Proton transfer to charged platinum electrodes. A molecular dynamics trajectory study.

PubMed

Wilhelm, Florian; Schmickler, Wolfgang; Spohr, Eckhard

2010-05-05

A recently developed empirical valence bond (EVB) model for proton transfer on Pt(111) electrodes (Wilhelm et al 2008 J. Phys. Chem. C 112 10814) has been applied in molecular dynamics (MD) simulations of a water film in contact with a charged Pt surface. A total of seven negative surface charge densities σ between -7.5 and -18.9 µC cm(-2) were investigated. For each value of σ, between 30 and 84 initial conditions of a solvated proton within a water slab were sampled, and the trajectories were integrated until discharge of a proton occurred on the charged surfaces. We have calculated the mean rates for discharge and for adsorption of solvated protons within the adsorbed water layer in contact with the metal electrode as a function of surface charge density. For the less negative values of σ we observe a Tafel-like exponential increase of discharge rate with decreasing σ. At the more negative values this exponential increase levels off and the discharge process is apparently transport limited. Mechanistically, the Tafel regime corresponds to a stepwise proton transfer: first, a proton is transferred from the bulk into the contact water layer, which is followed by transfer of a proton to the charged surface and concomitant discharge. At the more negative surface charge densities the proton transfer into the contact water layer and the transfer of another proton to the surface and its discharge occur almost simultaneously.

NMR Stratagems for the Study of Multiple Kinetic Hydrogen/Deuterium Isotope Effectsof Proton Exchange. Example: Di-p-fluorophenylformamidine/THF

NASA Astrophysics Data System (ADS)

Limbach, Hans-Heinrich; Meschede, Ludger; Scherer, Gerd

1989-05-01

Stratagems are presented for the determination of kinetic isotope effects of proton exchange reactions by dynamic NMR spectroscopy. In such experiments, lineshape analyses and/or polarization transfer experiments are performed on the exchanging protons or deuterons as well as on remote spins, as a function of the deuterium fraction in the mobile proton sites. These methods are NMR analogs of previous proton inventory techniques involving classical kinetic methods. A theory is developed in order to derive the kinetic isotope effects as well as the number of transferred protons from the experimental NMR spectra. The technique is then applied to the problem of proton exchange in the system 15N,15N'-di-p-fluorophenylibrmamidine, a nitrogen analog of formic acid, dissolved in tetrahydrofuran-d8 (THF). DFFA forms two conformers in THF to which s-trans and s-cis structures have been assigned. Only the s-trans conformer is able to dimerize and exchange protons. Lineshape simulations and magnetization transfer experiments were carried out at 189,2 K, at a concentration of 0.02 mol l-1, as a function of the deuterium fraction D in the 1H-15N sites. Using 1H NMR spectroscopy, a linear dependence of the inverse proton lifetimes on D was observed. From this it was concluded that two protons are transported in the rate limiting step of the proton exchange. This result is expected for a double proton transfer in an s-trans dimer with a cyclic structure. The full kinetic HH/HD/DD isotope effects of 233:11:1 at 189 K were determined through 19F NMR experiments on the same samples. The deviation from the rule of geometric mean, although substantial, is much smaller than found in previous studies of intramolecular HH transfer reactions. Possible causes of this effect are discussed.

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortiz-Sanchez, Juan Manuel; Gelabert, Ricard; Moreno, Miquel

2008-12-07

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a ({pi},{pi}*) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet ({pi},{pi}*) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fittedmore » to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.« less

Copper-Containing Nitrite Reductase Employing Proton-Coupled Spin-Exchanged Electron-Transfer and Multiproton Synchronized Transfer to Reduce Nitrite.

PubMed

Qin, Xin; Deng, Li; Hu, Caihong; Li, Li; Chen, Xiaohua

2017-10-20

The possible catalytic mechanism of the reduction of nitrite by copper-containing nitrite reductases (CuNiRs) is examined by using the M06 function according to two copper models, which include type-one copper (T1Cu) and type-two copper (T2Cu) sites. Examinations confirm that the protonation of two residues, His255 and Asp98, near the T2Cu site, can modulate the redox states of T1Cu and T2Cu, but cannot directly cause electron transfer from T1Cu to T2Cu. The electron hole remains at the T2Cu site when only one residue, His255 or Asp98, is protonated. However, the hole resides at the T1Cu site when both His255 and Asp98 are protonated. Then, the first protonation of nitrite takes place through indirect proton transfer from protonated His255 through the bridging H 2 O and Asp98 with three protons moving together, which cannot cause the cleavage of the HO-NO bond. Subsequently, the substrate is required to obtain another proton from reprotonated His255 through the bridging H 2 O. The reprotonation of nitrite induces the generation of nitric oxide (NO) and H 2 O at the T2Cu site through a special double-proton-coupled spin-exchanged electron-transfer mechanism with indirect proton transfer from His255 to the substrate, a beta-electron of T2Cu I shift to the NO cation, and the remaining alpha-electron changing spin direction at the same time. These results may provide useful information to better understand detailed proton-/electron-transfer reactions for the catalytic processes of CuNiR. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spying on the neighbors' pool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xantheas, S. S.

2016-12-01

The structure and properties of the aqueous proton is of fundamental interest in many areas of chemistry and biology. Acids and bases are molecules that are able to transfer (donate / accept) a proton according to Brønsted and Lowry, a process that was further explained by Lewis in terms of changes in their electronic structure in an attempt to offer a generalization of the Arrhenius theory. Simple proton transfers or the ones coupled to an electron transfer determine speciation, valence and reactivity in aqueous media and explain electrochemical processes, while voltage-gated proton channels have severe implications to the function ofmore » a number of tissues and species.« less

Reply to the 'Comment on "Proton transport in barium stannate: classical, semi-classical and quantum regime"'.

PubMed

Geneste, Grégory; Hermet, Jessica; Dezanneau, Guilhem

2017-08-09

We respond to the erroneous criticisms about our modeling of proton transport in barium stannate [G. Geneste et al., Phys. Chem. Chem. Phys., 2015, 17, 19104]. In this previous work, we described, on the basis of density-functional calculations, proton transport in the classical and semi-classical regimes, and provided arguments in favor of an adiabatic picture for proton transfer at low temperature. We re-explain here our article (with more detail and precision), the content of which has been distorted in the Comment, and reiterate our arguments in this reply. We refute all criticisms. They are completely wrong in the context of our article. Even though a few of them are based on considerations probably true in some metals, they make no sense here since they do not correspond to the content of our work. It has not been understood in the Comment that two competitive configurations, associated with radically different transfer mechanisms, have been studied in our work. It has also not been understood in the Comment that the adiabatic regime described for transfer occurs in the protonic ground state, in a very-low barrier configuration with the protonic ground state energy larger than the barrier. Serious confusion has been made in the Comment with the case of H in metals like Nb or Ta, leading to the introduction of the notion of (protonic) "excited-state proton transfer", relevant for H in some metals, but (i) that does not correspond to the (ground state) adiabatic transfers here described, and (ii) that does not correspond to what is commonly described as the "adiabatic limit for proton transfer" in the scientific literature. We emphasize, accordingly, the large differences between proton transfer in the present oxide and hydrogen jumps in metals like Nb or Ta, and the similarities between proton transfer in the present oxide and in acid-base solutions. We finally describe a scenario for proton transfer in the present oxide regardless of the temperature regime.

The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway.

PubMed

ter Beek, Josy; Krause, Nils; Reimann, Joachim; Lachmann, Peter; Ädelroth, Pia

2013-10-18

The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.

Endpoint Model of Exclusive Processes

NASA Astrophysics Data System (ADS)

Dagaonkar, Sumeet; Jain, Pankaj; Ralston, John P.

2018-07-01

The endpoint model explains the scaling laws observed in exclusive hadronic reactions at large momentum transfer in all experimentally important regimes. The model, originally conceived by Feynman and others, assumes a single valence quark carries most of the hadron momentum. The quark wave function is directly related to the momentum transfer dependence of the reaction. After extracting the momentum dependence of the quark wave function from one process, it explains all the others. Endpoint quark-counting rules relate the number of quarks in a hadron to the power-law. A universal linear endpoint behavior explains the proton electromagnetic form factors F1 and F2, proton-proton scattering at fixed-angle, the t-dependence of proton-proton scattering at large s>> t, and Compton scattering at fixed t. The model appears to be the only comprehensive mechanism consistent with all experimental information.

Chemical dynamics of the first proton-coupled electron transfer of water oxidation on TiO2 anatase.

PubMed

Chen, Jia; Li, Ye-Fei; Sit, Patrick; Selloni, Annabella

2013-12-18

Titanium dioxide (TiO2) is a prototype, water-splitting (photo)catalyst, but its performance is limited by the large overpotential for the oxygen evolution reaction (OER). We report here a first-principles density functional theory study of the chemical dynamics of the first proton-coupled electron transfer (PCET), which is considered responsible for the large OER overpotential on TiO2. We use a periodic model of the TiO2/water interface that includes a slab of anatase TiO2 and explicit water molecules, sample the solvent configurations by first principles molecular dynamics, and determine the energy profiles of the two electronic states involved in the electron transfer (ET) by hybrid functional calculations. Our results suggest that the first PCET is sequential, with the ET following the proton transfer. The ET occurs via an inner sphere process, which is facilitated by a state in which one electronic hole is shared by the two oxygen ions involved in the transfer.

Proton transport through aqueous Nafion membrane

NASA Astrophysics Data System (ADS)

Son, D. N.; Kasai, H.

2009-08-01

We introduce a new model for proton transport through a single proton-conducting channel of an aqueous Nafion membrane based on a mechanism in which protons move under electrostatic effect provided by the sulfonate ( SO3 -groups of the Nafion side chains, the spin effect of active components, the hydrogen bonding effect with water molecules, and the screening effect of water media. This model can describe the proton transport within various levels of humidification ranging from the low humidity to the high humidity as a function of operating temperature. At low humidity, this model approaches to the so-called surface mechanism, while at high humidity, it approaches the well-known Grotthuss one. Proton motion is considered as the transfer from cluster to cluster under a potential energy. A proton-proton interaction is comprised in the calculation. Using Green function method, we obtained the proton current as a function of the Nafion membrane temperature. We found that the lower the temperature, the higher the proton current transfer through the Nafion membrane in low temperatures compared to the critical point 10K, which separates magnetic regime from non-magnetic regime. The increasing of proton current at very low temperatures is attributed to the spin effect. As the membrane temperature is higher than 40 ° C , the decreasing of proton current is attributed to the loss of water uptake and the polymer contraction. The results of this study are qualitatively in good agreement with experiments. The expression for the critical temperature is also presented as a function of structural and tunable parameters, and interpreted by experimental data. in here

Anion Photoelectron Spectroscopy of the Homogenous 2-Hydroxypyridine Dimer Electron Induced Proton Transfer System

NASA Astrophysics Data System (ADS)

Vlk, Alexandra; Stokes, Sarah; Wang, Yi; Hicks, Zachary; Zhang, Xinxing; Blando, Nicolas; Frock, Andrew; Marquez, Sara; Bowen, Kit; Bowen Lab JHU Team

Anion photoelectron spectroscopic (PES) and density functional theory (DFT) studies on the dimer anion of (2-hydroxypyridine)2-are reported. The experimentally measured vertical detachment energy (VDE) of 1.21eV compares well with the theoretically predicted values. The 2-hydroxypyridine anionic dimer system was investigated because of its resemblance to the nitrogenous heterocyclic pyrimidine nucleobases. Experimental and theoretical results show electron induced proton transfer (EIPT) in both the lactim and lactam homogeneous dimers. Upon electron attachment, the anion can serve as the intermediate between the two neutral dimers. A possible double proton transfer process can occur from the neutral (2-hydroxypyridine)2 to (2-pyridone)2 through the dimer anion. This potentially suggests an electron catalyzed double proton transfer mechanism of tautomerization. Research supported by the NSF Grant No. CHE-1360692.

Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

Proton transfer in malonaldehyde: From reaction path to Schrödinger's Cat

NASA Astrophysics Data System (ADS)

Fillaux, François; Nicolaï, Béatrice

2005-11-01

Proton transfer in the chelated form of malonaldehyde is commonly supposed to occur between two tautomers, across a transition state involving changes of the chemical bonding. We show that this view is in conflict with rotational spectra. The molecule is better thought of as a superposition of indistinguishable and non-separable C s tautomers and proton tunneling is totally decoupled from the other degrees of freedom. Double minimum potential functions are determined from experiments and ab initio calculations.

Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum.

PubMed

Siletsky, Sergey A; Mamedov, Mahir D; Lukashev, Evgeniy P; Balashov, Sergei P; Dolgikh, Dmitriy A; Rubin, Andrei B; Kirpichnikov, Mikhail P; Petrovskaya, Lada E

2016-11-01

A retinal protein from Exiguobacterium sibiricum (ESR) functions as a light-driven proton pump. Unlike other proton pumps, it contains Lys96 instead of a usual carboxylic residue in the internal proton donor site. Nevertheless, the reprotonation of the Schiff base occurs fast, indicating that Lys96 facilitates proton transfer from the bulk. In this study we examined kinetics of light-induced transmembrane electrical potential difference, ΔΨ, generated in proteoliposomes reconstituted with ESR. We show that total magnitude of ΔΨ is comparable to that produced by bacteriorhodopsin but its kinetic components and their pH dependence are substantially different. The results are in agreement with the earlier finding that proton uptake precedes reprotonation of the Schiff base in ESR, suggesting that Lys96 is unprotonated in the initial state and gains a proton transiently in the photocycle. The electrogenic phases and the photocycle transitions related to proton transfer from the bulk to the Schiff base are pH dependent. At neutral pH, they occur with τ 0.5ms and 4.5ms. At alkaline pH, the fast component ceases and Schiff base reprotonation slows. At pH8.4, a spectrally silent electrogenic component with τ 0.25ms is detected, which can be attributed to proton transfer from the bulk to Lys96. At pH5.1, the amplitude of ΔΨ decreases 10 fold, reflecting a decreased yield and rate of proton transfer, apparently from protonation of the acceptor (Asp85-His57 pair) in the initial state. The features of the photoelectric potential generation correlate with the ESR structure and proposed mechanism of proton transfer. Copyright © 2016 Elsevier B.V. All rights reserved.

Polarization-transfer measurement to a large-virtuality bound proton in the deuteron

NASA Astrophysics Data System (ADS)

Yaron, I.; Izraeli, D.; Achenbach, P.; Arenhövel, H.; Beričič, J.; Böhm, R.; Bosnar, D.; Cohen, E. O.; Debenjak, L.; Distler, M. O.; Esser, A.; Friščić, I.; Gilman, R.; Korover, I.; Lichtenstadt, J.; Merkel, H.; Middleton, D. G.; Mihovilovič, M.; Müller, U.; Piasetzky, E.; Pochodzalla, J.; Ron, G.; Schlimme, B. S.; Schoth, M.; Schulz, F.; Sfienti, C.; Širca, S.; Strauch, S.; Thiel, M.; Tyukin, A.; Weber, A.; A1 Collaboration

2017-06-01

We report the measurement of the ratio of polarization-transfer components, Px /Pz, in the 2H (e → ,e‧ p →) n reaction at low and high missing momenta, in search of differences between free and bound protons. The observed deviation of Px /Pz from that of a free proton, which is similar to that observed in 4He, indicates that the effect in nuclei is a function of the virtuality of the knock-out proton and the missing momentum direction, but not the average nuclear density. There is a general agreement between the data and calculations, which assume free proton form factors, however, the measurements are consistently about 10% higher.

Ground state intermolecular proton transfer in the supersystems thymine-(H2O)n and thymine-(CH3OH)n, n = 1,2: a theoretical study.

PubMed

Delchev, Vassil B; Shterev, Ivan G

2009-04-01

Twelve binary and eight ternary supersystems between thymine and methanol, and water were investigated in the ground state at the B3LYP and MP2 levels of theory using B3LYP/6-311 + + G(d,p) basis functions. The thermodynamics of complex formations and the mechanisms of intermolecular proton transfers were clarified in order to find out the most stable H-boned system. It was established that the energy barriers of the water/methanol-assisted proton transfers are several times lower than those of the intramolecular proton transfers in the DNA/RNA bases. The X-ray powder spectra of thymine, and this precrystallized from water and methanol showed that water molecules are incorporated in the crystal lattice of thymine forming H-bridges between thymine molecules.

Time-resolved and steady-state fluorescence studies of excited-state proton-transfer reactions of proflavine

NASA Astrophysics Data System (ADS)

De Silvestri, S.; Laporta, P.

1984-01-01

Time-resolved and steady-state fluorescence studies of proflavine in aqueous solution are presented. The observation of a monoexponential fluorescence decay with a time constant decreasing with increasing pH and the presence of an anomalous red-shift in the fluorescence spectrum as a function of pH indicate the existence of a complex proton-transfer mechanism in the excited state. A reaction scheme is proposed and the corresponding proton-transfer rates are evaluated. An excited-state pK value of 12.85 is obtained for the equilibrium between the cationic form of proflavine and the same form dissociated at an amino group.

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase

PubMed Central

Pisliakov, Andrei V.; Hino, Tomoya; Shiro, Yoshitsugu; Sugita, Yuji

2012-01-01

Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb 3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. PMID:22956904

Insights into proton translocation in cbb3 oxidase from MD simulations.

PubMed

Carvalheda, Catarina A; Pisliakov, Andrei V

2017-05-01

Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb 3 ) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb 3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337. Copyright © 2017 Elsevier B.V. All rights reserved.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

PubMed

Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

2008-04-21

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Protonation of Excited State Pyrene-1-Carboxylate by Phosphate and Organic Acids in Aqueous Solution Studied by Fluorescence Spectroscopy

PubMed Central

Zelent, Bogumil; Vanderkooi, Jane M.; Coleman, Ryan G.; Gryczynski, Ignacy; Gryczynski, Zygmunt

2006-01-01

Pyrene-1-carboxylic acid has a pK of 4.0 in the ground state and 8.1 in the singlet electronic excited state. In the pH range of physiological interest (pH ∼5–8), the ground state compound is largely ionized as pyrene-1-carboxylate, but protonation of the excited state molecule occurs when a proton donor reacts with the carboxylate during the excited state lifetime of the fluorophore. Both forms of the pyrene derivatives are fluorescent, and in this work the protonation reaction was measured by monitoring steady-state and time-resolved fluorescence. The rate of protonation of pyrene-COO− by acetic, chloroacetic, lactic, and cacodylic acids is a function of ΔpK, as predicted by Marcus theory. The rate of proton transfer from these acids saturates at high concentration, as expected for the existence of an encounter complex. Trihydrogen-phosphate is a much better proton donor than dihydrogen- and monohydrogen-phosphate, as can be seen by the pH dependence. The proton-donating ability of phosphate does not saturate at high concentrations, but increases with increasing phosphate concentration. We suggest that enhanced rate of proton transfer at high phosphate concentrations may be due to the dual proton donating and accepting nature of phosphate, in analogy to the Grotthuss mechanism for proton transfer in water. It is suggested that in molecular structures containing multiple phosphates, such as membrane surfaces and DNA, proton transfer rates will be enhanced by this mechanism. PMID:16920831

Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities

PubMed Central

Miller, David C.; Tarantino, Kyle T.; Knowles, Robert R.

2016-01-01

Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter we aim to highlight the origins, development and evolution of PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups. PMID:27573270

A catalytic role of surface silanol groups in CO2 capture on the amine-anchored silica support.

PubMed

Cho, Moses; Park, Joonho; Yavuz, Cafer T; Jung, Yousung

2018-05-03

A new mechanism of CO2 capture on the amine-functionalized silica support is demonstrated using density functional theory calculations, in which the silica surface not only acts as a support to anchor amines, but also can actively participate in the CO2 capture process through a facile proton transfer reaction with the amine groups. The surface-mediated proton transfer mechanism in forming a carbamate-ammonium product has lower kinetic barrier (8.1 kcal mol-1) than the generally accepted intermolecular mechanism (12.7 kcal mol-1) under dry conditions, and comparable to that of the water-assisted intermolecular mechanism (6.0 kcal mol-1) under humid conditions. These findings suggest that the CO2 adsorption on the amine-anchored silica surface would mostly occur via the rate-determining proton transfer step that is catalyzed by the surface silanol groups.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plautz, Tia E.; Johnson, R. P.; Sadrozinski, H. F.-W.

Purpose: To characterize the modulation transfer function (MTF) of the pre-clinical (phase II) head scanner developed for proton computed tomography (pCT) by the pCT collaboration. To evaluate the spatial resolution achievable by this system. Methods: Our phase II proton CT scanner prototype consists of two silicon telescopes that track individual protons upstream and downstream from a phantom, and a 5-stage scintillation detector that measures a combination of the residual energy and range of the proton. Residual energy is converted to water equivalent path length (WEPL) of the protons in the scanned object. The set of WEPL values and associated pathsmore » of protons passing through the object over a 360° angular scan is processed by an iterative parallelizable reconstruction algorithm that runs on GP-GPU hardware. A custom edge phantom composed of water-equivalent polymer and tissue-equivalent material inserts was constructed. The phantom was first simulated in Geant4 and then built to perform experimental beam tests with 200 MeV protons at the Northwestern Medicine Chicago Proton Center. The oversampling method was used to construct radial and azimuthal edge spread functions and modulation transfer functions. The spatial resolution was defined by the 10% point of the modulation transfer function in units of lp/cm. Results: The spatial resolution of the image was found to be strongly correlated with the radial position of the insert but independent of the relative stopping power of the insert. The spatial resolution varies between roughly 4 and 6 lp/cm in both the the radial and azimuthal directions depending on the radial displacement of the edge. Conclusion: The amount of image degradation due to our detector system is small compared with the effects of multiple Coulomb scattering, pixelation of the image and the reconstruction algorithm. Improvements in reconstruction will be made in order to achieve the theoretical limits of spatial resolution.« less

Proton-deuteron double scattering

NASA Technical Reports Server (NTRS)

Wilson, J. W.

1974-01-01

A simple but accurate form for the proton-deuteron elastic double scattering amplitude, which includes both projectile and target recoil motion and is applicable at all momentum transfer, is derived by taking advantage of the restricted range of Fermi momentum allowed by the deuteron wave function. This amplitude can be directly compared to approximations which have neglected target recoil or are limited to small momentum transfer; the target recoil and large momentum transfer effects are evaluated explicitly within the context of a Gaussian model.

Identifying the proton transfer reaction mechanism via a proton-bound dimeric intermediate for esomeprazoles by a kinetic method combined with density functional theory calculations.

PubMed

Cao, Xiaoji; Zhang, Feifei; Zhu, Kundan; Ye, Xuemin; Shen, Lingxiao; Chen, Jiaoyu; Mo, Weimin

2014-05-15

Esomeprazole analogs are a class of important proton pump inhibitors for the treatment of gastro-esophageal reflux diseases. Understanding the fragmentation reaction mechanism of the protonated esomeprazole analogs will facilitate the characterization of their complex metabolic fate in humans. In this paper, the kinetic method and theoretical calculations were applied to evaluate the fragmentation of protonated esomeprazole analogs. All collision-induced dissociation (CID) mass spectrometry experiments were carried out using electrospray ionization (ESI) ion trap mass spectrometry in positive ion mode. Also the accurate masses of fragments were measured on by ESI quadrupole time-of-flight (QTOF) MS in positive ion mode. Theoretical calculations were carried out by the density functional theory (DFT) method with the 6-31G(d) basis set in the Gaussian 03 program. In the fragmentation of the protonated esomeprazole analogs, C-S bond breakage is observed, which gives rise to protonated 2-(sulfinylmethylene)pyridines and protonated benzimidazoles. DFT calculations demonstrate that the nitrogen atom of the pyridine part is the thermodynamically most favorable protonation site, and the C-S bond cleavage is triggered by the transfer of this ionizing proton from the nitrogen atom of the pyridine part to the carbon atom of the benzimidazole part to which the sulfinyl is attached. Moreover, with the kinetic plot, the intensity ratios of two protonated product ions yield a linear relationship with the differences in proton affinities of the corresponding neutral molecules, which provides strong experimental evidence that the reaction proceeds via proton-bound 2-(sulfinylmethylene)pyridine/benzimidazole complex intermediates. The kinetic method combined with theoretical calculations was successfully applied to probe the proton transfer reaction by proton-bound 2-(sulfinylmethylene)pyridine/benzimidazole complexes in the fragmentation of protonated esomeprazole analogs by ESI CID MS, which is a strong evidence that the kinetic method can be applied in identifying a proton-bound dimeric intermediate in the fragmentation of protonated ions. Copyright © 2014 John Wiley & Sons, Ltd.

Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

PubMed

Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon

2018-02-28

The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.

Moving protons with pendant amines: proton mobility in a nickel catalyst for oxidation of hydrogen.

PubMed

O'Hagan, Molly; Shaw, Wendy J; Raugei, Simone; Chen, Shentan; Yang, Jenny Y; Kilgore, Uriah J; DuBois, Daniel L; Bullock, R Morris

2011-09-14

Proton transport is ubiquitous in chemical and biological processes, including the reduction of dioxygen to water, the reduction of CO(2) to formate, and the production/oxidation of hydrogen. In this work we describe intramolecular proton transfer between Ni and positioned pendant amines for the hydrogen oxidation electrocatalyst [Ni(P(Cy)(2)N(Bn)(2)H)(2)](2+) (P(Cy)(2)N(Bn)(2) = 1,5-dibenzyl-3,7-dicyclohexyl-1,5-diaza-3,7-diphosphacyclooctane). Rate constants are determined by variable-temperature one-dimensional NMR techniques and two-dimensional EXSY experiments. Computational studies provide insight into the details of the proton movement and energetics of these complexes. Intramolecular proton exchange processes are observed for two of the three experimentally observable isomers of the doubly protonated Ni(0) complex, [Ni(P(Cy)(2)N(Bn)(2)H)(2)](2+), which have N-H bonds but no Ni-H bonds. For these two isomers, with pendant amines positioned endo to the Ni, the rate constants for proton exchange range from 10(4) to 10(5) s(-1) at 25 °C, depending on isomer and solvent. No exchange is observed for protons on pendant amines positioned exo to the Ni. Analysis of the exchange as a function of temperature provides a barrier for proton exchange of ΔG(‡) = 11-12 kcal/mol for both isomers, with little dependence on solvent. Density functional theory calculations and molecular dynamics simulations support the experimental observations, suggesting metal-mediated intramolecular proton transfers between nitrogen atoms, with chair-to-boat isomerizations as the rate-limiting steps. Because of the fast rate of proton movement, this catalyst may be considered a metal center surrounded by a cloud of exchanging protons. The high intramolecular proton mobility provides information directly pertinent to the ability of pendant amines to accelerate proton transfers during catalysis of hydrogen oxidation. These results may also have broader implications for proton movement in homogeneous catalysts and enzymes in general, with specific implications for the proton channel in the Ni-Fe hydrogenase enzyme.

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

PubMed

Luo, Zhoujie; Gao, Ya; Zhu, Tong; Zhang, John Zenghui; Xia, Fei

2017-08-31

Water molecules can serve as proton shuttles for proton transfer in the C-H bond insertion reactions catalyzed by transition metal complexes. Recently, the control experiments performed for C-H bond insertion of phenol and anisol by gold carbenes show that large discrepancy exists in the yields of hydrogenated and deuterated products. Thus, we conducted a detailed theoretical analysis on the function of water molecules in the C-H bond insertion reactions. The comparison of calculated results and control experiments indicates that the solution water molecules play a crucial role of proton shuttle in C-H bond insertion. In particular, it was found that the hydroxyl groups in phenols were capable of donating protons via water shuttles for the production of C-H products, which had a substantial influence on the yields of inserted products. The hydroxyl groups instead of C-H bonds in phenols function like "proton reservoirs" in the C-H bond insertion, which we call the "proton self-sufficient" (PSS) function of phenol. The PSS function of phenol indicates that the substrates with and without proton reservoirs will lead to different C-H bond insertion products.

Resolving the negative potential side (n-side) water-accessible proton pathway of F-type ATP synthase by molecular dynamics simulations.

PubMed

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-10-19

The rotation of F(1)F(o)-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane F(o) domain, which is coupled to the ATP-producing F(1) domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the "locked" and "open" conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F(1)F(o)-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode.

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study.

PubMed

Panek, Jarosław J; Filarowski, Aleksander; Jezierska-Mazzarello, Aneta

2013-10-21

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Polarization transfer in the {sup 4}He(e(pol), e'p(pol)) {sup 3}He reaction at Q{sup 2} = 0.8 and 1.3 GeV/c){sup 2}.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paolone, M.; Malace, S. P.; Strauch, S.

2010-08-12

Proton recoil polarization was measured in the quasielastic 4He(e(pol),e{prime}p(pol)){sup 3}H reaction at Q{sup 2}=0.8 and 1.3(GeV/c){sup 2} with unprecedented precision. The polarization-transfer coefficients are found to differ from those of the {sup 1}H(e(pol),e{prime}p(pol)) reaction, contradicting a relativistic distorted-wave approximation and favoring either the inclusion of medium-modified proton form factors predicted by the quark-meson coupling model or a spin-dependent charge-exchange final-state interaction. For the first time, the polarization-transfer ratio is studied as a function of the virtuality of the proton.

Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

DOE PAGES

Bondar, Ana-Nicoleta; Smith, Jeremy C.

2017-07-25

Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. Here, we compare the protonation-coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter- and intra-helical carboxylate/hydroxyl hydrogen-bonding motifs.more » Specifically, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen-bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.« less

Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bondar, Ana-Nicoleta; Smith, Jeremy C.

Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. Here, we compare the protonation-coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter- and intra-helical carboxylate/hydroxyl hydrogen-bonding motifs.more » Specifically, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen-bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.« less

Excited state proton transfer in strongly enhanced GFP (sGFP2).

PubMed

van Oort, Bart; ter Veer, Mirelle J T; Groot, Marie Louise; van Stokkum, Ivo H M

2012-07-07

Proton transfer is an elementary process in biology. Green fluorescent protein (GFP) has served as an important model system to elucidate the mechanistic details of this reaction, because in GFP proton transfer can be induced by light absorption. We have used pump-dump-probe spectroscopy to study how proton transfer through the 'proton-wire' around the chromophore is affected by a combination of mutations in a modern GFP variety (sGFP2). The results indicate that in H(2)O, after absorption of a photon, a proton is transferred (A* → I*) in 5 ps, and back-transferred from a ground state intermediate (I → A) in 0.3 ns, similar to time constants found with GFPuv, although sGFP2 shows less heterogeneous proton transfer. This suggests that the mutations left the proton-transfer largely unchanged, indicating the robustness of the proton-wire. We used pump-dump-probe spectroscopy in combination with target analysis to probe suitability of the sGFP2 fluorophore for super-resolution microscopy.

Activation Thermodynamics and H/D Kinetic Isotope Effect of the Hox to HredH+ Transition in [FeFe] Hydrogenase.

PubMed

Ratzloff, Michael W; Wilker, Molly B; Mulder, David W; Lubner, Carolyn E; Hamby, Hayden; Brown, Katherine A; Dukovic, Gordana; King, Paul W

2017-09-20

Molecular complexes between CdSe nanocrystals and Clostridium acetobutylicum [FeFe] hydrogenase I (CaI) enabled light-driven control of electron transfer for spectroscopic detection of redox intermediates during catalytic proton reduction. Here we address the route of electron transfer from CdSe→CaI and activation thermodynamics of the initial step of proton reduction in CaI. The electron paramagnetic spectroscopy of illuminated CdSe:CaI showed how the CaI accessory FeS cluster chain (F-clusters) functions in electron transfer with CdSe. The H ox →H red H + reduction step measured by Fourier-transform infrared spectroscopy showed an enthalpy of activation of 19 kJ mol -1 and a ∼2.5-fold kinetic isotope effect. Overall, these results support electron injection from CdSe into CaI involving F-clusters, and that the H ox →H red H + step of catalytic proton reduction in CaI proceeds by a proton-dependent process.

Pendant Hydrogen-Bond Donors in Cobalt Catalysts Independently Enhance CO2 Reduction

PubMed Central

2018-01-01

The bioinspired incorporation of pendant proton donors into transition metal catalysts is a promising strategy for converting environmentally deleterious CO2 to higher energy products. However, the mechanism of proton transfer in these systems is poorly understood. Herein, we present a series of cobalt complexes with varying pendant secondary and tertiary amines in the ligand framework with the aim of disentangling the roles of the first and second coordination spheres in CO2 reduction catalysis. Electrochemical and kinetic studies indicate that the rate of catalysis shows a first-order dependence on acid, CO2, and the number of pendant secondary amines, respectively. Density functional theory studies explain the experimentally observed trends and indicate that pendant secondary amines do not directly transfer protons to CO2, but instead bind acid molecules from solution. Taken together, these results suggest a mechanism in which noncooperative pendant amines facilitate a hydrogen-bonding network that enables direct proton transfer from acid to the activated CO2 substrate. PMID:29632886

Pendant Hydrogen-Bond Donors in Cobalt Catalysts Independently Enhance CO2 Reduction.

PubMed

Chapovetsky, Alon; Welborn, Matthew; Luna, John M; Haiges, Ralf; Miller, Thomas F; Marinescu, Smaranda C

2018-03-28

The bioinspired incorporation of pendant proton donors into transition metal catalysts is a promising strategy for converting environmentally deleterious CO 2 to higher energy products. However, the mechanism of proton transfer in these systems is poorly understood. Herein, we present a series of cobalt complexes with varying pendant secondary and tertiary amines in the ligand framework with the aim of disentangling the roles of the first and second coordination spheres in CO 2 reduction catalysis. Electrochemical and kinetic studies indicate that the rate of catalysis shows a first-order dependence on acid, CO 2 , and the number of pendant secondary amines, respectively. Density functional theory studies explain the experimentally observed trends and indicate that pendant secondary amines do not directly transfer protons to CO 2 , but instead bind acid molecules from solution. Taken together, these results suggest a mechanism in which noncooperative pendant amines facilitate a hydrogen-bonding network that enables direct proton transfer from acid to the activated CO 2 substrate.

Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer.

PubMed

Gupta, Ashutosh; Jaeger, Heather M; Compaan, Katherine R; Schaefer, Henry F

2012-05-17

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases

PubMed Central

Szőri-Dorogházi, Emma; Maróti, Gergely; Szőri, Milán; Nyilasi, Andrea; Rákhely, Gábor; Kovács, Kornél L.

2012-01-01

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis. PMID:22511957

An antilock molecular braking system.

PubMed

Sun, Wei-Ting; Huang, Shou-Ling; Yao, Hsuan-Hsiao; Chen, I-Chia; Lin, Ying-Chih; Yang, Jye-Shane

2012-08-17

A light-driven molecular brake displaying an antilock function is constructed by introducing a nonradiative photoinduced electron transfer (PET) decay channel to compete with the trans (brake-off) → cis (brake-on) photoisomerization. A fast release of the brake can be achieved by deactivating the PET process through addition of protons. The cycle of irradiation-protonation-irradiation-deprotonation conducts the brake function and mimics the antilock braking system (ABS) of vehicles.

A Ratio-Analysis Method to the Dynamics of Excited State Proton Transfer: Pyranine in Water and Micelles.

PubMed

Sahu, Kalyanasis; Nandi, Nilanjana; Dolai, Suman; Bera, Avisek

2018-06-05

Emission spectrum of a fluorophore undergoing excited state proton transfer (ESPT) often exhibits two distinct bands each representing emissions from protonated and deprotonated forms. The relative contribution of the two bands, best represented by an emission intensity ratio (R) (intensity maximum of the protonated band / intensity maximum of the deprotonated band), is an important parameter which usually denotes feasibility or promptness of the ESPT process. However, the use of ratio is only limited to the interpretation of steady-state fluorescence spectra. Here, for the first time, we exploit the time-dependence of the ratio (R(t)), calculated from time-resolved emission spectra (TRES) at different times, to analyze ESPT dynamics. TRES at different times were fitted with a sum of two lognormal-functions representing each peaks and then, the peak intensity ratio, R(t) was calculated and further fitted with an analytical function. Recently, a time-resolved area-normalized emission spectra (TRANES)-based analysis was presented where the decay of protonated emission or the rise of deprotonated emission intensity conveniently accounts for the ESPT dynamics. We show that these two methods are equivalent but the new method provides more insights on the nature of the ESPT process.

Subunit III-depleted cytochrome c oxidase provides insight into the process of proton uptake by proteins

PubMed Central

Varanasi, Lakshman; Hosler, Jonathan P.

2011-01-01

We review studies of subunit III-depleted cytochrome c oxidase (CcO III (−)) that elucidate the structural basis of steady-state proton uptake from solvent into an internal proton transfer pathway. The removal of subunit III from R. sphaeroides CcO makes proton uptake into the D pathway a rate-determining step, such that measurements of the pH dependence of steady-state O2 consumption can be used to compare the rate and functional pKa of proton uptake by D pathways containing different initial proton acceptors. The removal of subunit III also promotes spontaneous suicide inactivation by CcO, greatly shortening its catalytic lifespan. Because the probability of suicide inactivation is controlled by the rate at which the D pathway delivers protons to the active site, measurements of catalytic lifespan provide a second method to compare the relative efficacy of proton uptake by engineered CcO III (−) forms. These simple experimental systems have been used to explore general questions of proton uptake by proteins, such as the functional value of an initial proton acceptor, whether an initial acceptor must be surface-exposed, which side chains will function as initial proton acceptors and whether multiple acceptors can speed proton uptake. PMID:22023935

Size and shape dependent deprotonation potential and proton affinity of nanodiamond

NASA Astrophysics Data System (ADS)

Barnard, Amanda S.; Per, Manolo C.

2014-11-01

Many important reactions in biology and medicine involve proton abstraction and transfer, and it is integral to applications such as drug delivery. Unlike electrons, which are quantum mechanically delocalized, protons are instantaneously localized on specific residues in these reactions, which can be a distinct advantage. However, the introduction of nanoparticles, such as non-toxic nanodiamonds, to this field complicates matters, as the number of possible sites increases as the inverse radius of the particle. In this paper we present \\gt {{10}4} simulations that map the size- and shape-dependence of the deprotonation potential and proton affinity of nanodiamonds in the range 1.8-2.7 nm in average diameter. We find that while the average deprotonation potential and proton affinities decrease with size, the site-specific values are inhomogeneous over the surface of the particles, exhibiting strong shape-dependence. The proton affinity is strongly facet-dependent, whereas the deprotonation potential is edge/corner-dependent, which creates a type of spatial hysteresis in the transfer of protons to and from the nanodiamond, and provides new opportunities for selective functionalization.

Analysis of the critical step in catalytic carbodiimide transformation: proton transfer from amines, phosphines, and alkynes to guanidinates, phosphaguanidinates, and propiolamidinates with Li and Al catalysts.

PubMed

Rowley, Christopher N; Ong, Tiow-Gan; Priem, Jessica; Richeson, Darrin S; Woo, Tom K

2008-12-15

While lithium amides supported by tetramethylethylenediamine (TMEDA) are efficient catalysts in the synthesis of substituted guanidines via the guanylation of an amine with carbodiimide, as well as the guanylation of phosphines and conversion of alkynes into propiolamidines, aluminum amides are only efficient catalysts for the guanylation of amides. Density functional theory (DFT) calculations were used to explain this difference in activity. The origin of this behavior is apparent in the critical step where a proton is transferred from the substrate to a metal guanidinate. The activation energies of these steps are modest for amines, phosphines, and alkynes when a lithium catalyst was used, but are prohibitively high for the analogous reactions with phosphines and alkynes for aluminum amide catalysts. Energy decomposition analysis (EDA) indicates that these high activations energies are due to the high energetic cost of the detachment of a chelating guanidinate nitrogen from the aluminum in the proton transfer transition state. Amines are able to adopt an ideal geometry for facile proton transfer to the aluminum guanidinate and concomitant Al-N bond formation, while phosphines and alkynes are not.

Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging?

NASA Astrophysics Data System (ADS)

Paul, Suvendu; Karar, Monaj; Das, Biswajit; Mallick, Arabinda; Majumdar, Tapas

2017-12-01

Fluoride ion sensing mechanism of 3,3‧-bis(indolyl)-4-chlorophenylmethane has been analyzed with density functional and time-dependent density functional theories. Extensive theoretical calculations on molecular geometry & energy, charge distribution, orbital energies & electronic distribution, minima on potential energy surface confirmed strong hydrogen bonded sensor-anion complex with incomplete proton transfer in S0. In S1, strong hydrogen bonding extended towards complete ESDPT. The distinct and single minima on the PES of the sensor-anion complex for both ground and first singlet excited states confirmed the concerted proton transfer mechanism. Present study well reproduced the experimental spectroscopic data and provided ESDPT as probable fluoride sensing mechanism.

Ultrafast Intramolecular Electron and Proton Transfer in Bis(imino)isoindole Derivatives.

PubMed

Driscoll, Eric; Sorenson, Shayne; Dawlaty, Jahan M

2015-06-04

Concerted motion of electrons and protons in the excited state is pertinent to a wide range of chemical phenomena, including those relevant for solar-to-fuel light harvesting. The excited state dynamics of small proton-bearing molecules are expected to serve as models for better understanding such phenomena. In particular, for designing the next generation of multielectron and multiproton redox catalysts, understanding the dynamics of more than one proton in the excited state is important. Toward this goal, we have measured the ultrafast dynamics of intramolecular excited state proton transfer in a recently synthesized dye with two equivalent transferable protons. We have used a visible ultrafast pump to initiate the proton transfer in the excited state, and have probed the transient absorption of the molecule over a wide bandwidth in the visible range. The measurement shows that the signal which is characteristic of proton transfer emerges within ∼710 fs. To identify whether both protons were transferred in the excited state, we have measured the ultrafast dynamics of a related derivative, where only a single proton was available for transfer. The measured proton transfer time in that molecule was ∼427 fs. The observed dynamics in both cases were reasonably fit with single exponentials. Supported by the ultrafast observations, steady-state fluorescence, and preliminary computations of the relaxed excited states, we argue that the doubly protonated derivative most likely transfers only one of its two protons in the excited state. We have performed calculations of the frontier molecular orbitals in the Franck-Condon region. The calculations show that in both derivatives, the excitation is primarily from the HOMO to LUMO causing a large rearrangement of the electronic charge density immediately after photoexcitation. In particular, charge density is shifted away from the phenolic protons and toward the proton acceptor nitrogens. The proton transfer is hypothesized to occur both due to enhanced acidity of the phenolic proton and enhanced basicity of the nitrogen in the excited state. We hope this study can provide insight for better understanding of the general class of excited state concerted electron-proton dynamics.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

PubMed Central

Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

2013-01-01

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

Sugar Radical Formation by a Proton Coupled Hole Transfer in 2′-Deoxyguanosine Radical Cation (2′-dG•+): A Theoretical Treatment

PubMed Central

Kumar, Anil; Sevilla, Michael D.

2009-01-01

Previous experimental and theoretical work has established that electronic excitation of a guanine cation radical in nucleosides or in DNA itself leads to sugar radical formation by deprotonation from the dexoxyribose sugar. In this work we investigate a ground electronic state pathway for such sugar radical formation in a hydrated one electron oxidized 2′-deoxyguanosine (dG•+ + 7H2O), using density functional theory (DFT) with the B3LYP functional and the 6-31G* basis set. We follow the stretching of the C5′-H bond in dG•+ to gain an understanding of the energy requirements to transfer the hole from the base to sugar ring and then to deprotonate to proton acceptor sites in solution and on the guanine ring. The geometries of reactant (dG•+ + 7H2O), transition state (TS) for deprotonation of C5′ site and product (dG(•C5′, N7-H+) + 7 H2O) were fully optimized. The zero point energy (ZPE) corrected activation energy (TS) for the proton transfer (PT) from C5′ is calculated to be 9.0 kcal/mol and is achieved by stretching the C5′-H bond by 0.13 Å from its equilibrium bond distance (1.099 Å). Remarkably, this small bond stretch is sufficient to transfer the “hole” (positive charge and spin) from guanine to the C5′ site on the deoxyribose group. Beyond the TS, the proton (H+) spontaneously adds to water to form a hydronium ion (H3O+) as an intermediate. The proton subsequently transfers to the N7 site of the guanine (product). The 9 kcal/mol barrier suggests slow thermal conversion of the cation radical to the sugar radical but also suggests that localized vibrational excitations would be sufficient to induce rapid sugar radical formation in DNA base cation radicals. PMID:19754084

Gas-phase ion-molecule reactions for the identification of the sulfone functionality in protonated analytes in a linear quadrupole ion trap mass spectrometer.

PubMed

Tang, Weijuan; Sheng, Huaming; Kong, John Y; Yerabolu, Ravikiran; Zhu, Hanyu; Max, Joann; Zhang, Minli; Kenttämaa, Hilkka I

2016-06-30

The oxidation of sulfur atoms is an important biotransformation pathway for many sulfur-containing drugs. In order to rapidly identify the sulfone functionality in drug metabolites, a tandem mass spectrometric method based on ion-molecule reactions was developed. A phosphorus-containing reagent, trimethyl phosphite (TMP), was allowed to react with protonated analytes with various functionalities in a linear quadrupole ion trap mass spectrometer. The reaction products and reaction efficiencies were measured. Only protonated sulfone model compounds were found to react with TMP to form a characteristic [TMP adduct-MeOH] product ion. All other protonated compounds investigated, with functionalities such as sulfoxide, N-oxide, hydroxylamino, keto, carboxylic acid, and aliphatic and aromatic amino, only react with TMP via proton transfer and/or addition. The specificity of the reaction was further demonstrated by using a sulfoxide-containing anti-inflammatory drug, sulindac, as well as its metabolite sulindac sulfone. A method based on functional group-selective ion-molecule reactions in a linear quadrupole ion trap mass spectrometer has been demonstrated for the identification of the sulfone functionality in protonated analytes. A characteristic [TMP adduct-MeOH] product ion was only formed for the protonated sulfone analytes. The applicability of the TMP reagent in identifying sulfone functionalities in drug metabolites was also demonstrated. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Electron, proton and hydrogen-atom transfers in photosynthetic water oxidation.

PubMed Central

Tommos, Cecilia

2002-01-01

When photosynthetic organisms developed so that they could use water as an electron source to reduce carbon dioxide, the stage was set for efficient proliferation. Algae and plants spread globally and provided the foundation for our atmosphere and for O(2)-based chemistry in biological systems. Light-driven water oxidation is catalysed by photosystem II, the active site of which contains a redox-active tyrosine denoted Y(Z), a tetramanganese cluster, calcium and chloride. In 1995, Gerald Babcock and co-workers presented the hypothesis that photosynthetic water oxidation occurs as a metallo-radical catalysed process. In this model, the oxidized tyrosine radical is generated by coupled proton/electron transfer and re-reduced by abstracting hydrogen atoms from substrate water or hydroxide-ligated to the manganese cluster. The proposed function of Y(Z) requires proton transfer from the tyrosine site upon oxidation. The oxidation mechanism of Y(Z) in an inhibited and O(2)-evolving photosystem II is discussed. Domino-deprotonation from Y(Z) to the bulk solution is shown to be consistent with a variety of data obtained on metal-depleted samples. Experimental data that suggest that the oxidation of Y(Z) in O(2)-evolving samples is coupled to proton transfer in a hydrogen-bonding network are described. Finally, a dielectric-dependent model for the proton release that is associated with the catalytic cycle of photosystem II is discussed. PMID:12437877

Proton transfer in organic scaffolds

NASA Astrophysics Data System (ADS)

Basak, Dipankar

This dissertation focuses on the fundamental understanding of the proton transfer process and translating the knowledge into design/development of new organic materials for efficient non-aqueous proton transport. For example, what controls the shuttling of a proton between two basic sites? a) Distance between two groups? or b) the basicity? c) What is the impact of protonation on molecular conformation when the basic sites are attached to rigid scaffolds? For this purpose, we developed several tunable proton sponges and studied proton transfer in these scaffolds theoretically as well as experimentally. Next we moved our attention to understand long-range proton conduction or proton transport. We introduced liquid crystalline (LC) proton conductor based on triphenylene molecule and established that activation energy barrier for proton transport is lower in the LC phase compared to the crystalline phase. Furthermore, we investigated the impact of several critical factors: the choice of the proton transferring groups, mobility of the charge carriers, intrinsic vs. extrinsic charge carrier concentrations and the molecular architectures on long-range proton transport. The outcome of this research will lead to a deeper understanding of non-aqueous proton transfer process and aid the design of next generation proton exchange membrane (PEM) for fuel cell.

Activation Thermodynamics and H/D Kinetic Isotope Effect of the H ox to H red H + Transition in [FeFe] Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ratzloff, Michael W.; Wilker, Molly B.; Mulder, David W.

Molecular complexes between CdSe nanocrystals and Clostridium acetobutylicum [FeFe] hydrogenase I (CaI) enabled light-driven control of electron transfer for spectroscopic detection of redox intermediates during catalytic proton reduction. Here in this paper we address the route of electron transfer from CdSe→CaI and activation thermodynamics of the initial step of proton reduction in CaI. The electron paramagnetic spectroscopy of illuminated CdSe:CaI showed how the CaI accessory FeS cluster chain (F-clusters) functions in electron transfer with CdSe. The H ox→H redH + reduction step measured by Fourier-transform infrared spectroscopy showed an enthalpy of activation of 19 kJ mol -1 and a ~2.5-foldmore » kinetic isotope effect. Overall these results support electron injection from CdSe into CaI involving F-clusters, and that the H ox→H redH + step of catalytic proton reduction in CaI proceeds by a proton-dependent process.« less

Activation Thermodynamics and H/D Kinetic Isotope Effect of the H ox to H red H + Transition in [FeFe] Hydrogenase

DOE PAGES

Ratzloff, Michael W.; Wilker, Molly B.; Mulder, David W.; ...

2017-08-29

Molecular complexes between CdSe nanocrystals and Clostridium acetobutylicum [FeFe] hydrogenase I (CaI) enabled light-driven control of electron transfer for spectroscopic detection of redox intermediates during catalytic proton reduction. Here in this paper we address the route of electron transfer from CdSe→CaI and activation thermodynamics of the initial step of proton reduction in CaI. The electron paramagnetic spectroscopy of illuminated CdSe:CaI showed how the CaI accessory FeS cluster chain (F-clusters) functions in electron transfer with CdSe. The H ox→H redH + reduction step measured by Fourier-transform infrared spectroscopy showed an enthalpy of activation of 19 kJ mol -1 and a ~2.5-foldmore » kinetic isotope effect. Overall these results support electron injection from CdSe into CaI involving F-clusters, and that the H ox→H redH + step of catalytic proton reduction in CaI proceeds by a proton-dependent process.« less

Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

PubMed Central

2015-01-01

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment. PMID:24960612

Umbrella sampling of proton transfer in a creatine-water system

NASA Astrophysics Data System (ADS)

Ivchenko, Olga; Bachert, Peter; Imhof, Petra

2014-04-01

Proton transfer reactions are among the most common processes in chemistry and biology. Proton transfer between creatine and surrounding solvent water is underlying the chemical exchange saturation transfer used as a contrast in magnetic resonance imaging. The free energy barrier, determined by first-principles umbrella sampling simulations (EaDFT 3 kcal/mol) is in the same order of magnitude as the experimentally obtained activation energy. The underlying mechanism is a first proton transfer from the guanidinium group to the water pool, followed by a second transition where a proton is "transferred back" from the nearest water molecule to the deprotonated nitrogen atom of creatine.

Competition between Hydrogen Bonding and Proton Transfer during Specific Anion Recognition by Dihomooxacalix[4]arene Bidentate Ureas.

PubMed

Martínez-González, Eduardo; González, Felipe J; Ascenso, José R; Marcos, Paula M; Frontana, Carlos

2016-08-05

Competition between hydrogen bonding and proton transfer reactions was studied for systems composed of electrogenerated dianionic species from dinitrobenzene isomers and substituted dihomooxacalix[4]arene bidentate urea derivatives. To analyze this competition, a second-order ErCrCi mechanism was considered where the binding process is succeeded by proton transfer and the voltammetric responses depend on two dimensionless parameters: the first related to hydrogen bonding reactions, and the second one to proton transfer processes. Experimental results indicated that, upon an increase in the concentration of phenyl-substituted dihomooxacalix[4]arene bidentate urea, voltammetric responses evolve from diffusion-controlled waves (where the binding process is at chemical equilibrium) into irreversible kinetic responses associated with proton transfer. In particular, the 1,3-dinitrobenzene isomer showed a higher proton transfer rate constant (∼25 M(-1) s(-1)) compared to that of the 1,2-dinitrobenzene (∼5 M(-1) s(-1)), whereas the 1,4-dinitrobenzene did not show any proton transfer effect in the experimental conditions employed.

Proton-Coupled Electron Transfer in Artificial Photosynthetic Systems.

PubMed

Mora, S Jimena; Odella, Emmanuel; Moore, Gary F; Gust, Devens; Moore, Thomas A; Moore, Ana L

2018-02-20

Artificial photosynthetic constructs can in principle operate more efficiently than natural photosynthesis because they can be rationally designed to optimize solar energy conversion for meeting human demands rather than the multiple needs of an organism competing for growth and reproduction in a complex ecosystem. The artificial photosynthetic constructs described in this Account consist primarily of covalently linked synthetic chromophores, electron donors and acceptors, and proton donors and acceptors that carry out the light absorption, electron transfer, and proton-coupled electron transfer (PCET) processes characteristic of photosynthetic cells. PCET is the movement of an electron from one site to another accompanied by proton transfer. PCET and the transport of protons over tens of angstroms are important in all living cells because they are a fundamental link between redox processes and the establishment of transmembrane gradients of proton electrochemical potential, known as proton-motive force (PMF), which is the unifying concept in bioenergetics. We have chosen a benzimidazole phenol (BIP) system as a platform for the study of PCET because with appropriate substitutions it is possible to design assemblies in which one or multiple proton transfers can accompany oxidation of the phenol. In BIP, oxidation of the phenol increases its acidity by more than ten pK a units; thus, electrochemical oxidation of the phenol is associated with a proton transfer to the imidazole. This is an example of a PCET process involving transfer of one electron and one proton, known as electron-proton transfer (EPT). When the benzimidazole moiety of BIP is substituted at the 4-position with good proton acceptor groups such as aliphatic amines, experimental and theoretical results indicate that two proton transfers occur upon one-electron oxidation of the phenol. This phenomenon is described as a one-electron-two-proton transfer (E2PT) process and results in translocation of protons over ∼7 Å via a Grotthuss-type mechanism, where the protons traverse a network of internally H-bonded sites. In the case of the E2TP process involving BIP analogues with amino group substituents, the thermodynamic price paid in redox potential to move a proton to the final proton acceptor is ∼300 mV. In this example, the decrease in redox potential limits the oxidizing power of the resulting phenoxyl radical. Thus, unlike the biological counterpart, the artificial construct is thermodynamically incapable of effectively advancing the redox state of a water oxidation catalyst. The design of systems where multiple proton transfer events are coupled to an oxidation reaction while a relatively high redox potential is maintained remains an outstanding challenge. The ability to control proton transfer and activity at defined distances and times is key to achieving proton management in the vicinity of catalysts operating at low overpotential in myriad biochemically important processes. Artificial photosynthetic constructs with well-defined structures, such as the ones described in this Account, can provide the means for discovering design principles upon which efficient redox catalysts for electrolysis and fuel cells can be based.

Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.

What's new in the proton transfer reaction from pyranine to water? A femtosecond study of the proton transfer dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prayer, C.; Gustavsson, T.; Tran-Thi, T.-H.

1996-04-01

The proton transfer from excited pyranine to water is studied by the femtosecond fluorescence upconversion technique. It is shown for the first time that the proton transfer reaction in water proceeds by three successive steps: the solvent cage relaxation, the specific solute-solvent hydrogen-bond formation and finally the ion pair dissociation/diffusion.

Modeling of S-Nitrosothiol-Thiol Reactions of Biological Significance: HNO Production by S-Thiolation Requires a Proton Shuttle and Stabilization of Polar Intermediates.

PubMed

Ivanova, Lena V; Cibich, Daniel; Deye, Gregory; Talipov, Marat R; Timerghazin, Qadir K

2017-04-18

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S-thiolation reaction between thiols and S-nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S-thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge-separated zwitterionic intermediate structure RSS + (R)N(H)O - (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S-S bond formation are asynchronous, resulting in a high activation barrier (>40 kcal mol -1 ), making the reaction infeasible. However, the barrier can decrease below the S-N bond dissociation energy in RSNOs (≈30 kcal mol -1 ) upon transition into an aqueous environment that stabilizes Zi and provides a proton shuttle to synchronize the proton transfer and the S-S bond formation. These mechanistic features suggest that S-thiolation can easily lend itself to enzymatic catalysis and thus can be a possible route of endogenous HNO production. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic resonance imaging using chemical exchange saturation transfer

NASA Astrophysics Data System (ADS)

Park, Jaeseok

2012-10-01

Magnetic resonance imaging (MRI) has been widely used as a valuable diagnostic imaging modality that exploits water content and water relaxation properties to provide both structural and functional information with high resolution. Chemical exchange saturation transfer (CEST) in MRI has been recently introduced as a new mechanism of image contrast, wherein exchangeable protons from mobile proteins and peptides are indirectly detected through saturation transfer and are not observable using conventional MRI. It has been demonstrated that CEST MRI can detect important tissue metabolites and byproducts such as glucose, glycogen, and lactate. Additionally, CEST MRI is sensitive to pH or temperature and can calibrate microenvironment dependent on pH or temperature. In this work, we provide an overview on recent trends in CEST MRI, introducing general principles of CEST mechanism, quantitative description of proton transfer process between water pool and exchangeable solute pool in the presence or absence of conventional magnetization transfer effect, and its applications

Proton transfer in microbial electrolysis cells

DOE PAGES

Borole, Abhijeet P.; Lewis, Alex J.

2017-02-15

Proton transfer and electron transfer are of prime importance in the development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations have to be identified. Here in this study, the proton transfer rate was quantified for a microbial electrolysis cell (MEC) and its dependence on process parameters was investigated using a proton balance model. The reaction system consisted of a biomass-derived pyrolytic aqueous stream as amore » substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate and organic loading rate up to a maximum of 0.36 ± 0.01 moles per m 2 per h, equivalent to a hydrogen production rate of 9.08 L per L per day. Higher rates of hydrogen production, reaching 11.7 ± 0.2 L per L per day were achieved, when additional protons were provided via the cathode buffer. Electrochemical impedance spectroscopy shows that proton transfer was the dominant resistance in the production of hydrogen. The quantification of proton transfer rates for MECs with potential for biorefinery application and the demonstration of high hydrogen production rates approaching those required for commercial consideration indicate the strong potential of this technology for renewable hydrogen production. Understanding the transport phenomenon in bioelectrochemical cells is of great significance since these systems have potential for wide-ranging applications including energy production, bioremediation, chemical and nanomaterial synthesis, electro-fermentation, energy storage, desalination, and produced water treatment. Electron transfer in anode biofilms has been investigated extensively, but proton transfer studies are also important, since many cathodic half reactions require protons as the reactant. Determination of transport rates via proton balance was investigated in microbial electrolysis cells, which can be applied to other forms of microbial electrochemical systems. Lastly, these systems have a unique niche in the development of future biorefineries as a means of recovering energy from waste streams with potential for water recycle, making them an integral part of the water–energy nexus focus area.« less

Proton transfer in microbial electrolysis cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borole, Abhijeet P.; Lewis, Alex J.

Proton transfer and electron transfer are of prime importance in the development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations have to be identified. Here in this study, the proton transfer rate was quantified for a microbial electrolysis cell (MEC) and its dependence on process parameters was investigated using a proton balance model. The reaction system consisted of a biomass-derived pyrolytic aqueous stream as amore » substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate and organic loading rate up to a maximum of 0.36 ± 0.01 moles per m 2 per h, equivalent to a hydrogen production rate of 9.08 L per L per day. Higher rates of hydrogen production, reaching 11.7 ± 0.2 L per L per day were achieved, when additional protons were provided via the cathode buffer. Electrochemical impedance spectroscopy shows that proton transfer was the dominant resistance in the production of hydrogen. The quantification of proton transfer rates for MECs with potential for biorefinery application and the demonstration of high hydrogen production rates approaching those required for commercial consideration indicate the strong potential of this technology for renewable hydrogen production. Understanding the transport phenomenon in bioelectrochemical cells is of great significance since these systems have potential for wide-ranging applications including energy production, bioremediation, chemical and nanomaterial synthesis, electro-fermentation, energy storage, desalination, and produced water treatment. Electron transfer in anode biofilms has been investigated extensively, but proton transfer studies are also important, since many cathodic half reactions require protons as the reactant. Determination of transport rates via proton balance was investigated in microbial electrolysis cells, which can be applied to other forms of microbial electrochemical systems. Lastly, these systems have a unique niche in the development of future biorefineries as a means of recovering energy from waste streams with potential for water recycle, making them an integral part of the water–energy nexus focus area.« less

Aqueous proton transfer across single-layer graphene

DOE PAGES

Achtyl, Jennifer L.; Unocic, Raymond R.; Xu, Lijun; ...

2015-03-17

Proton transfer across single-layer graphene proceeds with large computed energy barriers and is thought to be unfavourable at room temperature unless nanoscale holes or dopants are introduced, or a potential bias is applied. Here we subject single-layer graphene supported on fused ​silica to cycles of high and low pH, and show that protons transfer reversibly from the aqueous phase through the graphene to the other side where they undergo acid–base chemistry with the silica hydroxyl groups. After ruling out diffusion through macroscopic pinholes, the protons are found to transfer through rare, naturally occurring atomic defects. Computer simulations reveal low energymore » barriers of 0.61–0.75 eV for aqueous proton transfer across hydroxyl-terminated atomic defects that participate in a Grotthuss-type relay, while ​pyrylium-like ether terminations shut down proton exchange. In conclusion, unfavourable energy barriers to helium and ​hydrogen transfer indicate the process is selective for aqueous protons.« less

Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

PubMed Central

Sharma, Vivek; Enkavi, Giray; Vattulainen, Ilpo; Róg, Tomasz; Wikström, Mårten

2015-01-01

Molecular oxygen acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the reduction of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochemical gradient, which drives the synthesis of ATP. Based on kinetic experiments on the O–O bond splitting transition of the catalytic cycle (A → PR), it has been proposed that the electron transfer to the binuclear iron–copper center of O2 reduction initiates the proton pump mechanism. This key electron transfer event is coupled to an internal proton transfer from a conserved glutamic acid to the proton-loading site of the pump. However, the proton may instead be transferred to the binuclear center to complete the oxygen reduction chemistry, which would constitute a short-circuit. Based on atomistic molecular dynamics simulations of cytochrome c oxidase in an explicit membrane–solvent environment, complemented by related free-energy calculations, we propose that this short-circuit is effectively prevented by a redox-state–dependent organization of water molecules within the protein structure that gates the proton transfer pathway. PMID:25646428

Infrared spectra of proton transfer complexes of the cycleanine alkaloid in solid state

NASA Astrophysics Data System (ADS)

Kasende, Okuma E.; de Waal, D.

2003-01-01

Proton transfer complexes obtained between the cycleanine alkaloid and hydrogen chloride, hydrogen bromide and nitric acids have been investigated by infrared spectroscopic technique between 4000 and 400 cm -1 in KBr. The vibrational perturbations brought about by proton transfer complex formation, discussed in terms of preferred site of interaction, show that the proton of the inorganic acids is transferred to cycleanine through one of its N sites.

Self-interaction effects on charge-transfer collisions

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Andrade, Xavier; ...

2017-04-27

In this article, we investigate the role of the self-interaction error in the simulation of collisions using time-dependent density functional theory (TDDFT) and Ehrenfest dynamics. In addition, we compare many different approximations of the exchange and correlation potential, using as a test system the collision of H + + CH 4 at 30 eV. We find that semilocal approximations, like the Perdew-Burke- Ernzerhof (PBE), and even hybrid functionals, such as the Becke, 3-parameter, Lee-Yang-Parr (B3LYP), produce qualitatively incorrect predictions for the scattering of the proton. This discrepancy appears because the self-interaction error allows the electrons to jump too easily tomore » the proton, leading to radically different forces with respect to the non-self-interacting case. Lastly, from our results, we conclude that using a functional that is self-interaction free is essential to properly describing charge-transfer collisions between ions and molecules in TDDFT.« less

Single mutations that redirect internal proton transfer in the ba3 oxidase from Thermus thermophilus

PubMed Central

Smirnova, Irina; Chang, Hsin-Yang; von Ballmoos, Christoph; Ädelroth, Pia; Gennis, Robert B.; Brzezinski, Peter

2014-01-01

The ba3-type cytochrome c oxidase from Thermus thermophilus is a membrane-bound proton pump. Results from earlier studies have shown that with the aa3-type oxidases proton uptake to the catalytic site and “pump site” occur simultaneously. However, with the ba3 oxidase the pump site is loaded before proton transfer to the catalytic site because the proton transfer to the latter is slower than with the aa3 oxidases. In addition, the timing of formation and decay of catalytic intermediates is different in the two types of oxidases. In the present study, we have investigated two mutant ba3 CytcOs in which residues of the proton pathway leading to the catalytic site as well as the pump site were exchanged, Thr312Val and Tyr244Phe. Even though the ba3 CytcO uses only a single proton pathway for transfer of the substrate and “pumped” protons, the amino-acid residue substitutions had distinctly different effects on the kinetics of proton transfer to the catalytic site and the pump site, respectively. The results indicate that the rates of these reactions can be modified independently by replacement of single residues within the proton pathway. Furthermore, the data suggest that the Thr312Val and Tyr244Phe mutations interfere with a structural rearrangement in the proton pathway that is rate limiting for proton transfer to the catalytic site. PMID:24004023

Synthesis, characterization, crystal structure and solution studies of a novel proton transfer (charge transfer) complex of 2,2‧-dipyridylamine with 2,6-pyridine dicarboxylic acid

NASA Astrophysics Data System (ADS)

Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Zarghampour, Fereshteh; Moghimi, Abolghasem; García-Granda, Santiago; Mendoza-Meroño, Rafael

2015-06-01

Reaction between 2,2‧-dipyridylamine (DPA) and 2,6-pyridine dicarboxylic acid (dipicolinic acid, dipicH2), in water results in the formation of a proton transfer or charge transfer (CT) complex, (DPAH)+(dipicH)-·H2O, 1. The characterization was performed using 1H NMR and FTIR spectroscopy, elemental analysis and X-ray crystallography. The crystal system is triclinic with space group P1. The structural investigations exhibit that the hydrogen bonds and π-π stacking interactions stabilize the crystal structure of proton transfer complex. The protonation constants of 2,6-pyridine dicarboxylic acid, 2,2‧-dipyridylamine and the equilibrium constants for dipic-DPA (1:1) proton transfer system were calculated by potentiometric pH titration method using Hyperquad2008 program. The stoichiometries of the proton transfer species in solution was in agreement with the solid state result.

Protons in non-ionic aqueous reverse micelles.

PubMed

Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

2007-05-03

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

A DFT study on NHC-catalyzed intramolecular aldehyde-ketone crossed-benzoin reaction: mechanism, regioselectivity, stereoselectivity, and role of NHC.

PubMed

Zhang, Wei; Wang, Yang; Wei, Donghui; Tang, Mingsheng; Zhu, Xinju

2016-07-06

A systematic theoretical study has been carried out to understand the mechanism and stereoselectivity of N-heterocyclic carbene (NHC)-catalyzed intramolecular crossed-benzoin reaction of enolizable keto-aldehyde using density functional theory (DFT) calculations. The calculated results reveal that the most favorable pathway contains four steps, i.e., the nucleophilic attack of NHC on the carbonyl carbon atom of a formyl group, the formation of a Breslow intermediate, a ring-closure process coupled with proton transfer, and regeneration of the catalyst. For the formation of the Breslow intermediate via the [1,2]-proton transfer process, apart from the direct proton transfer mechanism, the base Et3N and the in situ generated Brønsted acid Et3N·H(+) mediated proton transfer mechanisms have also been investigated; the free energy barriers for the crucial proton transfer steps are found to be significantly lowered by explicit inclusion of the Brønsted acid Et3N·H(+). The computational results show that the ring-closure process is the stereoselectivity-determining step, in which two chirality centers assigned on the coupling carbon atoms are formed, and the S-configured diastereomer is the predominant product, which is in good agreement with the experimental observations. NCI and NBO analyses are employed to disclose the origin of stereoselectivity and regioselectivity. Moreover, a global reaction index (GRI) analysis has been performed to confirm that NHC mainly plays the role of a Lewis base. The mechanistic insights obtained in the present study should be valuable for the rational design of an effective organocatalyst for this kind of reaction with high stereoselectivity and regioselectivity.

Concerted electron-proton transfer in the optical excitation of hydrogen-bonded dyes.

PubMed

Westlake, Brittany C; Brennaman, M Kyle; Concepcion, Javier J; Paul, Jared J; Bettis, Stephanie E; Hampton, Shaun D; Miller, Stephen A; Lebedeva, Natalia V; Forbes, Malcolm D E; Moran, Andrew M; Meyer, Thomas J; Papanikolas, John M

2011-05-24

The simultaneous, concerted transfer of electrons and protons--electron-proton transfer (EPT)--is an important mechanism utilized in chemistry and biology to avoid high energy intermediates. There are many examples of thermally activated EPT in ground-state reactions and in excited states following photoexcitation and thermal relaxation. Here we report application of ultrafast excitation with absorption and Raman monitoring to detect a photochemically driven EPT process (photo-EPT). In this process, both electrons and protons are transferred during the absorption of a photon. Photo-EPT is induced by intramolecular charge-transfer (ICT) excitation of hydrogen-bonded-base adducts with either a coumarin dye or 4-nitro-4'-biphenylphenol. Femtosecond transient absorption spectral measurements following ICT excitation reveal the appearance of two spectroscopically distinct states having different dynamical signatures. One of these states corresponds to a conventional ICT excited state in which the transferring H(+) is initially associated with the proton donor. Proton transfer to the base (B) then occurs on the picosecond time scale. The other state is an ICT-EPT photoproduct. Upon excitation it forms initially in the nuclear configuration of the ground state by application of the Franck-Condon principle. However, due to the change in electronic configuration induced by the transition, excitation is accompanied by proton transfer with the protonated base formed with a highly elongated (+)H ─ B bond. Coherent Raman spectroscopy confirms the presence of a vibrational mode corresponding to the protonated base in the optically prepared state.

Proton Transfer in Perfluorosulfonic Acid Fuel Cell Membranes with Differing Pendant Chains and Equivalent Weights.

PubMed

Thomaz, Joseph E; Lawler, Christian M; Fayer, Michael D

2017-05-04

Proton transfer in the nanoscopic water channels of polyelectrolyte fuel cell membranes was studied using a photoacid, 8-hydroxypyrene-1,3,6-trisulfonic acid sodium salt (HPTS), in the channels. The local environment of the probe was determined using 8-methoxypyrene-1,3,6-trisulfonic acid sodium salt (MPTS), which is not a photoacid. Three fully hydrated membranes, Nafion (DuPont) and two 3M membranes, were studied to determine the impact of different pendant chains and equivalent weights on proton transfer. Fluorescence anisotropy and excited state population decay data that characterize the local environment of the fluorescent probes and proton transfer dynamics were measured. The MPTS lifetime and anisotropy results show that most of the fluorescent probes have a bulk-like water environment with a relatively small fraction interacting with the channel wall. Measurements of the HPTS protonated and deprotonated fluorescent bands' population decays provided information on the proton transport dynamics. The decay of the protonated band from ∼0.5 ns to tens of nanoseconds is in part determined by dissociation and recombination with the HPTS, providing information on the ability of protons to move in the channels. The dissociation and recombination is manifested as a power law component in the protonated band fluorescence decay. The results show that equivalent weight differences between two 3M membranes resulted in a small difference in proton transfer. However, differences in pendant chain structure did significantly influence the proton transfer ability, with the 3M membranes displaying more facile transfer than Nafion.

Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin.

PubMed

Ge, Xiaoxia; Gunner, M R

2016-05-01

Bacteriorhodopsin, a light activated protein that creates a proton gradient in halobacteria, has long served as a simple model of proton pumps. Within bacteriorhodopsin, several key sites undergo protonation changes during the photocycle, moving protons from the higher pH cytoplasm to the lower pH extracellular side. The mechanism underlying the long-range proton translocation between the central (the retinal Schiff base SB216, D85, and D212) and exit clusters (E194 and E204) remains elusive. To obtain a dynamic view of the key factors controlling proton translocation, a systematic study using molecular dynamics simulation was performed for eight bacteriorhodopsin models varying in retinal isomer and protonation states of the SB216, D85, D212, and E204. The side-chain orientation of R82 is determined primarily by the protonation states of the residues in the EC. The side-chain reorientation of R82 modulates the hydrogen-bond network and consequently possible pathways of proton transfer. Quantum mechanical intrinsic reaction coordinate calculations of proton-transfer in the methyl guanidinium-hydronium-hydroxide model system show that proton transfer via a guanidinium group requires an initial geometry permitting proton donation and acceptance by the same amine. In all the bacteriorhodopsin models, R82 can form proton wires with both the CC and the EC connected by the same amine. Alternatively, rare proton wires for proton transfer from the CC to the EC without involving R82 were found in an O' state where the proton on D85 is transferred to D212. © 2016 Wiley Periodicals, Inc.

Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides

PubMed Central

Liu, Jian; McLuckey, Scott A.

2012-01-01

The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation. PMID:23264749

Probing the coupling between proton and electron transfer in Photosystem II core complexes containing a 3-fluorotyrosine

PubMed Central

Rappaport, Fabrice; Boussac, Alain; Force, Dee Ann; Peloquin, Jeffrey; Brynda, Marcin; Sugiura, Miwa; Un, Sun; Britt, R. David; Diner, Bruce A.

2009-01-01

The catalytic cycle of numerous enzymes involves the coupling between proton transfer and electron transfer. Yet, the understanding of this coordinated transfer in biological systems remains limited, likely because its characterization relies on the controlled but experimentally challenging modifications of the free energy changes associated with either the electron or proton transfer. We have performed such a study here in Photosystem II. The driving force for electron transfer from TyrZ to P680•+ has been decreased by ~ 80 meV by mutating the axial ligand of P680, and that for proton transfer upon oxidation of TyrZ by substituting a 3-fluorotyrosine (3F-TyrZ) for TyrZ. In Mn-depleted Photosystem II, the dependence upon pH of the oxidation rates of TyrZ and 3F-TyrZ were found to be similar. However, in the pH range where the phenolic hydroxyl of TyrZ is involved in a H-bond with a proton acceptor, the activation energy of the oxidation of 3F-TyrZ is decreased by 110 meV, a value which correlates with the in vitro finding of a 90 meV stabilization energy to the phenolate form of 3F-Tyr when compared to Tyr (Seyedsayamdost et al., 2006, JACS 128:1569–79). Thus, when the phenol of YZ acts as a H-bond-donor, its oxidation by P680•+ is controlled by its prior deprotonation. This contrasts with the situation prevailing at lower pH, where the proton acceptor is protonated and therefore unavailable, in which the oxidation-induced proton transfer from the phenolic hydroxyl of TyrZ has been proposed to occur concertedly with the electron transfer to P680•+. This suggests a switch between a concerted proton/electron transfer at pHs < 7.5 to a sequential one at pHs > 7.5 and illustrates the roles of the H-bond and of the likely salt-bridge existing between the phenolate and the nearby proton acceptor in determining the coupling between proton and electron transfer. PMID:19265377

Timing of electron and proton transfer in the ba(3) cytochrome c oxidase from Thermus thermophilus.

PubMed

von Ballmoos, Christoph; Lachmann, Peter; Gennis, Robert B; Ädelroth, Pia; Brzezinski, Peter

2012-06-05

Heme-copper oxidases are membrane-bound proteins that catalyze the reduction of O(2) to H(2)O, a highly exergonic reaction. Part of the free energy of this reaction is used for pumping of protons across the membrane. The ba(3) oxidase from Thermus thermophilus presumably uses a single proton pathway for the transfer of substrate protons used during O(2) reduction as well as for the transfer of the protons that are pumped across the membrane. The pumping stoichiometry (0.5 H(+)/electron) is lower than that of most other (mitochondrial-like) oxidases characterized to date (1 H(+)/electron). We studied the pH dependence and deuterium isotope effect of the kinetics of electron and proton transfer reactions in the ba(3) oxidase. The results from these studies suggest that the movement of protons to the catalytic site and movement to a site located some distance from the catalytic site [proposed to be a "proton-loading site" (PLS) for pumped protons] are separated in time, which allows individual investigation of these reactions. A scenario in which the uptake and release of a pumped proton occurs upon every second transfer of an electron to the catalytic site would explain the decreased proton pumping stoichiometry compared to that of mitochondrial-like oxidases.

Computational study of the structure-free radical scavenging relationship of procyanidins.

PubMed

Mendoza-Wilson, Ana María; Castro-Arredondo, Sergio Ivan; Balandrán-Quintana, René Renato

2014-10-15

Procyanidins (PCs) are effective free radical scavengers, however, their antioxidant ability is variable because they have different degrees of polymerisation, are composed by distinct types of subunits and are very susceptible to changes in conformation. In this work the structure-free radical scavenging relationship of monomers, dimers and trimers of PCs was studied through the hydrogen atom transfer (HAT), sequential proton-loss electron-transfer (SPLET) and single electron transfer followed by proton transfer (SET-PT) mechanisms in aqueous phase, employing the Density Functional Theory (DFT) computational method. The structure-free radical scavenging relationship of PCs showed a very similar behaviour in HAT and SET-PT mechanisms, but very different in the SPLET mechanism. The structural factor that showed more effects on the ability of PCs to scavenge free radicals in aqueous phase was the conformation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development and application of a water calorimeter for the absolute dosimetry of short-range particle beams.

PubMed

Renaud, J; Rossomme, S; Sarfehnia, A; Vynckier, S; Palmans, H; Kacperek, A; Seuntjens, J

2016-09-21

In this work, we describe a new design of water calorimeter built to measure absorbed dose in non-standard radiation fields with reference depths in the range of 6-20 mm, and its initial testing in clinical electron and proton beams. A functioning calorimeter prototype with a total water equivalent thickness of less than 30 mm was constructed in-house and used to obtain measurements in clinical accelerator-based 6 MeV and 8 MeV electron beams and cyclotron-based 60 MeV monoenergetic and modulated proton beams. Corrections for the conductive heat transfer due to dose gradients and non-water materials was also accounted for using a commercial finite element method software package. Absorbed dose to water was measured with an associated type A standard uncertainty of approximately 0.4% and 0.2% for the electron and proton beam experiments, respectively. In terms of thermal stability, drifts were on the order of a couple of hundred µK min -1 , with a short-term variation of 5-10 µK. Heat transfer correction factors ranged between 1.021 and 1.049. The overall combined standard uncertainty on the absorbed dose to water was estimated to be 0.6% for the 6 MeV and 8 MeV electron beams, as well as for the 60 MeV monoenergetic protons, and 0.7% for the modulated 60 MeV proton beam. This study establishes the feasibility of developing an absorbed dose transfer standard for short-range clinical electrons and protons and forms the basis for a transportable dose standard for direct calibration of ionization chambers in the user's beam. The largest contributions to the combined standard uncertainty were the positioning (⩽0.5%) and the correction due to conductive heat transfer (⩽0.4%). This is the first time that water calorimetry has been used in such a low energy proton beam.

Development and application of a water calorimeter for the absolute dosimetry of short-range particle beams

NASA Astrophysics Data System (ADS)

Renaud, J.; Rossomme, S.; Sarfehnia, A.; Vynckier, S.; Palmans, H.; Kacperek, A.; Seuntjens, J.

2016-09-01

In this work, we describe a new design of water calorimeter built to measure absorbed dose in non-standard radiation fields with reference depths in the range of 6-20 mm, and its initial testing in clinical electron and proton beams. A functioning calorimeter prototype with a total water equivalent thickness of less than 30 mm was constructed in-house and used to obtain measurements in clinical accelerator-based 6 MeV and 8 MeV electron beams and cyclotron-based 60 MeV monoenergetic and modulated proton beams. Corrections for the conductive heat transfer due to dose gradients and non-water materials was also accounted for using a commercial finite element method software package. Absorbed dose to water was measured with an associated type A standard uncertainty of approximately 0.4% and 0.2% for the electron and proton beam experiments, respectively. In terms of thermal stability, drifts were on the order of a couple of hundred µK min-1, with a short-term variation of 5-10 µK. Heat transfer correction factors ranged between 1.021 and 1.049. The overall combined standard uncertainty on the absorbed dose to water was estimated to be 0.6% for the 6 MeV and 8 MeV electron beams, as well as for the 60 MeV monoenergetic protons, and 0.7% for the modulated 60 MeV proton beam. This study establishes the feasibility of developing an absorbed dose transfer standard for short-range clinical electrons and protons and forms the basis for a transportable dose standard for direct calibration of ionization chambers in the user’s beam. The largest contributions to the combined standard uncertainty were the positioning (⩽0.5%) and the correction due to conductive heat transfer (⩽0.4%). This is the first time that water calorimetry has been used in such a low energy proton beam.

FTIR spectroscopic study on individual amino acid residues in the proton pumping process of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Liu, Xiaomei

1998-05-01

My thesis project has concentrated on clarifying the role of individual amino acids such as tyrosine, arginine and threonine in the active proton transferring process of Bacteriorhodopsin(bR). BR is a protein found in the purple membrane of Halobacteria salinarium. The main function of bR is to transfer a proton from the interior side of the cell to the external medium upon illumination by visible light. BR belongs to a family of retinal- containing membrane proteins which includes rhodopsin, a visual receptor found in the eye, and sensory rhodopsin I, a light receptor for phototaxis found in H. salinarium. Complete understanding of the proton transferring mechanism of bR can help explain the energy transduction and active ion transport in biological systems. This information also provides insight into other members of the retinal-containing protein family. To study the behavior of a single amino acid in a protein which consists of 248 amino acids, I employed the Fourier transform infrared (FTIR) difference spectroscopy technique. This was combined with the recently developed genetic engineering method of site directed isotope labeling (SDIL). As complementary work, I also characterized the vibrational properties of individual amino acids in various environments. Because of the high resolution and sensitivity of FTIR difference spectroscopy, along with the ability of SDIL to detect structural changes at the single amino acid level, we are able to determine changes in the structure of specific amino acids at different steps in bR photocycle. My research results provide strong evidence for a proton pump model. This model predicts the participation of tyrosine 185 and one or more threonines in a hydrogen bonded chain which can transfer proton across the membrane. My data also suggest a more accurate model for the proton release step which involves arginine 82.

Time-dependent calculations of transfer ionization by fast proton-helium collision in one-dimensional kinematics

NASA Astrophysics Data System (ADS)

Serov, Vladislav V.; Kheifets, A. S.

2014-12-01

We analyze a transfer ionization (TI) reaction in the fast proton-helium collision H++He →H0+He2 ++ e- by solving a time-dependent Schrödinger equation (TDSE) under the classical projectile motion approximation in one-dimensional kinematics. In addition, we construct various time-independent analogs of our model using lowest-order perturbation theory in the form of the Born series. By comparing various aspects of the TDSE and the Born series calculations, we conclude that the recent discrepancies of experimental and theoretical data may be attributed to deficiency of the Born models used by other authors. We demonstrate that the correct Born series for TI should include the momentum-space overlap between the double-ionization amplitude and the wave function of the transferred electron.

Coupled-Sturmian and perturbative treatments of electron transfer and ionization in high-energy p-He+ collisions

NASA Astrophysics Data System (ADS)

Winter, Thomas G.; Alston, Steven G.

1992-02-01

Cross sections have been determined for electron transfer and ionization in collisions between protons and He+ ions at proton energies from several hundred kilo-electron-volts to 2 MeV. A coupled-Sturmian approach is taken, extending the work of Winter [Phys. Rev. A 35, 3799 (1987)] and Stodden et al. [Phys. Rev. A 41, 1281 (1990)] to high energies where perturbative approaches are expected to be valid. An explicit connection is made with the first-order Born approximation for ionization and the impulse version of the distorted, strong-potential Born approximation for electron transfer. The capture cross section is shown to be affected by the presence of target basis functions of positive energy near v2/2, corresponding to the Thomas mechanism.

Quantum-mechanical analysis of amino acid residues function in the proton transport during F0F1-ATP synthase catalytic cycle

NASA Astrophysics Data System (ADS)

Ivontsin, L. A.; Mashkovtseva, E. V.; Nartsissov, Ya R.

2017-11-01

Implications of quantum-mechanical approach to the description of proton transport in biological systems are a tempting subject for an overlapping of fundamental physics and biology. The model of proton transport through the integrated membrane enzyme FoF1-ATP synthase responsible for ATP synthesis was developed. The estimation of the mathematical expectation of the proton transfer time through the half-channel was performed. Observed set of proton pathways through the inlet half-channel showed the nanosecond timescale highly dependable of some amino acid residues. There were proposed two types of crucial amino acids: critically localized (His245) and being a part of energy conserving system (Asp119).

Nanogranular SiO2 proton gated silicon layer transistor mimicking biological synapses

NASA Astrophysics Data System (ADS)

Liu, M. J.; Huang, G. S.; Feng, P.; Guo, Q. L.; Shao, F.; Tian, Z. A.; Li, G. J.; Wan, Q.; Mei, Y. F.

2016-06-01

Silicon on insulator (SOI)-based transistors gated by nanogranular SiO2 proton conducting electrolytes were fabricated to mimic synapse behaviors. This SOI-based device has both top proton gate and bottom buried oxide gate. Electrical transfer properties of top proton gate show hysteresis curves different from those of bottom gate, and therefore, excitatory post-synaptic current and paired pulse facilitation (PPF) behavior of biological synapses are mimicked. Moreover, we noticed that PPF index can be effectively tuned by the spike interval applied on the top proton gate. Synaptic behaviors and functions, like short-term memory, and its properties are also experimentally demonstrated in our device. Such SOI-based electronic synapses are promising for building neuromorphic systems.

Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

PubMed

Chakravorty, Dhruva K; Hammes-Schiffer, Sharon

2010-06-02

The two proton transfer reactions catalyzed by ketosteroid isomerase (KSI) involve a dienolate intermediate stabilized by hydrogen bonds with Tyr14 and Asp99. Molecular dynamics simulations based on an empirical valence bond model are used to examine the impact of mutating these residues on the hydrogen-bonding patterns, conformational changes, and van der Waals and electrostatic interactions during the proton transfer reactions. While the rate constants for the two proton transfer steps are similar for wild-type (WT) KSI, the simulations suggest that the rate constant for the first proton transfer step is smaller in the mutants due to the significantly higher free energy of the dienolate intermediate relative to the reactant. The calculated rate constants for the mutants D99L, Y14F, and Y14F/D99L relative to WT KSI are qualitatively consistent with the kinetic experiments indicating a significant reduction in the catalytic rates along the series of mutants. In the simulations, WT KSI retained two hydrogen-bonding interactions between the substrate and the active site, while the mutants typically retained only one hydrogen-bonding interaction. A new hydrogen-bonding interaction between the substrate and Tyr55 was observed in the double mutant, leading to the prediction that mutation of Tyr55 will have a greater impact on the proton transfer rate constants for the double mutant than for WT KSI. The electrostatic stabilization of the dienolate intermediate relative to the reactant was greater for WT KSI than for the mutants, providing a qualitative explanation for the significantly reduced rates of the mutants. The active site exhibited restricted motion during the proton transfer reactions, but small conformational changes occurred to facilitate the proton transfer reactions by strengthening the hydrogen-bonding interactions and by bringing the proton donor and acceptor closer to each other with the proper orientation for proton transfer. Thus, these calculations suggest that KSI forms a preorganized active site but that the structure of this preorganized active site is altered upon mutation. Moreover, small conformational changes due to stochastic thermal motions are required within this preorganized active site to facilitate the proton transfer reactions.

A cluster of carboxylic groups in PsbO protein is involved in proton transfer from the water oxidizing complex of Photosystem II.

PubMed

Shutova, Tatiana; Klimov, Vyacheslav V; Andersson, Bertil; Samuelsson, Göran

2007-06-01

The hypothesis presented here for proton transfer away from the water oxidation complex of Photosystem II (PSII) is supported by biochemical experiments on the isolated PsbO protein in solution, theoretical analyses of better understood proton transfer systems like bacteriorhodopsin and cytochrome oxidase, and the recently published 3D structure of PS II (Pdb entry 1S5L). We propose that a cluster of conserved glutamic and aspartic acid residues in the PsbO protein acts as a buffering network providing efficient acceptors of protons derived from substrate water molecules. The charge delocalization of the cluster ensures readiness to promptly accept the protons liberated from substrate water. Therefore protons generated at the catalytic centre of PSII need not be released into the thylakoid lumen as generally thought. The cluster is the beginning of a localized, fast proton transfer conduit on the lumenal side of the thylakoid membrane. Proton-dependent conformational changes of PsbO may play a role in the regulation of both supply of substrate water to the water oxidizing complex and the resultant proton transfer.

Proton transfer events in GFP.

PubMed

Di Donato, Mariangela; van Wilderen, Luuk J G W; Van Stokkum, Ivo H M; Stuart, Thomas Cohen; Kennis, John T M; Hellingwerf, Klaas J; van Grondelle, Rienk; Groot, Marie Louise

2011-09-28

Proton transfer is one of the most important elementary processes in biology. Green fluorescent protein (GFP) serves as an important model system to elucidate the mechanistic details of this reaction, because in GFP proton transfer can be induced by light absorption. Illumination initiates proton transfer through a 'proton-wire', formed by the chromophore (the proton donor), water molecule W22, Ser205 and Glu222 (the acceptor), on a picosecond time scale. To obtain a more refined view of this process, we have used a combined approach of time resolved mid-infrared spectroscopy and visible pump-dump-probe spectroscopy to resolve with atomic resolution how and how fast protons move through this wire. Our results indicate that absorption of light by GFP induces in 3 ps (10 ps in D(2)O) a shift of the equilibrium positions of all protons in the H-bonded network, leading to a partial protonation of Glu222 and to a so-called low barrier hydrogen bond (LBHB) for the chromophore's proton, giving rise to dual emission at 475 and 508 nm. This state is followed by a repositioning of the protons on the wire in 10 ps (80 ps in D(2)O), ultimately forming the fully deprotonated chromophore and protonated Glu222.

Conserved phosphoryl transfer mechanisms within kinase families and the role of the C8 proton of ATP in the activation of phosphoryl transfer

PubMed Central

2012-01-01

Background The kinome is made up of a large number of functionally diverse enzymes, with the classification indicating very little about the extent of the conserved kinetic mechanisms associated with phosphoryl transfer. It has been demonstrated that C8-H of ATP plays a critical role in the activity of a range of kinase and synthetase enzymes. Results A number of conserved mechanisms within the prescribed kinase fold families have been identified directly utilizing the C8-H of ATP in the initiation of phosphoryl transfer. These mechanisms are based on structurally conserved amino acid residues that are within hydrogen bonding distance of a co-crystallized nucleotide. On the basis of these conserved mechanisms, the role of the nucleotide C8-H in initiating the formation of a pentavalent intermediate between the γ-phosphate of the ATP and the substrate nucleophile is defined. All reactions can be clustered into two mechanisms by which the C8-H is induced to be labile via the coordination of a backbone carbonyl to C6-NH2 of the adenyl moiety, namely a "push" mechanism, and a "pull" mechanism, based on the protonation of N7. Associated with the "push" mechanism and "pull" mechanisms are a series of proton transfer cascades, initiated from C8-H, via the tri-phosphate backbone, culminating in the formation of the pentavalent transition state between the γ-phosphate of the ATP and the substrate nucleophile. Conclusions The "push" mechanism and a "pull" mechanism are responsible for inducing the C8-H of adenyl moiety to become more labile. These mechanisms and the associated proton transfer cascades achieve the proton transfer via different family-specific conserved sets of amino acids. Each of these mechanisms would allow for the regulation of the rate of formation of the pentavalent intermediate between the ATP and the substrate nucleophile. Phosphoryl transfer within kinases is therefore a specific event mediated and regulated via the coordination of the adenyl moiety of ATP and the C8-H of the adenyl moiety. PMID:22397702

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2015-11-21

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at highmore » temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes.« less

Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels.

PubMed

Tahat, Amani; Martí, Jordi

2016-07-01

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 Å(-3) have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Combined TDDFT and AIM Insights into Photoinduced Excited State Intramolecular Proton Transfer (ESIPT) Mechanism in Hydroxyl- and Amino-Anthraquinone Solution.

PubMed

Zheng, Daoyuan; Zhang, Mingzhen; Zhao, Guangjiu

2017-10-23

Time-dependent density functional theory (TDDFT) and atoms in molecules (AIM) theory are combined to study the photoinduced excited state intramolecular proton transfer (ESIPT) dynamics for eight anthraquinones (AQs) derivatives in solution. The calculated absorption and emission spectra are consistent with the available experimental data, verifying the suitability of the theory selected. The systems with the excited-state exothermic proton transfer, such as 1-HAQ, 1,5-DHAQ and TFAQ, emit completely from transfer structure (T), while the reactions for those without ESIPT including 1,4-DHAQ and AAAQ appear to be endothermic. Three reaction properties of three systems (1,8-DHAQ, DCAQ and CAAQ) are between the exothermic and endothermic, sensitive to the solvent. Energy scanning shows that 1,4-DHAQ and AAAQ exhibit the higher ESIPT energy barriers compared to 1-HAQ, 1,5-DHAQ and TFAQ with the "barrierless" ESIPT process. The ESIPT process is facilitated by the strengthening of hydrogen bonds in excited state. With AIM theory, it is observed that the change in electrons density ρ(r) and potential energy density V(r) at BCP position between ground state and excited state are crucial factors to quantitatively elucidate the ESIPT.

Concerted electron-proton transfer in the optical excitation of hydrogen-bonded dyes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westlake, Brittany C.; Brennaman, Kyle M.; Concepcion, Javier J.

2011-05-24

The simultaneous, concerted transfer of electrons and protons—electron-proton transfer (EPT)—is an important mechanism utilized in chemistry and biology to avoid high energy intermediates. There are many examples of thermally activated EPT in ground-state reactions and in excited states following photoexcitation and thermal relaxation. Here we report application of ultrafast excitation with absorption and Raman monitoring to detect a photochemically driven EPT process (photo-EPT). In this process, both electrons and protons are transferred during the absorption of a photon. Photo-EPT is induced by intramolecular charge-transfer (ICT) excitation of hydrogen-bonded-base adducts with either a coumarin dye or 4-nitro-4'-biphenylphenol. Femtosecond transient absorption spectralmore » measurements following ICT excitation reveal the appearance of two spectroscopically distinct states having different dynamical signatures. One of these states corresponds to a conventional ICT excited state in which the transferring H⁺ is initially associated with the proton donor. Proton transfer to the base (B) then occurs on the picosecond time scale. The other state is an ICT-EPT photoproduct. Upon excitation it forms initially in the nuclear configuration of the ground state by application of the Franck–Condon principle. However, due to the change in electronic configuration induced by the transition, excitation is accompanied by proton transfer with the protonated base formed with a highly elongated ⁺H–B bond. Coherent Raman spectroscopy confirms the presence of a vibrational mode corresponding to the protonated base in the optically prepared state.« less

Acid-induced exchange of the imino proton in G.C pairs.

PubMed Central

Nonin, S; Leroy, J L; Gueron, M

1996-01-01

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine. PMID:8604298

Acid-induced exchange of the imino proton in G.C pairs.

PubMed

Nonin, S; Leroy, J L; Gueron, M

1996-02-15

Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine.

A method to calculate fission-fragment yields Y(Z,N) versus proton and neutron number in the Brownian shape-motion model

DOE PAGES

Moller, Peter; Ichikawa, Takatoshi

2015-12-23

In this study, we propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q 2), neck d, left nascent fragment spheroidal deformation ϵ f1, right nascent fragment deformation ϵ f2 and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method tomore » calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the “compound-system” model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition.« less

Imaging of endogenous exchangeable proton signals in the human brain using frequency labeled exchange transfer imaging.

PubMed

Yadav, Nirbhay N; Jones, Craig K; Hua, Jun; Xu, Jiadi; van Zijl, Peter C M

2013-04-01

To image endogenous exchangeable proton signals in the human brain using a recently reported method called frequency labeled exchange transfer (FLEX) MRI. As opposed to labeling exchangeable protons using saturation (i.e., chemical exchange saturation transfer, or CEST), FLEX labels exchangeable protons with their chemical shift evolution. The use of short high-power frequency pulses allows more efficient labeling of rapidly exchanging protons, while time domain acquisition allows removal of contamination from semi-solid magnetization transfer effects. FLEX-based exchangeable proton signals were detected in human brain over the 1-5 ppm frequency range from water. Conventional magnetization transfer contrast and the bulk water signal did not interfere in the FLEX spectrum. The information content of these signals differed from in vivo CEST data in that the average exchange rate of these signals was 350-400 s(-1) , much faster than the amide signal usually detected using direct saturation (∼30 s(-1) ). Similarly, fast exchanging protons could be detected in egg white in the same frequency range where amide and amine protons of mobile proteins and peptides are known to resonate. FLEX MRI in the human brain preferentially detects more rapidly exchanging amide/amine protons compared to traditional CEST experiments, thereby changing the information content of the exchangeable proton spectrum. This has the potential to open up different types of endogenous applications as well as more easy detection of rapidly exchanging protons in diaCEST agents or fast exchanging units such as water molecules in paracest agents without interference of conventional magnetization transfer contrast. Copyright © 2013 Wiley Periodicals, Inc.

Study of ring influence and electronic response to proton transfer reactions. Reaction electronic flux analysis.

PubMed

Herrera, Barbara

2011-05-01

In this article, a theoretical study of 1-5 proton transfers is presented. Two model systems which represent 1-5 proton transfer, 3-hidroxy-2-propenimine and salicyldenaniline have been studied as shown in Fig. 1. For this purpose, a DFT/B3LYP/6-311+G**, reaction force and reaction electronic flux analysis is made. The obtained results indicate that both proton transfers exhibit energetic and electronic differences emphasizing the role of the neighbor ring and the impact of conjugation on electronic properties.

Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerlits, Oksana; Wymore, Troy; Das, Amit

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

DOE PAGES

Gerlits, Oksana; Wymore, Troy; Das, Amit; ...

2016-03-09

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

PubMed

Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey

2016-04-11

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scaling violations of the proton structure function F2 at small x

NASA Astrophysics Data System (ADS)

Abt, I.; Ahmed, T.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bärwolff, H.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bergstein, H.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Biddulph, P.; Binder, E.; Bischoff, A.; Bizot, J. C.; Blobel, V.; Borras, K.; Bosetti, P. C.; Boudry, V.; Bourdarios, C.; Brasse, F.; Braun, U.; Braunschweig, W.; Bruncko, D.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Colombo, M.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Danilov, M.; Dann, A. W. E.; Dau, W. D.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; Devel, M.; De Roeck, A.; Dingus, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Drescher, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebbinghaus, R.; Eberle, M.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellis, N. N.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Fensome, I. F.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Flauger, W.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Fuhrmann, P.; Gabathuler, E.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gellrich, A.; Gennis, M.; Genzel, H.; Gerhards, R.; Godfrey, L.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goodall, A. M.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Greif, H.; Grindhammer, G.; Gruber, C.; Haack, J.; Hajduk, L.; Hamon, O.; Handschuh, D.; Hanlon, E. M.; Hapke, M.; Harjes, J.; Haydar, R.; Haynes, W. J.; Heatherington, J.; Hedberg, V.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herma, R.; Herynek, I.; Hildesheim, W.; Hill, P.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Huet, Ph.; Hufnagel, H.; Huot, N.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kasarian, S.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Kaufmann, H. H.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Langkau, R.; Lanius, P.; Laporte, J. F.; Lebedev, A.; Leuschner, A.; Leverenz, C.; Levonian, S.; Lewin, D.; Ley, Ch.; Lindner, A.; Lindström, G.; Linsel, F.; Lipinski, J.; Loch, P.; Lohmander, H.; Lopez, G. C.; Lüers, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, A.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milone, V.; Monnier, E.; Moreau, F.; Moreels, J.; Morris, J. V.; Müller, K.; Murín, P.; Murray, S. A.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Niebergall, F.; Niebuhr, C.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Orenstein, S.; Ould-Saada, F.; Pascaud, C.; Patel, G. D.; Peppel, E.; Peters, S.; Phillips, H. T.; Phillips, J. P.; Pichler, Ch.; Pilgram, W.; Pitzl, D.; Prell, S.; Prosi, R.; Rädel, G.; Raupach, F.; Rauschnabel, K.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Robertson, S. M.; Robmann, P.; Roosen, R.; Rostovtsev, A.; Royon, C.; Rudowicz, M.; Ruffer, M.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Savitsky, M.; Schacht, P.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmitz, W.; Schöning, A.; Schröder, V.; Schulz, M.; Schwab, B.; Schwind, A.; Scobel, W.; Seehausen, U.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Smolik, L.; Soloviev, Y.; Spitzer, H.; Staroba, P.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stösslein, U.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Tichomirov, I.; Truöl, P.; Turnau, J.; Tutas, J.; Urban, L.; Usik, A.; Valkar, S.; Valkarova, A.; Vallée, C.; Van Esch, P.; Vartapetian, A.; Vazdik, Y.; Vecko, M.; Verrecchia, P.; Vick, R.; Villet, G.; Vogel, E.; Wacker, K.; Walker, I. W.; Walther, A.; Weber, G.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wolff, Th.; Womersley, L. A.; Wright, A. E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Závada, P.; Zeitnitz, C.; Ziaeepour, H.; Zimmer, M.; Zimmermann, W.; Zomer, F.; H1 Collaboration

1994-01-01

An analysis is presented of scaling violations of the proton structure function F2( x, Q2) measured with the H1 detector at HERA in the range of Bjorken x values between x = 3 × 10 -4 and 10 -2 for four-momentum transfers Q> 2 larger than 8.7 GeV 2. The structure function F2( x, Q2) is observed to rise linearly with ln Q2. Under the assumption that the observed scaling violations at small x ⩽ 0.01 are described correctly by perturbative QCD, an estimate is obtained of the gluon distribution function G( x, Q02) at Q22 = 20 GeV 2.

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander; Hammes-Schiffer, Sharon

2015-11-17

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approachmore » in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences (applications to molecular electrocatalysts).« less

Cavity hydration dynamics in cytochrome c oxidase and functional implications

PubMed Central

Son, Chang Yun; Cui, Qiang

2017-01-01

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport. PMID:28973914

The Effect of Isotopic Substitution on Quantum Proton Transfer Across Short Water Bridges in Biological Systems

NASA Astrophysics Data System (ADS)

Blazejewski, Jacob; Schultz, Chase; Mazzuca, James

2015-03-01

Many biological systems utilize water chains to transfer charge over long distances by means of an excess proton. This study examines how quantum effects impact these reactions in a small model system. The model consists of a water molecule situated between an imidazole donor and acceptor group, which simulate a fixed amino acid backbone. A one dimensional energy profile is evaluated using density functional theory at the 6-31G*/B3LYP level, which generates a barrier with a width of 0.6 Å and a height of 20.7 kcal/mol. Quantum transmission probability is evaluated by solving the time dependent Schrödinger equation on a grid. Isotopic effects are examined by performing calculations with both hydrogen and deuterium. The ratio of hydrogen over the deuterium shows a 130-fold increase in transmission probability at low temperatures. This indicates a substantial quantum tunneling effect. The study of higher dimensional systems as well as increasing the number of water molecules in the chain will be necessary to fully describe the proton transfer process. Alma College Provost's Office.

Measurement of Lactate Content and Amide Proton Transfer Values in the Basal Ganglia of a Neonatal Piglet Hypoxic-Ischemic Brain Injury Model Using MRI.

PubMed

Zheng, Y; Wang, X-M

2017-04-01

As amide proton transfer imaging is sensitive to protein content and intracellular pH, it has been widely used in the nervous system, including brain tumors and stroke. This work aimed to measure the lactate content and amide proton transfer values in the basal ganglia of a neonatal piglet hypoxic-ischemic brain injury model by using MR spectroscopy and amide proton transfer imaging. From 58 healthy neonatal piglets (3-5 days after birth; weight, 1-1.5 kg) selected initially, 9 piglets remained in the control group and 43 piglets, in the hypoxic-ischemic brain injury group. Single-section amide proton transfer imaging was performed at the coronal level of the basal ganglia. Amide proton transfer values of the bilateral basal ganglia were measured in all piglets. The ROI of MR spectroscopy imaging was the right basal ganglia, and the postprocessing was completed with LCModel software. After hypoxic-ischemic insult, the amide proton transfer values immediately decreased, and at 0-2 hours, they remained at their lowest level. Thereafter, they gradually increased and finally exceeded those of the control group at 48-72 hours. After hypoxic-ischemic insult, the lactate content increased immediately, was maximal at 2-6 hours, and then gradually decreased to the level of the control group. The amide proton transfer values were negatively correlated with lactate content ( r = -0.79, P < .05). This observation suggests that after hypoxic-ischemic insult, the recovery of pH was faster than that of lactate homeostasis. © 2017 by American Journal of Neuroradiology.

Noninvasive amide proton transfer magnetic resonance imaging in evaluating the grading and cellularity of gliomas.

PubMed

Bai, Yan; Lin, Yusong; Zhang, Wei; Kong, Lingfei; Wang, Lifu; Zuo, Panli; Vallines, Ignacio; Schmitt, Benjamin; Tian, Jie; Song, Xiaolei; Zhou, Jinyuan; Wang, Meiyun

2017-01-24

Using noninvasive magnetic resonance imaging techniques to accurately evaluate the grading and cellularity of gliomas is beneficial for improving the patient outcomes. Amide proton transfer imaging is a noninvasive molecular magnetic resonance imaging technique based on chemical exchange saturation transfer mechanism that detects endogenous mobile proteins and peptides in biological tissues. Between August 2012 and November 2015, a total number of 44 patients with pathologically proven gliomas were included in this study. We compared the capability of amide proton transfer magnetic resonance imaging with that of noninvasive diffusion-weighted imaging and noninvasive 3-dimensional pseudo-continuous arterial spin imaging in evaluating the grading and cellularity of gliomas. Our results reveal that amide proton transfer magnetic resonance imaging is a superior imaging technique to diffusion-weighted imaging and 3-dimensional pseudo-continuous arterial spin imaging in the grading of gliomas. In addition, our results showed that the Ki-67 index correlated better with the amide proton transfer-weighted signal intensity than with the apparent diffusion coefficient value or the cerebral blood flow value in the gliomas. Amide proton transfer magnetic resonance imaging is a promising method for predicting the grading and cellularity of gliomas.

Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase.

PubMed

Zelleke, Theodros; Marx, Dominik

2017-01-18

The rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase, which is proton abstraction from the native substrate methylamine, is investigated using accelerated QM/MM molecular dynamics simulations at room temperature. Generation of the multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace maps two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 Å, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms-the OD2 site-is slightly favored in methylamine dehydrogenase by approximately 2 kcal mol -1 , both kinetically and thermodynamically. Mechanistic analyses reveal that the hydrogen bond between Thr122β and OD1 is always present in the transition state independently of the proton transfer channel. Population analysis confirms that the electronic charge gained upon oxidation of the substrate is delocalized within the ring systems of the tryptophan tryptophylquinone cofactor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Redox reaction characteristics of riboflavin: a fluorescence spectroelectrochemical analysis and density functional theory calculation.

PubMed

Chen, Wei; Chen, Jie-Jie; Lu, Rui; Qian, Chen; Li, Wen-Wei; Yu, Han-Qing

2014-08-01

Riboflavin (RF), the primary redox active component of flavin, is involved in many redox processes in biogeochemical systems. Despite of its wide distribution and important roles in environmental remediation, its redox behaviors and reaction mechanisms in hydrophobic sites remain unclear yet. In this study, spectroelectrochemical analysis and density functional theory (DFT) calculation were integrated to explore the redox behaviors of RF in dimethyl sulfoxide (DMSO), which was used to create a hydrophobic environment. Specifically, cyclic voltafluorometry (CVF) and derivative cyclic voltafluorometry (DCVF) were employed to track the RF concentration changing profiles. It was found that the reduction contained a series of proton-coupled electron transfers dependent of potential driving force. In addition to the electron transfer-chemical reaction-electron transfer process, a disproportionation (DISP1) process was also identified to be involved in the reduction. The redox potential and free energy of each step obtained from the DFT calculations further confirmed the mechanisms proposed based on the experimental results. The combination of experimental and theoretical approaches yields a deep insight into the characteristics of RF in environmental remediation and better understanding about the proton-coupled electron transfer mechanisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Cytochrome bc1 complexes of microorganisms.

PubMed Central

Trumpower, B L

1990-01-01

The cytochrome bc1 complex is the most widely occurring electron transfer complex capable of energy transduction. Cytochrome bc1 complexes are found in the plasma membranes of phylogenetically diverse photosynthetic and respiring bacteria, and in the inner mitochondrial membrane of all eucaryotic cells. In all of these species the bc1 complex transfers electrons from a low-potential quinol to a higher-potential c-type cytochrome and links this electron transfer to proton translocation. Most bacteria also possess alternative pathways of quinol oxidation capable of circumventing the bc1 complex, but these pathways generally lack the energy-transducing, protontranslocating activity of the bc1 complex. All cytochrome bc1 complexes contain three electron transfer proteins which contain four redox prosthetic groups. These are cytochrome b, which contains two b heme groups that differ in their optical and thermodynamic properties; cytochrome c1, which contains a covalently bound c-type heme; and a 2Fe-2S iron-sulfur protein. The mechanism which links proton translocation to electron transfer through these proteins is the proton motive Q cycle, and this mechanism appears to be universal to all bc1 complexes. Experimentation is currently focused on understanding selected structure-function relationships prerequisite for these redox proteins to participate in the Q-cycle mechanism. The cytochrome bc1 complexes of mitochondria differ from those of bacteria, in that the former contain six to eight supernumerary polypeptides, in addition to the three redox proteins common to bacteria and mitochondria. These extra polypeptides are encoded in the nucleus and do not contain redox prosthetic groups. The functions of the supernumerary polypeptides of the mitochondrial bc1 complexes are generally not known and are being actively explored by genetically manipulating these proteins in Saccharomyces cerevisiae. Images PMID:2163487

Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH.

PubMed

Tamogami, Jun; Sato, Keitaro; Kurokawa, Sukuna; Yamada, Takumi; Nara, Toshifumi; Demura, Makoto; Miyauchi, Seiji; Kikukawa, Takashi; Muneyuki, Eiro; Kamo, Naoki

2016-02-23

Proteorhodopsin (PR) is an outward light-driven proton pump observed in marine eubacteria. Despite many structural and functional similarities to bacteriorhodopsin (BR) in archaea, which also acts as an outward proton pump, the mechanism of the photoinduced proton release and uptake is different between two H(+)-pumps. In this study, we investigated the pH dependence of the photocycle and proton transfer in PR reconstituted with the phospholipid membrane under alkaline conditions. Under these conditions, as the medium pH increased, a blue-shifted photoproduct (defined as Ma), which is different from M, with a pKa of ca. 9.2 was produced. The sequence of the photoinduced proton uptake and release during the photocycle was inverted with the increase in pH. A pKa value of ca. 9.5 was estimated for this inversion and was in good agreement with the pKa value of the formation of Ma (∼ 9.2). In addition, we measured the photoelectric current generated by PRs attached to a thin polymer film at varying pH. Interestingly, increases in the medium pH evoked bidirectional photocurrents, which may imply a possible reversal of the direction of the proton movement at alkaline pH. On the basis of these findings, a putative photocycle and proton transfer scheme in PR under alkaline pH conditions was proposed.

Hydration of Concrete: The First Steps.

PubMed

Thissen, Peter; Natzeck, Carsten; Giraudo, Nicolas; Weidler, Peter; Wöll, Christof

2018-04-12

Concrete is the most important construction material used by mankind and, at the same time, one of the most complex substances known in materials science. Since this mineral compound is highly porous, a better understanding of its surface chemistry, and in particular the reaction with water, is urgently required to understand and avoid corrosion of infrastructure like buildings and bridges. We have gained insight into proton transfer from concrete upon contact with water by applying the so-called Surface Science approach to a well-defined mineral, Wollastonite. Data from IR (infrared) spectroscopy reveal that exposure of this calcium-silicate (CS) substrate to H 2 O leads to dissociation and the formation of OH-species. This proton transfer is a chemical reaction of key importance, since on the one hand it triggers the conversion of cement into concrete (a calcium-silicate-hydrate phase), but on the other hand also governs the corrosion of concrete. Interestingly, we find that no proton transfer takes place when the same surface is exposed to methanol. In order to understand this unexpected difference, the analysis of the spectroscopic data obtained was aided by a detailed, first-principles computational study employing density functional theory (DFT). The combined experimental and theoretical effort allows derivation of a consistent picture of proton transfer reactions occurring in CS and CSH phases. Implications for strategies to protect this backbone of urban infrastructure from corrosion in harsh, aqueous environments will be discussed. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proton transfer from water to ketyl radical anion: Assessment of critical size of hydrated cluster and free energy barrier in solution from first principles simulations

NASA Astrophysics Data System (ADS)

Biswas, Sohag; Dasgupta, Teesta; Mallik, Bhabani S.

2016-09-01

We present the reactivity of an organic intermediate by studying the proton transfer process from water to ketyl radical anion using gas phase electronic structure calculations and the metadynamics method based first principles molecular dynamics (FPMD) simulations. Our results indicate that during the micro solvation of anion by water molecules systematically, the presence of minimum three water molecules in the gas phase cluster is sufficient to observe the proton transfer event. The analysis of trajectories obtained from initial FPMD simulation of an aqueous solution of the anion does not show any evident of complete transfer of the proton from water. The cooperativity of water molecules and the relatively weak anion-water interaction in liquid state prohibit the full release of the proton. Using biasing potential through first principles metadynamics simulations, we report the observation of proton transfer reaction from water to ketyl radical anion with a barrier height of 16.0 kJ/mol.

Alternative initial proton acceptors for the D pathway of Rhodobacter sphaeroides cytochrome c oxidase

PubMed Central

Varanasi, Lakshman; Hosler, Jonathan

2011-01-01

In order to characterize protein structures that control proton uptake, forms of cytochrome c oxidase (CcO) containing a carboxyl or a thiol group in line with the initial, internal waters of the D pathway for proton transfer have been assayed in the presence and absence of subunit III. Subunit III provides approximately half of the protein surrounding the entry region of the D pathway. The mutant N139D-D132N contains a carboxyl group 6Å within the D pathway and lacks the normal, surface-exposed proton acceptor, Asp-132. With subunit III, the steady-state activity of this mutant is slow but once subunit III is removed its activity is the same as wild-type CcO lacking subunit III (∼1800 H+ s-1). Thus, a carboxyl group ∼25% within the pathway enhances proton uptake even though the carboxyl has no direct contact with bulk solvent. Protons from solvent apparently move to internal Asp-139 through a short file of waters, normally blocked by subunit III. Cysteine-139 also supports rapid steady-state proton uptake, demonstrating that an anion other than a carboxyl can attract and transfer protons into the D pathway. When both Asp-132 and Asp/Cys-139 are present, the removal of subunit III increases CcO activity to rates greater than that of normal CcO due to simultaneous proton uptake by two initial acceptors. The results show how the environment of the initial proton acceptor for the D pathway in these CcO forms dictates the pH range of CcO activity, with implications for the function of Asp-132, the normal proton acceptor. PMID:21344856

Classical Molecular Dynamics with Mobile Protons.

PubMed

Lazaridis, Themis; Hummer, Gerhard

2017-11-27

An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

The excited-state intramolecular proton transfer in Nsbnd H-type dye molecules with a seven-membered-ring intramolecular hydrogen bond: A theoretical insight

NASA Astrophysics Data System (ADS)

Yuan, Huijuan; Feng, Songyan; Wen, Keke; Guo, Xugeng; Zhang, Jinglai

2018-02-01

Excited-state intramolecular proton transfer (ESIPT) reactions of a series of N(R)sbnd H ⋯ N-type seven-membered-ring hydrogen-bonding compounds were explored by employing density functional theory/time-dependent density functional theory calculations with the PBE0 functional. Our results indicate that the absorption and emission spectra predicted theoretically match very well the experimental findings. Additionally, as the electron-withdrawing strength of R increases, the intramolecular H-bond of the Nsbnd S1 form gradually enhances, and the forward energy barrier along the ESIPT reaction gradually decreases. For compound 4, its ESIPT reaction is found to be a barrierless process due to the involvement of a strong electron-withdrawing COCF3 group. It is therefore a reasonable presumption that the ESIPT efficiency of these N(R)sbnd H ⋯ N-type seven-membered-ring H-bonding systems can be improved when a strong electron-withdrawing group in R is introduced.

Car-Parrinello molecular dynamics study of the intramolecular vibrational mode-sensitive double proton-transfer mechanisms in porphycene.

PubMed

Walewski, Łukasz; Waluk, Jacek; Lesyng, Bogdan

2010-02-18

Car-Parrinello molecular dynamics simulations were carried out to help interpret proton-transfer processes observed experimentally in porphycene under thermodynamic equilibrium conditions (NVT ensemble) as well as during selective, nonequilibrium vibrational excitations of the molecular scaffold (NVE ensemble). In the NVT ensemble, the population of the trans form in the gas phase at 300 K is 96.5%, and of the cis-1 form is 3.5%, in agreement with experimental data. Approximately 70% of the proton-transfer events are asynchronous double proton transfers. According to the high resolution simulation data they consist of two single transfer events that rapidly take place one after the other. The average time-period between the two consecutive jumps is 220 fs. The gas phase reaction rate estimate at 300 K is 3.6 ps, which is comparable to experimentally determined rates. The NVE ensemble nonequilibrium ab initio MD simulations, which correspond to selective vibrational excitations of the molecular scaffold generated with high resolution laser spectroscopy techniques, exhibit an enhancing property of the 182 cm(-1) vibrational mode and an inhibiting property of the 114 cm(-1) one. Both of them influence the proton-transfer rate, in qualitative agreement with experimental findings. Our ab initio simulations provide new predictions regarding the influence of double-mode vibrational excitations on proton-transfer processes. They can help in setting up future programmable spectroscopic experiments for the proton-transfer translocations.

Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein.

PubMed

Nadal-Ferret, Marc; Gelabert, Ricard; Moreno, Miquel; Lluch, José M

2015-12-14

In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1. Expectation values of the geometry reveal that the proton shared between the chromophore and W22, and the proton shared between Ser205 and Glu222 are very close to the center of the respective hydrogen bonds, giving support to the claim that the first transient intermediate detected after photoexcitation (I0*) has characteristics similar to those of a low-barrier hydrogen bond [Di Donato et al., Phys. Chem. Chem. Phys., 2012, 13, 16295]. A quantum dynamical calculation of the evolution in the excited state shows an even larger probability of finding those two protons close to the center compared to in the ground state, but no formation of the proton-transferred product is observed. A QM/MM photoactive state geometry optimization, initiated using a configuration obtained by taking the A minimum and moving the protons to the product side, yields a minimum energy structure with the protons transferred and in which the His148 residue is substantially closer to the now anionic chromophore. These results indicate that: (1) proton transfer is not possible if structural relaxation of the surroundings of the chromophore is prevented; (2) protons H1 and H3 especially are found very close to the point halfway between the donor and acceptor after photoexcitation when the zero-point energy is considered; (3) a geometrical parameter exists (the His148-Cro distance) under which the structure with the protons transferred is not a minimum, and that, if included, should lead to the fluorescing I* structure. The existence of an oscillating stationary state between the reactants and products of the triple proton transfer reaction can explain the dual emission reported for the I0* intermediate of wtGFP.

Proton conduction within the reaction centers of Rhodobacter capsulatus: the electrostatic role of the protein.

PubMed

Maróti, P; Hanson, D K; Baciou, L; Schiffer, M; Sebban, P

1994-06-07

Light-induced charge separation in the photosynthetic reaction center results in delivery of two electrons and two protons to the terminal quinone acceptor QB. In this paper, we have used flash-induced absorbance spectroscopy to study three strains that share identical amino acid sequences in the QB binding site, all of which lack the protonatable amino acids Glu-L212 and Asp-L213. These strains are the photosynthetically incompetent site-specific mutant Glu-L212/Asp-L213-->Ala-L212/Ala-L213 and two different photocompetent derivatives that carry both alanine substitutions and an intergenic suppressor mutation located far from QB (class 3 strain, Ala-Ala + Arg-M231-->Leu; class 4 strain, Ala-Ala + Asn-M43-->Asp). At pH 8 in the double mutant, we observe a concomitant decrease of nearly 4 orders of magnitude in the rate constants of second electron and proton transfer to QB compared to the wild type. Surprisingly, these rates are increased to about the same extent in both types of suppressor strains but remain > 2 orders of magnitude smaller than those of the wild type. In the double mutant, at pH 8, the loss of Asp-L213 and Glu-L212 leads to a substantial stabilization (> or = 60 meV) of the semiquinone energy level. Both types of compensatory mutations partially restore, to nearly the same level, the original free energy difference for electron transfer from primary quinone QA to QB. The pH dependence of the electron and proton transfer processes in the double-mutant and the suppressor strains suggests that when reaction centers of the double mutant are shifted to lower pH (1.5-2 units), they function like those of the suppressor strains at physiological pH. Our data suggest that the main effect of the compensatory mutations is to partially restore the negative electrostatic environment of QB and to increase an apparent "functional" pK of the system for efficient proton transfer to the active site. This emphasizes the role of the protein in tuning the electrostatic environment of its cofactors and highlights the possible long-range electrostatic effects.

Measurement of the Neutron F2 Structure Function via Spectator Tagging with CLAS

NASA Astrophysics Data System (ADS)

Baillie, N.; Tkachenko, S.; Zhang, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Keppel, C. E.; Kuhn, S. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Adikaram, D.; Aghasyan, M.; Amaryan, M. J.; Anghinolfi, M.; Arrington, J.; Avakian, H.; Baghdasaryan, H.; Battaglieri, M.; Biselli, A. S.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Daniel, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Dey, B.; Djalali, C.; Dodge, G.; Domingo, J.; Doughty, D.; Dupre, R.; Dutta, D.; Ent, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fradi, A.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Graham, L.; Guegan, B.; Guidal, M.; Guler, N.; Guo, L.; Hafidi, K.; Heddle, D.; Hicks, K.; Holtrop, M.; Hungerford, E.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ispiryan, M.; Isupov, E. L.; Jawalkar, S. S.; Jo, H. S.; Kalantarians, N.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Klimenko, A.; Kubarovsky, V.; Kuleshov, S. V.; Kvaltine, N. D.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Mao, Y.; Markov, N.; McKinnon, B.; Mineeva, T.; Morrison, B.; Moutarde, H.; Munevar, E.; Nadel-Turonski, P.; Ni, A.; Niccolai, S.; Niculescu, I.; Niculescu, G.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L.; Park, K.; Park, S.; Pasyuk, E.; Anefalos Pereira, S.; Pisano, S.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Schott, D.; Schumacher, R. A.; Seder, E.; Sharabian, Y. G.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Stoler, P.; Strauch, S.; Taiuti, M.; Tang, W.; Ungaro, M.; Vineyard, M. F.; Voutier, E.; Watts, D. P.; Weinstein, L. B.; Weygand, D. P.; Wood, M. H.; Zana, L.; Zhao, B.

2012-04-01

We report on the first measurement of the F2 structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲100MeV/c and their angles to ≳100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F2n data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65

Measurement of the neutron F 2 structure function via spectator tagging with CLAS

DOE PAGES

Baillie, N.; Tkachenko, S.; Zhang, J.; ...

2012-04-01

We report on the first measurement of the F 2 structure function of the neutron from semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≈< 100 MeV and their angles to ≈> 100 degrees relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F 2 n data collected cover the nucleon resonance and deep-inelastic regions over a wide range of x for 0.65 < Q 2 < 4.52 GeV 2, with uncertainties from nuclear correctionsmore » estimated to be less than a few percent. These measurements provide the first determination of the neutron to proton structure function ratio F 2 n/F 2 p at 0.2 ≈< x ≈< 0.8, essentially free of nuclear corrections.« less

A measurement of the proton structure function F2( x, Q2)

NASA Astrophysics Data System (ADS)

Ahmed, T.; Aid, S.; Akhundov, A.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bergstein, H.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegge, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Danilov, M.; Dau, W. D.; Daum, K.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, V.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herma, R.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Linsel, F.; Lipinski, J.; List, B.; Loch, P.; Lohmander, H.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Savitsky, M.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Seehausen, U.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Soloviev, Y.; Spiekermann, J.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Vecko, M.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

A measurement of the proton structure function F2( x, Q2) is reported for momentum transfers squared Q2 between 4.5 GeV 2 and 1600 GeV 2 and for Bjorken x between 1.8 × 10 -14 and 0.13 using data collected by the HERA experiment H1 in 1993. It is observed that F2 increases significantly with decreasing x, confirming our previous measurement made with one tenth of the data available in this analysis. The Q2 dependence is approximately logarithmic over the full kinematic range covered. The subsample of deep inelastic events with a large pseudo-rapidity gap in the hadronic energy flow close to the proton remnant is used to measure the "diffractive" contribution to F2.

Electron Transfer Ion/Ion Reactions in a Three-Dimensional Quadrupole Ion Trap: Reactions of Doubly and Triply Protonated Peptides with SO2·−

PubMed Central

Pitteri, Sharon J.; Chrisman, Paul A.; Hogan, Jason M.; McLuckey, Scott A.

2005-01-01

Ion–ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2·−. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2·− give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2·− shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide. PMID:15762593

Femtochemistry of Intramolecular Charge and Proton Transfer Reactions in Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douhal, Abderrazzak; Sanz, Mikel; Carranza, Maria Angeles

2005-03-17

We report on the first observation of ultrafast intramolecular charge- and proton-transfer reactions in 4'-dimethylaminoflavonol (DAMF) in solution. Upon femtosecond excitation of a non-planar structure of DMAF in apolar medium, the intramolecular charge transfer (ICT) does not occur, and a slow (2 ps) proton motion takes place. However, in polar solvents, the ICT is very fast (100-200 fs) and the produced structure is stabilized that proton motion takes place in few or tens of ps.

Polarization Transfer in Proton Compton Scattering at High Momentum Transfer

NASA Astrophysics Data System (ADS)

Hamilton, D. J.; Mamyan, V. H.; Aniol, K. A.; Annand, J. R.; Bertin, P. Y.; Bimbot, L.; Bosted, P.; Calarco, J. R.; Camsonne, A.; Chang, G. C.; Chang, T.-H.; Chen, J.-P.; Choi, Seonho; Chudakov, E.; Danagoulian, A.; Degtyarenko, P.; de Jager, C. W.; Deur, A.; Dutta, D.; Egiyan, K.; Gao, H.; Garibaldi, F.; Gayou, O.; Gilman, R.; Glamazdin, A.; Glashausser, C.; Gomez, J.; Hansen, J.-O.; Hayes, D.; Higinbotham, D.; Hinton, W.; Horn, T.; Howell, C.; Hunyady, T.; Hyde-Wright, C. E.; Jiang, X.; Jones, M. K.; Khandaker, M.; Ketikyan, A.; Kubarovsky, V.; Kramer, K.; Kumbartzki, G.; Laveissière, G.; Lerose, J.; Lindgren, R. A.; Margaziotis, D. J.; Markowitz, P.; McCormick, K.; Meziani, Z.-E.; Michaels, R.; Moussiegt, P.; Nanda, S.; Nathan, A. M.; Nikolenko, D. M.; Nelyubin, V.; Norum, B. E.; Paschke, K.; Pentchev, L.; Perdrisat, C. F.; Piasetzky, E.; Pomatsalyuk, R.; Punjabi, V. A.; Rachek, I.; Radyushkin, A.; Reitz, B.; Roche, R.; Roedelbronn, M.; Ron, G.; Sabatie, F.; Saha, A.; Savvinov, N.; Shahinyan, A.; Shestakov, Y.; Širca, S.; Slifer, K.; Solvignon, P.; Stoler, P.; Tajima, S.; Sulkosky, V.; Todor, L.; Vlahovic, B.; Weinstein, L. B.; Wang, K.; Wojtsekhowski, B.; Voskanyan, H.; Xiang, H.; Zheng, X.; Zhu, L.

2005-06-01

Compton scattering from the proton was investigated at s=6.9 GeV2 and t=-4.0 GeV2 via polarization transfer from circularly polarized incident photons. The longitudinal and transverse components of the recoil proton polarization were measured. The results are in disagreement with a prediction of perturbative QCD based on a two-gluon exchange mechanism, but agree well with a prediction based on a reaction mechanism in which the photon interacts with a single quark carrying the spin of the proton.

Sulfate-reducing bacteria: Microbiology and physiology

NASA Technical Reports Server (NTRS)

Peck, H. D.

1985-01-01

The sulfate reducing bacteria, the first nonphotosynthetic anaerobic bacteria demonstrated to contain c type cytochromes, perform electron transfer coupled to phosphorylation. A new bioenergetic scheme for the formation of a proton gradient for growth of Desulfovibrio on organic substrates and sulfate involving vectors electron transfer and consistent with the cellular localization of enzymes and electron transfer components was proposed. Hydrogen is produced in the cytoplasm from organic substrates and, as a permease molecule diffuses rapidly across the cytoplasmic membrane, it is oxidized to protons and electrons by the periplasmic hydrogenase. The electrons only are transferred across the cytoplasmic membrane to the cytoplasm where they are used to reduce sulfate to sulfide. The protons are used for transport or to drive a reversible ATPOSE. The net effect is the transfer of protons across the cytoplasmic membrane with the intervention of a proton pump. This type of H2 cycling is relevant to the bioenergetics of other types of anaerobic microorganisms.

Non-Transition-Metal Catalytic System for N 2 Reduction to NH 3: A Density Functional Theory Study of Al-Doped Graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Yong-Hui; Hu, Shuangli; Sheng, Xiaolan

The prevalent catalysts for natural and artificial N 2 fixation are known to hinge upon transition-metal (TM) elements. In this paper, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N 2 to NH 3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N 2 and its various downstream N xH y intermediates. The initial hydrogenation of N 2 canmore » readily take place via an internal H-transfer process with the assistance of a Li + ion as an additive. Finally, in view of the recurrence of H transfer in the first step of N 2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N 2 fixation.« less

Non-Transition-Metal Catalytic System for N 2 Reduction to NH 3: A Density Functional Theory Study of Al-Doped Graphene

DOE PAGES

Tian, Yong-Hui; Hu, Shuangli; Sheng, Xiaolan; ...

2018-01-16

The prevalent catalysts for natural and artificial N 2 fixation are known to hinge upon transition-metal (TM) elements. In this paper, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N 2 to NH 3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N 2 and its various downstream N xH y intermediates. The initial hydrogenation of N 2 canmore » readily take place via an internal H-transfer process with the assistance of a Li + ion as an additive. Finally, in view of the recurrence of H transfer in the first step of N 2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N 2 fixation.« less

Thermally triggered polyrotaxane translational motion helps proton transfer.

PubMed

Ge, Xiaolin; He, Yubin; Liang, Xian; Wu, Liang; Zhu, Yuan; Yang, Zhengjin; Hu, Min; Xu, Tongwen

2018-06-12

Synthetic polyelectrolytes, capable of fast transporting protons, represent a challenging target for membrane engineering in so many fields, for example, fuel cells, redox flow batteries, etc. Inspired by the fast advance in molecular machines, here we report a rotaxane based polymer entity assembled via host-guest interaction and prove that by exploiting the thermally triggered translational motion (although not in a controlled manner) of mechanically bonded rotaxane, exceptionally fast proton transfer can be fulfilled at an external thermal input. The relative motion of the sulfonated axle to the ring in rotaxane happens at ~60 °C in our cases and because of that a proton conductivity (indicating proton transfer rate) of 260.2 mS cm -1 , which is much higher than that in the state-of-the-art Nafion, is obtained at a relatively low ion-exchange capacity (representing the amount of proton transfer groups) of 0.73 mmol g -1 .

A novel salt of antidiabetic drug metformin resulting from a proton transfer reaction: Synthesis, characterization, crystal structure and solution studies

NASA Astrophysics Data System (ADS)

Ghasemi, Fatemeh; Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Refahi, Masoud; García-Granda, Santiago; Mendoza-Meroño, Rafael

2017-03-01

Reaction between N,N-dimethylebiguanidine, Met = Metformin, and 4-hydroxy-2,6-pyridinedicarboxylic acid, HO-dipicH2, results in the formation of a novel proton transfer compound, [MetH2][HO-dipicH]2·H2O, 1. The characterization was performed using FTIR, UV-Vis, 1H and 13C NMR spectroscopy and X-ray crystallography. The crystal system is triclinic with space group P 1 bar and two molecules per unit cell. The protonation constants of O-dipic and Met, in all of probability protonated forms, and the equilibrium constants for the O-dipic-Met proton transfer system were investigated by the potentiometric pH titration method using the Hyperquad2008 program. The stoichiometry of the proton transfer species in solution were in agreement with the solid state result.

F"orster-type mechanism of the redox-driven proton pump

NASA Astrophysics Data System (ADS)

Mourokh, Lev; Smirnov, Anatoly; Nori, Franco

2007-03-01

We propose a model to describe an electronically-driven proton pump in the cytochrome c oxidase (CcO). We examine the situation when the electron transport between the two sites embedded into the inner membrane of the mitochondrion occurs in parallel with the proton transfer from the protonable site that is close to the negative (inner) side of the membrane to the other protonable site located nearby the positive (outer) surface of the membrane. In addition to the conventional electron and proton tunnelings between the sites, the Coulomb interaction between electrons and protons localized on the corresponding sites leads to so-called F"orster transfer, i.e. to the process when the simultaneous electron and proton tunnelings are accompanied by the resonant energy transfer between the electrons and protons. Our calculations based on reasonable parameters have demonstrated that the F"orster process facilitates the proton pump at physiological temperatures. We have examined the effects of an electron voltage build-up, external temperature, and molecular electrostatics driving the electron and proton energies to the resonant conditions, and have shown that these parameters can control the proton pump operation.

Rates of proton transfer to Fe-S-based clusters: comparison of clusters containing {MFe(mu(2)-S)(2)}n+ and {MFe(3)(mu(3)-S)(4)}n+ (M = Fe, Mo, or W) cores.

PubMed

Bates, Katie; Garrett, Brendan; Henderson, Richard A

2007-12-24

The rates of proton transfer from [pyrH]+ (pyr = pyrrolidine) to the binuclear complexes [Fe2S2Cl4]2- and [S2MS2FeCl2]2- (M = Mo or W) are reported. The reactions were studied using stopped-flow spectrophotometry, and the rate constants for proton transfer were determined from analysis of the kinetics of the substitution reactions of these clusters with the nucleophiles Br- or PhS- in the presence of [pyrH]+. In general, Br- is a poor nucleophile for these clusters, and proton transfer occurs before Br- binds, allowing direct measure of the rate of proton transfer from [pyrH]+ to the cluster. In contrast, PhS- is a better nucleophile, and a pathway in which PhS- binds preferentially to the cluster prior to proton transfer from [pyrH]+ usually operates. For the reaction of [Fe2S2Cl4]2- with PhS- in the presence of [pyrH]+ both pathways are observed. Comparison of the results presented in this paper with analogous studies reported earlier on cuboidal Fe-S-based clusters allows discussion of the factors which affect the rates of proton transfer in synthetic clusters including the nuclearity of the cluster core, the metal composition, and the nature of the terminal ligands. The possible relevance of these findings to the protonation sites of natural Fe-S-based clusters, including FeMo-cofactor from nitrogenase, are presented.

Conformational flexibility of arginine-82 as source for the heterogeneous and pH-dependent kinetics of the primary proton transfer step in the bacteriorhodopsin photocycle: An electrostatic model

NASA Astrophysics Data System (ADS)

Scharnagl, Christina; Fischer, Sighart F.

1996-11-01

We use equilibrium thermodynamic concepts to relate protein conformational and protonation substates and their pH-dependent population to kinetic schemes for the rise of the M intermediate in the photocycle of bacteriorhodopsin. Conformational flexibility of arginine R82 is described by a two-state model. The analysis accounts for the electrostatic coupling between its orientation and hydrogen ion titration and presents a structural basis for the linkage between the protonation states of the primary proton acceptor, aspartate D85, and the extracellular release group, glutamate E204. We find that the charge state of D85 is a significant determinant for the orientation of R82. The molecular model predicts the following: the primary proton transfer to D85 can be described by a kinetic scheme with two heterogeneous substates. They control the event with different activation parameters due to the reorientation of R82 away from the chromophore binding site. Their population depends on the external pH and the proton exchange equilibrium between the membrane buried residues and the bulk aqueous solvent. Proton transfer in the physiologic pH range is strongly activated and followed by the reorientation of R82 which shifts the equilibrium toward complete transfer. In the alkaline pH region a different mechanism operates, which involves the increased population of a substate with already reoriented R82 as a consequence of the deprotonation of E204, leading to accelerated proton transfer. Assuming full proton exchange equilibrium with the bulk water on the millisecond time scale leads to an increased population of substates which are non-productive for proton transfer.

An evaluation of spatial resolution of a prototype proton CT scanner.

PubMed

Plautz, Tia E; Bashkirov, V; Giacometti, V; Hurley, R F; Johnson, R P; Piersimoni, P; Sadrozinski, H F-W; Schulte, R W; Zatserklyaniy, A

2016-12-01

To evaluate the spatial resolution of proton CT using both a prototype proton CT scanner and Monte Carlo simulations. A custom cylindrical edge phantom containing twelve tissue-equivalent inserts with four different compositions at varying radial displacements from the axis of rotation was developed for measuring the modulation transfer function (MTF) of a prototype proton CT scanner. Two scans of the phantom, centered on the axis of rotation, were obtained with a 200 MeV, low-intensity proton beam: one scan with steps of 4°, and one scan with the phantom continuously rotating. In addition, Monte Carlo simulations of the phantom scan were performed using scanners idealized to various degrees. The data were reconstructed using an iterative projection method with added total variation superiorization based on individual proton histories. Edge spread functions in the radial and azimuthal directions were obtained using the oversampling technique. These were then used to obtain the modulation transfer functions. The spatial resolution was defined by the 10% value of the modulation transfer function (MTF 10% ) in units of line pairs per centimeter (lp/cm). Data from the simulations were used to better understand the contributions of multiple Coulomb scattering in the phantom and the scanner hardware, as well as the effect of discretization of proton location. The radial spatial resolution of the prototype proton CT scanner depends on the total path length, W, of the proton in the phantom, whereas the azimuthal spatial resolution depends both on W and the position, u - , at which the most-likely path uncertainty is evaluated along the path. For protons contributing to radial spatial resolution, W varies with the radial position of the edge, whereas for protons contributing to azimuthal spatial resolution, W is approximately constant. For a pixel size of 0.625 mm, the radial spatial resolution of the image reconstructed from the fully idealized simulation data ranged between 6.31 ± 0.36 lp/cm for W = 197 mm i.e., close to the center of the phantom, and 13.79 ± 0.36 lp/cm for W = 97 mm, near the periphery of the phantom. The azimuthal spatial resolution ranged from 6.99 ± 0.23 lp/cm at u - = 75 mm (near the center) to 11.20 ± 0.26 lp/cm at u - = 20 mm (near the periphery). Multiple Coulomb scattering limits the radial spatial resolution for path lengths greater than approximately 130 mm, and the azimuthal spatial resolution for positions of evaluation greater than approximately 40 mm for W = 199 mm. The radial spatial resolution of the image reconstructed from data from the 4° stepped experimental scan ranged from 5.11 ± 0.61 lp/cm for W = 197 mm to 8.58 ± 0.50 lp/cm for W = 97 mm. In the azimuthal direction, the spatial resolution ranged from 5.37 ± 0.40 lp/cm at u - = 75 mm to 7.27 ± 0.39 lp/cm at u - = 20 mm. The continuous scan achieved the same spatial resolution as that of the stepped scan. Multiple Coulomb scattering in the phantom is the limiting physical factor of the achievable spatial resolution of proton CT; additional loss of spatial resolution in the prototype system is associated with scattering in the proton tracking system and inadequacies of the proton path estimate used in the iterative reconstruction algorithm. Improvement in spatial resolution may be achievable by improving the most likely path estimate by incorporating information about high and low density materials, and by minimizing multiple Coulomb scattering in the proton tracking system.

An evaluation of spatial resolution of a prototype proton CT scanner

PubMed Central

Plautz, Tia E.; Bashkirov, V.; Giacometti, V.; Hurley, R. F.; Piersimoni, P.; Sadrozinski, H. F.-W.; Schulte, R. W.; Zatserklyaniy, A.

2016-01-01

Purpose: To evaluate the spatial resolution of proton CT using both a prototype proton CT scanner and Monte Carlo simulations. Methods: A custom cylindrical edge phantom containing twelve tissue-equivalent inserts with four different compositions at varying radial displacements from the axis of rotation was developed for measuring the modulation transfer function (MTF) of a prototype proton CT scanner. Two scans of the phantom, centered on the axis of rotation, were obtained with a 200 MeV, low-intensity proton beam: one scan with steps of 4°, and one scan with the phantom continuously rotating. In addition, Monte Carlo simulations of the phantom scan were performed using scanners idealized to various degrees. The data were reconstructed using an iterative projection method with added total variation superiorization based on individual proton histories. Edge spread functions in the radial and azimuthal directions were obtained using the oversampling technique. These were then used to obtain the modulation transfer functions. The spatial resolution was defined by the 10% value of the modulation transfer function (MTF10%) in units of line pairs per centimeter (lp/cm). Data from the simulations were used to better understand the contributions of multiple Coulomb scattering in the phantom and the scanner hardware, as well as the effect of discretization of proton location. Results: The radial spatial resolution of the prototype proton CT scanner depends on the total path length, W, of the proton in the phantom, whereas the azimuthal spatial resolution depends both on W and the position, u−, at which the most-likely path uncertainty is evaluated along the path. For protons contributing to radial spatial resolution, W varies with the radial position of the edge, whereas for protons contributing to azimuthal spatial resolution, W is approximately constant. For a pixel size of 0.625 mm, the radial spatial resolution of the image reconstructed from the fully idealized simulation data ranged between 6.31 ± 0.36 lp/cm for W = 197 mm i.e., close to the center of the phantom, and 13.79 ± 0.36 lp/cm for W = 97 mm, near the periphery of the phantom. The azimuthal spatial resolution ranged from 6.99 ± 0.23 lp/cm at u− = 75 mm (near the center) to 11.20 ± 0.26 lp/cm at u− = 20 mm (near the periphery). Multiple Coulomb scattering limits the radial spatial resolution for path lengths greater than approximately 130 mm, and the azimuthal spatial resolution for positions of evaluation greater than approximately 40 mm for W = 199 mm. The radial spatial resolution of the image reconstructed from data from the 4° stepped experimental scan ranged from 5.11 ± 0.61 lp/cm for W = 197 mm to 8.58 ± 0.50 lp/cm for W = 97 mm. In the azimuthal direction, the spatial resolution ranged from 5.37 ± 0.40 lp/cm at u− = 75 mm to 7.27 ± 0.39 lp/cm at u− = 20 mm. The continuous scan achieved the same spatial resolution as that of the stepped scan. Conclusions: Multiple Coulomb scattering in the phantom is the limiting physical factor of the achievable spatial resolution of proton CT; additional loss of spatial resolution in the prototype system is associated with scattering in the proton tracking system and inadequacies of the proton path estimate used in the iterative reconstruction algorithm. Improvement in spatial resolution may be achievable by improving the most likely path estimate by incorporating information about high and low density materials, and by minimizing multiple Coulomb scattering in the proton tracking system. PMID:27908179

Reaction cycle and thermodynamics in bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1992-01-01

Light causes the all-trans to 13-cis isomerization of the retinal in bacteriorhodopsin; the thermal relaxation leading back to the initial state drives proton transport first via proton transfer between the retinal Schiff base and D85 and then between the Schiff base and D96. The reaction sequence and thermodynamics of this photocycle are described by measuring time-resolved absorption changes with a gated multichannel analyzer between 100 ns and 100 ms, at six temperatures between 5 degrees C and 30 degrees C. Analysis of the energetics of the chromophore reaction sequence is on the basis of a recently proposed model (Varo & Lanyi, Biochemistry 30, 5016-5022, 1991) which consists of a single cycle and many reversible reactions: BR -hv-->K<==>L<==>M1-->M2<==>N<==>O-->BR. The existence of the M1-->M2 reaction, which functions as the switch in the proton transfer, is confirmed by spectroscopic evidence. The calculated thermodynamic parameters indicate that the exchange of free energy between the protein and the protons is at the switch step. Further, a large entropy decrease at this reaction suggests a protein conformation change which will conserve delta G for driving the completion of the reaction cycle. The results provide insights to mechanism and energy coupling in this system, with possible relevance to the general question of how ion pumps function.

Selective heteronuclear Hartmann-Hahn: A multiple-pulse sequence for selective magnetization transfer in the structural elucidation of “isotagged” oligosaccharides

NASA Astrophysics Data System (ADS)

Meng, Xi; Nguyen, William H.; Nowick, James S.; Shaka, A. J.

2010-03-01

A new selective heteronuclear Hartmann-Hahn (SHEHAHA) multiple-pulse mixing sequence is proposed for the solution structure elucidation of milligram amounts of peracetylated oligosaccharides in which the acetyl groups are enriched in carbon-13, so-called “isotags”. SHEHAHA accomplishes exclusive in-phase magnetization transfer between the isotag carbonyl 13C and the proximal proton on the sugar ring. Relayed transfer around the sugar rings by proton-proton TOCSY is suppressed, while the heteronuclear transfer from the labeled carbonyl carbon to the proximal ring proton is maintained. The sequence is broadband in the sense that all acetyl groups simultaneously give good signal transfer to their respective nearest proton neighbors. The 1H-detected spectra have decent sensitivity and excellent resolution, giving patterns that unambiguously identify common structural subunits in human glycans. Peracetylated maltitol is shown as a test case of the method. Lineshapes are pure absorption, allowing facile measurement of vicinal proton-proton couplings. Linkage points can be deduced, and the 2D correlation spectra may be useful for more ambitious prediction algorithms and machine identification by a spectral database.

C-PCM based calculation of energy profiles for proton transfer in phosphorus-containing acid- N, N-dimethylformamide complexes

NASA Astrophysics Data System (ADS)

Fedorova, I. V.; Khatuntseva, E. A.; Krest'yaninov, M. A.; Safonova, L. P.

2016-02-01

Proton transfer along the hydrogen bond in complexes of DMF with H3PO4, H3PO3, CH3H2PO3, and their dimers has been investigated by the B3LYP/6-31++G** method in combination with the C-PCM model. When the Oacid···ODMF distance ( R) in the scanning procedure is not fixed, the energy profile in all cases has a single well. When this distance is fixed, there can be a proton transfer in all of the complexes in the gas phase at R > 2.6 Å; if solvation is taken into account, proton transfer can take place at R > 2.4 Å ( R > 2.5 Å for DMF complexes with CH3H2PO3 and its dimer). The height of the energy barrier to proton transfer increases with increasing R. Proton transfer is energetically most favorable in the DMF-phosphoric acid complexes. The structural and energetic characteristics of the hydrogen-bonded complexes calculated on the basis of the solvation model are compared with the same parameters for the complexes in the gas phase.

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

PubMed Central

Chakravorty, Dhruva K.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2009-01-01

Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme. PMID:19799395

Pendant acid-base groups in molecular catalysts: H-bond promoters or proton relays? Mechanisms of the conversion of CO2 to CO by electrogenerated iron(0)porphyrins bearing prepositioned phenol functionalities.

PubMed

Costentin, Cyrille; Passard, Guillaume; Robert, Marc; Savéant, Jean-Michel

2014-08-20

Two derivatives of iron tetraphenylporphyrin bearing prepositioned phenolic functionalities on two of the opposed phenyl groups prove to be remarkable catalysts for the reduction of CO2 to CO when generated electrochemically at the Fe(0) oxidation state. In one case, the same substituents are present on the two other phenyls, whereas in the other the two other phenyls are perfluorinated. They are taken as examples of the possible role of pendant acid-base groups in molecular catalysis. The prepositioned phenol groups incorporated into the catalyst molecule induce strong stabilization of the initial Fe(0)CO2 adduct through H-bonding, confirmed by DFT calculations. This positive factor is partly counterbalanced by the necessity, resulting from the same stabilization, to inject an additional electron to trigger catalysis. Thanks to the preprotonation of the initial Fe(0)CO2 adduct, the potential required for this second electron transfer is not very distant from the potential at which the adduct is generated by addition of CO2 to the Fe(0) complex. The protonation step involves an internal phenolic group and the reprotonation of the phenoxide ion thus generated by added phenol. The prepositioned phenol groups thus play both the role of H-bonding stabilizers and high-concentration proton donors. They play the same role in the second electron transfer step which closes the catalytic loop concertedly with the breaking of one of the two C-O bonds of CO2 and with proton transfer. It is also remarkable that reprotonation by added phenol is concerted with the three other events.

D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine YZ for proton exit during water oxidation.

PubMed

Nagao, Ryo; Ueoka-Nakanishi, Hanayo; Noguchi, Takumi

2017-12-08

In photosynthetic water oxidation, two water molecules are converted into one oxygen molecule and four protons at the Mn 4 CaO 5 cluster in photosystem II (PSII) via the S-state cycle. Efficient proton exit from the catalytic site to the lumen is essential for this process. However, the exit pathways of individual protons through the PSII proteins remain to be identified. In this study, we examined the involvement of a hydrogen-bond network near the redox-active tyrosine Y Z in proton transfer during the S-state cycle. We focused on spectroscopic analyses of a site-directed variant of D1-Asn-298, a residue involved in a hydrogen-bond network near Y Z We found that the D1-N298A mutant of Synechocystis sp. PCC 6803 exhibits an O 2 evolution activity of ∼10% of the wild-type. D1-N298A and the wild-type D1 had very similar features of thermoluminescence glow curves and of an FTIR difference spectrum upon Y Z oxidation, suggesting that the hydrogen-bonded structure of Y Z and electron transfer from the Mn 4 CaO 5 cluster to Y Z were little affected by substitution. In the D1-N298A mutant, however, the flash-number dependence of delayed luminescence showed a monotonic increase without oscillation, and FTIR difference spectra of the S-state cycle indicated partial and significant inhibition of the S 2 → S 3 and S 3 → S 0 transitions, respectively. These results suggest that the D1-N298A substitution inhibits the proton transfer processes in the S 2 → S 3 and S 3 → S 0 transitions. This in turn indicates that the hydrogen-bond network near Y Z can be functional as a proton transfer pathway during photosynthetic water oxidation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

2016-04-01

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Revealing proton shape fluctuations with incoherent diffraction at high energy

DOE PAGES

Mantysaari, H.; Schenke, B.

2016-08-30

The di erential cross section of exclusive di ractive vector meson production in electron proton collisions carries important information on the geometric structure of the proton. More speci cally, the coherent cross section as a function of the transferred transverse momentum is sensitive to the size of the proton, while the incoherent, or proton dissociative cross section is sensitive to uctuations of the gluon distribution in coordinate space. We show that at high energies the experimentally measured coherent and incoherent cross sections for the production of J= mesons are very well reproduced within the color glass condensate framework when strongmore » geometric uctuations of the gluon distribution in the proton are included. For meson production we also nd reasonable agreement. We study in detail the dependence of our results on various model parameters, including the average proton shape, analyze the e ect of saturation scale and color charge uctuations and constrain the degree of geometric uctuations.« less

Proton-coupled electron transfer versus hydrogen atom transfer: generation of charge-localized diabatic states.

PubMed

Sirjoosingh, Andrew; Hammes-Schiffer, Sharon

2011-03-24

The distinction between proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms is important for the characterization of many chemical and biological processes. PCET and HAT mechanisms can be differentiated in terms of electronically nonadiabatic and adiabatic proton transfer, respectively. In this paper, quantitative diagnostics to evaluate the degree of electron-proton nonadiabaticity are presented. Moreover, the connection between the degree of electron-proton nonadiabaticity and the physical characteristics distinguishing PCET from HAT, namely, the extent of electronic charge redistribution, is clarified. In addition, a rigorous diabatization scheme for transforming the adiabatic electronic states into charge-localized diabatic states for PCET reactions is presented. These diabatic states are constructed to ensure that the first-order nonadiabatic couplings with respect to the one-dimensional transferring hydrogen coordinate vanish exactly. Application of these approaches to the phenoxyl-phenol and benzyl-toluene systems characterizes the former as PCET and the latter as HAT. The diabatic states generated for the phenoxyl-phenol system possess physically meaningful, localized electronic charge distributions that are relatively invariant along the hydrogen coordinate. These diabatic electronic states can be combined with the associated proton vibrational states to generate the reactant and product electron-proton vibronic states that form the basis of nonadiabatic PCET theories. Furthermore, these vibronic states and the corresponding vibronic couplings may be used to calculate rate constants and kinetic isotope effects of PCET reactions.

Measuring Interference of Drug-Like Molecules with the Respiratory Chain: Toward the Early Identification of Mitochondrial Uncouplers in Lead Finding

PubMed Central

Matter, Hans; Diekert, Kerstin; Dörner, Wolfgang; Dröse, Stefan; Licher, Thomas

2013-01-01

Abstract The electron transport chain (ETC) couples electron transfer between donors and acceptors with proton transport across the inner mitochondrial membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate (ATP). Proton transfer is based on the activity of complex I–V proteins in the ETC. The overall electrical activity of these proteins can be measured by proton transfer using Solid Supported Membrane technology. We tested the activity of complexes I, III, and V in a combined assay, called oxidative phosphorylation assay (oxphos assay), by activating each complex with the corresponding substrate. The oxphos assay was used to test in-house substances from different projects and several drugs currently available on the market that have reported effects on mitochondrial functions. The resulting data were compared to the influence of the respective compounds on mitochondria as determined by oxygen consumption and to data generated with an ATP depletion assay. The comparison shows that the oxidative phosphorylation assay provides both a rapid approach for detecting interaction of compounds with respiratory chain proteins and information on their mode of interaction. Therefore, the oxphos assay is a useful tool to support structure activity relationship studies by allowing early identification of mitotoxicity and for analyzing the outcome of phenotypic screens that are susceptible to the generation of mitotoxicity-related artifacts. PMID:23992120

White light generation by carbonyl based indole derivatives due to proton transfer: an efficient fluorescence sensor.

PubMed

Singla, Nidhi; Bhadram, Venkata Srinu; Narayana, Chandrabhas; Chowdhury, Papia

2013-04-04

The motivation of the present work is to understand the optical, chemical, and electrical aspects of the proton transfer mechanism of indole (I) and some carbonyl based indole derivatives: indole-3-carboxaldehyde (I3C) and indole-7-carboxaldehyde (I7C) for both powder form and their liquid solution. Structural information for indole derivatives (isolated molecule and in solution) is obtained with density functional theory (DFT) and time dependent DFT (TD-DFT) methods. Calculated transition energies are used to generate UV-vis, FTIR, Raman, and NMR spectra which are later verified with the experimental spectra. The occurrence of different conformers [cis (N(c)), trans (N(t)), and zwitterion (Z*)] have been interpreted by Mulliken charge, natural bond orbital (NBO) analysis, and polarization versus electric field (P-E loop) studies. (1)H and (13)C NMR and molecular vibrational frequencies of the fundamental modes established the stability of Nc due to the presence of intramolecular hydrogen bonding (IHB) in the ground state (S0). Computed/experimental UV-vis absorption/emission studies reveal the creation of new species: zwitterion (Z*) and anion (A*) in the excited state (S1) due to excited state intramolecular and intermolecular proton transfer (ESI(ra)PT and ESI(er)PT). Increased electrical conductivity (σ(ac)) with temperature and increased ferroelectric polarization at higher field verifies proton conduction in I7C.

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

NASA Astrophysics Data System (ADS)

Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

2016-09-01

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

Polarization Transfer in Proton Compton Scattering at High Momentum Transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

D.J. Hamilton; Vahe Mamyan

2004-10-01

Compton scattering from the proton was investigated at s = 6.9 GeV{sup 2} and t = -4.0 TeV{sup 2} via polarization transfer from circularly polarized incident photons. The longitudinal and transverse components of the recoil proton polarization were measured. The results are in excellent agreement with a prediction based on a reaction mechanism in which the photon interacts with a single quark carrying the spin of the proton and in disagreement with a prediction of pQCD based on a two-gluon exchange mechanism.

Dynamic study of excited state hydrogen-bonded complexes of harmane in cyclohexane-toluene mixtures.

PubMed

Carmona, Carmen; Balón, Manuel; Galán, Manuel; Guardado, Pilar; Muñoz, María A

2002-09-01

Photoinduced proton transfer reactions of harmane or 1-methyl-9H-pyrido[3,4-b]indole (HN) in the presence of the proton donor hexafluoroisopropanol (HFIP) in cyclohexane-toluene mixtures (CY-TL; 10% vol/vol of TL) have been studied. Three excited state species have been identified: a 1:2 hydrogen-bonded proton transfer complex (PTC), between the pyridinic nitrogen of the substrate and the proton donor, a hydrogen-bonded cation-like exciplex (CL*) with a stoichiometry of at least 1:3 and a zwitterionic exciplex (Z*). Time-resolved fluorescence measurements evidence that upon excitation of ground state PTC, an excited state equilibrium is established between PTC* and the cationlike exciplex, CL*, lambdaem approximately/= 390 nm. This excited state reaction is assisted by another proton donor molecule. Further reaction of CL* with an additional HFIP molecule produces the zwitterionic species, Z*, lambda(em) approximately/= 500 nm. From the analysis of the multiexponential decays, measured at different emission wavelengths and as a function of HFIP concentration, the mechanism of these excited state reactions has been established. Thus, three rate constants and three reciprocal lifetimes have been determined. The simultaneous study of 1,9-dimethyl-9H-pyrido[3,4-b]indole (MHN) under the same experimental conditions has helped to understand the excited state kinetics of these processes.

Charging of Proteins in Native Mass Spectrometry

NASA Astrophysics Data System (ADS)

Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.; Tainer, John A.; Williams, Evan R.

2017-02-01

Factors that influence the charging of protein ions formed by electrospray ionization from aqueous solutions in which proteins have native structures and function were investigated. Protein ions ranging in molecular weight from 12.3 to 79.7 kDa and pI values from 5.4 to 9.6 were formed from different solutions and reacted with volatile bases of gas-phase basicities higher than that of ammonia in the cell of a Fourier-transform ion cyclotron resonance mass spectrometer. The charge-state distribution of cytochrome c ions formed from aqueous ammonium or potassium acetate is the same. Moreover, ions formed from these two solutions do not undergo proton transfer to 2-fluoropyridine, which is 8 kcal/mol more basic than ammonia. These results provide compelling evidence that proton transfer between ammonia and protein ions does not limit protein ion charge in native electrospray ionization. Both circular dichroism and ion mobility measurements indicate that there are differences in conformations of proteins in pure water and aqueous ammonium acetate, and these differences can account for the difference in the extent of charging and proton-transfer reactivities of protein ions formed from these solutions. The extent of proton transfer of the protein ions with higher gas-phase basicity bases trends with how closely the protein ions are charged to the value predicted by the Rayleigh limit for spherical water droplets approximately the same size as the proteins. These results indicate that droplet charge limits protein ion charge in native mass spectrometry and are consistent with these ions being formed by the charged residue mechanism.

Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

DOE PAGES

Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John -Paul; ...

2015-05-05

Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implicationsmore » for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.« less

SU-E-T-236: Deconvolution of the Total Nuclear Cross-Sections of Therapeutic Protons and the Characterization of the Reaction Channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulmer, W.

2015-06-15

Purpose: The knowledge of the total nuclear cross-section Qtot(E) of therapeutic protons Qtot(E) provides important information in advanced radiotherapy with protons, such as the decrease of fluence of primary protons, the release of secondary particles (neutrons, protons, deuterons, etc.), and the production of nuclear fragments (heavy recoils), which usually undergo β+/− decay by emission of γ-quanta. Therefore determination of Qtot(E) is an important tool for sophisticated calculation algorithms of dose distributions. This cross-section can be determined by a linear combination of shifted Gaussian kernels and an error-function. The resonances resulting from deconvolutions in the energy space can be associated withmore » typical nuclear reactions. Methods: The described method of the determination of Qtot(E) results from an extension of the Breit-Wigner formula and a rather extended version of the nuclear shell theory to include nuclear correlation effects, clusters and highly excited/virtually excited nuclear states. The elastic energy transfer of protons to nucleons (the quantum numbers of the target nucleus remain constant) can be removed by the mentioned deconvolution. Results: The deconvolution of the term related to the error-function of the type cerf*er((E-ETh)/σerf] is the main contribution to obtain various nuclear reactions as resonances, since the elastic part of energy transfer is removed. The nuclear products of various elements of therapeutic interest like oxygen, calcium are classified and calculated. Conclusions: The release of neutrons is completely underrated, in particular, for low-energy protons. The transport of seconary particles, e.g. cluster formation by deuterium, tritium and α-particles, show an essential contribution to secondary particles, and the heavy recoils, which create γ-quanta by decay reactions, lead to broadening of the scatter profiles. These contributions cannot be accounted for by one single Gaussian kernel for the description of lateral scatter.« less

A measurement of the proton structure function F2( x, Q2) at low x and low Q2 at HERA

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Borras, K.; Botterweck, F.; Boudry, V.; Bourov, S.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jacquet, M.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Levonian, S.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Walter, T.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Nunnemann, T.; Nyberg-Werther, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stöβlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Valĺee, C.; Van Esch, P.; Van Mechelen, P.; Vandenplas, D.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Wallny, R.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1997-02-01

The results of a measurement of the proton structure function F2( x, Q2) and the virtual photon-proton cross section are reported for momentum transfers squared Q2 between 0.35 GeV 2 and 3.5 GeV 2 and for Bjorken- x values down to 6 × 10 -6 using data collected by the HERA experiment H1 in 1995. The data represent an increase in kinematic reach to lower x and Q2 values of about a factor of 5 compared to previous H1 measurements. Including measurements from fixed target experiments the rise of F2 with decreasing x is found to be less steep for the lowest Q2 values measured. Phenomenological models at low Q2 are compared with the data.

Production of Hydrogen by Electrocatalysis: Making the H-H Bond by Combining Protons and Hydrides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullock, R. Morris; Appel, Aaron M.; Helm, Monte L.

2014-03-25

Generation of hydrogen by reduction of two protons by two electrons can be catalysed by molecular electrocatalysts. Determination of the thermodynamic driving force for elimination of H2 from molecular complexes is important for the rational design of molecular electrocatalysts, and allows the design of metal complexes of abundant, inexpensive metals rather than precious metals (“Cheap Metals for Noble Tasks”). The rate of H2 evolution can be dramatically accelerated by incorporating pendant amines into diphosphine ligands. These pendant amines in the second coordination sphere function as protons relays, accelerating intramolecular and intermolecular proton transfer reactions. The thermodynamics of hydride transfer frommore » metal hydrides and the acidity of protonated pendant amines (pKa of N-H) contribute to the thermodynamics of elimination of H2; both of the hydricity and acidity can be systematically varied by changing the substituents on the ligands. A series of Ni(II) electrocatalysts with pendant amines have been developed. In addition to the thermochemical considerations, the catalytic rate is strongly influenced by the ability to deliver protons to the correct location of the pendant amine. Protonation of the amine endo to the metal leads to the N-H being positioned appropriately to favor rapid heterocoupling with the M-H. Designing ligands that include proton relays that are properly positioned and thermodynamically tuned is a key principle for molecular electrocatalysts for H2 production as well as for other multi-proton, multi-electron reactions important for energy conversions. The research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for DOE.« less

Photocatalytic Conversion of Nitrobenzene to Aniline through Sequential Proton-Coupled One-Electron Transfers from a Cadmium Sulfide Quantum Dot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jensen, Stephen C.; Bettis Homan, Stephanie; Weiss, Emily A.

2016-01-28

This paper describes the use of cadmium sulfide quantum dots (CdS QDs) as visible-light photocatalysts for the reduction of nitrobenzene to aniline through six sequential photoinduced, proton-coupled electron transfers. At pH 3.6–4.3, the internal quantum yield of photons-to-reducing electrons is 37.1% over 54 h of illumination, with no apparent decrease in catalyst activity. Monitoring of the QD exciton by transient absorption reveals that, for each step in the catalytic cycle, the sacrificial reductant, 3-mercaptopropionic acid, scavenges the excitonic hole in ~5 ps to form QD•–; electron transfer to nitrobenzene or the intermediates nitrosobenzene and phenylhydroxylamine then occurs on the nanosecondmore » time scale. The rate constants for the single-electron transfer reactions are correlated with the driving forces for the corresponding proton-coupled electron transfers. This result suggests, but does not prove, that electron transfer, not proton transfer, is rate-limiting for these reactions. Nuclear magnetic resonance analysis of the QD–molecule systems shows that the photoproduct aniline, left unprotonated, serves as a poison for the QD catalyst by adsorbing to its surface. Performing the reaction at an acidic pH not only encourages aniline to desorb but also increases the probability of protonated intermediates; the latter effect probably ensures that recruitment of protons is not rate-limiting.« less

Structural insights into electron transfer in caa3-type cytochrome oxidase

PubMed Central

Lyons, Joseph A.; Aragão, David; Slattery, Orla; Pisliakov, Andrei V.; Soulimane, Tewfik; Caffrey, Martin

2012-01-01

Summary Paragraph Cytochrome c oxidase is a member of the heme copper oxidase superfamily (HCO)1. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c2–4. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented. PMID:22763450

Solvent Dependence of Double Proton Transfer in the Formic Acid-Formamidine Complex: Path Integral Molecular Dynamics Investigation.

PubMed

Kungwan, Nawee; Ngaojampa, Chanisorn; Ogata, Yudai; Kawatsu, Tsutomu; Oba, Yuki; Kawashima, Yukio; Tachikawa, Masanori

2017-10-05

Solvent dependence of double proton transfer in the formic acid-formamidine (FA-FN) complex at room temperature was investigated by means of ab initio path integral molecular dynamics (AIPIMD) simulation with taking nuclear quantum and thermal effects into account. The conductor-like screening model (COSMO) was applied for solvent effect. In comparison with gas phase, double proton delocalization between two heavy atoms (O and N) in FA-FN were observed with reduced proton transfer barrier height in low dielectric constant medium (<4.8). For dielectric constant medium at 4.8, the chance of finding these two protons are more pronounced due to the solvent effect which completely washes out the proton transfer barrier. In the case of higher dielectric constant medium (>4.8), the ionic species becomes more stable than the neutral ones and the formate anion and formamidium cation are thermodynamically stable. For ab initio molecular dynamics simulation, in low dielectric constant medium (<4.8) a reduction of proton transfer barrier with solvent effect is found to be less pronounced than the AIPIMD due to the absence of nuclear quantum effect. Moreover, the motions of FA-FN complex are significantly different with increasing dielectric constant medium. Such a difference is revealed in detail by the principal component analysis.

An integrated experimental and theoretical reaction path search: analyses of the multistage reaction of an ionized diethylether dimer involving isomerization, proton transfer, and dissociation.

PubMed

Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

2018-05-30

An ionization-induced multistage reaction of an ionized diethylether (DEE) dimer involving isomerization, proton transfer, and dissociation is investigated by combining infrared (IR) spectroscopy, tandem mass spectrometry, and a theoretical reaction path search. The vertically-ionized DEE dimer isomerizes to a hydrogen-bonded cluster of protonated DEE and the [DEE-H] radical through barrierless intermolecular proton transfer from the CH bond of the ionized moiety. This isomerization process is confirmed by IR spectroscopy and the theoretical reaction path search. The multiple dissociation pathways following the isomerization are analyzed by tandem mass spectrometry. The isomerized cluster dissociates stepwise into a [protonated DEE-acetaldehyde (AA)] cluster, protonated DEE, and protonated AA. The structure of the fragment ion is also analyzed by IR spectroscopy. The reaction map of the multistage processes is revealed through a harmony of these experimental and theoretical methods.

Ultrafast Spectroscopy of Proton-Coupled Electron Transfer (PCET) in Photocatalysis

DTIC Science & Technology

2016-07-08

AFRL-AFOSR-VA-TR-2016-0244 Ultrafast Spectroscopy of Proton-Coupled Electron Transfer (PCET) in Photocatalysis Jahan Dawlaty UNIVERSITY OF SOUTHERN...TITLE AND SUBTITLE Ultrafast Spectroscopy of Proton-Coupled Electron Transfer (PCET) in Photocatalysis 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550...298 Back (Rev. 8/98) DISTRIBUTION A: Distribution approved for public release. Final Report: AFOSR YIP Grant FA9550-13-1-0128: Ultrafast Spectroscopy

Photodynamics of intramolecular proton transfer in polar and nonpolar biflavonoid solutions

NASA Astrophysics Data System (ADS)

Bondarev, S. L.; Knyukshto, V. N.; Tikhomirov, S. A.; Buganov, O. V.; Pyrko, A. N.

2012-10-01

Using methods of steady state luminescence and femtosecond spectroscopy, we have studied the mechanism of intramolecular proton transfer in synthesized 3,7-dihydroxy-2,8-di(4-methoxyphenyl)-4H,6H-pyrano[3,2- g]chromen-4,6-dion in polar and nonpolar solutions, films, and polycrystals at 293 and 77 K. In an excited singlet state, intramolecular proton transfer occurs in two stages. At the first stage, a tautomer with one transferred proton (OTP tautomer) is formed from the Franck-Condon state within τ1 = 0.6 ps. At the second stage, the second proton is transferred within τ2 = 3.1 ps and a tautomer with two transferred protons (TTP tautomer) is formed, which fluoresces in toluene at 293 K with a high quantum yield, Φ f = 0.66, and the fluorescence spectrum of which is characterized by a large Stokes shift, 9900 cm-1. At 293 K, polar solvents (dimethylformamide, dimethyl sulfoxide, ethanol, etc.) solvate the BFV molecule in the ground state, while, in the excited state, an OTP tautomer is mainly formed. In polar ethanol at 77 K, a dual fluorescence spectrum is observed, which is caused by the fluorescence emission of polysolvates with λ{max/ f } = 460 nm and TTP phototautomers at λ{max/ f }= 610 nm.

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase.

PubMed

Kaila, Ville R I; Verkhovsky, Michael I; Hummer, Gerhard; Wikström, Mårten

2009-10-01

Cytochrome c oxidase (CcO) is the terminal enzyme of aerobic respiration. The energy released from the reduction of molecular oxygen to water is used to pump protons across the mitochondrial or bacterial membrane. The pump function introduces a mechanistic requirement of a valve that prevents protons from flowing backwards during the process. It was recently found that Glu-242, a key amino acid in transferring protons to be pumped across the membrane and to the site of oxygen reduction, fulfils the function of such a valve by preventing simultaneous contact to the pump site and to the proton-conducting D-channel (Kaila V.R.I. et al. Proc. Natl. Acad. Sci. USA 105, 2008). Here we have incorporated the valve model into the framework of the reaction mechanism. The function of the Glu valve is studied by exploring how the redox state of the surrounding metal centers, dielectric effects, and membrane potential, affects the energetics and leaks of this valve. Parallels are drawn between the dynamics of Glu-242 and the long-standing obscure difference between the metastable O(H) and stable O states of the binuclear center. Our model provides a suggestion for why reduction of the former state is coupled to proton translocation while reduction of the latter is not.

Emission of neutron–proton and proton–proton pairs in neutrino scattering

DOE PAGES

Ruiz Simo, I.; Amaro, J. E.; Barbaro, M. B.; ...

2016-11-10

For this paper, we use a recently developed model of relativistic meson-exchange currents to compute the neutron–proton and proton–proton yields in (νμ, μ -)scattering from 12C in the 2p–2h channel. We compute the response functions and cross sections with the relativistic Fermi gas model for different kinematics from intermediate to high momentum transfers. We find a large contribution of neutron–proton configurations in the initial state, as compared to proton–proton pairs. In the case of charge-changing neutrino scattering the 2p–2h cross section of proton–proton emission (i.e.,np in the initial state) is much larger than for neutron–proton emission (i.e.,two neutrons in themore » initial state) by a (ω, q)-dependent factor. The different emission probabilities of distinct species of nucleon pairs are produced in our model only by meson-exchange currents, mainly by the Δ isobar current. We also analyze other effects including exchange contributions and the effect of the axial and vector currents.« less

New observations of the low energy proton inner belt

NASA Astrophysics Data System (ADS)

Guild, T. B.; Mazur, J. E.; Looper, M. D.; Blake, J. B.

2013-12-01

We present preliminary results of the trapped low energy (6-32 MeV) proton population in the inner radiation belt (L>1.8) from May, 2008 through present. These observations were made by the High Linear Energy Transfer (HiLET) proton telescope, part of the TWIN-ES instrument suite on the TWINS-2 spacecraft. This collimated telescope measures pitch-angle-resolved proton fluxes as it rises through the inner radiation belt twice per day. We present pitch angle distributions of low energy protons as a function of L, and show how the flux and pitch angle distributions change from the deep solar minimum of 2009 through the rising phase of solar cycle 24. Particular emphasis will be given to inner belt dynamics throughout this interval, both gradual and abrupt, and a discussion of the candidate processes responsible for these changes will be given.

Transverse relaxation of scalar-coupled protons.

PubMed

Segawa, Takuya F; Baishya, Bikash; Bodenhausen, Geoffrey

2010-10-25

In a preliminary communication (B. Baishya, T. F. Segawa, G. Bodenhausen, J. Am. Chem. Soc. 2009, 131, 17538-17539), we recently demonstrated that it is possible to obtain clean echo decays of protons in biomolecules despite the presence of homonuclear scalar couplings. These unmodulated decays allow one to determine apparent transverse relaxation rates R(2) (app) of individual protons. Herein, we report the observation of R(2) (app) for three methyl protons, four amide H(N) protons, and all 11 backbone H(α) protons in cyclosporin A. If the proton resonances overlap, their R(2) (app) rates can be measured by transferring their magnetization to neighboring (13)C nuclei, which are less prone to overlap. The R(2) (app) rates of protons attached to (13)C are faster than those attached to (12)C because of (13)C-(1)H dipolar interactions. The differences of these rates allow the determination of local correlation functions. Backbone H(N) and H(α) protons that have fast decay rates R(2) (app) also feature fast longitudinal relaxation rates R(1) and intense NOESY cross peaks that are typical of crowded environments. Variations of R(2) (app) rates of backbone H(α) protons in similar amino acids reflect differences in local environments.

Proton transfer mediated by the vibronic coupling in oxygen core ionized states of glyoxalmonoxime studied by infrared-X-ray pump-probe spectroscopy.

PubMed

Felicíssimo, V C; Guimarães, F F; Cesar, A; Gel'mukhanov, F; Agren, H

2006-11-30

The theory of IR-X-ray pump-probe spectroscopy beyond the Born-Oppenheimer approximation is developed and applied to the study of the dynamics of intramolecular proton transfer in glyoxalmonoxime leading to the formation of the tautomer 2-nitrosoethenol. Due to the IR pump pulses the molecule gains sufficient energy to promote a proton to a weakly bound well. A femtosecond X-ray pulse snapshots the wave packet route and, hence, the dynamics of the proton transfer. The glyoxalmonoxime molecule contains two chemically nonequivalent oxygen atoms that possess distinct roles in the hydrogen bond, a hydrogen donor and an acceptor. Core ionizations of these form two intersecting core-ionized states, the vibronic coupling between which along the OH stretching mode partially delocalizes the core hole, resulting in a hopping of the core hole from one site to another. This, in turn, affects the dynamics of the proton transfer in the core-ionized state. The quantum dynamical simulations of X-ray photoelectron spectra of glyoxalmonoxime driven by strong IR pulses demonstrate the general applicability of the technique for studies of intramolecular proton transfer in systems with vibronic coupling.

Polarization Transfer in Wide-Angle Compton Scattering and Single-Pion Photoproduction from the Proton

NASA Astrophysics Data System (ADS)

Fanelli, C.; Cisbani, E.; Hamilton, D. J.; Salmé, G.; Wojtsekhowski, B.; Ahmidouch, A.; Annand, J. R. M.; Baghdasaryan, H.; Beaufait, J.; Bosted, P.; Brash, E. J.; Butuceanu, C.; Carter, P.; Christy, E.; Chudakov, E.; Danagoulian, S.; Day, D.; Degtyarenko, P.; Ent, R.; Fenker, H.; Fowler, M.; Frlez, E.; Gaskell, D.; Gilman, R.; Horn, T.; Huber, G. M.; de Jager, C. W.; Jensen, E.; Jones, M. K.; Kelleher, A.; Keppel, C.; Khandaker, M.; Kohl, M.; Kumbartzki, G.; Lassiter, S.; Li, Y.; Lindgren, R.; Lovelace, H.; Luo, W.; Mack, D.; Mamyan, V.; Margaziotis, D. J.; Markowitz, P.; Maxwell, J.; Mbianda, G.; Meekins, D.; Meziane, M.; Miller, J.; Mkrtchyan, A.; Mkrtchyan, H.; Mulholland, J.; Nelyubin, V.; Pentchev, L.; Perdrisat, C. F.; Piasetzky, E.; Prok, Y.; Puckett, A. J. R.; Punjabi, V.; Shabestari, M.; Shahinyan, A.; Slifer, K.; Smith, G.; Solvignon, P.; Subedi, R.; Wesselmann, F. R.; Wood, S.; Ye, Z.; Zheng, X.

2015-10-01

Wide-angle exclusive Compton scattering and single-pion photoproduction from the proton have been investigated via measurement of the polarization transfer from a circularly polarized photon beam to the recoil proton. The wide-angle Compton scattering polarization transfer was analyzed at an incident photon energy of 3.7 GeV at a proton scattering angle of θcmp=70 ° . The longitudinal transfer KLL, measured to be 0.645 ±0.059 ±0.048 , where the first error is statistical and the second is systematic, has the same sign as predicted for the reaction mechanism in which the photon interacts with a single quark carrying the spin of the proton. However, the observed value is ˜3 times larger than predicted by the generalized-parton-distribution-based calculations, which indicates a significant unknown contribution to the scattering amplitude.

Polarization Transfer in Wide-Angle Compton Scattering and Single-Pion Photoproduction from the Proton

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanelli, C.; Cisbani, E.; Hamilton, D. J.

Wide-angle exclusive Compton scattering and single-pion photoproduction from the proton have been investigated via measurement of the polarization transfer from a circularly polarized photon beam to the recoil proton. The wide-angle Compton scattering polarization transfer was analyzed at an incident photon energy of 3.7 GeV at a proton scattering angle of theta(p)(cm) cm = 70 degrees. The longitudinal transfer K-LL, measured to be 0.645 +/- 0.059 +/- 0.048, where the first error is statistical and the second is systematic, has the same sign as predicted for the reaction mechanism in which the photon interacts with a single quark carrying themore » spin of the proton. However, the observed value is similar to 3 times larger than predicted by the generalized-parton-distribution-based calculations, which indicates a significant unknown contribution to the scattering amplitude.« less

Nonlinear optical properties of rhenium(I) complexes: Influence of the extended π-conjugated connectors and proton abstraction.

PubMed

Yu, Hai-Ling; Hong, Bo; Yang, Ning; Zhao, Hong-Yan

2015-09-01

The photoinduced proton-coupled electron transfer chemistry is very crucial to the development of nonlinear optical (NLO) materials with large first hyperpolarizability contrast. We have performed a systematic investigation on the geometric structures, NLO switching, and simulated absorption spectra of rhenium(I) complexes via density functional theory (DFT). The results show that the first hyperpolarizabilities (βvec) increase remarkably with further extending of the organic connectors. In addition, the solvent leads to a slight enhancement of the hyperpolarizability and frequency dependent hyperpolarizability. Furthermore, the proton abstraction plays an important role in tuning the second-order NLO response. It is found that deprotonation not only increases the absolute value of βvec but also changes the sign of βvec from positive to negative. This different sign can be explained by the opposite dipole moments. The efficient enhancement of first hyperpolarizability is attributed to the better delocalization of the π-electron system and the more obvious degree of charge transfer. Therefore, these kinds of complexes might be promising candidates for designed as proton driven molecular second-order NLO switching. Copyright © 2015 Elsevier Inc. All rights reserved.

Semiclassical study of quantum coherence and isotope effects in ultrafast electron transfer reactions coupled to a proton and a phonon bath.

PubMed

Venkataraman, Charulatha

2011-11-28

The linearized semiclassical initial value representation is employed to describe ultrafast electron transfer processes coupled to a phonon bath and weakly coupled to a proton mode. The goal of our theoretical investigation is to understand the influence of the proton on the electronic dynamics in various bath relaxation regimes. More specifically, we study the impact of the proton on coherences and analyze if the coupling to the proton is revealed in the form of an isotope effect. This will be important in distinguishing reactions in which the proton does not undergo significant rearrangement from those in which the electron transfer is accompanied by proton transfer. Unlike other methodologies widely employed to describe nonadiabatic electron transfer, this approach treats the electronic and nuclear degrees of freedom consistently. However, due to the linearized approximation, quantum interference effects are not captured accurately. Our study shows that at small phonon bath reorganization energies, coherent oscillations and isotope effect are observed in both slow and fast bath regimes. The coherences are more substantially damped by deuterium in comparison to the proton. Further, in contrast to the dynamics of the spin-boson model, the coherences are not long-lived. At large bath reorganization energies, the decay is incoherent in the slow and fast bath regimes. In this case, the extent of the isotope effect depends on the relative relaxation timescales of the proton mode and the phonon bath. The isotope effect is magnified for baths that relax on picosecond timescales in contrast to baths that relax in femtoseconds.

Mechanism for the Excited-State Multiple Proton Transfer Process of Dihydroxyanthraquinone Chromophores.

PubMed

Zhou, Qiao; Du, Can; Yang, Li; Zhao, Meiyu; Dai, Yumei; Song, Peng

2017-06-22

The single and dual cooperated proton transfer dynamic process in the excited state of 1,5-dihydroxyanthraquinone (1,5-DHAQ) was theoretically investigated, taking solvent effects (ethanol) into account. The absorption and fluorescence spectra were simulated, and dual fluorescence exhibited, which is consistent with previous experiments. Analysis of the calculated IR and Raman vibration spectra reveals that the intramolecular hydrogen bonding interactions (O 20 -H 21 ···O 24 and O 22 -H 23 ···O 25 ) are strengthened following the excited proton transfer process. Finally, by constructing the potential energy surfaces of the ground state, first excited singlet state, and triplet state, the mechanism of the intramolecular proton transfer of 1,5-DHAQ can be revealed.

Resolution of concerted versus sequential mechanisms in photo-induced double-proton transfer reaction in 7-azaindole H-bonded dimer

PubMed Central

Catalán, Javier; del Valle, Juan Carlos; Kasha, Michael

1999-01-01

The experimental and theoretical bases for a synchronous or concerted double-proton transfer in centro-symmetric H-bonded electronically excited molecular dimers are presented. The prototype model is the 7-azaindole dimer. New research offers confirmation of a concerted mechanism for excited-state biprotonic transfer. Recent femtosecond photoionization and coulombic explosion techniques have given rise to time-of-flight MS observations suggesting sequential two-step biprotonic transfer for the same dimer. We interpret the overall species observed in the time-of-flight experiments as explicable without conflict with the concerted mechanism of proton transfer. PMID:10411876

Size-restricted proton transfer within toluene-methanol cluster ions.

PubMed

Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek; Furlani, Thomas; DeLeon, Robert L; Garvey, James F

2008-11-20

To understand the interaction between toluene and methanol, the chemical reactivity of [(C6H5CH3)(CH3OH) n=1-7](+) cluster ions has been investigated via tandem quadrupole mass spectrometry and through calculations. Collision Induced Dissociation (CID) experiments show that the dissociated intracluster proton transfer reaction from the toluene cation to methanol clusters, forming protonated methanol clusters, only occurs for n = 2-4. For n = 5-7, CID spectra reveal that these larger clusters have to sequentially lose methanol monomers until they reach n = 4 to initiate the deprotonation of the toluene cation. Metastable decay data indicate that for n = 3 and n = 4 (CH3OH)3H(+) is the preferred fragment ion. The calculational results reveal that both the gross proton affinity of the methanol subcluster and the structure of the cluster itself play an important role in driving this proton transfer reaction. When n = 3, the cooperative effect of the methanols in the subcluster provides the most important contribution to allow the intracluster proton transfer reaction to occur with little or no energy barrier. As n >or= 4, the methanol subcluster is able to form ring structures to stabilize the cluster structures so that direct proton transfer is not a favored process. The preferred reaction product, the (CH3OH)3H(+) cluster ion, indicates that this size-restricted reaction is driven by both the proton affinity and the enhanced stability of the resulting product.

Measurement of the neutron F2 structure function via spectator tagging with CLAS.

PubMed

Baillie, N; Tkachenko, S; Zhang, J; Bosted, P; Bültmann, S; Christy, M E; Fenker, H; Griffioen, K A; Keppel, C E; Kuhn, S E; Melnitchouk, W; Tvaskis, V; Adhikari, K P; Adikaram, D; Aghasyan, M; Amaryan, M J; Anghinolfi, M; Arrington, J; Avakian, H; Baghdasaryan, H; Battaglieri, M; Biselli, A S; Branford, D; Briscoe, W J; Brooks, W K; Burkert, V D; Carman, D S; Celentano, A; Chandavar, S; Charles, G; Cole, P L; Contalbrigo, M; Crede, V; D'Angelo, A; Daniel, A; Dashyan, N; De Vita, R; De Sanctis, E; Deur, A; Dey, B; Djalali, C; Dodge, G; Domingo, J; Doughty, D; Dupre, R; Dutta, D; Ent, R; Egiyan, H; El Alaoui, A; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fedotov, G; Fegan, S; Fradi, A; Gabrielyan, M Y; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Gohn, W; Golovatch, E; Gothe, R W; Graham, L; Guegan, B; Guidal, M; Guler, N; Guo, L; Hafidi, K; Heddle, D; Hicks, K; Holtrop, M; Hungerford, E; Hyde, C E; Ilieva, Y; Ireland, D G; Ispiryan, M; Isupov, E L; Jawalkar, S S; Jo, H S; Kalantarians, N; Khandaker, M; Khetarpal, P; Kim, A; Kim, W; King, P M; Klein, A; Klein, F J; Klimenko, A; Kubarovsky, V; Kuleshov, S V; Kvaltine, N D; Livingston, K; Lu, H Y; MacGregor, I J D; Mao, Y; Markov, N; McKinnon, B; Mineeva, T; Morrison, B; Moutarde, H; Munevar, E; Nadel-Turonski, P; Ni, A; Niccolai, S; Niculescu, I; Niculescu, G; Osipenko, M; Ostrovidov, A I; Pappalardo, L; Park, K; Park, S; Pasyuk, E; Anefalos Pereira, S; Pisano, S; Pozdniakov, S; Price, J W; Procureur, S; Prok, Y; Protopopescu, D; Raue, B A; Ricco, G; Rimal, D; Ripani, M; Rosner, G; Rossi, P; Sabatié, F; Saini, M S; Salgado, C; Schott, D; Schumacher, R A; Seder, E; Sharabian, Y G; Sober, D I; Sokhan, D; Stepanyan, S; Stepanyan, S S; Stoler, P; Strauch, S; Taiuti, M; Tang, W; Ungaro, M; Vineyard, M F; Voutier, E; Watts, D P; Weinstein, L B; Weygand, D P; Wood, M H; Zana, L; Zhao, B

2012-04-06

We report on the first measurement of the F(2) structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲100 MeV/c and their angles to ≳100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F(2)(n) data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65

Physical consequences of the mitochondrial targeting of single-walled carbon nanotubes probed computationally

NASA Astrophysics Data System (ADS)

Chistyakov, V. A.; Zolotukhin, P. V.; Prazdnova, E. V.; Alperovich, I.; Soldatov, A. V.

2015-06-01

Experiments by F. Zhou and coworkers (2010) [16] showed that mitochondria are the main target of the cellular accumulation of single-walled carbon nanotubes (SWCNTs). Our in silico experiments, based on geometrical optimization of the system consisting of SWCNT+proton within Density Functional Theory, revealed that protons can bind to the outer side of SWCNT so generating a positive charge. Calculation results allow one to propose the following mechanism of SWCNTs mitochondrial targeting. SWCNTs enter the space between inner and outer membranes of mitochondria, where the excess of protons has been formed by diffusion. In this compartment SWCNTs are loaded with protons and acquire positive charges distributed over their surface. Protonation of hydrophobic SWCNTs can also be carried out within the mitochondrial membrane through interaction with the protonated ubiquinone. Such "charge loaded" particles can be transferred as "Sculachev ions" through the inner membrane of the mitochondria due to the potential difference generated by the inner membrane. Physiological consequences of the described mechanism are discussed.

Proton transfer along water bridges in biological systems with density-functional tight-binding

NASA Astrophysics Data System (ADS)

Reiss, Krystle; Wise, Abigail; Mazzuca, James

2015-03-01

When examining the dynamics of charge transfer in high dimensional enzymatic systems, the cost of quantum mechanical treatment of electrons increases exponentially with the size of the system. As a semi-empirical method, density-functional tight-binding aids in shortening these calculation times, but can be inaccurate in the regime where bonds are being formed and broken. To address these inaccuracies with respect to proton transfer in an enzymatic system, DFTB is being used to calculate small model systems containing only a single amino acid residue donor, represented by an imidazole molecule, and a water acceptor. When DFTB calculations are compared to B3LYP geometry calculations of the donor molecule, we observe a bond angle error on the order of 1.2 degrees and a bond length error on the order of 0.011 Å. As we move forward with small donor-acceptor systems, comparisons between DFTB and B3LYP energy profiles will provide a better clue as to what extent improvements need to be made. To improve the accuracy of the DFTB calculations, the internuclear repulsion term may be altered. This would result in energy profiles that closely resemble those produced by higher-level theory. Alma College Provost's Office.

On-resonance Variable Delay Multi Pulse Scheme for Imaging of Fast-exchanging Protons and semi-solid Macromolecules

PubMed Central

Xu, Jiadi; Chan, Kannie W.Y.; Xu, Xiang; Yadav, Nibhay; Liu, Guanshu; van Zijl, Peter C. M.

2016-01-01

Purpose To develop an on-resonance variable delay multi-pulse (VDMP) scheme to image magnetization transfer contrast (MTC) as well as the chemical exchange saturation transfer (CEST) contrast of total fast-exchanging protons (TFP) with exchange rate above about 1 kHz. Methods A train of high power binomial pulses was applied at the water resonance. The inter-pulse delay, called mixing time, was varied to observe its effect on the water signal reduction, allowing separation and quantification of MTC and CEST contributions due to their different proton transfer rates. The fast-exchanging protons in CEST and MTC are labeled together with the short T2 components in MTC and separated out using a variable mixing time. Results Phantom studies of selected metabolite solutions (glucose, glutamate, creatine, myo-inositol), bovine serum albumin (BSA) and hair conditioner show the capability of on-resonance VDMP to separate out exchangeable protons with exchange rates above 1 kHz. Quantitative MTC and TFP maps were acquired on healthy mouse brains using this method showing strong gray/white matter contrast for the slowly transferring MTC protons while the TFP map was more uniform across the brain but somewhat higher in gray matter. Conclusions The new method provides a simple way of imaging fast-exchanging protons, as well as MTC components with a slow transfer rate. PMID:26900759

Substitutions of S101 decrease proton and hydride transfers in the oxidation of betaine aldehyde by choline oxidase.

PubMed

Gadda, Giovanni; Yuan, Hongling

2017-11-15

Choline oxidase oxidizes choline to glycine betaine, with two flavin-mediated reactions to convert the alcohol substrate to the carbon acid product. Proton abstraction from choline or hydrated betaine aldehyde in the wild-type enzyme occurs in the mixing time of the stopped-flow spectrophotometer, thereby precluding a mechanistic investigation. Mutagenesis of S101 rendered the proton transfer reaction amenable to study. Here, we have investigated the aldehyde oxidation reaction catalyzed by the mutant enzymes using steady-state and rapid kinetics with betaine aldehyde. Stopped-flow traces for the reductive half-reaction of the S101T/V/C variants were biphasic, corresponding to the reactions of proton abstraction and hydride transfer. In contrast, the S101A enzyme yielded monophasic traces like wild-type choline oxidase. The rate constants for proton transfer in the S101T/C/V variants decreased logarithmically with increasing hydrophobicity of residue 101, indicating a behavior different from that seen previously with choline for which no correlation was determined. The rate constants for hydride transfer also showed a logarithmic decrease with increasing hydrophobicity at position 101, which was similar to previous results with choline as a substrate for the enzyme. Thus, the hydrophilic character of S101 is necessary not only for efficient hydride transfer but also for the proton abstraction reaction. Copyright © 2017. Published by Elsevier Inc.

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Nanoscale measurements of proton tracks using fluorescent nuclear track detectors

PubMed Central

Sawakuchi, Gabriel O.; Ferreira, Felisberto A.; McFadden, Conor H.; Hallacy, Timothy M.; Granville, Dal A.; Sahoo, Narayan; Akselrod, Mark S.

2016-01-01

Purpose: The authors describe a method in which fluorescence nuclear track detectors (FNTDs), novel track detectors with nanoscale spatial resolution, are used to determine the linear energy transfer (LET) of individual proton tracks from proton therapy beams by allowing visualization and 3D reconstruction of such tracks. Methods: FNTDs were exposed to proton therapy beams with nominal energies ranging from 100 to 250 MeV. Proton track images were then recorded by confocal microscopy of the FNTDs. Proton tracks in the FNTD images were fit by using a Gaussian function to extract fluorescence amplitudes. Histograms of fluorescence amplitudes were then compared with LET spectra. Results: The authors successfully used FNTDs to register individual proton tracks from high-energy proton therapy beams, allowing reconstruction of 3D images of proton tracks along with delta rays. The track amplitudes from FNTDs could be used to parameterize LET spectra, allowing the LET of individual proton tracks from therapeutic proton beams to be determined. Conclusions: FNTDs can be used to directly visualize proton tracks and their delta rays at the nanoscale level. Because the track intensities in the FNTDs correlate with LET, they could be used further to measure LET of individual proton tracks. This method may be useful for measuring nanoscale radiation quantities and for measuring the LET of individual proton tracks in radiation biology experiments. PMID:27147359

Nanoscale measurements of proton tracks using fluorescent nuclear track detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sawakuchi, Gabriel O., E-mail: gsawakuchi@mdanderson.org; Sahoo, Narayan; Ferreira, Felisberto A.

Purpose: The authors describe a method in which fluorescence nuclear track detectors (FNTDs), novel track detectors with nanoscale spatial resolution, are used to determine the linear energy transfer (LET) of individual proton tracks from proton therapy beams by allowing visualization and 3D reconstruction of such tracks. Methods: FNTDs were exposed to proton therapy beams with nominal energies ranging from 100 to 250 MeV. Proton track images were then recorded by confocal microscopy of the FNTDs. Proton tracks in the FNTD images were fit by using a Gaussian function to extract fluorescence amplitudes. Histograms of fluorescence amplitudes were then compared withmore » LET spectra. Results: The authors successfully used FNTDs to register individual proton tracks from high-energy proton therapy beams, allowing reconstruction of 3D images of proton tracks along with delta rays. The track amplitudes from FNTDs could be used to parameterize LET spectra, allowing the LET of individual proton tracks from therapeutic proton beams to be determined. Conclusions: FNTDs can be used to directly visualize proton tracks and their delta rays at the nanoscale level. Because the track intensities in the FNTDs correlate with LET, they could be used further to measure LET of individual proton tracks. This method may be useful for measuring nanoscale radiation quantities and for measuring the LET of individual proton tracks in radiation biology experiments.« less

Quantitative description of proton exchange processes between water and endogenous and exogenous agents for WEX, CEST, and APT experiments.

PubMed

Zhou, Jinyuan; Wilson, David A; Sun, Phillip Zhe; Klaus, Judith A; Van Zijl, Peter C M

2004-05-01

The proton exchange processes between water and solutes containing exchangeable protons have recently become of interest for monitoring pH effects, detecting cellular mobile proteins and peptides, and enhancing the detection sensitivity of various low-concentration endogenous and exogenous species. In this work, the analytic expressions for water exchange (WEX) filter spectroscopy, chemical exchange-dependent saturation transfer (CEST), and amide proton transfer (APT) experiments are derived by the use of Bloch equations with exchange terms. The effects of the initial states for the system, the difference between a steady state and a saturation state, and the relative contributions of the forward and backward exchange processes are discussed. The theory, in combination with numerical calculations, provides a useful tool for designing experimental schemes and assessing magnetization transfer (MT) processes between water protons and solvent-exchangeable protons. As an example, the case of endogenous amide proton exchange in the rat brain at 4.7 T is analyzed in detail. Copyright 2004 Wiley-Liss, Inc.

Photoluminescence of radiation-induced color centers in lithium fluoride thin films for advanced diagnostics of proton beams

NASA Astrophysics Data System (ADS)

Piccinini, M.; Ambrosini, F.; Ampollini, A.; Picardi, L.; Ronsivalle, C.; Bonfigli, F.; Libera, S.; Nichelatti, E.; Vincenti, M. A.; Montereali, R. M.

2015-06-01

Systematic irradiation of thermally evaporated 0.8 μm thick polycrystalline lithium fluoride films on glass was performed by proton beams of 3 and 7 MeV energies, produced by a linear accelerator, in a fluence range from 1011 to 1015 protons/cm2. The visible photoluminescence spectra of radiation-induced F2 and F3+ laser active color centers, which possess almost overlapping absorption bands at about 450 nm, were measured under laser pumping at 458 nm. On the basis of simulations of the linear energy transfer with proton penetration depth in LiF, it was possible to obtain the behavior of the measured integrated photoluminescence intensity of proton irradiated LiF films as a function of the deposited dose. The photoluminescence signal is linearly dependent on the deposited dose in the interval from 103 to about 106 Gy, independently from the used proton energies. This behavior is very encouraging for the development of advanced solid state radiation detectors based on optically transparent LiF thin films for proton beam diagnostics and two-dimensional dose mapping.

Detection of Ketones by a Novel Technology: Dipolar Proton Transfer Reaction Mass Spectrometry (DP-PTR-MS)

NASA Astrophysics Data System (ADS)

Pan, Yue; Zhang, Qiangling; Zhou, Wenzhao; Zou, Xue; Wang, Hongmei; Huang, Chaoqun; Shen, Chengyin; Chu, Yannan

2017-05-01

Proton transfer reaction mass spectrometry (PTR-MS) has played an important role in the field of real-time monitoring of trace volatile organic compounds (VOCs) due to its advantages such as low limit of detection (LOD) and fast time response. Recently, a new technology of proton extraction reaction mass spectrometry (PER-MS) with negative ions OH- as the reagent ions has also been presented, which can be applied to the detection of VOCs and even inorganic compounds. In this work, we combined the functions of PTR-MS and PER-MS in one instrument, thereby developing a novel technology called dipolar proton transfer reaction mass spectrometry (DP-PTR-MS). The selection of PTR-MS mode and PER-MS mode was achieved in DP-PTR-MS using only water vapor in the ion source and switching the polarity. In this experiment, ketones (denoted by M) were selected as analytes. The ketone (molecular weight denoted by m) was ionized as protonated ketone [M + H]+ [mass-to-charge ratio ( m/z) m + 1] in PTR-MS mode and deprotonated ketone [M - H]- ( m/z m - 1) in PER-MS mode. By comparing the m/z value of the product ions in the two modes, the molecular weight of the ketone can be positively identified as m. Results showed that whether it is a single ketone sample or a mixed sample of eight kinds of ketones, the molecular weights can be detected with DP-PTR-MS. The newly developed DP-PTR-MS not only maintains the original advantages of PTR-MS and PER-MS in sensitive and rapid detection of ketones, but also can estimate molecular weight of ketones.

Mechanism of tyrosine D oxidation in Photosystem II.

PubMed

Saito, Keisuke; Rutherford, A William; Ishikita, Hiroshi

2013-05-07

Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II [Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473(7345):55-60], we investigated the H-bonding environment of the redox-active tyrosine D (TyrD) and obtained insights that help explain its slow redox kinetics and the stability of TyrD(•). The water molecule distal to TyrD, located ~4 Å away from the phenolic O of TyrD, corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to the phenolic O of TyrD, corresponds to the presence of the unoxidized tyrosine. The H(+) released on oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasiirreversible, explaining the great stability of the TyrD(•). A symmetry-related proton pathway associated with tyrosine Z is pointed out, and this is associated with one of the Cl(-) sites. This may represent a proton pathway functional in the water oxidation cycle.

A delicate case of unidirectional proton transfer from water to an aromatic heterocyclic anion.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2016-11-21

We present the characteristic proton transfer process from water to the pyrazole anion, infrared signatures of hydroxyl groups and the free energy profile of the process in aqueous solution combining first principles simulations, wavelet analysis and metadynamics. Our results show that the presence of minimum three water molecules in the gas phase cluster with a particular arrangement is sufficient to facilitate the proton transfer process from water to the anion. The overall reaction is very rapid in aqueous solution, and the free energy barrier for this process is found to be 4.2 kcal mol -1 . One of the earlier reported fundamental reasons for the transfer of proton from water to the anion is the change in the acidity of OH groups surrounding the anion. We have correlated the stretching frequencies of the surrounding OH groups with this acidity. We find that the development of less energetic vibrational states, and the OH mode having lowest average stretching frequency contains the most acidic proton. A large frequency shift of the OH mode belonging to one of the surrounding water molecules is observed during the transfer of proton from water to the anion; this shift is due to the change in acidity of the adjacent hydroxyl groups in the vicinity of the anion.

Artificial synapse network on inorganic proton conductor for neuromorphic systems.

PubMed

Zhu, Li Qiang; Wan, Chang Jin; Guo, Li Qiang; Shi, Yi; Wan, Qing

2014-01-01

The basic units in our brain are neurons, and each neuron has more than 1,000 synapse connections. Synapse is the basic structure for information transfer in an ever-changing manner, and short-term plasticity allows synapses to perform critical computational functions in neural circuits. Therefore, the major challenge for the hardware implementation of neuromorphic computation is to develop artificial synapse network. Here in-plane lateral-coupled oxide-based artificial synapse network coupled by proton neurotransmitters are self-assembled on glass substrates at room-temperature. A strong lateral modulation is observed due to the proton-related electrical-double-layer effect. Short-term plasticity behaviours, including paired-pulse facilitation, dynamic filtering and spatiotemporally correlated signal processing are mimicked. Such laterally coupled oxide-based protonic/electronic hybrid artificial synapse network proposed here is interesting for building future neuromorphic systems.

Sterics level the rates of proton transfer to [Ni(XPh){PhP(CH₂CH₂PPh₂)₂}]⁺ (X = O, S or Se).

PubMed

Alwaaly, Ahmed; Henderson, Richard A

2014-09-04

Rates of proton transfers between lutH(+) (lut = 2,6-dimethylpyridine) and [Ni(XPh)(PhP{CH2CH2PPh2}2)](+) (X = O, S or Se) are slow and show little variation (k(O) : k(S) : k(Se) = 1 : 12 : 9). This unusual behaviour is a consequence of sterics affecting the optimal interaction between the reactants prior to proton transfer.

Pathways of proton transfer in the light-driven pump bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1993-01-01

The mechanism of proton transport in the light-driven pump bacteriorhodopsin is beginning to be understood. Light causes the all-trans to 13-cis isomerization of the retinal chromophore. This sets off a sequential and directed series of transient decreases in the pKa's of a) the retinal Schiff base, b) an extracellular proton release complex which includes asp-85, and c) a cytoplasmic proton uptake complex which includes asp-96. The timing of these pKa changes during the photoreaction cycle causes sequential proton transfers which result in the net movement of a proton across the protein, from the cytoplasmic to the extracellular surface.

Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

PubMed

Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

2009-10-07

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

Determination of the longitudinal proton structure function FL(x,Q2) at low x

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arndt, C.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Blümlein, J.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; de Roeck, A.; de Wolf, E. A.; Dirkmann, M.; Dixon, P.; di Nezza, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Erdmann, W.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krehbiel, H.; Krücker, D.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Levonian, S.; Lindström, G.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Noyes, G. W.; Nunnemann, T.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Reinshagen, S.; Riemersma, S.; Rick, H.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steiner, H.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tutas, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; van Esch, P.; van Mechelen, P.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wünsch, E.; ŽáČek, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; Zuber, K.; Zurnedden, M.

1997-02-01

A measurement of the inclusive cross section for the deep-inelastic scattering of positrons off protons at HERA is presented at momentum transfers 8.5 <= Q2 <= 35 GeV2 and large inelasticity = 0.7, i.e. for the Bjorken-x range 0.00013 <= x <= 0.00055. Using a next-to-leading order QCD fit to the structure function F2 at lower y values, the contribution of F2 to the measured cross section at high y is calculated and, by subtraction, the longitudinal structure function FL is determined for the first time with an average value of FL = 0.52+/-0.03 (stat)+0.25-0.22 (syst) at Q2 = 15.4 GeV2 and x = 0.000243.

In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

PubMed

Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

2016-10-24

The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Water Molecules Gating a Photoinduced One-Electron Two-Protons Transfer in a Tyrosine/Histidine (Tyr/His) Model of Photosystem II.

PubMed

Chararalambidis, Georgios; Das, Shyamal; Trapali, Adelais; Quaranta, Annamaria; Orio, Maylis; Halime, Zakaria; Fertey, Pierre; Guillot, Régis; Coutsolelos, Athanassios; Leibl, Winfried; Aukauloo, Ally; Sircoglou, Marie

2018-05-22

We investigate a biomimetic model of a Tyr Z /His 190 pair, a hydrogen-bonded phenol/imidazole covalently attached to a porphyrin sensitizer. Laser flash photolysis in the presence of an external electron acceptor reveals the need for water molecules to unlock the light-induced oxidation of the phenol through an intramolecular pathway. Kinetics monitoring encompasses two fast phases with distinct spectral properties. The first phase is related to a one-electron transfer from the phenol to the porphyrin radical cation coupled with a domino two-proton transfer leading to the ejection of a proton from the imidazole-phenol pair. The second phase concerns conveying the released proton to the porphyrin N 4 coordinating cavity. Our study provides an unprecedented example of a light-induced electron-transfer process in a Tyr Z /His 190 model of photosystem II, evidencing the movement of both the phenol and imidazole protons along an isoenergetic pathway. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fourier transform infrared difference and time-resolved infrared detection of the electron and proton transfer dynamics in photosynthetic water oxidation.

PubMed

Noguchi, Takumi

2015-01-01

Photosynthetic water oxidation, which provides the electrons necessary for CO₂ reduction and releases O₂ and protons, is performed at the Mn₄CaO₅ cluster in photosystem II (PSII). In this review, studies that assessed the mechanism of water oxidation using infrared spectroscopy are summarized focusing on electron and proton transfer dynamics. Structural changes in proteins and water molecules between intermediates known as Si states (i=0-3) were detected using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Electron flow in PSII and proton release from substrate water were monitored using the infrared changes in ferricyanide as an exogenous electron acceptor and Mes buffer as a proton acceptor. Time-resolved infrared (TRIR) spectroscopy provided information on the dynamics of proton-coupled electron transfer during the S-state transitions. In particular, a drastic proton movement during the lag phase (~200μs) before electron transfer in the S3→S0 transition was detected directly by monitoring the infrared absorption of a polarizable proton in a hydrogen bond network. Furthermore, the proton release pathways in the PSII proteins were analyzed by FTIR difference measurements in combination with site-directed mutagenesis, isotopic substitutions, and quantum chemical calculations. Therefore, infrared spectroscopy is a powerful tool for understanding the molecular mechanism of photosynthetic water oxidation. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamamoto, Takeshi; Kato, Shigeki

2007-06-14

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schroedinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schroedinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes inmore » this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.« less

Suicide Inhibition of Cytochrome P450 Enzymes by Cyclopropylamines via a Ring-opening Mechanism: Proton-Coupled Electron Transfer Makes a Difference

NASA Astrophysics Data System (ADS)

Zhang, Xiaoqian; Li, Xiao-Xi; Liu, Yufang; Wang, Yong

2017-01-01

N-benzyl-N-cyclopropylamine (BCA) has been attracting great interests for decades for its partial suicide inactivation role to cytochrome P450 (P450) via a ring-opening mechanism besides acting as a role of normal substrates. Understanding the mechanism of such partial inactivation is vital to the clinical drug design. Thus, density functional theoretical (DFT) calculations were carried out on such P450-catalyzed reactions, not only on the metabolic pathway, but on the ring-opening inactivation one. Our theoretical results demonstrated that, in the metabolic pathway, besides the normal carbinolamine, an unexpected enamine was formed via the dual hydrogen abstraction (DHA) process, in which the competition between rotation of the H-abstracted substrate radical and the rotation of hydroxyl group of the protonated Cpd II moiety plays a significant role in product branch; In the inactivation pathway, the well-noted single electron transfer (SET) mechanism-involved process was invalidated for its high energy barrier, a proton-coupled electron transfer (PCET(ET)) mechanism plays a role. Our results are consistent with other related theoretical works on heteroatom-hydrogen (X-H, X = O, N) activation and revealed new features. The revealed mechanisms will play a positive role in relative drug design.

Theoretical Insights Into the Excited State Double Proton Transfer Mechanism of Deep Red Pigment Alkannin.

PubMed

Zhao, Jinfeng; Dong, Hao; Zheng, Yujun

2018-02-08

As the most important component of deep red pigments, alkannin is investigated theoretically in detail based on time-dependent density functional theory (TDDFT) method. Exploring the dual intramolecular hydrogen bonds (O1-H2···O3 and O4-H5···O6) of alkannin, we confirm the O1-H2···O3 may play a more important role in the first excited state than the O4-H5···O6 one. Infrared (IR) vibrational analyses and subsequent charge redistribution also support this viewpoint. Via constructing the S 1 -state potential energy surface (PES) and searching transition state (TS) structures, we illuminate the excited state double proton transfer (ESDPT) mechanism of alkannin is the stepwise process that can be first launched by the O1-H2···O3 hydrogen bond wire in gas state, acetonitrile (CH 3 CN) and cyclohexane (CYH) solvents. We present a novel mechanism that polar aprotic solvents can contribute to the first-step proton transfer (PT) process in the S 1 state, and nonpolar solvents play important roles in lowering the potential energy barrier of the second-step PT reaction.

Excited-State Proton Transfer on the Surface of a Therapeutic Protein, Protamine.

PubMed

Awasthi, Ankur A; Singh, Prabhat K

2017-11-16

Proton transfer reactions on biosurfaces play an important role in a myriad of biological processes. Herein, the excited-state proton transfer reaction of 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) has been investigated in the presence of an important therapeutic protein, Protamine (PrS), using ground-state absorption, steady-state, and detailed time-resolved emission measurements. HPTS forms a 1:1 complex with Protamine with a high association constant of 2.6 × 10 4 M -1 . The binding of HPTS with Protamine leads to a significant modulation in the ground-state prototropic equilibrium causing a downward shift of 1.1 unit in the acidity constant (pK a ). In contrast to a large number of reports of slow proton transfer of HPTS on biosurfaces, interestingly, HPTS registers a faster proton transfer event in the presence of Protamine as compared to that of even the bulk aqueous buffer medium. Furthermore, the dimensionality of the proton diffusion process is also significantly reduced on the surface of Protamine that is in contrast to the behavior of HPTS in the bulk aqueous buffer medium, where the proton diffusion process is three-dimensional. The effect of ionic strength on the binding of HPTS toward PrS suggests a predominant role of electrostatic interaction between anionic HPTS and cationic Protamine, which is further supported by molecular docking simulations which predict that the most preferable binding site for HPTS on the surface of Protamine is surrounded by multiple cationic arginine residues.

On-resonance variable delay multipulse scheme for imaging of fast-exchanging protons and semisolid macromolecules.

PubMed

Xu, Jiadi; Chan, Kannie W Y; Xu, Xiang; Yadav, Nirbhay; Liu, Guanshu; van Zijl, Peter C M

2017-02-01

To develop an on-resonance variable delay multipulse (VDMP) scheme to image magnetization transfer contrast (MTC) and the chemical exchange saturation transfer (CEST) contrast of total fast-exchanging protons (TFP) with exchange rate above approximately 1 kHz. A train of high power binomial pulses was applied at the water resonance. The interpulse delay, called mixing time, was varied to observe its effect on the water signal reduction, allowing separation and quantification of MTC and CEST contributions as a result of their different proton transfer rates. The fast-exchanging protons in CEST and MTC are labeled together with the short T 2 components in MTC and separated out using a variable mixing time. Phantom studies of selected metabolite solutions (glucose, glutamate, creatine, myo-inositol), bovine serum albumin (BSA), and hair conditioner show the capability of on-resonance VDMP to separate out exchangeable protons with exchange rates above 1 kHz. Quantitative MTC and TFP maps were acquired on healthy mouse brains using this method, showing strong gray/white matter contrast for the slowly transferring MTC protons, whereas the TFP map was more uniform across the brain but somewhat higher in gray matter. The new method provides a simple way of imaging fast-exchanging protons and MTC components with a slow transfer rate. Magn Reson Med 77:730-739, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Competing Pathways in the photo- Proton-Coupled Electron Transfer Reduction of fac -[Re(bpy)(CO) 3 (4,4'-bpy] +* by Hydroquinone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, David J.; Brennaman, M. Kyle; Bettis, Stephanie E.

2011-08-04

The emitting metal-to-ligand charge transfer (MLCT) excited state of fac-[Re{sup I}(bpy)(CO)₃(4,4'-bpy)] + (1) (bpy is 2,2'-bipyridine, 4,4'-bpy is 4,4'-bipyridine), [Re II(bpy –•)(CO)₃(4,4'-bpy)] +*, is reductively quenched by 1,4-hydroquinone (H₂Q) in CH₃CN at 23 ± 2 °C by competing pathways to give a common electron–proton-transfer intermediate. In one pathway, electron transfer (ET) quenching occurs to give Re{sup I}(bpy –•)(CO)₃(4,4'-bpy)]⁰ with k = (1.8 ± 0.2) × 10⁹ M –1 s –1, followed by proton transfer from H₂Q to give [Re I(bpy)(CO)₃(4,4'-bpyH •)] +. Protonation triggers intramolecular bpy –•→ 4,4'-bpyH{sup +} electron transfer. In the second pathway, preassociationmore » occurs between the ground state and H₂Q at high concentrations. Subsequent Re → bpy MLCT excitation of the adduct is followed by electron–proton transfer from H₂Q in concert with intramolecular bpy –•→ 4,4'-bpyH + electron transfer to give [Re I(bpy)(CO)₃(4,4'-bpyH •)] + with k = (1.0 ± 0.4) × 10⁹ s –1 in 3:1 CH₃CN/H₂O.« less

A modular, energy-based approach to the development of nickel containing molecular electrocatalysts for hydrogen production and oxidation.

PubMed

Shaw, Wendy J; Helm, Monte L; DuBois, Daniel L

2013-01-01

This review discusses the development of molecular electrocatalysts for H2 production and oxidation based on nickel. A modular approach is used in which the structure of the catalyst is divided into first, second, and outer coordination spheres. The first coordination sphere consists of the ligands bound directly to the metal center, and this coordination sphere can be used to control such factors as the presence or absence of vacant coordination sites, redox potentials, hydride donor abilities and other important thermodynamic parameters. The second coordination sphere includes functional groups such as pendent acids or bases that can interact with bound substrates such as H2 molecules and hydride ligands, but that do not form strong bonds with the metal center. These functional groups can play diverse roles such as assisting the heterolytic cleavage of H2, controlling intra- and intermolecular proton transfer reactions, and providing a physical pathway for coupling proton and electron transfer reactions. By controlling both the hydride donor ability of the catalysts using the first coordination sphere and the proton donor abilities of the functional groups in the second coordination sphere, catalysts can be designed that are biased toward H2 production, oxidation, or bidirectional (catalyzing both H2 oxidation and production). The outer coordination sphere is defined as that portion of the catalytic system that is beyond the second coordination sphere. This coordination sphere can assist in the delivery of protons and electrons to and from the catalytically active site, thereby adding another important avenue for controlling catalytic activity. Many features of these simple catalytic systems are good models for enzymes, and these simple systems provide insights into enzyme function and reactivity that may be difficult to probe in enzymes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Amide Proton Transfer Imaging Allows Detection of Glioma Grades and Tumor Proliferation: Comparison with Ki-67 Expression and Proton MR Spectroscopy Imaging.

PubMed

Su, C; Liu, C; Zhao, L; Jiang, J; Zhang, J; Li, S; Zhu, W; Wang, J

2017-09-01

Prognosis in glioma depends strongly on tumor grade and proliferation. In this prospective study of patients with untreated primary cerebral gliomas, we investigated whether amide proton transfer-weighted imaging could reveal tumor proliferation and reliably distinguish low-grade from high-grade gliomas compared with Ki-67 expression and proton MR spectroscopy imaging. This study included 42 patients with low-grade ( n = 28) or high-grade ( n = 14) glioma, all of whom underwent conventional MR imaging, proton MR spectroscopy imaging, and amide proton transfer-weighted imaging on the same 3T scanner within 2 weeks before surgery. We assessed metabolites of choline and N -acetylaspartate from proton MR spectroscopy imaging and the asymmetric magnetization transfer ratio at 3.5 ppm from amide proton transfer-weighted imaging and compared them with histopathologic grade and immunohistochemical expression of the proliferation marker Ki-67 in the resected specimens. The asymmetric magnetization transfer ratio at 3.5 ppm values measured by different readers showed good concordance and were significantly higher in high-grade gliomas than in low-grade gliomas (3.61% ± 0.155 versus 2.64% ± 0.185, P = .0016), with sensitivity and specificity values of 92.9% and 71.4%, respectively, at a cutoff value of 2.93%. The asymmetric magnetization transfer ratio at 3.5 ppm values correlated with tumor grade ( r = 0.506, P = .0006) and Ki-67 labeling index ( r = 0.502, P = .002). For all patients, the asymmetric magnetization transfer ratio at 3.5 ppm correlated positively with choline ( r = 0.43, P = .009) and choline/ N -acetylaspartate ratio ( r = 0.42, P = .01) and negatively with N -acetylaspartate ( r = -0.455, P = .005). These correlations held for patients with low-grade gliomas versus those with high-grade gliomas, but the correlation coefficients were higher in high-grade gliomas (choline: r = 0.547, P = .053; N -acetylaspartate: r = -0.644, P = .017; choline/ N -acetylaspartate: r = 0.583, P = .036). The asymmetric magnetization transfer ratio at 3.5 ppm may serve as a potential biomarker not only for assessing proliferation, but also for predicting histopathologic grades in gliomas. © 2017 by American Journal of Neuroradiology.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Water-Mediated Proton Hopping on an Iron Oxide Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merte, L. R.; Peng, Guowen; Bechstein, Ralf

2012-05-18

The diffusion of hydrogen atoms across solid oxide surfaces is often assumed to be accelerated by the presence of water molecules. Here we present a high-resolution, high-speed scanning tunneling microscopy (STM) study of the diffusion of H atoms on an FeO thin film. STM movies directly reveal a water-mediated hydrogen diffusion mechanism on the oxide surface at temperatures between 100 and 300 kelvin. Density functional theory calculations and isotope-exchange experiments confirm the STM observations, and a proton-transfer mechanism that proceeds via an H3O+-like transition state is revealed. This mechanism differs from that observed previously for rutile TiO2(110), where water dissociationmore » is a key step in proton diffusion.« less

Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

PubMed

Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

2015-09-28

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I.

PubMed

Le Breton, Nolwenn; Wright, John J; Jones, Andrew J Y; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

2017-11-15

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A( 1 H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

Alternating electron and proton transfer steps in photosynthetic water oxidation

PubMed Central

Klauss, André; Haumann, Michael; Dau, Holger

2012-01-01

Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel–production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese–calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S2 → S3 transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (). The rate-determining elementary step (τ, approximately 30 µs at 20 °C) in the long-distance proton relocation toward the protein–water interface is characterized by a high activation energy (Ea = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S0 → S1 transition are similar (τ, approximately 100 µs; Ea = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established. PMID:22988080

Alternating electron and proton transfer steps in photosynthetic water oxidation.

PubMed

Klauss, André; Haumann, Michael; Dau, Holger

2012-10-02

Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel-production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese-calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S(2) → S(3) transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (Y Z OX). The rate-determining elementary step (τ, approximately 30 µs at 20 °C) in the long-distance proton relocation toward the protein-water interface is characterized by a high activation energy (E(a) = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S(0) → S(1) transition are similar (τ, approximately 100 µs; E(a) = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established.

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Nonadiabatic dynamics of photo-induced proton-coupled electron transfer reactions via ring-polymer surface hopping

NASA Astrophysics Data System (ADS)

Shakib, Farnaz; Huo, Pengfei

Photo-induced proton-coupled electron transfer reactions (PCET) are at the heart of energy conversion reactions in photocatalysis. Here, we apply the recently developed ring-polymer surface-hopping (RPSH) approach to simulate the nonadiabatic dynamics of photo-induced PCET. The RPSH method incorporates ring-polymer (RP) quantization of the proton into the fewest-switches surface-hopping (FSSH) approach. Using two diabatic electronic states, corresponding to the electron donor and acceptor states, we model photo-induced PCET with the proton described by a classical isomorphism RP. From the RPSH method, we obtain numerical results that are comparable to those obtained when the proton is treated quantum mechanically. This accuracy stems from incorporating exact quantum statistics, such as proton tunnelling, into approximate quantum dynamics. Additionally, RPSH offers the numerical accuracy along with the computational efficiency. Namely, compared to the FSSH approach in vibronic representation, there is no need to calculate a massive number of vibronic states explicitly. This approach opens up the possibility to accurately and efficiently simulate photo-induced PCET with multiple transferring protons or electrons.

Effect of proton transfer on the electronic coupling in DNA

NASA Astrophysics Data System (ADS)

Rak, Janusz; Makowska, Joanna; Voityuk, Alexander A.

2006-06-01

The effects of single and double proton transfer within Watson-Crick base pairs on donor-acceptor electronic couplings, Vda, in DNA are studied on the bases of quantum chemical calculations. Four dimers [AT,AT], [GC,GC], [GC,AT] and [GC,TA)] are considered. Three techniques - the generalized Mulliken-Hush scheme, the fragment charge method and the diabatic states method - are employed to estimate Vda for hole transfer between base pairs. We show that both single- and double proton transfer (PT) reactions may substantially affect the electronic coupling in DNA. The electronic coupling in [AT,AT] is predicted to be most sensitive to PT. Single PT within the first base pair in the dimer leads to increase in the hole transfer efficiency by a factor of 4, while proton transfer within the second pair should substantially, by 2.7 times, decrease the rate of charge transfer. Thus, directional asymmetry of the PT effects on the electronic coupling is predicted. The changes in the Vda matrix elements correlate with the topological properties of orbitals of donor and acceptor and can be qualitatively rationalized in terms of resonance structures of donor and acceptor. Atomic pair contributions to the Vda matrix elements are also analyzed.

On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations.

PubMed

Hong, G; Cornish, A J; Hegg, E L; Pachter, R

2011-05-01

Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159→Ser198→Glu156→water460→Cys178→DTMA([Fe-Fe](H)) and (Glu282→Ser319→Glu279→water612→Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe-Fe](H) sub-cluster in DdH was readily observed in our results, specifically when [Fe-Fe](H) was in the reduced state ([Fe(I)-Fe(I)]) or in the mixed valence state for the protonated distal iron Fe(d) ([Fe(I)-Fe(II)-H(-)](H)). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in CpI. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe-Fe] hydrogenases in which the proton binds at Fe(d), providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs. Published by Elsevier B.V.

Measurement of the structure function of the nearly free neutron using spectator tagging in inelastic 2H(e ,e'ps )X scattering with CLAS

NASA Astrophysics Data System (ADS)

Tkachenko, S.; Baillie, N.; Kuhn, S. E.; Zhang, J.; Arrington, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Kalantarians, N.; Keppel, C. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anefalos Pereira, S.; Avakian, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fleming, J. A.; Garillon, B.; Gevorgyan, N.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gothe, R. W.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Hicks, K.; Ho, D.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Jo, H. S.; Keller, D.; Khandaker, M.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, V.; Kuleshov, S. V.; Lenisa, P.; Lewis, S.; Livingston, K.; Lu, H.; MacCormick, M.; MacGregor, I. J. D.; Markov, N.; Mayer, M.; McKinnon, B.; Mineeva, T.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munoz Camacho, C.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Phillips, J. J.; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Rimal, D.; Ripani, M.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Sabatié, F.; Schott, D.; Schumacher, R. A.; Seder, E.; Senderovich, I.; Sharabian, Y. G.; Simonyan, A.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Strauch, S.; Tang, W.; Ungaro, M.; Vlassov, A. V.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D.; Wei, X.; Weinstein, L. B.; Wood, M. H.; Zana, L.; Zonta, I.; CLAS Collaboration

2014-04-01

Background: Much less is known about neutron structure than that of the proton due to the absence of free neutron targets. Neutron information is usually extracted from data on nuclear targets such as deuterium, requiring corrections for nuclear binding and nucleon off-shell effects. These corrections are model dependent and have significant uncertainties, especially for large values of the Bjorken scaling variable x . As a consequence, the same data can lead to different conclusions, for example, about the behavior of the d quark distribution in the proton at large x . Purpose: The Barely Off-shell Nucleon Structure experiment at Jefferson Lab measured the inelastic electron-deuteron scattering cross section, tagging spectator protons in coincidence with the scattered electrons. This method reduces nuclear binding uncertainties significantly and has allowed for the first time a (nearly) model-independent extraction of the neutron structure function F2(x ,Q2) in the resonance and deep-inelastic regions. Method: A novel compact radial time projection chamber was built to detect protons with momentum between 70 and 150 MeV/c and over a nearly 4 π angular range. For the extraction of the free-neutron structure function F2n, spectator protons at backward angles (>100∘ relative to the momentum transfer) and with momenta below 100 MeV/c were selected, ensuring that the scattering took place on a nearly free neutron. The scattered electrons were detected with Jefferson Lab's CLAS spectrometer, with data taken at beam energies near 2, 4, and 5 GeV. Results: The extracted neutron structure function F2n and its ratio to the inclusive deuteron structure function F2d are presented in both the resonance and the deep-inelastic regions for momentum transfer squared Q2 between 0.7 and 5 GeV2/c2 , invariant mass W between 1 and 2.7 GeV/c2 , and Bjorken x between 0.25 and 0.6 (in the deep-inelastic scattering region). The dependence of the semi-inclusive cross section on the spectator proton momentum and angle is investigated, and tests of the spectator mechanism for different kinematics are performed. Conclusions: Our data set on the structure function ratio F2n/F2d can be used to study neutron resonance excitations, test quark-hadron duality in the neutron, develop more precise parametrizations of structure functions, and investigate binding effects (including possible mechanisms for the nuclear EMC effect) and provide a first glimpse of the asymptotic behavior of d /u at x →1 .

Mammalian complex I pumps 4 protons per 2 electrons at high and physiological proton motive force in living cells.

PubMed

Ripple, Maureen O; Kim, Namjoon; Springett, Roger

2013-02-22

Mitochondrial complex I couples electron transfer between matrix NADH and inner-membrane ubiquinone to the pumping of protons against a proton motive force. The accepted proton pumping stoichiometry was 4 protons per 2 electrons transferred (4H(+)/2e(-)) but it has been suggested that stoichiometry may be 3H(+)/2e(-) based on the identification of only 3 proton pumping units in the crystal structure and a revision of the previous experimental data. Measurement of proton pumping stoichiometry is challenging because, even in isolated mitochondria, it is difficult to measure the proton motive force while simultaneously measuring the redox potentials of the NADH/NAD(+) and ubiquinol/ubiquinone pools. Here we employ a new method to quantify the proton motive force in living cells from the redox poise of the bc(1) complex measured using multiwavelength cell spectroscopy and show that the correct stoichiometry for complex I is 4H(+)/2e(-) in mouse and human cells at high and physiological proton motive force.

Communication: Charge transfer dominates over proton transfer in the reaction of nitric acid with gas-phase hydrated electrons

NASA Astrophysics Data System (ADS)

Lengyel, Jozef; Med, Jakub; Slavíček, Petr; Beyer, Martin K.

2017-09-01

The reaction of HNO3 with hydrated electrons (H2O)n- (n = 35-65) in the gas phase was studied using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and ab initio molecular dynamics simulations. Kinetic analysis of the experimental data shows that OH-(H2O)m is formed primarily via a reaction of the hydrated electron with HNO3 inside the cluster, while proton transfer is not observed and NO3-(H2O)m is just a secondary product. The reaction enthalpy was determined using nanocalorimetry, revealing a quite exothermic charge transfer with -241 ± 69 kJ mol-1. Ab initio molecular dynamics simulations indicate that proton transfer is an allowed reaction pathway, but the overall thermochemistry favors charge transfer.

Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2.

PubMed

Wawrzyniak, Piotr K; Alia, A; Schaap, Roland G; Heemskerk, Mattijs M; de Groot, Huub J M; Buda, Francesco

2008-12-14

Bacteriochlorophyll-histidine complexes are ubiquitous in nature and are essential structural motifs supporting the conversion of solar energy into chemically useful compounds in a wide range of photosynthesis processes. A systematic density functional theory study of the NMR chemical shifts for histidine and for bacteriochlorophyll-a-histidine complexes in the light-harvesting complex II (LH2) is performed using the BLYP functional in combination with the 6-311++G(d,p) basis set. The computed chemical shift patterns are consistent with available experimental data for positive and neutral(tau) (N(tau) protonated) crystalline histidines. The results for the bacteriochlorophyll-a-histidine complexes in LH2 provide evidence that the protein environment is stabilizing the histidine close to the Mg ion, thereby inducing a large charge transfer of approximately 0.5 electronic equivalent. Due to this protein-induced geometric constraint, the Mg-coordinated histidine in LH2 appears to be in a frustrated state very different from the formal neutral(pi) (N(pi) protonated) form. This finding could be important for the understanding of basic functional mechanisms involved in tuning the electronic properties and exciton coupling in LH2.

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

The response of a thermoluminescent dosimeter to low energy protons in the range 30-100 keV.

PubMed

Chu, T C; Lin, S Y; Hsu, C C; Li, J P

2001-11-01

This study demonstrates the thermoluminescence (TL) response of CaF2:Tm (commercial name TLD-300) to 30-100 keV protons which were generated by means of a Cockcroft-Walton accelerator. The phenomenon in which the total thermoluminescent output from CaF2:Tm (TLD-300) decreases with proton energy from 30 to 100 keV (with increase of LET) can be interpreted by the track structure theory (TST). The analysis of the glow peaks: P2 (131 degrees C), P3 (153.5 degrees C) and P6 (259 degrees C), of TLD-300 show the oscillatory decreasing phenomenon as a function of incident proton energy, which can be interpreted with the TST and the oscillatory emission of electrons in a thermoluminescent dosimeter (TLD) that is caused by resonant or quasi-resonant charge transfer in ion-atom interactions in this TLD-300.

A Simple Geometric Model for the Marcus Theory of Proton Transfer

ERIC Educational Resources Information Center

McLennan, Duncan J.

1976-01-01

Uses the intersecting parabola model to derive an equation that relates the observed free energy of activation for a slow proton transfer to the overall thermodynamic free energy change in the reaction. (MLH)

Piston-assisted proton pumping in Complex I of mitochondria membranes

NASA Astrophysics Data System (ADS)

Mourokh, Lev; Filonenko, Ilan

2014-03-01

Proton-pumping mechanism of Complex I remains mysterious because its electron and proton paths are well separated and the direct Coulomb interaction seems to be negligible. The structure of this enzyme was resolved very recently and its functionality was connected the shift of the helix HL. We model the helix as a piston oscillating between the protons and electrons. We assume that positive charges are accumulated near the edges of the helix. In the oxidized state, the piston is attracted to electrons, so its distance to the proton sites increases, the energy of these sites decreases and the sites can be populated. When electrons proceed to the drain, elastic forces return the piston to the original position and the energies of populated proton sites increase, so the protons can be transferred to the positive site of the membrane. In this work, we explore a simplified model when the interaction of the piston with electrons is replaced by a periodic force. We derive quantum Heisenberg equations for the proton operators and solve them jointly with the Langevin equation for the piston position. We show that the proton pumping is possible in such structure with parameters closely resembling the real system. We also address the feasibility of using such mechanism in nanoelectronics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mautner, M.M.N.

The ionization energy of ferrocene (Cp{sub 2}Fe) was measured by charge-transfer equilibria as 6.81 {plus minus} 0.07 eV (157.1 {plus minus} 1.6 kcal/mol). The proton affinity was obtained from equilibrium temperature studies as 207 {plus minus} 1 kcal/mol. The protonation of Cp{sub 2}Fe also involves a significant entropy change of +6.3 cal/mol{center dot}K. Deuteration experiments show that, in the protonation of Cp{sub 2}Fe, the incoming proton goes to a sterically unique position and does not exchange with the ring protons. This is consistent with protonation on iron, but ring protonation exclusively in an exo position or an agostic ring-to-iron bridgedmore » structure are also possible. The results suggest that the proton affinity at Fe is greater by at least 5 kcal/mol than for ring protonation. The solvation energies of Cp{sub 2}Fe{sup +} and Cp{sub 2}FeH{sup +} by a CH{sub 3}CN molecule, 11.4 and 12.9 kcal/mol, respectively, are weaker than those of most gas-phase cations, and the attachment energies of dimethyl ether and benzene, <9 kcal/mol, are even weaker. These results support that the weak solution basicity of Cp{sub 2}Fe is due to inefficient ion solvation. The kinetics of proton transfer between Cp{sub 2}Fe and some cyclic compounds is unusually slow, with reaction efficiencies of 0.1-0.01, without significant temperature dependence. These are the first proton-transfer reactions to show such behavior, which may be due to a combination of an energy barrier and steric hindrance. Proton transfer is also observed from (RCN){sub 2}H{sup +} dimer ions to Cp{sub 2}Fe. These reactions may be direct or involve ligand switching, and in several cases either mechanism is endothermic and entropy-driven.« less

Medicago truncatula Mtha1-2 mutants loose metabolic responses to mycorrhizal colonization.

PubMed

Hubberten, Hans-Michael; Sieh, Daniela; Zöller, Daniela; Hoefgen, Rainer; Krajinski, Franziska

2015-01-01

Bidirectional nutrient transfer is one of the key features of the arbuscular mycorrhizal symbiosis. Recently we were able to identify a Medicago truncatula mutant (mtha1-2) that is defective in the uptake of phosphate from the periarbuscular space due to a lack of the energy providing proton gradient provided by the symbiosis specific proton ATPase MtHA1 In order to further characterize the impact of fungal colonization on the plant metabolic status, without the beneficial aspect of improved mineral nutrition, we performed leaf ion analyses in mutant and wildtype plants with and without fungal colonization. Although frequency of fungal colonization was unaltered, the mutant did not show a positive growth response to mycorrhizal colonization. This indicates that nutrient transfer into the plant cell fails in the truncated arbuscules due to lacking expression of a functional MtHA1 protein. The leaves of wildtype plants showed clear metabolic responses to root mycorrhizal colonization, whereas no changes of leaf metabolite levels of mycorrhizal mtha1-2 plants were detected, even though they were colonized. These results show that MtHa1 is indispensable for a functional mycorrhizal symbiosis and, moreover, suggest that fungal root colonization per se does not depend on nutrient transfer to the plant host.

Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans

PubMed Central

ter Beek, Josy; Krause, Nils; Ädelroth, Pia

2016-01-01

Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed. PMID:27030968

Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans.

PubMed

ter Beek, Josy; Krause, Nils; Ädelroth, Pia

2016-01-01

Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed.

First steps towards a gas-phase acidity ladder for derivatized fullerene dications

NASA Astrophysics Data System (ADS)

Petrie, Simon; Javahery, Gholamreza; Bohme, Diethard K.

1993-03-01

C2+60 can be derivatized by gas-phase ion/molecule reactions with polar hydrogen-bearing molecules. The adduct dications so produced may then undergo proton transfer to neutrals. The occurrence or absence of proton transfer as a secondary process gives information on the gas-phase acidity of the dicationic species C60·(XH)2+in. We have performed studies using a selected-ion flow tube at 294 ± 2 K and 0.35 ± 0.01 Torr, and have used observed reactivity of such dicationic fullerene adducts to determine upper or lower limits to their apparent and absolute gas-phase acidities. We present also a rationale for assessing the proton-transfer reactivity of dications via the apparent gas-phase acidity of these species, rather than the traditional use of gas-phase basicities or proton affinities. We propose that further studies of proton transfer from polycharged fullerene adducts may provide considerable useful information to model the reactivity of polyprotonated proteins and other large molecular polycatiions which can now be produced by techniques such as electrospray ionization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loew, G.H.; Axe, F.U.; Collins, J.R.

In this study, we have investigated the plausibility of a key postulated transformation of the proximal imidazole ligand (His 175) to an imidazolate by proton transfer to a nearby aspartate (Asp 235) absent in Mb. The proton relay system studied included not only models for the His 175 and Asp 235 residues but also for a nearby Trp 191 residue that could also interact with Asp 235 through hydrogen bonding and polarization. Two semiempirical quantum mechanical methods, Am1 and MNDO/H, with improved capabilities of describing H-bonded systems, were used to calculate the enthalpies of the three tautomeric forms of themore » proton relay system corresponding to the proton on the His, Asp, and Trp, respectively. These calculations were made for several models of the effect of the iron. Relative tautomeric enthalpies were calculated both with H-atom only optimization, keeping the heavy atoms fixed in their X-ray positions, and additional optimization that allowed the model Asp residue to relax. Transition-state enthalpies for the proton transfer from His to Asp were also calculated. The results of these studies suggest that the crucial postulated proton transfer from His to Asp is energetically favored, but only in the presence of the interaction of the iron with the imidazole ligand. Another stable form of the cluster, with competing proton transfer from the Trp to the Asp, was found only when the Asp position was allowed to optimize.« less

Double proton transfer behavior and one-electron oxidation effect in double H-bonded glycinamide-formic acid complex.

PubMed

Li, Ping; Bu, Yuxiang

2004-11-22

The behavior of double proton transfer occurring in a representative glycinamide-formic acid complex has been investigated at the B3LYP/6-311 + + G( * *) level of theory. Thermodynamic and, especially, kinetic parameters, such as tautomeric energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the double proton transfer process, such as geometrical changes, interaction energies, and intrinsic reaction coordinate calculations have also been studied. Computational results show that the participation of a formic acid molecule favors the proceeding of the proton transfer for glycinamide compared with that without mediate-assisted case. The double proton transfer process proceeds with a concerted mechanism rather than a stepwise one since no ion-pair complexes have been located during the proton transfer process. The calculated barrier heights are 11.48 and 0.85 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 2.95 and 2.61 kcal/mol to 8.53 and -1.76 kcal/mol if further inclusion of zero-point vibrational energy corrections, where the negative barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to that occurring between glycinamide and formamide. Furthermore, solvent effects on the thermodynamic and kinetic processes have also been predicted qualitatively employing the isodensity surface polarized continuum model within the framework of the self-consistent reaction field theory. Additionally, the oxidation process for the double H-bonded glycinamide-formic acid complex has also been investigated. Contrary to that neutral form possessing a pair of two parallel intermolecular H bonds, only a single H bond with a comparable strength has been found in its ionized form. The vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.40 and 8.69 eV, respectively, where ionization is mainly localized on the glycinamide fragment. Like that ionized glycinamide-formamide complex, the proton transfer in the ionized complex is characterized by a single-well potential, implying that the proton initially attached to amide N4 in the glycinamide fragment cannot be transferred to carbonyl O13 in the formic acid fragment at the geometry of the optimized complex. Copyright 2004 American Institute of Physics.

Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase.

PubMed

Wikström, Mårten; Ribacka, Camilla; Molin, Mika; Laakkonen, Liisa; Verkhovsky, Michael; Puustinen, Anne

2005-07-26

The membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from O2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. O2 reduction produces water at the bimetallic heme a3/CuB active site next to a hydrophobic cavity deep within the membrane. Water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism. Here, we show by molecular dynamics simulations that the conserved arginine/heme a3 delta-propionate ion pair provides a gate, which exhibits reversible thermal opening that is governed by the redox state and the water molecules in the cavity. An important role of this gate in the proton-pumping mechanism is supported by site-directed mutagenesis experiments. Transport of the product water out of the enzyme must be rigidly controlled to prevent water-mediated proton leaks that could compromise the proton-pumping function. Exit of product water is observed through the same arginine/propionate gate, which provides an explanation for the observed extraordinary spatial specificity of water expulsion from the enzyme.

Computing Wigner distributions and time correlation functions using the quantum thermal bath method: application to proton transfer spectroscopy.

PubMed

Basire, Marie; Borgis, Daniel; Vuilleumier, Rodolphe

2013-08-14

Langevin dynamics coupled to a quantum thermal bath (QTB) allows for the inclusion of vibrational quantum effects in molecular dynamics simulations at virtually no additional computer cost. We investigate here the ability of the QTB method to reproduce the quantum Wigner distribution of a variety of model potentials, designed to assess the performances and limits of the method. We further compute the infrared spectrum of a multidimensional model of proton transfer in the gas phase and in solution, using classical trajectories sampled initially from the Wigner distribution. It is shown that for this type of system involving large anharmonicities and strong nonlinear coupling to the environment, the quantum thermal bath is able to sample the Wigner distribution satisfactorily and to account for both zero point energy and tunneling effects. It leads to quantum time correlation functions having the correct short-time behavior, and the correct associated spectral frequencies, but that are slightly too overdamped. This is attributed to the classical propagation approximation rather than the generation of the quantized initial conditions themselves.

Measurements of the separated longitudinal structure function FL from hydrogen and deuterium targets at low Q2

NASA Astrophysics Data System (ADS)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; Abbott, D.; Adams, G. S.; Afanasev, A.; Ahmidouch, A.; Angelescu, T.; Arrington, J.; Asaturyan, R.; Avery, S.; Baker, O. K.; Benmouna, N.; Berman, B. L.; Biselli, A.; Blok, H. P.; Boeglin, W. U.; Bosted, P. E.; Brash, E.; Breuer, H.; Chang, G.; Chant, N.; Christy, M. E.; Connell, S. H.; Dalton, M. M.; Danagoulian, S.; Day, D.; Dodario, T.; Dunne, J. A.; Dutta, D.; El Khayari, N.; Ent, R.; Fenker, H. C.; Frolov, V. V.; Gaskell, D.; Garrow, K.; Gilman, R.; Gueye, P.; Hafidi, K.; Hinton, W.; Holt, R. J.; Horn, T.; Huber, G. M.; Jackson, H.; Jiang, X.; Jones, M. K.; Joo, K.; Kelly, J. J.; Keppel, C. E.; Kuhn, J.; Kinney, E.; Klein, A.; Kubarovsky, V.; Liang, Y.; Lolos, G.; Lung, A.; Mack, D.; Malace, S.; Markowitz, P.; Mbianda, G.; McGrath, E.; Mckee, D.; Meekins, D. G.; Mkrtchyan, H.; Napolitano, J.; Navasardyan, T.; Niculescu, G.; Nozar, M.; Ostapenko, T.; Papandreou, Z.; Potterveld, D.; Reimer, P. E.; Reinhold, J.; Roche, J.; Rock, S. E.; Schulte, E.; Segbefia, E.; Smith, C.; Smith, G. R.; Stoler, P.; Tadevosyan, V.; Tang, L.; Telfeyan, J.; Todor, L.; Ungaro, M.; Uzzle, A.; Vidakovic, S.; Villano, A.; Vulcan, W. F.; Warren, G.; Wesselmann, F.; Wojtsekhowski, B.; Wood, S. A.; Yan, C.; Zihlmann, B.

2018-04-01

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. However, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q2<1 GeV2 , and compare them with parton distribution parametrization and kT factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q2 scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R , than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE PAGES

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; ...

2018-04-26

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

NASA Astrophysics Data System (ADS)

MacLeod, N. A.; Simons, J. P.

2007-03-01

Protonated neurotransmitters have been produced in the gas phase via a novel photochemical scheme: complexes of the species of interest, 1-phenylethylamine, 2-amino-1-phenylethanol and the diastereo-isomers, ephedrine and pseudoephedrine, with a suitable proton donor, phenol (or indole), are produced in a supersonic expansion and ionized by resonant two photon ionization of the donor. Efficient proton transfer generates the protonated neurotransmitters, complexed to a phenoxy radical. Absorption of infrared radiation, and subsequent evaporation of the phenoxy tag, coupled with time of flight mass spectrometry, provides vibrational spectra of the protonated (and also hydrated) complexes for comparison with the results of quantum chemical computation. Comparison with the conformational structures of the neutral neurotransmitters (established previously) reveals the effect of protonation on their structure. The photochemical proton transfer strategy allows spectra to be recorded from individual laser shots and their quality compares favourably with that obtained using electro-spray or matrix assisted laser desorption ion sources.

Cell kill by megavoltage protons with high LET.

PubMed

Kuperman, Vadim Y

2016-07-21

The aim of the current study is to develop a radiobiological model which describes the effect of linear energy transfer (LET) on cell survival and relative biological effectiveness (RBE) of megavoltage protons. By assuming the existence of critical sites within a cell, analytical expression for cell survival S as a function of LET is derived. The obtained results indicate that in cases where dose per fraction is small, [Formula: see text] is a linear-quadratic (LQ) function of dose while both alpha and beta radio-sensitivities are non-linearly dependent on LET. In particular, in the current model alpha increases with increasing LET while beta decreases. Conversely, in the case of large dose per fraction, the LQ dependence of [Formula: see text] on dose is invalid. The proposed radiobiological model predicts cell survival probability and RBE which, in general, deviate from the results obtained by using conventional LQ formalism. The differences between the LQ model and that described in the current study are reflected in the calculated RBE of protons.

Evidence of quantum correlations in the H/D-transfer dynamics in the hydrogen bonds in partially deuterated benzoic acid crystals

NASA Astrophysics Data System (ADS)

Takeda, Sadamu; Tsuzumitani, Akihiko; Chatzidimitriou-Dreismann, C. A.

1992-10-01

A precise investigation of spin—lattice relaxation rates for protons and deuterons of partially deuterated benzoic acid crystals showed a remarkable quenching of the transfer rate of an HD pair in hydrogen-bonded dimeric units of carboxyl groups with increasing concentration of D in the surrounding hydrogen bonds. A similar effect was also observed for partially deuterated crystals of acetylenedicarboxylic acid. This finding supports recent theoretical predictions of thermally activated protonic quantum correlation in condensed matter and proposes a new mechanism for the proton transfer in hydrogen bonds in condensed matter.

Inhibited proton transfer enhances Au-catalyzed CO2-to-fuels selectivity.

PubMed

Wuttig, Anna; Yaguchi, Momo; Motobayashi, Kenta; Osawa, Masatoshi; Surendranath, Yogesh

2016-08-09

CO2 reduction in aqueous electrolytes suffers efficiency losses because of the simultaneous reduction of water to H2 We combine in situ surface-enhanced IR absorption spectroscopy (SEIRAS) and electrochemical kinetic studies to probe the mechanistic basis for kinetic bifurcation between H2 and CO production on polycrystalline Au electrodes. Under the conditions of CO2 reduction catalysis, electrogenerated CO species are irreversibly bound to Au in a bridging mode at a surface coverage of ∼0.2 and act as kinetically inert spectators. Electrokinetic data are consistent with a mechanism of CO production involving rate-limiting, single-electron transfer to CO2 with concomitant adsorption to surface active sites followed by rapid one-electron, two-proton transfer and CO liberation from the surface. In contrast, the data suggest an H2 evolution mechanism involving rate-limiting, single-electron transfer coupled with proton transfer from bicarbonate, hydronium, and/or carbonic acid to form adsorbed H species followed by rapid one-electron, one-proton, or H recombination reactions. The disparate proton coupling requirements for CO and H2 production establish a mechanistic basis for reaction selectivity in electrocatalytic fuel formation, and the high population of spectator CO species highlights the complex heterogeneity of electrode surfaces under conditions of fuel-forming electrocatalysis.

Correlations and currents in 3He studied with the (e, e'pp) reaction

NASA Astrophysics Data System (ADS)

Groep, David Leo

2000-01-01

Nucleon-nucleon correlations, especially those of short-range character, can be well studied with electron-induced two-nucleon knockout reactions at intermediate electron energies. However, these reactions are not only driven by one-body currents, i.e., coupling of the virtual photon to one of the nucleons of a correlated pair, a process that directly probes NN-correlations. Also two-body currents, resulting from intermediate Delta-excitation and coupling to exchanged mesons, as well as final state interactions, influence the experimental cross section. Exclusive measurements of the three-body breakup of 3He offer the opportunity to compare data to microscopic calculations. The relative importance of competing two-proton knockout mechanisms can be investigated by varying the energy and momentum of the virtual photon. The experiment was performed with the electron beam extracted from the Amsterdam Pulse Stretcher (AmPS) at NIKHEF; the incident electron energy was 564 MeV. A cryogenic, high-pressure 3He gas target was used with a thickness of 270 mg/cm^2. Scattered electrons were detected in the QDQ magnetic spectrometer and both emitted protons in the HADRON plastic scintillator arrays. Cross sections were determined for three values of the three-momentum transfer of the virtual photon (q=305, 375, and 445 MeV/c) at an energy transfer value omega of 220 MeV. At q=375 MeV/c, measurements were performed over a continuous range in energy transfer from 170 to 290 MeV. The data are compared to results of continuum-Faddeev calculations performed by Golak et al., that account for rescattering among the emitted nucleons. Various potential models were used in the calculations: Bonn-B, CD-Bonn, Nijmegen-93 and Argonne v18 . Presentation of the data as a function of the missing or neutron momentum, pm, shows that the cross section decreases exponentially as a function of pm. Calculations performed with only a one-body hadronic current operator show fair agreement with data obtained at pm < 100 MeV/c at omega = 220 MeV for all q-values. It can therefore be concluded that at omega = 220 MeV and pm < 100 MeV/c the cross section is dominated by direct knockout of two protons via a one-body hadronic current. At higher neutron momentum values, data and theoretical predictions differ up to a fac tor of five for all values of omega. Within the range of energy transfer values probed in this experiment, the high pm domain is expected to be strongly influenced by intermediate excitation in the proton-neutron pair. Within specific regions of phase space, where two nucleons are emitted with comparable momentum vectors, rescattering processes strongly influence the cross section. For a such a region, measured at q=445 MeV/c, good agreement was found between data and the continuum- Faddeev calculations as a function of the pn momentum difference in the final state. Information on the wave function of 3He may be obtained in the domain omega = 220 MeV and pm < 100 MeV/c by representing the cross section as a function of pdiff1, which can be related to the relative momentum of the constituents of the two-proton pair in the initial state. The observed decrease of the cross section reflects the behaviour of the wave function and is well reproduced by calculations. At present, the data do not permit to express preference for any one of the potential models considered.

Isotope effects associated with tunneling and double proton transfer in the hydrogen bonds of benzoic acid

NASA Astrophysics Data System (ADS)

Xue, Q.; Horsewill, A. J.; Johnson, M. R.; Trommsdorff, H. P.

2004-06-01

The isotope effects associated with double proton transfer in the hydrogen bonds of benzoic acid (BA) dimers have been measured using field-cycling 1H NMR relaxometry and quasielastic neutron scattering. By studying mixed isotope (hydrogen and deuterium) samples, the dynamics of three isotopologues, BA-HH, BA-HD, and BA-DD, have been investigated. Low temperature measurements provide accurate measurements of the incoherent tunneling rate, k0. This parameter scales accurately with the mass number, m, according to the formula k0=(E/m)e-F√m providing conclusive evidence that the proton transfer process is a strongly correlated motion of two hydrons. Furthermore, we conclude that the tunneling pathway is the same for the three isotopologue species. Measurements at higher temperatures illuminate the through barrier processes that are mediated via intermediate or excited vibrational states. In parallel with the investigation of proton transfer dynamics, the theoretical and experimental aspects of studying spin-lattice relaxation in single crystals of mixed isotope samples are investigated in depth. Heteronuclear dipolar interactions between 1H and 2H isotopes contribute significantly to the overall proton spin-lattice relaxation and it is shown that these must be modeled correctly to obtain accurate values for the proton transfer rates. Since the sample used in the NMR measurements was a single crystal, full account of the orientation dependence of the spin-lattice relaxation with respect to the applied B field was incorporated into the data analysis.

Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture

NASA Astrophysics Data System (ADS)

Kasai, Yukako; Yoshida, Norio; Nakano, Haruyuki

2015-05-01

The co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water-acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is more stable than the neutral form. The reaction free energy is -10.6 kcal mol-1. On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol-1. The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.

Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine-cysteine peptides in solution

PubMed Central

Petruk, Ariel A.; Bartesaghi, Silvina; Trujillo, Madia; Estrin, Darío A.; Murgida, Daniel; Kalyanaraman, Balaraman; Marti, Marcelo A.; Radi, Rafael

2012-01-01

Experimental studies in hemeproteins and model Tyr/Cys-containing peptides exposed to oxidizing and nitrating species suggest that intramolecular electron transfer (IET) between tyrosyl radicals (Tyr-O●) and Cys residues controls oxidative modification yields. The molecular basis of this IET process is not sufficiently understood with structural atomic detail. Herein, we analyzed using molecular dynamics and quantum mechanics-based computational calculations, mechanistic possibilities for the radical transfer reaction in Tyr/Cys-containing peptides in solution and correlated them with existing experimental data. Our results support that Tyr-O● to Cys radical transfer is mediated by an acid/base equilibrium that involves deprotonation of Cys to form the thiolate, followed by a likely rate-limiting transfer process to yield cysteinyl radical and a Tyr phenolate; proton uptake by Tyr completes the reaction. Both, the pKa values of the Tyr phenol and Cys thiol groups and the energetic and kinetics of the reversible IET are revealed as key physico-chemical factors. The proposed mechanism constitutes a case of sequential, acid/base equilibrium-dependent and solvent-mediated, proton-coupled electron transfer and explains the dependency of oxidative yields in Tyr/Cys peptides as a function of the number of alanine spacers. These findings contribute to explain oxidative modifications in proteins that contain sequence and/or spatially close Tyr-Cys residues. PMID:22640642

Chemistry, photophysics, and ultrafast kinetics of two structurally related Schiff bases containing the naphthalene or quinoline ring

NASA Astrophysics Data System (ADS)

Fita, P.; Luzina, E.; Dziembowska, T.; Radzewicz, Cz.; Grabowska, A.

2006-11-01

The two structurally related Schiff bases, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) and 2-hydroxynaphthylidene-1'-naphthylamine (HNAN), were studied by means of steady-state and time resolved optical spectroscopies as well as time-dependent density functional theory (TDDFT) calculations. The first one, HNAQ, is stable as a keto tautomer in the ground state and in the excited state in solutions, therefore it was used as a model of a keto tautomer of HNAN which exists mainly in its enol form in the ground state at room temperature. Excited state intramolecular proton transfer in the HNAN molecule leads to a very weak (quantum yield of the order of 10-4) strongly Stokes-shifted fluorescence. The characteristic time of the proton transfer (about 30fs) was estimated from femtosecond transient absorption data supported by global analysis and deconvolution techniques. Approximately 35% of excited molecules create a photochromic form whose lifetime was beyond the time window of the experiment (2ns). The remaining ones reach the relaxed S1 state (of a lifetime of approximately 4ps), whose emission is present in the decay associated difference spectra. Some evidence for the back proton transfer from the ground state of the keto form with the characteristic time of approximately 13ps was also found. The energies and orbital characteristics of main electronic transitions in both molecules calculated by TDDFT method are also discussed.

Resonance energy transfer improves the biological function of bacteriorhodopsin within a hybrid material built from purple membranes and semiconductor quantum dots.

PubMed

Rakovich, Aliaksandra; Sukhanova, Alyona; Bouchonville, Nicolas; Lukashev, Evgeniy; Oleinikov, Vladimir; Artemyev, Mikhail; Lesnyak, Vladimir; Gaponik, Nikolai; Molinari, Michael; Troyon, Michel; Rakovich, Yury P; Donegan, John F; Nabiev, Igor

2010-07-14

Purple membrane (PM) from bacteria Halobacterium salinarum contains a photochromic protein bacteriorhodopsin (bR) arranged in a 2D hexagonal nanocrystalline lattice (Figure 1 ). Absorption of light by the protein-bound chromophore retinal results in pumping the protons through the PM creating an electrochemical gradient which is then used by the ATPases to energize the cellular processes. Energy conversion, photochromism, and photoelectrism are the inherent effects which are employed in many bR technical applications. bR, along with the other photosensitive proteins, is not able to deal with the excess energy of photons in UV and blue spectral region and utilizes less than 0.5% of the energy from the available incident solar light for its biological function. Here, we proceed with optimization of bR functions through the engineering of a "nanoconverter" of solar energy based on semiconductor quantum dots (QDs) tagged with the PM. These nanoconverters are able to harvest light from deep-UV to the visible region and to transfer this additionally collected energy to bR via Förster resonance energy transfer (FRET). We show that specific nanobio-optical and spatial coupling of QDs (donor) and bR retinal (acceptor) provide a means to achieve FRET with efficiency approaching 100%. We have finally demonstrated that the integration of QDs within PM significantly increases the efficiency of light-driven transmembrane proton pumping, which is the main bR biological function. This new QD-PM hybrid material will have numerous optoelectronic, photonic, and photovoltaic applications based on its energy conversion, photochromism, and photoelectrism properties.

Virtual Compton scattering and the generalized polarizabilities of the proton at Q2=0.92 and 1.76 GeV2

NASA Astrophysics Data System (ADS)

Fonvieille, H.; Laveissière, G.; Degrande, N.; Jaminion, S.; Jutier, C.; Todor, L.; Di Salvo, R.; Van Hoorebeke, L.; Alexa, L. C.; Anderson, B. D.; Aniol, K. A.; Arundell, K.; Audit, G.; Auerbach, L.; Baker, F. T.; Baylac, M.; Berthot, J.; Bertin, P. Y.; Bertozzi, W.; Bimbot, L.; Boeglin, W. U.; Brash, E. J.; Breton, V.; Breuer, H.; Burtin, E.; Calarco, J. R.; Cardman, L. S.; Cavata, C.; Chang, C.-C.; Chen, J.-P.; Chudakov, E.; Cisbani, E.; Dale, D. S.; de Jager, C. W.; De Leo, R.; Deur, A.; d'Hose, N.; Dodge, G. E.; Domingo, J. J.; Elouadrhiri, L.; Epstein, M. B.; Ewell, L. A.; Finn, J. M.; Fissum, K. G.; Fournier, G.; Frois, B.; Frullani, S.; Furget, C.; Gao, H.; Gao, J.; Garibaldi, F.; Gasparian, A.; Gilad, S.; Gilman, R.; Glamazdin, A.; Glashausser, C.; Gomez, J.; Gorbenko, V.; Grenier, P.; Guichon, P. A. M.; Hansen, J. O.; Holmes, R.; Holtrop, M.; Howell, C.; Huber, G. M.; Hyde, C. E.; Incerti, S.; Iodice, M.; Jardillier, J.; Jones, M. K.; Kahl, W.; Kato, S.; Katramatou, A. T.; Kelly, J. J.; Kerhoas, S.; Ketikyan, A.; Khayat, M.; Kino, K.; Kox, S.; Kramer, L. H.; Kumar, K. S.; Kumbartzki, G.; Kuss, M.; Leone, A.; LeRose, J. J.; Liang, M.; Lindgren, R. A.; Liyanage, N.; Lolos, G. J.; Lourie, R. W.; Madey, R.; Maeda, K.; Malov, S.; Manley, D. M.; Marchand, C.; Marchand, D.; Margaziotis, D. J.; Markowitz, P.; Marroncle, J.; Martino, J.; McCormick, K.; McIntyre, J.; Mehrabyan, S.; Merchez, F.; Meziani, Z. E.; Michaels, R.; Miller, G. W.; Mougey, J. Y.; Nanda, S. K.; Neyret, D.; Offermann, E. A. J. M.; Papandreou, Z.; Pasquini, B.; Perdrisat, C. F.; Perrino, R.; Petratos, G. G.; Platchkov, S.; Pomatsalyuk, R.; Prout, D. L.; Punjabi, V. A.; Pussieux, T.; Quémenér, G.; Ransome, R. D.; Ravel, O.; Real, J. S.; Renard, F.; Roblin, Y.; Rowntree, D.; Rutledge, G.; Rutt, P. M.; Saha, A.; Saito, T.; Sarty, A. J.; Serdarevic, A.; Smith, T.; Smirnov, G.; Soldi, K.; Sorokin, P.; Souder, P. A.; Suleiman, R.; Templon, J. A.; Terasawa, T.; Tieulent, R.; Tomasi-Gustaffson, E.; Tsubota, H.; Ueno, H.; Ulmer, P. E.; Urciuoli, G. M.; Vanderhaeghen, M.; Van der Meer, R. L. J.; Van De Vyver, R.; Vernin, P.; Vlahovic, B.; Voskanyan, H.; Voutier, E.; Watson, J. W.; Weinstein, L. B.; Wijesooriya, K.; Wilson, R.; Wojtsekhowski, B. B.; Zainea, D. G.; Zhang, W.-M.; Zhao, J.; Zhou, Z.-L.

2012-07-01

Virtual Compton scattering (VCS) on the proton has been studied at the Jefferson Laboratory using the exclusive photon electroproduction reaction ep→epγ. This paper gives a detailed account of the analysis which has led to the determination of the structure functions PLL-PTT/ɛ and PLT and the electric and magnetic generalized polarizabilities (GPs) αE(Q2) and βM(Q2) at values of the four-momentum transfer squared Q2=0.92 and 1.76 GeV2. These data, together with the results of VCS experiments at lower momenta, help building a coherent picture of the electric and magnetic GPs of the proton over the full measured Q2 range and point to their nontrivial behavior.

Reduction and Reoxidation of Humic Acid: Influence on Spectroscopic Properties and Proton Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maurer, F.; Christl, I; Kretzschmar, R

2010-01-01

Previous studies on proton and metal binding to humic substances have not considered a potential influence of reduction and oxidation of functional groups. Therefore, we investigated how proton binding of a purified soil humic acid was affected by reduction. Reduction of the humic acid was carried out using an electrochemical cell that allowed us to measure the amounts of electrons and protons involved in reduction reactions. We further applied spectroscopic methods (UV-vis, fluorescence, FT-IR, C-1s NEXAFS) to detect possible chemical changes in the humic acid induced by reduction and reoxidation. The effect of reduction on proton binding was determined withmore » acid-base titrations in the pH range 4-10 under controlled redox conditions. During reduction, 0.54 mol kg{sup -1} protons and 0.55 mol kg{sup -1} electrons were transferred to humic acid. NICA-Donnan modeling revealed an equivalent increase in proton-reactive sites (0.52 mol kg{sup -1}) in the alkaline pH-range. Our results indicate that reduction of humic acid increased the amount of proton-reactive sites by 15% compared to the untreated state. Spectroscopic differences between the untreated and reduced humic acid were minor, apart from a lower UV-vis absorption of the reduced humic acid between 400 and 700 nm.« less

Mammalian Complex I Pumps 4 Protons per 2 Electrons at High and Physiological Proton Motive Force in Living Cells*

PubMed Central

Ripple, Maureen O.; Kim, Namjoon; Springett, Roger

2013-01-01

Mitochondrial complex I couples electron transfer between matrix NADH and inner-membrane ubiquinone to the pumping of protons against a proton motive force. The accepted proton pumping stoichiometry was 4 protons per 2 electrons transferred (4H+/2e−) but it has been suggested that stoichiometry may be 3H+/2e− based on the identification of only 3 proton pumping units in the crystal structure and a revision of the previous experimental data. Measurement of proton pumping stoichiometry is challenging because, even in isolated mitochondria, it is difficult to measure the proton motive force while simultaneously measuring the redox potentials of the NADH/NAD+ and ubiquinol/ubiquinone pools. Here we employ a new method to quantify the proton motive force in living cells from the redox poise of the bc1 complex measured using multiwavelength cell spectroscopy and show that the correct stoichiometry for complex I is 4H+/2e− in mouse and human cells at high and physiological proton motive force. PMID:23306206

Proton Transfer Dynamics at the Membrane/Water Interface: Dependence on the Fixed and Mobile pH Buffers, on the Size and Form of Membrane Particles, and on the Interfacial Potential Barrier

PubMed Central

Cherepanov, Dmitry A.; Junge, Wolfgang; Mulkidjanian, Armen Y.

2004-01-01

Crossing the membrane/water interface is an indispensable step in the transmembrane proton transfer. Elsewhere we have shown that the low dielectric permittivity of the surface water gives rise to a potential barrier for ions, so that the surface pH can deviate from that in the bulk water at steady operation of proton pumps. Here we addressed the retardation in the pulsed proton transfer across the interface as observed when light-triggered membrane proton pumps ejected or captured protons. By solving the system of diffusion equations we analyzed how the proton relaxation depends on the concentration of mobile pH buffers, on the surface buffer capacity, on the form and size of membrane particles, and on the height of the potential barrier. The fit of experimental data on proton relaxation in chromatophore vesicles from phototropic bacteria and in bacteriorhodopsin-containing membranes yielded estimates for the interfacial potential barrier for H+/OH− ions of ∼120 meV. We analyzed published data on the acceleration of proton equilibration by anionic pH buffers and found that the height of the interfacial barrier correlated with their electric charge ranging from 90 to 120 meV for the singly charged species to >360 meV for the tetra-charged pyranine. PMID:14747306

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

PubMed Central

Dodson, M. L.; Walker, Ross C.; Lloyd, R. Stephen

2012-01-01

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N–terminal amine. PMID:22384015

Importance of a serine proximal to the C(4a) and N(5) flavin atoms for hydride transfer in choline oxidase.

PubMed

Yuan, Hongling; Gadda, Giovanni

2011-02-08

Choline oxidase catalyzes the flavin-dependent, two-step oxidation of choline to glycine betaine with the formation of an aldehyde intermediate. In the first oxidation reaction, the alcohol substrate is initially activated to its alkoxide via proton abstraction. The substrate is oxidized via transfer of a hydride from the alkoxide α-carbon to the N(5) atom of the enzyme-bound flavin. In the wild-type enzyme, proton and hydride transfers are mechanistically and kinetically uncoupled. In this study, we have mutagenized an active site serine proximal to the C(4a) and N(5) atoms of the flavin and investigated the reactions of proton and hydride transfers by using substrate and solvent kinetic isotope effects. Replacement of Ser101 with threonine, alanine, cysteine, or valine resulted in biphasic traces in anaerobic reductions of the flavin with choline investigated in a stopped-flow spectrophotometer. Kinetic isotope effects established that the kinetic phases correspond to the proton and hydride transfer reactions catalyzed by the enzyme. Upon removal of Ser101, there is an at least 15-fold decrease in the rate constants for proton abstraction, irrespective of whether threonine, alanine, valine, or cysteine is present in the mutant enzyme. A logarithmic decrease spanning 4 orders of magnitude is seen in the rate constants for hydride transfer with increasing hydrophobicity of the side chain at position 101. This study shows that the hydrophilic character of a serine residue proximal to the C(4a) and N(5) flavin atoms is important for efficient hydride transfer.

The tropolone-isobutylamine complex: a hydrogen-bonded troponoid without dominant π-π interactions.

PubMed

Vealey, Zachary N; Mercado, Brandon Q; Vaccaro, Patrick H

2016-10-01

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...π, or ion-π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C 4 H 12 N + ·C 7 H 5 O 2 - , has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz. π-π, C-H...π, and ion-π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor-acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

Charging of Proteins in Native Mass Spectrometry

DOE PAGES

Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.; ...

2016-10-12

Factors that influence the charging of protein ions formed by electrospray ionization from aqueous solutions in which proteins have native structures and function were investigated. Protein ions ranging in molecular weight from 12.3 to 79.7 kDa and pI values from 5.4 to 9.6 were formed from different solutions and reacted with volatile bases of gas-phase basicities higher than that of ammonia in the cell of a Fourier-transform ion cyclotron resonance mass spectrometer. The charge-state distribution of cytochrome c ions formed from aqueous ammonium or potassium acetate is the same. Moreover, ions formed from these two solutions do not undergo protonmore » transfer to 2-fluoropyridine, which is 8 kcal/mol more basic than ammonia. These results provide compelling evidence that proton transfer between ammonia and protein ions does not limit protein ion charge in native electrospray ionization. Both circular dichroism and ion mobility measurements indicate that there are differences in conformations of proteins in pure water and aqueous ammonium acetate, and these differences can account for the difference in the extent of charging and proton-transfer reactivities of protein ions formed from these solutions. The extent of proton transfer of the protein ions with higher gas-phase basicity bases trends with how closely the protein ions are charged to the value predicted by the Rayleigh limit for spherical water droplets approximately the same size as the proteins. These results indicate that droplet charge limits protein ion charge in native mass spectrometry and are consistent with these ions being formed by the charged residue mechanism.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.

Factors that influence the charging of protein ions formed by electrospray ionization from aqueous solutions in which proteins have native structures and function were investigated. Protein ions ranging in molecular weight from 12.3 to 79.7 kDa and pI values from 5.4 to 9.6 were formed from different solutions and reacted with volatile bases of gas-phase basicities higher than that of ammonia in the cell of a Fourier-transform ion cyclotron resonance mass spectrometer. The charge-state distribution of cytochrome c ions formed from aqueous ammonium or potassium acetate is the same. Moreover, ions formed from these two solutions do not undergo protonmore » transfer to 2-fluoropyridine, which is 8 kcal/mol more basic than ammonia. These results provide compelling evidence that proton transfer between ammonia and protein ions does not limit protein ion charge in native electrospray ionization. Both circular dichroism and ion mobility measurements indicate that there are differences in conformations of proteins in pure water and aqueous ammonium acetate, and these differences can account for the difference in the extent of charging and proton-transfer reactivities of protein ions formed from these solutions. The extent of proton transfer of the protein ions with higher gas-phase basicity bases trends with how closely the protein ions are charged to the value predicted by the Rayleigh limit for spherical water droplets approximately the same size as the proteins. These results indicate that droplet charge limits protein ion charge in native mass spectrometry and are consistent with these ions being formed by the charged residue mechanism.« less

Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.

PubMed

Rankin, Joel A; Mauban, Robert C; Fellner, Matthias; Desguin, Benoît; McCracken, John; Hu, Jian; Varganov, Sergey A; Hausinger, Robert P

2018-03-09

Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( k H / k D of 3.11 ± 0.17) was established using 2-α- 2 H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 Å) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.

Measurement of polarization-transfer to bound protons in carbon and its virtuality dependence

NASA Astrophysics Data System (ADS)

Izraeli, D.; Brecelj, T.; Achenbach, P.; Ashkenazi, A.; Böhm, R.; Cohen, E. O.; Distler, M. O.; Esser, A.; Gilman, R.; Kolar, T.; Korover, I.; Lichtenstadt, J.; Mardor, I.; Merkel, H.; Mihovilovič, M.; Müller, U.; Olivenboim, M.; Piasetzky, E.; Ron, G.; Schlimme, B. S.; Schoth, M.; Sfienti, C.; Širca, S.; Štajner, S.; Strauch, S.; Thiel, M.; Weber, A.; Yaron, I.; A1 Collaboration

2018-06-01

We measured the ratio Px /Pz of the transverse to longitudinal components of polarization transferred from electrons to bound protons in 12C by the 12C (e → ,e‧ p →) process at the Mainz Microtron (MAMI). We observed consistent deviations from unity of this ratio normalized to the free-proton ratio, (Px /Pz) 12C /(Px /Pz) 1H, for both s- and p-shell knocked out protons, even though they are embedded in averaged local densities that differ by about a factor of two. The dependence of the double ratio on proton virtuality is similar to the one for knocked out protons from 2H and 4He, suggesting a universal behavior. It further implies no dependence on average local nuclear density.

Depth dependence of absorbed dose, dose equivalent and linear energy transfer spectra of galactic and trapped particles in polyethylene and comparison with calculations of models

NASA Technical Reports Server (NTRS)

Badhwar, G. D.; Cucinotta, F. A.; Wilson, J. W. (Principal Investigator)

1998-01-01

A matched set of five tissue-equivalent proportional counters (TEPCs), embedded at the centers of 0 (bare), 3, 5, 8 and 12-inch-diameter polyethylene spheres, were flown on the Shuttle flight STS-81 (inclination 51.65 degrees, altitude approximately 400 km). The data obtained were separated into contributions from trapped protons and galactic cosmic radiation (GCR). From the measured linear energy transfer (LET) spectra, the absorbed dose and dose-equivalent rates were calculated. The results were compared to calculations made with the radiation transport model HZETRN/NUCFRG2, using the GCR free-space spectra, orbit-averaged geomagnetic transmission function and Shuttle shielding distributions. The comparison shows that the model fits the dose rates to a root mean square (rms) error of 5%, and dose-equivalent rates to an rms error of 10%. Fairly good agreement between the LET spectra was found; however, differences are seen at both low and high LET. These differences can be understood as due to the combined effects of chord-length variation and detector response function. These results rule out a number of radiation transport/nuclear fragmentation models. Similar comparisons of trapped-proton dose rates were made between calculations made with the proton transport model BRYNTRN using the AP-8 MIN trapped-proton model and Shuttle shielding distributions. The predictions of absorbed dose and dose-equivalent rates are fairly good. However, the prediction of the LET spectra below approximately 30 keV/microm shows the need to improve the AP-8 model. These results have strong implications for shielding requirements for an interplanetary manned mission.

A quantum chemical study of the mechanism for proton-coupled electron transfer leading to proton pumping in cytochrome c oxidase

NASA Astrophysics Data System (ADS)

Blomberg, Margareta R. A.; Siegbahn, Per E. M.

2010-10-01

The proton pumping mechanism in cytochrome c oxidase, the terminal enzyme in the respiratory chain, has been investigated using hybrid DFT with large chemical models. In previous studies, a gating mechanism was suggested based on electrostatic interpretations of kinetic experiments. The predictions from that analysis are tested here. The main result is that the suggestion of a positively charged transition state for proton transfer is confirmed, while some other suggestions for the gating are not supported. It is shown that a few critical relative energy values from the earlier studies are reproduced with quite high accuracy using the present model calculations. Examples are the forward barrier for proton transfer from the N-side of the membrane to the pump-loading site when the heme a cofactor is reduced, and the corresponding back leakage barrier when heme a is oxidised. An interesting new finding is an unexpected double-well potential for proton transfer from the N-side to the pump-loading site. In the intermediate between the two transition states found, the proton is bound to PropD on heme a. A possible purpose of this type of potential surface is suggested here. The accuracy of the present values are discussed in terms of their sensitivity to the choice of dielectric constant. Only one energy value, which is not critical for the present mechanism, varies significantly with this choice and is therefore less certain.

Proton-coupled electron-transfer reduction of dioxygen catalyzed by a saddle-distorted cobalt phthalocyanine.

PubMed

Honda, Tatsuhiko; Kojima, Takahiko; Fukuzumi, Shunichi

2012-03-07

Proton-coupled electron-transfer reduction of dioxygen (O(2)) to afford hydrogen peroxide (H(2)O(2)) was investigated by using ferrocene derivatives as reductants and saddle-distorted (α-octaphenylphthalocyaninato)cobalt(II) (Co(II)(Ph(8)Pc)) as a catalyst under acidic conditions. The selective two-electron reduction of O(2) by dimethylferrocene (Me(2)Fc) and decamethylferrocene (Me(10)Fc) occurs to yield H(2)O(2) and the corresponding ferrocenium ions (Me(2)Fc(+) and Me(10)Fc(+), respectively). Mechanisms of the catalytic reduction of O(2) are discussed on the basis of detailed kinetics studies on the overall catalytic reactions as well as on each redox reaction in the catalytic cycle. The active species to react with O(2) in the catalytic reaction is switched from Co(II)(Ph(8)Pc) to protonated Co(I)(Ph(8)PcH), depending on the reducing ability of ferrocene derivatives employed. The protonation of Co(II)(Ph(8)Pc) inhibits the direct reduction of O(2); however, the proton-coupled electron transfer from Me(10)Fc to Co(II)(Ph(8)Pc) and the protonated [Co(II)(Ph(8)PcH)](+) occurs to produce Co(I)(Ph(8)PcH) and [Co(I)(Ph(8)PcH(2))](+), respectively, which react immediately with O(2). The rate-determining step is a proton-coupled electron-transfer reduction of O(2) by Co(II)(Ph(8)Pc) in the Co(II)(Ph(8)Pc)-catalyzed cycle with Me(2)Fc, whereas it is changed to the electron-transfer reduction of [Co(II)(Ph(8)PcH)](+) by Me(10)Fc in the Co(I)(Ph(8)PcH)-catalyzed cycle with Me(10)Fc. A single crystal of monoprotonated [Co(III)(Ph(8)Pc)](+), [Co(III)Cl(2)(Ph(8)PcH)], produced by the proton-coupled electron-transfer reduction of O(2) by Co(II)(Ph(8)Pc) with HCl, was obtained, and the crystal structure was determined in comparison with that of Co(II)(Ph(8)Pc). © 2012 American Chemical Society

A glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase.

PubMed

Dementin, Sébastien; Burlat, Bénédicte; De Lacey, Antonio L; Pardo, Alejandro; Adryanczyk-Perrier, Géraldine; Guigliarelli, Bruno; Fernandez, Victor M; Rousset, Marc

2004-03-12

Kinetic, EPR, and Fourier transform infrared spectroscopic analysis of Desulfovibrio fructosovorans [NiFe] hydrogenase mutants targeted to Glu-25 indicated that this amino acid participates in proton transfer between the active site and the protein surface during the catalytic cycle. Replacement of that glutamic residue by a glutamine did not modify the spectroscopic properties of the enzyme but cancelled the catalytic activity except the para-H(2)/ortho-H(2) conversion. This mutation impaired the fast proton transfer from the active site that allows high turnover numbers for the oxidation of hydrogen. Replacement of the glutamic residue by the shorter aspartic acid slowed down this proton transfer, causing a significant decrease of H(2) oxidation and hydrogen isotope exchange activities, but did not change the para-H(2)/ortho-H(2) conversion activity. The spectroscopic properties of this mutant were totally different, especially in the reduced state in which a non-photosensitive nickel EPR spectrum was obtained.

Proton Transfers in a Channelrhodopsin-1 Studied by Fourier Transform Infrared (FTIR) Difference Spectroscopy and Site-directed Mutagenesis*

PubMed Central

Ogren, John I.; Yi, Adrian; Mamaev, Sergey; Li, Hai; Spudich, John L.; Rothschild, Kenneth J.

2015-01-01

Channelrhodopsin-1 from the alga Chlamydomonas augustae (CaChR1) is a low-efficiency light-activated cation channel that exhibits properties useful for optogenetic applications such as a slow light inactivation and a red-shifted visible absorption maximum as compared with the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Previously, both resonance Raman and low-temperature FTIR difference spectroscopy revealed that unlike CrChR2, CaChR1 under our conditions exhibits an almost pure all-trans retinal composition in the unphotolyzed ground state and undergoes an all-trans to 13-cis isomerization during the primary phototransition typical of other microbial rhodopsins such as bacteriorhodopsin (BR). Here, we apply static and rapid-scan FTIR difference spectroscopy along with site-directed mutagenesis to characterize the proton transfer events occurring upon the formation of the long-lived conducting P2380 state of CaChR1. Assignment of carboxylic C=O stretch bands indicates that Asp-299 (homolog to Asp-212 in BR) becomes protonated and Asp-169 (homolog to Asp-85 in BR) undergoes a net change in hydrogen bonding relative to the unphotolyzed ground state of CaChR1. These data along with earlier FTIR measurements on the CaChR1 → P1 transition are consistent with a two-step proton relay mechanism that transfers a proton from Glu-169 to Asp-299 during the primary phototransition and from the Schiff base to Glu-169 during P2380 formation. The unusual charge neutrality of both Schiff base counterions in the P2380 conducting state suggests that these residues may function as part of a cation selective filter in the open channel state of CaChR1 as well as other low-efficiency ChRs. PMID:25802337

Proton transfers in a channelrhodopsin-1 studied by Fourier transform infrared (FTIR) difference spectroscopy and site-directed mutagenesis.

PubMed

Ogren, John I; Yi, Adrian; Mamaev, Sergey; Li, Hai; Spudich, John L; Rothschild, Kenneth J

2015-05-15

Channelrhodopsin-1 from the alga Chlamydomonas augustae (CaChR1) is a low-efficiency light-activated cation channel that exhibits properties useful for optogenetic applications such as a slow light inactivation and a red-shifted visible absorption maximum as compared with the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Previously, both resonance Raman and low-temperature FTIR difference spectroscopy revealed that unlike CrChR2, CaChR1 under our conditions exhibits an almost pure all-trans retinal composition in the unphotolyzed ground state and undergoes an all-trans to 13-cis isomerization during the primary phototransition typical of other microbial rhodopsins such as bacteriorhodopsin (BR). Here, we apply static and rapid-scan FTIR difference spectroscopy along with site-directed mutagenesis to characterize the proton transfer events occurring upon the formation of the long-lived conducting P2 (380) state of CaChR1. Assignment of carboxylic C=O stretch bands indicates that Asp-299 (homolog to Asp-212 in BR) becomes protonated and Asp-169 (homolog to Asp-85 in BR) undergoes a net change in hydrogen bonding relative to the unphotolyzed ground state of CaChR1. These data along with earlier FTIR measurements on the CaChR1 → P1 transition are consistent with a two-step proton relay mechanism that transfers a proton from Glu-169 to Asp-299 during the primary phototransition and from the Schiff base to Glu-169 during P2 (380) formation. The unusual charge neutrality of both Schiff base counterions in the P2 (380) conducting state suggests that these residues may function as part of a cation selective filter in the open channel state of CaChR1 as well as other low-efficiency ChRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Optogenetic Acidification of Synaptic Vesicles and Lysosomes

PubMed Central

Grauel, M. Katharina; Wozny, Christian; Bentz, Claudia; Blessing, Anja; Rosenmund, Tanja; Jentsch, Thomas J.; Schmitz, Dietmar; Hegemann, Peter; Rosenmund, Christian

2016-01-01

Acidification is required for the function of many intracellular organelles, but methods to acutely manipulate their intraluminal pH have not been available. Here we present a targeting strategy to selectively express the light-driven proton pump Arch3 on synaptic vesicles. Our new tool, pHoenix, can functionally replace endogenous proton pumps, enabling optogenetic control of vesicular acidification and neurotransmitter accumulation. Under physiological conditions, glutamatergic vesicles are nearly full, as additional vesicle acidification with pHoenix only slightly increased the quantal size. By contrast, we found that incompletely filled vesicles exhibited a lower release probability than full vesicles, suggesting preferential exocytosis of vesicles with high transmitter content. Our subcellular targeting approach can be transferred to other organelles, as demonstrated for a pHoenix variant that allows light-activated acidification of lysosomes. PMID:26551543

Optogenetic acidification of synaptic vesicles and lysosomes.

PubMed

Rost, Benjamin R; Schneider, Franziska; Grauel, M Katharina; Wozny, Christian; Bentz, Claudia; Blessing, Anja; Rosenmund, Tanja; Jentsch, Thomas J; Schmitz, Dietmar; Hegemann, Peter; Rosenmund, Christian

2015-12-01

Acidification is required for the function of many intracellular organelles, but methods to acutely manipulate their intraluminal pH have not been available. Here we present a targeting strategy to selectively express the light-driven proton pump Arch3 on synaptic vesicles. Our new tool, pHoenix, can functionally replace endogenous proton pumps, enabling optogenetic control of vesicular acidification and neurotransmitter accumulation. Under physiological conditions, glutamatergic vesicles are nearly full, as additional vesicle acidification with pHoenix only slightly increased the quantal size. By contrast, we found that incompletely filled vesicles exhibited a lower release probability than full vesicles, suggesting preferential exocytosis of vesicles with high transmitter content. Our subcellular targeting approach can be transferred to other organelles, as demonstrated for a pHoenix variant that allows light-activated acidification of lysosomes.

Fine structure in the transition region: reaction force analyses of water-assisted proton transfers.

PubMed

Yepes, Diana; Murray, Jane S; Santos, Juan C; Toro-Labbé, Alejandro; Politzer, Peter; Jaque, Pablo

2013-07-01

We have analyzed the variation of the reaction force F(ξ) and the reaction force constant κ(ξ) along the intrinsic reaction coordinates ξ of the water-assisted proton transfer reactions of HX-N = Y (X,Y = O,S). The profile of the force constant of the vibration associated with the reactive mode, k ξ (ξ), was also determined. We compare our results to the corresponding intramolecular proton transfers in the absence of a water molecule. The presence of water promotes the proton transfers, decreasing the energy barriers by about 12 - 15 kcal mol(-1). This is due in part to much smaller bond angle changes being needed than when water is absent. The κ(ξ) profiles along the intrinsic reaction coordinates for the water-assisted processes show striking and intriguing differences in the transition regions. For the HS-N = S and HO-N = S systems, two κ(ξ) minima are obtained, whereas for HO-N = O only one minimum is found. The k ξ (ξ) show similar behavior in the transition regions. We propose that this fine structure reflects the degree of synchronicity of the two proton migrations in each case.

A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

2017-12-01

We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

Molecular reorganization of selected quinoline derivatives in the ground and excited states—Investigations via static DFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Błaziak, Kacper; Panek, Jarosław J.; Jezierska, Aneta, E-mail: aneta.jezierska@chem.uni.wroc.pl

2015-07-21

Quinoline derivatives are interesting objects to study internal reorganizations due to the observed excited-state-induced intramolecular proton transfer (ESIPT). Here, we report on computations for selected 12 quinoline derivatives possessing three kinds of intramolecular hydrogen bonds. Density functional theory was employed for the current investigations. The metric and electronic structure simulations were performed for the ground state and first excited singlet and triplet states. The computed potential energy profiles do not show a spontaneous proton transfer in the ground state, whereas excited states exhibit this phenomenon. Atoms in Molecules (AIM) theory was applied to study the nature of hydrogen bonding, whereasmore » Harmonic Oscillator Model of aromaticity index (HOMA) provided data of aromaticity evolution as a derivative of the bridge proton position. The AIM-based topological analysis confirmed the presence of the intramolecular hydrogen bonding. In addition, using the theory, we were able to provide a quantitative illustration of bonding transformation: from covalent to the hydrogen. On the basis of HOMA analysis, we showed that the aromaticity of both rings is dependent on the location of the bridge proton. Further, the computed results were compared with experimental data available. Finally, ESIPT occurrence was compared for the three investigated kinds of hydrogen bridges, and competition between two bridges in one molecule was studied.« less

Theoretical investigation on the excited state intramolecular proton transfer in Me2N substituted flavonoid by the time-dependent density functional theory method

NASA Astrophysics Data System (ADS)

Yin, Hang; Shi, Ying

2018-05-01

Not Available Project supported by the National Basic Research Program of China (Grant No. 2013CB922204), the National Natural Science Foundation of China (Grant Nos. 11574115 and 11704146), and the Natural Science Foundation of Jilin Province, China (Grant No. 20150101063JC).

A measurement and QCD analysis of the proton structure function F2 ( x, Q2) at HERA

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançoni, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; BurgerF. W. Büsser, J.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; De Roeck, A.; De Wolf, E. A.; Dirkmann, M.; Dixon, P.; Di Nezza, P.; Dlugosz, W.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Fahr, A. B.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Griffiths, R.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hampel, M.; Haynes, W. J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbie, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Lander, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Laporte, J.-F.; Lebedev, A.; Lehner, F.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindström, G.; Lindstroem, M.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lohmander, H.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merz, T.; Meyer, A.; MeyerH. Meyer, A.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Rick, H.; Riech, V.; Riedlberger, J.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, H.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabl, F.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Steiner, H.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; Van Esch, P.; Van Mechelen, P.; Vazdik, Y.; Verrecchi, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walther, A.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zomer, F.; Zsembery, J.; Zuber, K.; zurNedden, M.; Kaufmannxa, O.; H1 Collaboration

1996-02-01

A new measurement of the proton structure function F2 ( x, Q2) is reported for momentum transfers squared Q2 between ].5 GeV 2 and 5000 GeV 2 and for Bjorken x between 3 · 10 -5 and 0.32 using data collected by the HERA experiment H1 in 1994. The data represent an increase in statistics by a factor of ten with respect to the analysis of the 1993 data. Substantial extension of the kinematic range towards low Q2 and x has been achieved using dedicated data samples and events with initial state photon radiation. The structure function is found to increase significantly with decreasing x, even in the lowest accessible Q2 region. The data are well described by a Next to Leading Order QCD fit and the gluon density is extracted.

Laser photolysis studies of the phenolic H-atom transfer mechanism for a triplet π,π ∗ ketone in solution revisited

NASA Astrophysics Data System (ADS)

Yamaji, Minoru; Aoyama, Yutaka; Furukawa, Takashi; Itoh, Takao; Tobita, Seiji

2006-03-01

The mechanism of the H-atom transfer from phenols or thiophenols to triplet π,π ∗ 5,12-naphthacenequinone (5,12-NQ) has been examined by means of laser flash photolysis at 295 K. Based on the Hammett plots and the Rehm-Weller equation for the quenching rate constants, the phenolic H-atom transfer from phenols or thiophenols to triplet π,π ∗ 5,12-NQ is shown to proceed via the electron transfer followed by proton transfer. The previously proposed mechanism for H-atom transfer of π,π ∗ triplets, that proton transfer is followed by electron transfer, was not verified in the present systems.

Sequential Proton Loss Electron Transfer in Deactivation of Iron(IV) Binding Protein by Tyrosine Based Food Components.

PubMed

Tang, Ning; Skibsted, Leif H

2017-08-02

The iron(IV) binding protein ferrylmyoglobin, MbFe(IV)═O, was found to be reduced by tyrosine based food components in aqueous solution through a sequential proton loss electron transfer reaction mechanism without binding to the protein as confirmed by isothermal titration calorimetry. Dopamine and epinephrine are the most efficient food components reducing ferrylmyoglobin to oxymyoglobin, MbFe(II)O 2 , and metmyoglobin, MbFe(III), as revealed by multivariate curve resolution alternating least-squares with second order rate constants of 33.6 ± 2.3 L/mol/s (ΔH ⧧ of 19 ± 5 kJ/mol, ΔS ⧧ of -136 ± 18 J/mol K) and 228.9 ± 13.3 L/mol/s (ΔH ⧧ of 110 ± 7 kJ/mol, ΔS ⧧ of 131 ± 25 J/mol K), respectively, at pH 7.4 and 25 °C. The other tyrosine based food components were found to reduce ferrylmyoglobin to metmyoglobin with similar reduction rates at pH 7.4 and 25 °C. These reduction reactions were enhanced by protonation of ferrylmyoglobin and facilitated proton transfer at acidic conditions. Enthalpy-entropy compensation effects were observed for the activation parameters (ΔH ⧧ and ΔS ⧧ ), indicating the common reaction mechanism. Moreover, principal component analysis combined with heat map were performed to understand the relationship between density functional theory calculated molecular descriptors and kinetic data, which was further modeled by partial least squares for quantitative structure-activity relationship analysis. In addition, a three tyrosine residue containing protein, lysozyme, was also found to be able to reduce ferrylmyoglobin with a second order rate constant of 66 ± 28 L/mol/s as determined by a competitive kinetic method.

Proton-transfer lasers based on solid copolymers of modified 2-(2'-hydroxyphenyl)benzimidazoles with methacrylate monomers

NASA Astrophysics Data System (ADS)

Costela, A.; García-Moreno, I.; Mallavia, Ricardo; Amat-Guerri, F.; Barroso, J.; Sastre, R.

1998-06-01

We report on the lasing action of two newly synthesized 2-(2'-hydroxyphenyl) benzimidazole derivatives copolymerized with methyl methacrylate. The laser samples were transversely pumped with a N 2 laser at 337 nm. The influence on the proton-transfer laser performance of the distance between the chromophore group and the polymeric main chain and of the rigidity of the polymeric host matrix, were studied. Significant increases in lasing efficiency and photostability are demonstrated for some of the new materials, as compared to those previously obtained with related proton-transfer dyes also covalently bound to methacrylic monomers.

An efficient buffer-mediated control between free radical substitution and proton-coupled electron transfer: dehalogenation of iodoethane by the α-hydroxyethyl radical in aqueous solution.

PubMed

Ljubić, Ivan; Matasović, Brunislav; Bonifačić, Marija

2013-11-07

A remarkable buffer-mediated control between free-radical substitution (FRS) and proton-coupled electron transfer (PCET) is demonstrated for the reaction between iodoethane and the α-hydroxyethyl radical in neutral aqueous solution in the presence of bicarbonate or phosphate buffer. The reaction is initiated by the γ-radiolysis of the water solvent, and the products, either the iodine atom (FRS) or anion (PCET), are analysed using ion chromatographic and spectrophotometric techniques. A detailed insight into the mechanism is gained by employing density functional theory (M06-2X), Møller-Plesset perturbation treatment to the second order (MP2), and multireference methods (CASSCF/CASPT2). Addition of a basic buffer anion is indispensable for the reaction to occur and the competition between the two channels depends subtly on its proton accepting affinity, with FRS being the dominant channel in the phosphate and PCET in the bicarbonate containing solutions. Unlike the former, the latter channel sustains a chain-like process which significantly enhances the dehalogenation. The present systems furnish an example of the novel PCET/FRS dichotomy, as well as insights into possibilities of its efficient control.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

PubMed

Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

2015-01-01

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel.

PubMed

Rogers, Julie M G; Polishchuk, Alexei L; Guo, Lin; Wang, Jun; DeGrado, William F; Gai, Feng

2011-04-05

The structure and function of the influenza A M2 proton channel have been the subject of intensive investigations in recent years because of their critical role in the life cycle of the influenza virus. Using a truncated version of the M2 proton channel (i.e., M2TM) as a model, here we show that fluctuations in the fluorescence intensity of a dye reporter that arise from both fluorescence quenching via the mechanism of photoinduced electron transfer (PET) by an adjacent tryptophan (Trp) residue and local motions of the dye molecule can be used to probe the conformational dynamics of membrane proteins. Specifically, we find that the dynamics of the conformational transition between the N-terminal open and C-terminal open states of the M2TM channel occur on a timescale of about 500 μs and that the binding of either amantadine or rimantadine does not inhibit the pH-induced structural equilibrium of the channel. These results are consistent with the direct occluding mechanism of inhibition which suggests that the antiviral drugs act by sterically occluding the channel pore.

A mechanistic study and computational prediction of iron, cobalt and manganese cyclopentadienone complexes for hydrogenation of carbon dioxide.

PubMed

Ge, Hongyu; Chen, Xiangyang; Yang, Xinzheng

2016-10-13

A series of cobalt and manganese cyclopentadienone complexes are proposed and examined computationally as promising catalysts for hydrogenation of CO 2 to formic acid with total free energies as low as 20.0 kcal mol -1 in aqueous solution. Density functional theory study of the newly designed cobalt and manganese complexes and experimentally reported iron cyclopentadienone complexes reveals a stepwise hydride transfer mechanism with a water or a methanol molecule assisted proton transfer for the cleavage of H 2 as the rate-determining step.

Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasai, Yukako; Yoshida, Norio, E-mail: noriwo@chem.kyushu-univ.jp; Nakano, Haruyuki

2015-05-28

The co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water–acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is moremore » stable than the neutral form. The reaction free energy is −10.6 kcal mol{sup −1}. On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol{sup −1}. The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.« less

Spectrophotometric study on the proton transfer reaction between 2-amino-4-methylpyridine with 2,6-dichloro-4-nitrophenol in methanol, acetonitrile and the binary mixture 50% methanol + 50% acetonitrile

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2016-02-01

Proton transfer reaction between 2-amino-4-methylpyridine (2AMP) as the proton acceptor with 2,6-dichloro-4-nitrophenol (DCNP) as the proton donor has been investigated spectrophotometrically in methanol (MeOH), acetonitrile (AN) and a binary mixture composed of 50% MeOH and 50% AN (AN-Me). The composition of the complex has been investigated utilizing Job's and photometric titration methods to be 1:1. Minimum-maximum absorbance equation has been applied to estimate the formation constant of the proton transfer reaction (KPT) where it reached high values in the investigated solvent confirming its high stability. The formation constant recorded higher value in AN compared with MeOH and mixture of AN-Me. Based on the formation of stable proton transfer complex, a sensitive spectrophotometric method was suggested for quantitative determination of 2AMP. The Lambert-Beer's law was obeyed in the concentration range 0.5-8 μg mL- 1 with small values of limits of detection and quantification. The solid complex between 2AMP with DCNP has been synthesized and characterized by elemental analysis to be 1:1 in concordant with the molecular stoichiometry in solution. Further analysis of the solid complex was carried out using infrared and 1H NMR spectroscopy.

Highly oriented photosynthetic reaction centers generate a proton gradient in synthetic protocells

PubMed Central

Altamura, Emiliano; Milano, Francesco; Tangorra, Roberto R.; Trotta, Massimo; Omar, Omar Hassan; Stano, Pasquale

2017-01-01

Photosynthesis is responsible for the photochemical conversion of light into the chemical energy that fuels the planet Earth. The photochemical core of this process in all photosynthetic organisms is a transmembrane protein called the reaction center. In purple photosynthetic bacteria a simple version of this photoenzyme catalyzes the reduction of a quinone molecule, accompanied by the uptake of two protons from the cytoplasm. This results in the establishment of a proton concentration gradient across the lipid membrane, which can be ultimately harnessed to synthesize ATP. Herein we show that synthetic protocells, based on giant lipid vesicles embedding an oriented population of reaction centers, are capable of generating a photoinduced proton gradient across the membrane. Under continuous illumination, the protocells generate a gradient of 0.061 pH units per min, equivalent to a proton motive force of 3.6 mV⋅min−1. Remarkably, the facile reconstitution of the photosynthetic reaction center in the artificial lipid membrane, obtained by the droplet transfer method, paves the way for the construction of novel and more functional protocells for synthetic biology. PMID:28320948

Faster proton transfer dynamics of water on SnO2 compared to TiO2.

PubMed

Kumar, Nitin; Kent, Paul R C; Bandura, Andrei V; Kubicki, James D; Wesolowski, David J; Cole, David R; Sofo, Jorge O

2011-01-28

Proton jump processes in the hydration layer on the iso-structural TiO(2) rutile (110) and SnO(2) cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O-H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates.

pH-dependent reduction potentials and proton-coupled electron transfer mechanisms in hydrogen-producing nickel molecular electrocatalysts.

PubMed

Horvath, Samantha; Fernandez, Laura E; Appel, Aaron M; Hammes-Schiffer, Sharon

2013-04-01

The nickel-based P2(Ph)N2(Bn) electrocatalysts comprised of a nickel atom and two 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane ligands catalyze H2 production in acetonitrile. Recent electrochemical experiments revealed a linear dependence of the Ni(II/I) reduction potential on pH with a slope of 57 mV/pH unit, implicating a proton-coupled electron transfer (PCET) process with the same number of electrons and protons transferred. The combined theoretical and experimental studies herein provide an explanation for this pH dependence in the context of the overall proposed catalytic mechanism. In the proposed mechanisms, the catalytic cycle begins with a series of intermolecular proton transfers from an acid to the pendant amine ligand and electrochemical electron transfers to the nickel center to produce the doubly protonated Ni(0) species, a precursor to H2 evolution. The calculated Ni(II/I) reduction potentials of the doubly protonated species are in excellent agreement with the experimentally observed reduction potential in the presence of strong acid, suggesting that the catalytically active species leading to the peak observed in these cyclic voltammetry (CV) experiments is doubly protonated. The Ni(I/0) reduction potential was found to be slightly more positive than the Ni(II/I) reduction potential, indicating that the Ni(I/0) reduction occurs spontaneously after the Ni(II/I) reduction, as implied by the experimental observation of a single CV peak. These results suggest that the PCET process observed in the CV experiments is a two-electron/two-proton process corresponding to an initial double protonation followed by two reductions. On the basis of the experimental and theoretical data, the complete thermodynamic scheme and the Pourbaix diagram were generated for this catalyst. The Pourbaix diagram, which identifies the most thermodynamically stable species at each reduction potential and pH value, illustrates that this catalyst undergoes different types of PCET processes for various pH ranges. These thermodynamic insights will aid in the design of more effective molecular catalysts for H2 production.

Tuning the photoluminescence of graphene quantum dots through the charge transfer effect of functional groups.

PubMed

Jin, Sung Hwan; Kim, Da Hye; Jun, Gwang Hoon; Hong, Soon Hyung; Jeon, Seokwoo

2013-02-26

The band gap properties of graphene quantum dots (GQDs) arise from quantum confinement effects and differ from those in semimetallic graphene sheets. Tailoring the size of the band gap and understanding the band gap tuning mechanism are essential for the applications of GQDs in opto-electronics. In this study, we observe that the photoluminescence (PL) of the GQDs shifts due to charge transfers between functional groups and GQDs. GQDs that are functionalized with amine groups and are 1-3 layers thick and less than 5 nm in diameter were successfully fabricated using a two-step cutting process from graphene oxides (GOs). The functionalized GQDs exhibit a redshift of PL emission (ca. 30 nm) compared to the unfunctionalized GQDs. Furthermore, the PL emissions of the GQDs and the amine-functionalized GQDs were also shifted by changes in the pH due to the protonation or deprotonation of the functional groups. The PL shifts resulted from charge transfers between the functional groups and GQDs, which can tune the band gap of the GQDs. Calculations from density functional theory (DFT) are in good agreement with our proposed mechanism for band gap tuning in the GQDs through the use of functionalization.

QM/MM Calculation of the Enzyme Catalytic Cycle Mechanism for Copper- and Zinc-Containing Superoxide Dismutase.

PubMed

Lintuluoto, Masami; Yamada, Chiaki; Lintuluoto, Juha M

2017-08-03

The entire enzyme catalytic mechanism including the electron and the proton transfers of the copper- and zinc-containing extracellular superoxide dismutase (SOD3) was investigated by using QM/MM method. In the first step, the electron transfer from O 2 ·- to SOD3 occurred without the bond formation between the donor and the acceptor and formed the triplet oxygen molecule and reduced SOD3. In the reduced SOD3, the distorted tetrahedral structure of Cu(I) atom was maintained. The reduction of Cu(II) atom induced the protonation of His113, which bridges between the Cu(II) and Zn(II) atoms in the resting state. Since the protonation of His113 broke the bond between Cu(I) and His113, three-coordinated Cu(I) was formed. Further, we suggest the binding of O 2 ·- formed hydrogen peroxide and the resting state after both the Cu reduction and the protonation of His113. The protonation of His113 caused the conformational change of Arg186 located at the entrance of the reactive site. The electrostatic potential surface around the reactive site showed that Arg186 plays an important role as electrostatic guidance for the negatively charged substrates only after the protonation of His113. The rotation of Arg186 switched the proton supply routes via Glu108 or Glu179 for transferring two protons from the bulk solvent.

Probing membrane protein structure using water polarization transfer solid-state NMR.

PubMed

Williams, Jonathan K; Hong, Mei

2014-10-01

Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins. Copyright © 2014 Elsevier Inc. All rights reserved.

Unfolding the Quantum Nature of Proton Bound Symmetric Dimers of (MeOH)2H+ and (Me2O)2H+: a Theoretical Study

NASA Astrophysics Data System (ADS)

Tan, Jake Acedera; Kuo, Jer-Lai

2014-06-01

A proton under a tug of war between two competing Lewis bases is a common motif in biological systems and proton transfer processes. Over the past decades, model compounds for such motifs can be prepared by delicate stoichiometric control of salt solutions. Unfortunately, condensed phase studies, which aims to identify the key vibrational signatures are complicated to analyze. As a result, gas-phase studies do provide promising insights on the behavior of the shared proton. This study attempts to understand the quantum nature of the shared proton under theoretical paradigms. Proton bound symmetric dimers of (MeOH)2H+ and (Me2O)2H+ are chosen as the model compounds. The simulation is performed using Density Functional Theory (DFT) at the B3LYP level with 6-311+G(d,p) as the basis set. It was found out that stretching mode of shared proton couples with several other normal modes and its corresponding oscillator strength do distribute to other normal modes. J.R. Roscioli, L.R. McCunn and M.A. Johnson. Science 2007, 316, 249 T.E. DeCoursey. Physiol. Rev., 2003, 83, 475 E.S. Stoyanov. Psys. Chem. Phys., 2000,2,1137

Verification of the electron/proton coupled mechanism for phenolic H-atom transfer using a triplet π,π ∗ carbonyl

NASA Astrophysics Data System (ADS)

Yamaji, Minoru; Oshima, Juro; Hidaka, Motohiko

2009-06-01

Evidence for the coupled electron/proton transfer mechanism of the phenolic H-atom transfer between triplet π,π ∗ 3,3'-carbonylbis(7-diethylaminocoumarin) and phenol derivatives is obtained by using laser photolysis techniques. It was confirmed that the quenching rate constants of triplet CBC by phenols having positive Hammett constants do not follow the Rehm-Weller equation for electron transfer while those by phenols with negative Hammett constants do it. From the viewpoint of thermodynamic parameters for electron transfer, the crucial factors for phenolic H-atom transfer to π,π ∗ triplet are discussed.

FTIR Study of the Photoactivation Process of Xenopus (6-4) Photolyase†

PubMed Central

Yamada, Daichi; Zhang, Yu; Iwata, Tatsuya; Hitomi, Kenichi; Getzoff, Elizabeth D.; Kandori, Hideki

2012-01-01

Photolyases (PHRs) are blue-light activated DNA repair enzymes that maintain genetic integrity by reverting UV-induced photoproducts into normal bases. The FAD chromophore of PHRs has four different redox states: oxidized (FADox), anion radical (FAD•−), neutral radical (FADH•) and fully reduced (FADH−). We combined difference Fourier-transform infrared (FTIR) spectroscopy with UV-visible spectroscopy to study the detailed photoactivation process of Xenopus (6-4) PHR. Two photons produce the enzymatically active, fully reduced PHR from oxidized FAD: FADox is converted to semiquinone via light-induced one-electron and one-proton transfers, and then to FADH− by light-induced one-electron transfer. We successfully trapped FAD•− at 200 K, where electron transfer occurs, but proton transfer does not. UV-visible spectroscopy following 450-nm illumination of FADox at 277 K defined the FADH•/FADH− mixture and allowed calculation of difference FTIR spectra among the four redox states. The absence of a characteristic C=O stretching vibration indicated that the proton donor is not a protonated carboxylic acid. Structural changes in Trp and Tyr are suggested from UV-visible and FTIR analysis of FAD•− at 200 K. Spectral analysis of amide-I vibrations revealed structural perturbation of the protein’s β-sheet during initial electron transfer (FAD•− formation), transient increase in α-helicity during proton transfer (FADH• formation) and reversion to the initial amide-I signal following subsequent electron transfer (FADH− formation). Consequently, in (6-4) PHR, unlike cryptochrome-DASH, formation of enzymatically active FADH− did not perturb α-helicity. Protein structural changes in the photoactivation of (6-4) PHR are discussed on the basis of the present FTIR observations. PMID:22747528

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

PubMed

Fekete, Attila; Komáromi, István

2016-12-07

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Comparison of forward and backward pp pair knockout in 3He(e,e'pp)n

NASA Astrophysics Data System (ADS)

Baghdasaryan, H.; Weinstein, L. B.; Laget, J. M.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anghinolfi, M.; Ball, J.; Battaglieri, M.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Daniel, A.; Dashyan, N.; De Sanctis, E.; De Vita, R.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Fedotov, G.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Gothe, R. W.; Griffioen, K. A.; Guegan, B.; Guidal, M.; Hafidi, K.; Hicks, K.; Hyde, C. E.; Ireland, D. G.; Ishkhanov, B. S.; Jenkins, D.; Jo, H. S.; Joo, K.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; Kubarovsky, A.; Kubarovsky, V.; Kuhn, S. E.; Kuleshov, S. V.; Kvaltine, N. D.; Lu, H. Y.; MacGregor, I. J. D.; McKinnon, B.; Mirazita, M.; Mokeev, V.; Moutarde, H.; Munevar, E.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Paolone, M.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Park, S.; Pisano, S.; Pozdniakov, S.; Procureur, S.; Raue, B. A.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Saini, M. S.; Saylor, N. A.; Schott, D.; Schumacher, R. A.; Seraydaryan, H.; Smith, E. S.; Sober, D. I.; Sokan, D.; Stepanyan, S. S.; Stepanyan, S.; Strauch, S.; Taiuti, M.; Tang, W.; Tkachenko, S.; Voskanyan, H.; Voutier, E.; Wood, M. H.; Zana, L.; Zhao, B.

2012-06-01

Measuring nucleon-nucleon short range correlations (SRCs) has been a goal of the nuclear physics community for many years. They are an important part of the nuclear wave function, accounting for almost all of the high-momentum strength. They are closely related to the EMC effect. While their overall probability has been measured, measuring their momentum distributions is more difficult. In order to determine the best configuration for studying SRC momentum distributions, we measured the 3He(e,e'pp)n reaction, looking at events with high-momentum protons (pp>0.35 GeV/c) and a low-momentum neutron (pn<0.2 GeV/c). We examined two angular configurations: either both protons emitted forward or one proton emitted forward and one backward (with respect to the momentum transfer, q⃗). The measured relative momentum distribution of the events with one forward and one backward proton was much closer to the calculated initial-state pp relative momentum distribution, indicating that this is the preferred configuration for measuring SRC.

Polarization phenomena in quantum chromodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodsky, S.J.

1994-12-01

The author discusses a number of interrelated hadronic spin effects which test fundamental features of perturbative and nonperturbative QCD. For example, the anomalous magnetic moment of the proton and the axial coupling g{sub A} on the nucleon are shown to be related to each other for fixed proton radius, independent of the form of the underlying three-quark relativistic quark wavefunction. The renormalization scale and scheme ambiguities for the radiative corrections to the Bjorken sum rule for the polarized structure functions can be eliminated by using commensurate scale relations with other observables. Other examples include (a) new constraints on the shapemore » and normalization of the polarized quark and gluon structure functions of the proton at large and small x{sub bj}; (b) consequences of the principle of hadron retention in high x{sub F} inclusive reactions; (c) applications of hadron helicity conservation to high momentum transfer exclusive reactions; and (d) the dependence of nuclear structure functions and shadowing on virtual photon polarization. The author also discusses the implications of a number of measurements which are in striking conflict with leading-twist perturbative QCD predictions, such as the extraordinarily large spin correlation A{sub NN} observed in large angle proton-proton scattering, the anomalously large {rho}{pi} branching ratio of the J/{psi}, and the rapidly changing polarization dependence of both J/{psi} and continuum lepton pair hadroproduction observed at large x{sub F}. The azimuthal angular dependence of the Drell-Yan process is shown to be highly sensitive to the projectile distribution amplitude, the fundamental valence light-cone wavefunction of the hadron.« less

Intrinsic uncoupling of mitochondrial proton pumps. 2. Modeling studies.

PubMed

Pietrobon, D; Zoratti, M; Azzone, G F; Caplan, S R

1986-02-25

The thermodynamic and kinetic properties associated with intrinsic uncoupling in a six-state model of a redox proton pump have been studied by computing the flow-force relations for different degrees of coupling. Analysis of these relations shows the regulatory influence of the thermodynamic forces on the extent and relative contributions of redox slip and proton slip. Inhibition has been introduced into the model in two different ways, corresponding to possible modes of action of experimental inhibitors. Experiments relating the rate of electron transfer to delta microH at static head upon progressive inhibition of the pumps have been simulated considering (1) the limiting case that the nonzero rate of electron transfer at static head is only due to intrinsic uncoupling (no leaks) and (2) the experimentally observed case that about 30% of the nonzero rate of electron transfer at static head is due to a constant proton leakage conductance in parallel with the pumps, the rest being due to intrinsic uncoupling. The same simulations have been performed for experiments in which the rate of electron transfer is varied by varying the substrate concentration rather than by using an inhibitor. The corresponding experimental results obtained by measuring delta microH and the rate of electron transfer at different succinate concentrations in rat liver mitochondria are presented. Comparison between simulated behavior and experimental results leads to the general conclusion that the typical relationship between rate of electron transfer and delta microH found in mitochondria at static head could certainly be a manifestation of some degree of intrinsic uncoupling in the redox proton pumps.(ABSTRACT TRUNCATED AT 250 WORDS)

NMR studies of double proton transfer in hydrogen bonded cyclic N,N'-diarylformamidine dimers: conformational control, kinetic HH/HD/DD isotope effects and tunneling.

PubMed

Lopez, Juan Miguel; Männle, Ferdinand; Wawer, Iwona; Buntkowsky, Gerd; Limbach, Hans-Heinrich

2007-08-28

Using dynamic NMR spectroscopy, the kinetics of the degenerate double proton transfer in cyclic dimers of polycrystalline (15)N,(15)N'-di-(4-bromophenyl)-formamidine (DBrFA) have been studied including the kinetic HH/HD/DD isotope effects in a wide temperature range. This transfer is controlled by intermolecular interactions, which in turn are controlled by the molecular conformation and hence the molecular structure. At low temperatures, rate constants were determined by line shape analysis of (15)N NMR spectra obtained using cross-polarization (CP) and magic angle spinning (MAS). At higher temperatures, in the microsecond time scale, rate constants and kinetic isotope effects were obtained by a combination of longitudinal (15)N and (2)H relaxation measurements. (15)N CPMAS line shape analysis was also employed to study the non-degenerate double proton transfer of polycrystalline (15)N,(15)N'-diphenyl-formamidine (DPFA). The kinetic results are in excellent agreement with the kinetics of DPFA and (15)N,(15)N'-di-(4-fluorophenyl)-formamidine (DFFA) studied previously for solutions in tetrahydrofuran. Two large HH/HD and HD/DD isotope effects are observed in the whole temperature range which indicates a concerted double proton transfer mechanism in the domain of the reaction energy surface. The Arrhenius curves are non-linear indicating a tunneling mechanism. Arrhenius curve simulations were performed using the Bell-Limbach tunneling model. The role of the phenyl group conformation and hydrogen bond compression on the barrier of the proton transfer is discussed.

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus

PubMed Central

Chang, Hsin-Yang; Choi, Sylvia K.; Vakkasoglu, Ahmet Selim; Chen, Ying; Hemp, James; Fee, James A.; Gennis, Robert B.

2012-01-01

The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba3-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a3 to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a3, and for Glu126II (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126II, and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a3, was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a3 or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a3 is a good candidate to be the proton loading site. PMID:22431640

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus.

PubMed

Chang, Hsin-Yang; Choi, Sylvia K; Vakkasoglu, Ahmet Selim; Chen, Ying; Hemp, James; Fee, James A; Gennis, Robert B

2012-04-03

The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a(3), and for Glu126(II) (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126(II), and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a(3), was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a(3) or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a(3) is a good candidate to be the proton loading site.

Proton transfer mass spectrometry at 11 hPa with a circular glow discharge: Sensitivities and applications

NASA Astrophysics Data System (ADS)

Hanson, D. R.; Koppes, M.; Stoffers, A.; Harsdorf, R.; Edelen, K.

2009-04-01

The design and testing of a circular glow discharge ion source on a custom built proton transfer mass spectrometer are described. Also, issues important for quantitative measurements of volatile organic compounds using this instrument were investigated. Detailed calibration procedures based on gravimetry are presented, and representative outdoor air data are shown. Calibrations yield a good sensitivity, up to a few Hz/pptv for some compounds, and the detection limit (S/N = 3) is ~100 pptv or better for methanol, acetaldehyde and acetone (5 s sampling time with a 5 s zero). Detection limits are much lower for most other compounds due to high sensitivity and low background. For ions with m/z > ~90 the background signals are very low and species that appear efficiently at these m/z can be detected at the 10 pptv level in a few seconds. Ion breakup processes for alcohols show that a major product ion of mono-functional alcohols is at 57 u, presumably C4H9+. Oxalic acid is an interesting case in that a major product ion appears on an even mass, 46 u, presumably CO2H2+. The circular glow discharge source is easy to construct and deploy in proton transfer mass spectrometry studies at ~11 hPa. Continuous use of the system over time periods of many days and stable operation over time periods of months to years between disassembly and cleaning demonstrates its robustness.

Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses.

PubMed

Yamagiwa, Raika; Kurahashi, Takuya; Takeda, Mariko; Adachi, Mayuho; Nakamura, Hiro; Arai, Hiroyuki; Shiro, Yoshitsugu; Sawai, Hitomi; Tosha, Takehiko

2018-05-01

Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N 2 O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO 2 - ) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Theoretical studies of charge transfer and proton transfer complex formation between 3,5-dinitrobenzic acid and 1,2-dimethylimidazole

NASA Astrophysics Data System (ADS)

Afroz, Ziya; Faizan, Mohd.; Alam, Mohammad Jane; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

Natural atomic charge analysis and molecular electrostatic potential (MEP) surface analysis of hydrogen bonded charge transfer (HBCT) and proton transfer (PT) complex of 3,5-dinitrobenzoic acid (DNBA) and 1,2-dimethylimidazole (DMI) have been investigated by theoretical modelling using widely employed DFT/B3LYP/6-311G(d,p) level of theory. Along with this analysis, Hirshfeld surface study of the intermolecular interactions and associated 2D finger plot for reported PT complex between DNBA and DMI have been explored.

Proton elastic scattering at 200 A MeV and high momentum transfers of 1.7-2.7 fm-1 as a probe of the nuclear matter density of 6He

NASA Astrophysics Data System (ADS)

Chebotaryov, S.; Sakaguchi, S.; Uesaka, T.; Akieda, T.; Ando, Y.; Assie, M.; Beaumel, D.; Chiga, N.; Dozono, M.; Galindo-Uribarri, A.; Heffron, B.; Hirayama, A.; Isobe, T.; Kaki, K.; Kawase, S.; Kim, W.; Kobayashi, T.; Kon, H.; Kondo, Y.; Kubota, Y.; Leblond, S.; Lee, H.; Lokotko, T.; Maeda, Y.; Matsuda, Y.; Miki, K.; Milman, E.; Motobayashi, T.; Mukai, T.; Nakai, S.; Nakamura, T.; Ni, A.; Noro, T.; Ota, S.; Otsu, H.; Ozaki, T.; Panin, V.; Park, S.; Saito, A.; Sakai, H.; Sasano, M.; Sato, H.; Sekiguchi, K.; Shimizu, Y.; Stefan, I.; Stuhl, L.; Takaki, M.; Taniue, K.; Tateishi, K.; Terashima, S.; Togano, Y.; Tomai, T.; Wada, Y.; Wakasa, T.; Wakui, T.; Watanabe, A.; Yamada, H.; Yang, Zh; Yasuda, M.; Yasuda, J.; Yoneda, K.; Zenihiro, J.

2018-05-01

Differential cross sections of p-^6He elastic scattering were measured in inverse kinematics at an incident energy of 200 A MeV, covering the high momentum transfer region of 1.7-2.7 fm^{-1}. The sensitivity of the elastic scattering at low and high momentum transfers to the density distribution was investigated quantitatively using relativistic impulse approximation calculations. In the high momentum transfer region, where the present data were taken, the differential cross section has an order of magnitude higher sensitivity to the inner part of the ^6He density relative to the peripheral part (15:1). This feature makes the obtained data valuable for the deduction of the inner part of the ^6He density. The data were compared to a set of calculations assuming different proton and neutron density profiles of ^6He. The data are well reproduced by the calculation assuming almost the same profiles of proton and neutron densities around the center of ^6He, and a proton profile reproducing the known point-proton radius of 1.94 fm. This finding is consistent with the assumption that the ^6He nucleus consists of a rigid α-like core with a two-neutron halo.

Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

NASA Astrophysics Data System (ADS)

Martens, Sabrina M.; Marta, Rick A.; Martens, Jonathan K.; McMahon, Terry B.

2012-10-01

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm-1. The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs.

PubMed

Wu, Xiuxiu; Karsili, Tolga N V; Domcke, Wolfgang

2017-01-14

It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G - with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G - nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G - -A and 8-oxo-G - -C base pairs are likely too short-lived to be efficient electron-transfer repair agents.

Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.

PubMed

Unno, Masaki; Ishikawa-Suto, Kumiko; Kusaka, Katsuhiro; Tamada, Taro; Hagiwara, Yoshinori; Sugishima, Masakazu; Wada, Kei; Yamada, Taro; Tomoyori, Katsuaki; Hosoya, Takaaki; Tanaka, Ichiro; Niimura, Nobuo; Kuroki, Ryota; Inaka, Koji; Ishihara, Makiko; Fukuyama, Keiichi

2015-04-29

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

Exploring Nucleon Spin Structure Through Neutrino Neutral-Current Interactions in MicroBooNE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodruff, Katherine

2017-02-02

The net contribution of the strange quark spins to the proton spin,more » $$\\Delta s$$, can be determined from neutral current elastic neutrino-proton interactions at low momentum transfer combined with data from electron-proton scattering. The probability of neutrino-proton interactions depends in part on the axial form factor, which represents the spin structure of the proton and can be separated into its quark flavor contributions. Low momentum transfer neutrino neutral current interactions can be measured in MicroBooNE, a high-resolution liquid argon time projection chamber (LArTPC) in its first year of running in the Booster Neutrino Beamline at Fermilab. The signal for these interactions in MicroBooNE is a single short proton track. We present our work on the automated reconstruction and classification of proton tracks in LArTPCs, an important step in the determination of neutrino- nucleon cross sections and the measurement of $$\\Delta s$$.« less

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

PubMed Central

Marreiros, Bruno C.; Sena, Filipa V.; Sousa, Filipe M.; Oliveira, A. Sofia F.; Soares, Cláudio M.; Batista, Ana P.; Pereira, Manuela M.

2017-01-01

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains. These proteins contribute indirectly to the establishment of the transmembrane difference of electrochemical potential by catalyzing the reduction of quinone by oxidation of NAD(P)H. NDH-2s are widespread enzymes being present in the three domains of life. In this work, we explored the catalytic mechanism of NDH-2 by investigating the common elements of all NDH-2s, based on the rationale that conservation of such elements reflects their structural/functional importance. We observed conserved sequence motifs and structural elements among 1762 NDH-2s. We identified two proton pathways possibly involved in the protonation of the quinone. Our results led us to propose the first catalytic mechanism for NDH-2 family, in which a conserved glutamate residue, E172 (in NDH-2 from Staphylococcus aureus) plays a key role in proton transfer to the quinone pocket. This catalytic mechanism may also be extended to the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, such as sulfide:quinone oxidoreductases. PMID:28181562

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube.

PubMed

Duster, Adam W; Lin, Hai

2017-09-14

Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.

Concerted One-Electron Two-Proton Transfer Processes in Models Inspired by the Tyr-His Couple of Photosystem II

DOE PAGES

Huynh, Mioy T.; Mora, S. Jimena; Villalba, Matias; ...

2017-05-09

Nature employs a TyrZ-His pair as a redox relay that couples proton transfer to the redox process between P680 and the water oxidizing catalyst in photosystem II. Artificial redox relays composed of different benzimidazole–phenol dyads (benzimidazole models His and phenol models Tyr) with substituents designed to simulate the hydrogen bond network surrounding the TyrZ-His pair have been prepared. Furthermore, when the benzimidazole substituents are strong proton acceptors such as primary or tertiary amines, theory predicts that a concerted two proton transfer process associated with the electrochemical oxidation of the phenol will take place. Furthermore, theory predicts a decrease in themore » redox potential of the phenol by ~300 mV and a small kinetic isotope effect (KIE). Indeed, electrochemical, spectroelectrochemical, and KIE experimental data are consistent with these predictions. Our results were obtained by using theory to guide the rational design of artificial systems and have implications for managing proton activity to optimize efficiency at energy conversion sites involving water oxidation and reduction.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanov, Sergei D., E-mail: sergei.ivanov@unirostock.de; Grant, Ian M.; Marx, Dominik

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently andmore » thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.« less

An abnormally slow proton transfer reaction in a simple HBO derivative due to ultrafast intramolecular-charge transfer events.

PubMed

Alarcos, Noemí; Gutierrez, Mario; Liras, Marta; Sánchez, Félix; Douhal, Abderrazzak

2015-07-07

We report on the steady-state, picosecond and femtosecond time-resolved studies of a charge and proton transfer dye 6-amino-2-(2'-hydroxyphenyl)benzoxazole (6A-HBO) and its methylated derivative 6-amino-2-(2'-methoxyphenyl)benzoxazole (6A-MBO), in different solvents. With femtosecond resolution and comparison with the photobehaviour of 6A-MBO, we demonstrate for 6A-HBO in solution, the photoproduction of an intramolecular charge-transfer (ICT) process at S1 taking place in ∼140 fs or shorter, followed by solvent relaxation in the charge transferred species. The generated structure (syn-enol charge transfer conformer) experiences an excited-state intramolecular proton-transfer (ESIPT) reaction to produce a keto-type tautomer. This subsequent proton motion occurs in 1.2 ps (n-heptane), 14 ps (DCM) and 35 ps (MeOH). In MeOH, it is assisted by the solvent molecules and occurs through tunneling for which we got a large kinetic isotope effect (KIE) of about 13. For the 6A-DBO (deuterated sample in CD3OD) the global proton-transfer reaction takes place in 200 ps, showing a remarkable slow KIE regime. The slow ESIPT reaction in DCM (14 ps), not through tunnelling as it is not sensitive to OH/OD exchange, has however to overcome an energy barrier using intramolecular as well as solvent coordinates. The rich ESIPT dynamics of 6A-HBO in the used solutions is governed by an ICT reaction, triggered by the amino group, and it is solvent dependent. Thus, the charge injection to a 6A-HBO molecular frame makes the ICT species more stable, and the phenol group less acidic, slowing down the subsequent ESIPT reaction. Our findings bring new insights into the coupling between ICT and ESIPT reactions on the potential-energy surfaces of several barriers.

Infrared laser driven double proton transfer. An optimal control theory study

NASA Astrophysics Data System (ADS)

Abdel-Latif, Mahmoud K.; Kühn, Oliver

2010-02-01

Laser control of ultrafast double proton transfer is investigated for a two-dimensional model system describing stepwise and concerted transfer pathways. The pulse design has been done by employing optimal control theory in combination with the multiconfiguration time-dependent Hartree wave packet propagation. The obtained laser fields correspond to multiple pump-dump pulse sequences. Special emphasis is paid to the relative importance of stepwise and concerted transfer pathways for the driven wave packet and its dependence on the parameters of the model Hamiltonian as well as on the propagation time. While stepwise transfer is dominating in all cases considered, for high barrier systems concerted transfer proceeding via tunneling can make a contribution.

Photochemical reaction of 2-(3-benzoylphenyl)propionic acid (ketoprofen) with basic amino acids and dipeptides.

PubMed

Suzuki, Tadashi; Shinoda, Mio; Osanai, Yohei; Isozaki, Tasuku

2013-08-22

Photoreaction of 2-(3-benzoylphenyl)propionic acid (ketoprofen, KP) with basic amino acids (histidine, lysine, and arginine) and dipeptides (carnosine and anserine) including a histidine moiety in phosphate buffer solution (pH 7.4) has been investigated with transient absorption spectroscopy. With UV irradiation KP(-) gave rise to a carbanion through a decarboxylation reaction, and the carbanion easily abstracted a proton from the surrounding molecule to yield a 3-ethylbenzophenone ketyl biradical (EBPH). The dipeptides as well as the basic amino acids were found to accelerate the proton transfer reaction whereas alanine and glycine had no effect on the reaction, revealing that these amino acids having a protonated side chain act as a proton donor. The formation quantum yield of EBPH was estimated to be fairly large by means of an actinometrical method with benzophenone, and the bimolecular reaction rate constant for the proton transfer between the carbanion and the protonated basic amino acids or the protonated dipeptides was successfully determined. It has become apparent that the bimolecular reaction rate constant for the proton transfer depended on the acid dissociation constant for the side chain of the amino acids for the first time. This reaction mechanism was interpreted by difference of the heat of reaction for each basic amino acid based on the thermodynamical consideration. These results strongly suggest that the side chain of the basic amino acid residue in protein should play an important role for photochemistry of KP in vivo.

Time-resolved generation of membrane potential by ba3 cytochrome c oxidase from Thermus thermophilus coupled to single electron injection into the O and OH states.

PubMed

Siletsky, Sergey A; Belevich, Ilya; Belevich, Nikolai P; Soulimane, Tewfik; Wikström, Mårten

2017-11-01

Two electrogenic phases with characteristic times of ~14μs and ~290μs are resolved in the kinetics of membrane potential generation coupled to single-electron reduction of the oxidized "relaxed" O state of ba 3 oxidase from T. thermophilus (O→E transition). The rapid phase reflects electron redistribution between Cu A and heme b. The slow phase includes electron redistribution from both Cu A and heme b to heme a 3 , and electrogenic proton transfer coupled to reduction of heme a 3 . The distance of proton translocation corresponds to uptake of a proton from the inner water phase into the binuclear center where heme a 3 is reduced, but there is no proton pumping and no reduction of Cu B . Single-electron reduction of the oxidized "unrelaxed" state (O H →E H transition) is accompanied by electrogenic reduction of the heme b/heme a 3 pair by Cu A in a "fast" phase (~22μs) and transfer of protons in "middle" and "slow" electrogenic phases (~0.185ms and ~0.78ms) coupled to electron redistribution from the heme b/heme a 3 pair to the Cu B site. The "middle" and "slow" electrogenic phases seem to be associated with transfer of protons to the proton-loading site (PLS) of the proton pump, but when all injected electrons reach Cu B the electronic charge appears to be compensated by back-leakage of the protons from the PLS into the binuclear site. Thus proton pumping occurs only to the extent of ~0.1 H + /e - , probably due to the formed membrane potential in the experiment. Copyright © 2017 Elsevier B.V. All rights reserved.

Respiratory Complex I in Bos taurus and Paracoccus denitrificans Pumps Four Protons across the Membrane for Every NADH Oxidized.

PubMed

Jones, Andrew J Y; Blaza, James N; Varghese, Febin; Hirst, Judy

2017-03-24

Respiratory complex I couples electron transfer between NADH and ubiquinone to proton translocation across an energy-transducing membrane to support the proton-motive force that drives ATP synthesis. The proton-pumping stoichiometry of complex I ( i.e. the number of protons pumped for each two electrons transferred) underpins all mechanistic proposals. However, it remains controversial and has not been determined for any of the bacterial enzymes that are exploited as model systems for the mammalian enzyme. Here, we describe a simple method for determining the proton-pumping stoichiometry of complex I in inverted membrane vesicles under steady-state ADP-phosphorylating conditions. Our method exploits the rate of ATP synthesis, driven by oxidation of NADH or succinate with different sections of the respiratory chain engaged in catalysis as a proxy for the rate of proton translocation and determines the stoichiometry of complex I by reference to the known stoichiometries of complexes III and IV. Using vesicles prepared from mammalian mitochondria (from Bos taurus ) and from the bacterium Paracoccus denitrificans , we show that four protons are pumped for every two electrons transferred in both cases. By confirming the four-proton stoichiometry for mammalian complex I and, for the first time, demonstrating the same value for a bacterial complex, we establish the utility of P. denitrificans complex I as a model system for the mammalian enzyme. P. denitrificans is the first system described in which mutagenesis in any complex I core subunit may be combined with quantitative proton-pumping measurements for mechanistic studies. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Enhancement of proton transfer in ion channels by membrane phosphate headgroups.

PubMed

Wyatt, Debra L; de Godoy, Carlos Marcelo G; Cukierman, Samuel

2009-05-14

The transfer of protons (H+) in gramicidin (gA) channels is markedly distinct in monoglyceride and phospholipid membranes. In this study, the molecular groups that account for those differences were investigated using a new methodology. The rates of H+ transfer were measured in single gA channels reconstituted in membranes made of plain ceramides or sphingomyelins and compared to those in monoglyceride and phospholipid bilayers. Single-channel conductances to protons (gH) were significantly larger in sphingomyelin than in ceramide membranes. A novel and unsuspected finding was that H+ transfer was heavily attenuated or completely blocked in ceramide (but not in sphingomyelin) membranes in low-ionic-strength solutions. It is reasoned that H-bond dynamics at low ionic strengths between membrane ceramides and gA makes channels dysfunctional. The rate of H+ transfer in gA channels in ceramide membranes is significantly higher than that in monoglyceride bilayers. This suggests that solvation of the hydrophobic surface of gA channels by two acyl chains in ceramides stabilizes the gA channels and the water wire inside the pore, leading to an enhancement of H+ transfer in relation to that occurring in monoglyceride membranes. gH values in gA channels are similar in ceramide and monoglyceride bilayers and in sphingomyelin and phospholipid membranes. It is concluded that phospho headgroups in membranes have significant effects on the rate of H+ transfer at the membrane gA channel/solution interfaces, enhancing the entry and exit rates of protons in channels.

Alternative ground states enable pathway switching in biological electron transfer

DOE PAGES

Abriata, Luciano A.; Alvarez-Paggi, Damian; Ledesma, Gabirela N.; ...

2012-10-10

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant CuA redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronicmore » wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. In conclusion, these findings suggest a unique role for alternative or “invisible” electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein–protein interactions and membrane potential may optimize and regulate electron–proton energy transduction.« less

Evidence for Coherent Transfer of para-Hydrogen-Induced Polarization at Low Magnetic Fields.

PubMed

Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Kaptein, Robert; Vieth, Hans-Martin; Ivanov, Konstantin L

2013-08-01

We have investigated the mechanism of para-hydrogen-induced polarization (PHIP) transfer from the original strongly aligned protons to other nuclei at low external magnetic fields. Although it is known that PHIP is efficiently transferred at low fields, the nature of the transfer mechanism, that is, coherent spin mixing or cross-relaxation, is not well established. Polarization transfer kinetics for individual protons of styrene was, for the first time, measured and modeled theoretically. Pronounced oscillations were observed indicating a coherent transfer mechanism. Spin coherences were excited by passing through an avoided level crossing of the nuclear spin energy levels. Transfer at avoided level crossings is selective with respect to spin order. Our work provides evidence that the coherent PHIP transfer mechanism is dominant at low magnetic fields.

Investigation of the antioxidant and radical scavenging activities of some phenolic Schiff bases with different free radicals.

PubMed

Marković, Zoran; Đorović, Jelena; Petrović, Zorica D; Petrović, Vladimir P; Simijonović, Dušica

2015-11-01

The antioxidant properties of some phenolic Schiff bases in the presence of different reactive particles such as (•)OH, (•)OOH, (CH2=CH-O-O(•)), and (-•)O2 were investigated. The thermodynamic values, ΔH BDE, ΔH IP, and ΔH PA, were used for this purpose. Three possible mechanisms for transfer of hydrogen atom, concerted proton-electron transfer (CPET), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) were considered. These mechanisms were tested in solvents of different polarity. On the basis of the obtained results it was shown that SET-PT antioxidant mechanism can be the dominant mechanism when Schiff bases react with radical cation, while SPLET and CPET are competitive mechanisms for radical scavenging of hydroxy radical in all solvents under investigation. Examined Schiff bases react with the peroxy radicals via SPLET mechanism in polar and nonpolar solvents. The superoxide radical anion reacts with these Schiff bases very slowly.

Entanglement and co-tunneling of two equivalent protons in hydrogen bond pairs

NASA Astrophysics Data System (ADS)

Smedarchina, Zorka; Siebrand, Willem; Fernández-Ramos, Antonio

2018-03-01

A theoretical study is reported of a system of two identical symmetric hydrogen bonds, weakly coupled such that the two mobile protons can move either separately (stepwise) or together (concerted). It is modeled by two equivalent quartic potentials interacting through dipolar and quadrupolar coupling terms. The tunneling Hamiltonian has two imaginary modes (reaction coordinates) and a potential with a single maximum that may turn into a saddle-point of second order and two sets of (inequivalent) minima. Diagonalization is achieved via a modified Jacobi-Davidson algorithm. From this Hamiltonian the mechanism of proton transfer is derived. To find out whether the two protons move stepwise or concerted, a new tool is introduced, based on the distribution of the probability flux in the dividing plane of the transfer mode. While stepwise transfer dominates for very weak coupling, it is found that concerted transfer (co-tunneling) always occurs, even when the coupling vanishes since the symmetry of the Hamiltonian imposes permanent entanglement on the motions of the two protons. We quantify this entanglement and show that, for a wide range of parameters of interest, the lowest pair of states of the Hamiltonian represents a perfect example of highly entangled quantum states in continuous variables. The method is applied to the molecule porphycene for which the observed tunneling splitting is calculated in satisfactory agreement with experiment, and the mechanism of double-proton tunneling is found to be predominantly concerted. We show that, under normal conditions, when they are in the ground state, the two porphycene protons are highly entangled, which may have interesting applications. The treatment also identifies the conditions under which such a system can be handled by conventional one-instanton techniques.

Absorption and Emission of the Apigenin and Luteolin Flavonoids: A TDDFT Investigation

NASA Astrophysics Data System (ADS)

Amat, Anna; Clementi, Catia; de Angelis, Filippo; Sgamellotti, Antonio; Fantacci, Simona

2009-09-01

The absorption and emission properties of the two components of the yellow color extracted from weld (Reseda luteola L.), apigenin and luteolin, have been extensively investigated by means of DFT and TDDFT calculations. Our calculations reproduce the absorption spectra of both flavonoids in good agreement with the experimental data and allow us to assign the transitions giving rise to the main spectral features. For apigenin, we have also computed the electronic spectrum of the monodeprotonated species, providing a rationale for the red-shift of the experimental spectrum with increasing pH. The fluorescence emission of both apigenin and luteolin has then been investigated. Excited-state TDDFT geometry optimizations have highlighted an excited-state intramolecular proton transfer (ESIPT) from the 5-hydroxyl to the 4-carbonyl oxygen of the substituted benzopyrone moiety. By computing the potential energy curves at the ground and excited states as a function of an approximate proton transfer coordinate for apigenin, we have been able to trace an ESIPT pathway and thus explain the double emission observed experimentally.

Reoriention of diprotonated DABCO (1,4-Diazabicyclo[2.2.2]octane) cation and proton transfer in organic ferroelectric adduct DABCO-2(2-Chlorobenzoic acid)

NASA Astrophysics Data System (ADS)

Asaji, Tetsuo

2018-05-01

Temperature dependences of 1H NMR as well as 35Cl NQR spin-lattice relaxation times T1 were investigated of a ferroelectric molecular adduct with Tc = 323 K, in which 1,4-diazabicyclo[2.2.2]octane (DABCO) is sandwiched between two 2-chlorobenzoic acid (2-ClBA). The NQR frequencies clearly show that proton transfer from 2-ClBA to DABCO is occurred and the molecular adduct consists of diprotonated DABCO cation and two 2-chlorobenzoate anions. The correlation time of reorientational motion of the diprotonated DABCO molecule was determined as a function of temperature. The activation energy Ea of the motion was estimated as 22 kJ mol-1 below Tc. The steep decrease of the NQR T1 with Ea = 50 kJ mol-1, observed above ca. 280 K in the ferroelectric phase, suggests a slow fluctuation of electric field gradient at chlorine nucleus.

Proton-coupled electron transfer in the catalytic cycle of Alcaligenes xylosoxidans copper-dependent nitrite reductase.

PubMed

Leferink, Nicole G H; Han, Cong; Antonyuk, Svetlana V; Heyes, Derren J; Rigby, Stephen E J; Hough, Michael A; Eady, Robert R; Scrutton, Nigel S; Hasnain, S Samar

2011-05-17

We demonstrated recently that two protons are involved in reduction of nitrite to nitric oxide through a proton-coupled electron transfer (ET) reaction catalyzed by the blue Cu-dependent nitrite reductase (Cu NiR) of Alcaligenes xylosoxidans (AxNiR). Here, the functionality of two putative proton channels, one involving Asn90 and the other His254, is studied using single (N90S, H254F) and double (N90S--H254F) mutants. All mutants studied are active, indicating that protons are still able to reach the active site. The H254F mutation has no effect on the catalytic activity, while the N90S mutation results in ~70% decrease in activity. Laser flash-photolysis experiments show that in H254F and wild-type enzyme electrons enter at the level of the T1Cu and then redistribute between the two Cu sites. Complete ET from T1Cu to T2Cu occurs only when nitrite binds at the T2Cu site. This indicates that substrate binding to T2Cu promotes ET from T1Cu, suggesting that the enzyme operates an ordered mechanism. In fact, in the N90S and N90S--H254F variants, where the T1Cu site redox potential is elevated by ∼60 mV, inter-Cu ET is only observed in the presence of nitrite. From these results it is evident that the Asn90 channel is the main proton channel in AxNiR, though protons can still reach the active site if this channel is disrupted. Crystallographic structures provide a clear structural rationale for these observations, including restoration of the proton delivery via a significant movement of the loop connecting the T1Cu ligands Cys130 and His139 that occurs on binding of nitrite. Notably, a role for this loop in facilitating interaction of cytochrome c(551) with Cu NiR has been suggested previously based on a crystal structure of the binary complex.

Fine Tuning of Redox Networks on Multiheme Cytochromes from Geobacter sulfurreducens Drives Physiological Electron/Proton Energy Transduction

PubMed Central

Morgado, Leonor; Dantas, Joana M.; Bruix, Marta; Londer, Yuri Y.; Salgueiro, Carlos A.

2012-01-01

The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e−/H+ coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e−/H+ transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e−/H+ transfer at the physiological pH range for cellular growth. PMID:22899897

Proton transfer complexes based on some π-acceptors having acidic protons with 3-amino-6-[2-(2-thienyl)vinyl]-1,2,4-triazin-5(4 H)-one donor: Synthesis and spectroscopic characterizations

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-05-01

Charge transfer complexes based on 3-amino-6-[2-(2-thienyl)vinyl]-1,2,4-triazin-5(4 H)-one (ArNH 2) organic basic donor and pi-acceptors having acidic protons such as picric acid (PiA), hydroquinone (Q(OH) 2) and 3,5-dinitrobenzene (DNB) have been synthesized and spectroscopically studied. The sbnd NH3+ ammonium ion was formed under the acid-base theory through proton transfer from an acidic to basic centers in all charge transfer complexes resulted. The values of formation constant ( KCT) and molar extinction coefficient ( ɛCT) which were estimated from the spectrophotometric studies have a dramatic effect for the charge transfer complexes with differentiation of pi-acceptors. For further studies the vibrational spectroscopy of the [( ArNH3+)(PiA -)] (1), [( ArNH3+)(Q (OH)2-)] (2) and [( ArNH3+)(DNB -)] (3) of (1:1) charge transfer complexes of (donor: acceptor) were characterized by elemental analysis, infrared spectra, Raman spectra, 1H and 13CNMR spectra. The experimental data of elemental analyses of the charge transfer complexes (1), (2) and (3) were in agreement with calculated data. The IR and Raman spectra of (1), (2) and (3) are indicated to the presence of bands around 3100 and 1600 cm -1 distinguish to sbnd NH3+. The thermogravimetric analysis (TG) and differential scanning calorimetry (DSC) techniques were performed to give knowledge about thermal stability behavior of the synthesized charge transfer complexes. The morphological features of start materials and charge transfer complexes were investigated using scanning electron microscopy (SEM) and optical microscopy.

Effects of membrane curvature and pH on proton pumping activity of single cytochrome bo3 enzymes.

PubMed

Li, Mengqiu; Khan, Sanobar; Rong, Honglin; Tuma, Roman; Hatzakis, Nikos S; Jeuken, Lars J C

2017-09-01

The molecular mechanism of proton pumping by heme-copper oxidases (HCO) has intrigued the scientific community since it was first proposed. We have recently reported a novel technology that enables the continuous characterisation of proton transport activity of a HCO and ubiquinol oxidase from Escherichia coli, cytochrome bo 3 , for hundreds of seconds on the single enzyme level (Li et al. J Am Chem Soc 137 (2015) 16055-16063). Here, we have extended these studies by additional experiments and analyses of the proton transfer rate as a function of proteoliposome size and pH at the N- and P-side of single HCOs. Proton transport activity of cytochrome bo 3 was found to decrease with increased curvature of the membrane. Furthermore, proton uptake at the N-side (proton entrance) was insensitive to pH between pH6.4-8.4, while proton release at the P-side had an optimum pH of ~7.4, suggesting that the pH optimum is related to proton release from the proton exit site. Our previous single-enzyme experiments identified rare, long-lived conformation states of cytochrome bo 3 where protons leak back under turn-over conditions. Here, we analyzed and found that ~23% of cytochrome bo 3 proteoliposomes show ΔpH half-lives below 50s after stopping turnover, while only ~5% of the proteoliposomes containing a non-pumping mutant, E286C cytochrome bo 3 exhibit such fast decays. These single-enzyme results confirm our model in which HCO exhibit heterogeneous pumping rates and can adopt rare leak states in which protons are able to rapidly flow back. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Measurement and investigation of proton irradiation-induced charge transfer inefficiency in PPD CIS at different integration times

NASA Astrophysics Data System (ADS)

Xue, Yuanyuan; Wang, Zujun; Zhang, Fengqi; Bian, Jingying; Yao, Zhibin; He, Baoping; Liu, Minbo; Sheng, Jiangkun; Ma, Wuying; Dong, Guantao; Jin, Junshan

2018-04-01

Charge transfer inefficiency (CTI) is an important parameter for photodiode (PPD) CMOS image sensors (CISs). A test system was built and used to measure the CTI of PPD CIS devices at different integration times. The radiation effects of 3 MeV and 10 MeV protons on the CTI were investigated. The experiments were carried out at the EN Tandem Van de Graaff accelerator at proton fluences in the range 1010 to 1011 p/cm2. The CTI was measured within the 2 h following proton radiations. The dependence of CTI on integration time, proton energy and fluence were investigated. The CTI was observed to increase after proton irradiation: with the effect of irradiation with 3 MeV proton being more severe than that with 10 MeV protons. The CTI was also observed to decrease with increasing integration time, which is thought to be related to the charge density in the space charge region (SCR) of the CIS devices. This work has provided a simple method to measure the CTI and helped us to understand proton radiation effects on the CTI of PPD CISs.

Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein

PubMed Central

Landon, Céline; Berthault, Patrick; Vovelle, Françoise; Desvaux, Hervé

2001-01-01

Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas–protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by ∼12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure. PMID:11274467

Six-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Yuewei; Gralla, Edith Butler; Schumacher, Mikhail

Reduction of superoxide (O{sub 2}{sup -}) by manganese-containing superoxide dismutase occurs through either a 'prompt protonation' pathway, or an 'inner-sphere' pathway, with the latter leading to formation of an observable Mn-peroxo complex. We recently reported that wild-type (WT) manganese superoxide dismutases (MnSODs) from Saccharomyces cerevisiae and Candida albicans are more gated toward the 'prompt protonation' pathway than human and bacterial MnSODs and suggested that this could result from small structural changes in the second coordination sphere of manganese. We report here that substitution of a second-sphere residue, Tyr34, by phenylalanine (Y34F) causes the MnSOD from S. cerevisiae to react exclusivelymore » through the 'inner-sphere' pathway. At neutral pH, we have a surprising observation that protonation of the Mn-peroxo complex in the mutant yeast enzyme occurs through a fast pathway, leading to a putative six-coordinate Mn3+ species, which actively oxidizes O{sub 2}{sup -} in the catalytic cycle. Upon increasing pH, the fast pathway is gradually replaced by a slow proton-transfer pathway, leading to the well-characterized five-coordinate Mn{sup 3+}. We here propose and compare two hypothetical mechanisms for the mutant yeast enzyme, diffeeing in the structure of the Mn-peroxo complex yet both involving formation of the active six-coordinate Mn{sup 3+} and proton transfer from a second-sphere water molecule, which has substituted for the -OH of Tyr34, to the Mn-peroxo complex. Because WT and the mutant yeast MnSOD both rest in the 2+ state and become six-coordinate when oxidized up from Mn{sup 2+}, six-coordinate Mn{sup 3+} species could also actively function in the mechanism of WT yeast MnSODs.« less

Spin-locking vs. chemical exchange saturation transfer MRI for investigating chemical exchange process between water and labile metabolite protons

PubMed Central

Jin, Tao; Autio, Joonas; Obata, Takayuki; Kim, Seong-Gi

2010-01-01

Chemical exchange saturation transfer (CEST) and spin-locking (SL) experiments were both able to probe the exchange process between protons of non-equivalent chemical environments. To compare the characteristics of the CEST and SL approaches in the study of chemical exchange effects, we performed CEST and SL experiments at varied pH and concentrated metabolites with exchangeable amide, amine, and hydroxyl protons at 9.4 T. Our results show that: i) On-resonance SL is most sensitive to chemical exchanges in the intermediate exchange regime and is able to detect hydroxyl and amine protons on a millimolar concentration scale. Off-resonance SL and CEST approaches are sensitive to slow-exchanging protons when an optimal SL or saturation pulse power matches the exchanging rate, respectively. ii) Offset frequency-dependent SL and CEST spectra are very similar, and can be explained well with an SL model recently developed by Trott and Palmer. iii) The exchange rate and population of metabolite protons can be determined from offset-dependent SL or CEST spectra or from on-resonance SL relaxation dispersion measurements. iv) The asymmetry of the magnetization transfer ratio (MTRasym) is highly dependent on the choice of saturation pulse power. In the intermediate exchange regime, MTRasym becomes complicated and should be interpreted with care. PMID:21500270

Two-proton transfer reactions on even Ni and Zn isotopes

NASA Astrophysics Data System (ADS)

Boucenna, A.; Kraus, L.; Linck, I.; Chan, Tsan Ung

1990-10-01

New levels strongly excited by 112-MeV 12C ions on even Ni and Zn isotopes are Jπ assigned on kinematical and geometrical arguments, crude shell-model calculations, and distorted-wave Born approximation angular-distribution analysis. These tentative assignments are supported by the Bansal-French model. Because of the contribution of additional collective effects, the two-proton transfer reaction spectra are less selectively fed than those obtained with the analogous two-neutron transfer reactions induced on the same targets in a similar energy range.

Polarization transfer observables in elastic electron-proton scattering at Q 2 = 2.5 , 5.2, 6.8, and 8.5   GeV 2

DOE PAGES

Puckett, Andrew J. R.; Brash, E. J.; Jones, M. K.; ...

2017-11-06

In this paper, interest in the behavior of nucleon electromagnetic form factors at large momentum transfers has steadily increased since the discovery, using polarization observables, of the rapid decrease of the ratio G p E/G p M of the proton's electric and magnetic form factors for momentum transfers Q 2 ≳ 1 GeV 2, in strong disagreement with previous extractions of this ratio using the traditional Rosenbluth separation technique.

Polarization transfer observables in elastic electron-proton scattering at Q 2 = 2.5 , 5.2, 6.8, and 8.5   GeV 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puckett, Andrew J. R.; Brash, E. J.; Jones, M. K.

In this paper, interest in the behavior of nucleon electromagnetic form factors at large momentum transfers has steadily increased since the discovery, using polarization observables, of the rapid decrease of the ratio G p E/G p M of the proton's electric and magnetic form factors for momentum transfers Q 2 ≳ 1 GeV 2, in strong disagreement with previous extractions of this ratio using the traditional Rosenbluth separation technique.

Space Radiation Risk Assessment for Future Lunar Missions

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee Y.; Ponomarev, Artem; Atwell, Bill; Cucinotta, Francis A.

2007-01-01

For lunar exploration mission design, radiation risk assessments require the understanding of future space radiation environments in support of resource management decisions, operational planning, and a go/no-go decision. The future GCR flux was estimated as a function of interplanetary deceleration potential, which was coupled with the estimated neutron monitor rate from the Climax monitor using a statistical model. A probability distribution function for solar particle event (SPE) occurrence was formed from proton fluence measurements of SPEs occurred during the past 5 solar cycles (19-23). Large proton SPEs identified from impulsive nitrate enhancements in polar ice for which the fluences are greater than 2 10(exp 9) protons/sq cm for energies greater than 30 MeV, were also combined to extend the probability calculation for high level of proton fluences. The probability with which any given proton fluence level of a SPE will be exceeded during a space mission of defined duration was then calculated. Analytic energy spectra of SPEs at different ranks of the integral fluences were constructed over broad energy ranges extending out to GeV, and representative exposure levels were analyzed at those fluences. For the development of an integrated strategy for radiation protection on lunar exploration missions, effective doses at various points inside a spacecraft were calculated with detailed geometry models representing proposed transfer vehicle and habitat concepts. Preliminary radiation risk assessments from SPE and GCR were compared for various configuration concepts of radiation shelter in exploratory-class spacecrafts.

Measurement of transparency ratios for protons from short-range correlated pairs

NASA Astrophysics Data System (ADS)

Hen, O.; Hakobyan, H.; Shneor, R.; Piasetzky, E.; Weinstein, L. B.; Brooks, W. K.; May-Tal Beck, S.; Gilad, S.; Korover, I.; Beck, A.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anefalos Pereira, S.; Arrington, J. R.; Baghdasaryan, H.; Ball, J.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Bono, J.; Boiarinov, S.; Briscoe, W. J.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fleming, J. A.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Griffioen, K. A.; Guo, L.; Hafidi, K.; Harrison, N.; Heddle, D.; Hicks, K.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jo, H. S.; Joo, K.; Keller, D.; Khandaker, M.; Khetarpal, P.; Kim, A.; Klein, F. J.; Koirala, S.; Kubarovsky, A.; Kubarovsky, V.; Kuhn, S. E.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Martinez, D.; Mayer, M.; McKinnon, B.; Mineeva, T.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munevar, E.; Munoz Camacho, C.; Mustapha, B.; Nadel-Turonski, P.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Park, S.; Pasyuk, E.; Phelps, E.; Phillips, J. J.; Pisano, S.; Pivnyuk, N.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Raue, B. A.; Rimal, D.; Ripani, M.; Ritchie, B. G.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Schott, D.; Schumacher, R. A.; Seraydaryan, H.; Sharabian, Y. G.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S. S.; Stepanyan, S.; Strauch, S.; Taiuti, M.; Tang, W.; Taylor, C. E.; Tian, Ye; Tkachenko, S.; Ungaro, M.; Vernarsky, B.; Vlassov, A.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Wood, M. H.; Zachariou, N.; Zana, L.; Zhang, J.; Zheng, X.; Zonta, I.

2013-05-01

Nuclear transparency, Tp (A), is a measure of the average probability for a struck proton to escape the nucleus without significant re-interaction. Previously, nuclear transparencies were extracted for quasi-elastic A (e ,e‧ p) knockout of protons with momentum below the Fermi momentum, where the spectral functions are well known. In this Letter we extract a novel observable, the transparency ratio, Tp (A) /Tp(12 C), for knockout of high-missing-momentum protons from the breakup of short-range correlated pairs (2N-SRC) in Al, Fe and Pb nuclei relative to C. The ratios were measured at momentum transfer Q2 ⩾ 1.5(GeV /c) 2 and xB ⩾ 1.2 where the reaction is expected to be dominated by electron scattering from 2N-SRC. The transparency ratios of the knocked-out protons coming from 2N-SRC breakup are 20-30% lower than those of previous results for low missing momentum. They agree with Glauber calculations and agree with renormalization of the previously published transparencies as proposed by recent theoretical investigations. The new transparencies scale as A - 1 / 3, which is consistent with dominance of scattering from nucleons at the nuclear surface.

Protomers of benzocaine: solvent and permittivity dependence.

PubMed

Warnke, Stephan; Seo, Jongcheol; Boschmans, Jasper; Sobott, Frank; Scrivens, James H; Bleiholder, Christian; Bowers, Michael T; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin; von Helden, Gert

2015-04-01

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid that finds an application as a local anesthetic, is found to adopt in its protonated form at least two populations of distinct structures in the gas phase, and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization process. Here, we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry to yield gas-phase IR spectra of simultaneously m/z and drift-time-resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species: the N- and O-protonated forms. Density functional theory calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution-phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation have been suggested.

Proton radiation damage experiment on P-Channel CCD for an X-ray CCD camera onboard the ASTRO-H satellite

NASA Astrophysics Data System (ADS)

Mori, Koji; Nishioka, Yusuke; Ohura, Satoshi; Koura, Yoshiaki; Yamauchi, Makoto; Nakajima, Hiroshi; Ueda, Shutaro; Kan, Hiroaki; Anabuki, Naohisa; Nagino, Ryo; Hayashida, Kiyoshi; Tsunemi, Hiroshi; Kohmura, Takayoshi; Ikeda, Shoma; Murakami, Hiroshi; Ozaki, Masanobu; Dotani, Tadayasu; Maeda, Yukie; Sagara, Kenshi

2013-12-01

We report on a proton radiation damage experiment on P-channel CCD newly developed for an X-ray CCD camera onboard the ASTRO-H satellite. The device was exposed up to 109 protons cm-2 at 6.7 MeV. The charge transfer inefficiency (CTI) was measured as a function of radiation dose. In comparison with the CTI currently measured in the CCD camera onboard the Suzaku satellite for 6 years, we confirmed that the new type of P-channel CCD is radiation tolerant enough for space use. We also confirmed that a charge-injection technique and lowering the operating temperature efficiently work to reduce the CTI for our device. A comparison with other P-channel CCD experiments is also discussed. We performed a proton radiation damage experiment on a new P-channel CCD. The device was exposed up to 109 protons cm-2 at 6.7 MeV. We confirmed that it is radiation tolerant enough for space use. We confirmed that a charge-injection technique reduces the CTI. We confirmed that lowering the operating temperature also reduces the CTI.

A-Site Cation Substitutions in Strained Y-Doped BaZrO 3 Multilayer Films Leading to Fast Proton Transport Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aruta, Carmela; Han, Chu; Zhou, Si

Proton-conducting perovskite oxides form a class of solid electrolytes for novel electrochemical devices operating at moderate temperatures. Here, we use hard X-ray photoelectron spectroscopy, scanning transmission electron microscopy, and density functional theory calculations to investigate the structure and elucidate the origin of the fast proton transport properties of strained ultrathin films of Y-doped BaZrO 3 grown by pulsed lased deposition on NdGaO 3. Our study shows that our BaZr 0.8Y 0.2O 3 films incorporate a significant amount of Y dopants, and to a lesser extent also Zr ions, substituting for Ba 2+, and that these substitutional defects agglomerate forming columnarmore » regions crossing vertically from the surface to the interface the entire film. In conclusion, our calculations also show that, in regions rich in Y substitutions for both Zr and Ba, the proton transfer process involves nearly zero-energy barriers, indicating that A-site cation substitutions by Y lead to fast transport pathways and hence are responsible for the previously observed enhanced values of the proton conductivity of these perovskite oxide films.« less

Glycerol dehydratation by the B12-independent enzyme may not involve the migration of a hydroxyl group: a computational study.

PubMed

Feliks, Mikolaj; Ullmann, G Matthias

2012-06-21

A combination of continuum electrostatic and density functional calculations has been employed to study the mechanism of the B(12)-independent glycerol dehydratase, a novel glycyl-radical enzyme involved in the microbial conversion of glycerol to 3-hydroxylpropionaldehyde. The calculations indicate that the dehydratation of glycerol by the B(12)-independent enzyme does not need to involve a mechanistically complicated migration of the middle hydroxyl group to one of the two terminal positions of a molecule, as previously suggested. Instead, the reaction can proceed in three elementary steps. First, a radical transfer from the catalytically active Cys433 to the ligand generates a substrate-related intermediate. Second, a hydroxyl group splits off at the middle position of the ligand and is protonated by the neighboring His164 to form a water molecule. The other active site residue Glu435 accepts a proton from one of the terminal hydroxyl groups of the ligand and a C═O double bond is created. Third, the reaction is completed by a radical back transfer from the product-related intermediate to Cys433. On the basis of our calculations, the catalytic functions of the active site residues have been suggested. Cys433 is a radical relay site; His164 and Glu435 make up a proton accepting/donating system; Asn156, His281, and Asp447 form a network of hydrogen bonds responsible for the electrostatic stabilization of the transition state. A synergistic participation of these residues in the reaction seems to be crucial for the catalysis.

SU-E-T-549: Modeling Relative Biological Effectiveness of Protons for Radiation Induced Brain Necrosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mirkovic, D; Peeler, C; Grosshans, D

Purpose: To develop a model of the relative biological effectiveness (RBE) of protons as a function of dose and linear energy transfer (LET) for induction of brain necrosis using clinical data. Methods: In this study, treatment planning information was exported from a clinical treatment planning system (TPS) and used to construct a detailed Monte Carlo model of the patient and the beam delivery system. The physical proton dose and LET were computed in each voxel of the patient volume using Monte Carlo particle transport. A follow-up magnetic resonance imaging (MRI) study registered to the treatment planning CT was used tomore » determine the region of the necrosis in the brain volume. Both, the whole brain and the necrosis volumes were segmented from the computed tomography (CT) dataset using the contours drawn by a physician and the corresponding voxels were binned with respect to dose and LET. The brain necrosis probability was computed as a function of dose and LET by dividing the total volume of all necrosis voxels with a given dose and LET with the corresponding total brain volume resulting in a set of NTCP-like curves (probability as a function of dose parameterized by LET). Results: The resulting model shows dependence on both dose and LET indicating the weakness of the constant RBE model for describing the brain toxicity. To the best of our knowledge the constant RBE model is currently used in all clinical applications which may Result in increased rate of brain toxicities in patients treated with protons. Conclusion: Further studies are needed to develop more accurate brain toxicity models for patients treated with protons and other heavy ions.« less

The matrix effect in secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Seah, M. P.; Shard, A. G.

2018-05-01

Matrix effects in the secondary ion mass spectrometry (SIMS) of selected elemental systems have been analyzed to investigate the applicability of a mathematical description of the matrix effect, called here the charge transfer (CT) model. This model was originally derived for proton exchange and organic positive secondary ions, to characterise the enhancement or suppression of intensities in organic binary systems. In the systems considered in this paper protons are specifically excluded, which enables an assessment of whether the model applies for electrons as well. The present importance is in organic systems but, here we analyse simpler inorganic systems. Matrix effects in elemental systems cannot involve proton transfer if there are no protons present but may be caused by electron transfer and so electron transfer may also be involved in the matrix effects for organic systems. There are general similarities in both the magnitudes of the ion intensities as well as the matrix effects for both positive and negative secondary ions in both systems and so the CT model may be more widely applicable. Published SIMS analyses of binary elemental mixtures are analyzed. The data of Kim et al., for the Pt/Co system, provide, with good precision, data for such a system. This gives evidence for the applicability of the CT model, where electron, rather than proton, transfer is the matrix enhancing and suppressing mechanism. The published data of Prudon et al., for the important Si/Ge system, provides further evidence for the effects for both positive and negative secondary ions and allows rudimentary rules to be developed for the enhancing and suppressing species.

Photo-induced water oxidation at the aqueous GaN (101¯0) interface: Deprotonation kinetics of the first proton-coupled electron-transfer step

DOE PAGES

Ertem, Mehmed Z.; Kharche, Neerav; Batista, Victor S.; ...

2015-03-12

Photoeclectrochemical water splitting plays a key role in a promising path to the carbon-neutral generation of solar fuels. Wurzite GaN and its alloys ( e.g., GaN/ZnO and InGaN) are demonstrated photocatalysts for water oxidation, and they can drive the overall water splitting reaction when coupled with co-catalysts for proton reduction. In the present work, we investigate the water oxidation mechanism on the prototypical GaN (101¯0) surface using a combined ab initio molecular dynamics and molecular cluster model approach taking into account the role of water dissociation and hydrogen bonding within the first solvation shell of the hydroxylated surface. The investigationmore » of free-energy changes for the four proton-coupled electron-transfer (PCET) steps of the water oxidation mechanism shows that the first PCET step for the conversion of –Ga-OH to –Ga-O˙⁻ requires the highest energy input. We further examine the sequential PCETs, with the proton transfer (PT) following the electron transfer (ET), and find that photo-generated holes localize on surface –NH sites is thermodynamically more favorable than –OH sites. However, proton transfer from –OH sites with subsequent localization of holes on oxygen atoms is kinetically favored owing to hydrogen bonding interactions at the GaN (101¯0)–water interface. We find that the deprotonation of surface –OH sites is the limiting factor for the generation of reactive oxyl radical ion intermediates and consequently for water oxidation.« less

Proton radiation-induced miRNA signatures in mouse blood: Characterization and comparison with 56Fe-ion and gamma radiation

PubMed Central

Templin, Thomas; Young, Erik F.; Smilenov, Lubomir B.

2013-01-01

Purpose Previously, we showed that microRNA (miRNA) signatures derived from the peripheral blood of mice are highly specific for both radiation energy (γ-rays or high linear energy transfer [LET] 56Fe ions) and radiation dose. Here, we investigate to what extent miRNA expression signatures derived from mouse blood can be used as biomarkers for exposure to 600 MeV proton radiation. Materials and methods We exposed mice to 600 MeV protons, using doses of 0.5 or 1.0 Gy, isolated total RNA at 6 h or 24 h after irradiation, and used quantitative real-time polymerase chain reaction (PCR) to determine the changes in miRNA expression. Results A total of 26 miRNA were differentially expressed after proton irradiation, in either one (77%) or multiple conditions (23%). Statistical classifiers based on proton, γ, and 56Fe-ion miRNA expression signatures predicted radiation type and proton dose with accuracies of 81% and 88%, respectively. Importantly, gene ontology analysis for proton-irradiated cells shows that genes targeted by radiation-induced miRNA are involved in biological processes and molecular functions similar to those controlled by miRNA in γ ray- and 56Fe-irradiated cells. Conclusions Mouse blood miRNA signatures induced by proton, γ, or 56Fe irradiation are radiation type- and dose-specific. These findings underline the complexity of the miRNA-mediated radiation response. PMID:22551419

High-level ab initio potential energy surface and dynamics of the F– + CH3I SN2 and proton-transfer reactions† †Electronic supplementary information (ESI) available: Benchmark classical and adiabatic relative energies (Table S1), vibrational frequencies of all the stationary points (Tables S2 and S3), direct/indirect trajectory separation function parameters (Table S4), entrance-channel potential (Fig. S1), structures of the minima and saddle points corresponding to the abstraction channel (Fig. S2), reaction probabilities (Fig. S3), trajectory integration time distributions (Fig. S4), trajectory integration time vs. I– velocity distributions (Fig. S5), and mechanism-specific reaction probabilities (Fig. S6). See DOI: 10.1039/c7sc00033b Click here for additional data file.

PubMed Central

Olasz, Balázs; Szabó, István

2017-01-01

Bimolecular nucleophilic substitution (SN2) and proton transfer are fundamental processes in chemistry and F– + CH3I is an important prototype of these reactions. Here we develop the first full-dimensional ab initio analytical potential energy surface (PES) for the F– + CH3I system using a permutationally invariant fit of high-level composite energies obtained with the combination of the explicitly-correlated CCSD(T)-F12b method, the aug-cc-pVTZ basis, core electron correlation effects, and a relativistic effective core potential for iodine. The PES accurately describes the SN2 channel producing I– + CH3F via Walden-inversion, front-side attack, and double-inversion pathways as well as the proton-transfer channel leading to HF + CH2I–. The relative energies of the stationary points on the PES agree well with the new explicitly-correlated all-electron CCSD(T)-F12b/QZ-quality benchmark values. Quasiclassical trajectory computations on the PES show that the proton transfer becomes significant at high collision energies and double-inversion as well as front-side attack trajectories can occur. The computed broad angular distributions and hot internal energy distributions indicate the dominance of indirect mechanisms at lower collision energies, which is confirmed by analyzing the integration time and leaving group velocity distributions. Comparison with available crossed-beam experiments shows usually good agreement. PMID:28507692

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus

PubMed Central

Khurana, Ekta; Peraro, Matteo Dal; DeVane, Russell; Vemparala, Satyavani; DeGrado, William F.; Klein, Michael L.

2009-01-01

The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion is essential for the uncoating and further replication of the viral genetic material. The x-ray crystal [Stouffer AL, et al. (2008) Nature 451:596–599] and solution NMR [Schnell JR, Chou JJ (2008) Nature 451:591–595] structures of the transmembrane region of the M2 homo-tetrameric bundle both revealed pores with narrow constrictions at one end, leaving a question as to how protons enter the channel. His-37, which is essential for proton-gating and selective conduction of protons, lies in the pore of the crystallographic and NMR structures. Here, we explore the different protonation states of the His-37 residues of the M2 bundle in a bilayer using molecular dynamics (MD) simulations. When the His-37 residues are neutral, the protein prefers an Openout-Closedin conformation in which the channel is open to the environment on the outside of the virus but closed to the interior environment of the virus. Diffusion of protons into the channel from the outside of the virus and protonation of His-37 residues in the tetramer stabilizes an oppositely gated Closedout-Openin conformation. Thus, protons might be conducted through a transporter-like mechanism, in which the protein alternates between Openout-Closedin and Closedout-Openin conformations, and His-37 is protonated/deprotonated during each turnover. The transporter-like mechanism is consistent with the known properties of the M2 bundle, including its relatively low rate of proton flux and its strong rectifying behavior. PMID:19144924

Analytical linear energy transfer model including secondary particles: calculations along the central axis of the proton pencil beam

NASA Astrophysics Data System (ADS)

Marsolat, F.; De Marzi, L.; Pouzoulet, F.; Mazal, A.

2016-01-01

In proton therapy, the relative biological effectiveness (RBE) depends on various types of parameters such as linear energy transfer (LET). An analytical model for LET calculation exists (Wilkens’ model), but secondary particles are not included in this model. In the present study, we propose a correction factor, L sec, for Wilkens’ model in order to take into account the LET contributions of certain secondary particles. This study includes secondary protons and deuterons, since the effects of these two types of particles can be described by the same RBE-LET relationship. L sec was evaluated by Monte Carlo (MC) simulations using the GATE/GEANT4 platform and was defined by the ratio of the LET d distributions of all protons and deuterons and only primary protons. This method was applied to the innovative Pencil Beam Scanning (PBS) delivery systems and L sec was evaluated along the beam axis. This correction factor indicates the high contribution of secondary particles in the entrance region, with L sec values higher than 1.6 for a 220 MeV clinical pencil beam. MC simulations showed the impact of pencil beam parameters, such as mean initial energy, spot size, and depth in water, on L sec. The variation of L sec with these different parameters was integrated in a polynomial function of the L sec factor in order to obtain a model universally applicable to all PBS delivery systems. The validity of this correction factor applied to Wilkens’ model was verified along the beam axis of various pencil beams in comparison with MC simulations. A good agreement was obtained between the corrected analytical model and the MC calculations, with mean-LET deviations along the beam axis less than 0.05 keV μm-1. These results demonstrate the efficacy of our new correction of the existing LET model in order to take into account secondary protons and deuterons along the pencil beam axis.

Real-time observation of intramolecular proton transfer in the electronic ground state of chloromalonaldehyde: an ab initio study of time-resolved photoelectron spectra.

PubMed

do N Varella, Márcio T; Arasaki, Yasuki; Ushiyama, Hiroshi; Takatsuka, Kazuo; Wang, Kwanghsi; McKoy, Vincent

2007-02-07

The authors report on studies of time-resolved photoelectron spectra of intramolecular proton transfer in the ground state of chloromalonaldehyde, employing ab initio photoionization matrix elements and effective potential surfaces of reduced dimensionality, wherein the couplings of proton motion to the other molecular vibrational modes are embedded by averaging over classical trajectories. In the simulations, population is transferred from the vibrational ground state to vibrationally hot wave packets by pumping to an excited electronic state and dumping with a time-delayed pulse. These pump-dump-probe simulations demonstrate that the time-resolved photoelectron spectra track proton transfer in the electronic ground state well and, furthermore, that the geometry dependence of the matrix elements enhances the tracking compared with signals obtained with the Condon approximation. Photoelectron kinetic energy distributions arising from wave packets localized in different basins are also distinguishable and could be understood, as expected, on the basis of the strength of the optical couplings in different regions of the ground state potential surface and the Franck-Condon overlaps of the ground state wave packets with the vibrational eigenstates of the ion potential surface.

Synthesis, spectroscopic characterization and structural studies of a new proton transfer (H-bonded) complex of o-phenylenediamine with L-tartaric acid

NASA Astrophysics Data System (ADS)

Khan, Ishaat M.; Ahmad, Afaq

2013-10-01

A proton transfer or H-bonded (CT) complex of o-phenylenediamine (OPD) as donor with L-tartaric acid (TART) as acceptor was synthesized and characterized by spectral techniques such as FTIR, 1H NMR, elemental analysis, TGA-TDA, X-ray crystallography and spectrophotometric studies. The structural investigations exhibit that the cation [OPD+] and anion [TART-] are linked together through strong N+-H⋯O- type hydrogen bonds due to transfer of proton from acceptor to donor. Formed H-bonded complex exhibits well resolved proton transfer bands in the regions where neither donor nor acceptor has any absorption. The stoichiometry of the H-bonded complex (HBC) was found to be 1:1, determined by straight line methods. Spectrophotometric studies have been performed at room temperature and Benesi-Hildebrand equation was used to determine formation constant (KCT), molar extinction coefficient (ɛCT) and also transition energy (ECT) of the H-bonded complex. Spectrophotomeric and crystallographic studies have ascertained the formation of 1:1 H-bonded complex. Thermal analysis (TGA-DTA) was also used to confirm the thermal fragmentation and the stability of the synthesized H-bonded complex.

Crystal structure of acetanilide at 15 and 295 K by neutron diffraction. Lack of evidence for proton transfer along the N-H...O hydrogen bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, S.W.; Eckert, J.; Barthes, M.

1995-11-02

The crystal structure of acetanilide C{sub 8}H{sub 9}NO, M{sub r} = 135.17, orthorhombic, space group Pbca, Z=8, has been determined from neutron diffraction data at 15 and 295 K. The crystal data obtained are presented. This new investigation of the structure of acetanilide has been undertaken in order to assess a recent suggestion that confirmational substates in the amide proton position may be responsible for the vibrational anomalies. We found no evidence for multiple conformations or transfer along the N-H...O hydrogen bond of the amide proton at either temperature. However the intramolecular O...H6 distance from O to the nearest phenylmore » ring proton is unusually short and the amide proton has relatively close contacts with one of the phenyl and one of the methyl protons, which may well affect the vibrational parameters of the respective molecular groups. 44 refs., 6 figs., 5 tabs.« less

Effect of protons on the redox chemistry of colloidal zinc oxide nanocrystals.

PubMed

Valdez, Carolyn N; Braten, Miles; Soria, Ashley; Gamelin, Daniel R; Mayer, James M

2013-06-12

Electron transfer (ET) reactions of colloidal 3-5 nm diameter ZnO nanocrystals (NCs) with molecular reagents are explored in aprotic solvents. Addition of an excess of the one-electron reductant Cp*2Co (Cp* = pentamethylcyclopentadienyl) gives NCs that are reduced by up to 1-3 electrons per NC. Protons can be added stoichiometrically to the NCs by either a photoreduction/oxidation sequence or by addition of acid. The added protons facilitate the reduction of the ZnO NCs. In the presence of acid, NC reduction by Cp*2Co can be increased to over 15 electrons per NC. The weaker reductant Cp*2Cr transfers electrons only to ZnO NCs in the presence of protons. Cp*2M(+) counterions are much less effective than protons at stabilizing reduced NCs. With excess Cp*2Co or Cp*2Cr, the extent of reduction increases roughly linearly with the number of protons added. Some of the challenges in understanding these results are discussed.

Minimal proton channel enables H2 oxidation and production with a water-soluble nickel-based catalyst.

PubMed

Dutta, Arnab; Lense, Sheri; Hou, Jianbo; Engelhard, Mark H; Roberts, John A S; Shaw, Wendy J

2013-12-11

Hydrogenase enzymes use first-row transition metals to interconvert H2 with protons and electrons, reactions that are important for the storage and recovery of energy from intermittent sources such as solar, hydroelectric, and wind. Here we present Ni(P(Cy)2N(Gly)2)2, a water-soluble molecular electrocatalyst with the amino acid glycine built into the diphosphine ligand framework. Proton transfer between the outer coordination sphere carboxylates and the second coordination sphere pendant amines is rapid, as observed by cyclic voltammetry and FTIR spectroscopy, indicating that the carboxylate groups may participate in proton transfer during catalysis. This complex oxidizes H2 (1-33 s(-1)) at low overpotentials (150-365 mV) over a range of pH values (0.1-9.0) and produces H2 under identical solution conditions (>2400 s(-1) at pH 0.5). Enzymes employ proton channels for the controlled movement of protons over long distances-the results presented here demonstrate the effects of a simple two-component proton channel in a synthetic molecular electrocatalyst.

Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

PubMed Central

Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

2015-01-01

Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein

PubMed Central

Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Muñoz, Victor

2013-01-01

A battery of thermodynamic, kinetic, and structural approaches has indicated that the small α-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ∼7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ∼15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any given condition because the native structure is less stable for the protonated form. PMID:24205082

Mechanisms and rates of proton transfer to coordinated carboxydithioates: studies on [Ni(S2CR){PhP(CH2CH2PPh2)2}](+) (R = Me, Et, Bu(n) or Ph).

PubMed

Alwaaly, Ahmed; Clegg, William; Henderson, Richard A; Probert, Michael R; Waddell, Paul G

2015-02-21

The complexes [Ni(S2CR)(triphos)]BPh4 (R = Me, Et, Bu(n) or Ph; triphos = PhP{CH2CH2PPh2}2) have been prepared and characterised. X-ray crystallography (for R = Et, Ph, C6H4Me-4, C6H4OMe-4 and C6H4Cl-4) shows that the geometry of the five-coordinate nickel in the cation is best described as distorted trigonal bipyramidal, containing a bidentate carboxydithioate ligand with the two sulfur atoms spanning axial and equatorial sites, the other axial site being occupied by the central phosphorus of triphos. The reactions of [Ni(S2CR)(triphos)](+) with mixtures of HCl and Cl(-) in MeCN to form equilibrium solutions containing [Ni(SH(S)CR)(triphos)](2+) have been studied using stopped-flow spectrophotometry. The kinetics show that proton transfer is slower than the diffusion-controlled limit and involves at least two coupled equilibria. The first step involves the rapid association between [Ni(S2CR)(triphos)](+) and HCl to form the hydrogen-bonded precursor, {[Ni(S2CR)(triphos)](+)HCl} (K) and this is followed by the intramolecular proton transfer (k) to produce [Ni(SH(S)CR)(triphos)](2+). In the reaction of [Ni(S2CMe)(triphos)](+) the rate law is consistent with the carboxydithioate ligand undergoing chelate ring-opening after protonation. It seems likely that chelate ring-opening occurs for all [Ni(S2CR)(triphos)](+), but only with [Ni(S2CMe)(triphos)](+) is the protonation step sufficiently fast that chelate ring-opening is rate-limiting. With all other systems, proton transfer is rate-limiting. DFT calculations indicate that protonation can occur at either sulfur atom, but only protonation at the equatorial sulfur results in chelate ring-opening. The ways in which protonation of either sulfur atom complicates the analyses and interpretation of the kinetics are discussed.

Role of Amine Functionality for CO2 Chemisorption on Silica.

PubMed

Hahn, Maximilian W; Jelic, Jelena; Berger, Edith; Reuter, Karsten; Jentys, Andreas; Lercher, Johannes A

2016-03-03

The mechanism of CO2 adsorption on primary, secondary, and bibasic aminosilanes synthetically functionalized in porous SiO2 was qualitatively and quantitatively investigated by a combination of IR spectroscopy, thermogravimetry, and quantum mechanical modeling. The mode of CO2 adsorption depends particularly on the nature of the amine group and the spacing between the aminosilanes. Primary amines bonded CO2 preferentially through the formation of intermolecular ammonium carbamates, whereas CO2 was predominantly stabilized as carbamic acid, when interacting with secondary amines. Ammonium carbamate formation requires the transfer of the carbamic acid proton to a second primary amine group to form the ammonium ion and hence two (primary) amine groups are required to bind one CO2 molecule. The higher base strength of secondary amines enables the stabilization of carbamic acid, which is thereby hindered to interact further with nearby amine functions, because their association with Si-OH groups (either protonation or hydrogen bonding) does not allow further stabilization of carbamic acid as carbamate. Steric hindrance of the formation of intermolecular ammonium carbamates leads to higher uptake capacities for secondary amines functionalized in porous SiO2 at higher amine densities. In aminosilanes possessing a primary and a secondary amine group, the secondary amine group tends to be protonated by Si-OH groups and therefore does not substantially interact with CO2.

Watching proton transfer in real time: Ultrafast photoionization-induced proton transfer in phenol-ammonia complex cation.

PubMed

Shen, Ching-Chi; Tsai, Tsung-Ting; Wu, Jun-Yi; Ho, Jr-Wei; Chen, Yi-Wei; Cheng, Po-Yuan

2017-10-28

In this paper, we give a full account of our previous work [C. C. Shen et al., J. Chem. Phys. 141, 171103 (2014)] on the study of an ultrafast photoionization-induced proton transfer (PT) reaction in the phenol-ammonia (PhOH-NH 3 ) complex using ultrafast time-resolved ion photofragmentation spectroscopy implemented by the photoionization-photofragmentation pump-probe detection scheme. Neutral PhOH-NH 3 complexes prepared in a free jet are photoionized by femtosecond 1 + 1 resonance-enhanced multiphoton ionization via the S 1 state. The evolving cations are then probed by delayed pulses that result in ion fragmentation, and the ionic dynamics is followed by measuring the parent-ion depletion as a function of the pump-probe delay time. By comparing with systems in which PT is not feasible and the steady-state ion photofragmentation spectra, we concluded that the observed temporal evolutions of the transient ion photofragmentation spectra are consistent with an intracomplex PT reaction after photoionization from the initial non-PT to the final PT structures. Our experiments revealed that PT in [PhOH-NH 3 ] + cation proceeds in two distinct steps: an initial impulsive wave-packet motion in ∼70 fs followed by a slower relaxation of about 1 ps that stabilizes the system into the final PT configuration. These results indicate that for a barrierless PT system, even though the initial PT motions are impulsive and ultrafast, the time scale to complete the reaction can be much slower and is determined by the rate of energy dissipation into other modes.

Watching proton transfer in real time: Ultrafast photoionization-induced proton transfer in phenol-ammonia complex cation

NASA Astrophysics Data System (ADS)

Shen, Ching-Chi; Tsai, Tsung-Ting; Wu, Jun-Yi; Ho-Wei, Jr.; Chen, Yi-Wei; Cheng, Po-Yuan

2017-10-01

In this paper, we give a full account of our previous work [C. C. Shen et al., J. Chem. Phys. 141, 171103 (2014)] on the study of an ultrafast photoionization-induced proton transfer (PT) reaction in the phenol-ammonia (PhOH-NH3) complex using ultrafast time-resolved ion photofragmentation spectroscopy implemented by the photoionization-photofragmentation pump-probe detection scheme. Neutral PhOH-NH3 complexes prepared in a free jet are photoionized by femtosecond 1 + 1 resonance-enhanced multiphoton ionization via the S1 state. The evolving cations are then probed by delayed pulses that result in ion fragmentation, and the ionic dynamics is followed by measuring the parent-ion depletion as a function of the pump-probe delay time. By comparing with systems in which PT is not feasible and the steady-state ion photofragmentation spectra, we concluded that the observed temporal evolutions of the transient ion photofragmentation spectra are consistent with an intracomplex PT reaction after photoionization from the initial non-PT to the final PT structures. Our experiments revealed that PT in [PhOH-NH3]+ cation proceeds in two distinct steps: an initial impulsive wave-packet motion in ˜70 fs followed by a slower relaxation of about 1 ps that stabilizes the system into the final PT configuration. These results indicate that for a barrierless PT system, even though the initial PT motions are impulsive and ultrafast, the time scale to complete the reaction can be much slower and is determined by the rate of energy dissipation into other modes.

Kinetics of proton transfer from tetra(4-nitro-5- tert-butyl)phthalocyanine to nitrogen-containing bases in benzene

NASA Astrophysics Data System (ADS)

Petrov, O. A.; Kuzmina, E. L.; Maizlish, V. E.; Rodionov, A. V.

2014-01-01

The acid-basic interaction between tetra(4-nitro-5- tert-butyl)phthalocyanine and pyridine, 2-methylpyridine, morpholine, piperidine, n-butylamine, diethylamine, and triethylamine in benzene is studied. It is found that the intermolecular transfer of protons of NH groups from tetra(4-nitro-5- tert-butyl)phthalocyanine to morpholine and diethylamine is characterized by unusually low values of the reaction constant rates. The effect of the structure of tetra(4-nitro-5- tert-butyl)phthalocyanine and tetra(3-nitro-5- tert-butyl)phthalocyanine, and of the nature of the base on the kinetic parameters of acid-base interaction is demonstrated. A structure is proposed for complexes with the transfer of displaced phthalocyanines' protons. It is found that they undergo decomposition over time.

Ion-to-Neutral Ratios and Thermal Proton Transfer in Matrix-Assisted Laser Desorption/Ionization

NASA Astrophysics Data System (ADS)

Lu, I.-Chung; Chu, Kuan Yu; Lin, Chih-Yuan; Wu, Shang-Yun; Dyakov, Yuri A.; Chen, Jien-Lian; Gray-Weale, Angus; Lee, Yuan-Tseh; Ni, Chi-Kung

2015-07-01

The ion-to-neutral ratios of four commonly used solid matrices, α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), sinapinic acid (SA), and ferulic acid (FA) in matrix-assisted laser desorption/ionization (MALDI) at 355 nm are reported. Ions are measured using a time-of-flight mass spectrometer combined with a time-sliced ion imaging detector. Neutrals are measured using a rotatable quadrupole mass spectrometer. The ion-to-neutral ratios of CHCA are three orders of magnitude larger than those of the other matrices at the same laser fluence. The ion-to-neutral ratios predicted using the thermal proton transfer model are similar to the experimental measurements, indicating that thermal proton transfer reactions play a major role in generating ions in ultraviolet-MALDI.

New insights into proton surface mobility processes in PEMFC catalysts using isotopic exchange methods.

PubMed

Ferreira-Aparicio, Paloma

2009-09-01

The surface chemistry and the adsorption/desorption/exchange behavior of a proton-exchange membrane fuel cell catalyst are analyzed as a case study for the development of tailor-made support materials of enhanced performance and stability. By using H2, D2, and CO as probe molecules, the relevance of some surface functional groups of the catalyst support on several diffusion processes taking place during the adsorption is shown. Sulfonic groups associated with the vulcanized carbon black surface have been detected by means of spectroscopic techniques (X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy) and by analysis of the desorbed products during temperature-programmed desorption tests by mass spectrometry. Such hydrophilic species have been observed to favor proton surface mobility and exchange with Pt-adsorbed deuterium even in the presence of adsorbed CO. This behavior is relevant both for the proper characterization of these kinds of catalysts using adsorption probes and for the design of new surface-modified carbon supports, enabling alternative proton-transfer pathways throughout the catalytic layers toward the membrane.

The role of proton shuttling mechanisms in solvent-free and catalyst-free acetalization reactions of imines.

PubMed

Lillo, Victor J; Mansilla, Javier; Saá, José M

2018-06-06

Proton transfer is central to the understanding of chemical processes. More so in addition reactions of the type NuH + E → Nu-EH taking place under solvent-free and catalyst-free conditions. Herein we show that the addition of alcohols or amines (the NuH component) to imine derivatives (the E component), in 1 : 1 ratio, under solvent-free and catalyst-free conditions, are efficient methods to access N,O and N,N-acetal derivatives. In addition, computational studies reveal that they are catalyzed reactions involving two or even three NuH molecules operating in a cooperative manner as H-bonded NuH(NuH)nNuH associates (many body effects) in the transition state through a concerted proton shuttling mechanism (addition of alcohols) or stepwise proton shuttling mechanism (addition of amines), thereby facilitating the key proton transfer step.

Quantification of diesel exhaust gas phase organics by a thermal desorption proton transfer reaction mass spectrometer

NASA Astrophysics Data System (ADS)

Erickson, M. H.; Wallace, H. W.; Jobson, B. T.

2012-02-01

A new approach was developed to measure the total abundance of long chain alkanes (C12 and above) in urban air using thermal desorption with a proton transfer reaction mass spectrometer (PTR-MS). These species are emitted in diesel exhaust and may be important precursors to secondary organic aerosol production in urban areas. Long chain alkanes undergo dissociative proton transfer reactions forming a series of fragment ions with formula CnH2n+1. The yield of the fragment ions is a function of drift conditions. At a drift field strength of 80 Townsends, the most abundant ion fragments from C10 to C16 n-alkanes were m/z 57, 71 and 85. The PTR-MS is insensitive to n-alkanes less than C8 but displays an increasing sensitivity for larger alkanes. Higher drift field strengths yield greater normalized sensitivity implying that the proton affinity of the long chain n-alkanes is less than H2O. Analysis of diesel fuel shows the mass spectrum was dominated by alkanes (CnH2n+1), monocyclic aromatics, and an ion group with formula CnH2n-1 (m/z 97, 111, 125, 139). The PTR-MS was deployed in Sacramento, CA during the Carbonaceous Aerosols and Radiative Effects Study field experiment in June 2010. The ratio of the m/z 97 to 85 ion intensities in ambient air matched that found in diesel fuel. Total diesel exhaust alkane concentrations calculated from the measured abundance of m/z 85 ranged from the method detection limit of ~1 μg m-3 to 100 μg m-3 in several air pollution episodes. The total diesel exhaust alkane concentration determined by this method was on average a factor of 10 greater than the sum of alkylbenzenes associated with spark ignition vehicle exhaust.

Tuning of Nafion® by HKUST-1 as coordination network to enhance proton conductivity for fuel cell applications

NASA Astrophysics Data System (ADS)

Kim, Hee Jin; Talukdar, Krishan; Choi, Sang-June

2016-02-01

Metal-organic frameworks can be intentionally coordinated to achieve improved proton conductivity because they have highly ordered structures and modular nature that serve as a scaffold to anchor acidic groups and develop efficient proton transfer pathways for fuel cell application. Using the concept of a coordination network, the conductivity of Nafion® was tuned by the incorporation of HKUST-1. It has CuII-paddle wheel type nodes and 1,3,5-benzenetricarboxylate struts, feature accessible sites that provides an improved protonic channel depending on the water content. In spite of the fact that HKUST-1 is neutral, coordinated water molecules are contributed adequately acidic by CuII to supply protons to enhance proton conductivity. Water molecules play a vital part in transfer of proton as conducting media and serve as triggers to change proton conductivity through reforming hydrogen bonding networks by water adsorption/desorption process. Increased ion exchange capacity and proton conductivity with lower water uptake of the H3PO4-doped material, and improved thermal stability (as confirmed by thermogravimetric analysis) were achieved. The structure of HKUST-1 was confirmed via field emission scanning electron microscopy and X-ray diffraction, while the porosity and adsorption desorption capacity were characterized by porosity analysis.

Proton Transfers at the Air-Water Interface

NASA Astrophysics Data System (ADS)

Mishra, Himanshu

Proton transfer reactions at the interface of water with hydrophobic media, such as air or lipids, are ubiquitous on our planet. These reactions orchestrate a host of vital phenomena in the environment including, for example, acidification of clouds, enzymatic catalysis, chemistries of aerosol and atmospheric gases, and bioenergetic transduction. Despite their importance, however, quantitative details underlying these interactions have remained unclear. Deeper insight into these interfacial reactions is also required in addressing challenges in green chemistry, improved water quality, self-assembly of materials, the next generation of micro-nanofluidics, adhesives, coatings, catalysts, and electrodes. This thesis describes experimental and theoretical investigation of proton transfer reactions at the air-water interface as a function of hydration gradients, electrochemical potential, and electrostatics. Since emerging insights hold at the lipid-water interface as well, this work is also expected to aid understanding of complex biological phenomena associated with proton migration across membranes. Based on our current understanding, it is known that the physicochemical properties of the gas-phase water are drastically different from those of bulk water. For example, the gas-phase hydronium ion, H3O +(g), can protonate most (non-alkane) organic species, whereas H 3O+(aq) can neutralize only relatively strong bases. Thus, to be able to understand and engineer water-hydrophobe interfaces, it is imperative to investigate this fluctuating region of molecular thickness wherein the 'function' of chemical species transitions from one phase to another via steep gradients in hydration, dielectric constant, and density. Aqueous interfaces are difficult to approach by current experimental techniques because designing experiments to specifically sample interfacial layers (< 1 nm thick) is an arduous task. While recent advances in surface-specific spectroscopies have provided valuable information regarding the structure of aqueous interfaces, but structure alone is inadequate to decipher the function. By similar analogy, theoretical predictions based on classical molecular dynamics have remained limited in their scope. Recently, we have adapted an analytical electrospray ionization mass spectrometer (ESIMS) for probing reactions at the gas-liquid interface in real time. This technique is direct, surface-specific, and provides unambiguous mass-to-charge ratios of interfacial species. With this innovation, we have been able to investigate the following: 1. How do anions mediate proton transfers at the air-water interface? 2. What is the basis for the negative surface potential at the air-water interface? 3. What is the mechanism for catalysis 'on-water'? In addition to our experiments with the ESIMS, we applied quantum mechanics and molecular dynamics to simulate our experiments toward gaining insight at the molecular scale. Our results unambiguously demonstrated the role of electrostatic-reorganization of interfacial water during proton transfer events. With our experimental and theoretical results on the 'superacidity' of the surface of mildly acidic water, we also explored implications on atmospheric chemistry and green chemistry. Our most recent results explained the basis for the negative charge of the air-water interface and showed that the water-hydrophobe interface could serve as a site for enhanced autodissociation of water compared to the condensed phase. In a nutshell, this thesis presents an in-depth account of complementary experiments and theory employed to answer the questions listed above. It is primarily based on the following articles: 1. H. Mishra, S. Enami, L. A. Stewart, R. J. Nielsen, M. R. Hoffmann, W. A. Goddard III, A. J. Colussi, Proceedings of the National Academy of Sciences (2012), 109(46), 18679--18683; 2. H. Mishra, S. Enami, R. J. Nielsen, W. A. Goddard III, M.R. Hoffmann, A. J. Colussi, Proceedings of the National Academy of Sciences (2012), 109(26), 10228--10232; 3. H. Mishra, R. J. Nielsen, S. Enami, M. R. Hoffmann, A. J. Colussi, W. A. Goddard III, International Journal of Quantum Chemistry (2013), 113(4), 413--417; 4. S. Enami, H. Mishra, M. R. Hoffmann, A. J. Colussi, Journal of Physical Chemistry A (2012), 116 (24), 6027--6032. On the recommendation of the thesis committee, Appendix I and II have been added based on the following articles: S. Enami, H. Mishra, M. R. Hoffmann, A. J. Colussi, Journal of Chemical Physics (2012) 136(15), 154707, 1-7, and H. Mishra, C. J. Yu, D. P. Chen, W. A. Goddard, N. F. Dalleska, M. R. Hoffmann, M. S. Diallo, Environmental Science & Technology, (2012) 46(16), 8998-9004.

Theoretical insights of proton transfer and hydrogen bonded charge transfer complex of 1,2-dimethylimidazolium-3,5-dinitrobenzoate crystal

NASA Astrophysics Data System (ADS)

Afroz, Ziya; Faizan, Mohd.; Alam, Mohammad Jane; Ahmad, Shabbir; Ahmad, Afaq

2018-04-01

Proton transfer (PT) and hydrogen bonded charge transfer (HBCT) 1:1 complex of 1,2-dimethylimidazole (DMI) and 3,5-dinitrobenzoic acid (DNBA) have been theoretically analyzed and compared with reported experimental results. Both the structures in the isolated gaseous state have been optimized at DFT/B3LYP/6-311G(d,p) level of theory and further, the PT energy barrier has been calculated from potential energy surface scan. Along with structural investigations, theoretical vibrational spectra have been inspected and compared with the FTIR spectrum. Moreover, frontier molecular analysis has also been carried out.

Anolyte recirculation effects in buffered and unbuffered single-chamber air-cathode microbial fuel cells.

PubMed

Zhang, Liang; Zhu, Xun; Kashima, Hiroyuki; Li, Jun; Ye, Ding-Ding; Liao, Qiang; Regan, John M

2015-03-01

Two identical microbial fuel cells (MFCs) with a floating air-cathode were operated under either buffered (MFC-B) or bufferless (MFC-BL) conditions to investigate anolyte recirculation effects on enhancing proton transfer. With an external resistance of 50 Ω and recirculation rate of 1.0 ml/min, MFC-BL had a 27% lower voltage (9.7% lower maximal power density) but a 64% higher Coulombic efficiency (CE) than MFC-B. MFC-B had a decreased voltage output, batch time, and CE with increasing recirculation rate resulting from more oxygen transfer into the anode. However, increasing the recirculation rate within a low range significantly enhanced proton transfer in MFC-BL, resulting in a higher voltage output, a longer batch time, and a higher CE. A further increase in recirculation rate decreased the batch time and CE of MFC-BL due to excess oxygen transfer into anode outweighing the proton-transfer benefits. The unbuffered MFC had an optimal recirculation rate of 0.35 ml/min. Copyright © 2014 Elsevier Ltd. All rights reserved.

Stepwise vs concerted excited state tautomerization of 2-hydroxypyridine: Ammonia dimer wire mediated hydrogen/proton transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esboui, Mounir, E-mail: mounir.esboui@fst.rnu.tn; Technical and Vocational Training Corporation, Hail College of Technology, P.O. Box 1960, Hail 81441

The stepwise and concerted excited state intermolecular proton transfer (PT) and hydrogen transfer (HT) reactions in 2-hydroxypyridine-(NH{sub 3}){sub 2} complex in the gas phase under Cs symmetry constraint and without any symmetry constraints were performed using quantum chemical calculations. It shows that upon excitation, the hydrogen bonded in 2HP-(NH{sub 3}){sub 2} cluster facilitates the releasing of both hydrogen and proton transfer reactions along ammonia wire leading to the formation of the 2-pyridone tautomer. For the stepwise mechanism, it has been found that the proton and the hydrogen may transfer consecutively. These processes are distinguished from each other through charge translocationmore » analysis and the coupling between the motion of the proton and the electron density distribution along ammonia wire. For the complex under Cs symmetry, the excited state HT occurs on the A″({sup 1}πσ{sup ∗}) and A′({sup 1}nσ{sup ∗}) states over two accessible energy barriers along reaction coordinates, and excited state PT proceeds mainly through the A′({sup 1}ππ{sup ∗}) and A″({sup 1}nπ{sup ∗}) potential energy surfaces. For the unconstrained complex, potential energy profiles show two {sup 1}ππ{sup ∗}-{sup 1}πσ{sup ∗} conical intersections along enol → keto reaction path indicating that proton and H atom are localized, respectively, on the first and second ammonia of the wire. Moreover, the concerted excited state PT is competitive to take place with the stepwise process, because it proceeds over low barriers of 0.14 eV and 0.11 eV with respect to the Franck-Condon excitation of enol tautomer, respectively, under Cs symmetry and without any symmetry constraints. These barriers can be probably overcome through tunneling effect.« less

Sibling rivalry: intrinsic luminescence from two xanthene dye monoanions, resorufin and fluorescein, provides evidence for excited-state proton transfer in the latter.

PubMed

Kjær, Christina; Brøndsted Nielsen, Steen; Stockett, Mark H

2017-09-20

While the emission spectrum of fluorescein monoanions isolated in vacuo displays a broad and featureless band, that of resorufin, also belonging to the xanthene family, has a sharp band maximum, clear vibronic structure, and experiences a small Stokes shift. Excited-state proton transfer in fluorescein can account for the differences.

Kinetic Effects Of Increased Proton Transfer Distance On Proton-Coupled Oxidations Of Phenol-Amines

PubMed Central

Rhile, Ian J.

2011-01-01

To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh2NH2 substituent (1). Spectroscopic, structural, thermochemical and computational studies show that the two amino-phenols are very similar, except that the O⋯N distance (dON) is >0.1 Å longer in 2 than in 1. The difference in dON is 0.13 ± 0.03 Å from X-ray crystallography and 0.165 Å from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations •OAr–NH3+ by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. two orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C6H4OMe)3•+ (3a+) occurs at (1.4 ± 0.1) × 104 M-1 s-1, only a factor of two slower than the closely related reaction of 1 with N(C6H4OMe)2(C6H4Br)•+ (3b+). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG°(2 + 3a+) = +0.078 V vs. ΔG°(1 + 3b+) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Brønsted α, Δln(k)/Δln(Keq)). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the two phenols emphasizes the importance of the highly anharmonic O⋯H⋯N potential energy surface and the influence of proton vibrational excited states. PMID:21919508

Internal proton transfer and H2 rotations in the H5(+) cluster: a marked influence on its thermal equilibrium state.

PubMed

de Tudela, Ricardo Pérez; Barragán, Patricia; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

2011-03-31

Classical and path integral Monte Carlo (CMC, PIMC) "on the fly" calculations are carried out to investigate anharmonic quantum effects on the thermal equilibrium structure of the H5(+) cluster. The idea to follow in our computations is based on using a combination of the above-mentioned nuclear classical and quantum statistical methods, and first-principles density functional (DFT) electronic structure calculations. The interaction energies are computed within the DFT framework using the B3(H) hybrid functional, specially designed for hydrogen-only systems. The global minimum of the potential is predicted to be a nonplanar configuration of C(2v) symmetry, while the next three low-lying stationary points on the surface correspond to extremely low-energy barriers for the internal proton transfer and to the rotation of the H2 molecules, around the C2 axis of H5(+), connecting the symmetric C(2v) minima in the planar and nonplanar orientations. On the basis of full-dimensional converged PIMC calculations, results on the quantum vibrational zero-point energy (ZPE) and state of H5(+) are reported at a low temperature of 10 K, and the influence of the above-mentioned topological features of the surface on its probability distributions is clearly demonstrated.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Dynamics of Charge Transfer in DNA Wires: A Proton-Coupled Approach

NASA Astrophysics Data System (ADS)

Behnia, Sohrab; Fathizadeh, Samira; Ziaei, Javid; Akhshani, Afshin

2017-12-01

The advent of molecular electronics has fueled interest in studying DNA as a nanowire. The well-known Peyrard-Bishop-Dauxois (PBD) model, which was proposed for the purpose of understanding the mechanism of DNA denaturation, has a limited number of degrees of freedom. In addition, considering the Peyrard-Bishop-Holstein (PBH) model as a means of studying the charge transfer effect, in which the dynamical motion is described via the PBD model, may apply limitations on observing all the phenomena. Therefore, we have attempted to add the mutual interaction of a proton and electron in the form of proton-coupled electron transfer (PCET) to the PBH model. PCET has been implicated in a variety of oxidative processes that ultimately lead to mutations. When we have considered the PCET approach to DNA based on a proton-combined PBH model, we were able to extract the electron and proton currents independently. In this case, the reciprocal influence of electron and proton current is considered. This interaction does not affect the general form of the electronic current in DNA, but it changes the threshold of the occurrence of phenomena such as negative differential resistance. It is worth mentioning that perceiving the structural properties of the attractors in phase space via the Rényi dimension and concentrating on the critical regions through a scalogram can present a clear picture of the critical points in such phenomena.

Spin-locking versus chemical exchange saturation transfer MRI for investigating chemical exchange process between water and labile metabolite protons.

PubMed

Jin, Tao; Autio, Joonas; Obata, Takayuki; Kim, Seong-Gi

2011-05-01

Chemical exchange saturation transfer (CEST) and spin-locking (SL) experiments were both able to probe the exchange process between protons of nonequivalent chemical environments. To compare the characteristics of the CEST and SL approaches in the study of chemical exchange effects, we performed CEST and SL experiments at varied pH and concentrated metabolite phantoms with exchangeable amide, amine, and hydroxyl protons at 9.4 T. Our results show that: (i) on-resonance SL is most sensitive to chemical exchanges in the intermediate-exchange regime and is able to detect hydroxyl and amine protons on a millimolar concentration scale. Off-resonance SL and CEST approaches are sensitive to slow-exchanging protons when an optimal SL or saturation pulse power matches the exchanging rate, respectively. (ii) Offset frequency-dependent SL and CEST spectra are very similar and can be explained well with an SL model recently developed by Trott and Palmer (J Magn Reson 2002;154:157-160). (iii) The exchange rate and population of metabolite protons can be determined from offset-dependent SL or CEST spectra or from on-resonance SL relaxation dispersion measurements. (iv) The asymmetry of the magnetization transfer ratio (MTR(asym)) is highly dependent on the choice of saturation pulse power. In the intermediate-exchange regime, MTR(asym) becomes complicated and should be interpreted with care. Copyright © 2010 Wiley-Liss, Inc.

Two-proton transfer reactions on even Ni and Zn isotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boucenna, A.; Kraus, L.; Linck, I.

New levels strongly excited by 112-MeV {sup 12}C ions on even Ni and Zn isotopes are {ital J}{sup {pi}} assigned on kinematical and geometrical arguments, crude shell-model calculations, and distorted-wave Born approximation angular-distribution analysis. These tentative assignments are supported by the Bansal-French model. Because of the contribution of additional collective effects, the two-proton transfer reaction spectra are less selectively fed than those obtained with the analogous two-neutron transfer reactions induced on the same targets in a similar energy range.

Proton Mediated Chemistry and Catalysis in a Self-Assembled Supramolecular Host

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pluth, Michael; Bergman, Robert; Raymond, Kenneth

2009-04-10

Synthetic supramolecular host assemblies can impart unique reactivity to encapsulated guest molecules. Synthetic host molecules have been developed to carry out complex reactions within their cavities, despite the fact that they lack the type of specifically tailored functional groups normally located in the analogous active sites of enzymes. Over the past decade, the Raymond group has developed a series of self-assembled supramolecules and the Bergman group has developed and studied a number of catalytic transformations. In this Account, we detail recent collaborative work between these two groups, focusing on chemical catalysis stemming from the encapsulation of protonated guests and expandingmore » to acid catalysis in basic solution. We initially investigated the ability of a water-soluble, self-assembled supramolecular host molecule to encapsulate protonated guests in its hydrophobic core. Our study of encapsulated protonated amines revealed rich host-guest chemistry. We established that self-exchange (that is, in-out guest movement) rates of protonated amines were dependent on the steric bulk of the amine rather than its basicity. The host molecule has purely rotational tetrahedral (T) symmetry, so guests with geminal N-methyl groups (and their attendant mirror plane) were effectively desymmetrized; this allowed for the observation and quantification of the barriers for nitrogen inversion followed by bond rotation. Furthermore, small nitrogen heterocycles, such as N-alkylaziridines, N-alkylazetidines, and N-alkylpyrrolidines, were found to be encapsulated as proton-bound homodimers or homotrimers. We further investigated the thermodynamic stabilization of protonated amines, showing that encapsulation makes the amines more basic in the cavity. Encapsulation raises the effective basicity of protonated amines by up to 4.5 pK{sub a} units, a difference almost as large as that between the moderate and strong bases carbonate and hydroxide. The thermodynamic stabilization of protonated guests was translated into chemical catalysis by taking advantage of the potential for accelerating reactions that take place via positively charged transition states, which could be potentially stabilized by encapsulation. Orthoformates, generally stable in neutral or basic solution, were found to be suitable substrates for catalytic hydrolysis by the assembly. Orthoformates small enough to undergo encapsulation were readily hydrolyzed by the assembly in basic solution, with rate acceleration factors up to 3900 compared with those of the corresponding uncatalyzed reactions. Furthering the analogy to enzymes that obey Michaelis-Menten kinetics, we observed competitive inhibition with the inhibitor NPr{sub 4}{sup +}, thereby confirming that the interior cavity of the assembly was the active site for catalysis. Mechanistic studies revealed that the assembly is required for catalysis and that the rate-limiting step of the reaction involves proton transfer from hydronium to the encapsulated substrate. Encapsulation in the assembly changes the orthoformate hydrolysis from an A-1 mechanism (in which decomposition of the protonated substrate is the rate-limiting step) to an A-S{sub E}2 mechanism (in which proton transfer is the rate-limiting step). The study of hydrolysis in the assembly was next extended to acetals, which were also catalytically hydrolyzed by the assembly in basic solution. Acetal hydrolysis changed from the A-1 mechanism in solution to an A-2 mechanism inside the assembly, where attack of water on the protonated substrate is rate limiting. This work provides rare examples of assembly-catalyzed reactions that proceed with substantial rate accelerations despite the absence of functional groups in the cavity and with mechanisms fully elucidated by quantitative kinetic studies.« less

Coupled sensitizer-catalyst dyads: electron-transfer reactions in a perylene-polyoxometalate conjugate.

PubMed

Odobel, Fabrice; Séverac, Marjorie; Pellegrin, Yann; Blart, Errol; Fosse, Céline; Cannizzo, Caroline; Mayer, Cédric R; Elliott, Kristopher J; Harriman, Anthony

2009-01-01

Ultrafast discharge of a single-electron capacitor: A variety of intramolecular electron-transfer reactions are apparent for polyoxometalates functionalized with covalently attached perylene monoimide chromophores, but these are restricted to single-electron events. (et=electron transfer, cr=charge recombination, csr=charge-shift reaction, PER=perylene, POM=polyoxometalate).A new strategy is introduced that permits covalent attachment of an organic chromophore to a polyoxometalate (POM) cluster. Two examples are reported that differ according to the nature of the anchoring group and the flexibility of the linker. Both POMs are functionalized with perylene monoimide units, which function as photon collectors and form a relatively long-lived charge-transfer state under illumination. They are reduced to a stable pi-radical anion by electrolysis or to a protonated dianion under photolysis in the presence of aqueous triethanolamine. The presence of the POM opens up an intramolecular electron-transfer route by which the charge-transfer state reduces the POM. The rate of this process depends on the molecular conformation and appears to involve through-space interactions. Prior reduction of the POM leads to efficient fluorescence quenching, again due to intramolecular electron transfer. In most cases, it is difficult to resolve the electron-transfer products because of relatively fast reverse charge shift that occurs within a closed conformer. Although the POM can store multiple electrons, it has not proved possible to use these systems as molecular-scale capacitors because of efficient electron transfer from the one-electron-reduced POM to the excited singlet state of the perylene monoimide.

Constituent Quark and Diquark Properties from Small Angle Proton--Proton Elastic Scattering at High Energies

NASA Astrophysics Data System (ADS)

Bialas, A.; Bzdak, A.

2007-01-01

Small momentum transfer elastic proton-proton cross-section at high energies is calculated assuming the nucleon composed of two constituents -- a quark and a diquark. A comparison to data (described very well up to -t approx 2 GeV2/c) allows to determine some properties of the constituents. While quark turns out fairly small, the diquark appears to be rather large, comparable to the size of the proton.

Theoretical studies for excited-state tautomerization in the 7-azaindole-(CH3OH)n (n = 1 and 2) complexes in the gas phase.

PubMed

Fang, Hua; Kim, Yongho

2011-12-01

The excited-state tautomerization of 7-azaindole (7AI) complexes bonded with either one or two methanol molecule(s) was studied by systematic quantum mechanical calculations in the gas phases. Electronic structures and energies for the reactant, transition state (TS), and product were computed at the complete active space self-consistent field (CASSCF) levels with the second-order multireference perturbation theory (MRPT2) to consider the dynamic electron correlation. The time-dependent density functional theory (TDDFT) was also used for comparison. The excited-state double proton transfer (ESDPT) in 7AI-CH(3)OH occurs in a concerted but asynchronous mechanism. Similarly, such paths are also found in the two transition states during the excited-state triple proton transfer (ESTPT) of the 7AI-(CH(3)OH)(2) complex. In the first TS, the pyrrole ring proton first migrated to methanol, while in the second the methanol proton moved first to the pyridine ring. The CASSCF level with the MRPT2 correction showed that the former path was much preferable to the latter, and the ESDPT is much slower than the ESTPT. Additionally, the vibrational-mode enhanced tautomerization in the 7AI-(CH(3)OH)(2) complex was also studied. We found that the excitation of the low-frequency mode shortens the reaction path to increase the tautomerization rate. Overall, most TDDFT methods used in this study predicted different TS structures and barriers from the CASSCF methods with MRPT2 corrections. © 2011 American Chemical Society

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Double proton transfer in the complex of acetic acid with methanol: Theory versus experiment

NASA Astrophysics Data System (ADS)

Fernández-Ramos, Antonio; Smedarchina, Zorka; Rodríguez-Otero, Jesús

2001-01-01

To test the approximate instanton approach to intermolecular proton-transfer dynamics, we report multidimensional ab initio bimolecular rate constants of HH, HD, and DD exchange in the complex of acetic acid with methanol in tetrahydrofuran-d8, and compare them with the NMR (nuclear magnetic resonance) experiments of Gerritzen and Limbach. The bimolecular rate constants are evaluated as products of the exchange rates and the equilibrium rate constants of complex formation in solution. The two molecules form hydrogen-bond bridges and the exchange occurs via concerted transfer of two protons. The dynamics of this transfer is evaluated in the complete space of 36 vibrational degrees of freedom. The geometries of the two isolated molecules, the complex, and the transition states corresponding to double proton transfer are fully optimized at QCISD (quadratic configuration interaction including single and double substitutions) level of theory, and the normal-mode frequencies are calculated at MP2 (Møller-Plesset perturbation theory of second order) level with the 6-31G (d,p) basis set. The presence of the solvent is taken into account via single-point calculations over the gas phase geometries with the PCM (polarized continuum model). The proton exchange rate constants, calculated with the instanton method, show the effect of the structure and strength of the hydrogen bonds, reflected in the coupling between the tunneling motion and the other vibrations of the complex. Comparison with experiment, which shows substantial kinetic isotopic effects (KIE), indicates that tunneling prevails over classic exchange for the whole temperature range of observation. The unusual behavior of the experimental KIE upon single and double deuterium substitution is well reproduced and is related to the synchronicity of two-atom tunneling.

Advantages of Chemical Exchange-Sensitive Spin-Lock (CESL) Over Saturation Transfer (CEST) for Hydroxyl- and Amine-Water Proton Exchange Studies

PubMed Central

Jin, Tao; Kim, Seong-Gi

2014-01-01

The chemical exchange (CE) rate of endogenous hydroxyl and amine protons with water is often comparable to the difference in their chemical shifts. These intermediate exchange (IMEX) processes have been imaged by the CE saturation transfer (CEST) approach with low-power and long-duration irradiation. However, its sensitivity is not optimal, and more importantly, the signal is contaminated by slow magnetization transfer processes. Here, the property of CEST signals is compared to a CE-sensitive spin-locking (CESL) technique irradiating at the labile proton frequency. Firstly, using a higher power and shorter irradiation in CE-MRI yields i) increasing selectivity to faster chemical exchange rates by higher sensitivity to faster exchanges and less sensitivity to slower CE and magnetization transfer processes, and ii) decreasing in vivo asymmetric magnetization transfer contrast measured at ±15 ppm. The sensitivity gain of CESL over CEST is higher for a higher-power and shorter irradiation. Unlike CESL, CEST signals oscillate at a very high power and short irradiation. Secondly, time-dependent CEST and CESL signals are well modeled by analytical solutions of CE-MRI with asymmetric population approximation (CEAPA), which can be used for quantitative CE-MRI, and validated by simulations of Bloch-McConnell equations and phantom experiments. Lastly, in vivo amine-water proton exchange contrast measured at 2.5 ppm with ω1 of 500 Hz is 18% higher in sensitivity for CESL than CEST at 9.4 T. Overall, CESL provides better exchange rate selectivity and sensitivity than CEST; therefore, CESL is more suitable for CE-MRI of IMEX protons. PMID:25199631

Molecular mechanisms for generating transmembrane proton gradients

PubMed Central

Gunner, M.R.; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun

2013-01-01

Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side. PMID:23507617

Collision-induced dissociation processes of protonated benzoic acid and related compounds: competitive generation of protonated carbon dioxide or protonated benzene.

PubMed

Xu, Sihang; Pavlov, Julius; Attygalle, Athula B

2017-04-01

Upon activation in the gas phase, protonated benzoic acid (m/z 123) undergoes fragmentation by several mechanisms. In addition to the predictable water loss followed by a CO loss, the m/z 123 ion more intriguingly eliminates a molecule of benzene to generate protonated carbon dioxide (H - O +  ═ C ≡ O, m/z 45), or a molecule of carbon dioxide to yield protonated benzene (m/z 79). Experimental evidence shows that the incipient proton ambulates during the fragmentation processes. For the CO 2 or benzene loss, protonated benzoic acid transfers the charge-imparting proton initially to the ortho position and then to the ipso position to generate a transient species which dissociates to form an ion-neutral complex between benzene and protonated CO 2 . The formation of the m/z 45 ion is not a phenomenon unique to benzoic acid: spectra from protonated isophthalic acid, terephthalic acid, trans-cinnamic acid and some aliphatic acids also displayed a peak for m/z 45. However, the m/z 45 peak is structurally diagnostic only for certain benzene polycarboxylic acids because the spectra of compounds with two carboxyl groups on adjacent ring carbons do not produce a peak at m/z 45. For the m/z 79 ion to be formed, an intramolecular reaction should take place in which protonated CO 2 within the ion-neutral complex acts as the attacking electrophile to transfer a proton to benzene. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Proton elastic form factor ratios to Q2=3.5GeV2 by polarization transfer

NASA Astrophysics Data System (ADS)

Punjabi, V.; Perdrisat, C. F.; Aniol, K. A.; Baker, F. T.; Berthot, J.; Bertin, P. Y.; Bertozzi, W.; Besson, A.; Bimbot, L.; Boeglin, W. U.; Brash, E. J.; Brown, D.; Calarco, J. R.; Cardman, L. S.; Chai, Z.; Chang, C.-C.; Chen, J.-P.; Chudakov, E.; Churchwell, S.; Cisbani, E.; Dale, D. S.; Leo, R. De; Deur, A.; Diederich, B.; Domingo, J. J.; Epstein, M. B.; Ewell, L. A.; Fissum, K. G.; Fleck, A.; Fonvieille, H.; Frullani, S.; Gao, J.; Garibaldi, F.; Gasparian, A.; Gerstner, G.; Gilad, S.; Gilman, R.; Glamazdin, A.; Glashausser, C.; Gomez, J.; Gorbenko, V.; Green, A.; Hansen, J.-O.; Howell, C. R.; Huber, G. M.; Iodice, M.; de Jager, C. W.; Jaminion, S.; Jiang, X.; Jones, M. K.; Kahl, W.; Kelly, J. J.; Khayat, M.; Kramer, L. H.; Kumbartzki, G.; Kuss, M.; Lakuriki, E.; Laveissière, G.; Lerose, J. J.; Liang, M.; Lindgren, R. A.; Liyanage, N.; Lolos, G. J.; Macri, R.; Madey, R.; Malov, S.; Margaziotis, D. J.; Markowitz, P.; McCormick, K.; McIntyre, J. I.; Meer, R. L.; Michaels, R.; Milbrath, B. D.; Mougey, J. Y.; Nanda, S. K.; Offermann, E. A.; Papandreou, Z.; Pentchev, L.; Petratos, G. G.; Piskunov, N. M.; Pomatsalyuk, R. I.; Prout, D. L.; Quéméner, G.; Ransome, R. D.; Raue, B. A.; Roblin, Y.; Roche, R.; Rutledge, G.; Rutt, P. M.; Saha, A.; Saito, T.; Sarty, A. J.; Smith, T. P.; Sorokin, P.; Strauch, S.; Suleiman, R.; Takahashi, K.; Templon, J. A.; Todor, L.; Ulmer, P. E.; Urciuoli, G. M.; Vernin, P.; Vlahovic, B.; Voskanyan, H.; Wijesooriya, K.; Wojtsekhowski, B. B.; Woo, R. J.; Xiong, F.; Zainea, G. D.; Zhou, Z.-L.

2005-05-01

The ratio of the proton elastic electromagnetic form factors, GEp/GMp, was obtained by measuring Pt and Pℓ, the transverse and longitudinal recoil proton polarization components, respectively, for the elastic e→p→ep→reaction in the four-momentum transfer squared range of 0.5 to 3.5GeV2. In the single-photon exchange approximation, GEp/GMp is directly proportional to Pt/Pℓ. The simultaneous measurement of Pt and Pℓ in a polarimeter reduces systematic uncertainties. The results for GEp/GMp show a systematic decrease with increasing Q2, indicating for the first time a definite difference in the distribution of charge and magnetization in the proton. The data have been reanalyzed and their systematic uncertainties have become significantly smaller than those reported previously.

On the possibility for precision measurements of differential cross sections for elastic proton–proton scattering at the Protvino accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denisov, S. P., E-mail: denisov@ihep.ru; Kozelov, A. V.; Petrov, V. A.

Elastic-scattering data were analyzed, and it was concluded on the basis of this analysis that precisionmeasurements of differential cross sections for elastic proton–proton scattering at the accelerator of the Institute for High Energy Physics (IHEP, Protvino, Russia) over a broad momentum-transfer range are of importance and topical interest. The layout of the respective experimental facility detecting the scattered particle and recoil proton and possessing a high momentum-transfer resolution was examined along with the equipment constituting this facility. The facility in question is able to record up to a billion events of elastic proton–proton scattering per IHEP accelerator run (20 days).more » Other lines of physics research with this facility are briefly discussed.« less

Multiple electron processes of He and Ne by proton impact

NASA Astrophysics Data System (ADS)

Terekhin, Pavel Nikolaevich; Montenegro, Pablo; Quinto, Michele; Monti, Juan; Fojon, Omar; Rivarola, Roberto

2016-05-01

A detailed investigation of multiple electron processes (single and multiple ionization, single capture, transfer-ionization) of He and Ne is presented for proton impact at intermediate and high collision energies. Exclusive absolute cross sections for these processes have been obtained by calculation of transition probabilities in the independent electron and independent event models as a function of impact parameter in the framework of the continuum distorted wave-eikonal initial state theory. A binomial analysis is employed to calculate exclusive probabilities. The comparison with available theoretical and experimental results shows that exclusive probabilities are needed for a reliable description of the experimental data. The developed approach can be used for obtaining the input database for modeling multiple electron processes of charged particles passing through the matter.

Measurement of the beam asymmetry Σ for π0 and η photoproduction on the proton at Eγ=9 GeV

NASA Astrophysics Data System (ADS)

Al Ghoul, H.; Anassontzis, E. G.; Austregesilo, A.; Barbosa, F.; Barnes, A.; Beattie, T. D.; Bennett, D. W.; Berdnikov, V. V.; Black, T.; Boeglin, W.; Briscoe, W. J.; Brooks, W. K.; Cannon, B. E.; Chernyshov, O.; Chudakov, E.; Crede, V.; Dalton, M. M.; Deur, A.; Dobbs, S.; Dolgolenko, A.; Dugger, M.; Dzhygadlo, R.; Egiyan, H.; Eugenio, P.; Fanelli, C.; Foda, A. M.; Frye, J.; Furletov, S.; Gan, L.; Gasparian, A.; Gerasimov, A.; Gevorgyan, N.; Goetzen, K.; Goryachev, V. S.; Guo, L.; Hakobyan, H.; Hardin, J.; Henderson, A.; Huber, G. M.; Ireland, D. G.; Ito, M. M.; Jarvis, N. S.; Jones, R. T.; Kakoyan, V.; Kamel, M.; Klein, F. J.; Kliemt, R.; Kourkoumeli, C.; Kuleshov, S.; Kuznetsov, I.; Lara, M.; Larin, I.; Lawrence, D.; Levine, W. I.; Livingston, K.; Lolos, G. J.; Lyubovitskij, V.; Mack, D.; Mattione, P. T.; Matveev, V.; McCaughan, M.; McCracken, M.; McGinley, W.; McIntyre, J.; Mendez, R.; Meyer, C. A.; Miskimen, R.; Mitchell, R. E.; Mokaya, F.; Moriya, K.; Nerling, F.; Nigmatkulov, G.; Ochoa, N.; Ostrovidov, A. I.; Papandreou, Z.; Patsyuk, M.; Pedroni, R.; Pennington, M. R.; Pentchev, L.; Peters, K. J.; Pooser, E.; Pratt, B.; Qiang, Y.; Reinhold, J.; Ritchie, B. G.; Robison, L.; Romanov, D.; Salgado, C.; Schumacher, R. A.; Schwarz, C.; Schwiening, J.; Semenov, A. Yu.; Semenova, I. A.; Seth, K. K.; Shepherd, M. R.; Smith, E. S.; Sober, D. I.; Somov, A.; Somov, S.; Soto, O.; Sparks, N.; Staib, M. J.; Stevens, J. R.; Strakovsky, I. I.; Subedi, A.; Tarasov, V.; Taylor, S.; Teymurazyan, A.; Tolstukhin, I.; Tomaradze, A.; Toro, A.; Tsaris, A.; Vasileiadis, G.; Vega, I.; Walford, N. K.; Werthmüller, D.; Whitlatch, T.; Williams, M.; Wolin, E.; Xiao, T.; Zarling, J.; Zhang, Z.; Zihlmann, B.; Mathieu, V.; Nys, J.; GlueX Collaboration

2017-04-01

We report measurements of the photon beam asymmetry Σ for the reactions γ ⃗p →p π0 and γ ⃗p →p η from the GlueX experiment using a 9 GeV linearly polarized, tagged photon beam incident on a liquid hydrogen target in Jefferson Lab's Hall D. The asymmetries, measured as a function of the proton momentum transfer, possess greater precision than previous π0 measurements and are the first η measurements in this energy regime. The results are compared with theoretical predictions based on t -channel, quasiparticle exchange and constrain the axial-vector component of the neutral meson production mechanism in these models.

Determination of the quenching correction factors for plastic scintillation detectors in therapeutic high-energy proton beams

PubMed Central

Wang, L L W; Perles, L A; Archambault, L; Sahoo, N; Mirkovic, D; Beddar, S

2013-01-01

The plastic scintillation detectors (PSD) have many advantages over other detectors in small field dosimetry due to its high spatial resolution, excellent water equivalence and instantaneous readout. However, in proton beams, the PSDs will undergo a quenching effect which makes the signal level reduced significantly when the detector is close to Bragg peak where the linear energy transfer (LET) for protons is very high. This study measures the quenching correction factor (QCF) for a PSD in clinical passive-scattering proton beams and investigates the feasibility of using PSDs in depth-dose measurements in proton beams. A polystyrene based PSD (BCF-12, ϕ0.5mm×4mm) was used to measure the depth-dose curves in a water phantom for monoenergetic unmodulated proton beams of nominal energies 100, 180 and 250 MeV. A Markus plane-parallel ion chamber was also used to get the dose distributions for the same proton beams. From these results, the QCF as a function of depth was derived for these proton beams. Next, the LET depth distributions for these proton beams were calculated by using the MCNPX Monte Carlo code, based on the experimentally validated nozzle models for these passive-scattering proton beams. Then the relationship between the QCF and the proton LET could be derived as an empirical formula. Finally, the obtained empirical formula was applied to the PSD measurements to get the corrected depth-dose curves and they were compared to the ion chamber measurements. A linear relationship between QCF and LET, i.e. Birks' formula, was obtained for the proton beams studied. The result is in agreement with the literature. The PSD measurements after the quenching corrections agree with ion chamber measurements within 5%. PSDs are good dosimeters for proton beam measurement if the quenching effect is corrected appropriately. PMID:23128412

Determination of the quenching correction factors for plastic scintillation detectors in therapeutic high-energy proton beams

NASA Astrophysics Data System (ADS)

Wang, L. L. W.; Perles, L. A.; Archambault, L.; Sahoo, N.; Mirkovic, D.; Beddar, S.

2012-12-01

Plastic scintillation detectors (PSDs) have many advantages over other detectors in small field dosimetry due to their high spatial resolution, excellent water equivalence and instantaneous readout. However, in proton beams, the PSDs undergo a quenching effect which makes the signal level reduced significantly when the detector is close to the Bragg peak where the linear energy transfer (LET) for protons is very high. This study measures the quenching correction factor (QCF) for a PSD in clinical passive-scattering proton beams and investigates the feasibility of using PSDs in depth-dose measurements in proton beams. A polystyrene-based PSD (BCF-12, ϕ0.5 mm × 4 mm) was used to measure the depth-dose curves in a water phantom for monoenergetic unmodulated proton beams of nominal energies 100, 180 and 250 MeV. A Markus plane-parallel ion chamber was also used to get the dose distributions for the same proton beams. From these results, the QCF as a function of depth was derived for these proton beams. Next, the LET depth distributions for these proton beams were calculated by using the MCNPX Monte Carlo code, based on the experimentally validated nozzle models for these passive-scattering proton beams. Then the relationship between the QCF and the proton LET could be derived as an empirical formula. Finally, the obtained empirical formula was applied to the PSD measurements to get the corrected depth-dose curves and they were compared to the ion chamber measurements. A linear relationship between the QCF and LET, i.e. Birks' formula, was obtained for the proton beams studied. The result is in agreement with the literature. The PSD measurements after the quenching corrections agree with ion chamber measurements within 5%. PSDs are good dosimeters for proton beam measurement if the quenching effect is corrected appropriately.

Tunneling dynamics of double proton transfer in formic acid and benzoic acid dimers

NASA Astrophysics Data System (ADS)

Smedarchina, Zorka; Fernández-Ramos, Antonio; Siebrand, Willem

2005-04-01

Direct dynamics calculations based on instanton techniques are reported of tunneling splittings due to double proton transfer in formic and benzoic acid dimers. The results are used to assign the observed splittings to levels for which the authors of the high-resolution spectra could not provide a definitive assignment. In both cases the splitting is shown to be due mainly to the zero-point level rather than to the vibrationally or electronically excited level whose spectrum was investigated. This leads to zero-point splittings of 375MHz for (DCOOH)2 and 1107MHz for the benzoic acid dimer. Thus, contrary to earlier calculations, it is found that the splitting is considerably larger in the benzoic than in the formic acid dimer. The calculations are extended to solid benzoic acid where the asymmetry of the proton-transfer potential induced by the crystal can be overcome by suitable doping. This has allowed direct measurement of the interactions responsible for double proton transfer, which were found to be much larger than those in the isolated dimer. To account for this observation both static and dynamic effects of the crystal forces on the intradimer hydrogen bonds are included in the calculations. The same methodology, extended to higher temperatures, is used to calculate rate constants for HH, HD, and DD transfers in neat benzoic acid crystals. The results are in good agreement with reported experimental rate constants measured by NMR relaxometry and, if allowance is made for small structural changes induced by doping, with the transfer matrix elements observed in doped crystals. Hence the method used allows a unified description of tunneling splittings in the gas phase and in doped crystals as well as of transfer rates in neat crystals.

Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.

PubMed

Haines, Brandon E; Steussy, C Nicklaus; Stauffacher, Cynthia V; Wiest, Olaf

2012-10-09

HMG-CoA reductase catalyzes the four-electron reduction of HMG-CoA to mevalonate and is an enzyme of considerable biomedical relevance because of the impact of its statin inhibitors on public health. Although the reaction has been studied extensively using X-ray crystallography, there are surprisingly no computational studies that test the mechanistic hypotheses suggested for this complex reaction. Theozyme and quantum mechanical (QM)/molecular mechanical (MM) calculations up to the B3LYP/6-31g(d,p)//B3LYP/6-311++g(2d,2p) level of theory were employed to generate an atomistic description of the enzymatic reaction process and its energy profile. The models generated here predict that the catalytically important Glu83 is protonated prior to hydride transfer and that it acts as the general acid or base in the reaction. With Glu83 protonated, the activation energies calculated for the sequential hydride transfer reactions, 21.8 and 19.3 kcal/mol, are in qualitative agreement with the experimentally determined rate constant for the entire reaction (1 s(-1) to 1 min(-1)). When Glu83 is not protonated, the first hydride transfer reaction is predicted to be disfavored by >20 kcal/mol, and the activation energy is predicted to be higher by >10 kcal/mol. While not involved in the reaction as an acid or base, Lys267 is critical for stabilization of the transition state in forming an oxyanion hole with the protonated Glu83. Molecular dynamics simulations and MM/Poisson-Boltzmann surface area free energy calculations predict that the enzyme active site stabilizes the hemithioacetal intermediate better than the aldehyde intermediate. This suggests a mechanism in which cofactor exchange occurs before the breakdown of the hemithioacetal. Slowing the conversion to aldehyde would provide the enzyme with a mechanism to protect it from solvent and explain why the free aldehyde is not observed experimentally. Our results support the hypothesis that the pK(a) of an active site acidic group is modulated by the redox state of the cofactor. The oxidized cofactor and deprotonated Glu83 are closer in space after hydride transfer, indicating that indeed the cofactor may influence the pK(a) of Glu83 through an electrostatic interaction. The enzyme is able to catalyze the transfer of a hydride to the structurally and electronically distinct substrates by maintaining the general shape of the active site and adjusting the electrostatic environment through acid-base chemistry. Our results are in good agreement with the well-studied hydride transfer reactions catalyzed by liver alcohol dehydrogenase in calculated energy profile and reaction geometries despite different mechanistic functionalities.

Quantum treatment of protons with the reduced explicitly correlated Hartree-Fock approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirjoosingh, Andrew; Pak, Michael V.; Brorsen, Kurt R.

2015-06-07

The nuclear-electronic orbital (NEO) approach treats select nuclei quantum mechanically on the same level as the electrons and includes nonadiabatic effects between the electrons and the quantum nuclei. The practical implementation of this approach is challenging due to the significance of electron-nucleus dynamical correlation. Herein, we present a general extension of the previously developed reduced NEO explicitly correlated Hartree-Fock (RXCHF) approach, in which only select electronic orbitals are explicitly correlated to each quantum nuclear orbital via Gaussian-type geminal functions. Approximations of the electronic exchange between the geminal-coupled electronic orbitals and the other electronic orbitals are also explored. This general approachmore » enables computationally tractable yet accurate calculations on molecular systems with quantum protons. The RXCHF method is applied to the hydrogen cyanide (HCN) and FHF{sup −} systems, where the proton and all electrons are treated quantum mechanically. For the HCN system, only the two electronic orbitals associated with the CH covalent bond are geminal-coupled to the proton orbital. For the FHF{sup −} system, only the four electronic orbitals associated with the two FH covalent bonds are geminal-coupled to the proton orbital. For both systems, the RXCHF method produces qualitatively accurate nuclear densities, in contrast to mean field-based NEO approaches. The development and implementation of the RXCHF method provide the framework to perform calculations on systems such as proton-coupled electron transfer reactions, where electron-proton nonadiabatic effects are important.« less

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study.

PubMed

Magalhães, Pedro R; Oliveira, A Sofia F; Campos, Sara R R; Soares, Cláudio M; Baptista, António M

2017-02-27

Cytochrome c oxidase (CcO) couples the reduction of dioxygen to water with transmembrane proton pumping, which leads to the generation of an electrochemical gradient. In this study we analyze how one of the components of the electrochemical gradient, the difference in pH across the membrane, or ΔpH, influences the protonation states of residues in CcO. We modified our continuum electrostatics/Monte Carlo (CE/MC) method in order to include the ΔpH and applied it to the study of CcO, in what is, to our best knowledge, the first CE/MC study of CcO in the presence of a pH gradient. The inclusion of a transmembrane pH gradient allows for the identification of residues whose titration behavior depends on the pH on both sides of the membrane. Among the several residues with unusual titration profiles, three are well-known key residues in the proton transfer process of CcO: E286 I , Y288 I , and K362 I . All three residues have been previously identified as being critical for the catalytic or proton pumping functions of CcO. Our results suggest that when the pH gradient increases, these residues may be part of a regulatory mechanism to stem the proton flow.

Artificial photosynthetic antennas and reaction centers

DOE PAGES

Llansola-Portoles, Manuel J.; Gust, Devens; Moore, Thomas A.; ...

2017-03-01

Presently, the world is experiencing an unprecedented crisis associated with the CO2 produced by the use of fossil fuels to power our economies. As evidenced by the increasing levels in the atmosphere, the reduction of CO2 to biomass by photosynthesis cannot keep pace with production with the result that nature has lost control of the global carbon cycle. In order to restore control of the global carbon cycle to solar-driven processes, highly efficient artificial photosynthesis can augment photosynthesis in specific ways and places. The increased efficiency of artificial photosynthesis can provide both renewable carbon-based fuels and lower net atmospheric levelsmore » of CO2, which will preserve land and support the ecosystem services upon which all life on Earth depends. The development of artificial photosynthetic antennas and reaction centers contributes to the understanding of natural photosynthesis and to the knowledge base necessary for the development of future scalable technologies. This review focuses on the design and study of molecular and hybrid molecular-semiconductor nanoparticle based systems, all of which are inspired by functions found in photosynthesis and some of which are inspired by components of photosynthesis. In addition to constructs illustrating energy transfer, photoinduced electron transfer, charge shift reactions and proton coupled electron transfer, our review covers systems that produce proton motive force.« less

Artificial photosynthetic antennas and reaction centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Llansola-Portoles, Manuel J.; Gust, Devens; Moore, Thomas A.

Presently, the world is experiencing an unprecedented crisis associated with the CO2 produced by the use of fossil fuels to power our economies. As evidenced by the increasing levels in the atmosphere, the reduction of CO2 to biomass by photosynthesis cannot keep pace with production with the result that nature has lost control of the global carbon cycle. In order to restore control of the global carbon cycle to solar-driven processes, highly efficient artificial photosynthesis can augment photosynthesis in specific ways and places. The increased efficiency of artificial photosynthesis can provide both renewable carbon-based fuels and lower net atmospheric levelsmore » of CO2, which will preserve land and support the ecosystem services upon which all life on Earth depends. The development of artificial photosynthetic antennas and reaction centers contributes to the understanding of natural photosynthesis and to the knowledge base necessary for the development of future scalable technologies. This review focuses on the design and study of molecular and hybrid molecular-semiconductor nanoparticle based systems, all of which are inspired by functions found in photosynthesis and some of which are inspired by components of photosynthesis. In addition to constructs illustrating energy transfer, photoinduced electron transfer, charge shift reactions and proton coupled electron transfer, our review covers systems that produce proton motive force.« less

The controlled relay of multiple protons required at the active site of nitrogenase.

PubMed

Dance, Ian

2012-07-07

The enzyme nitrogenase, when reducing natural and unnatural substrates, requires large numbers of protons per chemical catalytic cycle. The active face of the catalytic site (the FeMo-cofactor, FeMo-co) is situated in a protein domain which is largely hydrophobic and anhydrous, and incapable of serial provision of multiple protons. Through detailed analysis of the high quality protein crystal structures available the characteristics of a chain of water molecules leading from the protein surface to a key sulfur atom (S3B) of FeMo-co are described. The first half of the water chain from the surface inwards is branched, slightly variable, and able to accommodate exogenous small molecules: this is dubbed the proton bay. The second half, from the proton bay to S3B, is comprised of a single chain of eight hydrogen bonded water molecules. This section is strictly conserved, and is intimately involved in hydrogen bonds with homocitrate, an essential component that chelates Mo. This is the proton wire, and a detailed Grotthuss mechanism for serial translocation of protons through this proton wire to S3B is proposed. This controlled serial proton relay from the protein surface to S3B is an essential component of the intramolecular hydrogenation paradigm for the complete chemical mechanisms of nitrogenase. Each proton reaching S3B, instigated by electron transfer to FeMo-co, becomes a hydrogen atom that migrates to other components of the active face of FeMo-co and to bound substrates and intermediates, allowing subsequent multiple proton transfers along the proton wire. Experiments to test the proposed mechanism of proton supply are suggested. The water chain in nitrogenase is comparable with the purported proton pumping pathway of cytochrome c oxidase.

Momentum loss in proton-nucleus and nucleus-nucleus collisions

NASA Technical Reports Server (NTRS)

Khan, Ferdous; Townsend, Lawrence W.

1993-01-01

An optical model description, based on multiple scattering theory, of longitudinal momentum loss in proton-nucleus and nucleus-nucleus collisions is presented. The crucial role of the imaginary component of the nucleon-nucleon transition matrix in accounting for longitudinal momentum transfer is demonstrated. Results obtained with this model are compared with Intranuclear Cascade (INC) calculations, as well as with predictions from Vlasov-Uehling-Uhlenbeck (VUU) and quantum molecular dynamics (QMD) simulations. Comparisons are also made with experimental data where available. These indicate that the present model is adequate to account for longitudinal momentum transfer in both proton-nucleus and nucleus-nucleus collisions over a wide range of energies.

Investigation of Chemical Exchange at Intermediate Exchange Rates using a Combination of Chemical Exchange Saturation Transfer (CEST) and Spin-Locking methods (CESTrho)

PubMed Central

Kogan, Feliks; Singh, Anup; Cai, Keija; Haris, Mohammad; Hariharan, Hari; Reddy, Ravinder

2011-01-01

Proton exchange imaging is important as it allows for visualization and quantification of the distribution of specific metabolites with conventional MRI. Current exchange mediated MRI methods suffer from poor contrast as well as confounding factors that influence exchange rates. In this study we developed a new method to measure proton exchange which combines chemical exchange saturation transfer (CEST) and T1ρ magnetization preparation methods (CESTrho). We demonstrated that this new CESTrho sequence can detect proton exchange in the slow to intermediate exchange regimes. It has a linear dependence on proton concentration which allows it to be used to quantitatively measure changes in metabolite concentration. Additionally, the magnetization scheme of this new method can be customized to make it insensitive to changes in exchange rate while retaining its dependency on solute concentration. Finally, we showed the feasibility of using CESTrho in vivo. This sequence is able to detect proton exchange at intermediate exchange rates and is unaffected by the confounding factors that influence proton exchange rates thus making it ideal for the measurement of metabolites with exchangeable protons in this exchange regime. PMID:22009759

Investigation of chemical exchange at intermediate exchange rates using a combination of chemical exchange saturation transfer (CEST) and spin-locking methods (CESTrho).

PubMed

Kogan, Feliks; Singh, Anup; Cai, Keija; Haris, Mohammad; Hariharan, Hari; Reddy, Ravinder

2012-07-01

Proton exchange imaging is important as it allows for visualization and quantification of the distribution of specific metabolites with conventional MRI. Current exchange mediated MRI methods suffer from poor contrast as well as confounding factors that influence exchange rates. In this study we developed a new method to measure proton exchange which combines chemical exchange saturation transfer and T(1)(ρ) magnetization preparation methods (CESTrho). We demonstrated that this new CESTrho sequence can detect proton exchange in the slow to intermediate exchange regimes. It has a linear dependence on proton concentration which allows it to be used to quantitatively measure changes in metabolite concentration. Additionally, the magnetization scheme of this new method can be customized to make it insensitive to changes in exchange rate while retaining its dependency on solute concentration. Finally, we showed the feasibility of using CESTrho in vivo. This sequence is able to detect proton exchange at intermediate exchange rates and is unaffected by the confounding factors that influence proton exchange rates thus making it ideal for the measurement of metabolites with exchangeable protons in this exchange regime. Copyright © 2011 Wiley Periodicals, Inc.

Transfer of a proton between H2 and O2.

PubMed

Kluge, Lars; Gärtner, Sabrina; Brünken, Sandra; Asvany, Oskar; Gerlich, Dieter; Schlemmer, Stephan

2012-11-13

The proton affinities of hydrogen and oxygen are very similar. Therefore, it has been discussed that the proton transfer from the omnipresent H(3)(+) to molecular oxygen in the near thermoneutral reaction H(3)(+) + O(2) <--> O(2)H(+) + H(2) effectively binds the interstellar oxygen in O(2)H(+). In this work, the proton transfer reaction has been investigated in a low-temperature 22-pole ion trap from almost room temperature (280 K) down to the lowest possible temperature limited by freeze out of oxygen gas (about 40 K at a low pressure). The Arrhenius behaviour of the rate coefficient for the forward reaction shows that it is subject to an activation energy of E(A)/k=113 K. Thus, the forward reaction can proceed only in higher temperature molecular clouds. Applying laser-induced reactions to the given reaction (in the backward direction), a preliminary search for spectroscopic signatures of O(2)H(+) in the infrared was unsuccessful, whereas the forward reaction has been successfully used to probe the population of the lowest ortho and para levels of H(3)(+).

Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study.

PubMed

Omidyan, Reza; Iravani, Maryam

2016-11-14

The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH 2 ) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S 1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S 1 /S 0 ), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study

NASA Astrophysics Data System (ADS)

Omidyan, Reza; Iravani, Maryam

2016-11-01

The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH2) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S1/S0), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

Electron scattering from high-momentum neutrons in deuterium

NASA Astrophysics Data System (ADS)

Klimenko, A. V.; Kuhn, S. E.; Butuceanu, C.; Egiyan, K. S.; Griffioen, K. A.; Adams, G.; Ambrozewicz, P.; Anghinolfi, M.; Asryan, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Barrow, S.; Batourine, V.; Battaglieri, M.; Bedlinskiy, I.; Bektasoglu, M.; Bellis, M.; Benmouna, N.; Biselli, A. S.; Bouchigny, S.; Boiarinov, S.; Bradford, R.; Branford, D.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Cazes, A.; Chen, S.; Cole, P. L.; Coltharp, P.; Cords, D.; Corvisiero, P.; Crabb, D.; Cummings, J. P.; Dashyan, N. B.; Devita, R.; Sanctis, E. De; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; Dharmawardane, K. V.; Djalali, C.; Dodge, G. E.; Donnelly, J.; Doughty, D.; Dugger, M.; Dytman, S.; Dzyubak, O. P.; Egiyan, H.; Elouadrhiri, L.; Eugenio, P.; Fatemi, R.; Fedotov, G.; Fersch, R. G.; Feuerbach, R. J.; Funsten, H.; Garçon, M.; Gavalian, G.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Gonenc, A.; Gordon, C. I. O.; Gothe, R. W.; Guidal, M.; Guillo, M.; Guler, N.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hakobyan, R. S.; Hardie, J.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Joo, K.; Juengst, H. G.; Kellie, J. D.; Khandaker, M.; Kim, W.; Klein, A.; Klein, F. J.; Kossov, M.; Kramer, L. H.; Kubarovsky, V.; Kuhn, J.; Kuleshov, S. V.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Li, Ji; Livingston, K.; McAleer, S.; McKinnon, B.; McNabb, J. W. C.; Mecking, B. A.; Mehrabyan, S.; Melone, J. J.; Mestayer, M. D.; Meyer, C. A.; Mibe, T.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morand, L.; Morrow, S. A.; Mueller, J.; Mutchler, G. S.; Nadel-Turonski, P.; Napolitano, J.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Osipenko, M.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Paterson, C.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Pozdniakov, S.; Preedom, B. M.; Price, J. W.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Ronchetti, F.; Rosner, G.; Rossi, P.; Sabatié, F.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Stoler, P.; Strauch, S.; Taiuti, M.; Tedeschi, D. J.; Thoma, U.; Tkabladze, A.; Tkachenko, S.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Weinstein, L. B.; Weygand, D. P.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Zana, L.; Zhang, J.; Zhao, B.

2006-03-01

We report results from an experiment measuring the semiinclusive reaction H2(e,e'ps) in which the proton ps is moving at a large angle relative to the momentum transfer. If we assume that the proton was a spectator to the reaction taking place on the neutron in deuterium, the initial state of that neutron can be inferred. This method, known as spectator tagging, can be used to study electron scattering from high-momentum (off-shell) neutrons in deuterium. The data were taken with a 5.765 GeV electron beam on a deuterium target in Jefferson Laboratory's Hall B, using the CEBAF large acceptance spectrometer. A reduced cross section was extracted for different values of final state missing mass W*, backward proton momentum p→s, and momentum transfer Q2. The data are compared to a simple plane wave impulse approximation (PWIA) spectator model. A strong enhancement in the data observed at transverse kinematics is not reproduced by the PWIA model. This enhancement can likely be associated with the contribution of final state interactions (FSI) that were not incorporated into the model. Within the framework of the simple spectator model, a “bound neutron structure function” F2neff was extracted as a function of W* and the scaling variable x* at extreme backward kinematics, where the effects of FSI appear to be smaller. For ps>0.4GeV/c, where the neutron is far off-shell, the model overestimates the value of F2neff in the region of x* between 0.25 and 0.6. A dependence of the bound neutron structure function on the neutron's “off-shell-ness” is one possible effect that can cause the observed deviation.

Two-Dimensional Metal-Free Organic Multiferroic Material for Design of Multifunctional Integrated Circuits.

PubMed

Tu, Zhengyuan; Wu, Menghao; Zeng, Xiao Cheng

2017-05-04

Coexistence of ferromagnetism and ferroelectricity in a single 2D material is highly desirable for integration of multifunctional units in 2D material-based circuits. We report theoretical evidence of C 6 N 8 H organic network as being the first 2D organic multiferroic material with coexisting ferromagnetic and ferroelectric properties. The ferroelectricity stems from multimode proton-transfer within the 2D C 6 N 8 H network, in which a long-range proton-transfer mode is enabled by the facilitation of oxygen molecule when the network is exposed to the air. Such oxygen-assisted ferroelectricity also leads to a high Curie temperature and coupling between ferroelectricity and ferromagnetism. We also find that hydrogenation and carbon doping can transform the 2D g-C 3 N 4 network from an insulator to an n-type/p-type magnetic semiconductor with modest bandgap. Akin to the dopant induced n/p channels in silicon wafer, a variety of dopant created functional units can be integrated into the g-C 3 N 4 wafer by design for nanoelectronic applications.

Quasi-four-body treatment of charge transfer in the collision of protons with atomic helium: II. Second-order non-Thomas mechanisms and the cross sections

NASA Astrophysics Data System (ADS)

Safarzade, Zohre; Akbarabadi, Farideh Shojaei; Fathi, Reza; Brunger, Michael J.; Bolorizadeh, Mohammad A.

2018-05-01

A fully quantum mechanical four-body treatment of charge transfer collisions between energetic protons and atomic helium is developed here. The Pauli exclusion principle is applied to both the wave function of the initial and final states as well as the operators involved in the interaction. Prior to the collision, the helium atom is assumed as a two-body system composed of the nucleus, He2+, and an electron cloud composed of two electrons. Nonetheless, four particles are assumed in the final state. As the double interactions contribute extensively in single charge transfer collisions, the Faddeev-Lovelace-Watson scattering formalism describes it best physically. The treatment of the charge transfer cross section, under this quasi-four-body treatment within the FWL formalism, showed that other mechanisms leading to an effect similar to the Thomas one occur at the same scattering angle. Here, we study the two-body interactions which are not classically described but which lead to an effect similar to the Thomas mechanism and finally we calculate the total singlet and triplet amplitudes as well as the angular distributions of the charge transfer cross sections. As the incoming projectiles are assumed to be plane waves, the present results are calculated for high energies; specifically a projectile energy of 7.42 MeV was assumed as this is where experimental results are available in the literature for comparison. Finally, when possible we compare the present results with the other available theoretical data.

Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for Production and Oxidation of Hydrogen.

PubMed

Raugei, Simone; Helm, Monte L; Hammes-Schiffer, Sharon; Appel, Aaron M; O'Hagan, Molly; Wiedner, Eric S; Bullock, R Morris

2016-01-19

Understanding how to control the movement of protons and electrons is crucial to the design of fast, efficient electrocatalysts for H2 production and oxidation based on earth-abundant metals. Our work seeks to address fundamental questions about proton movement. We have demonstrated that incorporating a pendant amine functioning as a proton relay in the second coordination sphere of a metal complex helps proton mobility, resulting in faster and more energy-efficient catalysts. Proton-transfer reactions can be rate-limiting and are influenced by several factors, such as pKa values, steric effects, hydrogen bonding, and solvation/desolvation of the exogenous base and acid employed. The presence of multiple protonation sites introduces branching points along the catalytic cycle, making less productive pathways accessible or leading to the formation of stable off-cycle species. Using ligands with only one pendant amine mitigates this problem and results in catalysts with high rates for production of H2, although generally at higher overpotentials. For H2 oxidation catalysts, iron complexes with a high H2 binding affinity were developed. However, these iron complexes had a pKa mismatch between the protonated metal center and the protonated pendant amine, and consequently intramolecular proton movement was slow. Taken altogether, our results demonstrate the necessity of optimizing the entire catalytic cycle because optimization of a specific catalytic step can negatively influence another step and not necessarily lead to a better catalytic performance. We discuss a general procedure, based on thermodynamic arguments, which allows the simultaneous minimization of the free-energy change of each catalytic step, yielding a nearly flat free-energy surface, with no large barriers due to energy mismatches from either high- or low-energy intermediates.

Theoretical Analysis of Cobalt Hangman Porphyrins: Ligand Dearomatization and Mechanistic Implications for Hydrogen Evolution

DOE PAGES

Solis, Brian H.; Maher, Andrew G.; Honda, Tatsuhiko; ...

2014-11-06

The design of molecular electrocatalysts for hydrogen evolution has been targeted as a strategy for the conversion of solar energy to chemical fuels. In cobalt hangman porphyrins, a carboxylic acid group on a xanthene backbone is positioned over a metalloporphyrin to serve as a proton relay. A key proton-coupled electron transfer (PCET) step along the hydrogen evolution pathway occurs via a sequential ET-PT mechanism in which electron transfer (ET) is followed by proton transfer (PT). Herein theoretical calculations are employed to investigate the mechanistic pathways of these hangman metalloporphyrins. The calculations confirm the ET-PT mechanism by illustrating that the calculatedmore » reduction potentials for this mechanism are consistent with experimental data. Under strong-acid conditions, the calculations indicate that this catalyst evolves H 2 by protonation of a formally Co(II) hydride intermediate, as suggested by previous experiments. Under weak-acid conditions, however, the calculations reveal a mechanism that proceeds via a phlorin intermediate, in which the meso carbon of the porphyrin is protonated. In the first electrochemical reduction, the neutral Co(II) species is reduced to a monoanionic singlet Co(I) species. Subsequent reduction leads to a dianionic doublet, formally a Co(0) complex in which substantial mixing of Co and porphyrin orbitals indicates ligand redox noninnocence. The partial reduction of the ligand disrupts the aromaticity in the porphyrin ring. As a result of this ligand dearomatization, protonation of the dianionic species is significantly more thermodynamically favorable at the meso carbon than at the metal center, and the ET-PT mechanism leads to a dianionic phlorin species. According to the proposed mechanism, the carboxylate group of this dianionic phlorin species is reprotonated, the species is reduced again, and H 2 is evolved from the protonated carboxylate and the protonated carbon. This proposed mechanism is a guidepost for future experimental studies of proton relays involving noninnocent ligand platforms.« less

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE PAGES

Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...

2017-05-01

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Measurement of D ∗ meson cross sections at HERA and determination of the gluon density in the proton using NLO QCD

NASA Astrophysics Data System (ADS)

Adloff, C.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Bate, P.; Beck, M.; Beglarian, A.; Behnke, O.; Behrend, H.-J.; Beier, C.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Biddulph, P.; Bizot, J. C.; Boudry, V.; Braunschweig, W.; Brisson, V.; Brown, D. P.; Brückner, W.; Bruel, P.; Bruncko, D.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burrage, A.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Chabert, E.; Charlet, M.; Clarke, D.; Clerbaux, B.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cvach, J.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davidsson, M.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Demirchyan, R.; Diaconu, C.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Donovan, K. T.; Dowell, J. D.; Droutskoi, A.; Ebert, J.; Eckerlin, G.; Eckstein, D.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Enzenberger, M.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Fleischer, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gassner, J.; Gayler, J.; Gerhards, R.; Ghazaryan, S.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haustein, V.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Hengstmann, S.; Henschel, H.; Heremans, R.; Herynek, I.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoffmann, D.; Horisberger, R.; Hurling, S.; Ibbotson, M.; İşsever, Ç.; Jacquet, M.; Jaffre, M.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jones, M.; Jung, H.; Kästli, H. K.; Kander, M.; Kant, D.; Kapichine, M.; Karlsson, M.; Karschnik, O.; Katzy, J.; Kaufmann, O.; Kausch, M.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, K.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Lahmann, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Lendermann, V.; Levonian, S.; Lindstroem, M.; List, B.; Lobo, G.; Lobodzinska, E.; Lubimov, V.; Lüders, S.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martin, G.; Martyn, H.-U.; Martyniak, J.; Maxfield, S. J.; McMahon, T. R.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Mikocki, S.; Milstead, D.; Moeck, J.; Mohr, R.; Mohrdieck, S.; Moreau, F.; Morris, J. V.; Müller, D.; Müller, K.; Murin, P.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nikitin, D.; Nix, O.; Nowak, G.; Nunnemann, T.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panassik, V.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Rabbertz, K.; Rauschenberger, J.; Reimer, P.; Reisert, B.; Reyna, D.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Scheins, J.; Schilling, F.-P.; Schleif, S.; Schleper, P.; Schmidt, D.; Schmidt, D.; Schoeffel, L.; Schröder, V.; Schultz-Coulon, H.-C.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Sirois, Y.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Spaskov, V.; Specka, A.; Spiekermann, J.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stiewe, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Swart, M.; Tapprogge, S.; Taševský, M.; Tchernshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Udluft, S.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Haecke, A.; Van Mechelen, P.; Vazdik, Y.; Villet, G.; Wacker, K.; Wallny, R.; Walter, T.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wittmann, E.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žaček, J.; Zálešak, J.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1999-04-01

With the H1 detector at the ep collider HERA, D ∗ meson production cross sections have been measured in deep inelastic scattering with four-momentum transfers Q2 > 3 GeV 2 and in photoproduction at energies around Wγp ≈ 88 GeV and 194 GeV. Next-to-Leading Order QCD calculations are found to describe the differential cross sections within theoretical and experimental uncertainties. Using these calculations, the NLO gluon momentum distribution in the proton, xgg( xg), has been extracted in the momentum fraction range 7.5 × 10 -4 < xg < 4 × 10 -2 at average scales μ2 = 25 to 50 GeV 2. The gluon momentum fraction xg has been obtained from the measured kinematics of the scattered electron and the D ∗ meson in the final state. The results compare well with the gluon distribution obtained from the analysis of scaling violations of the proton structure function F2.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Kiyoung; Li, Ning; Kwak, Yeonju

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Stereochemistry of 1,2-elimination and proton-transfer reactions: toward a unified understanding.

PubMed

Mohrig, Jerry R

2013-07-16

Many mechanistic and stereochemical studies have focused on the breaking of the C-H bond through base-catalyzed elimination reactions. When we began our research, however, chemists knew almost nothing about the stereospecificity of addition-elimination reactions involving conjugated acyclic carbonyl compounds, even though the carbonyl group is a pivotal functional group in organic chemistry. Over the last 25 years, we have studied the addition-elimination reactions of β-substituted acyclic esters, thioesters, and ketones in order to reach a comprehensive understanding of how electronic effects influence their stereochemistry. This Account brings together our understanding of the stereochemistry of 1,2-elimination and proton-transfer reactions, describing how each study has built upon previous work and contributed to our understanding of this field. When we began, chemists thought that anti stereospecificity in base-catalyzed 1,2-elimination reactions occurred via concerted E2 mechanisms, which provide a smooth path for anti elimination. Unexpectedly, we discovered that some E1cBirrev reactions produce the same anti stereospecificity as E2 reactions even though they proceed through diffusionally equilibrated, "free" enolate-anion intermediates. This result calls into question the conventional wisdom that anti stereochemistry must result from a concerted mechanism. While carrying out our research, we developed insights ranging from the role of historical contingency in the evolution of hydratase-dehydratase enzymes to the influence of buffers on the stereochemistry of H/D exchange in D2O. Negative hyperconjugation is the most important concept for understanding our results. This idea provides a unifying view for the largely anti stereochemistry in E1cBirrev elimination reactions and a basis for understanding the stereoelectronic influence of electron-withdrawing β-substituents on proton-transfer reactions.

Experimental and Theoretical Studies on Gas-Phase Fragmentation Reactions of Protonated Methyl Benzoate: Concomitant Neutral Eliminations of Benzene, Carbon Dioxide, and Methanol

NASA Astrophysics Data System (ADS)

Xia, Hanxue; Zhang, Yong; Attygalle, Athula B.

2018-06-01

Protonated methyl benzoate, upon activation, fragments by three distinct pathways. The m/z 137 ion for the protonated species generated by helium-plasma ionization (HePI) was mass-selected and subjected to collisional activation. In one fragmentation pathway, the protonated molecule generated a product ion of m/z 59 by eliminating a molecule of benzene (Pathway I). The m/z 59 ion (generally recognized as the methoxycarbonyl cation) produced in this way, then formed a methyl carbenium ion in situ by decarboxylation, which in turn evoked an electrophilic aromatic addition reaction on the benzene ring by a termolecular process to generate the toluenium cation (Pathway II). Moreover, protonated methyl benzoate undergoes also a methanol loss (Pathway III). However, it is not a simple removal of a methanol molecule after a protonation on the methoxy group. The incipient proton migrates to the ring and randomizes to a certain degree before a subsequent transfer of one of the ring protons to the alkoxy group for the concomitant methanol elimination. The spectrum recorded from deuteronated methyl benzoate showed two peaks at m/z 105 and 106 for the benzoyl cation at a ratio of 2:1, confirming the charge-imparting proton is mobile. However, the proton transfer from the benzenium intermediate to the methoxy group for the methanol loss occurs before achieving a complete state of scrambling. [Figure not available: see fulltext.

Proton Linear Energy Transfer measurement using Emulsion Cloud Chamber

NASA Astrophysics Data System (ADS)

Shin, Jae-ik; Park, Seyjoon; Kim, Haksoo; Kim, Meyoung; Jeong, Chiyoung; Cho, Sungkoo; Lim, Young Kyung; Shin, Dongho; Lee, Se Byeong; Morishima, Kunihiro; Naganawa, Naotaka; Sato, Osamu; Kwak, Jungwon; Kim, Sung Hyun; Cho, Jung Sook; Ahn, Jung Keun; Kim, Ji Hyun; Yoon, Chun Sil; Incerti, Sebastien

2015-04-01

This study proposes to determine the correlation between the Volume Pulse Height (VPH) measured by nuclear emulsion and Linear Energy Transfer (LET) calculated by Monte Carlo simulation based on Geant4. The nuclear emulsion was irradiated at the National Cancer Center (NCC) with a therapeutic proton beam and was installed at 5.2 m distance from the beam nozzle structure with various thicknesses of water-equivalent material (PMMA) blocks to position with specific positions along the Bragg curve. After the beam exposure and development of the emulsion films, the films were scanned by S-UTS developed in Nagoya University. The proton tracks in the scanned films were reconstructed using the 'NETSCAN' method. Through this procedure, the VPH can be derived from each reconstructed proton track at each position along the Bragg curve. The VPH value indicates the magnitude of energy loss in proton track. By comparison with the simulation results obtained using Geant4, we found the correlation between the LET calculated by Monte Carlo simulation and the VPH measured by the nuclear emulsion.

Measurement of HONO, HNCO, and other inorganic acids by negative-ion proton-transfer chemical-ionization mass spectrometry (NI-PT-CIMS): application to biomass burning emissions

Treesearch

J. M. Roberts; P. Veres; C. Warneke; J. A. Neuman; R. A. Washenfelder; S. S. Brown; M. Baasandorj; J. B. Burkholder; I. R. Burling; T. J. Johnson; R. J. Yokelson; J. de Gouw

2010-01-01

A negative-ion proton transfer chemical ionization mass spectrometric technique (NI-PT-CIMS), using acetate as the reagent ion, was applied to the measurement of volatile inorganic acids of atmospheric interest: hydrochloric (HCl), nitrous (HONO), nitric 5 (HNO3), and isocyanic (HNCO) acids. Gas phase calibrations through the sampling inlet showed the method to be...

Fluorescence excitation and excited state intramolecular relaxation dynamics of jet-cooled methyl-2-hydroxy-3-naphthoate

NASA Astrophysics Data System (ADS)

McCarthy, Annemarie; Ruth, Albert A.

2013-11-01

Two distinct S0 → S1 fluorescence excitation spectra of methyl-2-hydroxy-3-napthoate (MHN23) have been obtained by monitoring fluorescence separately in the short (˜410 nm) and long (˜650 nm) wavelength emission bands. The short wavelength fluorescence is assigned to two MHN23 conformers which do not undergo excited state intramolecular proton transfer (ESIPT). Analysis of the 'long wavelength' fluorescence excitation spectrum, which arises from the proton transfer tautomer of MHN23 indicates an average lifetime of τ ⩾ 18 ± 2 fs for the initially excited states. Invoking the results of Catalan et al. [J. Phys. Chem. A, 1999, 103, 10921], who determined the N tautomer to decay predominantly via a fast non-radiative process, the limit of the rate of intramolecular excited proton transfer in MHN23 is calculated as, kpt ⩽ 1 × 1012 s-1.

Proton transfer reaction mass spectrometry: on-line trace gas analysis at the ppb level

NASA Astrophysics Data System (ADS)

Hansel, A.; Jordan, A.; Holzinger, R.; Prazeller, P.; Vogel, W.; Lindinger, W.

1995-11-01

A system for trace gas analysis using proton transfer reaction mass spectrometry (PTR-MS) has been developed which allows for on-line measurements of components with concentrations as low as 1 ppb. The method is based on reactions of H3O+ ions, which perform non-dissociative proton transfer to most of the common organic trace constituents but do not react with any of the components present in clean air. Examples of analysis of breath taken from smokers and non-smokers as well as from patients suffering from cirrhosis of the liver, and of air in buildings as well as of ambient air taken at a road crossing demonstrate the wide range of applicability of this method. An enhanced level of acetonitrile in the breath is a most suitable indicator that a person is a smoker. Enhanced levels of propanol strongly indicate that a person has a severe liver deficiency.

Dynamic correlation effects in fully differential cross sections for 75-keV proton-impact ionization of helium

NASA Astrophysics Data System (ADS)

Niu, Xiaojie; Sun, Shiyan; Wang, Fujun; Jia, Xiangfu

2017-08-01

The effect of final-state dynamic correlation is investigated for helium single ionization by 75-keV proton impact analyzing fully differential cross sections (FDCS). The final state is represented by a continuum correlated wave (CCW-PT) function which accounts for the interaction between the projectile and the residual target ion (PT interaction). This continuum correlated wave function partially includes the correlation of electron-projectile and electron-target relative motion as coupling terms of the wave equation. The transition matrix is evaluated using the CCW-PT function and the Born initial state. The analytical expression of the transition matrix has been obtained. We have shown that this series is strongly convergent and analyzed the contribution of their different terms to the FDCS within the perturbation method. Illustrative computations are performed in the scattering plane and in the perpendicular plane. Both the correlation effects and the PT interaction are checked by the preset calculations. Our results are compared with absolute experimental data as well as other theoretical models. We have shown that the dynamic correlation plays an important role in the single ionization of atoms by proton impact at intermediate projectile energies, especially at large transverse momentum transfer. While overall agreement between theory and the experimental data is encouraging, detailed agreement is lacking. The need for more theoretical and experimental work is emphasized.

A SIFT study of the reactions of H2ONO+ ions with several types of organic molecules

NASA Astrophysics Data System (ADS)

Smith, David; Wang, Tianshu; Spanel, Patrik

2003-11-01

A selected ion flow tube (SIFT) study has been carried out of the reactions of hydrated nitrosonium ions, NO+H2O, which theory has equated to protonated nitrous acid ions, H2ONO+. One objective of this study was to investigate if this ion exhibits the properties of both a cluster ion and a protonated acid in their reactions with a variety of organic molecules. The chosen reactant molecules comprise two each of the following types--amines, terpenes, aromatic hydrocarbons, esters, carboxylic acids, ketones, aldehydes and alcohols. The reactant H2ONO+ (NO+H2O) ions are formed in a discharge ion source and injected into helium carrier gas where they are partially vibrationally excited and partially dissociated to NO+ ions. Hence, the reactions of the H2ONO+ ions had to be studies simultaneously with NO+ ions, the reactions of the latter ions readily being studied by selectively injecting NO+ ions into the carrier gas. The results of this study indicate that the H2ONO+ ions undergo a wide variety of reaction processes that depend on the properties of the reactant molecules such as their ionisation energies and proton affinities. These processes include charge transfer with compounds, M, that have low ionisation energies (producing M+), proton transfer with compounds possessing large proton affinities (MH+), hydride ion transfer (M---H+), alkyl radical (M---R+), alkoxide radical transfer (M---OR+), ion-molecule association (NO+H2OM) and ligand switching (NO+M), producing the ions given in parentheses.

Modeling the impact of preflushing on CTE in proton irradiated CCD-based detectors

NASA Astrophysics Data System (ADS)

Philbrick, R. H.

2002-04-01

A software model is described that performs a "real world" simulation of the operation of several types of charge-coupled device (CCD)-based detectors in order to accurately predict the impact that high-energy proton radiation has on image distortion and modulation transfer function (MTF). The model was written primarily to predict the effectiveness of vertical preflushing on the custom full frame CCD-based detectors intended for use on the proposed Kepler Discovery mission, but it is capable of simulating many other types of CCD detectors and operating modes as well. The model keeps track of the occupancy of all phosphorous-silicon (P-V), divacancy (V-V) and oxygen-silicon (O-V) defect centers under every CCD electrode over the entire detector area. The integrated image is read out by simulating every electrode-to-electrode charge transfer in both the vertical and horizontal CCD registers. A signal level dependency on the capture and emission of signal is included and the current state of each electrode (e.g., barrier or storage) is considered when distributing integrated and emitted signal. Options for performing preflushing, preflashing, and including mini-channels are available on both the vertical and horizontal CCD registers. In addition, dark signal generation and image transfer smear can be selectively enabled or disabled. A comparison of the charge transfer efficiency (CTE) data measured on the Hubble space telescope imaging spectrometer (STIS) CCD with the CTE extracted from model simulations of the STIS CCD show good agreement.

Theoretical simulations on the antioxidant mechanism of naturally occurring flavonoid: A DFT approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Praveena, R.; Sadasivam, K.

Synthetic antioxidants such as butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT) are found to be toxic, hence non-carcinogenic naturally occurring radical scavengers especially flavonoids have gained considerable importance in the past two decades. In the present investigation, the radical scavenging activity of C-glycosyl flavonoids is evaluated using theoretical approach which could broaden its scope in therapeutic applications. Gas and solvent phase studies of structural and molecular characteristics of C-glycosyl flavonoid, isovitexin is investigated through hydrogen atom transfer mechanism (HAT), Electron transfer-proton transfer (ET–PT) and Sequential proton loss electron transfer (SPLET) by Density functional theory (DFT) using hybrid parameters. The computedmore » values of the adiabatic ionization potential, electron affinity, hardness, softness, electronegativity and electrophilic index indicate that isovitexin possess good radical scavenging activity. The behavior of different –OH groups in polyphenolic compounds is assessed by considering electronic effects of the neighbouring groups and the overall geometry of molecule which in turn helps in analyzing the antioxidant capacity of the polyphenolic molecule. The studies indicate that the H–atom abstraction from 4’–OH site is preferred during the radical scavenging process. From Mulliken spin density analysis and FMOs, B–ring is found to be more delocalized center and capable of electron donation. Comparison of antioxidant activity of vitexin and isovitexin leads to the conclusion that isovitexin acts as a better radical scavenger. This is an evidence for the importance of position of glucose unit in the flavonoid.« less

Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization - a mass spectrometry, ion mobility and molecular modeling study.

PubMed

Tintaru, Aura; Chendo, Christophe; Wang, Qi; Viel, Stéphane; Quéléver, Gilles; Peng, Ling; Posocco, Paola; Pricl, Sabrina; Charles, Laurence

2014-01-15

Tandem mass spectrometry and ion mobility spectrometry experiments were performed on multiply charged molecules formed upon conjugation of a poly(amidoamine) (PAMAM) dendrimer with a poly(ethylene oxide) (PEO) linear polymer to evidence any conformational modification as a function of their charge state (2+ to 4+) and of the adducted cation (H(+)vs Li(+)). Experimental findings were rationalized by molecular dynamics simulations. The G0 PAMAM head-group could accommodate up to three protons, with protonated terminal amine group enclosed in a pseudo 18-crown-6 ring formed by the PEO segment. This particular conformation enabled a hydrogen bond network which allowed long-range proton transfer to occur during collisionally activated dissociation. In contrast, lithium adduction was found to mainly occur onto oxygen atoms of the polyether, each Li(+) cation being coordinated by a 12-crown-4 pseudo structure. As a result, for the studied polymeric segment (Mn=1500gmol(-1)), PEO-PAMAM hybrid molecules exhibited a more expanded shape when adducted to lithium as compared to proton. Copyright © 2013 Elsevier B.V. All rights reserved.

New insights into the nonadiabatic state population dynamics of model proton-coupled electron transfer reactions from the mixed quantum-classical Liouville approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shakib, Farnaz A.; Hanna, Gabriel, E-mail: gabriel.hanna@ualberta.ca

In a previous study [F. A. Shakib and G. Hanna, J. Chem. Phys. 141, 044122 (2014)], we investigated a model proton-coupled electron transfer (PCET) reaction via the mixed quantum-classical Liouville (MQCL) approach and found that the trajectories spend the majority of their time on the mean of two coherently coupled adiabatic potential energy surfaces. This suggested a need for mean surface evolution to accurately simulate observables related to ultrafast PCET processes. In this study, we simulate the time-dependent populations of the three lowest adiabatic states in the ET-PT (i.e., electron transfer preceding proton transfer) version of the same PCET modelmore » via the MQCL approach and compare them to the exact quantum results and those obtained via the fewest switches surface hopping (FSSH) approach. We find that the MQCL population profiles are in good agreement with the exact quantum results and show a significant improvement over the FSSH results. All of the mean surfaces are shown to play a direct role in the dynamics of the state populations. Interestingly, our results indicate that the population transfer to the second-excited state can be mediated by dynamics on the mean of the ground and second-excited state surfaces, as part of a sequence of nonadiabatic transitions that bypasses the first-excited state surface altogether. This is made possible through nonadiabatic transitions between different mean surfaces, which is the manifestation of coherence transfer in MQCL dynamics. We also investigate the effect of the strength of the coupling between the proton/electron and the solvent coordinate on the state population dynamics. Drastic changes in the population dynamics are observed, which can be understood in terms of the changes in the potential energy surfaces and the nonadiabatic couplings. Finally, we investigate the state population dynamics in the PT-ET (i.e., proton transfer preceding electron transfer) and concerted versions of the model. The PT-ET results confirm the participation of all of the mean surfaces, albeit in different proportions compared to the ET-PT case, while the concerted results indicate that the mean of the ground- and first-excited state surfaces only plays a role, due to the large energy gaps between the ground- and second-excited state surfaces.« less

Ultrafast proton shuttling in Psammocora cyan fluorescent protein.

PubMed

Kennis, John T M; van Stokkum, Ivo H M; Peterson, Dayna S; Pandit, Anjali; Wachter, Rebekka M

2013-09-26

Cyan, green, yellow, and red fluorescent proteins (FPs) homologous to green fluorescent protein (GFP) are used extensively as model systems to study fundamental processes in photobiology, such as the capture of light energy by protein-embedded chromophores, color tuning by the protein matrix, energy conversion by Förster resonance energy transfer (FRET), and excited-state proton transfer (ESPT) reactions. Recently, a novel cyan fluorescent protein (CFP) termed psamFP488 was isolated from the genus Psammocora of reef building corals. Within the cyan color class, psamFP488 is unusual because it exhibits a significantly extended Stokes shift. Here, we applied ultrafast transient absorption and pump-dump-probe spectroscopy to investigate the mechanistic basis of psamFP488 fluorescence, complemented with fluorescence quantum yield and dynamic light scattering measurements. Transient absorption spectroscopy indicated that, upon excitation at 410 nm, the stimulated cyan emission rises in 170 fs. With pump-dump-probe spectroscopy, we observe a very short-lived (110 fs) ground-state intermediate that we assign to the deprotonated, anionic chromophore. In addition, a minor fraction (14%) decays with 3.5 ps to the ground state. Structural analysis of homologous proteins indicates that Glu-167 is likely positioned in sufficiently close vicinity to the chromophore to act as a proton acceptor. Our findings support a model where unusually fast ESPT from the neutral chromophore to Glu-167 with a time constant of 170 fs and resulting emission from the anionic chromophore forms the basis of the large psamFP488 Stokes shift. When dumped to the ground state, the proton on neutral Glu is very rapidly shuttled back to the anionic chromophore in 110 fs. Proton shuttling in excited and ground states is a factor of 20-4000 faster than in GFP, which probably results from a favorable hydrogen-bonding geometry between the chromophore phenolic oxygen and the glutamate acceptor, possibly involving a short hydrogen bond. At any time in the reaction, the proton is localized on either the chromophore or Glu-167, which implies that most likely no low-barrier hydrogen bond exists between these molecular groups. This work supports the notion that proton transfer in biological systems, be it in an electronic excited or ground state, can be an intrinsically fast process that occurs on a 100 fs time scale. PsamFP488 represents an attractive model system that poses an ultrafast proton transfer regime in discrete steps. It constitutes a valuable model system in addition to wild type GFP, where proton transfer is relatively slow, and the S65T/H148D GFP mutant, where the effects of low-barrier hydrogen bonds dominate.

Quantification of in vivo pH-weighted amide proton transfer (APT) MRI in acute ischemic stroke

NASA Astrophysics Data System (ADS)

Zhou, Iris Y.; Igarashi, Takahiro; Guo, Yingkun; Sun, Phillip Z.

2015-03-01

Amide proton transfer (APT) imaging is a specific form of chemical exchange saturation transfer (CEST) MRI that probes the pH-dependent amide proton exchange.The endogenous APT MRI is sensitive to tissue acidosis, which may complement the commonly used perfusion and diffusion scans for characterizing heterogeneous ischemic tissue damage. Whereas the saturation transfer asymmetry analysis (MTRasym) may reasonably compensate for direct RF saturation, in vivo MTRasym is however, susceptible to an intrinsically asymmetric shift (MTR'asym). Specifically, the reference scan for the endogenous APT MRI is 7 ppm upfield from that of the label scan, and subjects to concomitant RF irradiation effects, including nuclear overhauser effect (NOE)-mediated saturation transfer and semisolid macromolecular magnetization transfer. As such, the commonly used asymmetry analysis could not fully compensate for such slightly asymmetric concomitant RF irradiation effects, and MTRasym has to be delineated in order to properly characterize the pH-weighted APT MRI contrast. Given that there is very little change in relaxation time immediately after ischemia and the concomitant RF irradiation effects only minimally depends on pH, the APT contrast can be obtained as the difference of MTRasym between the normal and ischemic regions. Thereby, the endogenous amide proton concentration and exchange rate can be solved using a dual 2-pool model, and the in vivo MTR'asym can be calculated by subtracting the solved APT contrast from asymmetry analysis (i.e., MTR'asym =MTRasym-APTR). In addition, MTR'asym can be quantified using the classical 2-pool exchange model. In sum, our study delineated the conventional in vivo pH-sensitive MTRasym contrast so that pHspecific contrast can be obtained for imaging ischemic tissue acidosis.

Monitoring the Reaction Process During the S2 → S3 Transition in Photosynthetic Water Oxidation Using Time-Resolved Infrared Spectroscopy.

PubMed

Sakamoto, Hiroki; Shimizu, Tatsuki; Nagao, Ryo; Noguchi, Takumi

2017-02-08

Photosynthetic water oxidation performed at the Mn 4 CaO 5 cluster in photosystem II plays a crucial role in energy production as electron and proton sources necessary for CO 2 fixation. Molecular oxygen, a byproduct, is a source of the oxygenic atmosphere that sustains life on earth. However, the molecular mechanism of water oxidation is not yet well-understood. In the reaction cycle of intermediates called S states, the S 2 → S 3 transition is particularly important; it consists of multiple processes of electron transfer, proton release, and water insertion, and generates an intermediate leading to O-O bond formation. In this study, we monitored the reaction process during the S 2 → S 3 transition using time-resolved infrared spectroscopy to clarify its molecular mechanism. A change in the hydrogen-bond interaction of the oxidized Y Z • radical, an immediate electron acceptor of the Mn 4 CaO 5 cluster, was clearly observed as a ∼100 μs phase before the electron-transfer phase with a time constant of ∼350 μs. This observation provides strong experimental evidence that rearrangement of the hydrogen-bond network around Y Z • , possibly due to the movement of a water molecule located near Y Z • to the Mn site, takes place before the electron transfer. The electron transfer was coupled with proton release, as revealed by a relatively high deuterium kinetic isotope effect of 1.9. This proton release, which decreases the redox potential of the Mn 4 CaO 5 cluster to facilitate electron transfer to Y Z • , was proposed to determine, as a rate-limiting step, the relatively slow electron-transfer rate of the S 2 → S 3 transition.

Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

PubMed

Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

2016-09-21

The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen bonding of the slightly acidic water in the nanoscale channel.

Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

PubMed

Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

2014-01-21

The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

Measurements of GEp/GMp to high Q2 and search for 2{gamma} contribution in elastic ep at Jefferson Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vina Punjabi, Charles Perdrisat

2010-05-01

The ratio, μpGEp/GMp, where μp is the proton magnetic moment, has been measured extensively over the last decade at the Jefferson Laboratory, using the polarization transfer method. This ratio is extracted directly from the measured ratio of transverse to longitudinal polarizations components of the recoiling proton in elastic electron-proton scattering. The polarization transfer results are of unprecedented high precision and accuracy, due in large part to the small systematic uncertainties associated with the experimental technique. Prior to these measurements, the form factors were empirically observed to exhibit dipole forms, such that μpGEp/GMp ≈ 1 over all regions of momentum transfermore » studied. With the Hall A results confirming that the ratio μpGEp/GMp shows a steady decrease below unity as a function of Q2, beginning around Q2 ≈ 1 GeV2, discussions revolving around the implication of this deviation from dipole behavior for the structure of the proton have been accompanied by renewed experimental interest in these elastic form factors. Starting in the fall of 2007, two new experiments, GEp-III and GEp-2γ in Hall C at JLab, measured the form factor ratio, GEp/GMp; the GEp-III experiment pushed the highest Q2 limit from 5.6 to 8.49 GeV2, with intermediate points at 5.2 and 6.8 GeV2, and the GEp-2γ experiment measured the ratio in three different kinematics at the constant value Q2=2.5 GeV2, by changing beam energy and detector angles. Preliminary results from both experiments are reported.« less

Measurement of the Generalized Polarizabilities of the Proton in Virtual Compton Scattering at Q2=0.92 and 1.76 GeV2

NASA Astrophysics Data System (ADS)

Laveissière, G.; Todor, L.; Degrande, N.; Jaminion, S.; Jutier, C.; di Salvo, R.; van Hoorebeke, L.; Alexa, L. C.; Anderson, B. D.; Aniol, K. A.; Arundell, K.; Audit, G.; Auerbach, L.; Baker, F. T.; Baylac, M.; Berthot, J.; Bertin, P. Y.; Bertozzi, W.; Bimbot, L.; Boeglin, W. U.; Brash, E. J.; Breton, V.; Breuer, H.; Burtin, E.; Calarco, J. R.; Cardman, L. S.; Cavata, C.; Chang, C.-C.; Chen, J.-P.; Chudakov, E.; Cisbani, E.; Dale, D. S.; de Jager, C. W.; de Leo, R.; Deur, A.; D'Hose, N.; Dodge, G. E.; Domingo, J. J.; Elouadrhiri, L.; Epstein, M. B.; Ewell, L. A.; Finn, J. M.; Fissum, K. G.; Fonvieille, H.; Fournier, G.; Frois, B.; Frullani, S.; Furget, C.; Gao, H.; Gao, J.; Garibaldi, F.; Gasparian, A.; Gilad, S.; Gilman, R.; Glamazdin, A.; Glashausser, C.; Gomez, J.; Gorbenko, V.; Grenier, P.; Guichon, P. A.; Hansen, J. O.; Holmes, R.; Holtrop, M.; Howell, C.; Huber, G. M.; Hyde-Wright, C. E.; Incerti, S.; Iodice, M.; Jardillier, J.; Jones, M. K.; Kahl, W.; Kato, S.; Katramatou, A. T.; Kelly, J. J.; Kerhoas, S.; Ketikyan, A.; Khayat, M.; Kino, K.; Kox, S.; Kramer, L. H.; Kumar, K. S.; Kumbartzki, G.; Kuss, M.; Leone, A.; Lerose, J. J.; Liang, M.; Lindgren, R. A.; Liyanage, N.; Lolos, G. J.; Lourie, R. W.; Madey, R.; Maeda, K.; Malov, S.; Manley, D. M.; Marchand, C.; Marchand, D.; Margaziotis, D. J.; Markowitz, P.; Marroncle, J.; Martino, J.; McCormick, K.; McIntyre, J.; Mehrabyan, S.; Merchez, F.; Meziani, Z. E.; Michaels, R.; Miller, G. W.; Mougey, J. Y.; Nanda, S. K.; Neyret, D.; Offermann, E. A.; Papandreou, Z.; Pasquini, B.; Perdrisat, C. F.; Perrino, R.; Petratos, G. G.; Platchkov, S.; Pomatsalyuk, R.; Prout, D. L.; Punjabi, V. A.; Pussieux, T.; Quémenér, G.; Ransome, R. D.; Ravel, O.; Real, J. S.; Renard, F.; Roblin, Y.; Rowntree, D.; Rutledge, G.; Rutt, P. M.; Saha, A.; Saito, T.; Sarty, A. J.; Serdarevic, A.; Smith, T.; Smirnov, G.; Soldi, K.; Sorokin, P.; Souder, P. A.; Suleiman, R.; Templon, J. A.; Terasawa, T.; Tieulent, R.; Tomasi-Gustaffson, E.; Tsubota, H.; Ueno, H.; Ulmer, P. E.; Urciuoli, G. M.; Vanderhaeghen, M.; van de Vyver, R.; van der Meer, R. L.; Vernin, P.; Vlahovic, B.; Voskanyan, H.; Voutier, E.; Watson, J. W.; Weinstein, L. B.; Wijesooriya, K.; Wilson, R.; Wojtsekhowski, B. B.; Zainea, D. G.; Zhang, W.-M.; Zhao, J.; Zhou, Z.-L.

2004-09-01

We report a virtual Compton scattering study of the proton at low c.m. energies. We have determined the structure functions PLL-PTT/ɛ and PLT, and the electric and magnetic generalized polarizabilities (GPs) αE(Q2) and βM(Q2) at momentum transfer Q2=0.92 and 1.76 GeV2. The electric GP shows a strong falloff with Q2, and its global behavior does not follow a simple dipole form. The magnetic GP shows a rise and then a falloff; this can be interpreted as the dominance of a long-distance diamagnetic pion cloud at low Q2, compensated at higher Q2 by a paramagnetic contribution from πN intermediate states.

Measurement of the beam asymmetry Σ for π 0 and η photoproduction on the proton at E γ = 9 GeV

DOE PAGES

Al Ghoul, H.; Anassontzis, E. G.; Austregesilo, A.; ...

2017-04-24

In this paper, we report measurements of the photon beam asymmetrymore » $$\\Sigma$$ for the reactions $$\\vec{\\gamma}p\\to p\\pi^0$$ and $$\\vec{\\gamma}p\\to p\\eta $$ from the GLUEX experiment using a 9 GeV linearly polarized, tagged photon beam incident on a liquid hydrogen target in Jefferson Lab's Hall D. The asymmetries, measured as a function of the proton momentum transfer, possess greater precision than previous $$\\pi^0$$ measurements and are the first $$\\eta$$ measurements in this energy regime. Lastly, the results are compared with theoretical predictions based on $t$-channel, quasi-particle exchange and constrain the axial-vector component of the neutral meson production mechanism in these models.« less

A spectroscopic investigation of the Schiff base reprotonation mechanism of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Russell, Terence Stephen

This thesis reports time-resolved visible spectroscopy experiments performed on the light-driven proton pumping protein, bacteriorhodopsin (bR), and a number of artificially produced analogs. These analogs comprise a variety of single and double amino acid substitutions produced in several of the residues previously implicated in proton transport in bR. Also addressed are the results of resonance Raman and FTIR difference spectroscopy which provide information about the vibrational modes of the protein. The results from these experiments confirm aspects of both structural and functional models of bR based on previous electron diffraction and spectroscopic data. During a phase of the proton pumping photocycle in bR known as Schiff base reprotonation (also referred to as M intermediate decay), a proton is transferred over a 12 A distance from a proton donor residue (Asp-96) to the light-absorbing active site. The behavior of the M intermediate was monitored by time-resolved visible spectroscopy. In the single substitution known as D96N, the Asp-96 residue was replaced with a less efficient proton donor, asparagine. This mutant exhibited an M intermediate which decayed slowly in comparison to that of wild-type bR. However, this effect was reversed with the double substitution, T46D/D96N. This result indicates that the proton donor group can be moved to another nearby location and still yield a system functionally similar to the native protein. Replacement of the donor group with a histidine, His-96, resulted in a photocycle similar to D96N above pH 7. However, below this pH, the M intermediate is not detected. FTIR difference spectroscopy indicates that the protonation state of the substituted His-96 residue influences the structure of the active site of bR which suggests that a proton that is associated with His-96 may move towards the active site and thereby block M intermediate formation. Finally, the residue Thr-89 was replaced with an asparagine. This substitution altered not only the vibrational modes of the protein but also its visible absorption, which indicates that Thr-89 interacts directly with the active site of bR. These results are used to correct and extend an overall molecular model of the proton transport mechanism in bacteriorhodopsin.

A pathway for protons in nitric oxide reductase from Paracoccus denitrificans.

PubMed

Reimann, Joachim; Flock, Ulrika; Lepp, Håkan; Honigmann, Alf; Adelroth, Pia

2007-05-01

Nitric oxide reductase (NOR) from P. denitrificans is a membrane-bound protein complex that catalyses the reduction of NO to N(2)O (2NO+2e(-)+2H(+)-->N(2)O+H(2)O) as part of the denitrification process. Even though NO reduction is a highly exergonic reaction, and NOR belongs to the superfamily of O(2)-reducing, proton-pumping heme-copper oxidases (HCuOs), previous measurements have indicated that the reaction catalyzed by NOR is non-electrogenic, i.e. not contributing to the proton electrochemical gradient. Since electrons are provided by donors in the periplasm, this non-electrogenicity implies that the substrate protons are also taken up from the periplasm. Here, using direct measurements in liposome-reconstituted NOR during reduction of both NO and the alternative substrate O(2), we demonstrate that protons are indeed consumed from the 'outside'. First, multiple turnover reduction of O(2) resulted in an increase in pH on the outside of the NOR-vesicles. Second, comparison of electrical potential generation in NOR-liposomes during oxidation of the reduced enzyme by either NO or O(2) shows that the proton transfer signals are very similar for the two substrates proving the usefulness of O(2) as a model substrate for these studies. Last, optical measurements during single-turnover oxidation by O(2) show electron transfer coupled to proton uptake from outside the NOR-liposomes with a tau=15 ms, similar to results obtained for net proton uptake in solubilised NOR [U. Flock, N.J. Watmough, P. Adelroth, Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen, Biochemistry 44 (2005) 10711-10719]. NOR must thus contain a proton transfer pathway leading from the periplasmic surface into the active site. Using homology modeling with the structures of HCuOs as templates, we constructed a 3D model of the NorB catalytic subunit from P. denitrificans in order to search for such a pathway. A plausible pathway, consisting of conserved protonatable residues, is suggested.

Lysosomal ROS formation.

PubMed

Nohl, Hans; Gille, Lars

2005-01-01

Ubiquinone is inhomogenously distributed in subcellular biomembranes. Apart from mitochondria, where ubiquinone has bioenergetic and pathophysiological functions, unusually high levels of ubiquinone have also been reported in Golgi vesicles and lysosomes. In lysosomes, the interior differs from other organelles in its low pH value which is important to ensure optimal activity of hydrolytic enzymes. Since redox-cycling of ubiquinone is associated with the acceptance and release of protons, we assumed that ubiquinone is part of a redox chain contributing to unilateral proton distribution. A similar function of ubiquinone was earlier suggested by Crane to operate in Golgi vesicles. Support for the involvement of ubiquinone in a presumed couple of redox carriers came from our observation that almost 70% of total lysosomal ubiquinone was in the divalently reduced state. Further reduction was seen in the presence of external NADH. Analysis of the components involved in the transfer of reducing equivalents from cytosolic NADH to ubiquinone revealed the existence of an FAD-containing NADH dehydrogenase. The latter was found to reduce ubiquinone by means of a b-type cytochrome. Proton translocation into the interior was linked to the activity of the novel lysosomal redox chain. Oxygen was found to be the terminal electron acceptor, thereby also regulating acidification of the lysosomal matrix. In contrast to mitochondrial respiration, oxygen was only trivalently reduced giving rise to the release of HO radicals. The role of this novel proton-pumping redox chain and the significance of the associated ROS formation has to be elucidated.

WE-D-17A-06: Optically Stimulated Luminescence Detectors as ‘LET-Meters’ in Proton Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Granville, D; Sahoo, N; Sawakuchi, GO

Purpose: To demonstrate and evaluate the potential of optically stimulated luminescence (OSL) detectors (OSLDs) for measurements of linear energy transfer (LET) in therapeutic proton beams. Methods: Batches of Al2O2:C OSLDs were irradiated with an absorbed dose of 0.2 Gy in un-modulated proton beams of varying LET (0.67 keV/μm to 2.58 keV/μm). The OSLDs were read using continuous wave (CW-OSL) and pulsed (P-OSL) stimulation modes. We parameterized and calibrated three characteristics of the OSL signals as functions of LET: CW-OSL curve shape, P-OSL curve shape and the ratio of the two OSL emission band intensities (ultraviolet/blue ratio). Calibration curves were createdmore » for each of these characteristics to describe their behaviors as functions of LET. The true LET values were determined using a validated Monte Carlo model of the proton therapy nozzle used to irradiate the OSLDs. We then irradiated batches of OSLDs with an absorbed dose of 0.2 Gy at various depths in two modulated proton beams (140 MeV, 4 cm wide spread-out Bragg peak (SOBP) and 250 MeV, 10 cm wide SOBP). The LET values were calculated using the OSL response and the calibration curves. Finally, measured LET values were compared to the true values determined using Monte Carlo simulations. Results: The CW-OSL curve shape, P-OSL curve shape and the ultraviolet/blue-ratio provided proton LET estimates within 12.4%, 5.7% and 30.9% of the true values, respectively. Conclusion: We have demonstrated that LET can be measured within 5.7% using Al2O3:C OSLDs in the therapeutic proton beams used in this investigation. From a single OSLD readout, it is possible to measure both the absorbed dose and LET. This has potential future applications in proton therapy quality assurance, particularly for treatment plans based on optimization of LET distributions. This research was partially supported by the Natural Sciences and Engineering Research Council of Canada.« less

Artificial neuron synapse transistor based on silicon nanomembrane on plastic substrate

NASA Astrophysics Data System (ADS)

Liu, Minjie; Huang, Gaoshan; Feng, Ping; Guo, Qinglei; Shao, Feng; Tian, Ziao; Li, Gongjin; Wan, Qing; Mei, Yongfeng

2017-06-01

Silicon nanomembrane (SiNM) transistors gated by chitosan membrane were fabricated on plastic substrate to mimic synapse behaviors. The device has both a bottom proton gate (BG) and multiple side gates (SG). Electrical transfer properties of BG show hysteresis curves different from those of typical SiO2 gate dielectric. Synaptic behaviors and functions by linear accumulation and release of protons have been mimicked on this device: excitatory post-synaptic current (EPSC) and paired pulse facilitation behavior of biological synapses were mimicked and the paired-pulse facilitation index could be effectively tuned by the spike interval applied on the BG. Synaptic behaviors and functions, including short-term memory and long-term memory, were also experimentally demonstrated in BG mode. Meanwhile, spiking logic operation and logic modulation were realized in SG mode. Project supported by the National Natural Science Foundation of China (No. 51322201), the Specialized Research Fund for the Doctoral Program of Higher Education (No. 20120071110025), and Science and Technology Commission of Shanghai Municipality (No. 14JC1400200).

Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.

PubMed

Fukuda, Yohta; Tse, Ka Man; Nakane, Takanori; Nakatsu, Toru; Suzuki, Mamoru; Sugahara, Michihiro; Inoue, Shigeyuki; Masuda, Tetsuya; Yumoto, Fumiaki; Matsugaki, Naohiro; Nango, Eriko; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Song, Changyong; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Murphy, Michael E P; Inoue, Tsuyoshi; Iwata, So; Mizohata, Eiichi

2016-03-15

Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.

High-level ab initio potential energy surface and dynamics of the F- + CH3I SN2 and proton-transfer reactions.

PubMed

Olasz, Balázs; Szabó, István; Czakó, Gábor

2017-04-01

Bimolecular nucleophilic substitution (S N 2) and proton transfer are fundamental processes in chemistry and F - + CH 3 I is an important prototype of these reactions. Here we develop the first full-dimensional ab initio analytical potential energy surface (PES) for the F - + CH 3 I system using a permutationally invariant fit of high-level composite energies obtained with the combination of the explicitly-correlated CCSD(T)-F12b method, the aug-cc-pVTZ basis, core electron correlation effects, and a relativistic effective core potential for iodine. The PES accurately describes the S N 2 channel producing I - + CH 3 F via Walden-inversion, front-side attack, and double-inversion pathways as well as the proton-transfer channel leading to HF + CH 2 I - . The relative energies of the stationary points on the PES agree well with the new explicitly-correlated all-electron CCSD(T)-F12b/QZ-quality benchmark values. Quasiclassical trajectory computations on the PES show that the proton transfer becomes significant at high collision energies and double-inversion as well as front-side attack trajectories can occur. The computed broad angular distributions and hot internal energy distributions indicate the dominance of indirect mechanisms at lower collision energies, which is confirmed by analyzing the integration time and leaving group velocity distributions. Comparison with available crossed-beam experiments shows usually good agreement.

Minima in generalized oscillator strengths for initially excited hydrogen-like atoms

NASA Technical Reports Server (NTRS)

Matsuzawa, M.; Omidvar, K.; Inokuti, M.

1976-01-01

Generalized oscillator strengths for transitions from an initially excited state of a hydrogenic atom to final states (either discrete or continuum) have complicated structures, including minima and shoulders, as functions of the momentum transfer. Extensive calculations carried out in the present work have revealed certain systematics of these structures. Some implications of the minima to the energy dependence of the inner-shell ionization cross section of heavy atoms by proton impact are discussed.

Complexity in Acid–Base Titrations: Multimer Formation Between Phosphoric Acids and Imines

PubMed Central

Malm, Christian; Kim, Heejae; Wagner, Manfred

2017-01-01

Abstract Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid–base aggregates challenging. Here, we track such acid–base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid–base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid‐base association constant is only around six times larger than that for the acid binding to an acid‐base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. PMID:28597513

Photodissociation pathways and lifetimes of protonated peptides and their dimers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aravind, G.; Klaerke, B.; Rajput, J.

2012-01-07

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA{sub n} (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of {approx}200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of {approx}2 {mu}s. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in themore » dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.« less

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

NASA Astrophysics Data System (ADS)

Stawoska, I.; Dudzik, A.; Wasylewski, M.; Jemioła-Rzemińska, M.; Skoczowski, A.; Strzałka, K.; Szaleniec, M.

2017-06-01

The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, ( S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2' ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.

Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soniat, Marielle; Rick, Steven W., E-mail: srick@uno.edu; Kumar, Revati

2015-07-28

The role of the solvated excess proton and hydroxide ions in interfacial properties is an interesting scientific question with applications in a variety of aqueous behaviors. The role that charge transfer (CT) plays in interfacial behavior is also an unsettled question. Quantum calculations are carried out on clusters of water with an excess proton or a missing proton (hydroxide) to determine their CT. The quantum results are applied to analysis of multi-state empirical valence bond trajectories. The polyatomic nature of the solvated excess proton and hydroxide ion results in directionally dependent CT, depending on whether a water molecule is amore » hydrogen bond donor or acceptor in relation to the ion. With polyatomic molecules, CT also depends on the intramolecular bond distances in addition to intermolecular distances. The hydrated proton and hydroxide affect water’s liquid/vapor interface in a manner similar to monatomic ions, in that they induce a hydrogen-bonding imbalance at the surface, which results in charged surface waters. This hydrogen bond imbalance, and thus the charged waters at the surface, persists until the ion is at least 10 Å away from the interface.« less

Proton Translocation in Cytochrome c Oxidase: Insights from Proton Exchange Kinetics and Vibrational Spectroscopy

PubMed Central

Ishigami, Izumi; Hikita, Masahide; Egawa, Tsuyoshi; Yeh, Syun-Ru; Rousseau, Denis L.

2014-01-01

Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLOS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. PMID:25268561

A hybrid QM/MM simulation study of intramolecular proton transfer in the pyridoxal 5'-phosphate in the active site of transaminase: influence of active site interaction on proton transfer.

PubMed

Dutta Banik, Sindrila; Chandra, Amalendu

2014-09-25

Pyridoxal 5'-phosphate (PLP) Schiff base, a versatile cofactor, exhibits a tautomeric equilibrium that involves an intramolecular proton transfer between the N-protonated zwitterionic ketoenamine tautomer and the O-protonated covalent enolimine tautomer. It has been postulated that for the catalytic activity, the PLP has to be in the zwitterionic ketoenamine tautomeric form. However, the exact position of the tautomeric equilibrium of Schiff base in the active site of PLP-dependent enzyme is not known yet. In the present work, we investigated the tautomeric equilibrium for the external aldimine state of PLP aspartate (PLP-Asp) Schiff base in the active site of aspartate aminotransferase (AspAT) using combined quantum mechanical and molecular mechanical simulations. The main focus of the present study is to analyze the factors that control the tautomeric equilibrium in the active sites of various PLP-dependent enzymes. The results show that the ketoenamine tautomer is more preferred than the enolimine tautomer both in the gas and aqueous phases as well as in the active site of AspAT. Current simulations show that the active site of AspAT is more suitable for the ketoenamine tautomer compared to the enolimine tautomer. Interestingly, the Tyr225 acts as a proton donor to the phenolic oxygen in the ketoenamine tautomer, while in the covalent enolimine tautomer, it acts as a proton acceptor to the phenolic oxygen. Finally, the metadynamics study confirms this result. The calculated free energy barrier is about 7.5 kcal/mol. A comparative analysis of the microenvironment created by the active site residues of three different PLP-dependent enzymes (aspartate aminotransferase, Dopa decarboxylase, and Ala-racemase) has been carried out to understand the controlling factor(s) of the tautomeric equilibrium. The analysis shows that the intermolecular hydrogen bonding between active site residues and the phenolic oxygen of PLP shifts the tautomeric equilibrium toward the N-protonated ketoenamine tautomeric form.

Study of the efficiency for ion transfer through bent capillaries.

PubMed

Chen, Tsung-Chi; Xu, Wei; Garimella, Sandilya; Ouyang, Zheng

2012-11-01

Discontinuous atmospheric pressure interfaces (DAPIs) with bent capillaries represent a highly simplified and flexible means for introducing ions into a vacuum manifold for mass analysis or gas phase ion reactions. In this work, a series of capillaries of different radians and curvatures were used with DAPI for studying the impact of the capillary bending on the ion transfer. The variation of transfer efficiency was systematically characterized for dry and solvated ions. The efficiency loss for dry ions was less than one order of magnitude, even with a three-turn bent capillary. The transfer of solvated ions generated by electrospray was found to be minimally impacted by the bending of the transfer capillary. For multiply protonated ions, the transfer efficiency for ions at lower charge states could be relatively well retained, presumably due to the lower reactivity associated with proton transfer reaction and the compensation in intensity by conversion of ions at higher charge states. Copyright © 2012 John Wiley & Sons, Ltd.

Proton-Coupled Electron Transfer and a Tyrosine-Histidine Pair in a Photosystem II-Inspired β-Hairpin Maquette: Kinetics on the Picosecond Time Scale.

PubMed

Pagba, Cynthia V; McCaslin, Tyler G; Chi, San-Hui; Perry, Joseph W; Barry, Bridgette A

2016-02-25

Photosystem II (PSII) and ribonucleotide reductase employ oxidation and reduction of the tyrosine aromatic ring in radical transport pathways. Tyrosine-based reactions involve either proton-coupled electron transfer (PCET) or electron transfer (ET) alone, depending on the pH and the pKa of tyrosine's phenolic oxygen. In PSII, a subset of the PCET reactions are mediated by a tyrosine-histidine redox-driven proton relay, YD-His189. Peptide A is a PSII-inspired β-hairpin, which contains a single tyrosine (Y5) and histidine (H14). Previous electrochemical characterization indicated that Peptide A conducts a net PCET reaction between Y5 and H14, which have a cross-strand π-π interaction. The kinetic impact of H14 has not yet been explored. Here, we address this question through time-resolved absorption spectroscopy and 280-nm photolysis, which generates a neutral tyrosyl radical. The formation and decay of the neutral tyrosyl radical at 410 nm were monitored in Peptide A and its variant, Peptide C, in which H14 is replaced by cyclohexylalanine (Cha14). Significantly, both electron transfer (ET, pL 11, L = lyonium) and PCET (pL 9) were accelerated in Peptide A and C, compared to model tyrosinate or tyrosine at the same pL. Increased electronic coupling, mediated by the peptide backbone, can account for this rate acceleration. Deuterium exchange gave no significant solvent isotope effect in the peptides. At pL 9, but not at pL 11, the reaction rate decreased when H14 was mutated to Cha14. This decrease in rate is attributed to an increase in reorganization energy in the Cha14 mutant. The Y5-H14 mechanism in Peptide A is reminiscent of proton- and electron-transfer events involving YD-H189 in PSII. These results document a mechanism by which proton donors and acceptors can regulate the rate of PCET reactions.

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations.

PubMed

Tubert-Brohman, Ivan; Acevedo, Orlando; Jorgensen, William L

2006-12-27

Fatty acid amide hydrolase (FAAH) is a serine hydrolase that degrades anandamide, an endocannabinoid, and oleamide, a sleep-inducing lipid, and has potential applications as a therapeutic target for neurological disorders. Remarkably, FAAH hydrolyzes amides and esters with similar rates; however, the normal preference for esters reemerges when Lys142 is mutated to alanine. To elucidate the hydrolysis mechanisms and the causes behind this variation of selectivity, mixed quantum and molecular mechanics (QM/MM) calculations were carried out to obtain free-energy profiles for alternative mechanisms for the enzymatic hydrolyses. The methodology features free-energy perturbation calculations in Monte Carlo simulations with PDDG/PM3 as the QM method. For wild-type FAAH, the results support a mechanism, which features proton transfer from Ser217 to Lys142, simultaneous proton transfer from Ser241 to Ser217, and attack of Ser241 on the substrate's carbonyl carbon to yield a tetrahedral intermediate, which subsequently undergoes elimination with simultaneous protonation of the leaving group by a Lys142-Ser217 proton shuttle. For the Lys142Ala mutant, a striking multistep sequence is proposed with simultaneous proton transfer from Ser241 to Ser217, attack of Ser241 on the carbonyl carbon of the substrate, and elimination of the leaving group and its protonation by Ser217. Support comes from the free-energy results, which well reproduce the observation that the Lys142Ala mutation in FAAH decreases the rate of hydrolysis for oleamide significantly more than for methyl oleate.

Magnetization transfer contrast-suppressed imaging of amide proton transfer and relayed nuclear overhauser enhancement chemical exchange saturation transfer effects in the human brain at 7T.

PubMed

Xu, Xiang; Yadav, Nirbhay N; Zeng, Haifeng; Jones, Craig K; Zhou, Jinyuan; van Zijl, Peter C M; Xu, Jiadi

2016-01-01

To use the variable delay multipulse (VDMP) chemical exchange saturation transfer (CEST) approach to obtain clean amide proton transfer (APT) and relayed Nuclear Overhauser enhancement (rNOE) CEST images in the human brain by suppressing the conventional magnetization transfer contrast (MTC) and reducing the direct water saturation contribution. The VDMP CEST scheme consists of a train of RF pulses with a specific mixing time. The CEST signal with respect to the mixing time shows distinguishable characteristics for protons with different exchange rates. Exchange rate filtered CEST images are generated by subtracting images acquired at two mixing times at which the MTC signals are equal, while the APT and rNOE-CEST signals differ. Because the subtraction is performed at the same frequency offset for each voxel and the CEST signals are broad, no B0 correction is needed. MTC-suppressed APT and rNOE-CEST images of human brain were obtained using the VDMP method. The APT-CEST data show hyperintensity in gray matter versus white matter, whereas the rNOE-CEST images show negligible contrast between gray and white matter. The VDMP approach provides a simple and rapid way of recording MTC-suppressed APT-CEST and rNOE-CEST images without the need for B0 field correction. © 2015 Wiley Periodicals, Inc.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Hybrid quantum chemical studies for the methanol formation reaction assisted by the proton transfer mechanism in supercritical water: CH3Cl+nH2O-->CH3OH+HCl+(n-1)H2O

NASA Astrophysics Data System (ADS)

Hori, T.; Takahashi, H.; Nitta, T.

2003-10-01

The proton transfer along the chain of hydrogen bonds is involved in many chemical reactions in aqueous solution and known to play a decisive role. We have performed the hybrid quantum chemical simulations for the methanol formation reaction catalyzed by the proton transfer mechanism [CH3Cl+nH2O→CH3OH+HCl+(n-1)H2O, n=3] in supercritical water (SCW) to investigate the role of water solvent on the reaction. In the simulation, the electronic state of the chemically active solutes (CH3Cl+3H2O) has been determined quantum mechanically, while the static water solvent has been represented by a classical model. The activation free energy for the water-catalytic reaction in SCW has been found to be 9.6 kcal/mol, which is much lower than that in the gas phase (29.2 kcal/mol). The fractional charge analysis has revealed that the notable charge separation in the solute complex takes place at the transition state (TS) and the resulting huge dipole gives rise to the considerable stabilization of the TS as compared to the reactant. It has been shown that the reaction assisted by the proton transfer mechanism is energetically much favored than the ionic SN2 reaction (CH3Cl+OH-→CH3OH+Cl-, 18.8 kcal/mol). The present calculations suggest that the proton migrations through the chain of hydrogen bonds can be regarded as a probable candidate responsible for the anomalous reactivities observed in SCW.

Redox Modulation of Flavin and Tyrosine Determines Photoinduced Proton-coupled Electron Transfer and Photoactivation of BLUF Photoreceptors

PubMed Central

Mathes, Tilo; van Stokkum, Ivo H. M.; Stierl, Manuela; Kennis, John T. M.

2012-01-01

Photoinduced electron transfer in biological systems, especially in proteins, is a highly intriguing matter. Its mechanistic details cannot be addressed by structural data obtained by crystallography alone because this provides only static information on a given redox system. In combination with transient spectroscopy and site-directed manipulation of the protein, however, a dynamic molecular picture of the ET process may be obtained. In BLUF (blue light sensors using FAD) photoreceptors, proton-coupled electron transfer between a tyrosine and the flavin cofactor is the key reaction to switch from a dark-adapted to a light-adapted state, which corresponds to the biological signaling state. Particularly puzzling is the fact that, although the various naturally occurring BLUF domains show little difference in the amino acid composition of the flavin binding pocket, the reaction rates of the forward reaction differ quite largely from a few ps up to several hundred ps. In this study, we modified the redox potential of the flavin/tyrosine redox pair by site-directed mutagenesis close to the flavin C2 carbonyl and fluorination of the tyrosine, respectively. We provide information on how changes in the redox potential of either reaction partner significantly influence photoinduced proton-coupled electron transfer. The altered redox potentials allowed us furthermore to experimentally describe an excited state charge transfer intermediately prior to electron transfer in the BLUF photocycle. Additionally, we show that the electron transfer rate directly correlates with the quantum yield of signaling state formation. PMID:22833672

Protonation-Gated Dual Photochromism of a Chromene-Styryl Dye Hybrid.

PubMed

Berdnikova, Daria V; Paululat, Thomas; Jonusauskas, Gediminas; Peregudova, Svetlana M; Fedorova, Olga A

2017-10-20

A novel hybrid bisphotochromic system involving a chromene residue and a styryl dye fragment is described. Initially, the compound shows almost no photochromism due to intramolecular energy and electron transfer between the chromophores. Protonation of the hybrid system blocks the transfer processes and unlocks a dual photochromic activity that includes ring opening of the chromene fragment and E-Z-isomerization of the styryl dye residue. Deprotonation of any photoinduced form resets the system to the initial photoinactive form.

Hydrogen bonding between phosphate and amino acid side chains

NASA Astrophysics Data System (ADS)

Carmona, P.; Rodriguez, M. L.

1986-03-01

Hydrogen bonds between polar groups of amino acid side chains (histidine, lysine, glutamic acid) and phosphate ions have been studied by infrared spectroscopy. Proton transfer from amino acid groups to phosphate occur mainly in case that tribasic and dibasic phosphate ions take part in hydrogen bonds. Conformational changes and continuum are strongly related to the degree of proton transfer and hydration. It is pointed out that the aforementioned properties should be of great significance for nucleation and growth of prostatic and renal stones.

Visualization of Proton and Electron Transfer Processes of a Biochemical Reaction by μSR

NASA Astrophysics Data System (ADS)

Kiyotani, Tamiko; Kobayashi, Masayoshi; Tanaka, Ichiro; Niimura, Nobuo

For the last several years, we have discussed and conducted experiments toward realization of visualization of electron and proton transfer process in an enzyme reaction using muon. As the first step for exploring the useful application of the μSR for the biological system, which is "μSR in Biology". A first μSR experiment on biochemical reaction was conducted using the complex of a digestive enzyme, a kind of serine-protease and the inhibitor at J-PARC and PSI.

Catalytic four-electron reduction of O2 via rate-determining proton-coupled electron transfer to a dinuclear cobalt-μ-1,2-peroxo complex.

PubMed

Fukuzumi, Shunichi; Mandal, Sukanta; Mase, Kentaro; Ohkubo, Kei; Park, Hyejin; Benet-Buchholz, Jordi; Nam, Wonwoo; Llobet, Antoni

2012-06-20

Four-electron reduction of O(2) by octamethylferrocene (Me(8)Fc) occurs efficiently with a dinuclear cobalt-μ-1,2-peroxo complex, 1, in the presence of trifluoroacetic acid in acetonitrile. Kinetic investigations of the overall catalytic reaction and each step in the catalytic cycle showed that proton-coupled electron transfer from Me(8)Fc to 1 is the rate-determining step in the catalytic cycle.

Electron and Oxygen Atom Transfer Chemistry of Co(II) in a Proton Responsive, Redox Active Ligand Environment.

PubMed

Cook, Brian J; Pink, Maren; Pal, Kuntal; Caulton, Kenneth G

2018-05-21

The bis-pyrazolato pyridine complex LCo(PEt 3 ) 2 serves as a masked form of three-coordinate Co II and shows diverse reactivity in its reaction with several potential outer sphere oxidants and oxygen atom transfer reagents. N-Methylmorpholine N-oxide (NMO) oxidizes coordinated PEt 3 from LCo(PEt 3 ) 2 , but the final cobalt product is still divalent cobalt, in LCo(NMO) 2 . The thermodynamics of a variety of oxygen atom transfer reagents, including NMO, are calculated by density functional theory, to rank their oxidizing power. Oxidation of LCo(PEt 3 ) 2 with AgOTf in the presence of LiCl as a trapping nucleophile forms the unusual aggregate [LCo(PEt 3 ) 2 Cl(LiOTf) 2 ] 2 held together by Li + binding to very nucleophilic chloride on Co(III) and triflate binding to those Li + . In contrast, Cp 2 Fe + effects oxidation to trivalent cobalt, to form (HL)Co(PEt 3 ) 2 Cl + ; proton and the chloride originate from solvent in a rare example of CH 2 Cl 2 dehydrochlorination. An unexpected noncomplementary redox reaction is reported involving attack by 2e reductant PEt 3 nucleophile on carbon of the 1e oxidant radical Cp 2 Fe + , forming a P-C bond and H + ; this reaction competes in the reaction of LCo(PEt 3 ) 2 with Cp 2 Fe + .

Single- and Double-Strand Breaks of Dry DNA Exposed to Protons at Bragg-Peak Energies.

PubMed

Souici, Mounir; Khalil, Talat T; Muller, Dominique; Raffy, Quentin; Barillon, Rémi; Belafrites, Abdelfettah; Champion, Christophe; Fromm, Michel

2017-01-26

Ultrathin layers (<20 nm) of pBR322 plasmid DNA were deposited onto 2.5 μm thick polyester films and exposed to proton Bragg-peak energies (90-3000 keV) at various fluences. A quantitative analysis of radio-induced DNA damage is reported here in terms of single- and double-strand breaks (SSB and DSB, respectively). The corresponding yields as well as G-values and the cross sections exhibit fairly good agreement with the rare available data, stemming from close experimental conditions, namely, based on α particle irradiation. SSB/DSB rates appear to be linear when plotted against linear energy transfer (LET) in the whole energy range studied. All the data present a maximum in the 150-200 keV energy range; as for LET, it peaks at 90 keV. We also show that fragmentation starts to be significant for proton fluences greater than 1 × 10 11 cm -2 at the Bragg-peak energies. Finally, we determine the average proton track radial extension, r max , corresponding to an occupation probability of 100% DSB in the Bragg-peak region. The r max values determined are in excellent agreement with the radial extensions of proton tracks determined by simulation approaches in water. When plotted as a function of LET, both SSB and DSB cross sections bend back at high LETs.

Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.

PubMed

Goyal, Puja; Qian, Hu-Jun; Irle, Stephan; Lu, Xiya; Roston, Daniel; Mori, Toshifumi; Elstner, Marcus; Cui, Qiang

2014-09-25

We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.

Evidence for decoupled electron and proton transfer in the electrochemical oxidation of ammonia on Pt(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.

The two traditional mechanisms of the electrochemical ammonia oxidation consider only concerted proton-electron transfer elementary steps and thus they predict that the rate–potential relationship is independent of the pH on the pH-corrected RHE potential scale. In this letter we show that this is not the case: the increase of the solution pH shifts the onset of the NH 3-to-N 2 oxidation on Pt(100) to lower potentials and also leads to higher surface concentration of formed N Oad before the latter is oxidized to nitrite. Therefore, we present a new mechanism for the ammonia oxidation which incorporates a deprotonation step occurringmore » prior to the electron transfer. The deprotonation step yields a negatively charged surface-adsorbed species which is discharged in a subsequent electron transfer step before the N–N bond formation. The negatively charged species is thus a precursor for the formation of N 2 and NO. The new mechanism should be a future guide for computational studies aiming at the identification of intermediates and corresponding activation barriers for the elementary steps. As a result, ammonia oxidation is a new example of a bond-forming reaction on (100) terraces which involves decoupled proton-electron transfer.« less

Evidence for decoupled electron and proton transfer in the electrochemical oxidation of ammonia on Pt(100)

DOE PAGES

Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.; ...

2016-01-12

The two traditional mechanisms of the electrochemical ammonia oxidation consider only concerted proton-electron transfer elementary steps and thus they predict that the rate–potential relationship is independent of the pH on the pH-corrected RHE potential scale. In this letter we show that this is not the case: the increase of the solution pH shifts the onset of the NH 3-to-N 2 oxidation on Pt(100) to lower potentials and also leads to higher surface concentration of formed N Oad before the latter is oxidized to nitrite. Therefore, we present a new mechanism for the ammonia oxidation which incorporates a deprotonation step occurringmore » prior to the electron transfer. The deprotonation step yields a negatively charged surface-adsorbed species which is discharged in a subsequent electron transfer step before the N–N bond formation. The negatively charged species is thus a precursor for the formation of N 2 and NO. The new mechanism should be a future guide for computational studies aiming at the identification of intermediates and corresponding activation barriers for the elementary steps. As a result, ammonia oxidation is a new example of a bond-forming reaction on (100) terraces which involves decoupled proton-electron transfer.« less

Oxygen anion (O- ) and hydroxide anion (HO- ) reactivity with a series of old and new refrigerants.

PubMed

Le Vot, Clotilde; Lemaire, Joël; Pernot, Pascal; Heninger, Michel; Mestdagh, Hélène; Louarn, Essyllt

2018-04-01

The reactivity of a series of commonly used halogenated compounds (trihalomethanes, chlorofluorocarbon, hydrochlorofluorocarbon, fluorocarbons, and hydrofluoroolefin) with hydroxide and oxygen anion is studied in a compact Fourier transform ion cyclotron resonance. O - is formed by dissociative electron attachment to N 2 O and HO - by a further ion-molecule reaction with ammonia. Kinetic experiments are performed by increasing duration of introduction of the studied molecule at a constant pressure. Hydroxide anion reactions mainly proceed by proton transfer for all the acidic compounds. However, nucleophilic substitution is observed for chlorinated and brominated compounds. For fluorinated compounds, a specific elimination of a neutral fluorinated alkene is observed in our results in parallel with the proton transfer reaction. Oxygen anion reacts rapidly and extensively with all compounds. Main reaction channels result from nucleophilic substitution, proton transfer, and formal H 2 + transfer. We highlight the importance of transfer processes (atom or ion) in the intermediate ion-neutral complex, explaining part of the observed reactivity and formed ions. In this paper, we present the first reactivity study of anions with HFO 1234yf. Finally, the potential of O - and HO - as chemical ionization reagents for trace analysis is discussed. Copyright © 2017 John Wiley & Sons, Ltd.

Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malik, Radhika; Viola, Ronald E.

2010-10-28

The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identificationmore » of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.« less

Hard two-photon contribution to elastic lepton-proton scattering determined by the OLYMPUS experiment

NASA Astrophysics Data System (ADS)

Hasell, D. K.; OLYMPUS Collaboration

2018-02-01

The OLYMPUS collaboration has recently made a precise measurement of the positron-proton to electron-proton elastic scattering cross section ratio, R 2γ, over a wide range of the virtual photon polarization, 0.456 < ɛ < 0.978. This provides a direct measure of hard two-photon exchange in elastic lepton-proton scattering widely thought to explain the discrepancy observed between unpolarized and polarized measurements of the proton form factor ratio, {μ }p{G}Ep/{G}Mp. The OLYMPUS results are small, within 1% on unity, over the range of momentum transfers measured and significantly lower than theoretical calculations that can explain part of the observed discrepancy in terms of two-photon exchange at higher momentum transfers. However, the results are in reasonable agreement with predictions based on phenomenological fits to the available form factor data. The motivation for measuring R 2γ will be presented followed by a description of the OLYMPUS experiment. The importance of radiative corrections in the analysis will be shown also. Then we will present the OLYMPUS results and compare with results from two similar experiments and theoretical calculations.

Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qi; Underwood, Tracy S.A.; Kung, Jong

2016-05-01

Purpose: Clinical proton beam therapy has been based on the use of a generic relative biological effectiveness (RBE) of ∼1.1. However, emerging data have suggested that Fanconi anemia (FA) and homologous recombination pathway defects can lead to a variable RBE, at least in vitro. We investigated the role of SLX4 (FANCP), which acts as a docking platform for the assembly of multiple structure-specific endonucleases, in the response to proton irradiation. Methods and Materials: Isogenic cell pairs for the study of SLX4, XPF/ERCC1, MUS81, and SLX1 were irradiated at the mid-spread-out Bragg peak of a clinical proton beam (linear energy transfer 2.5 keV/μm)more » or with 250 kVp x-rays, and the clonogenic survival fractions were determined. To estimate the RBE of the protons relative to cobalt-60 photons (Co60Eq), we assigned a RBE(Co60Eq) of 1.1 to x-rays to correct the physical dose measured. Standard DNA repair foci assays were used to monitor the damage responses, and the cell cycle distributions were assessed by flow cytometry. The poly(ADP-ribose) polymerase inhibitor olaparib was used for comparison. Results: Loss of SLX4 function resulted in an enhanced proton RBE(Co60Eq) of 1.42 compared with 1.11 for wild-type cells (at a survival fraction of 0.1; P<.05), which correlated with increased persistent DNA double-strand breaks in cells in the S/G{sub 2} phase. Genetic analysis identified the SLX4-binding partner MUS81 as a mediator of resistance to proton radiation. Both proton irradiation and olaparib treatment resulted in a similar prolonged accumulation of RAD51 foci in SLX4/MUS81-deficient cells, suggesting a common defect in the repair of DNA replication fork-associated damage. Conclusions: A defect in the FA pathway at the level of SLX4 results in hypersensitivity to proton radiation, which is, at least in part, due to impaired MUS81-mediated processing of replication forks that stall at clustered DNA damage. In vivo and clinical studies are needed to confirm these findings in human cancers.« less

Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation.

PubMed

Liu, Qi; Underwood, Tracy S A; Kung, Jong; Wang, Meng; Lu, Hsiao-Ming; Paganetti, Harald; Held, Kathryn D; Hong, Theodore S; Efstathiou, Jason A; Willers, Henning

2016-05-01

Clinical proton beam therapy has been based on the use of a generic relative biological effectiveness (RBE) of ∼1.1. However, emerging data have suggested that Fanconi anemia (FA) and homologous recombination pathway defects can lead to a variable RBE, at least in vitro. We investigated the role of SLX4 (FANCP), which acts as a docking platform for the assembly of multiple structure-specific endonucleases, in the response to proton irradiation. Isogenic cell pairs for the study of SLX4, XPF/ERCC1, MUS81, and SLX1 were irradiated at the mid-spread-out Bragg peak of a clinical proton beam (linear energy transfer 2.5 keV/μm) or with 250 kVp x-rays, and the clonogenic survival fractions were determined. To estimate the RBE of the protons relative to cobalt-60 photons (Co60Eq), we assigned a RBE(Co60Eq) of 1.1 to x-rays to correct the physical dose measured. Standard DNA repair foci assays were used to monitor the damage responses, and the cell cycle distributions were assessed by flow cytometry. The poly(ADP-ribose) polymerase inhibitor olaparib was used for comparison. Loss of SLX4 function resulted in an enhanced proton RBE(Co60Eq) of 1.42 compared with 1.11 for wild-type cells (at a survival fraction of 0.1; P<.05), which correlated with increased persistent DNA double-strand breaks in cells in the S/G2 phase. Genetic analysis identified the SLX4-binding partner MUS81 as a mediator of resistance to proton radiation. Both proton irradiation and olaparib treatment resulted in a similar prolonged accumulation of RAD51 foci in SLX4/MUS81-deficient cells, suggesting a common defect in the repair of DNA replication fork-associated damage. A defect in the FA pathway at the level of SLX4 results in hypersensitivity to proton radiation, which is, at least in part, due to impaired MUS81-mediated processing of replication forks that stall at clustered DNA damage. In vivo and clinical studies are needed to confirm these findings in human cancers. Copyright © 2016 Elsevier Inc. All rights reserved.

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rode, Michał F.; Sobolewski, Andrzej L.; Jankowska, Joanna

2016-04-07

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H) -ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale ofmore » this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.« less

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle*

PubMed Central

Yano, Naomine; Muramoto, Kazumasa; Shimada, Atsuhiro; Takemura, Shuhei; Baba, Junpei; Fujisawa, Hidenori; Mochizuki, Masao; Shinzawa-Itoh, Kyoko; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, Shinya

2016-01-01

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H3O+ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O2 bound to heme a3. To block backward proton movement, the water channel remains closed after O2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu198, which bridges the Mg2+ and CuA (the initial electron acceptor from cytochrome c) sites, suggest that the CuA-Glu198-Mg2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg2+-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO. PMID:27605664

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

PubMed

Yano, Naomine; Muramoto, Kazumasa; Shimada, Atsuhiro; Takemura, Shuhei; Baba, Junpei; Fujisawa, Hidenori; Mochizuki, Masao; Shinzawa-Itoh, Kyoko; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, Shinya

2016-11-11

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H 3 O + through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O 2 bound to heme a 3 To block backward proton movement, the water channel remains closed after O 2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O 2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg 2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu 198 , which bridges the Mg 2+ and Cu A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu A -Glu 198 -Mg 2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg 2+ -containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein's electronic polarization contributes significantly to its catalytic function

NASA Astrophysics Data System (ADS)

Xiang, Yun; Duan, Lili; Zhang, John Z. H.

2011-05-01

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.

Capturing the radical ion-pair intermediate in DNA guanine oxidation

PubMed Central

Jie, Jialong; Liu, Kunhui; Wu, Lidan; Zhao, Hongmei; Song, Di; Su, Hongmei

2017-01-01

Although the radical ion pair has been frequently invoked as a key intermediate in DNA oxidative damage reactions and photoinduced electron transfer processes, the unambiguous detection and characterization of this species remain formidable and unresolved due to its extremely unstable nature and low concentration. We use the strategy that, at cryogenic temperatures, the transient species could be sufficiently stabilized to be detectable spectroscopically. By coupling the two techniques (the cryogenic stabilization and the time-resolved laser flash photolysis spectroscopy) together, we are able to capture the ion-pair transient G+•⋯Cl− in the chlorine radical–initiated DNA guanine (G) oxidation reaction, and provide direct evidence to ascertain the intricate type of addition/charge separation mechanism underlying guanine oxidation. The unique spectral signature of the radical ion-pair G+•⋯Cl− is identified, revealing a markedly intense absorption feature peaking at 570 nm that is distinctive from G+• alone. Moreover, the ion-pair spectrum is found to be highly sensitive to the protonation equilibria within guanine-cytosine base pair (G:C), which splits into two resolved bands at 480 and 610 nm as the acidic proton transfers along the central hydrogen bond from G+• to C. We thus use this exquisite sensitivity to track the intrabase-pair proton transfer dynamics in the double-stranded DNA oligonucleotides, which is of critical importance for the description of the proton-coupled charge transfer mechanisms in DNA. PMID:28630924

Voltammetric Perspectives on the Acidity Scale and H+/H2 Process in Ionic Liquid Media.

PubMed

Bentley, Cameron L; Bond, Alan M; Zhang, Jie

2018-03-19

Nonhaloaluminate ionic liquids (ILs) have received considerable attention as alternatives to molecular solvents in diverse applications spanning the fields of physical, chemical, and biological science. One important and often overlooked aspect of the implementation of these designer solvents is how the properties of the IL formulation affect (electro)chemical reactivity. This aspect is emphasized herein, where recent (voltammetric) studies on the energetics of proton (H + ) transfer and electrode reaction mechanisms of the H + H 2 process in IL media are highlighted and discussed. The energetics of proton transfer, quantified using the pK 3 a (minus logarithm of acidity equilibrium constant, K a ) formalism, is strongly governed by the constituent IL anion, and to a lesser extent, the IL cation. The H + /H 2 process, a model inner-sphere reaction, also displays electrochemical characteristics that are strongly IL-dependent. Overall, these studies highlight the need to carry out systematic investigations to resolve IL structure and function relationships in order to realize the potential of these diverse and versatile solvents. Expected final online publication date for the Annual Review of Analytical Chemistry Volume 11 is June 12, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.

PubMed

Kóna, Juraj

2008-01-21

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.

Measurement of the generalized polarizabilities of the proton in virtual Compton scattering at Q2=0.92 and 1.76 GeV2.

PubMed

Laveissière, G; Todor, L; Degrande, N; Jaminion, S; Jutier, C; Di Salvo, R; Van Hoorebeke, L; Alexa, L C; Anderson, B D; Aniol, K A; Arundell, K; Audit, G; Auerbach, L; Baker, F T; Baylac, M; Berthot, J; Bertin, P Y; Bertozzi, W; Bimbot, L; Boeglin, W U; Brash, E J; Breton, V; Breuer, H; Burtin, E; Calarco, J R; Cardman, L S; Cavata, C; Chang, C-C; Chen, J-P; Chudakov, E; Cisbani, E; Dale, D S; de Jager, C W; De Leo, R; Deur, A; d'Hose, N; Dodge, G E; Domingo, J J; Elouadrhiri, L; Epstein, M B; Ewell, L A; Finn, J M; Fissum, K G; Fonvieille, H; Fournier, G; Frois, B; Frullani, S; Furget, C; Gao, H; Gao, J; Garibaldi, F; Gasparian, A; Gilad, S; Gilman, R; Glamazdin, A; Glashausser, C; Gomez, J; Gorbenko, V; Grenier, P; Guichon, P A M; Hansen, J O; Holmes, R; Holtrop, M; Howell, C; Huber, G M; Hyde-Wright, C E; Incerti, S; Iodice, M; Jardillier, J; Jones, M K; Kahl, W; Kato, S; Katramatou, A T; Kelly, J J; Kerhoas, S; Ketikyan, A; Khayat, M; Kino, K; Kox, S; Kramer, L H; Kumar, K S; Kumbartzki, G; Kuss, M; Leone, A; LeRose, J J; Liang, M; Lindgren, R A; Liyanage, N; Lolos, G J; Lourie, R W; Madey, R; Maeda, K; Malov, S; Manley, D M; Marchand, C; Marchand, D; Margaziotis, D J; Markowitz, P; Marroncle, J; Martino, J; McCormick, K; McIntyre, J; Mehrabyan, S; Merchez, F; Meziani, Z E; Michaels, R; Miller, G W; Mougey, J Y; Nanda, S K; Neyret, D; Offermann, E A J M; Papandreou, Z; Pasquini, B; Perdrisat, C F; Perrino, R; Petratos, G G; Platchkov, S; Pomatsalyuk, R; Prout, D L; Punjabi, V A; Pussieux, T; Quémenér, G; Ransome, R D; Ravel, O; Real, J S; Renard, F; Roblin, Y; Rowntree, D; Rutledge, G; Rutt, P M; Saha, A; Saito, T; Sarty, A J; Serdarevic, A; Smith, T; Smirnov, G; Soldi, K; Sorokin, P; Souder, P A; Suleiman, R; Templon, J A; Terasawa, T; Tieulent, R; Tomasi-Gustaffson, E; Tsubota, H; Ueno, H; Ulmer, P E; Urciuoli, G M; Vanderhaeghen, M; Van De Vyver, R; Van der Meer, R L J; Vernin, P; Vlahovic, B; Voskanyan, H; Voutier, E; Watson, J W; Weinstein, L B; Wijesooriya, K; Wilson, R; Wojtsekhowski, B B; Zainea, D G; Zhang, W-M; Zhao, J; Zhou, Z-L

2004-09-17

We report a virtual Compton scattering study of the proton at low c.m. energies. We have determined the structure functions P(LL)-P(TT)/epsilon and P(LT), and the electric and magnetic generalized polarizabilities (GPs) alpha(E)(Q2) and beta(M)(Q2) at momentum transfer Q(2)=0.92 and 1.76 GeV2. The electric GP shows a strong falloff with Q2, and its global behavior does not follow a simple dipole form. The magnetic GP shows a rise and then a falloff; this can be interpreted as the dominance of a long-distance diamagnetic pion cloud at low Q2, compensated at higher Q2 by a paramagnetic contribution from piN intermediate states.

Proton nuclear magnetic resonance studies on the variant-3 neurotoxin from Centruroides sculpturatus Ewing: Sequential assignment of resonances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nettesheim, D.G.; Klevit, R.E.; Drobny, G.

1989-02-21

The authors report the sequential assignment of resonances to specific residues in the proton nuclear magnetic resonance spectrum of the variant-3 neurotoxin from the scorpion Centruroides sculpturatus Ewing (range southwestern U.S.A.). A combination of two-dimensional NMR experiments such as 2D-COSY, 2D-NOESY, and single- and double-RELAY coherence transfer spectroscopy has been employed on samples of the protein dissolved in D{sub 2}O and in H{sub 2}O for assignment purposes. These studies provide a basis for the determination of the solution-phase conformation of this protein and for undertaking detailed structure-function studies of these neurotoxins that modulate the flow of sodium current by bindingmore » to the sodium channels of excitable membranes.« less

Hydrogen bonding in malonaldehyde: a density functional and reparametrized semiempirical approach

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Hrenar, Tomica; Došlić, Nadja

2003-08-01

Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core-core functions for the O-H and H-H interactions were used and a new functional form for the O-O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed.

Catalytic mechanism of human N-acetylserotonin methyltransferase: a theoretical investigation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Ting; Li, Jieqiong; He, Chaozheng; He, Hongqing; Zhang, Jinglai

2015-11-01

The methyl-transfer mechanism of human N-acetylserotonin methyltransferase and the roles of several residues around the active sites are investigated by density function theory method. This enzyme will catalyse the conversion of N-acetylserotonin and S-adenosyl-L-methionine (SAM) into melatonin and S-asenosylhomocysteine, which is the terminal step in the melatonin (N-acetyl-5-methoxytryptamine) biosynthesis. The calculated results confirm that the methyl transfer and proton transfer will take place via a SN2 step with a concerted mechanism, which is different from the experimental estimation via a water bridge. The residues H255, D256, E311, and R252 play an important role in reducing the barrier height and inducing methyl transfer. In addition, a full SAM molecule is considered in this work, which is never explored in previous reports. We find that some residues around the SAM in the centre of active site are essential factors to influence the mechanism and barrier height. So a truncated SAM model may not be suitable for all reactions.

Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines.

PubMed

Malm, Christian; Kim, Heejae; Wagner, Manfred; Hunger, Johannes

2017-08-10

Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Astrophysical S factor for the radiative capture {sup 12}N(p,{gamma}){sup 13}O determined from the {sup 14}N({sup 12}N,{sup 13}O){sup 13}C proton transfer reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banu, A.; Al-Abdullah, T.; Fu, C.

2009-02-15

The cross section of the radiative proton capture reaction on the drip line nucleus {sup 12}N was investigated using the asymptotic normalization coefficient (ANC) method. We have used the {sup 14}N({sup 12}N,{sup 13}O){sup 13}C proton transfer reaction at 12 MeV/nucleon to extract the ANC for {sup 13}O{yields}{sup 12}N+p and calculate from it the direct component of the astrophysical S factor of the {sup 12}N(p,{gamma}){sup 13}O reaction. The optical potentials used and the distorted-wave Born approximation analysis of the proton transfer reaction are discussed. For the entrance channel, the optical potential was inferred from an elastic scattering measurement carried out atmore » the same time as the transfer measurement. From the transfer, we determined the square of the ANC, C{sub p{sub 1/2}}{sup 2}({sup 13}O{sub g.s.})=2.53{+-}0.30 fm{sup -1}, and hence a value of 0.33(4) keV b was obtained for the direct astrophysical S factor at zero energy. Constructive interference at low energies between the direct and resonant captures leads to an enhancement of S{sub total}(0)=0.42(6) keV b. The {sup 12}N(p,{gamma}){sup 13}O reaction was investigated in relation to the evolution of hydrogen-rich massive Population III stars, for the role that it may play in the hot pp-chain nuclear burning processes, possibly occurring in such objects.« less

Froissart bound and self-similarity based models of proton structure functions

NASA Astrophysics Data System (ADS)

Choudhury, D. K.; Saikia, Baishali

2018-03-01

Froissart bound implies that the total proton-proton cross-section (or equivalently proton structure function) cannot rise faster than log2s ˜log2 1 x. Compatibility of such behavior with the notion of self-similarity in proton structure function was suggested by us sometime back. In the present work, we generalize and improve it further by considering more recent self-similarity based models of proton structure functions and compare with recent data as well as with the model of Block, Durand, Ha and McKay.

Hydrogen-bonded ring closing and opening of protonated methanol clusters H(+)(CH3OH)(n) (n = 4-8) with the inert gas tagging.

PubMed

Li, Ying-Cheng; Hamashima, Toru; Yamazaki, Ryoko; Kobayashi, Tomohiro; Suzuki, Yuta; Mizuse, Kenta; Fujii, Asuka; Kuo, Jer-Lai

2015-09-14

The preferential hydrogen bond (H-bond) structures of protonated methanol clusters, H(+)(MeOH)n, in the size range of n = 4-8, were studied by size-selective infrared (IR) spectroscopy in conjunction with density functional theory calculations. The IR spectra of bare clusters were compared with those with the inert gas tagging by Ar, Ne, and N2, and remarkable changes in the isomer distribution with the tagging were found for clusters with n≥ 5. The temperature dependence of the isomer distribution of the clusters was calculated by the quantum harmonic superposition approach. The observed spectral changes with the tagging were well interpreted by the fall of the cluster temperature with the tagging, which causes the transfer of the isomer distribution from the open and flexible H-bond network types to the closed and rigid ones. Anomalous isomer distribution with the tagging, which has been recently found for protonated water clusters, was also found for H(+)(MeOH)5. The origin of the anomaly was examined by the experiments on its carrier gas dependence.

Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression.

PubMed

Bar-Shir, Amnon; Liu, Guanshu; Liang, Yajie; Yadav, Nirbhay N; McMahon, Michael T; Walczak, Piotr; Nimmagadda, Sridhar; Pomper, Martin G; Tallman, Keri A; Greenberg, Marc M; van Zijl, Peter C M; Bulte, Jeff W M; Gilad, Assaf A

2013-01-30

Synthetic chemistry has revolutionized the understanding of many biological systems. Small compounds that act as agonists and antagonists of proteins, and occasionally as imaging probes, have contributed tremendously to the elucidation of many biological pathways. Nevertheless, the function of thousands of proteins is still elusive, and designing new imaging probes remains a challenge. Through screening and characterization, we identified a thymidine analogue as a probe for imaging the expression of herpes simplex virus type-1 thymidine kinase (HSV1-TK). To detect the probe, we used chemical exchange saturation transfer magnetic resonance imaging (CEST-MRI), in which a dynamic exchange process between an exchangeable proton and the surrounding water protons is used to amplify the desired contrast. Initially, five pyrimidine-based molecules were recognized as putative imaging agents, since their exchangeable imino protons resonate at 5-6 ppm from the water proton frequency and their detection is therefore less affected by endogenous CEST contrast or confounded by direct water saturation. Increasing the pK(a) value of the imino proton by reduction of its 5,6-double bond results in a significant reduction of the exchange rate (k(ex)) between this proton and the water protons. This reduced k(ex) of the dihydropyrimidine nucleosides fulfills the "slow to intermediate regime" condition for generating high CEST-MRI contrast. Consequently, we identified 5-methyl-5,6-dihydrothymidine as the optimal probe and demonstrated its feasibility for in vivo imaging of HSV1-TK. In light of these findings, this new approach can be generalized for designing specific probes for the in vivo imaging of a variety of proteins and enzymes.

Mechanism of [m+h]+ formation in atmospheric pressure photoionization mass spectrometry: identification of propionitrile in acetonitrile with high mass accuracy measurement and tandem mass spectrometry and evidence for its involvement in the protonation phenomenon.

PubMed

Kamel, Amin; Jeanville, Patrick; Colizza, Kevin; J-Rivera, Lauren Elizabeth

2008-11-01

The role of propionitrile in the production of [M+H]+ under atmospheric pressure photoionization (APPI) was investigated. In dopant-assisted APPI using acetone and anisole, protonated acetone and anisole radical cations were the most prominent ions observed. In dopant-free or direct APPI in acetonitrile, however, a major ion in acetonitrile was detected and identified as propionitrile, using high accuracy mass measurement and collision induced dissociation studies. Vaporizing ca. 10(-5) M althiazide and bendroflumethazide under direct APPI in acetonitrile produced their corresponding protonated species [M+H]+. In addition to protonated acetonitrile, its dimers, and acetonitrile/water clusters, protonated propionitrile, propionitrile dimer, and propionitrile/water clusters were also observed. The role of propionitrile, an impurity in acetonitrile and/or a possible product of ion-molecule reaction, in the production of [M+H]+ of althiazide and bendroflumethazide was further investigated in the absence of dopant using propionitrile-d5. The formation of [M+D]+ species was observed, suggesting a possible role of propionitrile in the protonation process. Additionally, an increase in the [M+H]+ signal of althiazide and bendroflumethazide was observed as a function of propionitrile concentration in acetonitrile. Theoretical data from the literature supported the assumption that one possible mechanism, among others, for the formation of [M+H]+ could be attributed to photo-initiated isomerization of propionitrile. The most stable isomers of propionitrile, based on their calculated ionization energy (IE) and relative energy (DeltaE), were assumed to undergo proton transfer to the analytes, and mechanisms were proposed.