Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications

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

Hou, Gao-Lei; Valiev, Marat; Wang, Xue-Bin

Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO 2(CH 2) nCO 2 -[HO 2(CH 2) nCO 2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that uponmore » formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO 4 -[HO 2(CH 2) 2CO 2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO 2(CH 2) 2CO 2 -[HO 2(CH 2) 2CO 2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.« less

A theoretical investigation into the strength of N-NO2 bonds, ring strain and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX.

PubMed

Wang, Bao-Guo; Ren, Fu-de; Shi, Wen-Jing

2015-11-01

Changes in N-NO2 bond strength, ring strain energy and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX were investigated using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. Analysis of electron density shifts was also carried out. The results indicate that H-bonding energy correlates well with the increment of ring strain energy. Upon complex formation, the strength of the N-NO2 trigger-bond is enhanced, suggesting reduced sensitivity, while judged by the increased ring strain energy, sensitivity is increased. However, some features of the molecular surface electrostatic potential, such as a local maximum above the N-NO2 bond and ring, σ + (2) and electrostatic balance parameter ν, remain essentially unchanged upon complex formation, and only a small change in the impact sensitivity h 50 is suggested. It is not sufficient to determine sensitivity solely on the basis of trigger bond or ring strain; as a global feature of a molecule, the molecular surface electrostatic potential is available to help judge the change of sensitivity in H-bonded complexes. Graphical Abstract The strengthened N-NO2 bond suggests reduced sensitivity, while it is reverse by theincreased ring strain energy upon the complex formation. However, the molecular surfaceelectrostatic potential (V S) shows the little change of h 50. The V S should be taken into accountin the analysis of explosive sensitivity in the H-bonded complex.

Spectrophotometric and spectroscopic studies of charge transfer complexes of p-toluidine as an electron donor with picric acid as an electron acceptor in different solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Khan, Ishaat M.; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with π-acceptor picric acid have been studied spectrophotometrically in various solvents such as carbon tetrachloride, chloroform, dichloromethane acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in non-polar solvent is high. The stoichiometry of the complex was found to be 1:1 ratio by straight-line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength ( f), transition dipole moment ( μEN), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complex was shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents that were used.

Spectroscopic studies of multiple charge transfer complexes of p-toluidine with π-acceptor picric acid in different polar solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with π-acceptor picric acid have been studied spectrophotometrically in various solvents such as acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in less polar solvent is high. The stoichiometry of the complex was found to be 1: 1 ratio by straight line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant ( K CT), molar extinction coefficient (ɛCT), standard free energy (Δ G°), oscillator strength ( f), transition dipole moment (μEN), resonance energy ( R N) and ionization potential ( I D). The results indicate that the formation constant ( K CT) for the complex were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used.

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

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

Chakraborty, Kaushik; Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitablemore » statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4–DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3–DNA complex.« less

Synthesis, crystallographic, spectral, and spectrophotometric studies of proton transfer complex of 1,2-dimethylimidazole with 3,5-dinitrobenzoic acid in different polar solvents

NASA Astrophysics Data System (ADS)

Miyan, Lal; Zulkarnain; Ahmad, Afaq

2017-04-01

The molecular interaction between 1, 2-dimethylimidazole (DMI) and 3,5-dinitrobenzoic acid (DNBA) has been investigated in methanol at room temperature. The stoichiometry of the synthesized CT complex was found to be 1:1 using the straight line method of Benesi-Hildebrand equation. The structure of the resulting CT complex was isolating and characterized using X-ray crystallography, FTIR and 1H NMR spectroscopic techniques. The thermal composition and stability of the CT complex were analyzed using thermogravimetric and differential thermal analysis (TGA and DTA). UV-visible spectrophotometric technique was used to the determine the various important physical parameters such as formation constant (KCT), molar extinction coefficient (εCT), energy of interaction (ECT), ionization potential (ID), resonance energy (RN), free energy (ΔG°), oscillator strength (ƒ) and transition dipole moment (μN). The effect of polarity of the solvent and concentration of acceptor on these parameters have been investigated. The results indicate that charge transfer complex (CTC) is more stable in less polar solvent due to the high value of the formation constant. A polymeric network through hydrogen bonding interaction between neighboring moieties was observed. This has also been attributed to the formation of 1:1 type CT complex.

Role of B800 in carotenoid-bacteriochlorophyll energy and electron transfer in LH2 complexes from the purple bacterium Rhodobacter sphaeroides.

PubMed

Polívka, Tomas; Niedzwiedzki, Dariusz; Fuciman, Marcel; Sundström, Villy; Frank, Harry A

2007-06-28

The role of the B800 in energy and electron transfer in LH2 complexes has been studied using femtosecond time-resolved transient absorption spectroscopy. The B800 site was perturbed by application of lithium dodecyl sulfate (LDS), and comparison of treated and untreated LH2 complexes from Rhodobacter sphaeroides incorporating carotenoids neurosporene, spheroidene, and spheroidenone was used to explore the role of B800 in carotenoid to bacteriochlorophyll-a (BChla) energy transfer and carotenoid radical formation. Efficiencies of the S1-mediated energy transfer in the LDS-treated complexes were 86, 61, and 57% in the LH2 complexes containing neurosporene, spheroidene, and spheroidenone, respectively. Analysis of the carotenoid S1 lifetimes in solution, LDS-treated, and untreated LH2 complexes allowed determination of B800/B850 branching ratio in the S1-mediated energy transfer. It is shown that B800 is a major acceptor, as approximately 60% of the energy from the carotenoid S1 state is accepted by B800. This value is nearly independent of conjugation length of the carotenoid. In addition to its role in energy transfer, the B800 BChla is the only electron acceptor in the event of charge separation between carotenoid and BChla in LH2 complexes, which is demonstrated by prevention of carotenoid radical formation in the LDS-treated LH2 complexes. In the untreated complexes containing neurosporene and spheroidene, the carotenoid radical is formed with a time constant of 300-400 fs. Application of different excitation wavelengths and intensity dependence of the carotenoid radical formation showed that the carotenoid radical can be formed only after excitation of the S2 state of carotenoid, although the S2 state itself is not a precursor of the charge-separated state. Instead, either a hot S1 state or a charge-transfer state lying between S2 and S1 states of the carotenoid are discussed as potential precursors of the charge-separated state.

Charge-transfer complexes of sulfamethoxazole drug with different classes of acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; El-Korashy, Sabry A.; El-Deen, Ibrahim M.; El-Sayed, Shaima M.

2010-09-01

The charge-transfer complexes of the donor sulfamethoxazole (SZ) with iodine (I 2), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), p-chloranil (CHL) and picric acid (PA) have been studied spectrophotometrically in chloroform or methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CT-complexes in case of four acceptors. The stoichiometry of the complexes was found to be 1:1 ratio by molar ratio method between donor and acceptor with maximum absorption bands (CT band). The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ G°), oscillator strength (ƒ), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complexes were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used. IR, 1H NMR, mass spectra, UV-Vis techniques, elemental analyses (CHN) and TG-DTG investigation were used to characterize the four sulfamethoxazole charge-transfer complexes.

Effects of low-energy electron irradiation on formation of nitrogen–vacancy centers in single-crystal diamond

DOE PAGES

Schwartz, J.; Aloni, S.; Ogletree, D. F.; ...

2012-04-20

Exposure to beams of low-energy electrons (2-30 keV) in a scanning electron microscope locally induces formation of NV-centers without thermal annealing in diamonds that have been implanted with nitrogen ions. In this study, we find that non-thermal, electron-beam-induced NV-formation is about four times less efficient than thermal annealing. But NV-center formation in a consecutive thermal annealing step (800°C) following exposure to low-energy electrons increases by a factor of up to 1.8 compared to thermal annealing alone. Finally, these observations point to reconstruction of nitrogen-vacancy complexes induced by electronic excitations from low-energy electrons as an NV-center formation mechanism and identify localmore » electronic excitations as a means for spatially controlled room-temperature NV-center formation.« less

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

Spectrophotometric and spectroscopic studies of charge transfer complexes of p-toluidine as an electron donor with picric acid as an electron acceptor in different solvents.

PubMed

Singh, Neeti; Khan, Ishaat M; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with pi-acceptor picric acid have been studied spectrophotometrically in various solvents such as carbon tetrachloride, chloroform, dichloromethane acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in non-polar solvent is high. The stoichiometry of the complex was found to be 1:1 ratio by straight-line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant (K(CT)), molar extinction coefficient (epsilon(CT)), standard free energy (DeltaG(o)), oscillator strength (f), transition dipole moment (mu(EN)), resonance energy (R(N)) and ionization potential (I(D)). The results indicate that the formation constant (K(CT)) for the complex was shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents that were used. Copyright 2010 Elsevier B.V. All rights reserved.

Hydrogen-bond formation between isoindolo[2,1-a]indol-6-one and aliphatic alcohols in n-hexane.

PubMed

Demeter, Attila; Bérces, Tibor

2005-03-17

The spectroscopic, kinetic, and equilibrium properties of isoindolo[2,1-a]indol-6-one (I) were studied in n-hexane in the presence and absence of alcohols (X). Hydrogen-bonded-complex formation was found to occur between the alcohol and the ground state as well as the excited state of the I molecule. The spectra of I and its singly complexed derivative (IX) are similar; however, that of IX is red shifted. The extent of red shift increases with the hydrogen-bonding ability of the alcohol. Equilibrium constant measurements were made to determine the hydrogen-bond basicity (beta(2)(H)) for I and the singlet excited (1)I. The beta(2)(H) value for (1)I is found to be about twice that of the ground-state I. Time-resolved fluorescence decay measurements indicate that the reaction of singlet excited I with fluorinated alcohols is diffusion controlled, while the rate of complexation with nonfluorinated (weaker hydrogen bonding) aliphatic alcohols depends on the Gibbs energy change in the complexation reaction. The quantitative correlation between the rate coefficient of complexation of (1)I with alcohols and the Gibbs energy change in the complexation process allowed us to estimate the rate coefficient for the complexation of the ground-state I with alcohols. The formation of the singlet excited hydrogen-bonded complex is irreversible; (1)IX disappears in a first order and an alcohol induced second order reaction. The first order decay is predominantly due to internal conversion to the ground state, the rate of which depends on the ionization energy of the complexing alcohol.

Selective CO2 conversion to formate conjugated with H2O oxidation utilizing semiconductor/complex hybrid photocatalysts.

PubMed

Sato, Shunsuke; Arai, Takeo; Morikawa, Takeshi; Uemura, Keiko; Suzuki, Tomiko M; Tanaka, Hiromitsu; Kajino, Tsutomu

2011-10-05

Photoelectrochemical reduction of CO(2) to HCOO(-) (formate) over p-type InP/Ru complex polymer hybrid photocatalyst was highly enhanced by introducing an anchoring complex into the polymer. By functionally combining the hybrid photocatalyst with TiO(2) for water oxidation, selective photoreduction of CO(2) to HCOO(-) was achieved in aqueous media, in which H(2)O was used as both an electron donor and a proton source. The so-called Z-scheme (or two-step photoexcitation) system operated with no external electrical bias. The selectivity for HCOO(-) production was >70%, and the conversion efficiency of solar energy to chemical energy was 0.03-0.04%.

A first-principles study of carbon-related energy levels in GaN. I. Complexes formed by substitutional/interstitial carbons and gallium/nitrogen vacancies

NASA Astrophysics Data System (ADS)

Matsubara, Masahiko; Bellotti, Enrico

2017-05-01

Various forms of carbon based complexes in GaN are studied with first-principles calculations employing Heyd-Scuseria-Ernzerhof hybrid functionals within the framework of the density functional theory. We consider carbon complexes made of the combinations of single impurities, i.e., CN-CGa, CI-CN , and CI-CGa , where CN, CGa , and CI denote C substituting nitrogen, C substituting gallium, and interstitial C, respectively, and of neighboring gallium/nitrogen vacancies ( VGa / VN ), i.e., CN-VGa and CGa-VN . Formation energies are computed for all these configurations with different charge states after full geometry optimizations. From our calculated formation energies, thermodynamic transition levels are evaluated, which are related to the thermal activation energies observed in experimental techniques such as deep level transient spectroscopy. Furthermore, the lattice relaxation energies (Franck-Condon shift) are computed to obtain optical activation energies, which are observed in experimental techniques such as deep level optical spectroscopy. We compare our calculated values of activation energies with the energies of experimentally observed C-related trap levels and identify the physical origins of these traps, which were unknown before.

Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics.

PubMed

Urakawa, Atsushi; Iannuzzi, Marcella; Hutter, Jürg; Baiker, Alfons

2007-01-01

Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.

Neighbor effect in complexation of a conjugated polymer.

PubMed

Sosorev, Andrey; Zapunidi, Sergey

2013-09-19

Charge-transfer complex (CTC) formation between a conjugated polymer and low-molecular-weight organic acceptor is proposed to be driven by the neighbor effect. Formation of a CTC on the polymer chain results in an increased probability of new CTC formation near the existing one. We present an analytical model for CTC distribution considering the neighbor effect, based on the principles of statistical mechanics. This model explains the experimentally observed threshold-like dependence of the CTC concentration on the acceptor content in a polymer:acceptor blend. It also allows us to evaluate binding energies of the complexes.

Defect states of complexes involving a vacancy on the boron site in boronitrene

NASA Astrophysics Data System (ADS)

Ngwenya, T. B.; Ukpong, A. M.; Chetty, N.

2011-12-01

First principles calculations have been performed to investigate the ground state properties of freestanding monolayer hexagonal boronitrene (h-BN). We have considered monolayers that contain native point defects and their complexes, which form when the point defects bind with the boron vacancy on the nearest-neighbor position. The changes in the electronic structure are analyzed to show the extent of localization of the defect-induced midgap states. The variations in formation energies suggest that defective h-BN monolayers that contain carbon substitutional impurities are the most stable structures, irrespective of the changes in growth conditions. The high energies of formation of the boron vacancy complexes suggest that they are less stable, and their creation by ion bombardment would require high-energy ions compared to point defects. Using the relative positions of the derived midgap levels for the double vacancy complex, it is shown that the quasi-donor-acceptor pair interpretation of optical transitions is consistent with stimulated transitions between electron and hole states in boronitrene.

Analysis of the Enhanced Stability of R(+)-Alpha Lipoic Acid by the Complex Formation with Cyclodextrins

PubMed Central

Ikuta, Naoko; Sugiyama, Hironori; Shimosegawa, Hiroshi; Nakane, Rie; Ishida, Yoshiyuki; Uekaji, Yukiko; Nakata, Daisuke; Pallauf, Kathrin; Rimbach, Gerald; Terao, Keiji; Matsugo, Seiichi

2013-01-01

R(+)-alpha lipoic acid (RALA) is one of the cofactors for mitochondrial enzymes and, therefore, plays a central role in energy metabolism. RALA is unstable when exposed to low pH or heat, and therefore, it is difficult to use enantiopure RALA as a pharma- and nutra-ceutical. In this study, we have aimed to stabilize RALA through complex formation with cyclodextrins (CDs). α-CD, β-CD and γ-CD were used for the formation of these RALA-CD complexes. We confirmed the complex formation using differential scanning calorimetry and showed by using HPLC analysis that complexed RALA is more stable than free RALA when subjected to humidity and high temperature or acidic pH conditions. Scanning electron microscopy studies showed that the particle size and shape differed depending on the cyclodextrin used for complexation. Further, the complexes of CD and RALA showed a different particle size distribution pattern compared with that of CD itself or that of the physical mixture of RALA and CD. PMID:23434662

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach.

PubMed

Rubinstein, Alexander I; Sabirianov, Renat F; Namavar, Fereydoon

2016-10-14

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander I.; Sabirianov, Renat F.; Namavar, Fereydoon

2016-10-01

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ˜80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Reaction mechanism of Ru(II) piano-stool complexes: umbrella sampling QM/MM MD study.

PubMed

Futera, Zdeněk; Burda, Jaroslav V

2014-07-15

Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru(II) (η(6) -benzene)(en)Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)-N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross-link formation. One feasible pathway leading to Ru(II) guanine-guanine cross-link with synchronous releasing of the benzene ligand is predicted. The cross-linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds-DNA. Copyright © 2014 Wiley Periodicals, Inc.

Computer-aided molecular modeling techniques for predicting the stability of drug cyclodextrin inclusion complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Faucci, Maria Teresa; Melani, Fabrizio; Mura, Paola

2002-06-01

Molecular modeling was used to investigate factors influencing complex formation between cyclodextrins and guest molecules and predict their stability through a theoretical model based on the search for a correlation between experimental stability constants ( Ks) and some theoretical parameters describing complexation (docking energy, host-guest contact surfaces, intermolecular interaction fields) calculated from complex structures at a minimum conformational energy, obtained through stochastic methods based on molecular dynamic simulations. Naproxen, ibuprofen, ketoprofen and ibuproxam were used as model drug molecules. Multiple Regression Analysis allowed identification of the significant factors for the complex stability. A mathematical model ( r=0.897) related log Ks with complex docking energy and lipophilic molecular fields of cyclodextrin and drug.

Unexpected Trimerization of Pyrazine in the Coordination Sphere of Low-Valent Titanocene Fragments.

PubMed

Jung, Thomas; Beckhaus, Rüdiger; Klüner, Thorsten; Höfener, Sebastian; Klopper, Wim

2009-08-11

The titanium mediated trimerization of pyrazine leads to the formation of a tris-chelate complex employing a 4a,4b,8a,8b,12a,12b-hexahydrodiyprazino[2,3-f:2',3'-h]quinoxaline ligand (HATH6, 3). The driving force in the formation of the (Cp*2Ti)3(HATH6) complex 2 is attributed to the formation of six Ti-N bonds. We show that density functional theory (DFT) fails to predict quantitatively correct results. Therefore, post-Hartree-Fock methods, such as second-order Møller-Plesset perturbation theory (MP2), in combination with coupled-cluster (CC) methods must be used. Both MP2 and CCSD(T) levels of theory provide endothermic trimerization energies, showing that the plain pyrazine trimer is not stable with respect to decomposition into its monomers. Complete basis set (CBS) results for the MP2 level of theory were computed using explicitly correlated wave functions. With these, we estimate the CCSD(T) CBS limit of the hypothetical trimerization energy to be +0.78 eV. Thus, the trimerization is facilitated by the formation of six Ti-N bonds with a calculated formation energy of -1.32 eV per bond.

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon

PubMed Central

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-01-01

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H+ translocation across the cytoplasmic membrane that then drives Na+ translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na+/H+ antiporter module. The electrochemical Na+ gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na+/H+ antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains. PMID:25049407

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon.

PubMed

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-08-05

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H(+) translocation across the cytoplasmic membrane that then drives Na(+) translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na(+)/H(+) antiporter module. The electrochemical Na(+) gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na(+)/H(+) antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains.

Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline-3-hydroxy-4-methoxybenzaldehyde

NASA Astrophysics Data System (ADS)

Sharma, K. P.; Reddi, R. S. B.; Bhattacharya, S.; Rai, R. N.

2012-06-01

The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV-Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied.

Simple method for determining binding energies of fullerene and complex atomic negative ions

NASA Astrophysics Data System (ADS)

Felfli, Zineb; Msezane, Alfred

2017-04-01

A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

Three Dimensional Energetics of Left Ventricle Flows Using Time-Resolved DPIV

NASA Astrophysics Data System (ADS)

Pierrakos, Olga; Vlachos, Pavlos

2006-11-01

Left ventricular (LV) flows in the human heart are very complex and in the presence of unhealthy or prosthetic heart valves (HV), the complexity of the flow is further increased. Yet to date, no study has documented the complex 3D hemodynamic characteristics and energetics of LV flows. We present high sampling frequency Time Resolved DPIV results obtained in a flexible, transparent LV documenting the evolution of eddies and turbulence. The purpose is to characterize the energetics of the LV flow field in the presence of four orientations of the most commonly implanted mechanical bileaflet HV and a porcine valve. By decomposing the energy scales of the flow field, the ultimate goal is to quantify the total energy losses associated with vortex ring formation and turbulence dissipation. The energies associated to vortex ring formation give a measure of the energy trapped within the structure while estimations of the turbulence dissipation rate (TDR) give a measure of the energy dissipated at the smaller scales. For the first time in cardiovascular applications, an LES-based PIV method, which overcomes the limitations of conventional TDR estimation methods that assume homogeneous isotropic turbulence, was employed. We observed that energy lost at the larger scales (vortex ring) is much higher than the energy lost at the smaller scales due to turbulence dissipation.

Energy minimization for self-organized structure formation and actuation

NASA Astrophysics Data System (ADS)

Kofod, Guggi; Wirges, Werner; Paajanen, Mika; Bauer, Siegfried

2007-02-01

An approach for creating complex structures with embedded actuation in planar manufacturing steps is presented. Self-organization and energy minimization are central to this approach, illustrated with a model based on minimization of the hyperelastic free energy strain function of a stretched elastomer and the bending elastic energy of a plastic frame. A tulip-shaped gripper structure illustrates the technological potential of the approach. Advantages are simplicity of manufacture, complexity of final structures, and the ease with which any electroactive material can be exploited as means of actuation.

Amine-free reversible hydrogen storage in formate salts catalyzed by ruthenium pincer complex without pH control or solvent change.

PubMed

Kothandaraman, Jotheeswari; Czaun, Miklos; Goeppert, Alain; Haiges, Ralf; Jones, John-Paul; May, Robert B; Prakash, G K Surya; Olah, George A

2015-04-24

Due to the intermittent nature of most renewable energy sources, such as solar and wind, energy storage is increasingly required. Since electricity is difficult to store, hydrogen obtained by electrochemical water splitting has been proposed as an energy carrier. However, the handling and transportation of hydrogen in large quantities is in itself a challenge. We therefore present here a method for hydrogen storage based on a CO2 (HCO3 (-) )/H2 and formate equilibrium. This amine-free and efficient reversible system (>90 % yield in both directions) is catalyzed by well-defined and commercially available Ru pincer complexes. The formate dehydrogenation was triggered by simple pressure swing without requiring external pH control or the change of either the solvent or the catalyst. Up to six hydrogenation-dehydrogenation cycles were performed and the catalyst performance remained steady with high selectivity (CO free H2 /CO2 mixture was produced). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic and physical measurements on charge-transfer complexes: Interactions between norfloxacin and ciprofloxacin drugs with picric acid and 3,5-dinitrobenzoic acid acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Elfalaky, A.; Elesh, Eman

2011-03-01

Charge-transfer complexes formed between norfloxacin (nor) or ciprofloxacin (cip) drugs as donors with picric acid (PA) and/or 3,5-dinitrobenzoic acid (DNB) as π-acceptors have been studied spectrophotometrically in methanol solvent at room temperature. The results indicated the formation of CT-complexes with molar ratio1:1 between donor and acceptor at maximum CT-bands. In the terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength ( f), transition dipole moment (μ), resonance energy ( RN) and ionization potential ( ID) were estimated. IR, H NMR, UV-Vis techniques, elemental analyses (CHN) and TG-DTG investigations were used to characterize the structural of charge-transfer complexes. It indicates that the CT interaction was associated with a proton migration from each acceptor to nor or cip donors which followed by appearing intermolecular hydrogen bond. In addition, X-ray investigation was carried out to scrutinize the crystal structure of the resulted CT-complexes.

A Molecular Copper Catalyst for Hydrogenation of CO­2 to Formate

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

Zall, Christopher M.; Linehan, John C.; Appel, Aaron M.

2015-09-04

There is widespread interest in the hydrogenation of CO2 to energy-rich products such as formate. However, first-row transition metal complexes that catalyze the hydrogenation of CO2 to formate remain rare. Copper phosphine complexes are widely used in the reduction of organic substrates but have not previously been used as catalysts for the conversion of H2 and CO2 to formate. Here we demonstrate that the triphosphine-ligated copper(I) complex LCu(MeCN)PF6 is an active catalyst for CO2 hydrogenation in the presence of a suitable base. Screening of bases and studies of catalytic reactions by in operando spectroscopy revealed important and unusual roles formore » the base in promoting H2 activation and turnover.« less

Hydrogen passivation and multiple hydrogen-Hg vacancy complex impurities (nH-VHg, n = 1,2,3,4) in Hg0.75Cd0.25Te

NASA Astrophysics Data System (ADS)

Xue, L.; Tang, D. H.; Qu, X. D.; Sun, L. Z.; Lu, Wei; Zhong, J. X.

2011-09-01

Using first-principles method within the framework of the density functional theory, we study the formation energies and the binding energies of multiple hydrogen-mercury vacancy complex impurities (nH-VHg, n = 1,2,3,4) in Hg0.75Cd0.25Te. We find that, when mercury vacancies exist in Hg0.75Cd0.25Te, the formation of the complex impurity between H and VHg (1H-VHg) is easy and its binding energy is up to 0.56 eV. In this case, the deep acceptor level of mercury vacancy is passivated. As the hydrogen concentration increases, we find that the complex impurity between VHg and two hydrogen atoms (2H-VHg) is more stable than 1H-VHg. This complex passivates both the two acceptor levels introduced by mercury vacancy and neutralizes the p-type dopant characteristics of VHg in Hg0.75Cd0.25Te. Moreover, we find that the complex impurities formed by one VHg and three or four H atoms (3H-VHg, 4H-VHg) are still stable in Hg0.75Cd0.25Te, changing the VHg doped p-type Hg0.75Cd0.25Te to n-type material.

Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

NASA Astrophysics Data System (ADS)

Remko, Milan

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

A tethering complex drives the terminal stage of SNARE-dependent membrane fusion

NASA Astrophysics Data System (ADS)

D'Agostino, Massimo; Risselada, Herre Jelger; Lürick, Anna; Ungermann, Christian; Mayer, Andreas

2017-11-01

Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.

PubMed

Costa, Kyle C; Wong, Phoebe M; Wang, Tiansong; Lie, Thomas J; Dodsworth, Jeremy A; Swanson, Ingrid; Burn, June A; Hackett, Murray; Leigh, John A

2010-06-15

In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.

Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions

NASA Technical Reports Server (NTRS)

Shortt, Brian; Chutjian, Ara; Orient, Otto

2008-01-01

A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

Nickel Complexes of a Binucleating Ligand Derived from an SCS Pincer

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

Peterson, Sonja M.; Helm, Monte L.; Appel, Aaron M.

2015-01-01

A binucleating ligand has been prepared that contains an SCS pincer and three oxygen donor ligands in a partial crown ether loop. To enable metalation with Ni0, a bromoarene precursor was used and resulted in the formation of a nickel-bromide complex in the SCS pincer. Reaction of the nickel complex with a lithium salt yielded a heterobimetallic complex with bromide bridging the two metal centers. The solid-state structures were determined for this heterobimetallic complex and the nickel-bromide precursor, and the two complexes were characterized electrochemically to determine the influence of coordinating the second metal. This research was supported by themore » US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. MLH 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. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

Time-dependent density functional theory study of the luminescence properties of gold phosphine thiolate complexes.

PubMed

Guidez, Emilie B; Aikens, Christine M

2015-04-09

The origin of the emission of the gold phosphine thiolate complex (TPA)AuSCH(CH3)2 (TPA = 1,3,5-triaza-7-phosphaadamantanetriylphosphine) is investigated using time-dependent density functional theory (TDDFT). This system absorbs light at 3.6 eV, which corresponds mostly to a ligand-to-metal transition with some interligand character. The P-Au-S angle decreases upon relaxation in the S1 and T1 states. Our calculations show that these two states are strongly spin-orbit coupled at the ground state geometry. Ligand effects on the optical properties of this complex are also discussed by looking at the simple AuP(CH3)3SCH3 complex. The excitation energies differ by several tenths of an electronvolt. Excited state optimizations show that the excited singlet and triplet of the (TPA)AuSCH(CH3)2 complex are bent. On the other hand, the Au-S bond breaks in the excited state for the simple complex, and TDDFT is no longer an adequate method. The excited state energy landscape of gold phosphine thiolate systems is very complex, with several state crossings. This study also shows that the formation of the [(TPA)AuSCH(CH3)2]2 dimer is favorable in the ground state. The inclusion of dispersion interactions in the calculations affects the optimized geometries of both ground and excited states. Upon excitation, the formation of a Au-Au bond occurs, which results in an increase in energy of the low energy excited states in comparison to the monomer. The experimentally observed emission of the (TPA)AuSCH(CH3)2 complex at 1.86 eV cannot be unambiguously assigned and may originate from several excited states.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II.

PubMed

Pathak, Vinay; Prasad, Ankush; Pospíšil, Pavel

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex.

Formation of singlet oxygen by decomposition of protein hydroperoxide in photosystem II

PubMed Central

Pathak, Vinay; Prasad, Ankush

2017-01-01

Singlet oxygen (1O2) is formed by triplet-triplet energy transfer from triplet chlorophyll to O2 via Type II photosensitization reaction in photosystem II (PSII). Formation of triplet chlorophyll is associated with the change in spin state of the excited electron and recombination of triplet radical pair in the PSII antenna complex and reaction center, respectively. Here, we have provided evidence for the formation of 1O2 by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. Protein hydroperoxide is formed by protein oxidation initiated by highly oxidizing chlorophyll cation radical and hydroxyl radical formed by Type I photosensitization reaction. Under highly oxidizing conditions, protein hydroperoxide is oxidized to protein peroxyl radical which either cyclizes to dioxetane or recombines with another protein peroxyl radical to tetroxide. These highly unstable intermediates decompose to triplet carbonyls which transfer energy to O2 forming 1O2. Data presented in this study show for the first time that 1O2 is formed by decomposition of protein hydroperoxide in PSII membranes deprived of Mn4O5Ca complex. PMID:28732060

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

NASA Astrophysics Data System (ADS)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents.

Spectroscopic and thermal investigations of charge-transfer complexes formed between sulfadoxine drug and different types of acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.

2011-01-01

Charge-transfer reactions between sulfadoxine (SDOX) as a donor with iodine (I 2), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), p-chloranil (CHL) and picric acid (PA) have been studied in solid and solution forms. The stoichiometry of all complexes was found to be 1:1 by molar ratio method between donor and acceptor at a CT-band absorption bands. The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength (ƒ), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complexes were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used. IR, 1H NMR and UV-Vis spectroscopic techniques, Elemental analyses (CHN) and TG-DTG investigation were used to characterize the four sulfadoxine charge-transfer complexes.

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

PubMed Central

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-01-01

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. PMID:27288028

Density functional theory study of HfCl4, ZrCl4, and Al(CH3)3 decomposition on hydroxylated SiO2: Initial stage of high-k atomic layer deposition

NASA Astrophysics Data System (ADS)

Jeloaica, L.; Estève, A.; Djafari Rouhani, M.; Estève, D.

2003-07-01

The initial stage of atomic layer deposition of HfO2, ZrO2, and Al2O3 high-k films, i.e., the decomposition of HfCl4, ZrCl4, and Al(CH3)3 precursor molecules on an OH-terminated SiO2 surface, is investigated within density functional theory. The energy barriers are determined using artificial activation of vibrational normal modes. For all precursors, reaction proceeds through the formation of intermediate complexes that have equivalent formation energies (˜-0.45 eV), and results in HCl and CH4 formation with activation energies of 0.88, 0.91, and 1.04 eV for Hf, Zr, and Al based precursors, respectively. The reaction product of Al(CH3)3 decomposition is found to be more stable (by -1.45 eV) than the chemisorbed intermediate complex compared to the endothermic decomposition of HfCl4 and ZrCl4 chemisorbed precursors (0.26 and 0.29 eV, respectively).

Reactions in 1,1,1-trifluoroacetone triggered by low energy electrons (0-10 eV): from simple bond cleavages to complex unimolecular reactions.

PubMed

Illenberger, Eugen; Meinke, Martina C

2014-08-21

The impact of low energy electrons (0-10 eV) to 1,1,1-trifluoroacetone yields a variety of fragment anions which are formed via dissociative electron attachment (DEA) through three pronounced resonances located at 0.8 eV, near 4 eV, and in the energy range 8-9 eV. The fragment ions arise from different reactions ranging from the direct cleavage of one single or double bond (formation of F(-), CF3(-), O(-), (M-H)(-), and M-F)(-)) to remarkably complex unimolecular reactions associated with substantial geometric and electronic rearrangement in the transitory intermediate (formation of OH(-), FHF(-), (M-HF)(-), CCH(-), and HCCO(-). The ion CCH(-), for example, is formed by an excision of unit from the target molecule through the concerted cleavage of four bonds and recombination to H2O within the neutral component of the reaction.

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

NASA Astrophysics Data System (ADS)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Electrocatalytic Oxidation of Formate with Nickel Diphosphane Dipeptide Complexes. Effect of Ligands Modified with Amino Acids

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

Galan, Brandon R.; Reback, Matthew L.; Jain, Avijita

2013-09-03

A series of nickel bis-diphosphine complexes with dipeptides appended to the ligands were investigated for the catalytic oxidation of formate. Typical rates of ~7 s -1 were found, similar to the parent complex (~8 s -1), with amino acid size and positioning contributing very little to rate or operating potential. Hydroxyl functionalities did result in lower rates, which were recovered by protecting the hydroxyl group. The results suggest that the overall dielectric introduced by the dipeptides does not play an important role in catalysis, but free hydroxyl groups do influence activity suggesting contributions from intra- or intermolecular interactions. These observationsmore » are important in developing a fundamental understanding of the affect that an enzyme-like outer coordination sphere can have upon molecular catalysts. This work was funded by the US DOE Basic Energy Sciences, Chemical Sciences, Geoscience and Biosciences Division (BRG, AJ, AMA, WJS), the US DOE Basic Energy Sciences, Physical Bioscience program (MLR). Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Terabit bandwidth-adaptive transmission using low-complexity format-transparent digital signal processing.

PubMed

Zhuge, Qunbi; Morsy-Osman, Mohamed; Chagnon, Mathieu; Xu, Xian; Qiu, Meng; Plant, David V

2014-02-10

In this paper, we propose a low-complexity format-transparent digital signal processing (DSP) scheme for next generation flexible and energy-efficient transceiver. It employs QPSK symbols as the training and pilot symbols for the initialization and tracking stage of the receiver-side DSP, respectively, for various modulation formats. The performance is numerically and experimentally evaluated in a dual polarization (DP) 11 Gbaud 64QAM system. Employing the proposed DSP scheme, we conduct a system-level study of Tb/s bandwidth-adaptive superchannel transmissions with flexible modulation formats including QPSK, 8QAM and 16QAM. The spectrum bandwidth allocation is realized in the digital domain instead of turning on/off sub-channels, which improves the performance of higher order QAM. Various transmission distances ranging from 240 km to 6240 km are demonstrated with a colorless detection for hardware complexity reduction.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation.

PubMed

Chernia, Zelig; Tsori, Yoav

2018-03-14

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

NASA Astrophysics Data System (ADS)

Chernia, Zelig; Tsori, Yoav

2018-03-01

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Selective Co-Encapsulation Inside an M6 L4 Cage.

PubMed

Leenders, Stefan H A M; Becker, René; Kumpulainen, Tatu; de Bruin, Bas; Sawada, Tomohisa; Kato, Taito; Fujita, Makoto; Reek, Joost N H

2016-10-17

There is broad interest in molecular encapsulation as such systems can be utilized to stabilize guests, facilitate reactions inside a cavity, or give rise to energy-transfer processes in a confined space. Detailed understanding of encapsulation events is required to facilitate functional molecular encapsulation. In this contribution, it is demonstrated that Ir and Rh-Cp-type metal complexes can be encapsulated inside a self-assembled M 6 L 4 metallocage only in the presence of an aromatic compound as a second guest. The individual guests are not encapsulated, suggesting that only the pair of guests can fill the void of the cage. Hence, selective co-encapsulation is observed. This principle is demonstrated by co-encapsulation of a variety of combinations of metal complexes and aromatic guests, leading to several ternary complexes. These experiments demonstrate that the efficiency of formation of the ternary complexes depends on the individual components. Moreover, selective exchange of the components is possible, leading to formation of the most favorable complex. Besides the obvious size effect, a charge-transfer interaction may also contribute to this effect. Charge-transfer bands are clearly observed by UV/Vis spectrophotometry. A change in the oxidation potential of the encapsulated electron donor also leads to a shift in the charge-transfer energy bands. As expected, metal complexes with a higher oxidation potential give rise to a higher charge-transfer energy and a larger hypsochromic shift in the UV/Vis spectrum. These subtle energy differences may potentially be used to control the binding and reactivity of the complexes bound in a confined space. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

PubMed Central

Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

2010-01-01

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

In situ synthesis, photometric and spectroscopic studies of chelating system during the 1,4,7,10,13,16-hexaoxacyclooctadecane charge transfer reaction with different acceptors

NASA Astrophysics Data System (ADS)

Hossan, Aisha S. M.; Abou-Melha, Hanaa M.; Refat, Moamen S.

2011-08-01

Electron donor acceptor complexes (EDA) of the 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6) as a rich donor were spectrophotometrically discussed and synthesized in solid form according the interactions with different nine of usual π-acceptors like 2,3,5,6-tetrachlorocyclohexa-2,5-diene-1,4-dione (p-chloranil; p-CHL), tetrachloro-1,2-benzoquinone (o-chloranil; o-CHL), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), tetracyanoquinodimethane (TCNQ), 2,6-dichloroquinone-4-chloroimide (DCQ), 2,6-dibromoquinone-4-chloroimide (DBQ), 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone (chloranilic acid; CLA), N-bromosuccinimide (NBS), 2,4,6-trinitrophenol (picric acid; PA). Spectroscopic and physical data such as formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ G°), oscillator strength ( f), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( Ip) were estimated in chloroform or methanol at 25 °C. Based on the elemental analysis and photometric titrations the CT-complexes were formed indicated the formation of 1:1 charge-transfer complexes for the o-CHL, TCNQ, DCQ, DBQ and NBS acceptors but 1:3 ratio for p-CHL, DDQ, CLA and PA, respectively. The charge-transfer interactions were interpretative according to the formation of dative ion pairs [18C6 rad +, A rad -], where A is acceptor. All of the resulting charge transfer complexes were isolated in amorphous form and the complexes formations on IR and 1H NMR spectra were discussed.

Preparation, characterization and molecular modeling studies of the inclusion complex of Caffeine with Beta-cyclodextrin

NASA Astrophysics Data System (ADS)

Prabu, Samikannu; Swaminathan, Meenakshisundaram; Sivakumar, Krishnamoorthy; Rajamohan, Rajaram

2015-11-01

The formation through supramolecular interaction of a host-guest inclusion complex of caffeine (CA) with nano-hydrophobic cavity beta-cyclodextrin (β-CD) is achieved by a physical mixture, a kneading method and a co-precipitation method. The formation of the inclusion complex of CA with β-CD in solution state is confirmed by UV-visible spectrophotometer, fluorescence spectrophotometer and time-resolved fluorescence spectrophotometer. The stoichiometry of the inclusion complex is 1:1; the imidazole ring and pyrimidine ring of caffeine is deeply entrapped in the beta-cyclodextrin as confirmed by spectral shifts. The Benesi-Hildebrand plot is used to calculate the binding constant of the inclusion complex of CA with β-CD at room temperature. The Gibbs free energy change of the inclusion complex process is calculated and the process is found to be spontaneous. The thermal stability of the inclusion complex of CA with β-CD is analyzed using differential scanning calorimetry. The crystal structure modification of a solid inclusion complex is confirmed by scanning electron microscopy image analysis. The formation of the inclusion complex of CA with β-CD in the solid phase is also confirmed by FT-IR and XRD. The formation of the inclusion complex between CA and β-CD, as confirmed by molecular docking studies, is in good relationship with the results obtained through different experimental methods.

Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes.

PubMed

Dai, Yumei; Wang, Yuhua; Huang, Zhengguo; Wang, Hongke; Yu, Lei

2012-01-01

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H(2)O)(n) (n = 1-3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H(2)O)(n) (n = 1-3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1-3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H(2)O)(3) complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.

Defect formation energy in pyrochlore: the effect of crystal size

NASA Astrophysics Data System (ADS)

Wang, Jianwei; Ewing, Rodney C.; Becker, Udo

2014-09-01

Defect formation energies of point defects of two pyrochlores Gd2Ti2O7 and Gd2Zr2O7 as a function of crystal size were calculated. Density functional theory with plane-wave basis sets and the projector-augmented wave method were used in the calculations. The results show that the defect formation energies of the two pyrochlores diverge as the size decreases to the nanometer range. For Gd2Ti2O7 pyrochlore, the defect formation energy is higher at nanometers with respect to that of the bulk, while it is lower for Gd2Zr2O7. The lowest defect formation energy for Gd2Zr2O7 is found at 15-20 Å. The different behaviors of the defect formation energies as a function of crystal size are caused by different structural adjustments around the defects as the size decreases. For both pyrochlore compositions at large sizes, the defect structures are similar to those of the bulk. As the size decreases, for Gd2Ti2O7, additional structure distortions appear at the surfaces, which cause the defect formation energy to increase. For Gd2Zr2O7, additional oxygen Frenkel pair defects are introduced, which reduce the defect formation energy. As the size further decreases, increased structure distortions occur at the surfaces, which cause the defect formation energy to increase. Based on a hypothesis that correlates the energetics of defect formation and radiation response for complex oxides, the calculated results suggest that at nanometer range Gd2Ti2O7 pyrochlore is expected to have a lower radiation tolerance, and those of Gd2Zr2O7 pyrochlore to have a higher radiation tolerance. The highest radiation tolerance for Gd2Zr2O7 pyrochlore is expected to be found at ˜2 nanometers.

The influence of projectile ion induced chemistry on surface pattern formation

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

Karmakar, Prasanta, E-mail: prasantak@vecc.gov.in; Satpati, Biswarup

We report the critical role of projectile induced chemical inhomogeneity on surface nanostructure formation. Experimental inconsistency is common for low energy ion beam induced nanostructure formation in the presence of uncontrolled and complex contamination. To explore the precise role of contamination on such structure formation during low energy ion bombardment, a simple and clean experimental study is performed by selecting mono-element semiconductors as the target and chemically inert or reactive ion beams as the projectile as well as the source of controlled contamination. It is shown by Atomic Force Microscopy, Cross-sectional Transmission Electron Microscopy, and Electron Energy Loss Spectroscopy measurementsmore » that bombardment of nitrogen-like reactive ions on Silicon and Germanium surfaces forms a chemical compound at impact zones. Continuous bombardment of the same ions generates surface instability due to unequal sputtering and non-uniform re-arrangement of the elemental atom and compound. This instability leads to ripple formation during ion bombardment. For Argon-like chemically inert ion bombardment, the chemical inhomogeneity induced boost is absent; as a result, no ripples are observed in the same ion energy and fluence.« less

Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species.

PubMed

Brites, Vincent; Cimas, Alvaro; Spezia, Riccardo; Sieffert, Nicolas; Lisy, James M; Gaigeot, Marie-Pierre

2015-03-10

Combined theoretical DFT-MD and RRKM methodologies and experimental spectroscopic infrared predissociation (IRPD) strategies to map potential energy surfaces (PES) of complex ionic clusters are presented, providing lowest and high energy conformers, thresholds to isomerization, and cluster formation pathways. We believe this association not only represents a significant advance in the field of mapping minima and transition states on the PES but also directly measures dynamical pathways for the formation of structural conformers and isomers. Pathways are unraveled over picosecond (DFT-MD) and microsecond (RRKM) time scales while changing the amount of internal energy is experimentally achieved by changing the loss channel for the IRPD measurements, thus directly probing different kinetic and isomerization pathways. Demonstration is provided for Li(+)(H2O)3,4 ionic clusters. Nonstatistical formation of these ionic clusters by both direct and cascade processes, involving isomerization processes that can lead to trapping of high energy conformers along the paths due to evaporative cooling, has been unraveled.

Defect interactions in GaAs single crystals

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1984-01-01

The two-sublattice structural configuration of GaAs and deviations from stoichiometry render the generation and interaction of electrically active point defects (and point defect complexes) critically important for device applications and very complex. Of the defect-induced energy levels, those lying deep into the energy band are very effective lifetime ""killers". The level 0.82 eV below the condition band, commonly referred to as EL2, is a major deep level, particularly in melt-grown GaAs. This level is associated with an antisite defect complex (AsGa - VAS). Possible mechanisms of its formation and its annihilation were further developed.

A quantum-rovibrational-state-selected study of the reaction in the collision energy range of 0.05-10.00 eV: translational, rotational, and vibrational energy effects.

PubMed

Xu, Yuntao; Xiong, Bo; Chang, Yih-Chung; Pan, Yi; Lo, Po Kam; Lau, Kai Chung; Ng, C Y

2017-04-12

We report detailed absolute integral cross sections (σ's) for the quantum-rovibrational-state-selected ion-molecule reaction in the center-of-mass collision energy (E cm ) range of 0.05-10.00 eV, where (vvv) = (000), (100), and (020), and . Three product channels, HCO + + OH, HOCO + + H, and CO + + H 2 O, are identified. The measured σ(HCO + ) curve [σ(HCO + ) versus E cm plot] supports the hypothesis that the formation of the HCO + + OH channel follows an exothermic pathway with no potential energy barriers. Although the HOCO + + H channel is the most exothermic, the σ(HOCO + ) is found to be significantly lower than the σ(HCO + ). The σ(HOCO + ) curve is bimodal, indicating two distinct mechanisms for the formation of HOCO + . The σ(HOCO + ) is strongly inhibited at E cm < 0.4 eV, but is enhanced at E cm > 0.4 eV by (100) vibrational excitation. The E cm onsets of σ(CO + ) determined for the (000) and (100) vibrational states are in excellent agreement with the known thermochemical thresholds. This observation, along with the comparison of the σ(CO + ) curves for the (100) and (000) states, shows that kinetic and vibrational energies are equally effective in promoting the CO + channel. We have also performed high-level ab initio quantum calculations on the potential energy surface, intermediates, and transition state structures for the titled reaction. The calculations reveal potential barriers of ≈0.5-0.6 eV for the formation of HOCO + , and thus account for the low σ(HOCO + ) and its bimodal profile observed. The E cm enhancement for σ(HOCO + ) at E cm ≈ 0.5-5.0 eV can be attributed to the direct collision mechanism, whereas the formation of HOCO + at low E cm < 0.4 eV may involve a complex mechanism, which is mediated by the formation of a loosely sticking complex between HCO + and OH. The direct collision and complex mechanisms proposed also allow the rationalization of the vibrational inhibition at low E cm and the vibrational enhancement at high E cm observed for the σ(HOCO + ).

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

PubMed

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

Ionization dynamics of the water trimer: A direct ab initio MD study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Takada, Tomoya

2013-03-01

Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ˜15 fs after the ionization). In complex channel, an ion-radical contact pair (H3O+-OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50-100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

Absorption spectrometric and thermodynamic study of charge transfer complexes of menadione (Vitamin K 3) with a series of phenols

NASA Astrophysics Data System (ADS)

Pal, Purnendu; Bhattacharya, Sumanta; Mukherjee, Asok K.; Mukherjee, Dulal C.

2005-03-01

The electron donor-acceptor (EDA) interactions between menadione (i.e., 2-methyl-1,4-naphthoquinone, which is also called 'Vitamin K 3') and a series of phenols (viz., phenol, resorcinol and p-quinol) have been studied in CCl 4 medium. In all the cases, charge transfer (CT) bands have been located. The CT transition energies ( hνCT) of the complexes are found to change systematically with change in the number and position of the -OH groups in the aromatic ring of the phenol moiety. From the trends in the hνCT values, the Hückel parameters ( hÖ and kC-Ö) for the -OH group have been obtained. The CT transition energies are well correlated with the ionisation potentials of the phenols. From an analysis of this variation the electron affinity of Vitamin K 3 has been found to be 2.28 eV. The stoichiometry of the complexes in each case has been found to be 1(menadione):2 (phenol). Formation constants of the complexes have been determined at four different temperatures from which the enthalpies and entropies of formation of the complexes have been estimated.

Absorption spectrometric and thermodynamic study of charge transfer complexes of menadione (Vitamin K3) with a series of phenols.

PubMed

Pal, Purnendu; Bhattacharya, Sumanta; Mukherjee, Asok K; Mukherjee, Dulal C

2005-03-01

The electron donor-acceptor (EDA) interactions between menadione (i.e., 2-methyl-1,4-naphthoquinone, which is also called 'Vitamin K3') and a series of phenols (viz., phenol, resorcinol and p-quinol) have been studied in CCl4 medium. In all the cases, charge transfer (CT) bands have been located. The CT transition energies (h nu(CT)) of the complexes are found to change systematically with change in the number and position of the -OH groups in the aromatic ring of the phenol moiety. From the trends in the h nu(CT) values, the Hückel parameters (h(O) and k(C-O)) for the -OH group have been obtained. The CT transition energies are well correlated with the ionisation potentials of the phenols. From an analysis of this variation the electron affinity of Vitamin K3 has been found to be 2.28 eV. The stoichiometry of the complexes in each case has been found to be 1(menadione):2 (phenol). Formation constants of the complexes have been determined at four different temperatures from which the enthalpies and entropies of formation of the complexes have been estimated.

Exploring interaction of TNF and orthopoxviral CrmB protein by surface plasmon resonance and free energy calculation.

PubMed

Ivanisenko, Nikita V; Tregubchak, Tatiana V; Saik, Olga V; Ivanisenko, Vladimir A; Shchelkunov, Sergei N

2014-01-01

Inhibition of the activity of the tumor necrosis factor (TNF) has become the main strategy for treating inflammatory diseases. The orthopoxvirus TNF-binding proteins can bind and efficiently neutralize TNF. To analyze the mechanisms of the interaction between human (hTNF) or mouse (mTNF) TNF and the cowpox virus N-terminal binding domain (TNFBD-CPXV), also the variola virus N-terminal binding domain (TNFBD-VARV) and to define the amino acids most importantly involved in the formation of complexes, computer models, derived from the X-ray structure of a homologous hTNF/TNFRII complex, were used together with experiments. The hTNF/TNFBD-CPXV, hTNF/TNFBD-VARV, mTNF/TNFBD-CPXV, and mTNF/TNFBD-VARV complexes were used in the molecular dynamics (MD) simulations and MM/GBSA free energy calculations. The complexes were ordered as hTNF/TNFBD-CPXV, hTNF/TNFBD-VARV, mTNF/TNFBD-CPXV and mTNF/TNFBD-VARV according to increase in the binding affinity. The calculations were in agreement with surface plasmon resonance (SPR) measurements of the binding constants. Key residues involved in complex formation were identified.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Gibbs energies of transferring triglycine from water into H2O-DMSO solvent

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Kuz'mina, K. I.; Lan, Pham Thi; Kuz'mina, I. A.; Sharnin, V. A.

2014-08-01

The Gibbs energies of transferring triglycine (3Gly, glycyl-glycyl-glycine) from water into mixtures of water with dimethyl sulfoxide (χDMSO = 0.05, 0.10, and 0.15 mole fractions) at 298.15 K are determined from the interphase distribution. An increased dimethyl sulfoxide (DMSO) concentration in the solvent slightly raises the positive values of Δtr G ○(3Gly), possibly indicating the formation of more stable 3Gly-H2O solvated complexes than ones of 3Gly-DMSO. It is shown that the change in the Gibbs energy of transfer of 3Gly is determined by the enthalpy component. The relationship of 3Gly and 18-crown-6 ether (18C6) solvation's contributions to the change in the Gibbs energy of [3Gly18C6] molecular complex formation in H2O-DMSO solvents is analyzed, and the key role of 3Gly solvation's contribution to the change in the stability of [3Gly18C6] upon moving from H2O to mixtures with DMSO is revealed.

Imaging protein complex formation in the autophagy pathway: analysis of the interaction of LC3 and Atg4BC74A in live cells using Förster resonance energy transfer and fluorescence recovery after photobleaching

NASA Astrophysics Data System (ADS)

Kraft, Lewis J.; Kenworthy, Anne K.

2012-01-01

The protein microtubule-associated protein 1, light chain 3 (LC3) functions in autophagosome formation and plays a central role in the autophagy pathway. Previously, we found LC3 diffuses more slowly in cells than is expected for a freely diffusing monomer, suggesting it may constitutively associate with a macromolecular complex containing other protein components of the pathway. In the current study, we used Förster resonance energy transfer (FRET) microscopy and fluorescence recovery after photobleaching (FRAP) to investigate the interactions of LC3 with Atg4BC74A, a catalytically inactive mutant of the cysteine protease involved in lipidation and de-lipidation of LC3, as a model system to probe protein complex formation in the autophagy pathway. We show Atg4BC74A is in FRET proximity with LC3 in both the cytoplasm and nucleus of living cells, consistent with previous biochemical evidence that suggests these proteins directly interact. In addition, overexpressed Atg4BC74A diffuses significantly more slowly than predicted based on its molecular weight, and its translational diffusion coefficient is significantly slowed upon coexpression with LC3 to match that of LC3 itself. Taken together, these results suggest Atg4BC74A and LC3 are contained within the same multiprotein complex and that this complex exists in both the cytoplasm and nucleoplasm of living cells.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin.

PubMed

Wade, Kristin R; Hotze, Eileen M; Kuiper, Michael J; Morton, Craig J; Parker, Michael W; Tweten, Rodney K

2015-02-17

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin

PubMed Central

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.

2015-01-01

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT. PMID:25646411

First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-07-01

We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

Complexes of dipolar excitons in layered quasi-two-dimensional nanostructures

NASA Astrophysics Data System (ADS)

Bondarev, Igor V.; Vladimirova, Maria R.

2018-04-01

We discuss neutral and charged complexes (biexcitons and trions) formed by indirect excitons in layered quasi-two-dimensional semiconductor heterostructures. Indirect excitons—long-lived neutral Coulomb-bound pairs of electrons and holes of different layers—have been known for semiconductor coupled quantum wells and have recently been reported for van der Waals heterostructures such as double bilayer graphene and transition-metal dichalcogenides. Using the configuration space approach, we derive the analytical expressions for the trion and biexciton binding energies as a function of interlayer distance. The method captures essential kinematics of complex formation to reveal significant binding energies, up to a few tens of meV for typical interlayer distances ˜3 -5 Å , with the trion binding energy always being greater than that of the biexciton. Our results can contribute to the understanding of more complex many-body phenomena such as exciton Bose-Einstein condensation and Wigner-like electron-hole crystallization in layered semiconductor heterostructures.

[Studies by means of 1H NMR spectroscopy of complex formation of aromatic biologically active compounds with antibiotic topotecan].

PubMed

Mosunov, A A; Kostiukov, V V; Evstigneev, M P

2012-01-01

The analysis of heteroassociation of antibiotic topotecan (TPT) with aromatic biologically active compounds (BAC): caffeine, mutagens ethidium bromide and proflavine, antibiotic daunomycin, vitamins flavin-mononucleotide and nicotinamide, has been carried out in the work using 1H NMR spectroscopy data. The equilibrium constants of heteroassociation and induced chemical shifts of the protons have been obtained in the complexes with BAC. It is found that the complex formation TPT-BAC has the nature of stacking of the chromophores, additionally stabilized in the case of proflavine by intermolecular hydrogen bond. Calculation of the basic components of the Gibbs free energy of the complexation reactions is carried out, and the factors which stabilize and destabilize the heterocomplexes of molecules are revealed.

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Enhanced Respiratory Chain Supercomplex Formation in Response to Exercise in Human Skeletal Muscle.

PubMed

Greggio, Chiara; Jha, Pooja; Kulkarni, Sameer S; Lagarrigue, Sylviane; Broskey, Nicholas T; Boutant, Marie; Wang, Xu; Conde Alonso, Sonia; Ofori, Emmanuel; Auwerx, Johan; Cantó, Carles; Amati, Francesca

2017-02-07

Mitochondrial dysfunction is a hallmark of multiple metabolic complications. Physical activity is known to increase mitochondrial content in skeletal muscle, counteracting age-related decline in muscle function and protecting against metabolic and cardiovascular complications. Here, we investigated the effect of 4 months of exercise training on skeletal muscle mitochondria electron transport chain complexes and supercomplexes in 26 healthy, sedentary older adults. Exercise differentially modulated respiratory complexes. Complex I was the most upregulated complex and not stoichiometrically associated to the other complexes. In contrast to the other complexes, complex I was almost exclusively found assembled in supercomplexes in muscle mitochondria. Overall, supercomplex content was increased after exercise. In particular, complexes I, III, and IV were redistributed to supercomplexes in the form of I+III 2 +IV. Taken together, our results provide the first evidence that exercise affects the stoichiometry of supercomplex formation in humans and thus reveal a novel adaptive mechanism for increased energy demand. Copyright © 2017 Elsevier Inc. All rights reserved.

Hydride-Meisenheimer Complex Formation and Protonation as Key Reactions of 2,4,6-Trinitrophenol Biodegradation by Rhodococcus erythropolis

PubMed Central

Rieger, Paul-Gerhard; Sinnwell, Volker; Preuß, Andrea; Francke, Wittko; Knackmuss, Hans-Joachim

1999-01-01

Biodegradation of 2,4,6-trinitrophenol (picric acid) by Rhodococcus erythropolis HLPM-1 proceeds via initial hydrogenation of the aromatic ring system. Here we present evidence for the formation of a hydride-Meisenheimer complex (anionic ς-complex) of picric acid and its protonated form under physiological conditions. These complexes are key intermediates of denitration and productive microbial degradation of picric acid. For comparative spectroscopic identification of the hydride complex, it was necessary to synthesize this complex for the first time. Spectroscopic data revealed the initial addition of a hydride ion at position 3 of picric acid. This hydride complex readily picks up a proton at position 2, thus forming a reactive species for the elimination of nitrite. Cell extracts of R. erythropolis HLPM-1 transform the chemically synthesized hydride complex into 2,4-dinitrophenol. Picric acid is used as the sole carbon, nitrogen, and energy source by R. erythropolis HLPM-1. PMID:9973345

DNA-lipid complexes: stability of honeycomb-like and spaghetti-like structures.

PubMed Central

May, S; Ben-Shaul, A

1997-01-01

A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the "spaghetti" complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The "honeycomb" complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/A of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer. PMID:9370436

Trap formation and energy transfer in pheophorbide a-DAB-dendrimers and pyropheophorbide a-fullerene C 60 hexaadduct molecular systems

NASA Astrophysics Data System (ADS)

Röder, Beate; Ermilov, Eugeny A.; Hackbarth, Steffen; Helmreich, Matthias; Jux, Norbert

2006-04-01

The photophysical properties of DAB-dendrimers from 1 st to 4 th generation as well as Diaminohexane - all substituted with the in maximum achievable quantity of pheophorbide a (Pheo) molecules were studied in comparison with a novel hexapyropheophorbide a - fullerene hexaadduct (FHP6) and a fullerene [6:0]-hexaadduct which carries twelve pyropheophorbide a units (FHP12) using both steady-state and time-resolved spectroscopic methods. It was found that neighboring dye molecules covalently linked to one DAB- or fullerene moiety due to the length and high flexibility of carbon chains could stack with each other. This structural property is the reason for the possibility of formation different types of energy traps, which were resolved experimentally. The dipole-dipole resonance Förster energy transfer between the dye molecules coupled to one complex caused a very fast and efficient delivery of the excitation to a trap. As result the fluorescence as well as the singlet oxygen quantum yields of the different complexes were reduced with increasing number of dye molecules per complex. Nevertheless in every case the singlet oxygen generation was less influenced then the fluorescence quantum yield, exposing the complex to a non-negligible amount of excited oxygen in the singlet state. While the fullerene complexes turned out to be stable under these conditions, the DAB-dendrimer-backbones were completely fragmented to small rudiments carrying just one or a small number of dye molecules.

Optimization of high quality Cu2ZnSnS4 thin film by low cost and environment friendly sol-gel technique for thin film solar cells applications

NASA Astrophysics Data System (ADS)

Chaudhari, J. J.; Joshi, U. S.

2018-05-01

In this study kesterite Cu2ZnSnS4 (CZTS) thin films suitable for absorber layer in thin film solar cells (TFSCs) were successfully fabricated on glass substrate by sol-gel method. The effects of complexing agent on formation of CZTS thin films have been investigated. X-ray diffraction (XRD) analysis confirms formation of polycrystalline CZTS thin films with single phase kesterite structure. XRD and Raman spectroscopy analysis of CZTS thin films with optimized concentration of complexing agent confirmed formation of kesterite phase in CZTS thin films. The direct optical band gap energy of CZTS thin films is found to decrease from 1.82 to 1.50 eV with increase of concentration of complexing agent triethanolamine. Morphological analysis of CZTS thin films shows smooth, uniform and densely packed CZTS grains and increase in the grain size with increase of concentration of complexing agent. Hall measurements revealed that concentration of charge carrier increases and resistivity decreases in CZTS thin films as amount of complexing agent increases.

Prebiotic molecules formation through the gas-phase reaction between HNO and CH2CHOH2+

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Martínez, Henar; Largo, Antonio; Barrientos, Carmen

2017-07-01

Context. Knowing how the molecules that are present in the ISM can evolve to more complex ones is an interesting topic in interstellar chemistry. The study of possible reactions between detected species can help to understand the evolution in complexity of the interstellar matter and also allows knowing the formation of new molecules which could be candidates to be detected. We focus our attention on two molecules detected in space, vinyl alcohol (CH2CHOH) and azanone (HNO). Aims: We aim to carry out a theoretical study of the ion-molecule reaction between protonated vinyl alcohol and azanone. The viability of formation of complex organic molecules (COMs) from these reactants is expected to provide some insight into the formation of prebiotic species through gas phase reactions. Methods: The reaction of protonated vinyl alcohol with azanone has been theoretically studied by using ab initio methods. Stationary points on the potential energy surface (PES) were characterized at the second-order Moller-Plesset level in conjunction with the aug-cc-pVTZ (correlation-consistent polarized valence triple-zeta) basis set. In addition, the electronic energies were refined by means of single-point calculations at the CCSD(T) level (coupled cluster single and double excitation model augmented with a non-iterative treatment of triple excitations) with the same basis set. Results: From a thermodynamic point of view, twelve products, composed of carbon, oxygen, nitrogen, and hydrogen which could be precursors in the formation of more complex biological molecules, can be obtained from this reaction. Among these, we focus especially on ionized glycine and two of its isomers. The analysis of the PES shows that only formation of cis- and trans-O-protonated imine acetaldehyde, CH2NHCOH+ and, CHNHCHOH+, are viable under interstellar conditions. Conclusions: The reaction of protonated vinyl alcohol with azanone can evolve in the interstellar medium to more complex organic molecules of prebiotic interest. Our results suggest that imine acetaldehyde could be a feasible candidate molecule to be searched for in space.

The equilibrium constant of complex formation in solution: A study utilizing a dielectric constant method

NASA Astrophysics Data System (ADS)

Loh, C. W.

1980-03-01

A method was developed for determining equilibrium constants, heat of reaction, and change in free energy and entropy during a 1:1 complex formation in solutions. The measurements were carried out on ternary systems containing two interacting solutes in an inert solvent. The procedures was applied to the investigation of hydrogen bond complex formations in two mixtures systems, phenol and pyridine in carbon tetrachloride, and 4, 5, 6, 7-tetrachloro-2-trifluoromethylbenzimidazole (TTFB) and alkyl acetate in styrene. The first mixture system was studied in order to compare the results with those obtained by other methods. Results for the second mixture system indicated strong association between molecules of TTFB and alkyl acetate and suggested that the blocking of valinomycin-mediated bilayer membrane conductance by substituted benzimidazoles was due to competition for a limited number of adsorption sites on the membrane surface.

High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase.

PubMed

Kaiyawet, Nopporn; Lonsdale, Richard; Rungrotmongkol, Thanyada; Mulholland, Adrian J; Hannongbua, Supot

2015-02-10

Thymidylate synthase (TS) is a promising cancer target, due to its crucial function in thymine synthesis. It performs the reductive methylation of 2'-deoxyuridine-5'-phosphate (dUMP) to thymidine-5'-phosphate (dTMP), using N-5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) as a cofactor. After the formation of the dUMP/mTHF/TS noncovalent complex, and subsequent conformational activation, this complex has been proposed to react via nucleophilic attack (Michael addition) by Cys146, followed by methylene-bridge formation to generate the ternary covalent intermediate. Herein, QM/MM (B3LYP-D/6-31+G(d)-CHARMM27) methods are used to model the formation of the ternary covalent intermediate. A two-dimensional potential energy surface reveals that the methylene-bridged intermediate is formed via a concerted mechanism, as indicated by a single transition state on the minimum energy pathway and the absence of a stable enolate intermediate. A range of different QM methods (B3LYP, MP2 and SCS-MP2, and different basis sets) are tested for the calculation of the activation energy barrier for the formation of the methylene-bridged intermediate. We test convergence of the QM/MM results with respect to size of the QM region. Inclusion of Arg166, which interacts with the nucleophilic thiolate, in the QM region is important for reliable results; the MM model apparently does not reproduce energies for distortion of the guanidinium side chain correctly. The spin component scaled-Møller-Plessett perturbation theory (SCS-MP2) approach was shown to be in best agreement (within 1.1 kcal/mol) while the results obtained with MP2 and B3LYP also yielded acceptable values (deviating by less than 3 kcal/mol) compared with the barrier derived from experiment. Our results indicate that using a dispersion-corrected DFT method, or a QM method with an accurate treatment of electron correlation, increases the agreement between the calculated and experimental activation energy barriers, compared with the semiempirical AM1 method. These calculations provide important insight into the reaction mechanism of TS and may be useful in the design of new TS inhibitors.

Impacts of natural disturbance on soil carbon dynamics in forest ecosystems

Treesearch

Steven T. Overby; Stephen C. Hart; Daniel G. Neary

2002-01-01

Forest soils are entities within themselves, self-organized and highly resilient over time. The transfer of energy bound in carbon (C) molecules drives the organization and functions of this biological system (Fisher and Binkley, 2000; Paul and Clark, 1996). Photosynthetic organisms reduce atmospheric C and store energy from solar radiation in the formation of complex...

Thermochemistry of Alane Complexes for Hydrogen Storage: A Theoretical and Experimental Investigation

PubMed Central

2011-01-01

Knowledge of the relative stabilities of alane (AlH3) complexes with electron donors is essential for identifying hydrogen storage materials for vehicular applications that can be regenerated by off-board methods; however, almost no thermodynamic data are available to make this assessment. To fill this gap, we employed the G4(MP2) method to determine heats of formation, entropies, and Gibbs free energies of formation for 38 alane complexes with NH3−nRn (R = Me, Et; n = 0−3), pyridine, pyrazine, triethylenediamine (TEDA), quinuclidine, OH2−nRn (R = Me, Et; n = 0−2), dioxane, and tetrahydrofuran (THF). Monomer, bis, and selected dimer complex geometries were considered. Using these data, we computed the thermodynamics of the key formation and dehydrogenation reactions that would occur during hydrogen delivery and alane regeneration, from which trends in complex stability were identified. These predictions were tested by synthesizing six amine−alane complexes involving trimethylamine, triethylamine, dimethylethylamine, TEDA, quinuclidine, and hexamine and obtaining upper limits of ΔG° for their formation from metallic aluminum. Combining these computational and experimental results, we establish a criterion for complex stability relevant to hydrogen storage that can be used to assess potential ligands prior to attempting synthesis of the alane complex. On the basis of this, we conclude that only a subset of the tertiary amine complexes considered and none of the ether complexes can be successfully formed by direct reaction with aluminum and regenerated in an alane-based hydrogen storage system. PMID:22962624

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.

Infrared and density functional theory studies of isoprene-water complexes in noble gas matrices

NASA Astrophysics Data System (ADS)

Ito, Fumiyuki

2017-11-01

The interaction of 2-methyl-1,3-butadiene (isoprene) with a H2O molecule in low-temperature noble gas matrices (Ar or Kr) was investigated using infrared absorption spectroscopy. Vibrational peaks arising from 1:1 isoprene-H2O adducts were assigned and compared with the results of quantum chemical calculations. The comparison led to the conclusion that the H2O molecule in the complex preferentially H-bonds to one of the two unsaturated Cdbnd C bonds, and that the binding energy of the complex is comparable to that of the C6H6-H2O complex. The present study suggests that the change in the charge distribution of isoprene due to the formation of a complex with H2O may lead to alteration of the reactivity with respect to the insertion of OH radicals, thereby influencing the formation of aerosols in the atmosphere.

Complex Pattern Formation from Current-Driven Dynamics of Single-Layer Epitaxial Islands on Crystalline Conducting Substrates

NASA Astrophysics Data System (ADS)

Kumar, Ashish; Dasgupta, Dwaipayan; Maroudas, Dimitrios

We report a systematic study of complex pattern formation resulting from the driven dynamics of single-layer homoepitaxial islands on face-centered cubic (FCC) crystalline conducting substrate surfaces under the action of an externally applied electric field. The analysis is based on an experimentally validated nonlinear model of mass transport via island edge atomic diffusion, which also accounts for edge diffusional anisotropy. We analyze the morphological stability and simulate the field-driven evolution of rounded islands for an electric field oriented along the fast diffusion direction. For larger than critical island sizes on {110} and {100} FCC substrates, we show that multiple necking instabilities generate complex island patterns, including void-containing islands, mediated by sequences of breakup and coalescence events and distributed symmetrically with respect to the electric field direction. We analyze the dependence of the formed patterns on the original island size and on the duration of application of the external field. Starting from a single large rounded island, we characterize the evolution of the number of daughter islands and their average size and uniformity. The analysis reveals that the pattern formation kinetics follows a universal scaling relation. Division of Materials Sciences & Engineering, Office of Basic Energy Sciences, U.S. Department of Energy (Award No.: DE-FG02-07ER46407).

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

PubMed

Krystek, S; Stouch, T; Novotny, J

1993-12-05

An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.

PubMed

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Polysaccharide chemistry regulates kinetics of calcite nucleation through competition of interfacial energies.

PubMed

Giuffre, Anthony J; Hamm, Laura M; Han, Nizhou; De Yoreo, James J; Dove, Patricia M

2013-06-04

Calcified skeletons are produced within complex assemblages of proteins and polysaccharides whose roles in mineralization are not well understood. Here we quantify the kinetics of calcite nucleation onto a suite of high-purity polysaccharide (PS) substrates under controlled conditions. The energy barriers to nucleation are PS-specific by a systematic relationship to PS charge density and substrate structure that is rooted in minimization of the competing substrate-crystal and substrate-liquid interfacial energies. Chitosan presents a low-energy barrier to nucleation because its near-neutral charge favors formation of a substrate-crystal interface, thus reducing substrate interactions with water. Progressively higher barriers are measured for negatively charged alginates and heparin that favor contact with the solution over the formation of new substrate-crystal interfaces. The findings support a directing role for PS in biomineral formation and demonstrate that substrate-crystal interactions are one end-member in a larger continuum of competing forces that regulate heterogeneous crystal nucleation.

Polysaccharide chemistry regulates kinetics of calcite nucleation through competition of interfacial energies

PubMed Central

Hamm, Laura M.; Han, Nizhou; De Yoreo, James J.; Dove, Patricia M.

2013-01-01

Calcified skeletons are produced within complex assemblages of proteins and polysaccharides whose roles in mineralization are not well understood. Here we quantify the kinetics of calcite nucleation onto a suite of high-purity polysaccharide (PS) substrates under controlled conditions. The energy barriers to nucleation are PS-specific by a systematic relationship to PS charge density and substrate structure that is rooted in minimization of the competing substrate–crystal and substrate–liquid interfacial energies. Chitosan presents a low-energy barrier to nucleation because its near-neutral charge favors formation of a substrate–crystal interface, thus reducing substrate interactions with water. Progressively higher barriers are measured for negatively charged alginates and heparin that favor contact with the solution over the formation of new substrate–crystal interfaces. The findings support a directing role for PS in biomineral formation and demonstrate that substrate–crystal interactions are one end-member in a larger continuum of competing forces that regulate heterogeneous crystal nucleation. PMID:23690577

Thermodynamics and Kinetics of Na+/K+-Formate Ion Pairs Association in Polarizable Water: A Molecular Dynamics Study

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

Nguyen, Phuong T.; Nguyen, Van T.; Annapureddy, Harsha V.

2012-12-03

To elevate our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on interactions between two alkali cations (Na+ and K+) with a formate anion in water. A very complex free energy landscape was observed, much more so than alkali-halide ion pairs. Furthermore, stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, a finding that agrees with experimental and theoretical studies of these systems. The kinetics of ion-pair interconversions were studied using transition rate theory, along with a variety of theoretical approachesmore » such as the Kramers and Grote Hynes theories. These rate results were used to predict solvent effects on dynamical features of contact ion-pair association, in which faster dynamics were found for K+-formate pairs than for Na+-formate pairs. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.« less

Abiogenic synthesis of nucleotides on the surface of small space bodies with high energy particles

NASA Astrophysics Data System (ADS)

Simakov, M. B.; Kuzicheva, E. A.; Antropov, A. E.; Dodonova, N. Ya

Abiotic formation of such complex biochemical compounds as nucleotides and oligopeptides on the surface of interstellar and interplanetary dust particles (IDP) by cosmic radiation was examined. In order to study the formation of organic compounds on IDPs, solid films prepared from nucleososide and inorganic phosphate were irradiated with high energy protons. Irradiated products were analyzed with HPLC. The natural nucleotides were detected. The main products were 5' AMP (3.2%) and 2'3' cAMP (2.7%). The results were compared with others experiments on the action of ultraviolet radiation with different wavelengths, γ-radiation and heat on solid mixtures of biologically significant compounds. The experiment on abiogenic synthesis of nucleotides on board of space satellite "BION-11" was compared also. The present results suggest that a considerable amount of complex biochemical compounds formed in extraterrestrial environments could have been supplied to the primitive earth before the origin of life.

Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei.

PubMed

Worm, Petra; Stams, Alfons J M; Cheng, Xu; Plugge, Caroline M

2011-01-01

Transcription of genes coding for formate dehydrogenases (fdh genes) and hydrogenases (hyd genes) in Syntrophobacter fumaroxidans and Methanospirillum hungatei was studied following growth under different conditions. Under all conditions tested, all fdh and hyd genes were transcribed. However, transcription levels of the individual genes varied depending on the substrate and growth conditions. Our results strongly suggest that in syntrophically grown S. fumaroxidans cells, the [FeFe]-hydrogenase (encoded by Sfum_844-46), FDH1 (Sfum_2703-06) and Hox (Sfum_2713-16) may confurcate electrons from NADH and ferredoxin to protons and carbon dioxide to produce hydrogen and formate, respectively. Based on bioinformatic analysis, a membrane-integrated energy-converting [NiFe]-hydrogenase (Mhun_1741-46) of M. hungatei might be involved in the energy-dependent reduction of CO(2) to formylmethanofuran. The best candidates for F(420)-dependent N(5),N(10)-methyl-H(4) MPT and N(5),N(10),-methylene-H(4)MPT reduction are the cytoplasmic [NiFe]-hydrogenase and FDH1. 16S rRNA ratios indicate that in one of the triplicate co-cultures of S. fumaroxidans and M. hungatei, less energy was available for S. fumaroxidans. This led to enhanced transcription of genes coding for the Rnf-complex (Sfum_2694-99) and of several fdh and hyd genes. The Rnf-complex probably reoxidized NADH with ferredoxin reduction, followed by ferredoxin oxidation by the induced formate dehydrogenases and hydrogenases.

Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.

PubMed

Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R

2016-04-07

We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O.

Trapping in water - an important prerequisite for complex reactivity in astrophysical ices: the case of acetone (CH3)2C = O and ammonia NH3

NASA Astrophysics Data System (ADS)

Fresneau, Aurélien; Danger, Grégoire; Rimola, Albert; Theule, Patrice; Duvernay, Fabrice; Chiavassa, Thierry

2014-10-01

Water is the most abundant compound in interstellar and cometary ices. Laboratory experiments on ice analogues have shown that water has a great influence on the chemical activity of these ices. In this study, we investigated the reactivity of acetone-ammonia ices, showing that water is an essential component in chemical reactions with high activation energies. In a water-free binary ice, acetone and ammonia do not react due to high activation energy, as the reactants desorb before reacting (at 120 and 140 K, respectively). By contrast, our study shows that under experimental conditions of ˜150 K, this reaction does occur in the presence of water. Here, water traps reactants in the solid phase above their desorption temperatures, allowing them to gather thermal energy as the reaction proceeds. Using infrared spectroscopy and mass spectrometry associated with isotopic labelling, as well as quantum chemical calculations, 2-aminopropan-2-ol (2HN-C(CH3)2-OH) was identified as the acetone-ammonia reaction product. The formation of this product may represent the first step towards formation of 2-aminoisobutyric acid (AIB) in the Strecker synthesis. The activation energy for the formation of 2-aminopropan-2-ol was measured to be 42 ± 3 kJ mol-1, while its desorption energy equalled 61.3 ± 0.1 kJ mol-1. Our work demonstrates that astrophysical water, rather than being a non-thermally reactive species, is crucial for the evolution of complex chemistry occurring in the Universe.

A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

NASA Astrophysics Data System (ADS)

Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

2009-04-01

MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

Coarse-grained simulations of protein-protein association: an energy landscape perspective.

PubMed

Ravikumar, Krishnakumar M; Huang, Wei; Yang, Sichun

2012-08-22

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

PubMed Central

Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun

2012-01-01

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. PMID:22947945

Molecular cell biology and physiology of solute transport

PubMed Central

Caplan, Michael J.; Seo-Mayer, Patricia; Zhang, Li

2010-01-01

Purpose of review An enormous body of research has been focused on exploring the mechanisms through which epithelial cells establish their characteristic polarity. It is clear that under normal circumstances cell–cell contacts mediated by the calcium-dependent adhesion proteins of the intercellular adhesion junctions are required to initiate complete polarization. Furthermore, formation of the tight, or occluding, junctions that limit paracellular permeability has long been thought to help to establish polarity by preventing the diffusion of membrane proteins between the two plasmalemmal domains. This review will discuss several selected kinases and protein complexes and highlight their relevance to transporting epithelial cell polarization. Recent findings Recent work has shed new light on the roles of junctional complexes in establishing and maintaining epithelial cell polarity. In addition, work from several laboratories, suggests that the formation of these junctions is tied to processes that regulate cellular energy metabolism. Summary Junctional complexes and energy sensing kinases constitute a novel class of machinery whose capacity to generate and modulate epithelial cell polarity is likely to have wide ranging and important physiological ramifications. PMID:18695392

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermodynamics of the complex formation of copper(II) with L-phenylalanine in aqueous ethanol solutions

NASA Astrophysics Data System (ADS)

Burov, D. M.; Ledenkov, S. F.; Vandyshev, V. N.

2013-05-01

Constants of the acid dissociation and complexation of L-phenylalanine (HPhe) with copper(II) ions are determined by potentiometry in aqueous ethanol solutions containing 0 to 0.7 molar fraction of alcohol. Changes in the Gibbs energy for the transfer from water to a binary solvent of L-phenylalanine, Phe- anion, and [CuPhe]+ complex are calculated. It is found that the weakening of solvation of the ligand donor groups in solvents with high ethanol contents is accompanied by an increase in the stability of [CuPhe]+ complex.

Pnicogen bonds between X═PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases.

PubMed

Alkorta, Ibon; Sánchez-Sanz, Goar; Elguero, José; Del Bene, Janet E

2014-02-27

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the pnicogen bonded complexes formed between the acids O═PH3, S═PH3, HN═PH3, and H2C═PH3 and the bases NH3, NCH, N2, PH3, and PCH. All nitrogen and phosphorus bases form complexes in which the bases are lone pair electron donors. The binding energies of complexes involving the stronger bases NH3, NCH, and PH3 differentiate among the acids, but the binding energies of complexes with the weaker bases do not. These complexes are stabilized by charge transfer from the lone pair orbital of N or P to the σ*P═A orbital of X═PH3, where A is the atom of X directly bonded to P. PCH also forms complexes with the X═PH3 acids as a π electron donor to the σ*P═A orbital. The binding energies and the charge-transfer energies of the π complexes are greater than those of the complexes in which PCH is a lone pair donor. Whether the positive charge on P increases, decreases, or remains the same upon complex formation, the chemical shieldings of (31)P decrease in the complexes relative to the corresponding monomers. (1p)J(P-N) and (1p)J(P-P) values correlate best with the corresponding P-N and P-P distances as a function of the nature of the base. (1)J(P-A) values do not correlate with P-A distances. Rather, the absolute values of (1)J(P-O), (1)J(P-S), and (1)J(P-N) decrease upon complexation. Decreasing (1)J(P-A) values correlate linearly with increasing complex binding energies. In contrast, (1)J(P-C) values increase upon complexation and correlate linearly with increasing binding energies.

Influence of structural features of carrageenan on the formation of polyelectrolyte complexes with chitosan.

PubMed

Volod'ko, A V; Davydova, V N; Glazunov, V P; Likhatskaya, G N; Yermak, I M

2016-03-01

The polyelectrolyte complexes (PEC) of carrageenans (CG)-κ-, κ/β-, λ-and x-CG with chitosan were obtained. The formation of PEC was detected by Fourier-transform infrared (FTIR) spectroscopy and by centrifugation in a Percoll gradient. The influence of the structural peculiarities of CG on its interaction with chitosan was studied. The results of centrifugation showed that x-CG with a high degree of sulphation (SD) was completely bound to chitosan, unlike low SD κ-CG and κ/β-CG. Binding constant values showed there was a high affinity of CG for chitosan. CG with flexible macromolecule conformation and high SD exhibited the greatest binding affinity for chitosan. The full-atomic 3D-structures of the PEC κ-CG: chitosan in solution have been obtained by the experiments in silico for the first time. The amino groups of chitosan make the largest contribution to the energy of the complex formation by means of hydrogen and ionic bonds. The most probable complexes have stoichiometries of 1:1 and 1:1.5. Copyright © 2015 Elsevier B.V. All rights reserved.

Unusual Complex Formation and Chemical Reaction of Haloacetate Anion on the Exterior Surface of Cucurbit[6]uril in the Gas Phase

NASA Astrophysics Data System (ADS)

Choi, Tae Su; Ko, Jae Yoon; Heo, Sung Woo; Ko, Young Ho; Kim, Kimoon; Kim, Hugh I.

2012-10-01

Noncovalent interactions of cucurbit[6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB[6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular SN2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular SN2 reaction of haloacetate, which correlate well with the experimental observation.

Molecular modeling studies of HIV-1 reverse transcriptase nonnucleoside inhibitors: total energy of complexation as a predictor of drug placement and activity.

PubMed Central

Kroeger Smith, M. B.; Rouzer, C. A.; Taneyhill, L. A.; Smith, N. A.; Hughes, S. H.; Boyer, P. L.; Janssen, P. A.; Moereels, H.; Koymans, L.; Arnold, E.

1995-01-01

Computer modeling studies have been carried out on three nonnucleoside inhibitors complexed with human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), using crystal coordinate data from a subset of the protein surrounding the binding pocket region. Results from the minimizations of solvated complexes of 2-cyclopropyl-4-methyl-5,11-dihydro-5H-dipyrido[3,2-b :2',3'-e][1,4] diazepin-6-one (nevirapine), alpha-anilino-2, 6-dibromophenylacetamide (alpha-APA), and 8-chloro-tetrahydro-imidazo(4,5,1-jk)(1,4)-benzodiazepin-2(1H)-thi one (TIBO) show that all three inhibitors maintain a very similar conformational shape, roughly overlay each other in the binding pocket, and appear to function as pi-electron donors to aromatic side-chain residues surrounding the pocket. However, side-chain residues adapt to each bound inhibitor in a highly specific manner, closing down around the surface of the drug to make tight van der Waals contacts. Consequently, the results from the calculated minimizations reveal that only when the inhibitors are modeled in a site constructed from coordinate data obtained from their particular RT complex can the calculated binding energies be relied upon to predict the correct orientation of the drug in the pocket. In the correct site, these binding energies correlate with EC50 values determined for all three inhibitors in our laboratory. Analysis of the components of the binding energy reveals that, for all three inhibitors, solvation of the drug is endothermic, but solvation of the protein is exothermic, and the sum favors complex formation. In general, the protein is energetically more stable and the drug less stable in their complexes as compared to the reactant conformations. For all three inhibitors, interaction with the protein in the complex is highly favorable. Interactions of the inhibitors with individual residues correlate with crystallographic and site-specific mutational data. pi-Stacking interactions are important in binding and correlate with drug HOMO RHF/6-31G* energies. Modeling results are discussed with respect to the mechanism of complex formation and the design of nonnucleoside inhibitors that will be more effective against mutants of HIV-1 RT that are resistant to the currently available drugs. PMID:8535257

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

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

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

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

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic–inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm –1 for Pb(II) and ca. 1580 cm –1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. These complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

DOE PAGES

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.; ...

2016-09-07

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Electrically active induced energy levels and metastability of B and N vacancy-complexes in 4H–SiC

NASA Astrophysics Data System (ADS)

Igumbor, E.; Olaniyan, O.; Mapasha, R. E.; Danga, H. T.; Omotoso, E.; Meyer, W. E.

2018-05-01

Electrically active induced energy levels in semiconductor devices could be beneficial to the discovery of an enhanced p or n-type semiconductor. Nitrogen (N) implanted into 4H–SiC is a high energy process that produced high defect concentrations which could be removed during dopant activation annealing. On the other hand, boron (B) substituted for silicon in SiC causes a reduction in the number of defects. This scenario leads to a decrease in the dielectric properties and induced deep donor and shallow acceptor levels. Complexes formed by the N, such as the nitrogen-vacancy centre, have been reported to play a significant role in the application of quantum bits. In this paper, results of charge states thermodynamic transition level of the N and B vacancy-complexes in 4H–SiC are presented. We explore complexes where substitutional N/N or B/B sits near a Si (V) or C (V) vacancy to form vacancy-complexes (NV, NV, NV, NV, BV, BV, BV and BV). The energies of formation of the N related vacancy-complexes showed the NV to be energetically stable close to the valence band maximum in its double positive charge state. The NV is more energetically stable in the double negative charge state close to the conduction band minimum. The NV on the other hand, induced double donor level and the NV induced a double acceptor level. For B related complexes, the BV and BV were energetically stable in their single positive charge state close to the valence band maximum. As the Fermi energy is varied across the band gap, the neutral and single negative charge states of the BV become more stable at different energy levels. B and N related complexes exhibited charge state controlled metastability behaviour.

Study on reaction mechanism by analysis of kinetic energy spectra of light particles and formation of final products

NASA Astrophysics Data System (ADS)

Giardina, G.; Mandaglio, G.; Nasirov, A. K.; Anastasi, A.; Curciarello, F.; Fazio, G.

2018-05-01

The sensitivity of reaction mechanism in the formation of compound nucleus (CN) by the analysis of kinetic energy spectra of light particles and of reaction products are shown. The dependence of the P CN fusion probability of reactants and W sur survival probability of CN against fission at its deexcitation on the mass and charge symmetries in the entrance channel of heavy-ion collisions, as well as on the neutron numbers is discussed. The possibility of conducting a complex program of investigations of the complete fusion by reliable ways depends on the detailed and refined methods of experimental and theoretical analyses.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Interaction of metal ions and amino acids - Possible mechanisms for the adsorption of amino acids on homoionic smectite clays

NASA Technical Reports Server (NTRS)

Gupta, A.; Loew, G. H.; Lawless, J.

1983-01-01

A semiempirical molecular orbital method is used to characterize the binding of amino acids to hexahydrated Cu(2+) and Ni(2+), a process presumed to occur when they are adsorbed in the interlamellar space of homoionic smectite clays. Five alpha-amino acids, beta-alanine, and gamma-aminobutyric acid were used to investigate the metal ion and amino acid specificity in binding. It was assumed that the alpha, beta, and gamma-amino acids would bind as bidentate anionic ligands, forming either 1:1 or 1:2 six-coordinated five, six, and seven-membered-ring chelate complexes, respectively. Energies of complex formation, optimized geometries, and electron and spin distribution were determined; and steric constraints of binding of the amino acids to the ion-exchanged cations in the interlamellar spacing of a clay were examined. Results indicate that hexahydrated Cu(2+) forms more stable complexes than hexahydrated Ni(2+) with all the amino acids studied. However, among these amino acids, complex formation does not favor the adsorption of the biological subset. Calculated energetics of complex formation and steric constraints are shown to predict that 1:1 rather than 1:2 metal-amino acid complexes are generally favored in the clay.

Hydrogen incorporation into BN fullerene-like nanostructures: A first-principles study

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Abbaszadeh, B.; Ahaz, B.

2011-10-01

We performed density functional theory calculations to investigate the possibility of formation of endohedrally H@(BN) n-fullerene ( n: 24, 36, 60) and H@C 60 complexes for potential applications in solid-state quantum-computers. Spin-polarized approach within the generalized gradient approximation with the Perdew-Burke-Ernzerhof functional was used for the total energies and structural relaxation calculations. The calculated binding energies show that H atom being incorporated into B 60N 60 nanocage can form most stable complexes while the B 24N 24 and C 60 nanocages might form unstable complex with positive binding energy. We have also examined the penetration of an H atom into the respective nanocages and the calculated barrier energies indicate that the H atom prefers to penetrate into the B 24N 24 and B 60N 60 nanocages with barrier energy of about 0.47 eV (10.84 kcal/mol). Furthermore the binding characteristic is rationalized by analyzing the electronic structures. Our findings reveal that the B 60N 60 nanocage has fascinating potential application in future solid-state quantum-computers.

Defect studies in copper-based p-type transparent conducting oxides

NASA Astrophysics Data System (ADS)

Ameena, Fnu

Among other intrinsic open-volume defects, copper vacancy (VCu) has been theoretically identified as the major acceptor in p-type Cu-based semiconducting transparent oxides, which has potential as low-cost photovoltaic absorbers in semi-transparent solar cells. A series of positron annihilation experiments with pure Cu, Cu2O, and CuO presented strong presence of VCu and its complexes in the copper oxides. The lifetime data also showed that the density of VCu was becoming higher as the oxidation state of Cu increased which was consistent with the decrease in the formation energy of VCu. Doppler broadening measurements further indicated that electrons with low momentum made more contribution to the contributed as pure Cu oxidizes to copper oxides. The metastable defects are known to be generated in Cu2O upon illumination and it has been known to affect the performance of Cu2O-based hetero-junctions used in solar cells. The metastable effect was studied using positron annihilation lifetime spectroscopy and its data showed the change in the defect population upon light exposure and the minimal effect of light-induced electron density increase in the bulk of materials to the average lifetime of the positrons. The change in the defect population is concluded to be related to the dissociation and association of VCu -- V Cu complexes. For example, the shorter lifetime under light was ascribed to the annihilation with smaller size vacancies, which explains the dissociation of the complexes with light illumination. Doppler broadening of the annihilation was independent of light illumination, which suggested that the chemical nature of the defects remained without change upon their dissociation and association -- only the size distribution of copper vacancies varied. The delafossite metal oxides, CuMIIIO2 are emerging wide-bandgap p-type semiconductors. In this research, the formation energies of structural vacancies are calculated using Van Vechten cavity model as an attempt to study the effect of the size of the MIII cation in the delafossites starting from Cu2O. Comparison of the formation energies between Cu2O and delafossite oxides clearly showed that the equilibrium concentration of the vacancies depended strongly on the structural parameters varied by the presence of different MIII cations. In particular, the size of the MIII cation greatly influenced the defect formation energies of VCu. It was observed from our calculations, as the size increases the formation energy decreases.

Hydrogen Financial Analysis Scenario Tool (H2FAST). Web Tool User's Manual

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

Bush, B.; Penev, M.; Melaina, M.

The Hydrogen Financial Analysis Scenario Tool (H2FAST) provides a quick and convenient indepth financial analysis for hydrogen fueling stations. This manual describes how to use the H2FAST web tool, which is one of three H2FAST formats developed by the National Renewable Energy Laboratory (NREL). Although all of the formats are based on the same financial computations and conform to generally accepted accounting principles (FASAB 2014, Investopedia 2014), each format provides a different level of complexity and user interactivity.

The effect of zero-point energy differences on the isotope dependence of the formation of ozone: a classical trajectory study.

PubMed

Schinke, Reinhard; Fleurat-Lessard, Paul

2005-03-01

The effect of zero-point energy differences (DeltaZPE) between the possible fragmentation channels of highly excited O(3) complexes on the isotope dependence of the formation of ozone is investigated by means of classical trajectory calculations and a strong-collision model. DeltaZPE is incorporated in the calculations in a phenomenological way by adjusting the potential energy surface in the product channels so that the correct exothermicities and endothermicities are matched. The model contains two parameters, the frequency of stabilizing collisions omega and an energy dependent parameter Delta(damp), which favors the lower energies in the Maxwell-Boltzmann distribution. The stabilization frequency is used to adjust the pressure dependence of the absolute formation rate while Delta(damp) is utilized to control its isotope dependence. The calculations for several isotope combinations of oxygen atoms show a clear dependence of relative formation rates on DeltaZPE. The results are similar to those of Gao and Marcus [J. Chem. Phys. 116, 137 (2002)] obtained within a statistical model. In particular, like in the statistical approach an ad hoc parameter eta approximately 1.14, which effectively reduces the formation rates of the symmetric ABA ozone molecules, has to be introduced in order to obtain good agreement with the measured relative rates of Janssen et al. [Phys. Chem. Chem. Phys. 3, 4718 (2001)]. The temperature dependence of the recombination rate is also addressed.

MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes.

PubMed

Bastiani, Michele; Liu, Libin; Hill, Michelle M; Jedrychowski, Mark P; Nixon, Susan J; Lo, Harriet P; Abankwa, Daniel; Luetterforst, Robert; Fernandez-Rojo, Manuel; Breen, Michael R; Gygi, Steven P; Vinten, Jorgen; Walser, Piers J; North, Kathryn N; Hancock, John F; Pilch, Paul F; Parton, Robert G

2009-06-29

Polymerase I and transcript release factor (PTRF)/Cavin is a cytoplasmic protein whose expression is obligatory for caveola formation. Using biochemistry and fluorescence resonance energy transfer-based approaches, we now show that a family of related proteins, PTRF/Cavin-1, serum deprivation response (SDR)/Cavin-2, SDR-related gene product that binds to C kinase (SRBC)/Cavin-3, and muscle-restricted coiled-coil protein (MURC)/Cavin-4, forms a multiprotein complex that associates with caveolae. This complex can constitutively assemble in the cytosol and associate with caveolin at plasma membrane caveolae. Cavin-1, but not other cavins, can induce caveola formation in a heterologous system and is required for the recruitment of the cavin complex to caveolae. The tissue-restricted expression of cavins suggests that caveolae may perform tissue-specific functions regulated by the composition of the cavin complex. Cavin-4 is expressed predominantly in muscle, and its distribution is perturbed in human muscle disease associated with Caveolin-3 dysfunction, identifying Cavin-4 as a novel muscle disease candidate caveolar protein.

Mobile multiwave lidar

NASA Astrophysics Data System (ADS)

Gritsuta, A. N.; Klimkin, A. V.; Kokhanenko, G. P.; Kuryak, A. N.; Osipov, K. Y.; Ponomarev, Yu. N.; Simonova, G. V.

2018-04-01

The task that faced the authors was construction of a mobile lidar complex for detection and investigation of aerosol-gas formations in the atmosphere. The complex must be constructed of commercial industrially produced components as much as possible. Many of engineering solutions had been previously worked out by the authors when the first lidar of such type was developed. The complex is designed for study of capabilities of lidar sensing for remote investigation of aerosol-gas formations by their fluorescence and Raman scattering spectra, as well as topographyc objects by fluorescence spectra of their surfaces. The complex has been tested in 2016, and may be applied for atmospheric sensing, for detection of potentially hazardous and dangerous admixtures above the cities, industrial and agricultural emissions, including emissions after disclosures of agricultural animal burial sites. The complex is mounted on a motor vehicle chassis and is energy-independent, and that allow using it for remote sensing of different objects in different natural conditions. Probing distance: 30 000 meters in elastic scattering channel and 5 000 meters in fluorescence channel.

Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

NASA Astrophysics Data System (ADS)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

Electrical and thermal modeling of a large-format lithium titanate oxide battery system.

DOT National Transportation Integrated Search

2015-04-01

The future of mass transportation is clearly moving towards the increased efficiency of hybrid and electric vehicles. Electrical : energy storage is a key component in most of these advanced vehicles, with the system complexity and vehicle cost shift...

Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments.

PubMed

Binzel, Daniel W; Khisamutdinov, Emil F; Guo, Peixuan

2014-04-15

The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles but has been limited by particle instability. It has been shown that the three-way junction of bacteriophage phi29 motor pRNA has unusual stability and can self-assemble from three fragments with high efficiency. It is generally believed that RNA and DNA folding is energy landscape-dependent, and the folding of RNA is driven by enthalpy. Here we examine the thermodynamic characteristics of the 3WJ components as 2'-fluoro RNA, DNA, and RNA. It was seen that the three fragments existed either in 3WJ complex or as monomers, with the intermediate of dimers almost undetectable. It seems that the three fragments can lead to the formation of the 3WJ complex efficiently within a rapid time. A low dissociation constant (apparent KD) of 11.4 nM was determined for RNA, inclusion of 2'-F pyrimidines strengthened the KD to 4.5 nM, and substitution of DNA weakened it to 47.7 nM. The ΔG°37, were -36, -28, and -15 kcal/mol for 3WJ2'-F, 3WJRNA, and 3WJDNA, respectively. It is found that the formation of the three-component complex was governed by entropy, instead of enthalpy, as usually found in RNA complexes. Here entropy-driven is referring to a dominating entropic contribution to the increased stability of the 3WJ(2'-F and 3WJ(RNA) compared to the 3WJ(DNA,) instead of referring to the absolute role or total energy governing 3WJ folding. [corrected].

Structural, luminescence, thermodynamic and theoretical studies on mononuclear complexes of Eu(III) with pyridine monocarboxylate-N-oxides in aqueous solution

NASA Astrophysics Data System (ADS)

Dumpala, Rama Mohana Rao; Rawat, Neetika; Boda, Anil; Ali, Sk. Musharaf; Tomar, B. S.

2018-02-01

The mononuclear complexes formed by Eu(III) with three isomeric pyridine monocarboxylate-N-oxides namely picolinic acid-N-oxide (PANO), nicotinic acid-N-oxide (NANO) and isonicotinic acid-N-oxide (IANO) in aqueous solutions were studied by potentiometry, luminescence spectroscopy and isothermal titration calorimetry (ITC) to determine the speciation, coordination, luminescence properties and thermodynamic parameters of the complexes formed during the course of the reaction. More stable six membered chelate complexes with stoichiometry (MLi, i = 1-4) are formed by Eu(III) with PANO while non chelating ML and ML2 complexes are formed by NANO and IANO. The stability of Eu(III) complexes follow the order PANO > IANO > NANO. The ITC studies inferred an endothermic and innersphere complex formation of Eu(III)-PANO and Eu(III)-IANO whereas an exothermic and outer-sphere complex formation for Eu(III)-NANO. The luminescence life time data further supported the ITC results. Density functional theoretical calculations were carried out to optimize geometries of the complexes and to estimate the energies, structural parameters (bond distances, bond angles) and charges on individual atoms of the same. Theoretical approximations are found to be in good agreement with the experimental observations.

Interaction of UV laser pulses with reactive dusty plasmas

NASA Astrophysics Data System (ADS)

van de Wetering, Ferdi; Beckers, Job; Nijdam, Sander; Oosterbeek, Wouter; Kovacevic, Eva; Berndt, Johannes

2016-09-01

This contribution deals with the effects of UV photons on the synthesis and transport of nanoparticles in reactive complex plasmas (capacitively coupled RF discharge). First measurements showed that the irradiation of a reactive acetylene-argon plasma with high-energy, ns UV laser pulses (355 nm, 75 mJ pulse energy, repetition frequency 10Hz) can have a large effect on the global discharge characteristics. One particular example concerns the formation of a dust void in the center of the discharge. At sufficiently high pulse energies, this formation of a dust free region - which occurs without laser irradiation-is totally suppressed. Moreover the experiments indicate that the laser pulses influence the early stages of the particle formation. Although the interaction between the laser and the plasma is not yet fully understood, it is remarkable that these localized nanosecond laser pulses can influence the plasma on a global scale. Besides new insights into fundamental problems, this phenomenon opens also new possibilities for the controlled manipulation of particle growth and particle transport in reactive plasmas.

The Permian Whitehill Formation (Karoo Basin, South Africa): deciphering the complexity and potential of an unconventional gas resource

NASA Astrophysics Data System (ADS)

Götz, Annette E.

2014-05-01

A key energy policy objective of the South African government is to diversify its energy mix from coal which constitutes 85% of the current mix. Gas will play a key role in the future South African economy with demand coming from electricity generation and gas-to-liquids projects. A study on world shale reserves conducted by the Energy Information Agency (EIA) in 2011 concluded that there could be as much as 485 Tcf recoverable reserves of shale gas in the South African Karoo Basin. However, the true extent and commercial viability is still unknown, due to the lack of exploration drilling and modern 3D seismic. The present study compiles existing data from literature review and new data from outcrop analogue studies on the Permian Whitehill Formation, the main target formation for future shale gas production, including thickness, depth, maturity, TOC, lithologies, sedimentary and organic facies, and dolerite occurrence to provide a first reference dataset for further investigations and resource estimates.

Electrochemiluminescence detection of TNT by resonance energy transfer through the formation of a TNT-amine complex.

PubMed

Qi, Wenjing; Xu, Min; Pang, Lei; Liu, Zhongyuan; Zhang, Wei; Majeed, Saadat; Xu, Guobao

2014-04-14

2,4,6-Trinitrotoluene (TNT) is a widely used nitroaromatic explosive with significant detrimental effects on the environment and human health. Its detection is of great importance. In this study, both electrochemiluminescence (ECL)-based detection of TNT through the formation of a TNT-amine complex and the detection of TNT through electrochemiluminescence resonance energy transfer (ECRET) are developed for the first time. 3-Aminopropyltriethoxysilane (APTES)-modified [Ru(phen)3](2+) (phen=1,10-phenanthroline)-doped silica nanoparticles (RuSiNPs) with uniform sizes of (73±3) nm were synthesized. TNT can interact with APTES-modified RuSiNPs through charge transfer from electron-rich amines in the RuSiNPs to the electron-deficient aromatic ring of TNT to form a red TNT-amine complex. The absorption spectrum of this complex overlaps with the ECL spectrum of the APTES-modified RuSiNPs/triethylamine system. As a result, ECL signals of the APTES-modified RuSiNPs/triethylamine system are turned off in the presence of TNT owing to resonance energy transfer from electrochemically excited RuSiNPs to the TNT-amine complex. This ECRET method has been successfully applied for the sensitive determination of TNT with a linear range from 1×10(-9) to 1×10(-6) M with a fast response time within 1 min. The limit of detection is 0.3 nM. The method exhibits good selectivity towards 2,4-dinitrotoluene, p-nitrotoluene, nitrobenzene, phenol, p-quinone, 8-hydroxyquinoline, p-phenylenediamine, K3[Fe(CN)6], Fe(3+), NO3(-), NO2(-), Cr(3+), Fe(2+), Pb(2+), SO3(2-), formaldehyde, oxalate, proline, and glycine. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The reactions of SO3 with HO2 radical and H2O...HO2 radical complex. Theoretical study on the atmospheric formation of HSO5 and H2SO4.

PubMed

Gonzalez, Javier; Torrent-Sucarrat, Miquel; Anglada, Josep M

2010-03-07

The influence of a single water molecule on the gas-phase reactivity of the HO(2) radical has been investigated by studying the reactions of SO(3) with the HO(2) radical and with the H(2)O...HO(2) radical complex. The naked reaction leads to the formation of the HSO(5) radical, with a computed binding energy of 13.81 kcal mol(-1). The reaction with the H(2)O...HO(2) radical complex can give two different products, namely (a) HSO(5) + H(2)O, which has a binding energy that is computed to be 4.76 kcal mol(-1) more stable than the SO(3) + H(2)O...HO(2) reactants (Delta(E + ZPE) at 0K) and an estimated branching ratio of about 34% at 298K and (b) sulfuric acid and the hydroperoxyl radical, which is computed to be 10.51 kcal mol(-1) below the energy of the reactants (Delta(E + ZPE) at 0K), with an estimated branching ratio of about 66% at 298K. The fact that one of the products is H(2)SO(4) may have relevance in the chemistry of the atmosphere. Interestingly, the water molecule acts as a catalyst, [as it occurs in (a)] or as a reactant [as it occurs in (b)]. For a sake of completeness we have also calculated the anharmonic vibrational frequencies for HO(2), HSO(5), the HSO(5)...H(2)O hydrogen bonded complex, H(2)SO(4), and two H(2)SO(4)...H(2)O complexes, in order to help with the possible experimental identification of some of these species.

A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.

Substitutional and interstitial oxygen in wurtzite GaN

NASA Astrophysics Data System (ADS)

Wright, A. F.

2005-11-01

Density-functional theory was used to compute energy-minimum configurations and formation energies of substitutional and interstitial oxygen (O) in wurtzite GaN. The results indicate that O substituted at a N site (ON) acts as a single donor with the ionized state (ON+1) being the most stable O state in p-type GaN. In n-type GaN, interstitial O (OI) is predicted to be a double acceptor and O substituted at a Ga site (OGa) is predicted to be a triple acceptor. The formation energies of these two species are comparable to that of ON in n-type GaN and, as such, they should form and compensate the ON donors. The extent of compensation was estimated for both Ga-rich and N-rich conditions with a total O concentration of 1017cm-3. Ga-rich conditions yielded negligible compensation and an ON concentration in excess of 9.9×1016cm-3. N-rich conditions yielded a 25% lower ON concentration, due to the increased stability of OI and OGa relative to ON, and moderate compensation. These findings are consistent with experimental results indicating that O acts as a donor in GaN(O). Complexes of ON with the Mg acceptor and OI with the Si donor were examined. Binding energies for charge-conserving reactions were ⩾0.5eV, indicating that these complexes can exist in equilibrium at room temperature. Complexes of ON with the Ga vacancy in n-type GaN were also examined and their binding energies were 1.2 and 1.4eV, indicating that appreciable concentrations can exist in equilibrium even at elevated temperatures.

Energy for the interface system of (Nb, Mo)C/γ-Fe

NASA Astrophysics Data System (ADS)

Zhou, Yanyuan; Wang, Zhenqiang; Zhao, Jiaying; Leng, Zhe; Niu, Zhongyi; Guo, Chunhuan; Zhang, Zhengyan; Yang, Zhigang; Yao, Chunfa; Jiang, Fengchun

2017-08-01

The interfacial energies of MC/γ-Fe and formation energies of MC carbides have been investigated using first-principles calculations based on density functional theory (DFT). Results show that the replacement of Nb by Mo in the NbC lattice is unfavorable with respect to the formation energy. However, it reduces the lattice parameter of MC and decreases the σ_{{chemical}} (interfacial chemical energy) of MC/γ-Fe, thus favoring the formation of complex (Nb, Mo)C carbide. The substitution of Nb by Mo at the interface of MC/γ-Fe system promotes the hybridizations of Mo-1NNFe and C-1NNFe (or 2NNFe) (the first or second nearest neighboring Fe atoms), which leads to a decrease in σ_{{chemical}}. The influence of bond energy is estimated using the discrete lattice plane/nearest neighbor broken bond (DLP/NNBB) model. It is found that the reduced σ_{{chemical}} is attributed to the much smaller value of e_{{{{Fe-C}}}} - e_{{{{Mo-C}}}} (the difference between Fe-C and Mo-C interactions) compared to e_{{{{Fe-C}}}} - e_{{{{Nb-C}}}} (the difference between Fe-C and Nb-C interactions). The results obtained from the analysis of the precipitates in Nb- and Nb-Mo-bearing steels are in a good agreement with the calculations.

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

NASA Astrophysics Data System (ADS)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.; Moon, Y.; Rai, K. B.; Woo, S. H.; Ahn, J. R.

2016-08-01

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalated at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.

Low-energy electron-induced chemistry of condensed methanol: implications for the interstellar synthesis of prebiotic molecules.

PubMed

Boamah, Mavis D; Sullivan, Kristal K; Shulenberger, Katie E; Soe, ChanMyae M; Jacob, Lisa M; Yhee, Farrah C; Atkinson, Karen E; Boyer, Michael C; Haines, David R; Arumainayagam, Christopher R

2014-01-01

In the interstellar medium, UV photolysis of condensed methanol (CH3OH), contained in ice mantles surrounding dust grains, is thought to be the mechanism that drives the formation of "complex" molecules, such as methyl formate (HCOOCH3), dimethyl ether (CH3OCH3), acetic acid (CH3COOH), and glycolaldehyde (HOCH2CHO). The source of this reaction-initiating UV light is assumed to be local because externally sourced UV radiation cannot penetrate the ice-containing dark, dense molecular clouds. Specifically, exceedingly penetrative high-energy cosmic rays generate secondary electrons within the clouds through molecular ionizations. Hydrogen molecules, present within these dense molecular clouds, are excited in collisions with these secondary electrons. It is the UV light, emitted by these electronically excited hydrogen molecules, that is generally thought to photoprocess interstellar icy grain mantles to generate "complex" molecules. In addition to producing UV light, the large numbers of low-energy (< 20 eV) secondary electrons, produced by cosmic rays, can also directly initiate radiolysis reactions in the condensed phase. The goal of our studies is to understand the low-energy, electron-induced processes that occur when high-energy cosmic rays interact with interstellar ices, in which methanol, a precursor of several prebiotic species, is the most abundant organic species. Using post-irradiation temperature-programmed desorption, we have investigated the radiolysis initiated by low-energy (7 eV and 20 eV) electrons in condensed methanol at - 85 K under ultrahigh vacuum (5 x 10(-10) Torr) conditions. We have identified eleven electron-induced methanol radiolysis products, which include many that have been previously identified as being formed by methanol UV photolysis in the interstellar medium. These experimental results suggest that low-energy, electron-induced condensed phase reactions may contribute to the interstellar synthesis of "complex" molecules previously thought to form exclusively via UV photons.

Formation and Recondensation of Complex Organic Molecules During Protostellar Luminosity Outbursts

NASA Technical Reports Server (NTRS)

Taquet, Vianney; Wirstrom, Eva S.; Charnley, Steven B.

2016-01-01

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion-molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

Formation and Recondensation of Complex Organic Molecules during Protostellar Luminosity Outbursts

NASA Astrophysics Data System (ADS)

Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

2016-04-01

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion-molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

Influence of bidentate ligand donor types on the formation and stability in 2 + 1 fac-[MI(CO)3]+ (M = Re, 99mTc) complexes.

PubMed

Hayes, Thomas R; Bottorff, Shalina C; Slocumb, Winston S; Barnes, Charles L; Clark, Aurora E; Benny, Paul D

2017-01-24

In the last two decades, a number of chelate strategies have been proposed for the fac-[M I (CO) 3 ] + (M = Re, 99m Tc) core in radiopharmaceutical applications. However, the development of new ligands/complexes with improved function and in vivo performance has been limited in recent years. Expanding on our previous studies using the 2 + 1 labeling strategy, a series of bidentate ligands (neutral vs. anionic) containing an aromatic amine in combination with monodentate pyridine analogs or imidazole were explored to determine the influence of the bidentate and monodentate ligands on the formation and stability of the respective complexes. The 2 + 1 complexes with Re and 99m Tc were synthesized in two steps and characterized by standard radio/chemical methods. X-ray characterization and density functional theory analysis of the Re 2 + 1 complexes with the complete bidentate series with 4-dimethylaminopyridine were conducted, indicating enhanced ligand binding energies of the neutral over anionic ligands. In the 99m Tc studies, anionic bidentate ligands had significantly higher formation yields of the 2 + 1 product, but neutral ligands appear to have increased stability in an amino acid challenge assay. Both bidentate series exhibited improved stability by increasing the basicity of the pyridine ligands.

Influence of Bidentate Ligand Donor Types on the Formation and Stability in 2+1 fac-[MI(CO)3]+ (M = Re, 99mTc) Complexes

PubMed Central

Hayes, Thomas R.; Bottorff, Shalina C.; Slocumb, Winston S.; Barnes, Charles L.; Clark, Aurora E.; Benny, Paul D.

2017-01-01

In the last two decades, a number of chelate strategies have been proposed for the fac-[MI(CO)3]+ (M = Re, 99mTc) core in radiopharmaceutical applications. However, the development of new ligands/complexes with improved function and in vivo performance has been limited in recent years. Expanding on our previous studies using the 2+1 labeling strategy, a series of bidentate ligands (neutral vs. anionic) containing an aromatic amine in combination with monodentate pyridine analogs or imidazole were explored to determine the influence of the bidentate and monodentate ligands on the formation and stability of the respective complexes. The 2+1 complexes with Re and 99mTc were synthesized in two steps and characterized by standard radio/chemical methods. X-ray characterization and density functional theory analysis of the Re 2+1 complexes with the complete bidentate series with 4-dimethylaminopyridine were conducted, indicating enhanced ligand binding energies of the neutral over anionic ligands. In the 99mTc studies, anionic bidentate ligands had significantly higher formation yields of the 2+1 product, but neutral ligands appear to have increased stability in an amino acid challenge assay. Both bidentate series exhibited improved stability by increasing the basicity of the pyridine ligands. PMID:28045466

Forming metal-intermetallic or metal-ceramic composites by self-propagating high-temperature reactions

DOEpatents

Rawers, James C.; Alman, David E.; Petty, Jr., Arthur V.

1996-01-01

Industrial applications of composites often require that the final product have a complex shape. In this invention intermetallic or ceramic phases are formed from sheets of unreacted elemental metals. The process described in this invention allows the final product shape be formed prior to the formation of the composite. This saves energy and allows formation of shaped articles of metal-intermetallic composites composed of brittle materials that cannot be deformed without breaking.

The role of shock waves in the formation of organic compounds in the primeval atmosphere.

NASA Technical Reports Server (NTRS)

Hochstim, A. R.

1971-01-01

It is shown that shock waves from micrometeorites, meteors, meteorites, and thunder are of interest from the viewpoint of contributing significantly to the total accumulation of organic compounds in primeval times. The multitude of recombination reactions occurring in connection with shock waves could be an important factor in the formation of more complex compounds. Lower bound kinetic energies available to micrometeorites, cometary meteorites, stony and iron meteorites are calculated.

About the Barriers to Reaction of CCl4 with HFeOH and FeCl2

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

Ginovska-Pangovska, Bojana; Camaioni, Donald M.; Dupuis, Michel

2011-08-11

The reactivity of iron nanoparticles in aqueous environments has received considerable attention due to their potential utilization in environmental remediation technologies. As part of a broader program aiming at an improved understanding of the mechanisms involved in the degradation of harmful chlorocarbons, joint experimental and computational studies of model systems were initiated. We previously reported on the reaction of one and two Fe atoms reactions with carbon tetrachloride (CCl4) in direct mimic of “atom-dropping” experiments, with insights into the formation of novel iron-carbon-chlorine complexes, their structures and possible reaction mechanisms. Increasing the level of complexity, we report here on themore » modeling of the reaction of HFeOH and CCl4 as companion research of recent ultra high vacuum experiments of the reaction of Fe with water and CCl4. HFeOH is a stable molecular species formed in the reaction of Fe with H2O. Experimentally the (Fe, H2O, CCl4) system showed no reactivity up to the desorption temperature of CCl4. Electron correlated CCSD(T) calculations (at DFT(B3LYP) optimized structures) indicated an energy barrier to reactivity of 24.5 kcal/mol following the formation of a stable ( 7.5 kcal/mol) long-range precursor complex. This finding is consistent with the lack of experimentally detected reaction products. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Complex Organic Molecules Formation in Space Through Gas Phase Reactions: A Theoretical Approach

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

2017-02-01

Chemistry in the interstellar medium (ISM) is capable of producing complex organic molecules (COMs) of great importance to astrobiology. Gas phase and grain surface chemistry almost certainly both contribute to COM formation. Amino acids as building blocks of proteins are some of the most interesting COMs. The simplest one, glycine, has been characterized in meteorites and comets and, its conclusive detection in the ISM seems to be highly plausible. In this work, we analyze the gas phase reaction of glycine and {{{CH}}5}+ to establish the role of this process in the formation of alanine or other COMs in the ISM. Formation of protonated α- and β-alanine in spite of being exothermic processes is not viable under interstellar conditions because the different paths leading to these isomers present net activation energies. Nevertheless, glycine can evolve to protonated 1-imide-2, 2-propanediol, protonated amino acetone, protonated hydroxyacetone, and protonated propionic acid. However, formation of acetic acid and protonated methylamine is also a favorable process and therefore will be a competitive channel with the evolution of glycine to COMs.

Energetics analysis of interstitial loops in single-phase concentrated solid-solution alloys

NASA Astrophysics Data System (ADS)

Wang, Xin-Xin; Niu, Liang-Liang; Wang, Shaoqing

2018-04-01

Systematic energetics analysis on the shape preference, relative stability and radiation-induced segregation of interstitial loops in nickel-containing single-phase concentrated solid-solution alloys have been conducted using atomistic simulations. It is shown that the perfect loops prefer rhombus shape for its low potential energy, while the Frank faulted loops favor ellipse for its low potential energy and the possible large configurational entropy. The decrease of stacking fault energy with increasing compositional complexity provides the energetic driving force for the formation of faulted loops, which, in conjunction with the kinetic factors, explains the experimental observation that the fraction of faulted loops rises with increasing compositional complexity. Notably, the kinetics is primarily responsible for the absence of faulted loops in nickel-cobalt with a very low stacking fault energy. We further demonstrate that the simultaneous nickel enrichment and iron/chromium depletion on interstitial loops can be fully accounted for by their energetics.

Anaerobic Formate and Hydrogen Metabolism.

PubMed

Sawers, R Gary; Blokesch, Melanie; Böck, August

2004-12-01

During fermentative growth, Escherichia coli degrades carbohydrates via the glycolytic route into two pyruvate molecules. Pyruvate can be reduced to lactate or nonoxidatively cleaved by pyruvate formate lyase into acetyl-coenzyme A (acetyl-CoA) and formate. Acetyl-CoA can be utilized for energy conservation in the phosphotransacetylase (PTA) and acetate kinase (ACK) reaction sequence or can serve as an acceptor for reducing equivalents gathered during pyruvate formation, through the action of alcohol dehydrogenase (AdhE). Formic acid is strongly acidic and has a redox potential of -420 mV under standard conditions and therefore can be classified as a high-energy compound. Its disproportionation into CO2 and molecular hydrogen (Em,7 -420 mV) via the formate hydrogenlyase (FHL) system is therefore of high selective value. The FHL reaction involves the participation of at least seven proteins, most of which are metalloenzymes, with requirements for iron, molybdenum, nickel, or selenium. Complex auxiliary systems incorporate these metals. Reutilization of the hydrogen evolved required the evolution of H2 oxidation systems, which couple the oxidation process to an appropriate energy-conserving terminal reductase. E. coli has two hydrogen-oxidizing enzyme systems. Finally, fermentation is the "last resort" of energy metabolism, since it gives the minimal energy yield when compared with respiratory processes. Consequently, fermentation is used only when external electron acceptors are absent. This has necessitated the establishment of regulatory cascades, which ensure that the metabolic capability is appropriately adjusted to the physiological condition. Here we review the genetics, biochemistry, and regulation of hydrogen metabolism and its hydrogenase maturation system.

Localization of superoxide anion production to mitochondrial electron transport chain in 3-NPA-treated cells

PubMed Central

Bacsi, Attila; Woodberry, Mitchell; Widger, William; Papaconstantinou, John; Mitra, Sankar; Peterson, Johnny W.; Boldogh, Istvan

2011-01-01

3-Nitropropionic acid (3-NPA), an inhibitor of succinate dehydrogenase (SDH) at complex II of the mitochondrial electron transport chain induces cellular energy deficit and oxidative stress-related neurotoxicity. In the present study, we identified the site of reactive oxygen species production in mitochondria. 3-NPA increased O2•− generation in mitochondria respiring on the complex I substrates pyruvate + malate, an effect fully inhibited by rotenone. Antimycin A increased O2•− production in the presence of complex I and/or II substrates. Addition of 3-NPA markedly increased antimycin A-induced O2•− production by mitochondria incubated with complex I substrates, but 3-NPA inhibited O2•− formation driven with the complex II substrate succinate. At 0.6 μM, myxothiazol inhibits complex III, but only partially decreases complex I activity, and allowed 3-NPA-induced O2•− formation; however, at 40 μM myxothiazol (which completely inhibits both complexes I and III) eliminated O2•− production from mitochondria respiring via complex I substrates. These results indicate that in the presence of 3-NPA, mitochondria generate O2•− from a site between the ubiquinol pool and the 3-NPA block in the respiratory complex II. PMID:17011837

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

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

Moutanabbir, O.; Scholz, R.; Goesele, U.

We present a detailed study of the thermal evolution of H ion-induced vacancy related complexes and voids in bulk GaN implanted under ion-cut conditions. By using transmission electron microscopy, we found that the damage band in as-implanted GaN is decorated with a high density of nanobubbles of approx1-2 nm in diameter. Variable energy Doppler broadening spectroscopy showed that this band contains vacancy clusters and voids. In addition to vacancy clusters, the presence of V{sub Ga}, V{sub Ga}-H{sub 2}, and V{sub Ga}V{sub N} complexes was evidenced by pulsed low-energy positron lifetime spectroscopy. Subtle changes upon annealing in these vacancy complexes weremore » also investigated. As a general trend, a growth in open-volume defects is detected in parallel to an increase in both size and density of nanobubbles. The observed vacancy complexes appear to be stable during annealing. However, for temperatures above 450 deg. C, unusually large lifetimes were measured. These lifetimes are attributed to the formation of positronium in GaN. Since the formation of positronium is not possible in a dense semiconductor, our finding demonstrates the presence of sufficiently large open-volume defects in this temperature range. Based on the Tao-Eldrup model, the average lattice opening during thermal annealing was quantified. We found that a void diameter of 0.4 nm is induced by annealing at 600 deg. C. The role of these complexes in the subsurface microcracking is discussed.« less

Hydrogen bond docking site competition in methyl esters

NASA Astrophysics Data System (ADS)

Zhao, Hailiang; Tang, Shanshan; Du, Lin

2017-06-01

The Osbnd H ⋯ O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119 cm- 1) > TFE-MF (93 cm- 1) > TFE-MTFA (44 cm- 1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6 kJ mol- 1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

PubMed

Higo, Junichi; Dasgupta, Bhaskar; Mashimo, Tadaaki; Kasahara, Kota; Fukunishi, Yoshifumi; Nakamura, Haruki

2015-07-30

A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did. © 2015 Wiley Periodicals, Inc.

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.

The causes of altered chlorophyll fluorescence quenching induction in the Arabidopsis mutant lacking all minor antenna complexes.

PubMed

Townsend, Alexandra J; Saccon, Francesco; Giovagnetti, Vasco; Wilson, Sam; Ungerer, Petra; Ruban, Alexander V

2018-03-13

Non-photochemical quenching (NPQ) of chlorophyll fluorescence is the process by which excess light energy is harmlessly dissipated within the photosynthetic membrane. The fastest component of NPQ, known as energy-dependent quenching (qE), occurs within minutes, but the site and mechanism of qE remain of great debate. Here, the chlorophyll fluorescence of Arabidopsis thaliana wild type (WT) plants was compared to mutants lacking all minor antenna complexes (NoM). Upon illumination, NoM exhibits altered chlorophyll fluorescence quenching induction (i.e. from the dark-adapted state) characterised by three different stages: (i) a fast quenching component, (ii) transient fluorescence recovery and (iii) a second quenching component. The initial fast quenching component originates in light harvesting complex II (LHCII) trimers and is dependent upon PsbS and the formation of a proton gradient across the thylakoid membrane (ΔpH). Transient fluorescence recovery is likely to occur in both WT and NoM plants, but it cannot be overcome in NoM due to impaired ΔpH formation and a reduced zeaxanthin synthesis rate. Moreover, an enhanced fluorescence emission peak at ~679 nm in NoM plants indicates detachment of LHCII trimers from the bulk antenna system, which could also contribute to the transient fluorescence recovery. Finally, the second quenching component is triggered by both ΔpH and PsbS and enhanced by zeaxanthin synthesis. This study indicates that minor antenna complexes are not essential for qE, but reveals their importance in electron stransport, ΔpH formation and zeaxanthin synthesis. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C60 : Synthesis, Supramolecular Formation and Excited-State Processes.

PubMed

Hu, Yi; Thomas, Michael B; Jinadasa, R G Waruna; Wang, Hong; D'Souza, Francis

2017-09-18

Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin-zinc porphyrin dyad, H 2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 10 4  m -1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H 2 P, and electron transfer to the coordinated ImC 60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×10 9  s -1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex photochemical events occurring in natural photosynthesis and its implications in building light energy harvesting devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding.

PubMed

Kalra, P; Reddy, T V; Jayaram, B

2001-12-06

A theoretically rigorous and computationally tractable methodology for the prediction of the free energies of binding of protein-ligand complexes is presented. The method formulated involves developing molecular dynamics trajectories of the enzyme, the inhibitor, and the complex, followed by a free energy component analysis that conveys information on the physicochemical forces driving the protein-ligand complex formation and enables an elucidation of drug design principles for a given receptor from a thermodynamic perspective. The complexes of HIV-1 protease with two peptidomimetic inhibitors were taken as illustrative cases. Four-nanosecond-level all-atom molecular dynamics simulations using explicit solvent without any restraints were carried out on the protease-inhibitor complexes and the free proteases, and the trajectories were analyzed via a thermodynamic cycle to calculate the binding free energies. The computed free energies were seen to be in good accord with the reported data. It was noted that the net van der Waals and hydrophobic contributions were favorable to binding while the net electrostatics, entropies, and adaptation expense were unfavorable in these protease-inhibitor complexes. The hydrogen bond between the CH2OH group of the inhibitor at the scissile position and the catalytic aspartate was found to be favorable to binding. Various implicit solvent models were also considered and their shortcomings discussed. In addition, some plausible modifications to the inhibitor residues were attempted, which led to better binding affinities. The generality of the method and the transferability of the protocol with essentially no changes to any other protein-ligand system are emphasized.

Free energy decomposition of protein-protein interactions.

PubMed

Noskov, S Y; Lim, C

2001-08-01

A free energy decomposition scheme has been developed and tested on antibody-antigen and protease-inhibitor binding for which accurate experimental structures were available for both free and bound proteins. Using the x-ray coordinates of the free and bound proteins, the absolute binding free energy was computed assuming additivity of three well-defined, physical processes: desolvation of the x-ray structures, isomerization of the x-ray conformation to a nearby local minimum in the gas-phase, and subsequent noncovalent complex formation in the gas phase. This free energy scheme, together with the Generalized Born model for computing the electrostatic solvation free energy, yielded binding free energies in remarkable agreement with experimental data. Two assumptions commonly used in theoretical treatments; viz., the rigid-binding approximation (which assumes no conformational change upon complexation) and the neglect of vdW interactions, were found to yield large errors in the binding free energy. Protein-protein vdW and electrostatic interactions between complementary surfaces over a relatively large area (1400--1700 A(2)) were found to drive antibody-antigen and protease-inhibitor binding.

Molecular Architecture of Plant Thylakoids under Physiological and Light Stress Conditions: A Study of Lipid–Light-Harvesting Complex II Model Membranes[C][W

PubMed Central

Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Puzio, Michal; Luchowski, Rafal; Grudzinski, Wojciech; Mazur, Radoslaw; Garstka, Maciej; Maksymiec, Waldemar; Kulik, Andrzej; Dietler, Giovanni; Gruszecki, Wieslaw I.

2013-01-01

In this study, we analyzed multibilayer lipid-protein membranes composed of the photosynthetic light-harvesting complex II (LHCII; isolated from spinach [Spinacia oleracea]) and the plant lipids monogalcatosyldiacylglycerol and digalactosyldiacylglycerol. Two types of pigment-protein complexes were analyzed: those isolated from dark-adapted leaves (LHCII) and those from leaves preilluminated with high-intensity light (LHCII-HL). The LHCII-HL complexes were found to be partially phosphorylated and contained zeaxanthin. The results of the x-ray diffraction, infrared imaging microscopy, confocal laser scanning microscopy, and transmission electron microscopy revealed that lipid-LHCII membranes assemble into planar multibilayers, in contrast with the lipid-LHCII-HL membranes, which form less ordered structures. In both systems, the protein formed supramolecular structures. In the case of LHCII-HL, these structures spanned the multibilayer membranes and were perpendicular to the membrane plane, whereas in LHCII, the structures were lamellar and within the plane of the membranes. Lamellar aggregates of LHCII-HL have been shown, by fluorescence lifetime imaging microscopy, to be particularly active in excitation energy quenching. Both types of structures were stabilized by intermolecular hydrogen bonds. We conclude that the formation of trans-layer, rivet-like structures of LHCII is an important determinant underlying the spontaneous formation and stabilization of the thylakoid grana structures, since the lamellar aggregates are well suited to dissipate excess energy upon overexcitation. PMID:23898030

Molecular architecture of plant thylakoids under physiological and light stress conditions: a study of lipid-light-harvesting complex II model membranes.

PubMed

Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Puzio, Michal; Luchowski, Rafal; Grudzinski, Wojciech; Mazur, Radoslaw; Garstka, Maciej; Maksymiec, Waldemar; Kulik, Andrzej; Dietler, Giovanni; Gruszecki, Wieslaw I

2013-06-01

In this study, we analyzed multibilayer lipid-protein membranes composed of the photosynthetic light-harvesting complex II (LHCII; isolated from spinach [Spinacia oleracea]) and the plant lipids monogalcatosyldiacylglycerol and digalactosyldiacylglycerol. Two types of pigment-protein complexes were analyzed: those isolated from dark-adapted leaves (LHCII) and those from leaves preilluminated with high-intensity light (LHCII-HL). The LHCII-HL complexes were found to be partially phosphorylated and contained zeaxanthin. The results of the x-ray diffraction, infrared imaging microscopy, confocal laser scanning microscopy, and transmission electron microscopy revealed that lipid-LHCII membranes assemble into planar multibilayers, in contrast with the lipid-LHCII-HL membranes, which form less ordered structures. In both systems, the protein formed supramolecular structures. In the case of LHCII-HL, these structures spanned the multibilayer membranes and were perpendicular to the membrane plane, whereas in LHCII, the structures were lamellar and within the plane of the membranes. Lamellar aggregates of LHCII-HL have been shown, by fluorescence lifetime imaging microscopy, to be particularly active in excitation energy quenching. Both types of structures were stabilized by intermolecular hydrogen bonds. We conclude that the formation of trans-layer, rivet-like structures of LHCII is an important determinant underlying the spontaneous formation and stabilization of the thylakoid grana structures, since the lamellar aggregates are well suited to dissipate excess energy upon overexcitation.

Hydrogen bonding effects on the reorganization energy for photoinduced charge separation reaction between porphyrin and quinone studied by nanosecond laser flash photolysis.

PubMed

Yago, Tomoaki; Gohdo, Masao; Wakasa, Masanobu

2010-02-25

Alcohol concentration dependences of photoinduced charge separation (CS) reaction of zinc tetraphenyl-porphyrin (ZnTPP) and duroquinone (DQ) were investigated in benzonitrile by a nanosecond laser flash photolysis technique. The photoinduced CS reaction was accelerated by the addition of alcohols, whereas the addition of acetonitrile caused little effect on the CS reactions. The simple theory was developed to calculate an increase in reorganization energies induced by the hydrogen bonding interactions between DQ and alcohols using the chemical equilibrium constants for the hydrogen bonding complexes through the concerted pathway and the stepwise one. The experimental results were analyzed by using the Marcus equation where we took into account the hydrogen bonding effects on the reorganization energy and the reaction free energy for the CS reaction. The observed alcohol concentration dependence of the CS reaction rates was well explained by the formation of the hydrogen bonding complexes through the concerted pathway, demonstrating the increase in the reorganization energy by the hydrogen bonding interactions.

Bonds Between Metal Atoms: A New Mode of Transition Metal Chemistry.

ERIC Educational Resources Information Center

Cotton, F. Albert; Chisholm, Malcolm H.

1982-01-01

Discusses polynuclear metal clusters (containing two or more metal atoms bonded to one another as well as to nonmetallic elements), including their formation and applications. Studies of bonds between metal atoms reveal superconductors, organic-reaction catalysts, and photosensitive complexes that may play a role in solar energy. (JN)

Reducing uncertainties in energy dissipation measurements in atomic force spectroscopy of molecular networks and cell-adhesion studies.

PubMed

Biswas, Soma; Leitao, Samuel; Theillaud, Quentin; Erickson, Blake W; Fantner, Georg E

2018-06-20

Atomic force microscope (AFM) based single molecule force spectroscopy (SMFS) is a valuable tool in biophysics to investigate the ligand-receptor interactions, cell adhesion and cell mechanics. However, the force spectroscopy data analysis needs to be done carefully to extract the required quantitative parameters correctly. Especially the large number of molecules, commonly involved in complex networks formation; leads to very complicated force spectroscopy curves. One therefore, generally characterizes the total dissipated energy over a whole pulling cycle, as it is difficult to decompose the complex force curves into individual single molecule events. However, calculating the energy dissipation directly from the transformed force spectroscopy curves can lead to a significant over-estimation of the dissipated energy during a pulling experiment. The over-estimation of dissipated energy arises from the finite stiffness of the cantilever used for AFM based SMFS. Although this error can be significant, it is generally not compensated for. This can lead to significant misinterpretation of the energy dissipation (up to the order of 30%). In this paper, we show how in complex SMFS the excess dissipated energy caused by the stiffness of the cantilever can be identified and corrected using a high throughput algorithm. This algorithm is then applied to experimental results from molecular networks and cell-adhesion measurements to quantify the improvement in the estimation of the total energy dissipation.

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

PubMed

Guo, Xunmin; Wang, Sufan; Xia, Andong; Su, Hongmei

2007-07-05

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes

PubMed Central

Bastiani, Michele; Liu, Libin; Hill, Michelle M.; Jedrychowski, Mark P.; Nixon, Susan J.; Lo, Harriet P.; Abankwa, Daniel; Luetterforst, Robert; Fernandez-Rojo, Manuel; Breen, Michael R.; Gygi, Steven P.; Vinten, Jorgen; Walser, Piers J.; North, Kathryn N.; Hancock, John F.; Pilch, Paul F.

2009-01-01

Polymerase I and transcript release factor (PTRF)/Cavin is a cytoplasmic protein whose expression is obligatory for caveola formation. Using biochemistry and fluorescence resonance energy transfer–based approaches, we now show that a family of related proteins, PTRF/Cavin-1, serum deprivation response (SDR)/Cavin-2, SDR-related gene product that binds to C kinase (SRBC)/Cavin-3, and muscle-restricted coiled-coil protein (MURC)/Cavin-4, forms a multiprotein complex that associates with caveolae. This complex can constitutively assemble in the cytosol and associate with caveolin at plasma membrane caveolae. Cavin-1, but not other cavins, can induce caveola formation in a heterologous system and is required for the recruitment of the cavin complex to caveolae. The tissue-restricted expression of cavins suggests that caveolae may perform tissue-specific functions regulated by the composition of the cavin complex. Cavin-4 is expressed predominantly in muscle, and its distribution is perturbed in human muscle disease associated with Caveolin-3 dysfunction, identifying Cavin-4 as a novel muscle disease candidate caveolar protein. PMID:19546242

Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex

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

Bhattacharya, Papri; Heiden, Zachariah M.; Wiedner, Eric S.

We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo-15NH3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo=15NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo=15NR generates a terminal Mo≡N nitride, and a [Mo-15NH]+ complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo-15NH3 complex and the formation of Mo=15NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Officemore » of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.« less

Efficient collective swimming by harnessing vortices through deep reinforcement learning.

PubMed

Verma, Siddhartha; Novati, Guido; Koumoutsakos, Petros

2018-06-05

Fish in schooling formations navigate complex flow fields replete with mechanical energy in the vortex wakes of their companions. Their schooling behavior has been associated with evolutionary advantages including energy savings, yet the underlying physical mechanisms remain unknown. We show that fish can improve their sustained propulsive efficiency by placing themselves in appropriate locations in the wake of other swimmers and intercepting judiciously their shed vortices. This swimming strategy leads to collective energy savings and is revealed through a combination of high-fidelity flow simulations with a deep reinforcement learning (RL) algorithm. The RL algorithm relies on a policy defined by deep, recurrent neural nets, with long-short-term memory cells, that are essential for capturing the unsteadiness of the two-way interactions between the fish and the vortical flow field. Surprisingly, we find that swimming in-line with a leader is not associated with energetic benefits for the follower. Instead, "smart swimmer(s)" place themselves at off-center positions, with respect to the axis of the leader(s) and deform their body to synchronize with the momentum of the oncoming vortices, thus enhancing their swimming efficiency at no cost to the leader(s). The results confirm that fish may harvest energy deposited in vortices and support the conjecture that swimming in formation is energetically advantageous. Moreover, this study demonstrates that deep RL can produce navigation algorithms for complex unsteady and vortical flow fields, with promising implications for energy savings in autonomous robotic swarms.

First-principles characterization of native-defect-related optical transitions in ZnO

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

Lyons, J. L.; Varley, J. B.; Steiauf, D.

We investigate the electrical and optical properties of oxygen vacancies (VO), zinc vacancies (V Zn), hydrogenated V Zn, and isolated dangling bonds in ZnO using hybrid functional calculations. While the formation energy of V O is high in n-type ZnO, indicating that this center is unlikely to form, our results for optical absorption signals associated with V O are consistent with those observed in irradiated samples, and give rise to emission with a peak at less than 1 eV. Under realistic growth conditions, we find that VZn is the lowest-energy native defect in n-type ZnO, acting as an acceptor thatmore » is likely to compensate donor doping. Turning to optical transitions, we first examine N O as a case study, since N-related transitions have been identified in experiments on ZnO. Here, we also examine how hydrogen, often unintentionally present in ZnO, forms stable complexes with V Zn and modifies its optical properties. Compared with isolated V Zn, V Zn-H complexes have charge-state transition levels lower in the band gap as well as have lower formation energies. These complexes also lead to characteristic vibrational frequencies which compare favorably with experiment. Oxygen dangling bonds show behavior mostly consistent with V Zn, while zinc dangling bonds give rise to transition levels near the ZnO conduction-band minimum and emission peaking near 2.4 eV. Lastly, we discuss our results in view of the available experimental literature.« less

First-principles characterization of native-defect-related optical transitions in ZnO

DOE PAGES

Lyons, J. L.; Varley, J. B.; Steiauf, D.; ...

2017-07-21

We investigate the electrical and optical properties of oxygen vacancies (VO), zinc vacancies (V Zn), hydrogenated V Zn, and isolated dangling bonds in ZnO using hybrid functional calculations. While the formation energy of V O is high in n-type ZnO, indicating that this center is unlikely to form, our results for optical absorption signals associated with V O are consistent with those observed in irradiated samples, and give rise to emission with a peak at less than 1 eV. Under realistic growth conditions, we find that VZn is the lowest-energy native defect in n-type ZnO, acting as an acceptor thatmore » is likely to compensate donor doping. Turning to optical transitions, we first examine N O as a case study, since N-related transitions have been identified in experiments on ZnO. Here, we also examine how hydrogen, often unintentionally present in ZnO, forms stable complexes with V Zn and modifies its optical properties. Compared with isolated V Zn, V Zn-H complexes have charge-state transition levels lower in the band gap as well as have lower formation energies. These complexes also lead to characteristic vibrational frequencies which compare favorably with experiment. Oxygen dangling bonds show behavior mostly consistent with V Zn, while zinc dangling bonds give rise to transition levels near the ZnO conduction-band minimum and emission peaking near 2.4 eV. Lastly, we discuss our results in view of the available experimental literature.« less

Ab initio prediction of fast non-equilibrium transport of nascent polarons in SrI 2: a key to high-performance scintillation [First-principles study of hole polaron formation and migration in strontium iodide

DOE PAGES

Zhou, Fei; Sadigh, Babak; Aberg, Daniel; ...

2016-08-12

The excellent light yield proportionality of europium-doped strontium iodide (SrI 2:Eu) has resulted in state-of-the-art γ-ray detectors with remarkably high-energy resolution, far exceeding that of most halide compounds. In this class of materials, the formation of self-trapped hole polarons is very common. However, polaron formation is usually expected to limit carrier mobilities and has been associated with poor scintillator light-yield proportionality and resolution. Here using a recently developed first-principles method, we perform an unprecedented study of polaron transport in SrI 2, both for equilibrium polarons, as well as nascent polarons immediately following a self-trapping event. We propose a rationale formore » the unexpected high-energy resolution of SrI 2. We identify nine stable hole polaron configurations, which consist of dimerised iodine pairs with polaron-binding energies of up to 0.5 eV. They are connected by a complex potential energy landscape that comprises 66 unique nearest-neighbour migration paths. Ab initio molecular dynamics simulations reveal that a large fraction of polarons is born into configurations that migrate practically barrier free at room temperature. Consequently, carriers created during γ-irradiation can quickly diffuse away reducing the chance for nonlinear recombination, the primary culprit for non-proportionality and resolution reduction. We conclude that the flat, albeit complex, landscape for polaron migration in SrI 2 is a key for understanding its outstanding performance. This insight provides important guidance not only for the future development of high-performance scintillators but also of other materials, for which large polaron mobilities are crucial such as batteries and solid-state ionic conductors.« less

Chemical dynamics simulations of the monohydrated OH-(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

NASA Astrophysics Data System (ADS)

Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L.

2015-06-01

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH-(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I-, and to a lesser extent CH2I- (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]-. In contrast, for the unsolvated OH- + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH-(H2O) + CH3IߙSN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I- post-reaction complex for the SN2 reaction is negligible.

The fine tuning of carotenoid-chlorophyll interactions in light-harvesting complexes: an important requisite to guarantee efficient photoprotection via triplet-triplet energy transfer in the complex balance of the energy transfer processes

NASA Astrophysics Data System (ADS)

Di Valentin, Marilena; Carbonera, Donatella

2017-08-01

Triplet-triplet energy transfer (TTET) from the chlorophyll to the carotenoid triplet state is the process exploited by photosynthetic systems to protect themselves from singlet oxygen formation under light-stress conditions. A deep comprehension of the molecular strategies adopted to guarantee TTET efficiency, while at the same time maintaining minimal energy loss and efficient light-harvesting capability, is still lacking. The paramagnetic nature of the triplet state makes electron paramagnetic resonance (EPR) the method of choice when investigating TTET. In this review, we focus on our extended comparative study of two photosynthetic antenna complexes, the Peridinin-chlorophyll a-protein of dinoflagellates and the light-harvesting complex II of higher plants, in order to point out important aspects of the molecular design adopted in the photoprotection strategy. We have demonstrated that a proper analysis of the EPR data allows one to identify the pigments involved in TTET and, consequently, gain an insight into the structure of the photoprotective sites. The structural information has been complemented by a detailed description of the electronic structure provided by hyperfine spectroscopy. All these elements represent the fundamental building blocks toward a deeper understanding of the requirements for efficient photoprotection, which is fundamental to guarantee the prolonged energy conversion action of photosynthesis.

Selective CO2 reduction conjugated with H2O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

NASA Astrophysics Data System (ADS)

Morikawa, T.; Sato, S.; Arai, T.; Uemura, K.; Yamanaka, K. I.; Suzuki, T. M.; Kajino, T.; Motohiro, T.

2013-12-01

We developed a new hybrid photocatalyst for CO2 reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (ECBM) of the semiconductor and the CO2 reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO2 to formate using water as an electron donor and a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO2 reduction with a TiO2 photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.

The H2O-CH3F Complex: a Combined Microwave and Infrared Spectroscopic Study Supported by Structure Calculations

NASA Astrophysics Data System (ADS)

Gnanasekar, Sharon Priya; Goubet, Manuel; Arunan, Elangannan; Georges, Robert; Soulard, Pascale; Asselin, Pierre; Huet, T. R.; Pirali, Olivier

2015-06-01

The H2O-CH3F complex could have two geometries, one with a hydrogen bond and one with the newly proposed carbon bond. While in general carbon bonds are weaker than hydrogen bonds, this complex appears to have comparable energies for the two structures. Infrared (IR) and microwave (MW) spectroscopic measurements using, respectively, the Jet-AILES apparatus and the FTMW spectrometer at the PhLAM laboratory, have been carried out to determine the structure of this complex. The IR spectrum shows the formation of the CH3F- H2O hydrogen bonded complex and small red-shifts in OH frequency most probably due to (CH3F)m-(H2O)n clusters. Noticeably, addition of CH_3F in the mixture promotes the formation of small water clusters. Preliminary MW spectroscopic measurements indicate the formation of the hydrogen bonded complex. So far, we have no experimental evidence for the carbon bonded structure. However, calculations of the Ar-CH3F complex show three energetically equivalent structures: a T-shape, a "fluorine" bond and a carbon bond. The MW spectrum of the (Ar)n-CH3F complexes is currently under analysis. Mani, D; Arunan, E. Phys. Chem. Chem. Phys. 2013, 15, 14377. Cirtog, M; Asselin, P; Soulard, P; Tremblay, B; Madebene, B; Alikhani, M. E; Georges, R; Moudens, A; Goubet, M; Huet, T.R; Pirali, O; Roy, P. J. Phys. Chem. A. 2011, 115, 2523 Kassi, S; Petitprez, D; Wlodarczak, G. J. Mol. Struct. 2000, 517-518, 375

FORMATION AND RECONDENSATION OF COMPLEX ORGANIC MOLECULES DURING PROTOSTELLAR LUMINOSITY OUTBURSTS

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

Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

2016-04-10

During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The modelmore » calculations presented here demonstrate that ion–molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.« less

Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

NASA Astrophysics Data System (ADS)

Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.

2015-10-01

The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

Reaction of iminopropadienones with amines: mechanistic explanations of zwitterionic intermediate, ketene and ketenimine formation.

PubMed

Koch, Rainer; Finnerty, Justin J; Bruhn, Torsten; Borget, Fabien; Wentrup, Curt

2008-09-25

The complex reaction of thermally generated iminopropadienones with amines in the gas phase and upon matrix deposition and its varying product composition is investigated using density functional theory. In the high energy gas phase addition a single amine molecule reacts readily with iminopropadienone with the decisive step being a 1,3-hydrogen shift and activation barriers of at least 100 kJ/mol. In accordance with the experiment, the formation of ketenes is favored. In the condensed phase of an amine matrix, the utilization of amine dimers both as reagents and as explicit solvents lowers the activation energy required to a feasible 20-30 kJ/mol and predicts ketenimines as the main products, as observed experimentally.

Spectroscopic, computational and electrochemical studies on the formation of the copper complex of 1-amino-4-hydroxy-9,10-anthraquinone and effect of it on superoxide formation by NADH dehydrogenase.

PubMed

Roy, Sanjay; Mondal, Palash; Sengupta, Partha Sarathi; Dhak, Debasis; Santra, Ramesh Chandra; Das, Saurabh; Guin, Partha Sarathi

2015-03-28

A 1 : 2 copper(II) complex of 1-amino-4-hydroxy-9,10-anthraquinone (QH) having the molecular formula CuQ2 was prepared and characterized by elemental analysis, NMR, FTIR, UV-vis and mass spectroscopy. The powder diffraction of the solid complex, magnetic susceptibility and ESR spectra were also recorded. The presence of the planar anthraquinone moiety in the complex makes it extremely difficult to obtain a single crystal suitable for X-ray diffraction studies. To overcome this problem, density functional theory (DFT) was used to evaluate an optimized structure of CuQ2. In the optimized structure, it was found that there is a tilt of the two planar aromatic anthraquinone rings of the complex with respect to each other in the two planes containing the O-Cu(II)-O plane. The present study is an important addition to the understanding of the structural aspects of metal-anthracyclines because there are only a few reports on the actual structures of metal-anthracyclines. The theoretical vibrational spectrum of the complex was assigned with the help of vibrational energy distribution analysis (VEDA) using potential energy distribution (PED) and compared with experimental results. Being important in producing the biochemical action of this class of molecules, the electrochemical behavior of the complex was studied in aqueous and non-aqueous solvents to find certain electrochemical parameters. In aqueous media, reduction involves a kinetic effect during electron transfer at an electrode surface, which was characterized very carefully using cyclic voltammetry. Electrochemical studies showed a significant modification in the electrochemical properties of 1-amino-4-hydroxy-9,10-anthraquinone (QH) when bound to Cu(II) in the complex compared to those observed for free QH. This suggests that the copper complex might be a good choice as a biologically active molecule, which was reflected in the lack of stimulated superoxide generation by the complex.

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

Krasnokutski, Serge A., E-mail: skrasnokutskiy@yahoo.com; Huisken, Friedrich, E-mail: friedrich.huisken@uni-jena.de

The reaction of carbon atoms with benzene has been investigated in liquid helium droplets at T = 0.37 K. We found an addition of the carbon atom to form an initial intermediate complex followed by a ring opening and the formation of a seven-membered ring. In contrast to a previous gas phase study, the reaction is frozen after these steps and the loss of hydrogen does not occur. A calorimetric technique was applied to monitor the energy balance of the reaction. It was found that more than 267 kJ mol{sup −1} were released in this reaction. This estimation is inmore » line with quantum chemical calculations of the formation energy of a seven-membered carbon ring. It is suggested that reactions of this kind could be responsible for the low abundance of small polycyclic aromatic hydrocarbon molecules in the interstellar medium. We also found the formation of weakly bonded water-carbon adducts, in which the carbon atom is linked to the oxygen atom of the water molecule with a binding energy of about 33.4 kJ mol{sup −1}.« less

Enhancement of photoisomerization of polymethine dyes in complexes with biomacromolecules

NASA Astrophysics Data System (ADS)

Tatikolov, Alexander S.; Akimkin, Timofei M.; Pronkin, Pavel G.; Yarmoluk, Sergiy M.

2013-01-01

Photochemical processes (photoisomerization and generation of the triplet state) of the thiacarbocyanine dyes 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2), 3,3'-diethyl-9-methylthiacarbocyanine iodide (DMTC), and 3,3',9-triethylthiacarbocyanine iodide (TETC) in complexes with biomacromolecules—DNA and chondroitin-4-sulfate—were studied by flash photolysis. It has been shown that, along with generation of the triplet state, enhancement of the photoisomer formation is observed for Cyan 2 and DMTC complexed with the biomolecules. This effect can be explained by the influence of the biopolymer matrix on the potential energy curves of the photoisomerization process.

Experimental and theoretical insight into the cooperativity effect in composite wax powder and ternary complex of coronene with CH4 and Mn+ (Mn+ = Li+, Na+, K+, Be2+, Mg2+ or Ca2+)

NASA Astrophysics Data System (ADS)

Jiang, Le-tao; Bai, Pei-kang; Wang, Jian-hong; Liu, Bin; Li, Yu-xin

2018-01-01

The experimental infrared (IR) spectrum of composite wax powder was investigated. The frequency shifts of the C=C anti-symmetrical stretching mode were observed and the experimental cooperativity effect involving Na+...π interaction was suggested. In order to further reveal the nature of cooperativity effect, the interaction energies in Mn+...coronene...CH4 (Mn+ = Li+, Na+, K+, Be2+, Mg2+ or Ca2+) as the model systems of composite wax powder were calculated by using the B3LYP, M06-2X and MP2 methods with 6-311++G** basis set. The results show that the Mn+...π interactions were strengthened upon the formation of ternary complexes. Although the changes of absolute values of the interactions between CH4 and coronene were not obvious, the relative values were considerably significant upon the formation of ternary complexes. The cooperativity effect was perhaps the reason for the formation of notable advantage of composite wax powder upon the introduction of surfactant with cation into wax powder. Reduced density gradient and atoms-in-molecules analysis confirm the cooperativity effect in Mn+...coronene...CH4, and reveal the nature of the formation of the predominant advantage of composite wax powder.

Solvent-coordinate free-energy landscape view of water-mediated ion-pair dissociation

NASA Astrophysics Data System (ADS)

Yonetani, Yoshiteru

2017-12-01

Water-mediated ion-pair dissociation is studied by molecular dynamics simulations of NaCl in water. Multidimensional free-energy analysis clarifies the relation between two essential solvent coordinates: the water coordination number and water-bridge formation. These two are related in a complex way. Both are necessary to describe ion-pair dissociation. The mechanism constructed with both solvent variables clearly shows the individual roles. The water coordination number is critical for starting ion-pair dissociation. Water-bridge formation is also important because it increases the likelihood of ion-pair dissociation by reducing the dissociation free-energy barrier. Additional Ca-Cl and NH4-Cl calculations show that these conclusions are unaffected by changes in the ion charge and shape. The present results will contribute to future explorations of many other molecular events such as surface water exchange and protein-ligand dissociation because the same mechanism is involved in such events.

VUV Dissociative Photoionization of Quinoline in the 7-26 eV Photon Energy Range

NASA Astrophysics Data System (ADS)

Leach, Sydney; Jochims, Hans-Werner; Baumgärtel, Helmut; Champion, Norbert

2018-05-01

The dissociative photoionization of quinoline was studied by photoionization mass spectrometry and ion yield measurements over a synchrotron photon excitation energy range 7-26 eV. The ionic and neutral products were identified with the aid of thermochemical calculations that, in some cases, led to deeper understanding of photodissociation pathways and the determination of upper limits of heats of formation of ionic and neutral dissociation products. A detailed comparison between the 20 eV photon excitation and 70 eV electron impact mass spectra, coupled with estimation of thermochemical appearance energies, leads to assignment of the dissociative ionization cation and neutral products for each detected ion. Reaction schemes for formation of these products are proposed in a number of cases. Ion intensities in the photon and electron impact mass spectra were used to consider extending a rule of charge retention in simple bond cleavage to more complex cases of dissociative ionization.

Reactions in Nitroimidazole and Methylnitroimidazole Triggered by Low-Energy (0-8 eV) Electrons.

PubMed

Tanzer, Katrin; Feketeová, Linda; Puschnigg, Benjamin; Scheier, Paul; Illenberger, Eugen; Denifl, Stephan

2015-06-25

Low-energy electrons (0-8 eV) effectively decompose 4-nitroimidazole (4NI) and the two methylated isomers 1-methyl-5-nitroimidazole and 1-methyl-4-nitroimidazole via dissociative electron attachment (DEA). The involved unimolecular decompositions range from simple bond cleavages (loss of H(•), formation of NO2(-)) to complex reactions possibly leading to a complete degradation of the target molecule (formation of CN(-), etc.). At energies below 2 eV, the entire rich chemistry induced by DEA is completely quenched by methylation, as demonstrated in a previous communication (Tanzer, K.; Feketeová, L.; Puschnigg, B.; Scheier, P.; Illenberger. E.; Denifl, S. Angew. Chem., Int. Ed. 2014, 53, 12240). The observation that in 4NI neutral radicals and radical anions are formed via DEA at high efficiency already at threshold (0 eV) may have significant implications for the development of nitroimidazole-based radiosensitizers in tumor radiation therapy.

Thermodynamics of formation for the 18-crown-6-triglycine molecular complex in water-dimethylsulfoxide solvents

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Lan, Pham Thi; Sharnin, V. A.

2014-06-01

The effect of a water-dimethylsulfoxide (DMSO) solvent on the formation of a molecular complex of 18-crown-6 (18C6) with triglycine (diglycylglycine, 3Gly) is studied via calorimetric titration. It is found that switching from water to an H2O-DMSO mixture with DMSO mole fraction of 0.30 is accompanied by a monotonic increase in the stability of [3Gly18C6] complex, from log K ∘ = 1.10 to log K ∘ = 2.44, and an increase in the exothermicity of the reaction of its formation, from -5.9 to -16.9 kJ/mol. It is shown that the [3Gly18C6] complex exhibits enthalpy stabilization with negative values of enthalpy and entropy over the investigated range of H2O-DMSO solvents. Analysis of the reagents' solvation characteristics reveals that the increase in the reaction's exothermicity of transfer is due to differences in the solvation of [3Gly18C6] and 18C6 with a small solvation contribution from 3Gly. It is concluded that the change in the Gibbs energy of the reaction 3Glysolv + 18C6solv ↔ [3Gly18C6]solv is due to differences in the change in the solvation state of the complex and the peptide (Δtr G ∘([3Gly18C6])-Δtr G ∘(3Gly)).

Spectroscopic and theoretical studies of charge-transfer interaction of 1-(2-pyridylazo)-2-napthol with nitroaromatics

NASA Astrophysics Data System (ADS)

Karmakar, Animesh; Singh, Bula

2017-05-01

1-(2-Pyridylazo)-2-napthol (hereafter 1Q) is widely used as a chelating ligand applied in chelatometric, spectrophotometric analysis of metal ions. It appeared from the literature survey that no inclusion complex of 1Q was reported with nitroaromatics. The formation of charge-transfer complex gives an opportunity to improve the physico-chemical properties of different donors. So the complex of 1Q with 4-nitrophenol (4-NP), 2,4-dinitrophenol (2,4-DNP), picric acid (PA), and 3,5-dinitrosalicylic acid (3,5-DNSA) was described in this work in methanol medium. The ground and excited state binding constants and other spectroscopic data have been determined using UV-vis and fluorescence spectroscopic studies. All the complexes have been synthesized and characterized using FT-IR, 1H NMR, and elemental analysis. Spectroscopic data reveal that 1Q joins by a N+sbnd Hsbnd O- type hydrogen bond with nitroaromatics. Job's plot of the continuous variation of absorbance indicates that stoichiometry of CT-complex was 1:1. Thermal stability of the synthesized complex has determined by TGA-DTA analysis. Energy-minimization DFT calculation further supported the formation of the H-bonded charge-transfer adduct.

Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

PubMed

Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

2018-01-25

Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

Femtosecond-picosecond laser photolysis studies on the dynamics of excited charge-transfer complexes: Aromatic hydrocarbon-acid anhydride, -tetracyanoethylene, and -tetracyanoquinodimethane systems in acetonitrile solutions

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

Asahi, Tsuyoshi; Mataga, Noboru

1991-03-07

Formation processes of contact ion pairs (CIP) from the excited Franck-Condon (FC) state of charge-transfer (CT) complexes of aromatic hydrocarbons with acid anhydride as well as cyano compound acceptors in acetonitrile solution and charge recombination (CR) rates (k{sub CR}{sup CIP}) of produced CIP states have been investigated by femtosecond and picosecond laser phototlysis and time-resolved absorption spectral measurements covering a wide range of free energy gap-{Delta}G{degree}{sub ip} between the ion pair and the ground state. It has been confirmed that the CIP formation becomes faster and k{sub CR}{sup CIP} of the produced CIP increases with increase of the strengths ofmore » the electron donor (D) and acceptor (A) in the complex, i.e., with decrease of the {minus}{Delta}G{degree}{sub ip} value. This peculiar energy gap dependence of k{sub CR}{sup CIP}, quite different from the bell-shaped one observed in the case of the solvent-separated ion pairs (SSIP) or loose ion pairs (LIP) formed by encounter between fluorescer and quencher in the fluoresence quenching reaction, has been interpreted by assuming the change of electronic and geometrical structures of CIP depending on the strengths of D and A.« less

Formation of plasmon pulses in the cooperative decay of excitons of quantum dots near a metal surface

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

Shesterikov, A. B.; Gubin, M. Yu.; Gladush, M. G.

The formation of pulses of surface electromagnetic waves at a metal–dielectric boundary is considered in the process of cooperative decay of excitons of quantum dots distributed near a metal surface in a dielectric layer. It is shown that the efficiency of exciton energy transfer to excited plasmons can, in principle, be increased by selecting the dielectric material with specified values of the complex permittivity. It is found that in the mean field approximation, the semiclassical model of formation of plasmon pulses in the system under study is reduced to the pendulum equation with the additional term of nonlinear losses.

Native and hydrogen-containing point defects in Mg3N2 : A density functional theory study

NASA Astrophysics Data System (ADS)

Lange, Björn; Freysoldt, Christoph; Neugebauer, Jörg

2010-06-01

The formation energy and solubility of hydrogen in magnesium nitride bulk (antibixbyite Mg3N2 ) have been studied employing density functional theory in the generalized gradient approximation. The effect of doping and the presence of native defects and complex formation have been taken into account. Our results show that magnesium nitride is a nearly defect-free insulator with insignificant hydrogen-storage capacity. Based on this insight we derive a model that highlights the role of the formation and presence of the parasitic Mg3N2 inclusions in the activation of p -doped GaN in optoelectronic devices.

Ion energy/momentum effects during ion assisted growth of niobium nitride films

NASA Astrophysics Data System (ADS)

Klingenberg, Melissa L.

The research described herein was performed to better understand and discern ion energy vs. ion momentum effects during ion beam assisted (IBAD) film growth and their effects on residual stress, crystalline structure, morphology, and composition, which influence film tribological properties. NbxN y was chosen for this research because it is a refractory material that can possess a large number of crystalline structures, and it has been found to have good tribological properties. To separate the effects of momentum transfer per arriving atom (p/a), which considers bombarding species mass, energy, and ion-to-atom transport ratio, from those of energy deposition per arriving atom (E/a), a mass independent parameter, different inert ion beams (krypton, argon, and neon) were used to create a matrix of coatings formed using similar energy deposition, but different momentum transfer and vice versa. Deposition was conducted in a research-scale IBAD system using electron beam evaporation, a radio frequency ion source, and a neutral nitrogen gas backfill. Films were characterized using x-ray diffraction, atomic force microscopy, Rutherford backscattering spectrometry, and residual stress analysis. Direct and quantifiable effects of bombardment were observed; however, energy deposition and momentum transfer effects could not be completely separated, confirming that thin film processes are complex. Complexities arose from ion-specific interactions (ion size, recoil energy, per cent reflected neutrals, Penning ionization, etc.) and chemistry effects that are not considered by the simple models. Overall, it can be stated that bombardment promoted nitride formation, nanocrystallinity, and compressive stress formation; influenced morphology (which influenced post-deposition oxygen uptake) and stress evolution; increased lattice parameter; modified crystalline phase and texture; and led to inert gas incorporation. High stress levels correlated strongly with material disorder and closed-structured morphologies.

Collapse of charged scalar field in dilaton gravity

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

Borkowska, Anna; Rogatko, Marek; Moderski, Rafal

2011-04-15

We elaborated the gravitational collapse of a self-gravitating complex charged scalar field in the context of the low-energy limit of the string theory, the so-called dilaton gravity. We begin with the regular spacetime and follow the evolution through the formation of an apparent horizon and the final central singularity.

Adhesion and formation of microbial biofilms in complex microfluidic devices

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

Kumar, Aloke; Karig, David K; Neethirajan, Suresh

2012-01-01

Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles inmore » the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.« less

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

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

Shin, H.-C.; Ahn, S. J.; Kim, H. W.

2016-08-22

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalatedmore » at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.« less

Hole Polaron Diffusion in the Final Discharge Product of Lithium–Sulfur Batteries

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

Liu, Zhixiao; Balbuena, Perla B.; Mukherjee, Partha P.

Poor electronic conductivity of bulk lithium sulfide (Li 2S) is a critical challenge for the debilitating performance of the lithium–sulfur battery. In this study we focus on investigating the thermodynamic and kinetic properties of native defects in Li 2S based on a first-principles approach. It is found that the hole polaron p + can form in Li 2S by removing a 3p electron from an S 2– anion. The p + diffusion barrier is only 90 meV, which is much lower than the Li vacancy (V Li –) diffusion barrier. Hence p + has the potential to serve as amore » charge carrier in the discharge product. Once the vacancy–polaron complex (V Li -––2p +) forms, the charge transport will be hindered due to the relatively higher diffusion barrier of the complex. Heteroatom dopants, which can decrease the p + formation energy and increase V Li – formation energy, are expected to be introduced to the discharge product to improve the electronic conductivity.« less

Hole Polaron Diffusion in the Final Discharge Product of Lithium–Sulfur Batteries

DOE PAGES

Liu, Zhixiao; Balbuena, Perla B.; Mukherjee, Partha P.

2017-07-24

Poor electronic conductivity of bulk lithium sulfide (Li 2S) is a critical challenge for the debilitating performance of the lithium–sulfur battery. In this study we focus on investigating the thermodynamic and kinetic properties of native defects in Li 2S based on a first-principles approach. It is found that the hole polaron p + can form in Li 2S by removing a 3p electron from an S 2– anion. The p + diffusion barrier is only 90 meV, which is much lower than the Li vacancy (V Li –) diffusion barrier. Hence p + has the potential to serve as amore » charge carrier in the discharge product. Once the vacancy–polaron complex (V Li -––2p +) forms, the charge transport will be hindered due to the relatively higher diffusion barrier of the complex. Heteroatom dopants, which can decrease the p + formation energy and increase V Li – formation energy, are expected to be introduced to the discharge product to improve the electronic conductivity.« less

Electric-Field Control of Oxygen Vacancies and Magnetic Phase Transition in a Cobaltite/Manganite Bilayer

NASA Astrophysics Data System (ADS)

Cui, B.; Song, C.; Li, F.; Zhong, X. Y.; Wang, Z. C.; Werner, P.; Gu, Y. D.; Wu, H. Q.; Saleem, M. S.; Parkin, S. S. P.; Pan, F.

2017-10-01

Manipulation of oxygen vacancies (VO ) in single oxide layers by varying the electric field can result in significant modulation of the ground state. However, in many oxide multilayers with strong application potentials, e.g., ferroelectric tunnel junctions and solid-oxide fuel cells, understanding VO behavior in various layers under an applied electric field remains a challenge, owing to complex VO transport between different layers. By sweeping the external voltage, a reversible manipulation of VO and a corresponding fixed magnetic phase transition sequence in cobaltite/manganite (SrCoO3 -x/La0.45Sr0.55MnO3 -y ) heterostructures are reported. The magnetic phase transition sequence confirms that the priority of electric-field-induced VO formation or annihilation in the complex bilayer system is mainly determined by the VO formation energies and Gibbs free-energy differences, which is supported by theoretical analysis. We not only realize a reversible manipulation of the magnetic phase transition in an oxide bilayer but also provide insight into the electric-field control of VO engineering in heterostructures.

Energy Capture and Use in Plants and Bacteria. Final Technical Report

DOE R&D Accomplishments Database

Boyer, P. D.

1993-12-31

The project has centered on elucidation of the mechanism of ATP synthase. The metabolic importance of ATP and the complexity of the ATP synthase have made the problem particularly important and challenging. The development of the binding change mechanism depended upon our recognition of features that were novel in bioenergetics and indeed to the field of enzymology. One important feature of mechanism is that the principal way that energy input from transmembrane proton movement is coupled to ATP formation is to drive conformational changes that cause the release of ATP readily formed and tightly bound at a catalytic site. Another is that three equivalent catalytic sites on the enzyme show strong catalytic cooperativity as they proceed sequentially through different conformations. A more speculative features is that this cooperativity and energy coupling involve a rotational movement of minor subunits relative to the catalytic subunits. During this period these studies have extended and clarified aspects of the synthase mechanism. During assessments of interactions of Mg{sup 2+} and ADP with the synthase we recognized unexpectedly that whether ADP and P{sub i}, or their complexes with Mg{sup 2+} served as substrates for ATP formation by photophosphorylation was not known. Our studies showed that MgADP and free P{sub i} act as substrates.

Gallium diffusion in zinc oxide via the paired dopant-vacancy mechanism

NASA Astrophysics Data System (ADS)

Sky, T. N.; Johansen, K. M.; Riise, H. N.; Svensson, B. G.; Vines, L.

2018-02-01

Isochronal and isothermal diffusion experiments of gallium (Ga) in zinc oxide (ZnO) have been performed in the temperature range of 900-1050 °C. The samples used consisted of a sputter-deposited and highly Ga-doped ZnO film at the surface of a single-crystal bulk material. We use a novel reaction diffusion (RD) approach to demonstrate that the diffusion behavior of Ga in ZnO is consistent with zinc vacancy (VZn) mediation via the formation and dissociation of GaZnVZn complexes. In the RD modeling, experimental diffusion data are fitted utilizing recent density-functional-theory estimates of the VZn formation energy and the binding energy of GaZnVZn. From the RD modeling, a migration energy of 2.3 eV is deduced for GaZnVZn, and a total/effective activation energy of 3.0 eV is obtained for the Ga diffusion. Furthermore, and for comparison, employing the so-called Fair model, a total/effective activation energy of 2.7 eV is obtained for the Ga diffusion, reasonably close to the total value extracted from the RD-modeling.

Homogenous Nucleation and Crystal Growth in a Model Liquid from Direct Energy Landscape Sampling Simulation

NASA Astrophysics Data System (ADS)

Walter, Nathan; Zhang, Yang

Nucleation and crystal growth are understood to be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of molecular dynamics' temporal constraints. Herein, we circumvent this temporal limitation by using a brutal-force, metadynamics-like, adaptive basin-climbing algorithm and directly sample the free-energy landscape of a model liquid Argon. The algorithm biases the system to evolve from an amorphous liquid like structure towards an FCC crystal through inherent structure, and then traces back the energy barriers. Consequently, the sampled timescale is macroscopically long. We observe that the formation of a crystal involves two processes, each with a unique temperature-dependent energy barrier. One barrier corresponds to the crystal nucleus formation; the other barrier corresponds to the crystal growth. We find the two processes dominate in different temperature regimes. Compared to other computation techniques, our method requires no assumptions about the shape or chemical potential of the critical crystal nucleus. The success of this method is encouraging for studying the crystallization of more complex

The effect of substituted moiety on the optoelectronic and photophysical properties of tris (phenylbenzimidazolinato) Ir (III) carbene complexes and the OLED performance: a theoretical study

NASA Astrophysics Data System (ADS)

Srivastava, Ruby

2015-06-01

Density functional theory (DFT) and time-dependent density functional theory (TDDFT) are used to analyse theoretically the optoelectronic, photophysical properties and organic light-emitting diode performance of a series of fac-mer blue-emitting Iridium (III) carbene complexes. Swain-Lupton constant is used to discuss the substituents effect. 5d-orbital splitting and d-d* transitions are calculated to assess the efficiency of the studied complexes. The reorganisation energies (λ), transfer integrals, mobilities, radiative decay rate (kr), and triplet exciton generation fraction (χT) are also calculated. Due to the higher χT of these complexes, the formation of triplet exciton will be more and it will cause a faster intersystem crossing. Two host materials are proposed and host-guest match (Dexter-Förster energy) is also discussed. We hope that this unified work will surely help to design new blue-emitting phosphorescent materials in future.

Complexes of carboxyl-containing polymer and monosubstituted bipyridinium salts

NASA Astrophysics Data System (ADS)

Merekalova, N. D.; Bondarenko, G. N.; Krylsky, D. W.; Zakirov, M. I.; Talroze, R. V.

2013-09-01

Semi-empirical PM3 method for the quantum calculations of molecular electronic structure based on NDDO integral approximation is used to investigate the complex formation of monosubstituted 4,4‧-bipyridinium salts BpyR (Hal) containing a halide anion interacting with the quaternary nitrogen atom and carboxylic group of the two-units construct. Significant effect of the BpyR (Hal) electronic structure is unveiled that contributes in two different structures of these salts, namely, partial charge transfer complex and ion pair structure, both having stable energy minima. We demonstrate that (i) the structure of the N-substituent modulates the energy and electronic characteristics of monosubstituted salts BpyR with chlorine and bromine anions and (ii) the coulomb interactions between quaternary N-atom, halogen anion, and the proton of carboxylic group stimulate the transformation of the charge transfer complex into the ion pair structure. Results of calculations are compared with the experimental FTIR spectra of blends of BpyR(Hal) with Eudragit copolymer.

A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.

PubMed

Winkler, Andreas; Heintz, Udo; Lindner, Robert; Reinstein, Jochen; Shoeman, Robert L; Schlichting, Ilme

2013-07-01

The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy sources, depending on environmental conditions including aerobic respiration or, in the absence of oxygen, photosynthesis. Photosynthetic genes are repressed at high oxygen tension, but at intermediate levels their partial expression prepares the bacterium for using light energy. Illumination, however, enhances repression under semiaerobic conditions. Here, we describe molecular details of two proteins mediating oxygen and light control of photosynthesis-gene expression: the light-sensing antirepressor AppA and the transcriptional repressor PpsR. Our crystal structures of both proteins and their complex and hydrogen/deuterium-exchange data show that light activation of AppA-PpsR2 affects the PpsR effector region within the complex. DNA binding studies demonstrate the formation of a light-sensitive ternary AppA-PpsR-DNA complex. We discuss implications of these results for regulation by light and oxygen, highlighting new insights into blue light-mediated signal transduction.

IR, 1H NMR, mass, XRD and TGA/DTA investigations on the ciprofloxacin/iodine charge-transfer complex.

PubMed

Refat, Moamen S; El-Hawary, W F; Moussa, Mohamed A A

2011-05-01

The charge-transfer complex (CTC) of ciprofloxacin drug (CIP) as a donor with iodine (I(2)) as a sigma acceptor has been studied spectrophotometrically in CHCl(3). At maximum absorption bands, the stoichiometry of CIP:iodine system was found to be 1:1 ratio according to molar ratio method. The essential spectroscopic data like formation constant (K(CT)), molar extinction coefficient (ɛ(CT)), standard free energy (ΔG°), oscillator strength (f), transition dipole moment (μ), resonance energy (R(N)) and ionization potential (I(D)) were estimated. The spectroscopic techniques such as IR, (1)H NMR, mass and UV-vis spectra and elemental analyses (CHN) as well as TG-DTG and DTA investigations were used to characterize the chelating behavior of CIP/iodine charge-transfer complex. The iodine CT interaction was associated with a presence of intermolecular hydrogen bond. The X-ray investigation was carried out to investigate the iodine doping in the synthetic CT complex. Copyright © 2011 Elsevier B.V. All rights reserved.

The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.

PubMed

Zhuang, Zhihao; Yoder, Bonita L; Burgers, Peter M J; Benkovic, Stephen J

2006-02-21

Numerous proteins that function in DNA metabolic pathways are known to interact with the proliferating cell nuclear antigen (PCNA). The important function of PCNA in stimulating various cellular activities requires its topological linkage with DNA. Loading of the circular PCNA onto duplex DNA requires the activity of a clamp-loader [replication factor C (RFC)] complex and the energy derived from ATP hydrolysis. The mechanistic and structural details regarding PCNA loading by the RFC complex are still developing. In particular, the positive identification of a long-hypothesized structure of an open clamp-RFC complex as an intermediate in loading has remained elusive. In this study, we capture an open yeast PCNA clamp in a complex with RFC through fluorescence energy transfer experiments. We also follow the topological transitions of PCNA in the various steps of the clamp-loading pathway through both steady-state and stopped-flow fluorescence studies. We find that ATP effectively drives the clamp-loading process to completion with the formation of the closed PCNA bound to DNA, whereas ATPgammaS cannot. The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm.

The role of the VZn-NO-H complex in the p-type conductivity in ZnO.

PubMed

Amini, M N; Saniz, R; Lamoen, D; Partoens, B

2015-02-21

Past research efforts aiming at obtaining stable p-type ZnO have been based on complexes involving nitrogen doping. A recent experiment by (J. G. Reynolds et al., Appl. Phys. Lett., 2013, 102, 152114) demonstrated a significant (∼10(18) cm(-3)) p-type behavior in N-doped ZnO films after appropriate annealing. The p-type conductivity was attributed to a VZn-NO-H shallow acceptor complex, formed by a Zn vacancy (VZn), N substituting O (NO), and H interstitial (Hi). We present here a first-principles hybrid functional study of this complex compared to the one without hydrogen. Our results confirm that the VZn-NO-H complex acts as an acceptor in ZnO. We find that H plays an important role, because it lowers the formation energy of the complex with respect to VZn-NO, a complex known to exhibit (unstable) p-type behavior. However, this additional H atom also occupies the hole level at the origin of the shallow behavior of VZn-NO, leaving only two states empty higher in the band gap and making the VZn-NO-H complex a deep acceptor. Therefore, we conclude that the cause of the observed p-type conductivity in experiment is not the presence of the VZn-NO-H complex, but probably the formation of the VZn-NO complex during the annealing process.

Principles, efficiency, and blueprint character of solar-energy conversion in photosynthetic water oxidation.

PubMed

Dau, Holger; Zaharieva, Ivelina

2009-12-21

Photosynthesis in plants and cyanobacteria involves two protein-cofactor complexes which are denoted as photosystems (PS), PSII and PSI. These solar-energy converters have powered life on earth for approximately 3 billion years. They facilitate light-driven carbohydrate formation from H(2)O and CO(2), by oxidizing the former and reducing the latter. PSII splits water in a process driven by light. Because all attractive technologies for fuel production driven by solar energy involve water oxidation, recent interest in this process carried out by PSII has increased. In this Account, we describe and apply a rationale for estimating the solar-energy conversion efficiency (eta(SOLAR)) of PSII: the fraction of the incident solar energy absorbed by the antenna pigments and eventually stored in form of chemical products. For PSII at high concentrations, approximately 34% of the incident solar energy is used for creation of the photochemistry-driving excited state, P680*, with an excited-state energy of 1.83 eV. Subsequent electron transfer results in the reduction of a bound quinone (Q(A)) and oxidation of the Tyr(Z) within 1 micros. This radical-pair state is stable against recombination losses for approximately 1 ms. At this level, the maximal eta(SOLAR) is 23%. After the essentially irreversible steps of quinone reduction and water oxidation (the final steps catalyzed by the PSII complex), a maximum of 50% of the excited-state energy is stored in chemical form; eta(SOLAR) can be as high as 16%. Extending our considerations to a photosynthetic organism optimized to use PSII and PSI to drive H(2) production, the theoretical maximum of the solar-energy conversion efficiency would be as high as 10.5%, if all electrons and protons derived from water oxidation were used for H(2) formation. The above performance figures are impressive, but they represent theoretical maxima and do not account for processes in an intact organism that lower these yields, such as light saturation, photoinhibitory, protective, and repair processes. The overpotential for catalysis of water oxidation at the Mn(4)Ca complex of PSII may be as low as 0.3 V. To address the specific energetics of water oxidation at the Mn complex of PSII, we propose a new conceptual framework that will facilitate quantitative considerations on the basis of oxidation potentials and pK values. In conclusion, photosynthetic water oxidation works at high efficiency and thus can serve as both an inspiring model and a benchmark in the development of future technologies for production of solar fuels.

Influence of complex configurations on properties of pygmy dipole resonances

NASA Astrophysics Data System (ADS)

Arsenyev, N. N.; Severyukhin, A. P.; Voronov, V. V.; Van Giai, Nguyen

2018-05-01

Starting from the quasiparticle random phase approximation based on the Skyrme interaction SLy5, we study the effects of phonon-phonon coupling (PPC) on the low-energy electric dipole responses in some spherical nuclei. The inclusion of the PPC results in the formation of low-energy 1‑ states. There is an impact of the PPC effect on low-energy E1 strength. The PPC effect on the electric dipole polarizability is discussed. We predict a strong increase of the summed E1 strength below 10 MeV, with increasing neutron number from 48Ca till 58Ca.

Triplet excited state spectra and dynamics of carotenoids from the thermophilic purple photosynthetic bacterium Thermochromatium tepidum

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

Niedzwiedzki, Dariusz; Kobayashi, Masayuki; Blankenship, R. E.

Light-harvesting complex 2 from the anoxygenic phototrophic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption, fluorescence and flash photolysis spectroscopy. Steady-state absorption and fluorescence measurements show that carotenoids play a negligible role as supportive energy donors and transfer excitation to bacteriochlorophyll-a with low energy transfer efficiency of ~30%. HPLC analysis determined that the dominant carotenoids in the complex are rhodopin and spirilloxanthin. Carotenoid excited triplet state formation upon direct (carotenoid) or indirect (bacteriochlorophyll-a Q{sub x} band) excitation shows that carotenoid triplets are mostly localized on spirilloxanthin. In addition, no triplet excitation transfer between carotenoids was observed. Suchmore » specific carotenoid composition and spectroscopic results strongly suggest that this organism optimized carotenoid composition in the light-harvesting complex 2 in order to maximize photoprotective capabilities of carotenoids but subsequently drastically suppressed their supporting role in light-harvesting process.« less

Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

PubMed

Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

2014-02-01

Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

Formation of Clustered DNA Damage after High-LET Irradiation: A Review

NASA Technical Reports Server (NTRS)

Hada, Megumi; Georgakilas, Alexandros G.

2008-01-01

Radiation can cause as well as cure cancer. The risk of developing radiation-induced cancer has traditionally been estimated from cancer incidence among survivors of the atomic bombs in Hiroshima and Nagasaki. These data provide the best estimate of human cancer risk over the dose range for low linear energy transfer (LET) radiations, such as X- or gamma-rays. The situation of estimating the real biological effects becomes even more difficult in the case of high LET particles encountered in space or as the result of domestic exposure to particles from radon gas emitters or other radioactive emitters like uranium-238. Complex DNA damage, i.e., the signature of high-LET radiations comprises by closely spaced DNA lesions forming a cluster of DNA damage. The two basic groups of complex DNA damage are double strand breaks (DSBs) and non-DSB oxidative clustered DNA lesions (OCDL). Theoretical analysis and experimental evidence suggest there is increased complexity and severity of complex DNA damage with increasing LET (linear energy transfer) and a high mutagenic or carcinogenic potential. Data available on the formation of clustered DNA damage (DSBs and OCDL) by high-LET radiations are often controversial suggesting a variable response to dose and type of radiation. The chemical nature and cellular repair mechanisms of complex DNA damage have been much less characterized than those of isolated DNA lesions like an oxidized base or a single strand break especially in the case of high-LET radiation. This review will focus on the induction of clustered DNA damage by high-LET radiations presenting the earlier and recent relative data.

Spectroscopic and thermal investigations on the charge transfer interaction between risperidone as a schizophrenia drug with some traditional π-acceptors: Part 2

NASA Astrophysics Data System (ADS)

El-Habeeb, Abeer A.; Al-Saif, Foziah A.; Refat, Moamen S.

2013-03-01

The focus of present investigation was to assess the utility of non-expensive techniques in the evaluation of risperidone (Ris) in solid and solution states with different traditional π-acceptors and subsequent incorporation of the analytical determination into pharmaceutical formulation for a faster release of risperidone. Charge-transfer complexes (CTC) of risperidone with picric acid (PA), 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ), tetracyanoquinodimethane (TCNQ), tetracyano ethylene (TCNE), tetrabromo-p-quinon (BL) and tetrachloro-p-quinon (CL) have been studied spectrophotometrically in absolute methanol at room temperature. The stoichiometries of the complexes were found to be 1:1 ratio by the photometric molar ratio between risperidone and the π-acceptors. The equilibrium constants, molar extinction coefficient (ɛCT) and spectroscopic-physical parameters (standard free energy (ΔGo), oscillator strength (f), transition dipole moment (μ), resonance energy (RN) and ionization potential (ID)) of the complexes were determined upon the modified Benesi-Hildebrand equation. Risperidone in pure form was applied in this study. The results indicate that the formation constants for the complexes depend on the nature of electron acceptors and donor, and also the spectral studies of the complexes were determined by (infrared, Raman, and 1H NMR) spectra and X-ray powder diffraction (XRD). The most stable mono-protonated form of Ris is characterized by the formation of +Nsbnd H (pyrimidine ring) intramolecular hydrogen bonded. In the high-wavenumber spectral region ˜3400 cm-1, the bands of the +Nsbnd H stretching vibrations and of the pyrimidine nitrogen atom could be potentially useful to discriminate the investigated forms of Ris. The infrared spectra of both Ris complexes are confirming the participation of +Nsbnd H pyrimidine ring in the donor-acceptor interaction.

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

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

Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de

2014-10-07

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry ofmore » the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.« less

Core-Shell Coating Silicon Anode Interfaces with Coordination Complex for Stable Lithium-Ion Batteries.

PubMed

Zhou, Jinqiu; Qian, Tao; Wang, Mengfan; Xu, Na; Zhang, Qi; Li, Qun; Yan, Chenglin

2016-03-02

In situ core-shell coating was used to improve the electrochemical performance of Si-based anodes with polypyrrole-Fe coordination complex. The vast functional groups in the organometallic coordination complex easily formed hydrogen bonds when in situ modifying commercial Si nanoparticles. The incorporation of polypyrrole-Fe resulted in the conformal conductive coating surrounding each Si nanoparticle, not only providing good electrical connection to the particles but also promoting the formation of a stable solid-electrolyte-interface layer on the Si electrode surface, enhancing the cycling properties. As an anode material for Li-ion batteries, modified silicon powders exhibited high reversible capacity (3567 mAh/g at 0.3 A/g), good rate property (549.12 mAh/g at 12 A/g), and excellent cycling performance (reversible capacity of 1500 mAh/g after 800 cycles at 1.2 A/g). The constructed novel concept of core-shell coating Si particles presented a promising route for facile and large-scale production of Si-based anodes for extremely durable Li-ion batteries, which provided a wide range of applications in the field of energy storage of the renewable energy derived from the solar energy, hydropower, tidal energy, and geothermal heat.

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

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

Valba, O. V., E-mail: valbaolga@gmail.com; Nechaev, S. K., E-mail: sergei.nechaev@gmail.com; Tamm, M. V., E-mail: thumm.m@gmail.com

2012-02-15

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energymore » between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.« less

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

PubMed Central

2017-01-01

Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein–protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein–protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol–1 from experimental values. Statistical error estimates were in the order of thermal noise. We conclude that the presented method has promising potential for broad applicability to quantitatively describe protein–protein and various other kinds of complex formation. PMID:28898077

Primary damage formation in bcc iron

NASA Astrophysics Data System (ADS)

Stoller, R. E.; Odette, G. R.; Wirth, B. D.

1997-11-01

Primary defect formation in bee iron has been extensively investigated using the methods of molecular dynamics (MD) and Monte Carlo (MC) simulation. This research has employed a modified version of the Finnis-Sinclair interatomic potential. MD was used in the simulation of displacement cascades with energies up to 40 keV and to examine the migration of the interstitial clusters that were observed to form in the cascade simulations. Interstitial cluster binding energies and the stable cluster configurations were determined by structural relaxation and energy minimization using a MC method with simulated annealing. Clusters containing up to 19 interstitials were examined. Taken together with the previous work, these new simulations provide a reasonably complete description of primary defect formation in iron. The results of the displacement cascade simulations have been used to characterize the energy and temperature dependence of primary defect formation in terms of two parameters: (1) the number of surviving point defects and (2) the fraction of the surviving defects that are contained in clusters. The number of surviving point defects is expressed as a fraction of the atomic displacements calculated using the secondary displacement model of Norgett-Robinson-Torrens (NRT). Although the results of the high energy simulations are generally consistent with those obtained at lower energies, two notable exceptions were observed. The first is that extensive subcascade formation at 40 keV leads to a higher defect survival fraction than would be predicted from extrapolation of the results obtained for energies up to 20 keV. The stable defect fraction obtained from the MD simulations is a smoothly decreasing function up to 20 keV. Subcascade formation leads to a slight increase in this ratio at 40 keV, where the value is about the same as at 10 keV. Secondly, the potential for a significant level of in-cascade vacancy clustering was observed. Previous cascade studies employing this potential have reported extensive interstitial clustering, but little evidence of vacancy clustering. Interstitial clusters were found to be strongly bound, with binding energies in excess of 1 eV. The larger clusters exhibited a complex, 3D structure and were composed of <111> crowdions. These clusters were observed to migrate by collective <111> translations with an activation energy on the order of 0.1 eV.

Nanoplasma Formation by High Intensity Hard X-rays

PubMed Central

Tachibana, T.; Jurek, Z.; Fukuzawa, H.; Motomura, K.; Nagaya, K.; Wada, S.; Johnsson, P.; Siano, M.; Mondal, S.; Ito, Y.; Kimura, M.; Sakai, T.; Matsunami, K.; Hayashita, H.; Kajikawa, J.; Liu, X.-J.; Robert, E.; Miron, C.; Feifel, R.; Marangos, J. P.; Tono, K.; Inubushi, Y.; Yabashi, M.; Son, S.-K.; Ziaja, B.; Yao, M.; Santra, R.; Ueda, K.

2015-01-01

Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo- and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays. PMID:26077863

A fluorescent chemosensor for Zn(II). Exciplex formation in solution and the solid state.

PubMed

Bencini, Andrea; Berni, Emanuela; Bianchi, Antonio; Fornasari, Patrizia; Giorgi, Claudia; Lima, Joao C; Lodeiro, Carlos; Melo, Maria J; de Melo, J Seixas; Parola, Antonio Jorge; Pina, Fernando; Pina, Joao; Valtancoli, Barbara

2004-07-21

The macrocyclic phenanthrolinophane 2,9-[2,5,8-triaza-5-(N-anthracene-9-methylamino)ethyl]-[9]-1,10-phenanthrolinophane (L) bearing a pendant arm containing a coordinating amine and an anthracene group forms stable complexes with Zn(II), Cd(II) and Hg(II) in solution. Stability constants of these complexes were determined in 0.10 mol dm(-3) NMe(4)Cl H(2)O-MeCN (1:1, v/v) solution at 298.1 +/- 0.1 K by means of potentiometric (pH metric) titration. The fluorescence emission properties of these complexes were studied in this solvent. For the Zn(II) complex, steady-state and time-resolved fluorescence studies were performed in ethanol solution and in the solid state. In solution, intramolecular pi-stacking interaction between phenanthroline and anthracene in the ground state and exciplex emission in the excited state were observed. From the temperature dependence of the photostationary ratio (I(Exc)/I(M)), the activation energy for the exciplex formation (E(a)) and the binding energy of the exciplex (-DeltaH) were determined. The crystal structure of the [ZnLBr](ClO(4)).H(2)O compound was resolved, showing that in the solid state both intra- and inter-molecular pi-stacking interactions are present. Such interactions were also evidenced by UV-vis absorption and emission spectra in the solid state. The absorption spectrum of a thin film of the solid complex is red-shifted compared with the solution spectra, whereas its emission spectrum reveals the unique featureless exciplex band, blue shifted compared with the solution. In conjunction with X-ray data the solid-state data was interpreted as being due to a new exciplex where no pi-stacking (full overlap of the pi-electron cloud of the two chromophores - anthracene and phenanthroline) is observed. L is a fluorescent chemosensor able to signal Zn(II) in presence of Cd(II) and Hg(II), since the last two metal ions do not give rise either to the formation of pi-stacking complexes or to exciplex emission in solution.

Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.

PubMed

Stafford, Amy J; Ensign, Daniel L; Webb, Lauren J

2010-11-25

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

Single Molecule Measurements of Interaction Free Energies Between the Proteins Within Binary and Ternary SNARE Complexes

PubMed Central

Liu, W.; Montana, Vedrana; Parpura, Vladimir; Mohideen, U.

2010-01-01

We use an Atomic Force Microscope based single molecule measurements to evaluate the activation free energy in the interaction of SNARE proteins syntaxin 1A, SNAP25B and synaptobrevin 2 which regulate intracellular fusion of vesicles with target membranes. The dissociation rate of the binary syntaxin-synaptobrevin and the ternary syntaxin-SNAP25B-synaptobrevin complex was measured from the rupture force distribution as a function of the rate of applied force. The temperature dependence of the spontaneous dissociation rate was used to obtain the activation energy to the transition state of 19.8 ± 3.5 kcal/mol = 33 ± 6 kBT and 25.7 ± 3.0 kcal/mol = 43 ± 5 kBT for the binary and ternary complex, respectively. They are consistent with those measured previously for the ternary complex in lipid membranes and are of order expected for bilayer fusion and pore formation. The ΔG was 12.4–16.6 kcal/mol = 21–28 kBT and 13.8–18.0 kcal/mol = 23–30 kBT for the binary and ternary complex, respectively. The ternary complex was more stable by 1.4 kcal/mol = 2.3 kBT, consistent with the spontaneous dissociation rates. The higher adhesion energies and smaller molecular extensions measured with SNAP25B point to its possible unique and important physiological role in tethering/docking the vesicle in closer proximity to the plasma membrane and increasing the probability for fusion completion. PMID:20107522

Thermodynamics and kinetics of Na+/K+-formate ion pairs association in polarizable water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Nguyen, Phuong T. M.; Nguyen, Van T.; Annapureddy, Harsha V. R.; Dang, Liem X.; Do, D. D.

2012-12-01

To enhance our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on the interactions between two alkali cations (Na+ and K+) with a formate anion in water. A very complex free energy landscape was observed, much more so than alkali-halide ion pairs. Furthermore, a stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, which is in agreement with experimental and theoretical studies [1-4]. The kinetics of ion-pair inter-conversions was studied using the transition rate theory, along with a number of theoretical approaches such as the Kramers and Grote-Hynes theories. These kinetic results were used to predict solvent effects on dynamical features of ion-pair association, in which we have found that the dynamics of K+-formate pairs is faster than Na+-formate pairs.

Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

PubMed

Georgieva, I; Mihaylov, Tz; Trendafilova, N

2014-06-01

The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Selective CO{sub 2} reduction conjugated with H{sub 2}O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

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

Morikawa, T., E-mail: morikawa@mosk.tytlabs.co.jp; Sato, S., E-mail: morikawa@mosk.tytlabs.co.jp; Arai, T., E-mail: morikawa@mosk.tytlabs.co.jp

2013-12-10

We developed a new hybrid photocatalyst for CO{sub 2} reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (E{sub CBM}) of the semiconductor and the CO{sub 2} reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO{sub 2} to formate using water as an electron donor andmore » a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO{sub 2} reduction with a TiO{sub 2} photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.« less

Morphology-Induced Collective Behaviors: Dynamic Pattern Formation in Water-Floating Elements

PubMed Central

Nakajima, Kohei; Ngouabeu, Aubery Marchel Tientcheu; Miyashita, Shuhei; Göldi, Maurice; Füchslin, Rudolf Marcel; Pfeifer, Rolf

2012-01-01

Complex systems involving many interacting elements often organize into patterns. Two types of pattern formation can be distinguished, static and dynamic. Static pattern formation means that the resulting structure constitutes a thermodynamic equilibrium whose pattern formation can be understood in terms of the minimization of free energy, while dynamic pattern formation indicates that the system is permanently dissipating energy and not in equilibrium. In this paper, we report experimental results showing that the morphology of elements plays a significant role in dynamic pattern formation. We prepared three different shapes of elements (circles, squares, and triangles) floating in a water-filled container, in which each of the shapes has two types: active elements that were capable of self-agitation with vibration motors, and passive elements that were mere floating tiles. The system was purely decentralized: that is, elements interacted locally, and subsequently elicited global patterns in a process called self-organized segregation. We showed that, according to the morphology of the selected elements, a different type of segregation occurs. Also, we quantitatively characterized both the local interaction regime and the resulting global behavior for each type of segregation by means of information theoretic quantities, and showed the difference for each case in detail, while offering speculation on the mechanism causing this phenomenon. PMID:22715370

Organic photochemical storage of solar energy. Progress report, February 1, 1979-January 31, 1980

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

Jones, G. II

1980-02-01

Study of valence isomerization of organic compounds has focused on two mechanisms of photosensitization involving either electron donor-acceptor interaction or energy transfer. The quenching of fluorescent sensitizers by isomerizable substrates results in the formation of excited complexes. These sensitizer-substrate pairs are highly polarized, leading to changes in bond order for the substrates. For several substrates such as quadricyclene, hexamethyldewarbenzene, and a nonbornadiene derivative, this perturbation results in efficient valence isomerization. Isomerization observed on irradiation of charge transfer complexes of isomerizable substrates is consistent with a similar exciplex - template mechanism. The energy transfer mechanism of photosensitization has been studied bymore » measuring the temperature dependence of quantum yield for isomerization of dimethyl norbornadiene-2,3-dicarboxylate sensitized by benzanthrone. From temperature and quencher concentration profiles quenching constants have been obtained which are consistent with an endoergic triplet energy transfer mechanism. The thermal upconversion of the low energy triplet of benzanthrone results in a threefold increase in isomerization quantum yield over a 90/sup 0/ temperature range.« less

Thermodynamics of surface defects at the aspirin/water interface

NASA Astrophysics Data System (ADS)

Schneider, Julian; Zheng, Chen; Reuter, Karsten

2014-09-01

We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics simulations. To this end, we adopt and modify existing approaches to calculate binding free energies of biological ligand/receptor complexes to be applicable to common surface defects, such as step edges and kink sites. We obtain statistically accurate and reliable free energy values for the aspirin/water interface, which can be applied to estimate the distribution of defects using well-established thermodynamic relations. As a show case we calculate the free energy upon dissolving molecules from kink sites at the interface. This free energy can be related to the solubility concentration and we obtain solubility values in excellent agreement with experimental results.

Solubility profiles, hydration and desolvation of curcumin complexed with γ-cyclodextrin and hydroxypropyl-γ-cyclodextrin

NASA Astrophysics Data System (ADS)

Shityakov, Sergey; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Roewer, Norbert; Förster, Carola; Broscheit, Jens

2017-04-01

In this study, we investigated curcumin (CUR) solubility profiles and hydration/desolvation effects of this substance formulated with γ-cyclodextrin (γ-CD) and hydroxypropyl-γ-cyclodextrin (HP-γ-CD) excipients. The CUR/HP-γ-CD complex was found to be more stable in solution with the highest apparent stability constant for CUR/HP-γ-CD (Kc = 1.58*104 M-1) as the more soluble form in distilled water. The in silico calculations, including molecular docking, Monte Carlo (MC), and molecular dynamics (MD) simulations, indicated that water molecules play an important role in host-guest complexation mediating the CUR binding to cyclodextrins via hydrogen bond formations. The CUR hydration/desolvation effects contributed to the complex formation by elevating the CUR binding affinity to both CDs. The CUR/HP-γ-CD complex after the CUR hydration was determined with a minimal Gibbs free energy of binding (ΔGbind = -9.93 kcal*mol-1) due to the major hydrophobic (vdW) forces. Overall, the results of this study can aid a development of cyclodextrin-based drug delivery vectors, signifying the importance of water molecules during the formulation processes.

Analysis of XeC1 Emission in a Hollow Cathode Discharge.

DTIC Science & Technology

1981-06-01

excited homopolar molecule, e.g., Xe2 , Hg2 The term exciplex refers to an electronically excited heteropolar complex, e.g., KrF , XeOH , XeCl , which...HCI Products, k9 = 5.4 x 10 cm /sec. (25) Figure 9 summarizes the main energy pathways for XeCI exciplex formation via three body recombination and

Investigation of the host-guest complexation between 4-sulfocalix[4]arene and nedaplatin for potential use in drug delivery

NASA Astrophysics Data System (ADS)

Fahmy, Sherif Ashraf; Ponte, Fortuna; Abd El-Rahman, Mohamed K.; Russo, Nino; Sicilia, Emilia; Shoeib, Tamer

2018-03-01

Macromolecules including macrocyclic species have been reported to have the potential to encapsulate biologically active compounds such as drugs through host-guest complexation to increase their solubility, stability and bioavailability. In this paper the first experimental and theoretical investigation of the complexation between nedaplatin, a second generation antineoplastic drug, and p-4-sulfocalix[4]arene, a macromolecule possessing a bipolar amphiphilic structure with good biocompatibility and relatively low haemolytic toxicity for potential use as a drug delivery system is presented. Data from 1H NMR, UV, Job's plot analysis, HPLC and DFT calculations are detailed and suggest the formation of a 1:1 complex. The stability constant of the complex was experimentally estimated to be 3.6 × 104 M- 1 and 2.1 × 104 M- 1 which correspond to values of - 6.2 and - 5.9 kcal mol- 1, respectively for the free energy of complexation while the interaction free energy is calculated to be - 4.9 kcal mol- 1. The formed species is shown to be stabilised in solution through hydrogen bonding between the host and the guest which may allow for this strategy to be effective for potential use in drug delivery.

Sequential energy and charge transfer processes in mixed host-guest complexes of subphthalocyanine, porphyrin and phthalocyanine chromophores.

PubMed

Menting, Roel; Ng, Dennis K P; Röder, Beate; Ermilov, Eugeny A

2012-11-14

Porphyrins, phthalocyanines and subphthalocyanines are three attractive classes of chromophores with intriguing properties making them suitable for the design of artificial photosynthetic systems. The assembly of these components by a supramolecular approach is of particular interest as it provides a facile means to build multi-chromophoric arrays with various architectures and tuneable photophysical properties. In this paper, we show the formation of mixed host-guest supramolecular complexes that consist of a β-cyclodextrin-conjugated subphthalocyanine, a tetrasulfonated porphyrin and a series of silicon(IV) phthalocyanines substituted axially with two β-cyclodextrins via different spacers. We found that the three components form supramolecular complexes held by host-guest interactions in aqueous solution. Upon excitation of the subphthalocyanine part of the complex, the excitation energy is delivered to the phthalocyanine unit via excitation energy transfer and the porphyrin chromophore acts as an energy transfer bridge enabling this process. It was shown that photo-induced charge transfer also takes place. A sequential electron transfer process from the porphyrin unit to the phthalocyanine moiety and subsequently from the subphthalocyanine moiety to the porphyrin unit takes place, and the probability of this process is controlled by the linker between β-cyclodextrin and phthalocyanine. The lifetime of the charge-separated state was found to be 1.7 ns by transient absorption spectroscopy.

Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

PubMed

Gu, Quanli; Knee, J L

2012-09-14

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

Optimizing energy functions for protein-protein interface design.

PubMed

Sharabi, Oz; Yanover, Chen; Dekel, Ayelet; Shifman, Julia M

2011-01-15

Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.

How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1

PubMed Central

2017-01-01

Abstract Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein–DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation. PMID:28633355

Studying the dynamics of SLP-76, Nck, and Vav1 multimolecular complex formation in live human cells with triple-color FRET.

PubMed

Pauker, Maor H; Hassan, Nirit; Noy, Elad; Reicher, Barak; Barda-Saad, Mira

2012-04-24

Protein-protein interactions regulate and control many cellular functions. A multimolecular complex consisting of the adaptor proteins SLP-76 (Src homology 2 domain-containing leukocyte protein of 76 kD), Nck, and the guanine nucleotide exchange factor Vav1 is recruited to the T cell side of the interface with an antigen-presenting cell during initial T cell activation. This complex is crucial for regulation of the actin machinery, antigen recognition, and signaling in T cells. We studied the interactions between these proteins as well as the dynamics of their recruitment into a complex that governs cytoskeletal reorganization. We developed a triple-color Förster resonance energy transfer (3FRET) system to observe the dynamics of the formation of this trimolecular signaling complex in live human T cells and to follow the three molecular interactions in parallel. Using the 3FRET system, we demonstrated that dimers of Nck and Vav1 were constitutively formed independently of both T cell activation and the association between SLP-76 and Nck. After T cell receptor stimulation, SLP-76 was phosphorylated, which enabled the binding of Nck. A point mutation in the proline-rich site of Vav1, which abolishes its binding to Nck, impaired actin rearrangement, suggesting that Nck-Vav1 dimers play a critical role in regulation of the actin machinery. We suggest that these findings revise the accepted model of the formation of a complex of SLP-76, Nck, and Vav1 and demonstrate the use of 3FRET as a tool to study signal transduction in live cells.

Our Galactic Neighbor Hosts Complex Organic Molecules

NASA Astrophysics Data System (ADS)

Hensley, Kerry

2018-03-01

For the first time, data from the Atacama Large Millimeter/submillimeter Array (ALMA) reveal the presence of methyl formate and dimethyl ether in a star-forming region outside our galaxy. This discovery has important implications for the formation and survival of complex organic compounds importantfor the formation of life in low-metallicity galaxies bothyoung and old.No Simple Picture of Complex Molecule FormationALMA, pictured here with the Magellanic Clouds above, has observed organic molecules in our Milky Way Galaxy and beyond. [ESO/C. Malin]Complex organic molecules (those with at least six atoms, one or more of which must be carbon) are the precursors to the building blocks of life. Knowing how and where complex organic molecules can form is a key part of understanding how life came to be on Earth and how it might arise elsewhere in the universe. From exoplanet atmospheres to interstellar space, complex organic molecules are ubiquitous in the Milky Way.In our galaxy, complex organic molecules are often found in the intense environments of hot cores clumps of dense molecular gas surrounding the sites of star formation. However, its not yet fully understood how the complex organic molecules found in hot cores come to be. One possibility is that the compounds condense onto cold dust grains long before the young stars begin heating their natal shrouds. Alternatively, they might assemble themselves from the hot, dense gas surrounding the blazing protostars.Composite infrared and optical image of the N 113 star-forming region in the LMC. The ALMA coverage is indicated by the gray line. Click to enlarge. [Sewio et al. 2018]Detecting Complexity, a Galaxy AwayUsing ALMA, a team of researchers led by Marta Sewio (NASA Goddard Space Flight Center) recently detected two complex organic molecules methyl formate and dimethyl ether for the first time in our neighboring galaxy, the Large Magellanic Cloud (LMC). Previous searches for organic molecules in the LMC detected small amounts of methanol, the parentmolecule of the two newly-discovered compounds. By revealing the spectral signatures of dimethyl ether and methyl formate, Sewio and collaboratorsfurther prove thatorganic chemistry is hard at work in hot cores in the LMC.This discovery is momentous because dwarf galaxies like theLMC tend to have a lower abundance of the heavy elements that make up complex organic molecules most importantly, oxygen, carbon, and nitrogen. Beyond lacking the raw materials necessary to create complex molecules, the gas of low-metallicity galaxies does a poorer job preventing the penetration of high-energy photons. The impinging photons warm dust grains, resulting in a lower probability of forming and maintaining complex organic molecules. Despite this, organic molecules appear to beable todevelop and persist which has exciting implications for organic chemistry in low-metallicity environments.ALMA observation of emission by methyl formate in a hot core in the LMC.[Adapted from Sewio et al. 2018]A Lens into the PastIn the early universe, before the budding galaxies have had time to upcycle their abundant hydrogen into heavier elements, organic chemistry is thought to proceed slowly or not at all. The discovery of complex organic molecules in a nearby low-metallicity galaxy upends this theory and propels us toward a better understanding of the organic chemistry in the early universe.CitationMarta Sewio et al 2018ApJL853L19. doi:10.3847/2041-8213/aaa079

New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

PubMed

Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

2016-03-07

This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

Mechanism for chelated sulfate formation from SO2 and bis (triphenylphosphine) platinum

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Structure and energy surface calculations using the atom superposition and electron delocalization molecular orbital theory show that the first step in the reaction between SO2 and the dioxygen complex (PPh3)2PtO2 is the coordination of SO2 with one oxygen atom of the complex, followed by metal-oxygen bond breaking and reorientation, leading to a five-membered cyclic structure. This then rearranges to form the bidentate coordinated sulfate. Alternative pathways are considered and are found to be less favorable.

Modeling of protein binary complexes using structural mass spectrometry data

PubMed Central

Kamal, J.K. Amisha; Chance, Mark R.

2008-01-01

In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints—positive and/or negative—in the docking step and are also used to decide the type of energy filter—electrostatics or desolvation—in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure. PMID:18042684

Kinetics of porous silicon growth studied using flicker-noise spectroscopy

NASA Astrophysics Data System (ADS)

Parkhutik, V.; Timashev, S.

2000-05-01

The mechanism of the formation of porous silicon (PS) is studied using flicker noise spectroscopy (FNS), a new phenomenological method that allows us to analyze the evolution of nonlinear dissipative systems in time, space and energy. FNS is based on the ideas of deterministic chaos in complex macro- and microsystems. It allows us to obtain a set of empiric parameters ("passport data") which characterize the state of the system and change of its properties due to the evolution in time, energy, and space. The FNS method permits us to get new information about the kinetics of growth of PS and its properties. Thus, the PS formation mechanisms at n-Si and p-Si, as revealed using the FNS, seem to be essentially different. p-Si shows larger "memory" in the sequence of individual events involved in PS growth than n-Si (if anodized without light illumination). The influence of the anodization variables (such as current density, HF concentration, duration of the process, light illumination) onto the "passport data" of PS is envisaged. The increase of the current density increases memory of the PS formation process, when each forthcoming individual event is more correlated with the preceding one. Increasing current density triggers electrochemical reactions that are negligible at lower currents. Light illumination also produces a positive effect onto the "memory" of the system. The FNS makes it possible to distinguish different stages of the continuous anodization process which are apparently associated with increasing pore length. Thus, FNS is a very sensitive tool in analysis of the PS formation and other complex electrochemical systems as well.

Simulation studies of the Cl- + CH3I SN2 nucleophilic substitution reaction: Comparison with ion imaging experiments

NASA Astrophysics Data System (ADS)

Zhang, Jiaxu; Lourderaj, Upakarasamy; Sun, Rui; Mikosch, Jochen; Wester, Roland; Hase, William L.

2013-03-01

In the previous work of Mikosch et al. [Science 319, 183 (2008)], 10.1126/science.1150238, ion imaging experiments were used to study the Cl- + CH3I → ClCH3 + I- reaction at collision energies Erel of 0.39, 0.76, 1.07, and 1.9 eV. For the work reported here MP2(fc)/ECP/d direct dynamics simulations were performed to obtain an atomistic understanding of the experiments. There is good agreement with the experimental product energy and scattering angle distributions for the highest three Erel, and at these energies 80% or more of the reaction is direct, primarily occurring by a rebound mechanism with backward scattering. At 0.76 eV there is a small indirect component, with isotropic scattering, involving formation of the pre- and post-reaction complexes. All of the reaction is direct at 1.07 eV. Increasing Erel to 1.9 eV opens up a new indirect pathway, the roundabout mechanism. The product energy is primarily partitioned into relative translation for the direct reactions, but to CH3Cl internal energy for the indirect reactions. The roundabout mechanism transfers substantial energy to CH3Cl rotation. At Erel = 0.39 eV both the experimental product energy partitioning and scattering are statistical, suggesting the reaction is primarily indirect with formation of the pre- and post-reaction complexes. However, neither MP2 nor BhandH/ECP/d simulations agree with experiment and, instead, give reaction dominated by direct processes as found for the higher collision energies. Decreasing the simulation Erel to 0.20 eV results in product energy partitioning and scattering which agree with the 0.39 eV experiment. The sharp transition from a dominant direct to indirect reaction as Erel is lowered from 0.39 to 0.20 eV is striking. The lack of agreement between the simulations and experiment for Erel = 0.39 eV may result from a distribution of collision energies in the experiment and/or a shortcoming in both the MP2 and BhandH simulations. Increasing the reactant rotational temperature from 75 to 300 K for the 1.9 eV collisions, results in more rotational energy in the CH3Cl product and a larger fraction of roundabout trajectories. Even though a ClCH3-I- post-reaction complex is not formed and the mechanistic dynamics are not statistical, the roundabout mechanism gives product energy partitioning in approximate agreement with phase space theory.

Computational repositioning of ethno medicine elucidated gB-gH-gL complex as novel anti herpes drug target

PubMed Central

2013-01-01

Background Herpes viruses are important human pathogens that can cause mild to severe lifelong infections with high morbidity. They remain latent in the host cells and can cause recurrent infections that might prove fatal. These viruses are known to infect the host cells by causing the fusion of viral and host cell membrane proteins. Fusion is achieved with the help of conserved fusion machinery components, glycoproteins gB, heterodimer gH-gL complex along with other non-conserved components. Whereas, another important glycoprotein gD without which viral entry to the cell is not possible, acts as a co-activator for the gB-gH-gL complex formation. Thus, this complex formation interface is the most promising drug target for the development of novel anti-herpes drug candidates. In the present study, we propose a model for binding of gH-gL to gB glycoprotein leading from pre to post conformational changes during gB-gH-gL complex formation and reported the key residues involved in this binding activity along with possible binding site locations. To validate the drug targetability of our proposed binding site, we have repositioned some of the most promising in vitro, in vivo validated anti-herpes molecules onto the proposed binding site of gH-gL complex in a computational approach. Methods Hex 6.3 standalone software was used for protein-protein docking studies. Arguslab 4.0.1 and Accelrys® Discovery Studio 3.1 Visualizer softwares were used for semi-flexible docking studies and visualizing the interactions respectively. Protein receptors and ethno compounds were retrieved from Protein Data Bank (PDB) and Pubchem databases respectively. Lipinski’s Filter, Osiris Property Explorer and Lazar online servers were used to check the pharmaceutical fidelity of the drug candidates. Results Through protein-protein docking studies, it was identified that the amino acid residues VAL342, GLU347, SER349, TYR355, SER388, ASN395, HIS398 and ALA387 of gH-gL complex play an active role in its binding activity with gB. Semi flexible docking analysis of the most promising in vitro, in vivo validated anti-herpes molecules targeting the above mentioned key residues of gH-gL complex showed that all the analyzed ethno medicinal compounds have successfully docked into the proposed binding site of gH-gL glycoprotein with binding energy range between -10.4 to -6.4 K.cal./mol. Conclusions Successful repositioning of the analyzed compounds onto the proposed binding site confirms the drug targetability of gH-gL complex. Based on the free binding energy and pharmacological properties, we propose (3-chloro phenyl) methyl-3,4,5 trihydroxybenzoate as worth a small ethno medicinal lead molecule for further development as potent anti-herpes drug candidate targeting gB-gH-gL complex formation interface. PMID:23587166

Direct evidence of an elongation factor-Tu/Ts·GTP·Aminoacyl-tRNA quaternary complex.

PubMed

Burnett, Benjamin J; Altman, Roger B; Ferguson, Angelica; Wasserman, Michael R; Zhou, Zhou; Blanchard, Scott C

2014-08-22

During protein synthesis, elongation factor-Tu (EF-Tu) bound to GTP chaperones the entry of aminoacyl-tRNA (aa-tRNA) into actively translating ribosomes. In so doing, EF-Tu increases the rate and fidelity of the translation mechanism. Recent evidence suggests that EF-Ts, the guanosine nucleotide exchange factor for EF-Tu, directly accelerates both the formation and dissociation of the EF-Tu-GTP-Phe-tRNA(Phe) ternary complex (Burnett, B. J., Altman, R. B., Ferrao, R., Alejo, J. L., Kaur, N., Kanji, J., and Blanchard, S. C. (2013) J. Biol. Chem. 288, 13917-13928). A central feature of this model is the existence of a quaternary complex of EF-Tu/Ts·GTP·aa-tRNA(aa). Here, through comparative investigations of phenylalanyl, methionyl, and arginyl ternary complexes, and the development of a strategy to monitor their formation and decay using fluorescence resonance energy transfer, we reveal the generality of this newly described EF-Ts function and the first direct evidence of the transient quaternary complex species. These findings suggest that EF-Ts may regulate ternary complex abundance in the cell through mechanisms that are distinct from its guanosine nucleotide exchange factor functions. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Formation of amino acids and nucleic acid constituents from simulated primitive planetary atmospheres by irradiation with high-energy protons

NASA Astrophysics Data System (ADS)

Kobayashi, K.; Yamanashi, H.; Ohashi, A.; Kaneko, T.; Miyakawa, S.; Saito, T.

It is suggested that primitive Earth atmosphere was only slightly reduced, which w as composed of carbon dioxide, carbon monoxide, nitrogen and water. It has been shown that bioorganic compounds can be hardly formed by energies as UV light, heat and spark discharges. We therefore examined possible formation pat hways of bioorganic compounds in the primitive E arth. A mixt ure of carbon monoxide, nitrogen and water was irradiated with high-energy prot ons generated by a van de Graaff accelerator, whi c h simulated an action of cosm ic rays. Aqueous solution of the product was hydr olyzed, and then analyzed by chromatography and mass spectrometry. A wide variety of amino acids and uracil, one of the nucle ic acid bases, wer e identified. Ribose, the RNA sugar, has not been identified, but formation of reducing polyols was suggested. A mino acids and uracil were also formed from a mixture of carbo n dioxide, carbon monoxide, nitrogen and water, and their yields correlated to the ratio of carbon monoxide and nitrogen in the mixture. Since a certain percentage of carbon monoxide could be expected to be in it [1], cosmic radiation can be regarded as an effective energ so urce for prebiotic formation of life's building blocks in they primitive Earth [2]. In the conventional scenario of chemical evolution, amino acids were formed in t he primitive ocean from such intermediates as HCN an d HCHO formed in t he atmosphere. T his scenario seem s not to be possible due to the following reasons: (1) The irradiation products were quit e complex organic com pound s whose molecular weights were ca. 1000, and they gave amino acids after hydrolysis. (2) Energy yields of amino ac ids in the hydrolysates were comparable to those of HCN and HCHO in the irradiation pro duct s. (3) Irradiation products from a mixture of carbon monoxide and nitrogen without water als o gave amino acids aft er hydrolysis. T hes e observations strongly sugge s t e d that complex precursors of bioor ganic com poun ds could be formed directly in the atmosphere. A new scenario of chemical evolution via complex organics toward the origin of life will be prop o s e d. [1] J. Kasting, Origins Life Evol. Biosph ere, 20, 199 (1990). [2] K. Kobay ashi , et al., Origins Life Evol. Biosphere, 28, 155 (1998). * Present address: Rensselaer Polytechnic Ins titut e.

Synergy of elastic and inelastic energy loss on ion track formation in SrTiO 3

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

Weber, William J.; Zarkadoula, Eva; Pakarinen, Olli H.

2015-01-12

While the interaction of energetic ions with solids is well known to result in inelastic energy loss to electrons and elastic energy loss to atomic nuclei in the solid, the coupled effects of these energy losses on defect production, nanostructure evolution and phase transformations in ionic and covalently bonded materials are complex and not well understood due to dependencies on electron-electron scattering processes, electron-phonon coupling, localized electronic excitations, diffusivity of charged defects, and solid-state radiolysis. Here we show that a colossal synergy occurs between inelastic energy loss and pre-existing atomic defects created by elastic energy loss in single crystal strontiummore » titanate (SrTiO 3), resulting in the formation of nanometer-sized amorphous tracks, but only in the narrow region with pre-existing defects. These defects locally decrease the electronic and atomic thermal conductivities and increase electron-phonon coupling, which locally increase the intensity of the thermal spike for each ion. This work identifies a major gap in understanding on the role of defects in electronic energy dissipation and electron-phonon coupling; it also provides insights for creating novel interfaces and nanostructures to functionalize thin film structures, including tunable electronic, ionic, magnetic and optical properties.« less

A quasi-classical study of energy transfer in collisions of hyperthermal H atoms with SO2 molecules.

PubMed

da Silva, Ramon S; Garrido, Juan D; Ballester, Maikel Y

2017-08-28

A deep understanding of energy transfer processes in molecular collisions is at central attention in physical chemistry. Particularly vibrational excitation of small molecules colliding with hot light atoms, via a metastable complex formation, has shown to be an efficient manner of enhancing reactivity. A quasi-classical trajectory study of translation-to-vibration energy transfer (T-V ET) in collisions of hyperthermal H( 2 S) atoms with SO 2 (X̃ 1 A ' ) molecules is presented here. For such a study, a double many-body expansion potential energy surface previously reported for HSO 2 ( 2 A) is used. This work was motivated by recent experiments by Ma et al. studying collisions of H + SO 2 at the translational energy of 59 kcal/mol [J. Ma et al., Phys. Rev. A 93, 040702 (2016)]. Calculations reproduce the experimental evidence that during majority of inelastic non-reactive collision processes, there is a metastable intermediate formation (HOSO or HSO 2 ). Nevertheless, the analysis of the trajectories shows that there are two distinct mechanisms in the T-V ET process: direct and indirect. Direct T-V processes are responsible for the high population of SO 2 with relatively low vibrational excitation energy, while indirect ones dominate the conversion from translational energy to high values of the vibrational counterpart.

Energy transfer of highly vibrationally excited phenanthrene and diphenylacetylene.

PubMed

Hsu, Hsu Chen; Tsai, Ming-Tsang; Dyakov, Yuri; Ni, Chi-Kung

2011-05-14

The energy transfer between Kr atoms and highly vibrationally excited, rotationally cold phenanthrene and diphenylacetylene in the triplet state was investigated using crossed-beam/time-of-flight mass spectrometer/time-sliced velocity map ion imaging techniques. Compared to the energy transfer between naphthalene and Kr, energy transfer between phenanthrene and Kr shows a larger cross-section for vibrational to translational (V → T) energy transfer, a smaller cross-section for translational to vibrational and rotational (T → VR) energy transfer, and more energy transferred from vibration to translation. These differences are further enlarged in the comparison between naphthalene and diphenylacetylene. In addition, less complex formation and significant increases in the large V → T energy transfer probabilities, termed supercollisions in diphenylacetylene and Kr collisions were observed. The differences in the energy transfer between these highly vibrationally excited molecules are attributed to the low-frequency vibrational modes, especially those vibrations with rotation-like wide-angle motions.

Heat capacity changes in carbohydrates and protein-carbohydrate complexes.

PubMed

Chavelas, Eneas A; García-Hernández, Enrique

2009-05-13

Carbohydrates are crucial for living cells, playing myriads of functional roles that range from being structural or energy-storage devices to molecular labels that, through non-covalent interaction with proteins, impart exquisite selectivity in processes such as molecular trafficking and cellular recognition. The molecular bases that govern the recognition between carbohydrates and proteins have not been fully understood yet. In the present study, we have obtained a surface-area-based model for the formation heat capacity of protein-carbohydrate complexes, which includes separate terms for the contributions of the two molecular types. The carbohydrate model, which was calibrated using carbohydrate dissolution data, indicates that the heat capacity contribution of a given group surface depends on its position in the saccharide molecule, a picture that is consistent with previous experimental and theoretical studies showing that the high abundance of hydroxy groups in carbohydrates yields particular solvation properties. This model was used to estimate the carbohydrate's contribution in the formation of a protein-carbohydrate complex, which in turn was used to obtain the heat capacity change associated with the protein's binding site. The model is able to account for protein-carbohydrate complexes that cannot be explained using a previous model that only considered the overall contribution of polar and apolar groups, while allowing a more detailed dissection of the elementary contributions that give rise to the formation heat capacity effects of these adducts.

Molecular structures and thermodynamic properties of monohydrated gaseous iodine compounds: Modelling for severe accident simulation

NASA Astrophysics Data System (ADS)

Sudolská, Mária; Cantrel, Laurent; Budzák, Šimon; Černušák, Ivan

2014-03-01

Monohydrated complexes of iodine species (I, I2, HI, and HOI) have been studied by correlated ab initio calculations. The standard enthalpies of formation, Gibbs free energy and the temperature dependence of the heat capacities at constant pressure were calculated. The values obtained have been implemented in ASTEC nuclear accident simulation software to check the thermodynamic stability of hydrated iodine compounds in the reactor coolant system and in the nuclear containment building of a pressurised water reactor during a severe accident. It can be concluded that iodine complexes are thermodynamically unstable by means of positive Gibbs free energies and would be represented by trace level concentrations in severe accident conditions; thus it is well justified to only consider pure iodine species and not hydrated forms.

Enzymology below 200 K: The kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase

PubMed Central

Heyes, Derren J.; Ruban, Alexander V.; Wilks, Helen M.; Hunter, C. Neil

2002-01-01

The chlorophyll biosynthesis enzyme protochlorophyllide reductase (POR) catalyzes the light-dependent reduction of protochlorophyllide (Pchlide) into chlorophyllide in the presence of NADPH. As POR is light-dependent, catalysis can be initiated by illumination of the enzyme-substrate complex at low temperatures, making it an attractive model for studying aspects of biological proton and hydride transfers. The early stages in the photoreduction, involving Pchlide binding and an initial photochemical reaction, have been studied in vitro by using low-temperature fluorescence and absorbance measurements. Formation of the ternary POR-NADPH-Pchlide complex produces red shifts in the fluorescence and absorbance maxima of Pchlide, allowing the dissociation constant for Pchlide binding to be measured. We demonstrate that the product of an initial photochemical reaction, which can occur below 200 K, is a nonfluorescent intermediate with a broad absorbance band at 696 nm (A696) that is suggested to represent an ion radical complex. The temperature dependence of the rate of A696 formation has allowed the activation energy for the photochemical step to be calculated and has shown that POR catalysis can proceed at much lower temperatures than previously thought. Calculations of differences in free energy between various reaction intermediates have been calculated; these, together with the quantum efficiency for Pchlide conversion, suggest a quantitative model for the thermodynamics of the light-driven step of Pchlide reduction. PMID:12177453

Charge transfer complex states in diketopyrrolopyrrole polymers and fullerene blends: Implications for organic solar cell efficiency

NASA Astrophysics Data System (ADS)

Moghe, D.; Yu, P.; Kanimozhi, C.; Patil, S.; Guha, S.

2011-12-01

The spectral photocurrent characteristics of two donor-acceptor diketopyrrolopyrrole (DPP)-based copolymers (PDPP-BBT and TDPP-BBT) blended with a fullerene derivative [6,6]-phenyl C61-butyric acid methyl ester (PCBM) were studied using Fourier-transform photocurrent spectroscopy (FTPS) and monochromatic photocurrent (PC) method. PDPP-BBT:PCBM shows the onset of the lowest charge transfer complex (CTC) state at 1.42 eV, whereas TDPP-BBT:PCBM shows no evidence of the formation of a midgap CTC state. The FTPS and PC spectra of P3HT:PCBM are also compared. The larger singlet state energy difference of TDPP-BBT and PCBM compared to PDPP-BBT/P3HT and PCBM obliterates the formation of a midgap CTC state resulting in an enhanced photovoltaic efficiency over PDPP-BBT:PCBM.

Temporal profiling of orexin receptor-arrestin-ubiquitin complexes reveals differences between receptor subtypes.

PubMed

Dalrymple, Matthew B; Jaeger, Werner C; Eidne, Karin A; Pfleger, Kevin D G

2011-05-13

Orexin G protein-coupled receptors (OxRs) and their cognate agonists have been implicated in a number of disorders since their recent discovery, ranging from narcolepsy to formation of addictive behavior. Bioluminescence resonance energy transfer assays of agonist-occupied OxRs provided evidence for a strong dose-dependent interaction with both trafficking proteins β-arrestin 1 and 2 that required unusually high agonist concentrations compared with inositol phosphate signaling. This appears to be reflected in functional differences in potency with respect to orexin A (OxA) and OxR2-dependent ERK1/2 phosphorylation after 90 min compared with 2 min, potentially consistent with β-arrestin-mediated versus G protein-mediated signaling, respectively. Furthermore, extended bioluminescence resonance energy transfer kinetic data monitoring OxA-dependent receptor-β-arrestin and β-arrestin-ubiquitin proximity suggested subtype-specific differences in receptor trafficking, with OxR2 activation resulting in more sustained receptor-β-arrestin-ubiquitin complex formation than elicited by OxR1 activation. Enzyme-linked immunosorbent assay (ELISA) data also revealed that OxR1 underwent significantly more rapid recycling compared with OxR2. Finally, we have observed sustained OxA-dependent ERK1/2 phosphorylation in the presence of OxR2 compared with OxR1. Although both OxR subtypes could be classified as class B receptors for β-arrestin usage based on the initial strength of interaction with both β-arrestins, our temporal profiling revealed tangible differences between OxR subtypes. Consequently, OxR1 appears to fit uneasily into the commonly used β-arrestin classification scheme. More importantly, it is hoped that this improved profiling capability, enabling the subtleties of protein complex formation, stability, and duration to be assessed in live cells, will help unlock the therapeutic potential of targeting these receptors.

Probing Aspergillus niger glucose oxidase with pentacyanoferrate(III) aza- and thia-complexes.

PubMed

Kulys, J; Tetianec, L; Ziemys, A

2006-10-01

Complexes of pentacyanoferrate(III) and biologically relevant ligands, such as pyridine, pyrazole, imidazole, histidine, and other aza- and thia-heterocycles, were synthesized. Their spectral, electrochemical properties, electron exchange constants, electronic structure parameters, and reactivity with glucose oxidase from Aspergillus niger were determined. The formation of the complexes following ammonia replacement by the ligands was associated with the appearance of a new band of absorbance in the visible spectrum. The constants of the complexes formation calculated at a ligand-pentacyanoferrate(III) concentrations ratio of 10:1, were 7.5 x 10(-5), 7.7 x 10(-5), and 1.8 x 10(-3) s(-1) for benzotriazole, benzimidazole, and aminothiazole ligands, respectively. The complexes showed quasi-reversible redox conversion at a glassy carbon electrode. The redox potential of the complexes spanned the potential range from 70 to 240 mV vs. saturated calomel electrode (SCE) at pH7.2. For most of the complexes self-exchange constants (k(11)) were similar to or larger than that of hexacyanoferrate(III) (ferricyanide). The complexes containing pyridine derivatives and thia-heterocyclic ligands held a lower value of k(11) than that of ferricyanide. All complexes reacted with reduced glucose oxidase at pH7.2. The reactivity of the complex containing pyrazole was the largest in comparison to the rest of the complexes. Correlations between the complexes' reactivity and both the free energy of reaction and k(11) shows that the reactivity of pentacyanoferrates obeys the principles of Marcus's electron transfer theory. The obtained data suggest that large negative charges of the complexes decrease their reactivity.

Synthesis of charge transfer complex of chloranilic acid as acceptor with p-nitroaniline as donor: Crystallographic, UV-visible spectrophotometric and antimicrobial studies

NASA Astrophysics Data System (ADS)

Zulkarnain; Khan, Ishaat M.; Ahmad, Afaq; Miyan, Lal; Ahmad, Musheer; Azizc, Nafe

2017-08-01

The charge transfer interaction between p-nitroaniline (PNA) and chloranilic (CAA) acid was studied spectrophotometrically in methanol at different temperatures within the range 298-328 K. This experimental work explores the nature of charge-transfer interactions that play a significant role in chemistry and biology. Structure of synthesized charge transfer (CT) complex was investigated by different technique such as X-ray crystallography, FTIR, 1HNMR, UV-visible spectroscopy, XRD and TGA-DTA, which indicates the presence of N+sbnd Hrbd2bd O- bond between donor and acceptor moieties. Spectrophotometric studies of CT complexes were carried out in methanol at different temperatures to estimate thermodynamic parameters such as formation constant (KCT), molar absorptivity (εCT), free energy change (ΔG), enthalpy change (ΔH), resonance energy (RN), oscillator strength (f), transition dipole moment (μEN) and interaction energy (ECT) were also calculated. The effect of temperatures on all the parameters was studied in methanol. 1:1 stoichiometric of CT-complex was ascertained by Benesi-Hildebrand plots giving straight line, which are good agreement with other analysis. Synthesized CT complex was screened for its antimicrobial activity such as antibacterial activity against two gram-positive bacteria, Staphylococcus aureus and bacillus subtilis and two gram negative bacteria Escherichia coli and pseudomonas aeruginosa, and antifungal activity against fungi Fusarium oxysporum, and Aspergillus flavus.

Silicon supported lipid-DNA thin film structures at varying temperature studied by energy dispersive X-ray diffraction and neutron reflectivity.

PubMed

Domenici, F; Castellano, C; Dell'Unto, F; Albinati, A; Congiu, A

2011-11-01

Non-viral gene transfection by means of lipid-based nanosystems, such as solid supported lipid assemblies, is often limited due to their lack of stability and the consequent loss of efficiency. Therefore not only a detailed thermo-lyotropic study of these DNA-lipid complexes is necessary to understand their interaction mechanisms, but it can also be considered as a first step in conceiving and developing new transfection biosystems. The aim of our study is a structural characterization of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC)-dimethyl-dioctadecyl-ammonium bromide (DDAB)-DNA complex at varying temperature using the energy dispersive X-ray diffraction (EDXD) and neutron reflectivity (NR) techniques. We have shown the formation of a novel thermo-lyotropic structure of DOPC/DDAB thin film self-organized in multi-lamellar planes on (100)-oriented silicon support by spin coating, thus enlightening its ability to include DNA strands. Our NR measurements indicate that the DOPC/DDAB/DNA complex forms temperature-dependent structures. At 65°C and relative humidity of 100% DNA fragments are buried between single lamellar leaflets constituting the hydrocarbon core of the lipid bilayers. This finding supports the consistency of the hydrophobic interaction model, which implies that the coupling between lipid tails and hypo-hydrated DNA single strands could be the driving force of DNA-lipid complexation. Upon cooling to 25°C, EDXD analysis points out that full-hydrated DOPC-DDAB-DNA can switch in a different metastable complex supposed to be driven by lipid heads-DNA electrostatic interaction. Thermotropic response analysis also clarifies that DOPC has a pivotal role in promoting the formation of our observed thermophylic silicon supported lipids-DNA assembly. Copyright © 2011 Elsevier B.V. All rights reserved.

Extracorporeal shock wave stimulates expression of the angiogenic genes via mechanosensory complex in endothelial cells: mimetic effect of fluid shear stress in endothelial cells.

PubMed

Ha, Chang Hoon; Kim, Sunghyen; Chung, Jihwa; An, Shung Hyen; Kwon, Kihwan

2013-10-09

Extracorporeal shock wave has been used in the noninvasive treatment of various diseases including musculoskeletal disorders. In particular, shock wave with low energy level showed anti-inflammatory effect and increased angiogenesis in ischemic tissues. However, the detailed cellular pathway in endothelial signaling is not fully understood. We investigate the role of shock wave with low energy level in angiogenic gene expression and underlying molecular mechanism by comparing the laminar and oscillatory fluid shear stresses in endothelial cells. We show that shock wave with low energy level (0.012-0.045 mJ/mm(2)) stimulated phosphorylation of Akt, eNOS and Erk 1/2 in a time-dependent manner which is similar to the effect of laminar fluid shear stress. The transfection of endothelial cells with siRNA encoding VEGFR2, VE-cadherin and PECAM-1 inhibited shock wave-induced phosphorylation of Akt, eNOS and Erk 1/2 and angiogenic gene expressions, including Akt, eNOS, KLF2/4, and Nur77. Moreover, mechanical stimulation through extracorporeal shock wave induced endothelial cell migration and tube formation. Our results demonstrate that shock wave-induced Akt/eNOS phosphorylation and angiogenic gene expression were mediated through the mechanosensory complex formation involving VEGFR-2, VE-cadherin and PECAM-1 which was similar to the effect of laminar shear stress. © 2013.

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

PubMed Central

Faponle, Abayomi S; Quesne, Matthew G; Sastri, Chivukula V; Banse, Frédéric; de Visser, Sam P

2015-01-01

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O–O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L52). Direct C–O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L52)FeIII(OOH)]2+ should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O–O bond, whereas a heterolytic O–O bond breaking in heme iron(III)–hydroperoxo is found. PMID:25399782

Understanding the mechanism of DNA deactivation in ion therapy of cancer cells: hydrogen peroxide action*

NASA Astrophysics Data System (ADS)

Piatnytskyi, Dmytro V.; Zdorevskyi, Oleksiy O.; Perepelytsya, Sergiy M.; Volkov, Sergey N.

2015-11-01

Changes in the medium of biological cells under ion beam irradiation has been considered as a possible cause of cell function disruption in the living body. The interaction of hydrogen peroxide, a long-lived molecular product of water radiolysis, with active sites of DNA macromolecule was studied, and the formation of stable DNA-peroxide complexes was considered. The phosphate groups of the macromolecule backbone were picked out among the atomic groups of DNA double helix as a probable target for interaction with hydrogen peroxide molecules. Complexes consisting of combinations including: the DNA phosphate group, H2O2 and H2O molecules, and Na+ counterion, were considered. The counterions have been taken into consideration insofar as under the natural conditions they neutralise DNA sugar-phosphate backbone. The energy of the complexes have been determined by considering the electrostatic and the Van der Waals interactions within the framework of atom-atom potential functions. As a result, the stability of various configurations of molecular complexes was estimated. It was shown that DNA phosphate groups and counterions can form stable complexes with hydrogen peroxide molecules, which are as stable as the complexes with water molecules. It has been demonstrated that the formation of stable complexes of H2O2-Na+-PO4- may be detected experimentally by observing specific vibrations in the low-frequency Raman spectra. The interaction of H2O2 molecule with phosphate group of the double helix backbone can disrupt DNA biological function and induce the deactivation of the cell genetic apparatus. Thus, the production of hydrogen peroxide molecules in the nucleus of living cells can be considered as an additional mechanism by which high-energy ion beams destroy tumour cells during ion beam therapy. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

The effect of alloying nickel with iron on the supersonic ballistic stage of high energy displacement cascades

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.

2016-06-23

Previous experimental and theoretical studies suggest that the production of extended defect structures by collision cascades is inhibited in equiatomic NiFe, in comparison to pure Ni. It is also known that the production of such extend defect structures results from the formation of subcascades by high-energy recoils and their subsequent interaction. A detailed analysis of the ballistics of 40 keV cascades in Ni and NiFe is performed to identify the formation of such subcascades and to assess their spatial distribution. It is found that subcascades in Ni and NiFe are created with nearly identical energies and distributed similarly in space.more » This suggests that the differences in production of extended defect structures is not related to processes taking place in the ballistic phase of the collision cascade. Lastly, these results can be generalized to other, more chemically complex, concentrated alloys where the elements have similar atomic numbers, such as many high-entropy alloys.« less

The effect of alloying nickel with iron on the supersonic ballistic stage of high energy displacement cascades

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

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.

Previous experimental and theoretical studies suggest that the production of extended defect structures by collision cascades is inhibited in equiatomic NiFe, in comparison to pure Ni. It is also known that the production of such extend defect structures results from the formation of subcascades by high-energy recoils and their subsequent interaction. A detailed analysis of the ballistics of 40 keV cascades in Ni and NiFe is performed to identify the formation of such subcascades and to assess their spatial distribution. It is found that subcascades in Ni and NiFe are created with nearly identical energies and distributed similarly in space.more » This suggests that the differences in production of extended defect structures is not related to processes taking place in the ballistic phase of the collision cascade. Lastly, these results can be generalized to other, more chemically complex, concentrated alloys where the elements have similar atomic numbers, such as many high-entropy alloys.« less

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study.

PubMed

Mudedla, Sathish Kumar; Azhagiya Singam, Ettayapuram Ramaprasad; Balamurugan, Kanagasabai; Subramanian, Venkatesan

2015-11-11

The complexation of small interfering RNA (siRNA) with positively charged gold nanoclusters has been studied in the present investigation with the help of classical molecular dynamics and steered molecular dynamics simulations accompanied by free energy calculations. The results show that gold nanoclusters form a stable complex with siRNA. The wrapping of siRNA around the gold nanocluster depends on the size and charge on the surface of the gold cluster. The binding pattern of the gold nanocluster with siRNA is also influenced by the presence of another cluster. The interaction between the positively charged amines in the gold nanocluster and the negatively charged phosphate group in the siRNA is responsible for the formation of complexes. The binding free energy value increases with the size of the gold cluster and the number of positive charges present on the surface of the gold nanocluster. The results reveal that the binding energy of small gold nanoclusters increases in the presence of another gold nanocluster while the binding of large gold nanoclusters decreases due to the introduction of another gold nanocluster. Overall, the findings have clearly demonstrated the effect of size and charge of gold nanoclusters on their interaction pattern with siRNA.

Observation of CO2 and solvent adduct ions during negative mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric analysis of monohydric alcohols.

PubMed

Zhou, Xibin; Zhang, Yahe; Zhao, Suoqi; Hsu, Chang Samuel; Shi, Quan

2013-12-15

Monohydric alcohols are common in natural products, bio-oils, and medicine. We have found that monohydric alcohols can form O3 (ions containing three oxygen atoms) and O4 adduct ions in negative electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which would significantly affect the composition analysis of alcohols, especially in a complex mixture. It is necessary to study the reaction pathways and the method to eliminate or reduce the 'artifact' adducts. Octadecanol, cholesterol, squalanol and two complex monohydric alcohol mixtures were selected as model compounds. These samples were subjected to negative ion ESI FT-ICR MS analysis. The composition and formation mechanism of adducts were studied by the ultrahigh-resolution accurate mass measurement for elemental composition, along with the MS(2) isolation and collision-induced dissociation (CID) experiments for structural determination. The reaction pathway of O3 adduct formation is the coupling of a monohydric alcohol ion with a CO2 to form a stable O3 ionic species by likely a covalent bond (source of CO2 is not clear). The O4 species are formed by O3 ionic species adducted with an alcohol molecule of the solvent, such as methanol or ethanol, by likely a hydrogen bond. These adduct ions could be eliminated or reduced by increasing collision energy. However, excessive collision energy would fragment monohydric alcohol ions. The formation mechanisms of O3 and O4 adducts from monohydric alcohols in negative ion ESI FT-ICR MS were proposed. The solvent adduction effects can be eliminated or reduced by optimizing the collision energy of CID in FT-ICR MS. Copyright © 2013 John Wiley & Sons, Ltd.

Reaction with cyanide of hydroxylamine oxidoreductase of Nitrosomonas europaea.

PubMed

Logan, M S; Balny, C; Hooper, A B

1995-07-18

Hydroxylamine oxidoreductase (HAO) catalyzes the reaction NH2OH+H2O-->HNO2+4e- + 4H+, a step in the energy-generating oxidation of ammonia to nitrite by the bacterium Nitrosomonas europaea. Each subunit of HAO contains 7 c-hemes and 1 heme P460. The latter, c-heme cross-linked from a methylene carbon to the ring of a protein tyrosine, forms part of the active site. The iron of heme P460 is probably linked by a bridging ligand to the iron of a c-heme. Here, the reaction of cyanide with ferric HAO was studied by optical, transient, and steady state kinetic techniques. The molecules, F-, Cl-, Br-, N3-, SCN-, and OCN- did not react with HAO. A single molecule of cyanide bound with high affinity to heme P460 of HAO. The optical and kinetic characteristics of formation of the monocyano complex of HAO resembled those of cyanide derivatives of other heme proteins. Cyanide, in the monocyano complex, was a noncompetitive inhibitor and remained bound during turnover. HAO was found in two forms. The most common form, HAO-A, formed only the monocyano derivative of heme P460, whereas the other, HAO-B, formed a mono- and dicyano complex. The optical properties and kinetics of formation of the mono- and dicyano complexes were different enough to easily allow independent analysis. The optical and kinetic characteristics of formation of the monocyano complex of heme P460 of HAO A and B were very similar. The dicyano complex of HAO-B appeared to result from the addition of a second molecule of cyanide to heme P460. The rate of conversion of the monocyano to the dicyano complex was stimulated 100-fold by the binding of substrate. Formation of the monoheme complex inhibited enzyme activity. The kinetic constants for the first-order formation of the monocyano derivative and the inhibition of substrate oxidation (under either transient or steady-state conditions) were different. The apparent discrepancy could be resolved by the hypothesis that HAO is functionally a dimer in which electrons rapidly equilibrate between the c-hemes of each subunit but not between oligomers. The results form the basis for the use of cyanide as a probe of the active site of HAO.

Reaction mechanism of molybdoenzyme formate dehydrogenase.

PubMed

Leopoldini, Monica; Chiodo, Sandro G; Toscano, Marirosa; Russo, Nino

2008-01-01

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.

First-principles study of defect formation in a photovoltaic semiconductor Cu2ZnGeSe4

NASA Astrophysics Data System (ADS)

Nishihara, Hironori; Maeda, Tsuyoshi; Wada, Takahiro

2018-02-01

The formation energies of neutral Cu, Zn, Ge, and Se vacancies in kesterite-type Cu2ZnGeSe4 were evaluated by first-principles pseudopotential calculations using plane-wave basis functions. The calculations were performed at typical points in Cu-(Zn1/2Ge1/2)-Se and Cu3Se2-ZnSe-GeSe2 pseudoternary phase diagrams for Cu2ZnGeSe4. The results were compared with those for Cu2ZnSnSe4, Cu2ZnGeS4, and Cu2ZnSnS4 calculated using the same version of the CASTEP program code. The results indicate that Cu vacancies are easily formed in Cu2ZnGeSe4 under the Cu-poor condition as in the above compounds and CuInSe2, suggesting that Cu2ZnGeSe4 is also a preferable p-type absorber material for thin-film solar cells. The formation energies of possible antisite defects, such as CuZn and CuGe, and of possible complex defects, such as CuZn+ZnCu, were also calculated and compared within the above materials. The antisite defect of CuZn, which has the smallest formation energy within the possible defects, is concluded to be the most hardly formed in Cu2ZnGeSe4 among the compounds.

A quantum dynamical study of the He++2He-->He2++He reaction

NASA Astrophysics Data System (ADS)

Xie, Junkai; Poirier, Bill; Gellene, Gregory I.

2003-11-01

The temperature dependent rate of the He++2He→He2++He three-body association reaction is studied using two complementary quantum dynamical models. Model I presumes a two-step, reverse Lindemann mechanism, where the intermediate energized complex, He2+*, is interpreted as the rotational resonance states of He2+. The energy and width of these resonances are determined via "exact" quantum calculation using highly accurate potential-energy curves. Model II uses an alternate quantum rate expression as the thermal average of the cumulative recombination probability, N(E). This microcanonical quantity is computed approximately, over the He2+ space only, with the third-body interaction modeled using a special type of absorbing potential. Because Model II implicitly incorporates both the two-step reverse Lindemann mechanism, and a one-step, reverse collision induced dissociation mechanism, the relative importance of the two formation mechanisms can be estimated by a comparison of the Model I and Model II results. For T<300 K, the reaction is found to be dominated by the two-step mechanism, and a formation rate in good agreement with the available experimental results is obtained with essentially no adjustable parameters in the theory. Interestingly, a nonmonotonic He2+ formation rate is observed, with a maximum identified near 25 K. This maximum is associated with just two reaction intermediate resonance states, the lowest energy states that can contribute significantly to the formation kinetics.

Crustal fingering: solidification on a viscously unstable interface

NASA Astrophysics Data System (ADS)

Fu, Xiaojing; Jimenez-Martinez, Joaquin; Cueto-Felgueroso, Luis; Porter, Mark; Juanes, Ruben

2017-11-01

Motivated by the formation of gas hydrates in seafloor sediments, here we study the volumetric expansion of a less viscous gas pocket into a more viscous liquid when the gas-liquid interfaces readily solidify due to hydrate formation. We first present a high-pressure microfluidic experiment to study the depressurization-controlled expansion of a Xenon gas pocket in a water-filled Hele-Shaw cell. The evolution of the pocket is controlled by three processes: (1) volumetric expansion of the gas; (2) rupturing of existing hydrate films on the gas-liquid interface; and (3) formation of new hydrate films. These result in gas fingering leading to a complex labyrinth pattern. To reproduce these observations, we propose a phase-field model that describes the formation of hydrate shell on viscously unstable interfaces. We design the free energy of the three-phase system to rigorously account for interfacial effects, gas compressibility and phase transitions. We model the hydrate shell as a highly viscous fluid with shear-thinning rheology to reproduce shell-rupturing behavior. We present high-resolution numerical simulations of the model, which illustrate the emergence of complex crustal fingering patterns as a result of gas expansion dynamics modulated by hydrate growth at the interface.

Chenier plain genesis explained by feedbacks between waves, mud, and sand

NASA Astrophysics Data System (ADS)

Nardin, William; Fagherazzi, Sergio

2017-04-01

Cheniers are sandy ridges parallel to the coast established by high energy waves. Here we discuss ontogeny of chenier plains through dimensional analysis and numerical results from the morphodynamic model Delft3D-SWAN. Our results show that wave energy and inner-shelf slope play an important role in the formation of chenier plains. In our numerical experiments, waves affect chenier plain development in three ways: by winnowing coarse sediment from the mudflat, by eroding mud and accumulating sand over the beach during extreme wave events. We further show that different sediment characteristics and wave climates can lead to three alternative coastal landscapes: strand plains, mudflats, or the more complex chenier plains. Low inner-shelf slopes are the most favorable for strand plain and chenier plain formation, while high slopes decrease the likelihood of mudflat development and preservation.

Chenier plain development: feedbacks between waves, mud and sand

NASA Astrophysics Data System (ADS)

Nardin, W.; Fagherazzi, S.

2015-12-01

Cheniers are sandy ridges parallel to the coast established by high energy waves. Here we discuss Chenier plains ontogeny through dimensional analysis and numerical results from the morphodynamic model Delft3D-SWAN. Our results show that wave energy and shelf slope play an important role in the formation of Chenier plains. In our numerical experiments waves affect Chenier plain development in three ways: by winnowing sediment from the mudflat, by eroding mud and accumulating sand over the beach during extreme wave events. We further show that different sediment characteristics and wave climates can lead to three alternative coastal landscapes: strand plains, mudflats, or the more complex Chenier plains. Low inner-shelf slopes are the most favorable for strand plain and Chenier plain formation, while high slopes decrease the likelihood of mudflat development and preservation.

Clinical trial tests drug for tumors associated with Krebs-cycle dysfunction | Center for Cancer Research

Cancer.gov

The Krebs cycle is part of the complex process where cells turn food into energy. One of the elements of the Krebs cycle is succinate dehydrogenase (SDH). Loss of SDH activity in cells has been linked to tumor formation. This new trial is studying guadecitabine for tumors associated with Krebs cycle dysfunction. Learn more...

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

Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Sharma, Amrish; Mudahar, Isha, E-mail: isha@pbi.ac.in

First principle calculations based on density functional theory were performed to calculate the structural and electronic properties of C{sub 20}-N{sub m}@C{sub n} dimer complexes. The calculated binding energies of the complexes formed are comparable to C{sub 60} dimer which ensures their stability. The bond lengths of these dimer complexes were found to be nearly same as pure complexes C{sub 20}-C{sub n}. Further, nitrogen (N) atoms were encapsulated inside the secondary cage (C{sub n}) of dimer complexes and the number of N atoms depends on diameter of the cage. The HOMO-LUMO gaps of new proposed complexes indicate the increase in gapmore » as compared to pure complexes. Mulliken charge analysis of these complexes has been studied which shows the significant charge transfer from the N atoms to the secondary cage of these complexes. The study propose the formation of the new dimer complexes which are stable and are able to encapsulate atoms which are otherwise reactive in free space.« less

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy† †Electronic supplementary information (ESI) available: Synthesis schemes, experimental methods, NMR spectra, X-ray crystallographic information, emission spectra, cyclic voltammetry, electronic structure calculations, data analysis and numerical methods, and other additional figures. CCDC 1561879. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04055e

PubMed Central

Kohler, Lars; Hadt, Ryan G.; Zhang, Xiaoyi; Liu, Cunming

2017-01-01

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)–Ru(ii) analogs of the homodinuclear Cu(i)–Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations. PMID:29629153

Chemical dynamics simulations of the monohydrated OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. Atomic-level mechanisms and comparison with experiment

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

Xie, Jing; Hase, William L., E-mail: bill.hase@ttu.edu; Otto, Rico

2015-06-28

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH{sup −}(H{sub 2}O) + CH{sub 3}I reaction. The S{sub N}2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH{sub 2}I{sup −}, and to a lesser extent CH{sub 2}I{sup −} (H{sub 2}O), becomes important. The S{sub N}2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of S{sub N}2 and proton transfer pre-reaction complexes and intermediates, includingmore » [CH{sub 3}--I--OH]{sup −}. In contrast, for the unsolvated OH{sup −} + CH{sub 3}I S{sub N}2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH{sup −}(H{sub 2}O) + CH{sub 3}I S{sub N}2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the S{sub N}2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H{sub 2}O molecule is unimportant. The S{sub N}2 reaction is dominated by events in which H{sub 2}O leaves the reactive system as CH{sub 3}OH is formed or before CH{sub 3}OH formation. Formation of solvated products is unimportant and participation of the (H{sub 2}O)CH{sub 3}OH---I{sup −} post-reaction complex for the S{sub N}2 reaction is negligible.« less

Phylogenetic Evidence for H2 based Electron Bifurcation In Early Life

NASA Astrophysics Data System (ADS)

Adams, M. W.; Boyd, E. S.; Schut, G.; Peters, J.

2012-12-01

Energy conservation is a fundamental underpinning of all life and is accomplished by electron transport phosphorylation and/or substrate level phosphorylation. A third mechanism, known as flavin-based electron bifurcation, has recently been established as a mechanism by which life can conserve energy. In this mechanism, a flavin-containing multienzyme complex catalyzes the thermodynamically unfavorable reduction of low potential ferredoxin using electron donors with higher potentials, such as NAD(P)H or H2. Such endergonic reactions are driven forward through the simultaneous oxidation of the electron donor with higher potential acceptors such as NAD+ or heterodisulfide. Membrane associated energy converting [NiFe]hydrogenases (Ech, Eha) link the oxidation of ferredoxin with the production of H2 and in the process conserve energy in the form of an ion (Na+/H+) gradient. Ech/Eha exhibit a modular composition represented by a Na+/H+ antiporter domain and a [NiFe] hydrogenase domain. In addition, Ech/Eha can be accompanied by a formate dehyrogenase, carbon monoxide dehydrogenase, or an FAD/NAD(P)H module that enables coupling with these substrates. Representatives of Ech/Eha have been identified among anaerobic Archaea and Bacteria, including deeply rooted methanogens, sulfur-reducing Crenarcheota/Euryarchaeota as well as Thermotogae. Ech exhibit extensive homology to a number of subunits within the NADH quinone oxidoreductase or complex I family (Nuo, Fpo). Metabolically, Ech generally couple the oxidation of carbon monooxide, formate or ferredoxin to the production of H2. In contrast, the Eha complex couples the translocation of Na+ and the oxidation of H2 to the reduction of ferredoxin, which is then available for the reduction of CO2 in methanogens. In the case of Eha, the gradient of Na+/H+ produced through translocation coupled to ferredoxin oxidation can in be used to drive the phosphorylation of ADP via an ATP synthase complex, thereby representing one of the most simple forms of ATP production supporting life. This finding is consistent with phylogenetic analyses which indicate a close phylogenetic relationship between Ech/Eha and Nuo/Fpo, with [NiFe]-hydrogenase typically involved in H2 oxidation forming divergent lineages. This suggests that Ech/Eha are most likely to represent an ancestor of the Complex I family and the [NiFe]-hydrogenase family. A concatenation and phylogenetic analysis of the large and small subunits of Ech and Nuo was performed and and additional modules enabling coupling with CO2 (Eha), CO (Ech-CODH), and formate (Ech-Fdh) through H2-based electron bifurcation were overlaid on this phylogeny. The results suggest an origin for H2-based electron bifurcation via Ech/Eha among CO2 reducing hydrogenotrophic methanogenic Archaea or sulfur-reducing Archaea, with evolution towards coupling with formate and CO. These results provide insight into the evolutionary relationships between electron bifurcation-enabled ionic gradients capable of driving phosphorylation and electron transport-based phosphorylation. Moreover, these observations suggest that electron bifurcation may have been important in overcoming key metabolic bottlenecks and may have enabled life to access small energetic gradients to support metabolism on early Earth.

The influence of dissolved H2O content in supercritical carbon dioxide to the inclusion complexes formation of ketoprofen/β-cyclodextrin

NASA Astrophysics Data System (ADS)

Goenawan, Joshua; Trisanti, P. N.; Sumarno

2015-12-01

This work studies the relation between dissolved H2O content in supercritical carbon dioxide (SC-CO2) with the formation of ketoprofen (KP)/β-cyclodextrin(CD) inclusion complexes. The process involves a physical mixture of these two compounds into contact with the supercritical carbon dioxide which had been previously saturated with H2O over a certain duration. The pressure used for saturation process is 130 bar and saturation temperature was ranged between 30 °C to 50 °C. The inclusion process was achieved by keeping it for 2 hours at 160 bar and 200 bar with inclusion temperature of 50 °C. The results enable us to suggest explanations for the inclusion formation. The inclusion complexes can be formed by contacting the dissolved H2O in SC-CO2 to the physical mixture of KP and CD. An increase in the temperature of saturation process resulted in an increase of dissolved H2O content in the supercritical carbon dioxide. The increasing levels of this water soluble resulted an increase in the inclusion complexes that has been formed. The formation of inclusion complexes includes the water molecules enhancing the emptying of the CD cavities and being replaced by KP, towards a more stable energy state. The drug release used for analyzing the dissolution rate of the KP/CD complexes. The results vary from 79,85% to 99,98% after 45 minutes which is above the rate that has been assigned by Farmakope Indonesia at 70% dissolution rate for KP. The use of SC-CO2 offers a new methods for increasing the rate of dissolution of drugs that are hydrophobic such as KP. CO2 used as a supercritical fluid because of its relatively low cost, easily obtainable supercritical conditions, and lack of toxicity. The material samples were characterized by DSC and Spectrophotometer UV-vis technique.

Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Shock, Everetr L.; Koretsky, Carla M.

1995-04-01

Regression of standard state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state allows evaluation of standard partial molal entropies ( overlineSo) of aqueous metal-organic complexes involving monovalent organic acid ligands. These values of overlineSo provide the basis for correlations that can be used, together with correlation algorithms among standard partial molal properties of aqueous complexes and equation-of-state parameters, to estimate thermodynamic properties including equilibrium constants for complexes between aqueous metals and several monovalent organic acid ligands at the elevated pressures and temperatures of many geochemical processes which involve aqueous solutions. Data, parameters, and estimates are given for 270 formate, propanoate, n-butanoate, n-pentanoate, glycolate, lactate, glycinate, and alanate complexes, and a consistent algorithm is provided for making other estimates. Standard partial molal entropies of association ( Δ -Sro) for metal-monovalent organic acid ligand complexes fall into at least two groups dependent upon the type of functional groups present in the ligand. It is shown that isothermal correlations among equilibrium constants for complex formation are consistent with one another and with similar correlations for inorganic metal-ligand complexes. Additional correlations allow estimates of standard partial molal Gibbs free energies of association at 25°C and 1 bar which can be used in cases where no experimentally derived values are available.

A "turn-on" fluorescent microbead sensor for detecting nitric oxide.

PubMed

Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

2015-01-01

Nitric oxide (NO) is a messenger molecule involved in numerous physical and pathological processes in biological systems. Therefore, the development of a highly sensitive material able to detect NO in vivo is a key step in treating cardiovascular and a number of types of cancer-related diseases, as well as neurological dysfunction. Here we describe the development of a fluorescent probe using microbeads to enhance the fluorescence signal. Microbeads are infused with the fluorophore, dansyl-piperazine (Ds-pip), and quenched when the fluorophore is coordinated with a rhodium (Rh)-complex, ie, Rh2(AcO(-))4(Ds-pip). In contrast, they are able to fluoresce when the transition-metal complex is replaced by NO. To confirm the "on/off" mechanism for detecting NO, we investigated the structural molecular properties using the Fritz Haber Institute ab initio molecular simulations (FHI-AIMS) package. According to the binding energy calculation, NO molecules bind more strongly and rapidly with the Rh-core of the Rh-complex than with Ds-pip. This suggests that NO can bond strongly with the Rh-core and replace Ds-pip, even though Ds-pip is already near the Rh-core. However, the recovery process takes longer than the quenching process because the recovery process needs to overcome the energy barrier for formation of the transition state complex, ie, NO-(AcO(-))4-(Ds-pip). Further, we confirm that the Rh-complex with the Ds-pip structure has too small an energy gap to give off visible light from the highest unoccupied molecular orbital/lowest unoccupied molecular orbital energy level.

Efficient whole cell biocatalyst for formate-based hydrogen production.

PubMed

Kottenhahn, Patrick; Schuchmann, Kai; Müller, Volker

2018-01-01

Molecular hydrogen (H 2 ) is an attractive future energy carrier to replace fossil fuels. Biologically and sustainably produced H 2 could contribute significantly to the future energy mix. However, biological H 2 production methods are faced with multiple barriers including substrate cost, low production rates, and low yields. The C1 compound formate is a promising substrate for biological H 2 production, as it can be produced itself from various sources including electrochemical reduction of CO 2 or from synthesis gas. Many microbes that can produce H 2 from formate have been isolated; however, in most cases H 2 production rates cannot compete with other H 2 production methods. We established a formate-based H 2 production method utilizing the acetogenic bacterium Acetobacterium woodii . This organism can use formate as sole energy and carbon source and possesses a novel enzyme complex, the hydrogen-dependent CO 2 reductase that catalyzes oxidation of formate to H 2 and CO 2 . Cell suspensions reached specific formate-dependent H 2 production rates of 71 mmol g protein -1 h -1 (30.5 mmol g CDW -1 h -1 ) and maximum volumetric H 2 evolution rates of 79 mmol L -1 h -1 . Using growing cells in a two-step closed batch fermentation, specific H 2 production rates reached 66 mmol g CDW -1 h -1 with a volumetric H 2 evolution rate of 7.9 mmol L -1  h -1 . Acetate was the major side product that decreased the H 2 yield. We demonstrate that inhibition of the energy metabolism by addition of a sodium ionophore is suitable to completely abolish acetate formation. Under these conditions, yields up to 1 mol H 2 per mol formate were achieved. The same ionophore can be used in cultures utilizing formate as specific switch from a growing phase to a H 2 production phase. Acetobacterium woodii reached one of the highest formate-dependent specific H 2 productivity rates at ambient temperatures reported so far for an organism without genetic modification and converted the substrate exclusively to H 2 . This makes this organism a very promising candidate for sustainable H 2 production and, because of the reversibility of the A. woodii enzyme, also a candidate for reversible H 2 storage.

Electrostatic Rate Enhancement and Transient Complex of Protein-Protein Association

PubMed Central

Alsallaq, Ramzi; Zhou, Huan-Xiang

2012-01-01

The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to ~105 – 106 M−1s−1. Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys. J. 1997;73:2441–2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by kD = kD0 exp(−*/ kBT), where kD and kD0 are the rates in the presence and absence of electrostatic interactions, respectively, * is the average electrostatic interaction energy in a “transient-complex” ensemble, and kBT is thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007, 15:215–224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. PMID:17932929

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

NASA Astrophysics Data System (ADS)

Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

2018-04-01

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

PubMed

Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

2018-04-23

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

A computational study of the CO dissociation in cyclopentadienyl ruthenium complexes relevant to the racemization of alcohols.

PubMed

Stewart, Beverly; Nyhlen, Jonas; Martín-Matute, Belén; Bäckvall, Jan-E; Privalov, Timofei

2013-01-28

The formation of an active 16-electron ruthenium sec-alkoxide complex via loss of the CO ligand is an important step in the mechanism of the racemization of sec-alcohols by (η(5)-Ph(5)C(5))Ru(CO)(2)X ruthenium complexes with X = Cl and O(t)Bu. Here we show with accurate DFT calculations the potential energy profile of the CO dissociation pathway for a series of relevant (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes, where X = Cl, O(t)Bu, H and COO(t)Bu. We have found that the CO dissociation energy increases in the following order: O(t)Bu (lowest), Cl, COO(t)Bu and H (highest). Using the distance between ruthenium and C(CO), r = Ru-C(CO), as a constraint, and by optimizing all other degrees of freedom for a range of Ru-CO distances, we obtained relative energies, ΔE(r) and geometries of a sufficient number of transient structures with the elongated Ru-CO bond up to r = 3.4 Å. Our calculations provide a quantitative understanding of the CO ligand dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)Cl and (η(5)-Ph(5)C(5))Ru(CO)(2)(O(t)Bu) complexes, which is relevant to the mechanism of their catalytic activity in the racemization of alcohols. We recently reported that exchange of the CO ligand by isotopically labeled (13)CO in the Ru-O(t)Bu complex occurs twenty times faster than that in the Ru-Cl complex. This corresponds to a difference of 1.8 kcal mol(-1) in the CO dissociation energy (at room temperature). This is in very good agreement with the calculated difference between the two potential energy curves for Ru-O(t)Bu and Ru-Cl complexes, which is about 1.8-2 kcal mol(-1) around the corresponding transition states of the CO dissociation. The calculated difference in the total energy for CO dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes is related to the stabilization provided by the X group in the final 16-electron complexes, which are formed via product-like transition states. In addition to the calculated transition states of CO dissociation in Ru-O(t)Bu and Ru-Cl complexes, the calculated transient structures with the elongated Ru-CO bond provide insight into how the geometry of the ruthenium complex with a potent heteroatom donor group (X) gradually changes when one of the COs is dissociating.

Discrete structural features among interface residue-level classes.

PubMed

Sowmya, Gopichandran; Ranganathan, Shoba

2015-01-01

Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs.

Discrete structural features among interface residue-level classes

PubMed Central

2015-01-01

Background Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. Results Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. Conclusions Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs. PMID:26679043

Ultrafast time-resolved carotenoid to-bacteriochlorophyll energy transfer in LH2 complexes from photosynthetic bacteria.

PubMed

Cong, Hong; Niedzwiedzki, Dariusz M; Gibson, George N; LaFountain, Amy M; Kelsh, Rhiannon M; Gardiner, Alastair T; Cogdell, Richard J; Frank, Harry A

2008-08-28

Steady-state and ultrafast time-resolved optical spectroscopic investigations have been carried out at 293 and 10 K on LH2 pigment-protein complexes isolated from three different strains of photosynthetic bacteria: Rhodobacter (Rb.) sphaeroides G1C, Rb. sphaeroides 2.4.1 (anaerobically and aerobically grown), and Rps. acidophila 10050. The LH2 complexes obtained from these strains contain the carotenoids, neurosporene, spheroidene, spheroidenone, and rhodopin glucoside, respectively. These molecules have a systematically increasing number of pi-electron conjugated carbon-carbon double bonds. Steady-state absorption and fluorescence excitation experiments have revealed that the total efficiency of energy transfer from the carotenoids to bacteriochlorophyll is independent of temperature and nearly constant at approximately 90% for the LH2 complexes containing neurosporene, spheroidene, spheroidenone, but drops to approximately 53% for the complex containing rhodopin glucoside. Ultrafast transient absorption spectra in the near-infrared (NIR) region of the purified carotenoids in solution have revealed the energies of the S1 (2(1)Ag-)-->S2 (1(1)Bu+) excited-state transitions which, when subtracted from the energies of the S0 (1(1)Ag-)-->S2 (1(1)Bu+) transitions determined by steady-state absorption measurements, give precise values for the positions of the S1 (2(1)Ag-) states of the carotenoids. Global fitting of the ultrafast spectral and temporal data sets have revealed the dynamics of the pathways of de-excitation of the carotenoid excited states. The pathways include energy transfer to bacteriochlorophyll, population of the so-called S* state of the carotenoids, and formation of carotenoid radical cations (Car*+). The investigation has found that excitation energy transfer to bacteriochlorophyll is partitioned through the S1 (1(1)Ag-), S2 (1(1)Bu+), and S* states of the different carotenoids to varying degrees. This is understood through a consideration of the energies of the states and the spectral profiles of the molecules. A significant finding is that, due to the low S1 (2(1)Ag-) energy of rhodopin glucoside, energy transfer from this state to the bacteriochlorophylls is significantly less probable compared to the other complexes. This work resolves a long-standing question regarding the cause of the precipitous drop in energy transfer efficiency when the extent of pi-electron conjugation of the carotenoid is extended from ten to eleven conjugated carbon-carbon double bonds in LH2 complexes from purple photosynthetic bacteria.

Energetics of drug-DNA interactions.

PubMed

Chaires, J B

1997-01-01

Understanding the thermodynamics of drug binding to DNA is of both practical and fundamental interest. The practical interest lies in the contribution that thermodynamics can make to the rational design process for the development of new DNA targeted drugs. Thermodynamics offer key insights into the molecular forces that drive complex formation that cannot be obtained by structural or computational studies alone. The fundamental interest in these interactions lies in what they can reveal about the general problems of parsing and predicting ligand binding free energies. For these problems, drug-DNA interactions offer several distinct advantages, among them being that the structures of many drug-DNA complexes are known at high resolution and that such structures reveal that in many cases the drug acts as a rigid body, with little conformational change upon binding. Complete thermodynamic profiles (delta G, delta H, delta S, delta Cp) for numerous drug-DNA interactions have been obtained, with the help of high-sensitivity microcalorimetry. The purpose of this article is to offer a perspective on the interpretation of these thermodynamics parameters, and in particular how they might be correlated with known structural features. Obligatory conformational changes in the DNA to accommodate intercalators and the loss of translational and rotational freedom upon complex formation both present unfavorable free energy barriers for binding. Such barriers must be overcome by favorable free energy contributions from the hydrophobic transfer of ligand from solution into the binding site, polyelectrolyte contributions from coupled ion release, and molecular interactions (hydrogen and ionic bonds, van der Waals interactions) that form within the binding site. Theoretical and semiempirical tools that allow estimates of these contributions to be made will be discussed, and their use in dissecting experimental data illustrated. This process, even at the current level of approximation, can shed considerable light on the drug-DNA binding process.

Theoretical insights into the structures and mechanical properties of HMX/NQ cocrystal explosives and their complexes, and the influence of molecular ratios on their bonding energies.

PubMed

Li, Yong-Xiang; Chen, Shu-Sen; Ren, Fu-de

2015-09-01

Molecular dynamics (MD) methods were employed to study the binding energies and mechanical properties of selected crystal planes of 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/nitroguanidine (NQ) cocrystals at different molecular molar ratios. The densities and detonation velocities of the cocrystals at different molar ratios were estimated. The intermolecular interaction and bond dissociation energy (BDE) of the N-NO2 bond in the HMX:NQ (1:1) complex were calculated using the B3LYP, MP2(full) and M06-2X methods with the 6-311++G(d,p) and 6-311++G(2df,2p) basis sets. The results indicated that the HMX/NQ cocrystal prefers cocrystalizing in a 1:1 molar ratio, and the cocrystallization is dominated by the (0 2 0) and (1 0 0) facets. The K, G, and E values of the ratio of 1:1 are smaller than those of the other ratios, and the 1:1 cocrystal has the best ductility. The N-NO2 bond becomes stronger upon the formation of the intermolecular H-bonding interaction and the sensitivity of HMX decreases in the cocrystal. This sensitivity change in the HMX/NQ cocrystal originates not only from the formation of the intermolecular interaction but also from the increment of the BDE of N-NO2 bond in comparison with isolated HMX. The HMX/NQ (1:1) cocrystal exhibits good detonation performance. Reduced density gradient (RDG) reveals the nature of cocrystallization. Analysis of the surface electrostatic potential further confirmed that the sensitivity decreases in complex (or cocrystal) in comparison with that in isolated HMX.

Osmotically Induced Reversible Transitions in Lipid-DNA Mesophases

PubMed Central

Danino, Dganit; Kesselman, Ellina; Saper, Gadiel; Petrache, Horia I.; Harries, Daniel

2009-01-01

We follow the effect of osmotic pressure on isoelectric complexes that self-assemble from mixtures of DNA and mixed neutral and cationic lipids. Using small angle x-ray diffraction and freeze-fracture cryo-electron microscopy, we find that lamellar complexes known to form in aqueous solutions can reversibly transition to hexagonal mesophases under high enough osmotic stress exerted by adding a neutral polymer. Using molecular spacings derived from x-ray diffraction, we estimate the reversible osmotic pressure-volume (Π-V) work needed to induce this transition. We find that the transition free energy is comparable to the work required to elastically bend lipid layers around DNA. Consistent with this, the required work is significantly lowered by an addition of hexanol, which is known to soften lipid bilayers. Our findings not only help to resolve the free-energy contributions associated with lipid-DNA complex formation, but they also demonstrate the importance that osmotic stress can have to the macromolecular phase geometry in realistic biological environments. PMID:19348739

Investigation of flavonoids bearing different substituents on ring C and their cu2+ complex binding with bovine serum albumin: structure-affinity relationship aspects.

PubMed

Shi, Shuyun; Zhang, Yuping; Chen, Xiaoqin; Peng, Mijun

2011-10-12

The effects of 1:1 flavonoid-Cu(2+) complexes of four flavonoids with different C-ring substituents, quercetin (QU), luteolin (LU), taxifolin (TA), and (+)-catechin (CA), on bovine serum albumin (BSA) were investigated and compared with corresponding free flavonoids by spectroscopic analysis in an attempt to characterize the chemical association taking place. The results indicated that all of the quenching mechanisms were based on static quenching combined with nonradiative energy transfer. Cu(2+) chelation changed the binding constants for BSA depending on the structures of flavonoids and the detected concentrations. The reduced hydroxyl groups, increased steric hindrance, and hydrophilicity of Cu(2+) chelation may be the main reasons for the reduced binding constants, whereas the formation of stable flavonoid-Cu(2+) complexes and synergistic action could increase the binding constants. The changed trends of critical energy transfer distance (R(0)) for Cu(2+) chelation were contrary to those of binding constants.

Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands

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

Xu, Huifang; Xu, David C.; Wang, Yifeng

Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal–ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r Mn+), Gibbs free energy of formation (ΔG° f,Mn+), and solvation energy (ΔG° s,Mn+)] by 2.303RT log K ML = (α* MLΔG° f,Mn+ – β* MLr Mn+ +more » γ* MLΔG° s,Mn+ – δ* ML), where the coefficients (α* ML, β* ML, γ* ML, and intercept δ* ML) are determined by fitting the equation to the existing experimental data. Coefficients β* ML and γ* ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG° f,Mn+) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α* ML is an index for the softness or hardness of a complexing ligand. Proton (H +) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid–base interactions is determined by the term α* MLΔG° f,Mn+; a positive product of α* ML and ΔG° f,Mn+ indicates that the acid–base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β* MLr Mn+ and γ* MLΔG° s,Mn+, which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. As a result, the new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.« less

Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands

DOE PAGES

Xu, Huifang; Xu, David C.; Wang, Yifeng

2017-10-26

Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal–ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r Mn+), Gibbs free energy of formation (ΔG° f,Mn+), and solvation energy (ΔG° s,Mn+)] by 2.303RT log K ML = (α* MLΔG° f,Mn+ – β* MLr Mn+ +more » γ* MLΔG° s,Mn+ – δ* ML), where the coefficients (α* ML, β* ML, γ* ML, and intercept δ* ML) are determined by fitting the equation to the existing experimental data. Coefficients β* ML and γ* ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG° f,Mn+) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α* ML is an index for the softness or hardness of a complexing ligand. Proton (H +) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid–base interactions is determined by the term α* MLΔG° f,Mn+; a positive product of α* ML and ΔG° f,Mn+ indicates that the acid–base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β* MLr Mn+ and γ* MLΔG° s,Mn+, which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. As a result, the new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.« less

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Photosynthetic dioxygen formation studied by time-resolved delayed fluorescence measurements--method, rationale, and results on the activation energy of dioxygen formation.

PubMed

Buchta, Joachim; Grabolle, Markus; Dau, Holger

2007-06-01

The analysis of the time-resolved delayed fluorescence (DF) measurements represents an important tool to study quantitatively light-induced electron transfer as well as associated processes, e.g. proton movements, at the donor side of photosystem II (PSII). This method can provide, inter alia, insights in the functionally important inner-protein proton movements, which are hardly detectable by conventional spectroscopic approaches. The underlying rationale and experimental details of the method are described. The delayed emission of chlorophyll fluorescence of highly active PSII membrane particles was measured in the time domain from 10 mus to 60 ms after each flash of a train of nanosecond laser pulses. Focusing on the oxygen-formation step induced by the third flash, we find that the recently reported formation of an S4-intermediate prior to the onset of O-O bond formation [M. Haumann, P. Liebisch, C. Müller, M. Barra, M. Grabolle, H. Dau, Science 310, 1019-1021, 2006] is a multiphasic process, as anticipated for proton movements from the manganese complex of PSII to the aqueous bulk phase. The S4-formation involves three or more likely sequential steps; a tri-exponential fit yields time constants of 14, 65, and 200 mus (at 20 degrees C, pH 6.4). We determine that S4-formation is characterized by a sizable difference in Gibbs free energy of more than 90 meV (20 degrees C, pH 6.4). In the second part of the study, the temperature dependence (-2.7 to 27.5 degrees C) of the rate constant of dioxygen formation (600/s at 20 degrees C) was investigated by analysis of DF transients. If the activation energy is assumed to be temperature-independent, a value of 230 meV is determined. There are weak indications for a biphasicity in the Arrhenius plot, but clear-cut evidence for a temperature-dependent switch between two activation energies, which would point to the existence of two distinct rate-limiting steps, is not obtained.

Visualization of complex DNA double-strand breaks in a tumor treated with carbon ion radiotherapy

PubMed Central

Oike, Takahiro; Niimi, Atsuko; Okonogi, Noriyuki; Murata, Kazutoshi; Matsumura, Akihiko; Noda, Shin-Ei; Kobayashi, Daijiro; Iwanaga, Mototaro; Tsuchida, Keisuke; Kanai, Tatsuaki; Ohno, Tatsuya; Shibata, Atsushi; Nakano, Takashi

2016-01-01

Carbon ion radiotherapy shows great potential as a cure for X-ray-resistant tumors. Basic research suggests that the strong cell-killing effect induced by carbon ions is based on their ability to cause complex DNA double-strand breaks (DSBs). However, evidence supporting the formation of complex DSBs in actual patients is lacking. Here, we used advanced high-resolution microscopy with deconvolution to show that complex DSBs are formed in a human tumor clinically treated with carbon ion radiotherapy, but not in a tumor treated with X-ray radiotherapy. Furthermore, analysis using a physics model suggested that the complexity of radiotherapy-induced DSBs is related to linear energy transfer, which is much higher for carbon ion beams than for X-rays. Visualization of complex DSBs in clinical specimens will help us to understand the anti-tumor effects of carbon ion radiotherapy. PMID:26925533

Divacancy complexes induced by Cu diffusion in Zn-doped GaAs

NASA Astrophysics Data System (ADS)

Elsayed, M.; Krause-Rehberg, R.; Korff, B.; Ratschinski, I.; Leipner, H. S.

2013-08-01

Positron annihilation spectroscopy was applied to investigate the nature and thermal behavior of defects induced by Cu diffusion in Zn-doped p-type GaAs crystals. Cu atoms were intentionally introduced in the GaAs lattice through thermally activated diffusion from a thin Cu capping layer at 1100 °C under defined arsenic vapor pressure. During isochronal annealing of the obtained Cu-diffused GaAs in the temperature range of 450-850 K, vacancy clusters were found to form, grow and finally disappear. We found that annealing at 650 K triggers the formation of divacancies, whereas further increasing in the annealing temperature up to 750 K leads to the formation of divacancy-copper complexes. The observations suggest that the formation of these vacancy-like defects in GaAs is related to the out-diffusion of Cu. Two kinds of acceptors are detected with a concentration of about 1016 - 1017 cm-3, negative ions and arsenic vacancy copper complexes. Transmission electron microscopy showed the presence of voids and Cu precipitates which are not observed by positron measurements. The positron binding energy to shallow traps is estimated using the positron trapping model. Coincidence Doppler broadening spectroscopy showed the presence of Cu in the immediate vicinity of the detected vacancies. Theoretical calculations suggested that the detected defect is VGaVAs-2CuGa.

Effects of collision energy and vibrational excitation of CH3 + cations on its reactivity with hydrocarbons: But-2-yne CH3CCCH3 as reagent partner

NASA Astrophysics Data System (ADS)

Cernuto, Andrea; Lopes, Allan; Romanzin, Claire; Cunha de Miranda, Barbara; Ascenzi, Daniela; Tosi, Paolo; Tonachini, Glauco; Maranzana, Andrea; Polášek, Miroslav; Žabka, Jan; Alcaraz, Christian

2017-10-01

The methyl carbocation is ubiquitous in gaseous environments, such as planetary ionospheres, cometary comae, and the interstellar medium, as well as combustion systems and plasma setups for technological applications. Here we report on a joint experimental and theoretical study on the mechanism of the reaction CH3 + + CH3CCCH3 (but-2-yne, also known as dimethylacetylene), by combining guided ion beam mass spectrometry experiments with ab initio calculations of the potential energy hypersurface. Such a reaction is relevant in understanding the chemical evolution of Saturn's largest satellite, Titan. Two complementary setups have been used: in one case, methyl cations are generated via electron ionization, while in the other case, direct vacuum ultraviolet photoionization with synchrotron radiation of methyl radicals is used to study internal energy effects on the reactivity. Absolute reactive cross sections have been measured as a function of collision energy, and product branching ratios have been derived. The two most abundant products result from electron and hydride transfer, occurring via direct and barrierless mechanisms, while other channels are initiated by the electrophilic addition of the methyl cation to the triple bond of but-2-yne. Among the minor channels, special relevance is placed on the formation of C5H7 +, stemming from H2 loss from the addition complex. This is the only observed condensation product with the formation of new C—C bonds, and it might represent a viable pathway for the synthesis of complex organic species in astronomical environments and laboratory plasmas.

Reconstructing the eruption magnitude and energy budgets for the pre-historic eruption of the monogenetic ˜5 ka Mt. Gambier Volcanic Complex, south-eastern Australia

NASA Astrophysics Data System (ADS)

van Otterloo, Jozua; Cas, Raymond A. F.

2013-12-01

Understanding explosive volcanic eruptions, especially phreatomagmatic eruptions, their intensities and energy budgets is of major importance when it comes to risk and hazard studies. With only a few historic occurrences of phreatomagmatic activity, a large amount of our understanding comes from the study of pre-historic volcanic centres, which causes issues when it comes to preservation and vegetation. In this research, we show that using 3D geometrical modelling it is possible to obtain volume estimates for different deposits of a pre-historic, complex, monogenetic centre, the Mt. Gambier Volcanic Complex, south-eastern Australia. Using these volumes, we further explore the energy budgets and the magnitude of this eruption (VEI 4), including dispersal patterns (eruption columns varying between 5 and 10 km, dispersed towards north-east to south), to further our understanding of intraplate, monogenetic eruptions involving phreatomagmatic activity. We also compare which thermodynamic model fits best in the creation of the maar crater of Mt. Gambier: the major-explosion-dominated model or the incremental growth model. In this case, the formation of most of the craters can best be explained by the latter model.

Detection of ochratoxin A (OTA) in coffee using chemiluminescence resonance energy transfer (CRET) aptasensor.

PubMed

Jo, Eun-Jung; Mun, Hyoyoung; Kim, Su-Ji; Shim, Won-Bo; Kim, Min-Gon

2016-03-01

We report a chemiluminescence resonance energy transfer (CRET) aptasensor for the detection of ochratoxin A (OTA) in roasted coffee beans. The aptamer sequences used in this study are 5'-DNAzyme-Linker-OTA aptamer-3'-dabcyl. Dabcyl at the end of the OTA aptamer region plays as a quencher in CRET aptasensor. When hemin and OTA are added, the dabcyl-labeled OTA aptamer approaches to the G-quadruplex-hemin complex by formation of the G-quadruplex-OTA complex. The G-quadruplex-hemin complexes possess horseradish peroxidase (HRP)-like activity, and therefore, the HRP-mimicking DNAzyme (HRPzyme) catalyzes peroxidation in the presence of luminol and H2O2. Resonance energy transfer between luminol (donor) and dabcyl (acceptor) enables quenching of chemiluminescence signals. The signal decreases with increasing the concentration of OTA within the range of 0.1-100ngmL(-1) (limit of detection 0.22ngmL(-1)), and the level of recovery of the respective 1ngmL(-1) and 10ngmL(-1) spiked coffee samples was 71.5% and 93.3%. These results demonstrated the potential of the proposed method for OTA analysis in diverse foods. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microhydration of caesium compounds: Cs, CsOH, CsI and Cs₂I₂ complexes with one to three H₂O molecules of nuclear safety interest.

PubMed

Sudolská, Mária; Cantrel, Laurent; Cernušák, Ivan

2014-04-01

Structure and thermodynamic properties (standard enthalpies of formation and Gibbs free energies) of hydrated caesium species of nuclear safety interest, Cs, CsOH, CsI and its dimer Cs₂I₂, with one up to three water molecules, are calculated to assess their possible existence in severe accident occurring to a pressurized water reactor. The calculations were performed using the coupled cluster theory including single, double and non-iterative triple substitutions (CCSD(T)) in conjunction with the basis sets (ANO-RCC) developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. Thermodynamic properties obtained by these correlated ab initio calculations (entropies and thermal capacities at constant pressure as a function of temperature) are used in nuclear accident simulations using ASTEC/SOPHAEROS software. Interaction energies, standard enthalpies and Gibbs free energies of successive water molecules addition determine the ordering of the complexes. CsOH forms the most hydrated stable complexes followed by CsI, Cs₂I₂, and Cs. CsOH still exists in steam atmosphere even at quite high temperature, up to around 1100 K.

Photoprotection and triplet energy transfer in higher plants: the role of electronic and nuclear fluctuations.

PubMed

Cupellini, Lorenzo; Jurinovich, Sandro; Prandi, Ingrid G; Caprasecca, Stefano; Mennucci, Benedetta

2016-04-28

Photosynthetic organisms employ several photoprotection strategies to avoid damage due to the excess energy in high light conditions. Among these, quenching of triplet chlorophylls by neighboring carotenoids (Cars) is fundamental in preventing the formation of singlet oxygen. Cars are able to accept the triplets from chlorophylls by triplet energy transfer (TET). We have here studied TET rates in CP29, a minor light-harvesting complex (LHC) of the Photosystem II in plants. A fully atomistic strategy combining classical molecular dynamics of the LHC in its natural environment with a hybrid time-dependent density functional theory/polarizable MM description of the TET is used. We find that the structural fluctuations of the pigment-protein complex can largely enhance the transfer rates with respect to those predicted using the crystal structure, reducing the triplet quenching times in the subnanosecond scale. These findings add a new perspective for the interpretation of the photoprotection function and its relation with structural motions of the LHC.

Electrostatic rate enhancement and transient complex of protein-protein association.

PubMed

Alsallaq, Ramzi; Zhou, Huan-Xiang

2008-04-01

The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to approximately 10(5)-10(6) M(-1) s(-1). Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys J 1997;73:2441-2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by $k_{\\bf D}$ = $k_{D}0\\ {exp} ( - \\langle U_{el} \\rangle;{\\star}/k_{B} T),$ where k(D) and k(D0) are the rates in the presence and absence of electrostatic interactions, respectively, U(el) is the average electrostatic interaction energy in a "transient-complex" ensemble, and k(B)T is the thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with the experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007;15:215-224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. (c) 2007 Wiley-Liss, Inc.

Thiol surface complexation on growing CdS clusters

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

Swayambunathan, V.; Hayes, D.; Schmidt, K.H.

1990-05-09

The growth of small CdS colloidal particles has been initiated by pulse radiolytic release of sulfide from thiol (3-mercapto-1,2-propanediol, RSH) in the presence of Cd{sup 2+} ions. The kinetics and stoichiometry of the ensuring reactions were followed by conductivity, absorption spectroscopy, and light-scattering techniques. The final CdS product has been identified by electron diffraction. The formation of Cd-thiolate complexes at the surface of the particles is indicated by conductivity and by energy dispersive analysis of X-ray (EDAX) results. The rate of formation of CdS clusters is strongly pH dependent due to the pH effect on the stability of Dd{sup 2+}/HS{supmore » {minus}} complexes. At low pHs (4.0-5.3) the growth mechanism is proposed to be primarily a cluster-molecule process. At this pH range Cd{sup 2+} ions at the CdS particle surface complex with thiolate ions stronger than in the bulk of the solution. The size control of the particles by thiols is proposed to result from a competition of thiolate ions with HS{sup {minus}} ions for cadmium ions at the surface of the growing particles.« less

Self-optimizing charge-transfer energy phenomena in metallosupramolecular complexes by dynamic constitutional self-sorting.

PubMed

Legrand, Yves-Marie; van der Lee, Arie; Barboiu, Mihail

2007-11-12

In this paper we report an extended series of 2,6-(iminoarene)pyridine-type ZnII complexes [(Lii)2Zn]II, which were surveyed for their ability to self-exchange both their ligands and their aromatic arms and to form different homoduplex and heteroduplex complexes in solution. The self-sorting of heteroduplex complexes is likely to be the result of geometric constraints. Whereas the imine-exchange process occurs quantitatively in 1:1 mixtures of [(Lii)2Zn]II complexes, the octahedral coordination process around the metal ion defines spatial-frustrated exchanges that involve the selective formation of heterocomplexes of two, by two different substituents; the bulkiest ones (pyrene in principle) specifically interact with the pseudoterpyridine core, sterically hindering the least bulky ones, which are intermolecularly stacked with similar ligands of neighboring molecules. Such a self-sorting process defined by the specific self-constitution of the ligands exchanging their aromatic substituents is self-optimized by a specific control over their spatial orientation around a metal center within the complex. They ultimately show an improved charge-transfer energy function by virtue of the dynamic amplification of self-optimized heteroduplex architectures. These systems therefore illustrate the convergence of the combinatorial self-sorting of the dynamic combinatorial libraries (DCLs) strategy and the constitutional self-optimized function.

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

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

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

DOE PAGES

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.; ...

2018-02-08

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Energy transfer of highly vibrationally excited biphenyl.

PubMed

Hsu, Hsu Chen; Dyakov, Yuri; Ni, Chi-Kung

2010-11-07

The energy transfer between Kr atoms and highly vibrationally excited, rotationally cold biphenyl in the triplet state was investigated using crossed-beam/time-of-flight mass spectrometer/time-sliced velocity map ion imaging techniques. Compared to the energy transfer of naphthalene, energy transfer of biphenyl shows more forward scattering, less complex formation, larger cross section for vibrational to translational (V→T) energy transfer, smaller cross section for translational to vibrational and rotational (T→VR) energy transfer, larger total collisional cross section, and more energy transferred from vibration to translation. Significant increase in the large V→T energy transfer probabilities, termed supercollisions, was observed. The difference in the energy transfer of highly vibrationally excited molecules between rotationally cold naphthalene and rotationally cold biphenyl is very similar to the difference in the energy transfer of highly vibrationally excited molecules between rotationally cold naphthalene and rotationally hot naphthalene. The low-frequency vibrational modes with out-of-plane motion and rotationlike wide-angle motion are attributed to make the energy transfer of biphenyl different from that of naphthalene.

Density functional studies of the defect-induced electronic structure modifications in bilayer boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-05-01

The van der Waals interaction-corrected density functional theory is used in this study to investigate the formation, energetic stability, and inter-layer cohesion in bilayer hexagonal boronitrene. The effect of inter-layer separation on the electronic structure is systematically investigated. The formation and energetic stability of intrinsic defects are also investigated at the equilibrium inter-layer separation. It is found that nonstoichiometric defects, and their complexes, that induce excess nitrogen or excess boron, in each case, are relatively more stable in the atmosphere that corresponds to the excess atomic species. The modifications of the electronic structure due to formation of complexes are also investigated. It is shown that van der Waals density functional theory gives an improved description of the cohesive properties but not the electronic structure in bilayer boronitrene compared to other functionals. We identify energetically favourable topological defects that retain the energy gap in the electronic structure, and discuss their implications for band gap engineering in low-n layer boronitrene insulators. The relative strengths and weaknesses of the functionals in predicting the properties of bilayer boronitrene are also discussed.

Formation of VP-Zn complexes in bulk InP(Zn) by migration of P vacancies from the (110) surface

NASA Astrophysics Data System (ADS)

Slotte, J.; Saarinen, K.; Ebert, Ph.

2006-05-01

We apply a combination of positron annihilation spectroscopy and scanning tunneling microscopy to show that thermally generated P vacancies diffuse from the InP surface toward the bulk. The defect observed in the bulk can be identified as a complex consisting of a P vacancy and a Zn impurity. We infer that this pair is formed when the diffusing positive P vacancy is trapped at the Zn dopant. A rough estimate for the migration energy of the P vacancy results in a value of 1.3eV .

Intrahippocampal Glutamine Administration Inhibits mTORC1 Signaling and Impairs Long-Term Memory

ERIC Educational Resources Information Center

Rozas, Natalia S.; Redell, John B.; Pita-Almenar, Juan D.; McKenna, James, III.; Moore, Anthony N.; Gambello, Michael J.; Dash, Pramod K.

2015-01-01

The mechanistic Target of Rapamycin Complex 1 (mTORC1), a key regulator of protein synthesis and cellular growth, is also required for long-term memory formation. Stimulation of mTORC1 signaling is known to be dependent on the availability of energy and growth factors, as well as the presence of amino acids. In vitro studies using serum- and amino…

Notable effects of metal salts on UV-vis absorption spectra of α-, β-, γ-, and δ-tocopheroxyl radicals in acetonitrile solution. The complex formation between tocopheroxyls and metal cations.

PubMed

Mukai, Kazuo; Kohno, Yutaro; Ouchi, Aya; Nagaoka, Shin-ichi

2012-08-02

The measurements of the UV-vis absorption spectra of α-, β-, γ-, and δ-tocopheroxyl (α-, β-, γ-, and δ-Toc(•)) radicals were performed by reacting aroxyl (ArO(•)) radical with α-, β-, γ-, and δ-tocopherol (α-, β-, γ-, and δ-TocH), respectively, in acetonitrile solution including three kinds of alkali and alkaline earth metal salts (LiClO(4), NaClO(4), and Mg(ClO(4))(2)) (MX or MX(2)), using stopped-flow spectrophotometry. The maximum wavelengths (λ(max)) of the absorption spectra of the α-, β-, γ-, and δ-Toc(•) located at 425-428 nm without metal salts increased with increasing concentrations of metal salts (0-0.500 M) in acetonitrile and approached some constant values, suggesting (Toc(•)···M(+) (or M(2+))) complex formations. Similarly, the values of the apparent molar extinction coefficient (ε(max)) increased drastically with increasing concentrations of metal salts in acetonitrile and approached some constant values. The result suggests that the formations of Toc(•) dimers were suppressed by the metal ion complex formations of Toc(•) radicals. The stability constants (K) were determined for Li(+), Na(+), and Mg(2+) complexes of α-, β-, γ-, and δ-Toc(•). The K values increased in the order of NaClO(4) < LiClO(4) < Mg(ClO(4))(2), being independent of the kinds of Toc(•) radicals. Furthermore, the K values increased in the order of δ- < γ- < β- < α-Toc(•) radicals for each metal salt. The alkali and alkaline earth metal salts having a smaller ionic radius of the cation and a larger charge of the cation gave a larger shift of the λ(max) value, a larger ε(max) value, and a larger K value. The result of the DFT molecular orbital calculations indicated that the α-, β-, γ-, and δ-Toc(•) radicals were stabilized by the (1:1) complex formation with metal cations (Li(+), Na(+), and Mg(2+)). Stabilization energy (E(S)) due to the complex formation increased in the order of Na(+) < Li(+) < Mg(2+) complexes, being independent of the kinds of Toc(•) radicals. The calculated result also indicated that the metal cations coordinate to the O atom at the sixth position of α-, β-, γ-, and δ-Toc(•) radicals.

Energetics of dendrimer binding to HIV-1 gp120-CD4 complex and mechanismic aspects of its role as an entry-inhibitor

NASA Astrophysics Data System (ADS)

Saurabh, Suman; Sahoo, Anil Kumar; Maiti, Prabal K.

2016-10-01

Experiments and computational studies have established that de-protonated dendrimers (SPL7013 and PAMAM) act as entry-inhibitors of HIV. SPL7013 based Vivagel is currently under clinical development. The dendrimer binds to gp120 in the gp120-CD4 complex, destabilizes it by breaking key contacts between gp120 and CD4 and prevents viral entry into target cells. In this work, we provide molecular details and energetics of the formation of the SPL7013-gp120-CD4 ternary complex and decipher modes of action of the dendrimer in preventing viral entry. It is also known from experiments that the dendrimer binds weakly to gp120 that is not bound to CD4. It binds even more weakly to the CD4-binding region of gp120 and thus cannot directly block gp120-CD4 complexation. In this work, we examine the feasibility of dendrimer binding to the gp120-binding region of CD4 and directly blocking gp120-CD4 complex formation. We find that the process of the dendrimer binding to CD4 can compete with gp120-CD4 binding due to comparable free energy change for the two processes, thus creating a possibility for the dendrimer to directly block gp120-CD4 complexation by binding to the gp120-binding region of CD4.

Demonstration of thermal dissipation of absorbed quanta during energy-dependent quenching of chlorophyll fluorescence in photosynthetic membranes.

PubMed

Yahyaoui, W; Harnois, J; Carpentier, R

1998-11-27

When plant leaves or chloroplasts are exposed to illumination that exceeds their photosynthetic capacity, photoprotective mechanisms such as described by the energy-dependent (non-photochemical) quenching of chlorophyll fluorescence are involved. The protective action is attributed to an increased rate constant for thermal dissipation of absorbed quanta. We applied photoacoustic spectroscopy to monitor thermal dissipation in spinach thylakoid membranes together with simultaneous measurement of chlorophyll fluorescence in the presence of inhibitors of opposite action on the formation of delta pH across the thylakoid membrane (tentoxin and nigericin/valinomycin). A linear relationship between the appearance of fluorescence quenching during formation of the delta pH and the reciprocal variation of thermal dissipation was demonstrated. Dicyclohexylcarbodiimide, which is known to prevent protonation of the minor light-harvesting complexes of photosystem II, significantly reduced the formation of fluorescence quenching and the concurrent increase in thermal dissipation. However, the addition of exogenous ascorbate to activate the xanthophyll de-epoxidase increased non-photochemical fluorescence quenching without affecting the measured thermal dissipation. It is concluded that a portion of energy-dependent fluorescence quenching that is independent of de-epoxidase activity can be readily measured by photoacoustic spectroscopy as an increase in thermal deactivation processes.

Crystallization of glass-forming liquids: Specific surface energy

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

Schmelzer, Jürn W. P., E-mail: juern-w.schmelzer@uni-rostock.de; Abyzov, Alexander S.

2016-08-14

A generalization of the Stefan-Skapski-Turnbull relation for the melt-crystal specific interfacial energy is developed in terms of the generalized Gibbs approach extending its standard formulation to thermodynamic non-equilibrium states. With respect to crystal nucleation, this relation is required in order to determine the parameters of the critical crystal clusters being a prerequisite for the computation of the work of critical cluster formation. As one of its consequences, a relation for the dependence of the specific surface energy of critical clusters on temperature and pressure is derived applicable for small and moderate deviations from liquid-crystal macroscopic equilibrium states. Employing the Stefan-Skapski-Turnbullmore » relation, general expressions for the size and the work of formation of critical crystal clusters are formulated. The resulting expressions are much more complex as compared to the respective relations obtained via the classical Gibbs theory. Latter relations are retained as limiting cases of these more general expressions for moderate undercoolings. By this reason, the formulated, here, general relations for the specification of the critical cluster size and the work of critical cluster formation give a key for an appropriate interpretation of a variety of crystallization phenomena occurring at large undercoolings which cannot be understood in terms of the Gibbs’ classical treatment.« less

Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

PubMed

Varadwaj, Pradeep Risikrishna

2010-05-01

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density rho ( c ), the Laplacian of electron charge density nabla(2)rho(c), and the total energy density (H ( c )) at the critical points between the interatomic regions that the interaction N...H is indeed electrostatic in origin (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) < 0) and HX ((rho(c) > 0, nabla(2)rho(c) < 0 and H(c) < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E((2)), caused by charge transfer mechanism shows that the interaction N...H is n(N) --> BD*(HX) delocalization.

Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda.

PubMed

Piekarska, B; Konieczny, L; Rybarska, J; Stopa, B; Zemanek, G; Szneler, E; Król, M; Nowak, M; Roterman, I

2001-11-01

Moderate heating (40-50 degrees C) of immunoglobulins makes them accessible for binding with Congo Red and some related highly associated dyes. The binding is specific and involves supramolecular dye ligands presenting ribbon-like micellar bodies. The L chain lambda dimer, which upon heating disclosed the same binding requirement with respect to supramolecular dye ligands, was used in this work to identify the site of their attachment. Two clearly defined dye-protein (L lambda chain) complexes arise upon heating, here called complex I and complex II. The first is formed at low temperatures (up to 40-45 degrees C) and hence by a still native protein, while the formation of the second one is associated with domain melting above 55 degrees C. They contain 4 and 8 dye molecules bound per L chain monomer, respectively. Complex I also forms efficiently at high dye concentration even at ambient temperature. Complex I and its formation was the object of the present studies. Three structural events that could make the protein accessible to penetration by the large dye ligand were considered to occur in L chains upon heating: local polypeptide chain destabilization, VL-VL domain incoherence, and protein melting. Of these three possibilities, local low-energy structural alteration was found to correlate best with the formation of complex I. It was identified as decreased packing stability of the N-terminal polypeptide chain fragment, which as a result made the V domain accessible for dye penetration. The 19-amino acid N-terminal fragment becomes susceptible to proteolytic cleavage after being replaced by the dye at its packing locus. Its splitting from the dye-protein complex was proved by amino acid sequence analysis. The emptied packing locus, which becomes the site that holds the dye, is bordered by strands of amino acids numbered 74-80 and 105-110, as shown by model analysis. The character of the temperature-induced local polypeptide chain destabilization and its possible role in intramolecular antibody signaling is discussed. Copyright 2001 John Wiley & Sons, Inc.

Direct decarbonylation of furfural to furan: A density functional theory study on Pt-graphene

NASA Astrophysics Data System (ADS)

Fellah, Mehmet Ferdi

2017-05-01

The catalytic mechanism of direct decarbonylation of furfural to furan on Pt graphene surface has been investigated by means of density functional theory (DFT) calculations. The main catalytic mechanism proposed in this study has six steps such as furfural adsorption, dissociation of H from adsorbed furfural, dissociation of carbon monoxide (molecularly) from adsorbed complex, furan formation and desorption of products. It has been concluded that the rate determining step for direct decarbonylation of furfural to furan is furan formation step and global activation barrier for this catalytic system is 82 kJ/mol consisting of zero point energy and thermal energy corrections. Pt-graphene structure has an important role on the catalytic decarbonylation of furfural to furan without any other reactants. This accordingly points out that Pt doped graphene structure might be an encouraging catalyst for direct decarbonylation of furfural to furan molecule as a valuable chemical material.

Hybrid Functional Study of Sodium and Potassium Incorporation in Cu2ZnSnS4

NASA Astrophysics Data System (ADS)

Tse, Kin Fai; Wong, Manhoi; Zhang, Yiou; Zhang, Jingzhao; Zhu, Junyi

The thermodynamics of Na and K incorporation and its effects in Cu2ZnSnS4 (CZTS) is studied using density functional theory with hybrid functional. The allowed chemical potential of Na/K in CZTS is established. Formation energy calculations shows that Na can be significantly incorporated as both substitutional defects and interstitial defects, and incorporation of K related defects are generally less favorable. Transition energy calculations is performed showing that both Na and K exhibit benign defect properties and act as a p-type dopant. The qualitative disagreement between GGA with rigid band edge shifting and HSE calculations, formation of defect complexes, and implications in experiment will also be discussed. The understandings on the defect properties of Na and K provides an essential knowledge to further understand the surfactant effects of Na and K observed in experiments. This work is supported by General Research Fund Ref. No: 14319416.

Inefficient jet-induced star formation in Centaurus A. High resolution ALMA observations of the northern filaments

NASA Astrophysics Data System (ADS)

Salomé, Q.; Salomé, P.; Miville-Deschênes, M.-A.; Combes, F.; Hamer, S.

2017-12-01

NGC 5128 (Centaurus A) is one of the best targets to study AGN feedback in the local Universe. At 13.5 kpc from the galaxy, optical filaments with recent star formation lie along the radio jet direction. This region is a testbed for positive feedback, here through jet-induced star formation. Atacama Pathfinder EXperiment (APEX) observations have revealed strong CO emission in star-forming regions and in regions with no detected tracers of star formation activity. In cases where star formation is observed, this activity appears to be inefficient compared to the Kennicutt-Schmidt relation. We used the Atacama Large Millimeter/submillimeter Array (ALMA) to map the 12CO(1-0) emission all along the filaments of NGC 5128 at a resolution of 1.3'' 23.8pc. We find that the CO emission is clumpy and is distributed in two main structures: (i) the Horseshoe complex, located outside the HI cloud, where gas is mostly excited by shocks and where no star formation is observed, and (ii) the Vertical filament, located at the edge of the HI shell, which is a region of moderate star formation. We identified 140 molecular clouds using a clustering method applied to the CO data cube. A statistical study reveals that these clouds have very similar physical properties, such as size, velocity dispersion, and mass, as in the inner Milky Way. However, the range of radius available with the present ALMA observations does not enable us to investigate whether or not the clouds follow the Larson relation. The large virial parameter αvir of the clouds suggests that gravity is not dominant and clouds are not gravitationally unstable. Finally, the total energy injection in the northern filaments of Centaurus A is of the same order as in the inner part of the Milky Way. The strong CO emission detected in the northern filaments is an indication that the energy injected by the jet acts positively in the formation of dense molecular gas. The relatively high virial parameter of the molecular clouds suggests that the injected kinetic energy is too strong for star formation to be efficient. This is particularly the case in the horseshoe complex, where the virial parameter is the largest and where strong CO is detected with no associated star formation. This is the first evidence of AGN positive feedback in the sense of forming molecular gas through shocks, associated with low star formation efficiency due to turbulence injection by the interaction with the radio jet. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2015.1.01019.S.The full Table A.1 and a catalogue of the molecular clouds are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/608/A98

Rational design of a molecularly imprinted polymer for dinotefuran: theoretical and experimental studies aimed at the development of an efficient adsorbent for microextraction by packed sorbent.

PubMed

Silva, Camilla Fonseca; Borges, Keyller Bastos; do Nascimento, Clebio Soares

2017-12-18

In this work, we studied theoretically the formation process of a molecularly imprinted polymer (MIP) for dinotefuran (DNF), testing distinct functional monomers (FM) in various solvents through density functional theory calculations. The results revealed that the best conditions for MIP synthesis were established with methacrylic acid (MAA) as FM in a 1 : 4 stoichiometry and with chloroform as the solvent. This protocol showed the most favourable stabilization energies for the pre-polymerization complexes. Furthermore, the formation of the FM/template complex is enthalpy driven and the occurrence of hydrogen bonds between the DNF and MAA plays a major role in the complex stability. To confirm the theoretical results, MIP was experimentally synthesized considering the best conditions found at the molecular level and characterized by scanning electron microscopy and thermogravimetric analysis. After that, the synthesized material was efficiently employed in microextraction by packed sorbent combined with high-performance liquid chromatography in a preliminary study of the recovery of DNF from water and artificial saliva samples.

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

PubMed

Hatakeyama, Makoto; Sakamoto, Yuki; Ogata, Koji; Sumida, Yuto; Sumida, Tomoe; Hosoya, Takamitsu; Nakamura, Shinichiro

2017-10-11

In this study, three reaction mechanisms of a benzyne-nickel (Ni) complex ([Ni(C 6 H 4 )(dcpe)]) with iodomethane during the methylation process were investigated, namely (a) S N 2 reaction of the benzyne-Ni complex with iodomethane, (b) concerted σ-bond metathesis during the bond breaking/forming processes, and (c) oxidative addition of iodomethane to the Ni-center and the subsequent reductive elimination process. DFT calculations revealed that the reaction barrier of the S N 2 reaction is slightly lower than those of the other mechanisms. The results of orbital analyses suggest that [Ni(C 6 H 4 )(dcpe)] forms a metallacycle structure between benzyne and the Ni II (3d 8 ) center instead of the η 2 -structure with the Ni 0 (3d 10 ) center. The metallacycle structures became inappropriate as the intermediates of oxidative addition in the formation of the Ni II -Me bond, avoiding further oxidation to the high-valent Ni IV . The high free energy along σ-bond metathesis was generated from the steric hindrance, thus invoking methylation and Ni-I bond formation concertedly.

Advances in Understanding of Swift Heavy-Ion Tracks in Complex Ceramics

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

Lang, Maik; Devanathan, Ram; Toulemonde, Marcel

2015-02-01

Tracks produced by swift heavy ions in ceramics are of interest for fundamental science as well as for applications covering different fields such as nanotechnology or fission-track dating of minerals. In the case of pyrochlores with general formula A2B2O7, the track structure and radiation sensitivity shows a clear dependence on the composition. Ion irradiated Gd2Zr2O7, e.g., retains its crystallinity while amorphous tracks are produced in Gd2Ti2O7. Tracks in Ti-containing compositions have a complex morphology consisting of an amorphous core surrounded by a shell of a disordered, defect-fluorite phase. The size of the amorphous core decreases with decreasing energy loss andmore » with increasing Zr content, while the shell thickness seems to be similar over a wide range of energy loss values. The large data set and the complex track structure has made pyrochlore an interesting model system for a general theoretical description of track formation including thermal spike calculations (providing the spatial and temporal evolution of temperature around the ion trajectory) and molecular dynamics (MD) simulations (describing the response of the atomic system).Recent MD advances consider the sudden temperature increase by inserting data from the thermal spike. The combination allows the reproduction of the core-shell track characteristic and sheds light on the early stages of track formation including recrystallization of the molten material produced by the thermal spike.« less

Classical trajectory studies of gas phase reaction dynamics and kinetics using ab initio potential energy surfaces

NASA Technical Reports Server (NTRS)

Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.

1989-01-01

Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.

Role of halogen and hydrogen bonds for stabilization of antithyroid drugs with hypohalous acids (HOX, X = I, Br, and Cl) adducts

NASA Astrophysics Data System (ADS)

El-Sheshtawy, Hamdy S.; El-Mehasseb, Ibrahim

2017-11-01

The mechanism for the inhibition of thyroid hormones by the thioamide-like antithyroid drug is a key process in the thyroid gland function. Therefore, in this study theoretical investigation of the molecular interaction between two antithyroid drugs, namely methimazol (MMI) and thiazoline-2-thione (T2T), with the hypohalous acids (HOX, X = I, Br, and Cl), which act as heme-linked halogenated species to tyrosine residue was discussed. The calculations were performed by M06-2X and MP2 using aug-cc-pVDZ level of theory. In addition, wB97xd/6-31G* level of theory was used in order to account for the dispersion forces. The results show the possible formation of three adducts, which is stabilized by halogen bond (I), both halogen and hydrogen bonds (II), two hydrogen bonds (III). The binding energies of the complexes reveals stabilization in the order III > II > I. The binding energies of the complexes was increased with increasing the electron affinity and polarizability of halogen atom, the dipole moment of the complexes (I and II), the electrostatic potential on halogen atom (Vmax:i.e σ-hole), and the charge-transfer process through the halogen bond in I. On the other hand, the binding energies of the complexes decreased with increasing the halogen atom electronegativity and the dipole moment of complex III. Natural bond orbital (NBO) analysis was used to investigate the molecular orbital interactions and the charge transfer process upon complexation.

Synthesis and Reactivity of Tripodal Complexes Containing Pendant Bases

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

Blacquiere, Johanna M.; Pegis, Michael L.; Raugei, Simone

2014-09-02

The synthesis of a new tripodal ligand family is reported, with tertiary-amine groups in the second-coordination sphere. The ligands are tris(amido)amine derivatives, with the pendant amines attached via a peptide coupling strategy. They were designed to be used in new catalysts for the oxygen reduction reaction (ORR), in which the pendant acid/base group could improve catalyst performance. Two members of the new ligand family were each metallated with Co(II) and Zn(II) to afford trigonal monopyramidal complexes. Reaction of the cobalt complexes, [Co(L)]-, with dioxygen reversibly generates a small amount of a Co(III)-superoxo species, which was characterized by EPR. Protonation ofmore » the zinc complex Zn[N{CH2CH2NC(O)CH2N(CH2Ph)2}3)-– ([Zn(TNBn)]-) with one equivalent of acid occurs with displacement and dissociation of an amide ligand. Addition of excess acid to the any of the complexes [M(L)]- results in complete proteolysis and formation of the ligands H3L. This decomposition limits the use of these complexes as catalysts for the ORR. An alternative ligand with two pyridyl arms was also prepared but could not be metallated. These studies highlight the importance of stability of the primary-coordination sphere of ORR electrocatalysts to both oxidative and acidic conditions. This 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.« less

Interaction of the ginsenosides with κ-casein and their effects on amyloid fibril formation by the protein: Multi-spectroscopic approaches.

PubMed

Chen, Fanbo; Wang, Yunhua; Yang, Miao; Yin, Jianyuan; Meng, Qin; Bu, Fengquan; Sun, Dandan; Liu, Jihua

2016-07-01

The interaction of the ginsenosides (GS) including ginsenoside Rg1, Rb1 and Re with κ-casein and the effects of GS inhibiting amyloid fibril formation by κ-casein have been investigated in vitro by fluorescence and ultraviolet spectra. Results showed that Rg1 and Rb1 had dose-dependent inhibitory effects on reduced and carboxymethylated κ-casein (RCMκ-CN) fibril formation, while Re resulted in an increase in the rate of fibril formation. The enhancement in RLS intensity was attributed to the formation of new complex between GS and RCMκ-CN, and the corresponding thermodynamic parameters (ΔH, ΔS and ΔG) were assayed. The steady-state ultraviolet-visible absorption spectra had also been tested to observe if the ground-state complex formed, and it showed the same result as RLS spectra. The binding constants and the number of binding sites between GS and RCMκ-CN at different temperatures had been evaluated from relevant fluorescence data. According to the Förster non-radiation energy transfer theory, the binding distance between RCMκ-CN and GS was calculated. The fluorescence lifetime of RCMκ-CN was longer in the presence of GS than in absence of GS, which was evident that the hydrophobic interaction plays a major role in the binding of GS to RCMκ-CN. From the results of synchronous fluorescence, it could be deduced that the polarity around RCMκ-CN Trp97 residue decreased and the hydrophobicity increased after addition of Rg1 or Rb1. Based on all the above results, it is explained that Rg1 and Rb1 inhibited amyloid fibril formation by κ-casein because the molecular spatial conformation and physical property of κ-casein changed causing by the complex formation between GS and κ-casein. Copyright © 2016 Elsevier B.V. All rights reserved.

Reactions in trifluoroacetic acid (CF 3COOH) induced by low energy electron attachment

NASA Astrophysics Data System (ADS)

Langer, Judith; Stano, Michal; Gohlke, Sascha; Foltin, Victor; Matejcik, Stefan; Illenberger, Eugen

2006-02-01

Dissociative electron attachment to trifluoroacetic acid (CF 3COOH) is characterized by an intense low energy shape resonance located near 1 eV and a comparatively weaker core excited resonance located near 7 eV. The shape resonance decomposes into the fragment ions CF 3COO -, CF 2COO -, and CF2-. The underlying reactions include simple bond cleavage but also more complex sequences involving multiple bond cleavages, rearrangement in the precursor ion and formation of new molecules (HF, CO 2). The core excited resonance additionally decomposes into F -, CF3- and probably metastable CO2-.

Synthesis, spectral, DFT modeling, cytotoxicity and microbial studies of novel Zr(IV), Ce(IV) and U(VI) piroxicam complexes

NASA Astrophysics Data System (ADS)

El-Shwiniy, Walaa H.; Zordok, Wael A.

2018-06-01

The Zr(IV), Ce(IV) and U(VI) piroxicam anti-inflammatory drug complexes were prepared and characterized using elemental analyses, conductance, IR, UV-Vis, magnetic moment, IHNMR and thermal analysis. The ratio of metal: Pir is found to be 1:2 in all complexes estimated by using molar ratio method. The conductance data reveal that Zr(IV) and U(VI) chelates are non-electrolytes except Ce(IV) complex is electrolyte. Infrared spectroscopic confirm that the Pir behaves as a bidentate ligand co-ordinated to the metal ions via the oxygen and nitrogen atoms of ν(Cdbnd O)carbonyl and ν(Cdbnd N)pyridyl, respectively. The kinetic parameters of thermogravimetric and its differential, such as activation energy, entropy of activation, enthalpy of activation, and Gibbs free energy evaluated using Coats-Redfern and Horowitz-Metzger equations for Pir and complexes. The geometry of the piroxicam drug in the Free State differs significantly from that in the metal complex. In the time of metal ion-drug bond formation the drug switches-on from the closed structure (equilibrium geometry) to the open one. The antimicrobial tests were assessed towards some types of bacteria and fungi. The in vitro cell cytotoxicity of the complexes in comparison with Pir against colon carcinoma (HCT-116) cell line was measured. Optimized geometrical structure of piroxicam ligand by using DFT calculations.

Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots.

PubMed

Kuttner, Yosef Y; Engel, Stanislav

2018-02-01

A rational design of protein complexes with defined functionalities and of drugs aimed at disrupting protein-protein interactions requires fundamental understanding of the mechanisms underlying the formation of specific protein complexes. Efforts to develop efficient small-molecule or protein-based binders often exploit energetic hot spots on protein surfaces, namely, the interfacial residues that provide most of the binding free energy in the complex. The molecular basis underlying the unusually high energy contribution of the hot spots remains obscure, and its elucidation would facilitate the design of interface-targeted drugs. To study the nature of the energetic hot spots, we analyzed the backbone dynamic properties of contact surfaces in several protein complexes. We demonstrate that, in most complexes, the backbone dynamic landscapes of interacting surfaces form complementary "stability patches," in which static areas from the opposing surfaces superimpose, and that these areas are predominantly located near the geometric center of the interface. We propose that a diminished enthalpy-entropy compensation effect augments the degree to which residues positioned within the complementary stability patches contribute to complex affinity, thereby giving rise to the energetic hot spots. These findings offer new insights into the nature of energetic hot spots and the role that backbone dynamics play in facilitating intermolecular recognition. Mapping the interfacial stability patches may provide guidance for protein engineering approaches aimed at improving the stability of protein complexes and could facilitate the design of ligands that target complex interfaces. © 2017 Wiley Periodicals, Inc.

Chemical complexity induced by efficient ice evaporation in the Barnard 5 molecular cloud

NASA Astrophysics Data System (ADS)

Taquet, V.; Wirström, E. S.; Charnley, S. B.; Faure, A.; López-Sepulcre, A.; Persson, C. M.

2017-10-01

Cold gas-phase water has recently been detected in a cold dark cloud, Barnard 5 located in the Perseus complex, by targeting methanol peaks as signposts for ice mantle evaporation. Observed morphology and abundances of methanol and water are consistent with a transient non-thermal evaporation process only affecting the outermost ice mantle layers, possibly triggering a more complex chemistry. Here we present the detection of the complex organic molecules (COMs) acetaldehyde (CH3CHO) and methyl formate (CH3OCHO), as well as formic acid (HCOOH) and ketene (CH2CO), and the tentative detection of di-methyl ether (CH3OCH3) towards the "methanol hotspot" of Barnard 5 located between two dense cores using the single dish OSO 20 m, IRAM 30 m, and NRO 45 m telescopes. The high energy cis-conformer of formic acid is detected, suggesting that formic acid is mostly formed at the surface of interstellar grains and then evaporated. The detection of multiple transitions for each species allows us to constrain their abundances through LTE and non-LTE methods. All the considered COMs show similar abundances between 1 and 10% relative to methanol depending on the assumed excitation temperature. The non-detection of glycolaldehyde, an isomer of methyl formate, with a [glycolaldehyde]/[methyl formate] abundance ratio lower than 6%, favours gas phase formation pathways triggered by methanol evaporation. According to their excitation temperatures derived in massive hot cores, formic acid, ketene, and acetaldehyde have been designated as "lukewarm" COMs whereas methyl formate and di-methyl ether were defined as "warm" species. Comparison with previous observations of other types of sources confirms that lukewarm and warm COMs show similar abundances in low-density cold gas whereas the warm COMs tend to be more abundant than the lukewarm species in warm protostellar cores. This abundance evolution suggests either that warm COMs are indeed mostly formed in protostellar environments and/or that lukewarm COMs are efficiently depleted by increased hydrogenation efficiency around protostars.

A mechanistic approach on the self-organization of the two-component thermoreversible hydrogel of riboflavin and melamine.

PubMed

Saha, Abhijit; Manna, Swarup; Nandi, Arun K

2007-12-18

The riboflavin (R) and melamine (M) supramolecular complex in the mole ratio of 3:1 (RM31) produces a thermoreversible gel in aqueous medium. The gelation mechanism has been elucidated from morphological investigations using optical, electron, and atomic force microscopy together with time-dependent circular dichroism (CD) and photoluminescence (PL) spectroscopy. Optical microscopy indicates spherulitic morphology at lower gelation temperature (

THE COMPLETE, TEMPERATURE RESOLVED EXPERIMENTAL SPECTRUM OF METHYL FORMATE (HCOOCH{sub 3}) BETWEEN 214.6 AND 265.4 GHz

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

McMillan, James P.; Fortman, Sarah M.; Neese, Christopher F.

2016-05-20

Because methyl formate (HCOOCH{sub 3}) is abundant in the interstellar medium and has a strong, complex spectrum, it is a major contributor to the list of identified astrophysical lines. Because of its spectral complexity, with many low lying torsional and vibrational states, the quantum mechanical (QM) analysis of its laboratory spectrum is challenging and thus incomplete. As a result it is assumed that methyl formate is also one of the major contributors to the lists of unassigned lines in astrophysical spectra. This paper provides a characterization, without the need for QM analysis, of the spectrum of methyl formate between 214.6more » and 265.4 GHz for astrophysically significant temperatures. The experimental basis for this characterization is a set of 425 spectra, with absolute intensity calibration, recorded between 248 and 408 K. Analysis of these spectra makes possible the calculation of the Complete Experimental Spectrum of methyl formate as a function of temperature. Of the 7132 strongest lines reported in this paper, 2523 are in the QM catalogs. Intensity differences of 5%–10% from those calculated via QM models were also found. Results are provided in a frequency point-by-point catalog that is well suited for the simulation of overlapped spectra. The common astrophysical line frequency, line strength, and lower state energy catalog is also provided.« less

The Complete, Temperature Resolved Experimental Spectrum of Methyl Formate (HCOOCH3) between 214.6 and 265.4 GHz

NASA Astrophysics Data System (ADS)

McMillan, James P.; Fortman, Sarah M.; Neese, Christopher F.; De Lucia, Frank C.

2016-05-01

Because methyl formate (HCOOCH3) is abundant in the interstellar medium and has a strong, complex spectrum, it is a major contributor to the list of identified astrophysical lines. Because of its spectral complexity, with many low lying torsional and vibrational states, the quantum mechanical (QM) analysis of its laboratory spectrum is challenging and thus incomplete. As a result it is assumed that methyl formate is also one of the major contributors to the lists of unassigned lines in astrophysical spectra. This paper provides a characterization, without the need for QM analysis, of the spectrum of methyl formate between 214.6 and 265.4 GHz for astrophysically significant temperatures. The experimental basis for this characterization is a set of 425 spectra, with absolute intensity calibration, recorded between 248 and 408 K. Analysis of these spectra makes possible the calculation of the Complete Experimental Spectrum of methyl formate as a function of temperature. Of the 7132 strongest lines reported in this paper, 2523 are in the QM catalogs. Intensity differences of 5%-10% from those calculated via QM models were also found. Results are provided in a frequency point-by-point catalog that is well suited for the simulation of overlapped spectra. The common astrophysical line frequency, line strength, and lower state energy catalog is also provided.

Trifluoperazine Regulation of Calmodulin Binding to Fas: A Computational Study

PubMed Central

Pan, Di; Yan, Qi; Chen, Yabing; McDonald, Jay M; Song, Yuhua

2011-01-01

Death-inducing signaling complex (DISC) formation is a critical step in Fas-mediated signaling for apoptosis. Previous experiments have demonstrated that the calmodulin (CaM) antagonist, trifluoperazine (TFP) regulates CaM-Fas binding and affects Fas-mediated DISC formation. In this study, we investigated the anti-cooperative characteristics of TFP binding to CaM and the effect of TFP on the CaM-Fas interaction from both structural and thermodynamic perspectives using combined molecular dynamics simulations and binding free energy analyses. We studied the interactions of different numbers of TFP molecules with CaM and explored the effects of the resulting conformational changes in CaM on CaM-Fas binding. Results from these analyses showed that the number of TFP molecules bound to CaM directly influenced α-helix formation and hydrogen bond occupancy within the α-helices of CaM, contributing to the conformational and motion changes in CaM. These changes affected CaM binding to Fas, resulting in secondary structural changes in Fas and conformational and motion changes of Fas in CaM-Fas complexes, potentially perturbing the recruitment of Fas-associated death domain (FADD) for DISC formation. The computational results from this study reveal the structural and molecular mechanisms that underlie the role of the CaM antagonist, TFP, in regulation of CaM-Fas binding and Fas-mediated DISC formation in a concentration-dependent manner. PMID:21656570

3D-structured illumination microscopy reveals clustered DNA double-strand break formation in widespread γH2AX foci after high LET heavy-ion particle radiation.

PubMed

Hagiwara, Yoshihiko; Niimi, Atsuko; Isono, Mayu; Yamauchi, Motohiro; Yasuhara, Takaaki; Limsirichaikul, Siripan; Oike, Takahiro; Sato, Hiro; Held, Kathryn D; Nakano, Takashi; Shibata, Atsushi

2017-12-12

DNA double-strand breaks (DSBs) induced by ionising radiation are considered the major cause of genotoxic mutations and cell death. While DSBs are dispersed throughout chromatin after X-rays or γ-irradiation, multiple types of DNA damage including DSBs, single-strand breaks and base damage can be generated within 1-2 helical DNA turns, defined as a complex DNA lesion, after high Linear Energy Transfer (LET) particle irradiation. In addition to the formation of complex DNA lesions, recent evidence suggests that multiple DSBs can be closely generated along the tracks of high LET particle irradiation. Herein, by using three dimensional (3D)-structured illumination microscopy, we identified the formation of 3D widespread γH2AX foci after high LET carbon-ion irradiation. The large γH2AX foci in G 2 -phase cells encompassed multiple foci of replication protein A (RPA), a marker of DSBs undergoing resection during homologous recombination. Furthermore, we demonstrated by 3D analysis that the distance between two individual RPA foci within γH2AX foci was approximately 700 nm. Together, our findings suggest that high LET heavy-ion particles induce clustered DSB formation on a scale of approximately 1 μm 3 . These closely localised DSBs are considered to be a risk for the formation of chromosomal rearrangement after heavy-ion irradiation.

Photodissociation of van der Waals clusters of isoprene with oxygen, C{sub 5}H{sub 8}-O{sub 2}, in the wavelength range 213-277 nm

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

Vidma, Konstantin V.; Frederix, Pim W. J. M.; Parker, David H.

2012-08-07

The speed and angular distribution of O atoms arising from the photofragmentation of C{sub 5}H{sub 8}-O{sub 2}, the isoprene-oxygen van der Waals complex, in the wavelength region of 213-277 nm has been studied with the use of a two-color dissociation-probe method and the velocity map imaging technique. Dramatic enhancement in the O atoms photo-generation cross section in comparison with the photodissociation of individual O{sub 2} molecules has been observed. Velocity map images of these 'enhanced' O atoms consisted of five channels, different in their kinetic energy, angular distribution, and wavelength dependence. Three channels are deduced to be due to themore » one-quantum excitation of the C{sub 5}H{sub 8}-O{sub 2} complex into the perturbed Herzberg III state ({sup 3}{Delta}{sub u}) of O{sub 2}. This excitation results in the prompt dissociation of the complex giving rise to products C{sub 5}H{sub 8}+O+O when the energy of exciting quantum is higher than the complex photodissociation threshold, which is found to be 41740 {+-} 200 cm{sup -1} (239.6{+-}1.2 nm). This last threshold corresponds to the photodissociation giving rise to an unexcited isoprene molecule. The second channel, with threshold shifted to the blue by 1480 {+-} 280 cm{sup -1}, corresponds to dissociation with formation of rovibrationally excited isoprene. A third channel was observed at wavelengths up to 243 nm with excitation below the upper photodissociation threshold. This channel is attributed to dissociation with the formation of a bound O atom C{sub 5}H{sub 8}-O{sub 2}+hv{yields} C{sub 5}H{sub 8}-O{sub 2}({sup 3}{Delta}{sub u}) {yields} C{sub 5}H{sub 8}O + O and/or to dissociation of O{sub 2} with borrowing of the lacking energy from incompletely cooled complex internal degrees of freedom C{sub 5}H{sub 8}{sup *}-O{sub 2}+hv{yields} C{sub 5}H{sub 8}{sup *}-O{sub 2}({sup 3}{Delta}{sub u}) {yields} C{sub 5}H{sub 8}+ O + O. The kinetic energy of the O atoms arising in two other observed channels corresponds to O atoms produced by photodissociation of molecular oxygen in the excited a {sup 1}{Delta}{sub g} and b {sup 1}{Sigma}{sub g}{sup +} singlet states as the precursors. This indicates the formation of singlet oxygen O{sub 2}(a {sup 1}{Delta}{sub g}) and O{sub 2}(b {sup 1}{Sigma}{sub g}{sup +}) after excitation of the C{sub 5}H{sub 8}-O{sub 2} complex. Cooperative excitation of the complex with a simultaneous change of the spin of both partners {sup 1}X-{sup 3}O{sub 2}+h{nu}{yields}{sup 3}X-{sup 1}O{sub 2}{yields}{sup 3}X +{sup 1}O{sub 2} is suggested as a source of singlet oxygen O{sub 2}(a {sup 1}{Delta}{sub g}) and O{sub 2}(b {sup 1}{Sigma}{sub g}{sup +}). This cooperative excitation is in agreement with little or no vibrational excitation of O{sub 2}(a {sup 1}{Delta}{sub g}), produced from the C{sub 5}H{sub 8}-O{sub 2} complex as studied in the current paper as well as from the C{sub 3}H{sub 6}-O{sub 2} and CH{sub 3}I-O{sub 2} complexes reported in our previous paper [Baklanov et al., J. Chem. Phys. 126, 124316 (2007)]. The formation of O{sub 2}(a {sup 1}{Delta}{sub g}) from C{sub 5}H{sub 8}-O{sub 2} was observed at {lambda}{sub pump}= 213-277 nm with the yield going down towards the long wavelength edge of this interval. This spectral profile is interpreted as the red-side wing of the band of a cooperative transition {sup 1}X-{sup 3}O{sub 2}+h{nu}{yields}{sup 3}X(T{sub 2})-{sup 1}O{sub 2}(a {sup 1}{Delta}{sub g}) in the C{sub 5}H{sub 8}-O{sub 2} complex.« less

Dynamic Changes of IsiA-Containing Complexes during Long-Term Iron Deficiency in Synechocystis sp. PCC 6803.

PubMed

Ma, Fei; Zhang, Xin; Zhu, Xi; Li, Tianpei; Zhan, Jiao; Chen, Hui; He, Chenliu; Wang, Qiang

2017-01-09

Iron stress-induced protein A (IsiA), a major chlorophyll-binding protein in the thylakoid membrane, is significantly induced under iron deficiency conditions. Using immunoblot analysis and 77 K fluorescence spectroscopy combined with sucrose gradient fractionation, we monitored dynamic changes of IsiA-containing complexes in Synechocystis sp. PCC 6803 during exposure to long-term iron deficiency. Within 3 days of exposure to iron deficiency conditions, the initially induced free IsiA proteins preferentially conjugated to PS I trimer to form IsiA 18 -PS I trimers, which serve as light energy collectors for efficiently transmitting energy to PS I. With prolonged iron deficiency, IsiA proteins assembled either into IsiA aggregates or into two other types of IsiA-PS I supercomplexes, namely IsiA-PS I high fluorescence supercomplex (IHFS) and IsiA-PS I low fluorescence supercomplex (ILFS). Further analysis revealed a role for IsiA as an energy dissipater in the IHFS and as an energy collector in the ILFS. The trimeric structure of PS I mediated by PsaL was found to be indispensable for the formation of IHFS/ILFS. Dynamic changes in IsiA-containing complexes in cyanobacteria during long-term iron deficiency may represent an adaptation to iron limitation stress for flexible light energy distribution, which balances electron transfer between PS I and PS II, thus minimizing photooxidative damage. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Characterizing the Protostars in the Herschel Survey of Cygnus-X

NASA Astrophysics Data System (ADS)

Kirk, James; Hora, J. L.; Smith, H. A.; Herschel Cygnus-X Group

2014-01-01

The Cygnus-X complex is an extremely active region of massive star formation at a distance of ~1.4 kpc which can be studied with higher sensitivity and less confusion than more distant regions. The study of this region is important in improving our understanding of the formation processes and protostellar phases of massive stars. A previous Spitzer Legacy survey of Cygnus-X mapped the distributions of Class I and Class II YSOs within the region and studied the interaction between massive young stars and clusters of YSOs. Using data from the recent Herschel survey of the region, taken with the PACS and SPIRE instrument (70-500 microns), we are expanding this study of star formation to the youngest and most deeply embedded objects. Using these data we will expand the sample of massive protostars and YSOs in Cygnus-X, analyze the population of infrared dark clouds and their embedded objects, construct Spectral Energy Distributions (SEDs) using pre-existing Spitzer and near-IR data sets (1-500 microns), and fit these sources with models of protostars to derive luminosities and envelope masses. The derived luminosities and masses will enable us to create evolutionary diagrams and test models of high-mass star formation. We will also investigate what role OB associations, such as Cyg OB2, play in causing subsequent star formation in neighboring clouds, providing us with a comprehensive picture of star formation within this extremely active complex.

Host-guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V.

PubMed

Begel, Svetlana; Puchta, Ralph; van Eldik, Rudi

2013-01-01

The selectivity of the cryptands [2.2.bpy] and [2.bpy.bpy] for the endohedral complexation of alkali, alkaline-earth and earth metal ions was predicted on the basis of the DFT (B3LYP/LANL2DZp) calculated structures and complex-formation energies. The cavity size in both cryptands lay between that for [2.2.2] and [bpy.bpy.bpy], such that the complexation of K(+), Sr(2+) and Tl(3+) is most favorable. While the [2.2.bpy] is moderately larger, preferring Rb(+) complexation and demonstrating equal priority for Sr(2+) and Ba(2+), the slightly smaller [2.bpy.bpy] yields more stable cryptates with Na(+) and Ca(2+). Although the CH2-units containing molecular bars fixed at the bridgehead nitrogen atoms determine the flexibility of the cryptands, the twist angles associated with the bipyridine and glycol building blocks also contribute considerably.

Cation-π interaction of the univalent sodium cation with [2.2.2]paracyclophane: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Makrlík, Emanuel; Sýkora, David; Böhm, Stanislav; Vaňura, Petr

2018-02-01

By employing electrospray ionization mass spectrometry (ESI-MS), it was proven experimentally that the univalent sodium cation (Na+) forms with [2.2.2]paracyclophane (C24H24) the cationic complex [Na(C24H24)]+. Further, applying quantum chemical DFT calculations, the most probable structure of the [Na(C24H24)]+ complex was derived. In the resulting complex with a symmetry very close to C3, the "central" cation Na+, fully located in the cavity of the parent [2.2.2]paracyclophane ligand, is bound to all three benzene rings of [2.2.2]paracyclophane via cation-π interaction. Finally, the interaction energy, E(int), of the considered cation-π complex [Na(C24H24)]+ was found to be -267.3 kJ/mol, confirming the formation of this fascinating complex species as well.

Infrared spectroscopy and density functional calculations on titanium-dinitrogen complexes

NASA Astrophysics Data System (ADS)

Yoo, Hae-Wook; Choi, Changhyeok; Cho, Soo Gyeong; Jung, Yousung; Choi, Myong Yong

2018-04-01

Titanium-nitrogen complexes were generated by laser ablated titanium (Ti) atoms and N2 gas molecules in this study. These complexes were isolated on the pre-deposited solid Ar matrix on the pre-cooled KBr window (T ∼ 5.4 K), allowing infrared spectra to be measured. Laser ablation experiments with 15N2 isotope provided distinct isotopic shifts in the infrared spectra that strongly implicated the formation of titanium-nitrogen complexes, Ti(NN)x. Density functional theory (DFT) calculations were employed to investigate the molecular structures, electronic ground state, relative energies, and IR frequencies of the anticipated Ti(NN)x complexes. Based on laser ablation experiments and DFT calculations, we were able to assign multiple Ti(NN)x (x = 1-6) species. Particularly, Ti(NN)5 and Ti(NN)6, which have high nitrogen content, may serve as good precursors in preparing polynitrogens.

The phase behavior of cationic lipid-DNA complexes.

PubMed Central

May, S; Harries, D; Ben-Shaul, A

2000-01-01

We present a theoretical analysis of the phase behavior of solutions containing DNA, cationic lipids, and nonionic (helper) lipids. Our model allows for five possible structures, treated as incompressible macroscopic phases: two lipid-DNA composite (lipoplex) phases, namely, the lamellar (L(alpha)(C)) and hexagonal (H(II)(C)) complexes; two binary (cationic/neutral) lipid phases, that is, the bilayer (L(alpha)) and inverse-hexagonal (H(II)) structures, and uncomplexed DNA. The free energy of the four lipid-containing phases is expressed as a sum of composition-dependent electrostatic, elastic, and mixing terms. The electrostatic free energies of all phases are calculated based on Poisson-Boltzmann theory. The phase diagram of the system is evaluated by minimizing the total free energy of the three-component mixture with respect to all the compositional degrees of freedom. We show that the phase behavior, in particular the preferred lipid-DNA complex geometry, is governed by a subtle interplay between the electrostatic, elastic, and mixing terms, which depend, in turn, on the lipid composition and lipid/DNA ratio. Detailed calculations are presented for three prototypical systems, exhibiting markedly different phase behaviors. The simplest mixture corresponds to a rigid planar membrane as the lipid source, in which case, only lamellar complexes appear in solution. When the membranes are "soft" (i.e., low bending modulus) the system exhibits the formation of both lamellar and hexagonal complexes, sometimes coexisting with each other, and with pure lipid or DNA phases. The last system corresponds to a lipid mixture involving helper lipids with strong propensity toward the inverse-hexagonal phase. Here, again, the phase diagram is rather complex, revealing a multitude of phase transitions and coexistences. Lamellar and hexagonal complexes appear, sometimes together, in different regions of the phase diagram. PMID:10733951

Synthesis, and spectroscopic studies of charge transfer complex of 1,2-dimethylimidazole as an electron donor with π-acceptor 2,4-dinitro-1-naphthol in different polar solvents

NASA Astrophysics Data System (ADS)

Miyan, Lal; Khan, Ishaat M.; Ahmad, Afaq

2015-07-01

The charge transfer (CT) complex of 1,2-dimethylimidazole (DMI) as an electron donor with π acceptor 2,4-dinitro-1-naphthol (DNN) has been studied spectrophotometrically in different solvents like chloroform, acetonitrile, methanol, methylene chloride, etc. at room temperature. The CT complex which is formed through the transfer of lone pair electrons from DMI to DNN exhibits well resolved CT bands and the regions of these bands were remarkably different from those of the donor and acceptor. The stoichiometry of the CT complex was found to be 1:1 by a straight-line method between donor and acceptor with maximum absorption bands. The novel CT complex has been characterized by FTIR, TGA-DTA, powder XRD, 1H NMR and 13C NMR spectroscopic techniques. The Benesi-Hildebrand equation has been used to determine the formation constant (KCT), molar extinction coefficient (εCT), standard gibbs free energy (ΔG°) and other physical parameters of the CT complex. The formation constant recorded higher values and molar extinction coefficient recorded lower values in chloroform compared with methylene chloride, methanol and acetonitrile, confirming the strong interaction between the molecular orbital's of donor and acceptor in the ground state in less polar solvent. This CT complex has been studied by absorption spectra of donor 1,2-dimethylimidazole (DMI) and acceptor 2,4-dinitro-1-naphthol (DNN) by using the spectrophotometric technique in various solvents at room temperature.

Comparison of ibuprofen release from minitablets and capsules containing ibuprofen: β-cyclodextrin complex.

PubMed

Salústio, P J; Cabral-Marques, H M; Costa, P C; Pinto, J F

2011-05-01

Mixtures containing ibuprofen (IB) complexed with β-cyclodextrin (βCD) obtained by two complexation methods [suspension/solution (with water removed by air stream, spray- and freeze-drying) and kneading technique] were processed into pharmaceutical dosage forms (minitablets and capsules). Powders (IB, βCD and IBβCD) were characterized for moisture content, densities (true and bulk), angle of repose and Carr's index, X-ray and NMR. From physical mixtures and IBβCD complexes without other excipients were prepared 2.5-mm-diameter minitablets and capsules. Minitablets were characterized for the energy of compaction, tensile strength, friability, density and IB release (at pH 1.0 and 7.2), whereby capsules were characterized for IB release. The results from the release of IB were analyzed using different parameters, namely, the similarity factor (f(2)), the dissolution efficiency (DE) and the amounts released at a certain time (30, 60 and 180 min) and compared statistically (α=0.05). The release of IB from the minitablets showed no dependency on the amount of water used in the formation of the complexes. Differences were due to the compaction force used or the presence of a shell for the capsules. The differences observed were mostly due to the characteristics of the particles (dependent on the method considered on the formation of the complexes) and neither to the dosage form nor to the complex of the IB. Copyright © 2011 Elsevier B.V. All rights reserved.

Transformations in oxides induced by high-energy ball-milling.

PubMed

Šepelák, Vladimir; Bégin-Colin, Sylvie; Le Caër, Gérard

2012-10-21

This paper, by no means exhaustive, focuses on high-energy ball-milling of oxides, on their mechanically induced changes and on the consequences of such changes on their physical and chemical properties. High-energy ball-milling offers a fortunate combination of technical simplicity and of complexity both of physical mechanisms which act during milling and of mechanosynthesized materials. Its basic interest, which stems from the large diversity of routes it offers to prepare oxides either directly or indirectly, is illustrated with various families of oxides. The direct path is to be favoured when as-milled oxides are of interest per se because of their nanocrystalline characteristics, their defects or their modified structures which result from mechanically driven phase transformations. The indirect path consists of a sequence of steps starting with mechanically activated oxides which may be subsequently just annealed or submitted to a combination of thermal treatments, with the possible occurrence of various chemical reactions, to prepare the sought-after materials with potential gains in processing temperatures and times. High energy ball-milling of oxides is more and more currently used to activate powders and to prepare nano-oxides at moderate temperatures. The interest of an activation step is well illustrated by the broad development of doped titania powders, synthesized by heat treatment of pre-ground reactants, for photocatalytic applications or to develop antibacterial materials. Another important class of applications of high-energy ball-milling is the formation of composites. It is exemplified here with the case of oxide-dispersed strengthened alloys whose properties are considerably improved by a dispersion of ultra-stable nanosized oxides whose formation mechanisms were recently described. The basic understanding of the mechanisms by which oxides or oxide mixtures evolve by high-energy ball-milling appears to be less advanced than it is for metallic materials essentially because of the overall complexity of the oxide structures, of their surfaces, of their defects and of their mechanical behavior.

Statistical self-similarity of hotspot seamount volumes modeled as self-similar criticality

USGS Publications Warehouse

Tebbens, S.F.; Burroughs, S.M.; Barton, C.C.; Naar, D.F.

2001-01-01

The processes responsible for hotspot seamount formation are complex, yet the cumulative frequency-volume distribution of hotspot seamounts in the Easter Island/Salas y Gomez Chain (ESC) is found to be well-described by an upper-truncated power law. We develop a model for hotspot seamount formation where uniform energy input produces events initiated on a self-similar distribution of critical cells. We call this model Self-Similar Criticality (SSC). By allowing the spatial distribution of magma migration to be self-similar, the SSC model recreates the observed ESC seamount volume distribution. The SSC model may have broad applicability to other natural systems.

Nucleosome Positioning and Epigenetics

NASA Astrophysics Data System (ADS)

Schwab, David; Bruinsma, Robijn

2008-03-01

The role of chromatin structure in gene regulation has recently taken center stage in the field of epigenetics, phenomena that change the phenotype without changing the DNA sequence. Recent work has also shown that nucleosomes, a complex of DNA wrapped around a histone octamer, experience a sequence dependent energy landscape due to the variation in DNA bend stiffness with sequence composition. In this talk, we consider the role nucleosome positioning might play in the formation of heterochromatin, a compact form of DNA generically responsible for gene silencing. In particular, we discuss how different patterns of nucleosome positions, periodic or random, could either facilitate or suppress heterochromatin stability and formation.

Thermal regeneration of an electrochemical concentration cell

DOEpatents

Krumpelt, Michael; Bates, John K.

1981-01-01

A system and method for thermally regenerating an electrochemical concentration cell having first and second aluminum electrodes respectively positioned in contact with first and second electrolytes separated by an ion exchange member, the first and second electrolytes being composed of different concentrations of an ionic solvent and a salt, preferably an aluminum halide. The ionic solvent may be either organic or inorganic with a relatively low melting point, the ionic solvent and the salt form a complex wherein the free energy of formation of said complex is less than about -5 Kcal/mole. A distillation column using solar heat or low grade industrial waste heat receives the first and second electrolytes and thermally decomposes the salt-solvent complex to provide feed material for the two half cells.

Design Principles for Metal Oxide Redox Materials for Solar-Driven Isothermal Fuel Production.

PubMed

Michalsky, Ronald; Botu, Venkatesh; Hargus, Cory M; Peterson, Andrew A; Steinfeld, Aldo

2015-04-01

The performance of metal oxides as redox materials is limited by their oxygen conductivity and thermochemical stability. Predicting these properties from the electronic structure can support the screening of advanced metal oxides and accelerate their development for clean energy applications. Specifically, reducible metal oxide catalysts and potential redox materials for the solar-thermochemical splitting of CO 2 and H 2 O via an isothermal redox cycle are examined. A volcano-type correlation is developed from available experimental data and density functional theory. It is found that the energy of the oxygen-vacancy formation at the most stable surfaces of TiO 2 , Ti 2 O 3 , Cu 2 O, ZnO, ZrO 2 , MoO 3 , Ag 2 O, CeO 2 , yttria-stabilized zirconia, and three perovskites scales with the Gibbs free energy of formation of the bulk oxides. Analogously, the experimental oxygen self-diffusion constants correlate with the transition-state energy of oxygen conduction. A simple descriptor is derived for rapid screening of oxygen-diffusion trends across a large set of metal oxide compositions. These general trends are rationalized with the electronic charge localized at the lattice oxygen and can be utilized to predict the surface activity, the free energy of complex bulk metal oxides, and their oxygen conductivity.

Kinetics and thermodynamics of bovine serum albumin interactions with Congo red dye.

PubMed

de Paula, Hauster Maximiler Campos; Coelho, Yara Luiza; Agudelo, Alvaro Javier Patiño; Rezende, Jaqueline de Paula; Ferreira, Gabriel Max Dias; Ferreira, Guilherme Max Dias; Pires, Ana Clarissa Dos Santos; da Silva, Luis Henrique Mendes

2017-11-01

To optimize the therapeutic applications of Congo red (CR), a potential inhibitor of protein aggregation, the kinetics and thermodynamics of the interactions between CR and a model protein need to be understood. We used surface plasmon resonance (SPR) and fluorescence techniques to determine the dynamics and thermodynamic parameters for the formation of complexes between CR and bovine serum albumin (BSA). CR interacts with BSA through a transition complex; the activation energy for association (E act(a) ) was determined to be 35.88kJmol -1 , while the activation enthalpy (ΔH ‡ ), entropy (ΔS ‡ ), and Gibbs free energy (ΔG ‡ ) are 33.41kJmol -1 , 0.18Jmol -1 K -1 , and 33.35kJmol -1 , respectively. When this intermediate transforms into the final CR-BSA complex, the entropy of the system increases and part of the absorbed energy is released; this process is associated with a reverse activation energy (E act(d) ) of 20.17kJmol -1 , and values of ΔH ‡ , ΔS ‡ , and ΔG ‡ of 17.69kJmol -1 , -162.86Jmol -1 K -1 , and 66.25kJmol -1 , respectively. A comparison of the SPR and fluorescence results suggests that there is more than one site where BSA interacts with CR. Copyright © 2017 Elsevier B.V. All rights reserved.

Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides

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

Adams, Peter G.; Mothersole, David J.; Ng, Irene W.

2011-01-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre–light-harvesting 1–PufX (RC–LH1–PufX) ‘core’ complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX -). Lower rates of LH2more » assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX - mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC–LH1–PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX - membranes, resulting in locally ordered clusters of monomeric RC–LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation.« less

Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides.

PubMed

Adams, Peter G; Mothersole, David J; Ng, Irene W; Olsen, John D; Hunter, C Neil

2011-09-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation. 2011 Elsevier B.V. All rights reserved.

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni 0.5Co 0.5, Ni 0.5Fe 0.5, Ni 0.8Fe 0.2 and Ni 0.8Cr 0.2

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

Zhao, Shijun; Stocks, George Malcolm; Zhang, Yanwen

2016-08-03

It has been shown that concentrated solid solution alloys possess unusual electronic, magnetic, transport, mechanical and radiation-resistant properties that are directly related to underlying chemical complexity. Because every atom experiences a different local atomic environment, the formation and migration energies of vacancies and interstitials in these alloys exhibit a distribution, rather than a single value as in a pure metal or dilute alloy. In this study, using ab initio calculations based on density functional theory and special quasirandom structure, we have characterized the distribution of defect formation energy and migration barrier in four Ni-based solid-solution alloys: Ni 0.5Co 0.5, Nimore » 0.5Fe 0.5, Ni 0.8Fe 0.2 and Ni 0.8Cr 0.2. As defect formation energies in finite-size models depend sensitively on the elemental chemical potential, we have developed a computationally efficient method for determining it which takes into account the global composition and the local short-range order. In addition we have compared the results of our ab initio calculations to those obtained from available embedded atom method (EAM) potentials. Our results indicate that the defect formation and migration energies are closely related to the specific atomic size in the structure, which further determines the elemental diffusion properties. In conclusion, different EAM potentials yield different features of defect energetics in concentrated alloys, pointing to the need for additional potential development efforts in order to allow spatial and temporal scale-up of defect and simulations, beyond those accessible to ab initio methods.« less

Theory of p-type Zinc Oxide

NASA Astrophysics Data System (ADS)

Zhang, Shengbai

2002-03-01

Recent advances in bipolar doping of wide gap semiconductors challenge our understanding of impurity and defect properties in these materials, as theories based on equilibrium thermodynamics cannot keep up with these recent developments. For ZnO, the puzzling experimental results involve doping with nitrogen(M. Joseph, H. Tabata, and T. Kawai, Jpn. J. Appl. Phys. 38), L1205 (1999)., arsenic(Y. R. Ryu, S. Zhu, D. C. Look, J. M. Wrobel, H. M. Jeong, and H. W. White, J. Crys. Growth 216), 330 (2000)., and phosphorus(T. Aoki, Y. Hatanaka, and D. C. Look, Appl. Phys. Lett. 76), 3257 (2000).. In this talk, I will discuss some recent theoretical efforts trying to explain the experiments by first-principles total energy calculations. I will first discuss the acceptor level positions for group I and group V impurities. A general trend is observed(C. H. Park, S. B. Zhang, and S.-H. Wei, submitted to Phys. Rev. B.) that substitutional group V impurities on O range from relatively deep (e.g. N) to very deep (e.g. P and As) with high formation energies, whereas substitutional group I impurities on Zn are shallow acceptors. However, substitutional group I impurities are unstable against the formation of interstitials that are donors. A careful examination of N doping in Ref. [1] suggests that one can kinetically suppress the formation of N2 molecules by engineering dopant sources/footnoteY. Yan, S. B. Zhang, and S. T. Pantelides, Phys. Rev. Lett. 86, 5723 (2001).. This leads to significantly enhanced N solubility and hence p-type ZnO. For As [2], our preliminary studies show that the formation energy of AsO is so high that it is an exothermic process to form low-energy complexes that act effectively as relatively shallow acceptors.

Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni0.5Co0.5, Ni0.5Fe0.5, Ni0.8Fe0.2 and Ni0.8Cr0.2.

PubMed

Zhao, Shijun; Stocks, G Malcolm; Zhang, Yanwen

2016-09-14

It has been shown that concentrated solid solution alloys possess unusual electronic, magnetic, transport, mechanical and radiation-resistant properties that are directly related to underlying chemical complexity. Because every atom experiences a different local atomic environment, the formation and migration energies of vacancies and interstitials in these alloys exhibit a distribution, rather than a single value as in a pure metal or dilute alloy. Using ab initio calculations based on density functional theory and special quasirandom structures, we have characterized the distribution of defect formation energy and migration barrier in four Ni-based solid-solution alloys: Ni0.5Co0.5, Ni0.5Fe0.5, Ni0.8Fe0.2, and Ni0.8Cr0.2. As defect formation energies in finite-size models depend sensitively on the elemental chemical potential, we have developed a computationally efficient method for determining it which takes into account the global composition and the local short-range order. In addition we have compared the results of our ab initio calculations to those obtained from available embedded atom method (EAM) potentials. Our results indicate that the defect formation and migration energies are closely related to the specific atoms in the structure, which further determines the elemental diffusion properties. Different EAM potentials yield different features of defect energetics in concentrated alloys, pointing to the need for additional potential development efforts in order to allow spatial and temporal scale-up of defect and simulations, beyond those accessible to ab initio methods.

AMPK Signaling in the Dorsal Hippocampus Negatively Regulates Contextual Fear Memory Formation

PubMed Central

Han, Ying; Luo, Yixiao; Sun, Jia; Ding, Zengbo; Liu, Jianfeng; Yan, Wei; Jian, Min; Xue, Yanxue; Shi, Jie; Wang, Ji-Shi; Lu, Lin

2016-01-01

Both the formation of long-term memory (LTM) and dendritic spine growth that serves as a physical basis for the long-term storage of information require de novo protein synthesis. Memory formation also critically depends on transcription. Adenosine monophosphate-activated protein kinase (AMPK) is a transcriptional regulator that has emerged as a major energy sensor that maintains cellular energy homeostasis. However, still unknown is its role in memory formation. In the present study, we found that AMPK is primarily expressed in neurons in the hippocampus, and then we demonstrated a time-dependent decrease in AMPK activity and increase in mammalian target of rapamycin complex 1 (mTORC1) activity after contextual fear conditioning in the CA1 but not CA3 area of the dorsal hippocampus. Using pharmacological methods and adenovirus gene transfer to bidirectionally regulate AMPK activity, we found that increasing AMPK activity in the CA1 impaired the formation of long-term fear memory, and decreasing AMPK activity enhanced fear memory formation. These findings were associated with changes in the phosphorylation of AMPK and p70s6 kinase (p70s6k) and expression of BDNF and membrane GluR1 and GluR2 in the CA1. Furthermore, the prior administration of an mTORC1 inhibitor blocked the enhancing effect of AMPK inhibition on fear memory formation, suggesting that this negative regulation of contextual fear memory by AMPK in the CA1 depends on the mTORC1 signaling pathway. Finally, we found that AMPK activity regulated hippocampal spine growth associated with memory formation. In summary, our results indicate that AMPK is a key negative regulator of plasticity and fear memory formation. PMID:26647974

Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions.

PubMed

Suárez, Dimas; Díaz, Natalia; Francisco, Evelio; Martín Pendás, Angel

2018-04-17

The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent interactions. The lack of a pair density in density functional theory (DFT), which precludes the direct IQA decomposition of the characteristic exchange-correlation energy, has been recently overcome by means of a scaling technique, which can largely expand the applicability of the method. To better assess the utility of the augmented IQA methodology to derive quantum chemical decompositions at the atomic and molecular levels, we report the results of Hartree-Fock (HF) and DFT calculations on the complexes included in the S66 and the ionic H-bond databases of benchmark geometry and binding energies. For all structures, we perform single-point and geometry optimizations using HF and selected DFT methods with triple-ζ basis sets followed by full IQA calculations. Pairwise dispersion energies are accounted for by the D3 method. We analyze the goodness of the HF-D3 and DFT-D3 binding energies, the magnitude of numerical errors, the fragment and atomic distribution of formation energies, etc. It is shown that fragment-based IQA decomposes the formation energies in comparable terms to those of perturbative approaches and that the atomic IQA energies hold the promise of rigorously quantifying atomic and group energy contributions in larger biomolecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Peng, Yuan; Wang, Junling, E-mail: jlwang@ntu.edu.sg; Zheng, Jianwei

Single n-type dopant in CuO has either a deep donor level or limited solubility, inefficient in generating free electrons. We have performed ab-initio study of the donor-acceptor codoping to obtain n-type CuO. Our results show that N codoping can slightly improve the donor level of Zr and In by forming shallower n-type complexes (Zr{sub Cu}-N{sub O} and 2In{sub Cu}-N{sub O}), but their formation energies are too high to be realized in experiments. However, Li codoping with Al and Ga is found to be relatively easy to achieve. 2Al{sub Cu}-Li{sub Cu} and 2Ga{sub Cu}-Li{sub Cu} have shallower donor levels than singlemore » Al and Ga by 0.14 eV and 0.08 eV, respectively, and their formation energies are reasonably low to act as efficient codopants. Moreover, Li codoping with both Al and Ga produce an empty impurity band just below the host conduction band minimum, which may reduce the donor ionization energy at high codoping concentrations.« less

Growth and structural evolution of Sn on Ag(001): Epitaxial monolayer to thick alloy film

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

Chakraborty, Suvankar; Menon, Krishnakumar S. R., E-mail: krishna.menon@saha.ac.in

The growth and structure of Sn on Ag(001), from submonolayer to thick film coverages at room temperature, are studied using low energy electron diffraction, x-ray photoemission spectroscopy and angle-resolved photoemission spectroscopy (ARPES) techniques. The authors observe different growth modes for submonolayer Sn coverages and for higher Sn coverages. Systematic surface structural evolution, consistent with the substitution of surface Ag atoms by Sn atoms, is observed for submonolayer Sn coverages while an ordered Ag-Sn bulk alloy film is formed for higher Sn coverages with an Ag overlayer. For monolayer coverage of Sn, a pseudomorphic growth of a Sn layer without alloyingmore » is determined. ARPES results also confirm the presence of an ordered Ag overlayer on the bulk Ag-Sn alloy film, suggesting the formation of an Ag/Ag{sub 3}Sn/Ag(001) sandwich structure at the surface for higher Sn coverages. The present results illustrate the complex interplay of atomic mobilities, surface free-energies, and alloy formation energies in determining the growth and structural properties of the system.« less

Cosmic Star Formation: A Simple Model of the SFRD(z)

NASA Astrophysics Data System (ADS)

Chiosi, Cesare; Sciarratta, Mauro; D’Onofrio, Mauro; Chiosi, Emanuela; Brotto, Francesca; De Michele, Rosaria; Politino, Valeria

2017-12-01

We investigate the evolution of the cosmic star formation rate density (SFRD) from redshift z = 20 to z = 0 and compare it with the observational one by Madau and Dickinson derived from recent compilations of ultraviolet (UV) and infrared (IR) data. The theoretical SFRD(z) and its evolution are obtained using a simple model that folds together the star formation histories of prototype galaxies that are designed to represent real objects of different morphological type along the Hubble sequence and the hierarchical growing of structures under the action of gravity from small perturbations to large-scale objects in Λ-CDM cosmogony, i.e., the number density of dark matter halos N(M,z). Although the overall model is very simple and easy to set up, it provides results that mimic results obtained from highly complex large-scale N-body simulations well. The simplicity of our approach allows us to test different assumptions for the star formation law in galaxies, the effects of energy feedback from stars to interstellar gas, the efficiency of galactic winds, and also the effect of N(M,z). The result of our analysis is that in the framework of the hierarchical assembly of galaxies, the so-called time-delayed star formation under plain assumptions mainly for the energy feedback and galactic winds can reproduce the observational SFRD(z).

Defect charge states in Si doped hexagonal boron-nitride monolayer

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Molepo, M. P.; Andrew, R. C.; Chetty, N.

2016-02-01

We perform ab initio density functional theory calculations to investigate the energetics, electronic and magnetic properties of isolated stoichiometric and non-stoichiometric substitutional Si complexes in a hexagonal boron-nitride monolayer. The Si impurity atoms substituting the boron atom sites SiB giving non-stoichiometric complexes are found to be the most energetically favourable, and are half-metallic and order ferromagnetically in the neutral charge state. We find that the magnetic moments and magnetization energies increase monotonically when Si defects form a cluster. Partial density of states and standard Mulliken population analysis indicate that the half-metallic character and magnetic moments mainly arise from the Si 3p impurity states. The stoichiometric Si complexes are energetically unfavorable and non-magnetic. When charging the energetically favourable non-stoichiometric Si complexes, we find that the formation energies strongly depend on the impurity charge states and Fermi level position. We also find that the magnetic moments and orderings are tunable by charge state modulation q  =  -2, -1, 0, +1, +2. The induced half-metallic character is lost (retained) when charging isolated (clustered) Si defect(s). This underlines the potential of a Si doped hexagonal boron-nitride monolayer for novel spin-based applications.

Quantitative ROESY analysis of computational models: structural studies of citalopram and β-cyclodextrin complexes by (1) H-NMR and computational methods.

PubMed

Ali, Syed Mashhood; Shamim, Shazia

2015-07-01

Complexation of racemic citalopram with β-cyclodextrin (β-CD) in aqueous medium was investigated to determine atom-accurate structure of the inclusion complexes. (1) H-NMR chemical shift change data of β-CD cavity protons in the presence of citalopram confirmed the formation of 1 : 1 inclusion complexes. ROESY spectrum confirmed the presence of aromatic ring in the β-CD cavity but whether one of the two or both rings was not clear. Molecular mechanics and molecular dynamic calculations showed the entry of fluoro-ring from wider side of β-CD cavity as the most favored mode of inclusion. Minimum energy computational models were analyzed for their accuracy in atomic coordinates by comparison of calculated and experimental intermolecular ROESY peak intensities, which were not found in agreement. Several least energy computational models were refined and analyzed till calculated and experimental intensities were compatible. The results demonstrate that computational models of CD complexes need to be analyzed for atom-accuracy and quantitative ROESY analysis is a promising method. Moreover, the study also validates that the quantitative use of ROESY is feasible even with longer mixing times if peak intensity ratios instead of absolute intensities are used. Copyright © 2015 John Wiley & Sons, Ltd.

Influence of carbon nanotubes on the optical properties of plasticized solid polymer electrolytes

NASA Astrophysics Data System (ADS)

Ibrahim, Suriani; Yasin, Siti Mariah Mohd; Johan, Mohd Rafie

2013-07-01

Polyethylene oxide (PEO) based solid polymer electrolyte films complexed with lithium hexafluorophosphate (LiPF6), ethylene carbonate (EC) and carbon nanotubes (CNTs) are prepared by solution-casting technique. The complexation of doping materials with polymer is confirmed by X-ray diffraction and infrared studies. The incorporation of LiPF6, EC and CNTs into the host polymer shows a significant increase in conductivity of 10-10 and 10-3 S cm-1. The optical properties such as direct and indirect band gaps are investigated for pure and doped polymer films within a wavelength range of 200-400 nm. It is found that the energy gaps and band edge values shift towards lower energies upon doping. It is shown that LiPF6, EC and CNTs are responsible for the formation of defects in polymer electrolytes, which increases the degree of disorder in the films.

Coordination chemistry in magnesium battery electrolytes: how ligands affect their performance.

PubMed

Shao, Yuyan; Liu, Tianbiao; Li, Guosheng; Gu, Meng; Nie, Zimin; Engelhard, Mark; Xiao, Jie; Lv, Dongping; Wang, Chongmin; Zhang, Ji-Guang; Liu, Jun

2013-11-04

Magnesium battery is potentially a safe, cost-effective, and high energy density technology for large scale energy storage. However, the development of magnesium battery has been hindered by the limited performance and the lack of fundamental understandings of electrolytes. Here, we present a study in understanding coordination chemistry of Mg(BH₄)₂ in ethereal solvents. The O donor denticity, i.e. ligand strength of the ethereal solvents which act as ligands to form solvated Mg complexes, plays a significant role in enhancing coulombic efficiency of the corresponding solvated Mg complex electrolytes. A new electrolyte is developed based on Mg(BH₄)₂, diglyme and LiBH₄. The preliminary electrochemical test results show that the new electrolyte demonstrates a close to 100% coulombic efficiency, no dendrite formation, and stable cycling performance for Mg plating/stripping and Mg insertion/de-insertion in a model cathode material Mo₆S₈ Chevrel phase.

Coordination Chemistry in magnesium battery electrolytes: how ligands affect their performance

DOE PAGES

Shao, Yuyan; Liu, Tianbiao L.; Li, Guosheng; ...

2013-11-04

Magnesium battery is potentially a safe, cost-effective, and high energy density technology for large scale energy storage. However, the development of magnesium battery has been hindered by the limited performance and the lack of fundamental understandings of electrolytes. Here, we present a coordination chemistry study of Mg(BH 4) 2 in ethereal solvents. The O donor denticity, i.e. ligand strength of the ethereal solvents which act as ligands to form solvated Mg complexes, plays a significant role in enhancing coulombic efficiency of the corresponding solvated Mg complex electrolytes. A new and safer electrolyte is developed based on Mg(BH4)2, diglyme and optimizedmore » LiBH4 additive. The new electrolyte demonstrates 100% coulombic efficiency, no dendrite formation, and stable cycling performance with the cathode capacity retention of ~90% for 300 cycles in a prototype magnesium battery.« less

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

PubMed

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Ab initio prediction of fast non-equilibrium transport of nascent polarons in SrI2: a key to high-performance scintillation

NASA Astrophysics Data System (ADS)

Zhou, Fei; Sadigh, Babak; Erhart, Paul; Åberg, Daniel

2016-08-01

The excellent light yield proportionality of europium-doped strontium iodide (SrI2:Eu) has resulted in state-of-the-art γ-ray detectors with remarkably high-energy resolution, far exceeding that of most halide compounds. In this class of materials, the formation of self-trapped hole polarons is very common. However, polaron formation is usually expected to limit carrier mobilities and has been associated with poor scintillator light-yield proportionality and resolution. Here using a recently developed first-principles method, we perform an unprecedented study of polaron transport in SrI2, both for equilibrium polarons, as well as nascent polarons immediately following a self-trapping event. We propose a rationale for the unexpected high-energy resolution of SrI2. We identify nine stable hole polaron configurations, which consist of dimerised iodine pairs with polaron-binding energies of up to 0.5 eV. They are connected by a complex potential energy landscape that comprises 66 unique nearest-neighbour migration paths. Ab initio molecular dynamics simulations reveal that a large fraction of polarons is born into configurations that migrate practically barrier free at room temperature. Consequently, carriers created during γ-irradiation can quickly diffuse away reducing the chance for non-linear recombination, the primary culprit for non-proportionality and resolution reduction. We conclude that the flat, albeit complex, landscape for polaron migration in SrI2 is a key for understanding its outstanding performance. This insight provides important guidance not only for the future development of high-performance scintillators but also of other materials, for which large polaron mobilities are crucial such as batteries and solid-state ionic conductors.

Young stellar population and ongoing star formation in the H II complex Sh2-252

NASA Astrophysics Data System (ADS)

Jose, Jessy; Pandey, A. K.; Samal, M. R.; Ojha, D. K.; Ogura, K.; Kim, J. S.; Kobayashi, N.; Goyal, A.; Chauhan, N.; Eswaraiah, C.

2013-07-01

In this paper, an extensive survey of the star-forming complex Sh2-252 has been undertaken with an aim to explore its hidden young stellar population as well as to understand the structure and star formation history for the first time. This complex is composed of five prominent embedded clusters associated with the subregions A, C, E, NGC 2175s and Teu 136. We used Two Micron All Sky Survey-near-infrared and Spitzer-Infrared Array Camera, Multiband Imaging Photometer for Spitzer photometry to identify and classify the young stellar objects (YSOs) by their infrared (IR) excess emission. Using the IR colour-colour criteria, we identified 577 YSOs, of which, 163 are Class I, 400 are Class II and 14 are transition disc YSOs, suggesting a moderately rich number of YSOs in this complex. Spatial distribution of the candidate YSOs shows that they are mostly clustered around the subregions in the western half of the complex, suggesting enhanced star formation activity towards its west. Using the spectral energy distribution and optical colour-magnitude diagram-based age analyses, we derived probable evolutionary status of the subregions of Sh2-252. Our analysis shows that the region A is the youngest (˜0.5 Myr), the regions B, C and E are of similar evolutionary stage (˜1-2 Myr) and the clusters NGC 2175s and Teu 136 are slightly evolved (˜2-3 Myr). Morphology of the region in the 1.1 mm map shows a semicircular shaped molecular shell composed of several clumps and YSOs bordering the western ionization front of Sh2-252. Our analyses suggest that next generation star formation is currently under way along this border and that possibly fragmentation of the matter collected during the expansion of the H II region as one of the major processes is responsible for such stars. We observed the densest concentration of YSOs (mostly Class I, ˜0.5 Myr) at the western outskirts of the complex, within a molecular clump associated with water and methanol masers and we suggest that it is indeed a site of cluster formation at a very early evolutionary stage, sandwiched between the two relatively evolved CH II regions A and B.

Exocyst and autophagy-related membrane trafficking in plants.

PubMed

Pecenková, Tamara; Markovic, Vedrana; Sabol, Peter; Kulich, Ivan; Žárský, Viktor

2017-12-18

Endomembrane traffic in eukaryotic cells functions partially as a means of communication; delivery of membrane in one direction has to be balanced with a reduction at the other end. This effect is typically the case during the defence against pathogens. To combat pathogens, cellular growth and differentiation are suppressed, while endomembrane traffic is poised towards limiting the pathogen attack. The octameric exocyst vesicle-tethering complex was originally discovered as a factor facilitating vesicle-targeting and vesicle-plasma membrane (PM) fusion during exocytosis prior to and possibly during SNARE complex formation. Interestingly, it was recently implicated both in animals and plants in autophagy membrane traffic. In animal cells, the exocyst is integrated into the mTOR-regulated energy metabolism stress/starvation pathway, participating in the formation and especially initiation of an autophagosome. In plants, the first functional link was to autophagy-related anthocyanin import to the vacuole and to starvation. In this concise review, we summarize the current knowledge of exocyst functions in autophagy and defence in plants that might involve unconventional secretion and compare it with animal conditions. Formation of different exocyst complexes during undisturbed cell growth, as opposed to periods of cellular stress reactions involving autophagy, might contribute to the coordination of endomembrane trafficking pathways. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Evidence of bovine serum albumin-viologen herbicide binding interaction and associated structural modifications

NASA Astrophysics Data System (ADS)

Roy, Swarup; Saxena, Shailendra K.; Mishra, Suryakant; Yogi, Priyanka; Sagdeo, P. R.; Kumar, Rajesh

2017-07-01

The binding ability of viologen herbicide with bovine serum albumin (BSA) has been investigated to understand viologen associated hazards by investigating ethyl viologen's (EV) binding using various spectroscopies and in-silico molecular docking approaches. Apparent association constant (1.3 × 104 L/mol), calculated using UV-Vis spectra indicating a moderate complex formation between BSA and EV. A static mode of fluorescence quenching has been observed as evident from inverse temperature dependence of Stern-Volmer quenching constant which also confirms an EV-BSA complex formation. Emission and time resolved fluorescence studies reveal that the emission quenching of BSA with EV is initiated by static quenching mechanism. A moderately strong binding affinity between EV and BSA has been observed (binding constant value of 7.58 × 104 L/Mol) using fluorescence quenching titration, obtained at 298 K. Quantitative measurements of thermodynamic parameters like enthalpy and entropy changes clearly indicates hydrophobic force responsible for EV-BSA complex formation. The binding distance between EV and BSA was found to be 4.48 nm are involved in non-radiative energy transfer process. Furthermore, from the circular dichroism spectra it was observed that addition of EV is also found to change the secondary structure of BSA which leads to decrease in α-helix. Above mentioned results are found to be in consonance with molecular docking simulations and supports the EV-BSA binding.

Low-Energy Collisions of Protonated Enantiopure Amino Acids with Chiral Target Gases

NASA Astrophysics Data System (ADS)

Kulyk, K.; Rebrov, O.; Ryding, M.; Thomas, R. D.; Uggerud, E.; Larsson, M.

2017-12-01

Here we report on the gas-phase interactions between protonated enantiopure amino acids ( l- and d-enantiomers of Met, Phe, and Trp) and chiral target gases [( R)- and ( S)-2-butanol, and ( S)-1-phenylethanol] in 0.1-10.0 eV low-energy collisions. Two major processes are seen to occur over this collision energy regime, collision-induced dissociation and ion-molecule complex formation. Both processes were found to be independent of the stereo-chemical composition of the interacting ions and targets. These data shed light on the currently debated mechanisms of gas-phase chiral selectivity by demonstrating the inapplicability of the three-point model to these interactions, at least under single collision conditions. [Figure not available: see fulltext.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

Carbene-aerogen bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Sabouri, Ayda

2017-04-01

Through the use of ab initio calculations, the possibility of formation of σ-hole interaction between ZO3 (Z = Ar, Kr and Xe) and carbene species is investigated. Since singlet carbenes show a negative electrostatic potential on their divalent carbon atom, they can favourably interact with the positive electrostatic potential generated by the σ-hole of Z atom of ZO3. The characteristic of this interaction, termed as 'carbene-aerogen' bond, is analysed in terms of geometric, interaction energies and electronic features. The energy decomposition analysis indicates that for all complexes analysed here, the electrostatic energy is more negative than the polarisation or dispersion energy term. According to the electron density analysis, some partial covalent character can be ascribed to XeṡṡṡC interactions. In addition, the carbene-aerogen bond exhibits cooperative effects with the HṡṡṡO hydrogen-bonding interaction in ternary complexes where both interactions coexist. For a given carbene, the amount of these cooperative effects increases with the size of the Z atom. The results obtained in this work may be helpful for the extension and future application of σ-hole intermolecular interactions as well as coordination chemistry.

Vacancy-mediated dehydrogenation of sodium alanate

PubMed Central

Gunaydin, Hakan; Houk, Kendall N.; Ozoliņš, Vidvuds

2008-01-01

Clarification of the mechanisms of hydrogen release and uptake in transition-metal-doped sodium alanate, NaAlH4, a prototypical high-density complex hydride, has fundamental importance for the development of improved hydrogen-storage materials. In this and most other modern hydrogen-storage materials, H2 release and uptake are accompanied by long-range diffusion of metal species. Using first-principles density-functional theory calculations, we have determined that the activation energy for Al mass transport via AlH3 vacancies is Q = 85 kJ/mol·H2, which is in excellent agreement with experimentally measured activation energies in Ti-catalyzed NaAlH4. The activation energy for an alternate decomposition mechanism via NaH vacancies is found to be significantly higher: Q = 112 kJ/mol·H2. Our results suggest that bulk diffusion of Al species is the rate-limiting step in the dehydrogenation of Ti-doped samples of NaAlH4 and that the much higher activation energies measured for uncatalyzed samples are controlled by other processes, such as breaking up of AlH4− complexes, formation/dissociation of H2 molecules, and/or nucleation of the product phases. PMID:18299582

Temporal evolution of ion spectral structures during a geomagnetic storm: Observations and modeling

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2016-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. We present a case study of the temporal evolution of H+, He+, and O+ spectral structures throughout the geomagnetic storm of 2 October 2013. We use data from the Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometer onboard Van Allen Probe A to analyze the spectral structures in the energy range of 1- 50 keV. We find that the characteristics of the ion structures follow a cyclic pattern, the observed features changing dramatically as the storm starts and then returning to its initial pre-storm state. Quiet, pre-storm times are characterized by multiple and often complex flux structures at narrow energy bands. During the storm main phase, the observed features become simple, with no nose structures or only one nose structure present in the energy-time spectrograms. As the inner magnetosphere recovers from the storm, more complex structures appear once again. Additionally, the heavy ion spectral features are generally more complex than the H+ features, with multiple noses being observed more often in the heavy ion spectra. We use a model of ion drift and losses due to charge exchange to understand the formation of the spectral features and their species dependence.

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.

PubMed

Baum, Bernhard; Muley, Laveena; Smolinski, Michael; Heine, Andreas; Hangauer, David; Klebe, Gerhard

2010-04-09

Additivity of functional group contributions to protein-ligand binding is a very popular concept in medicinal chemistry as the basis of rational design and optimized lead structures. Most of the currently applied scoring functions for docking build on such additivity models. Even though the limitation of this concept is well known, case studies examining in detail why additivity fails at the molecular level are still very scarce. The present study shows, by use of crystal structure analysis and isothermal titration calorimetry for a congeneric series of thrombin inhibitors, that extensive cooperative effects between hydrophobic contacts and hydrogen bond formation are intimately coupled via dynamic properties of the formed complexes. The formation of optimal lipophilic contacts with the surface of the thrombin S3 pocket and the full desolvation of this pocket can conflict with the formation of an optimal hydrogen bond between ligand and protein. The mutual contributions of the competing interactions depend on the size of the ligand hydrophobic substituent and influence the residual mobility of ligand portions at the binding site. Analysis of the individual crystal structures and factorizing the free energy into enthalpy and entropy demonstrates that binding affinity of the ligands results from a mixture of enthalpic contributions from hydrogen bonding and hydrophobic contacts, and entropic considerations involving an increasing loss of residual mobility of the bound ligands. This complex picture of mutually competing and partially compensating enthalpic and entropic effects determines the non-additivity of free energy contributions to ligand binding at the molecular level. (c) 2010 Elsevier Ltd. All rights reserved.

Sensitized green emission of terbium with dibenzoylmethane and 1, 10 phenanthroline in polyvinyl alcohol and polyvinyl pyrrolidone blends

NASA Astrophysics Data System (ADS)

Kumar, Brijesh; Kaur, Gagandeep; Rai, S. B.

2017-12-01

Tb doped polyvinyl alcohol: polyvinyl pyrrolidone blends with dibenzoylmethane (DBM) and 1, 10 Phenanthroline (Phen) have been prepared by solution cast technique. Bond formation amongst the ligands and Tb3 + ions in the doped polymer has been confirmed employing Fourier Transform Infrared (FTIR) techniques. Optical properties of the Tb3 + ions have been investigated using UV-Vis absorption, excitation and fluorescence studies excited by different radiations. Addition of dimethylbenzoate and 1, 10 Phenanthroline to the polymer blend increases the luminescence from Tb3 + ions along with energy transfer from the polymer blend itself. Luminescence decay curve analysis affirms the non-radiative energy transfer from DBM and Phen to Tb3 + ions, which is identified as the reason behind this enhancement. The fluorescence decay time of PVA-PVP host decreases from 6.02 ns to 2.31 ns showing an evidence of energy transfer from the host blend to the complexed Tb ions. Similarly the lifetime of DBM and Phen and both in the blend reduces in the complexed system showing the feasibility of energy transfer from these excited DBM and Phen to Tb3 + and is proposed as the cause of the above observations. These entire phenomena have been explained by the energy level diagram.

TRANSPARENT TESTA GLABRA1 and GLABRA1 Compete for Binding to GLABRA3 in Arabidopsis

PubMed Central

Pesch, Martina; Schultheiß, Ilka; Klopffleisch, Karsten; Clemen, Christoph S.; Hülskamp, Martin

2015-01-01

The MBW (for R2R3MYB, basic helix-loop-helix [bHLH], and WD40) genes comprise an evolutionarily conserved gene cassette that regulates several traits such as (pro)anthocyanin and anthocyanin biosynthesis and epidermal cell differentiation in plants. Trichome differentiation in Arabidopsis (Arabidopsis thaliana) is governed by GLABRA1 (GL1; R2R3MYB), GL3 (bHLH), and TRANSPARENT TESTA GLABRA1 (TTG1; WD40). They are thought to form a trimeric complex that acts as a transcriptional activation complex. We provide evidence that these three MBW proteins form either GL1 GL3 or GL3 TTG1 dimers. The formation of each dimer is counteracted by the respective third protein in yeast three-hybrid assays, pulldown experiments (luminescence-based mammalian interactome), and fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer studies. We further show that two target promoters, TRIPTYCHON (TRY) and CAPRICE (CPC), are differentially regulated: GL1 represses the activation of the TRY promoter by GL3 and TTG1, and TTG1 suppresses the activation of the CPC promoter by GL1 and GL3. Our data suggest that the transcriptional activation by the MBW complex involves alternative complex formation and that the two dimers can differentially regulate downstream genes. PMID:25926482

Linear σ-hole⋯CO⋯σ-hole intermolecular interactions between carbon monoxide and dihalogen molecules XY (X, Y=Cl, Br).

PubMed

Yang, Xing; Yang, Fan; Wu, Rui-Zhi; Yan, Chao-Xian; Zhou, Da-Gang; Zhou, Pan-Pan; Yao, Xiaojun

2017-09-01

Carbon monoxide can interact with two dihalogen molecules XY (X, Y=Cl, Br) in the form of X(Y)⋯COX(Y)⋯CO⋯X(Y)X(Y) trimeric complex, and their nature and characteristics were investigated at MP2/aug-cc-pVDZ level without and with counterpoise method, together with single point calculations at CCSD(T)/aug-cc-pVDZ level. The optimized geometries, stretching modes and interaction energies of a series of X(Y)⋯COX(Y)⋯CO⋯X(Y)X(Y) trimeric complexes were obtained and discussed. The cooperativity in these complexes was evaluated. EDA analyses reveal that the electrostatic interaction is the dominant net driving force in each trimer, but the contributions of other interactions like exchange, dispersion and polarization interactions are also important. QTAIM and NCI analyses confirm the existence of attractive halogen-bonding interactions. Additionally, EDDMF analysis was employed for the component dimers of these trimers, which indicates that the formation of halogen-bonding interactions is closely related to the charge shift and the rearrangement of electronic density in the formation of these complexes. The results would provide valuable insight into for these linear halogen bonds. Copyright © 2017 Elsevier Inc. All rights reserved.

Noncovalent Interactions and Internal Dynamics in Pyridine-Ammonia: A Combined Quantum-Chemical and Microwave Spectroscopy Study.

PubMed

Spada, Lorenzo; Tasinato, Nicola; Vazart, Fanny; Barone, Vincenzo; Caminati, Walther; Puzzarini, Cristina

2017-04-06

The 1:1 complex of ammonia with pyridine is characterized by using state-of-the-art quantum-chemical computations combined with pulsed-jet Fourier-transform microwave spectroscopy. The computed potential energy landscape indicates the formation of a stable σ-type complex, which is confirmed experimentally: analysis of the rotational spectrum shows the presence of only one 1:1 pyridine-ammonia adduct. Each rotational transition is split into several components owing to the internal rotation of NH 3 around its C 3 axis and to the hyperfine structure of both 14 N quadrupolar nuclei, thus providing unequivocal proof that the two molecules form a σ-type complex involving both a N-H⋅⋅⋅N and a C-H⋅⋅⋅N hydrogen bond. The dissociation energy (BSSE- and ZPE-corrected) is estimated to be 11.5 kJ mol -1 . This work represents the first application of an accurate yet efficient computational scheme, designed for the investigation of small biomolecules, to a molecular cluster. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-Covalent Interactions and Internal Dynamics in Pyridine-Ammonia a Combined Quantum-Chemical and Microwave Spectroscopy Study

NASA Astrophysics Data System (ADS)

Spada, Lorenzo; Tasinato, Nicola; Vazart, Fanny; Barone, Vincenzo; Caminati, Walther; Puzzarini, Cristina

2017-06-01

The 1:1 complex of ammonia with pyridine has been characterized by using state-of-the-art quantum-chemical computations combined with pulsed-jet Fourier-Transform microwave spectroscopy. The computed potential energy landscape pointed out the formation of a stable σ-type complex, which has been confirmed experimentally: the analysis of the rotational spectrum showed the presence of only one 1:1 pyridine - ammonia adduct. Each rotational transition is split into several components due to the internal rotation of NH_3 around its C_3 axis and to the hyperfine structure of both ^{14}N quadrupolar nuclei, thus providing the unequivocal proof that the two molecules form a σ-type complex involving both a N-H\\cdotsN and a C-H\\cdotsN hydrogen bond. The dissociation energy (BSSE and ZPE corrected) has been estimated to be 11.5 kJ\\cdotmol^{-1}. This work represents the first application of an accurate, yet efficient computational scheme, designed for the investigation of small biomolecules, to a molecular cluster.

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

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

Sullivan, Sarah M.; Holyoak, Todd

2008-09-17

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection

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

Sullivan, S.M.; Holyoak, T.

2009-05-26

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Exploring hydride-π interactions and their tuning by σ-hole bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Asadollahi, Soheila; Mousavian, Parisasadat

2018-01-01

In the present work, ab initio calculations are performed to investigate the geometry, interaction energy and bonding properties of binary complexes formed between metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CH3) and a series of π-acidic heteroaromatic rings. In all the resulting complexes, the heteroaromatic ring acts as a Lewis acid (electron acceptor), while the H atom of the HMX molecule acts as a Lewis base (electron donor). The nature of this interaction, called 'hydride-π' interaction, is explored in terms of molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. The results show that the interaction energies of these hydride-π interactions are between -1.24 and -2.72 kcal/mol. Furthermore, mutual influence between the hydride-π and halogen- or pnicogen-bonding interactions is studied in complexes in which these interactions coexist. For a given π-acidic ring, the formation of the pnicogen-bonding induces a larger enhancing effect on the strength of hydride-π bond than the halogen-bonding.

Theoretical and Experimental Study of Inclusion Complexes of β-Cyclodextrins with Chalcone and 2',4'-Dihydroxychalcone.

PubMed

Sancho, Matias I; Andujar, Sebastian; Porasso, Rodolfo D; Enriz, Ricardo D

2016-03-31

The inclusion complexes formed by chalcone and 2',4'-dihydroxychalcone with β-cyclodextrin have been studied combining experimental (phase solubility diagrams, Fourier transform infrared spectroscopy) and molecular modeling (molecular dynamics, quantum mechanics/molecular mechanics calculations) techniques. The formation constants of the complexes were determined at different temperatures, and the thermodynamic parameters of the process were obtained. The inclusion of chalcone in β-cyclodextrin is an exothermic process, while the inclusion of 2',4'-dihydroxychalcone is endothermic. Free energy profiles, derived from umbrella sampling using molecular dynamics simulations, were constructed to analyze the binding affinity and the complexation reaction at a molecular level. Hybrid QM/MM calculations were also employed to obtain a better description of the energetic and structural aspects of the complexes. The intermolecular interactions that stabilize both inclusion complexes were characterized by means of quantum atoms in molecules theory and reduce density gradient method. The calculated interactions were experimentally observed using FTIR.

Temporal Profiling of Orexin Receptor-Arrestin-Ubiquitin Complexes Reveals Differences between Receptor Subtypes*

PubMed Central

Dalrymple, Matthew B.; Jaeger, Werner C.; Eidne, Karin A.; Pfleger, Kevin D. G.

2011-01-01

Orexin G protein-coupled receptors (OxRs) and their cognate agonists have been implicated in a number of disorders since their recent discovery, ranging from narcolepsy to formation of addictive behavior. Bioluminescence resonance energy transfer assays of agonist-occupied OxRs provided evidence for a strong dose-dependent interaction with both trafficking proteins β-arrestin 1 and 2 that required unusually high agonist concentrations compared with inositol phosphate signaling. This appears to be reflected in functional differences in potency with respect to orexin A (OxA) and OxR2-dependent ERK1/2 phosphorylation after 90 min compared with 2 min, potentially consistent with β-arrestin-mediated versus G protein-mediated signaling, respectively. Furthermore, extended bioluminescence resonance energy transfer kinetic data monitoring OxA-dependent receptor-β-arrestin and β-arrestin-ubiquitin proximity suggested subtype-specific differences in receptor trafficking, with OxR2 activation resulting in more sustained receptor-β-arrestin-ubiquitin complex formation than elicited by OxR1 activation. Enzyme-linked immunosorbent assay (ELISA) data also revealed that OxR1 underwent significantly more rapid recycling compared with OxR2. Finally, we have observed sustained OxA-dependent ERK1/2 phosphorylation in the presence of OxR2 compared with OxR1. Although both OxR subtypes could be classified as class B receptors for β-arrestin usage based on the initial strength of interaction with both β-arrestins, our temporal profiling revealed tangible differences between OxR subtypes. Consequently, OxR1 appears to fit uneasily into the commonly used β-arrestin classification scheme. More importantly, it is hoped that this improved profiling capability, enabling the subtleties of protein complex formation, stability, and duration to be assessed in live cells, will help unlock the therapeutic potential of targeting these receptors. PMID:21378163

Decanuclear Ln10 Wheels and Vertex-Shared Spirocyclic Ln5 Cores: Synthesis, Structure, SMM Behavior, and MCE Properties.

PubMed

Das, Sourav; Dey, Atanu; Kundu, Subrata; Biswas, Sourav; Narayanan, Ramakirushnan Suriya; Titos-Padilla, Silvia; Lorusso, Giulia; Evangelisti, Marco; Colacio, Enrique; Chandrasekhar, Vadapalli

2015-11-16

The reaction of a Schiff base ligand (LH3) with lanthanide salts, pivalic acid and triethylamine in 1:1:1:3 and 4:5:8:20 stoichiometric ratios results in the formation of decanuclear Ln10 (Ln = Dy (1), Tb (2), and Gd (3)) and pentanuclear Ln5 complexes (Ln = Gd (4), Tb (5), and Dy (6)), respectively. The formation of Ln10 and Ln5 complexes are fully governed by the stoichiometry of the reagents used. Detailed magnetic studies on these complexes (1-6) have been carried out. Complex 1 shows a SMM behavior with an effective energy barrier for the reversal of the magnetization (Ueff) = 16.12(8) K and relaxation time (τo) = 3.3×10(-5) s under 4000 Oe direct current (dc) field. Complex 6 shows the frequency dependent maxima in the out-of-phase signal under zero dc field, without achieving maxima above 2 K. Complexes 3 and 4 show a large magnetocaloric effect with the following characteristic values: -ΔSm = 26.6 J kg(-1) K(-1) at T = 2.2 K for 3 and -ΔSm = 27.1 J kg(-1) K(-1) at T = 2.4 K for 4, both for an applied field change of 7 T. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of angular momentum alignment and strong magnetic fields on the formation of protostellar discs

NASA Astrophysics Data System (ADS)

Gray, William J.; McKee, Christopher F.; Klein, Richard I.

2018-01-01

Star-forming molecular clouds are observed to be both highly magnetized and turbulent. Consequently, the formation of protostellar discs is largely dependent on the complex interaction between gravity, magnetic fields, and turbulence. Studies of non-turbulent protostellar disc formation with realistic magnetic fields have shown that these fields are efficient in removing angular momentum from the forming discs, preventing their formation. However, once turbulence is included, discs can form in even highly magnetized clouds, although the precise mechanism remains uncertain. Here, we present several high-resolution simulations of turbulent, realistically magnetized, high-mass molecular clouds with both aligned and random turbulence to study the role that turbulence, misalignment, and magnetic fields have on the formation of protostellar discs. We find that when the turbulence is artificially aligned so that the angular momentum is parallel to the initial uniform field, no rotationally supported discs are formed, regardless of the initial turbulent energy. We conclude that turbulence and the associated misalignment between the angular momentum and the magnetic field are crucial in the formation of protostellar discs in the presence of realistic magnetic fields.

Ligational behavior of clioquinol antifungal drug towards Ag(I), Hg(II), Cr(III) and Fe(III) metal ions: Synthesis, spectroscopic, thermal, morphological and antimicrobial studies

NASA Astrophysics Data System (ADS)

El-Megharbel, Samy M.; Refat, Moamen S.

2015-04-01

This article presents a synthesis, characterization, theoretical and biological (anti-bacterial, and anti-fugal) evaluation studies of Ag(I), Hg(II), Cr(III) and Fe(III) complexes of clioquinol (CQ) drug ligand. Structures of the titled complexes cited herein were discussed using elemental analyses and spectral measurements e.g., IR, 1H NMR, and electronic studies. The results confirmed the formation of the clioquinol complexes by three molar ratios (1:1) for Ag(I), (1:2) for Hg(II) and (1:3) for both Cr(III) and Fe(III) metal ions. The clioquinol reacts as a bidentate chelate bound to all respected metal ions through the oxygen and nitrogen of quinoline-8-ol. The metal(II) ions coordinated to clioquinol ligand through deprotonation of sbnd OH terminal group. Infrared and 1H NMR spectral data confirm that coordination is via the oxygen of phenolic group and nitrogen atom of quinoline moiety. The molar conductance measurements of the CQ complexes in DMSO correspond to be non-electrolyte nature. Thus, these complexes may be formulated as [Ag(CQ)(H2O)2] H2O, [Hg(CQ)2]ṡ2H2O, [Cr(CQ)3] and [Fe(CQ)3]H2O. The Coats-Redfern method, the kinetic thermodynamic parameters like activation energies (E∗), entropies (ΔS∗), enthalpies (ΔH∗), and Gibbs free energies (ΔG∗) of the thermal decomposition reactions have been deduced from thermogravimetric curves (TG) with helpful of differential thermo gravimetric (DTG) curves. The narrow size distribution in nano-scale range for the clioquinol complexes have been discussed using X-ray powder diffraction (XRD), scanning electron microscope (SEM), and X-ray energy dispersive spectrometer (EDX) analyzer.

Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

NASA Astrophysics Data System (ADS)

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

2017-09-01

New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained. An important aim of this work is analysis of the interaction energies between the filled natural bond orbitals (NBOs) and the empty ones in order to shed the light on the ease of electron delocalization among bonds in the novel hydrogen bonded complex.

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.

PubMed

Callegari, D; Ranaghan, K E; Woods, C J; Minari, R; Tiseo, M; Mor, M; Mulholland, A J; Lodola, A

2018-03-14

Osimertinib is a third-generation inhibitor approved for the treatment of non-small cell lung cancer. It overcomes resistance to first-generation inhibitors by incorporating an acrylamide group which alkylates Cys797 of EGFR T790M. The mutation of a residue in the P-loop (L718Q) was shown to cause resistance to osimertinib, but the molecular mechanism of this process is unknown. Here, we investigated the inhibitory process for EGFR T790M (susceptible to osimertinib) and EGFR T790M/L718Q (resistant to osimertinib), by modelling the chemical step ( i.e. , alkylation of Cys797) using QM/MM simulations and the recognition step by MD simulations coupled with free-energy calculations. The calculations indicate that L718Q has a negligible impact on both the activation energy for Cys797 alkylation and the free-energy of binding for the formation of the non-covalent complex. The results show that Gln718 affects the conformational space of the EGFR-osimertinib complex, stabilizing a conformation of acrylamide which prevents reaction with Cys797.

A density functional theory study of the correlation between analyte basicity, ZnPc adsorption strength, and sensor response.

PubMed

Tran, N L; Bohrer, F I; Trogler, W C; Kummel, A C

2009-05-28

Density functional theory (DFT) simulations were used to determine the binding strength of 12 electron-donating analytes to the zinc metal center of a zinc phthalocyanine molecule (ZnPc monomer). The analyte binding strengths were compared to the analytes' enthalpies of complex formation with boron trifluoride (BF(3)), which is a direct measure of their electron donating ability or Lewis basicity. With the exception of the most basic analyte investigated, the ZnPc binding energies were found to correlate linearly with analyte basicities. Based on natural population analysis calculations, analyte complexation to the Zn metal of the ZnPc monomer resulted in limited charge transfer from the analyte to the ZnPc molecule, which increased with analyte-ZnPc binding energy. The experimental analyte sensitivities from chemiresistor ZnPc sensor data were proportional to an exponential of the binding energies from DFT calculations consistent with sensitivity being proportional to analyte coverage and binding strength. The good correlation observed suggests DFT is a reliable method for the prediction of chemiresistor metallophthalocyanine binding strengths and response sensitivities.

Assessment of CO2 Mineralization and Dynamic Rock Properties at the Kemper Pilot CO2 Injection Site

NASA Astrophysics Data System (ADS)

Qin, F.; Kirkland, B. L.; Beckingham, L. E.

2017-12-01

CO2-brine-mineral reactions following CO2 injection may impact rock properties including porosity, permeability, and pore connectivity. The rate and extent of alteration largely depends on the nature and evolution of reactive mineral interfaces. In this work, the potential for geochemical reactions and the nature of the reactive mineral interface and corresponding hydrologic properties are evaluated for samples from the Lower Tuscaloosa, Washita-Fredericksburg, and Paluxy formations. These formations have been identified as future regionally extensive and attractive CO2 storage reservoirs at the CO2 Storage Complex in Kemper County, Mississippi, USA (Project ECO2S). Samples from these formations were obtained from the Geological Survey of Alabama and evaluated using a suite of complementary analyses. The mineral composition of these samples will be determined using petrography and powder X-ray Diffraction (XRD). Using these compositions, continuum-scale reactive transport simulations will be developed and the potential CO2-brine-mineral interactions will be examined. Simulations will focus on identifying potential reactive minerals as well as the corresponding rate and extent of reactions. The spatial distribution and accessibility of minerals to reactive fluids is critical to understanding mineral reaction rates and corresponding changes in the pore structure, including pore connectivity, porosity and permeability. The nature of the pore-mineral interface, and distribution of reactive minerals, will be determined through imaging analysis. Multiple 2D scanning electron microscopy (SEM) backscattered electron (BSE) images and energy dispersive x-ray spectroscopy (EDS) images will be used to create spatial maps of mineral distributions. These maps will be processed to evaluate the accessibility of reactive minerals and the potential for flow-path modifications following CO2 injection. The "Establishing an Early CO2 Storage Complex in Kemper, MS" project is funded by the U.S. Department of Energy's National Energy Technology Laboratory and cost-sharing partners.

Graphene sheets stabilized on genetically engineered M13 viral templates as conducting frameworks for hybrid energy-storage materials.

PubMed

Oh, Dahyun; Dang, Xiangnan; Yi, Hyunjung; Allen, Mark A; Xu, Kang; Lee, Yun Jung; Belcher, Angela M

2012-04-10

Utilization of the material-specific peptide-substrate interactions of M13 virus broadens colloidal stability window of graphene. The homogeneous distribution of graphene is maintained in weak acids and increased ionic strengths by complexing with virus. This graphene/virus conducting template is utilized in the synthesis of energy-storage materials to increase the conductivity of the composite electrode. Successful formation of the hybrid biological template is demonstrated by the mineralization of bismuth oxyfluoride as a cathode material for lithium-ion batteries, with increased loading and improved electronic conductivity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogenation of Carbon Dioxide to Methanol Catalyzed by Iron, Cobalt, and Manganese Cyclopentadienone Complexes: Mechanistic Insights and Computational Design.

PubMed

Ge, Hongyu; Chen, Xiangyang; Yang, Xinzheng

2017-07-03

Density functional theory study of the hydrogenation of carbon dioxide to methanol catalyzed by iron, cobalt, and manganese cyclopentadienone complexes reveals a self-promoted mechanism, which features a methanol- or water-molecule-assisted proton transfer for the cleavage of H 2 . The total free energy barrier of the formation of methanol from CO 2 and H 2 catalyzed by Knölker's iron cyclopentadienone complex, [2,5-(SiMe 3 ) 2 -3,4-(CH 2 ) 4 (η 5 -C 4 COH)]Fe(CO) 2 H, is 26.0 kcal mol -1 in the methanol solvent. We also evaluated the catalytic activities of 8 other experimentally reported iron cyclopentadienone complexes and 37 iron, cobalt, and manganese cyclopentadienone complexes proposed in this study. In general, iron and manganese complexes have relatively higher catalytic activities. Among all calculated complexes, [2,5-(SiMe 3 ) 2 -3,4-CH 3 CHSCH 2 (η 5 -C 4 COH)]Fe(CO) 2 H (1 Fe-Casey-S-CH3 ) is the most active one with a total free energy barrier of 25.1 kcal mol -1 in the methanol solvent. Such a low barrier indicates that 1 Fe-Casey-S-CH3 is a very promising low-cost and high efficiency catalyst for the conversion of CO 2 and H 2 to methanol under mild conditions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Architectural elements from Lower Proterozoic braid-delta and high-energy tidal flat deposits in the Magaliesberg Formation, Transvaal Supergroup, South Africa

NASA Astrophysics Data System (ADS)

Eriksson, Patrick G.; Reczko, Boris F. F.; Jaco Boshoff, A.; Schreiber, Ute M.; Van der Neut, Markus; Snyman, Carel P.

1995-06-01

Three architectural elements are identified in the Lower Proterozoic Magaliesberg Formation (Pretoria Group, Transvaal Supergroup) of the Kaapvaal craton, South Africa: (1) medium- to coarse-grained sandstone sheets; (2) fine- to medium-grained sandstone sheets; and (3) mudrock elements. Both sandstone sheet elements are characterised by horizontal lamination and planar cross-bedding, with lesser trough cross-bedding, channel-fills and wave ripples, as well as minor desiccated mudrock partings, double-crested and flat-topped ripples. Due to the local unimodal palaeocurrent patterns in the medium- to coarse-grained sandstone sheets, they are interpreted as ephemeral braid-delta deposits, which were subjected to minor marine reworking. The predominantly bimodal to polymodal palaeocurrent trends in the fine- to medium-grained sandstone sheets are inferred to reflect high-energy macrotidal processes and more complete reworking of braid-delta sands. The suspension deposits of mudrocks point to either braid-delta channel abandonment, or uppermost tidal flat sedimentation. The depositional model comprises ephemeral braid-delta systems which debouched into a high-energy peritidal environment, around the margins of a shallow epeiric sea on the Kaapvaal craton. Braid-delta and tidal channel dynamics are inferred to have been similar. Fine material in the Magaliesberg Formation peritidal complexes indicates that extensive aeolian removal of clay does not seem applicable to this example of the early Proterozoic.

Thermal regeneration of an electrochemical concentration cell

DOEpatents

Krumpelt, M.; Bates, J.K.

1980-05-09

A system and method are described for thermally regenerating an electrochemical concentration cell having first and second aluminum electrodes respectively positioned in contact with first and second electrolytes separated by an ion exchange member, the first and second electrolytes being composed of different concentrations of an ionic solvent and a salt, preferably an aluminum halide. The ionic solvent may be either organic or inorganic with a relatively low melting point, the ionic solvent and the salt form a complex wherein the free energy of formation of said complex is less than about -5 kcal/mole. A distillation column using solar heat or low grade industrial waste heat receives the first and second electrolytes and thermally decomposes the salt-solvent complex to provide feed material for the two half cells.

Photochemical Approaches to Complex Chemotypes: Applications in Natural Product Synthesis.

PubMed

Kärkäs, Markus D; Porco, John A; Stephenson, Corey R J

2016-09-14

The use of photochemical transformations is a powerful strategy that allows for the formation of a high degree of molecular complexity from relatively simple building blocks in a single step. A central feature of all light-promoted transformations is the involvement of electronically excited states, generated upon absorption of photons. This produces transient reactive intermediates and significantly alters the reactivity of a chemical compound. The input of energy provided by light thus offers a means to produce strained and unique target compounds that cannot be assembled using thermal protocols. This review aims at highlighting photochemical transformations as a tool for rapidly accessing structurally and stereochemically diverse scaffolds. Synthetic designs based on photochemical transformations have the potential to afford complex polycyclic carbon skeletons with impressive efficiency, which are of high value in total synthesis.

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro

2011-10-20

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

Dynamics of Fos-Jun-NFAT1 complexes

PubMed Central

Ramirez-Carrozzi, Vladimir R.; Kerppola, Tom K.

2001-01-01

Transcription initiation in eukaryotes is controlled by nucleoprotein complexes formed through cooperative interactions among multiple transcription regulatory proteins. These complexes may be assembled via stochastic collisions or defined pathways. We investigated the dynamics of Fos-Jun-NFAT1 complexes by using a multicolor fluorescence resonance energy transfer assay. Fos-Jun heterodimers can bind to AP-1 sites in two opposite orientations, only one of which is populated in mature Fos-Jun-NFAT1 complexes. We studied the reversal of Fos-Jun binding orientation in response to NFAT1 by measuring the efficiencies of energy transfer from donor fluorophores linked to opposite ends of an oligonucleotide to an acceptor fluorophore linked to one subunit of the heterodimer. The reorientation of Fos-Jun by NFAT1 was not inhibited by competitor oligonucleotides or heterodimers. The rate of Fos-Jun reorientation was faster than the rate of heterodimer dissociation at some binding sites. The facilitated reorientation of Fos-Jun heterodimers therefore can enhance the efficiency of Fos-Jun-NFAT1 complex formation. We also examined the influence of the preferred orientation of Fos-Jun binding on the stability and transcriptional activity of Fos-Jun-NFAT1 complexes. Complexes formed at sites where Fos-Jun favored the same binding orientation in the presence and absence of NFAT1 exhibited an 8-fold slower dissociation rate than complexes formed at sites where Fos-Jun favored the opposite binding orientation. Fos-Jun-NFAT1 complexes also exhibited greater transcription activation at promoter elements that favored the same orientation of Fos-Jun binding in the presence and absence of NFAT1. Thus, the orientation of heterodimer binding can influence both the dynamics and promoter selectivity of multiprotein transcription regulatory complexes. PMID:11320240

Dynamics of Fos-Jun-NFAT1 complexes.

PubMed

Ramirez-Carrozzi, V R; Kerppola, T K

2001-04-24

Transcription initiation in eukaryotes is controlled by nucleoprotein complexes formed through cooperative interactions among multiple transcription regulatory proteins. These complexes may be assembled via stochastic collisions or defined pathways. We investigated the dynamics of Fos-Jun-NFAT1 complexes by using a multicolor fluorescence resonance energy transfer assay. Fos-Jun heterodimers can bind to AP-1 sites in two opposite orientations, only one of which is populated in mature Fos-Jun-NFAT1 complexes. We studied the reversal of Fos-Jun binding orientation in response to NFAT1 by measuring the efficiencies of energy transfer from donor fluorophores linked to opposite ends of an oligonucleotide to an acceptor fluorophore linked to one subunit of the heterodimer. The reorientation of Fos-Jun by NFAT1 was not inhibited by competitor oligonucleotides or heterodimers. The rate of Fos-Jun reorientation was faster than the rate of heterodimer dissociation at some binding sites. The facilitated reorientation of Fos-Jun heterodimers therefore can enhance the efficiency of Fos-Jun-NFAT1 complex formation. We also examined the influence of the preferred orientation of Fos-Jun binding on the stability and transcriptional activity of Fos-Jun-NFAT1 complexes. Complexes formed at sites where Fos-Jun favored the same binding orientation in the presence and absence of NFAT1 exhibited an 8-fold slower dissociation rate than complexes formed at sites where Fos-Jun favored the opposite binding orientation. Fos-Jun-NFAT1 complexes also exhibited greater transcription activation at promoter elements that favored the same orientation of Fos-Jun binding in the presence and absence of NFAT1. Thus, the orientation of heterodimer binding can influence both the dynamics and promoter selectivity of multiprotein transcription regulatory complexes.

Acetonitrile-water hydrogen-bonded interaction: Matrix-isolation infrared and ab initio computation

NASA Astrophysics Data System (ADS)

Gopi, R.; Ramanathan, N.; Sundararajan, K.

2015-08-01

The 1:1 hydrogen-bonded complex of acetonitrile (CH3CN) and water (H2O) was trapped in Ar and N2 matrices and studied using infrared technique. Ab initio computations showed two types of complexes formed between CH3CN and H2O, a linear complex A with a Ctbnd N⋯H interaction between nitrogen of CH3CN and hydrogen of H2O and a cyclic complex B, in which the interactions are between the hydrogen of CH3CN with oxygen of H2O and hydrogen of H2O with π cloud of sbnd Ctbnd N of CH3CN. Vibrational wavenumber calculations revealed that both the complexes A and B were minima on the potential energy surface. Interaction energies computed at B3LYP/6-311++G(d,p) showed that linear complex A is more stable than cyclic complex B. Computations identified a blue shift of ∼11.5 cm-1 and a red shift of ∼6.5 cm-1 in the CN stretching mode for the complexes A and B, respectively. Experimentally, we observed a blue shift of ∼15.0 and ∼8.3 cm-1 in N2 and Ar matrices, respectively, in the CN stretching mode of CH3CN, which supports the formation of complex A. The Onsager Self Consistent Reaction Field (SCRF) model was used to explain the influence of matrices on the complexes A and B. To understand the nature of the interactions, Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were carried out for the complexes A and B.

Reproducing the observed energy-dependent structure of Earth's electron radiation belts during storm recovery with an event-specific diffusion model

DOE PAGES

Ripoll, J. -F.; Reeves, Geoffrey D.; Cunningham, Gregory Scott; ...

2016-06-11

Here, we present dynamic simulations of energy-dependent losses in the radiation belt “slot region” and the formation of the two-belt structure for the quiet days after the 1 March storm. The simulations combine radial diffusion with a realistic scattering model, based data-driven spatially and temporally resolved whistler-mode hiss wave observations from the Van Allen Probes satellites. The simulations reproduce Van Allen Probes observations for all energies and L shells (2–6) including (a) the strong energy dependence to the radiation belt dynamics (b) an energy-dependent outer boundary to the inner zone that extends to higher L shells at lower energies andmore » (c) an “S-shaped” energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. We find that the characteristic energy-dependent structure of the radiation belts and slot region is dynamic and can be formed gradually in ~15 days, although the “S shape” can also be reproduced by assuming equilibrium conditions. The highest-energy electrons (E > 300 keV) of the inner region of the outer belt (L ~ 4–5) also constantly decay, demonstrating that hiss wave scattering affects the outer belt during times of extended plasmasphere. Through these simulations, we explain the full structure in energy and L shell of the belts and the slot formation by hiss scattering during storm recovery. We show the power and complexity of looking dynamically at the effects over all energies and L shells and the need for using data-driven and event-specific conditions.« less

Titanium embedded cage structure formation in Al{sub n}Ti{sup +} clusters and their interaction with Ar

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

Torres, M. B., E-mail: begonia@ubu.es; Vega, A.; Balbás, L. C.

2014-05-07

Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al{sub n}Ti{sup +} [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > n{sub c} determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al{sub n}Ti{sup +}, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic propertiesmore » of singly titanium doped cationic clusters, Al{sub n}Ti{sup +} (n = 16–21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at n{sub c} = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (n{sub c} = 21) and their neutral counterparts (n{sub c} = 20). For the Al {sub n} Ti {sup +} · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al{sub n}Ti{sup +} clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For n{sub c} = 21, the smallest size of endohedral Ti doped cationic clusters, the Ar binding energy decreases drastically, whereas the Ar-cluster distance increases substantially, point to Ar physisorption, as assumed by the experimentalists. Calculated Ar adsorption energies agree well with available experimental binding energies.« less

Structural characterization of molecular complexes formed by trimethoprim and cimitidine with 2,3,5,6-tetrachloro-1,4-benzoquinone

NASA Astrophysics Data System (ADS)

Balraj, C.; Ganesh, K.; Elango, K. P.

2011-07-01

Spectroscopic and spectrofluorimetric techniques have been employed to investigate the structure of the charge transfer (CT) complexes of Trimethoprim (TMP) and Cimitidine (CTD) drugs with 2,3,5,6-tetrachloro-1,4-benzoquinone ( p-chloranil, p-CHL). The stoichiometry of the complexes was found to be 1:2 for TMP- p-CHL system and 1:1 for CTD- p-CHL system. The thermodynamic results indicated that the formation of molecular complex between the donors and the acceptor is spontaneous and endothermic. The results of electronic spectral studies indicated that the formation constant for CTD- p-CHL system is found to be higher than that for TMP- p-CHL system. The observation is well supported by the results of fluorescence quenching studies and the association constants calculated for CTD- p-CHL system is 36.2 × 10 3 mol L -1 and that for TMP- p-CHL system is 2.6 × 10 3 mol L -1. The kinetic results, in both the cases, indicated that the interaction is first order each with respect to the concentration of the donor and the acceptor. The physico-chemical parameters viz. oscillator strength, dipole moment, ionization potential and dissociation energy of the complexes were also determined and discussed. Structural characterization of the complexes were done using FT-IR and 1H NMR spectral techniques and the results indicated that, in TMP, the free NH 2 group while in CTD the pyrazole N sbnd H moiety involves in complexation with the acceptor, p-CHL.

DFT study of uranyl peroxo complexes with H2O, F-, OH-, CO3(2-), and NO3(-).

PubMed

Odoh, Samuel O; Schreckenbach, Georg

2013-05-06

The structural and electronic properties of monoperoxo and diperoxo uranyl complexes with aquo, fluoride, hydroxo, carbonate, and nitrate ligands have been studied using scalar relativistic density functional theory (DFT). Only the complexes in which the peroxo ligands are coordinated to the uranyl moiety in a bidentate mode were considered. The calculated binding energies confirm that the affinity of the peroxo ligand for the uranyl group far exceeds that of the F(-), OH(-), CO3(2-), NO3(-), and H2O ligands. The formation of the monoperoxo complexes from UO2(H2O)5(2+) and HO2(-) were found to be exothermic in solution. In contrast, the formation of the monouranyl-diperoxo, UO2(O2)2X2(4-) or UO2(O2)2X(4-/3-) (where X is any of F(-), OH(-), CO3(2-), or NO3(-)), complexes were all found to be endothermic in aqueous solution. This suggests that the monoperoxo species are the terminal monouranyl peroxo complexes in solution, in agreement with recent experimental work. Overall, we find that the properties of the uranyl-peroxo complexes conform to well-known trends: the coordination of the peroxo ligand weakens the U-O(yl) bonds, stabilizes the σ(d) orbitals and causes a mixing between the uranyl π- and peroxo σ- and π-orbitals. The weakening of the U-O(yl) bonds upon peroxide coordination results in uranyl stretching vibrational frequencies that are much lower than those obtained after the coordination of carbonato or hydroxo ligands.

Electrically active induced energy levels and metastability of B and N vacancy-complexes in 4H-SiC.

PubMed

Igumbor, E; Olaniyan, O; Mapasha, R E; Danga, H T; Omotoso, E; Meyer, W E

2018-05-10

Electrically active induced energy levels in semiconductor devices could be beneficial to the discovery of an enhanced p or n-type semiconductor. Nitrogen (N) implanted into 4H-SiC is a high energy process that produced high defect concentrations which could be removed during dopant activation annealing. On the other hand, boron (B) substituted for silicon in SiC causes a reduction in the number of defects. This scenario leads to a decrease in the dielectric properties and induced deep donor and shallow acceptor levels. Complexes formed by the N, such as the nitrogen-vacancy centre, have been reported to play a significant role in the application of quantum bits. In this paper, results of charge states thermodynamic transition level of the N and B vacancy-complexes in 4H-SiC are presented. We explore complexes where substitutional N[Formula: see text]/N[Formula: see text] or B[Formula: see text]/B[Formula: see text] sits near a Si (V[Formula: see text]) or C (V[Formula: see text]) vacancy to form vacancy-complexes (N[Formula: see text]V[Formula: see text], N[Formula: see text]V[Formula: see text], N[Formula: see text]V[Formula: see text], N[Formula: see text]V[Formula: see text], B[Formula: see text]V[Formula: see text], B[Formula: see text]V[Formula: see text], B[Formula: see text]V[Formula: see text] and B[Formula: see text]V[Formula: see text]). The energies of formation of the N related vacancy-complexes showed the N[Formula: see text]V[Formula: see text] to be energetically stable close to the valence band maximum in its double positive charge state. The N[Formula: see text]V[Formula: see text] is more energetically stable in the double negative charge state close to the conduction band minimum. The N[Formula: see text]V[Formula: see text] on the other hand, induced double donor level and the N[Formula: see text]V[Formula: see text] induced a double acceptor level. For B related complexes, the B[Formula: see text]V[Formula: see text] and B[Formula: see text]V[Formula: see text] were energetically stable in their single positive charge state close to the valence band maximum. As the Fermi energy is varied across the band gap, the neutral and single negative charge states of the B[Formula: see text]V[Formula: see text] become more stable at different energy levels. B and N related complexes exhibited charge state controlled metastability behaviour.

Stomatin-Like Protein 2 Is Required for In Vivo Mitochondrial Respiratory Chain Supercomplex Formation and Optimal Cell Function

PubMed Central

Mitsopoulos, Panagiotis; Chang, Yu-Han; Wai, Timothy; König, Tim; Dunn, Stanley D.; Langer, Thomas

2015-01-01

Stomatin-like protein 2 (SLP-2) is a mainly mitochondrial protein that is widely expressed and is highly conserved across evolution. We have previously shown that SLP-2 binds the mitochondrial lipid cardiolipin and interacts with prohibitin-1 and -2 to form specialized membrane microdomains in the mitochondrial inner membrane, which are associated with optimal mitochondrial respiration. To determine how SLP-2 functions, we performed bioenergetic analysis of primary T cells from T cell-selective Slp-2 knockout mice under conditions that forced energy production to come almost exclusively from oxidative phosphorylation. These cells had a phenotype characterized by increased uncoupled mitochondrial respiration and decreased mitochondrial membrane potential. Since formation of mitochondrial respiratory chain supercomplexes (RCS) may correlate with more efficient electron transfer during oxidative phosphorylation, we hypothesized that the defect in mitochondrial respiration in SLP-2-deficient T cells was due to deficient RCS formation. We found that in the absence of SLP-2, T cells had decreased levels and activities of complex I-III2 and I-III2-IV1-3 RCS but no defects in assembly of individual respiratory complexes. Impaired RCS formation in SLP-2-deficient T cells correlated with significantly delayed T cell proliferation in response to activation under conditions of limiting glycolysis. Altogether, our findings identify SLP-2 as a key regulator of the formation of RCS in vivo and show that these supercomplexes are required for optimal cell function. PMID:25776552

3D-structured illumination microscopy reveals clustered DNA double-strand break formation in widespread γH2AX foci after high LET heavy-ion particle radiation

PubMed Central

Hagiwara, Yoshihiko; Niimi, Atsuko; Isono, Mayu; Yamauchi, Motohiro; Yasuhara, Takaaki; Limsirichaikul, Siripan; Oike, Takahiro; Sato, Hiro; Held, Kathryn D.; Nakano, Takashi; Shibata, Atsushi

2017-01-01

DNA double-strand breaks (DSBs) induced by ionising radiation are considered the major cause of genotoxic mutations and cell death. While DSBs are dispersed throughout chromatin after X-rays or γ-irradiation, multiple types of DNA damage including DSBs, single-strand breaks and base damage can be generated within 1–2 helical DNA turns, defined as a complex DNA lesion, after high Linear Energy Transfer (LET) particle irradiation. In addition to the formation of complex DNA lesions, recent evidence suggests that multiple DSBs can be closely generated along the tracks of high LET particle irradiation. Herein, by using three dimensional (3D)-structured illumination microscopy, we identified the formation of 3D widespread γH2AX foci after high LET carbon-ion irradiation. The large γH2AX foci in G2-phase cells encompassed multiple foci of replication protein A (RPA), a marker of DSBs undergoing resection during homologous recombination. Furthermore, we demonstrated by 3D analysis that the distance between two individual RPA foci within γH2AX foci was approximately 700 nm. Together, our findings suggest that high LET heavy-ion particles induce clustered DSB formation on a scale of approximately 1 μm3. These closely localised DSBs are considered to be a risk for the formation of chromosomal rearrangement after heavy-ion irradiation. PMID:29312614

Strain-Engineered Oxygen Vacancies in CaMnO3 Thin Films.

PubMed

Chandrasena, Ravini U; Yang, Weibing; Lei, Qingyu; Delgado-Jaime, Mario U; Wijesekara, Kanishka D; Golalikhani, Maryam; Davidson, Bruce A; Arenholz, Elke; Kobayashi, Keisuke; Kobata, Masaaki; de Groot, Frank M F; Aschauer, Ulrich; Spaldin, Nicola A; Xi, Xiaoxing; Gray, Alexander X

2017-02-08

We demonstrate a novel pathway to control and stabilize oxygen vacancies in complex transition-metal oxide thin films. Using atomic layer-by-layer pulsed laser deposition (PLD) from two separate targets, we synthesize high-quality single-crystalline CaMnO 3 films with systematically varying oxygen vacancy defect formation energies as controlled by coherent tensile strain. The systematic increase of the oxygen vacancy content in CaMnO 3 as a function of applied in-plane strain is observed and confirmed experimentally using high-resolution soft X-ray absorption spectroscopy (XAS) in conjunction with bulk-sensitive hard X-ray photoemission spectroscopy (HAXPES). The relevant defect states in the densities of states are identified and the vacancy content in the films quantified using the combination of first-principles theory and core-hole multiplet calculations with holistic fitting. Our findings open up a promising avenue for designing and controlling new ionically active properties and functionalities of complex transition-metal oxides via strain-induced oxygen-vacancy formation and ordering.

The Feedback of Star Formation Based on Large-scale Spectroscopic Mapping Technology

NASA Astrophysics Data System (ADS)

Li, H. X.

2017-05-01

Star Formation is a fundamental topic in astrophysics. Although there is a popular model of low-mass star formation, every step of the process is full of physical and chemical complexity. One of the key questions is the dynamical feedback during the process of star formation. The answer of this question will help us to understand the star formation and the evolution of molecular clouds. We have identified outflows and bubbles in the Taurus molecular cloud based on the ˜ 100 deg2 Five College Radio Astronomy Observatory 12CO(1-0) and 13CO(1-0) maps and the Spitzer young stellar object (YSO) catalog. In the main 44 deg2 area of Taurus, we found 55 outflows, of which 31 were previously unknown. We also found 37 bubbles in the entire 100 deg2 area of Taurus, all of which had not been identified before. After visual inspection, we developed an interactive IDL pipeline to confirm the outflows and bubbles. This sample covers a contiguous region with a linear spatial dynamic range of ˜ 1000. Among the 55 outflows, we found that bipolar, monopolar redshifted, and monopolar blueshifted outflows account for 45%, 44%, and 11%, respectively. There are more red lobes than blue ones. The occurrence of more red lobes may result from the fact that Taurus is thin. Red lobes tend to be smaller and younger. The total mass and energy of red lobes are similar to blue lobes on average. There are 3 expanding bubbles and 34 broken bubbles among all the bubbles in Taurus. There are more outflow-driving YSOs in Class I, Flat, and Class II while few outflow-driving YSOs in Class III, which indicates that outflows more likely appear in the earlier stage (Class I) than in the later phase (Class III) of star formation. There are more bubble-driving YSOs of Class II and Class III while there are few bubble-driving YSOs of Class I and Flat, implying that the bubble structures are more likely to occur in the later stage of star formation. The total kinetic energy of the identified outflows is estimated to be ˜ 3.9 × 1045 erg, which is 1% of the cloud turbulent energy. The total kinetic energy of the detected bubbles is estimated to be ˜ 9.2 × 1046 erg, which is 29% of the turbulent energy of Taurus. The energy injection rate from the outflows is ˜ 1.3 × 1033 erg s-1, 0.4-2 times the turbulent dissipation rate of the cloud. The energy injection rate from bubbles is ˜ 6.4 × 1033 erg s-1, 2-10 times the turbulent dissipation rate of the cloud. The gravitational binding energy of the cloud is ˜ 1.5 × 1048 erg, 385 and 16 times the energy of outflows and bubbles, respectively. We conclude that neither outflows nor bubbles can provide sufficient energy to balance the overall gravitational binding energy and the turbulent energy of Taurus. However, in the current epoch, stellar feedback is sufficient to maintain the observed turbulence in Taurus. We studied the methods of spectral data processing for large-scale surveys, which is helpful in developing the data-processing software of FAST (Five-hundred-meter Aperture Spherical radio Telescope).

Ab Initio Study of Aluminium Impurity and Interstitial-Substitutional Complexes in Ge Using a Hybrid Functional (HSE)

NASA Astrophysics Data System (ADS)

Igumbor, E.; Mapasha, R. E.; Meyer, W. E.

2017-07-01

The results of an ab initio modelling of aluminium substitutional impurity ({\\hbox {Al}}_Ge), aluminium interstitial in Ge [{\\hbox {I}}_Al for the tetrahedral (T) and hexagonal (H) configurations] and aluminium interstitial-substitutional pairs in Ge ({\\hbox {I}}_Al{\\hbox {Al}}_Ge) are presented. For all calculations, the hybrid functional of Heyd, Scuseria, and Ernzerhof in the framework of density functional theory was used. Defects formation energies, charge state transition levels and minimum energy configurations of the {\\hbox {Al}}_Ge, {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge were obtained for -2, -1, 0, +1 and +2 charge states. The calculated formation energy shows that for the neutral charge state, the {\\hbox {I}}_Al is energetically more favourable in the T than the H configuration. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge forms with formation energies of -2.37 eV and -2.32 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge is energetically more favourable when the interstitial atom is at the T site with a binding energy of 0.8 eV. The {\\hbox {I}}_Al in the T configuration, induced a deep donor (+2/+1) level at EV+0.23 eV and the {\\hbox {Al}}_Ge induced a single acceptor level (0/-1) at EV+0.14 eV in the band gap of Ge. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge induced double-donor levels are at E_V+0.06 and E_V+0.12 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge exhibit properties of charge state-controlled metastability.

Nanoscale Charge Balancing Mechanism in Calcium-Silicate-Hydrate Gels: Novel Complex Disordered Materials from First-principles

NASA Astrophysics Data System (ADS)

Ozcelik, Ongun; White, Claire

Alkali-activated materials which have augmented chemical compositions as compared to ordinary Portland cement are sustainable technologies that have the potential to lower CO2 emissions associated with the construction industry. In particular, calcium-silicate-hydrate (C-S-H) gel is altered at the atomic scale due to changes in its chemical composition. Here, based on first-principles calculations, we predict a charge balancing mechanism at the molecular level in C-S-H gels when alkali atoms are introduced into their structure. This charge balancing process is responsible for the formation of novel structures which possess superior mechanical properties compared to their charge unbalanced counterparts. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these charge balancing effects on the structures is assessed by analyzing their formation energies, local bonding environments, diffusion barriers and mechanical properties. These results provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental mechanisms that play a crucial role in these complex disordered materials. We acknowledge funding from the Princeton Center for Complex Materials, a MRSEC supported by NSF.

A Mussel-Derived One-Component Adhesive Coacervate

PubMed Central

Wei, Wei; Tan, Yerpeng; Rodriguez, N. Martinez; Yu, Jing; Israelachvili, Jacob N.; Waite, J. Herbert

2013-01-01

Marine organisms process and deliver many of their underwater coatings and adhesives as complex fluids. In marine mussels, one such fluid, secreted during the formation of adhesive plaques, consists of a concentrated colloidal suspension of a mussel foot protein (mfp) known as Mfp-3S. Results of this study suggest that Mfp-3S becomes a complex fluid by a liquid-liquid phase separation from equilibrium solution at a pH and ionic strength reminiscent of conditions created by the mussel foot during plaque formation. The pH dependence of phase separation and its sensitivity indicate that inter/intra-molecular electrostatic interactions are partially responsible for driving the phase separation. Hydrophobic interactions between the nonpolar Mfp-3S proteins provide another important driving force for coacervation. As complex coacervation typically results from charge-charge interactions between polyanions and polycations, Mfp-3S is thus unique in being the only known protein that coacervates with itself. The Mfp-3S coacervate was shown to have an effective interfacial energy of ≤ 1 mJ/m2 which explains its tendency to spread over or engulf most surfaces. Of particular interest to biomedical applications is the extremely high adsorption capacity of coacervated Mfp-3S on hydroxyapatite. PMID:24060881

Transcriptome Response to Embolism Formation in Stems of Populus trichocarpa Provides Insight into Signaling and the Biology of Refilling1[W][OA

PubMed Central

Secchi, Francesca; Gilbert, Matthew E.; Zwieniecki, Maciej A.

2011-01-01

The mechanism of embolism repair in transpiring plants is still not understood, despite significant scientific effort. The refilling process is crucial to maintaining stem transport capacity and ensuring survival for plants experiencing dynamic changes in water stress. Refilling air-filled xylem vessels requires an energy and water source that can only be provided by adjacent living parenchyma cells. Here, we report an analysis of the transcriptome response of xylem parenchyma cells after embolism formation in Populus trichocarpa trees. Genes encoding aquaporins, ion transporters, and carbohydrate metabolic pathways were up-regulated, and there was a significant reduction in the expression of genes responding to oxidative stress. Thus, a novel view of the plant response to embolism emerges that suggests a role for oxygen in embolized vessels as a signal triggering xylem refilling and for the activity of cation transport as having a significant role in the generation of the energy gradient necessary to heal embolized vessels. These findings redefine current hypotheses surrounding the refilling phenomenon and provide insight into the complexity of the biological response to the seemingly simple physical event of xylem embolism formation. PMID:21951466

A theoretical study of the dynamic behavior of alkane hydroxylation by a compound I model of cytochrome P450.

PubMed

Yoshizawa, K; Kamachi, T; Shiota, Y

2001-10-10

Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.

Lamellar cationic lipid-DNA complexes from lipids with a strong preference for planar geometry: A Minimal Electrostatic Model.

PubMed

Perico, Angelo; Manning, Gerald S

2014-11-01

We formulate and analyze a minimal model, based on condensation theory, of the lamellar cationic lipid (CL)-DNA complex of alternately charged lipid bilayers and DNA monolayers in a salt solution. Each lipid bilayer, composed by a random mixture of cationic and neutral lipids, is assumed to be a rigid uniformly charged plane. Each DNA monolayer, located between two lipid bilayers, is formed by the same number of parallel DNAs with a uniform separation distance. For the electrostatic calculation, the model lipoplex is collapsed to a single plane with charge density equal to the net lipid and DNA charge. The free energy difference between the lamellar lipoplex and a reference state of the same number of free lipid bilayers and free DNAs, is calculated as a function of the fraction of CLs, of the ratio of the number of CL charges to the number of negative charges of the DNA phosphates, and of the total number of planes. At the isoelectric point the free energy difference is minimal. The complex formation, already favoured by the decrease of the electrostatic charging free energy, is driven further by the free energy gain due to the release of counterions from the DNAs and from the lipid bilayers, if strongly charged. This minimal model compares well with experiment for lipids having a strong preference for planar geometry and with major features of more detailed models of the lipoplex. © 2014 Wiley Periodicals, Inc.

Understanding pH Effects on Trichloroethylene and Perchloroethylene Adsorption to Iron in Permeable Reactive Barriers for Groundwater Remediation.

PubMed

Luo, Jing; Farrell, James

2013-01-01

Metallic iron filings are becoming increasing used in permeable reactive barriers for remediating groundwater contaminated by chlorinated solvents. Understanding solution pH effects on rates of reductive dechlorination in permeable reactive barriers is essential for designing remediation systems that can meet treatment objectives under conditions of varying groundwater properties. The objective of this research was to investigate how the solution pH value affects adsorption of trichloroethylene (TCE) and perchloroethylene (PCE) on metallic iron surfaces. Because adsorption is first required before reductive dechlorination can occur, pH effects on halocarbon adsorption energies may explain pH effects on dechlorination rates. Adsorption energies for TCE and PCE were calculated via molecular mechanics simulations using the Universal force field and a self-consistent reaction field charge equilibration scheme. A range in solution pH values was simulated by varying the amount of atomic hydrogen adsorbed on the iron. The potential energies associated TCE and PCE complexes were dominated by electrostatic interactions, and complex formation with the surface was found to result in significant electron transfer from the iron to the adsorbed halocarbons. Adsorbed atomic hydrogen was found to lower the energies of TCE complexes more than those for PCE. Attractions between atomic hydrogen and iron atoms were more favorable when TCE versus PCE was adsorbed to the iron surface. These two findings are consistent with the experimental observation that changes in solution pH affect TCE reaction rates more than those for PCE.

A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

NASA Astrophysics Data System (ADS)

Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

2016-10-01

Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.

A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

PubMed Central

Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

2016-01-01

Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation. PMID:27731375

Nitrogen fixation and hydrogen metabolism in cyanobacteria.

PubMed

Bothe, Hermann; Schmitz, Oliver; Yates, M Geoffrey; Newton, William E

2010-12-01

This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.

A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation.

PubMed

Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

2016-10-12

Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2k B T, in the range of previously proposed rough parts of landscapes models during dissociation.

Insight into π-hole interactions containing the inorganic heterocyclic compounds S2N2/SN2P2.

PubMed

Lu, Bo; Zhang, Xueying; Meng, Lingpeng; Zeng, Yanli

2017-08-01

Similar to σ-hole interactions, the π-hole interaction has attracted much attention in recent years. According to the positive electrostatic potentials above and below the surface of inorganic heterocyclic compounds S 2 N 2 and three SN 2 P 2 isomers (heterocyclic compounds 1-4), and the negative electrostatic potential outside the X atom of XH 3 (X = N, P, As), S 2 N 2 /SN 2 P 2 ⋯XH 3 (X = N, P, As) complexes were constructed and optimized at the MP2/aug-cc-pVTZ level. The X atom of XH 3 (X = N, P, As) is almost perpendicular to the ring of the heterocyclic compounds. The π-hole interaction energy becomes greater as the trend goes from 1⋯XH 3 to 4⋯XH 3 . These π-hole interactions are weak and belong to "closed-shell" noncovalent interactions. According to the energy decomposition analysis, of the three attractive terms, the dispersion energy contributes more than the electrostatic energy. The polarization effect also plays an important role in the formation of π-hole complexes, with the contrasting phenomena of decreasing electronic density in the π-hole region and increasing electric density outside the X atom of XH 3 (X = N, P, As). Graphical abstract Computed density difference plots for the complexes 3⋯NH 3 (a 1 ), 3⋯PH 3 (b 1 ), 3⋯AsH 3 (c 1 ) and electron density shifts for the complexes 3⋯NH 3 (a 2 ), 3⋯PH 3 (b 2 ),3⋯AsH 3 (c 2 ) on the 0.001 a.u. contour.

A model complex of a possible intermediate in the mechanism of action of peptide deformylase: first example of an (N2S)zinc(II)-formate complex.

PubMed

Chang, S C; Sommer, R D; Rheingold, A L; Goldberg, D P

2001-11-21

The synthesis and crystallographic characterization of a new (N2S)zinc-alkyl complex and (N2S)zinc-formate complex is described; the bonding mode of the formate complex has implications for the mechanism of action of the enzyme peptide deformylase.

Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex.

PubMed

Bello, Martiniano; Correa-Basurto, José

2016-04-01

Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.

Methods for converging correlation energies within the dielectric matrix formalism

NASA Astrophysics Data System (ADS)

Dixit, Anant; Claudot, Julien; Gould, Tim; Lebègue, Sébastien; Rocca, Dario

2018-03-01

Within the dielectric matrix formalism, the random-phase approximation (RPA) and analogous methods that include exchange effects are promising approaches to overcome some of the limitations of traditional density functional theory approximations. The RPA-type methods however have a significantly higher computational cost, and, similarly to correlated quantum-chemical methods, are characterized by a slow basis set convergence. In this work we analyzed two different schemes to converge the correlation energy, one based on a more traditional complete basis set extrapolation and one that converges energy differences by accounting for the size-consistency property. These two approaches have been systematically tested on the A24 test set, for six points on the potential-energy surface of the methane-formaldehyde complex, and for reaction energies involving the breaking and formation of covalent bonds. While both methods converge to similar results at similar rates, the computation of size-consistent energy differences has the advantage of not relying on the choice of a specific extrapolation model.

The crystal structure of halofantrine-ferriprotoporphyrin IX and the mechanism of action of arylmethanol antimalarials.

PubMed

de Villiers, Katherine A; Marques, Helder M; Egan, Timothy J

2008-08-01

The crystal structure of the complex formed between the antimalarial drug halofantrine and ferriprotoporphyrin IX (Fe(III)PPIX) has been determined by single crystal X-ray diffraction. The structure shows that halofantrine coordinates to the Fe(III) center through its alcohol functionality in addition to pi-stacking of the phenanthrene ring over the porphyrin. The length of the Fe(III)-O bond is consistent with an alkoxide and not an alcohol coordinating group. The iron porphyrin is five coordinate and monomeric. Changes in the electronic spectrum of Fe(III)PPIX upon addition of halofantrine base in acetonitrile solution are almost identical to those observed upon addition of quinidine free base in the same solvent. This suggests homologous binding. Molecular mechanics modeling of Fe(III)PPIX complexes of quinidine, quinine, 9-epiquinine and 9-epiquinidine based on this homology suggests that the antimalarially active quinidine and quinine can readily adopt conformations that permit formation of an intramolecular salt bridge between the protonated quinuclidine tertiary amino group and unprotonated heme propionate group, while the inactive epimers 9-epiquinidine and 9-epiquinine have to adopt high energy conformations in order to accommodate such salt bridge formation. We propose that salt bridge formation may interrupt formation of the hemozoin precursor dimer formed during the heme detoxification pathway and so account for the strong activity of the two active isomers.

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

Kozlovski, V. V.; Lebedev, A. A.; Bogdanova, E. V.

The model of conductivity compensation in SiC under irradiation with high-energy electrons is presented. The following processes are considered to cause a decrease in the free carrier concentration: (i) formation of deep traps by intrinsic point defects, Frenkel pairs produced by irradiation; (ii) 'deactivation' of the dopant via formation of neutral complexes including a dopant atom and a radiation-induced point defect; and (iii) formation of deep compensating traps via generation of charged complexes constituted by a dopant atom and a radiation-induced point defect. To determine the compensation mechanism, dose dependences of the deep compensation of moderately doped SiC (CVD) undermore » electron irradiation have been experimentally studied. It is demonstrated that, in contrast to n-FZ-Si, moderately doped SiC (CVD) exhibits linear dependences (with a strongly nonlinear dependence observed for Si). Therefore, the conductivity compensation in silicon carbide under electron irradiation occurs due to deep traps formed by primary radiation defects (vacancies and interstitial atoms) in the silicon and carbon sublattices. It is known that the compensation in silicon is due to the formation of secondary radiation defects that include a dopant atom. It is shown that, in contrast to n-SiC (CVD), primary defects in only the carbon sublattice of moderately doped p-SiC (CVD) cannot account for the compensation process. In p-SiC, either primary defects in the silicon sublattice or defects in both sublattices are responsible for the conductivity compensation.« less

Progress report for a research program in theoretical high energy physics

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

Feldman, D.; Fried, H.M.; Jevicki, A.

This year's research has dealt with: superstrings in the early universe; the invisible axion emissions from SN1987A; quartic interaction in Witten's superstring field theory; W-boson associated multiplicity and the dual parton model; cosmic strings and galaxy formation; cosmic strings and baryogenesis; quark flavor mixing; p -- /bar p/ scattering at TeV energies; random surfaces; ordered exponentials and differential equations; initial value and back-reaction problems in quantum field theory; string field theory and Weyl invariance; the renormalization group and string field theory; the evolution of scalar fields in an inflationary universe, with and without the effects of gravitational perturbations; cosmic stringmore » catalysis of skyrmion decay; inflation and cosmic strings from dynamical symmetry breaking; the physic of flavor mixing; string-inspired cosmology; strings at high-energy densities and complex temperatures; the problem of non-locality in string theory; string statistical mechanics; large-scale structures with cosmic strings and neutrinos; the delta expansion for stochastic quantization; high-energy neutrino flux from ordinary cosmic strings; a physical picture of loop bremsstrahlung; cylindrically-symmetric solutions of four-dimensional sigma models; large-scale structure with hot dark matter and cosmic strings; the unitarization of the odderon; string thermodynamics and conservation laws; the dependence of inflationary-universe models on initial conditions; the delta expansion and local gauge invariance; particle physics and galaxy formation; chaotic inflation with metric and matter perturbations; grand-unified theories, galaxy formation, and large-scale structure; neutrino clustering in cosmic-string-induced wakes; and infrared approximations to nonlinear differential equations. 17 refs.« less

Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation

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

Marshall, Richard S.; Vierstra, Richard D.

26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required formore » granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability.« less

Monodisperse self-assembly in a model with protein-like interactions

NASA Astrophysics Data System (ADS)

Wilber, Alex W.; Doye, Jonathan P. K.; Louis, Ard A.; Lewis, Anna C. F.

2009-11-01

We study the self-assembly behavior of patchy particles with "proteinlike" interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

Effect of Laser Power and Scan Speed on Melt Pool Characteristics of Commercially Pure Titanium (CP-Ti)

NASA Astrophysics Data System (ADS)

Kusuma, Chandrakanth; Ahmed, Sazzad H.; Mian, Ahsan; Srinivasan, Raghavan

2017-07-01

Selective laser melting (SLM) is an additive manufacturing technique that creates complex parts by selectively melting metal powder layer-by-layer using a laser. In SLM, the process parameters decide the quality of the fabricated component. In this study, single beads of commercially pure titanium (CP-Ti) were melted on a substrate of the same material using an in-house built SLM machine. Multiple combinations of laser power and scan speed were used for single bead fabrication, while the laser beam diameter and powder layer thickness were kept constant. This experimental study investigated the influence of laser power, scan speed, and laser energy density on the melt pool formation, surface morphology, geometry (width and height), and hardness of solidified beads. In addition, the observed unfavorable effect such as inconsistency in melt pool width formation is discussed. The results show that the quality, geometry, and hardness of solidified melt pool are significantly affected by laser power, scanning speed, and laser energy density.

Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation

DOE PAGES

Marshall, Richard S.; Vierstra, Richard D.

2018-04-06

26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required formore » granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability.« less

Resonances in positron-potassium (e +-K) system with natural and unnatural parities

NASA Astrophysics Data System (ADS)

Umair, M.; Jonsell, S.

2016-01-01

We present an investigation of resonances with natural and unnatural parities in the positron-potassium system using the complex scaling method. A model potential is used to represent the interaction between the core and the valence electron. Explicitly correlated Gaussian wave functions are used to represent the correlation effects between the valence electron, the positron and the K+ core. Resonance energies and widths for two partial waves (S- and P-wave) below the {{K}}(4p,5 s,5p,4 d,4f) excitation thresholds and positronium n = 2 formation threshold are calculated for natural parity. Resonance states for P e below the {{K}}(4d) excitation threshold and positronium n = 2, 3 formation thresholds are calculated for unnatural parity which has not been previously reported. Below both positronium thresholds we have found a dipole series of resonances, with binding energies scaling in good agreement with exceptions from an analytical calculation. The present results are compared with those in the literature.

Electrodeposited Cu2O doped with Cl: Electrical and optical properties

NASA Astrophysics Data System (ADS)

Pelegrini, S.; Tumelero, M. A.; Brandt, I. S.; Della Pace, R. D.; Faccio, R.; Pasa, A. A.

2018-04-01

For understanding the electrical and optical properties of electrodeposited Cl-doped Cu2O thin films, we have studied layers with increasing thickness and Cl concentrations of 0.8 and 1.2 at. %. The deposits were characterized by measuring the charge transport, the optical reflectance, and the photoluminescence. No significant decrease of electrical resistivity was observed in doped samples compared to undoped ones. A decrease of about five orders of magnitude was measured and ascribed to the presence of pinholes, as confirmed by scanning electron microscopy analyses. From optical measurements, we concluded that the Cl atoms are incorporated into substitutional sites of Cu2O lattices in agreement with photoluminescence results showing a strong reduction in the peak intensity of VO+2 defects in comparison to undoped layers. Computational calculation using density functional theory has pointed out high formation energy for single Cl related defects, but low formation energy for Cl-defect complexes, such as ClO + VCu, that strongly compensate the carriers generated by the Cl doping.

Synthesis, Spectral Characterization, Thermal and Optical Studies of Novel Complexes: 4-(Dimethylamino)benzylidene-4-acetamideaniline and 4-(Dimethylamino)benzylidene-4-nitroaniline.

PubMed

Neupane, Umesh; Rai, R N

2017-11-01

The phase diagram representing solid-liquid equilibrium of entire range of composition and thermodynamic studies of two binary organic systems of 4-dimethylaminobenzaldehyde (DMAB) with two NLO active compounds, p-aminoacetanilide (PAA) and p-nitroaniline (PNA), have been studied by solid state synthetic route. Both systems are independently forming a new entity called intermolecular complex (IMC) and two eutectics on either side of intermolecular complexes. The various thermodynamic parameters such as heat of mixing, entropy of fusion, roughness parameter, interfacial energy and excess thermodynamic functions of IMCs and eutectics were calculated using the heat of fusion values. The TGA and DTA studies were performed to understand the physico-chemical, thermal behavior and unique identity of newly synthesized organic complexes, 4-(dimethylamino)benzylidene-4-acetamideaniline (DMABPAA) and 4-(dimethylamino)benzylidene-4-nitroaniline (DMABPNA), and their respective enthalpy of fusion values were found to be 30.01 and 37.26 kJ mol - 1 . The higher melting point of both the novel complexes than their parent's compounds reveal the strong molecular interaction between parent components to yield the complex. The FTIR spectral analysis predicts the disappearance of aldehyde peaks of DMAB and NH 2 peaks of PAA and PNA while the appearance of entirely new peaks than that of parent's compounds are the supportive for the formation of new molecular entities. These findings are further supported by FTNMR spectrum studies by observation of disappearance of proton peak of aldehyde of DMAB and amine peaks of PAA and PNA rather formation of new imine proton peak or peaks were observed. The appearance of new peaks in Powder XRD of complexes than those of parent components is further indicative for the formation of complexes. The absorption spectrum of DMABPAA and DMABPNA showed intra-molecular charge-transfer (ICT) excited state absorption at 258 and 241 nm, respectively. Both the IMCs, DMABPAA and DMABPNA, show strong fluorescence with quantum yield 0.66 and 0.93, respectively, in methanol solution.

Association of phycoerythrin and phycocyanin: in vitro formation of a functional energy transferring phycobilisome complex of Porphyridium sordidum

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

Lipschultz, C.A.; Gantt, E.

1981-01-01

Functional in vitro association and dissociation of a phycobiliprotein complex, isolated from phycobilisomes of the red alga Porphyridium sordidum, were studied. The complex contained large bangiophyceaen phycoerythrin and cyanophytan phycocyanin in an equimolar ratio and had absorption maxima at 625, 567, and 550 nm and a shoulder at 495 nm. Emission at 655 nm (with excitation at 545 nm) from phycocyanin indicated functional coupling. The complex was stable over a wide buffer concentration range, and, notably, it was maximally stable in low phosphate, <0.01 M, unlike the phycobilisomes, which dissociate at this concentration. Its molecular weight was estimated to bemore » ca. 510 000, and by electron microscopy it was seen to consist of two units of similar size. The complex in 0.1 M phosphate was separated on a sucrose gradient into a homogeneous phycoerythrin band and a spectrally heterogeneous phycocyanin band. In vitro association of phycoerythrin and phycocyanin resulted in a complex with the same absorbance, emission, sedimentation, and molar pigment ratio as those of the native complex. The spectrally heterogeneous phycocyanin fractions from the dissociation gradient varied in the degree of association with phycoerythrin. Phycocyanin fractions absorbing from 622 to 633 nm exhibited high associability (>70%), whereas those with maxima at 617-620 nm had low associability (<30%). The presence of a 30 000 molecular weight polypeptide accompanied high associability, where it was ca. 2-fold more prominent. It is suggested that this polypeptide is involved in complex formation and could serve either in the stabilization of the conformational state of cyanophytan phycocyanin or as a direct linker between phycobiliproteins.« less

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

PubMed

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative density functional study of the complexes [UO2(CO3)3]4- and [(UO2)3(CO3)6]6- in aqueous solution.

PubMed

Schlosser, Florian; Moskaleva, Lyudmila V; Kremleva, Alena; Krüger, Sven; Rösch, Notker

2010-06-28

With a relativistic all-electron density functional method, we studied two anionic uranium(VI) carbonate complexes that are important for uranium speciation and transport in aqueous medium, the mononuclear tris(carbonato) complex [UO(2)(CO(3))(3)](4-) and the trinuclear hexa(carbonato) complex [(UO(2))(3)(CO(3))(6)](6-). Focusing on the structures in solution, we applied for the first time a full solvation treatment to these complexes. We approximated short-range effects by explicit aqua ligands and described long-range electrostatic interactions via a polarizable continuum model. Structures and vibrational frequencies of "gas-phase" models with explicit aqua ligands agree best with experiment. This is accidental because the continuum model of the solvent to some extent overestimates the electrostatic interactions of these highly anionic systems with the bulk solvent. The calculated free energy change when three mono-nuclear complexes associate to the trinuclear complex, agrees well with experiment and supports the formation of the latter species upon acidification of a uranyl carbonate solution.

Designing functionality in perovskite thin films using ion implantation techniques: Assessment and insights from first-principles calculations

DOE PAGES

Sharma, Vinit K.; Herklotz, Andreas; Ward, Thomas Zac; ...

2017-09-11

Ion implantation has been widely used in the semiconductor industry for decades to selectively control electron/hole doping for device applications. Recently, experimental studies on ion implantation into more structurally and electronically complex materials have been undertaken in which defect generation has been used to control a variety of functional phenomena. Of particular interest, are recent findings demonstrating that low doses of low energy helium ions into single crystal films can be used to tailor the structural properties. These initial experimental studies have shown that crystal symmetry can be continuously controlled by applying increasingly large doses of He ions into amore » crystal. The observed changes in lattice structure were then observed to correlate with functional changes, such as metal-insulator transition temperature2 and optical bandgap3. In these preliminary experimental studies, changes to lattice expansion was proposed to be the direct result of chemical pressure originating predominantly from the implanted He applying chemical pressure at interstitial sites. However, the influence of possible secondary knock-on damage arising from the He atoms transferring energy to the lattice through nuclear-nuclear collision with the crystal lattice remains largely unaddressed. In this work, we focus on a SrRuO3 model system to provide a comprehensive examination of the impact of common defects on structural and electronic properties, obtain calculated defect formation energies, and define defect migration barriers. Our model indicates that, while interstitial He can modify the crystal properties, a dose significantly larger than those reported in experimental studies would be required. The true origin of the observed structural changes is likely the result of a combination of secondary defects created during He implantation. Of particular importance, we observe that different defect types can generate greatly varied local electronic structures and that the formation energies and migration energy barriers vary by defect type. Thus, we may have identified a new method of selectively inducing controlled defect complexes into single crystal materials. Development of this approach would have a broad impact on both our ability to probe specific defect contributions in fundamental studies and allow a new level of control over functional properties driven by specific defect complexes.« less

The improvement of thermal characteristics of autoclave aerated concrete for energy efficient high-rise buildings application

NASA Astrophysics Data System (ADS)

Khavanov, Pavel; Fomina, Ekaterina; Kozhukhova, Natalia

2018-03-01

Nowadays, the problem of energy saving is very relevant. One of the ways to reduction energy consumption in construction materials production and construction of civil and industrial high-rise buildings is the application of claddings with heat-insulating performance. The concept of energy efficiency of high-rise buildings is closely related to environmental aspect and sustainability of applied construction materials; reducing service costs; energy saving and microclimate comfortability. A complexity of architectural and structural design as well as aesthetic characteristics of construction materials are also should be considered. The high interest focused on materials with combined properties. This work is oriented on the study of energy efficiency of buildings by improving heat-insulation and strength performance of autoclave aerated concrete. The applied method of sulfate activation of lime allows monitoring phase and structure formation in aerated concrete. The optimal mix design of aerated concrete with the compressive strength up to 8.5 MPa and decreased density up to 760 kg/m3 was proposed. Analysis of structure at macro-and microscale was performed as well as the criteria of an optimal porosity formation was considered a number, size, shape of pore and density of interior partition. SEM analysis and BET method were performed in this research work. The research results demonstrated the correlation between structure and vapor permeability resistance, also it was found that the increase of strength can lead to reduction of thermal conductivity.

Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon

PubMed Central

Kuhn, Patrick; Draycheva, Albena; Vogt, Andreas; Petriman, Narcis-Adrian; Sturm, Lukas; Drepper, Friedel; Warscheid, Bettina; Wintermeyer, Wolfgang

2015-01-01

Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex. PMID:26459600

Antimycobacterial action of a new glycolipid-peptide complex obtained from extracellular metabolites of Raoultella ornithinolytica.

PubMed

Fiołka, Marta J; Grzywnowicz, Krzysztof; Mendyk, Ewaryst; Zagaja, Mirosław; Szewczyk, Rafał; Rawski, Michał; Keller, Radosław; Rzymowska, Jolanta; Wydrych, Jerzy

2015-12-01

In this paper, an antimycobacterial component of extracellular metabolites of a gut bacterium Raoultella ornithinolytica from D. veneta earthworms was isolated and its antimycobacterial action was tested using Mycobacterium smegmatis. After incubation with the complex obtained, formation of pores and furrows in cell walls was observed using microscopic techniques. The cells lost their shape, stuck together and formed clusters. Surface-enhanced Raman spectroscopy analysis showed that, after incubation, the complex was attached to the cell walls of the Mycobacterium. Analyses of the component performed with Fourier transform infrared spectroscopy demonstrated high similarity to a bacteriocin nisin, but energy dispersive X-ray spectroscopy analysis revealed differences in the elemental composition of this antimicrobial peptide. The component with antimycobacterial activity was identified using mass spectrometry techniques as a glycolipid-peptide complex. As it exhibits no cytotoxicity on normal human fibroblasts, the glycolipid-peptide complex appears to be a promising compound for investigations of its activity against pathogenic mycobacteria. © 2015 APMIS. Published by John Wiley & Sons Ltd.

Complex collective dynamics of active torque-driven colloids at interfaces

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

Snezhko, Alexey

Modern self-assembly techniques aiming to produce complex structural order or functional diversity often rely on non-equilibrium conditions in the system. Light, electric, or magnetic fields are predominantly used to modify interaction profiles of colloidal particles during self-assembly or induce complex out-of-equilibrium dynamic ordering. The energy injection rate, properties of the environment are important control parameters that influence the outcome of active (dynamic) self-assembly. The current review is focused on a case of collective dynamics and self-assembly of particles with externally driven torques coupled to a liquid or solid interface. The complexity of interactions in such systems is further enriched bymore » strong hydrodynamic coupling between particles. Unconventionally ordered dynamic self-assembled patterns, spontaneous symmetry breaking phenomena, self-propulsion, and collective transport have been reported in torque-driven colloids. Some of the features of the complex collective behavior and dynamic pattern formation in those active systems have been successfully captured in simulations.« less

Fluorescence in complexes based on quinolines-derivatives: a search for better fluorescent probes.

PubMed

Mecca, Carolina Z P; Fonseca, Fernando L A; Bagatin, Izilda A

2016-11-05

Quinoline-derived fluorescent complexes were designed; synthesized by the reaction of 5-nitro-8-hydroxyquinoline and 5-chloro-8-hydroxyquinoline with Al(3+), Mg(2+), Zn(2+), and Cd(2+) salts (1-8); and characterized. The (1)H NMR spectra of complexes 1 and 5, containing Al(3+), were consistent with an octahedral structure having approximate D3 symmetry, and the results supported the favored facial isomer (fac). Data for complexes 2-4 and 6-8 supported the formation of tetrahedral structures. Intense luminescence was detected for complexes 5-8, even with the naked eye, as indicated by quantum yield values of 0.087, 0.094, 0.051, and 0.021, respectively. Furthermore, in contrast to 5-nitro-8-hydroxyquinoline, the 5-chloro-8-hydroxyquinoline ligand exhibited bands at different energies depending on the coordinated metal, which supported its potential application in ionic and biological probes, as well as in cell imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

[2.2.2]Paracyclophane as a receptor for the cesium cation in the gas phase

NASA Astrophysics Data System (ADS)

Makrlík, Emanuel; Sýkora, David; Böhm, Stanislav; Vaňura, Petr

2017-10-01

By using electrospray ionisation mass spectrometry, it was proven experimentally that the cesium cation (Cs+) forms with [2.2.2]paracyclophane (C24H24) the cationic complex [Cs(C24H24)]+. Further, applying quantum chemical calculations, the most probable structure of the [Cs(C24H24)]+ complex was derived. In the resulting complex with a symmetry very close to C3, the 'central' cation Cs+, fully located in the cavity of the parent [2.2.2]paracyclophane ligand, is bound to all three benzene rings of [2.2.2]paracyclophane via cation-π interaction. Finally, the interaction energy, E(int), of the considered cation-π complex [Cs(C24H24)]+ was found to be -73.2 kJ/mol, confirming the formation of this fascinating complex species as well. This means that [2.2.2]paracyclophane can be considered as a receptor for the Cs+ cation in the gas phase.

The Zinc-Schiff Base-Novicidin Complex as a Potential Prostate Cancer Therapy

PubMed Central

Milosavljevic, Vedran; Haddad, Yazan; Merlos Rodrigo, Miguel Angel; Moulick, Amitava; Polanska, Hana; Hynek, David; Heger, Zbynek; Kopel, Pavel; Adam, Vojtech

2016-01-01

Prostate cancer cells control energy metabolism by chelating intracellular zinc. Thus, zinc delivery has been a popular therapeutic approach for prostate cancer. Here, we propose the use of the membrane-penetrating peptide Novicidin connected to zinc-Schiff base as a carrier vehicle for the delivery of zinc to prostate cells. Mass spectrometry, electrochemistry and spectrophotometry confirmed the formation/stability of this complex and provided insight regarding the availability of zinc for complex interactions. This delivery system showed minor toxicity in normal PNT1A cells and high potency towards PC3 tumor cells. The complex preferentially penetrated PC3 tumor cells in contrast to confinement to the membranes of PNT1A. Furthermore, zinc uptake was confirmed in both cell lines. Molecular analysis was used to confirm the activation of zinc stress (e.g., ZnT-1) and apoptosis (e.g., CASP-1). Our results strongly suggest that the zinc-Schiff base-Novicidin complex has great potential as a novel anticancer drug. PMID:27727290

Formation of the acrosome complex in the bush cricket Gampsocleis gratiosa (Orthoptera: Tettigoniidae).

PubMed

Su, Cai Xia; Chen, Jie; Shi, Fu Ming; Guo, Ming Shen; Chang, Yan Lin

2017-07-01

The acrosome complex plays an indispensable role in the normal function of mature spermatozoa. However, the dynamic process of acrosome complex formation in insect remains poorly understood. Gampsocleis gratiosa Brunner von Wattenwyl possesses the typical characteristic of insect sperms, which is tractable in terms of size, and therefore was selected for the acrosome formation study in this report. The results show that acrosome formation can be divided into six phases: round, rotating, rhombic, cylindrical, transforming and mature phase, based on the morphological dynamics of acrosome complex and nucleus. In addition, the cytoskeleton plays a critical role in the process of acrosome formation. The results from this study indicate that: (1) glycoprotein is the major component of the acrosome proper; (2) the microfilament is one element of the acrosome complex, and may mediate the morphologic change of the acrosome complex; (3) the microtubules might also shape the nucleus and acrosome complex during the acrosome formation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molybdenum Hydride and Dihydride Complexes Bearing Diphosphine Ligands with a Pendant Amine: Formation of Complexes With Bound Amines

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

Zhang, Shaoguang; Bullock, R. Morris

2015-07-06

CpMo(CO)(PNP)H complexes (PNP = (R2PCH2)2NMe, R = Et or Ph) were synthesized by displacement of two CO ligands of CpMo(CO)3H by the PNP ligand; these complexes were characterized by IR and variable temperature 1H and 31P NMR spectroscopy. CpMo(CO)(PNP)H complexes are formed as mixture of cis and trans-isomers. Both cis-CpMo(CO)(PEtNMePEt)H and trans-CpMo(CO)(PPhNMePPh)H were analyzed by single crystal X-ray diffraction. Electrochemical oxidation of CpMo(CO)(PEtNMePEt)H and CpMo(CO)(PPhNMePPh)H in CH3CN are both irreversible at slow scan rates and quasi-reversible at higher scan rates, with E1/2 = -0.36 V (vs. Cp2Fe+/0) for CpMo(CO)(PEtNMePEt)H and E1/2 = -0.18 V for CpMo(CO)(PPhNMePPh)H. Hydride abstraction from CpMo(CO)(PNP)Hmore » with [Ph3C]+[A]- (A = B(C6F5)4 or BArF4; [ArF = 3,5-bis(trifluoromethyl)phenyl]) afforded “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes that feature the amine bound to the metal. Displacement of the κ3 Mo-N bond by CD3CN gives [CpMo(CO)(PNP)(CD3CN)]+. The kinetics of this reaction were studied by NMR spectroscopy, providing the activation parameters ΔH‡ = 22.1 kcal/mol, ΔS‡ = 1.89 cal/(mol·K), Ea = 22.7 kcal/mol. Protonation of CpMo(CO)(PEtNMePEt)H affords [CpMo(CO)(κ2-PEtNMePEt)(H)2]+ as a Mo dihydride complex, which loses H2 to generate [CpMo(CO)(κ3-PEtNMePEt)]+ at room temperature. CpMo(CO)(dppp)H (dppp = 1,2-bis(diphenylphosphino)propane) was studied as a Mo diphosphine analogue without a pendant amine, and the product of protonation of this complex gives [CpMo(CO)(dppp)(H)2]+. Our results show that the pendant amine has a strong driving force to form stable “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes, and also promotes hydrogen elimination from [CpMo(CO)(PNP)(H)2]+ complexes by formation of Mo-N dative bond. We thank the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy. We thank Monte Helm, Elliott Hulley and Deanna Miller for help on the crystallography, and Ming Fang for assistance on the electrochemical experiments.« less

A Computational Model for Thrombus Formation in Response to Cardiovascular Implantable Devices

NASA Astrophysics Data System (ADS)

Horn, John; Ortega, Jason; Maitland, Duncan

2014-11-01

Cardiovascular implantable devices elicit complex physiological responses within blood. Notably, alterations in blood flow dynamics and interactions between blood proteins and biomaterial surface chemistry may lead to the formation of thrombus. For some devices, such as stents and heart valves, this is an adverse outcome. For other devices, such as embolic aneurysm treatments, efficient blood clot formation is desired. Thus a method to study how biomedical devices induce thrombosis is paramount to device development and optimization. A multiscale, multiphysics computational model is developed to predict thrombus formation within the vasculature. The model consists of a set of convection-diffusion-reaction partial differential equations for blood protein constituents involved in the progression of the clotting cascades. This model is used to study thrombus production from endovascular devices with the goal of optimizing the device design to generate the desired clotting response. This work was performed in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Vortex formation through inertial wave focusing

NASA Astrophysics Data System (ADS)

Duran-Matute, Matias; Flor, Jan-Bert; Godeferd, Fabien

2011-11-01

We present a novel experimental and numerical study on the formation of columnar vortical structures by inertial waves in a rotating fluid. Two inertial-wave cones are generated by a vertically oscillating torus in a fluid in solid body rotation At the tip of the cones, there is a singular point towards which the energy of the waves gets focused. The particularity of this configuration, as compared to those of previous experiments (e.g. oscillating sphere or disc), is that the singular point's position within the fluid leads to complex non-linear wave interaction, which may lead to the formation of a localized vortex that expands in the vertical in the form of a Taylor column. Using detailed PIV measurements we consider the flow evolution from the localized wave overturning motion to the Taylor column formation as well as the inertial wave dynamics during this process, The results are discussed in the context of turbulence in rotating fluids. We acknowledge financial support from projects ANR ANISO and CIBLE.

Photosynthetic microorganism-mediated synthesis of akaganeite (beta-FeOOH) nanorods.

PubMed

Brayner, Roberta; Yéprémian, Claude; Djediat, Chakib; Coradin, Thibaud; Herbst, Fréderic; Livage, Jacques; Fiévet, Fernand; Couté, Alain

2009-09-01

Common Anabaena and Calothrix cyanobacteria and Klebsormidium green algae are shown to form intracellularly akaganeite beta-FeOOH nanorods of well-controlled size and unusual morphology at room temperature. X-ray diffraction (XRD), transmission electron microscopy (TEM), and scanning electron microscopy X-ray energy dispersive spectrometry (SEM-EDS) analyses are used to investigate particle structure, size, and morphology. A mechanism involving iron-siderophore complex formation is proposed and compared with iron biomineralization in magnetotactic bacteria.

Theoretical Insight into the Influences of Molecular Ratios on Stabilities and Mechanical Properties, Solvent Effect of HMX/FOX-7 Cocrystal Explosive

NASA Astrophysics Data System (ADS)

Wei, Yan-Ju; Ren, Fu-De; Shi, Wen-Jing; Zhao, Qi

2016-10-01

A molecular dynamics method was employed to study the binding energies of the selected crystal planes of the 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane/1,1-diamino-2,2-dinitroethylene (HMX/FOX-7) cocrystal in different molecular molar ratios. Mechanical properties, densities, and detonation velocities of the cocrystals in different ratios were estimated. The intermolecular interactions and bond dissociation energies (BDEs) of the N-NO2 bond in the HMX:FOX-7 (1:1) complex were calculated using the B3LYP and MP2(full) methods at the 6-311++G (d,p) and 6-311++G(2df,2p) basis sets. Solvent effects on stability are discussed. The results indicate that HMX/FOX-7 cocrystals prefer cocrystalizing in a 1:1 molar ratio, which has good mechanical properties. The N-NO2 bond becomes strong upon the formation of a complex and the sensitivity of HMX might decrease in cocrystals. The sensitivity change of HMX/FOX-7 originates from not only the formation of intermolecular interaction but also the increment in the N-NO2 BDE. HMX/FOX-7 cocrystals exhibit good detonation performance and meet the requirements of high-density energetic materials. Solvents with low dielectric constants may be chosen to obtain stable HMX/FOX-7 cocrystals.

Computational study of interfacial charge transfer complexes of 2-anthroic acid adsorbed on a titania nanocluster for direct injection solar cells

NASA Astrophysics Data System (ADS)

Manzhos, Sergei; Kotsis, Konstantinos

2016-09-01

Adsorption and light absorption properties of interfacial charge transfer complexes of 2-anthroic acid and titania, promising for direct-injection solar cells, are studied ab initio. The formation of interfacial charge transfer bands is observed. The intensity of visible absorption is relatively low, highlighting a key challenge facing direct injection cells. We show that the popular strategy of using a lower level of theory for geometry optimization followed by single point calculations of adsorption or optical properties introduces significant errors which have been underappreciated: by up to 3 eV in adsorption energies, by up to 5 times in light absorption intensity.

Antibody-mediated cofactor-driven reactions

DOEpatents

Schultz, Peter G.

1993-01-01

Chemical reactions capable of being rate-enhanced by auxiliary species which interact with the reactants but do not become chemically bound to them in the formation of the final product are performed in the presence of antibodies which promote the reactions. The antibodies contain regions within their antigen binding sites which recognize the auxiliary species in a conformation which promotes the reaction. The antigen binding site frequently recognizes a particular transition state complex or other high energy complex along the reaction coordinate, thereby promoting the progress of the reaction along the desired route as opposed to other less favorable routes. Various classes of reaction together with appropriate antigen binding site specificities tailored for each are disclosed.

Theoretical investigation on functional monomer and solvent selection for molecular imprinting of tramadol

NASA Astrophysics Data System (ADS)

Fonseca, Matheus C.; Nascimento, Clebio S.; Borges, Keyller B.

2016-02-01

The purpose of this Letter was to study for the first time the interaction process of tramadol (TRM) with distinct functional monomers (FM) in the formation of molecular imprinted polymer (MIP), using density functional theory (DFT) calculations at B3LYP/6-31G(d,p). As result we were able to establish that the best MIP synthesis conditions are obtained with acrylic acid as FM in 1:3 molar ratio and with chloroform as solvent. This condition presented the lowest stabilization energy for the pre-polymerization complexes. Besides, the intermolecular hydrogen bonds found between the template molecule and functional monomers play a primary role to the complex stability.

Microscopic progression in the free radical addition reaction: modeling, geometry, energy, and kinetics.

PubMed

Zhang, Yun; Huang, Hong; Liang, Zhiling; Liu, Houhe; Yi, Ling; Zhang, Jinhong; Zhang, Zhiqiang; Zhong, Cheng; Huang, Yugang; Ye, Guodong

2017-03-01

The free radical addition reaction is very important in UV curing. The benzoyl radical is the most commonly observed radical. In the addition process, the benzoyl radical adds to an acrylate monomer, forming a primary radical that has great value for subsequent research. In this article, a quantum chemical method was used to study the microscopic progression from the reactive complex to the saddle point. The reactions of three monomers (amylene, allyl methyl ether and methyl acrylate) with a benzoyl radical were evaluated in terms of geometry and energy. The results were also interpreted with an expanded version of the Polanyi rules and the interaction/deformation theory. The deformation energy of methyl acrylate was found to be the smallest, and the bond formation index showed that the transition state in the methyl acrylate system forms early, and can easily reach the saddle point. The activity of the monomer was ascertained by charge analysis and was further confirmed by the reaction rate. Mayer bond order curves depicted the constantly changing chemical bonds during formation and dissociation. Reduced density gradient analysis showed a weak interaction between the monomer and the benzoyl radical.

Chemical reaction CO+OH • → CO 2+H • autocatalyzed by carbon dioxide: Quantum chemical study of the potential energy surfaces

DOE PAGES

Masunov, Artem E.; Wait, Elizabeth; Vasu, Subith S.

2016-06-28

The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO 2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO 2 to OH radical and CO molecule, hydrogen transfer frommore » oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO 2 medium. Furthermore, tt may open a new venue for controlling reaction rates for chemical manufacturing.« less

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

Laskin, Julia

In this work, resonant ejection coupled with surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer is used to examine fragmentation kinetics of two singly protonated hexapeptides, RYGGFL and KYGGFL, containing the basic arginine residue and less basic lysine residue at the N-terminus. The kinetics of individual reaction channels at different collision energies are probed by applying a short ejection pulse (1 ms) in resonance with the cyclotron frequency of a selected fragment ion and varying the delay time between ion-surface collision and resonant ejection while keeping total reaction delay time constant. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of themore » experimental data provides accurate threshold energies and activation entropies of individual reaction channels. Substitution of arginine with less basic lysine has a pronounced effect on the observed fragmentation kinetics of several pathways, including the b2 ion formation, but has little or no effect on formation of the b5+H2O fragment ion. The combination of resonant ejection SID, time- and collision energy-resolved SID, and RRKM modeling of both types of experimental data provides a detailed mechanistic understanding of the primary dissociation pathways of complex gaseous ions.« less

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

Stoller, Roger E; Nordlund, Kai; Melerba, L

The processes that give rise to changes in the microstructure and the physical and mechanical properties of materials exposed to energetic particles are initiated by essentially elastic collisions between atoms in what has been called an atomic displacement cascade. The formation and evolution of this primary radiation damage mechanism are described to provide an overview of how stable defects are formed by displacement cascades, as well as the nature and morphology of the defects themselves. The impact of the primary variables cascade energy and irradiation temperature are discussed, along with a range of secondary factors that can influence damage formation.Radiation-inducedmore » changes in microstructure and mechanical properties in structural materials are the result of a complex set of physical processes initiated by the collision between an energetic particle (neutron or ion) and an atom in the lattice. This primary damage event is called an atomic displacement cascade. The simplest description of a displacement cascade is to view it as a series of many billiard-ball-like elastic collisions among the atoms in the material. This chapter describes the formation and evolution of this primary radiation damage mechanism to provide an overview of how stable defects are formed by displacement cascades, as well as the nature and morphology of the defects themselves. The impact of the relevant variables such as cascade energy and irradiation temperature is discussed, and defect formation in different materials is compared.« less

AMR Studies of Star Formation: Simulations and Simulated Observations

NASA Astrophysics Data System (ADS)

Offner, Stella; McKee, C. F.; Klein, R. I.

2009-01-01

Molecular clouds are typically observed to be approximately virialized with gravitational and turbulent energy in balance, yielding a star formation rate of a few percent. The origin and characteristics of the observed supersonic turbulence are poorly understood, and without continued energy injection the turbulence is predicted to decay within a cloud dynamical time. Recent observations and analytic work have suggested a strong connection between the initial stellar mass function, the core mass function, and turbulence characteristics. The role of magnetic fields in determining core lifetimes, shapes, and kinematic properties remains hotly debated. Simulations are a formidable tool for studying the complex process of star formation and addressing these puzzles. I present my results modeling low-mass star formation using the ORION adaptive mesh refinement (AMR) code. I investigate the properties of forming cores and protostars in simulations in which the turbulence is driven to maintain virial balance and where it is allowed to decay. I will discuss simulated observations of cores in dust emission and in molecular tracers and compare to observations of local star-forming clouds. I will also present results from ORION cluster simulations including flux-limited diffusion radiative transfer and show that radiative feedback, even from low-mass stars, has a significant effect on core fragmentation, disk properties, and the IMF. Finally, I will discuss the new simulation frontier of AMR multigroup radiative transfer.

The significance of ACTH for the process of formation of complex heparin compounds in the blood during immobilization stress

NASA Technical Reports Server (NTRS)

Kudryashov, B. A.; Shapiro, F. B.; Lomovskaya, F. B.; Lyapina, L. A.

1979-01-01

Adrenocorticotropin (ACTH) was administered to rats at different times following adrenalectomy. Adrenocorticotropin caused a significant increase in the formation of heparin complexes even in the absence of stress factor. When ACTH secretion is blocked, immobilization stress is not accompanied by an increase in the process of complex formation. The effect of ACTH on the formation of heparin complexes was mediated through its stimulation of the adrenal cortex.

Probing the Energetics of Antigen-Antibody Recognition by Titration Microcalorimetry

PubMed

Jelesarov; Leder; Bosshard

1996-06-01

Our understanding of the energetics that govern antigen-antibody recognition lags behind the increasingly rapid accumulation of structural information on antigen-antibody complexes. Thanks to the development of highly sensitive microcalorimeters, the thermodynamic parameters of antigen-antibody interactions can now be measured with precision and using only nanomole quantities of protein. The method of choice is isothermal titration calorimetry, in which a solution of the antibody (or antigen) is titrated with small aliquots of the antigen (or antibody) and the heat change accompanying the formation of the antigen-antibody complex is measured with a sensitivity as high as 0.1 μcal s-1. The free energy of binding (DeltaG), the binding enthalpy (DeltaH), and the binding entropy (DeltaS) are usually obtained from a single experiment, and no spectroscopic or radioactive label must be introduced into the antigen or antibody. The often large and negative change in heat capacity (DeltaCp) accompanying the formation of an antigen-antibody complex is obtained from DeltaH measured at different temperatures. The basic theory and the principle of the measurements are reviewed and illustrated by examples. The thermodynamic parameters relate to the dynamic physical forces that govern the association of the freely moving antigen and antibody into a well-structured and unique complex. This information complements the static picture of the antigen-antibody complex that results from X-ray diffraction analysis. Attempts to correlate dynamic and static aspects are discussed briefly.

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

PubMed

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

a Chiral Tag Study of the Absolute Configuration of Camphor

NASA Astrophysics Data System (ADS)

Pratt, David; Evangelisti, Luca; Smart, Taylor; Holdren, Martin S.; Mayer, Kevin J.; West, Channing; Pate, Brooks

2017-06-01

The chiral tagging method for rotational spectroscopy uses an established approach in chiral analysis of creating a complex with an enantiopure tag so that enantiomers of the molecule of interest are converted to diastereomer complexes. Since the diastereomers have distinct structure, they give distinguishable rotational spectra. Camphor was chosen as an example for the chiral tag method because it has spectral properties that could pose challenges to the use of three wave mixing rotational spectroscopy to establish absolute configuration. Specifically, one of the dipole moment components of camphor is small making three wave mixing measurements challenging and placing high accuracy requirements on computational chemistry for calculating the dipole moment direction in the principal axis system. The chiral tag measurements of camphor used the hydrogen bond donor 3-butyn-2-ol. Quantum chemistry calculations using the B3LYP-D3BJ method and the def2TZVP basis set identified 7 low energy isomers of the chiral complex. The two lowest energy complexes of the homochiral and heterochiral complexes are observed in a measurement using racemic tag. Absolute configuration is confirmed by the use of an enantiopure tag sample. Spectra with ^{13}C-sensitivity were acquired so that the carbon substitution structure of the complex could be obtained to provide a structure of camphor with correct stereochemistry. The chiral tag complex spectra can also be used to estimate the enantiomeric excess of the sample and analysis of the broadband spectrum indicates that the sample enantiopurity is higher than 99.5%. The structure of the complex is analyzed to determine the extent of geometry modification that occurs upon formation of the complex. These results show that initial isomer searches with fixed geometries will be accurate. The reduction in computation time from fixed geometry assumptions will be discussed.

Primary and aggregate color centers in proton irradiated LiF crystals and thin films for luminescent solid state detectors

NASA Astrophysics Data System (ADS)

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

2015-04-01

Proton beams of 3 MeV energy, produced by the injector of a linear accelerator for proton therapy, were used to irradiate at room temperature lithium fluoride crystals and polycrystalline thin films grown by thermal evaporation. The irradiation fluence range was 1011-1015 protons/cm2. The proton irradiation induced the stable formation of primary and aggregate color centers. Their formation was investigated by optical absorption and photoluminescence spectroscopy. The F2 and F3+ photoluminescence intensities, carefully measured in LiF crystals and thin films, show linear behaviours up to different maximum values of the irradiation fluence, after which a quenching is observed, depending on the nature of the samples (crystals and films). The Principal Component Analysis, applied to the absorption spectra of colored crystals, allowed to clearly identify the formation of more complex aggregate defects in samples irradiated at highest fluences.

Phenomenal enhancement of optical nonlinearity in PTZ-I based ZnS/ZnSe nanocomposites

NASA Astrophysics Data System (ADS)

Divyasree, M. C.; Shiju, E.; Vijisha, M. V.; Ramesan, M. T.; Chandrasekharan, K.

2018-05-01

The enhanced nonlinear optical properties of phenothiazine-iodine (PTZ-I) charge transfer complex (CTC) on composite formation with ZnS/ZnSe nanostructures are reported. The interaction between the components was confirmed by the FTIR spectra. Structural and morphological changes on nanocomposite formation were analyzed by scanning electron microscopy and X-ray diffraction spectra. The absorption and emission features of both the nanocomposites and their constituent components were studied. Nonlinear optical properties of all the samples in nanosecond regime were investigated by the Z-scan technique using Nd: YAG laser with 532 nm wavelength and 7 ns pulse width. The optical nonlinearity of PTZ-I CTC was found to be improved considerably on composite formation and the new systems can be proposed as excellent candidates for photonic devices. Enhanced optical nonlinearity of the composites could be attributed to charge/energy transfer mechanism between PTZ-I CTC and the nanostructures.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Multiple pickering emulsions stabilized by microbowls.

PubMed

Nonomura, Yoshimune; Kobayashi, Naoto; Nakagawa, Naoki

2011-04-19

Some researchers have focused on the adsorption of solid particles at fluid-fluid interfaces and prepared emulsions and foams called "Pickering emulsions/foams". However, while several reports exist on simple spherical emulsions, few reports are available on the formation of more complex structures. Here, we show that holes on particle surfaces are a key factor in establishing the variety and complexity of mesoscale structures. Microbowls, which are hollow particles with holes on their surfaces, form multiple emulsions (water-in-oil-in-water and oil-in-water-in-oil emulsions) by simply mixing them with water and oil. Furthermore, stable potato-like or coffee-bean-like emulsions are also obtained, although nonspherical emulsions are usually unstable because of their larger interfacial energies. These findings are useful in designing the building blocks of complex supracolloidal systems for pharmaceutical, food, and cosmetic products. © 2011 American Chemical Society

Photochemical Approaches to Complex Chemotypes: Applications in Natural Product Synthesis

PubMed Central

2016-01-01

The use of photochemical transformations is a powerful strategy that allows for the formation of a high degree of molecular complexity from relatively simple building blocks in a single step. A central feature of all light-promoted transformations is the involvement of electronically excited states, generated upon absorption of photons. This produces transient reactive intermediates and significantly alters the reactivity of a chemical compound. The input of energy provided by light thus offers a means to produce strained and unique target compounds that cannot be assembled using thermal protocols. This review aims at highlighting photochemical transformations as a tool for rapidly accessing structurally and stereochemically diverse scaffolds. Synthetic designs based on photochemical transformations have the potential to afford complex polycyclic carbon skeletons with impressive efficiency, which are of high value in total synthesis. PMID:27120289

DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

PubMed

Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

2017-09-24

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

Relative biological effectiveness for photons: implication of complex DNA double-strand breaks as critical lesions

NASA Astrophysics Data System (ADS)

Liang, Ying; Fu, Qibin; Wang, Xudong; Liu, Feng; Yang, Gen; Luo, Chunxiong; Ouyang, Qi; Wang, Yugang

2017-03-01

Current knowledge in radiobiology ascribes the adverse biological effects of ionizing radiation primarily to the induction of DNA double-strand breaks (DSBs), which is supposed to be potentially lethal and may be converted to lethal damage due to misrepair. Soft and ultrasoft x-rays have been found to bear elevated biological effectiveness for cell killing compared with conventional x-rays or 60Co γ-rays. This phenomenon is qualitatively interpreted as the increased level of DSB induction for low energy photons, however, a thorough quantitative reasoning is lacking. Here, we systematically compared the relative biological effectiveness (RBE) with relative DSB induction for photons from several hundreds of eV up to MeV. Although there is an approximate two-fold increase in the yields of DSB for low energy photons found in our calculation and a large number of experimental measurements, it is far from enough to account for the three- to four-fold increase in RBE. Further theoretical investigations show that DSB complexity (additional single-strand breaks and base damage within 10 base pairs) increases notably for low energy photons, which largely reconciles the discrepancy between RBE and DSB induction. Our theoretical results are in line with accumulating experimental evidence that complex DSBs are refractory to repair machinery and may contribute predominantly to the formation of lethal damage.

Heterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein-protein docking.

PubMed

Montaño, Sarita; Orozco, Esther; Correa-Basurto, José; Bello, Martiniano; Chávez-Munguía, Bibiana; Betanzos, Abigail

2017-02-01

EhCPADH is a protein complex involved in the virulence of Entamoeba histolytica, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecular dynamics simulations (MDS) and docking calculations were performed. Results predicted that the pEhCP112 proenzyme and the mEhCP112 mature enzyme were globular and peripheral membrane proteins. Interestingly, in pEhCP112, the propeptide appeared hiding the catalytic site (C167, H329, N348); while in mEhCP112, this site was exposed and its residues were found structurally closer than in pEhCP112. EhADH emerged as an extended peripheral membrane protein with high fluctuation in Bro1 and V shape domains. 500 ns-long MDS and protein-protein docking predictions evidenced different heterodimeric complexes with the lowest free energy. pEhCP112 interacted with EhADH by the propeptide and C-terminal regions and mEhCP112 by the C-terminal through hydrogen bonds. In contrast, EhADH bound to mEhCP112 by 442-479 residues, adjacent to the target cell-adherence region (480-600 residues), and by the Bro1 domain (9-349 residues). Calculations of the effective binding free energy and per residue free energy decomposition showed that EhADH binds to mEhCP112 with a higher binding energy than to pEhCP112, mainly through van der Waals interactions and the nonpolar part of solvation energy. The EhADH and EhCP112 structural relationship was validated in trophozoites by immunofluorescence, TEM, and immunoprecipitation assays. Experimental findings fair agreed with in silico results.

Bioastrophysical aspects of low energy ion irradiation of frozen anthracene containing water.

PubMed

Tuleta, M; Gabła, L; Madej, J

2001-08-13

The origin of life on Earth remains a fascinating mystery in spite of many theories existing on this subject. However, it seems that simple prebiotic molecules could play an essential role in the formation of more complex organisms. In our experiment, we synthesized a class of these molecules (quinones) bombarding frozen anthracene containing water with low energy hydrogen ions. This experiment roughly simulated the astrophysical conditions which one can find in the solar system. Thus, we can hypothesize that prebiotic molecules could be created by interaction of the solar wind with interplanetary dust grains. The delivery of these molecules to early Earth may have contributed to the generation of life on our planet.

Spectroscopic, structure and antimicrobial activity of new Y(III) and Zr(IV) ciprofloxacin

NASA Astrophysics Data System (ADS)

Sadeek, Sadeek A.; El-Shwiniy, Walaa H.; Zordok, Wael A.; El-Didamony, Akram M.

2011-02-01

The preparation and characterization of the new solid complexes [Y(CIP) 2(H 2O) 2]Cl 3·10H 2O and [ZrO(CIP) 2Cl]Cl·15H 2O formed in the reaction of ciprofloxacin (CIP) with YCl 3 and ZrOCl 2·8H 2O in ethanol and methanol, respectively, at room temperature were reported. The isolated complexes have been characterized with elemental analysis, IR spectroscopy, conductance measurements, UV-vis and 1H NMR spectroscopic methods and thermal analyses. The results support the formation of the complexes and indicate that ciprofloxacin reacts as a bidentate ligand bound to the metal ion through the pyridone oxygen and one carboxylato oxygen. The activation energies, E*; entropies, Δ S*; enthalpies, Δ H*; Gibbs free energies, Δ G*, of the thermal decomposition reactions have been derived from thermogravimetric (TGA) and differential thermogravimetric (DTG) curves, using Coats-Redfern and Horowitz-Metzeger methods. The proposed structure of the two complexes was detected by using the density functional theory (DFT) at the B3LYP/CEP-31G level of theory. The ligand as well as their metal complexes was also evaluated for their antibacterial activity against several bacterial species, such as Staphylococcus aureus ( S. aureus), Escherichia coli ( E. coli) and Pseudomonas aeruginosa ( P. aeruginosa) and antifungal screening was studied against two species ( Penicillium ( P. rotatum) and Trichoderma ( T. sp.)). This study showed that the metal complexes are more antibacterial as compared to free ligand and no antifungal activity observed for ligand and their complexes.

Formation Energies of Native Point Defects in Strained-Layer Superlattices (Postprint)

DTIC Science & Technology

2017-06-05

AFRL-RX-WP-JA-2017-0217 FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED-LAYER SUPERLATTICES (POSTPRINT) Zhi-Gang Yu...2016 Interim 11 September 2013 – 5 November 2016 4. TITLE AND SUBTITLE FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED-LAYER SUPERLATTICES...native point defect (NPD) formation energies and absence of mid-gap levels. In this Letter we use first-principles calculations to study the formation

The role of Rnf in ion gradient formation in Desulfovibrio alaskensis

DOE PAGES

Wang, Luyao; Bradstock, Peter; Li, Chuang; ...

2016-04-14

Rnf is a membrane protein complex that has been shown to be important in energy conservation. Here, Desulfovibrio alaskensis G20 and Rnf mutants of G20 were grown with different electron donor and acceptor combinations to determine the importance of Rnf in energy conservation and the type of ion gradient generated. The addition of the protonophore TCS strongly inhibited lactate-sulfate dependent growth whereas the sodium ionophore ETH2120 had no effect, indicating a role for the proton gradient during growth. Mutants in rnfA and rnfD were more sensitive to the protonophore at 5 µM than the parental strain, suggesting the importance ofmore » Rnf in the generation of a proton gradient. The electrical potential (ΔΨ), ΔpH and proton motive force were lower in thernfAmutant than in the parental strain of D.alaskensis G20. In conclusion, these results provide evidence that the Rnf complex in D. alaskensis functions as a primary proton pump whose activity is important for growth.« less