Theoretical studies on the unimolecular decomposition of ethylene glycol.

PubMed

Ye, Lili; Zhao, Long; Zhang, Lidong; Qi, Fei

2012-01-12

The unimolecular decomposition processes of ethylene glycol have been investigated with the QCISD(T) method with geometries optimized at the B3LYP/6-311++G(d,p) level. Among the decomposition channels identified, the H(2)O-elimination channels have the lowest barriers, and the C-C bond dissociation is the lowest-energy dissociation channel among the barrierless reactions (the direct bond cleavage reactions). The temperature and pressure dependent rate constant calculations show that the H(2)O-elimination reactions are predominant at low temperature, whereas at high temperature, the direct C-C bond dissociation reaction is dominant. At 1 atm, in the temperature range 500-2000 K, the calculated rate constant is expressed to be 7.63 × 10(47)T(-10.38) exp(-42262/T) for the channel CH(2)OHCH(2)OH → CH(2)CHOH + H(2)O, and 2.48 × 10(51)T(-11.58) exp(-43593/T) for the channel CH(2)OHCH(2)OH → CH(3)CHO + H(2)O, whereas for the direct bond dissociation reaction CH(2)OHCH(2)OH → CH(2)OH + CH(2)OH the rate constant expression is 1.04 × 10(71)T(-16.16) exp(-52414/T).

Effects of charge state on fragmentation pathways, dynamics, and activation energies of ubiquitin ions measured by blackbody infrared radiative dissociation.

PubMed

Jockusch, R A; Schnier, P D; Price, W D; Strittmatter, E F; Demirev, P A; Williams, E R

1997-03-15

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 10(12) s-1, respectively. These values for the 6+ and 7+ ions are 0.9-1.0 eV and 10(9) s-1, and those for the 10+ and 11+ ions are 1.6 eV and 10(16)-10(17) s-1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed.

Regulation of Catch Bonds by Rate of Force Application*

PubMed Central

Sarangapani, Krishna K.; Qian, Jin; Chen, Wei; Zarnitsyna, Veronika I.; Mehta, Padmaja; Yago, Tadayuki; McEver, Rodger P.; Zhu, Cheng

2011-01-01

The current paradigm for receptor-ligand dissociation kinetics assumes off-rates as functions of instantaneous force without impact from its prior history. This a priori assumption is the foundation for predicting dissociation from a given initial state using kinetic equations. Here we have invalidated this assumption by demonstrating the impact of force history with single-bond kinetic experiments involving selectins and their ligands that mediate leukocyte tethering and rolling on vascular surfaces during inflammation. Dissociation of bonds between L-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) loaded at a constant ramp rate to a constant hold force behaved as catch-slip bonds at low ramp rates that transformed to slip-only bonds at high ramp rates. Strikingly, bonds between L-selectin and 6-sulfo-sialyl Lewis X were impervious to ramp rate changes. This ligand-specific force history effect resembled the effect of a point mutation at the L-selectin surface (L-selectinA108H) predicted to contact the former but not the latter ligand, suggesting that the high ramp rate induced similar structural changes as the mutation. Although the A108H substitution in L-selectin eliminated the ramp rate responsiveness of its dissociation from PSGL-1, the inverse mutation H108A in P-selectin acquired the ramp rate responsiveness. Our data are well explained by the sliding-rebinding model for catch-slip bonds extended to incorporate the additional force history dependence, with Ala-108 playing a pivotal role in this structural mechanism. These results call for a paradigm shift in modeling the mechanical regulation of receptor-ligand bond dissociation, which includes conformational coupling between binding pocket and remote regions of the interacting molecules. PMID:21775439

Critical Role of Water and Oxygen Defects in C-O Scission during CO2 Reduction on Zn2GeO4(010).

PubMed

Yang, Jing; Li, Yanlu; Zhao, Xian; Fan, Weiliu

2018-03-27

Exploration of catalyst structure and environmental sensitivity for C-O bond scission is essential for improving the conversion efficiency because of the inertness of CO 2 . We performed density functional theory calculations to understand the influence of the properties of adsorbed water and the reciprocal action with oxygen vacancy on the CO 2 dissociation mechanism on Zn 2 GeO 4 (010). When a perfect surface was hydrated, the introduction of H 2 O was predicted to promote the scission step by two modes based on its appearance, with the greatest enhancement from dissociative adsorbed H 2 O. The dissociative H 2 O lowers the barrier and reaction energy of CO 2 dissociation through hydrogen bonding to preactivate the C-O bond and assisted scission via a COOH intermediate. The perfect surface with bidentate-binding H 2 O was energetically more favorable for CO 2 dissociation than the surface with monodentate-binding H 2 O. Direct dissociation was energetically favored by the former, whereas monodentate H 2 O facilitated the H-assisted pathway. The defective surface exhibited a higher reactivity for CO 2 decomposition than the perfect surface because the generation of oxygen vacancies could disperse the product location. When the defective surface was hydrated, the reciprocal action for vacancy and surface H 2 O on CO 2 dissociation was related to the vacancy type. The presence of H 2 O substantially decreased the reaction energy for the direct dissociation of CO 2 on O 2c1 - and O 3c2 -defect surfaces, which converts the endoergic reaction to an exoergic reaction. However, the increased decomposition barrier made the step kinetically unfavorable and reduced the reaction rate. When H 2 O was present on the O 2c2 -defect surface, both the barrier and reaction energy for direct dissociation were invariable. This result indicated that the introduction of H 2 O had little effect on the kinetics and thermodynamics. Moreover, the H-assisted pathway was suppressed on all hydrated defect surfaces. These results provide a theoretical perspective for the design of highly efficient catalysts.

Control of C-H Bond Activation by Mo-Oxo Complexes: pKa or Bond Dissociation Free Energy (BDFE)?

PubMed

Nazemi, Azadeh; Cundari, Thomas R

2017-10-16

A density functional theory (DFT) study (BMK/6-31+G(d)) was initiated to investigate the activation of benzylic carbon-hydrogen bonds by a molybdenum-oxo complex with a potentially redox noninnocent supporting ligand-a simple mimic of the active species of the enzyme ethylbenzene dehydrogenase (EBDH)-through deprotonation (C-H bond heterolysis) or hydrogen atom abstraction (C-H bond homolysis) routes. Activation free-energy barriers for neutral and anionic Mo-oxo complexes were high, but lower for anionic complexes than neutral complexes. Interesting trends as a function of substituents were observed that indicated significant H δ+ character in the transition states (TS), which was further supported by the preference for [2 + 2] addition over HAA for most complexes. Hence, it was hypothesized that C-H activation by these EBDH mimics is controlled more by the pK a than by the bond dissociation free energy of the C-H bond being activated. Therefore, the results suggest promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active-site mimics.

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

PubMed

Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

2005-06-16

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

Determination of metal-hydrogen bond dissociation energies by the deprotonation of transition metal hydride ions: application to MnH +

NASA Astrophysics Data System (ADS)

Stevens, Amy E.; Beauchamp, J. L.

1981-03-01

ICR trapped ion techniques are used to examine the kinetics of proton transfer from MnH + (formed as a fragment ion from HMn (CO) 5 by electron impact) to bases of varying strength. Deprotonation is rapid with bases whose proton affinity exceeds 196±3 kcal mol -1. This value for PA (Mn) yields the homolytic bond dissociation energy D0(Mn +-H) = 53±5 kcal mol -1.

In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

DOE PAGES

Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; ...

2015-03-23

Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of thismore » support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.« less

Active Thermochemical Tables: Sequential Bond Dissociation Enthalpies of Methane, Ethane, and Methanol and the Related Thermochemistry

DOE PAGES

Ruscic, Branko

2015-03-31

Active Thermochemical Tables (ATcT) thermochemistry for the sequential bond dissociations of methane, ethane, and methanol systems were obtained by analyzing and solving a very large thermochemical network (TN). Values for all possible C–H, C–C, C–O, and O–H bond dissociation enthalpies at 298.15 K (BDE 298) and bond dissociation energies at 0 K (D 0) are presented. The corresponding ATcT standard gas-phase enthalpies of formation of the resulting CH n, n = 4–0 species (methane, methyl, methylene, methylidyne, and carbon atom), C 2H n, n = 6–0 species (ethane, ethyl, ethylene, ethylidene, vinyl, ethylidyne, acetylene, vinylidene, ethynyl, and ethynylene), and COHmore » n, n = 4–0 species (methanol, hydroxymethyl, methoxy, formaldehyde, hydroxymethylene, formyl, isoformyl, and carbon monoxide) are also presented. The ATcT thermochemistry of carbon dioxide, water, hydroxyl, and carbon, oxygen, and hydrogen atoms is also included, together with the sequential BDEs of CO 2 and H 2O. The provenances of the ATcT enthalpies of formation, which are quite distributed and involve a large number of relevant determinations, are analyzed by variance decomposition and discussed in terms of principal contributions. The underlying reasons for periodic appearances of remarkably low and/or unusually high BDEs, alternating along the dissociation sequences, are analyzed and quantitatively rationalized. The present ATcT results are the most accurate thermochemical values currently available for these species.« less

Measuring Intermolecular Binding Energies by Laser Spectroscopy.

PubMed

Knochenmuss, Richard; Maity, Surajit; Féraud, Géraldine; Leutwyler, Samuel

2017-02-22

The ground-state dissociation energy, D0(S0), of isolated intermolecular complexes in the gas phase is a fundamental measure of the interaction strength between the molecules. We have developed a three-laser, triply resonant pump-dump-probe technique to measure dissociation energies of jet-cooled M•S complexes, where M is an aromatic chromophore and S is a closed-shell 'solvent' molecule. Stimulated emission pumping (SEP) via the S0→S1 electronic transition is used to precisely 'warm' the complex by populating high vibrational levels v" of the S0 state. If the deposited energy E(v") is less than D0(S0), the complex remains intact, and is then mass- and isomer-selectively detected by resonant two-photon ionization (R2PI) with a third (probe) laser. If the pumped level is above D0(S0), the hot complex dissociates and the probe signal disappears. Combining the fluorescence or SEP spectrum of the cold complex with the SEP breakoff of the hot complex brackets D0(S0). The UV chromophores 1-naphthol and carbazole were employed; these bind either dispersively via the aromatic rings, or form a hydrogen bond via the -OH or -NH group. Dissociation energies have been measured for dispersively bound complexes with noble gases (Ne, Kr, Ar, Xe), diatomics (N2, CO), alkanes (methane to n-butane), cycloalkanes (cyclopropane to cycloheptane), and unsaturated compounds (ethene, benzene). Hydrogen-bond dissociation energies have been measured for H2O, D2O, methanol, ethanol, ethers (oxirane, oxetane), NH3 and ND3.

Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory

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

DiLabio, Gino A., E-mail: Gino.DiLabio@nrc.ca; Department of Chemistry, University of British Columbia, Okanagan, 3333 University Way, Kelowna, British Columbia V1V 1V7; Koleini, Mohammad

2014-05-14

Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for themore » C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the “S66” set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the “D3” pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.« less

Bond Dissociation Free Energies (BDFEs) of the Acidic H-A Bonds in HA(*)(-) Radical Anions by Three Different Pathways.

PubMed

Zhao, Yongyu; Bordwell, Frederick G.

1996-09-20

Cleavage of radical anions, HA(*)(-), have been considered to give either H(*) + A(-) (path a) or H(-) + A(*) (path b), and factors determining the preferred mode of cleavage have been discussed. It is conceivable that cleavage to give a proton and a radical dianion, HA(*)(-) right harpoon over left harpoon H(+) + A(*)(2)(-) (path c), might also be feasible. A method, based on a thermodynamic cycle, to estimate the bond dissociation free energy (BDFE) by path c has been devised. Comparison of the BDFEs for cleavage of the radical anions derived from 24 nitroaromatic OH, SH, NH, and CH acids by paths a, b, c has shown that path c is favored thermodynamically.

The dissociative chemisorption of water on Ni(111): Mode- and bond-selective chemistry on metal surfaces

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

Farjamnia, Azar; Jackson, Bret, E-mail: jackson@chem.umass.edu

A fully quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of H{sub 2}O, HOD, and D{sub 2}O on Ni(111). For this late barrier system, excitation of both the bending and stretching modes significantly enhances dissociative sticking. The vibrational efficacies vary somewhat from mode-to-mode but are all relatively close to one, in contrast to methane dissociation, where the behavior is less statistical. Similar to methane dissociation, the motion of lattice atoms near the dissociating molecule can significantly modify the height of the barrier to dissociation, leading to a strong variation in dissociativemore » sticking with substrate temperature. Given a rescaling of the barrier height, our results are in reasonable agreement with measurements of the dissociative sticking of D{sub 2}O on Ni(111), for both laser-excited molecules with one or two quanta of excitation in the antisymmetric stretch and in the absence of laser excitation. Even without laser excitation, the beam contains vibrationally excited molecules populated at the experimental source temperature, and these make significant contributions to the sticking probability. At high collision energies, above the adiabatic barrier heights, our results correlate with these barrier heights and mode softening effects. At lower energies, dissociative sticking occurs primarily via vibrationally nonadiabatic pathways. We find a preference for O–H over O–D bond cleavage for ground state HOD molecules at all but the highest collision energies, and excitation of the O–H stretch gives close to 100% O–H selectivity at lower energies. Excitation of the O–D stretch gives a lower O–D cleavage selectivity, as the interaction with the surface leads to energy transfer from the O–D stretch into the O–H bond, when mode softening makes these vibrations nearly degenerate.« less

Density functional theory study of hydrogen atom abstraction from a series of para-substituted phenols: why is the Hammett σ(p)+ constant able to represent radical reaction rates?

PubMed

Yoshida, Tatsusada; Hirozumi, Koji; Harada, Masataka; Hitaoka, Seiji; Chuman, Hiroshi

2011-06-03

The rate of hydrogen atom abstraction from phenolic compounds by a radical is known to be often linear with the Hammett substitution constant σ(+), defined using the S(N)1 solvolysis rates of substituted cumyl chlorides. Nevertheless, a physicochemical reason for the above "empirical fact" has not been fully revealed. The transition states of complexes between the 2,2-diphenyl-1-picrylhydrazyl radical (dpph·) and a series of para-substituted phenols were determined by DFT (Density Functional Theory) calculations, and then the activation energy as well as the homolytic bond dissociation energy of the O-H bond and charge distribution in the transition state were calculated. The heterolytic bond dissociation energy of the C-Cl bond and charge distribution in the corresponding para-substituted cumyl chlorides were calculated in parallel. Excellent correlations among σ(+), charge distribution, and activation and bond dissociation energies revealed quantitatively that there is a strong similarity between the two reactions, showing that the electron-deficiency of the π-electron system conjugated with a substituent plays a crucial role in determining rates of the two reactions. The results provide a new insight into and physicochemical understanding of σ(+) in the hydrogen abstraction from substituted phenols by a radical.

Jet-Cooled Chlorofluorobenzyl Radicals: Spectroscopy and Mechanism

NASA Astrophysics Data System (ADS)

Yoon, Young; Lee, Sang

2016-06-01

Whereas the benzyl radical, a prototypic aromatic free radical, has been the subject of numerous spectroscopic studies, halo-substituted benzyl radicals have received less attention, due to the difficulties associated with production of radicals from precursors. In particular, chloro-substituted benzyl radicals have been much less studied because of the weak visible emission intensity and weak C-Cl bond dissociation energy. The jet-cooled chlorofluorobenzyl radicals were generated in a technique of corona excited supersonic jet expansion using a pinhole-type glass nozzle for the vibronic assignments and measurements of electronic energies of the D_1 → D_0 transition. The 2,4-,2.5-, and 2.6- chlorofluorobenzyl radicals were generated by corona discharge of corresponding precursors, chlorofluorotoluenes seeded in a large amount of helium carrier gas. The vibronic emission spectra were recorded with a long-path monochromator in the visible region. The emission spectra show the vibronic bands originating from two types of benzyl-type radicals, chlorofluorobenzyl and fluorobenzyl benzyl radicals, in which fluorobenzyl radicals were obtained by displacement of Cl by H produced by dissociation of methyl C-H bond. From the analysis of the spectra observed, we could determine the electronic energies in D_1 → D_0 transition and vibrational mode frequencies at the D_0 state of chlorofluorobenzyl radicals, which show the origin band of the electronic transition to be shifted to red region, comparing with the parental benzyl radical. From the quantitative analysis of the red-shift, it has been found that the additivity rule can be applied to dihalo-substituted benzyl radicals. In this presentation, the dissociation process of precursors in corona discharge is discussed in terms of bond dissociation energy as well as the spectroscopic analysis of the radicals. C. S. Huh, Y. W. Yoon, and S. K. Lee, J. Chem. Phys. 136, 174306 (2012). Y. W. Huh, S. Y. Chae, and S. K. Lee, Chem. Phys. Lett. 608, 6 (2014). Y. W. Yoon, S. Y. Chae, M. Lim, and S. K. Lee, Chem. Phys. Lett. 637, 148 (2015).

H2S adsorption on chromium, chromia, and gold/chromia surfaces: Photoemission studies

NASA Astrophysics Data System (ADS)

Rodriguez, J. A.; Chaturvedi, S.; Kuhn, M.; van Ek, J.; Diebold, U.; Robbert, P. S.; Geisler, H.; Ventrice, C. A., Jr.

1997-12-01

The reaction of H2S with chromium, chromia, and Au/chromia films grown on a Pt(111) crystal has been investigated using synchrotron-based high-resolution photoemission spectroscopy. At 300 K, H2S completely decomposes on polycrystalline chromium producing a chemisorbed layer of S that attenuates the Cr 3d valence features. No evidence was found for the formation of CrSx species. The dissociation of H2S on Cr3O4 and Cr2O3 films at room temperature produces a decrease of 0.3-0.8 eV in the work function of the surface and significant binding-energy shifts (0.2-0.6 eV) in the Cr 3p core levels and Cr 3d features in the valence region. The rate of dissociation of H2S increases following the sequence: Cr2O3

Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

NASA Astrophysics Data System (ADS)

Zhang, Yun; Zhang, Hao; Cui, Weidong; Chen, Hao

2011-09-01

Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen ( m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

Mechanisms and energetics of hydride dissociation reactions on surfaces of plasma-deposited silicon thin films

NASA Astrophysics Data System (ADS)

Singh, Tejinder; Valipa, Mayur S.; Mountziaris, T. J.; Maroudas, Dimitrios

2007-11-01

We report results from a detailed analysis of the fundamental silicon hydride dissociation processes on silicon surfaces and discuss their implications for the surface chemical composition of plasma-deposited hydrogenated amorphous silicon (a-Si:H) thin films. The analysis is based on a synergistic combination of first-principles density functional theory (DFT) calculations of hydride dissociation on the hydrogen-terminated Si(001)-(2×1) surface and molecular-dynamics (MD) simulations of adsorbed SiH3 radical precursor dissociation on surfaces of MD-grown a-Si :H films. Our DFT calculations reveal that, in the presence of fivefold coordinated surface Si atoms, surface trihydride species dissociate sequentially to form surface dihydrides and surface monohydrides via thermally activated pathways with reaction barriers of 0.40-0.55eV. The presence of dangling bonds (DBs) results in lowering the activation barrier for hydride dissociation to 0.15-0.20eV, but such DB-mediated reactions are infrequent. Our MD simulations on a-Si :H film growth surfaces indicate that surface hydride dissociation reactions are predominantly mediated by fivefold coordinated surface Si atoms, with resulting activation barriers of 0.35-0.50eV. The results are consistent with experimental measurements of a-Si :H film surface composition using in situ attenuated total reflection Fourier transform infrared spectroscopy, which indicate that the a-Si :H surface is predominantly covered with the higher hydrides at low temperatures, while the surface monohydride, SiH(s ), becomes increasingly more dominant as the temperature is increased.

Desulfurization of Thiophene on Au/TiC(001): Au−C Interactions and Charge Polarization

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

Rodriguez, J.; Liu, P; Takahashi, Y

2009-01-01

Photoemission and first-principles DF calculations were used to study the interaction of thiophene with TiC(001) and Au/TiC(001) surfaces. The adsorption strength of thiophene on TiC(001) is weak, and the molecule desorbs at temperatures below 200 K. The molecule binds to Ti centers of TiC(001) through its sulfur atom with negligible structural perturbations. In spite of the very poor desulfurization performance of TiC(001) or Au(111), a Au/TiC(001) system displays a hydrodesulfurization activity higher than that of conventional Ni/MoS{sub x} catalysts. The Au?TiC(001) interactions induce a polarization of electron density around Au which substantially increases the chemical reactivity of this metal. Aumore » nanoparticles drastically increase the hydrodesulfurization activity of TiC(001) by enhancing the bonding energy of thiophene and by helping in the dissociation of H{sub 2} to produce the hydrogen necessary for the hydrogenolysis of C-S bonds and the removal of sulfur. H{sub 2} spontaneously dissociates on small two-dimensional clusters of gold in contact with TiC(001). On these systems, the adsorption energy of thiophene is 0.45-0.65 eV larger than that on TiC(001) or Au(111). Thiophene binds in a ?5 configuration with a large elongation ({approx}0.2 {angstrom}) of the C-S bonds.« less

A general transformation to canonical form for potentials in pairwise interatomic interactions.

PubMed

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Computational study of C(sp3)-O bond formation at a PdIV centre.

PubMed

Canty, Allan J; Ariafard, Alireza; Camasso, Nicole M; Higgs, Andrew T; Yates, Brian F; Sanford, Melanie S

2017-03-14

This report describes a computational study of C(sp 3 )-OR bond formation from Pd IV complexes of general structure Pd IV (CH 2 CMe 2 -o-C 6 H 4 -C,C')(F)(OR)(bpy-N,N') (bpy = 2,2'-bipyridine). Dissociation of - OR from the different octahedral Pd IV starting materials results in a common square-pyramidal Pd IV cation. An S N 2-type attack by - OR ( - OR = phenoxide, acetate, difluoroacetate, and nitrate) then leads to C(sp 3 )-OR bond formation. In contrast, when - OR = triflate, concerted C(sp 3 )-C(sp 2 ) bond-forming reductive elimination takes place, and the calculations indicate this outcome is the result of thermodynamic rather than kinetic control. The energy requirements for the dissociation and S N 2 steps with different - OR follow opposing trends. The S N 2 transition states exhibit "PdCO" angles in a tight range of 151.5 to 153.0°, resulting from steric interactions between the oxygen atom and the gem-dimethyl group of the ligand. Conformational effects for various OR ligands and isomerisation of the complexes were also examined as components of the solution dynamics in these systems. In all cases, the trends observed computationally agree with those observed experimentally.

Growth behavior of surface cracks in pipeline steels exposed to near-neutral pH environments

NASA Astrophysics Data System (ADS)

Egbewande, Afolabi Taiwo

We perform Restrained hybrid Monte Carlo simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H 2O) 7. We find that, like in the bulk, hydrofluoric acid, is a weak acid also in the cubic HF(H2O)7 cluster, and that its acidity is higher at lower T. This latter phenomenon has a (vibrational) entropic origin, namely it is due to the reduction of the (negative) TDeltaS contribution to the variation of free energy between the reactant and product. We found also a temperature dependence of the reactions mechanism. At low T (≤225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an Eigen ion H9O 4 +, then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, krp. We find that at very low T (≤75 K), krp depends strongly on the temperature, while it is almost constant at higher Ts. With respect to the bulk, the HF dissociation in HF(H2O)7 is about one order of magnitude faster. This is due to a lower free energy barrier for dissociation in the cluster.

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

Liu, Zongyuan; Senanayake, Sanjaya D.; Rodriguez, Jose A.

Bulk metallic nickel is a poor catalyst for the reforming of oxygenates being deactivated by the deposition of coke. In contrast, Ni-ceria is an active system for the catalytic extraction of H 2 from the ethanol steam reforming reaction (ESR, C 2H 5OH + 3H 2O ↔ 2CO 2 + 6H 2). Numerous studies, with model (well-defined crystal surfaces) and technical (high surface area powders) catalysts, have been devoted to understand the fundamental role of each catalyst component, the performance of adjacent sites in the metal-oxide interface, and the complex mechanistic steps that convert two oxygenated reactants (ethanol and Hmore » 2O) into H 2. The size and low loading of Ni on ceria facilitate metal-oxide support interactions that probably enhance the reactivity of the system. To establish the precise role of both Ni and Ce is challenging. However it is clear that both Ni and Ce are associated with the dissociation of H 2O (OH + H), while ceria readily adsorbs and partially dissociates ethanol (i.e. ethoxy formation). The most difficult step of Csingle bondC bond dissociation likely occurs only on Ni or at the Ni-Ce interface. H 2O and OH remain as important agents for the prevention of excess C build up during the Csingle bondH/Csingle bondC dissociation process. Often, deactivation upon C build up, is a direct result of Ni sintering and decoupling of the Ni-Ce interactions. One strategy to maintain good activity and stability is to protect the Ni-Ce interaction, and this can be achieved through the use of solid solutions (Ce 1–xNi xO 2–y) or by employing stabilizing agents such as W (Ni xW yCe zO 2). In this paper, we present and discuss the most recent work for the ESR reaction and show the important role of ceria which participates directly in the reaction and also enhances catalytic activity through metal-support interactions.« less

Laser photolysis studies of ω-bond dissociation in aromatic carbonyls with a C-C triple bond stimulated by triplet sensitization.

PubMed

Yamaji, Minoru; Horimoto, Ami; Marciniak, Bronislaw

2017-07-14

We have prepared three types of carbonyl compounds, benzoylethynylmethyl phenyl sulfide (2@SPh), (p-benzoyl)phenylethynylmethyl phenyl sulfide (3@SPh) and p-(benzoylethynyl)benzyl phenyl sulfide (4@SPh) with benzoyl and phenylthiylmethyl groups, which are interconnected with a C-C triple bond and a phenyl ring. Laser flash photolysis of 3@SPh and 4@SPh in acetonitrile provided the transient absorption spectra of the corresponding triplet states where no chemical reactions were recognized. Upon laser flash photolysis of 2@SPh, the absorption band due to the phenylthiyl radical (PTR) was obtained, indicating that the C-S bond cleaved in the excited state. Triplet sensitization of these carbonyl compounds using acetone and xanthone was conducted using laser photolysis techniques. The formation of triplet 3@SPh was seen in the transient absorption, whereas the PTR formation was observed for 2@SPh and 4@SPh, indicating that the triplet states were reactive for the C-S bond dissociation. The C-S bond dissociation mechanism for 4@SPh upon triplet sensitization is discussed in comparison with those for 2@SPh and 3@SPh.

Trapping-mediated dissociative chemisorption of C3H8 and C3D8 on Ir(110)

NASA Astrophysics Data System (ADS)

Kelly, D.; Weinberg, W. H.

1996-07-01

We have employed molecular beam techniques to investigate the molecular trapping and trapping-mediated dissociative chemisorption of C3H8 and C3D8 on Ir(110) at low beam translational energies, Ei≤5 kcal/mol, and surface temperatures, Ts, from 85 to 1200 K. For Ts=85 K, C3H8 is molecularly adsorbed on Ir(110) with a trapping probability, ξ, equal to 0.94 at Ei=1.6 kcal/mol and ξ=0.86 at Ei=5 kcal/mol. At Ei=1.9 kcal/mol and Ts=85 K, ξ of C3D8 is equal to 0.93. From 150 K to approximately 700 K, the initial probabilities of dissociative chemisorption of propane decrease with increasing Ts. For Ts from 700 to 1200 K, however, the initial probability of dissociative chemisorption maintains the essentially constant value of 0.16. These observations are explained within the context of a kinetic model which includes both C-H (C-D) and C-C bond cleavage. Below 450 K propane chemisorption on Ir(110) arises essentially solely from C-H (C-D) bond cleavage, an unactivated mechanism (with respect to a gas-phase energy zero) for this system, which accounts for the decrease in initial probabilities of chemisorption with increasing Ts. With increasing Ts, however, C-C bond cleavage, the activation energy of which is greater than the desorption energy of physically adsorbed propane, increasingly contributes to the measured probability of dissociative chemisorption. The activation energies, referenced to the bottom of the physically adsorbed molecular well, for C-H and C-C bond cleavage for C3H8 on Ir(110) are found to be Er,CH=5.3±0.3 kcal/mol and Er,CC=9.9±0.6 kcal/mol, respectively. The activation energies for C-D and C-C bond cleavage for C3D8 on Ir(110) are 6.3±0.3 kcal/mol and 10.5±0.6 kcal/mol, respectively. The desorption activation energy of propane from Ir(110) is approximately 9.5 kcal/mol. These activation energies are compared to activation energies determined recently for ethane and propane adsorption on Ir(111), Ru(001), and Pt(110)-(1×2), and ethane activation on Ir(110).

Does the tautomeric status of the adenine bases change upon the dissociation of the A*·A(syn) Topal-Fresco DNA mismatch? A combined QM and QTAIM atomistic insight.

PubMed

Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M

2014-02-28

We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A*·A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader's quantum theory of atoms in molecules. It was found that the A*·A(syn) ↔ A·A*(syn) tautomerisation is the asynchronous concerted process. It was established that the A*·A(syn) DNA mismatch is stabilized by the N6H···N6 (6.35) and N1H···N7 (6.17) hydrogen (H) bonds, whereas the A·A*(syn) base mispair (Cs) by the N6H···N6 (8.82) and N7H···N1 (9.78) H-bonds and the C8H···HC2 HH-bond (0.30 kcal mol(-1)). Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···N6 and N1H···N7/N7H···N1 H-bonds are anti-cooperative and mutually weaken each other in the A*·A(syn) and A·A*(syn) mispairs. It was revealed that the A·A*(syn) DNA mismatch is a dynamically unstable structure with a short lifetime of 1.12 × 10(-13) s and any of its 6 low-frequency intermolecular vibrations can develop during this period of time. This observation makes it impossible to change the tautomeric status of the A bases upon the dissociation of the A*·A(syn) base mispair into the monomers during DNA replication.

A Theoretical Study of the Photodissociation Mechanism of Cyanoacetylene in Its Lowest Singlet and Triplet Excited States

NASA Astrophysics Data System (ADS)

Luo, Cheng; Du, Wei-Na; Duan, Xue-Mei; Li, Ze-Sheng

2008-11-01

Cyanoacetylene (H5-C4 ≡ C3-C2 ≡ N1) is a minor constituent of the atmosphere of Titan, and its photochemistry plays an important role in the formation of the haze surrounding the satellite. In this paper, the complete active space self-consistent field (CASSCF) and multiconfigurational second-order perturbation (CASPT2) approaches are employed to investigate the photochemical processes for cyanoacetylene in its first singlet and triplet excited states with the cc-pVTZ basis set. Fissions of the C4-H5 and C2-C3 bonds in S1 yield H(2S) + CCCN(A2Π) and HCC(A2Π) + CN(X2Σ+), respectively. In T1, the corresponding dissociation products are H(2S) + CCCN(X2Σ+) and HCC(X2Σ) + CN(X2Σ+). At the CASPT2(14,13)//CASSCF(14,13) + ZPE level, the barriers for the adiabatic dissociation of the C4-H5 and C2-C3 bonds are 6.11 and 6.94 eV in S1 and 5.71 and 6.39 eV in T1, respectively, taking the energy of S0 minimum as reference. Based on the calculated potential energy surfaces, the existence of a metastable excited molecule is anticipated upon 260-230 nm photoexcitation, which provides a probable approach for cyanoacetylene to polymerize. The internal conversion (IC) process through vibronic interaction followed by C4-H5 fission in the ground state is found to account for the observed diffuse character in the UV absorption spectrum below 240 nm.

Surface chemistry of PH 3, PF 3 and PCl 3 on Ru(0001)

NASA Astrophysics Data System (ADS)

Tao, H.-S.; Diebold, U.; Shinn, N. D.; Madey, T. E.

1994-06-01

The adsorption, desorption and decomposition of PH 3, PF 3 and PCl 3 on Ru(0001) have been studied by soft X-ray photoelectron spectroscopy (SXPS) using synchrotron radiation. Due to large chemical shifts in the P 2p core levels, different phosphorus containing surface species can be identified. We find that PF 3 adsorbs molecularly on Ru(0001) at 80 and 300 K. At 80 K, PH 3 saturates the surface with one layer of atomic hydrogen, elemental phosphorus, subhydride (i.e., PHx (0 < x < 3)) and PH 3, with a total phosphorus coverage of 0.4 ML. At 300 K, PH 3 decomposes into atomic hydrogen and elemental phosphorus with a phosphorus coverage of 0.8 ML. At 80 K, PCl 3 adsorbs dissociatively into atomic chlorine, elemental phosphorus, PCl and possibly PCl 2 and PCl 3 in the first monolayer. Formation of multilayers of PCl 3 is observed at 80 K. At 300 K, PCl 3 adsorbs dissociatively as atomic chlorine and elemental phosphorus with a saturation phosphorus coverage of 0.1 ML. The variation in total phosphorus uptake at 300 K from PX3 ( X = H, FandCl) adsorption is a result of competition between site blocking by dissociation fragments and displacement reactions. Annealing surfaces with adsorbed phosphorus to 1000 K results in formation of RuzP ( z = 1 or 2), which is manifested by the chemical shifts in the P2p core level, as well as the P LVV Auger transition. The recombination of adsorbed phosphorus and adsorbed X ( = H, FandCl) from decomposition is also observed, but is a minor reaction channel on the surface. Thermochemical data are used to analyze the different stabilities of PX 3 at 300 K, namely, PF 3 adsorbs molecularly and PH 3 and PCl 3 dissociate completely. First, we compare the heat of molecular adsorption and the heat of dissociative adsorption of PX 3 on Ru(0001), using an enthalpy approach, and find results consistent with experimental observations. Second, we compare the total bond energy difference between molecular adsorption and complete dissociation of PX 3 on Ru(0001). In particular, we apply Shustorovich's bond-order conservation-Morse potential (BOC-MP) method to estimate the heat of adsorption for PH 3 and PCl 3 and the bond energies of the relaxed P-X bonds of the adsorbed PX 3 on the surface. The bond strength difference among the relaxed P-X bonds (i.e., the relaxed P-F bond ( 475 {kJ}/{mol}) is much stronger than either the relaxed P-H bond ( 287 {kJ}/{mol}) or the relaxed P-Cl bond ( 288 {kJ}/{mol})) suggests that PF 3 is more stable than PH 3 and PCl 3 on Ru(0001) at 300 K. These values are used to evaluate the total bond energy differences between molecular adsorption and complete dissociation for each of the PX 3, and the results agree with the experimental trends.

A density functional theory model of mechanically activated silyl ester hydrolysis

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

Pill, Michael F.; Schmidt, Sebastian W.; Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel

2014-01-28

To elucidate the mechanism of the mechanically activated dissociation of chemical bonds between carboxymethylated amylose (CMA) and silane functionalized silicon dioxide, we have investigated the dissociation kinetics of the bonds connecting CMA to silicon oxide surfaces with density functional calculations including the effects of force, solvent polarizability, and pH. We have determined the activation energies, the pre-exponential factors, and the reaction rate constants of candidate reactions. The weakest bond was found to be the silyl ester bond between the silicon and the alkoxy oxygen atom. Under acidic conditions, spontaneous proton addition occurs close to the silyl ester such that neutralmore » reactions become insignificant. Upon proton addition at the most favored position, the activation energy for bond hydrolysis becomes 31 kJ mol{sup −1}, which agrees very well with experimental observation. Heterolytic bond scission in the protonated molecule has a much higher activation energy. The experimentally observed bi-exponential rupture kinetics can be explained by different side groups attached to the silicon atom of the silyl ester. The fact that different side groups lead to different dissociation kinetics provides an opportunity to deliberately modify and tune the kinetic parameters of mechanically activated bond dissociation of silyl esters.« less

Theoretical aspects of methyl acetate and methanol activation on MgO(100) and (501) catalyst surfaces with application in FAME production

NASA Astrophysics Data System (ADS)

Man, Isabela-Costinela; Soriga, Stefan Gabriel; Parvulescu, Vasile

2017-01-01

Density functional theory (DFT) calculations were carried out to study the activation of methyl acetate and methanol on MgO(100) and MgO(501) surfaces and integrated in the context of transesterification, interesterification and glycerolysis reactions used in biodiesel industry. First results indicate the importance of including of dispersion forces in the calculations. On MgO(100) the reverse reactions steps of Csbnd O and Csbnd H dissociations and on MgO(501) the same reverse reaction step of Csbnd H dissociations of methyl acetate are energetically favorable, while the dissociation of Csbnd O bond into methoxide and acetate fragments on the edge of MgO(501) was found to be exothermic with a low activation energy. For methanol, the dissociation of Osbnd H bond on MgO(100) surface in the presence of the second coadsorbed methanol molecule becomes more energetically favoured compared to the isolated molecule, due to the fact that the methoxide fragment is stabilized by intermolecular hydrogen bonding. This is reflected by the decrease of the activation energy of the forward reaction step and the increase of the activation energy of the backward reaction step, increasing the probability to have dissociated molecules among the undissociated ones. These results represent a step forward for better understanding from atomistic point of view the paths of these reactions on these surfaces for the corresponding catalytic processes.

The adsorption and thermal decomposition of PH 3 on Si(111)-(7 × 7)

NASA Astrophysics Data System (ADS)

Taylor, P. A.; Wallace, R. M.; Choyke, W. J.; Yates, J. T.

1990-11-01

The adsorption of PH 3, on Si(111)-(7 × 7) has been studied by Auger electron spectroscopy and temperature programmed desorption. PH 3 was found to exhibit two kinds of behavior on the surface. A small surface coverage of molecularly adsorbed PH 3 desorbs without any dissociative surface chemistry. For the majority of the adsorbed PH x species (3 ⩾ x ⩾ 1) dissociation occurs to form P(a) and H(a). At 120 K, PH 3 initially adsorbs as the reactive species with a sticking coefficient of S ≅ 1 up to ˜75% saturation. The reactive PH x species surface concentration saturates at (1.9 ± 0.3) × 10 14 PH x cm -2. Surface H(a), produc thermal decomposition, desorbs as H 2(g) at T > 700 K., and P(a) desorbs as P 2(g) at T > 900 K. Capping the Si-dangling bonds with atomic deuterium prevents PH 3 adsorption, indicating that the dangling bonds are the PH 3 adsorption sites. Isotopic studies involving Si-D surface species mixed with adsorbed PH x species indicate that PH 3 desorption does not occur through a recombination process. Finally, additional PH 3 may be adsorbed if the surface hydrogen produced by dissociation of PH 3 is removed. Evidence for P penetration into bulk Si(111) at 875 K is presented.

Influence of Brownian motion on blood platelet flow behavior and adhesive dynamics near a planar wall.

PubMed

Mody, Nipa A; King, Michael R

2007-05-22

We used the platelet adhesive dynamics computational method to study the influence of Brownian motion of a platelet on its flow characteristics near a surface in the creeping flow regime. Two important characterizations were done in this regard: (1) quantification of the platelet's ability to contact the surface by virtue of the Brownian forces and torques acting on it, and (2) determination of the relative importance of Brownian motion in promoting surface encounters in the presence of shear flow. We determined the Peclet number for a platelet undergoing Brownian motion in shear flow, which could be expressed as a simple linear function of height of the platelet centroid, H from the surface Pe (platelet) = . (1.56H + 0.66) for H > 0.3 microm. Our results demonstrate that at timescales relevant to shear flow in blood Brownian motion plays an insignificant role in influencing platelet motion or creating further opportunities for platelet-surface contact. The platelet Peclet number at shear rates >100 s-1 is large enough (>200) to neglect platelet Brownian motion in computational modeling of flow in arteries and arterioles for most practical purposes even at very close distances from the surface. We also conducted adhesive dynamics simulations to determine the effects of platelet Brownian motion on GPIbalpha-vWF-A1 single-bond dissociation dynamics. Brownian motion was found to have little effect on bond lifetime and caused minimal bond stressing as bond rupture forces were calculated to be less than 0.005 pN. We conclude from our results that, for the case of platelet-shaped cells, Brownian motion is not expected to play an important role in influencing flow characteristics, platelet-surface contact frequency, and dissociative binding phenomena under flow at physiological shear rates (>50 s(-1)).

Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX.

PubMed

Liu, Lin-Lin; Liu, Pei-Jin; Hu, Song-Qi; He, Guo-Qiang

2017-01-17

NO 2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10 -10  s -1 ) when the temperature was less than 1000 K.

Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX

NASA Astrophysics Data System (ADS)

Liu, Lin-Lin; Liu, Pei-Jin; Hu, Song-Qi; He, Guo-Qiang

2017-01-01

NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10-10 s-1) when the temperature was less than 1000 K.

UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture.

PubMed

Soorkia, Satchin; Dehon, Christophe; Kumar, S Sunil; Pedrazzani, Mélanie; Frantzen, Emilie; Lucas, Bruno; Barat, Michel; Fayeton, Jacqueline A; Jouvet, Christophe

2014-04-03

Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.

Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry

NASA Astrophysics Data System (ADS)

Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu

2017-07-01

Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.

Hydrogenated Benzene in Circumstellar Environments: Insights into the Photostability of Super-hydrogenated PAHs

NASA Astrophysics Data System (ADS)

Quitián-Lara, Heidy M.; Fantuzzi, Felipe; Nascimento, Marco A. C.; Wolff, Wania; Boechat-Roberty, Heloisa M.

2018-02-01

Polycyclic aromatic hydrocarbons (PAHs), comprised of fused benzene (C6H6) rings, emit infrared radiation (3–12 μm) due to the vibrational transitions of the C–H bonds of the aromatic rings. The 3.3 μm aromatic band is generally accompanied by the band at 3.4 μm assigned to the vibration of aliphatic C–H bonds of compounds such as PAHs with an excess of peripheral H atoms (H n –PAHs). Herein we study the stability of fully hydrogenated benzene (or cyclohexane, C6H12) under the impact of stellar radiation in the photodissociation region (PDR) of NGC 7027. Using synchrotron radiation and time-of-flight mass spectrometry, we investigated the ionization and dissociation processes at energy ranges of UV (10–200 eV) and soft X-rays (280–310 eV). Density Functional Theory (DFT) calculations were used to determine the most stable structures and the relevant low-lying isomers of singly charged C6H12 ions. Partial Ion Yield (PIY) analysis gives evidence of the higher tendency toward dissociation of cyclohexane in comparison to benzene. However, because of the high photoabsorption cross-section of benzene at the C1s resonance edge, its photodissociation and photoionization cross-sections are enhanced, leading to a higher efficiency of dissociation of benzene in the PDR of NGC 7027. We suggest that a similar effect is experienced by PAHs in X-ray photon-rich environments, which ultimately acts as an auxiliary protection mechanism of super-hydrogenated polycyclic hydrocarbons. Finally, we propose that the single photoionization of cyclohexane could enhance the abundance of branched molecules in interstellar and circumstellar media.

Photodissociation pathways and lifetimes of protonated peptides and their dimers

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

Aravind, G.; Klaerke, B.; Rajput, J.

2012-01-07

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA{sub n} (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of {approx}200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of {approx}2 {mu}s. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in themore » dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.« less

Electron-impact dissociative excitation and ionization of N{sub 2}D{sup +}

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

Fogle, M.; Bahati, E. M.; Bannister, M. E.

Absolute cross sections for electron-impact dissociation of N{sub 2}D{sup +} producing N{sub 2}{sup +}, ND{sup +}, and N{sup +} ion fragments were measured in the 5- to 100-eV range using a crossed electron-ion beams technique. In the 5- to 20-eV region, in which dissociative excitation (DE) is the principal contributing mechanism, N{sub 2}{sup +} production dominates. The N{sub 2}{sup +} + D dissociation channel shows a large resonant-like structure in the DE cross section, as observed previously in electron impact dissociation of triatomic dihydride species [M. Fogle, E. M. Bahati, M. E. Bannister, S. H. M. Deng, C. R. Vane,more » R. D. Thomas, and V. Zhaunerchyk, Phys. Rev. A 82, 042720 (2010)]. In the dissociative ionization (DI) region, 20- to 100-eV, N{sub 2}{sup +}, ND{sup +}, and N{sup +} ion fragment production are comparable. The observance of the ND{sup +} and N{sup +} ion fragments indicate breaking of the N - N bond along certain dissociation channels.« less

Elucidating the interaction between Ni and CeO x in ethanol steam reforming catalysts: A perspective of recent studies over model and powder systems

DOE PAGES

Liu, Zongyuan; Senanayake, Sanjaya D.; Rodriguez, Jose A.

2016-11-15

Bulk metallic nickel is a poor catalyst for the reforming of oxygenates being deactivated by the deposition of coke. In contrast, Ni-ceria is an active system for the catalytic extraction of H 2 from the ethanol steam reforming reaction (ESR, C 2H 5OH + 3H 2O ↔ 2CO 2 + 6H 2). Numerous studies, with model (well-defined crystal surfaces) and technical (high surface area powders) catalysts, have been devoted to understand the fundamental role of each catalyst component, the performance of adjacent sites in the metal-oxide interface, and the complex mechanistic steps that convert two oxygenated reactants (ethanol and Hmore » 2O) into H 2. The size and low loading of Ni on ceria facilitate metal-oxide support interactions that probably enhance the reactivity of the system. To establish the precise role of both Ni and Ce is challenging. However it is clear that both Ni and Ce are associated with the dissociation of H 2O (OH + H), while ceria readily adsorbs and partially dissociates ethanol (i.e. ethoxy formation). The most difficult step of Csingle bondC bond dissociation likely occurs only on Ni or at the Ni-Ce interface. H 2O and OH remain as important agents for the prevention of excess C build up during the Csingle bondH/Csingle bondC dissociation process. Often, deactivation upon C build up, is a direct result of Ni sintering and decoupling of the Ni-Ce interactions. One strategy to maintain good activity and stability is to protect the Ni-Ce interaction, and this can be achieved through the use of solid solutions (Ce 1–xNi xO 2–y) or by employing stabilizing agents such as W (Ni xW yCe zO 2). In this paper, we present and discuss the most recent work for the ESR reaction and show the important role of ceria which participates directly in the reaction and also enhances catalytic activity through metal-support interactions.« less

Influence of Brownian Motion on Blood Platelet Flow Behavior and Adhesive Dynamics near a Planar Wall

PubMed Central

Mody, Nipa A.; King, Michael R.

2008-01-01

We used the Platelet Adhesive Dynamics computational method to study the influence of Brownian motion of a platelet on its flow characteristics near a surface in the creeping flow regime. Two important characterizations were done in this regard: (1) quantification of the platelet’s ability to contact the surface by virtue of the Brownian forces and torques acting on it, and (2) determination of the relative importance of Brownian motion in promoting surface encounters in the presence of shear flow. We determined the Peclet number for a platelet undergoing Brownian motion in shear flow, which could be expressed as a simple linear function of height of the platelet centroid, H from the surface Pe (platelet) = γ. · (1.56H + 0.66) for H > 0.3 μm. Our results demonstrate that at timescales relevant to shear flow in blood, Brownian motion plays an insignificant role in influencing platelet motion or creating further opportunities for platelet-surface contact. The platelet Peclet number at shear rates > 100 s-1 is large enough (> 200) to neglect platelet Brownian motion in computational modeling of flow in arteries and arterioles for most practical purposes even at very close distances from the surface. We also conducted adhesive dynamics simulations to determine the effects of platelet Brownian motion on GPIbα-vWF-A1 single-bond dissociation dynamics. Brownian motion was found to have little effect on bond lifetime and caused minimal bond stressing as bond rupture forces were calculated to be less than 0.005 pN. We conclude from our results that for the case of platelet-shaped cells, Brownian motion is not expected to play an important role in influencing flow characteristics, platelet-surface contact frequency and dissociative binding phenomena under flow at physiological shear rates (> 50 s-1). PMID:17417890

Performance of an integrated approach for prediction of bond dissociation enthalpies of phenols extracted from ginger and tea

NASA Astrophysics Data System (ADS)

Nam, Pham Cam; Chandra, Asit K.; Nguyen, Minh Tho

2013-01-01

Integration of the (RO)B3LYP/6-311++G(2df,2p) with the PM6 method into a two-layer ONIOM is found to produce reasonably accurate BDE(O-H)s of phenolic compounds. The chosen ONIOM model contains only two atoms of the breaking bond as the core zone and is able to provide reliable evaluation for BDE(O-H) for phenols and tocopherol. Deviation of calculated values from experiment is ±(1-2) kcal/mol. BDE(O-H) of several curcuminoids and flavanoids extracted from ginger and tea are computed using the proposed model. The BDE(O-H) values of enol curcumin and epigallocatechin gallate are predicted to be 83.3 ± 2.0 and 76.0 ± 2.0 kcal/mol, respectively.

Competitive fragmentation pathways of acetic acid dimer explored by synchrotron VUV photoionization mass spectrometry and electronic structure calculations.

PubMed

Guan, Jiwen; Hu, Yongjun; Zou, Hao; Cao, Lanlan; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi

2012-09-28

In present study, photoionization and dissociation of acetic acid dimers have been studied with the synchrotron vacuum ultraviolet photoionization mass spectrometry and theoretical calculations. Besides the intense signal corresponding to protonated cluster ions (CH(3)COOH)(n)·H(+), the feature related to the fragment ions (CH(3)COOH)H(+)·COO (105 amu) via β-carbon-carbon bond cleavage is observed. By scanning photoionization efficiency spectra, appearance energies of the fragments (CH(3)COOH)·H(+) and (CH(3)COOH)H(+)·COO are obtained. With the aid of theoretical calculations, seven fragmentation channels of acetic acid dimer cations were discussed, where five cation isomers of acetic acid dimer are involved. While four of them are found to generate the protonated species, only one of them can dissociate into a C-C bond cleavage product (CH(3)COOH)H(+)·COO. After surmounting the methyl hydrogen-transfer barrier 10.84 ± 0.05 eV, the opening of dissociative channel to produce ions (CH(3)COOH)(+) becomes the most competitive path. When photon energy increases to 12.4 eV, we also found dimer cations can be fragmented and generate new cations (CH(3)COOH)·CH(3)CO(+). Kinetics, thermodynamics, and entropy factors for these competitive dissociation pathways are discussed. The present report provides a clear picture of the photoionization and dissociation processes of the acetic acid dimer in the range of the photon energy 9-15 eV.

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo.

PubMed

Schnier, P D; Klassen, J S; Strittmatter, E F; Williams, E R

1998-09-23

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.

Bond-selective photodissociation of partially deuterated ammonia molecules: Photodissociations of vibrationally excited NHD2 in the 5νNH state and NH2D in the 5νND state

NASA Astrophysics Data System (ADS)

Akagi, Hiroshi; Yokoyama, Keiichi; Yokoyama, Atsushi

2004-03-01

Ultraviolet photodissociation of NHD2 excited to the fourth overtone state of the NH stretching mode (5νNH) and NH2D excited to that of the ND stretching mode (5νND) has been investigated by using a crossed laser and molecular beams method. Branching ratio between the NH and ND bond dissociations has been determined by utilizing a (2+1) resonance enhanced multiphoton ionization scheme of H and D atoms. For the photolysis of NHD2 in the 5νNH state, the NH dissociation cross section is 5.1±1.4 times as large as the ND dissociation cross section per bond. On the other hand, for the photolysis of NH2D in the 5νND state, the ratio of the NH dissociation cross section per bond to the ND dissociation cross section decreases to 0.68±0.16. In comparison with the branching ratios for the photolysis of vibrationally unexcited NH2D and NHD2 [Koda and Back, Can. J. Chem. 55, 1380 (1977)], the present results indicate that the excitation of the NH stretching mode enhances the NH dissociation with ca. two times larger NH/ND branching ratio, whereas the excitation of the ND stretching mode results in the preferential ND dissociation with ca. 3-4 times larger ND/NH branching ratio than that for the vibrational ground states. The mechanism of the bond-selective enhancement has been discussed in terms of the energetics and dynamics of wave packet.

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity.

PubMed

Garratt, Shaun A; Hughes, Russell P; Kovacik, Ivan; Ward, Antony J; Willemsen, Stefan; Zhang, Donghui

2005-11-09

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.

Quantum-state-resolved reactivity of overtone excited CH 4 on Ni(111): Comparing experiment and theory

DOE PAGES

Hundt, P. Morten; van Reijzen, Maarten E.; Beck, Rainer D.; ...

2017-02-07

Quantum state resolved reactivity measurements probe the role of vibrational symmetry on the vibrational activation of the dissociative chemisorption of CH 4 on Ni(111). IR-IR double resonance excitation in a molecular beam was used to prepare CH 4 in three different vibrational symmetry components A 1, E, and F 2 of the 2ν 32 antisymmetric stretch overtone vibration as well as in the ν1+ν3 symmetric plus antisymmetric C-H stretch combination band of F 2 symmetry. We measured the quantum state specific dissociation probability S 0 (sticking coefficient) for each of the four vibrational states by detecting chemisorbed carbon on Ni(111)more » as the product of CH 4 dissociation by Auger electron spectroscopy. We also observe strong mode specificity, where S 0 for the most reactive state ν 1+ν 3 is an order of magnitude higher than for the least reactive, more energetic 2ν 3-E state. Our first principles quantum scattering calculations show that as molecules in the ν1 state approach the surface, the vibrational amplitude becomes localized on the reacting C-H bond, making them very reactive. We found that this behavior results from the weakening of the reacting C-H bond as the molecule approaches the surface, decoupling its motion from the three non-reacting C-H stretches. Similarly, we find that overtone normal mode states with more ν 1 character are more reactive: S 0(2ν 1) > S 0(ν 1+ν 3) > S 0(2ν 3). The 2ν 3 eigenstates excited in the experiment can be written as linear combinations of these normal mode states. The highly reactive 2ν 1 and ν 1+ν 3 normal modes, being of A 1 and F 2 symmetry, can contribute to the 2ν 3-A 1 and 2ν 3-F 2 eigenstates, respectively, boosting their reactivity over the E component, which contains no ν 1 character due to symmetry.« less

Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C 2H 4, C 2H 3F, and 1,1-C 2H 2F 2) near and above threshold

DOE PAGES

Gaire, B.; Gatton, A. S.; Wiegandt, F.; ...

2016-09-14

We have investigated bond-rearrangement driven by photo-double-ionization (PDI) near and above the double ionization threshold in a sequence of carbon-carbon double bonded hydrocarbon molecules: ethylene, fluoroethylene, and 1,1-difluoroethylene. We employ the kinematically complete cold target recoil ion momentum spectroscopy (COLTRIMS) method to resolve all photo-double-ionization events leading to two-ionic fragments. We observe changes in the branching ratios of different dissociative ionization channels depending on the presence of none, one, or two fluorine atoms. The role of the fluorine atom in the bond-rearrangement channels is intriguing as evident by the re-ordering of the threshold energies of the PDI in the fluorinatedmore » molecules. These effects offer a compelling argument that the electronegativity of the fluorine (or the polarity of the molecule) strongly influences the potential energy surfaces of the molcules and drives bond-rearrangement during the dissociation process. The energy sharing and the relative angle between the 3D-momentum vectors of the two electrons provide clear evidence of direct and indirect PDI processes.« less

Competing 1πσ* mediated dynamics in mequinol: O-H versus O-CH3 photodissociation pathways.

PubMed

Hadden, David J; Roberts, Gareth M; Karsili, Tolga N V; Ashfold, Michael N R; Stavros, Vasilios G

2012-10-14

Deactivation of excited electronic states through coupling to dissociative (1)πσ* states in heteroaromatic systems has received considerable attention in recent years, particularly as a mechanism that contributes to the ultraviolet (UV) photostability of numerous aromatic biomolecules and their chromophores. Recent studies have expanded upon this work to look at more complex species, which involves understanding competing dynamics on two different (1)πσ* potential energy surfaces (PESs) localized on different heteroatom hydride coordinates (O-H and N-H bonds) within the same molecule. In a similar spirit, the work presented here utilizes ultrafast time-resolved velocity map ion imaging to study competing dissociation pathways along (1)πσ* PESs in mequinol (p-methoxyphenol), localized at O-H and O-CH(3) bonds yielding H atoms or CH(3) radicals, respectively, over an excitation wavelength range of 298-238 nm and at 200 nm. H atom elimination is found to be operative via either tunneling under a conical intersection (CI) (298 ≥ λ ≥ 280 nm) or ultrafast internal conversion through appropriate CIs (λ ≤ 245 nm), both of which provide mechanisms for coupling onto the dissociative state associated with the O-H bond. In the intermediate wavelength range of 280 ≥ λ ≥ 245 nm, mediated H atom elimination is not observed. In contrast, we find that state driven CH(3) radical elimination is only observed in the excitation range 264 ≥ λ ≥ 238 nm. Interpretation of these experimental results is guided by: (i) high level complete active space with second order perturbation theory (CASPT2) calculations, which provide 1-D potential energy cuts of the ground and low lying singlet excited electronic states along the O-H and O-CH(3) bond coordinates; and (ii) calculated excitation energies using CASPT2 and the equation-of-motion coupled cluster with singles and doubles excitations (EOM-CCSD) formalism. From these comprehensive studies, we find that the dynamics along the O-H coordinate generally mimic H atom elimination previously observed in phenol, whereas O-CH(3) bond fission in mequinol appears to present notably different behavior to the CH(3) elimination dynamics previously observed in anisole (methoxybenzene).

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

PubMed

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

2017-04-18

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

Gas-Phase and Solution-Phase Homolytic Bond Dissociation Energies of H-N(+) Bonds in the Conjugate Acids of Nitrogen Bases.

PubMed

Liu, Wei-Zhong; Bordwell, Frederick G.

1996-07-12

The oxidation potentials of 19 nitrogen bases (abbreviated as B: six primary amines, five secondary amines, two tertiary amines, three anilines, pyridine, quinuclidine, and 1,4-diazabicyclo[2,2,2]octane), i.e., E(ox)(B) values in dimethyl sulfoxide (DMSO) and/or acetonitrile (AN), have been measured. Combination of these E(ox)(B) values with the acidity values of the corresponding acids (pK(HB)(+)) in DMSO and/or AN using the equation: BDE(HB)(+) = 1.37pK(HB)(+) + 23.1 E(ox)(B) + C (C equals 59.5 kcal/mol in AN and 73.3 kcal/mol in DMSO) gave estimates of solution phase homolytic bond dissociation energies of H-B(+) bonds. Gas-phase BDE values of H-B(+) bonds were estimated from updated proton affinities (PA) and adiabatic ionization potentials (aIP) using the equation, BDE(HB(+))(g) = PA + aIP - 314 kcal/mol. The BDE(HB)(+) values estimated in AN were found to be 5-11 kcal/mol higher than the corresponding gas phase BDE(HB(+))(g) values. These bond-strengthening effects in solution are interpreted as being due to the greater solvation energy of the HB(+) cation than that of the B(+*) radical cation.

The electrooxidation mechanism of formic acid on platinum and on lead ad-atoms modified platinum studied with the kinetic isotope effect

NASA Astrophysics Data System (ADS)

Bełtowska-Brzezinska, M.; Łuczak, T.; Stelmach, J.; Holze, R.

2014-04-01

Kinetics and mechanism of formic acid (FA) oxidation on platinum and upd-lead ad-atoms modified platinum electrodes have been studied using unlabelled and deuterated compounds. Poisoning of the electrode surface by CO-like species was prevented by suppression of dissociative chemisorption of FA due to a fast competitive underpotential deposition of lead ad-atoms on the Pt surface from an acidic solution containing Pb2+ cations. Modification of the Pt electrode with upd lead induced a catalytic effect in the direct electrooxidation of physisorbed FA to CO2. With increasing degree of H/D substitution, the rate of this reaction decreased in the order: HCOOH > DCOOH ≥ HCOOD > DCOOD. HCOOH was oxidized 8.5-times faster on a Pt/Pb electrode than DCOOD. This primary kinetic isotope effect proves that the C-H- and O-H-bonds are simultaneously cleaved in the rate determining step. A secondary kinetic isotope effect was found in the dissociative chemisorption of FA in the hydrogen adsorption-desorption range on a bare Pt electrode after H/D exchange in the C-H bond, wherein the influence of deuterium substitution in the O-H group was negligibly small. Thus the C-H bond cleavage is accompanied by the C-OH and not the O-H bond split in the FA decomposition, producing CO-like species on the Pt surface sites.

Efficient dehydrogenation of formic acid using Al12N12 nanocage: A DFT study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Nurazar, Roghaye

2014-11-01

We have studied the adsorption and decomposition of formic acid (HCOOH) on the surface of Al12N12 fullerene-like nanocage using density functional theory. Different adsorption modes were found for HCOOH on the Al12N12, i.e. molecular and dissociative monodentate or bidentate adsorption. Three reaction pathways were proposed to understand gas-phase HCOOH decomposition on the Al12N12 nanocage. Our results reveal that for the decomposition of HCOOH into CO2 and H2, the most favorable pathway should be the Csbnd H bond activation reaction. The reaction energies and the activation barriers obtained here suggest that for the dissociative adsorption configuration on the Al12N12 surface, the rate-determining step is the Csbnd H bond breaking.

Methane steam reforming rates over Pt, Rh and Ni(111) accounting for H tunneling and for metal lattice vibrations

NASA Astrophysics Data System (ADS)

German, Ernst D.; Sheintuch, Moshe

2017-02-01

Microkinetic models of methane steam reforming (MSR) over bare platinum and rhodium (111) surfaces are analyzed in present work using calculated rate constants. The individual rate constants are classified into three different sets: (i) rate constants of adsorption and desorption steps of CH4, H2O, CO and of H2; (ii) rate constants of dissociation and formation of A-H bonds (A = C, O, and H), and (iii) rate constants of dissociation and formation of C-O bond. The rate constants of sets (i) and (iii) are calculated using transition state theory and published thermochemical data. The rate constants of H-dissociation reactions (set (ii)) are calculated in terms of a previously-developed approach that accounts for thermal metal lattice vibrations and for H tunneling through a potential barrier of height which depends on distance of AH from a surface. Pre-exponential factors of several group (ii) steps were calculated to be usually lower than the traditional kBT/h due to tunneling effect. Surface composition and overall MSR rates over platinum and rhodium surfaces are compared with those over nickel surface showing that operating conditions strongly affect on the activity order of the catalysts.

Bond strengths of toluenes, anilines, and phenols: to hammett or not.

PubMed

Pratt, Derek A; DiLabio, Gino A; Mulder, Peter; Ingold, K U

2004-05-01

The Hammett equation correlates the effects of Y on many different chemical properties of YC(6)H(4)ZX families of compounds. One of the most surprising is that the Z-X bond dissociation enthalpy (BDE), a homolytic property, can be correlated for some 4-YC(6)H(4)ZX families with electrophilic substituent constants, sigma(p)(+)(Y), which were largely derived from the rates of the heterolytic S(N)1 solvolyses of para-substituted cumyl chlorides. Although there is no Hammett correlation of the C-X BDEs in 4-YC(6)H(4)CH(2)X (X = H, halide, OPh) families, there are good correlations of N-X BDEs with sigma(p)(+)(Y) in 4-YC(6)H(4)NHX (X = H, CH(3), OH, F) and excellent correlations of O-X BDEs with sigma(p)(+)(Y) in 4-YC(6)H(4)OX (X = H, CH(3), CH(2)Ph) families. The reasons for this varied behavior are discussed.

Decontamination of 2-Chloroethyl Ethyl Sulfide by Pulsed Corona Plasma

NASA Astrophysics Data System (ADS)

Li, Zhanguo; Hu, Zhen; Cao, Peng; Zhao, Hongjie

2014-11-01

Decontamination of 2-chloroethyl ethyl sulfide (2-CEES, CH3CH2SCH2CH2Cl) by pulsed corona plasma was investigated. The results show that 212.6 mg/m3 of 2-CEES, with the gas flow rate of 2 m3/h, can be decontaminated to 0.09 mg/m3. According to the variation of the inlet and outlet concentration of 2-CEES vapor with retention time, it is found that the reaction of 2-CEES in a pulsed corona plasma system follows the first order reaction, with the reaction rate constant of 0.463 s-1. The decontamination mechanism is discussed based on an analysis of the dissociation energy of chemical bonds and decontamination products. The C-S bond adjacent to the Cl atom will be destroyed firstly to form CH3CH2S· and ·CH2CH2Cl radicals. CH3CH2S· can be decomposed to ·C2H5 and ·S. ·S can be oxidized to SO2, while ·C2H5 can be finally oxidized to CO2 and H2O. The C-Cl bond in the ·CH2CH2Cl radical can be destroyed to form ·CH2CH2. and ·Cl, which can be mineralized to CO2, H2O and HCl. The H atom in the ·CH2CH2Cl radical can also be substituted by ·Cl to form CHCl2-CHCl2.

Shape-programmed nanofabrication: understanding the reactivity of dichalcogenide precursors.

PubMed

Guo, Yijun; Alvarado, Samuel R; Barclay, Joshua D; Vela, Javier

2013-04-23

Dialkyl and diaryl dichalcogenides are highly versatile and modular precursors for the synthesis of colloidal chalcogenide nanocrystals. We have used a series of commercially available dichalcogenide precursors to unveil the molecular basis for the outcome of nanocrystal preparations, more specifically, how precursor molecular structure and reactivity affect the final shape and size of II-VI semiconductor nanocrystals. Dichalcogenide precursors used were diallyl, dibenzyl, di-tert-butyl, diisopropyl, diethyl, dimethyl, and diphenyl disulfides and diethyl, dimethyl, and diphenyl diselenides. We find that the presence of two distinctively reactive C-E and E-E bonds makes the chemistry of these precursors much richer and interesting than that of other conventional precursors such as the more common phosphine chalcogenides. Computational studies (DFT) reveal that the dissociation energy of carbon-chalcogen (C-E) bonds in dichalcogenide precursors (R-E-E-R, E=S or Se) increases in the order (R): diallyl

Dissociative adsorption of a multifunctional compound on a semiconductor surface: a theoretical study of the adsorption of hydroxylamine on Ge(100).

PubMed

Park, Hyunkyung; Kim, Do Hwan

2018-06-06

The adsorption behavior of hydroxylamine on a Ge(100) surface was investigated using density functional theory (DFT) calculations. These calculations predicted that hydroxylamine, a multifunctional compound consisting of a hydroxyl group and an amine group, would initially become adsorbed through N-dative bonding, or alternatively through the hydroxyl group via O-H dissociative adsorption. An N-O dissociative reaction may also occur, mainly via N-dative molecular adsorption, and the N-O dissociative product was calculated to be the most stable of all the possible adsorption structures. The calculations furthermore indicated the formation of the N-O dissociative product from the N-dative structure to be nearly barrierless and the dissociated hydroxyl and amine groups to be bonded to two Ge atoms of adjacent Ge dimers. Simulated STM images suggested the change in electron density that would occur upon adsorption of hydroxylamine in various adsorption configurations, and specifically indicated the N-O dissociative product to have greater electron density around the amine groups, and the hydroxyl groups to mainly contribute electron density to the unoccupied electronic states.

Room-temperature activation of methane and dry re-forming with CO 2 on Ni-CeO 2 (111) surfaces: Effect of Ce 3+ sites and metal–support interactions on C–H bond cleavage

DOE PAGES

Lustemberg, Pablo G.; Ramírez, Pedro J.; Liu, Zongyuan; ...

2016-10-27

The results of core-level photoemission indicate that Ni-CeO 2(111) surfaces with small or medium coverages of nickel are able to activate methane at 300 K, producing adsorbed CH x and CO x (x = 2, 3) groups. Calculations based on density functional theory predict a relatively low activation energy of 0.6–0.7 eV for the cleavage of the first C–H bond in the adsorbed methane molecule. Ni and O centers of ceria work in a cooperative way in the dissociation of the C–H bond at room temperature, where a low Ni loading is crucial for the catalyst activity and stability. Themore » strong electronic perturbations in the Ni nanoparticles produced by the ceria supports of varying natures, such as stoichiometric and reduced, result in a drastic change in their chemical properties toward methane adsorption and dissociation as well as the dry reforming of methane reaction. Lastly, the coverage of Ni has a drastic effect on the ability of the system to dissociate methane and catalyze the dry re-forming process.« less

Room-temperature activation of methane and dry re-forming with CO 2 on Ni-CeO 2 (111) surfaces: Effect of Ce 3+ sites and metal–support interactions on C–H bond cleavage

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

Lustemberg, Pablo G.; Ramírez, Pedro J.; Liu, Zongyuan

The results of core-level photoemission indicate that Ni-CeO 2(111) surfaces with small or medium coverages of nickel are able to activate methane at 300 K, producing adsorbed CH x and CO x (x = 2, 3) groups. Calculations based on density functional theory predict a relatively low activation energy of 0.6–0.7 eV for the cleavage of the first C–H bond in the adsorbed methane molecule. Ni and O centers of ceria work in a cooperative way in the dissociation of the C–H bond at room temperature, where a low Ni loading is crucial for the catalyst activity and stability. Themore » strong electronic perturbations in the Ni nanoparticles produced by the ceria supports of varying natures, such as stoichiometric and reduced, result in a drastic change in their chemical properties toward methane adsorption and dissociation as well as the dry reforming of methane reaction. Lastly, the coverage of Ni has a drastic effect on the ability of the system to dissociate methane and catalyze the dry re-forming process.« less

Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin-binding protein A affect bond strength and fibronectin conformation

PubMed Central

Casillas-Ituarte, Nadia N.; Cruz, Carlos H. B.; Lins, Roberto D.; DiBartola, Alex C.; Howard, Jessica; Liang, Xiaowen; Höök, Magnus; Viana, Isabelle F. T.; Sierra-Hernández, M. Roxana; Lower, Steven K.

2017-01-01

The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands (e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous SNPs in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight 20-mer peptide variants containing amino acids Ala, Asn, Gln, His, Ile, and Lys at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 of FnBPA. Experimentally measured bond lifetimes (1/koff) and dissociation constants (Kd = koff/kon), determined by mechanically dissociating the Fn·peptide complex at loading rates relevant to the cardiovascular system, varied from the lowest-affinity H782A/K786A peptide (0.011 s, 747 μm) to the highest-affinity H782Q/K786N peptide (0.192 s, 15.7 μm). These atomic force microscopy results tracked remarkably well to metadynamics simulations in which peptide detachment was defined solely by the free-energy landscape. Simulations and SPR experiments suggested that an Fn conformational change may enhance the stability of the binding complex for peptides with K786I or H782Q/K786I (Kdapp = 0.2–0.5 μm, as determined by SPR) compared with the lowest-affinity double-alanine peptide (Kdapp = 3.8 μm). Together, these findings demonstrate that amino acid substitutions in Fn-binding repeat-9 can significantly affect bond strength and influence the conformation of Fn upon binding. They provide a mechanistic explanation for the observation of nonsynonymous SNPs in fnbA among clinical isolates of S. aureus that cause endovascular infections. PMID:28400484

Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin-binding protein A affect bond strength and fibronectin conformation.

PubMed

Casillas-Ituarte, Nadia N; Cruz, Carlos H B; Lins, Roberto D; DiBartola, Alex C; Howard, Jessica; Liang, Xiaowen; Höök, Magnus; Viana, Isabelle F T; Sierra-Hernández, M Roxana; Lower, Steven K

2017-05-26

The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands ( e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous SNPs in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight 20-mer peptide variants containing amino acids Ala, Asn, Gln, His, Ile, and Lys at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 of FnBPA. Experimentally measured bond lifetimes (1/ k off ) and dissociation constants ( K d = k off / k on ), determined by mechanically dissociating the Fn·peptide complex at loading rates relevant to the cardiovascular system, varied from the lowest-affinity H782A/K786A peptide (0.011 s, 747 μm) to the highest-affinity H782Q/K786N peptide (0.192 s, 15.7 μm). These atomic force microscopy results tracked remarkably well to metadynamics simulations in which peptide detachment was defined solely by the free-energy landscape. Simulations and SPR experiments suggested that an Fn conformational change may enhance the stability of the binding complex for peptides with K786I or H782Q/K786I ( K d app = 0.2-0.5 μm, as determined by SPR) compared with the lowest-affinity double-alanine peptide ( K d app = 3.8 μm). Together, these findings demonstrate that amino acid substitutions in Fn-binding repeat-9 can significantly affect bond strength and influence the conformation of Fn upon binding. They provide a mechanistic explanation for the observation of nonsynonymous SNPs in fnbA among clinical isolates of S. aureus that cause endovascular infections. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Hydropersulfides: H-Atom Transfer Agents Par Excellence.

PubMed

Chauvin, Jean-Philippe R; Griesser, Markus; Pratt, Derek A

2017-05-10

Hydropersulfides (RSSH) are formed endogenously via the reaction of the gaseous biotransmitter hydrogen sulfide (H 2 S) and disulfides (RSSR) and/or sulfenic acids (RSOH). RSSH have been investigated for their ability to store H 2 S in vivo and as a line of defense against oxidative stress, from which it is clear that RSSH are much more reactive to two-electron oxidants than thiols. Herein we describe the results of our investigations into the H-atom transfer chemistry of RSSH, contrasting it with the well-known H-atom transfer chemistry of thiols. In fact, RSSH are excellent H-atom donors to alkyl (k ∼ 5 × 10 8 M -1 s -1 ), alkoxyl (k ∼ 1 × 10 9 M -1 s -1 ), peroxyl (k ∼ 2 × 10 6 M -1 s -1 ), and thiyl (k > 1 × 10 10 M -1 s -1 ) radicals, besting thiols by as little as 1 order and as much as 4 orders of magnitude. The inherently high reactivity of RSSH to H-atom transfer is based largely on thermodynamic factors; the weak RSS-H bond dissociation enthalpy (∼70 kcal/mol) and the associated high stability of the perthiyl radical make the foregoing reactions exothermic by 15-34 kcal/mol. Of particular relevance in the context of oxidative stress is the reactivity of RSSH to peroxyl radicals, where favorable thermodynamics are bolstered by a secondary orbital interaction in the transition state of the formal H-atom transfer that drives the inherent reactivity of RSSH to match that of α-tocopherol (α-TOH), nature's premier radical-trapping antioxidant. Significantly, the reactivity of RSSH eclipses that of α-TOH in H-bond-accepting media because of their low H-bond acidity (α 2 H ∼ 0.1). This affords RSSH a unique versatility compared to other highly reactive radical-trapping antioxidants (e.g., phenols, diarylamines, hydroxylamines, sulfenic acids), which tend to have high H-bond acidities. Moreover, the perthiyl radicals that result are highly persistent under autoxidation conditions and undergo very rapid dimerization (k = 5 × 10 9 M -1 s -1 ) in lieu of reacting with O 2 or autoxidizable substrates.

Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

PubMed

Uddin, M; Coombe, D

2014-03-20

Molecular dynamics simulations of gas hydrate dissociation comparing the behavior of CH4 and CO2 hydrates are presented. These simulations were based on a structurally correct theoretical gas hydrate crystal, coexisting with water. The MD system was first initialized and stabilized via a thorough energy minimization, constant volume-temperature ensemble and constant volume-energy ensemble simulations before proceeding to constant pressure-temperature simulations for targeted dissociation pressure and temperature responses. Gas bubble evolution mechanisms are demonstrated as well as key investigative properties such as system volume, density, energy, mean square displacements of the guest molecules, radial distribution functions, H2O order parameter, and statistics of hydrogen bonds. These simulations have established the essential similarities between CH4 and CO2 hydrate dissociation. The limiting behaviors at lower temperature (no dissociation) and higher temperature (complete melting and formation of a gas bubble) have been illustrated for both hydrates. Due to the shift in the known hydrate stability curves between guest molecules caused by the choice of water model as noted by other authors, the intermediate behavior (e.g., 260 K) showed distinct differences however. Also, because of the more hydrogen-bonding capability of CO2 in water, as reflected in its molecular parameters, higher solubility of dissociated CO2 in water was observed with a consequence of a smaller size of gas bubble formation. Additionally, a novel method for analyzing hydrate dissociation based on H-bond breakage has been proposed and used to quantify the dissociation behaviors of both CH4 and CO2 hydrates. Activation energies Ea values from our MD studies were obtained and evaluated against several other published laboratory and MD values. Intrinsic rate constants were estimated and upscaled. A kinetic reaction model consistent with macroscale fitted kinetic models has been proposed to indicate the macroscopic consequences of this analysis.

A Molecular Dynamics Simulation of the Human Lysozyme – Camelid VHH HL6 Antibody System

PubMed Central

Su, Zhi-Yuan; Wang, Yeng-Tseng

2009-01-01

Amyloid diseases such as Alzheimer’s and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able to combat against wild-type human lysozyme for inhibiting in-vitro aggregations of the amyloidogenic variant (D67H). The present study is aimed at elucidating the unbinding mechanics between the D67H lysozyme and VHH HL6 antibody fragment by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different pulling velocities. The results of the simulation indicated that stretching forces of more than two nano Newton (nN) were required to dissociate the proteinantibody system, and the hydrogen bond dissociation pathways were computed. PMID:19468335

Partially linearized external models to active-space coupled-cluster through connected hextuple excitations.

PubMed

Xu, Enhua; Ten-No, Seiichiro L

2018-06-05

Partially linearized external models to active-space coupled-cluster through hextuple excitations, for example, CC{SDtqph} L , CCSD{tqph} L , and CCSD{tqph} hyb, are implemented and compared with the full active-space CCSDtqph. The computational scaling of CCSDtqph coincides with that for the standard coupled-cluster singles and doubles (CCSD), yet with a much large prefactor. The approximate schemes to linearize the external excitations higher than doubles are significantly cheaper than the full CCSDtqph model. These models are applied to investigate the bond dissociation energies of diatomic molecules (HF, F 2 , CuH, and CuF), and the potential energy surfaces of the bond dissociation processes of HF, CuH, H 2 O, and C 2 H 4 . Among the approximate models, CCSD{tqph} hyb provides very accurate descriptions compared with CCSDtqph for all of the tested systems. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Molecular Mechanisms, Thermodynamics, and Dissociation Kinetics of Knob-Hole Interactions in Fibrin*

PubMed Central

Kononova, Olga; Litvinov, Rustem I.; Zhmurov, Artem; Alekseenko, Andrey; Cheng, Chia Ho; Agarwal, Silvi; Marx, Kenneth A.; Weisel, John W.; Barsegov, Valeri

2013-01-01

Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs ‘A’ and ‘B’ in the central nodule of fibrin monomer to complementary holes ‘a’ and ‘b’ in the γ- and β-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using molecular dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob ‘A’ mimetic) and GHRP (knob ‘B’ mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; however, the dissociation kinetics were sensitive to variations in acidity (pH 5–7) and temperature (T = 25–37 °C). There were similar structural changes in holes ‘a’ and ‘b’ during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of the interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an “all-or-none” transition as it occurred through distinct two-step or single step pathways with or without intermediate states. The knob-hole bonds were stronger, tighter, and more brittle at pH 7 than at pH 5. The B:b knob-hole bonds were weaker, looser, and more compliant than the A:a knob-hole bonds at pH 7 but stronger, tighter, and less compliant at pH 5. Surprisingly, the knob-hole bonds were stronger, not weaker, at elevated temperature (T = 37 °C) compared with T = 25 °C due to the helix-to-coil transition in loop I that helps stabilize the bonds. These results provide detailed qualitative and quantitative characteristics underlying the most significant non-covalent interactions involved in fibrin polymerization. PMID:23720752

Spectral, coordination and thermal properties of 5-arylidene thiobarbituric acids

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; El-Marghany, Adel; Orabi, Adel; Ali, Alaa E.; Sayed, Reham

2013-04-01

Synthesis of 5-arylidine thiobarbituric acids containing different functional groups with variable electronic characters were described and their Co2+, Ni2+ and Cu2+ complexes. The stereochemistry and mode of bonding of 5-(substituted benzylidine)-2-TBA complexes were achieved based on elemental analysis, spectral (UV-VIS, IR, 1H NMR, MS), magnetic susceptibility and conductivity measurements. The ligands were of bidentate and tridentate bonding through S, N and O of pyrimidine nucleolus. All complexes were of octahedral configuration. The thermal data of the complexes pointed to their stability. The mechanism of the thermal decomposition is discussed. The thermodynamic parameters of the dissociation steps were evaluated and discussed.

Atomistic simulation of orientation dependence in shock-induced initiation of pentaerythritol tetranitrate.

PubMed

Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P

2013-01-24

The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

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

PubMed

Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

2018-05-30

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

Atomic-scale analysis of deposition and characterization of a-Si:H thin films grown from SiH radical precursor

NASA Astrophysics Data System (ADS)

Sriraman, Saravanapriyan; Aydil, Eray S.; Maroudas, Dimitrios

2002-07-01

Growth of hydrogenated amorphous silicon films (a-Si:H) on an initial H-terminated Si(001)(2 x1) substrate at T=500 K was studied through molecular-dynamics (MD) simulations of repeated impingement of SiH radicals to elucidate the effects of reactive minority species on the structural quality of the deposited films. The important reactions contributing to film growth were identified through detailed visualization of radical-surface interaction trajectories. These reactions include (i) insertion of SiH into Si-Si bonds, (ii) adsorption onto surface dangling bonds, (iii) surface H abstraction by impinging SiH radicals through an Eley-Rideal mechanism, (iv) surface adsorption by penetration into subsurface layers or dissociation leading to interstitial atomic hydrogen, (v) desorption of interstitial hydrogen into the gas phase, (vi) formation of higher surface hydrides through the exchange of hydrogen, and (vii) dangling-bond-mediated dissociation of surface hydrides into monohydrides. The MD simulations of a-Si:H film growth predict an overall surface reaction probability of 95% for the SiH radical that is in good agreement with experimental measurements. Structural and chemical characterization of the deposited films was based on the detailed analysis of evolution of the films' structure, surface morphology and roughness, surface reactivity, and surface composition. The analysis revealed that the deposited films exhibit high dangling bond densities and rough surface morphologies. In addition, the films are abundant in voids and columnar structures that are detrimental to producing device-quality a-Si:H thin films.

Competitive fragmentation pathways of acetic acid dimer explored by synchrotron VUV photoionization mass spectrometry and electronic structure calculations

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

Guan Jiwen; Hu Yongjun; Zou Hao

2012-09-28

In present study, photoionization and dissociation of acetic acid dimers have been studied with the synchrotron vacuum ultraviolet photoionization mass spectrometry and theoretical calculations. Besides the intense signal corresponding to protonated cluster ions (CH{sub 3}COOH){sub n}{center_dot}H{sup +}, the feature related to the fragment ions (CH{sub 3}COOH)H{sup +}{center_dot}COO (105 amu) via {beta}-carbon-carbon bond cleavage is observed. By scanning photoionization efficiency spectra, appearance energies of the fragments (CH{sub 3}COOH){center_dot}H{sup +} and (CH{sub 3}COOH)H{sup +}{center_dot}COO are obtained. With the aid of theoretical calculations, seven fragmentation channels of acetic acid dimer cations were discussed, where five cation isomers of acetic acid dimer are involved.more » While four of them are found to generate the protonated species, only one of them can dissociate into a C-C bond cleavage product (CH{sub 3}COOH)H{sup +}{center_dot}COO. After surmounting the methyl hydrogen-transfer barrier 10.84 {+-} 0.05 eV, the opening of dissociative channel to produce ions (CH{sub 3}COOH){sup +} becomes the most competitive path. When photon energy increases to 12.4 eV, we also found dimer cations can be fragmented and generate new cations (CH{sub 3}COOH){center_dot}CH{sub 3}CO{sup +}. Kinetics, thermodynamics, and entropy factors for these competitive dissociation pathways are discussed. The present report provides a clear picture of the photoionization and dissociation processes of the acetic acid dimer in the range of the photon energy 9-15 eV.« less

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical

NASA Astrophysics Data System (ADS)

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-01

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 1011 s-1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical.

PubMed

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-28

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 10 11 s -1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Gas-phase behaviour of Ru(II) cyclopentadienyl-derived complexes with N-coordinated ligands by electrospray ionization mass spectrometry: fragmentation pathways and energetics.

PubMed

Madeira, Paulo J Amorim; Morais, Tânia S; Silva, Tiago J L; Florindo, Pedro; Garcia, M Helena

2012-08-15

The gas-phase behaviour of six Ru(II) cyclopentadienyl-derived complexes with N-coordinated ligands, compounds with antitumor activities against several cancer lines, was studied. This was performed with the intent of establishing fragmentation pathways and to determine the Ru-L(N) and Ru-L(P) ligand bond dissociation energies. Such knowledge can be an important tool for the postulation of the mechanisms of action of these anticancer drugs. Two types of instruments equipped with electrospray ionisation were used (ion trap and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer). The dissociation energies were determined using energy-variable collision-induced dissociation measurements in the ion trap. The FTICR instrument was used to perform MS(n) experiments on one of the compounds and to obtain accurate mass measurements. Theoretical calculations were performed at the density functional theory (DFT) level using two different functionals (B3LYP and M06L) to estimate the dissociation energies of the complexes under study. The influence of the L(N) on the bond dissociation energy (D) of RuCp compounds with different nitrogen ligands was studied. The lability order of L(N) was: imidazole<1-butylimidazole<5-phenyl-1H-tetrazole<1-benzylimidazole. Both the functionals used gave the following ligand lability order: imidazole<1-benzylimidazole<5-phenyl-1H-tetrazole<1-butylimidazole. It is clear that there is an inversion between 1-benzylimidazole and 1-butylimidazole for the experimental and theoretical lability orders. The M06L functional afforded values of D closer to the experimental values. The type of phosphane (L(P) ) influenced the dissociation energies, with values of D being higher for Ru-L(N) with 1-butylimidazole when the phosphane was 1,2-bis(diphenylphosphino)ethane. The Ru-L(P) bond dissociation energy for triphenylphosphane was independent of the type of complex. The D values of Ru-L(N) and Ru-L(P) were determined for all six compounds and compared with the values calculated by the DFT method. For the imidazole-derived ligands the energy trend was rationalized in terms of the increasing extension of the σ-donation/π-backdonation effect. The bond dissociation energy of Ru-PPh(3) was independent of the fragmentations. Copyright © 2012 John Wiley & Sons, Ltd.

Bond Dissociation Energies of Tungsten Molecules: WC, WSi, WS, WSe, and WCl.

PubMed

Sevy, Andrew; Huffaker, Robert F; Morse, Michael D

2017-12-14

Resonant two-photon ionization spectroscopy was used to locate predissociation thresholds in WC, WSi, WS, WSe, and WCl, allowing bond dissociation energies to be measured for these species. Because of the high degree of vibronic congestion in the observed spectra, it is thought that the molecules dissociate as soon as the lowest separated atom limit is exceeded. From the observed predissociation thresholds, dissociation energies are assigned as D 0 (WC) = 5.289(8) eV, D 0 (WSi) = 3.103(10) eV, D 0 (WS) = 4.935(3) eV, D 0 (WSe) = 4.333(6) eV, and D 0 (WCl) = 3.818(6) eV. These results are combined with other data to obtain the ionization energy IE(WC) = 8.39(9) eV and the anionic bond dissociation energies of D 0 (W-C - ) = 6.181(17) eV, D 0 (W - -C) = 7.363(19) eV, D 0 (W-Si - ) ≤ 3.44(4) eV, and D 0 (W - -Si) ≤ 4.01(4) eV. Combination of the D 0 (WX) values with atomic enthalpies of formation also provides Δ f H 0K ° values for the gaseous WX molecules. Computational results are also provided, which shed some light on the electronic structure of these molecules.

O-H bond dissociation enthalpies in oximes: order restored.

PubMed

Pratt, Derek A; Blake, Jessie A; Mulder, Peter; Walton, John C; Korth, Hans-Gert; Ingold, Keith U

2004-09-01

The O-H bond dissociation enthalpies (BDEs) of 13 oximes, RR'C=NOH, having R and/or R' = H, alkyl, and aryl are reported. Experimental anchor points used to validate the results of theoretical calculations include (1) the O-H BDEs of (t-Bu)2C=NOH, t-Bu(i-Pr)C=NOH, and t-Bu(1-Ad)C=NOH determined earlier from the heat released in the reaction of (t-Bu)2C=NO* with (PhNH)2 in benzene and EPR spectroscopy (Mahoney, L. R.; Mendenhall, G. D.; Ingold, K. U. J. Am. Chem. Soc. 1973, 95, 8610), all of which were decreased by 1.7 kcal/mol to reflect a revision to the heat of formation of (E)-azobenzene (which has significant ramifications for other BDEs) and to correct for the heat of hydrogen bonding of (t-Bu)2C=NOH (alphaH2 = 0.43 measured in this work) to benzene, and (2) the measured rates of thermal decomposition of six RR'C=NOCH2Ph at 423 or 443 K, which were used to derive O-H BDEs for the corresponding RR'C=NOH. Claims (Bordwell, F. G.; Ji, G. Z. J. Org. Chem. 1992, 57, 3019; Bordwell, F. G.; Zhang, S. J. Am. Chem. Soc. 1995, 117, 4858; and Bordwell, F. G.; Liu, W.-Z. J. Am. Chem. Soc. 1996, 118, 10819) that the O-H BDEs in mono- and diaryloximes are significantly lower than those for alkyloximes due to delocalization of the unpaired electron into the aromatic ring have always been inconsistent with the known structures of iminoxyl radicals as are the purported perpendicular structures, i.e., phi(Calpha-C=N-O*) = 90 degrees, for sterically hindered dialkyl iminoxyl radicals. The present results confirm the 1973 conclusion that simple steric effects, not electron delocalization or dramatic geometric changes, are responsible for the rather small differences in oxime O-H BDEs. Copyright 2004 American Chemical Society

ELECTRONIC STRUCTURE FOR THE GROUND STATE OF T1H FROM RELATIVISTIC MULTICONFIGURATION SCF CALCULATIONS

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

Christiansen, P.A.; Pitzer, K.S.

The dissociation curve for the ground state of TlH was computed using a relativistic {omega}-{omega} coupling formalism. The relativistic effects represented by the Dirac equation were introduced using effective potentials generated from atomic Dirac-Fock wave functions using a generalization of the improved effective potential formulation of Christiansen, Lee, and Pitzer. The multiconfiguration SCF treatment used is a generalization of the two-component molecular spinor formalism of Lee, Ermler, and Pitzer. Using a five configuration wave function we were able to obtain approximately 85% of the experimental dissociation energy. Our computations indicate that the bond is principally sigma in form, despite themore » large spin-orbit splitting in atomic thallium. Furthermore the bond appears to be slightly ionic (Tl{sup +}H{sup -}) with about 0.3 extra electron charge on the hydrogen.« less

Electronic structure for the ground state of TlH from relativistic multiconfiguration SCF calculations

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

Christiansen, P.A.; Pitzer, K.S.

The dissociation curve for the ground state of TlH was computed using a relativistic ..omega..--..omega.. coupling formalism. The relativistic effects represented by the Dirac equation were introduced using effective potentials generated from atomic Dirac--Fock wave functions using a generalization of the improved effective potential formulation of Christiansen, Lee, and Pitzer. The multiconfiguration SCF treatment used is a generalization of the two-component molecular spinor formalism of Lee, Ermler, and Pitzer. Using a five configuration wave function we were able to obtain approximately 85% of the experimental dissociation energy. Our computations indicate that the bond is principally sigma in form, despite themore » large spin--orbit splitting in atomic thallium. Furthermore the bond appears to be slightly ionic (Tl/sup +/H/sup -/) with about 0.3 extra electron charge on the hydrogen.« less

Adsorption of small inorganic molecules on a defective MoS2 monolayer.

PubMed

González, César; Biel, Blanca; Dappe, Yannick J

2017-04-05

We present a theoretical study of molecular adsorption on defects on a MoS 2 monolayer. Based on Density Functional Theory, our calculations confirm that small inorganic molecules, such as CO 2 , CO, H 2 O, NO, NO 2 , H 2 and N 2 , remain bonded to the pristine monolayer through weak van der Waals interactions, suggesting that the molecules may easily diffuse over the clean monolayer. On the other hand, the introduction of defects can lead to three different situations, depending on the defect and the molecule considered: physisorption, chemical (strong) bonding to the metallic defects, namely the Mo substitutional atoms on the S vacancies, and dissociation, that can take place spontaneously at 0 K in some specific cases or by the effect of thermal agitation in molecules such as CO 2 or NO 2 on the S vacancy. Our energetic and electronic analyses provide an explanation to such bonding possibilities, showing that in the low interacting situations, the molecules tend to adopt a planar configuration parallel to the monolayer, while a molecular rotation is favored in order to facilitate the bond formation on the reactive sites. Finally, the ab initio based Scanning Tunneling Microscopy (STM) simulations show the fingerprint of each molecule adsorbed on the most reactive site. This work opens the way to the possibility of tuning the catalytic properties of MoS 2 by controlling the creation of specific defects in the MoS 2 monolayer.

Catalytic water dissociation by greigite Fe3S4 surfaces: density functional theory study

PubMed Central

Roldan, A.; de Leeuw, N. H.

2016-01-01

The iron sulfide mineral greigite, Fe3S4, has shown promising capability as a hydrogenating catalyst, in particular in the reduction of carbon dioxide to produce small organic molecules under mild conditions. We employed density functional theory calculations to investigate the {001},{011} and {111} surfaces of this iron thiospinel material, as well as the production of hydrogen ad-atoms from the dissociation of water molecules on the surfaces. We systematically analysed the adsorption geometries and the electronic structure of both bare and hydroxylated surfaces. The sulfide surfaces presented a higher flexibility than the isomorphic oxide magnetite, Fe3O4, allowing perpendicular movement of the cations above or below the top atomic sulfur layer. We considered both molecular and dissociative water adsorption processes, and have shown that molecular adsorption is the predominant state on these surfaces from both a thermodynamic and kinetic point of view. We considered a second molecule of water which stabilizes the system mainly by H-bonds, although the dissociation process remains thermodynamically unfavourable. We noted, however, synergistic adsorption effects on the Fe3S4{001} owing to the presence of hydroxyl groups. We concluded that, in contrast to Fe3O4, molecular adsorption of water is clearly preferred on greigite surfaces. PMID:27274698

Selective bond breaking mediated by state specific vibrational excitation in model HOD molecule through optimized femtosecond IR pulse: a simulated annealing based approach.

PubMed

Shandilya, Bhavesh K; Sen, Shrabani; Sahoo, Tapas; Talukder, Srijeeta; Chaudhury, Pinaki; Adhikari, Satrajit

2013-07-21

The selective control of O-H/O-D bond dissociation in reduced dimensionality model of HOD molecule has been explored through IR+UV femtosecond pulses. The IR pulse has been optimized using simulated annealing stochastic approach to maximize population of a desired low quanta vibrational state. Since those vibrational wavefunctions of the ground electronic states are preferentially localized either along the O-H or O-D mode, the femtosecond UV pulse is used only to transfer vibrationally excited molecule to the repulsive upper surface to cleave specific bond, O-H or O-D. While transferring from the ground electronic state to the repulsive one, the optimization of the UV pulse is not necessarily required except specific case. The results so obtained are analyzed with respect to time integrated flux along with contours of time evolution of probability density on excited potential energy surface. After preferential excitation from [line]0, 0> ([line]m, n> stands for the state having m and n quanta of excitations in O-H and O-D mode, respectively) vibrational level of the ground electronic state to its specific low quanta vibrational state ([line]1, 0> or [line]0, 1> or [line]2, 0> or [line]0, 2>) by using optimized IR pulse, the dissociation of O-D or O-H bond through the excited potential energy surface by UV laser pulse appears quite high namely, 88% (O-H ; [line]1, 0>) or 58% (O-D ; [line]0, 1>) or 85% (O-H ; [line]2, 0>) or 59% (O-D ; [line]0, 2>). Such selectivity of the bond breaking by UV pulse (if required, optimized) together with optimized IR one is encouraging compared to the normal pulses.

Density functional study of H2O molecule adsorption on α-U(001) surface.

PubMed

Huang, Shanqisong; Zeng, Xiu-Lin; Zhao, Feng-Qi; Ju, Xuehai

2016-04-01

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H2O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H2O molecular dissociate reaction. The long-bridge site is the most favorable site of H2O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H2O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H2O is -1.994 to -2.215 eV on U(001) surface, while the dissociating energy decreases to -3.351 to -3.394 eV with two hydrogen atoms dissociating from H2O. These phenomena also indicate that the Oads can promote the dehydrogenation of H2O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.

A shock tube and theory study of the dissociation of acetone and subsequent recombination of methyl radicals.

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

Saxena, A.; Kiefer, J. H.; Klippenstein, S. J.

The dissociation of acetone: CH{sub 3}C{double_bond}OCH{sub 3} {yields} CH{sub 3}C{double_bond}O + CH{sub 3}, quickly followed by CH{sub 3}CO {yields} CH{sub 3} + CO, has been examined with Laser-Schlieren measurements in incident shock waves over 32-717 Torr and 1429-1936 K using 5% acetone dilute in krypton. A few very low pressure experiments ({approx}10 Torr) were used in a marginal effort to resolve the extremely fast vibrational relaxation of this molecule. This effort was partly motivated as a test for molecular, 'roaming methyl' reactions, and also as a source of methyl radicals to test the application of a recent high-temperature mechanism formore » ethane decomposition [J.H. Kiefer, S. Santhanam, N.K. Srinivasan, R.S. Tranter, S.J. Klippenstein, M.A. Oehlschlaeger, Proc. Combust. Inst. 30 (2005) 1129-1135] on the reverse methyl combination. The gradient profiles show strong initial positive gradients and following negative values fully consistent with methyl radical formation and its following recombination. Thus C-C fission is certainly a large part of the process and molecular channels cannot be responsible for more than 30% of the dissociation. Rates obtained for the C-C fission show strong falloff well fit by variable reaction coordinate transition state theory when combined with a master equation. The calculated barrier is 82.8 kcal/mol, the fitted <{Delta}E>{sub down} = 400 (T/298) cm{sup -1}, similar to what was found in a recent study of C-C fission in acetaldehyde, and the extrapolated k{sub {infinity}} = 10{sup 25.86} T{sup -2.72} exp(?87.7 (kcal/mol)/RT), which agrees with the literature rate for CH{sub 3} + CH{sub 3}CO. Large negative (exothermic) gradients appearing late from methyl combination are accurately fit in both time of onset and magnitude by the earlier ethane dissociation mechanism. The measured dissociation rates are in close accord with one earlier shock-tube study [K. Sato, Y. Hidaka, Combust. Flame 122 (2000) 291-311], but show much less falloff than the high pressure experiments of Ernst et al. [J. Ernst, K. Spindler, H.Gg. Wagner, Ber. Bunsenges. Phys. Chem. 80 (1976) 645-650].« less

Nature of water and hydrogen reactions on transition metal surfaces studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tatarkhanov, Mouslim Magomedovich

Scanning Tunneling Microscopy (STM) has already been established as a tool for the investigation of simple reaction mechanisms. In this work I present results of two parallel studies using STM: first, hydrogen on Ru(0001) surface and second, water on Ru(0001) and Pd(111). In both studies initial stages of adsorption up to saturation monolayer coverage were investigated by variable temperature scanning tunneling microscopy (VT STM). The first step of the hydrogen adsorption study was the identification and characterization of the various coverage structures on clean Ru(0001). Hydrogen was found to adsorb dissociatively forming ( 3x3 )R30°, 3 domains of (2x1), (2x2)-3H and (1x1) for increasing coverages of theta=0.3 ML, 0.5 ML, 0.75 ML and 0.1 ML respectively. Some of these structures were observed to coexist at intermediate coverage values. In addition effects of impurities such as oxygen and carbon on hydrogen adsorption has been discussed. Next, near saturation coverage the interesting mechanism of how H 2 dissociates and binds to the surface of Ru(0001) has been observed. We found that the H2 dissociation takes place only on Ru sites where the metal atom is not bound to any H atom. Such active sites are formed when at least 3 H-vacancies aggregate by thermal diffusion. Sites formed by single H-vacancies (i.e. unoccupied Ru sites) or pairs of adjoining vacancies were found to be unreactive toward H2. H-vacancies were observed as single entities diffusing on the surface at 50 K and able to form transient triangular shaped aggregations where H2 molecules dissociated. It was found that the diffusion and aggregation of the H-vacancies is essential in creation of active sites where dissociative adsorption of hydrogen occurs. The first step of water studies was the initial stages of growth of water on the hexagonal surfaces of Pd(111) and Ru(0001) in the temperature range between 40 K and 130 K. In addition, DFT calculations and STM image simulations were used to validate the models. Below 130 K water dissociation does not occur at any appreciable rate and only molecular films are formed. At these temperatures the kinetics of water growth leads to structures where the molecules bind to the metal substrate through the O-lone pair while making 3 H-bonds with neighboring molecules and form clusters of hexagonal units with a honeycomb structure. This bonding geometry imposes limitations to the size of the clusters, with unsaturated H-bonds confined to the cluster periphery. It is found that growth proceeds by attachement of water molecules to the edge of the clusters by H-bonds. These molecules bind only weakly to the metal substrate and can hop around the edges. Comparison of DFT and STM image calculations with experiments shows that on Pd the edge-attached molecules form two different structures, a metastable one where the molecule is elevated by 2.7 A with respect to the cluster molecules, and another where they are elevated by only 0.4 A. On Ru only the less elevated (0.4 A higher) edge-attached molecules are observed. In next final step, water structures on Ru(0001) were studied at temperatures above 140K. STM findings were backed by x-ray absorption spectroscopy. Additional DFT calculations and STM simulations provided validation of proposed models. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H 2O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentiallymostly parallel to the surface. STM images show that the mixed H2O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H2O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripes geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

NASA Astrophysics Data System (ADS)

Nguyen, Huong T. H.; Tureček, František

2017-07-01

Peptide cation-radical fragment ions of the z-type, [●AXAR+], [●AXAK+], and [●XAR+], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS3-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO-NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [yn]+ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second ( B) excited electronic states in the peptide ion R-CH●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH+-C●(O-)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic Cα and amide nitrogen positions.

Tuning the oxidative power of free iron-sulfur clusters.

PubMed

Lang, Sandra M; Zhou, Shaodong; Schwarz, Helmut

2017-03-15

The gas-phase reactions between a series of di-iron sulfur clusters Fe 2 S x + (x = 1-3) and the small alkenes C 2 H 4 , C 3 H 6 , and C 4 H 8 have been investigated by means of Fourier-transform ion-cyclotron resonance mass spectrometry. For all studied alkenes, the reaction efficiency is found to increase in the order Fe 2 S + < Fe 2 S 2 + < Fe 2 S 3 + . In particular, Fe 2 S + and Fe 2 S 2 + only form simple association products, whereas the sulfur-rich Fe 2 S 3 + is able to dehydrogenate propene and 2-butene via desulfurization of the cluster and formation of H 2 S. This indicates an increased propensity to induce oxidation reactions, i.e. oxidative power, of Fe 2 S 3 + that is attributed to an increased formal oxidation state of the iron atoms. Furthermore, the ability of Fe 2 S 3 + to activate and dissociate the C-H bonds of the alkenes is observed to increase with increasing size of the alkene and thus correlates with the alkene ionization energy.

Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

PubMed

Ambrosek, David; González, Leticia

2007-10-07

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

Bond Strength and Reactivity Scales for Lewis Superacid Adducts: A Comparative Study with In(OTf)3 and Al(OTf)3.

PubMed

Compain, Guillaume; Sikk, Lauri; Massi, Lionel; Gal, Jean-François; Duñach, Elisabet

2017-03-17

Metal triflates, often called Lewis superacids, are potent catalysts for organic synthesis. However, the reactivity of a given Lewis superacid toward a given base is difficult to anticipate. A systematic screening of catalysts is often necessary when developing synthetic methodologies. Presented herein is the development of quantitative reactivity and bond strength scales by using mass spectrometry (MS). By applying a collision-induced dissociation (CID) technique to the adducts formed between Lewis superacids Al(OTf) 3 or In(OTf) 3 with a series of amides bases, including monodentate and bidentate ligands, different dissociation pathways were observed. Quantitative relative energy scales were established by performing energy-resolved mass spectrometry (ERMS) analysis on the adducts. ERMS of the adducts affords a bond strength scale when the fragmentation leads to the loss of a ligand, and reactivity scales when the dissociation leads to the C-F bond activation of one triflate anion or the deprotonation of the ligand. Al(OTf) 3 was found to bind stronger to amides than In(OTf) 3 and to provide the most reactive adducts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen-Atom Transfer Oxidation with H2O2 Catalyzed by [FeII(1,2-bis(2,2'-bipyridyl-6-yl)ethane(H2O)2]2+: Likely Involvement of a (μ-Hydroxo)(μ-1,2-peroxo)diiron(III) Intermediate.

PubMed

Khenkin, Alexander M; Vedichi, Madhu; Shimon, Linda J W; Cranswick, Matthew A; Klein, Johannes E M N; Que, Lawrence; Neumann, Ronny

2017-11-01

The iron(II) triflate complex ( 1 ) of 1,2-bis(2,2'-bipyridyl-6-yl)ethane, with two bipyridine moieties connected by an ethane bridge, was prepared. Addition of aqueous 30% H 2 O 2 to an acetonitrile solution of 1 yielded 2 , a green compound with λ max =710 nm. Moessbauer measurements on 2 showed a doublet with an isomer shift (δ) of 0.35 mm/s and a quadrupole splitting (Δ E Q ) of 0.86 mm/s, indicative of an antiferromagnetically coupled diferric complex. Resonance Raman spectra showed peaks at 883, 556 and 451 cm -1 that downshifted to 832, 540 and 441 cm -1 when 1 was treated with H 2 18 O 2 . All the spectroscopic data support the initial formation of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that oxidizes carbon-hydrogen bonds. At 0°C 2 reacted with cyclohexene to yield allylic oxidation products but not epoxide. Weak benzylic C-H bonds of alkylarenes were also oxidized. A plot of the logarithms of the second order rate constants versus the bond dissociation energies of the cleaved C-H bond showed an excellent linear correlation. Along with the observation that oxidation of the probe substrate 2,2-dimethyl-1-phenylpropan-1-ol yielded the corresponding ketone but no benzaldehyde, and the kinetic isotope effect, k H /k D , of 2.8 found for the oxidation of xanthene, the results support the hypothesis for a metal-based H-atom abstraction mechanism. Complex 2 is a rare example of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that can elicit the oxidation of carbon-hydrogen bonds.

Can Internal Conversion BE Controlled by Mode-Specific Vibrational Excitation in Polyatomic Molecules

NASA Astrophysics Data System (ADS)

Portnov, Alexander; Epshtein, Michael; Bar, Ilana

2017-06-01

Nonadiabatic processes, dominated by dynamic passage of reactive fluxes through conical intersections (CIs) are considered to be appealing means for manipulating reaction paths. One approach that is considered to be effective in controlling the course of dissociation processes is the selective excitation of vibrational modes containing a considerable component of motion. Here, we have chosen to study the predissociation of the model test molecule, methylamine and its deuterated isotopologues, excited to well-characterized quantum states on the first excited electronic state, S_{1}, by following the N-H(D) bond fission dynamics through sensitive H(D) photofragment probing. The branching ratios between slow and fast H(D) photofragments, the internal energies of their counter radical photofragments and the anisotropy parameters for fast H photofragments, confirm correlated anomalies for predissociation initiated from specific rovibronic states, reflecting the existence of a dynamic resonance in each molecule. This resonance strongly depends on the energy of the initially excited rovibronic states, the evolving vibrational mode on the repulsive S_{1} part during N-H(D) bond elongation, and the manipulated passage through the CI that leads to radicals excited with C-N-H(D) bending and preferential perpendicular bond breaking, relative to the photolyzing laser polarization, in molecules containing the NH_{2} group. The indicated resonance plays an important role in the bifurcation dynamics at the CI and can be foreseen to exist in other photoinitiated processes and to control their outcome.

Equilibrium Acidities and Homolytic Bond Dissociation Enthalpies of the Acidic C-H Bonds in P-(Para-substituted benzyl)triphenylphosphonium Cations and Related Cations.

PubMed

Zhang, Xian-Man; Fry, Albert J.; Bordwell, Frederick G.

1996-06-14

Equilibrium acidities (pK(HA)) of six P-(para-substituted benzyl)triphenylphosphonium (p-GC(6)H(4)CH(2)PPh(3)(+)) cations, P-allyltriphenylphosphonium cation, P-cinnamyltriphenylphosphonium cation, and As-(p-cyanobenzyl)triphenylarsonium cation, together with the oxidation potentials [E(ox)(A(-))] of their conjugate anions (ylides) have been measured in dimethyl sulfoxide (DMSO) solution. The acidifying effects of the alpha-triphenylphosphonium groups on the acidic C-H bonds in toluene and propene were found to be ca 25 pK(HA) units (34 kcal/mol). Introduction of an electron-withdrawing group such as 4-NO(2), 4-CN, or 4-Br into the para position of the benzyl ring in p-GC(6)H(4)CH(2)PPh(3)(+) cations resulted in an additional acidity increase, but introduction of the 4-OEt electron-donating group decreases the acidity. The equilibrium acidities of p-GC(6)H(4)CH(2)PPh(3)(+) cations were nicely linearly correlated with the Hammett sigma(-) constants of the substituents (G) with a slope of 4.78 pK(HA) units (R(2) = 0.992) (Figure 1). Reversible oxidation potentials of the P-(para-substituted benzyl)triphenylphosphonium ylides were obtained by fast scan cyclic voltammetry. The homolytic bond dissociation enthalpies (BDEs) of the acidic C-H bonds in these cations, estimated by combining their equilibrium acidities with the oxidation potentials of their corresponding conjugate anions, showed that the alpha-Ph(3)P(+) groups have negligible stabilizing or destabilizing effects on the adjacent radicals. The equilibrium acidity of As-(p-cyanobenzyl)triphenylarsonium cation is 4 pK(HA) units weaker than that of P-(p-cyanobenzyl)triphenylphosphonium cation, but the BDE of the acidic C-H bond in As-(p-cyanobenzyl)triphenylarsonium cation is ca 2 kcal/mol higher than that in P-(p-cyanobenzyl)triphenylphosphonium cation.

Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions

PubMed Central

Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

2015-01-01

A series of different types of wax esters (represented by RCOOR′) were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS3 (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2]+, [RCO]+ and [RCO – H2O]+ that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: 1) [RCOOH2]+ for saturated wax esters, 2) [RCOOH2]+, [RCO]+ and [RCO – H2O]+ for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and 3) [RCOOH2]+ and [RCO]+ for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R′]+ and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2]+ ions for all types of wax esters and [R′ – 2H]+ ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions. PMID:26178197

Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions.

PubMed

Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

2015-08-01

A series of different types of wax esters (represented by RCOOR') were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS(3) (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2](+), [RCO](+) and [RCO-H2O](+) that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: (1) [RCOOH2](+) for saturated wax esters, (2) [RCOOH2](+), [RCO](+) and [RCO-H2O](+) for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and (3) [RCOOH2](+) and [RCO](+) for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R'](+) and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2](+) ions for all types of wax esters and [R'-2H](+) ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions.

Does GaH5 exist?

NASA Astrophysics Data System (ADS)

Speakman, Lucas D.; Turney, Justin M.; Schaefer, Henry F.

2005-11-01

The existence or nonexistence of GaH5 has been widely discussed [N. M. Mitzel, Angew. Chem. Int. Ed. 42, 3856 (2003)]. Seven possible structures for gallium pentahydride have been systematically investigated using ab initio electronic structure theory. Structures and vibrational frequencies have been determined employing self-consistent field, coupled cluster including all single and double excitations (CCSD), and CCSD with perturbative triples levels of theory, with at least three correlation-consistent polarized-valence-(cc-pVXZ and aug-cc-pVXZ) type basis sets. The X˜A'1 state for GaH5 is predicted to be weakly bound complex 1 between gallane and molecular hydrogen, with Cs symmetry. The dissociation energy corresponding to GaH5→GaH3+H2 is predicted to be De=2.05kcalmol-1. The H-H stretching fundamental is predicted to be v =4060cm-1, compared to the tentatively assigned experimental feature of Wang and Andrews [J. Phys. Chem. A 107, 11371 (2003)] at 4087cm-1. A second Cs structure 2 with nearly equal energy is predicted to be a transition state, corresponding to a 90° rotation of the H2 bond. Thus the rotation of the hydrogen molecule is essentially free. However, hydrogen scrambling through the C2v structure 3 seems unlikely, as the activation barrier for scrambling is at least 30kcalmol-1 higher in energy than that for the dissociation of GaH5 to GaH3 and H2. Two additional structures consisting of GaH3 with a dihydrogen bond perpendicular to gallane (C3v structure 4) and an in-plane dihydrogen bond [Cs(III) structure 5] were also examined. A C3v symmetry second-order saddle point has nearly the same energy as the GaH3+H2 dissociation limit, while the Cs(III) structure 5 is a transition structure to the C3v structure. The C4v structure 6 and the D3h structure 7 are much higher in energy than GaH3+H2 by 88 and 103kcalmol-1, respectively.

First-principles study of the interaction of H2O with the GaSb (001) surface

NASA Astrophysics Data System (ADS)

Bermudez, V. M.

2013-05-01

The adsorption of H2O on the GaSb (001) surface, both clean and with pre-adsorbed H atoms, has been studied computationally using dispersion-corrected density functional theory. The model employed is the α-(4×3) reconstruction consisting of Ga-Sb dimers adsorbed on the Sb-terminated surface, a disordered version of which is believed to constitute the frequently observed Sb-rich (1×3) surface. On the clean surface, molecular adsorption of H2O at a coordinatively unsaturated Ga site is exothermic (ΔE = -0.57 eV), but dissociation of this adsorbed H2O is significantly endothermic (ΔE = +0.45 eV or more). Dissociation can form either a (HO)Ga-Sb(H) site involving a Ga-Sb dimer or a (H)Ga-O(H)-Sb bridge. Other reactions are also energetically feasible, depending on the bond strength of different inequivalent Ga-Sb dimers. The two structures have essentially the same energy, and both can undergo an exothermic reaction with a second H2O. For the (HO)Ga-Sb(H) site, this reaction leads to the breaking of the dimer bond and the adsorption of molecular water, while the (H)Ga-O(H)-Sb bridge transforms to (HO)Ga-O(H)-Sb with the release of H2. On the H-terminated surface, molecular adsorption of H2O can be suppressed and dissociative adsorption enhanced, which means that formation of an OH-terminated surface may be easier when starting with an H-terminated vs. a clean surface. The implications of these results for the growth of oxide/GaSb heterostructures via atomic layer deposition are discussed.

Cell membrane antigen-antibody complex dissociation by the widely used glycine-HCL method: an unreliable procedure for studying antibody internalization.

PubMed

Tsaltas, G; Ford, C H

1993-02-01

Methods following the process of binding and internalization of antibodies to cell surface antigens have often employed low pH isoosmolar buffers in order to dissociate surface antigen-antibody complexes. One of the most widely used buffers is a 0.05 M glycine-HCL buffer pH 2.8. Since the efficacy of action of this buffer was critical to a series of internalization experiments employing monoclonal antibodies (Mabs) to carcinoembryonic antigen (CEA) expressing cancer cell lines in this laboratory, we tested its performance in a number of different assays. Our results indicate that this buffer only partially dissociates antigen-antibody bonds and therefore can introduce major inaccuracies in internalization experiments.

Unified mechanism of alkali and alkaline earth catalyzed gasification reactions of carbon by CO2 and H2O

USGS Publications Warehouse

Chen, S.G.; Yang, R.T.

1997-01-01

From molecular orbital calculations, a unified mechanism is proposed for the gasification reactions of graphite by CO2 and H2O, both uncatalyzed and catalyzed by alkali and alkaline earth catalysts. In this mechanism, there are two types of oxygen intermediates that are bonded to the active edge carbon atoms: an in-plane semiquinone type, Cf(O), and an off-plane oxygen bonded to two saturated carbon atoms that are adjacent to the semiquinone species, C(O)Cf(O). The rate-limiting step is the decomposition of these intermediates by breaking the C-C bonds that are connected to Cf(O). A new rate equation is derived for the uncatalyzed reactions, and that for the catalyzed reactions is readily available from the proposed mechanism. The proposed mechanism can account for several unresolved experimental observations: TPD and TK (transient kinetics) desorption results of the catalyzed systems, the similar activation energies for the uncatalyzed and catalyzed reactions, and the relative activities of the alkali and alkaline earth elements. The net charge of the edge carbon active site is substantially changed by gaining electron density from the alkali or alkaline earth element (by forming C-O-M, where M stands for metal). The relative catalytic activities of these elements can be correlated with their abilities of donating electrons and changing the net charge of the edge carbon atom. As shown previously (Chen, S. G.; Yang, R. T. J. Catal. 1993, 141, 102), only clusters of the alkali compounds are active. This derives from the ability of the clusters to dissociate CO2 and H2O to form O atoms and the mobility of the dissociated O atoms facilitated by the clusters.

Unravelling the Electronic State of NO2 Product in Ultrafast Photodissociation of Nitromethane.

PubMed

Adachi, Shunsuke; Kohguchi, Hiroshi; Suzuki, Toshinori

2018-01-18

The primary photochemical reaction of nitromethane (NM) after ππ* excitation is known to be C-N bond cleavage (CH 3 NO 2 + hν → CH 3 + NO 2 ). On the other hand, NO 2 can be formed in both the ground and excited states, and identification of the electronic state of the NO 2 product has been a central subject in the experimental and theoretical studies. Here we present time-resolved photoelectron spectroscopy using vacuum-ultraviolet probe pulses to observe all transient electronic states of NM and the reaction products. The result indicates that ultrafast internal conversion occurs down to S 1 and S 0 within 24 fs, and the dissociation proceeds on the S 1 surface (τ diss ≲ 50 fs), leading to comparable product yields of NO 2 (A) and NO 2 (X). The overall dissociation quantum yield within our observation time window (<2 ps) is estimated to be 0.29.

Surface interaction of H2S, SO2, and SO3 on fullerene-like gallium nitride (GaN) nanostructure semiconductor

NASA Astrophysics Data System (ADS)

Salimifard, M.; Rad, A. Shokuhi; Mahanpoor, K.

2017-10-01

Density functional theory (DFT) using MPW1PW91 and B3LYP hybrid functionals was utilized for quantum-based investigations of three major sulfur compounds (H2S, SO2, and SO3) adsorption onto fullerene-like Ga12N12 nanocluster. All chemicals showed high chemisorption with the order of SO3>SO2>>H2S. Results of charge analysis showed that during adsorption, transfer of charge is from H2S to nanocluster while reverse direction of charge transfer is found for SO2 and SO3 molecules. Partial dissociation is found for adsorbates especially for SO2 and SO3 molecules. Results of thermochemistry analysis show negative values for enthalpy and Gibbs free energy of adsorption, confirming exothermic spontaneous process. Analysis of frontier molecular orbital (FMO) showed important role of orbital hybridizing towards formation of new bonds upon adsorption. As a result, we introduce Ga12N12 nanocluster as a strong adsorbent for sulfur compounds.

Effects of Charge State on Fragmentation Pathways, Dynamics, and Activation Energies of Ubiquitin Ions Measured by Blackbody Infrared Radiative Dissociation

PubMed Central

Jockusch, Rebecca A.; Schnier, Paul D.; Price, William D.; Strittmatter, Eric. F.; Demirev, Plamen A.; Williams*, Evan R.

2005-01-01

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 1012 s−1, respectively. These values for the 6+ and 7+ ions are 0.9–1.0 eV and 109 s−1, and those for the 10+ and 11+ ions are 1.6 eV and 1016–1017 s−1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed. PMID:9075403

Unimolecular dissociation of protonated trans-1,4-diphenyl-2-butene-1,4-dione in the gas phase: rearrangement versus simple cleavage.

PubMed

Wu, Lianming; Liu, David Q; Vogt, Frederick G

2006-01-01

Fragmentation mechanisms of trans-1,4-diphenyl-2-butene-1,4-dione were studied using a variety of mass spectrometric techniques. The major fragmentation pathways occur by various rearrangements by loss of H(2)O, CO, H(2)O and CO, and CO(2). The other fragmentation pathways via simple alpha cleavages were also observed but accounted for the minor dissociation channels in both a two-dimensional (2-D) linear ion trap and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The elimination of CO(2) (rather than CH(3)CHO or C(3)H(8)), which was confirmed by an exact mass measurement using the Q-TOF instrument, represented a major fragmentation pathway in the 2-D linear ion trap mass spectrometer. However, the elimination of H(2)O and CO becomes more competitive in the beam-type Q-TOF instrument. The loss of CO is observed in both the MS(2) experiment of m/z 237 and the MS(3) experiment of m/z 219 but via the different transition states. The data suggest that the olefinic double bond in protonated trans-1,4-diphenyl-2-butene-1,4-dione plays a key role in stabilizing the rearrangement transition states and increasing the bond dissociation (cleavage) energy to give favorable rearrangement fragmentation pathways. Copyright (c) 2006 John Wiley & Sons, Ltd.

Protonation switching to the least-basic heteroatom of carbamate through cationic hydrogen bonding promotes the formation of isocyanate cations.

PubMed

Kurouchi, Hiroaki; Sumita, Akinari; Otani, Yuko; Ohwada, Tomohiko

2014-07-07

We found that phenethylcarbamates that bear ortho-salicylate as an ether group (carbamoyl salicylates) dramatically accelerate OC bond dissociation in strong acid to facilitate generation of isocyanate cation (N-protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote CO bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>CO(+) H⋅⋅⋅O<) with the phenolic ether oxygen. This facilitates OC bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid-mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo CO bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

PubMed

Forbert, Harald; Masia, Marco; Kaczmarek-Kedziera, Anna; Nair, Nisanth N; Marx, Dominik

2011-03-23

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.

Hydrogen bonding as the origin of the switching behavior in dithiolated phenylene-vinylene oligomers

NASA Astrophysics Data System (ADS)

Obodo, J. T.; Gkionis, K.; Rungger, I.; Sanvito, S.; Schwingenschlögl, U.

2013-08-01

We investigate theoretically the switching behavior of a dithiolated phenylene-vinylene oligomer sandwiched between Au(111) electrodes using self-interaction corrected density-functional theory combined with the nonequilibrium Green's-function method for quantum transport. The molecule presents a configurational bistability, which can be exploited in constructing molecular memories, switches, and sensors. We find that protonation of the terminating thiol groups is at the origin of the change in conductance. H bonding at the thiol group weakens the S-Au bond and reduces by about one order of magnitude the transmission coefficient at the Fermi level, and thus the linear response conductance. Furthermore, protonation downshifts in energy the position of the highest occupied molecular orbital, so that the current of the protonated species is lower than that of the unprotonated one along the entire bias range investigated, from -1.5 to 1.5 V. A second protonation at the opposite thiol group has only minor effects and no further drastic reduction in transmission takes place. Our results allow us to re-interpret the experimental data originally attributing the conductance reduction to H dissociation.

Electron driven processes in sulphur containing compounds CH3SCH3 and CH3SSCH3

NASA Astrophysics Data System (ADS)

Kopyra, Janina; Władziński, Jakub

2015-06-01

Dissociative electron attachment to gas phase dimethyl sulphide (CH3SCH3) and dimethyl disulphide (CH3SSCH3) has been studied by means of a crossed beams apparatus. Cleavage of the C-S bond within CH3SCH3 and the S-S bond within CH3SSCH3 is observed within a resonance in the energy range below 2 eV and visible preferentially via the appearance of the fragment CH2S-. The striking finding is that the intensity of CH2S- generated from CH3SSCH3 is more than two orders of magnitude higher than the intensity of the respective anionic fragment generated from CH3SCH3. Our results clearly demonstrate that the CH3SSCH3 molecule, which contains disulphide bridge is substantially more sensitive towards electron attachment resulting mainly in dissociation along the S-S bridge.

CO dissociation and CO hydrogenation on smooth and ion-bombarded Pd(1 1 1): SFG and XPS spectroscopy at mbar pressures

NASA Astrophysics Data System (ADS)

Rupprechter, G.; Kaichev, V. V.; Unterhalt, H.; Morkel, M.; Bukhtiyarov, V. I.

2004-07-01

The CO dissociation probability on transition metals is often invoked to explain the product distribution (selectivity) of catalytic CO hydrogenation. Along these lines, we have investigated CO adsorption and dissociation on smooth and ion-bombarded Pd(1 1 1) at pressures up to 1 mbar using vibrational sum frequency generation (SFG) and X-ray photoelectron spectroscopy (XPS). Under high pressure, CO adsorbate structures were observed that were identical to high-coverage structures in UHV. On ion-bombarded surfaces an additional species was detected which was attributed to CO bridge bonded to defect (low-coordinated) sites. On both surfaces, no indications of CO dissociation were found even after hours of 0.1 mbar CO exposure. However, exposing CO/H 2 mixtures to ion-bombarded Pd(1 1 1) produced carbonaceous deposits suggesting CH xO species as precursors for CO bond cleavage and that the formation of CH xO is facilitated by surface defects. The relevance of the observations for CO hydrogenation on Pd catalysts is discussed.

Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy.

PubMed

Kwak, Kyungwon; Rosenfeld, Daniel E; Chung, Jean K; Fayer, Michael D

2008-11-06

Hydrogen bonds formed between C-H and various hydrogen bond acceptors play important roles in the structure of proteins and organic crystals, and the mechanisms of C-H bond cleavage reactions. Chloroform, a C-H hydrogen bond donor, can form weak hydrogen-bonded complexes with acetone and with dimethylsulfoxide (DMSO). When chloroform is dissolved in a mixed solvent consisting of acetone and DMSO, both types of hydrogen-bonded complexes exist. The two complexes, chloroform-acetone and chloroform-DMSO, are in equilibrium, and they rapidly interconvert by chloroform exchanging hydrogen bond acceptors. This fast hydrogen bond acceptor substitution reaction is probed using ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy. Deuterated chloroform is used in the experiments, and the 2D-IR spectrum of the C-D stretching mode is measured. The chemical exchange of the chloroform hydrogen bonding partners is tracked by observing the time-dependent growth of off-diagonal peaks in the 2D-IR spectra. The measured substitution rate is 1/30 ps for an acetone molecule to replace a DMSO molecule in a chloroform-DMSO complex and 1/45 ps for a DMSO molecule to replace an acetone molecule in a chloroform-acetone complex. Free chloroform exists in the mixed solvent, and it acts as a reactive intermediate in the substitution reaction, analogous to a SN1 type reaction. From the measured rates and the equilibrium concentrations of acetone and DMSO, the dissociation rates for the chloroform-DMSO and chloroform-acetone complexes are found to be 1/24 ps and 1/5.5 ps, respectively. The difference between the measured rate for the complete substitution reaction and the rate for complex dissociation corresponds to the diffusion limited rate. The estimated diffusion limited rate agrees well with the result from a Smoluchowski treatment of diffusive reactions.

Kinetic Investigation of Homogeneous H(2)-D(2) Equilibration Catalyzed by Pt-Au Cluster Compounds. Characterization of the Cluster [(H)Pt(AuPPh(3))(9)](NO(3))(2).

PubMed

Rubinstein, Leon I.; Pignolet, Louis H.

1996-11-06

The new Pt-Au hydrido cluster compound [(H)Pt(AuPPh(3))(9)](NO(3))(2) (3) has been synthesized and characterized by NMR, FABMS, and single-crystal X-ray diffraction [triclinic, P&onemacr;, a = 17.0452(1) Å, b = 17.4045(2) Å, c = 55.2353(1) Å, alpha = 89.891(1) degrees, beta = 85.287(1) degrees, gamma = 75.173(1) degrees, V = 15784.0(2) Å(3), Z = 4 (two molecules in asymmetric unit), residual R = 0.089 for 45 929 observed reflections and 3367 variables, Mo Kalpha radiation]. The Pt(AuP)(9) core geometry is a distorted icosahedron with three vertices vacant. The Pt-Au, Au-Au, and Au-P distances are within the normal ranges observed in other Pt-Au clusters. This cluster is a catalyst for H(2)-D(2) equilibration in homogeneous solution phase and has been used in a general mechanistic study of this reaction catalyzed by Pt-Au clusters. We previously proposed that a key step in the mechanism for catalytic H(2)-D(2) equilibration is the dissociation of a PPh(3) ligand to give a cluster with an open Au site for bonding of H(2) or D(2). This was based on qualitative observations that PPh(3) inhibited the rate of HD production with [Pt(AuPPh(3))(8)](NO(3))(2) (1) as catalyst. In order to test this hypothesis, phosphine inhibition (on the rate of HD production) and phosphine ligand exchange kinetic experiments were carried out with [(H)(PPh(3))Pt(AuPPh(3))(7)](NO(3))(2) (2) and 3. In this paper we show that the rate constant for phosphine dissociation determined from the PPh(3) inhibition rate study of H(2)-D(2) equilibration with cluster 2 is nearly identical to the rate constant for dissociative phosphine ligand exchange. The slower rate for H(2)-D(2) equilibration observed with 3 compared with 2 (5.5 x 10(-3) vs 7.7 x 10(-2) turnover s(-1)) is explained by its smaller rate constant for phosphine dissociation (2.8 x 10(-5) vs 2.9 x 10(-4) s(-1)). The fact that clusters 2 and 3 show similar kinetic behaviors suggests that the PPh(3) dissociation step in the catalytic H(2)-D(2) equilibration is general for 18-electron hydrido Pt-AuPPh(3) clusters.

Benzylic Fluorination of Aza-Heterocycles Induced by Single-Electron Transfer to Selectfluor.

PubMed

Danahy, Kelley E; Cooper, Julian C; Van Humbeck, Jeffrey F

2018-04-23

A selective and mild method for the benzylic fluorination of aromatic azaheterocycles with Selectfluor is described. These reactions take place by a previously unreported mechanism, in which electron transfer from the heterocyclic substrate to the electrophilic fluorinating agent Selectfluor eventually yields a benzylic radical, thus leading to the desired C-F bond formation. This mechanism enables high intra- and intermolecular selectivity for aza-heterocycles over other benzylic components with similar C-H bond-dissociation energies. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bond breaking and bond formation: how electron correlation is captured in many-body perturbation theory and density-functional theory.

PubMed

Caruso, Fabio; Rohr, Daniel R; Hellgren, Maria; Ren, Xinguo; Rinke, Patrick; Rubio, Angel; Scheffler, Matthias

2013-04-05

For the paradigmatic case of H(2) dissociation, we compare state-of-the-art many-body perturbation theory in the GW approximation and density-functional theory in the exact-exchange plus random-phase approximation (RPA) for the correlation energy. For an unbiased comparison and to prevent spurious starting point effects, both approaches are iterated to full self-consistency (i.e., sc-RPA and sc-GW). The exchange-correlation diagrams in both approaches are topologically identical, but in sc-RPA they are evaluated with noninteracting and in sc-GW with interacting Green functions. This has a profound consequence for the dissociation region, where sc-RPA is superior to sc-GW. We argue that for a given diagrammatic expansion, sc-RPA outperforms sc-GW when it comes to bond breaking. We attribute this to the difference in the correlation energy rather than the treatment of the kinetic energy.

Selective collision-induced fragmentation of ortho-hydroxybenzyl-aminated lysyl-containing tryptic peptides.

PubMed

Simon, E S; Papoulias, P G; Andrews, P C

2013-07-30

In protein studies that employ tandem mass spectrometry the manipulation of protonated peptide fragmentation through exclusive dissociation pathways may be preferred in some applications over the comprehensive amide backbone fragmentation that is typically observed. In this study, we characterized the selective cleavage of the side-chain Cζ-Nε bond of peptides with ortho-hydroxybenzyl-aminated lysine residues. Internal lysyl residues of representative peptides were derivatized via reductive amination with ortho-hydroxybenzaldehyde. The modified peptides were analyzed using collision-induced dissociation (CID) on an Orbitrap tandem mass spectrometer. Theoretical calculations using computational methods (density functional theory) were performed to investigate the potential dissociation mechanisms for the Cζ-Nε bond of the derivatized lysyl residue resulting in the formation of the observed product ions. Tandem mass spectra of the derivatized peptide ions exhibit product peaks corresponding to selective cleavage of the side-chain Cζ-Nε bond that links the derivative to lysine. The ortho-hydroxybenzyl derivative is released either as a neutral moiety [C7H6O1] or as a carbocation [C7H7O1](+) through competing pathways (retro-Michael versus Carbocation Elimination (CCE), respectively). The calculated transition state activation barriers indicate that the retro-Michael pathway is kinetically favored over CCE and both are favored over amide cleavage. The application of ortho-hydroxybenzyl amination is a promising peptide derivatization scheme for promoting selective dissociation pathways in the tandem mass spectrometry of protonated peptides. This can be implemented in the rational development of peptide reactive reagents for applications that may benefit from selective fragmentation paths (including crosslinking or MRM reagents). Copyright © 2013 John Wiley & Sons, Ltd.

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

NASA Astrophysics Data System (ADS)

Kamarchik, E.; Rodrigo, C.; Bowman, J. M.; Reisler, H.; Krylov, A. I.

2012-02-01

The dissociation of the hydroxymethyl radical, CH2OH, and its isotopolog, CD2OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH2OH and CH3O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH2OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ˜3000 cm-1 above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D0(CH2OH → CH2O + H) = 10 188 cm-1, D0(CD2OH → CD2O + H) = 10 167 cm-1, D0(CD2OH → CHDO + D) = 10 787 cm-1. All are in excellent agreement with the experimental results. For CH2OH, the barriers for the direct OH bond fission and isomerization are: 14 205 and 13 839 cm-1, respectively.

H2S adsorption and decomposition on the gradually reduced α-Fe2O3(001) surface: A DFT study

NASA Astrophysics Data System (ADS)

Lin, Changfeng; Qin, Wu; Dong, Changqing

2016-11-01

Reduction of iron based desulfurizer occurs during hot gas desulfurization process, which will affect the interaction between H2S and the desulfurizer surface. In this work, a detailed adsorption behavior and dissociation mechanism of H2S on the perfect and reduced α-Fe2O3(001) surfaces, as well as the correlation between the interaction characteristic and reduction degree of iron oxide, have been studied by using periodic density functional theory (DFT) calculations. Results demonstrate that H2S firstly chemisorbs on surface at relatively higher oxidation state (reduction degree χ < 33%), then dissociative adsorption occurs and becomes the main adsorption type after χ > 33%. Reduction of iron oxide benefits the H2S adsorption. Further, dissociation processes of H2S via molecular and dissociative adsorption were investigated. Results show that after reduction of Fe2O3 into the oxidation state around FeO and Fe, the reduced surface exhibits very strong catalytic capacity for H2S decomposition into S species. Meanwhile, the overall dissociation process on all surfaces is exothermic. These results provide a fundamental understanding of reduction effect of iron oxide on the interaction mechanism between H2S and desulfurizer surface, and indicate that rational control of reduction degree of desulfurizer is essential for optimizing the hot gas desulfurization process.

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.

Structure and spectra of H/sub 2/O in hydrated. beta. -alumina

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

Bates, J.B.; Dudney, N.J.; Brown, G.M.

1982-11-15

The structure and spectra of hydrated Li and Na ..beta..-alumina were investigated using neutron diffraction, infrared absorption, and Raman scattering. The dimensions of the hexagonal unit cell of a hydrated Li ..beta..-alumina crystal containing 1.55 H/sub 2/O molecules per unit cell are a = 5.591 A and c = 22.715 A. The oxygen atoms of the water molecules are located in the conduction plane between the mO, and the aBR sites; the protons, located above the below the plane, form bent hydrogen bonds with the O(4) oxygen ions. The HOH bond angle of water in Li ..beta..-alumina is 114/sup 0/more » and the Vertical BarO--HVertical Bar bond distance is 0.992 A. Based on polarized infrared spectra, H/sub 2/O adopts a similar structure and orientation in Na ..beta..-alumina. Spectra of absorbed H/sub 2/O, D/sub 2/O, and HDO species show that water molecules dissociate in Li ..beta..-alumina to form OH/sup -/ and H(H/sub 2/O)/sup +//sub n/ species. No evidence was found for the dissociation of water in Na ..beta..-alumina. The absorption coefficients determined for OH/sup -/ and H/sub 2/O in Li ..beta..-alumina include local field corrections. A large local field anisotropy at the protons of H/sub 2/O is responsible for the large ratio of the intensities of ..nu../sub 3/ and ..nu../sub 1/ observed for water in Li and Na ..beta..-alumina.« less

Elucidation of hydroxyl groups-antioxidant relationship in mono- and dihydroxyflavones based on O-H bond dissociation enthalpies.

PubMed

Treesuwan, Witcha; Suramitr, Songwut; Hannongbua, Supa

2015-06-01

Radical scavenging potential is the key to anti-oxidation of hydroxyflavones which generally found in fruits and vegetables. The objective of this work was to investigate the influence of hydroxyl group on the O-H bond dissociation enthalpies (BDE) from a series of mono- and dihydroxyflavones. Calculation at the B3LYP/6-31G(d,p) level reveals the important roles of an additional one hydroxyl group to boost the BDE of hydroxyflavones that were a stabilization of the generated radicals through attractive H-bond interactions, an ortho- and para-dihydroxyl effect, and a presence of the 3-OH in dihydroxyflavones. On the other hand, the meta-dihydroxyl effect and range-hydroxyl effect especially associated with the either 5-OH or 8-OH promoted greater BDE. Results did not only confirm that dihydroxyflavones had lower BDE than monohydroxyflavones but also suggest the selective potent hydroxyflavone molecules that are the 6'-hydroxyflavone (for monohydroxyflavone) and the 5',6'-, 7,8- and 3',4'-dihydroxyflavone which the corresponding radical preferable generated at C6'-O•, C8-O• and C4'-O•, respectively. Electron distribution was limited only over the two connected rings of hydroxyflavones while the expansion distribution into C-ring could be enhanced if the radical was formed especially for the 2',3'- and 5',6'dihydroxyflavone radicals. The delocalized bonds were strengthened after radical was generated. However the 5-O• in 5,6-dihydroxyflavone and the 3-O• in 3,6'-dihydroxyflavone increased the bond order at C4-O11 which might interrupt the conjugated delocalized bonds at the keto group.

Thermochemistry of Hydroxyl and Hydroperoxide Substituted Furan, Methylfuran, and Methoxyfuran.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W

2017-06-15

Reaction pathways are influenced by thermochemical properties, species stability, and chemical kinetics. Understanding these factors allows for an understanding of the reaction paths and formation of intermediate species. Enthalpies of formation (ΔH f,298 ° ), entropies (S 298 ° ), heat capacities (C p (T)), oxygen-hydrogen (O-H), oxygen-oxygen (O-O), and (R-O) bond dissociation energies (BDEs) are reported for hydroxyl and hydroperoxide substituted furan, methylfuran, and methoxyfuran species. Standard enthalpies of formation for parent and radical species have been determined using density functional theory B3LYP/6-31G(d,p), B3LYP/6-311G(2d,2p), and M06-2X/6-31G(d,p) along with higher-level CBS-QB3 and CBS-APNO composite methods. Isodesmic work reactions were employed to improve accuracy by canceling error and show consistency between the levels of theory. Corresponding O-H and O-O BDEs are determined and compared to other similar structures. The stability of the furan moiety coupled with the double-bond-forming capability of the oxygen moiety results in a number of bond energies significantly lower than one might have expected. Substituted hydroperoxides are calculated to have ROO-H BDEs between 86.9 and 94.2 kcal mol -1 , and their RO-OH BDEs show a large 49 kcal mol -1 range of -2.3-46.8 kcal mol -1 . Substituted alcohols also show a wide 48 kcal mol -1 range with RO-H BDEs, ranging from 59.3 to 106.9 kcal mol -1 . Bond lengths of parent and radical species are presented to highlight potential bonds of interest leading to furan ring opening. Group additivity is discussed, and groups for substituted furan, methylfuran, and methoxyfuran species are derived. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) density functional level and are used to determine the S 298 ° and C p (T) values.

Dipole and Coulomb forces in electron capture dissociation and electron transfer dissociation mass spectroscopy.

PubMed

Świerszcz, Iwona; Skurski, Piotr; Simons, Jack

2012-02-23

Ab initio electronic structure calculations were performed on a doubly charged polypeptide model H(+)-Lys(Ala)(19)-CO-CH(NH(2))-CH(2)-SS-CH(2)-(NH(2))CH-CO-(Ala)(19)-Lys-H(+) consisting of a C-terminal protonated Lys followed by a 19-Ala α-helix with a 20th Ala-like unit whose side chain is linked by a disulfide bond to a corresponding Ala-like unit connected to a second 19-Ala α-helix terminated by a second C-terminal-protonated Lys. The Coulomb potentials arising from the two charged Lys residues and dipole potentials arising from the two oppositely directed 72 D dipoles of the α-helices act to stabilize the SS bond's σ* orbital. The Coulomb potentials provide stabilization of 1 eV, while the two large dipoles generate an additional 4 eV. Such stabilization allows the SS σ* orbital to attach an electron and thereby generate disulfide bond cleavage products. Although calculations are performed only on SS bond cleavage, discussion of N-C(α) bond cleavage caused by electron attachment to amide π* orbitals is also presented. The magnitudes of the stabilization energies as well as the fact that they arise from Coulomb and dipole potentials are supported by results on a small model system consisting of a H(3)C-SS-CH(3) molecule with positive and negative fractional point charges to its left and right designed to represent (i) two positive charges ca. 32 Å distant (i.e., the two charged Lys sites of the peptide model) and (ii) two 72 D dipoles (i.e., the two α-helices). Earlier workers suggested that internal dipole forces in polypeptides could act to guide incoming free electrons (i.e., in electron capture dissociation (ECD)) toward the positive end of the dipole and thus affect the branching ratios for cleaving various bonds. Those workers argued that, because of the huge mass difference between an anion donor and a free electron, internal dipole forces would have a far smaller influence over the trajectory of a donor (i.e., in electron transfer dissociation (ETD)). The present findings suggest that, in addition to their effects on guiding electron or donor trajectories, dipole potentials (in combination with Coulomb potentials) also alter the energies of SS σ* and amide π* orbitals, which then affects the ability of these orbitals to bind an electron. Thus, both by trajectory-guiding and by orbital energy stabilization, Coulomb and dipole potentials can have significant influences on the branching ratios of ECD and ETC in which disulfide or N-C(α) bonds are cleaved. © 2012 American Chemical Society

Small Water Cluster Cations

NASA Astrophysics Data System (ADS)

Novakovskaya, Yu. V.; Stepanov, N. F.

Structures of water cluster cations (H_{2}O)^{+}_{n} with n ≤ 5 are optimized at the unrestricted Hartree-Fock level with the 4 - 31 + +G** basis set. Energetic characteristics of the cations are then estimated taking into account the second order perturbation corrections (MP2). After the electron detachment from a neutral cluster, the structure of the latter substantially changes, so that OH and H3O+ fragments can be distinguished in it. In some cations H3O+ is so strongly bonded to water molecules that it is reasonable to speak of the [H2n-1On-1]+ fragments. According to the position of OH, the structures form two groups. In one group, OH acts exclusively as the proton acceptor in H-bonds with water molecules, thus being terminal in the chain-like structures; in the other group it is directly bonded to H3O and, as a proton donor, forms an H-bond with water molecule. Cluster cations do not tend to dissociate into the fragments. However, an external influence of ≤ 0.4 eV is sufficient for the cations of the first group to dissociate into a free OH radical and a protonated cluster H+(H2O)n-1. Extrapolation of the calculated adiabatic ionization potentials of the water clusters to n → ∞ provides a value of 8.6 eV, which can be considered as an estimation of the electron work function of water. This value is close to the experimental photoelectric thresholds of amorphous ice (8.7 ± 0.1 eV) and water (9.39 ± 0.3 eV). Solvation of the electron lowers the value, and an energy of 7 eV can be sufficient for initiating conductivity. This prediction is in accord with the experiment: irradiating ice with ultraviolet light of the photon energy 6.5-6.8 eV initiates photoconductivity, and hydrogen peroxide and H3O+ ions are observed.

High-order above-threshold dissociation of molecules.

PubMed

Lu, Peifen; Wang, Junping; Li, Hui; Lin, Kang; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Zhang, Wenbin; Ma, Junyang; Li, Hanxiao; Zeng, Heping; He, Feng; Wu, Jian

2018-02-27

Electrons bound to atoms or molecules can simultaneously absorb multiple photons via the above-threshold ionization featured with discrete peaks in the photoelectron spectrum on account of the quantized nature of the light energy. Analogously, the above-threshold dissociation of molecules has been proposed to address the multiple-photon energy deposition in the nuclei of molecules. In this case, nuclear energy spectra consisting of photon-energy spaced peaks exceeding the binding energy of the molecular bond are predicted. Although the observation of such phenomena is difficult, this scenario is nevertheless logical and is based on the fundamental laws. Here, we report conclusive experimental observation of high-order above-threshold dissociation of H 2 in strong laser fields where the tunneling-ionized electron transfers the absorbed multiphoton energy, which is above the ionization threshold to the nuclei via the field-driven inelastic rescattering. Our results provide an unambiguous evidence that the electron and nuclei of a molecule as a whole absorb multiple photons, and thus above-threshold ionization and above-threshold dissociation must appear simultaneously, which is the cornerstone of the nowadays strong-field molecular physics. Copyright © 2018 the Author(s). Published by PNAS.

Factors influencing the regioselectivity of the oxidation of asymmetric secondary amines with singlet oxygen.

PubMed

Ushakov, Dmitry B; Plutschack, Matthew B; Gilmore, Kerry; Seeberger, Peter H

2015-04-20

Aerobic amine oxidation is an attractive and elegant process for the α functionalization of amines. However, there are still several mechanistic uncertainties, particularly the factors governing the regioselectivity of the oxidation of asymmetric secondary amines and the oxidation rates of mixed primary amines. Herein, it is reported that singlet-oxygen-mediated oxidation of 1° and 2° amines is sensitive to the strength of the α-C-H bond and steric factors. Estimation of the relative bond dissociation energy by natural bond order analysis or by means of one-bond C-H coupling constants allowed the regioselectivity of secondary amine oxidations to be explained and predicted. In addition, the findings were utilized to synthesize highly regioselective substrates and perform selective amine cross-couplings to produce imines. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The pure rotational spectrum of ZnS (X 1Σ +)

NASA Astrophysics Data System (ADS)

Zack, L. N.; Ziurys, L. M.

2009-10-01

The pure rotational spectrum of ZnS (X 1Σ +) has been measured using direct-absorption millimeter/sub-millimeter techniques in the frequency range 372-471 GHz. This study is the first spectroscopic investigation of this molecule. Spectra originating in four zinc isotopologues ( 64ZnS, 66ZnS, 68ZnS, and 67ZnS) were recorded in natural abundance in the ground vibrational state, and data from the v = 1 state were also measured for the two most abundant zinc species. Spectroscopic constants have been subsequently determined, and equilibrium parameters have been estimated. The equilibrium bond length was calculated to be re ˜ 2.0464 Å, which agrees well with theoretical predictions. In contrast, the dissociation energy of DE ˜ 3.12 eV calculated for ZnS, assuming a Morse potential, was significantly higher than past experimental and theoretical estimates, suggesting diabatic interaction with other potentials that lower the effective dissociation energy. Although ZnS is isovalent with ZnO, there appear to be subtle differences in bonding between the two species, as suggested by their respective force constants and bond length trends in the 3d series.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

Adsorption of ammonia at GaN(0001) surface in the mixed ammonia/hydrogen ambient - a summary of ab initio data

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

Kempisty, Paweł; Krukowski, Stanisław; Interdisciplinary Centre for Materials Modelling, Warsaw University, Pawińskiego 5a, 02-106 Warsaw

Adsorption of ammonia at NH{sub 3}/NH{sub 2}/H-covered GaN(0001) surface was analyzed using results of ab initio calculations. The whole configuration space of partially NH{sub 3}/NH{sub 2}/H-covered GaN(0001) surface was divided into zones of differently pinned Fermi level: at the Ga broken bond state for dominantly bare surface (region I), at the valence band maximum (VBM) for NH{sub 2} and H-covered surface (region II), and at the conduction band minimum (CBM) for NH{sub 3}-covered surface (region III). The electron counting rule (ECR) extension was formulated for the case of adsorbed molecules. The extensive ab intio calculations show the validity of themore » ECR in case of all mixed H-NH{sub 2}-NH{sub 3} coverages for the determination of the borders between the three regions. The adsorption was analyzed using the recently identified dependence of the adsorption energy on the charge transfer at the surface. For region I ammonia adsorbs dissociatively, disintegrating into a H adatom and a HN{sub 2} radical for a large fraction of vacant sites, while for region II adsorption of ammonia is molecular. The dissociative adsorption energy strongly depends on the Fermi level at the surface (pinned) and in the bulk (unpinned) while the molecular adsorption energy is determined by bonding to surface only, in accordance to the recently published theory. Adsorption of Ammonia in region III (Fermi level pinned at CBM) leads to an unstable configuration both molecular and dissociative, which is explained by the fact that broken Ga-bonds are doubly occupied by electrons. The adsorbing ammonia brings 8 electrons to the surface, necessitating the transfer of these two electrons from the Ga broken bond state to the Fermi level. This is an energetically costly process. Adsorption of ammonia at H-covered site leads to the creation of a NH{sub 2} radical at the surface and escape of H{sub 2} molecule. The process energy is close to 0.12 eV, thus not large, but the direct inverse process is not possible due to the escape of the hydrogen molecule.« less

A Computational Study on the Ground and Excited States of Nickel Silicide.

PubMed

Schoendorff, George; Morris, Alexis R; Hu, Emily D; Wilson, Angela K

2015-09-17

Nickel silicide has been studied with a range of computational methods to determine the nature of the Ni-Si bond. Additionally, the physical effects that need to be addressed within calculations to predict the equilibrium bond length and bond dissociation energy within experimental error have been determined. The ground state is predicted to be a (1)Σ(+) state with a bond order of 2.41 corresponding to a triple bond with weak π bonds. It is shown that calculation of the ground state equilibrium geometry requires a polarized basis set and treatment of dynamic correlation including up to triple excitations with CR-CCSD(T)L resulting in an equilibrium bond length of only 0.012 Å shorter than the experimental bond length. Previous calculations of the bond dissociation energy resulted in energies that were only 34.8% to 76.5% of the experimental bond dissociation energy. It is shown here that use of polarized basis sets, treatment of triple excitations, correlation of the valence and subvalence electrons, and a Λ coupled cluster approach is required to obtain a bond dissociation energy that deviates as little as 1% from experiment.

Initial decomposition of the condensed-phase β-HMX under shock waves: molecular dynamics simulations.

PubMed

Ge, Ni-Na; Wei, Yong-Kai; Ji, Guang-Fu; Chen, Xiang-Rong; Zhao, Feng; Wei, Dong-Qing

2012-11-26

We have performed quantum-based multiscale simulations to study the initial chemical processes of condensed-phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock wave loading. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed. The results show that the initial decomposition of shocked HMX is triggered by the N-NO(2) bond breaking under the low velocity impact (8 km/s). As the shock velocity increases (11 km/s), the homolytic cleavage of the N-NO(2) bond is suppressed under high pressure, the C-H bond dissociation becomes the primary pathway for HMX decomposition in its early stages. It is accompanied by a five-membered ring formation and hydrogen transfer from the CH(2) group to the -NO(2) group. Our simulations suggest that the initial chemical processes of shocked HMX are dependent on the impact velocity, which gain new insights into the initial decomposition mechanism of HMX upon shock loading at the atomistic level, and have important implications for understanding and development of energetic materials.

Bond Dissociation Energies for Diatomic Molecules Containing 3d Transition Metals: Benchmark Scalar-Relativistic Coupled-Cluster Calculations for 20 Molecules

DOE PAGES

Cheng, Lan; Gauss, Jürgen; Ruscic, Branko; ...

2017-01-12

Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the 20 diatomic molecules containing 3d transition metals in the 3dMLBE20 database ( J. Chem. Theory Comput. 2015, 11, 2036) are reported in this paper. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of 16 molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol. The discrepancies between theory and experiment remain substantial (more than 20 kJ/mol) for VH, CrH, CoH, and FeH. To explore the source of themore » latter discrepancies, the analysis used to determine the experimental dissociation energies for VH and CrH is revisited. It is shown that, if improved values are used for the heterolytic C–H dissociation energies of di- and trimethylamine involved in the experimental determination, the experimental values for the dissociation energies of VH and CrH are increased by 18 kJ/mol, such that D 0(VH) = 223 ± 7 kJ/mol and D 0(CrH) = 204 ± 7 kJ/mol (or D e(VH) = 233 ± 7 kJ/mol and D e(CrH) = 214 ± 7 kJ/mol). Finally, the new experimental values agree quite well with the calculated values, showing the consistency of the computation and the measured reaction thresholds.« less

Density-functional theory based on the electron distribution on the energy coordinate

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki

2018-03-01

We developed an electronic density functional theory utilizing a novel electron distribution n(ɛ) as a basic variable to compute ground state energy of a system. n(ɛ) is obtained by projecting the electron density n({\\boldsymbol{r}}) defined on the space coordinate {\\boldsymbol{r}} onto the energy coordinate ɛ specified with the external potential {\\upsilon }ext}({\\boldsymbol{r}}) of interest. It was demonstrated that the Kohn-Sham equation can also be formulated with the exchange-correlation functional E xc[n(ɛ)] that employs the density n(ɛ) as an argument. It turned out an exchange functional proposed in our preliminary development suffices to describe properly the potential energies of several types of chemical bonds with comparable accuracies to the corresponding functional based on local density approximation. As a remarkable feature of the distribution n(ɛ) it inherently involves the spatially non-local information of the exchange hole at the bond dissociation limit in contrast to conventional approximate functionals. By taking advantage of this property we also developed a prototype of the static correlation functional E sc including no empirical parameters, which showed marked improvements in describing the dissociations of covalent bonds in {{{H}}}2,{{{C}}}2{{{H}}}4 and {CH}}4 molecules.

Gas-Phase Chemistry of Arylimido-Functionalized Hexamolybdates [Mo6O19]2-

NASA Astrophysics Data System (ADS)

Cao, Jie; Wang, QianQian; Liu, Chang; An, ShuQi

2018-04-01

The gas-phase fragmentations of a series of arylimido derivatives of hexamolybdate [Mo6O18(NC6H5-n R n )]2- (2-10, where R = CH3, i-C3H7, OCH3, NO2; n = 1 or 2) versus the parent species [Mo6O19]2- (1) were systematically studied using electrospray tandem mass spectrometry (ESI). Fragmentation of 1 generates two molybdate fragments only, [Mo3O10]2- and [Mo4O13]2-, whereas decomposition of 2-10 went through two dissociation pathways in which path A generates a variety of molybdate fragments via breaking the Mo-N bond followed by the cleavages of the multiple Mo-O bonds, whereas path B produces a range of molybdate fragments with arylimido group via breaking the multiple Mo-O bonds on POM framework. Moreover, the presences of mixed-oxidation-state molybdate fragments are characteristic for the fragmentation. The gas-phase stability order obtained by energy-variable collision-induced dissociation (CID) experiment reveals that 2-10 are generally less stable than 1 and substitution on the benzene ring exerts a considerable effect on the stabilization of the hybrid clusters. [Figure not available: see fulltext.

Specific Cα-C Bond Cleavage of β-Carbon-Centered Radical Peptides Produced by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Nagoshi, Keishiro; Yamakoshi, Mariko; Sakamoto, Kenya; Takayama, Mitsuo

2018-04-01

Radical-driven dissociation (RDD) of hydrogen-deficient peptide ions [M - H + H]·+ has been examined using matrix-assisted laser dissociation/ionization in-source decay mass spectrometry (MALDI-ISD MS) with the hydrogen-abstracting matrices 4-nitro-1-naphthol (4,1-NNL) and 5-nitrosalicylic acid (5-NSA). The preferential fragment ions observed in the ISD spectra include N-terminal [a] + ions and C-terminal [x]+, [y + 2]+, and [w]+ ions which imply that β-carbon (Cβ)-centered radical peptide ions [M - Hβ + H]·+ are predominantly produced in MALDI conditions. RDD reactions from the peptide ions [M - Hβ + H]·+ successfully explains the fact that both [a]+ and [x]+ ions arising from cleavage at the Cα-C bond of the backbone of Gly-Xxx residues are missing from the ISD spectra. Furthermore, the formation of [a]+ ions originating from the cleavage of Cα-C bond of deuterated Ala(d3)-Xxx residues indicates that the [a]+ ions are produced from the peptide ions [M - Hβ + H]·+ generated by deuteron-abstraction from Ala(d3) residues. It is suggested that from the standpoint of hydrogen abstraction via direct interactions between the nitro group of matrix and hydrogen of peptides, the generation of the peptide radical ions [M - Hβ + H]·+ is more favorable than that of the α-carbon (Cα)-centered radical ions [M - Hα + H]·+ and the amide nitrogen-centered radical ions [M - HN + H]·+, while ab initio calculations indicate that the formation of [M - Hα + H]·+ is energetically most favorable. [Figure not available: see fulltext.

Rare Gases Inserted into Biological Building Blocks: A Theoretical Study of Glycine - Rg Compounds (Rg-Xe, Kr, Ar)

NASA Technical Reports Server (NTRS)

Chaban, Galina M.

2005-01-01

Compounds formed by insertion of rare-gas atoms (Xe, Kr, and Ar) into glycine molecule are investigated using accurate ab initio computational methods. Identification of such insertion compounds may open new frontiers in the field of rare-gas chemistry, such as possible existence of biological molecules that include chemically bound rare gas atoms. The most stable glycine-Rg configuration is found to correspond to insertion of Rg atoms into the 0-H bond of glycine. These NH2CH2COORgH compounds are metastable , but separated by sizable potential barriers from the Rg + glycine dissociation products. Preliminary calculations show that NH2CH2COOXeH compound is energetically stable with respect to another (3-body) dissociation channel (NH2CH2COO + Rg + H), while the corresponding Ar species is not stable in this respect. The compound with the inserted Kr is a borderline case, with the 3-body dissociation products being close in energy to the NH2CH2COOKrH minimum.

Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+-water.

PubMed

Chatterjee, Kuntal; Dopfer, Otto

2017-12-13

Polycyclic aromatic hydrocarbons (PAHs) are suggested to occur in interstellar media and ice grains. It is important to characterize hydrated PAHs and their cations to explore their stability in interstellar and biological media. Herein, the infrared photodissociation (IRPD) spectrum of the naphthalene + -H 2 O radical cation (Np + -H 2 O) recorded in the O-H and C-H stretch range is analysed by dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level to determine its structure and intermolecular bonding. Monohydration of Np + in its 2 A u ground electronic state leads to the formation of a bifurcated CHO ionic hydrogen bond (H-bond), in which the lone pairs of H 2 O bind to two adjacent CH proton donors of the two aromatic rings. The frequency-dependent branching ratios observed for IRPD of cold Np + -H 2 O-Ar clusters allows the estimation of the dissociation energy of Np + -H 2 O as D 0 ∼ 2800 ± 300 cm -1 . The monohydration motif of Np + differs qualitatively from that of the benzene cation in both structure and binding energy, indicating the strong influence of the multiple aromatic rings on the hydration of PAH + cations. This difference is rationalized by natural bond orbital analysis of the ionic H-bond motif. Comparison with neutral Np-H 2 O reveals the large change in structure and bond strength of the hydrated PAHs upon ionization. While neutral Np-H 2 O is stabilized by weak π H-bonds (OHπ, π-stacking), strong cation-dipole forces favour a planar bifurcated CHO ionic H-bond in Np + -H 2 O.

Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX

PubMed Central

Liu, Lin-lin; Liu, Pei-jin; Hu, Song-qi; He, Guo-qiang

2017-01-01

NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10−10 s−1) when the temperature was less than 1000 K. PMID:28094774

The role of Zn2+ dopants in the acid-basic catalysis on MgO(001) surface: Ab initio simulations of the dissociative chemisorption of R-O-R‧ and R-S-R‧ (R, R ‧ = H , CH3, C2H5)

NASA Astrophysics Data System (ADS)

Fonseca, Carla G.; Tavares, Sérgio R.; Soares, Carla V.; daFonseca, Bruno G.; Henrique, Fábio J. F. S.; Vaiss, Viviane S.; Souza, Wladmir F.; Chiaro, Sandra S. X.; Diniz, Renata; Leitão, Alexandre A.

2017-07-01

Ab initio calculations were performed to study the effect of the Zn2+ dopant on the reactivity and the catalytic activity of the MgO(001) surface toward molecular adsorption and dissociation reactions of the H2O, H2S, CH3CH2OH, CH3CH2SH and CH3SCH3 molecules. The electronic analysis showed that Zn2+ cation increased the reactivity of the surface locally. All molecules dissociate on both surfaces except for water and ethanol which only dissociate on the MgO:Zn(001) surface, confirming the increased reactivity in this surface. The ΔG ° for the dissociation reactions of the CH3CH2SH and CH3SCH3 molecules on pure MgO(001) surface is positive in the entire temperature range. On the other hand, the ΔG ° for H2S molecule is negative until 148.7 °C. In the case of the MgO:Zn(001) surface, the CH3CH2SH molecule dissociates in the entire temperature range and, for H2S molecule, the dissociation is spontaneous until 349.7 °C. The rate constants obtained for the dissociation reactions were very large because the reaction barriers are very low in both surfaces for all the studied molecules, except for CH3SCH3 molecule. The Zn-doped MgO(001) surface, besides being more reactive, presented a better catalytic activity than the MgO(001) surface for the dissociation of this molecule.

Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm

NASA Astrophysics Data System (ADS)

Talbert, Lance E.; Julian, Ryan R.

2018-04-01

Ultraviolet photodissociation or UVPD is an increasingly popular option for tandem-mass spectrometry experiments. UVPD can be carried out at many wavelengths, and it is important to understand how the results will be impacted by this choice. Here, we explore the utility of 213 nm photons for initiating bond-selective fragmentation. It is found that bonds previously determined to be labile at 266 nm, including carbon-iodine and sulfur-sulfur bonds, can also be cleaved with high selectivity at 213 nm. In addition, many carbon-sulfur bonds that are not subject to direct dissociation at 266 nm can be selectively fragmented at 213 nm. This capability can be used to site-specifically create alaninyl radicals that direct backbone dissociation at the radical site, creating diagnostic d-ions. Furthermore, the additional carbon-sulfur bond fragmentation capability leads to signature triplets for fragmentation of disulfide bonds. Absorption of amide bonds can enhance dissociation of nearby labile carbon-sulfur bonds and can be used for stochastic backbone fragmentation typical of UVPD experiments at shorter wavelengths. Several potential applications of the bond-selective fragmentation chemistry observed at 213 nm are discussed. [Figure not available: see fulltext.

Effect of kinetic and electronic energy on the reactions of Mn + with H2, HD, and D2

NASA Astrophysics Data System (ADS)

Elkind, J. L.; Armentrout, P. B.

1986-05-01

Reactions of several electronic states of Mn+ with H2, HD, and D2 have been examined using guided ion beam mass spectroscopy. The excitation function for the ground state of Mn+(7S) has two regions: one of very low reactivity at threshold and another more efficient pathway at higher energies. In contrast, the 5S and 5D states react efficiently at their thermodynamic thresholds. In reaction with HD, the 5S and 5D states produce ≊3 times as much MnH+ as MnD+ in the threshold region. This isotope effect is similar to that seen in previous studies of transition metal ion reactions. Reaction of Mn+(7S) with HD, on the other hand, exhibits an extreme isotope effect such that MnD+ is formed almost exclusively. The state dependence of the reactivity and reaction mechanisms is explained using simple molecular orbital concepts. The results are analyzed to yield a bond dissociation energy at 0 K for MnH+ of 2.06±0.15 eV (47.5±3.4 kcal/mol).

Anopheles gambiae Purine Nucleoside Phosphorylase: Catalysis, Structure, and Inhibition

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

Taylor,E.; Rinaldo-Matthis, A.; Li, L.

The purine salvage pathway of Anopheles gambiae, a mosquito that transmits malaria, has been identified in genome searches on the basis of sequence homology with characterized enzymes. Purine nucleoside phosphorylase (PNP) is a target for the development of therapeutic agents in humans and purine auxotrophs, including malarial parasites. The PNP from Anopheles gambiae (AgPNP) was expressed in Escherichia coli and compared to the PNPs from Homo sapiens (HsPNP) and Plasmodium falciparum (PfPNP). AgPNP has kcat values of 54 and 41 s-1 for 2'-deoxyinosine and inosine, its preferred substrates, and 1.0 s-1 for guanosine. However, the chemical step is fast formore » AgPNP at 226 s-1 for guanosine in pre-steady-state studies. 5'-Deaza-1'-aza-2'-deoxy-1'-(9-methylene)-Immucillin-H (DADMe-ImmH) is a transition-state mimic for a 2'-deoxyinosine ribocation with a fully dissociated N-ribosidic bond and is a slow-onset, tight-binding inhibitor with a dissociation constant of 3.5 pM. This is the tightest-binding inhibitor known for any PNP, with a remarkable Km/Ki* of 5.4 x 107, and is consistent with enzymatic transition state predictions of enhanced transition-state analogue binding in enzymes with enhanced catalytic efficiency. Deoxyguanosine is a weaker substrate than deoxyinosine, and DADMe-Immucillin-G is less tightly bound than DADMe-ImmH, with a dissociation constant of 23 pM for AgPNP as compared to 7 pM for HsPNP. The crystal structure of AgPNP was determined in complex with DADMe-ImmH and phosphate to a resolution of 2.2 Angstroms to reveal the differences in substrate and inhibitor specificity. The distance from the N1' cation to the phosphate O4 anion is shorter in the AgPNP{center_dot}DADMe-ImmH{center_dot}PO4 complex than in HsPNP{center_dot}DADMe-ImmH{center_dot}SO4, offering one explanation for the stronger inhibitory effect of DADMe-ImmH for AgPNP.« less

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

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

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Dissociation energy and dynamics of water clusters

NASA Astrophysics Data System (ADS)

Ch'ng, Lee Chiat

The state-to-state vibrational predissociation (VP) dynamics of water clusters were studied following excitation of a vibrational mode of each cluster. Velocity-map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated center-of-mass translational energy distributions. Product energy distributions and dissociation energies were determined. Following vibrational excitation of the HCl stretch fundamental of the HCl-H2O dimer, HCl fragments were detected by 2 + 1 REMPI via the f 3□2(nu' = 0) ← X 1Sigma+(nu'' = 0) and V1Sigma + (nu' = 11 and 12) ← X1Sigma+ (nu'' = 0) transitions. REMPI spectra clearly show HCl from dissociation produced in the ground vibrational state with J'' up to 11. The fragments' center-of-mass translational energy distributions were determined from images of selected rotational states of HCl and were converted to rotational state distributions of the water cofragment. All the distributions could be fit well when using a dimer dissociation energy of bond dissociation energy D0 = 1334 +/- 10 cm--1. The rotational distributions in the water cofragment pair-correlated with specific rotational states of HCl appear nonstatistical when compared to predictions of the statistical phase space theory. A detailed analysis of pair-correlated state distributions was complicated by the large number of water rotational states available, but the data show that the water rotational populations increase with decreasing translational energy. H2O fragments of this dimer were detected by 2 + 1 REMPI via the C˜1B1(000) ← X˜1A1(000) transition. REMPI clearly shows that H2O from dissociation is produced in the ground vibrational state. The fragment's center-of-mass translational energy distributions were determined from images of selected rotational states of H2O and were converted to rotational state distributions of the HCl cofragment. The distributions gave D0 = 1334 +/- 10 cm --1 and show a clear preference for rotational levels in the HCl fragment that minimize translational energy release. The usefulness of 2 + 1 REMPI detection of water fragment is discussed. The hydrogen bonding in water is dominated by pair-wise dimer interactions, and the predissociation of the water dimer following vibrational excitation is reported. The measured D0 values of (H 2O)2 and (D2O)2, 1105 and 1244 +/- 10 cm--1, respectively, are in excellent agreement with the calculated values of 1103 and 1244 +/- 5 cm--1. Pair-correlated water fragment rovibrational state distributions following vibrational predissociation of (H2O)2 and (D2O) 2 were obtained upon excitation of the hydrogen bonded OH and OD stretch fundamentals, respectively. Quasiclassical trajectory calculations, using an accurate full-dimensional potential energy surface, are in accord with and help to elucidate experiment. Experiment and theory find predominant excitation of the fragment bending mode upon hydrogen bond breaking. A minor channel is also observed in which both fragments are in the ground vibrational state and are highly rotationally excited. The theoretical calculations reveal equal probability of bending excitation in the donor and acceptor subunits, which is a result of interchange of donor and acceptor roles. The rotational distributions associated with the major channel, in which one water fragment has one quantum of bend, and the minor channel with both water fragments in the ground vibrational state are calculated, and are in agreement with experiment. (Abstract shortened by UMI.)

Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B⋯A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds.

PubMed

Alkorta, Ibon; Legon, Anthony C

2017-10-23

It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N₂, CO, HC≡CH, CH₂=CH₂, C₃H₆, PH₃, H₂S, HCN, H₂O, H₂CO and NH₃) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H₂O, F₂, Cl₂, Br₂, ClF, BrCl, H₃SiF, H₃GeF, F₂CO, CO₂, N₂O, NO₂F, PH₂F, AsH₂F, SO₂, SeO₂, SF₂, and SeF₂) can be represented to good approximation by means of the equation D e = c ' N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c ' is a constant, conveniently chosen to have the value 1.00 kJ mol -1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy.

Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

PubMed

Wei, YuJie

2008-03-01

We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

Far-UV photochemical bond cleavage of n-amyl nitrite: bypassing a repulsive surface.

PubMed

Minitti, Michael P; Zhang, Yao; Rosenberg, Martin; Brogaard, Rasmus Y; Deb, Sanghamitra; Sølling, Theis I; Weber, Peter M

2012-01-19

We have investigated the deep-UV photoinduced, homolytic bond cleavage of amyl nitrite to form NO and pentoxy radicals. One-color multiphoton ionization with ultrashort laser pulses through the S(2) state resonance gives rise to photoelectron spectra that reflect ionization from the S(1) state. Time-resolved pump-probe photoionization measurements show that upon excitation at 207 nm, the generation of NO in the v = 2 state is delayed, with a rise time of 283 (16) fs. The time-resolved mass spectrum shows the NO to be expelled with a kinetic energy of 1.0 eV, which is consistent with dissociation on the S(1) state potential energy surface. Combined, these observations show that the first step of the dissociation reaction involves an internal conversion from the S(2) to the S(1) state, which is followed by the ejection of the NO radical on the predissociative S(1) state potential energy surface.

Fast MAS 1H NMR Study of Water Adsorption and Dissociation on the (100) Surface of Ceria Nanocubes: A Fully Hydroxylated, Hydrophobic Ceria Surface

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

Gill, Lance; Beste, Ariana; Chen, Banghao

1H nuclear magnetic resonance (NMR) spectroscopy was used to study hydroxylic surface species on ceria nanocubes, a crystalline, high-surface-area CeO 2 that presents mostly (100) facets. Water adsorption and desorption experiments in combination with fast magic angle spinning (MAS, 20–40 kHz) 1H NMR provide high-resolution 1H spectra that allow the observation of ten resonance bands (water or hydroxyl) on or under the (100) surface. Assignments were made using a combination of adsorption and temperature-programmed desorption, quantitative spin counting, deuterium exchange, spin–lattice (T 1) and spin–spin (T 2) relaxation, and DFT calculations. In air, the (100) surface exists as a fullymore » hydroxylated surface. Water adsorption and dissociation on dry ceria surfaces occur first at oxygen vacancies, but Ce 3+ centers are not required since water dissociation is barrier-less on the fully oxidized surface. Surface $-$OH functionality occurs in two resolved bands representing isolated $-$OH (1 ppm) and hydrogen-bonded $-$OH (9 ppm), the latter being dominant. Deuterium exchange of surface hydroxyls with D 2O does not occur under mild or forcing conditions. Despite large differences in the T 1 of surface hydroxyls and physisorbed water, surface hydroxyl T 1 values are independent of the presence or absence of physisorbed water, demonstrating that the protons within these two functional group pools are not in intimate contact. These observations show that, once hydroxylated, the surface $-$OH functionality preferentially forms hydrogen bonds with surface lattice oxygen, i.e., the hydroxylated (100) surface of ceria is hydrophobic. Near this surface it is energetically more favorable for physisorbed water to hydrogen bond to itself rather than to the surface. DFT calculations support this notion. Impurity Na + remaining in incompletely washed ceria nanocubes increases the surface hydrophilicity. In conclusion, sharp, low-field resonances observed in spectra of noncalcined nanocubes arise from kinetically trapped subsurface $-$OH.« less

Fast MAS 1H NMR Study of Water Adsorption and Dissociation on the (100) Surface of Ceria Nanocubes: A Fully Hydroxylated, Hydrophobic Ceria Surface

DOE PAGES

Gill, Lance; Beste, Ariana; Chen, Banghao; ...

2017-03-22

1H nuclear magnetic resonance (NMR) spectroscopy was used to study hydroxylic surface species on ceria nanocubes, a crystalline, high-surface-area CeO 2 that presents mostly (100) facets. Water adsorption and desorption experiments in combination with fast magic angle spinning (MAS, 20–40 kHz) 1H NMR provide high-resolution 1H spectra that allow the observation of ten resonance bands (water or hydroxyl) on or under the (100) surface. Assignments were made using a combination of adsorption and temperature-programmed desorption, quantitative spin counting, deuterium exchange, spin–lattice (T 1) and spin–spin (T 2) relaxation, and DFT calculations. In air, the (100) surface exists as a fullymore » hydroxylated surface. Water adsorption and dissociation on dry ceria surfaces occur first at oxygen vacancies, but Ce 3+ centers are not required since water dissociation is barrier-less on the fully oxidized surface. Surface $-$OH functionality occurs in two resolved bands representing isolated $-$OH (1 ppm) and hydrogen-bonded $-$OH (9 ppm), the latter being dominant. Deuterium exchange of surface hydroxyls with D 2O does not occur under mild or forcing conditions. Despite large differences in the T 1 of surface hydroxyls and physisorbed water, surface hydroxyl T 1 values are independent of the presence or absence of physisorbed water, demonstrating that the protons within these two functional group pools are not in intimate contact. These observations show that, once hydroxylated, the surface $-$OH functionality preferentially forms hydrogen bonds with surface lattice oxygen, i.e., the hydroxylated (100) surface of ceria is hydrophobic. Near this surface it is energetically more favorable for physisorbed water to hydrogen bond to itself rather than to the surface. DFT calculations support this notion. Impurity Na + remaining in incompletely washed ceria nanocubes increases the surface hydrophilicity. In conclusion, sharp, low-field resonances observed in spectra of noncalcined nanocubes arise from kinetically trapped subsurface $-$OH.« less

MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

NASA Astrophysics Data System (ADS)

Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

2017-06-01

In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-05-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-01-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Mode Specific Electronic Friction in Dissociative Chemisorption on Metal Surfaces: H2 on Ag(111)

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Jiang, Bin; Guo, Hua; Tully, John C.

2017-06-01

Electronic friction and the ensuing nonadiabatic energy loss play an important role in chemical reaction dynamics at metal surfaces. Using molecular dynamics with electronic friction evaluated on the fly from density functional theory, we find strong mode dependence and a dominance of nonadiabatic energy loss along the bond stretch coordinate for scattering and dissociative chemisorption of H2 on the Ag(111) surface. Exemplary trajectories with varying initial conditions indicate that this mode specificity translates into modulated energy loss during a dissociative chemisorption event. Despite minor nonadiabatic energy loss of about 5%, the directionality of friction forces induces dynamical steering that affects individual reaction outcomes, specifically for low-incidence energies and vibrationally excited molecules. Mode-specific friction induces enhanced loss of rovibrational rather than translational energy and will be most visible in its effect on final energy distributions in molecular scattering experiments.

Block Copolymer-Based Supramolecular Elastomers with High Extensibility and Large Stress Generation Capability

NASA Astrophysics Data System (ADS)

Noro, Atsushi; Hayashi, Mikihiro

We prepared block copolymer-based supramolecular elastomers with high extensibility and large stress generation capability. Reversible addition fragmentation chain transfer polymerizations were conducted under normal pressure and high pressure to synthesize several large molecular weight polystyrene-b-[poly(butyl acrylate)-co-polyacrylamide]-b-polystyrene (S-Ba-S) block copolymers. Tensile tests revealed that the largest S-Ba-S with middle block molecular weight of 3140k achieved a breaking elongation of over 2000% with a maximum tensile stress of 3.6 MPa and a toughness of 28 MJ/m3 while the reference sample without any middle block hydrogen bonds, polystyrene-b-poly(butyl acrylate)-b-polystyrene with almost the same molecular weight, was merely viscous and not self-standing. Hence, incorporation of hydrogen bonds into a long soft middle block was found to be beneficial to attain high extensibility and large stress generation capability probably due to concerted combination of entropic changes and internal potential energy changes originaing from the dissociation of multiple hydrogen bonds by elongation. This work was supported by JSPS KAKENHI Grant Numbers 13J02357, 24685035, 15K13785, and 23655213 for M.H. and A.N. A.N. also expresses his gratitude for Tanaka Rubber Science & Technology Award by Enokagaku-Shinko Foundation, Japan.

Selectivity of peptide bond dissociation on excitation of a core electron: Effects of a phenyl group

NASA Astrophysics Data System (ADS)

Tsai, Cheng-Cheng; Chen, Jien-Lian; Hu, Wei-Ping; Lin, Yi-Shiue; Lin, Huei-Ru; Lee, Tsai-Yun; Lee, Yuan T.; Ni, Chi-Kung; Liu, Chen-Lin

2016-09-01

The selective dissociation of a peptide bond upon excitation of a core electron in acetanilide and N-benzylacetamide was investigated. The total-ion-yield near-edge X-ray absorption fine structure spectra were recorded and compared with the predictions from time-dependent density functional theory. The branching ratios for the dissociation of a peptide bond are observed as 16-34% which is quite significant. This study explores the core-excitation, the X-ray photodissociation pathways, and the theoretical explanation of the NEXAFS spectra of organic molecules containing both a peptide bond and a phenyl group.

Dissociative excitation of H2, HD, and D2 by electron impact

NASA Technical Reports Server (NTRS)

Carnahan, B. L.; Zipf, E. C.

1977-01-01

Time-of-flight techniques have been used to investigate the electron-impact dissociation of H2, HD, and D2 in order to determine the effect of isotopic mass variation in the target molecule on the dissociative excitation process. At incident electron energies near 100 eV, the time-of-flight spectrum produced from each molecule consists of atoms in the metastable 2s state and in high-lying long-lived Rydberg levels. The individual time-of-flight distributions, kinetic-energy spectra, and relative differential cross sections for these two species resulting from each molecule have been measured. The kinetic-energy spectrum of the Rydberg atoms produced from dissociative excitation of H2 was notably dissimilar in shape from the corresponding distributions produced from HD and D2. Also the 2s and Rydberg production cross sections differed between the three molecules. In the dissociation of the heteronuclear HD molecule, the ratio of fast H(2s) atoms to D(2s) atoms was about 1 to 1, while the same ratio comparing the Rydberg atoms was nearly 2 to 1. These differences indicate the influence of the mass variation on the position of the Franck-Condon region in the production of 2s atoms and on the competition between autoionization and dissociation in the formation of Rydberg fragments.

Molecular models of site-isolated cobalt, rhodium, and iridium catalysts supported on zeolites: Ligand bond dissociation energies

DOE PAGES

Chen, Mingyang; Serna, Pedro; Lu, Jing; ...

2015-09-28

The chemistry of zeolite-supported site-isolated cobalt, rhodium, and iridium complexes that are essentially molecular was investigated with density functional theory (DFT) and the results compared with experimentally determined spectra characterizing rhodium and iridium species formed by the reactions of Rh(C 2H 4) 2(acac) and Ir(C 2H 4) 2(acac) (acac = acetylacetonate) with acidic zeolites such as dealuminated HY zeolite. The experimental results characterize ligand exchange reactions and catalytic reactions of adsorbed ligands, including olefin hydrogenation and dimerization. Two molecular models were used to characterize various binding sites of the metal complexes in the zeolites, and the agreement between experimental andmore » calculated infrared frequencies and metal-ligand distances determined by extended X-ray absorption fine structure spectroscopy was generally very good. The calculated structures and energies indicate a metal-support-oxygen (M(I)-O) coordination number of two for most of the supported complexes and a value of three when the ligands include the radicals C 2H 5 or H. The results characterizing various isomers of the supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. Ligand bond dissociation energies (LDEs) are reported to explain the observed reactivity trends. The experimental observations of a stronger M-CO bond than M-(C 2H 4) bond for both Ir and Rh match the calculated LDEs, which show that the single-ligand LDEs of the mono and dual-ligand complexes for CO are similar to 12 and similar to 15 kcal/mol higher in energy (when the metal is Rh) and similar to 17 and similar to 20 kcal/mol higher (when the metal is Ir) than the single-ligand LDEs of the mono and dual ligand complexes for C 2H 4, respectively. The results provide a foundation for the prediction of the catalytic properties of numerous supported metal complexes, as summarized in detail here.« less

Thermochemistry of C7H16 to C10H22 alkane isomers: primary, secondary, and tertiary C-H bond dissociation energies and effects of branching.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W; Simmie, John M

2014-10-09

Standard enthalpies of formation (ΔH°f 298) of methyl, ethyl, primary and secondary propyl, and n-butyl radicals are evaluated and used in work reactions to determine internal consistency. They are then used to calculate the enthalpy of formation for the tert-butyl radical. Other thermochemical properties including standard entropies (S°(T)), heat capacities (Cp(T)), and carbon-hydrogen bond dissociation energies (C-H BDEs) are reported for n-pentane, n-heptane, 2-methylhexane, 2,3-dimethylpentane, and several branched higher carbon number alkanes and their radicals. ΔH°f 298 and C-H BDEs are calculated using isodesmic work reactions at the B3LYP (6-31G(d,p) and 6-311G(2d,2p) basis sets), CBS-QB3, CBS-APNO, and G3MP2B3 levels of theory. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) level for contributions to entropy and heat capacities. Enthalpy calculations for these hydrocarbon radical species are shown to have consistency with the CBS-QB3 and CBS-APNO methods using all work reactions. Our recommended ideal gas phase ΔH°f 298 values are from the average of all CBS-QB3, CBS-APNO, and for G3MP2B3, only where the reference and target radical are identical types, and are compared with literature values. Calculated values show agreement between the composite calculation methods and the different work reactions. Secondary and tertiary C-H bonds in the more highly branched alkanes are shown to have bond energies that are several kcal mol(-1) lower than the BDEs in corresponding smaller molecules often used as reference species. Entropies and heat capacities are calculated and compared to literature values (when available) when all internal rotors are considered.

QTAIM electron density study of natural chalcones

NASA Astrophysics Data System (ADS)

González Moa, María J.; Mandado, Marcos; Cordeiro, M. Natália D. S.; Mosquera, Ricardo A.

2007-09-01

QTAIM atomic and bond properties, ionization potential, and O-H bond dissociation energies calculated at the B3LYP/6-311++G(2d,2p) level indicate the natural chalcones bear a significant radical scavenging activity. However, their ionization potentials indicate they decrease the electron-transfer rate between antioxidant and oxygen that yields the pro-oxidative cations less than other natural antioxidants. Rings A and B display slight and similar positive charges, whereas ring B is involved in exocycle delocalization at a larger extension.

Charge transfer photodissociation of phenol on Ag(111)

NASA Astrophysics Data System (ADS)

Lee, Junseok; Ryu, Sunmin; Ku, Jong Seok; Kim, Seong Keun

2001-12-01

The photochemistry of phenol on Ag(111) has been investigated by post-irradiation temperature programmed desorption (TPD). Ultraviolet (UV) irradiation at 355 and 266 nm was found to affect only the chemisorption layer in direct contact with the metal surface, while leaving the multilayer virtually intact. The main photoinduced reaction was found to be photodissociation of the O-H bond of phenol. Two new peaks were observed at the mass of phenol in the post-irradiation TPD spectrum at 335 K and 455 K. These peaks were assigned to the recombinative desorption of phenoxy with the hydrogen from O-H bond photodissociation and from thermal C-H bond fission, respectively. The photodissociation cross section was measured at different wavelengths and coverages. A charge transfer type photodissociation mechanism was proposed, where hot electrons generated in the substrate by UV photons attach to the affinity level of the adsorbed phenol. The transition to the transient anionic potential then leads to facile dissociation of O-H bond. The affinity level of phenol has been estimated to lie at 3.2-3.5 eV above the Fermi level for the 1 ML case.

Blackbody infrared radiative dissociation of protonated oligosaccharides.

PubMed

Fentabil, Messele A; Daneshfar, Rambod; Kitova, Elena N; Klassen, John S

2011-12-01

The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel(6)), which is composed of β-(1→4)-linked glucopyranose rings, and five malto-oligosaccharides (Mal(x), where x=4-8), which are composed of α-(1→4)-linked glucopyranose units. At the temperatures investigated (85-160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B(1) and B(2)) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (E(a) and A) were determined. The E(a) and A-factors measured for protonated Mal(x) (x>4) are indistinguishable within error (~19 kcal mol(-1), 10(10) s(-1)), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel(6) (24 kcal mol(-1), 10(12) s(-1)) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage. © American Society for Mass Spectrometry, 2011

Blackbody infrared radiative dissociation of oligonucleotide anions.

PubMed

Klassen, J S; Schnier, P D; Williams, E R

1998-11-01

The dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [d(A)7(2-), d(AATTAAT)2-, d(TTAATTA)2-, and d(CCGGCCG)2-] were measured using blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. The oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5') phosphodiester bond to produce structurally informative a-base and w type ions. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained for the loss of base. The measured Arrhenius parameters are dependent on the identity of the nucleobase. The process involving the loss of an adenine base from the dianions, d(A)7(2-), d(AATTAAT)2-, and d(TTAATTA)2- has an average activation energy (Ea) of approximately 1.0 eV and a preexponential factor (A) of 10(10) s-1. Both guanine and cytosine base loss occurs for d(CCGGCCG)2-. The average Arrhenius parameters for the loss of cytosine and guanine are Ea = 1.32 +/- 0.03 eV and A = 10(13.3 +/- 0.3) s-1. No loss of thymine was observed for mixed adenine-thymine oligonucleotides. Neither base loss nor any other fragmentation reactions occur for d(T)7(2-) over a 600 s reaction delay at 207 degrees C, a temperature close to the upper limit accessible with our instrument. The Arrhenius parameters indicate that the preferred cleavage sites for mixed oligonucleotides of similar mass-to-charge ratio will be strongly dependent on the internal energy of the precursor ions. At low internal energies (effective temperatures below 475 K), loss of adenine and subsequent cleavage of the adjacent phosphoester bonds will dominate, whereas at higher energies, preferential cleavage at C and G residues will occur. The magnitude of the A factors < or = 10(13) s-1 measured for the loss of the three nucleobases (A, G, and C) is indicative of an entropically neutral or disfavored process as the rate limiting step for this reaction.

Non-adiabatic behavior in the homolytic and heterolytic bond dissociation of protonated hydrazine: A guided ion beam and theoretical investigation

NASA Astrophysics Data System (ADS)

McNary, Christopher P.; Armentrout, P. B.

2017-09-01

Threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer was performed on protonated hydrazine and its perdeuterated variant. The dominant dissociation pathways observed were endothermic homolytic and heterolytic cleavages of the N-N bond. The data were analyzed using a statistical model after accounting for internal and kinetic energy distributions, multiple collisions, and kinetic shifts to obtain 0 K bond dissociation energies. Comparison with literature thermochemistry demonstrates that both channels behave non-adiabatically. Heterolytic bond cleavage yields NH2+ + NH3 products, but the NH2+ fragment is in the spin-restricted excited 1A1 state and not in the spin-forbidden ground 3B1 state, whereas homolytic bond cleavage leads to dissociation to the NH3+ + NH2 product asymptote with NH2 in its excited 2A1 state rather than the energetically favored 2B1 state. The rationale for the non-adiabatic behavior observed in the homolytic bond cleavage is revealed by detailed theoretical calculations of the relevant potential energy surfaces and the relevant occupied valence molecular orbitals. These calculations suggest that the non-adiabatic behavior results from conservation of the σ and π character of the binding and lone pair electrons on the nitrogen atoms.

A matrix of heterobimetallic complexes for interrogation of hydrogen evolution reaction electrocatalysts.

PubMed

Ghosh, Pokhraj; Ding, Shengda; Chupik, Rachel B; Quiroz, Manuel; Hsieh, Chung-Hung; Bhuvanesh, Nattami; Hall, Michael B; Darensbourg, Marcetta Y

2017-12-01

Experimental and computational studies address key questions in a structure-function analysis of bioinspired electrocatalysts for the HER. Combinations of NiN 2 S 2 or [(NO)Fe]N 2 S 2 as donors to (η 5 -C 5 H 5 )Fe(CO) + or [Fe(NO) 2 ] +/0 generate a series of four bimetallics, gradually "softened" by increasing nitrosylation, from 0 to 3, by the non-innocent NO ligands. The nitrosylated NiFe complexes are isolated and structurally characterized in two redox levels, demonstrating required features of electrocatalysis. Computational modeling of experimental structures and likely transient intermediates that connect the electrochemical events find roles for electron delocalization by NO, as well as Fe-S bond dissociation that produce a terminal thiolate as pendant base well positioned to facilitate proton uptake and transfer. Dihydrogen formation is via proton/hydride coupling by internal S-H + ··· - H-Fe units of the "harder" bimetallic arrangements with more localized electron density, while softer units convert H - ···H - via reductive elimination from two Fe-H deriving from the highly delocalized, doubly reduced [Fe 2 (NO) 3 ] - derivative. Computational studies also account for the inactivity of a Ni 2 Fe complex resulting from entanglement of added H + in a pinched -S δ - ···H + ··· δ - S- arrangement.

Electride support boosts nitrogen dissociation over ruthenium catalyst and shifts the bottleneck in ammonia synthesis

DOE PAGES

Kitano, Masaaki; Kanbara, Shinji; Inoue, Yasunori; ...

2015-03-30

We actively sough novel approaches to efficient ammonia synthesis at an ambient pressure so as to reduce the cost of ammonia production and to allow for compact production facilities. It is accepted that the key is the development of a high-performance catalyst that significantly enhances dissociation of the nitrogen-nitrogen triple bond, which is generally considered a rate-determining step. Here we examine the kinetics of nitrogen and hydrogen isotope exchange and hydrogen adsorption/desorption reactions for a recently discovered efficient catalyst for ammonia synthesis --ruthenium-loaded 12CaO∙7AI 2O 3 electride (Ru/C12A7:more » $$\\bar{e}$$ )--and find that the rate controlling step of ammonia synthesis over Ru/C12A7:$$\\bar{e}$$ is not dissociation of the nitrogen-nitrogen triple bond but the subsequent formation of N-H n species. A mechanism of ammonia synthesis involving reversible storage and release of hydrogen atoms on the Ru/C12A7:$$\\bar{e}$$ surface is proposed on the basis of observed hydrogen adsorption/desorption kinetics.« less

Electride support boosts nitrogen dissociation over ruthenium catalyst and shifts the bottleneck in ammonia synthesis

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

Kitano, Masaaki; Kanbara, Shinji; Inoue, Yasunori

We actively sough novel approaches to efficient ammonia synthesis at an ambient pressure so as to reduce the cost of ammonia production and to allow for compact production facilities. It is accepted that the key is the development of a high-performance catalyst that significantly enhances dissociation of the nitrogen-nitrogen triple bond, which is generally considered a rate-determining step. Here we examine the kinetics of nitrogen and hydrogen isotope exchange and hydrogen adsorption/desorption reactions for a recently discovered efficient catalyst for ammonia synthesis --ruthenium-loaded 12CaO∙7AI 2O 3 electride (Ru/C12A7:more » $$\\bar{e}$$ )--and find that the rate controlling step of ammonia synthesis over Ru/C12A7:$$\\bar{e}$$ is not dissociation of the nitrogen-nitrogen triple bond but the subsequent formation of N-H n species. A mechanism of ammonia synthesis involving reversible storage and release of hydrogen atoms on the Ru/C12A7:$$\\bar{e}$$ surface is proposed on the basis of observed hydrogen adsorption/desorption kinetics.« less

Effect of contact time and force on monocyte adhesion to vascular endothelium.

PubMed Central

Rinker, K D; Prabhakar, V; Truskey, G A

2001-01-01

In this study we examined whether monocytic cell attachment to vascular endothelium was affected by elevating shear stress at a constant shear rate. Contact time, which is inversely related to the shear rate, was fixed and viscosity elevated with dextran to increase the shear stress (and hence the net force on the cell) independently of shear rate. At a fixed contact time, tethering frequencies increased, rolling velocities decreased, and median arrest durations increased with increasing shear stress. Rolling and short arrests (< 0.2 s) were well fit by a single exponential consistent with adhesion via the formation of a single additional bond. The cell dissociation constant, k(off), increased when the shear stress was elevated at constant shear rate. Firmly adherent cells arresting for at least 0.2 s were well fit by a stochastic model involving dissociation from multiple bonds. Therefore, at a fixed contact time and increasing shear stress, bonds formed more frequently for rolling cells resulting in more short arrests, and more bonds formed for firmly arresting cells resulting in longer arrest durations. Possible mechanisms for this increased adhesion include greater monocyte deformation and/or more frequent penetration of microvilli through steric and charge barriers. PMID:11259286

Periodic trends in bond dissociation energies. A theoretical study.

PubMed

Mó, Otilia; Yáñez, Manuel; Eckert-Maksić, Mirjana; Maksić, Zvonimir B; Alkorta, Ibón; Elguero, José

2005-05-19

Bond dissociation energies (BDEs) of all possible A-X single bonds involving the first- and second-row atoms, from Li to Cl, where the free valences are saturated by hydrogens, have been estimated through the use of the G3-theory and at the B3LYP/6-311+G(3df,2pd)//B3LYP/6-31G(2df,p) DFT level of theory. BDEs exhibit a periodical behavior. The A-X (A = Li, Be, B, Na, Mg, Al, and Si) BDEs show a steady increase along the first and the second row of the periodic table as a function of the atomic number Z(X). For A-X bonds involving electronegative atoms (A = C, N, O, F, P, S, and Cl) the bond energies achieve a maximum around Z(X) = 5. The same behavior is observed when BDEs are plotted against the electronegativity chi(X) of the atom X. Thus, for A-X bonds (A = Li, Be, B, Na, Mg, Al, Si), the BDEs for a fixed A increases, grosso modo, as the electronegativity differences between X and A increase, with some exceptions, which reflect the differences in the relaxation energies of the radicals produced upon the bond cleavage. A similar trend, albeit less pronounced, is found for single A-X bonds, where A = C, N, O, F, P, S, and Cl. However, there is an additional feature embodied in the enhancement of the strength of the A-boron bonds due to the ability of boron to act as a strong electron acceptor. The trends in bond lengths and charge densities at the bond critical points are in line with the aforementioned behavior.

Dissociation, absorption and ionization of some important sulfur oxoanions (S2On2- n = 2, 3, 4, 6, 7 and 8)

NASA Astrophysics Data System (ADS)

Abedi, M.; Farrokhpour, H.; Farnia, S.; Chermahini, A. Najafi

2015-08-01

In this work, a systematic theoretical study was performed on the dissociation, absorption and ionization of several important sulfur oxoanions (S2On2- (n = 2, 3, 4, 6, 7 and 8)). ΔEelec (thermal corrected energy), ΔH° and ΔG° of the dissociation reactions of the oxoanions to their radical monoanions were calculated using combined computational levels of theories such as Gaussian-3 (G3) and a new version of complete basis set method (CBS-4M) in different environments including gas phase, microhydrated in gas phase and different solvents. Calculations showed S2O72- is the most stable anion against the dissociation to its radical monoanions (SO4-rad + SO3-rad). It was also found that S2O42- has more tendency to dissociate to its radical anions (SO2-rad + SO2-rad) compared to the other anions. The absorption spectra of the anions were also calculated using the time-dependent density functional theory (TD-DFT) employing M062X functional. The effect of microhydration and electrostatic field of solvent on the different aspects (intensity, energy shift and assignment) of the absorption spectra of these anions were also discussed. It was observed that both hydrogen bonding and electrostatic effect of water increases the intensity of the absorption spectrum compared to the gas phase. Effect of microhydration in shifting the spectra to the shorter wavelength is considerably higher than the effect of electrostatic field of water. Finally, several gas phase ionization energies of the anions were calculated using the symmetry-adapted cluster-configuration interaction methodology (SAC-CI) and found that the first electron detachment energies of S2O22-, S2O32- and S2O42- are negative. Natural bonding orbital (NBO) calculations were also performed to assign the electron detachment bands of the anions.

Decomposition mechanism of formic acid on Cu (111) surface: A theoretical study

NASA Astrophysics Data System (ADS)

Jiang, Zhao; Qin, Pei; Fang, Tao

2017-02-01

The study of formic acid decomposition on transition metal surfaces is important to obtain useful information for vapor phase catalysis involving HCOOH and for the development of direct formic acid fuel cells. In this study, periodic density functional theory calculations have been employed to investigate the dissociation pathways of HCOOH on Cu (111) surface. About adsorption, it is found that the adsorption of HCOO, COOH, HCO, CO, OH and H on Cu (111) are considered chemisorption, whereas HCOOH, CO2, H2O and H2 have the weak interaction with Cu (111) surface. Furthermore, the minimum energy pathways are analyzed for the decomposition of HCOOH to CO2 and CO through the scission of Hsbnd O, Csbnd H and Csbnd O bonds. It is found that HCOOH, HCOO and COOH prefer to dissociate in the related reactions rather than desorb. For the decomposition, it is indicated that HCO and COOH are the main dissociated intermediates of trans-HCOOH, CO2 is the main dissociated intermediates of bidentate-HCOO, and CO is the main dissociated product of cis-COOH. The co-adsorbed H atom is beneficial for the formation of CO2 from cis-COOH. Besides, it is found that the most favorable path for HCOOH decomposition on Cu (111) surface is HCOOH-HCO-CO (Path 5), where the step of CO formation from HCO dehydrogenation is considered to be the rate-determining step. The results also show that CO is preferentially formed as the dominant product of HCOOH on Cu (111) surface.

Significant Quantum Effects in Hydrogen Activation

DOE PAGES

Kyriakou, Georgios; Davidson, Erlend R. M.; Peng, Guowen; ...

2014-03-31

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature revealmore » completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H 2 up to ~190 K and for D 2 up to ~140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H 2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D 2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Here, examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.« less

Catalytic Proton Coupled Electron Transfer from Metal Hydrides to Titanocene Amides, Hydrazides and Imides: Determination of Thermodynamic Parameters Relevant to Nitrogen Fixation.

PubMed

Pappas, Iraklis; Chirik, Paul J

2016-10-03

The hydrogenolysis of titanium-nitrogen bonds in a series of bis(cyclopentadienyl) titanium amides, hydrazides and imides by proton coupled electron transfer (PCET) is described. Twelve different N-H bond dissociation free energies (BDFEs) among the various nitrogen-containing ligands were measured or calculated, and effects of metal oxidation state and N-ligand substituent were determined. Two metal hydride complexes, (η 5 -C 5 Me 5 )(py-Ph)Rh-H (py-Ph = 2-pyridylphenyl, [Rh]-H) and (η 5 -C 5 R 5 )(CO) 3 Cr-H ([Cr] R -H, R= H, Me) were evaluated for formal H atom transfer reactivity and were selected due to their relatively weak M-H bond strengths yet ability to activate and cleave molecular hydrogen. Despite comparable M-H BDFEs, disparate reactivity between the two compounds was observed and was traced to the vastly different acidities of the M-H bonds and overall redox potentials of the molecules. With [Rh]-H, catalytic syntheses of ammonia, silylamine and N,N-dimethylhydrazine have been accomplished from the corresponding titanium(IV) complex using H 2 as the stoichiometric H atom source. The data presented in this study provides the thermochemical foundation for the synthesis of NH 3 by proton coupled electron transfer at a well-defined transition metal center.

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields.

PubMed

Li, Hui; Kling, Nora G; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A; Kling, Matthias F; Kaziannis, Spyros

2016-07-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3 (+), H2 (+), and H3 (+), originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2 (+) and H3 (+) involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy.

PubMed

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P; Nguyen, Huong T H; Dang, Andy; Tureček, František

2018-01-16

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z 4 + H] +● fragment ion-radicals of the R-C ● H-CONH- type, initially formed by N-C α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [ ● DAAR + H] + isomers and used to assign structures to the action spectra. The potential energy surface of [ ● DAAR + H] + isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [ ● XAAR + H] + ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H] ● -ETD fragments containing Asp, Asn, Glu, and Gln residues. Graphical Abstract ᅟ.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P.; Nguyen, Huong T. H.; Dang, Andy; Tureček, František

2018-01-01

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z4 + H]+● fragment ion-radicals of the R-C●H-CONH- type, initially formed by N-Cα bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [●DAAR + H]+ isomers and used to assign structures to the action spectra. The potential energy surface of [●DAAR + H]+ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [●XAAR + H]+ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone Cα positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]●-ETD fragments containing Asp, Asn, Glu, and Gln residues. [Figure not available: see fulltext.

Ab initio molecular dynamics of H2O adsorbed on solid MgO

NASA Astrophysics Data System (ADS)

Langel, Walter; Parrinello, Michele

1995-08-01

The Car-Parrinello method has been applied to study the adsorption of water on solid magnesium oxide with surface defects. A step consisting of an (100) and an (010) surface on an (011) base plane allows us to model the experimentally observed microfaceting. In and on this step dissociation of water into a hydroxyl group and a H-atom took place following a complicated pathway only accessible by the simulation of thermal motion. Under comparable conditions physisorption only was observed on a regular (001) plane. This solves an experimental controversy and it is in agreement with the observation, that disordered surfaces are more active in initiating the dissociation of the water molecules. Our work allows us to identify an important active center. We can also account for the experimentally observed broadening and shifting to the red of the stretching mode of hydrogen bonded hydroxyl groups, and we provide a detailed explanation of the origin of this effect. This allows us to verify earlier theories of hydrogen bonding such as that of the adiabatic separation of the proton dynamics.

Structural and Antioxidant Properties of Compounds Obtained from Fe2+ Chelation by Juglone and Two of Its Derivatives: DFT, QTAIM, and NBO Studies

PubMed Central

Tamafo Fouegue, Aymard Didier; Bikélé Mama, Désiré; Nkungli, Nyiang Kennet; Younang, Elie

2016-01-01

The chelating ability of juglone and two of its derivatives towards Fe2+ion and the antioxidant activity (AOA) of the resulting chelates and complexes (in the presence of H2O and CH3OH as ligands) in gas phase is reported via bond dissociation enthalpy, ionization potential, proton dissociation enthalpy, proton affinity, and electron transfer enthalpy. The DFT/B3LYP level of theory associated with the 6-31+G(d,p) and 6-31G(d) Pople-style basis sets on the atoms of the ligands and the central Fe(II), respectively, was used. Negative chelation free energies obtained revealed that juglone derivatives possessing the O-H substituent (L2) have the greatest ability to chelate Fe2+ ion. Apart from 1B, thermodynamic descriptors of the AOA showed that the direct hydrogen atom transfer is the preferred mechanism of the studied molecules. NBO analysis showed that the Fe-ligand bonds are all formed through metal to ligand charge transfer. QTAIM studies revealed that among all the Fe-ligand bonds, the O1-Fe bond of 1A is purely covalent. The aforementioned results show that the ligands can be used to fight against Fe(II) toxicity, thus preserving human health, and fight against the deterioration of industrial products. In addition, most of the complexes studied have shown a better AOA than their corresponding ligands. PMID:27774044

Active sites and states in the heterogeneous catalysis of carbon-hydrogen bonds.

PubMed

Somorjai, Gabor A; Marsh, Anderson L

2005-04-15

C-H bond activation for several alkenes (ethylene, propylene, isobutene, cyclohexene and 1-hexene) and alkanes (methane, ethane, n-hexane, 2-methylpentane and 3-methylpentane) has been studied on the (111) crystal face of platinum as a function of temperature at low (10(-6) Torr) and high (>/=1 Torr) pressures in the absence and presence of hydrogen pressures (>/=10 Torr). Sum frequency generation (SFG) vibrational spectroscopy has been used to characterize the adsorbate structures and high pressure scanning tunnelling microscopy (HP-STM) has been used to monitor their surface mobility under reaction conditions during hydrogenation, dehydrogenation and CO poisoning. C-H bond dissociation occurs at low temperatures, approximately 250 K, for all of these molecules, although only at high pressures for the weakly bound alkanes because of their low desorption temperatures. Bond dissociation is known to be surface structure sensitive and we find that it is also accompanied by the restructuring of the metal surface. The presence of hydrogen slows down dehydrogenation and for some of the molecules it influences the molecular rearrangement, thus altering reaction selectivity. Surface mobility of adsorbates is essential to produce catalytic activity. When surface diffusion is inhibited by CO adsorption, ordered surface structures form and the reaction is poisoned. Ethylene hydrogenation is surface structure insensitive, while cyclohexene hydrogenation and dehydrogenation are structure sensitive. n-Hexane and other C6 alkanes form either upright or flat-lying molecules on the platinum surface which react to produce branched isomers or benzene, respectively.

A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

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

Chang, Yih -Chung; Xiong, Bo; Bross, David H.

Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

DOE PAGES

Chang, Yih -Chung; Xiong, Bo; Bross, David H.; ...

2017-03-27

Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

Reaction of Si(100) with NH3: Rate-limiting steps and reactivity enhancement via electronic excitation

NASA Astrophysics Data System (ADS)

Bozso, F.; Avouris, Ph.

1986-09-01

We report on the low-temperature reaction of ammonia with Si(100)-(2×1). The dangling bonds in the clean Si surface promote NH3 dissociation even at temperatures as low as 90 K. The N atoms thus produced occupy subsurface sites, while the H atoms bind to surface Si atoms, tie up the dangling bonds, and inactivate the surface. Thermal or electronic-excitation-induced hydrogen desorption restores the dangling bonds and the reactivity of the surface. Silicon nitride film growth is achieved at 90 K by simultaneous exposure of the Si surface to NH3 and an electron beam.

Quadrupole type mass spectrometric study of the abstraction reaction between hydrogen atoms and ethane.

PubMed

Bayrakçeken, Fuat

2008-02-01

The reactions of photochemically generated deuterium atoms of selected initial translational energy with ethane have been investigated. At each initial energy the relative probability of the atoms undergoing reaction or energy loss on collision with ethane was investigated, and the phenomenological threshold energy was measured as 30+/-5kJmol(-1) for the abstraction from the secondary C-H bonds. The ratio of relative yields per bond, secondary:primary was approximately 3 at the higher energies studied. The correlation of threshold energies with bond dissociation energies, heats of reaction and activation energies is discussed for abstraction reactions with several hydrocarbons.

Intermolecular dissociation energies of dispersively bound complexes of aromatics with noble gases and nitrogen

NASA Astrophysics Data System (ADS)

Knochenmuss, Richard; Sinha, Rajeev K.; Leutwyler, Samuel

2018-04-01

We measured accurate intermolecular dissociation energies D0 of the supersonic jet-cooled complexes of 1-naphthol (1NpOH) with the noble gases Ne, Ar, Kr, and Xe and with N2, using the stimulated-emission pumping resonant two-photon ionization method. The ground-state values D0(S0) for the 1NpOHṡS complexes with S= Ar, Kr, Xe, and N2 were bracketed to be within ±3.5%; they are 5.67 ± 0.05 kJ/mol for S = Ar, 7.34 ± 0.07 kJ/mol for S = Kr, 10.8 ± 0.28 kJ/mol for S = Xe, 6.67 ± 0.08 kJ/mol for isomer 1 of the 1NpOHṡN2 complex, and 6.62 ± 0.22 kJ/mol for the corresponding isomer 2. For S = Ne, the upper limit is D0 < 3.36 kJ/mol. The dissociation energies increase by 1%-5% upon S0 → S1 excitation of the complexes. Three dispersion-corrected density functional theory (DFT-D) methods (B97-D3, B3LYP-D3, and ωB97X-D) predict that the most stable form of these complexes involves dispersive binding to the naphthalene "face." A more weakly bound edge isomer is predicted in which the S moiety is H-bonded to the OH group of 1NpOH; however, no edge isomers were observed experimentally. The B97-D3 calculated dissociation energies D0(S0) of the face complexes with Ar, Kr, and N2 agree with the experimental values within <5%, but the D0(S0) for Xe is 12% too low. The B3LYP-D3 and ωB97X-D calculated D0(S0) values exhibit larger deviations to both larger and smaller dissociation energies. For comparison to 1-naphthol, we calculated the D0(S0) of the carbazole complexes with S = Ne, Ar, Kr, Xe, and N2 using the same DFT-D methods. The respective experimental values have been previously determined to be within <2%. Again, the B97-D3 results are in the best overall agreement with experiment.

The physicochemical essence of the purine·pyrimidine transition mismatches with Watson-Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding.

PubMed

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

It was established for the first time by DFT and MP2 quantum-mechanical (QM) methods either in vacuum, so in the continuum with a low dielectric constant (ε = 4), typical for hydrophobic interfaces of specific protein-nucleic acid interactions, that the repertoire for the tautomerisation of the biologically important adenine · cytosine* (A · C*) mismatched DNA base pair, formed by the amino tautomer of the A and the imino mutagenic tautomer of the C, into the A*·C base mispair (∆G = 2.72 kcal mol(-1) obtained at the MP2 level of QM theory in the continuum with ε = 4), formed by the imino mutagenic tautomer of the A and the amino tautomer of the C, proceeds via the asynchronous concerted double proton transfer along two antiparallel H-bonds through the transition state (TSA · C* ↔ A* · C). The limiting stage of the A · C* → A* · C tautomerisation is the final proton transfer along the intermolecular N6H · · · N4 H-bond. It was found that the A · C*/A* · C DNA base mispairs with Watson-Crick geometry are associated by the N6H · · · N4/N4H · · · N6, N3H · · · N1/N1H · · · N3 and C2H · · · O2 H-bonds, respectively, while the TSA · C*↔ A* · C is joined by the N6-H-N4 covalent bridge and the N1H · · · N3 and C2H · · · O2 H-bonds. It was revealed that the A · C* ↔ A* · C tautomerisation is assisted by the true C2H · · · O2 H-bond, that in contrast to the two others conventional H-bonds exists along the entire intrinsic reaction coordinate (IRC) range herewith becoming stronger at the transition from vacuum to the continuum with ε = 4. To better understand the behavior of the intermolecular H-bonds and base mispairs along the IRC of the A · C* ↔ A* · C tautomerisation, the profiles of their electron-topological, energetical, geometrical, polar and charge characteristics are reported in this study. It was established based on the profiles of the H-bond energies that all three H-bonds are cooperative, mutually strengthening each other. The nine key points, providing a detailed physicochemical picture of the A · C* ↔ A* · C tautomerisation, were revealed and thoroughly examined along the IRC. It was shown that the A* · C base mispair with the population ~1 % obtained at the MP2 level of QM theory in the continuum with ε = 4 is thermodynamically and dynamically stable structure. Its lifetime was calculated to be 5.76 · 10(-10) s at the MP2 level of QM theory in the continuum with ε = 4. This lifetime, from the one side, enables all six low-frequency intermolecular vibrations to develop, but, from the other side, it is by order less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. This means that the A* · C base mispair "slips away from the hands" of the replication machinery into the A · C* mismatched base pair. Consequently, the authors came to the conclusion that exactly the A · C* base mispair is an active player of the point mutational events and is effectively dissociated by the replication machinery into the A and C* monomers in contrast to the A* · C base mispair, playing the mediated role of a provider of the A · C* base mispair in DNA that is synthesised.

Microsolvated Model for the Kinetics and Thermodynamics of Glycosidic Bond Dissociative Cleavage of Nucleoside D4G.

PubMed

Jiang, Yang; Xue, Ying; Zeng, Yi

2018-02-15

Using the microsolvated model that involves explicit water molecules and implicit solvent in the optimization, two proposed dissociative hydrolysis mechanisms of 2',3'-didehydro-2',3'-dideoxyguanosine (d4G) have been first investigated by means of M06-2X(CPCM, water)/6-31++G(d,p) method. The glycosidic bond dissociation for the generation of the oxacarbenium ion intermediate is the rate-determining step (RDS). The subsequent nucleophilic water attack from different side of the oxacarbenium ion intermediate gives either the α-product [(2S,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] or β-product [(2R,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] and is thus referred to as α-path (inversion) and β-path (retention). Two to five explicit water molecules (n = 2-5) are considered in the microsolvated model, and n = 3 or 4 is the smallest model capable of minimizing the activation energy for α-path and β-path, respectively. Our theoretical results suggest that α-path (n = 3) is more kinetically favorable with lower free energy barrier (RDS) of 27.7 kcal mol -1 , in contrast to that of 30.7 kcal mol -1 for the β-path (n = 4). The kinetic preference of the α-path is rationalized by NBO analysis. Whereas thte β-path is more thermodynamically favorable over the α-path, where the formation of β-product and α-product are exergonic and endergonic, respectively, providing theoretical support for the experimental observation that the β-cleavage product was the major one after sufficient reaction time. Comparisons of d4G with analogous cyclo-d4G and dG from kinetic free energy barriers and thermodynamic heterolytic dissociation energies were also carried out. Our kinetic and thermodynamic results manifest that the order of glycosidic bond stability should be d4G < cyclo-d4G < dG, which agrees well with the reported experimental stability order of d4G compounds and analogues and gives further understanding on the influence of 6-cyclopropylamino and unsaturated ribose to the glycosidic bond instability of d4G.

Birge-Sponer Estimation of the C-H Bond Dissociation Energy in Chloroform Using Infrared, Near-Infrared, and Visible Absorption Spectroscopy: An Experiment in Physical Chemistry

ERIC Educational Resources Information Center

Myrick, M. L.; Greer, A. E.; Nieuwland, A. A.; Priore, R. J.; Scaffidi, J.; Andreatta, Danielle; Colavita, Paula

2008-01-01

The fundamental and overtone vibrational absorption spectroscopy of the C-H unit in CHCl[subscript 3] is measured for transitions from the v = 0 energy level to v = 1 through v = 5 energy levels. The energies of the transitions exhibit a linearly-decreasing spacing between adjacent vibrational levels as the vibrational quantum number increases.…

Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain

PubMed Central

2016-01-01

Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were 13C2D2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward 13C2D2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA. PMID:25584637

Boosting effect of ortho-propenyl substituent on the antioxidant activity of natural phenols.

PubMed

Marteau, Clémentine; Guitard, Romain; Penverne, Christophe; Favier, Dominique; Nardello-Rataj, Véronique; Aubry, Jean-Marie

2016-04-01

Seven new antioxidants derived from natural or synthetic phenols have been designed as alternatives to BHT and BHA antioxidants. Influence of various substituents at the ortho, meta and para positions of the aromatic core of phenols on the bond dissociation enthalpy of the ArO-H bond was evaluated using a DFT method B3LYP/6-311++G(2d,2p)//B3LYP/6-311G(d,p). This prediction highlighted the ortho-propenyl group as the best substituent to decrease the bond dissociation enthalpy (BDE) value. The rate constants of hydrogen transfer from these phenols to DPPH radical in a non-polar and non-protic solvent have been measured and were found to be in agreement with the BDE calculations. For o-propenyl derivatives from 2-tert-butyl-4-methylphenol, BHA, creosol, isoeugenol and di-o-propenyl p-cresol, fewer radicals were trapped by a single phenol molecule, i.e. a lower stoichiometric number. Reaction mechanisms involving the evolution of the primary phenoxyl radical ArO are proposed to rationalise these effects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields

PubMed Central

Li, Hui; Kling, Nora G.; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A.; Kling, Matthias F.; Kaziannis, Spyros

2016-01-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3+, H2+, and H3+, originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2+ and H3+ involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules. PMID:26958589

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

NASA Astrophysics Data System (ADS)

Lichtenberg, Dennis L.

During this period some important breakthroughs were accomplished in understanding the relationships between molecular ionization energies and bond energies in transition metal complexes, in understanding the electronic factors of carbon-hydrogen bond activation by transition metals, in characterizing small molecule bonding interactions with transition metals, and in investigating intermolecular interactions in thin films of transition metal complexes. The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies was developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. The relationship was used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. The ionization energies were also used to correlate the rates of carbonyl substitution reactions of (eta(sup 5)-C5H4X)Rh(CO)2 complexes, and to reveal the factors that control the stability of the transition state. The investigations of the fundamental interactions of C-H sigma and sigma* orbitals metals were continued with study of eta(sup 3)-1-methylallyl metal complexes. Direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal was obtained. The ability to observe the electronic effects of intermolecular interactions by comparing the ionizations of metal complexes in the gas phase with the ionizations of thin solid organometallic films prepared in ultra-high vacuum was established. Most significantly, the scanning tunneling microscope imaging of these thin films was accomplished.

Thermal Dissociation of Halogen Azides

DTIC Science & Technology

1994-09-01

Proc. Int. Conf. L.asers 1986. (38) Radimacher, P.; Bittner, A. J.; Schatnc. G.; Wilner, H . Chem. Ber. (43) Hcidner. R. F.; Helvajian . H .; Hollaway. J...Winker, DJ. Bernard and T.A. Seder, H -gh Power Gas Lasers, Proceedings of the SPIE, I= (1990) 543. 6. R.F. Heidner, H . Helvajian , J.S. Holloway and J.B...34Production of NF(a’A) by Dissociation of Fluorine Azide," Journal of Physical Chemistry, vol. 93, pp. 4790-4796, 1989. 3. R.H. Heidner, H . Helvajian , J.S

Relativistic Corrections to the Properties of the Alkali Fluorides

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Partridge, Harry

1993-01-01

Relativistic corrections to the bond lengths, dissociation energies and harmonic frequencies of KF, RbF and CsF have been obtained at the self-consistent field level by dissociating to ions. The relativistic corrections to the bond lengths, harmonic frequencies and dissociation energies to the ions are very small, due to the ionic nature of these molecules and the similarity of the relativistic and nonrelativistic ionic radii.

Theoretical verification and extension of the McKean relationship between bond lengths and stretching frequencies

NASA Astrophysics Data System (ADS)

Larsson, J. A.; Cremer, D.

1999-08-01

Vibrational spectra contain explicit information on the electronic structure and the bonding situation of a molecule, which can be obtained by transforming the vibrational normal modes of a molecule into appropriate internal coordinate modes, which are localized in a fragment of the molecule and which are associated to that internal coordinate that describes the molecular fragment in question. It is shown that the adiabatic internal modes derived recently (Int. J. Quant. Chem., 67 (1998) 1) are the theoretical counterparts of McKean's isolated CH stretching modes (Chem. Soc. Rev., 7 (1978) 399). Adiabatic CH stretching frequencies obtained from experimental vibrational spectra can be used to determine CH bond lengths with high accuracy. Contrary to the concept of isolated stretching frequencies a generalization to any bond of a molecule is possible as is demonstrated for the CC stretching frequencies. While normal mode frequencies do not provide a basis to determine CC bond lengths and CC bond strengths, this is possible with the help of the adiabatic CC stretching frequencies. Measured vibrational spectra are used to describe different types of CC bonds in a quantitative way. For CH bonds, it is also shown that adiabatic stretching frequency leads to the definition of an ideal dissociation energy, which contrary to the experimentally determined dissociation energy is a direct measure of the bond strength. The difference between measured and ideal dissociation energies gives information on stabilization or destabilization of the radicals formed in a dissociation process.

Role of dispersion corrected hybrid GGA class in accurately calculating the bond dissociation energy of carbon halogen bond: A benchmark study

NASA Astrophysics Data System (ADS)

Kosar, Naveen; Mahmood, Tariq; Ayub, Khurshid

2017-12-01

Benchmark study has been carried out to find a cost effective and accurate method for bond dissociation energy (BDE) of carbon halogen (Csbnd X) bond. BDE of C-X bond plays a vital role in chemical reactions, particularly for kinetic barrier and thermochemistry etc. The compounds (1-16, Fig. 1) with Csbnd X bond used for current benchmark study are important reactants in organic, inorganic and bioorganic chemistry. Experimental data of Csbnd X bond dissociation energy is compared with theoretical results. The statistical analysis tools such as root mean square deviation (RMSD), standard deviation (SD), Pearson's correlation (R) and mean absolute error (MAE) are used for comparison. Overall, thirty-one density functionals from eight different classes of density functional theory (DFT) along with Pople and Dunning basis sets are evaluated. Among different classes of DFT, the dispersion corrected range separated hybrid GGA class along with 6-31G(d), 6-311G(d), aug-cc-pVDZ and aug-cc-pVTZ basis sets performed best for bond dissociation energy calculation of C-X bond. ωB97XD show the best performance with less deviations (RMSD, SD), mean absolute error (MAE) and a significant Pearson's correlation (R) when compared to experimental data. ωB97XD along with Pople basis set 6-311g(d) has RMSD, SD, R and MAE of 3.14 kcal mol-1, 3.05 kcal mol-1, 0.97 and -1.07 kcal mol-1, respectively.

Discontinuities-free complete-active-space state–specific multi–reference coupled cluster theory for describing bond stretching and dissociation

DOE PAGES

Zaporozhets, Irina A.; Ivanov, Vladimir V.; Lyakh, Dmitry I.; ...

2015-07-13

The earlier proposed multi-reference state-specific coupled-cluster theory with the complete active space reference suffered from a problem of energy discontinuities when the formal reference state was changing in the calculation of the potential energy curve (PEC). A simple remedy to the discontinuity problem is found and is presented in this work. It involves using natural complete active space self-consistent field active orbitals in the complete active space coupled-cluster calculations. As a result, the approach gives smooth PECs for different types of dissociation problems, as illustrated in the calculations of the dissociation of the single bond in the hydrogen fluorine moleculemore » and of the symmetric double-bond dissociation in the water molecule.« less

Comparative study on the effect of H2 pre-adsorption on CO oxidation in O2-poor atmosphere over Au/TiO2 and TiO2: Temperature programmed surface reaction by a multiplexed mass spectrometer testing

NASA Astrophysics Data System (ADS)

Si, Ruiru; Liu, Junfeng; Zhang, Yujuan; Chen, Xun; Dai, Wenxin; Fu, Xianzhi

2016-11-01

The behaviors of H2 pre-adsorption on CO oxidation in an O2-poor stream containing a trace H2O over Au/TiO2 and TiO2 have been investigated by a temperature programmed surface reaction testing, respectively. It was found that the H2 pre-adsorption could keep CO oxidation without H2O consumption over Au/TiO2, but suppress CO oxidation over TiO2. The chemisorption testing showed that the H2 adsorption at Au/TiO2 could benefit to the formation of Ti-bonded hydroxyl species (Ti4+-OH), while the H2 adsorption at TiO2 would consume the Ti-bonded hydroxyl species and form the bridge hydroxyl species (Ti4+-OH-Ti4+). These results show that only the Ti-bonded hydroxyl species (not all kinds of hydroxyl species) could act as the active species of oxidizing CO. Furthermore, it is suggested that the dissociative hydrogen adsorbed at Au sites could activate the lattice oxygen of TiO2 to form the active Ti-bonded hydroxyl species (hydrogen spillover from Au to TiO2), which exhibit a strong reducibility than the H directly adsorbed at TiO2.

Disilane chemisorption on Si(x)Ge(1-x)(100)-(2 x 1): molecular mechanisms and implications for film growth rates.

PubMed

Ng, Rachel Qiao-Ming; Tok, E S; Kang, H Chuan

2009-07-28

At low temperatures, hydrogen desorption is known to be the rate-limiting process in silicon germanium film growth via chemical vapor deposition. Since surface germanium lowers the hydrogen desorption barrier, Si(x)Ge((1-x)) film growth rate increases with the surface germanium fraction. At high temperatures, however, the molecular mechanisms determining the epitaxial growth rate are not well established despite much experimental work. We investigate these mechanisms in the context of disilane adsorption because disilane is an important precursor used in film growth. In particular, we want to understand the molecular steps that lead, in the high temperature regime, to a decrease in growth rate as the surface germanium increases. In addition, there is a need to consider the issue of whether disilane adsorbs via silicon-silicon bond dissociation or via silicon-hydrogen bond dissociation. It is usually assumed that disilane adsorption occurs via silicon-silicon bond dissociation, but in recent work we provided theoretical evidence that silicon-hydrogen bond dissociation is more important. In order to address these issues, we calculate the chemisorption barriers for disilane on silicon germanium using first-principles density functional theory methods. We use the calculated barriers to estimate film growth rates that are then critically compared to the experimental data. This enables us to establish a connection between the dependence of the film growth rate on the surface germanium content and the kinetics of the initial adsorption step. We show that the generally accepted mechanism where disilane chemisorbs via silicon-silicon bond dissociation is not consistent with the data for film growth kinetics. Silicon-hydrogen bond dissociation paths have to be included in order to give good agreement with the experimental data for high temperature film growth rate.

X-ray-induced dissociation of H.sub.2O and formation of an O.sub.2-H.sub.2 alloy at high pressure

DOEpatents

Mao, Ho-kwang [Washington, DC; Mao, Wendy L [Washington, DC

2011-11-29

A novel molecular alloy of O.sub.2 and H.sub.2 and a method of producing such a molecular alloy are provided. When subjected to high pressure and extensive x-radiation, H.sub.2O molecules cleaved, forming O--O and H--H bonds. In the method of the present invention, the O and H framework in ice VII was converted into a molecular alloy of O.sub.2 and H.sub.2. X-ray diffraction, x-ray Raman scattering, and optical Raman spectroscopy demonstrate that this crystalline solid differs from previously known phases.

3c/4e [small sigma, Greek, circumflex]-type long-bonding competes with ω-bonding in noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I): a NBO/NRT perspective.

PubMed

Zhang, Guiqiu; Li, Hong; Weinhold, Frank; Chen, Dezhan

2016-03-21

Noble-gas hydrides HNgY are frequently described as a single ionic form (H-Ng)(+)Y(-). We apply natural bond orbital (NBO) and natural resonance theory (NRT) analyses to a series of noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I) to gain quantitative insight into the resonance bonding of these hypervalent molecules. We find that each of the studied species should be better represented as a resonance hybrid of three leading resonance structures, namely, H-Ng(+ -):Y (I), H:(- +)Ng-Y (II), and H^Y (III), in which the "ω-bonded" structures I and II arise from the complementary donor-acceptor interactions nY → σ*HNg and nH → σ*NgY, while the "long-bond" ([small sigma, Greek, circumflex]-type) structure III arises from the nNg → [small sigma, Greek, circumflex]*HY/[small sigma, Greek, circumflex]HY interaction. The bonding for all of the studied molecules can be well described in terms of the continuously variable resonance weightings of 3c/4e ω-bonding and [small sigma, Greek, circumflex]-type long-bonding motifs. Furthermore, we find that the calculated bond orders satisfy a generalized form of "conservation of bond order" that incorporates both ω-bonding and long-bonding contributions [viz., (bHNg + bNgY) + bHY = bω-bonding + blong-bonding = 1]. Such "conservation" throughout the title series implies a competitive relationship between ω-bonding and [small sigma, Greek, circumflex]-type long-bonding, whose variations are found to depend in a chemically reasonable manner on the electronegativity of Y and the outer valence-shell character of the central Ng atom. The calculated bond orders are also found to exhibit chemically reasonable correlations with bond lengths, vibrational frequencies, and bond dissociation energies, in accord with Badger's rule and related empirical relationships. Overall, the results provide electronic principles and chemical insight that may prove useful in the rational design of noble-gas hydrides of technological interest.

Ab Initio energetics of SiO bond cleavage.

PubMed

Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Wondraczek, Lothar; Sierka, Marek

2017-10-15

A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol -1 , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H 2 O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol -1 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The investigation of adsorption and dissociation of H2O on Li2O (111) by ab initio theory

NASA Astrophysics Data System (ADS)

Kong, Xianggang; Yu, You; Ma, Shenggui; Gao, Tao; Lu, Tiecheng; Xiao, Chengjian; Chen, Xiaojun; Zhang, Chuanyu

2017-06-01

The adsorption and dissociation mechanism of H2O molecule on the Li2O (111) surface have been systematically studied by using the density functional theory calculations. The parallel and vertical configurations of H2O at six different symmetry adsorption sites on the Li2O (111) surface are considered. In our calculations, it is suggested that H2O can dissociate on the perfect Li2O surface, of which the corresponding adsorption energy is 1.118 eV. And the adsorption energy decrease to be 0.241 eV when oxygen atom of H2O bonds to lithium atom of the slab. The final configurations are sensitive to the initial molecular orientation. By Bader charge analysis, the charge transfer from slab to adsorbed H2O/OH can be found due to the downward shift of lowest-unoccupied molecular orbital. We also analyze the vibrational frequencies at the Brillouin Zone centre for H2O molecule adsorbed on the stoichiometric surface. Due to the slightly different structure parameters, the calculated values of the vibrational frequencies of hydroxyl group range from 3824 to 3767 cm-1. Our results agree well with experimental results performed in FT-IR spectrum, which showed that an absorption peak of OH group appeared at 3677 cm-1 at room temperature.

S K-edge XAS and DFT Calculations on Square Planar NiII-thiolate Complexes: Effects of Active and Passive H-bonding

PubMed Central

Dey, Abhishek; Green, Kayla N.; Jenkins, Roxanne M.; Jeffrey, Stephen P.; Darensbourg, Marcetta; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2008-01-01

S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc.; 2005; 127, 12046-12053.). These differences were analyzed using DFT calculations and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate the orbital involved in H-bonding is non-bonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated. PMID:17949080

Mussel-inspired histidine-based transient network metal coordination hydrogels

PubMed Central

Fullenkamp, Dominic E.; He, Lihong; Barrett, Devin G.; Burghardt, Wesley R.; Messersmith, Phillip B.

2013-01-01

Transient network hydrogels cross-linked through histidine-divalent cation coordination bonds were studied by conventional rheologic methods using histidine-modified star poly(ethylene glycol) (PEG) polymers. These materials were inspired by the mussel, which is thought to use histidine-metal coordination bonds to impart self-healing properties in the mussel byssal thread. Hydrogel viscoelastic mechanical properties were studied as a function of metal, pH, concentration, and ionic strength. The equilibrium metal-binding constants were determined by dilute solution potentiometric titration of monofunctional histidine-modified methoxy-PEG and were found to be consistent with binding constants of small molecule analogs previously studied. pH-dependent speciation curves were then calculated using the equilibrium constants determined by potentiometric titration, providing insight into the pH dependence of histidine-metal ion coordination and guiding the design of metal coordination hydrogels. Gel relaxation dynamics were found to be uncorrelated with the equilibrium constants measured, but were correlated to the expected coordination bond dissociation rate constants. PMID:23441102

Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations

NASA Astrophysics Data System (ADS)

Machida, Masahiko; Kato, Koichiro; Shiga, Motoyuki

2018-03-01

The isotopologs of liquid water, H2O, D2O, and T2O, are studied systematically by first principles PIMD simulations, in which the whole entity of the electrons and nuclei are treated quantum mechanically. The simulation results are in reasonable agreement with available experimental data on isotope effects, in particular, on the peak shift in the radial distributions of H2O and D2O and the shift in the evaporation energies. It is found that, due to differences in nuclear quantum effects, the H atoms in the OH bonds more easily access the dissociative region up to the hydrogen bond center than the D (T) atoms in the OD (OT) bonds. The accuracy and limitation in the use of the current density-functional-theory-based first principles PIMD simulations are also discussed. It is argued that the inclusion of the dispersion correction or relevant improvements in the density functionals are required for the quantitative estimation of isotope effects.

Vibrational Mode-Specific Reaction of Methane with a Nickel Surface

NASA Astrophysics Data System (ADS)

Beck, Rainer

2004-03-01

The dissociation of methane on a nickel catalyst is a key step in steam reforming of natural gas for hydrogen production. Despite substantial effort in both experiment and theory, there is still no atomic scale description of this important gas-surface reaction. To elucidate its dynamics, we have performed quantum state resolved studies of vibrationally excited methane reacting on the Ni(100) surface using pulsed laser and molecular beam techniques. We observed up to a factor of 5 greater reaction probability for methane-d2 with two quanta of excitation in one C-H bond versus a nearly isoenergetic state with one quanta in each of two C-H bonds. The observed reactivities point to a transition state structure which has one of the C-H bonds significantly elongated. Our results also clearly exclude the possibility of statistical models correctly describing the mechanism of this process and emphasize the importance of full-dimensional calculations of the reaction dynamics.

Influence of Au and TiO2 structures on hydrogen dissociation over TiO2/Au(100)

NASA Astrophysics Data System (ADS)

Nakamura, I.; Mantoku, H.; Furukawa, T.; Takahashi, A.; Fujitani, T.

2012-11-01

We performed H2-D2 exchange reactions over TiOx/Au(100) and compared the observed reaction kinetics with those reported for TiOx/Au(111) in order to clarify the influence of the Au and TiO2 structures on dissociation of H2 molecules. Low energy electron diffraction observations showed that the TiO2 produced on Au(100) was disordered, in contrast to the comparatively ordered TiO2 structure formed on Au(111). The activation energies and the turnover frequencies for HD formation over TiO2/Au(100) agreed well with those for TiO2/Au(111), clearly indicating that the hydrogen dissociation sites created over TiO2/Au(100) were the perimeter interface between stoichiometric TiO2 and Au, as was previously concluded for TiO2/Au(111). We concluded that the creation of active sites for hydrogen dissociation was independent of the Au and TiO2 structures consisting perimeter interface, and that local bonds that formed between Au and O atoms of stoichiometric TiO2 were essential for the creation of active sites.

Combined Experimental and Computational Study on the Unimolecular Decomposition of JP-8 Jet Fuel Surrogates. I. n-Decane (n-C10H22).

PubMed

Zhao, Long; Yang, Tao; Kaiser, Ralf I; Troy, Tyler P; Ahmed, Musahid; Belisario-Lara, Daniel; Ribeiro, Joao Marcelo; Mebel, Alexander M

2017-02-16

Exploiting a high temperature chemical reactor, we explored the pyrolysis of helium-seeded n-decane as a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) over a temperature range of 1100-1600 K at a pressure of 600 Torr. The nascent products were identified in situ in a supersonic molecular beam via single photon vacuum ultraviolet (VUV) photoionization coupled with a mass spectroscopic analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF). Our studies probe, for the first time, the initial reaction products formed in the decomposition of n-decane-including radicals and thermally labile closed-shell species effectively excluding mass growth processes. The present study identified 18 products: molecular hydrogen (H 2 ), C2 to C7 1-alkenes [ethylene (C 2 H 4 ) to 1-heptene (C 7 H 14 )], C1-C3 radicals [methyl (CH 3 ), vinyl (C 2 H 3 ), ethyl (C 2 H 5 ), propargyl (C 3 H 3 ), allyl (C 3 H 5 )], small C1-C3 hydrocarbons [methane (CH 4 ), acetylene (C 2 H 2 ), allene (C 3 H 4 ), methylacetylene (C 3 H 4 )], along with higher-order reaction products [1,3-butadiene (C 4 H 6 ), 2-butene (C 4 H 8 )]. On the basis of electronic structure calculations, n-decane decomposes initially by C-C bond cleavage (excluding the terminal C-C bonds) producing a mixture of alkyl radicals from ethyl to octyl. These alkyl radicals are unstable under the experimental conditions and rapidly dissociate by C-C bond β-scission to split ethylene (C 2 H 4 ) plus a 1-alkyl radical with the number of carbon atoms reduced by two and 1,4-, 1,5-, 1,6-, or 1,7-H shifts followed by C-C β-scission producing alkenes from propene to 1-octene in combination with smaller 1-alkyl radicals. The higher alkenes become increasingly unstable with rising temperature. When the C-C β-scission continues all the way to the propyl radical (C 3 H 7 ), it dissociates producing methyl (CH 3 ) plus ethylene (C 2 H 4 ). Also, at higher temperatures, hydrogen atoms can abstract hydrogen from C 10 H 22 to yield n-decyl radicals, while methyl (CH 3 ) can also abstract hydrogen or recombine with hydrogen to form methane. These n-decyl radicals can decompose via C-C-bond β-scission to C3 to C9 alkenes.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

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

Johnson, Eric L.; Davis, Quincy C.; Morse, Michael D.

The abrupt onset of predissociation in the congested electronic spectra of jet-cooled VC, VN, and VS has been observed using resonant two-photon ionization spectroscopy. It is argued that because of the high density of electronic states in these molecules, the predissociation threshold occurs at the thermochemical threshold for the production of separated atoms in their ground electronic states. As a result, the measured threshold represents the bond dissociation energy. Using this method, bond dissociation energies of D{sub 0}(V C) = 4.1086(25) eV, D{sub 0}(V N) = 4.9968(20) eV, and D{sub 0}(V S) = 4.5353(25) eV are obtained. From these values,more » enthalpies of formation are derived as Δ{sub f,0K}H°(V C(g)) = 827.0 ± 8 kJ mol{sup −1}, Δ{sub f,0K}H°(V N(g)) = 500.9 ± 8 kJ mol{sup −1}, and Δ{sub f,0K}H°(V S(g)) = 349.3 ± 8 kJ mol{sup −1}. Using a thermochemical cycle and the well-known ionization energies of V, VC, and VN, our results also provide D{sub 0}(V{sup +}–C) = 3.7242(25) eV and D{sub 0}(V{sup +}–N) = 4.6871(20) eV. These values are compared to previous measurements and to computational results. The precision of these bond dissociation energies makes them good candidates for testing computational chemistry methods, particularly those that employ density functional theory.« less

Bis(4-nitraminofurazanyl-3-azoxy)azofurazan and Derivatives: 1,2,5-Oxadiazole Structures and High-Performance Energetic Materials.

PubMed

Liu, Yuji; Zhang, Jiaheng; Wang, Kangcai; Li, Jinshan; Zhang, Qinghua; Shreeve, Jean'ne M

2016-09-12

Bis(4-nitraminofurazanyl-3-azoxy)azofurazan (1) and ten of its energetic salts were prepared and fully characterized. Computational analysis based on isochemical shielding surface and trigger bond dissociation enthalpy provide a better understanding of the thermal stabilities for nitramine-furazans. These energetic compounds exhibit good densities, high heats of formation, and excellent detonation velocity and pressure. Some representative compounds, for example, 1 (vD : 9541 m s(-1) ; P: 40.5 GPa), and 4 (vD : 9256 m s(-1) ; P: 38.0 GPa) exhibit excellent detonation performances, which are comparable with current high explosives such as RDX (vD : 8724 m s(-1) ; P: 35.2 GPa) and HMX (vD : 9059 m s(-1) ; P: 39.2 GPa). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Periodic density functional theory study of ethylene hydrogenation over Co3O4 (1 1 1) surface: The critical role of oxygen vacancies

NASA Astrophysics Data System (ADS)

Lu, Jinhui; Song, JiaJia; Niu, Hongling; Pan, Lun; Zhang, Xiangwen; Wang, Li; Zou, Ji-Jun

2016-05-01

Recently, metal oxides are attracting increasing interests as hydrogenation catalyst. Herein we studied the hydrogenation of ethylene on perfect and oxygen defective Co3O4 (1 1 1) using periodic density functional theory. The energetics and pathways of ethylene hydrogenation to ethane were determined. We have demonstrated that (i) H2 dissociation on Co3O4 is a complicated two-step process through a heterolytic cleavage, followed by the migration of H atom and finally yields the homolytic product on both perfect and oxygen defective Co3O4 (1 1 1) surfaces easily. (ii) After introducing the surface oxygen vacancy, the stepwise hydrogenation of ethylene by atomic hydrogen is much easier than that on perfect surface due to the weaker bond strength of OH group. The strength of Osbnd H bond is a crucial factor for the hydrogenation reaction which involves the breakage of Osbnd H bond. The formation of oxygen vacancy increases the electronic charges at the adjacent surface O, which reduces its capability of further gaining electrons from adsorbed atomic hydrogen and then weakens the strength of Osbnd H bond. These results emphasize the importance of the oxygen vacancies for hydrogenation on metal oxides.

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.

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

NASA Astrophysics Data System (ADS)

Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

2014-05-01

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

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.

Does a higher metal oxidation state necessarily imply higher reactivity toward H-atom transfer? A computational study of C-H bond oxidation by high-valent iron-oxo and -nitrido complexes.

PubMed

Geng, Caiyun; Ye, Shengfa; Neese, Frank

2014-04-28

In this work, the reactions of C-H bond activation by two series of iron-oxo ( (Fe(IV)), (Fe(V)), (Fe(VI))) and -nitrido model complexes ( (Fe(IV)), (Fe(V)), (Fe(VI))) with a nearly identical coordination geometry but varying iron oxidation states ranging from iv to vi were comprehensively investigated using density functional theory. We found that in a distorted octahedral coordination environment, the iron-oxo species and their isoelectronic nitrido analogues feature totally different intrinsic reactivities toward C-H bond cleavage. In the case of the iron-oxo complexes, the reaction barrier monotonically decreases as the iron oxidation state increases, consistent with the gradually enhanced electrophilicity across the series. The iron-nitrido complex is less reactive than its isoelectronic iron-oxo species, and more interestingly, a counterintuitive reactivity pattern was observed, i.e. the activation barriers essentially remain constant independent of the iron oxidation states. The detailed analysis using the Polanyi principle demonstrates that the different reactivities between these two series originate from the distinct thermodynamic driving forces, more specifically, the bond dissociation energies (BDEE-Hs, E = O, N) of the nascent E-H bonds in the FeE-H products. Further decomposition of the BDEE-Hs into the electron and proton affinity components shed light on how the oxidation states modulate the BDEE-Hs of the two series.

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

PubMed Central

Averett, Laurel E.; Schoenfisch, Mark H.; Akhremitchev, Boris B.; Gorkun, Oleg V.

2009-01-01

Abstract Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation. PMID:19917237

Characterization of π-stacking interactions between aromatic amino acids and quercetagetin

NASA Astrophysics Data System (ADS)

Akher, Farideh Badichi; Ebrahimi, Ali; Mostafavi, Najmeh

2017-01-01

In the present study, the π-stacking interactions between quercetagetin (QUE), which is one of the most representative flavonol compounds with biological and chemical activities, and some aromatic amino acid (AA) residues has been investigated by the quantum mechanical calculations. The trend in the absolute value of stacking interaction energy |ΔE| with respect to AAs is HIS > PHE > TYR > TPR. The results show that the sum of donor-acceptor interaction energy between AAs and QUE (∑E2) and the sum of electron densities ρ calculated at BCPs and CCPs between the rings (∑ρBCPs and ∑ρCCP) can be useful descriptors for prediction of the ΔE values of the complexes. The Osbnd H bond dissociation enthalpy (BDE) slightly decreases by the π-stacking interaction, which confirms the positive effect of that interaction on the antioxidant activity of QUE. A reverse trend is observed for BDE when is compared with the |ΔE| values. A reliable relationship is also observed between the Muliken spin density (MSD) distributions of the radical species and the most convenient Osbnd H bond dissociations. In addition, reactivity is in good correlation with the antioxidant activity of the complexes.

What is the best bonding model of the (σ-H-BR) species bound to a transition metal? Bonding analysis in complexes [(H)2Cl(PMe3)2M(σ-H-BR)] (M = Fe, Ru, Os).

PubMed

Pandey, Krishna K

2012-03-21

Density Functional Theory calculations have been performed for the σ-hydroboryl complexes of iron, ruthenium and osmium [(H)(2)Cl(PMe(3))(2)M(σ-H-BR)] (M = Fe, Ru, Os; R = OMe, NMe(2), Ph) at the BP86/TZ2P/ZORA level of theory in order to understand the interactions between metal and HBR ligands. The calculated geometries of the complexes [(H)(2)Cl(PMe(3))(2)Ru(HBNMe(2))], [(H)(2)Cl(PMe(3))(2)Os(HBR)] (R = OMe, NMe(2)) are in excellent agreement with structurally characterized complexes [(H)(2)Cl(P(i)Pr(3))(2)Os(σ-H-BNMe(2))], [(H)(2)Cl(P(i)Pr(3))(2)Os{σ-H-BOCH(2)CH(2)OB(O(2)CH(2)CH(2))}] and [(H)(2)Cl(P(i)Pr(3))(2)Os(σ-H-BNMe(2))]. The longer calculated M-B bond distance in complex [(H)(2)Cl(PMe(3))(2)M(σ-H-BNMe(2))] are due to greater B-N π bonding and as a result, a weaker M-B π-back-bonding. The B-H2 bond distances reveal that (i) iron complexes contain bis(σ-borane) ligand, (ii) ruthenium complexes contain (σ-H-BR) ligands with a stretched B-H2 bond, and (iii) osmium complexes contain hydride (H2) and (σ-H-BR) ligands. The H-BR ligands in osmium complexes are a better trans-directing ligand than the Cl ligand. Values of interaction energy, electrostatic interaction, orbital interaction, and bond dissociation energy for interactions between ionic fragments are very large and may not be consistent with M-(σ-H-BR) bonding. The EDA as well as NBO and AIM analysis suggest that the best bonding model for the M-σ-H-BR interactions in the complexes [(H)(2)Cl(PMe(3))(2)M(σ-H-BR)] is the interaction between neutral fragments [(H)(2)Cl(PMe(3))(2)M] and [σ-H-BR]. This becomes evident from the calculated values for the orbital interactions. The electron configuration of the fragments which is shown for C in Fig. 1 experiences the smallest change upon the M-σ-H-BR bond formation. Since model C also requires the least amount of electronic excitation and geometry changes of all models given by the ΔE(prep) values, it is clearly the most appropriate choice of interacting fragments. The π-bonding contribution is 14-22% of the total orbital contribution.

Electron Localization in Dissociating H 2 + by Retroaction of a Photoelectron onto Its Source

DOE PAGES

Waitz, M.; Asliturk, D.; Wechselberger, N.; ...

2016-01-26

We investigate the dissociation of H 2 + into a proton and a H 0 after single ionization with photons of an energy close to the threshold. We find that the p + and the H 0 do not emerge symmetrically in the case of the H 2 + dissociating along the 1sσ g ground state. Instead, a preference for the ejection of the p + in the direction of the escaping photoelectron can be observed. This symmetry breaking is strongest for very small electron energies. Our experiment is consistent with a recent prediction by Serov and Kheifets. In theirmore » model, which treats the photoelectron classically, the symmetry breaking is induced by the retroaction of the long-range Coulomb potential onto the dissociating H 2 +.« less

NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

PubMed

Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

2013-12-31

An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

Vibrational Mode-Specific Reaction of Methane on a Nickel Surface

NASA Astrophysics Data System (ADS)

Beck, Rainer D.; Maroni, Plinio; Papageorgopoulos, Dimitrios C.; Dang, Tung T.; Schmid, Mathieu P.; Rizzo, Thomas R.

2003-10-01

The dissociation of methane on a nickel catalyst is a key step in steam reforming of natural gas for hydrogen production. Despite substantial effort in both experiment and theory, there is still no atomic-scale description of this important gas-surface reaction. We report quantum state-resolved studies, using pulsed laser and molecular beam techniques, of vibrationally excited methane reacting on the nickel (100) surface. For doubly deuterated methane (CD2H2), we observed that the reaction probability with two quanta of excitation in one C-H bond was greater (by as much as a factor of 5) than with one quantum in each of two C-H bonds. These results clearly exclude the possibility of statistical models correctly describing the mechanism of this process and attest to the importance of full-dimensional calculations of the reaction dynamics.

Vibrational mode-specific reaction of methane on a nickel surface.

PubMed

Beck, Rainer D; Maroni, Plinio; Papageorgopoulos, Dimitrios C; Dang, Tung T; Schmid, Mathieu P; Rizzo, Thomas R

2003-10-03

The dissociation of methane on a nickel catalyst is a key step in steam reforming of natural gas for hydrogen production. Despite substantial effort in both experiment and theory, there is still no atomic-scale description of this important gas-surface reaction. We report quantum state-resolved studies, using pulsed laser and molecular beam techniques, of vibrationally excited methane reacting on the nickel (100) surface. For doubly deuterated methane (CD2H2), we observed that the reaction probability with two quanta of excitation in one C-H bond was greater (by as much as a factor of 5) than with one quantum in each of two C-H bonds. These results clearly exclude the possibility of statistical models correctly describing the mechanism of this process and attest to the importance of full-dimensional calculations of the reaction dynamics.

Dissociative adsorption of CH{sub 3}X (X = Br and Cl) on a silicon(100) surface revisited by density functional theory

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

Wang, Chen-Guang; Lash Miller Chemical Laboratories, Department of Chemistry and Institute of Optical Sciences, University of Toronto, Toronto, Ontario M5S 3H6; Huang, Kai, E-mail: khuang@chem.utoronto.ca, E-mail: wji@ruc.edu.cn

During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH{sub 3}X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH{sub 3}Br, insights havemore » been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH{sub 3}Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.« less

Theoretical and Experimental Insights into the Dissociation of 2-Hydroxyethylhydrazinium Nitrate Clusters Formed via Electrospray.

PubMed

Patrick, Amanda L; Vogelhuber, Kristen M; Prince, Benjamin D; Annesley, Christopher J

2018-03-01

Ionic liquids are used for myriad applications, including as catalysts, solvents, and propellants. Specifically, 2-hydroxyethylhydrazinium nitrate (HEHN) has been developed as a chemical propellant for space applications. The gas-phase behavior of HEHN ions and clusters is important in understanding its potential as an electrospray thruster propellant. Here, the unimolecular dissociation pathways of two clusters are experimentally observed, and theoretical modeling of hydrogen bonding and dissociation pathways is used to help rationalize those observations. The cation/deprotonated cation cluster [HEH 2 - H] + , which is observed from electrospray ionization, is calculated to be considerably more stable than the complementary cation/protonated anion adduct, [HEH + HNO 3 ] + , which is not observed experimentally. Upon collisional activation, a larger cluster [(HEHN) 2 HEH] + undergoes dissociation via loss of nitric acid at lower collision energies, as predicted theoretically. At higher collision energies, additional primary and secondary loss pathways open, including deprotonated cation loss, ion-pair loss, and double-nitric-acid loss. Taken together, these experimental and theoretical results contribute to a foundational understanding of the dissociation of protic ionic liquid clusters in the gas phase.

Creation and annealing of metastable defect states in CH3NH3PbI3 at low temperatures

NASA Astrophysics Data System (ADS)

Lang, F.; Shargaieva, O.; Brus, V. V.; Rappich, J.; Nickel, N. H.

2018-02-01

Methylammonium lead iodide (CH3NH3PbI3), an organic-inorganic perovskite widely used for optoelectronic applications, is known to dissociate under illumination with light at photon energies around 2.7 eV and higher. Here, we show that photo-induced dissociation is not limited to ambient temperatures but can be observed even at 5 K. The photo-induced dissociation of N-H bonds results in the formation of metastable states. Photoluminescence (PL) measurements reveal the formation of defect states that are located 100 meV within the bandgap. This is accompanied by a quenching of the band-to-band PL by one order of magnitude. Defect generation is reversible and annealing at 30 K recovers the band-to-band PL, while the light-induced defect states disappear concurrently.

Driving force analysis of proton tunnelling across a reactivity series for an enzyme-substrate complex.

PubMed

Hothi, Parvinder; Hay, Sam; Roujeinikova, Anna; Sutcliffe, Michael J; Lee, Michael; Leys, David; Cullis, Paul M; Scrutton, Nigel S

2008-11-24

Quantitative structure-activity relationships are widely used to probe C-H bond breakage by quinoprotein enzymes. However, we showed recently that p-substituted benzylamines are poor reactivity probes for the quinoprotein aromatic amine dehydrogenase (AADH) because of a requirement for structural change in the enzyme-substrate complex prior to C-H bond breakage. This rearrangement is partially rate limiting, which leads to deflated kinetic isotope effects for p-substituted benzylamines. Here we report reactivity (driving force) studies of AADH with p-substituted phenylethylamines for which the kinetic isotope effect (approximately 16) accompanying C-H/C-(2)H bond breakage is elevated above the semi-classical limit. We show bond breakage occurs by quantum tunnelling and that within the context of the environmentally coupled framework for H-tunnelling the presence of the p-substituent places greater demand on the apparent need for fast promoting motions. The crystal structure of AADH soaked with phenylethylamine or methoxyphenylethylamine indicates that the structural change identified with p-substituted benzylamines should not limit the reaction with p-substituted phenylethylamines. This is consistent with the elevated kinetic isotope effects measured with p-substituted phenylethylamines. We find a good correlation in the rate constant for proton transfer with bond dissociation energy for the reactive C-H bond, consistent with a rate that is limited by a Marcus-like tunnelling mechanism. As the driving force becomes larger, the rate of proton transfer increases while the Marcus activation energy becomes smaller. This is the first experimental report of the driving force perturbation of H-tunnelling in enzymes using a series of related substrates. Our study provides further support for proton tunnelling in AADH.

"Vibrational bonding": a new type of chemical bond is discovered.

PubMed

Rhodes, Christopher J; Macrae, Roderick M

2015-01-01

A long-sought but elusive new type of chemical bond, occurring on a minimum-free, purely repulsive potential energy surface, has recently been convincingly shown to be possible on the basis of high-level quantum-chemical calculations. This type of bond, termed a vibrational bond, forms because the total energy, including the dynamical energy of the nuclei, is lower than the total energy of the dissociated products, including their vibrational zero-point energy. For this to be the case, the ZPE of the product molecule must be very high, which is ensured by replacing a conventional hydrogen atom with its light isotope muonium (Mu, mass = 1/9 u) in the system Br-H-Br, a natural transition state in the reaction between Br and HBr. A paramagnetic species observed in the reaction Mu +Br2 has been proposed as a first experimental sighting of this species, but definitive identification remains challenging.

First-principles studies of H₂S adsorption and dissociation on metal surfaces

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

Alfonso, D R

2008-01-01

Density functional theory calculations were employed to investigate the molecular and dissociative adsorption of H₂S on the closed packed surfaces of a number of important noble metals (Ag(1 1 1), Au(1 1 1) and Cu(1 1 1)) and transition metals (Ir(1 1 1), Ni(1 1 1), Pd(1 1 1) and Pt(1 1 1)). Energy minima corresponding to adsorbed states were identified with H₂S binding preferentially at the top sites. The adsorption of other S moieties (SH and S) was also examined. SH and S were found to prefer bridge sites and hollow sites, respectively. The binding of H₂S and itsmore » S-containing dissociated species is stronger on the transition metals. The elementary reactions of abstraction of H from H₂S to form a surface SH intermediate and abstraction of H from SH to form a surface S intermediate as model pathways for the dissociation of H₂S were examined. Our results suggest that H₂S decomposition on the aforementioned transition metal surfaces is more facile, both thermodynamically and kinetically.« less

Hemi bonds and noncovalent interactions in the cational systems (XH2P: SHY)+

NASA Astrophysics Data System (ADS)

Li, Xiang; Li, An Yong

2016-08-01

Quantum chemistry ab initio MP2 and CCSD calculations were performed to investigate the P⋯S hemi bonds and noncovalent interactions in the radical cational systems (H3P:SH2)+, (FH2P:SH2)+ and (H3P:SHF)+. The hydride dimer (H3P:SH2)+ has a P⋯S hemi bonding structure and a H-bonding structure, (FH2P:SH2)+ has two hemi bonding structures and a proton-transferred H-bonding structure, (H3P:SHF)+ has two hemi bonding structures and three noncovalent structures. It is remarkable that these hemi bonds also have characters of pnicogen and chalcogen bonds. The binding energy, stability and bonding nature of the hemi bonds were presented.

Dissociative electron attachment studies on acetone

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

Prabhudesai, Vaibhav S., E-mail: vaibhav@tifr.res.in; Tadsare, Vishvesh; Ghosh, Sanat

Dissociative electron attachment (DEA) to acetone is studied in terms of the absolute cross section for various fragment channels in the electron energy range of 0–20 eV. H{sup −} is found to be the most dominant fragment followed by O{sup −} and OH{sup −} with only one resonance peak between 8 and 9 eV. The DEA dynamics is studied by measuring the angular distribution and kinetic energy distribution of fragment anions using Velocity Slice Imaging technique. The kinetic energy and angular distribution of H{sup −} and O{sup −} fragments suggest a many body break-up for the lone resonance observed. Themore » ab initio calculations show that electron is captured in the multi-centered anti-bonding molecular orbital which would lead to a many body break-up of the resonance.« less

Effect of pH and aging time on the kinetic dissociation of 243Am(III) from humic acid-coated gamma-Al2O3: a chelating resin exchange study.

PubMed

Wang, Xiangke; Chen, Changlun; Du, Jinzhou; Tan, Xiaoli; Di, Xu; Yu, Shaoming

2005-09-15

The chelating resin was studied to assess its influence on metal availability and mobility in the environment. The association of organic-inorganic colloid-borne trace elements was investigated in this work. The radionuclide 243Am(III) was chosen as the representative and chemical homologue for trivalent lanthanide and actinide ions present in radioactive nuclear waste. The kinetic dissociation behavior of 243Am(III) from humic acid-coated gamma-Al2O3 was studied at pH values of 4.0 +/- 0.1, 5.0 +/- 0.2, and 6.0 +/- 0.2 with a contact time of 2 days after the addition of a chelating cation exchanger resin. The concentrations of the components were: 243Am(III) 3.0 x 10(-7) mol/L, gamma-Al2O3 0.5 g/L, HA 10 mg/L (pH 4.0 +/- 0.1, 5.0 +/- 0.2, and 6.0 +/- 0.2) and 50 mg/L (pH 6.0 +/- 0.2), respectively. The kinetics of dissociation of 243Am(III) after different equilibration time with humic acid-coated gamma-Al2O3 was also investigated at pH 5.0 +/- 0.2. The experiments were carried out in air and at ambient temperature. The results suggest that the fraction of irreversible bonding of radionuclides to HA-coated Al2O3 increases with increasing pH and is independent of aging time. The assumption of two different 243Am(III)-HA-Al2O3 species, with "fast" and "slow" dissociation kinetics, is required to explain the experimental results. 243Am(III) species present on HA-Al2O3 colloids moves from the "fast" to the "slow" dissociating sites with the increase of aging time.

SK-Edge XAS And DFT Calculations on Square-Planar NiII-Thiolate Complexes: Effects of Active And Passive H-Bonding

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

Dey, A.; Green, K.N.; Jenkins, R.M.

S K-edge XAS for a low-spin Ni{sup II}-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin Fe{sup III}-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possiblemore » in metal-thiolate systems. In the high-spin Fe{sup III}-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin Ni{sup II}-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.« less

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction.

PubMed

Siu, Chi-Kit; Liu, Zhi-Feng; Tse, John S

2002-09-11

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.

Physical-chemical studies of proteins of squid nerve axoplasm, with special reference to the axon fibrous protein.

PubMed

DAVISON, P F; TAYLOR, E W

1960-03-01

The proteins in the axoplasm of the squid, Dosidicus gigas, have been resolved electrophoretically into a major fraction including the fibrous protein, and possibly its structural subunits, and a minor fraction including at least two proteins with low sedimentation coefficients. A partially reversible change in the structure of the fibrous protein occurs under the action of 0.4 M salt or high pH. These experiments have been interpreted to indicate that in the intact fiber one, or a few, protofibrils are arranged helically or longitudinally along the fiber axis, and linked by electrostatic bonds. On the dissociation of these bonds the separated protofibrils assume a less extended form and sediment more rapidly than the intact fibers. Some material with a lower sedimentation rate is also released on the dissociation. This fraction may comprise smaller chain fragments. The volume fraction and the approximate refractive index of the fibers have been calculated.

Physical-Chemical Studies of Proteins of Squid Nerve Axoplasm, with Special Reference to the Axon Fibrous Protein

PubMed Central

Davison, Peter F.; Taylor, Edwin W.

1960-01-01

The proteins in the axoplasm of the squid, Dosidicus gigas, have been resolved electrophoretically into a major fraction including the fibrous protein, and possibly its structural subunits, and a minor fraction including at least two proteins with low sedimentation coefficients. A partially reversible change in the structure of the fibrous protein occurs under the action of 0.4 M salt or high pH. These experiments have been interpreted to indicate that in the intact fiber one, or a few, protofibrils are arranged helically or longitudinally along the fiber axis, and linked by electrostatic bonds. On the dissociation of these bonds the separated protofibrils assume a less extended form and sediment more rapidly than the intact fibers. Some material with a lower sedimentation rate is also released on the dissociation. This fraction may comprise smaller chain fragments. The volume fraction and the approximate refractive index of the fibers have been calculated. PMID:13814536

Stark shift and electric-field-induced dissociation of excitons in monolayer MoS2 and h BN /MoS2 heterostructures

NASA Astrophysics Data System (ADS)

Haastrup, Sten; Latini, Simone; Bolotin, Kirill; Thygesen, Kristian S.

2016-07-01

Efficient conversion of photons into electrical current in two-dimensional semiconductors requires, as a first step, the dissociation of the strongly bound excitons into free electrons and holes. Here we calculate the dissociation rates and energy shift of excitons in monolayer MoS2 as a function of an applied in-plane electric field. The dissociation rates are obtained as the inverse lifetime of the resonant states of a two-dimensional hydrogenic Hamiltonian which describes the exciton within the Mott-Wannier model. The resonances are computed using complex scaling, and the effective masses and screened electron-hole interaction defining the hydrogenic Hamiltonian are computed from first principles. For field strengths above 0.1 V/nm the dissociation lifetime is shorter than 1 ps, which is below the lifetime associated with competing decay mechanisms. Interestingly, encapsulation of the MoS2 layer in just two layers of hexagonal boron nitride (h BN ), enhances the dissociation rate by around one order of magnitude due to the increased screening. This shows that dielectric engineering is an effective way to control exciton lifetimes in two-dimensional materials.

First-principles study for the enhanced sulfur tolerance of Ni(1 1 1) surface alloyed with Pb

NASA Astrophysics Data System (ADS)

Zhang, Yanxing; Yang, Zongxian

2018-04-01

The adsorption of H2S, HS, S, H and the dissociation of H2S on the Ni2Pb/Ni (1 1 1) are systematically studied using the first-principles method based on density functional theory. It is found that H2S dissociation barriers are greatly increased by alloying with Pb atoms in the Ni(1 1 1) surface, while the barrier for H2S formation is greatly reduced. In addition, the adsorption of sulfur atom is weakened a lot. The results indicate that alloying with Pb may be a good way to increase the sulfur tolerance of Ni based anode catalysts of solid oxide fuel cells.

O-H bond oxidation by a monomeric Mn(III)-OMe complex.

PubMed

Wijeratne, Gayan B; Day, Victor W; Jackson, Timothy A

2015-02-21

Manganese-containing, mid-valent oxidants (Mn(III)-OR) that mediate proton-coupled electron-transfer (PCET) reactions are central to a variety of crucial enzymatic processes. The Mn-dependent enzyme lipoxygenase is such an example, where a Mn(III)-OH unit activates fatty acid substrates for peroxidation by an initial PCET. This present work describes the quantitative generation of the Mn(III)-OMe complex, [Mn(III)(OMe)(dpaq)](+) (dpaq = 2-[bis(pyridin-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate) via dioxygen activation by [Mn(II)(dpaq)](+) in methanol at 25 °C. The X-ray diffraction structure of [Mn(III)(OMe)(dpaq)](+) exhibits a Mn-OMe group, with a Mn-O distance of 1.825(4) Å, that is trans to the amide functionality of the dpaq ligand. The [Mn(III)(OMe)(dpaq)](+) complex is quite stable in solution, with a half-life of 26 days in MeCN at 25 °C. [Mn(III)(OMe)(dpaq)](+) can activate phenolic O-H bonds with bond dissociation free energies (BDFEs) of less than 79 kcal mol(-1) and reacts with the weak O-H bond of TEMPOH (TEMPOH = 2,2'-6,6'-tetramethylpiperidine-1-ol) with a hydrogen/deuterium kinetic isotope effect (H/D KIE) of 1.8 in MeCN at 25 °C. This isotope effect, together with other experimental evidence, is suggestive of a concerted proton-electron transfer (CPET) mechanism for O-H bond oxidation by [Mn(III)(OMe)(dpaq)](+). A kinetic and thermodynamic comparison of the O-H bond oxidation reactivity of [Mn(III)(OMe)(dpaq)](+) to other M(III)-OR oxidants is presented as an aid to gain more insight into the PCET reactivity of mid-valent oxidants. In contrast to high-valent counterparts, the limited examples of M(III)-OR oxidants exhibit smaller H/D KIEs and show weaker dependence of their oxidation rates on the driving force of the PCET reaction with O-H bonds.

Linear Response Function of Bond-Order

PubMed Central

Suzuki, Nayuta; Mitsuta, Yuki; Okumura, Mitsutaka; Yamanaka, Shusuke

2016-01-01

We present the linear response function of bond-orders (LRF-BO) based on a real space integration scheme for molecular systems. As in the case of the LRF of density, the LRF-BO is defined as the response of the bond order of the molecule for the virtual perturbation. Our calculations show that the LRF-BO enables us not only to detect inductive and resonating effects of conjugating systems, but also to predict pKa values on substitution groups via linear relationships between the Hammett constants and the LRF-BO values for meta- and para-substituted benzoic acids. More importantly, the LRF-BO values for the O-H bonds strongly depend on the sites to which the virtual perturbation is applied, implying that the LRF-BO values include essential information about reaction mechanism of the acid-dissociation of substituted benzoic acids. PMID:27792148

Selective hydrogenation of amides to alcohols in water solvent over a heterogeneous CeO2-supported Ru catalyst.

PubMed

Tamura, Masazumi; Ishikawa, Susumu; Betchaku, Mii; Nakagawa, Yoshinao; Tomishige, Keiichi

2018-06-20

CeO2-supported Ru (Ru/CeO2) worked as an effective and reusable heterogeneous catalyst for the selective dissociation of the C-N bond in amides, particularly primary amides, with H2 in water solvent at low reaction temperature of 333 K, and high yields of the corresponding alcohols were obtained from primary amides.

Fixed-Node Diffusion Quantum Monte Carlo Method on Dissociation Energies and Their Trends for R-X Bonds (R = Me, Et, i-Pr, t-Bu).

PubMed

Hou, Aiqiang; Zhou, Xiaojun; Wang, Ting; Wang, Fan

2018-05-15

Achieving both bond dissociation energies (BDEs) and their trends for the R-X bonds with R = Me, Et, i-Pr, and t-Bu reliably is nontrivial. Density functional theory (DFT) methods with traditional exchange-correlation functionals usually have large error on both the BDEs and their trends. The M06-2X functional gives rise to reliable BDEs, but the relative BDEs are determined not as accurately. More demanding approaches such as some double-hybrid functionals, for example, G4 and CCSD(T), are generally required to achieve the BDEs and their trends reliably. The fixed-node diffusion quantum Monte Carlo method (FN-DMC) is employed to calculated BDEs of these R-X bonds with X = H, CH 3 , OCH 3 , OH, and F in this work. The single Slater-Jastrow wave function is adopted as trial wave function, and pseudopotentials (PPs) developed for quantum Monte Carlo calculations are chosen. Error of these PPs is modest in wave function methods, while it is more pronounced in DFT calculations. Our results show that accuracy of BDEs with FN-DMC is similar to that of M06-2X and G4, and trends in BDEs are calculated more reliably than M06-2X. Both BDEs and trends in BDEs of these bonds are reproduced reasonably with FN-DMC. FN-DMC using PPs can thus be applied to BDEs and their trends of similar chemical bonds in larger molecules reliably and provide valuable information on properties of these molecules.

The acid properties of dodecasubstituted porphyrins with a chemically active NH bond

NASA Astrophysics Data System (ADS)

Berezin, D. B.; Ivanova, Yu. B.; Sheinin, V. B.

2007-12-01

The NH acid properties of nonplanar dodecasubstituted porphyrins (H2P) were studied by the spectropotentiometric and spectrophotometric methods and by semiempirical quantum-chemical calculations. The reaction of H2P with a weak organic base DMSO proceeded with the formation of the H-associated form DMSO⋯H⋯PH or DMSO⋯H⋯P⋯H⋯DMSO. Strong bases KOH[222] and [NR4]OH reacted with the formation of mono-(HP-) or dianionic (P2-) forms. An increase in NH acidity along the series tetraphenylporphin < tetraphenyltetrabenzoporphin < β-octaethyltetraphenylporphin < dodecaphenylporphin < β-octabromotetraphenylporphin was to a great extent caused by the polarization of molecules, which accompanied saddle-nonplanar distortions of their structure, rather than β-substituent electronic effects. The quantitative characteristics obtained using the suggested system of criteria of the chemical activity of NH bonds (1H NMR spectral, kinetic, and quantum-chemical criteria) linearly correlated with H2P acid dissociation constants and could be used for alternative estimation of the acidity of tetrapyrrole compounds.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

NASA Astrophysics Data System (ADS)

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-01

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Enthalpy of formation of anisole: implications for the controversy on the O-H bond dissociation enthalpy in phenol.

PubMed

Simões, Ricardo G; Agapito, Filipe; Diogo, Hermínio P; da Piedade, Manuel E Minas

2014-11-20

Significant discrepancies in the literature data for the enthalpy of formation of gaseous anisole, ΔfHmo(PhOCH3, g), have fueled an ongoing controversy regarding the most reliable enthalpy of formation of the phenoxy radical and of the gas phase O-H bond dissociation enthalpy, DHo(PhO-H), in phenol. In the present work ΔfHmo(PhOCH3, g) was reassessed using a combination of calorimetric determinations and high-level (W2-F12) ab initio calculations. Static-bomb combustion calorimetry led to the standard molar enthalpy of formation of liquid anisole at 298.15 K, ΔfHmo(PhOCH3, l) = −(117.1 ± 1.4) kJ·mol(-1). The corresponding enthalpy of vaporization was obtained as, ΔvapHmo(PhOCH3) = 46.41 ± 0.26 kJ·mol(-1), by Calvet-drop microcalorimetry. These results give ΔfHmo(PhOCH3, g) = −(70.7 ± 1.4) kJ·mol(-1), in excellent agreement with ΔfHmo(PhOCH3, g) = −(70.8 ± 3.2) kJ·mol(-1), obtained from the W2-F12 calculations. The ΔfHmo(PhOCH3, g) here recommended leads to ΔfHmo(PhO•, g) = 55.5 ± 2.4 kJ·mol(-)1 and DH°(PhO-H) = 368.1 ± 2.6 kJ·mol(-1).

Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation

NASA Astrophysics Data System (ADS)

Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

2014-02-01

The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

Pauling's electronegativity equation and a new corollary accurately predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.

PubMed

Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A

2003-04-18

Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite accurately homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not reproduce experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously observed empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant.

On the behavior of Bronsted-Evans-Polanyi Relations for Transition Metal Oxides

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

Vojvodic, Aleksandra

2011-08-22

Versatile Broensted-Evans-Polanyi (BEP) relations are found from density functional theory for a wide range of transition metal oxides including rutiles and perovskites. For oxides, the relation depends on the type of oxide, the active site and the dissociating molecule. The slope of the BEP relation is strongly coupled to the adsorbate geometry in the transition state. If it is final state-like the dissociative chemisorption energy can be considered as a descriptor for the dissociation. If it is initial state-like, on the other hand, the dissociative chemisorption energy is not suitable as descriptor for the dissociation. Dissociation of molecules with strongmore » intramolecular bonds belong to the former and molecules with weak intramolecular bonds to the latter group. We show, for the prototype system La-perovskites, that there is a 'cyclic' behavior in the transition state characteristics upon change of the active transition metal of the oxide.« less

Molybdenum-carbon bond dissociation energies in Mo(CO) sub 6

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

Ganske, J.A.; Rosenfeld, R.N.

1990-05-17

The pressure dependence of the recombination rate constants for Mo(CO){sub n} (n = 3,4 and 5) with CO has been studied by time-resolved infrared laser absorption spectroscopy. These data, in conjunction with an RRKM model for unimolecular decay of the activated molecules (Mo(CO){sub 6})*, (Mo(CO){sub 5})*, and (Mo(CO){sub 4})*, have allowed the determination of the bond dissociation energies for several of the Mo-C bonds in Mo(CO){sub 6}. The first Mo-C bond dissociation energies for Mo(CO){sub 6}, Mo(CO){sub 5}, and Mo(CO){sub 4} are found to be DH{degree}((CO){sub 5}Mo{hor ellipsis}CO) = 35 {plus minus} 5 kcal/mol, DH{degree}((CO){sub 4}Mo{hor ellipsis}CO) = 27 {plusmore » minus} 5 kcal/mol, and DH{degree}((CO){sub 3}Mo{hor ellipsis}CO) = 31 {plus minus} 5 kcal/mol.« less

Dry reforming of methane on a highly-active Ni-CeO 2 catalyst: Effects of metal-support interactions on C–H bond breaking

DOE PAGES

Liu, Zongyuan; Grinter, David C.; Lustemberg, Pablo G.; ...

2016-05-04

Ni-CeO 2 is a highly efficient, stable and non-expensive catalyst for methane dry reforming at relative low temperatures (700 K). The active phase of the catalyst consists of small nanoparticles of nickel dispersed on partially reduced ceria. Experiments of ambient pressure XPS indicate that methane dissociates on Ni/CeO 2 at temperatures as low as 300 K, generating CH x and CO x species on the surface of the catalyst. Strong metal–support interactions activate Ni for the dissociation of methane. The results of density-functional calculations show a drop in the effective barrier for methane activation from 0.9 eV on Ni(111) tomore » only 0.15 eV on Ni/CeO 2–x(111). At 700 K, under methane dry reforming conditions, no signals for adsorbed CH x or C species are detected in the C1s XPS region. As a result, the reforming of methane proceeds in a clean and efficient way.« less

Assessing thermochemical data

NASA Astrophysics Data System (ADS)

Holmes, John L.; Aubry, Christiane; Wang, Xian

2007-11-01

This paper describes, with examples, a critical assessment of thermochemical data for some small molecules and free radicals. The available heats of formation, [Delta]fH° (all 298 K values). for simple alkyl hydroperoxides and di-alkyl peroxides were compared and new data are provided. The [Delta]fH° values, all ±5 kJ/mol, are: CH3OOH, -135; CH3CH2OOH, -168; n-C3H7OOH, -189; s-C3H7OOH, -205; t-C4H9OOH, -240; CH3OOCH3, -132; CH3CH2OOCH3, -165; C2H5OOC2H5, -198; n-C3H7OOn-C3H7, -240; s-C3H7OOs-C3H7, -272; t-C4H9OOt-C4H9, -342. These are consistent with established O-O bond dissociation energies and with additivity considerations. [Delta]fH° values for the corresponding alkoxy radicals are also addressed. A similar survey was applied to the homologous n-alkyl aldehydes, C2 to C8, for which recommended [Delta]fH° values, all ±1.5 kJ/mol, are: -166.5, -189, -207.5, -227, -248, -268 and -289, respectively. Particular attention was given to [Delta]fH°(CH3CO) = -10.3 ± 1.8 kJ/mol. The current NIST WebBook datum, [Delta]fH°(CS) = 280.3 kJ/mol, is arguably the best value, being consistent with related thermochemical data. Finally the [Delta]fH° values for the allylic free radicals CH2CHCH2, 174 ± 3 kJ/mol, CH2CHCH(OH), 4.5 ± 4 kJ/mol, and (CH2CH)2C(OH), 37 ± 4 kJ/mol, derived from experimental data and results of computational chemistry are described, together with some related homolytic bond strengths.

Theoretical study of photoacidity of HCN: the effect of complexation with water.

PubMed

Muchová, Eva; Spirko, Vladimir; Hobza, Pavel; Nachtigallová, Dana

2006-11-14

The character of the hydrogen bonding and the excited state proton transfer (ESPT) in the model system HCN...H(2)O is investigated. The PES of the two lowest excited states of the H(2)O...HCN complex was calculated using the CASPT2 method. The nonadiabatic coupling of the two states of the (pi-->pi*) and (pi-->sigma*) character is responsible for the excited state proton/hydrogen transfer. Compared to the ground state, the barrier for this process is significantly smaller. An increased number of water molecules in the complex with cyclic hydrogen-bonded network causes a large blue shift of the state of the (pi-->sigma*) character. The question of the dissociation of the complex in its excited state is also addressed.

Bond dissociation enthalpies of a pinoresinol lignin model compound

Treesearch

Thomas Elder

2014-01-01

ABSTRACT: The pinoresinol unit is one of the principal interunit linkages in lignin. As such, its chemistry and properties are of major importance in understanding the behavior or the polymer. This work examines the homolytic cleavage of the pinoresinol system, representing the initial step in thermal degradation. The bond dissociation enthalpy of this reaction has...

Surface electronic states of low-temperature H-plasma-exposed Ge(100)

NASA Astrophysics Data System (ADS)

Cho, Jaewon; Nemanich, R. J.

1992-11-01

The surface of low-temperature H-plasma-cleaned Ge(100) was studied by angle-resolved UV-photoemission spectroscopy and low-energy electron diffraction (LEED). The surface was prepared by an ex situ preclean followed by an in situ H-plasma exposure at a substrate temperature of 150-300 °C. Auger-electron spectroscopy indicated that the in situ H-plasma clean removed the surface contaminants (carbon and oxygen) from the Ge(100) surface. The LEED pattern varied from a 1×1 to a sharp 2×1, as the substrate temperature was increased. The H-induced surface state was identified at ~5.6 eV below EF, which was believed to be mainly due to the ordered or disordered monohydride phases. The annealing dependence of the spectra showed that the hydride started to dissociate at a temperature of 190 °C, and the dangling-bond surface state was identified. A spectral shift upon annealing indicated that the H-terminated surfaces were unpinned. After the H-plasma clean at 300 °C the dangling-bond surface state was also observed directly with no evidence of H-induced states.

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

Crystal structure and vibrational spectra of melaminium arsenate

NASA Astrophysics Data System (ADS)

Anbalagan, G.; Marchewka, M. K.; Pawlus, K.; Kanagathara, N.

2015-01-01

The crystals of the new melaminium arsenate (MAS) [C3H7N6+ṡH2AsO4-] were obtained by the slow evaporation of an aqueous solution at room temperature. Single crystal X-ray diffraction analysis reveals that the crystal belongs to triclinic system with centro symmetric space group P-1. The crystals are built up from single protonated melaminium residues and single dissociated arsenate H2AsO4- anions. The protonated melaminium ring is almost planar. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the melaminium and arsenate residues forms a three-dimensional network. Vibrational spectroscopic analysis is reported on the basis of FT-IR and FT-Raman spectra recorded at room temperature. Hydrogen bonded network present in the crystal gives notable vibrational effect. DSC has also been performed for the crystal shows no phase transition in the studied temperature range (113-293 K).

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Dehydrogenation involved Coulomb explosion of molecular C2H4FBr in an intense laser field

NASA Astrophysics Data System (ADS)

Pei, Minjie; Yang, Yan; Zhang, Jian; Sun, Zhenrong

2018-04-01

The dissociative double ionization (DDI) of molecular 1-fluo-2-bromoethane (FBE) in an intense laser field has been investigated by dc-slice imaging technology. The DDI channels involved with dehydrogenation are revealed and it's believed both the charge distribution and the bound character of real potential energy surfaces of parent ions play important roles in the dissociation process. The relationship between the potential energy surfaces of the precursor species and the photofragment ejection angles are also discussed and analyzed. Furthermore, the competition between the DDI channels has been studied and the Csbnd C bond cleavages dominate the DDI process at relative higher laser intensity.

The Biotin/Avidin complex adhesion force

NASA Astrophysics Data System (ADS)

Balsera, Manel A.; Izrailev, Sergei; Stepaniants, Sergey; Oono, Yoshitsugu; Schulten, Klaus

1997-03-01

The vitamin Biotin and the protein avidin form one of the strongest non-covalent bonds between biological molecules. We have performed molecular and stochastic dynamic modeling of the unbinding of this complex(Izrailev et al., Biophysical Journal, In press). These simulations provide insight into the effect of particular residues and water on the tight binding of the system. With the aid of simple phenomenological models we have related qualitatively our results to Atomic Force Microscopy adhesion force measurements (E.-L. Florin, V. T. Moy and H. E. Gaub Science) 264:415-417 and kinetic dissociation experiments( A. Chilcotti and P. S. Stayton, J. Am. Chem. Soc.) 117:10622-10628. We will discuss the difficulties preventing a more quantitative understanding of the unbinding force and kinetics.

Collision-Induced Dissociation Study of Strong Hydrogen-Bonded Cluster Ions Y-(HF) n (Y=F, O2) Using Atmospheric Pressure Corona Discharge Ionization Mass Spectrometry Combined with a HF Generator.

PubMed

Sakamoto, Kenya; Sekimoto, Kanako; Takayama, Mitsuo

2017-01-01

Hydrogen fluoride (HF) was produced by a homemade HF generator in order to investigate the properties of strong hydrogen-bonded clusters such as (HF) n . The HF molecules were ionized in the form of complex ions associated with the negative core ions Y - produced by atmospheric pressure corona discharge ionization (APCDI). The use of APCDI in combination with the homemade HF generator led to the formation of negative-ion HF clusters Y - (HF) n (Y=F, O 2 ), where larger clusters with n ≥4 were not detected. The mechanisms for the formation of the HF, F - (HF) n , and O 2 - (HF) n species were discussed from the standpoints of the HF generator and APCDI MS. By performing energy-resolved collision-induced dissociation (CID) experiments on the cluster ions F - (HF) n ( n =1-3), the energies for the loss of HF from F - (HF) 3 , F - (HF) 2 , and F - (HF) were evaluated to be 1 eV or lower, 1 eV or higher, and 2 eV, respectively, on the basis of their center-of-mass energy ( E CM ). These E CM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O 2 (HF) n ] - ( n =1-4) was discussed on the basis of the bond lengths of O 2 H-F - (HF) n and O 2 - H-F(HF) n obtained by ab initio calculations. The calculations indicated that [O 2 (HF) 4 ] - separated into O 2 H and F - (HF) 3 .

Dissociative Attachment Reactions of Electrons with Gas Phase Superacids

NASA Astrophysics Data System (ADS)

Liu, Xifan

Using the flowing afterglow Langmuir probe (FALP) technique, dissociative attachment coefficients beta for reactions of electrons with gas phase superacids HCo(PF_3)_4, HRh(PF _3)_4 and carbonyl hydride complexes HMn(CO)_5, HRe(CO) _5 have been determined under thermal conditions over the approximate temperature range 300~ 550 K. The superacids react relatively slowly (< 1/20 of beta_{rm max}) with free electrons in a thermal plasma, and the values of beta obtained this far do not show a correlation between acidity and beta. The pioneer researchers in this field had speculated that any superacid would be a rapid attacher of electrons; we found that this speculation is not true in general. The product distribution of electron attachment reaction to HCo(PF_3)_4 was found to be independent of temperature even though the beta (HCo(PF_3)_4 ) increases with temperature. This leads us to propose that the electron attachment process occurs well before the excited complex dissociates. In addition, the activation energy of HCo(PF_3)_4 for electron attachment has been derived from the Arrhenius plots. The carbonyl hydride complexes, HMn(CO) _5 and HRe(CO)_5, react relatively rapidly (>1/4 of beta_{rm max}) with free electrons in thermal plasma. This indicates that these reactions cannot be significantly endothermic. Observation of rapid attachment for these non-superacids shows that the Mn-CO and Re-CO bonds are weaker than the Mn-H and Re-H bonds, respectively. Comparisons between the carbonyl and trifluorophosphine cases implies that fast electron capture is related more to the CO ligand than to the transition -metal species.

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

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

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE PAGES

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad; ...

2017-10-06

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Multiconfiguration Pair-Density Functional Theory and Complete Active Space Second Order Perturbation Theory. Bond Dissociation Energies of FeC, NiC, FeS, NiS, FeSe, and NiSe.

PubMed

Sharkas, Kamal; Gagliardi, Laura; Truhlar, Donald G

2017-12-07

We investigate the performance of multiconfiguration pair-density functional theory (MC-PDFT) and complete active space second-order perturbation theory for computing the bond dissociation energies of the diatomic molecules FeC, NiC, FeS, NiS, FeSe, and NiSe, for which accurate experimental data have become recently available [Matthew, D. J.; Tieu, E.; Morse, M. D. J. Chem. Phys. 2017, 146, 144310-144320]. We use three correlated participating orbital (CPO) schemes (nominal, moderate, and extended) to define the active spaces, and we consider both the complete active space (CAS) and the separated-pair (SP) schemes to specify the configurations included for a given active space. We found that the moderate SP-PDFT scheme with the tPBE on-top density functional has the smallest mean unsigned error (MUE) of the methods considered. This level of theory provides a balanced treatment of the static and dynamic correlation energies for the studied systems. This is encouraging because the method is low in cost even for much more complicated systems.

Hydrogen-assisted versus hydroxyl-assisted CO dissociation over Co-doped Cu(111): A DFT study

NASA Astrophysics Data System (ADS)

Zha, Hao; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua

2018-03-01

First principle based density functional theory (DFT) was used to calculate the step-by-step hydrogenation and dissociation reaction network of carbon monoxide (CO) over Co-doped Cu(111) surface as a model for understanding the lateral interaction of surface hydroxyl species (OH) on these reactions. We discussed the Csbnd O bond length and the adsorption energy changes of reaction intermediates under different adsorption circumstances for purpose of making out the effect of surface hydroxyl on the reaction selectivity. Reaction intermediates co-adsorbed with H atom and hydroxyl could undergo H-assisted or OH-assisted routes. The calculations show that the OH-assisted route prefers with the formation of COH, CHOH and CH2OH while general H-assisted route prefers with the formation of HCO, CH2O and CH3O. Considering the rather low activation barrier of COH, CHOH and CH2OH to form CHX, the existence of hydroxyl on the surface is in favor of boosting the CHX and suppressing the methanol.

Density Functional Theory Calculations of the Dissociation of H[2] on (100) 2H-MoS[2] Surfaces: A Key Step in the Hydroprocessing of Crude Oil

ERIC Educational Resources Information Center

Todorova, Teodora; Alexiev, Valentin; Weber, Thomas

2006-01-01

Hydrogen activation on the (100) surface of MoS[2] structures was investigated by means of density functional theory calculations. Linear and quadratic synchronous transit methods with a conjugate gradient refinement of the saddle point were used to localize transition states. The calculations include heterolytic and homolytic dissociation of…

The photodissociation dynamics of the ethyl radical, C2H5, investigated by velocity map imaging.

PubMed

Steinbauer, Michael; Giegerich, Jens; Fischer, Kathrin H; Fischer, Ingo

2012-07-07

The photodissociation dynamics of the ethyl radical C(2)H(5) has been investigated by velocity map imaging. Ethyl was produced by flash pyrolysis from n-propyl nitrite and excited to the à (2)A(') (3s) Rydberg state around 250 nm. The energetically most favorable reaction channel in this wavelength region is dissociation to C(2)H(4) (ethene) + H. The H-atom dissociation products were ionized in a [1+1(')] process via the 1s-2p transition. The observed translational energy distribution is bimodal: A contribution of slow H-atoms with an isotropic angular distribution peaks at low translational energies. An expectation value for the fraction of excess energy released into translation of = 0.19 is derived from the data, typical for statistical dissociation reactions. In addition, a fast H-atom channel is observed, peaking around 1.8 eV. The latter shows an anisotropic distribution with β = 0.45. It originates from a direct dissociation process within less than a rotational period. Time-delay scans with varying extraction voltages indicate the presence of two rates for the formation of H-atoms. One rate with a sub-nanosecond time constant is associated with H-atoms with large translational energy; a second one with a time constant on the order of 100 ns is associated with H-atoms formed with low translational energy. The data confirm and extend those from previous experiments and remove some inconsistencies. Possible mechanisms for the dissociation are discussed in light of the new results as well as previous ones.

Structure and Bonding analysis of the cationic electrophilic phosphinidene complexes of iron, ruthenium, and osmium [(η(5)-C5Me5)(CO)2M{PN(i)Pr2}]+, [(η(5)-C5H5)(CO)2M{PNR2}]+ (R = Me, (i)Pr), and [(η(5)-C5H5)(PMe3)2M{PNMe2}]+ (M = Fe, Ru, Os).

PubMed

Pandey, Krishna K; Tiwari, Pradeep; Patidar, Pankaj

2012-11-29

Quantum-chemical DFT calculations for the electronic, molecular structure and M-PNR(2) bonding analyses of the experimentally known cationic electrophilic phosphinidene complexes [(η(5)-C(5)Me(5))(CO)(2)M{PN(i)Pr(2)}](+) and of the model complexes [(η(5)-C(5)H(5))(CO)(2)M{PNR(2)}](+) (R = (i)Pr, Me) and [(η(5)-C(5)H(5))(PMe(3))(2)M{PNMe(2)}](+) were carried out using BP86/TZ2P/ZORA level of theory. The calculated geometrical parameters of the studied complexes are in good agreement with the reported experimental values. The short M-P bond distances and calculated Pauling bond orders (range of 1.23-1.68), suggest the presence of M-P multiple bond characters. The Hirshfeld charge analysis shows that the overall charge flows from phosphinidene ligand to metal fragment. The M-P σ-bonding orbitals are well-occupied (>1.80e). The energy decomposition analysis revealed that the contribution of the electrostatic interaction ΔE(elstat) is, in all studied complexes, significantly larger (55.2-62.6%) than the orbital interactions ΔE(orb). The orbital interactions between metal and PNR(2) in [(η(5)-C(5)H(5))(L)(2)M{PNR(2)}](+) arise mainly from M ← PNR(2) σ-donation. The π-bonding contribution (19-36%) is much smaller than the σ-bonding. The interaction energies, as well as bond dissociation energies, depend on the auxiliary ligand framework around the metal and decrease in the order (η(5)-C(5)H(5)) > (η(5)-C(5)Me(5)) and CO > PMe(3). Upon substitution of R = (i)Pr with smaller group R = Me, the M-PNR(2) bond strength slightly decreases.

Synthesis and reactivity of dimeric Ar'TlTlAr' and trimeric (Ar"T1)3 (Ar', Ar" = bulky terphenyl group) thallium(I) derivatives: Tl(I)-Tl(I) bonding in species ligated by monodentate ligands.

PubMed

Wright, Robert J; Phillips, Andrew D; Hino, Shirley; Power, Philip P

2005-04-06

The synthesis and characterization of three new organothallium(I) compounds are reported. Reaction of (Ar'Li)(2) (Ar' = C(6)H(3)-2,6-(C(6)H(3)-2,6-Pr(i)(2))(2)) and Ar"Li (Ar" = C(6)H(3)-2,6-(C(6)H(3)-2,6-Me(2))(2)) with TlCl in Et(2)O afforded (Ar'Tl)(2) (1) and (Ar' 'Tl)(3) (2). The "dithallene" 1 is the heaviest group 13 dimetallene and features a planar, trans-bent structure with Ar'Tl-Tl = 119.74(14) degrees and Tl-Tl = 3.0936(8) A. Compound 2 is the first structurally characterized neutral, three-membered ring species of formula c-(MR)(3) (M = Al-Tl; R = organo group). The Tl(3) ring has Tl-Tl distances in the range ca. 3.21-3.37 A as well as pyramidal Tl geometries. The Tl-Tl bonds in 1 and 2 are outside the range (2.88-2.97 A) of Tl-Tl single bonds in R(2)TlTlR(2) compounds. The weak Tl-Tl bonding in 1 and 2 leads to their dissociation into Ar'Tl and Ar' 'Tl monomers in hexane. The Ar'Tl monomer behaves as a Lewis base and readily forms a 1:1 donor-acceptor complex with B(C(6)F(5))(3) to give Ar'TlB(C(6)F(5))(3), 3. Adduct 3 features an almost linear thallium C(ipso)-Tl-B angle of 174.358(7) degrees and a Tl-B distance of 2.311(2) A, which indicates strong association. Treatment of 1 with a variety of reagents resulted in no reactions. The lower reactivity of 1 is in accord with the reluctance of Tl(I) to undergo oxidation to Tl(III) due to the unreactive character of the 6s(2) electrons.

Supramolecular architecture of 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole.3H2O: Synthesis, spectroscopic investigations, DFT computation, MD simulations and docking studies

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.

2017-12-01

Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential of title molecule in the area of pharmaceutics, we have also calculated a series of drug likeness parameters. Possibly important biological activity of BMMBI molecule was also confirmed by molecular docking study.

Electric double layer at metal oxide surfaces:static properties of the cassiterite-water interface.

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

Vlcek, L.; Zhang, Z.; Machesky, M .L.

2007-03-24

The structure of water at the (110) surface of cassiterite ({alpha}-SnO{sub 2}) at ambient conditions was studied by means of molecular dynamics simulations and X-ray crystal truncation rod experiments and interpreted with the help of the revised MUSIC model of surface protonation. The interactions of the metal oxide in the simulations were described by a recently developed classical force field based on the SPC/E model of water. Two extreme cases of completely hydroxylated and nonhydroxylated surfaces were considered along with a mixed surface with 50% dissociation. To study the dependence of the surface properties on pH, neutral and negatively chargedmore » variants of the surfaces were constructed. Axial and lateral density distributions of water for different types of surfaces were compared to each other and to experimental axial density distributions found by X-ray experiments. Although significant differences were found between the structures of the studied interfaces, the axial distances between Sn and O atoms are very similar and therefore could not be clearly distinguished by the diffraction technique. The explanation of structures observed in the density distributions was provided by a detailed analysis of hydrogen bonding in the interfacial region. It revealed qualitatively different hydrating patterns formed at neutral hydroxylated and nonhydroxylated surfaces and suggested a preference for the dissociative adsorption of water. At negatively charged surfaces, however, the situation can be reversed by the electric field stabilizing a hydrogen bond network similar to that found at the neutral nonhydroxylated surface. Comparison with previously studied rutile ({alpha}-TiO{sub 2}) surfaces provided insight into the differences between the hydration of these two metal oxides, and an important role was ascribed to their different lattice parameters. A link to macroscopic properties was provided by the revised MUSIC surface protonation model. Explicit use of the Sn-O bond lengths based on ab initio calculations and H-bond configurations as inputs led to the prediction of a pH of zero net-proton induced surface charge (pH{sub pzc}) that agrees very well with those determined experimentally (about 4.4 at 298 K).« less

Electric double layer at metal oxide surfaces: Static properties of the cassiterite - Water Interface

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

Vlcek, Lukas; Zhang, Zhan; Machesky, Michael L.

2007-01-01

The structure of water at the (110) surface of cassiterite ({alpha}-SnO{sub 2}) at ambient conditions was studied by means of molecular dynamics simulations and X-ray crystal truncation rod experiments and interpreted with the help of the revised MUSIC model of surface protonation. The interactions of the metal oxide in the simulations were described by a recently developed classical force field based on the SPC/E model of water. Two extreme cases of completely hydroxylated and nonhydroxylated surfaces were considered along with a mixed surface with 50% dissociation. To study the dependence of the surface properties on pH, neutral and negatively chargedmore » variants of the surfaces were constructed. Axial and lateral density distributions of water for different types of surfaces were compared to each other and to experimental axial density distributions found by X-ray experiments. Although significant differences were found between the structures of the studied interfaces, the axial distances between Sn and O atoms are very similar and therefore could not be clearly distinguished by the diffraction technique. The explanation of structures observed in the density distributions was provided by a detailed analysis of hydrogen bonding in the interfacial region. It revealed qualitatively different hydrating patterns formed at neutral hydroxylated and nonhydroxylated surfaces and suggested a preference for the dissociative adsorption of water. At negatively charged surfaces, however, the situation can be reversed by the electric field stabilizing a hydrogen bond network similar to that found at the neutral nonhydroxylated surface. Comparison with previously studied rutile ({alpha}-TiO{sub 2}) surfaces provided insight into the differences between the hydration of these two metal oxides, and an important role was ascribed to their different lattice parameters. A link to macroscopic properties was provided by the revised MUSIC surface protonation model. Explicit use of the Sn-O bond lengths based on ab initio calculations and H-bond configurations as inputs led to the prediction of a pH of zero net-proton induced surface charge (pH{sub pzc}) that agrees very well with those determined experimentally (about 4.4 at 298 K).« less

Catch bonding in the forced dissociation of a polymer endpoint

NASA Astrophysics Data System (ADS)

Vrusch, Cyril; Storm, Cornelis

2018-04-01

Applying a force to certain supramolecular bonds may initially stabilize them, manifested by a lower dissociation rate. We show that this behavior, known as catch bonding and by now broadly reported in numerous biophysics bonds, is generically expected when either or both the trapping potential and the force applied to the bond possess some degree of nonlinearity. We enumerate possible scenarios and for each identify the possibility and, if applicable, the criterion for catch bonding to occur. The effect is robustly predicted by Kramers theory and Mean First Passage Time theory and confirmed in direct molecular dynamics simulation. Among the catch scenarios, one plays out essentially any time the force on the bond originates in a polymeric object, implying that some degree of catch bond behavior is to be expected in many settings relevant to polymer network mechanics or optical tweezer experiments.

Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis

NASA Astrophysics Data System (ADS)

Lyon, Yana A.; Beran, Gregory; Julian, Ryan R.

2017-07-01

Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers.

DFT and ab initio study of the unimolecular decomposition of the lowest singlet and triplet states of nitromethane

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

Manaa, M.R.; Fried, L.E.

1998-11-26

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C-NO{sub 2} bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. The authors perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C-N bond distance with 12--16 kcal/mol lower energy than does MCSCF.more » In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by FT methods based on Becke`s 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF and QCISD in the vicinity of the equilibrium structure. The computational methods predict bond dissociation energies 5--9 kcal/mol lower than the experimental value. DFT techniques based on Becke`s 3-parameter exchange functional show the best overall agreement with the higher level methods.« less

Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.

PubMed

Li, Xiaojun; Sun, Qingan; Jiang, Cai; Yang, Kailu; Hung, Li-Wei; Zhang, Junjie; Sacchettini, James C

2015-10-06

The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evidence for concerted ring opening and C-Br bond breaking in UV-excited bromocyclopropane.

PubMed

Pandit, Shubhrangshu; Preston, Thomas J; King, Simon J; Vallance, Claire; Orr-Ewing, Andrew J

2016-06-28

Photodissociation of gaseous bromocyclopropane via its A-band continuum has been studied at excitation wavelengths ranging from 230 nm to 267 nm. Velocity-map images of ground-state bromine atoms (Br), spin-orbit excited bromine atoms (Br(∗)), and C3H5 hydrocarbon radicals reveal the kinetic energies of these various photofragments. Both Br and Br(∗) atoms are predominantly generated via repulsive excited electronic states in a prompt photodissociation process in which the hydrocarbon co-fragment is a cyclopropyl radical. However, the images obtained at the mass of the hydrocarbon radical fragment identify a channel with total kinetic energy greater than that deduced from the Br and Br(∗) images, and with a kinetic energy distribution that exceeds the energetic limit for Br + cyclopropyl radical products. The velocity-map images of these C3H5 fragments have lower angular anisotropies than measured for Br and Br(∗), indicating molecular restructuring during dissociation. The high kinetic energy C3H5 signals are assigned to allyl radicals generated by a minor photochemical pathway which involves concerted C-Br bond dissociation and cyclopropyl ring-opening following single ultraviolet (UV)-photon absorption. Slow photofragments also contribute to the velocity map images obtained at the C3H5 radical mass, but the corresponding slow Br atoms are not observed. These features in the images are attributed to C3H5 (+) from the photodissociation of the C3H5Br(+) molecular cation following two-photon ionization of the parent compound. This assignment is confirmed by 118-nm vacuum ultraviolet ionization studies that prepare the molecular cation in its ground electronic state prior to UV photodissociation.

Ring-breaking electron attachment to uracil: following bond dissociations via evolving resonances.

PubMed

Gianturco, Franco A; Sebastianelli, F; Lucchese, R R; Baccarelli, I; Sanna, N

2008-05-07

Calculations are carried out at various distinct energies to obtain both elastic cross sections and S-matrix resonance indicators (poles) from a quantum treatment of the electron scattering from gas-phase uracil. The low-energy region confirms the presence of pi(*) resonances as revealed by earlier calculations and experiments which are compared with the present findings. They turn out to be little affected by bond deformation, while the transient negative ions (TNIs) associated with sigma(*) resonances in the higher energy region ( approximately 8 eV) indeed show that ring deformations which allow vibrational redistribution of the excess electron energy into the molecular target strongly affect these shape resonances: They therefore evolve along different dissociative pathways and stabilize different fragment anions. The calculations further show that the occurrence of conical intersections between sigma(*) and pi(*)-type potential energy surfaces (real parts) is a very likely mechanism responsible for energy transfers between different TNIs. The excess electron wavefunctions for such scattering states, once mapped over the molecular space, provide nanoscopic reasons for the selective breaking of different bonds in the ring region.

Theoretical Study of Trimethylacetic Acid Adsorption on CeO 2 (111) Surface

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

Wang, Weina; Thevuthasan, S.; Wang, Wenliang

We investigated trimethylacetic acid (TMAA) adsorption on stoichiometric and oxygen-deficient CeO 2(111) surfaces using density functional theory that accounts for the on-site Coulomb interaction via a Hubbard term (DFT+U) and long-range dispersion correction. Both the molecular state and dissociative state (TMAA → TMA– + H +) were identified on stoichiometric and oxygen-deficient CeO 2(111) surfaces. For the stoichiometric surface, two thermodynamically favorable configurations with adsorption energies of the order of -30 kcal/mol are identified; one is a molecule adsorption state, and the other one is a dissociative state. For the oxygen-deficient surface, dissociative states are more favorable than molecular states.more » Moreover, the most favorable configuration is the dissociative adsorption of TMAA with the adsorption energy of the order of -77 kcal/mol. The dissociated TMA moiety takes the position of oxygen vacancy, forming three Ce–O bonds. The signature vibrational frequencies for these thermodynamically stable structures are reported as well as their electronic structures. The effects of long-range dispersion interactions are found to be negligible for geometries but important for adsorption energies.« less

Theoretical Study of Trimethylacetic Acid Adsorption on CeO 2 (111) Surface

DOE PAGES

Wang, Weina; Thevuthasan, S.; Wang, Wenliang; ...

2016-01-11

We investigated trimethylacetic acid (TMAA) adsorption on stoichiometric and oxygen-deficient CeO 2(111) surfaces using density functional theory that accounts for the on-site Coulomb interaction via a Hubbard term (DFT+U) and long-range dispersion correction. Both the molecular state and dissociative state (TMAA → TMA– + H +) were identified on stoichiometric and oxygen-deficient CeO 2(111) surfaces. For the stoichiometric surface, two thermodynamically favorable configurations with adsorption energies of the order of -30 kcal/mol are identified; one is a molecule adsorption state, and the other one is a dissociative state. For the oxygen-deficient surface, dissociative states are more favorable than molecular states.more » Moreover, the most favorable configuration is the dissociative adsorption of TMAA with the adsorption energy of the order of -77 kcal/mol. The dissociated TMA moiety takes the position of oxygen vacancy, forming three Ce–O bonds. The signature vibrational frequencies for these thermodynamically stable structures are reported as well as their electronic structures. The effects of long-range dispersion interactions are found to be negligible for geometries but important for adsorption energies.« less

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

Lam, Chow-Shing; Adams, Jonathan D.; Butler, Laurie J.

We investigate the unimolecular dissociation of the vinoxy radical (CH 2CHO) prepared with high internal energy imparted from the photodissociation of chloroacetaldehyde (CH 2ClCHO) at 157 nm. Using a velocity map imaging apparatus, we measured the speed distribution of the recoiling chlorine atoms, Cl( 2P 3/2) and Cl( 2P 1/2), and derived from this the resulting distribution of kinetic energy, P(ET), imparted to the Cl + vinoxy fragments upon dissociation. Using conservation of energy, the distribution of kinetic energy was used to determine the total internal energy distribution in the radical. The P(ET) derived for the C–Cl bond fission presentedmore » in this work suggests the vinoxy radicals are mostly formed in the à state. We also took ion images at m/z = 42 and m/z = 15 to characterize the branching between the unimolecular dissociation channels of the vinoxy radical to H + ketene and methyl + CO products. Our results show a marked change in the branching ratio between the two channels from the previous study on the photodissociation of chloroacetaldehyde at 193 nm by Miller et al. (J. Chem. Phys., 2004, 121, 1830) in that the production of ketene is now favored over the production of methyl. To help analyze the data, we developed a model for the branching between the two channels that takes into account how the change in rotational energy en route to the products affects the vibrational energy available to surmount the barriers to the channels. The model predicts the portion of the C–Cl bond fission P(ET) that produces dissociative vinoxy radicals, then predicts the branching ratio between the H + ketene and CH 3 + CO product channels at each ET. The model uses Rice–Ramsperger–Kassel–Marcus rate constants at the correct sums and densities of vibrational states while accounting for angular momentum conservation. We find that the predicted portion of the P(ET) that produces H + ketene products best fits the experimental portion (that we derive by taking advantage of conservation of momentum) if we use a barrier height for the H + ketene channel that is 4.0 ± 0.5 kcal/mol higher than the isomerization barrier en route to CH 3 + CO products. Using the G4 computed isomerization barrier of 40.6 kcal/mol, this gives an experimentally determined barrier to the H + ketene channel of 44.6 kcal/mol. From these calculations, we also predict the branching ratio between the H + ketene and methyl + CO channels to be ~2.1:1.« less

Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex.

PubMed Central

Nonin-Lecomte, S; Lin, C H; Patel, D J

2001-01-01

The solution structure of an adenosine monophosphate (AMP)-DNA aptamer complex has been determined previously [Lin, C. H., and Patel, D. J. (1997) Chem. Biol. 4:817-832]. On a symmetrical aptamer complex containing the same binding loop, but with better resolved spectra, we have identified two additional hydrogen bond-mediated associations in the binding loop. One of these involves a rapidly exchanging G imino proton. The phosphate group of the AMP ligand was identified as the acceptor by comparison with other aptamer complexes. Imino proton exchange measurements also yielded the dissociation constants of the stem and binding loop base pairs. This study shows that nuclear magnetic resonance-based imino proton exchange is a good probe for detection of weak hydrogen-bond associations. PMID:11721004

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

Mei, Donghai; Lebarbier, Vanessa M.; Rousseau, Roger

In a combined experimental and first-principles density functional theory (DFT) study, benzene steam reforming (BSR) over MgAl 2O 4 supported Rh and Ir catalysts was investigated. Experimentally, it has been found that both highly dispersed Rh and Ir clusters (1-2 nm) on the MgAl 2O 4 spinel support are stable during the BSR in the temperature range of 700-850°C. Compared to the Ir/MgAl 2O 4 catalyst, the Rh/MgAl 2O 4 catalyst is more active with higher benzene turnover frequency and conversion. At typical steam conditions with the steam-to-carbon ratio > 12, the benzene conversion is only a weak function ofmore » the H 2O concentration in the feed. This suggests that the initial benzene decomposition step rather than the benzene adsorption is most likely the rate-determined step in BSR over supported Rh and Ir catalysts. In order to understand the differences between the two catalysts, we followed with a comparative DFT study of initial benzene decomposition pathways over two representative model systems for each supported metal (Rh and Ir) catalysts. A periodic terrace (111) surface and an amorphous 50-atom metal cluster with a diameter of 1.0 nm were used to represent the two supported model catalysts under low and high dispersion conditions. Our DFT results show that the decreasing catalyst particle size enhances the benzene decomposition on supported Rh catalysts by lowering both C-C and C-H bond scission. The activation barriers of the C-C and the C-H bond scission decrease from 1.60 and 1.61 eV on the Rh(111) surface to 1.34 and 1.26 eV on the Rh50 cluster. For supported Ir catalysts, the decreasing particle size only affects the C-C scission. The activation barrier of the C-C scission of benzene decreases from 1.60 eV on the Ir(111) surface to 1.35 eV on the Ir50 cluster while the barriers of the C-H scission are practically the same. The experimentally measured higher BSR activity on the supported highly dispersed Rh catalyst can be rationalized by the thermodynamic limitation for the very first C-C bond scission of benzene on the small Ir50 catalyst. The C-C bond scission of benzene on the small Ir50 catalyst is highly endothermic although the barrier is competitive with the barriers of both the C-C and the C-H bond-breakings on the small Rh50 catalyst. The calculations also imply that, for the supported Rh catalysts the C-C and C-H bond scissions are competitive, independently of the Rh cluster sizes. After the initial dissociation step via either the C-C or the C-H bond scission, the C-H bond breaking seems to be more favorable rather than the C-C bond breaking on the larger Rh terrace surface. This work was financially supported by the United States Department of Energy’s Office of Biomass Program’s. Computing time was granted by a user project at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Thermal regulation of methane hydrate dissociation: Implications for gas production models

USGS Publications Warehouse

Circone, S.; Kirby, S.H.; Stern, L.A.

2005-01-01

Thermal self-regulation of methane hydrate dissociation at pressure, temperature conditions along phase boundaries, illustrated by experiment in this report, is a significant effect with potential relevance to gas production from gas hydrate. In surroundings maintained at temperatures above the ice melting point, the temperature in the vicinity of dissociating methane hydrate will decrease because heat flow is insufficient to balance the heat absorbed by the endothermic reaction: CH4??nH2O (s) = CH4 (g) + nH2O (l). Temperature decreases until either all of the hydrate dissociates or a phase boundary is reached. At pressures above the quadruple point, the temperature-limiting phase boundary is that of the dissociation reaction itself. At lower pressures, the minimum temperature is limited by the H2O solid/liquid boundary. This change in the temperature-limiting phase boundary constrains the pressure, temperature conditions of the quadruple point for the CH4-H2O system to 2.55 ?? 0.02 MPa and 272.85 ?? 0.03 K. At pressures below the quadruple point, hydrate dissociation proceeds as the liquid H2O produced by dissociation freezes. In the laboratory experiments, dissociation is not impeded by the formation of ice byproduct per se; instead rates are proportional to the heat flow from the surroundings. This is in contrast to the extremely slow dissociation rates observed when surrounding temperatures are below the H2O solid/liquid boundary, where no liquid water is present. This "anomalous" or "self" preservation behavior, most pronounced near 268 K, cannot be accessed when surrounding temperatures are above the H2O solid/liquid boundary. ?? 2005 American Chemical Society.

Density functional theory and RRKM calculations of decompositions of the metastable E-2,4-pentadienal molecular ions.

PubMed

Solano Espinoza, Eduardo A; Vallejo Narváez, Wilmer E

2010-07-01

The potential energy profiles for the fragmentations that lead to [C(5)H(5)O](+) and [C(4)H(6)](+*) ions from the molecular ions [C(5)H(6)O](+*) of E-2,4-pentadienal were obtained from calculations at the UB3LYP/6-311G + + (3df,3pd)//UB3LYP/6-31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice-Ramsperger-Kassel-Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre-equilibrium and rate-controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C-H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E-2,4-pentadienal ions. The direct dissociation, however, can only become important in the high-energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2-hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion-neutral complex which, in turn, decomposes rapidly to the s-trans-1,3-butadiene ion [C(4)H(6)](+*). The predominating metastable channel is the second one, that is, a multi-step ring closure which starts with a rate-limiting cis-trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C(5)H(5)O](+). These results can be used to rationalize the CID mass spectrum of E-2,4-pentadienal in a low-energy regime. 2010 John Wiley & Sons, Ltd.

The divergent effects of strong NHC donation in catalysis† †Electronic supplementary information (ESI) available: Rate profiles for decomposition of u-GIIm and s-GIIm; X-ray crystallographic details; NOESY spectra, and derivation of the [PCy3]-independence of decomposition. CCDC 1400077. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc02592c

PubMed Central

Lummiss, Justin A. M.; Higman, Carolyn S.; Fyson, Devon L.; McDonald, Robert

2015-01-01

Strong σ-donation from NHC ligands (NHC = N-heterocyclic carbene) is shown to have profoundly conflicting consequences for the reactivity of transition-metal catalysts. Such donation is regarded as central to high catalyst activity in many contexts, of which the second-generation Grubbs metathesis catalysts (RuCl2(NHC)(PCy3)( 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CHPh), GII) offer an early, prominent example. Less widely recognized is the dramatically inhibiting impact of NHC ligation on initiation of GII, and on re-entry into the catalytic cycle from the resting-state methylidene species RuCl2(NHC)(PCy3)( 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CH2), GIIm. Both GII and the methylidene complexes are activated by dissociation of PCy3. The impact of NHC donicity on the rate of PCy3 loss is explored in a comparison of s-GIIm, vs.u-GIIm, in which the NHC ligand is saturated H2IMes or unsaturated IMes, respectively. PCy3 loss is nearly an order of magnitude slower for the IMes derivative (a difference that is replicated, albeit smaller, for the benzylidene precatalysts GII). Proposed as an overlooked contributor to these rate differences is an increase in the Ru–PCy3 bond strength arising from π-back-donation onto the phosphine ligand. Strong σ-donation from the IMes ligand, coupled with the inability of this unsaturated NHC to participate in significant π-backbonding, amplifies Ru → PCy3 π-back-donation. The resulting increase in Ru–P bond strength greatly inhibits entry into the active cycle. For s-GII, in contrast, the greater π-acceptor capacity of the NHC ligand enables competing Ru → H2IMes back-donation (as confirmed by NOE experiments, which reveal restricted rotation about the Ru–NHC bond for H2IMes, but not IMes). Ru → PCy3 back-donation is thus attenuated in the H2IMes complexes, accounting for the greater lability of the PCy3 ligand in s-GIIm and s-GII. Similarly inhibited initiation is predicted for other metal–NHC catalysts in which a π-acceptor ligand L must be dissociated to permit substrate binding. Conversely, enhanced reactivity can be expected where such L ligands are pure σ-donors. These effects are expected to be particularly dramatic where the NHC ligand has minimal π-acceptor capacity (as in the unsaturated Arduengo carbenes), and in geometries that maximize NHC–M–L orbital interactions. PMID:29861923

First time-dependent study of H{sub 2} and H{sub 3}{sup +} ortho-para chemistry in the diffuse interstellar medium: Observations meet theoretical predictions

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

Albertsson, T.; Semenov, D.; Henning, Th.

The chemistry in the diffuse interstellar medium (ISM) initiates the gradual increase of molecular complexity during the life cycle of matter. A key molecule that enables build-up of new molecular bonds and new molecules via proton donation is H{sub 3}{sup +}. Its evolution is tightly related to molecular hydrogen and thought to be well understood. However, recent observations of ortho and para lines of H{sub 2} and H{sub 3}{sup +} in the diffuse ISM showed a puzzling discrepancy in nuclear spin excitation temperatures and populations between these two key species. H{sub 3}{sup +}, unlike H{sub 2}, seems to be outmore » of thermal equilibrium, contrary to the predictions of modern astrochemical models. We conduct the first time-dependent modeling of the para-fractions of H{sub 2} and H{sub 3}{sup +} in the diffuse ISM and compare our results to a set of line-of-sight observations, including new measurements presented in this study. We isolate a set of key reactions for H{sub 3}{sup +} and find that the destruction of the lowest rotational states of H{sub 3}{sup +} by dissociative recombination largely controls its ortho/para ratio. A plausible agreement with observations cannot be achieved unless a ratio larger than 1:5 for the destruction of (1, 1)- and (1, 0)-states of H{sub 3}{sup +} is assumed. Additionally, an increased cosmic-ray ionization rate to 10{sup –15} s{sup –1} further improves the fit whereas variations of other individual physical parameters, such as density and chemical age, have only a minor effect on the predicted ortho/para ratios. Thus, our study calls for new laboratory measurements of the dissociative recombination rate and branching ratio of the key ion H{sub 3}{sup +} under interstellar conditions.« less

First Time-dependent Study of H2 and H_3^+ Ortho-Para Chemistry in the Diffuse Interstellar Medium: Observations Meet Theoretical Predictions

NASA Astrophysics Data System (ADS)

Albertsson, T.; Indriolo, N.; Kreckel, H.; Semenov, D.; Crabtree, K. N.; Henning, Th.

2014-05-01

The chemistry in the diffuse interstellar medium (ISM) initiates the gradual increase of molecular complexity during the life cycle of matter. A key molecule that enables build-up of new molecular bonds and new molecules via proton donation is H_3^+. Its evolution is tightly related to molecular hydrogen and thought to be well understood. However, recent observations of ortho and para lines of H2 and H_3^+ in the diffuse ISM showed a puzzling discrepancy in nuclear spin excitation temperatures and populations between these two key species. H_3^+, unlike H2, seems to be out of thermal equilibrium, contrary to the predictions of modern astrochemical models. We conduct the first time-dependent modeling of the para-fractions of H2 and H_3^+ in the diffuse ISM and compare our results to a set of line-of-sight observations, including new measurements presented in this study. We isolate a set of key reactions for H_3^+ and find that the destruction of the lowest rotational states of H_3^+ by dissociative recombination largely controls its ortho/para ratio. A plausible agreement with observations cannot be achieved unless a ratio larger than 1:5 for the destruction of (1, 1)- and (1, 0)-states of H_3^+ is assumed. Additionally, an increased cosmic-ray ionization rate to 10-15 s-1 further improves the fit whereas variations of other individual physical parameters, such as density and chemical age, have only a minor effect on the predicted ortho/para ratios. Thus, our study calls for new laboratory measurements of the dissociative recombination rate and branching ratio of the key ion H_{3}^{+} under interstellar conditions. Partly based on observations collected at the European Organization for Astronomical Research in the Southern Hemisphere, Chile, as part of program 088.C-0351.

A bond-order potential for the Al–Cu–H ternary system

DOE PAGES

Zhou, X. W.; Ward, D. K.; Foster, M. E.

2018-02-27

Al-Based Al–Cu alloys have a very high strength to density ratio, and are therefore important materials for transportation systems including vehicles and aircrafts. These alloys also appear to have a high resistance to hydrogen embrittlement, and as a result, are being explored for hydrogen related applications. To enable fundamental studies of mechanical behavior of Al–Cu alloys under hydrogen environments, we have developed an Al–Cu–H bond-order potential according to the formalism implemented in the molecular dynamics code LAMMPS. Our potential not only fits well to properties of a variety of elemental and compound configurations (with coordination varying from 1 to 12)more » including small clusters, bulk lattices, defects, and surfaces, but also passes stringent molecular dynamics simulation tests that sample chaotic configurations. Careful studies verified that this Al–Cu–H potential predicts structural property trends close to experimental results and quantum-mechanical calculations; in addition, it properly captures Al–Cu, Al–H, and Cu–H phase diagrams and enables simulations of H 2 dissociation, chemisorption, and absorption on Al–Cu surfaces.« less

A bond-order potential for the Al–Cu–H ternary system

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

Zhou, X. W.; Ward, D. K.; Foster, M. E.

Al-Based Al–Cu alloys have a very high strength to density ratio, and are therefore important materials for transportation systems including vehicles and aircrafts. These alloys also appear to have a high resistance to hydrogen embrittlement, and as a result, are being explored for hydrogen related applications. To enable fundamental studies of mechanical behavior of Al–Cu alloys under hydrogen environments, we have developed an Al–Cu–H bond-order potential according to the formalism implemented in the molecular dynamics code LAMMPS. Our potential not only fits well to properties of a variety of elemental and compound configurations (with coordination varying from 1 to 12)more » including small clusters, bulk lattices, defects, and surfaces, but also passes stringent molecular dynamics simulation tests that sample chaotic configurations. Careful studies verified that this Al–Cu–H potential predicts structural property trends close to experimental results and quantum-mechanical calculations; in addition, it properly captures Al–Cu, Al–H, and Cu–H phase diagrams and enables simulations of H 2 dissociation, chemisorption, and absorption on Al–Cu surfaces.« less

Dimers of nineteen-electron sandwich compounds: crystal and electronic structures, and comparison of reducing strengths.

PubMed

Mohapatra, Swagat K; Fonari, Alexandr; Risko, Chad; Yesudas, Kada; Moudgil, Karttikay; Delcamp, Jared H; Timofeeva, Tatiana V; Brédas, Jean-Luc; Marder, Seth R; Barlow, Stephen

2014-11-17

The dimers of some Group 8 metal cyclopentadienyl/arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the X-ray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central CC σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these CC bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2 ]2 , rather similar (-1.97 to -2.15 V vs. FeCp2 (+/0) in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perspective: A controversial benchmark system for water-oxide interfaces: H2O/TiO2(110)

NASA Astrophysics Data System (ADS)

Diebold, Ulrike

2017-07-01

The interaction of water with the single-crystalline rutile TiO2(110) surface has been the object of intense investigations with both experimental and computational methods. Not only is TiO2(110) widely considered the prototypical oxide surface, its interaction with water is also important in many applications where this material is used. At first, experimental measurements were hampered by the fact that preparation recipes for well-controlled surfaces had yet to be developed, but clear experimental evidence that water dissociation at defects including oxygen vacancies and steps emerged. For a perfect TiO2(110) surface, however, an intense debate has evolved whether or not water adsorbs as an intact molecule or if it dissociates by donating a proton to a so-called bridge-bonded surface oxygen atom. Computational studies agree that the energy difference between these two states is very small and thus depends sensitively on the computational setup and on the approximations used in density functional theory (DFT). While a recent molecular beam/STM experiment [Z.-T. Wang et al., Proc. Natl. Acad. Sci. U. S. A. 114(8), 1801-1805 (2017)] gives conclusive evidence for a slight preference (0.035 eV) for molecular water and a small activation energy of (0.36 eV) for dissociation, understanding the interface between liquid water and TiO2(110) arises as the next controversial frontier.

Dissociative double-photoionization of butadiene in the 25-45 eV energy range using 3-D multi-coincidence ion momentum imaging spectrometry

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

Oghbaie, Shabnam; Gisselbrecht, Mathieu; Laksman, Joakim

Dissociative double-photoionization of butadiene in the 25-45 eV energy range has been studied with tunable synchrotron radiation using full three-dimensional ion momentum imaging. Using ab initio calculations, the electronic states of the molecular dication below 33 eV are identified. The results of the measurement and calculation show that double ionization from π orbitals selectively triggers twisting about the terminal or central C–C bonds. We show that this conformational rearrangement depends upon the dication electronic state, which effectively acts as a gateway for the dissociation reaction pathway. For photon energies above 33 eV, three-body dissociation channels where neutral H-atom evaporation precedesmore » C–C charge-separation in the dication species appear in the correlation map. The fragment angular distributions support a model where the dication species is initially aligned with the molecular backbone parallel to the polarization vector of the light, indicating a high probability for double-ionization to the “gateway states” for molecules with this orientation.« less

High-order above-threshold dissociation of molecules

NASA Astrophysics Data System (ADS)

Lu, Peifen; Wang, Junping; Li, Hui; Lin, Kang; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Zhang, Wenbin; Ma, Junyang; Li, Hanxiao; Zeng, Heping; He, Feng; Wu, Jian

2018-03-01

Electrons bound to atoms or molecules can simultaneously absorb multiple photons via the above-threshold ionization featured with discrete peaks in the photoelectron spectrum on account of the quantized nature of the light energy. Analogously, the above-threshold dissociation of molecules has been proposed to address the multiple-photon energy deposition in the nuclei of molecules. In this case, nuclear energy spectra consisting of photon-energy spaced peaks exceeding the binding energy of the molecular bond are predicted. Although the observation of such phenomena is difficult, this scenario is nevertheless logical and is based on the fundamental laws. Here, we report conclusive experimental observation of high-order above-threshold dissociation of H2 in strong laser fields where the tunneling-ionized electron transfers the absorbed multiphoton energy, which is above the ionization threshold to the nuclei via the field-driven inelastic rescattering. Our results provide an unambiguous evidence that the electron and nuclei of a molecule as a whole absorb multiple photons, and thus above-threshold ionization and above-threshold dissociation must appear simultaneously, which is the cornerstone of the nowadays strong-field molecular physics.

The Bond Dissociation Energies of 1-Butene

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The bond dissociation energies of 1-butene and several calibration systems are computed using the G2(MP2) approach. The agreement between the calibration systems and experiment is very good. The computed values for 1-butene are compared with calibration systems and the agreement between the computed results for 1-butene and the "rule of thumb" values from the smaller systems is remarkably good.

Threshold collision-induced dissociation of diatomic molecules: a case study of the energetics and dynamics of O2- collisions with Ar and Xe.

PubMed

Ahu Akin, F; Ree, Jongbaik; Ervin, Kent M; Kyu Shin, Hyung

2005-08-08

The energetics and dynamics of collision-induced dissociation of O2- with Ar and Xe targets are studied experimentally using guided ion-beam tandem mass spectrometry. The cross sections and the collision dynamics are modeled theoretically by classical trajectory calculations. Experimental apparent threshold energies are 2.1 and 1.1 eV in excess of the thermochemical O2- bond dissociation energy for argon and xenon, respectively. Classical trajectory calculations confirm the observed threshold behavior and the dependence of cross sections on the relative kinetic energy. Representative trajectories reveal that the bond dissociation takes place on a short time scale of about 50 fs in strong direct collisions. Collision-induced dissociation is found to be remarkably restricted to the perpendicular approach of ArXe to the molecular axis of O2-, while collinear collisions do not result in dissociation. The higher collisional energy-transfer efficiency of xenon compared with argon is attributed to both mass and polarizability effects.

Palladium-Catalyzed Formal Cross-Coupling of Diaryl Ethers with Amines: Slicing the 4-O-5 Linkage in Lignin Models.

PubMed

Zeng, Huiying; Cao, Dawei; Qiu, Zihang; Li, Chao-Jun

2018-03-26

Lignin is the second most abundant organic matter on Earth, and is an underutilized renewable source for valuable aromatic chemicals. For future sustainable production of aromatic compounds, it is highly desirable to convert lignin into value-added platform chemicals instead of using fossil-based resources. Lignins are aromatic polymers linked by three types of ether bonds (α-O-4, β-O-4, and 4-O-5 linkages) and other C-C bonds. Among the ether bonds, the bond dissociation energy of the 4-O-5 linkage is the highest and the most challenging to cleave. To date, 4-O-5 ether linkage model compounds have been cleaved to obtain phenol, cyclohexane, cyclohexanone, and cyclohexanol. The first example of direct formal cross-coupling of diaryl ether 4-O-5 linkage models with amines is reported, in which dual C(Ar)-O bond cleavages form valuable nitrogen-containing derivatives. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Factors affecting hydrogen-tunneling contribution in hydroxylation reactions promoted by oxoiron(IV) porphyrin π-cation radical complexes.

PubMed

Cong, Zhiqi; Kinemuchi, Haruki; Kurahashi, Takuya; Fujii, Hiroshi

2014-10-06

Hydrogen atom transfer with a tunneling effect (H-tunneling) has been proposed to be involved in aliphatic hydroxylation reactions catalyzed by cytochrome P450 and synthetic heme complexes as a result of the observation of large hydrogen/deuterium kinetic isotope effects (KIEs). In the present work, we investigate the factors controlling the H-tunneling contribution to the H-transfer process in hydroxylation reaction by examining the kinetics of hydroxylation reactions at the benzylic positions of xanthene and 1,2,3,4-tetrahydronaphthalene by oxoiron(IV) 5,10,15,20-tetramesitylporphyrin π-cation radical complexes ((TMP(+•))Fe(IV)O(L)) under single-turnover conditions. The Arrhenius plots for these hydroxylation reactions of H-isotopomers have upwardly concave profiles. The Arrhenius plots of D-isotopomers, clear isosbestic points, and product analysis rule out the participation of thermally dependent other reaction processes in the concave profiles. These results provide evidence for the involvement of H-tunneling in the rate-limiting H-transfer process. These profiles are simulated using an equation derived from Bell's tunneling model. The temperature dependence of the KIE values (k(H)/k(D)) determined for these reactions indicates that the KIE value increases as the reaction temperature becomes lower, the bond dissociation energy (BDE) of the C-H bond of a substrate becomes higher, and the reactivity of (TMP(+•))Fe(IV)O(L) decreases. In addition, we found correlation of the slope of the ln(k(H)/k(D)) - 1/T plot and the bond strengths of the Fe═O bond of (TMP(+•))Fe(IV)O(L) estimated from resonance Raman spectroscopy. These observations indicate that these factors modulate the extent of the H-tunneling contribution by modulating the ratio of the height and thickness of the reaction barrier.

Hydrogen interaction kinetics of Ge dangling bonds at the Si0.25Ge0.75/SiO2 interface

NASA Astrophysics Data System (ADS)

Stesmans, A.; Nguyen Hoang, T.; Afanas'ev, V. V.

2014-07-01

The hydrogen interaction kinetics of the GePb1 defect, previously identified by electron spin resonance (ESR) as an interfacial Ge dangling bond (DB) defect occurring in densities ˜7 × 1012 cm-2 at the SiGe/SiO2 interfaces of condensation grown (100)Si/a-SiO2/Ge0.75Si0.25/a-SiO2 structures, has been studied as function of temperature. This has been carried out, both in the isothermal and isochronal mode, through defect monitoring by capacitance-voltage measurements in conjunction with ESR probing, where it has previously been demonstrated the defects to operate as negative charge traps. The work entails a full interaction cycle study, comprised of analysis of both defect passivation (pictured as GePb1-H formation) in molecular hydrogen (˜1 atm) and reactivation (GePb1-H dissociation) in vacuum. It is found that both processes can be suitably described separately by the generalized simple thermal (GST) model, embodying a first order interaction kinetics description based on the basic chemical reactions GePb1 + H2 → GePb1H + H and GePb1H → GePb1 + H, which are found to be characterized by the average activation energies Ef = 1.44 ± 0.04 eV and Ed = 2.23 ± 0.04 eV, and attendant, assumedly Gaussian, spreads σEf = 0.20 ± 0.02 eV and σEd = 0.15 ± 0.02 eV, respectively. The substantial spreads refer to enhanced interfacial disorder. Combination of the separately inferred kinetic parameters for passivation and dissociation results in the unified realistic GST description that incorporates the simultaneous competing action of passivation and dissociation, and which is found to excellently account for the full cycle data. For process times ta ˜ 35 min, it is found that even for the optimum treatment temperature ˜380 °C, only ˜60% of the GePb1 system can be electrically silenced, still far remote from device grade level. This ineffectiveness is concluded, for the major part, to be a direct consequence of the excessive spreads in the activation energies, ˜2-3 times larger than for the Si DB Pb defects at the standard thermal (111)Si/SiO2 interface which may be easily passivated to device grade levels, strengthened by the reduced difference between the average Ef and Ed values. Exploring the guidelines of the GST model indicates that passivation can be improved by decreasing Tan and attendant enlarging of ta, however, at best still leaving ˜2% defects unpassivated even for unrealistically extended anneal times. The average dissociation energy Ed ˜ 2.23 eV, concluded as representing the GePb1-H bond strength, is found to be smaller than the SiPb-H one, characterized by Ed ˜ 2.83 eV. An energy deficiency is encountered regarding the energy sum rule inherent to the GST-model, the origin of which is substantiated to lie with a more complex nature of the forward passivation process than basically depicted in the GST model. The results are discussed within the context of theoretical considerations on the passivation of interfacial Ge DBs by hydrogen.

Reactive molecular dynamics simulation of solid nitromethane impact on (010) surfaces induced and nonimpact thermal decomposition.

PubMed

Guo, Feng; Cheng, Xin-lu; Zhang, Hong

2012-04-12

Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Blue- and Red-Shifting Hydrogen Bonding: A Gas Phase FTIR and Ab Initio Study of RR'CO···DCCl3 and RR'S···DCCl3 Complexes.

PubMed

Behera, B; Das, Puspendu K

2018-05-10

Blue-shifting H-bonded (C-D···O) complexes between CDCl 3 and CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, and red-shifting H-bonded (C-D···S) complexes between CDCl 3 with (CH 3 ) 2 S and (C 2 H 5 ) 2 S have been identified by Fourier transform infrared spectroscopy in the gas phase at room temperature. With increasing partial pressure of the components, a new band appears in the C-D stretching region of the vibrational spectra. The intensity of this band decreases with an increase in temperature at constant pressure, which provides the basis for identification of the H-bonded bands in the spectrum. The C-D stretching frequency of CDCl 3 is blue-shifted by +7.1, +4, and +3.2 cm -1 upon complexation with CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO, respectively, and red-shifted by -14 and -19.2 cm -1 upon complexation with (CH 3 ) 2 S and (C 2 H 5 ) 2 S, respectively. By using quantum chemical calculations at the MP2/6-311++G** level, we predict the geometry, electronic structural parameters, binding energy, and spectral shift of H-bonded complexes between CDCl 3 and two series of compounds named RCOR' (H 2 CO, CH 3 HCO, (CH 3 ) 2 CO, and C 2 H 5 (CH 3 )CO) and RSR' (H 2 S, CH 3 HS, (CH 3 ) 2 S, and (C 2 H 5 ) 2 S) series. The calculated and observed spectral shifts follow the same trends. With an increase in basicity of the H-bond acceptor, the C-D bond length increases, force constant decreases, and the frequency shifts to the red from the blue. The potential energy scans of the above complexes are done, which show that electrostatic attraction between electropositive D and electron-rich O/S causes bond elongation and red shift, and the electronic and nuclear repulsions lead to bond contraction and blue shifts. The dominance of the two opposing forces at the equilibrium geometry of the complex determines the nature of the shift, which changes both in magnitude and in direction with the basicity of the hydrogen-bond acceptor.

Unexpected methyl migrations of ethanol dimer under synchrotron VUV radiation

NASA Astrophysics Data System (ADS)

Xiao, Weizhan; Hu, Yongjun; Li, Weixing; Guan, Jiwen; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi

2015-01-01

While methyl transfer is well known to occur in the enzyme- and metal-catalyzed reactions, the methyl transfer in the metal-free organic molecules induced by the photon ionization has been less concerned. Herein, vacuum ultraviolet single photon ionization and dissociation of ethanol dimer are investigated with synchrotron radiation photoionization mass spectroscopy and theoretical methods. Besides the protonated clusters cation (C2H5OH) ṡ H+ (m/z = 47) and the β-carbon-carbon bond cleavage fragment CH2O ṡ (C2H5OH)H+ (m/z = 77), the measured mass spectra revealed that a new fragment (C2H5OH) ṡ (CH3)+ (m/z = 61) appeared at the photon energy of 12.1 and 15.0 eV, where the neutral dimer could be vertically ionized to higher ionic state. Thereafter, the generated carbonium ions are followed by a Wagner-Meerwein rearrangement and then dissociate to produce this new fragment, which is considered to generate after surmounting a few barriers including intra- and inter-molecular methyl migrations by the aid of theoretical calculations. The appearance energy of this new fragment is measured as 11.55 ± 0.05 eV by scanning photoionization efficiency curve. While the signal intensity of fragment m/z = 61 starts to increase, the fragments m/z = 47 and 77 tend to slowly incline around 11.55 eV photon energy. This suggests that the additional fragment channels other than (C2H5OH) ṡ H+ and CH2O ṡ (C2H5OH)H+ have also been opened, which consume some dimer cations. The present report provides a clear description of the photoionization and dissociation processes of the ethanol dimer in the range of the photon energy 12-15 eV.

The interface of SrTiO3 and H2O from density functional theory molecular dynamics

PubMed Central

Spijker, P.; Foster, A. S.

2016-01-01

We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO3/H2O solid–liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO2 termination and 5% on the stepped TiO2-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to H2O bonding and surface corrugation. We find a featureless electronic density of states in and around the band gap energy region at the solid–liquid interface. The vibrational spectrum indicates redshifting of the O–H stretching band due to surface-to-liquid hydrogen bonding and blueshifting due to high-frequency stretching vibrations of OH fragments within the liquid, as well as strong suppression of the OH stretching band on the stepped surface. We find highly varying rates of proton transfer above different SrTiO3 surfaces, owing to differences in hydrogen bond strength and the degree of dissociation of incident water. Trends in proton dynamics and the mode of H2O adsorption among studied surfaces can be explained by the differential ionicity of the Ti–O and Sr–O bonds in the SrTiO3 crystal. PMID:27713660

Decomposition of multilayer benzene and n-hexane films on vanadium.

PubMed

Souda, Ryutaro

2015-09-21

Reactions of multilayer hydrocarbon films with a polycrystalline V substrate have been investigated using temperature-programmed desorption and time-of-flight secondary ion mass spectrometry. Most of the benzene molecules were dissociated on V, as evidenced by the strong depression in the thermal desorption yields of physisorbed species at 150 K. The reaction products dehydrogenated gradually after the multilayer film disappeared from the surface. Large amount of oxygen was needed to passivate the benzene decomposition on V. These behaviors indicate that the subsurface sites of V play a role in multilayer benzene decomposition. Decomposition of the n-hexane multilayer films is manifested by the desorption of methane at 105 K and gradual hydrogen desorption starting at this temperature, indicating that C-C bond scission precedes C-H bond cleavage. The n-hexane dissociation temperature is considerably lower than the thermal desorption temperature of the physisorbed species (140 K). The n-hexane multilayer morphology changes at the decomposition temperature, suggesting that a liquid-like phase formed after crystallization plays a role in the low-temperature decomposition of n-hexane.

Spectroscopy Identification of Benzyl-Type Radicals Generated by Corona Discharge of Precursors of Mixed Substituents

NASA Astrophysics Data System (ADS)

Yoon, Young Wook; Huh, Chang Soon; Lee, Sang Kuk

2012-06-01

We generated vibronically excited but jet-cooled benzyl-type radicals from corona discharge of precursor of mixed substituents using a technique of corona excited supersonic expansion coupled with a pinhole-type glass nozzle, from which the visible vibronic emission spectra were recorded with a long-path monochromator. The spectra exhibit the intensity variation of each species with discharging voltage, indicating the radical species generated in corona discharge is highly sensitive to excitation. From the analysis of the spectra, we found the Cl substituent is replaced in preference to the F substituent by the hydrogen atoms liberated from the dissociation of the C-H bond of the methyl group of the precursor, from which we proposed the possible mechanism for the elimination reaction of substituent in terms of the bond dissociation energy. Additionally, we obtained an accurate electronic energy in the D_1 → D_0 transition and the vibrational mode frequencies of newly detected benzyl-type radicals in the ground electronic state by comparison with those of ab initio calculations and the known spectroscopic data of precursors for the first time.

Ratio of entropy to enthalpy in thermal transitions in biological tissues.

PubMed

Jacques, Steven L

2006-01-01

Thermal transitions in biological tissues that have been reported in the literature are summarized in terms of the apparent molar entropy (DeltaS) and molar enthalpy (DeltaH) involved in the transition. A plot of DeltaS versus DeltaH for all the data yields a straight line, consistent with the definition of free energy, DeltaG=DeltaH+TDeltaS. Various bonds may be involved in cooperative bond breakage during thermal transitions; however, for the sake of description, the equivalent number of cooperative hydrogen bonds can be cited. Most of the tissue data behave as if 10 to 20 hydrogen bonds are cooperatively broken during coagulation, with one transition, the expression of heat shock protein, involving 90 cooperative hydrogen bonds. The data are consistent with DeltaS=a+bDeltaH, where a=-327.5 J(mol K) and b=31.47 x 10(-4) K(-1). If each additional hydrogen bond adds 19 x 10(3) Jmol to DeltaH, then each additional bond adds 59.8 J(mol K) to DeltaS. Hence, the dynamics of irreversible thermal transitions can be described in terms of one free parameter, the apparent number of cooperative hydrogen bonds broken during the transition.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-02-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides

NASA Astrophysics Data System (ADS)

Schaller-Duke, Ranelle M.; Bogala, Mallikharjuna R.; Cassady, Carolyn J.

2018-05-01

Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. [Figure not available: see fulltext.

UV photolysis of 4-iodo-, 4-bromo-, and 4-chlorophenol: Competition between C-Y (Y = halogen) and O-H bond fission

NASA Astrophysics Data System (ADS)

Sage, Alan G.; Oliver, Thomas A. A.; King, Graeme A.; Murdock, Daniel; Harvey, Jeremy N.; Ashfold, Michael N. R.

2013-04-01

The wavelength dependences of C-Y and O-H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O-H bond fission following excitation at wavelengths λ ≲ 240 nm, on repulsive ((n/π)σ*) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ˜11 000 cm-1. For Y = I and Br, this process occurs in competition with prompt C-I and C-Br bond cleavage on another (n/π)σ* PES, but no Cl/Cl* products unambiguously attributable to one photon induced C-Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C-I bond fission is observed following excitation of 4-IPhOH at all λ ≤ 330 nm; the wavelength dependent trends in I/I* product branching ratio, kinetic energy release, and recoil anisotropy suggest that (with regard to C-I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O-H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C-Y centred (n/π)σ* potentials across the series Y = I < Br < Cl and the concomitant reduction in C-Y bond strength, cf. that of the rival O-H bond, and (ii) the much increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the risks inherent in extrapolating photochemical behaviour measured for one molecule at one wavelength to other (related) molecules and to other excitation energies.

UV photolysis of 4-iodo-, 4-bromo-, and 4-chlorophenol: competition between C-Y (Y = halogen) and O-H bond fission.

PubMed

Sage, Alan G; Oliver, Thomas A A; King, Graeme A; Murdock, Daniel; Harvey, Jeremy N; Ashfold, Michael N R

2013-04-28

The wavelength dependences of C-Y and O-H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O-H bond fission following excitation at wavelengths λ ≲ 240 nm, on repulsive ((n∕π)σ∗) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ∼11,000 cm(-1). For Y = I and Br, this process occurs in competition with prompt C-I and C-Br bond cleavage on another (n∕π)σ∗ PES, but no Cl∕Cl∗ products unambiguously attributable to one photon induced C-Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C-I bond fission is observed following excitation of 4-IPhOH at all λ ≤ 330 nm; the wavelength dependent trends in I∕I∗ product branching ratio, kinetic energy release, and recoil anisotropy suggest that (with regard to C-I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O-H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C-Y centred (n∕π)σ∗ potentials across the series Y = I < Br < Cl and the concomitant reduction in C-Y bond strength, cf. that of the rival O-H bond, and (ii) the much increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the risks inherent in extrapolating photochemical behaviour measured for one molecule at one wavelength to other (related) molecules and to other excitation energies.

Carboxylate-assisted C–H activation of phenylpyridines with copper, palladium and ruthenium: a mass spectrometry and DFT study† †Electronic supplementary information (ESI) available: Details on the mass-spectrometry experiments and theoretical calculations, Hammett studies, potential energy surfaces, energies, optimized Gaussian geometries and laser-power dependence during the IRMPD spectra measurements. See DOI: 10.1039/c5sc01729g

PubMed Central

Gray, A.; Tsybizova, A.

2015-01-01

The C–H activation of 2-phenylpyridine, catalyzed by copper(ii), palladium(ii) and ruthenium(ii) carboxylates, was studied in the gas phase. ESI-MS, infrared multiphoton dissociation spectroscopy and quantum chemical calculations were combined to investigate the intermediate species in the reaction. Collision induced dissociation (CID) experiments and DFT calculations allowed estimation of the energy required for this C–H activation step and the subsequent acetic acid loss. Hammett plots constructed from the CID experiments using different copper carboxylates as catalysts revealed that the use of stronger acids accelerates the C–H activation step. The reasoning can be traced from the associated transition structures that suggest a concerted mechanism and the key effect of the carbon–metal bond pre-formation. Carboxylates derived from stronger acids make the metal atom more electrophilic and therefore shift the reaction towards the formation of C–H activated products. PMID:29861892

Dissociation energetics and mechanisms of leucine enkephalin (M + H)+ and (2M + X)+ ions (X = H, Li, Na, K, and Rb) measured by blackbody infrared radiative dissociation.

PubMed

Schnier, P D; Price, W D; Strittmatter, E F; Williams, E R

1997-08-01

The dissociation kinetics of protonated leucine enkephalin and its proton and alkali metal bound dimers were investigated by blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Protonated leucine enkephalin dissociates to form b(4) and (M-H(2)O)(+) ions with an average activation energy (E(a)) of 1.1 eV and an A factor of 10(10.5) s(-1). The value of the A factor indicates that these dissociation processes are rearrangements. The b(4) ions subsequently dissociate to form a(4) ions via a process with a relatively high activation energy (1.3 eV), but one that is entropically favored. For the cationized dimers, the thermal stability decreases with increasing cation size, consistent with a simple electrostatic interaction in these noncovalent ion-molecule complexes. The E(a) and A factors are indistinguishable within experimental error with values of approximately 1.5 eV and 10(17) s(-1), respectively. Although not conclusive, results from master equation modeling indicate that all these BIRD processes, except for b(4) --> a(4), are in the rapid energy exchange limit. In this limit, the internal energy of the precursor ion population is given by a Boltzmann distribution and information about the energetics and dynamics of the reaction are obtained directly from the measured Arrhenius parameters.

Shear bond strength of one-step self-etch adhesives: pH influence

PubMed Central

Poggio, Claudio; Beltrami, Riccardo; Scribante, Andrea; Colombo, Marco; Chiesa, Marco

2015-01-01

Background: The aim of this study was to compare the shear bond strength of four one-step self-etch adhesives with different pH values to enamel and dentin. Materials and Methods: In this in vitro study, 200 bovine permanent mandibular incisors were used. Four one-step self-etch adhesives with different pH values were tested both on enamel and on dentin: Adper™ Easy Bond Self-Etch Adhesive (pH = 0.8-1), Futurabond NR (pH=2), G-aenial Bond (pH = 1.5), Clearfil S3 Bond (pH = 2.7). After adhesive systems application, a nanohybrid composite resin was inserted into the bonded surface. The specimens were placed in a universal testing machine. The shear bond strength was performed at a cross-head speed of 1 mm/min until the sample rupture. The shear bond strength values (MPa) of the different groups were compared with analysis of variance after that Kolmogorov and Smirnov tests were applied to assess normality of distributions. P < 0.05 was considered as significant. Results: In enamel shear bond strength, the highest shear bond strength values were reported with Futurabond NR (P < 0.01); however, no significant differences were found with Clearfil S3 Bond. The others adhesive systems showed lower shear bond strength values with significant differences between them (P < 0.05). When comparing the dentin shear bond strength, the lowest shear bond strength values were reported with Clearfil S3 Bond (P < 0.05), while there were no significant differences among the other three products (P > 0.05). Conclusion: The pH values of adhesive systems did not influence significantly their shear bond strength to enamel or dentin. PMID:26005459

Studies of the kinetics and thermochemistry of the forward and reverse reaction Cl + C6H6 = HCl + C6H5.

PubMed

Alecu, I M; Gao, Yide; Hsieh, P-C; Sand, Jordan P; Ors, Ahmet; McLeod, A; Marshall, Paul

2007-05-17

The laser flash photolysis resonance fluorescence technique was used to monitor atomic Cl kinetics. Loss of Cl following photolysis of CCl4 and NaCl was used to determine k(Cl + C6H6) = 6.4 x 10(-12) exp(-18.1 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 578-922 K and k(Cl + C6D6) = 6.2 x 10(-12) exp(-22.8 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 635-922 K. Inclusion of literature data at room temperature leads to a recommendation of k(Cl + C6H6) = 6.1 x 10(-11) exp(-31.6 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) for 296-922 K. Monitoring growth of Cl during the reaction of phenyl with HCl led to k(C6H5 + HCl) = 1.14 x 10(-12) exp(+5.2 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 294-748 K, k(C6H5 + DCl) = 7.7 x 10(-13) exp(+4.9 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 292-546 K, an approximate k(C6H5 + C6H5I) = 2 x 10(-11) cm(3) molecule(-1) s(-1) over 300-750 K, and an upper limit k(Cl + C6H5I) < or = 5.3 x 10(-12) exp(+2.8 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 300-750 K. Confidence limits are discussed in the text. Third-law analysis of the equilibrium constant yields the bond dissociation enthalpy D(298)(C6H5-H) = 472.1 +/- 2.5 kJ mol(-1) and thus the enthalpy of formation Delta(f)H(298)(C6H5) = 337.0 +/- 2.5 kJ mol(-1).

Long-Lived Charge Separation at Heterojunctions between Semiconducting Single-Walled Carbon Nanotubes and Perylene Diimide Electron Acceptors

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

Kang, Hyun Suk; Sisto, Thomas J.; Peurifoy, Samuel

Nonfullerene electron acceptors have facilitated a recent surge in the efficiencies of organic solar cells, although fundamental studies of the nature of exciton dissociation at interfaces with nonfullerene electron acceptors are still relatively sparse. Semiconducting single-walled carbon nanotubes (s-SWCNTs), unique one-dimensional electron donors with molecule-like absorption and highly mobile charges, provide a model system for studying interfacial exciton dissociation. Here, we investigate excited-state photodynamics at the heterojunction between (6,5) s-SWCNTs and two perylene diimide (PDI)-based electron acceptors. Each of the PDI-based acceptors, hPDI2-pyr-hPDI2 and Trip-hPDI2, is deposited onto (6,5) s-SWCNT films to form a heterojunction bilayer. Transient absorption measurements demonstratemore » that photoinduced hole/electron transfer occurs at the photoexcited bilayer interfaces, producing long-lived separated charges with lifetimes exceeding 1.0 us. Both exciton dissociation and charge recombination occur more slowly for the hPDI2-pyr-hPDI2 bilayer than for the Trip-hPDI2 bilayer. To explain such differences, we discuss the potential roles of the thermodynamic charge transfer driving force available at each interface and the different molecular structure and intermolecular interactions of PDI-based acceptors. As a result, detailed photophysical analysis of these model systems can develop the fundamental understanding of exciton dissociation between organic electron donors and nonfullerene acceptors, which has not been systematically studied.« less

Long-Lived Charge Separation at Heterojunctions between Semiconducting Single-Walled Carbon Nanotubes and Perylene Diimide Electron Acceptors

DOE PAGES

Kang, Hyun Suk; Sisto, Thomas J.; Peurifoy, Samuel; ...

2018-04-13

Nonfullerene electron acceptors have facilitated a recent surge in the efficiencies of organic solar cells, although fundamental studies of the nature of exciton dissociation at interfaces with nonfullerene electron acceptors are still relatively sparse. Semiconducting single-walled carbon nanotubes (s-SWCNTs), unique one-dimensional electron donors with molecule-like absorption and highly mobile charges, provide a model system for studying interfacial exciton dissociation. Here, we investigate excited-state photodynamics at the heterojunction between (6,5) s-SWCNTs and two perylene diimide (PDI)-based electron acceptors. Each of the PDI-based acceptors, hPDI2-pyr-hPDI2 and Trip-hPDI2, is deposited onto (6,5) s-SWCNT films to form a heterojunction bilayer. Transient absorption measurements demonstratemore » that photoinduced hole/electron transfer occurs at the photoexcited bilayer interfaces, producing long-lived separated charges with lifetimes exceeding 1.0 us. Both exciton dissociation and charge recombination occur more slowly for the hPDI2-pyr-hPDI2 bilayer than for the Trip-hPDI2 bilayer. To explain such differences, we discuss the potential roles of the thermodynamic charge transfer driving force available at each interface and the different molecular structure and intermolecular interactions of PDI-based acceptors. As a result, detailed photophysical analysis of these model systems can develop the fundamental understanding of exciton dissociation between organic electron donors and nonfullerene acceptors, which has not been systematically studied.« less

Dissociative recombination of HCl+, H2Cl+, DCl+, and D2Cl+ in a flowing afterglow

NASA Astrophysics Data System (ADS)

Wiens, Justin P.; Miller, Thomas M.; Shuman, Nicholas S.; Viggiano, Albert A.

2016-12-01

Dissociative recombination of electrons with HCl+, H2Cl+, DCl+, and D2Cl+ has been measured under thermal conditions at 300, 400, and 500 K using a flowing afterglow-Langmuir probe apparatus. Measurements for HCl+ and DCl+ employed the variable electron and neutral density attachment mass spectrometry (VENDAMS) method, while those for H2Cl+ and D2Cl+ employed both VENDAMS and the more traditional technique of monitoring electron density as a function of reaction time. At 300 K, HCl+ and H2Cl+ recombine with kDR = 7.7±2.14.5 × 10-8 cm3 s-1 and 2.6 ± 0.8 × 10-7 cm3 s-1, respectively, whereas D2Cl+ is roughly half as fast as H2Cl+ with kDR = 1.1 ± 0.3 × 10-7 cm3 s-1 (2 σ confidence intervals). DCl+ recombines with a rate coefficient below the approximate detection limit of the method (≲5 × 10-8 cm3 s-1) at all temperatures. Relatively slow dissociative recombination rates have been speculated to be responsible for the large HCl+ and H2Cl+ abundances in interstellar clouds compared to current astrochemical models, but our results imply that the discrepancy must originate elsewhere.

The electrophoretically 'slow' and 'fast' forms of the alpha 2-macroglobulin molecule.

PubMed Central

Barrett, A J; Brown, M A; Sayers, C A

1979-01-01

alpha 2-Macroglobulin (alpha 2M) was isolated from human plasma by a four-step procedure: poly(ethylene glyco) fractionation, gel chromatography, euglobulin precipitation and immunoadsorption. No contaminants were detected in the final preparations by electrophoresis or immunoprecipitation. The protein ran as a single slow band in gel electrophoresis, and was designated 'S-alpha 2M'. S-alpha 2M bound about 2 mol of trypsin/mol. Treatment of S-alpha 2M with a proteinase or ammonium salts produced a form of the molecule more mobile in electrophoresis, and lacking proteinase-binding activity (F-alpha 2M). The electrophoretic mobility of the F-alpha 2M resulting from reaction with NH4+ salts was identical with that of proteinase complexes. We attribute the change in electrophoretic mobility of the alpha 2M to a conformation change, but there was no evidence of a change in pI or Strokes radius. Electrophoresis of S-alpha 2M in the presence of sodium dodecylsulphate gave results consistent with the view that the alpha 2M molecule is a tetramer of identical subunits, assembled as a non-covalent pair of disulphide-linked dimers. Some of the subunits seemed to be 'nicked' into two-thires-length and one-third-length chains, however. This was not apparent with F-alpha 2M produced by ammonium salts. F-alpha 2M produced by trypsin showed two new bands attributable to cleavage of the subunit polypeptide chain near the middle. Immunoassays of F-alpha 2M gave 'rockets' 12-29% lower than those with S-alpha 2M. The nature of the interactions between subunits in S-alpha 2M and F-alpha 2M was investigated by treating each form with glutaraldehyde before electrophoresis in the presence of sodium dodecyl sulphate. A much greater degree of cross-linking was observed with the F-alpha 2M, indicating that the subunits interact most closely in this form of the molecule. Exposure of S-alpha 2M to 3 M-urea or pH3 resulted in dissociation to the disulphide-bonded half-molecules; these did not show the proteinase-binding activity characteristic of the intact alpha 2M. F-alpha 2M was less easily dissociated than was S-alpha 2M. S-alpha 2M was readily dissociated to the quarter-subunits by mild reduction, with the formation of 3-4 new thiol groups per subunit. Inact reactive alpha 2M could then be regenerated in high yield by reoxidation of the subunits. F-alpha 2M formed by reaction with a proteinase or ammonium salts was not dissociated under the same conditions, although the interchain disulphide bonds were reduced. If the thiol groups of the quarter-subunits of S-alpha 2M were blocked by carboxymethylation, oxidative reassociation did not occur. Nevertheless treatment of these subunits with methylammonium salts or a proteinase caused the reassembly of half-molecules and intact (F-) tetramers. It is emphasized that F-alpha 2M does not have the properties of a denatured form of the protein... Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:91367

Production of the Q2 doubly excited states of the hydrogen molecule by electron impact in a single step

NASA Astrophysics Data System (ADS)

Santos, Leonardo O.; Rocha, Alexandre B.; Faria, Nelson Velho de Castro; Jalbert, Ginette

2017-03-01

We calculate the single step cross sections for excitation of Q 2 states of H2 and its subsequent dissociation. The cross section calculations were performed within the first Born approximation and the electronic wave functions were obtained via State-Averaged Multiconfigurational Self-Consistent Field followed by Configuration Interaction. We have assumed autoionization is the only important process competing with dissociation into neutral atoms. We have estimated its probability through a semi classical approach and compared with results of literature. Special attention was given to the Q 2 1Σg +(1) state which, as has been shown in a previous work, may dissociate into H(2 sσ) + H(2 sσ) fragments (some figures in this article are in colour only in the electronic version).

Modulators of actin-myosin dissociation: basis for muscle type functional differences during fatigue

PubMed Central

Karatzaferi, Christina; Adamek, Nancy

2017-01-01

The muscle types present with variable fatigue tolerance, in part due to the myosin isoform expressed. However, the critical steps that define “fatigability” in vivo of fast vs. slow myosin isoforms, at the molecular level, are not yet fully understood. We examined the modulation of the ATP-induced myosin subfragment 1 (S1) dissociation from pyrene-actin by inorganic phosphate (Pi), pH, and temperature using a specially modified stopped-flow system that allowed fast kinetics measurements at physiological temperature. We contrasted the properties of rabbit psoas (fast) and bovine masseter (slow) myosins (obtained from samples collected from New Zealand rabbits and from a licensed abattoir, respectively, according to institutional and national ethics permits). To identify ATP cycling biochemical intermediates, we assessed ATP binding to a preequilibrated mixture of actomyosin and variable [ADP], pH (pH 7 vs. pH 6.2), and Pi (zero, 15, or 30 added mM Pi) in a range of temperatures (5 to 45°C). Temperature and pH variations had little, if any, effect on the ADP dissociation constant (KADP) for fast S1, but for slow S1, KADP was weakened with increasing temperature or low pH. In the absence of ADP, the dissociation constant for phosphate (KPi) was weakened with increasing temperature for fast S1. In the presence of ADP, myosin type differences were revealed at the apparent phosphate affinity, depending on pH and temperature. Overall, the newly revealed kinetic differences between myosin types could help explain the in vivo observed muscle type functional differences at rest and during fatigue. PMID:28931538

Dissociation kinetics of Mn2+ complexes of NOTA and DOTA.

PubMed

Drahoš, Bohuslav; Kubíček, Vojtěch; Bonnet, Célia S; Hermann, Petr; Lukeš, Ivan; Tóth, Éva

2011-03-07

The kinetics of transmetallation of [Mn(nota)](-) and [Mn(dota)](2-) was investigated in the presence of Zn(2+) (5-50-fold excess) at variable pH (3.5-5.6) by (1)H relaxometry. The dissociation is much faster for [Mn(nota)](-) than for [Mn(dota)](2-) under both experimental and physiologically relevant conditions (t(½) = 74 h and 1037 h for [Mn(nota)](-) and [Mn(dota)](2-), respectively, at pH 7.4, c(Zn(2+)) = 10(-5) M, 25 °C). The dissociation of the complexes proceeds mainly via spontaneous ([Mn(nota)](-)k(0) = (2.6 ± 0.5) × 10(-6) s(-1); [Mn(dota)](2-)k(0) = (1.8 ± 0.6) × 10(-7) s(-1)) and proton-assisted pathways ([Mn(nota)](-)k(1) = (7.8 ± 0.1) × 10(-1) M(-1) s(-1); [Mn(dota)](2-)k(1) = (4.0 ± 0.6) × 10(-2) M(-1) s(-1), k(2) = (1.6 ± 0.1) × 10(3) M(-2) s(-1)). The observed suppression of the reaction rates with increasing Zn(2+) concentration is explained by the formation of a dinuclear Mn(2+)-L-Zn(2+) complex which is about 20-times more stable for [Mn(dota)](2-) than for [Mn(nota)](-) (K(MnLZn) = 68 and 3.6, respectively), and which dissociates very slowly (k(3)∼10(-5) M(-1) s(-1)). These data provide the first experimental proof that not all Mn(2+) complexes are kinetically labile. The absence of coordinated water makes both [Mn(nota)](-) and [Mn(dota)](2-) complexes inefficient for MRI applications. Nevertheless, the higher kinetic inertness of [Mn(dota)](2-) indicates a promising direction in designing ligands for Mn(2+) complexation.

The Onset of H + Ketene Products from Vinoxy Radicals Prepared by Photodissociation of Chloroacetaldehyde at 157 nm

DOE PAGES

Lam, Chow-Shing; Adams, Jonathan D.; Butler, Laurie J.

2016-04-19

We investigate the unimolecular dissociation of the vinoxy radical (CH 2CHO) prepared with high internal energy imparted from the photodissociation of chloroacetaldehyde (CH 2ClCHO) at 157 nm. Using a velocity map imaging apparatus, we measured the speed distribution of the recoiling chlorine atoms, Cl( 2P 3/2) and Cl( 2P 1/2), and derived from this the resulting distribution of kinetic energy, P(ET), imparted to the Cl + vinoxy fragments upon dissociation. Using conservation of energy, the distribution of kinetic energy was used to determine the total internal energy distribution in the radical. The P(ET) derived for the C–Cl bond fission presentedmore » in this work suggests the vinoxy radicals are mostly formed in the à state. We also took ion images at m/z = 42 and m/z = 15 to characterize the branching between the unimolecular dissociation channels of the vinoxy radical to H + ketene and methyl + CO products. Our results show a marked change in the branching ratio between the two channels from the previous study on the photodissociation of chloroacetaldehyde at 193 nm by Miller et al. (J. Chem. Phys., 2004, 121, 1830) in that the production of ketene is now favored over the production of methyl. To help analyze the data, we developed a model for the branching between the two channels that takes into account how the change in rotational energy en route to the products affects the vibrational energy available to surmount the barriers to the channels. The model predicts the portion of the C–Cl bond fission P(ET) that produces dissociative vinoxy radicals, then predicts the branching ratio between the H + ketene and CH 3 + CO product channels at each ET. The model uses Rice–Ramsperger–Kassel–Marcus rate constants at the correct sums and densities of vibrational states while accounting for angular momentum conservation. We find that the predicted portion of the P(ET) that produces H + ketene products best fits the experimental portion (that we derive by taking advantage of conservation of momentum) if we use a barrier height for the H + ketene channel that is 4.0 ± 0.5 kcal/mol higher than the isomerization barrier en route to CH 3 + CO products. Using the G4 computed isomerization barrier of 40.6 kcal/mol, this gives an experimentally determined barrier to the H + ketene channel of 44.6 kcal/mol. From these calculations, we also predict the branching ratio between the H + ketene and methyl + CO channels to be ~2.1:1.« less

Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds

PubMed Central

Rueda, Daniel; Sheen, Patricia; Gilman, Robert H.; Bueno, Carlos; Santos, Marco; Pando-Robles, Victoria; Batista, Cesar V.; Zimic, Mirko

2014-01-01

Recombinant wild-pyrazinamidase from H37Rv M. tuberculosis was analyzed by gel electrophoresis under differential reducing conditions to evaluate its quaternary structure. PZAse was fractionated by size exclusion chromatography under non-reducing conditions. PZAse activity was measured and mass spectrometry analysis was performed to determine the identity of proteins by de novo sequencing and to determine the presence of disulfide bonds. This study confirmed that M. tuberculosis wild type PZAse was able to form homo-dimers in vitro. Homo-dimers showed a slightly lower specific PZAse activity compared to monomeric PZAse. PZAse dimers were dissociated into monomers in response to reducing conditions. Mass spectrometry analysis confirmed the existence of disulfide bonds (C72-C138 and C138-C138) stabilizing the quaternary structure of the PZAse homo-dimer. PMID:25199451

Activation of Carbon-Hydrogen and Hydrogen-Hydrogen Bonds by Copper-Nitrenes: A Comparison of Density Functional Theory with Single- and Multireference Correlation Consistent Composite Approaches.

PubMed

Tekarli, Sammer M; Williams, T Gavin; Cundari, Thomas R

2009-11-10

The kinetics and thermodynamics of copper-mediated nitrene insertion into C-H and H-H bonds (the former of methane) have been studied using several levels of theory: B3LYP/6-311++G(d,p), B97-1/cc-pVTZ, PBE1KCIS/cc-pVTZ, and ccCA (correlation consistent Composite Approach). The results show no significant difference among the DFT methods. All three DFT methods predict the ground state of the copper-nitrene model complex, L'Cu(NH), to be a triplet, while single reference ccCA predicts the singlet to be the ground state. The contributions to the total ccCA energy indicate that the singlet state is favored at the MP2/CBS level of theory, while electron correlation beyond this level (CCSD(T)) favors a triplet state, resulting in a close energetic balance between the two states. A multireference ccCA method is applied to the nitrene active species and supports the assignment of a singlet ground state. In general, the largest difference in the model reaction cycles between DFT and ccCA methods is for processes involving radicals and bond dissociation.

Cocrystals of 6-propyl-2-thiouracil: N-H···O versus N-H···S hydrogen bonds.

PubMed

Tutughamiarso, Maya; Egert, Ernst

2011-11-01

In order to investigate the relative stability of N-H···O and N-H···S hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C(4)H(5)N(3)·2C(7)H(10)N(2)OS, (I), the `base pair' is connected by one N-H···S and one N-H···N hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-H···S hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C(9)H(11)N(3)O(2)·2C(7)H(10)N(2)OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C(7)H(10)N(2)OS, (III), is stabilized by pairwise N-H···O and N-H···S hydrogen bonds. In all three structures, N-H···S hydrogen bonds occur only within R(2)(2)(8) patterns, whereas N-H···O hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.

A first principles study of the oxidation energetics and kinetics of realgar

NASA Astrophysics Data System (ADS)

Renock, Devon; Becker, Udo

2010-08-01

Quantum-mechanical calculations allow resolving and quantifying in detail important aspects of reaction mechanisms such as spin transitions and oxygen dissociation that can be the major rate-limiting steps in redox processes on sulfide and oxide surfaces. In addition, this knowledge can help experimentalists in setting up the framework of rate equations that can be used to describe the kinetics of, e.g., oxidation processes. The unique molecular crystal structure of realgar, As 4S 4 clusters held together by van der Waals bonds, allows for a convenient quantum-mechanical (q.m.) cluster approach to investigate the thermodynamics and kinetic pathways of oxidation. The interaction of As 4S 4 clusters with oxygen and co-adsorbed ions provides a model system for understanding the molecular-scale processes that underpin empirically-derived rate expressions, and provides clues to the oxidation mechanisms of other sulfides and oxides. Two activated processes are shown to dominate the kinetics of oxidation by molecular oxygen: (i) a paramagnetic 3O to diamagnetic 1O spin transition and (ii) oxygen dissociation on the surface, in that order. The activation energies for the spin transition and O 2 dissociation step were determined to be 1.1 eV (106 kJ/mol) and 0.9 eV (87 kJ/mol), respectively, if molecular oxygen is the only reactant on the surface. In the case of As 4S 4, q.m. calculations reveal that 3O transfers its spin to the cluster and forms a low-spin, peroxo intermediate on the surface before dissociating. The adsorption of a hydroxide ion on the surface proximate to the 3O adsorption site changes the adsorption mechanism by lowering the activation energy barriers for both the spin transition (0.30 eV/29 kJ/mol) and the O 2 dissociation step (0.72 eV/69 kJ/mol). Thus, while spin transition is rate limiting for oxidation with O 2 alone, dissociation becomes the rate-limiting step for oxidation with co-adsorption of OH -. First-principles, periodic calculations of the realgar (1¯20) surface show that the energetics and structural changes that accompany oxidation of As 4S 4 clusters on the surface are similar to those involving individual As 4S 4 clusters. Thus, assuming that an As 4S 4 cluster with an adsorbed hydroxyl group is a reasonable approximation of the surface of As 4S 4 at high pH, the theoretically calculated oxidation rate (˜1 × 10 -10 mol m -2 s -1) is of the same order as empirically-derived rates from experiments at T = 298 K, pH = 8, and similar dissolved oxygen concentrations. In addition, the co-adsorption of other anions found in alkaline waters (i.e. carbonate, bicarbonate, sulfate, and sulfite) were shown to energetically promote the oxidation of As 4S 4 (on the order of 5-40 kJ/mol depending on the co-adsorbed anion, OH -, CO32-, HCO3-, SO42-, or SO32-, and accounting for changes in the hydration of products and reactants). The effect of the co-adsorbate on the kinetics and thermodynamics of oxidation is due to each adsorbate modifying the electronic and structural environment of the other adsorption site. Activation-energy barriers due to spin transitions are rarely discussed in the literature as key factors for controlling oxidation rates of mineral surfaces, even though the magnitude of these barriers is enough to alter the kinetics significantly. The attenuation of the activation energy by co-adsorbed anions suggests the possibility of pH- or p(co-adsorbate)-dependent activation energies that can be used to refine oxidation rate laws for sulfide minerals and other, especially semiconducting minerals, such as oxides.

Molecular-level understanding of ground- and excited-state O-H...O hydrogen bonding involving the tyrosine side chain: a combined high-resolution laser spectroscopy and quantum chemistry study.

PubMed

Biswal, Himansu S; Bhattacharyya, Surjendu; Wategaonkar, Sanjay

2013-12-16

The present study combines both laser spectroscopy and ab initio calculations to investigate the intermolecular OH⋅⋅⋅O hydrogen bonding of complexes of the tyrosine side chain model chromophore compounds phenol (PH) and para-cresol (pCR) with H2 O, MeOH, PH and pCR in the ground (S0 ) state as well as in the electronic excited (S1 ) state. All the experimental and computational findings suggest that the H-bond strength increases in the S1 state and irrespective of the hydrogen bond acceptor used, the dispersion energy contribution to the total interaction energy is about 10-15 % higher in the S1 state compared to that in the S0 state. The alkyl-substituted (methyl; +I effect) H-bond acceptor forms a significantly stronger H bond both in the S0 and the S1 state compared to H2 O, whereas the aryl-substituted (phenyl; -R effect) H-bond donor shows a minute change in energy compared to H2 O. The theoretical study emphasizes the significant role of the dispersive interactions in the case of the pCR and PH dimers, in particular the CH⋅⋅⋅O and the CH⋅⋅⋅π interactions between the donor and acceptor subunits in controlling the structure and the energetics of the aromatic dimers. The aromatic dimers do not follow the acid-base formalism, which states that the stronger the base, the more red-shifted is the XH stretching frequency, and consequently the stronger is the H-bond strength. This is due to the significant contribution of the dispersion interaction to the total binding energy of these compounds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.

PubMed

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R Ogorzalek; Julian, Ryan R; Loo, Joseph A

2015-11-15

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment

NASA Astrophysics Data System (ADS)

Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

2014-12-01

"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

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

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

DOE PAGES

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram; ...

2017-07-05

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

A cumulant functional for static and dynamic correlation

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

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2; Hosseini, Hessam

A functional for the cumulant energy is introduced. The functional is composed of a pair-correction and static and dynamic correlation energy components. The pair-correction and static correlation energies are functionals of the natural orbitals and the occupancy transferred between near-degenerate orbital pairs, rather than the orbital occupancies themselves. The dynamic correlation energy is a functional of the statically correlated on-top two-electron density. The on-top density functional used in this study is the well-known Colle-Salvetti functional. Using the cc-pVTZ basis set, the functional effectively models the bond dissociation of H{sub 2}, LiH, and N{sub 2} with equilibrium bond lengths and dissociationmore » energies comparable to those provided by multireference second-order perturbation theory. The performance of the cumulant functional is less impressive for HF and F{sub 2}, mainly due to an underestimation of the dynamic correlation energy by the Colle-Salvetti functional.« less

Observing electron localization in a dissociating H2+ molecule in real time

PubMed Central

Xu, H.; Li, Zhichao; He, Feng; Wang, X.; Atia-Tul-Noor, A.; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

2017-01-01

Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H2+ dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond—the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump–probe experiment. We demonstrate that in H2+ electron localization is complete in just 15 fs when the molecule’s internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation. PMID:28621332

Rates of ligand exchange between >FeIII-OH2 functional groups on a nanometer-sized aqueous cluster and bulk solution.

PubMed

Balogh, Edina; Todea, Ana Maria; Müller, Achim; Casey, William H

2007-08-20

Variable-temperature 17O NMR experiments were conducted on the nanometer-sized Keplerate Mo72Fe30 cluster, with the stoichiometry [Mo72Fe30O252(CH3COO)12[Mo2O7(H2O)]2[H2Mo2O8(H2O)](H2O)91]. approximately 150H2O. This molecule contains on its surface 30 Fe(H2O) groups forming a well-defined icosidodecahedron, and we estimated the rates of exchange of the isolated >FeIII-OH2 waters with bulk aqueous solution. Both longitudinal and transverse 17O-relaxation times were measured, as well as chemical shifts, and these parameters were then fit to the Swift-Connick equations in order to obtain the rate parameters. Correspondingly, we estimate: k(ex)298 = 6.7(+/-0.8) x 106 s-1, which is about a factor of approximately 4 x 104 times larger than the corresponding rate coefficient for the Fe(OH2)63+ ion of k(ex)298 = 1.6 x 102 s-1 (Grant and Jordan, 1981; Inorg. Chem. 20, 55-60) and DeltaH and DeltaS are 26.3 +/- 0.6 kJ mol-1 and -26 +/- 0.9 J mol-1 K-1, respectively. High-pressure 17O NMR experiments were also conducted, but the cluster decomposed slightly under pressure, which precluded confident quantitative estimation of the DeltaV. However, the increase in the reduced transverse-relaxation time with pressure suggests a dissociative character, such as a D or Id mechanism. The enhanced reactivity of waters on the Mo72Fe30 cluster is associated with an increase in the FeIII-OH2 bond length in the solid state of approximately 0.1 A relative to the Fe(OH2)63+ ion, suggesting that a correlation exists between the FeIII-OH2 bond length and k(ex)298. Although there are only few high-spin Fe(III) complexes where both exchange rates and structural data are available, these few seem to support a general correlation.

Variable (Tg, Ts) Measurements of Alkane Dissociative Sticking Coefficients

NASA Astrophysics Data System (ADS)

Valadez, Leticia; Dewitt, Kristy; Abbott, Heather; Kolasinski, Kurt; Harrision, Ian

2006-03-01

Dissociative sticking coefficients S(Tg, Ts) for CH4 and C2H6 on Pt(111) have been measured as a function of gas temperature (Tg) and surface temperature (Ts) using an effusive molecular beam. Microcanonical unimolecular rate theory (MURT) was employed to extract transition state characteristics [e.g., E0(CH4) = 52.5±3.5 kJ/mol-1 and E0(C2H6) = 26.5±3 kJ/mol-1]. MURT allows our S(Tg, Ts) values to be directly compared to other supersonic molecular beam and thermal equilibrium sticking measurements. The S(Tg, Ts) depend strongly on Ts, however, only for CH4 is a strong Tg dependence observed. The fairly weak Tg dependence for C2H6 suggests that vibrational mode specific behavior and/or molecular rotations play stronger roles in the dissociative chemisorption of C2H6 than they do for CH4. Interestingly, thermal S(Tg=Ts) predictions based on MURT modeling of our CH4/Pt(111) data are three orders of magnitude higher than recent thermal equilibrium measurements on supported Pt nanocrystallite catalysts [J. M. Wei, E. Iglesia, J. Phys. Chem. B 108, 4094 (2004)].

A DFT study and micro-kinetic analysis of acetylene selective hydrogenation on Pd-doped Cu(111) surfaces

NASA Astrophysics Data System (ADS)

Ma, Ling-Ling; Lv, Cun-Qin; Wang, Gui-Chang

2017-07-01

Semi-hydrogenation of acetylene in a hydrogen-rich stream is an industrially important process. Inspired by the recent experiments that Cu(111) surface doped by a small number of Pd atoms can exhibit excellent catalytic performance toward the dissociation of H2 molecule as well as the high selective hydrogenation of acetylene as compared with pure Cu and Pd metal alone at low-temperature, here we performed systematic first-principles calculations to investigate the corresponding reaction mechanism related to the acetylene hydrogenation processes on single atom alloys (SAAs) and monolayer Pd/Cu(111) (i.e.,1.00 ML Pd/Cu(111)) model catalysts in detail, and to explore the possible factors controlling the high selectivity on SAAs. Our results clearly demonstrate that the SAA catalyst has higher selectivity for the ethylene formation than that of 1.00 ML Pd/Cu(111), and lower activity for the acetylene conversion compared with that of 1.00 ML Pd/Cu(111). The relatively high selectivity on SAA is mainly due to the facile desorption of ethylene and moderate activity in the dissociation of molecular H2. The main factor which lowers the selectivity towards the ethylene formation on 1.00 ML Pd/Cu(111) is that this system has a higher capacity to promote the breaking of Csbnd H/Csbnd C bonds, which leads to the formation of carbonaceous deposits and polymers such as benzene, and thus reduces the selectivity for the ethylene formation. Meanwhile, it was found that the desorption energy of ethylene on these two surfaces was smaller than the energy barrier of further hydrogenation, which results in the absence of ethane on these two systems. Micro-kinetic model analysis provides a further valuable insight into the evidence for the key factors controlling the catalytic activity and selectivity towards the selective hydrogenation of acetylene. Our findings may help people to design a highly selective hydrogenation catalyst by controlling the balance between the H2 dissociation and Csbnd H/Csbnd C bond broken processes, and a good catalyst should be the one with the modest catalytic activity in the activation of molecular H2. At the same time, the present work provides an extremely significant mechanism of acetylene trimerization to form benzene and carbon formation.

Toward reliable modeling of S-nitrosothiol chemistry: Structure and properties of methyl thionitrite (CH3SNO), an S-nitrosocysteine model

NASA Astrophysics Data System (ADS)

Khomyakov, Dmitry G.; Timerghazin, Qadir K.

2017-07-01

Methyl thionitrite CH3SNO is an important model of S-nitrosated cysteine aminoacid residue (CysNO), a ubiquitous biological S-nitrosothiol (RSNO) involved in numerous physiological processes. As such, CH3SNO can provide insights into the intrinsic properties of the —SNO group in CysNO, in particular, its weak and labile S—N bond. Here, we report an ab initio computational investigation of the structure and properties of CH3SNO using a composite Feller-Peterson-Dixon scheme based on the explicitly correlated coupled cluster with single, double, and perturbative triple excitations calculations extrapolated to the complete basis set limit, CCSD(T)-F12/CBS, with a number of additive corrections for the effects of quadruple excitations, core-valence correlation, scalar-relativistic and spin-orbit effects, as well as harmonic zero-point vibrational energy with an anharmonicity correction. These calculations suggest that the S—N bond in CH3SNO is significantly elongated (1.814 Å) and has low stretching frequency and dissociation energy values, νS—N = 387 cm-1 and D0 = 32.4 kcal/mol. At the same time, the S—N bond has a sizable rotation barrier, △E0≠ = 12.7 kcal/mol, so CH3SNO exists as a cis- or trans-conformer, the latter slightly higher in energy, △E0 = 1.2 kcal/mol. The S—N bond properties are consistent with the antagonistic nature of CH3SNO, whose resonance representation requires two chemically opposite (antagonistic) resonance structures, CH3—S+=N—O- and CH3—S-/NO+, which can be probed using external electric fields and quantified using the natural resonance theory approach (NRT). The calculated S—N bond properties slowly converge with the level of correlation treatment, with the recently developed distinguished cluster with single and double excitations approximation (DCSD-F12) performing significantly better than the coupled cluster with single and double excitations (CCSD-F12), although still inferior to the CCSD(T)-F12 method that includes perturbative triple excitations. Double-hybrid density functional theory (DFT) calculations with mPW2PLYPD/def2-TZVPPD reproduce well the geometry, vibrational frequencies, and the S—N bond rotational barrier in CH3SNO, while hybrid DFT calculations with PBE0/def2-TZVPPD give a better S—N bond dissociation energy.

Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)-Substituted 1-H-Imidazole-2-carboxamide, A Potential Universal Reader for DNA Sequencing by Recognition Tunneling

PubMed Central

Liang, Feng; Li, Shengqing

2012-01-01

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunnelling in nanopores.[1] The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT> dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied. PMID:22461259

Fast and accurate predictions of covalent bonds in chemical space.

PubMed

Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

2016-05-07

We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSiP, HSiAs, HGeN, HGeP, HGeAs); and (v) H2 (+) single bond with 1 electron.

Mechanisms of formation of 8-oxoguanine due to reactions of one and two OH* radicals and the H2O2 molecule with guanine: A quantum computational study.

PubMed

Jena, N R; Mishra, P C

2005-07-28

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.

Collision induced dissociation of protonated N-nitrosodimethylamine by ion trap mass spectrometry: Ultimate carcinogens in gas phase

NASA Astrophysics Data System (ADS)

Kulikova, Natalia; Baker, Michael; Gabryelski, Wojciech

2009-12-01

Collision induced dissociation of protonated N-nitrosodimethylamine (NDMA) and isotopically labeled N-nitrosodimethyl-d6-amine (NDMA-d6) was investigated by sequential ion trap mass spectrometry to establish mechanisms of gas phase reactions leading to intriguing products of this potent carcinogen. The fragmentation of (NDMA + H+) occurs via two dissociation pathways. In the alkylation pathway, homolytic cleavage of the N-O bond of N-dimethyl, N'-hydroxydiazenium ion generates N-dimethyldiazenium distonic ion which reacts further by a CH3 radical loss to form methanediazonium ion. Both methanediazonium ion and its precursor are involved in ion/molecule reactions. Methanediazonium ion showed to be capable of methylating water and methanol molecules in the gas phase of the ion trap and N-dimethyldiazenium distonic ion showed to abstract a hydrogen atom from a solvent molecule. In the denitrosation pathway, a tautomerization of N-dimethyl, N'-hydroxydiazenium ion to N-nitrosodimethylammonium intermediate ion results in radical cleavage of the N-N bond of the intermediate ion to form N-dimethylaminium radical cation which reacts further through [alpha]-cleavage to generate N-methylmethylenimmonium ion. Although the reactions of NDMA in the gas phase are different to those for enzymatic conversion of NDMA in biological systems, each activation method generates the same products. We will show that collision induced dissociation of N-nitrosodiethylamine (NDEA) and N-nitrosodipropylamine (NDPA) is also a feasible approach to gain information on formation, stability, and reactivity of alkylating agents originating from NDEA and NDPA. Investigating such biologically relevant, but highly reactive intermediates in the condensed phase is hampered by the short life-times of these transient species.

The role of high oxygen vacancy concentration on modification of surface properties and H2S adsorption on the rutile TiO2 (110)

NASA Astrophysics Data System (ADS)

Wei, Shiqian; Wang, Fang; Dan, Meng; Zeng, Kaiyue; Zhou, Ying

2017-11-01

In this work, spin-polarized DFT + U method has been employed to investigate adsorption properties of H2S on the rutile TiO2 (110) surface with a high coverage of bridging oxygen vacancies (BOVs). The influence of different BOV coverage (θ-BOVs) on the surface electronic structure is examined. Defected states increase within the band gap with θ-BOVs increasing from 1/8 to 4/8 monolayer (ML). The high defected surface with θ-BOVs = 4/8 ML is determined to have a desired band structure and noticeable visible light response. In addition, H2S adsorption behaviors are noticeably affected by different H2S coverage (θ-H2S). Particularly, it is found molecular adsorption at θ-H2S ≤ 1/8 ML and dissociative adsorption at the higher θ-H2S. The maximization of spontaneous dissociation of H2S can be realized when the BOVs are all covered by H2S molecules. This work gains mechanistic insights into BOVs in tuning the surface properties and provides a guide for the effective utilization of the active surface sites on the rutile TiO2 (110) in the field of H2S splitting.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

PubMed

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-07

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

Novel germanetellones: XYGe=Te (X, Y = H, F, Cl, Br, I and CN) - structures and energetics. Comparison with the first synthetic successes.

PubMed

Jaufeerally, Naziah B; Abdallah, Hassan H; Ramasami, Ponnadurai; Schaefer, Henry F

2014-03-14

No stable germanetellone was described until Tbt(Dis)Ge=Te and Tbt(Tip)Ge=Te (Tbt = 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl, Dis = bis(trimethylsilyl)methyl and Tip = 2,4,6-triisopropylphenyl) were reported in 1997. Following these initial experiments, there has arisen considerable interest in Ge[double bond, length as m-dash]Te systems. An obvious question is: why have the simple XYGe=Te (X, Y = H, F, Cl, Br, I and CN) molecules not yet been isolated? In view of the present situation, theoretical information may be of great help for further advances in germanetellone chemistry. A systematic investigation of the XYGe=Te molecules is carried out using the second order Møller-Plesset perturbation theory (MP2) and density functional theory (DFT). The structures and energetics, including ionization potentials (IPad and IPad(ZPVE)), four different forms of neutral-anion separations (EAad, EAad(ZPVE), VEA and VDE) and the singlet-triplet gaps, are reported. The electronegativity (χ) reactivity descriptor for the halogens (F, Cl, Br and I) and the natural charge separations of the Ge=Te moiety are used to assess the interrelated properties of germanetellone and its derivatives. The results are analyzed, discussed and compared with analogous studies of telluroformaldehyde, silanetellone and their derivatives. The thermodynamic viabilities of some of the novel germanetellones have also been evaluated in terms of the bond dissociation enthalpies of Tbt(Dis)Ge=Te and Tbt(Tip)Ge=Te. The simple mono-substituted germanetellones appear to be slightly more thermodynamically favored than Tbt(Dis)Ge=Te and Tbt(Tip)Ge=Te, since the bond dissociation enthalpies of these kinetically stabilized germanetellones are about 28 and 51 kcal mol(-1) lower, respectively.

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

PubMed

Mo, Lixin; Zeng, Yanli; Li, Xiaoyan; Zhang, Xueying; Meng, Lingpeng

2016-07-01

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

Impact of resistance mutations on inhibitor binding to HIV-1 integrase

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

Chen, Qi; Buolamwini, John K.; Smith, Jeremy C.

2013-11-08

Here, HIV-1 integrase (IN) is essential for HIV-1 replication, catalyzing two key reaction steps termed 3' processing and strand transfer. Therefore, IN has become an important target for antiviral drug discovery. However, mutants have emerged, such as E92Q/N155H and G140S/Q148H, which confer resistance to raltegravir (RAL), the first IN strand transfer inhibitor (INSTI) approved by the FDA, and to the recently approved elvitegravir (EVG). To gain insights into the molecular mechanisms of ligand binding and drug resistance, we performed molecular dynamics (MD) simulations of homology models of the HIV-1 IN and four relevant mutants complexed with viral DNA and RAL.more » The results show that the structure and dynamics of the 140s loop, comprising residues 140 to 149, are strongly influenced by the IN mutations. In the simulation of the G140S/Q148H double mutant, we observe spontaneous dissociation of RAL from the active site, followed by an intrahelical swing-back of the 3' -OH group of nucleotide A17, consistent with the experimental observation that the G140S/Q148H mutant exhibits the highest resistance to RAL compared to other IN mutants. An important hydrogen bond between residues 145 and 148 is present in the wild-type IN but not in the G140S/Q148H mutant, accounting for the structural and dynamical differences of the 140s' loop and ultimately impairing RAL binding in the double mutant. End-point free energy calculations that broadly capture the experimentally known RAL binding profiles elucidate the contributions of the 140s' loop to RAL binding free energies and suggest possible approaches to overcoming drug resistance.« less

Relationships for the impact sensitivities of energetic C-nitro compounds based on bond dissociation energy.

PubMed

Li, Jinshan

2010-02-18

The ZPE-corrected C-NO(2) bond dissociation energies (BDEs(ZPE)) of a series of model C-nitro compounds and 26 energetic C-nitro compounds have been calculated using density functional theory methods. Computed results show that for C-nitro compounds the UB3LYP calculated BDE(ZPE) is less than the UB3P86 using the 6-31G** basis set, and the UB3P86 BDE(ZPE) changes slightly with the basis set varying from 6-31G** to 6-31++G**. For the series of model C-nitro compounds with different chemical skeletons, it is drawn from NBO analysis that the order of BDE(ZPE) is not only in line with that of the NAO bond order but also with that of the energy gap between C-NO(2) bonding and antibonding orbitals. It is found that for the energetic C-nitro compounds whose drop energies (Es(dr)) are below 24.5 J a good linear correlation exists between E(dr) and BDE(ZPE), implying that these compounds ignite through the C-NO(2) dissociation mechanism. After excluding the so-called trinitrotoluene mechanism compounds, a polynomial correlation of ln(E(dr)) with the BDE(ZPE) calculated at density functional theory levels has been established successfully for the 18 C-NO(2) dissociation energetic C-nitro compounds.

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

Zaporozhets, Irina A.; Ivanov, Vladimir V.; Lyakh, Dmitry I.

The earlier proposed multi-reference state-specific coupled-cluster theory with the complete active space reference suffered from a problem of energy discontinuities when the formal reference state was changing in the calculation of the potential energy curve (PEC). A simple remedy to the discontinuity problem is found and is presented in this work. It involves using natural complete active space self-consistent field active orbitals in the complete active space coupled-cluster calculations. As a result, the approach gives smooth PECs for different types of dissociation problems, as illustrated in the calculations of the dissociation of the single bond in the hydrogen fluorine moleculemore » and of the symmetric double-bond dissociation in the water molecule.« less

The competition of charge remote and charge directed fragmentation mechanisms in quaternary ammonium salt derivatized peptides--an isotopic exchange study.

PubMed

Cydzik, Marzena; Rudowska, Magdalena; Stefanowicz, Piotr; Szewczuk, Zbigniew

2011-12-01

Derivatization of peptides as quaternary ammonium salts (QAS) is a promising method for sensitive detection by electrospray ionization tandem mass spectrometry (Cydzik et al. J. Pept. Sci. 2011, 17, 445-453). The peptides derivatized by QAS at their N-termini undergo fragmentation according to the two competing mechanisms - charge remote (ChR) and charge directed (ChD). The absence of mobile proton in the quaternary salt ion results in ChR dissociation of a peptide bond. However, Hofmann elimination of quaternary salt creates an ion with one mobile proton leading to the ChD fragmentation. The experiments on the quaternary ammonium salts with deuterated N-alkyl groups or amide NH bonds revealed that QAS derivatized peptides dissociate according to the mixed ChR-ChD mechanism. The isotopic labeling allows differentiation of fragments formed according to ChR and ChD mechanisms. © The Author(s) 2011. This article is published with open access at Springerlink.com

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-). Theoretical evidence for a competitive charge transfer mechanism.

PubMed

Hu, Zhenming; Boyd, Russell J; Nakatsuji, Hiroshi

2002-03-20

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-) complexes have been investigated using the B3LYP and the symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theoretical methods. All the dicarbonyl complexes have singlet ground electronic states with large singlet-triplet separations. Thermal dissociations of CO from the parent dicarbonyls are energetically unfavorable. CO thermal dissociation is an activation process for [Cl(2)Rh(CO)(2)](-) while it is a repulsive potential for CpM(CO)(2). The natures of the main excited states of CpM(CO)(2) and [Cl(2)Rh(CO)(2)](-) are found to be quite different. For [Cl(2)Rh(CO)(2)](-), all the strong transitions are identified to be metal to ligand CO charge transfer (MLCT) excitations. A significant feature of the excited states of CpM(CO)(2) is that both MLCT excitation and a ligand Cp to metal and CO charge transfer excitation are strongly mixed in the higher energy states with the latter having the largest oscillator strength. A competitive charge transfer excited state has therefore been identified theoretically for CpRh(CO)(2) and CpIr(CO)(2). The wavelength dependence of the quantum efficiencies for the photoreactions of CpM(CO)(2) reported by Lees et al. can be explained by the existence of two different types of excited states. The origin of the low quantum efficiencies for the C-H/S-H bond activations of CpM(CO)(2) can be attributed to the smaller proportion of the MLCT excitation in the higher energy states.

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

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

Lichtenberger, D.L.

1991-10-01

The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies has been developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. This relationship has been used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. We have been able to obtain a direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal. The ionization energies have also been used to correlate the rates of carbonyl substitution reactions of ({eta}{sup 5}-C{sub 5}H{sub 4}X)Rh(CO){sub 2}more » complexes, and to reveal the electronic factors that control the stability of the transition state. The extent that the electronic features of these bonding interactions transfer to other chemical systems is being investigated in terms of the principle of additivity of ligand electronic effects. Specific examples under study include metal- phosphines, metal-halides, and metallocenes. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C{sub 60} molecule, buckminsterfullerene, and its interaction with a metal surface. The high-resolution valence ionizations in the gas phase reveal the high symmetry of the molecule, and studies of thin films of C{sub 60} reveal weak intermolecular interactions. Scanning tunneling and atomic force microscopy reveal the arrangement of spherical molecules on gold substrates, with significant delocalization of charge from the metal surface. 21 refs.« less

Collision-induced dissociation of [4Fe-4S] cubane cluster complexes: [Fe4S4Cl4 - x(SC2H5)x]2-/1- (x = 0-4)

NASA Astrophysics Data System (ADS)

Fu, You-Jun; Laskin, Julia; Wang, Lai-Sheng

2006-09-01

Collision-induced dissociation (CID) experiments on a series of [4Fe-4S] cluster ions, [Fe4S4Cl4 - x(SC2H5)x]2-/1- (x = 0-4), revealed that their fragmentation channels change with the coordination environment. Among the three Coulomb repulsion related channels for the doubly charged species, the collision induced electron detachment channel was found to become more significant from x = 0 to 4 due to the decreasing electron binding energies and the magnitude of repulsion Coulomb barrier, while both the ligand detachment of Cl- and the fission of the [Fe4S4]2+ core became more and more significant with the increase of the Cl- coordination, and eventually became the dominant channel at x = 0. From the parents containing the SC2H5 ligand, neutral losses of HSC2H5 (62 u) and/or HSCHCH2 (60 u) were observed. It was proposed that inter- and intra-ligand proton transfer could happen during the CID process, resulting in hydrogen coordination to the [4Fe-4S] cluster. In the presence of O2, [Fe4S4Cl3(SC2H5)]2- and [Fe4S4Cl4]2- can form the O2-substituted products [Fe4S4Cl2(SC2H5)O2]- and [Fe4S4Cl3O2]-, respectively. It was shown that the O2 complexation occurs by coordination to the empty iron site of the [4Fe-4S] cubane core after dissociation of one Cl- ligand.

Blackbody Infrared Radiative Dissociation of Oligonucleotide Anions

PubMed Central

Klassen, John S.; Schnier, Paul D.; Williams, Evan R.

2005-01-01

The dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [ d(A)72-, d(AATTAAT)2−, d(TTAATTA)2−, and d(CCGGCCG)2−] were measured using blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. The oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5′) phosphodiester bond to produce structurally informative a-base and w type ions. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained for the loss of base. The measured Arrhenius parameters are dependent on the identity of the nucleobase. The process involving the loss of an adenine base from the dianions, d(A)72-, d(AATTAAT)2−, and d(TTAATTA)2− has an average activation energy (Ea) of ~1.0 eV and a preexponential factor (A) of 1010 s−1. Both guanine and cytosine base loss occurs for d(CCGGCCG)2−. The average Arrhenius parameters for the loss of cytosine and guanine are Ea = 1.32 ± 0.03 eV and A = 1013.3±0.3 s−1. No loss of thymine was observed for mixed adenine–thymine oligonucleotides. Neither base loss nor any other fragmentation reactions occur for d(T)72- over a 600 s reaction delay at 207 °C, a temperature close to the upper limit accessible with our instrument. The Arrhenius parameters indicate that the preferred cleavage sites for mixed oligonucleotides of similar mass-to-charge ratio will be strongly dependent on the internal energy of the precursor ions. At low internal energies (effective temperatures below 475 K), loss of adenine and subsequent cleavage of the adjacent phosphoester bonds will dominate, whereas at higher energies, preferential cleavage at C and G residues will occur. The magnitude of the A factors ≤1013 s−1 measured for the loss of the three nucleobases (A, G, and C) is indicative of an entropically neutral or disfavored process as the rate limiting step for this reaction. PMID:9794082

Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

NASA Astrophysics Data System (ADS)

Klein, Erik; Lukeš, Vladimír

2006-11-01

In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

Infrared spectroscopy and molecular simulations of a polymeric sorbent and its enantioselective interactions with benzoin enantiomers.

PubMed

Tsui, Hung-Wei; Willing, Jonathan N; Kasat, Rahul B; Wang, Nien-Hwa Linda; Franses, Elias I

2011-11-10

Retention factors, k(R) and k(S), and enantioselectivities, S ≡ k(R)/k(S), of amylose tris[(S)-α-methylbenzylcarbamate] (AS) sorbent for benzoin (B) enantiomers were measured for various isopropyl alcohol (IPA)/n-hexane compositions of the high-performance liquid chromatography (HPLC) mobile phase. Novel data for pure n-hexane show that k(R) = 106, k(S) = 49.6, and S = 2.13. With some IPA from 0.5 to 10 vol %, with S = 1.8-1.4, the retention factors were smaller. Infrared spectra showed evidence of substantial hydrogen bonding (H-bonding) interactions in the pure polymer phase and additional H-bonding interactions between AS and benzoin. Density functional theory (DFT) was used to model the chain-chain and chain-benzoin H-bonding and other interactions. DFT was also used to predict fairly well the IR wavenumber shifts caused by the H-bonds. DFT simulations of IR bands of NH and C═O allowed for the first time the predictions of relative intensities and relative populations of H-bonding strengths. Molecular dynamics (MD) simulations were used to model a single 12-mer polymer chain. MD simulations predicted the existence of various potentially enantioselective cavities, two of which are sufficiently large to accommodate a benzoin molecule. Then "docking" studies of benzoin in AS with MD, Monte Carlo (MC), and MC/MD simulations were done to probe the AS-B interactions. The observed enantioselectivities are predicted to be primarily due to two H-bonds, of the kind AS CO···HO (R)-benzoin and AS NH···OC (R)-benzoin, and two π-π (phenyl-phenyl) interactions for (R)-benzoin and one H-bond, of type AS CO···HO (S)-benzoin, and one π-π interaction for (S)-benzoin. The MC/MD predictions are consistent with the HPLC and IR results.

Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question.

PubMed

Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M

2014-03-05

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form. Copyright © 2013 Wiley Periodicals, Inc.

Hydrogen-bonded diketopyrrolopyrrole (DPP) pigments as organic semiconductors

DOE PAGES

Glowacki, Eric Daniel; Coskun, Halime; Blood-Forsythe, Martin A.; ...

2014-10-13

Diketopyrrolopyrroles (DPPs) have recently gained attention as building-blocks for organic semiconducting polymers and small molecules, however the semiconducting properties of their hydrogen-bonded (H-bonded) pigment forms have not been explored. Herein we report on the performance of three archetypical H-bonded DPP pigments, which show ambipolar carrier mobilities in the range 0.01–0.06 cm 2/V s in organic field-effect transistors. Their semiconducting properties are correlated with crystal structure, where an H-bonded crystal lattice supports close and relatively cofacial π–π stacking. To better understand transport in these systems, density functional theory calculations were carried out, indicating theoretical maximum ambipolar mobility values of ~0.3 cmmore » 2/V s. Furthermore, based on these experimental and theoretical results, H-bonded DPPs represent a viable alternative to more established DPP-containing polymers and small molecules where H-bonding is blocked by N-alkylation.« less

Tracking the photodissociation dynamics of liquid nitromethane at 266 nm by femtosecond time-resolved broadband transient grating spectroscopy

NASA Astrophysics Data System (ADS)

Wu, Honglin; Song, Yunfei; Yu, Guoyang; Wang, Yang; Wang, Chang; Yang, Yanqiang

2016-05-01

Femtosecond time-resolved transient grating (TG) technique was employed to get insight into the photodissociation mechanism of liquid nitromethane (NM). Broadband white-light continuum was introduced as the probe to observe the evolution of electronic excited states of NM molecules and the formation of photodissociation products simultaneously. The reaction channel of liquid NM under 266 nm excitation was obtained that NM molecules in excited state S2 relax through two channels: about 73% relax to low lying S1 state through S2/S1 internal conversion with a time constant of 0.24 ps and then go back to the ground state through S1/S0 internal conversion; the other 27% will dissociate with a time constant of 2.56 ps. NO2 was found to be one of the products from the experimental TG spectra, which confirmed that C-N bond rupture was the primary dissociation channel of liquid NM.

Spectroscopic characterisation of interaction of ferulic acid with aldehyde dehydrogenase (ALDH).

PubMed

Kolawole, Ayodele O; Agaba, Ruth J; Oluwole, Matthew O

2017-05-01

Interaction of a pharmacological important phenolic, ferulic acid, with Aldehyde dehydrogenase (ALDH) at the simulative pH condition, was studied using spectroscopic approach. Ferulic acid caused a decrease in the fluorescence intensity formed from ALDH-ferulic acid complex resulting in mixed inhibition of ALDH activity (IC 50 =30.65μM). The intrinsic quenching was dynamic and induced altered conformation of ALDH and made the protein less compact but might not unfold it. ALDH has two binding sites for ferulic acid at saturating concentrations having association constant of 1.35×10 3 Lmol -1 and a dissociation constant of 9.7×10 7 Lmol -1 at 25°C indicating ALDH-ferulic acid complex formation is more favourable than its dissociation. The interaction was not spontaneous and endothermic and suggests the involvement of hydrophobic interactions with a FRET binding distance of 4.49nm. Change in pH near and far from isoelectric points of ferulic acid did not affect the bonding interaction. Using trehalose as viscosogen, the result from Stoke-Einstein hypothesis showed that ferulic acid-ALDH binding and dissociation equilibrium was diffusion controlled. These results clearly suggest the unique binding properties and lipophilicity influence of ferulic acid. Copyright © 2017 Elsevier B.V. All rights reserved.

Hydrolyzable Polyureas Bearing Hindered Urea Bonds

PubMed Central

2015-01-01

Hydrolyzable polymers are widely used materials that have found numerous applications in biomedical, agricultural, plastic, and packaging industrials. They usually contain ester and other hydrolyzable bonds, such as anhydride, acetal, ketal, or imine, in their backbone structures. Here, we report the first design of hydrolyzable polyureas bearing dynamic hindered urea bonds (HUBs) that can reversibly dissociate to bulky amines and isocyanates, the latter of which can be further hydrolyzed by water, driving the equilibrium to facilitate the degradation of polyureas. Polyureas bearing 1-tert-butyl-1-ethylurea bonds that show high dynamicity (high bond dissociation rate), in the form of either linear polymers or cross-linked gels, can be completely degraded by water under mild conditions. Given the simplicity and low cost for the production of polyureas by simply mixing multifunctional bulky amines and isocyanates, the versatility of the structures, and the tunability of the degradation profiles of HUB-bearing polyureas, these materials are potentially of very broad applications. PMID:25406025

Probing C-O bond activation on gas-phase transition metal clusters: Infrared multiple photon dissociation spectroscopy of Fe, Ru, Re, and W cluster CO complexes

NASA Astrophysics Data System (ADS)

Lyon, Jonathan T.; Gruene, Philipp; Fielicke, André; Meijer, Gerard; Rayner, David M.

2009-11-01

The binding of carbon monoxide to iron, ruthenium, rhenium, and tungsten clusters is studied by means of infrared multiple photon dissociation spectroscopy. The CO stretching mode is used to probe the interaction of the CO molecule with the metal clusters and thereby the activation of the C-O bond. CO is found to adsorb molecularly to atop positions on iron clusters. On ruthenium and rhenium clusters it also binds molecularly. In the case of ruthenium, binding is predominantly to atop sites, however higher coordinated CO binding is also observed for both metals and becomes prevalent for rhenium clusters containing more than nine atoms. Tungsten clusters exhibit a clear size dependence for molecular versus dissociative CO binding. This behavior denotes the crossover to the purely dissociative CO binding on the earlier transition metals such as tantalum.

Dissociative Photoionization of 1-Halogenated Silacyclohexanes: Silicon Traps the Halogen.

PubMed

Bodi, Andras; Sigurdardottir, Katrin Lilja; Kvaran, Ágúst; Bjornsson, Ragnar; Arnason, Ingvar

2016-11-23

The threshold photoelectron spectra and threshold photoionization mass spectra of 1-halogenated-1-silacyclohexanes, for the halogens X = F, Cl, Br, and I, have been obtained using synchrotron vacuum ultraviolet radiation and photoelectron photoion coincidence spectroscopy. As confirmed by a similar ionization onset and density functional theory molecular orbitals, the ionization to the ground state is dominated by electron removal from the silacyclohexane ring for X = F, Cl, and Br, and from the halogen lone pair for X = I. The breakdown diagrams show that the dissociative photoionization mechanism is also different for X = I. Whereas the parent ions decay by ethylene loss for X = F to Br in the low-energy regime, the iodine atom is lost for X = I. The first step is followed by a sequential ethylene loss at higher internal energies in each of the compounds. It is argued that the tendency of silicon to lower bond angles stabilizes the complex cation in which C 2 H 4 is η 2 -coordinated to it, and which precedes ethylene loss. Together with the relatively strong silicon-halogen bonds and the increased inductive effect of the silacyclohexane ring in stabilizing the cation, this explains the main differences observed in the fragmentation of the halogenated silacyclohexane and halogenated cyclohexane ions. The breakdown diagrams have been modeled taking into account slow dissociations at threshold and the resulting kinetic shift. The 0 K appearance energies have been obtained to within 0.08 eV for the ethylene loss for X = F to Br (10.56, 10.51, and 10.51 eV, respectively), the iodine atom loss for X = I (10.11 eV), the sequential ethylene loss for X = F to I (12.29, 12.01, 11.94, and 11.86 eV, respectively), and the minor channels of H loss for X = F (10.56 eV) and propylene loss in X = Cl (also at 10.56 eV). The appearance energies for the major channels likely correspond to the dissociative photoionization reaction energy.

UV photodissociation of proline-containing peptide ions: insights from molecular dynamics.

PubMed

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

NASA Astrophysics Data System (ADS)

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S2 and S3, lie close to 213 nm. Non-adiabatic MD simulation starting from S2 and S3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

Elucidating Direct Photolysis Mechanisms of Different Dissociation Species of Norfloxacin in Water and Mg2+ Effects by Quantum Chemical Calculations.

PubMed

Wang, Se; Wang, Zhuang

2017-11-11

The study of pollution due to combined antibiotics and metals is urgently needed. Photochemical processes are an important transformation pathway for antibiotics in the environment. The mechanisms underlying the effects of metal-ion complexation on the aquatic photochemical transformation of antibiotics in different dissociation forms are crucial problems in science, and beg solutions. Herein, we investigated the mechanisms of direct photolysis of norfloxacin (NOR) in different dissociation forms in water and metal ion Mg 2+ effects using quantum chemical calculations. Results show that different dissociation forms of NOR had different maximum electronic absorbance wavelengths (NOR 2+ < NOR⁰ < NOR⁺) and showed different photolysis reactivity. Analysis of transition states (TS) and reaction activation energies ( E a ) indicated NOR⁺ generally underwent loss of the piperazine ring (C10-N13 bond cleavage) and damage to piperazine ring (N13-C14 bond cleavage). For NOR 2+ , the main direct photolysis pathways were de-ethylation (N7-C8 bond cleavage) and decarboxylation (C2-C5 bond cleavage). Furthermore, the presence of Mg 2+ changed the order of the wavelength at maximum electronic absorbance (NOR⁺-Mg 2+ < NOR⁰-Mg 2+ < NOR 2+ -Mg 2+ ) and increased the intensities of absorbance peaks of all three dissociation species of NOR, implying that Mg 2+ played an important role in the direct photolysis of NOR⁰, NOR⁺, and NOR 2+ . The calculated TS results indicated that the presence of Mg 2+ increased E a for most direct photolysis pathways of NOR, while it decreased E a for some direct photolysis pathways such as the loss of the piperazine ring and the damage of the piperazine ring of NOR⁰ and the defluorination of NOR⁺.

Formation, structure and bond dissociation thresholds of gas-phase vanadium oxide cluster ions

NASA Astrophysics Data System (ADS)

Bell, R. C.; Zemski, K. A.; Justes, D. R.; Castleman, A. W.

2001-01-01

The formation and structure of gas-phase vanadium oxide cluster anions are examined using a guided ion beam mass spectrometer coupled with a laser vaporization source. The dominant peaks in the anion total mass distribution correspond to clusters having stoichiometries of the form (VO2)n(VO3)m(O2)q-. Collision-induced dissociation studies of the vanadium oxide species V2O4-6-, V3O6-9-, V4O8-10-, V5O11-13-, V6O13-15-, and V7O16-18- indicate that VO2, VO3, and V2O5 units are the main building blocks of these clusters. There are many similarities between the anion mass distribution and that of the cation distribution studied previously. The principal difference is a shift to higher oxygen content by one additional oxygen atom for the stoichiometric anions (VxOy-) as compared to the cations with the same number of vanadium atoms, which is attributed to the extra pair of electrons of the anionic species. The oxygen-rich clusters, VxOy(O2)-, are shown to more tightly adsorb molecular oxygen than those of the corresponding cationic clusters. In addition, the bond dissociation thresholds for the vanadium oxide clusters ΔE(V+-O)=6.09±0.28 eV, ΔE(OV+-O)=3.51±0.36 eV, and ΔE(O2V--O)=5.43±0.31 eV are determined from the energy-dependent collision-induced dissociation cross sections with Xe as the collision partner. To the best of our knowledge, this is the first bond dissociation energy reported for the breaking of the V-O bond of a vanadium oxide anion.

A theoretical study of three gas-phase reactions involving the production or loss of methane cations.

PubMed

Baptista, Leonardo; da Silveira, Enio F

2014-10-21

Hydrocarbon ions are important species in flames, spectroscopy and the interstellar medium. Their importance is reflected in the extensive body of literature on the structure and reactivity of carbocations. However, the geometry, electronic structure and reactivity of carbocations are difficult to assess. This study aims to contribute to the current knowledge of this subject by presenting a quantum mechanics description of methane cation dissociation using multiconfigurational methods. The geometric and electronic parameters of the minimum structure were determined for three main reaction paths: the dissociation CH4(+)→ CH2(+) + H2 and the dissociation-recombination processes CH4(+)↔ CH3(+) + H. The electronic and energetic effects of these reactions were analyzed, and it was found that each reaction path has a strong dependence on the methodology used as well as a strong multiconfigurational character during dissociation. The first doublet excited states are inner-shell excited states and may correspond to the ions that are expected to be formed after electron detachment. The rate coefficient for each reaction path was determined using variational transition state theory and RRKM/master equation calculations. The major dissociation paths, with their rate coefficients at the high-pressure limit, are CH4(+)(X(~)(2)B1) → CH3(+)(A(2)A1') + H((2)S) (k∞(T) = 1.42 × 10(+14) s(-1) exp(-37.12/RT)) and CH4(+)(X(~)(2)B1) → CH2(+)(A(2)A1) + H2((2)Σg(+)) (k∞(T) = 9.18 × 10(+14) s(-1) exp(-55.77/RT)). Our findings help to explain the abundance of ions formed from CH4 in the interstellar medium and to build models of chemical evolution.

pH at the micellar interface: synthesis of pH probes derived from salicylic acid, acid-base dissociation in sodium dodecyl sulfate micelles, and Poisson-Boltzmann simulation.

PubMed

Souza, T P; Zanette, D; Kawanami, A E; de Rezende, L; Ishiki, H M; do Amaral, A T; Chaimovich, H; Agostinho-Neto, A; Cuccovia, I M

2006-05-01

The study of the H+ concentration at the micellar interface is a convenient system for modeling the distribution of H+ at interfaces. We have synthesized salicylic acid derivatives to analyze the proton dissociation of both the carboxylic and phenol groups of the probes, determining spectrophotometrically the apparent pK(a)'s (pK(ap)) in sodium dodecyl sulfate, SDS, micelles with and without added salt. The synthesized probes were 2-hydroxy-5-(2-trimethylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumhexanoyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumundecanoyl)benzoate; 2-hydroxy-5-acetylbenzoic acid; and 2-hydroxy-5-dodecanoylbenzoic acid. Upon incorporation into SDS micelles the pK(ap)'s of both carboxylic and phenol groups increased by ca. 3 pH units and NaCl addition caused a decrease in the probe-incorporated pK(ap). The experimental results were fitted with a cell model Poisson-Boltzmann (P-B) equation taking in consideration the effect of salt on the aggregation number of SDS and using the distance of the dissociating group as a parameter. The conformations of the probes were analyzed theoretically using two dielectric constants, e.g., 2 and 78. Both the P-B analysis and conformation calculations can be interpreted by assuming that the acid groups dissociate very close to, or at, the interface. Our results are consistent with the assumption that the intrinsic pK(a)'s of both carboxylic and phenol groups of the salicylic acid probes used here can be taken as those in water. Using this assumption the micellar and salt effects on the pK(ap)'s of the (trialkylammonium)benzoate probes were described accurately using a cell model P-B analysis.

A P-H functionalized Al/P-based frustrated Lewis pair - hydrophosphination of nitriles, ring opening with cyclopropenones and evidence of P[double bond, length as m-dash]C double bond formation.

PubMed

Keweloh, Lukas; Aders, Niklas; Hepp, Alexander; Pleschka, Damian; Würthwein, Ernst-Ulrich; Uhl, Werner

2018-06-12

Hydroalumination of R-P(H)-C[triple bond, length as m-dash]C-tBu with bulky H-Al[CH(SiMe3)2]2 afforded the new P-H functionalized Al/P-based frustrated Lewis pair R-P(H)-C[[double bond, length as m-dash]C(H)-tBu]-AlR2 [R = CH(SiMe3)2; FLP 7]. A weak adduct of 7 with benzonitrile (8) was detected by NMR spectroscopy, but could not be isolated. tert-Butyl isocyanide afforded a similar, but isolable adduct (9), in which the isocyanide C atom was coordinated to aluminium. The unique reactivity of 7 became evident from its reactions with the heteroatom substituted nitriles PhO-C[triple bond, length as m-dash]N, PhCH2S-C[triple bond, length as m-dash]N and H8C4N-C[triple bond, length as m-dash]N. Hydrophosphination of the C[triple bond, length as m-dash]N triple bonds afforded imines at room temperature which were coordinated to the FLP by Al-N and P-C bonds to yield AlCPCN heterocycles (10 to 12). These processes depend on substrate activation by the FLP. Diphenylcyclopropenone and its sulphur derivative reacted with 7 by addition of the P-H bond to a C-C bond of the strained C3 ring and ring opening to afford the fragment (Z)-Ph-C(H)[double bond, length as m-dash]C(Ph)-C-X-Al (X = O, S). The C-O or C-S groups were coordinated to the FLP to yield AlCPCX heterocycles (13 and 14). The thiocarbonyl derived compound 14 contains an internally stabilized phosphenium cation with a localized P[double bond, length as m-dash]C bond, a trigonal planar coordinated P atom and a short P[double bond, length as m-dash]C distance (168.9 pm). Insight into formation mechanisms, the structural and energetic properties of FLP 7 and compounds 13 and 14 was gained by quantum chemical DFT calculations.

Mechanistic Insights on C-O and C-C Bond Activation and Hydrogen Insertion during Acetic Acid Hydrogenation Catalyzed by Ruthenium Clusters in Aqueous Medium

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

Shangguan, Junnan; Olarte, Mariefel V.; Chin, Ya-Huei

Catalytic pathways for acetic acid (CH3COOH) and hydrogen (H2) reactions on dispersed Ru clusters in the aqueous medium and the associated kinetic requirements for C-O and C-C bond cleavages and hydrogen insertion are established from rate and isotopic assessments. CH3COOH reacts with H2 in steps that either retain its carbon backbone and lead to ethanol, ethyl acetate, and ethane (47-95 %, 1-23 %, and 2-17 % carbon selectivities, respectively) or break its C-C bond and form methane (1-43 % carbon selectivities) at moderate temperatures (413-523 K) and H2 pressures (10-60 bar, 298 K). Initial CH3COOH activation is the kinetically relevantmore » step, during which CH3C(O)-OH bond cleaves on a metal site pair at Ru cluster surfaces nearly saturated with adsorbed hydroxyl (OH*) and acetate (CH3COO*) intermediates, forming an adsorbed acetyl (CH3CO*) and hydroxyl (OH*) species. Acetic acid turnover rates increase proportionally with both H2 (10-60 bar) and CH3COOH concentrations at low CH3COOH concentrations (<0.83 M), but decrease from first to zero order as the CH3COOH concentration and the CH3COO* coverages increase and the vacant Ru sites concomitantly decrease. Beyond the initial CH3C(O)-OH bond activation, sequential H-insertions on the surface acetyl species (CH3CO*) lead to C2 products and their derivative (ethanol, ethane, and ethyl acetate) and the competitive C-C bond cleavage of CH3CO* causes the eventual methane formation. The instantaneous carbon selectivities towards C2 species (ethanol, ethane, and ethyl acetate) increase linearly with the concentration of proton-type Hδ+ (derived from carboxylic acid dissociation) and chemisorbed H*. The selectivities towards C2 products decrease with increasing temperature, because of higher observed barriers for C-C bond cleavage than H-insertion. This study offers an interpretation of mechanism and energetics and provides kinetic evidence of carboxylic acid assisted proton-type hydrogen (Hδ+) shuffling during H-insertion steps in the aqueous phase, unlike those in the vapor phase, during the hydrogenation of acetic acid on Ru clusters.« less

Determination of the photolysis rate coefficient of monochlorodimethyl sulfide (MClDMS) in the atmosphere and its implications for the enhancement of SO2 production from the DMS + Cl2 reaction.

PubMed

Copeland, G; Lee, E P F; Williams, R G; Archibald, A T; Shallcross, D E; Dyke, J M

2014-01-01

In this work, the photolysis rate coefficient of CH3SCH2Cl (MClDMS) in the lower atmosphere has been determined and has been used in a marine boundary layer (MBL) box model to determine the enhancement of SO2 production arising from the reaction DMS + Cl2. Absorption cross sections measured in the 28000-34000 cm(-1) region have been used to determine photolysis rate coefficients of MClDMS in the troposphere at 10 solar zenith angles (SZAs). These have been used to determine the lifetimes of MClDMS in the troposphere. At 0° SZA, a photolysis lifetime of 3-4 h has been obtained. The results show that the photolysis lifetime of MClDMS is significantly smaller than the lifetimes with respect to reaction with OH (≈ 4.6 days) and with Cl atoms (≈ 1.2 days). It has also been shown, using experimentally derived dissociation energies with supporting quantum-chemical calculations, that the dominant photodissocation route of MClDMS is dissociation of the C-S bond to give CH3S and CH2Cl. MBL box modeling calculations show that buildup of MClDMS at night from the Cl2 + DMS reaction leads to enhanced SO2 production during the day. The extra SO2 arises from photolysis of MClDMS to give CH3S and CH2Cl, followed by subsequent oxidation of CH3S.

The effect of carbon-chain oxygenation in the carbon-carbon dissociation.

PubMed

Dos Santos, Lisandra Paulino; Baptista, Leonardo

2018-06-01

Currently, there is a trend of moving away from the use of fossil fuels to the use of biofuels. This modification changes the molecular structure of gasoline and diesel constituents, which should impact pollutant emissions and engine efficiency. An important property of automotive fuels is the resistance to autoignition. The goal of the present work is to evaluate thermochemical and kinetic parameters that govern the carbon-carbon bond dissociation and relate these parameters, in conjunction with molecular properties, to autoignition resistance. Three model reactions were investigated in the present work: dissociation of ethane, ethanol, and ethanal. All studies were conducted at the multiconfigurational level of theory, and the rate coefficients were evaluated from 300 to 2000 K. The comparison of dissociation energies and Arrhenius expressions indicates that autoignition resistance is related to the kinetic control of dissociation reactions and it is possible to relate the higher octane number of ethanol based fuels to the kinetics parameters of carbon-carbon bond fission. Graphical abstract Effect of the functional group in the Arrhenius parameters of the C-C dissociation. Arrhenius curves calculated at NEVPT2(6,6)/6-311G(2df,2pd).

Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

NASA Astrophysics Data System (ADS)

Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

2006-07-01

Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

Water clusters contributed to molecular interactions of ionizable organic pollutants with aromatized biochar via π-PAHB: Sorption experiments and DFT calculations.

PubMed

Zhang, Kun; Chen, Baoliang; Mao, Jiefei; Zhu, Lizhong; Xing, Baoshan

2018-05-08

Molecular interactions between biochars and ionizable organic pollutants (IOPs) are of great concern in natural environments, however the role of water clusters on the biochar surface remain unclear. The pH-dependent adsorption of aniline, phenol, 2-chlorophenol, 3-chlorophenol, 4-chlorophenol, 4-methylphenol and 4-nitrophenol onto bamboo wood derived biochar (BW700) as a model was conducted to identify conventional and novel interaction mechanisms between aromatized surface and IOPs. The dissociation constant (pK a,surface ) of surface functional groups of BW700 was characterized by acid-base titration and Zeta potential measurements. The pH-dependent adsorption behavior depended on the pK a,IOP of IOPs and also related to the pK a,surface of biochar surface. An obvious peak of adsorption coefficients (K d ) in the range of solution pH was shaped at pH peak  = (pK a,IOP  + pK a,surface )/2, which cannot be well explained by the conventional mechanisms such as hydrophobic effects, π-π interaction, electrostatic attractions, and hydrogen-binding. The contribution of ice-like adlayer (water clusters) on aromatic surface as H-acceptors is proposed for the first time to the adsorption peak of IOP as H-donors at pH peak . Density functional theory (DFT) calculations provided a possible structure of the complex combined with ice-like adlayer and aromatic substrate of BW700, and indicated that the adsorbing peak resulted from the multiple π-bond and polarization assisted H-bond (π-PAHB) interactions. Three distinct properties of π-PAHB were given, based on multiple π-bond, hydrophobicity-dependence and pH sensitivity. This novel mechanism extends the definition of H-bonds for better understanding the molecular interactions of IOP with carbonaceous materials and their environmental fate. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electrochemistry-Assisted Top-Down Characterization of Disulfide-Containing Proteins

PubMed Central

Zhang, Yun; Cui, Weidong; Zhang, Hao; Dewald, Howard D.; Chen, Hao

2013-01-01

Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then online ionized into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs. 73 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs. 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research. PMID:22448817

Electrochemistry-assisted top-down characterization of disulfide-containing proteins.

PubMed

Zhang, Yun; Cui, Weidong; Zhang, Hao; Dewald, Howard D; Chen, Hao

2012-04-17

Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with a top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then undergo online ionization into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows one to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs 75 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research.

Bond Dissociation Energies of the Tungsten Fluorides and Their Singly-Charged Ions: A Density Functional Survey

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Arnold, James (Technical Monitor)

1999-01-01

The dissociation of WF6 and the related singly-charged cations and anions into the lower fluorides and fluorine atoms has been investigated theoretically using density functional theory (B3LYP) and relativistic effective core potentials, with estimates of spin-orbit effects included using a simple model. The inclusion of spin-orbit is essential for a correct description of the thermochemistry. The total atomization energy of the neutral and anionic WF6 is reproduced to within 25 kcal/mol, but comparison of individual bond dissociation energies with available experimental data shows discrepancies of up to 10 kcal/mol. The results are nevertheless useful to help resolve discrepancies in experimental data and provide estimates of missing data.

From photoelectron detachment spectra of BrHBr{sup −}, BrDBr{sup −} and IHI{sup −}, IDI{sup −} to vibrational bonding of BrMuBr and IMuI

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

Manz, Jörn; Freie Universität Berlin, Institut für Chemie und Biochemie, 14195 Berlin; Sato, Kazuma

2015-04-28

Photoelectron detachment XLX{sup −}(00{sup 0}0) + hν → XLX(vib) + e{sup −} + KER (X = Br or I, L = H or D) at sufficiently low temperatures photoionizes linear dihalogen anions XLX{sup −} in the vibrational ground state (v{sub 1}v{sub 2}{sup l}v{sub 3} = 00{sup 0}0) and prepares the neutral radicals XLX(vib) in vibrational states (vib). At the same time, part of the photon energy (hν) is converted into kinetic energy release (KER) of the electron [R. B. Metz, S. E. Bradforth, and D. M. Neumark, Adv. Chem. Phys. 81, 1 (1992)]. The process may be described approximately inmore » terms of a Franck-Condon type transfer of the vibrational wavefunction representing XLX{sup −}(00{sup 0}0) from the domain close to the minimum of its potential energy surface (PES) to the domain close to the linear transition state of the PES of the neutral XLX. As a consequence, prominent peaks of the photoelectron detachment spectra (pds) correlate with the vibrational energies E{sub XLX,vib} of states XLX(vib) which are centered at linear transition state. The corresponding vibrational quantum numbers may be labeled vib = (v{sub 1}v{sub 2}{sup l}v{sub 3}) = (00{sup 0}v{sub 3}). Accordingly, the related most prominent peaks in the pds are labeled v{sub 3}. We construct a model PES which mimics the “true” PES in the domain of transition state such that it supports vibrational states with energies E{sub XLX,pds,00{sup 0}v{sub 3}} close to the peaks of the pds labeled v{sub 3} = 0, 2, and 4. Subsequently, the same model PES is also used to calculate approximate values of the energies E{sub XMuX,00{sup 0}0} of the isotopomers XMuX(00{sup 0}0). For the heavy isotopomers XHX and XDX, it turns out that all energies E{sub XLX,00{sup 0}v{sub 3}} are above the threshold for dissociation, which means that all heavy XLX(00{sup 0}v{sub 3}) with wavefunctions centered at the transition state are unstable resonances with finite lifetimes. Turning the table, bound states of the heavy XLX are van der Waals (vdW) bonded. In contrast, the energies E{sub XMuX,00{sup 0}0} of the light isotopomers XMuX(00{sup 0}0) are below the threshold for dissociation, with wavefunctions centered at the transition state. This means that XMuX(00{sup 0}0) are vibrationally bonded. This implies a fundamental change of the nature of chemical bonding, from vdW bonding of the heavy XHX, XDX to vibrational bonding of XMuX. For BrMuBr, the present results derived from experimental pds of BrHBr{sup −} and BrDBr{sup −} confirm the recent discovery of vibrational bonding based on quantum chemical ab initio calculations [D. G. Fleming, J. Manz, K. Sato, and T. Takayanagi, Angew. Chem., Int. Ed. 53, 13706 (2014)]. The extension from BrLBr to ILI means the discovery of a new example of vibrational bonding. These empirical results for the vibrational bonding of IMuI, derived from the photoelectron spectra of IHI{sup −} and IDI{sup −}, are supported by ab initio simulations of the spectra and of the wavefunction representing vibrational bonding of IMuI.« less

Bond Dissociation Energies for Substituted Polycyclic Aromatic Hydrocarbons and Their Cations

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)

1998-01-01

The B3LYP/4-31G approach is used to compute bond energies for a series of substituted benzene, naphthalene, and anthracene molecules and their cations. The benzene bond energies are compared with experiment. The trends in the bond energies are discussed. The ionization energies are also reported and compared with available experiments.

Microhydrated dihydrogen phosphate clusters probed by gas phase vibrational spectroscopy and first principles calculations

DOE PAGES

Sun, Shou -Tian; Jiang, Ling; Liu, J. W.; ...

2015-06-05

We report infrared multiple photon dissociation (IRMPD) spectra of cryogenically-cooled H 2PO 4 -(H 2O) n anions (n = 2–12) in the spectral range of the stretching and bending modes of the solute anion (600–1800 cm-1). The spectra cannot be fully understood using the standard technique of comparison to harmonic spectra of minimum-energy structures; a satisfactory assignment requires considering anharmonic effects as well as entropy-driven hydrogen bond network fluctuations. Aided by finite temperature ab initio molecular dynamics simulations, the observed changes in the position, width and intensity of the IRMPD bands with cluster size are related to the sequence ofmore » microsolvation. Due to stronger hydrogen bonding to the two terminal P=O groups, these are hydrated before the two P–OH groups. By n = 6, all four end groups are involved in the hydrogen bond network and by n = 12, the cluster spectra show similarities to the condensed phase spectrum of H 2PO 4 -(aq). Our results reveal some of the microscopic details concerning the formation of the aqueous solvation environment around H 2PO 4 -, provide ample testing grounds for the design of model solvation potentials for this biologically relevant anion, and support a new paradigm for the interpretation of IRMPD spectra of microhydrated ions.« less

A neural network potential energy surface for the NaH2 system and dynamics studies on the H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+) reaction.

PubMed

Wang, Shufen; Yuan, Jiuchuang; Li, Huixing; Chen, Maodu

2017-08-02

In order to study the dynamics of the reaction H( 2 S) + NaH(X 1 Σ + ) → Na( 2 S) + H 2 (X 1 Σ g + ), a new potential energy surface (PES) for the ground state of the NaH 2 system is constructed based on 35 730 ab initio energy points. Using basis sets of quadruple zeta quality, multireference configuration interaction calculations with Davidson correction were carried out to obtain the ab initio energy points. The neural network method is used to fit the PES, and the root mean square error is very small (0.00639 eV). The bond lengths, dissociation energies, zero-point energies and spectroscopic constants of H 2 (X 1 Σ g + ) and NaH(X 1 Σ + ) obtained on the new NaH 2 PES are in good agreement with the experiment data. On the new PES, the reactant coordinate-based time-dependent wave packet method is applied to study the reaction dynamics of H( 2 S) + NaH(X 1 Σ + ) → Na( 2 S) + H 2 (X 1 Σ g + ), and the reaction probabilities, integral cross-sections (ICSs) and differential cross-sections (DCSs) are obtained. There is no threshold in the reaction due to the absence of an energy barrier on the minimum energy path. When the collision energy increases, the ICSs decrease from a high value at low collision energy. The DCS results show that the angular distribution of the product molecules tends to the forward direction. Compared with the LiH 2 system, the NaH 2 system has a larger mass and the PES has a larger well at the H-NaH configuration, which leads to a higher ICS value in the H( 2 S) + NaH(X 1 Σ + ) → Na( 2 S) + H 2 (X 1 Σ g + ) reaction. Because the H( 2 S) + NaH(X 1 Σ + ) → Na( 2 S) + H 2 (X 1 Σ g + ) reaction releases more energy, the product molecules can be excited to a higher vibrational state.

A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search.

PubMed

Chen, Jianzhong; Shiyanov, Pavel; Schlager, John J; Green, Kari B

2012-02-01

It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs. © American Society for Mass Spectrometry, 2011

The effect of dimethyl sulfoxide (DMSO) on dentin bonding and nanoleakage of etch-and-rinse adhesives.

PubMed

Tjäderhane, Leo; Mehtälä, Pekka; Scaffa, Polliana; Vidal, Cristina; Pääkkönen, Virve; Breschi, Lorenzo; Hebling, Josimeri; Tay, Franklin R; Nascimento, Fabio D; Pashley, David H; Carrilho, Marcela R

2013-10-01

The objective was to examine the effect of a solvent dimethyl sulfoxide (DMSO) on resin-dentin bond durability, as well as potential functional mechanisms behind the effect. Microtensile bond strength (μTBS) was evaluated in extracted human teeth in two separate experiments. Dentin specimens were acid-etched and assigned to pre-treatment with 0.5mM (0.004%) DMSO as additional primer for 30s and to controls with water pre-treatment. Two-step etch-and-rinse adhesive (Scotchbond 1XT, 3M ESPE) was applied and resin composite build-ups were created. Specimens were immediately tested for μTBS or stored in artificial saliva for 6 and 12 months prior to testing. Additional immediate and 6-month specimens were examined for interfacial nanoleakage analysis under SEM. Matrix metalloproteinase (MMP) inhibition by DMSO was examined with gelatin zymography. Demineralized dentin disks were incubated in 100% DMSO to observe the optical clearing effect. The use of 0.5mM DMSO had no effect on immediate bond strength or nanoleakage. In controls, μTBS decreased significantly after storage, but increased significantly in DMSO-treated group. The control group had significantly lower μTBS than DMSO-group after 6 and 12 months. DMSO also eliminated the increase in nanoleakage seen in controls. 5% and higher DMSO concentrations significantly inhibited the gelatinases. DMSO induced optical clearing effect demonstrating collagen dissociation. DMSO as a solvent may be useful in improving the preservation of long-term dentin-adhesive bond strength. The effect may relate to dentinal enzyme inhibition or improved wetting of collagen by adhesives. The collagen dissociation required much higher DMSO concentrations than the 0.5mM DMSO used for bonding. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Hydrogen Sulfide as a Scavenger of Sulfur Atomic Cation.

PubMed

Fortenberry, Ryan C; Trabelsi, Tarek; Francisco, Joseph S

2018-06-07

The well-studied hydrogen sulfide molecule is shown here for the first time to form a S-S bond barrierlessly with sulfur atomic cation to produce stable H 2 SS + , a compound for which there is nearly no literature data. Previous work has shown that the reaction of hydrogen sulfide with neutral atomic sulfur will likely only take place at high pressures. Conversely, this work shows that hydrogen sulfide will readily bind with atomic sulfur cation first through the 1 4 A″ state from association of H 2 S with S + ( 4 S) and then will relax to the nearly degenerate 1 2 A' or 1 2 A″ states. S + ( 4 S) + H 2 S lies 29.5 kcal/mol above the 1 4 A″ H 2 SS + minimum. The 1 4 A″ H 2 SS + minimum in the S-S bond is also directly intersected by the doublet potential energy surface. As the S-S bond shortens in the association, the 1 2 A' and 1 2 A″ states split, falling 33.5 and 26.4 kcal/mol, respectively, below the 1 4 A″ state. Hence, this work is opening the door for novel synthesis of S-S bonds or potential removal of the common H 2 S toxin/pollutant through concatenation and subsequent precipitation.

Atypical cleavage of protonated N-fatty acyl amino acids derived from aspartic acid evidenced by sequential MS3 experiments.

PubMed

Boukerche, Toufik Taalibi; Alves, Sandra; Le Faouder, Pauline; Warnet, Anna; Bertrand-Michel, Justine; Bouchekara, Mohamed; Belbachir, Mohammed; Tabet, Jean-Claude

2016-12-01

Lipidomics calls for information on detected lipids and conjugates whose structural elucidation by mass spectrometry requires to rationalization of their gas phase dissociations toward collision-induced dissociation (CID) processes. This study focused on activated dissociations of two lipoamino acid (LAA) systems composed of N-palmitoyl acyl coupled with aspartic and glutamic acid mono ethyl esters (as LAA (*D) and LAA (*E) ). Although in MS/MS, their CID spectra show similar trends, e.g., release of water and ethanol, the [(LAA (*D/*E) +H)-C 2 H 5 OH] + product ions dissociate via distinct pathways in sequential MS 3 experiments. The formation of all the product ions is rationalized by charge-promoted cleavages often involving stepwise processes with ion isomerization into ion-dipole prior to dissociation. The latter explains the maleic anhydride or ketene neutral losses from N-palmitoyl acyl aspartate and glutamate anhydride fragment ions, respectively. Consequently, protonated palmitoyl acid amide is generated from LAA (*D), whereas LAA (*E) leads to the [*E+H-H 2 O] + anhydride. The former releases ammonia to provide acylium, which gives the C n H (2n-1) and C n H (2n-3) carbenium series. This should offer structural information, e.g., to locate either unsaturation(s) or alkyl group branching present on the various fatty acyl moieties of lipo-aspartic acid in further studies based on MS n experiments.

The role of multivalency in the association kinetics of patchy particle complexes.

PubMed

Newton, Arthur C; Groenewold, Jan; Kegel, Willem K; Bolhuis, Peter G

2017-06-21

Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles.

The role of multivalency in the association kinetics of patchy particle complexes

NASA Astrophysics Data System (ADS)

Newton, Arthur C.; Groenewold, Jan; Kegel, Willem K.; Bolhuis, Peter G.

2017-06-01

Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles.

Effects of membrane deformability and bond formation/dissociation rates on adhesion dynamics of a spherical capsule in shear flow.

PubMed

Zhang, Ziying; Du, Jun; Wei, Zhengying; Wang, Zhen; Li, Minghui

2018-02-01

Cellular adhesion plays a critical role in biological systems and biomedical applications. Cell deformation and biophysical properties of adhesion molecules are of significance for the adhesion behavior. In the present work, dynamic adhesion of a deformable capsule to a planar substrate, in a linear shear flow, is numerically simulated to investigate the combined influence of membrane deformability (quantified by the capillary number) and bond formation/dissociation rates on the adhesion behavior. The computational model is based on the immersed boundary-lattice Boltzmann method for the capsule-fluid interaction and a probabilistic adhesion model for the capsule-substrate interaction. Three distinct adhesion states, detachment, rolling adhesion and firm adhesion, are identified and presented in a state diagram as a function of capillary number and bond dissociation rate. The impact of bond formation rate on the state diagram is further investigated. Results show that the critical bond dissociation rate for the transition of rolling or firm adhesion to detachment is strongly related to the capsule deformability. At the rolling-adhesion state, smaller off rates are needed for larger capillary number to increase the rolling velocity and detach the capsule. In contrast, the critical off rate for firm-to-detach transition slightly increases with the capillary number. With smaller on rate, the effect of capsule deformability on the critical off rates is more pronounced and capsules with moderate deformability are prone to detach by the shear flow. Further increasing of on rate leads to large expansion of both rolling-adhesion and firm-adhesion regions. Even capsules with relatively large deformability can maintain stable rolling adhesion at certain off rate.

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

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

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

DOE PAGES

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.; ...

2017-05-03

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics.

PubMed

Masunov, Artëm E; Wait, Elizabeth E; Atlanov, Arseniy A; Vasu, Subith S

2017-05-18

In oxy-fuel combustion, the pure oxygen (O 2 ), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2 O) are free from pollution by nitrogen oxides. Moreover, high pressures result in the near-liquid density of CO 2 at supercritical state (sCO 2 ). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. To assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of the carbon dioxide molecule. All transition states and reactant and product complexes are reported for three reactions: H 2 CO + HO 2 → HCO + H 2 O 2 (R1), 2HO 2 → H 2 O 2 + O 2 (R2), and CO + OH → CO 2 + H (R3). In reaction R3, covalent binding of CO 2 to the OH radical and then the CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to the bimolecular OH + CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol and is expected to accelerate the reaction. In the case of hydroperoxyl self-reaction 2HO 2 → H 2 O 2 + O 2 the intermediates, containing covalent bonds to CO 2 are found not to be competitive. However, the spectator CO 2 molecule can stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates is also discovered in the H 2 CO + HO 2 → HCO + H 2 O 2 reaction, but these species lead to substantially higher activation barriers, which makes them unlikely to play a role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilizes the transition state and reduces the reaction barrier. These results indicate that the CO 2 environment is likely to have a catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2 .

An HMM-based algorithm for evaluating rates of receptor–ligand binding kinetics from thermal fluctuation data

PubMed Central

Ju, Lining; Wang, Yijie Dylan; Hung, Ying; Wu, Chien-Fu Jeff; Zhu, Cheng

2013-01-01

Motivation: Abrupt reduction/resumption of thermal fluctuations of a force probe has been used to identify association/dissociation events of protein–ligand bonds. We show that off-rate of molecular dissociation can be estimated by the analysis of the bond lifetime, while the on-rate of molecular association can be estimated by the analysis of the waiting time between two neighboring bond events. However, the analysis relies heavily on subjective judgments and is time-consuming. To automate the process of mapping out bond events from thermal fluctuation data, we develop a hidden Markov model (HMM)-based method. Results: The HMM method represents the bond state by a hidden variable with two values: bound and unbound. The bond association/dissociation is visualized and pinpointed. We apply the method to analyze a key receptor–ligand interaction in the early stage of hemostasis and thrombosis: the von Willebrand factor (VWF) binding to platelet glycoprotein Ibα (GPIbα). The numbers of bond lifetime and waiting time events estimated by the HMM are much more than those estimated by a descriptive statistical method from the same set of raw data. The kinetic parameters estimated by the HMM are in excellent agreement with those by a descriptive statistical analysis, but have much smaller errors for both wild-type and two mutant VWF-A1 domains. Thus, the computerized analysis allows us to speed up the analysis and improve the quality of estimates of receptor–ligand binding kinetics. Contact: jeffwu@isye.gatech.edu or cheng.zhu@bme.gatech.edu PMID:23599504

Negative cooperativity in binding of muscarinic receptor agonists and GDP as a measure of agonist efficacy.

PubMed

Jakubík, J; Janíčková, H; El-Fakahany, E E; Doležal, V

2011-03-01

Conventional determination of agonist efficacy at G-protein coupled receptors is measured by stimulation of guanosine-5'-γ-thiotriphosphate (GTPγS) binding. We analysed the role of guanosine diphosphate (GDP) in the process of activation of the M₂ muscarinic acetylcholine receptor and provide evidence that negative cooperativity between agonist and GDP binding is an alternative measure of agonist efficacy. Filtration and scintillation proximity assays measured equilibrium binding as well as binding kinetics of [³⁵S]GTPγS and [³H]GDP to a mixture of G-proteins as well as individual classes of G-proteins upon binding of structurally different agonists to the M₂ muscarinic acetylcholine receptor. Agonists displayed biphasic competition curves with the antagonist [³H]-N-methylscopolamine. GTPγS (1 µM) changed the competition curves to monophasic with low affinity and 50 µM GDP produced a similar effect. Depletion of membrane-bound GDP increased the proportion of agonist high-affinity sites. Carbachol accelerated the dissociation of [³H]GDP from membranes. The inverse agonist N-methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP. Carbachol affected both GDP association with and dissociation from G(i/o) G-proteins but only its dissociation from G(s/olf) G-proteins. These findings suggest the existence of a low-affinity agonist-receptor conformation complexed with GDP-liganded G-protein. Also the negative cooperativity between GDP and agonist binding at the receptor/G-protein complex determines agonist efficacy. GDP binding reveals differences in action of agonists versus inverse agonists as well as differences in activation of G(i/o) versus G(s/olf) G-proteins that are not identified by conventional GTPγS binding. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

Understanding Chemistry: Current and Possible

ERIC Educational Resources Information Center

Sanderson, R. T.

1976-01-01

Describes an instructional approach for teaching the cause-and-effect relationship between the qualities of atoms and the properties of their chemical compositions. Discusses atomic structure, ionization energies, homonuclear and heteronuclear bonding, and bond dissociation. (MLH)

ACTIVITY OF DISSOCIATED AND REASSOCIATED 19S ANTI-γ-GLOBULINS

PubMed Central

Schrohenloher, Ralph E.; Kunkel, Henry G.; Tomasi, Thomas B.

1964-01-01

19S anti-γ-globulins were isolated in a high state of purity from the sera of two patients with rheumatoid arthritis. Following reduction with ethyl mercaptan and alkylation by iodoacetamide, fragments were produced which retained the capacity to combine with 7S γ-globulin. The fragments from one of the 19S anti-γ-globulins agglutinated red cells coated with incomplete anti-Rh antibodies. This activity was shown by density gradient ultracentrifugation to be associated with low molecular weight fractions. The agglutination of the coated red cells by the fragments was strongly inhibited by normal and myeloma 7S γ-globulins and showed a greater specificity than the parent 19S material. Analytical ultracentrifuge experiments demonstrated that the fragments from either of the 19S anti-γ-globulins formed complexes with 7S γ-globulin. Reassociation of the dissociated fragments through reformation of disulfide bonds resulted in the formation of fast sedimenting molecules having properties similar to those of the untreated 19S material in respect to precipitation with aggregated γ-globulin and agglutination of coated red cells. PMID:14238936

Methanol electro-oxidation on platinum modified tungsten carbides in direct methanol fuel cells: a DFT study.

PubMed

Sheng, Tian; Lin, Xiao; Chen, Zhao-Yang; Hu, P; Sun, Shi-Gang; Chu, You-Qun; Ma, Chun-An; Lin, Wen-Feng

2015-10-14

In exploration of low-cost electrocatalysts for direct methanol fuel cells (DMFCs), Pt modified tungsten carbide (WC) materials are found to be great potential candidates for decreasing Pt usage whilst exhibiting satisfactory reactivity. In this work, the mechanisms, onset potentials and activity for electrooxidation of methanol were studied on a series of Pt-modified WC catalysts where the bare W-terminated WC(0001) substrate was employed. In the surface energy calculations of a series of Pt-modified WC models, we found that the feasible structures are mono- and bi-layer Pt-modified WCs. The tri-layer Pt-modified WC model is not thermodynamically stable where the top layer Pt atoms tend to accumulate and form particles or clusters rather than being dispersed as a layer. We further calculated the mechanisms of methanol oxidation on the feasible models via methanol dehydrogenation to CO involving C-H and O-H bonds dissociating subsequently, and further CO oxidation with the C-O bond association. The onset potentials for the oxidation reactions over the Pt-modified WC catalysts were determined thermodynamically by water dissociation to surface OH* species. The activities of these Pt-modified WC catalysts were estimated from the calculated kinetic data. It has been found that the bi-layer Pt-modified WC catalysts may provide a good reactivity and an onset oxidation potential comparable to pure Pt and serve as promising electrocatalysts for DMFCs with a significant decrease in Pt usage.

Reactions at the Metal Vertex of a Monometal Metallocarborane Cluster. The Chemistry of (closo-3,3-(PPh3)2-3-(HSO4)-3,1,2-RhC2B9H11) and (closo-3-(PPh3)-3,3-(NO3)-3,1,2RhC2B9H11).

DTIC Science & Technology

1982-03-09

4) produced by dissociation of PPh 3 from (2) or through an ionic species such as [closo-3,3- (PPh 3)2 -3,1,2-RhC 289 H ] [HSO4 (4a). Secondly, the...acetylene molecule and subsequent insertion into a metal-carbon bond has been observed in the linear oligomerization of acetylere catalyzed by [Ni(CO...monoxide were obtained from Liquid Carbonic and used without further treatment. Phenylacetylene (Aldrich) was distilled under vacuum before use and n

Tree species affect cation exchange capacity (CEC) and cation binding properties of organic matter in acid forest soils.

PubMed

Gruba, Piotr; Mulder, Jan

2015-04-01

Soil organic matter (SOM) in forest soil is of major importance for cation binding and acid buffering, but its characteristics may differ among soils under different tree species. We investigated acidity, cation exchange properties and Al bonding to SOM in stands of Scots pine, pedunculate oak, Norway spruce, European beech and common hornbeam in southern Poland. The content of total carbon (Ct) was by far the major contributor to total cation exchange capacity (CECt) even in loamy soils and a strong relationship between Ct and CECt was found. The slope of the regression of CECt to Ct increased in the order hornbeam≈oak

Parabola-like shaped pH-rate profile for phenols oxidation by aqueous permanganate.

PubMed

Du, Juanshan; Sun, Bo; Zhang, Jing; Guan, Xiaohong

2012-08-21

Oxidation of phenols by permanganate in the pH range of 5.0-9.0 generally exhibits a parabola-like shape with the maximum reaction rate obtained at pH close to phenols' pK(a). However, a monotonic increase or decrease is observed if phenols' pK(a) is beyond the pH range of 5.0-9.0. A proton transfer mechanism is proposed in which the undissociated phenol is directly oxidized by permanganate to generate products while a phenolate-permanganate adduct, intermediate, is formed between dissociated phenol and permanganate ion and this is the rate-limiting step for phenolates oxidation by permanganate. The intermediate combines with H(+) and then decomposes to products. Rate equations derived based on the steady-state approximation can well simulate the experimentally derived pH-rate profiles. Linear free energy relationships (LFERs) were established among the parameters obtained from the modeling, Hammett constants, and oxygen natural charges in phenols and phenolates. LFERs reveal that chlorine substituents have opposite influence on the susceptibility of phenols and phenolates to permanganate oxidation and phenolates are not necessarily more easily oxidized than their neutral counterparts. The chlorine substituents regulate the reaction rate of chlorophenolates with permanganate mainly by influencing the natural charges of the oxygen atoms of dissociated phenols while they influence the oxidation of undissociated chlorophenols by permanganate primarily by forming intramolecular hydrogen bonding with the phenolic group.

Spectroscopic and pH-metric studies of the complexation of 3-[2-(4-methylquinolin-2-yl)hydrazono]butan-2-one oxime compound.

PubMed

Seleem, H S; El-Inany, G A; Mousa, M; Hanafy, F I

2010-05-01

The electronic absorption spectra of the oximic quinolinyl hydrazone (MHQ; H(2)L) and its Co(II) and Cu(II)-complexes have been studied in Britton-Rhobinson buffer solutions of varying pH's in 75% dioxane-water. The dissociation constant of the hydrazone (pK(H)) as well as the stability constants (logK) of its chelates were determined spectrophotometrically and pH-metrically. The obtained data are in good agreement. Beer's law is valid in the ranges (0.64-6.99) and (2.36-6.48)mug/mL for Cu(II) and Co(II)-ions, respectively. On the other hand, the pK(H) and logK were determined pH-metrically in 75% solvent-water; (solvent=dioxane, ethanol, methanol and isopropanol). The variation of pK(H) or logK as a function of solvent parameters viz. 1/D, E(T), AN and pi* was used to evaluate the dissociation and stability constants in the aqueous medium. Furthermore, the reaction of the oximic hydrazone (H(2)L) with copper(II)-nitrate and chloride in addition to copper(I)-iodide afforded square planar mononuclear and binuclear complexes in which the oximic hydrazone showed three different modes of bonding. The obtained complexes reflect the strong bridging ability of the oximato group as well as its ambidentate and flexidentate characters. Copyright 2010 Elsevier B.V. All rights reserved.

Understanding and modulating the high-energy properties of noble-gas hydrides from their long-bonding: an NBO/NRT investigation on HNgCO+/CS+/OSi+ and HNgCN/NC (Ng = He, Ar, Kr, Xe, Rn) molecules.

PubMed

Zhang, Guiqiu; Song, Junjie; Fu, Lei; Tang, Kongshuang; Su, Yue; Chen, Dezhan

2018-04-18

The noble-gas hydrides, HNgX (X is an electronegative atom or fragment), represent potential high-energy materials because their two-body decomposition process, HNgX → Ng + HX, is strongly exoergic. Our previous studies have shown that each member of the HNgX (X = halogen atom or CN/NC fragment) molecules is composed of three leading resonance structures: two ω-bonding structures (H-Ng+ :X- and H:- Ng+-X) and one long-bonding structure (H∧X). The last one paints a novel [small sigma, Greek, circumflex]-type long-bonding picture. The present study focuses on the relationship between this novel bonding motif and the unusual energetic properties. We chose HNgCO+/CS+/OSi+/CN/NC, with the formula HNgAB (Ng = He, Ar, Kr, Xe, Rn; AB = CO+/CS+/OSi+/CN/NC) as the research system. We first investigated the bonding of HNgCO+ and its analogous HNgCS+/OSi+ species using NBO/NRT methods, and quantitatively compared the bonding with that in HNgCN/NC molecules. NBO/NRT results showed that each of the HNgCO+/CS+/OSi+ molecules could be better represented as a resonance hybrid of ω-bonding and long-bonding structures, but the long-bonding is much weaker than that in HNgCN/NC molecules. Furthermore, we introduced the long-bonding concept into the rationalization of the high-energy properties, and found a good correlation between the highly exothermic two-body dissociation channel and the long-bond order, bH-A. We also found that the long-bond order is highly tunable for these noble-gas hydrides due to its dependence on the nature of the electronegative AB fragments or the central noble-gas atoms, Ng. On the basis of these results, we could optimize the energetic properties by changing the long-bonding motif of our studied molecules. Overall, this study shows that the long-bonding model provides an easy way to rationalize and modulate the unusual energy properties of noble-gas hydrides, and that it is helpful to predict some noble-gas hydrides as potential energetic materials.

Engineering Improvements in a Bacterial Therapeutic Delivery System for Breast Cancer

DTIC Science & Technology

2009-09-01

curve is observed on the other platform (Supplementary Figure 2H). Although it is not the object of this article to explore a physical explanation for...light-directed oligonucleotide microarrays using a digital micromirror array.. Nat Biotechnol, 17(10), 974–978. [12] Matveeva, O. V., Shabalina, S. A...Rouillard, J. M., Whittam, T. S., Gulari, E., Tiedje, J. M., and Hashsham, S. A. (2006) On- chip non-equilibrium dissociation curves and dissociation

Adsorption and dissociation of sulfur-based toxic gas molecules on silicene nanoribbons: a quest for high-performance gas sensors and catalysts.

PubMed

Walia, Gurleen Kaur; Randhawa, Deep Kamal Kaur

2018-03-16

The adsorption behavior of sulfur-based toxic gases (H 2 S and SO 2 ) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restricting its dimensions into one dimension, construction of nanoribbons, and by introduction of a defect, its band gap can be tuned. Pristine armchair silicene nanoribbons (P-ASiNRs) have a very low sensitivity to gas molecules. Therefore, a defect was introduced by removal of one Si atom, leading to increased sensitivity. To deeply understand the impact of the aforementioned gases on silicene nanoribbons, electronic band structures, density of states, charge transfers, adsorption energies, electron densities, current-voltage characteristics and most stable adsorption configurations were calculated. H 2 S is dissociated completely into HS and H species when adsorbed onto defective armchair silicene nanoribbons (D-ASiNRs). Thus, D-ASiNR is a likely catalyst for dissociation of the H 2 S gas molecule. Conversely, upon SO 2 adsorption, P-ASiNR acts as a suitable sensor, whereas D-ASiNR provides enhanced sensitivity compared with P-ASiNR. On the basis of these results, D-ASiNR can be expected to be a disposable sensor for SO 2 detection as well as a catalyst for H 2 S reduction. Graphical abstract Comparison of I-V characteristics of pristine and defective armchair silicene nanoribbons with H 2 S and SO 2 adsorbed on them.

Alexithymia: its prevalence and correlates in a British undergraduate sample.

PubMed

Mason, O; Tyson, M; Jones, C; Potts, S

2005-03-01

Alexithymia is characterized by a difficulty identifying and describing emotional states, as well as an externally oriented thinking style. This study investigated the prevalence of alexithymia in a British undergraduate sample and assesses its relationship to both parental bonding and dissociation. The Toronto alexithymia scale (TAS-20), the Parental Bonding Instrument (PBI), and the Dissociative Experience Scale (DES) were administered to a sample of 181 male and 190 female undergraduate students from both arts and science subjects. Rates of alexithymia were comparable with those observed in some other countries. Contrary to predictions, females were found to have higher rates than males, and the highest presence of alexithymia was in female science students. As in previous studies, alexithymia was linked to both dissociation and perceptions of a lack of maternal care, though the degree of association to the latter was small. Dissociative experiences were predicted by both maternal overprotection and difficulties identifying feelings. Some qualified support was found for the relevance of early maternal bonding to later difficulties processing emotions. The presence of greater alexithymia in females, and female science students in particular, was discussed in reference to similar observations elsewhere. There was also an understandable relationship between 'difficulty identifying feelings' (TAS) and both depersonalization/derealization and absorption (DES).

Cross-Dehydrogenative Coupling Reactions Between P(O)-H and X-H (X = S, N, O, P) Bonds.

PubMed

Hosseinian, Akram; Farshbaf, Sepideh; Fekri, Leila Zare; Nikpassand, Mohammad; Vessally, Esmail

2018-05-26

P(O)-X (X = S, N, O, P) bond-containing compounds have extensive application in medicinal chemistry, agrochemistry, and material chemistry. These useful organophosphorus compounds also have many applications in organic synthesis. In light of the importance of titled compounds, there is continuing interest in the development of synthetic methods for P(O)-X bonds construction. In the last 4 years, the direct coupling reaction of P(O)-H compounds with thiols, alcohols, and amines/amides has received much attention because of the atom-economic character. This review aims to give an overview of new developments in cross-dehydrogenative coupling reactions between P(O)-H and X-H (X = S, N, O, P) bonds, with special emphasis on the mechanistic aspects of the reactions.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

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

Bie Haiying; Lu Jing; Yu Jiehui

Three novel thiocyanate supramolecular compounds have been synthesized and characterized by X-ray diffraction and fluorescent spectra. Compound [pipH]{sub 2}[Co(NCS){sub 4}] (pip=piperazine) 1 possesses a two-dimensional layer connected by the combination of N-H...N hydrogen bonds and weak S...S contacts. Under the same conditions, using nickel salt instead of cobalt salt as a starting material, we obtained a different two-dimensional supramolecular layer [pipH]{sub 2}[Ni(NCS){sub 4}] 2 connected by unusual N-H...S hydrogen bonds and weak S...S contacts. In order to observe the influence of the dimension of ligand on the self-assembly structure, dabco was used for substituting pip, and compound [dabcoH]{sub 2}[Ni(NCS){sub 4}]more » (dabco=1,4-Diazabicyclo[2.2.2] octane) 3 was gained, which constructed two-dimensional, highly wavy network with hourglass-shaped cavities only through N-H...S hydrogen bonds.« less

CO2 hydrate: Synthesis, composition, structure, dissociation behavior, and a comparison to structure I CH4 hydrate

USGS Publications Warehouse

Circone, S.; Stern, L.A.; Kirby, S.H.; Durham, W.B.; Chakoumakos, B.C.; Rawn, C.J.; Rondinone, A.J.; Ishii, Y.

2003-01-01

Structure I (sI) carbon dioxide (CO2) hydrate exhibits markedly different dissociation behavior from sI methane (CH4) hydrate in experiments in which equilibrated samples at 0.1 MPa are heated isobarically at 13 K/h from 210 K through the H2O melting point (273.15 K). The CO2 hydrate samples release only about 3% of their gas content up to temperatures of 240 K, which is 22 K above the hydrate phase boundary. Up to 20% is released by 270 K, and the remaining CO2 is released at 271.0 plusmn; 0.5 K, where the sample temperature is buffered until hydrate dissociation ceases. This reproducible buffering temperature for the dissociation reaction CO2??nH2O = CO2(g) + nH2O(1 to s) is measurably distinct from the pure H2O melting point at 273.15 K, which is reached as gas evolution ceases. In contrast, when si CH4 hydrate is heated at the same rate at 0.1 MPa, >95% of the gas is released within 25 K of the equilibrium temperature (193 K at 0.1 MPa). In conjunction with the dissociation study, a method for efficient and reproducible synthesis of pure polycrystalline CO2 hydrate with suitable characteristics for material properties testing was developed, and the material was characterized. CO2 hydrate was synthesized from CO2 liquid and H2O solid and liquid reactants at pressures between 5 and 25 MPa and temperatures between 250 and 281 K. Scanning electron microscopy (SEM) examination indicates that the samples consist of dense crystalline hydrate and 50-300 ??m diameter pores that are lined with euhedral cubic hydrate crystals. Deuterated hydrate samples made by this same procedure were analyzed by neutron diffraction at temperatures between 4 and 215 K; results confirm that complete conversion of water to hydrate has occurred and that the measured unit cell parameter and thermal expansion are consistent with previously reported values. On the basis of measured weight gain after synthesis and gas yields from the dissociation experiments, approximately all cages in the hydrate structure are filled such that n ??? 5.75.

Chemisorbed monolayers of corannulene penta-thioethers on gold.

PubMed

Angelova, Polina; Solel, Ephrath; Parvari, Galit; Turchanin, Andrey; Botoshansky, Mark; Gölzhäuser, Armin; Keinan, Ehud

2013-02-19

Penta(tert-butylthio)corannulene and penta(4-dimethylaminophenylthio)corannulene form highly stable monolayers on gold surfaces, as indicated by X-ray photoelectron spectroscopy (XPS). Formation of these homogeneous monolayers involves multivalent coordination of the five sulfur atoms to gold with the peripheral alkyl or aryl substituents pointing away from the surface. No dissociation of C-S bonds upon binding could be observed at room temperature. Yet, the XPS experiments reveal strong chemical bonding between the thioether groups and gold. Temperature-dependent XPS study shows that the thermal stability of the monolayers is higher than the typical stability of self-assembled monolayers (SAMs) of thiolates on gold.

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.

Ambient pressure XPS and IRRAS investigation of ethanol steam reforming on Ni–CeO 2(111) catalysts: An in situ study of C–C and O–H bond scission

DOE PAGES

Liu, Zongyuan; Duchon, Tomas; Wang, Huanru; ...

2016-03-31

Ambient-Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Infrared Reflection Absorption Spectroscopy (AP-IRRAS) have been used to elucidate the active sites and mechanistic steps associated with the ethanol steam reforming reaction (ESR) over Ni–CeO 2(111) model catalysts. Our results reveal that surface layers of the ceria substrate are both highly reduced and hydroxylated under reaction conditions while the small supported Ni nanoparticles are present as Ni 0/NixC. A multifunctional, synergistic role is highlighted in which Ni, CeO x and the interface provide an ensemble effect in the active chemistry that leads to H 2. Ni 0 is the active phase leading tomore » both C–C and C–H bond cleavage in ethanol and it is also responsible for carbon accumulation. On the other hand, CeO x is important for the deprotonation of ethanol/water to ethoxy and OH intermediates. The active state of CeO x is a Ce 3+(OH) x compound that results from extensive reduction by ethanol and the efficient dissociation of water. Additionally, we gain an important insight into the stability and selectivity of the catalyst by its effective water dissociation, where the accumulation of surface carbon can be mitigated by the increased presence of surface OH groups. As a result, the co-existence and cooperative interplay of Ni 0 and Ce 3+(OH) x through a metal–support interaction facilitate oxygen transfer, activation of ethanol/water as well as the removal of coke.« less

Copper-catalyzed aerobic oxidative N-S bond functionalization for C-S bond formation: regio- and stereoselective synthesis of sulfones and thioethers.

PubMed

Li, Xianwei; Xu, Yanli; Wu, Wanqing; Jiang, Chang; Qi, Chaorong; Jiang, Huanfeng

2014-06-23

A regio- and stereoselective synthesis of sulfones and thioethers by means of Cu(I)-catalyzed aerobic oxidative N-S bond cleavage of sulfonyl hydrazides, followed by cross-coupling reactions with alkenes and aromatic compounds to form the C sp 2-S bond, is described herein. N2 and H2O are the byproducts of this transformation, thus offering an environmentally benign process with a wide range of potential applications in organic synthesis and medicinal chemistry. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural changes of a-CNx thin films induced by thermal annealing

NASA Astrophysics Data System (ADS)

Aziz, Siti Aisyah Abd; Awang, Rozidawati

2018-04-01

In this work, amorphous carbon nitride (a-CNx) thin films were deposited by radio frequency plasma enhanced chemical vapor deposition (RF-PECVD) technique at different RF powers of 60, 70, 80, 90 and 100 W for 30 min. These films were prepared using a mixture of acetylene (C2H2) at 20 sccm and nitrogen (N2) gases at 50 sccm. The films were then annealed at 400 °C in a quartz tube furnace in argon (Ar) gas. The chemical bondings of the film were analyzed by Fourier Transform Infra-red Spectroscopy (FTIR) while surface morphology and film roughness were determined by Atomic Force Microscopy (AFM). The FTIR analysis reveals that annealing resulted in the loss of C-H and C-N bonds and formation of graphitic sp2C cluster with the dissociation of N and C in the films. AFM indicates that the film surface becomes less rough which effectually enhances structural modifications and the rearrangement of the microstructure of the films after annealing.

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

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

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE PAGES

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

2017-07-17

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Density functional study on structure and stability of bimetallic AuNZn (N<=6) clusters and their cations

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Neukermans, Sven; Janssens, Ewald; Silverans, Roger E.; Lievens, Peter

2003-10-01

A systematic study on the structure and stability of zinc doped gold clusters has been performed by density functional theory calculations. All the lowest-energy isomers found have a planar structure and resemble pure gold clusters in shape. Stable isomers tend to equally delocalize valence s electrons of the constituent atoms over the entire structure and maximize the number of Au-Zn bonds in the structure. This is because the Au-Zn bond is stronger than the Au-Au bond and gives an extra σ-bonding interaction by the overlap between vacant Zn 4p and valence Au 6s(5d) orbitals. No three-dimensional isomers were found for Au5Zn+ and Au4Zn clusters containing six delocalized valence electrons. This result reflects that these clusters have a magic number of delocalized electrons for two-dimensional systems. Calculated vertical ionization energies and dissociation energies as a function of the cluster size show odd-even behavior, in agreement with recent mass spectrometric observations [Tanaka et al., J. Am. Chem. Soc. 125, 2862 (2003)].

Effect of site-directed mutagenesis of His373 of yeast enolase on some of its physical and enzymatic properties.

PubMed

Brewer, J M; Glover, C V; Holland, M J; Lebioda, L

1997-06-20

The X-ray structure of yeast enolase shows His373 interacting with a water molecule also held by residues Glu168 and Glu211. The water molecule is suggested to participate in the catalytic mechanism (Lebioda, L. and Stec, B. (1991) Biochemistry 30, 2817-2822). Replacement of His373 with asparagine (H373N enolase) or phenylalanine (H373F enolase) reduces enzymatic activity to ca. 10% and 0.0003% of the native enzyme activity, respectively. H373N enolase exhibits a reduced Km for the substrate, 2-phosphoglycerate, and produces the same absorbance changes in the chromophoric substrate analogues TSP1 and AEP1, relative to native enolase. H373F enolase binds AEP less strongly, producing a smaller absorbance change than native enolase, and reacts very little with TSP. H373F enolase dissociates to monomers in the absence of substrate; H373N enolase subunit dissociation is less than H373F enolase but more than native enolase. Substrate and Mg2+ increase subunit association in both mutants. Differential scanning calorimetric experiments indicate that the interaction with substrate that stabilizes enolase to thermal denaturation involves His373. We suggest that the function of His373 in the enolase reaction may involve hydrogen bonding rather than acid/base catalysis, through interaction with the Glu168/Glu211/H2O system, which produces removal or addition of hydroxyl at carbon-3 of the substrate.

Arene-mercury complexes stabilized by gallium chloride: relative rates of H/D and arene exchange.

PubMed

Branch, Catherine S; Barron, Andrew R

2002-11-27

We have previously proposed that the Hg(arene)(2)(GaCl(4))(2) catalyzed H/D exchange reaction of C(6)D(6) with arenes occurs via an electrophilic aromatic substitution reaction in which the coordinated arene protonates the C(6)D(6). To investigate this mechanism, the kinetics of the Hg(C(6)H(5)Me)(2)(GaCl(4))(2) catalyzed H/D exchange reaction of C(6)D(6) with naphthalene has been studied. Separate second-order rate constants were determined for the 1- and 2-positions on naphthalene; that is, the initial rate of H/D exchange = k(1i)[Hg][C-H(1)] + k(2i)[Hg][C-H(2)]. The ratio of k(1i)/k(2i) ranges from 11 to 2.5 over the temperature range studied, commensurate with the proposed electrophilic aromatic substitution reaction. Observation of the reactions over an extended time period shows that the rates change with time, until they again reach a new and constant second-order kinetics regime. The overall form of the rate equation is unchanged: final rate = k(1f)[Hg][C-H(1)] + k(2f)[Hg][C-H(2)]. This change in the H/D exchange is accompanied by ligand exchange between Hg(C(6)D(6))(2)(GaCl(4))(2) and naphthalene to give Hg(C(10)H(8))(2)(GaCl(4))(2,) that has been characterized by (13)C CPMAS NMR and UV-visible spectroscopy. The activation parameters for the ligand exchange may be determined and are indicative of a dissociative reaction and are consistent with our previously calculated bond dissociation for Hg(C(6)H(6))(2)(AlCl(4))(2). The initial Hg(arene)(2)(GaCl(4))(2) catalyzed reaction of naphthalene with C(6)D(6) involves the deuteration of naphthalene by coordinated C(6)D(6); however, as ligand exchange progresses, the pathway for H/D exchange changes to where the protonation of C(6)D(6) by coordinated naphthalene dominates. The site selectivity for the H/D exchange is initially due to the electrophilic aromatic substitution of naphthalene. As ligand exchange occurs, this selectivity is controlled by the activation of the naphthalene C-H bonds by mercury.

Structure of zirconocene complexes relevant for olefin catalysis: infrared fingerprint of the Zr(C(5)H(5))(2)(OH)(CH(3)CN)(+) cation in the gas phase.

PubMed

Lagutschenkov, Anita; Springer, Andreas; Lorenz, Ulrich Joseph; Maitre, Philippe; Dopfer, Otto

2010-02-11

Cationic zirconocene complexes are active species in Ziegler-Natta catalysis for olefin polymerization. Their structure and metal-ligand bond strength strongly influence their activity. In the present work, the infrared multiphoton dissociation (IRMPD) spectrum of mass selected Zr(C(5)H(5))(2)(OH)(CH(3)CN)(+) cations was obtained in the 300-1500 cm(-1) fingerprint range by coupling a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization (ESI) source and the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO). The experimental efforts are complemented by quantum chemical calculations at the MP2 and B3LYP levels using the 6-311G* basis set. Vibrational assignments of transitions observed in the IRMPD spectra to modes of the Zr-O-H, C(5)H(5), and CH(3)CN moieties are based on comparison to calculated linear absorption spectra. Both the experimental data and the calculations provide unprecedented information about structure, metal-ligand bonding, charge distribution, and binding energy of the complex.

Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Aspartic Acid Complexes with Zn2+ and Cd2.

PubMed

Boles, Georgia C; Hightower, Randy L; Coates, Rebecca A; McNary, Christopher P; Berden, Giel; Oomens, Jos; Armentrout, P B

2018-04-12

Complexes of aspartic acid (Asp) cationized with Zn 2+ : Zn(Asp-H) + , Zn(Asp-H) + (ACN) where ACN = acetonitrile, and Zn(Asp-H) + (Asp); as well as with Cd 2+ , CdCl + (Asp), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. A series of low-energy conformers for each complex was found using quantum chemical calculations to identify the structures formed experimentally. The main binding motif observed for the heavy-metal complex, CdCl + (Asp)[N,CO,CO s ], is a charge-solvated, tridentate structure, where the metal center binds to the backbone amino group and carbonyl oxygens of the backbone and side-chain carboxylic acids. Likewise, the deprotonated Zn(Asp-H) + (ACN) and Zn(Asp-H) + (Asp) complexes show comparable [N,CO - ,CO s ](ACN) and [N,CO - ,CO s ][N,CO,CO s ] coordinations, respectively. Interestingly, there was only minor spectral evidence for the analogous Zn(Asp-H) + [N,CO - ,CO s ] binding motif, even though this species is predicted to be the lowest-energy conformer. Instead, rearrangement and partial dissociation of the amino acid are observed, as spectral features most consistent with the experimental spectrum are exhibited by a four-coordinate Zn(Asp-NH 4 ) + [CO 2 - ,CO s ](NH 3 ) complex. Analysis of the mechanistic pathway leading from the predicted lowest-energy conformer to the isobaric deaminated complex is explored theoretically. Further, comparison of the current work to that of Zn 2+ and Cd 2+ complexes of asparagine (Asn) allows additional conclusions regarding populated conformers and effects of carboxamide versus carboxylic acid binding to be drawn.

Characterization of epoxy carotenoids by fast atom bombardment collision-induced dissociation MS/MS.

PubMed

Maoka, Takashi; Fujiwara, Yasuhiro; Hashimoto, Keiji; Akimoto, Naoshige

2004-02-01

The characterization and structure of epoxy carotenoids possessing 5,6-epoxy, 5,8-epoxy and 3,6-epoxy end groups conjugated to the polyene chain were investigated using high-energy fast atom bombardment collision-induced dissociation MS/MS methods. In addition to [M - 80](+*), a characteristic fragment ion of an epoxy carotenoid, product ions resulting from the cleavage of C-C bonds in the polyene chain from the epoxy end group, such as m/z 181 (b ion) and 121 (c ion), were detected. On the other hand, diagnostic ions of m/z 286 (e-H ion) and 312 (f-H ion) were observed, not in the 5,6-epoxy or 5,8-epoxy carotenoid but in the 3,6-epoxy carotenoid. These fragmentation patterns can be used to distinguish 3,6-epoxy carotenoids from 5,6-epoxy or 5,8-epoxy carotenoids. The structure of an epoxy carotenoid, 3,6-epoxy-5,6-dihydro-7',8'-didehydro-beta,beta-carotene-5,3'-diol (8), isolated from oyster, was characterized using FAB CID-MS/MS by comparing fragmentation patterns with those of related known compounds.

Cluster transformation of [Cu3(μ3-H)(μ3-BH4)((PPh2)2NH)3](BF4) to [Cu3(μ3-H)(μ2,μ1-S2CH)((PPh2)2NH)3](BF4) via reaction with CS2. X-ray structural characterisation and reactivity of cationic clusters explored by multistage mass spectrometry and computational studies.

PubMed

Ma, Howard Z; Li, Jiaye; Canty, Allan J; O'Hair, Richard A J

2017-11-07

The copper nanocluster [Cu 3 (μ 3 -H)(μ 3 -BH 4 )L Ph 3 ](BF 4 ), 1a·BF4 (L Ph = (PPh 2 ) 2 NH = dppa), can potentially react with substrates at either the coordinated hydride or borohydride sites. Reaction of 1a·BF4 with CS 2 has given rise to [Cu 3 (μ 3 -H)(μ 2 ,μ 1 -S 2 CH)L Ph 3 ](BF 4 ), (2a·BF4), which was structurally characterised using electrospray ionisation (ESI) with high-resolution mass spectrometry (HRMS), X-ray crystallography, NMR, IR and UV-Vis spectroscopy. The copper(i) atoms adopt a planar trinuclear Cu 3 geometry coordinated on the bottom face by a μ 3 -hydride, on the top face by a μ 2 ,μ 1 -dithioformate and surrounded by three bridging L Ph ligands. Reaction of 1a·BF4 with elemental sulfur gives the known cluster [Cu 4 (L Ph -H + 2S) 3 ](BF 4 ), (3·BF4), which was structurally characterised via X-ray crystallography. ESI-MS of 2a·BF4 produces [Cu 3 (H)(S 2 CH)L Ph 3 ] + and its gas-phase ion chemistry was examined under multistage mass spectrometry conditions using collision-induced dissociation (CID). The primary product, [Cu 3 (H)(S 2 CH)L Ph 2 ] + , formed via ligand loss, undergoes further fragmentation via loss of thioformaldehyde to give [Cu 3 (S)L Ph 2 ] + . DFT calculations exploring rearrangement and fragmentation of the model system [Cu 3 (H)(S 2 CH)L Me 2 ] + (L Me = (PMe 2 ) 2 NH = dmpa) provide a feasible mechanism. Thus, coupling of the coordinated hydride with the dithioformate ligands gives [Cu 3 (S 2 CH 2 )L Me 2 ] + , which then undergoes CH 2 S extrusion via C-S bond cleavage to give [Cu 3 (S)L Me 2 ] + .

Effect of gallium environment on infrared emission in Er3+-doped gallium– antimony– sulfur glasses

PubMed Central

Jiao, Qing; Li, Ge; Li, Lini; Lin, Changgui; Wang, Guoxiang; Liu, Zijun; Dai, Shixun; Xu, Tiefeng; Zhang, Qinyuan

2017-01-01

Gallium-based Ga–Sb–S sulfide glasses was elaborated and studied. A relationship between the structure, composition, and optical properties of the glass has been established. The effects of the introduction of Ga on the structure using infrared and Raman spectroscopies and on the Er3+-doped IR emission have been discussed. The results show that incorporation of Ga induced the dissociation of [SbS3] pyramids units and the formation of tetrahedral [GaS4] units. The dissolved rare earth ions are separated around the Ga–S bonding and the infrared emission quenching are controlled. Moreover, continuous introduction of Er ions into the glass forms more Er–S bonds through the further aggregation surrounding the [GaS4] units. In return, the infrared emission intensity decreased with excessive Er ion addition. This phenomenon is correlated with the recurrence concentration quenching effect induced by the increase of [GaS4] units. PMID:28106143

Enantioselective C(sp3)‒H bond activation by chiral transition metal catalysts.

PubMed

Saint-Denis, Tyler G; Zhu, Ru-Yi; Chen, Gang; Wu, Qing-Feng; Yu, Jin-Quan

2018-02-16

Organic molecules are rich in carbon-hydrogen bonds; consequently, the transformation of C-H bonds to new functionalities (such as C-C, C-N, and C-O bonds) has garnered much attention by the synthetic chemistry community. The utility of C-H activation in organic synthesis, however, cannot be fully realized until chemists achieve stereocontrol in the modification of C-H bonds. This Review highlights recent efforts to enantioselectively functionalize C(sp 3 )-H bonds via transition metal catalysis, with an emphasis on key principles for both the development of chiral ligand scaffolds that can accelerate metalation of C(sp 3 )-H bonds and stereomodels for asymmetric metalation of prochiral C-H bonds by these catalysts. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Tuning the Ground State Symmetry of Acetylenyl Radicals

PubMed Central

2015-01-01

The lowest excited state of the acetylenyl radical, HCC, is a 2Π state, only 0.46 eV above the ground state, 2Σ+. The promotion of an electron from a π bond pair to a singly occupied σ hybrid orbital is all that is involved, and so we set out to tune those orbital energies, and with them the relative energetics of 2Π and 2Σ+ states. A strategy of varying ligand electronegativity, employed in a previous study on substituted carbynes, RC, was useful, but proved more difficult to apply for substituted acetylenyl radicals, RCC. However, π-donor/acceptor substitution is effective in modifying the state energies. We are able to design molecules with 2Π ground states (NaOCC, H2NCC (2A″), HCSi, FCSi, etc.) and vary the 2Σ+–2Π energy gap over a 4 eV range. We find an inconsistency between bond order and bond dissociation energy measures of the bond strength in the Si-containing molecules; we provide an explanation through an analysis of the relevant potential energy curves. PMID:27162981

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field.

PubMed

Ren, Fu-de; Cao, Duan-lin; Shi, Wen-jing

2016-04-01

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH3NO2 → CH3ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C-NO2 bond axis, the barriers of the isomerization are lower than the C-NO2 bond dissociation energies, leading to the preferences of the isomerization over the C-NO2 bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C-NO2 bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.

DFT simulation on H2 adsorption over Ni-decorated defective h-BN nanosheets

NASA Astrophysics Data System (ADS)

Zhou, Xuan; Chu, Wei; Zhou, Yanan; Sun, Wenjing; Xue, Ying

2018-05-01

Nickel doped defective h-BN nanosheets and their potential application on hydrogen storage were explored by density functional theory (DFT) calculation. Three types of defective h-BN (SW defect, VB and VN substrates) were modeled. In comparison with the SW defect, the B or N vacancy can improve the interaction between Ni atom and h-BN nanosheet strikingly. Furthermore, the Ni-doped SW defect sheet shows chemisorption on H2 molecules, and the Hsbnd H bond is partially dissociated. While on the VB sheet, Ni adatom interacts with H2 in the range of physisorption. However, the Ni-functionalized VN sheet exhibits a desirable adsorption on H2, and the corresponding energy varies from -0.40 to -0.51 eV, which is favorable for H2 adsorption and release at ambient conditions. As a result, the VN substrate is expected to a desirable support for H2 storage. Our work provides an insight into H2 storage on Ni-functionalized defective h-BN monolayer.

Hydrogen Bond Lifetimes and Energetics for Solute-Solvent Complexes Studied with 2D-IR Vibrational Echo Spectroscopy

PubMed Central

Zheng, Junrong; Fayer, Michael D.

2008-01-01

Weak π hydrogen bonded solute-solvent complexes are studied with ultrafast two dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute-solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory. PMID:17373792

G3//BMK and Its Application to Calculation of Bond Dissociation Enthalpies.

PubMed

Zheng, Wen-Rui; Fu, Yao; Guo, Qing-Xiang

2008-08-01

On the basis of systematic examinations it was found that the BMK functional significantly outperformed the other popular density functional theory methods including B3LYP, B3P86, KMLYP, MPW1P86, O3LYP, and X3LYP for the calculation of bond dissociation enthalpies (BDEs). However, it was also found that even the BMK functional might dramatically fail in predicting the BDEs of some chemical bonds. To solve this problem, a new composite ab initio method named G3//BMK was developed by combining the strengths of both the G3 theory and BMK. G3//BMK was found to outperform the G3 and G3//B3LYP methods. It could accurately predict the BDEs of diverse types of chemical bonds in various organic molecules within a precision of ca. 1.2 kcal/mol.

Negative cooperativity in binding of muscarinic receptor agonists and GDP as a measure of agonist efficacy

PubMed Central

Jakubík, J; Janíčková, H; El-Fakahany, EE; Doležal, V

2011-01-01

BACKGROUND AND PURPOSE Conventional determination of agonist efficacy at G-protein coupled receptors is measured by stimulation of guanosine-5′-γ−thiotriphosphate (GTPγS) binding. We analysed the role of guanosine diphosphate (GDP) in the process of activation of the M2 muscarinic acetylcholine receptor and provide evidence that negative cooperativity between agonist and GDP binding is an alternative measure of agonist efficacy. EXPERIMENTAL APPROACH Filtration and scintillation proximity assays measured equilibrium binding as well as binding kinetics of [35S]GTPγS and [3H]GDP to a mixture of G-proteins as well as individual classes of G-proteins upon binding of structurally different agonists to the M2 muscarinic acetylcholine receptor. KEY RESULTS Agonists displayed biphasic competition curves with the antagonist [3H]-N-methylscopolamine. GTPγS (1 µM) changed the competition curves to monophasic with low affinity and 50 µM GDP produced a similar effect. Depletion of membrane-bound GDP increased the proportion of agonist high-affinity sites. Carbachol accelerated the dissociation of [3H]GDP from membranes. The inverse agonist N-methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP. Carbachol affected both GDP association with and dissociation from Gi/o G-proteins but only its dissociation from Gs/olf G-proteins. CONCLUSIONS AND IMPLICATIONS These findings suggest the existence of a low-affinity agonist-receptor conformation complexed with GDP-liganded G-protein. Also the negative cooperativity between GDP and agonist binding at the receptor/G-protein complex determines agonist efficacy. GDP binding reveals differences in action of agonists versus inverse agonists as well as differences in activation of Gi/o versus Gs/olf G-proteins that are not identified by conventional GTPγS binding. PMID:20958290

Conformational Specific Infrared and Ultraviolet Spectroscopy of Cold YA(D-Pro)AA\\cdotH+ Ions: a Sterochemical "twist" on the Proline Effect

NASA Astrophysics Data System (ADS)

Harrilal, Christopher P.; DeBlase, Andrew F.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

2016-06-01

The "proline effect" is a well-known fragmentation phenomenon in mass spectrometry, in which y-fragments are produced preferentially over b-fragments during the collision induced dissociation of protonated L-proline containing peptide ions. This specific fragmentation channel is favored because of the high basicity of the secondary amine intermediate and the ring instability in alternative bn+ products [ASMS 2014, 25, 1705]. In contrast, peptides containing the D-Pro stereoisomer have been shown to largely favor the production of b4+ ions over y3+ ions. This strongly suggests that differences in the conformational preferences between the D-Pro and L-Pro diastereomers are likely to be responsible but structural evidence has been lacking to date. Using tandem mass spectrometry and IR-UV double resonant action spectroscopy we are able to compare the 3D structures of cold [YA(D-Pro)AA+H]+ to [YA(L-Pro)AA+H]+ ions. The UV action spectra reveals two major conformers in [YA(D-Pro)AA+H]+ and one major conformer in [YA(L-Pro)AA+H]+. Clear differences in the hydrogen bonding patterns are apparent between the two conformers observed in the D-Pro specie which are both distinct from the L-Pro diastereomer. Furthermore, conformer and diastereomer specific photofragmentation patterns are observed. It is also noted that a ten-fold photofragment enhancement unique to one of the D-Pro conformers is observed upon absorption of a resonant IR photon after UV excitation. Differences in the excited state photophysics between the two D-Pro conformers suggest that vibrational excitation of S1 turns on coupling to the dissociative -Tyr channel in one conformer, while this coupling is already present in the vibronic ground state of the other. Calculated harmonic spectra (M052X/6-31+G*) of conformers obtained from Monte Carlo searches to the experimental spectra.

QTAIM charge density study of natural cinnamic acids

NASA Astrophysics Data System (ADS)

González Moa, María J.; Mandado, Marcos; Mosquera, Ricardo A.

2006-06-01

B3LYP/6-311++G(2d,2p) 6d ionization potentials and O-H bond dissociation energies of natural cinnamic acids are consistent with an important antioxidant activity. The QTAIM analysis indicates that: (i) the benzene ring and the propenoic acid fragment of cinnamic acids behave as independent π systems; (ii) the ionization process consists in a loss of nearly 1 a.u. of π electron density by the atoms involved in HOMO accompanied by a reorganization of σ electron density that is mostly provided by the remaining atoms.

Infrared spectroscopy of extreme coordination: the carbonyls of U(+) and UO(2)(+).

PubMed

Ricks, Allen M; Gagliardi, Laura; Duncan, Michael A

2010-11-17

Uranium and uranium dioxide carbonyl cations produced by laser vaporization are studied with mass-selected ion infrared spectroscopy in the C-O stretching region. Dissociation patterns, spectra, and quantum chemical calculations establish that the fully coordinated ions are U(CO)(8)(+) and UO(2)(CO)(5)(+), with D(4d) square antiprism and D(5h) pentagonal bipyramid structures. Back-bonding in U(CO)(8)(+) causes a red-shifted CO stretch, but back-donation is inefficient for UO(2)(CO)(5)(+), producing a blue-shifted CO stretch characteristic of nonclassical carbonyls.

Photodissociation dynamics of propanal and isobutanal: The Norrish Type I pathway

NASA Astrophysics Data System (ADS)

Harrison, Aaron W.; Kable, Scott H.

2018-04-01

The Norrish Type I photodissociation of two aliphatic aldehydes, propanal and isobutanal, has been investigated using velocity-map imaging. The HCO photoproduct of this reaction was probed using a 1+1 resonance-enhanced multiphoton ionization scheme via the 3p2Π Rydberg state. The velocity map images of HCO+ were collected across a range of photolysis energies for both species from 30 500 to 33 000 cm-1 (λ = 312-327 nm). The corresponding translational energy distributions show that the majority of the available energy goes into the translational motion of the products (55%-68%) with this fraction increasing as the T1 barrier is approached. Analysis of the translational energy distributions was also used to determine the aldehyde α C-C bond dissociation energies which were found to be 339.8 ± 2.5 and 331.2 ± 2.5 kJ/mol for propanal and isobutanal, respectively. These values were also found to be in good agreement with the computed dissociation energies using G4 and CCSD(T)/aug-cc-pVTZ//M062X/aug-cc-pVTZ levels of theory. Furthermore, these dissociation energies, combined with the known ΔfH (0 K) of the reaction products, provided the ΔfH (0 K) of propanal and isobutanal which were calculated to be -167.3 ± 2.5 and -184.0 ± 2.5 kJ/mol, respectively.

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

Barc, B.; Ryszka, M.; Spurrell, J.

Multi-photon ionization (MPI) of the RNA base uracil has been studied in the wavelength range 220–270 nm, coinciding with excitation to the S{sub 2}(ππ*) state. A fragment ion at m/z = 84 was produced by 2-photon absorption at wavelengths ≤232 nm and assigned to C{sub 3}H{sub 4}N{sub 2}O{sup +} following CO abstraction. This ion has not been observed in alternative dissociative ionization processes (notably electron impact) and its threshold is close to recent calculations of the minimum activation energy for a ring opening conical intersection to a σ(n-π)π* closed shell state. Moreover, the predicted ring opening transition leaves a COmore » group at one end of the isomer, apparently vulnerable to abstraction. An MPI mass spectrum of uracil-water clusters is presented for the first time and compared with an equivalent dry measurement. Hydration enhances certain fragment ion pathways (particularly C{sub 3}H{sub 3}NO{sup +}) but represses C{sub 3}H{sub 4}N{sub 2}O{sup +} production. This indicates that hydrogen bonding to water stabilizes uracil with respect to neutral excited-state ring opening.« less

Initial mechanisms for the unimolecular decomposition of electronically excited bisfuroxan based energetic materials.

PubMed

Yuan, Bing; Bernstein, Elliot R

2017-01-07

Unimolecular decomposition of energetic molecules, 3,3'-diamino-4,4'-bisfuroxan (labeled as A) and 4,4'-diamino-3,3'-bisfuroxan (labeled as B), has been explored via 226/236 nm single photon laser excitation/decomposition. These two energetic molecules, subsequent to UV excitation, create NO as an initial decomposition product at the nanosecond excitation energies (5.0-5.5 eV) with warm vibrational temperature (1170 ± 50 K for A, 1400 ± 50 K for B) and cold rotational temperature (<55 K). Initial decomposition mechanisms for these two electronically excited, isolated molecules are explored at the complete active space self-consistent field (CASSCF(12,12)/6-31G(d)) level with and without MP2 correction. Potential energy surface calculations illustrate that conical intersections play an essential role in the calculated decomposition mechanisms. Based on experimental observations and theoretical calculations, NO product is released through opening of the furoxan ring: ring opening can occur either on the S 1 excited or S 0 ground electronic state. The reaction path with the lowest energetic barrier is that for which the furoxan ring opens on the S 1 state via the breaking of the N1-O1 bond. Subsequently, the molecule moves to the ground S 0 state through related ring-opening conical intersections, and an NO product is formed on the ground state surface with little rotational excitation at the last NO dissociation step. For the ground state ring opening decomposition mechanism, the N-O bond and C-N bond break together in order to generate dissociated NO. With the MP2 correction for the CASSCF(12,12) surface, the potential energies of molecules with dissociated NO product are in the range from 2.04 to 3.14 eV, close to the theoretical result for the density functional theory (B3LYP) and MP2 methods. The CASMP2(12,12) corrected approach is essential in order to obtain a reasonable potential energy surface that corresponds to the observed decomposition behavior of these molecules. Apparently, highly excited states are essential for an accurate representation of the kinetics and dynamics of excited state decomposition of both of these bisfuroxan energetic molecules. The experimental vibrational temperatures of NO products of A and B are about 800-1000 K lower than previously studied energetic molecules with NO as a decomposition product.

Oxygen adsorption onto pure and doped Al surfaces--the role of surface dopants.

PubMed

Lousada, Cláudio M; Korzhavyi, Pavel A

2015-01-21

Using density functional theory (DFT) with the PBE0 density functional we investigated the role of surface dopants in the molecular and dissociative adsorption of O2 onto Al clusters of types Al50, Al50Alad, Al50X and Al49X, where X represents a dopant atom of the following elements Si, Mg, Cu, Sc, Zr, and Ti. Each dopant atom was placed on the Al(111) surface as an adatom or as a substitutional atom, in the last case replacing a surface Al atom. We found that for the same dopant geometry, the closer is the ionization energy of the dopant element to that of elemental Al, the more exothermic is the dissociative adsorption of O2 and the stronger are the bonds between the resulting O atoms and the surface. Additionally we show that the Mulliken concept of electronegativity can be applied in the prediction of the dissociative adsorption energy of O2 on the doped surfaces. The Mulliken modified second-stage electronegativity of the dopant atom is proportional to the exothermicity of the dissociative adsorption of O2. For the same dopant element in an adatom position the dissociation of O2 is more exothermic when compared to the case where the dopant occupies a substitutional position. These observations are discussed in view of the overlap population densities of states (OPDOS) computed as the overlap between the electronic states of the adsorbate O atoms and the clusters. It is shown that a more covalent character in the bonding between the Al surface and the dopant atom causes a more exothermic dissociation of O2 and stronger bonding with the O atoms when compared to a more ionic character in the bonding between the dopant and the Al surface. The extent of the adsorption site reconstruction is dopant atom dependent and is an important parameter for determining the mode of adsorption, adsorption energy and electronic structure of the product of O2 adsorption. The PBE0 functional could predict the existence of the O2 molecular adsorption product for many of the cases investigated here.

Photoisomerization and photodissociation dynamics of reactive free radicals

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

Bise, Ryan T.

2000-08-01

The photofragmentation pathways of chemically reactive free radicals have been examined using the technique of fast beam photofragment translational spectroscopy. Measurements of the photodissociation cross-sections, product branching ratios, product state energy distributions, and angular distributions provide insight into the excited state potential energy surfaces and nonadiabatic processes involved in the dissociation mechanisms. Photodissociation spectroscopy and dynamics of the predissociativemore » $$\\tilde{A}$$ 2A 1 and $$\\tilde{B}$$ 2A 2 states of CH 3S have been investigated. At all photon energies, CH 3 + S( 3P j), was the main reaction channel. The translational energy distributions reveal resolved structure corresponding to vibrational excitation of the CH 3 umbrella mode and the S( 3P j) fine-structure distribution from which the nature of the coupled repulsive surfaces is inferred. Dissociation rates are deduced from the photofragment angular distributions, which depend intimately on the degree of vibrational excitation in the C-S stretch. Nitrogen combustion radicals, NCN, CNN and HNCN have also been studied. For all three radicals, the elimination of molecular nitrogen is the primary reaction channel. Excitation to linear excited triplet and singlet electronic states of the NCN radical generates resolved vibrational structure of the N 2 photofragment. The relatively low fragment rotational excitation suggests dissociation via a symmetric C 2V transition state. Resolved vibrational structure of the N 2 photofragment is also observed in the photodissociation of the HNCN radical. The fragment vibrational and rotational distributions broaden with increased excitation energy. Simple dissociation models suggest that the HNCN radical isomerizes to a cyclic intermediate (c-HCNN) which then dissociates via a tight cyclic transition state. In contrast to the radicals mentioned above, resolved vibrational structure was not observed for the ICNN radical due to extensive fragment rotational excitation, suggesting that intermediate bent states are strongly coupled along the dissociation pathway. The measurements performed in this Thesis have additionally refined the heats of formation and bond dissociation energies of these radicals and have unambiguously confirmed and added to the known electronic spectroscopy.« less

Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

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

Machesky, Michael L.; Predota, M.; Wesolowski, David J

The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming thatmore » the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite ({alpha}-SnO{sub 2}) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.« less

Reactions of methyl groups on a non-reducible metal oxide: The reaction of iodomethane on stoichiometric α-Cr 2O 3(0001)

DOE PAGES

Dong, Yujung; Brooks, John D.; Chen, Tsung-Liang; ...

2015-06-10

The reaction of iodomethane on the nearly stoichiometric α-Cr 2O 3(0001) surface produces gas phase ethylene, methane, and surface iodine adatoms. The reaction is first initiated by the dissociation of iodomethane into surface methyl fragments, -CH 3, and iodine adatoms. Methyl fragments bound at surface Cr cation sites undergo a rate-limiting dehydrogenation reaction to methylene, =CH 2. The methylene intermediates formed from methyl dehydrogenation can then undergo coupling reactions to produce ethylene via two principle reaction pathways: (1) direct coupling of methylene and (2) methylene insertion into the methyl surface bond to form surface ethyl groups which undergo β-H eliminationmore » to produce ethylene. The liberated hydrogen also combines with methyl groups to form methane. Iodine adatoms from the dissociation of iodomethane deactivate the surface by simple site blocking of the surface Cr 3+ cations.« less

Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

NASA Astrophysics Data System (ADS)

Medzihradszky, Katalin F.; Bohlen, Christopher J.

2012-05-01

A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

Kinetic, Spectroscopic, and Theoretical Assessment of Associative and Dissociative Methanol Dehydration Routes in Zeolites

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

Jones, Andrew J.; Iglesia, Enrique

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy-mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy–entropy trade-offs merely reflect the intervening role of temperature in activation free energies and the prevalence of moremore » complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H-bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.« less

Mutual control of axial and equatorial ligands: model studies with [Ni]-bacteriochlorophyll-a.

PubMed

Yerushalmi, Roie; Noy, Dror; Baldridge, Kim K; Scherz, Avigdor

2002-07-17

Modification of the metal's electronic environment by ligand association and dissociation in metalloenzymes is considered cardinal to their catalytic activity. We have recently presented a novel system that utilizes the bacteriochlorophyll (BChl) macrocycle as a ligand and reporter. This system allows for charge mobilization in the equatorial plane and experimental estimate of changes in the electronic charge density around the metal with no modification of the metal's chemical environment. The unique spectroscopy, electrochemistry and coordination chemistry of [Ni]-bacteriochlorophyll ([Ni]-BChl) enable us to follow directly fine details and steps involved in the function of the metal redox center. This approach is utilized here whereby electro-chemical reduction of [Ni]-BChl to the monoanion [Ni]-BChl(-) results in reversible dissociation of biologically relevant axial ligands. Similar ligand dissociation was previously detected upon photoexcitation of [Ni]-BChl (Musewald, C.; Hartwich, G.; Lossau, H.; Gilch, P.; Pollinger-Dammer, F.; Scheer, H.; Michel-Beyerle, M. E. J. Phys. Chem. B 1999, 103, 7055-7060 and Noy, D.; Yerushalmi, R.; Brumfeld, V.; Ashur, I.; Baldridge, K. K.; Scheer, H.; Scherz, A. J. Am. Chem. Soc. 2000, 122, 3937-3944). The electrochemical measurements and quantum mechanical (QM) calculations performed here for the neutral, singly reduced, monoligated, and singly reduced, monoligated [Ni]-BChl suggest the following: (a) Electroreduction, although resulting in a pi anion [Ni]-BChl(-) radical, causes electron density migration to the [Ni]-BChl core. (b) Reduction of nonligated [Ni]-BChl does not change the macrocycle conformation, whereas axial ligation results in a dramatic expansion of the metal core and a flattening of the highly ruffled macrocycle conformation. (c) In both the monoanion and singly excited [Ni]-BChl ([Ni]-BChl*), the frontier singly occupied molecular orbital (SOMO) has a small but nonnegligible metal character. Finally, (d) computationally, we found that a reduction of [Ni]-BChl*imidazole results in a weaker metal-axial ligand bond. Yet, it remains weakly bound in the gas phase. The experimentally observed ligand dissociation is accounted for computationally when solvation is considered. On the basis of the experimental observations and QM calculations, we propose a mechanism whereby alterations in the equatorial pi system and modulation of sigma bonding between the axial ligands and the metal core are mutually correlated. Such a mechanism highlights the dynamic role of axial ligands in regulating the activity of metal centers such as factor F430 (F430), a nickel-based coenzyme that is essential in methanogenic archea.

Interaction of benzene thiol and thiolate with small gold clusters.

PubMed

Letardi, Sara; Cleri, Fabrizio

2004-06-01

We studied the interaction between benzene thiol and thiolate molecules, and gold clusters made of 1 to 3 atoms, by means of ab initio density functional theory in the local density approximation. We find that the thiolate is energetically more stable than the thiol, however the process of detachment of H from the thiol appears to be possibly mediated by the intermediate step of H chemisorption on Au. Cleavage of the S-H bond is accompanied by a 90 degrees rotation of the molecule around the S-Au bond, showing a strong steric specificity. Such a rotation is induced by the relative energy shift of the S atom p orbitals with respect to the benzene pi ring and the Au d orbitals. By analyzing the correlation of the bond energy, bond lengths, and HOMO-LUMO gap with the number of S-Au bonds, we find that the thiolate S atom appears to prefer a low-coordination condition on Au clusters. (c) 2004 American Institute of Physics.

Molecular Structures and Sorption Mechanisms of Biochars as Heterogeneous Carbon Materials

NASA Astrophysics Data System (ADS)

Chen, Baoliang; Chen, Zaiming; Xiao, Xin; Fang, Qile

2015-04-01

Surface functional groups such as carboxyl play a vital role in the environmental applications of biochar as a soil amendment. However, the quantification of oxygen-containing groups on a biochar surface still lacks systematical investigation. An integrated method combining chemical and spectroscopic techniques was established to quantitatively identify the chemical states, dissociation constants (pKa), and contents of oxygen-containing groups on dairy manure-derived biochars prepared at 100-700 °C. The dissociation pH of carboxyl groups on the biochar surface covered a wide range of pH values (pH 2-11), due to the varied structural micro-environments and chemical states. For low temperature biochars (≤350 °C), carboxyl existed not only as hydrogen-bonded carboxyl and unbonded carboxyl groups but also formed esters at the surface of biochars. The esters consumed OH‒ via saponification in the alkaline pH region and enhanced the dissolution of organic matter from biochars. For high temperature biochars (≥500 °C), esters came from carboxyl were almost eliminated via carbonization (ester pyrolysis), while lactones were developed. The surface density of carboxyl groups on biochars decreased sharply with the increase of the biochar-producing temperature, but the total contents of the surface carboxyls for different biochars were comparable (with a difference < 3-fold) as a result of the expanded surface area at high pyrolytic temperatures. Understanding the wide pKa ranges and the abundant contents of carboxyl groups on biochars is a prerequisite to recognition of the multi-functional applications and biogeochemical cycling of biochars. A schematic diagram for the dissociation of acid/base groups on biochar surfaces and their related functions was depicted. The protonated biochars favor inorganic anion adsorption and ionizable organic chemical sorption, while the deprotonated biochars favor cationic nutrient retention, heavy metal immobilization, and the release of dissolved materials. For low temperature biochars (i.e., DM100, DM250 and DM350), the acid/base group dissociation directly controls the pH buffering properties of biochars. The resulting surface charges regulate biochars in nutrient retention, sorption/immobilization of hazardous pollutants and biochar particle dispersing properties. Meanwhile, dissociation of acid/base groups affects carbon and silica biogeochemical cycling by regulating the release of organic matter from the cleavage of esters and dissolution of the Si-containing minerals. For high temperature biochars (i.e., DM500 and DM700), the effect of acid/base dissociation on organic matter dissolution is eliminated, but other functions are similar. CGs are the major acid/base groups on biochar surfaces. In field applications, such abundant CGs are worthy of concern in terms of multiple functions of biochars, such as soil pH adjustment, soil nutrient retention, and toxic metals immobilization.

Guided ion beam and theoretical studies of the bond energy of SmS+

NASA Astrophysics Data System (ADS)

Armentrout, P. B.; Demireva, Maria; Peterson, Kirk A.

2017-12-01

Previous work has shown that atomic samarium cations react with carbonyl sulfide to form SmS+ + CO in an exothermic and barrierless process. To characterize this reaction further, the bond energy of SmS+ is determined in the present study using guided ion beam tandem mass spectrometry. Reactions of SmS+ with Xe, CO, and O2 are examined. Results for collision-induced dissociation processes with all three molecules along with the endothermicity of the SmS+ + CO → Sm+ + COS exchange reaction are combined to yield D0(Sm+-S) = 3.37 ± 0.20 eV. The CO and O2 reactions also yield a SmSO+ product, with measured endothermicities that indicate D0(SSm+-O) = 3.73 ± 0.16 eV and D0(OSm+-S) = 1.38 ± 0.27 eV. The SmS+ bond energy is compared with theoretical values characterized at several levels of theory, including CCSD(T) complete basis set extrapolations using all-electron basis sets. Multireference configuration interaction calculations with explicit spin-orbit calculations along with composite thermochemistry using the Feller-Peterson-Dixon method and all-electron basis sets were also explored for SmS+, and for comparison, SmO, SmO+, and EuO.

Guided ion beam and theoretical studies of the bond energy of SmS.

PubMed

Armentrout, P B; Demireva, Maria; Peterson, Kirk A

2017-12-07

Previous work has shown that atomic samarium cations react with carbonyl sulfide to form SmS + + CO in an exothermic and barrierless process. To characterize this reaction further, the bond energy of SmS + is determined in the present study using guided ion beam tandem mass spectrometry. Reactions of SmS + with Xe, CO, and O 2 are examined. Results for collision-induced dissociation processes with all three molecules along with the endothermicity of the SmS + + CO → Sm + + COS exchange reaction are combined to yield D 0 (Sm + -S) = 3.37 ± 0.20 eV. The CO and O 2 reactions also yield a SmSO + product, with measured endothermicities that indicate D 0 (SSm + -O) = 3.73 ± 0.16 eV and D 0 (OSm + -S) = 1.38 ± 0.27 eV. The SmS + bond energy is compared with theoretical values characterized at several levels of theory, including CCSD(T) complete basis set extrapolations using all-electron basis sets. Multireference configuration interaction calculations with explicit spin-orbit calculations along with composite thermochemistry using the Feller-Peterson-Dixon method and all-electron basis sets were also explored for SmS + , and for comparison, SmO, SmO + , and EuO.

Quasiparticle Interfacial Level Alignment of Highly Hybridized Frontier Levels: H2O on TiO2(110)

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

Migani, Annapaola; Mowbray, Duncan J.; Zhao, Jin

Knowledge of the frontier levels’ alignment prior to photoirradiation is necessary to achieve a complete quantitative description of H2O photocatalysis on TiO2(110). Although H2O on rutile TiO2(110) has been thoroughly studied both experimentally and theoretically, a quantitative value for the energy of the highest H2O occupied levels is still lacking. For experiment, this is due to the H2O levels being obscured by hybridization with TiO2(110) levels in the difference spectra obtained via ultraviolet photoemission spectroscopy (UPS). For theory, this is due to inherent difficulties in properly describing many-body effects at the H2O–TiO2(110) interface. Using the projected density of states (DOS)more » from state-of-the-art quasiparticle (QP) G0W0, we disentangle the adsorbate and surface contributions to the complex UPS spectra of H2O on TiO2(110). We perform this separation as a function of H2O coverage and dissociation on stoichiometric and reduced surfaces. Due to hybridization with the TiO2(110) surface, the H2O 3a1 and 1b1 levels are broadened into several peaks between 5 and 1 eV below the TiO2(110) valence band maximum (VBM). These peaks have both intermolecular and interfacial bonding and antibonding character. We find the highest occupied levels of H2O adsorbed intact and dissociated on stoichiometric TiO2(110) are 1.1 and 0.9 eV below the VBM. We also find a similar energy of 1.1 eV for the highest occupied levels of H2O when adsorbed dissociatively on a bridging O vacancy of the reduced surface. In both cases, these energies are significantly higher (by 0.6 to 2.6 eV) than those estimated from UPS difference spectra, which are inconclusive in this energy region. Finally, we apply self-consistent QPGW (scQPGW1) to obtain the ionization potential of the H2O–TiO2(110) interface.« less

Quasiparticle interfacial level alignment of highly hybridized frontier levels: H2O on TiO2(110).

PubMed

Migani, Annapaola; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje

2015-01-13

Knowledge of the frontier levels' alignment prior to photoirradiation is necessary to achieve a complete quantitative description of H2O photocatalysis on TiO2(110). Although H2O on rutile TiO2(110) has been thoroughly studied both experimentally and theoretically, a quantitative value for the energy of the highest H2O occupied levels is still lacking. For experiment, this is due to the H2O levels being obscured by hybridization with TiO2(110) levels in the difference spectra obtained via ultraviolet photoemission spectroscopy (UPS). For theory, this is due to inherent difficulties in properly describing many-body effects at the H2O-TiO2(110) interface. Using the projected density of states (DOS) from state-of-the-art quasiparticle (QP) G0W0, we disentangle the adsorbate and surface contributions to the complex UPS spectra of H2O on TiO2(110). We perform this separation as a function of H2O coverage and dissociation on stoichiometric and reduced surfaces. Due to hybridization with the TiO2(110) surface, the H2O 3a1 and 1b1 levels are broadened into several peaks between 5 and 1 eV below the TiO2(110) valence band maximum (VBM). These peaks have both intermolecular and interfacial bonding and antibonding character. We find the highest occupied levels of H2O adsorbed intact and dissociated on stoichiometric TiO2(110) are 1.1 and 0.9 eV below the VBM. We also find a similar energy of 1.1 eV for the highest occupied levels of H2O when adsorbed dissociatively on a bridging O vacancy of the reduced surface. In both cases, these energies are significantly higher (by 0.6 to 2.6 eV) than those estimated from UPS difference spectra, which are inconclusive in this energy region. Finally, we apply self-consistent QPGW (scQPGW1) to obtain the ionization potential of the H2O-TiO2(110) interface.

The dissociation of liquid silica at high pressure and temperature

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

Hicks, D; Boehly, T; Eggert, J

2005-11-17

Liquid silica at high pressure and temperature is shown to undergo significant structural modifications and profound changes in its electronic properties. Temperature measurements on shock waves in silica at 70-1000 GPa indicate that the specific heat of liquid SiO{sub 2} rises well above the Dulong-Petit limit, exhibiting a broad peak with temperature that is attributable to the growing structural disorder caused by bond-breaking in the melt. The simultaneous sharp rise in optical reflectivity of liquid SiO{sub 2} indicates that dissociation causes the electrical and therefore thermal conductivities of silica to attain metallic-like values of 1-5 x 10{sup 5} S/m andmore » 24-600 W/m.K respectively.« less

Toward improving CO2 dissociation and conversion to methanol via CO-hydrogenation on Cu(100) surface by introducing embedded Co nanoclusters as promoters: A DFT study

NASA Astrophysics Data System (ADS)

Qiu, Mei; Tao, Huilin; Li, Yali; Li, Yi; Ding, Kaining; Huang, Xin; Chen, Wenkai; Zhang, Yongfan

2018-01-01

The dissociation and hydrogenation of CO2 on Cu(100) surfaces that are modified by introducing Co nanoclusters with different size into the top layer have been investigated using density functional theory method. Our results show that on all surfaces the Co atoms are the sites for the adsorption of CO2, and in the early stage of introducing Co dopant, the chemisorption behavior of CO2 is sensitive to the amount of Co atom. According to the predicted pathways for the dissociation of CO2 to CO, it is interesting that the energy barrier decreases first and then increases as more Co atoms are dispersed on the surface, forming a ;V; shape. The minimum energy barrier of CO2 decomposition is predicted on the Cu(100) surface that contains four Co atoms aggregated together on the top layer, namely Co4/Cu(100) bimetallic surface. The most favorable reaction pathway for the hydrogenation of CO to methanol on such surface is further determined, which follows the sequence of CO* → HCO* → H2CO* → H3CO* → H3COH*, and the rate-limiting step is the hydrogenation of H3CO species with an activation barrier of 106.4 kJ/mol. It is noted that with respect to the pure Cu(100), since more stronger Cosbnd O adsorption bonds are formed on the Co-modified surface, the stability of formaldehyde intermediate is significantly enhanced. Correspondingly, the introducing of Co4 cluster tends to improve the productivity and selectivity towards methanol synthesis on Cu(100) surface.

DFT study of CO2 conversion on InZr3(110) surface.

PubMed

Zhang, Minhua; Dou, Maobin; Yu, Yingzhe

2017-11-01

Methanol and methane synthesis from CO 2 hydrogenation on a InZr 3 (110) surface has been studied using density functional theory calculations. The CO 2 can be chemically adsorbed via a polydentated configuration and the H 2 molecule can dissociate to H atoms spontaneously. The methanol is primarily formed via the HCOO route instead of the RWGS route, due to its higher activation barrier of 1.35 eV for HCO hydrogenation. In the HCOO route, the adsorbed CO 2 consecutively hydrogenates to form HCOO, H 2 COO and the H 3 CO species. The H 3 COH is produced via the reaction of H 3 CO with a surface OH group. Furthermore, the C-O bonds of CO, CHO, CH 2 O and CH 3 O species prefer to dissociate to C, CH, CH 2 CH 3 and surface O species. Methane is formed via the hydrogenation of CH x (x = 0-3) monomers with the highest activation barrier of 1.19 eV for CH 3 hydrogenation, which is higher than that of the hydrogenation of H 2 COO in methanol synthesis via the HCOO route. The surface O species formed during CO 2 hydrogenation reacts with the adsorbed H 2 molecule to produce an OH group which reacts with a surface H atom to form H 2 O with an activation barrier of 1.13 eV, which then desorbs to the gas phase. Our calculated results indicate that the InZr 3 alloy is a potential candidate catalyst for CO 2 utilization and conversion.

TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12

NASA Astrophysics Data System (ADS)

Kozlowski, Pawel; Liu, Hui; Kornobis, Karina; Lodowski, Piotr; Jaworska, Maria

2013-12-01

Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ*Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a MLCT (metal-to-ligand charge transfer) and a σ bonding-ligand charge transfer (SBLCT) states.

Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

NASA Astrophysics Data System (ADS)

Anders, Christian; Urbassek, Herbert M.

2017-01-01

Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

Synthesis, characterization and single crystal structures of chiral Schiff base and its tetranuclear palladium complex with Pdsbnd Osbnd Pd bridging and Pdsbnd Pd bonds

NASA Astrophysics Data System (ADS)

Rajegowda, H. R.; Kumar, P. Raghavendra; Hosamani, Amar; Butcher, R. J.; Naveen, S.; Lokanath, N. K.

2018-03-01

A new chiral Schiff base ligand 2-{N-[(2S)-(1-hydroxy-3-phenylpropan-2-yl]ethanimidoyl} phenol ((S)sbnd H2L) was obtained by acid catalyzed condensation of (2S)-(-)-2-amino-3-phenyl-1-propanol with 2‧-hydroxyacetophenone. The palladium complex was prepared by treating a solution of (S)sbnd H2L in acetone with a solution of Na2PdCl4 in water in 1:1 M ratio. The new ligand and its complex were characterized by FT-IR, 1H, 13C{1H} NMR spectroscopy, polarimetry and elemental analysis and their molecular structures were determined by single crystal X-ray diffraction. Both the compounds crystallizes in monoclinic system in the space group P21. There exists an intra [Osbnd H ⋯N (1.62(5) Å)] and intermolecular [Osbnd H ⋯O (1.53(5) Å) and Csbnd H ⋯O (2.59 Å)] hydrogen bonding and secondary interactions in the crystal of (S)sbnd H2L. The structure of the palladium complex was found very interesting wherein the ligand coordinated to metal center as tridentate dianionic (O-, N, O-) fashion, (S)-L, resulting in a tetranuclear palladium cluster, [Pd4((S)-L)4]. In these supramolecular structures phenolate oxygen coordinated to Pd(II) ion as Pdsbnd O terminal bonds [1.934(12) - 1.977(11) Å] and the alkoxide oxygen coordinated as Pdsbnd Osbnd Pd bridging bonds [1.993(11) - 2.012(12) Å]. The Pdsbnd N bond lengths found were in the range of 1.949(13) to 1.919(12) Å. There exists two asymmetric tetranuclear complex molecules in its crystal lattice. There exists very strong metal-metal bond interaction, Pd(2)sbnd Pd(3) [3.0410(18) Å] and Pd(6)sbnd Pd(7) [3.0517(19) Å] respectively in the two asymmetric units.

Phase Stability and Superconductivity of Compressed Argon-Hydrogen Compounds from First-Principles

NASA Astrophysics Data System (ADS)

Ishikawa, Takahiro; Nakanishi, Akitaka; Shimizu, Katsuya; Oda, Tatsuki

2017-12-01

We present the phase stability and superconductivity of Ar-H compounds under high pressure predicted by first-principles calculations and a genetic algorithm technique for crystal structure search. We found that insulating ArH4, earlier predicted to be metalized at 350 GPa, survives up to 700 GPa owing to the transition into a new phase Pnma at around 250 GPa and then decomposes into metallic ArH2 and pure solid hydrogen. At around 1500 GPa, the bonding form of ArH2 is changed by the dissociation of H2 molecules at the interstitial site of the argon lattice, and antibonding orbitals are partially filled, which causes an increase in the density of states at the Fermi level. Results showed that electron-phonon coupling is enhanced and the superconducting critical temperature is increased from 0.2 to 67 K.

Fascinating transformations of donor-acceptor complexes of group 13 metal (Al, Ga, In) derivatives with nitriles and isonitriles: from monomeric cyanides to rings and cages.

PubMed

Timoshkin, Alexey Y; Schaefer, Henry F

2003-08-20

Formation of the donor-acceptor complexes of group 13 metal derivatives with nitriles and isonitriles X(3)M-D (M = Al,Ga,In; X = H,Cl,CH(3); D = RCN, RNC; R = H,CH(3)) and their subsequent reactions have been theoretically studied at the B3LYP/pVDZ level of theory. Although complexation with MX(3) stabilizes the isocyanide due to the stronger M-C donor-acceptor bond, this stabilization (20 kJ mol(-1) at most) is not sufficient to make the isocyanide form more favorable. Relationships between the dissociation enthalpy DeltaH degrees (298)(diss), charge-transfer q(CT), donor-acceptor bond energy E(DA), and the shift of the vibrational stretching mode of the CN group upon coordination Deltaomega(CN) have been examined. For a given metal center, there is a good correlation between the energy of the donor-acceptor bond and the degree of a charge transfer. Prediction of the DeltaH degrees (298)(diss) on the basis of the shift of CN stretching mode is possible within limited series of cyanide complexes (for the fixed M,R); in contrast, complexes of the isocyanides exhibit very poor Deltaomega(CN) - DeltaH degrees (298)(diss) correlation. Subsequent X ligand transfer and RX elimination reactions yielding monomeric (including donor-acceptor stabilized) and variety of oligomeric cage and ring compounds with [MN]n, [MC]n, [MNC]n cores have been considered and corresponding to thermodynamic characteristics have been obtained for the first time. Monomeric aluminum isocyanides X(2)AlNC are more stable compared to Al-C bonded isomers; for gallium and indium situation is reversed, in qualitative agreement with Pearson's HSAB concept. Substitution of X by CN in MX(3) increases the dissociation enthalpy of the MX(2)CN-NH(3) complex compared to that for MX(3)-NH(3), irrespective of the substituent X. Mechanisms of the initial reaction of the X transfer have been studied for the case X = R = H. The process of hydrogen transfer from the metal to the carbon atom in H(3)M-CNH is thermodynamically favorable and is likely to be intramolecular. By contrast, intramolecular hydrogen transfer in H(3)M-NCH has been definitely ruled out. Head-to-tail dimeric species [H(3)M-(NC)H](2) are formed exothermically and exhibit low H.H distances, which can assist in hydrogen transfer, and are likely to be the starting point for H(2) elimination. Elimination of H(2), CH(4), and C(2)H(6) from X(3)M-(NC)R adducts is very favorable thermodynamically; by contrast, elimination of HCl and CH(3)Cl is highly unfavorable even if formation of oligomer species takes place. Thus, high-temperature generation of gas-phase rings and clusters has been predicted viable in the cases X = H,CH(3) and their presence in the reactor media should not be neglected. Moderate stability of [HMCH(2)NH](4) clusters (especially in the cases M = Ga, In) makes these species viable intermediates of gas-phase reactions. Their formation may be responsible for the carbon contamination in the course of metal organic chemical vapor deposition processes of group 13 binary nitrides.

Combined Experimental and Computational Study on the Unimolecular Decomposition of JP-8 Jet Fuel Surrogates. II: n-Dodecane (n-C12H26).

PubMed

Zhao, Long; Yang, Tao; Kaiser, Ralf I; Troy, Tyler P; Ahmed, Musahid; Ribeiro, Joao Marcelo; Belisario-Lara, Daniel; Mebel, Alexander M

2017-02-16

We investigated temperature-dependent products in the pyrolysis of helium-seeded n-dodecane, which represents a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) aviation fuel. The experiments were performed in a high temperature chemical reactor over a temperature range of 1200 K to 1600 K at a pressure of 600 Torr, with in situ identification of the nascent products in a supersonic molecular beam using single photon vacuum ultraviolet (VUV) photoionization coupled with the analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF). For the first time, the initial decomposition products of n-dodecane-including radicals and thermally labile closed-shell species-were probed in experiments, which effectively exclude mass growth processes. A total of 15 different products were identified, such as molecular hydrogen (H 2 ), C2 to C7 1-alkenes [ethylene (C 2 H 4 ) to 1-heptene (C 7 H 14 )], C1-C3 radicals [methyl (CH 3 ), ethyl (C 2 H 5 ), allyl (C 3 H 5 )], small C1-C3 hydrocarbons [acetylene (C 2 H 2 ), allene (C 3 H 4 ), methylacetylene (C 3 H 4 )], as well as the reaction products [1,3-butadiene (C 4 H 6 ), 2-butene (C 4 H 8 )] attributed to higher-order processes. Electronic structure calculations carried out at the G3(CCSD,MP2)//B3LYP/6-311G(d,p) level of theory combined with RRKM/master equation of rate constants for relevant reaction steps showed that n-dodecane decomposes initially by a nonterminal C-C bond cleavage and producing a mixture of alkyl radicals from ethyl to decyl with approximately equal branching ratios. The alkyl radicals appear to be unstable under the experimental conditions and to rapidly dissociate either directly by C-C bond β-scission to produce ethylene (C 2 H 4 ) plus a smaller 1-alkyl radical with the number of carbon atoms diminished by two or via 1,5-, 1,6-, or 1,7- 1,4-, 1,9-, or 1,8-H shifts followed by C-C β-scission producing alkenes from propene to 1-nonene together with smaller 1-alkyl radicals. The stability and hence the branching ratios of higher alkenes decrease as temperature increases. The C-C β-scission continues all the way to the propyl radical (C 3 H 7 ), which dissociates to methyl (CH 3 ) plus ethylene (C 2 H 4 ). In addition, at higher temperatures, another mechanism can contribute, in which hydrogen atoms abstract hydrogen from C 12 H 26 producing various n-dodecyl radicals and these radicals then decompose by C-C bond β-scission to C3 to C11 alkenes.

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation.

PubMed

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W; Harding, Lawrence B; Hase, William L; Klippenstein, Stephen J

2018-05-07

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C 2 H 4 O 3 , the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H 2 COO) and formaldehyde (H 2 CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (∼30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation

NASA Astrophysics Data System (ADS)

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W.; Harding, Lawrence B.; Hase, William L.; Klippenstein, Stephen J.

2018-05-01

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C2H4O3, the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H2COO) and formaldehyde (H2CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (˜30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Hydrogen bonded C-H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis

NASA Astrophysics Data System (ADS)

Isaev, A. N.

2016-03-01

Hydrogen bonded C-H···Y complexes formed by H2O, H2S molecules, hydrogen halides, and halogen-ions with methane, halogen substituted methane as well as with the C2H2 and NCH molecules were studied at the MP2/aug-cc-pVDZ level. The structure of NBOs corresponding to lone pair of acceptor Y, n Y, and vacant anti-σ-bond C-H of proton donor was analyzed and estimates of second order perturbation energy E(2) characterizing donor-acceptor n Y → σ C-H * charge-transfer interaction were obtained. Computational results for complexes of methane and its halogen substituted derivatives show that for each set of analogous structures, the EnY→σ*C-H (2) energy tends to grow with an increase in the s-component percentage in the lone pair NBO of acceptor Y. Calculations for different C···Y distances show that the equilibrium geometries of complexes lie in the region where the E(2) energy is highest and it changes symbatically with the length of the covalent E-H bond when the R(C···Y) distance is varied. The performed analysis allows us to divide the hydrogen bonded complexes into two groups, depending on the pattern of overlapping for NBOs of the hydrogen bridge.

Interaction of sulfur dioxide with titanium-carbide nanoparticles and surfaces: A density functional study

NASA Astrophysics Data System (ADS)

Liu, Ping; Rodriguez, José A.

2003-11-01

In the control of environmental pollution, metal carbides are potentially useful for trapping and destroying sulfur dioxide (SO2). In the present study, the density functional theory was employed to study the surface structures and electronic properties of the adsorbed SO2 on titanium carbides: metcar Ti8C12, nanocrystal Ti14C13, and a bulk TiC(001) surface. The geometries and orientations of SO2 were fully optimized on all these substrates. Our calculations show that, in spite of the high C/Ti ratio and C2 groups, metcar Ti8C12 exhibits extremely high activity towards SO2. The S-O bonds of SO2 spontaneously break on Ti8C12. The products of the decomposition reaction (S, O) interact simultaneously with Ti and C sites. The C atoms are not simple spectators, and their participation in the dissociation of SO2 is a key element for the energetics of this process. Nanocrystal Ti14C13 also displays a strong interaction with SO2. Although the dissociation of SO2 on Ti14C13 cannot proceed as easily as that on Ti8C12, it could occur by thermal activation even at very low temperature. SO2 is weakly bonded with the bulk TiC(001) surface. By thermal activation the dissociation of SO2 on a TiC(001) surface may also take place but it should be much more difficult than that on Ti14C13. Therefore, we suggest that the carbide nanoparticles (Ti8C12 and Ti14C13) should have special chemical activity towards SO2 removal associated with their "magic" structures.

N-H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers.

PubMed

Wategaonkar, Sanjay; Bhattacherjee, Aditi

2018-05-03

The N-H···S hydrogen bond, even though classified as an unconventional hydrogen bond, is found to bear important structural implications on protein structure and folding. In this article, we report a gas-phase study of the N-H···S hydrogen bond between the model compounds of histidine (benzimidazole, denoted BIM) and methionine (dimethyl sulfide, diethyl sulfide, and tetrahydrothiophene, denoted Me 2 S, Et 2 S, and THT, respectively). A combination of laser spectroscopic methods such as laser-induced fluorescence (LIF), two-color resonant two-photon ionization (2cR2PI), and fluorescence depletion by infrared spectroscopy (FDIR) is used in conjunction with DFT and ab initio calculations to characterize the nature of this prevalent H-bonding interaction in simple bimolecular complexes. A single conformer was found to exist for the BIM-Me 2 S complex, whereas the BIM-Et 2 S and BIM-THT complexes showed the presence of three and two conformers, respectively. These conformers were characterized on the basis of IR spectroscopic results and electronic structure calculations. Quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO), and energy decomposition (NEDA) analyses were performed to investigate the nature of the N-H···S H-bond. Comparison of the results with the N-H···O type of interactions in BIM and indole revealed that the strength of the N-H···S H-bond is similar to N-H···O in these binary gas-phase complexes.

Interfacial Connection Mechanisms in Calcium-Silicate-Hydrates/Polymer Nanocomposites: A Molecular Dynamics Study.

PubMed

Zhou, Yang; Hou, Dongshuai; Manzano, Hegoi; Orozco, Carlos A; Geng, Guoqing; Monteiro, Paulo J M; Liu, Jiaping

2017-11-22

Properties of organic/inorganic composites can be highly dependent on the interfacial connections. In this work, molecular dynamics, using pair-potential-based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium-silicate-hydrates (C-S-H) and organic functional groups of three different polymer species. The calculation results suggest that the affinity between C-S-H and polymers is influenced by the polarity of the functional groups and the diffusivity and aggregation tendency of the polymers. In the interfaces, the calcium counterions from C-S-H act as the coordination atoms in bridging the double-bonded oxygen atoms in the carboxyl groups (-COOH), and the Ca-O connection plays a dominant role in binding poly(acrylic acid) (PAA) due to the high bond strength defined by time-correlated function. The defective calcium-silicate chains provide significant numbers of nonbridging oxygen sites to accept H-bonds from -COOH groups. As compared with PAA, the interfacial interactions are much weaker between C-S-H and poly(vinyl alcohol) (PVA) or poly(ethylene glycol) (PEG). Predominate percentage of the -OH groups in the PVA form H-bonds with inter- and intramolecule, which results in the polymer intertwining and reduces the probability of H-bond connections between PVA and C-S-H. On the other hand, the inert functional groups (C-O-C) in poly(ethylene glycol) (PEG) make this polymer exhibit unfolded configurations and move freely with little restrictions. The interaction mechanisms interpreted in this organic-inorganic interface can give fundamental insights into the polymer modification of C-S-H and further implications to improving cement-based materials from the genetic level.

Lysosome-oriented, dual-stage pH-responsive polymeric micelles for β-Lapachone delivery.

PubMed

Zhou, Yinjian; Dong, Ying; Huang, Gang; Wang, Yiguang; Huang, Xiaonan; Zhang, Fayun; Boothman, David A; Gao, Jinming; Liang, Wei

2016-12-14

β-Lapachone (β-lap), a novel anticancer agent, is bioactivated by NADP(H):quinone oxidoreductase 1 (NQO1), an enzyme over-expressed in numerous tumors, including lung, pancreas, breast, and prostate cancers. Fast renal clearance and methemaglobinemia / hemolytic side-effects from the clinical formulation (β-lap-hydroxyl propyl-β-cyclodextrin complex) hindered its clinical translation. Here, we investigated a dual model pH responsive polymers for β-lap delivery. Three pH-sensitive linkages, including acylhydrazone, ketal and imine bonds for β-lap prodrug syntheses result in an aryl imine linkage the most optimal linkage. The conversion to β-lap was 2.8%, 4.5% and 100% at pH 7.4, 6.5 and 5.0 in 8 h, respectively. β-lap aryl imine prodrug conjugated ultra pH-sensitive (UPS) polymer reached high β-lap loading density (8.3%) and exhibited dual-stages responsiveness to pH variation. In pHs under pH t , at stage I, micelle immediately dissociation and subsequently entering stage II, micelles start quickly release β-lap. In vitro release study showed that the micelles constantly release β-lap (14.9 ± 0.1%) at pHs above pH t in 72 h, whereas boosted release of β-lap (79.4 ± 1.2%) at pH 5.0. Micelle intracellular distribution predominantly in the lysosome organelle guaranteed their pH responsive dissociation and subsequently β-lap controlled release. The M-P micelles retained NQO1-dependent cytotoxicity in A549 lung cancer cells, similar to free drug in both efficacy and mechanism of cell death. The lysosome-oriented dual-stage ultra pH responsive β-lap prodrug micelles potentially offer an alternative nanotherapeutic strategy for lung, as well as other NQO1+ cancer therapies.

Third-order Douglas-Kroll Relativistic Coupled-Cluster Theory through Connected Single, Double, Triple, and Quadruple Substitutions: Applications to Diatomic and Triatomic Hydrides

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

Hirata, So; Yanai, Takeshi; De Jong, Wibe A.

Coupled-cluster methods including through and up to the connected single, double, triple, and quadruple substitutions (CCSD, CCSDT, and CCSDTQ) have been automatically derived and implemented for sequential and parallel executions for use in conjunction with a one-component third-order Douglas-Kroll (DK3) approximation for relativistic corrections. A combination of the converging electron-correlation methods, the accurate relativistic reference wave functions, and the use of systematic basis sets tailored to the relativistic approximation has been shown to predict the experimental singlet-triplet separations within 0.02 eV (0.5 kcal/mol) for five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+), the experimental bond lengths within 0.002 angstroms,more » rotational constants within 0.02 cm-1, vibration-rotation constants within 0.01 cm-1, centrifugal distortion constants within 2 %, harmonic vibration frequencies within 9 cm-1 (0.4 %), anharmonic vibrational constants within 2 cm-1, and dissociation energies within 0.03 eV (0.8 kcal/mol) for twenty diatomic hydrides (BH, CH, NH, OH, FH, AlH, SiH, PH, SH, ClH, GaH, GeH, AsH, SeH, BrH, InH, SnH, SbH, TeH, and IH) containing main-group elements across the second through fifth periods of the periodic table. In these calculations, spin-orbit effects on dissociation energies, which were assumed to be additive, were estimated from the measured spin-orbit coupling constants of atoms and diatomic molecules, and an electronic energy in the complete-basis-set, complete-electron-correlation limit has been extrapolated by the formula which was in turn based on the exponential-Gaussian extrapolation formula of the basis set dependence.« less

3D H-bonding networks self-assembly from pyridinium derivatives and bis(maleonitriledithiolato)zincate(II)

NASA Astrophysics Data System (ADS)

Ren, Xiaoming; Xie, Jingli; Chen, Youcun; Kremer, Reinhard Karl

2003-11-01

The two ion-pair complexes, [pyH] 2[Zn(mnt) 2] ( 1) and [4,4'-bipyH 2]-[Zn(mnt) 2] ( 2), were synthesized, where mnt 2- denotes maleonitriledithiolate, and [pyH] +, [4,4'-bipyH 2] 2+ represent pyridinium and diprotonated 4,4'-bipyridinium, respectively. Their single crystal structures show that there are strong bifurcated H-bonding interactions between the cations of the pyridinium derivative and the [Zn(mnt) 2] 2- anions in both 1 and 2. The bifurcated H-bonding interactions between the N-H of the pyridiniums and the CN groups of the mnt 2- ligands give rise to a 2D layered H-bonding network, the adjacent layers come together in such way as mutual embrace to give a tight pack, thus 2D hydrogen-bonding sheets further develop into 3D H-bonding networks through weak C-H⋯S and π⋯π stacking interactions in 1. As for 2, the cations and anions connect into several types of H-bonding macrorings ([2+2], [3+3] and [4+4]), these H-bonding macrorings fuse to extend into 2D layered structure, the interpenetration between [3+3] and [4+4] type H-bonding macrorings in the adjacent layers give further rise to novel 3D extended H-bonding networks, in which there are clearly parallel stacks of cations and the chelate rings of anions.

Photodissociation of cis-, trans-, and 1,1-dichloroethylene in the ultraviolet range: characterization of Cl((2)P(J)) elimination.

PubMed

Hua, Linqiang; Zhang, Xiaopeng; Lee, Wei-Bin; Chao, Meng-Hsuan; Zhang, Bing; Lin, King-Chuen

2010-01-14

By using photofragment velocity imaging detection coupled with a (2 + 1) resonance-enhanced multiphoton ionization technique, the elimination channel of spin-orbit chlorine atoms in photodissociation of cis-, trans-, and 1,1-dichloroethylene at two photolysis wavelengths of 214.5 and 235 nm is investigated. Translational energy and angular distributions of Cl((2)P(J)) fragmentation are acquired. The Cl((2)P(J)) fragments are produced by two competing channels. The fast dissociation component with higher translational energy is characterized by a Gaussian distribution, resulting from a curve crossing of the initially excited (pi, pi*) state to nearby repulsive (pi, sigma*) and/or (n, sigma*). In contrast, the slow component with a lower translational energy is characterized by a Boltzmann distribution, which dissociates on the vibrationally hot ground state relaxed from the (pi, pi*) state via internal conversion. cis-C(2)H(2)Cl(2) is found to have a larger branching of Boltzmann component than the other two isomers. The fraction of available energy partitioning into translation increases along the trend of cis- < trans- < 1,1-C(2)H(2)Cl(2). This trend may be fitted by a rigid radical model and interpreted by means of a torque generated during the C-Cl bond cleavage. The anisotropy parameters are determined, and the transition dipole moments are expected to be essentially along the C horizontal lineC bond axis. The results are also predicted theoretically. The relative quantum yields of Cl((2)P(J)) have a similar value for the three isomers at the two photolysis wavelengths.

Hydrogen interaction kinetics of Ge dangling bonds at the Si{sub 0.25}Ge{sub 0.75}/SiO{sub 2} interface

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

Stesmans, A., E-mail: andre.stesmans@fys.kuleuven.be; Nguyen Hoang, T.; Afanas'ev, V. V.

2014-07-28

The hydrogen interaction kinetics of the GeP{sub b1} defect, previously identified by electron spin resonance (ESR) as an interfacial Ge dangling bond (DB) defect occurring in densities ∼7 × 10{sup 12} cm{sup −2} at the SiGe/SiO{sub 2} interfaces of condensation grown (100)Si/a-SiO{sub 2}/Ge{sub 0.75}Si{sub 0.25}/a-SiO{sub 2} structures, has been studied as function of temperature. This has been carried out, both in the isothermal and isochronal mode, through defect monitoring by capacitance-voltage measurements in conjunction with ESR probing, where it has previously been demonstrated the defects to operate as negative charge traps. The work entails a full interaction cycle study, comprised of analysis ofmore » both defect passivation (pictured as GeP{sub b1}-H formation) in molecular hydrogen (∼1 atm) and reactivation (GeP{sub b1}-H dissociation) in vacuum. It is found that both processes can be suitably described separately by the generalized simple thermal (GST) model, embodying a first order interaction kinetics description based on the basic chemical reactions GeP{sub b1} + H{sub 2} → GeP{sub b1}H + H and GeP{sub b1}H → GeP{sub b1} + H, which are found to be characterized by the average activation energies E{sub f} = 1.44 ± 0.04 eV and E{sub d} = 2.23 ± 0.04 eV, and attendant, assumedly Gaussian, spreads σE{sub f} = 0.20 ± 0.02 eV and σE{sub d} = 0.15 ± 0.02 eV, respectively. The substantial spreads refer to enhanced interfacial disorder. Combination of the separately inferred kinetic parameters for passivation and dissociation results in the unified realistic GST description that incorporates the simultaneous competing action of passivation and dissociation, and which is found to excellently account for the full cycle data. For process times t{sub a} ∼ 35 min, it is found that even for the optimum treatment temperature ∼380 °C, only ∼60% of the GeP{sub b1} system can be electrically silenced, still far remote from device grade level. This ineffectiveness is concluded, for the major part, to be a direct consequence of the excessive spreads in the activation energies, ∼2–3 times larger than for the Si DB P{sub b} defects at the standard thermal (111)Si/SiO{sub 2} interface which may be easily passivated to device grade levels, strengthened by the reduced difference between the average E{sub f} and E{sub d} values. Exploring the guidelines of the GST model indicates that passivation can be improved by decreasing T{sub an} and attendant enlarging of t{sub a}, however, at best still leaving ∼2% defects unpassivated even for unrealistically extended anneal times. The average dissociation energy E{sub d} ∼ 2.23 eV, concluded as representing the GeP{sub b1}-H bond strength, is found to be smaller than the SiP{sub b}-H one, characterized by E{sub d} ∼ 2.83 eV. An energy deficiency is encountered regarding the energy sum rule inherent to the GST-model, the origin of which is substantiated to lie with a more complex nature of the forward passivation process than basically depicted in the GST model. The results are discussed within the context of theoretical considerations on the passivation of interfacial Ge DBs by hydrogen.« less

The adsorption of methyl, acetylide, chlorine and phosphorus trifluoride on zinc oxide: A quantum-chemical study

NASA Astrophysics Data System (ADS)

Rodriguez, JoséA.

1989-11-01

The chemisorptions of methyl (CH 3), acetylide (H-CC), chlorine (Cl) and phosphorus trifluoride (PF 3) on ZnO(0001) and of Cl on ZnO(101¯0) have been examined employing semi-em- pirical quantum-chemical calculations (INDO/S) and neutral clusters of limited size (Zn 13O 13). CH 3, H-CC and Cl appear as strong electron acceptors when adsorbed on Zn sites of ZnO. The chemisorption bonds of these molecules are almost pure σ-bonds and are largely localized on the adsorption site. An increase in the work function of ZnO surfaces upon adsorption of CH 3, H-CC and Cl is predicted. The PF 3 molecule is a very weak acceptor of electrons when adsorbed on a-top sites of ZnO(0001). The bonding mechanism of CH 3, H-CC, Cl and PF 3 on the ZnO(0001) surface involves primarily the HOMO and LUMO of the adsorbate and the Zn(4s,4p) orbitals of the substrate. The effects of chemisorption on the C-H bonds of CH 3 and H-CC, the C-C bond of H-CC, and the P-F bonds of PF 3 are examined. On the basis of these INDO/S results, the possible UPS spectra for CH 3, H-CC and PF 3 adsorbed on ZnO(0001) are discussed and compared with results for adsorption on transition-metal surfaces. A general picture of the chemisorption bond of alkyls, acetylides, alkoxides, carboxylates and halogens on a-top sites of ZnO(0001) is obtained by comparing our results for adsorption of CH 3, H-CC and Cl with those previously reported for adsorption of methoxy, OH and formate.

Cocrystal assembled by 1,4-diiodotetrafluorobenzene and phenothiazine based on C-I...π/N/S halogen bond and other assisting interactions.

PubMed

Wang, Hui; Jin, Wei Jun

2017-04-01

The halogen-bonded cocrystal of 1,4-diiodotetrafluorobenzene (1,4-DITFB) with the butterfly-shape non-planar heterocyclic compound phenothiazine (PHT) was successfully assembled by the conventional solution-based method. X-ray single-crystal diffraction analysis reveals a 3:2 stoichiometric ratio for the cocrystal (1,4-DITFB/PHT), and the cocrystal structure is constructed via C-I...π, C-I...N and C-I...S halogen bonds as well as other assisting interactions (e.g. C-H...F/S hydrogen bond, C-H...H-C and C-F...F-C bonds). The small shift of the 1,4-DITFB vibrational band to lower frequencies in FT-IR and Raman spectroscopies provide evidence to confirm the existence of the halogen bond. In addition, the non-planarity of the PHT molecule in the cocrystal results in PHT emitting weak phosphorescence and relatively strong delayed fluorescence. Thus, a wide range of delayed fluorescence and weak phosphorescence could play a significant role in selecting a proper π-conjugated system to engineer functional cocrystal and luminescent materials by halogen bonds.

Synthesis, structure, and thermal properties of soluble hydrazinium germanium(IV) and tin(IV) selenide salts.

PubMed

Mitzi, David B

2005-05-16

The crystal structures of two hydrazinium-based germanium(IV) and tin(IV) selenide salts are determined. (N(2)H(5))(4)Ge(2)Se(6) (1) [I4(1)cd, a = 12.708(1) Angstroms, c = 21.955(2) Angstroms, Z = 8] and (N(2)H(4))(3)(N(2)H(5))(4)Sn(2)Se(6) (2) [P, a = 6.6475(6) Angstroms, b = 9.5474(9) Angstroms, c = 9.8830(10) Angstroms, alpha = 94.110(2) degrees, beta = 99.429(2) degrees, gamma = 104.141(2) degrees, Z = 1] each consist of anionic dimers of edge-sharing metal selenide tetrahedra, M(2)Se(6)(4-) (M = Ge or Sn), separated by hydrazinium cations and, for 2, additional neutral hydrazine molecules. Substantial hydrogen bonding exists among the hydrazine/hydrazinium molecules as well as between the hydrazinium cations and the selenide anions. Whereas the previously reported tin(IV) sulfide system, (N(2)H(5))(4)Sn(2)S(6), decomposes cleanly to microcrystalline SnS(2) when heated to 200 degrees C in an inert atmosphere, higher temperatures (>300 degrees C) are required to dissociate selenium from 1 and 2 for the analogous preparations of single-phase metal selenides. The metal chalcogenide salts are highly soluble in hydrazine, as well as in a variety of amines and DMSO, highlighting the potential usefulness of these compounds as precursors for the solution deposition of the corresponding metal chalcogenide films.

The near ultraviolet photodissociation dynamics of 2- and 3-substituted thiophenols: Geometric vs. electronic structure effects

NASA Astrophysics Data System (ADS)

Marchetti, Barbara; Karsili, Tolga N. V.; Cipriani, Maicol; Hansen, Christopher S.; Ashfold, Michael N. R.

2017-07-01

The near ultraviolet spectroscopy and photodissociation dynamics of two families of asymmetrically substituted thiophenols (2- and 3-YPhSH, with Y = F and Me) have been investigated experimentally (by H (Rydberg) atom photofragment translational spectroscopy) and by ab initio electronic structure calculations. Photoexcitation in all cases populates the 11ππ* and/or 11πσ* excited states and results in S-H bond fission. Analyses of the experimentally obtained total kinetic energy release (TKER) spectra yield the respective parent S-H bond strengths, estimates of ΔE(A ˜ -X ˜ ), the energy splitting between the ground (X ˜ ) and first excited (A ˜ ) states of the resulting 2-(3-)YPhS radicals, and reveal a clear propensity for excitation of the C-S in-plane bending vibration in the radical products. The companion theory highlights roles for both geometric (e.g., steric effects and intramolecular H-bonding) and electronic (i.e., π (resonance) and σ (inductive)) effects in determining the respective parent minimum energy geometries, and the observed substituent and position-dependent trends in S-H bond strength and ΔE(A ˜ -X ˜ ). 2-FPhSH shows some clear spectroscopic and photophysical differences. Intramolecular H-bonding ensures that most 2-FPhSH molecules exist as the syn rotamer, for which the electronic structure calculations return a substantial barrier to tunnelling from the photoexcited 11ππ* state to the 11πσ* continuum. The 11ππ* ← S0 excitation spectrum of syn-2-FPhSH thus exhibits resolved vibronic structure, enabling photolysis studies with a greater parent state selectivity. Structure apparent in the TKER spectrum of the H + 2-FPhS products formed when exciting at the 11ππ* ← S0 origin is interpreted by assuming unintended photoexcitation of an overlapping resonance associated with syn-2-FPhSH(v33 = 1) molecules. The present data offer tantalising hints that such out-of-plane motion influences non-adiabatic coupling in the vicinity of a conical intersection (between the 11πσ* and ground state potentials at extended S-H bond lengths) and thus the electronic branching in the eventual radical products.

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework.

PubMed

Machesky, Michael L; Predota, Milan; Wesolowski, David J; Vlcek, Lukas; Cummings, Peter T; Rosenqvist, Jörgen; Ridley, Moira K; Kubicki, James D; Bandura, Andrei V; Kumar, Nitin; Sofo, Jorge O

2008-11-04

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.

Gene-specific characterization of human histone H2B by electron capture dissociation.

PubMed

Siuti, Nertila; Roth, Michael J; Mizzen, Craig A; Kelleher, Neil L; Pesavento, James J

2006-02-01

The basis set of protein forms expressed by human cells from the H2B gene family was determined by Top Down Mass Spectrometry. Using Electron Capture Dissociation for MS/MS of H2B isoforms, direct evidence for the expression of unmodified H2B.Q, H2B.A, H2B.K/T, H2B.J, H2B.E, H2B.B, H2B.F, and monoacetylated H2B.A was obtained from asynchronous HeLa cells. H2B.A was the most abundant form, with the overall expression profile not changing significantly in cells arrested in mitosis by colchicine or during mid-S, mid-G2, G2/M, and mid-G1 phases of the cell cycle. Modest hyperacetylation of H2B family members was observed after sodium butyrate treatment.

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

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

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

Evaluation of bond strength of self-etching adhesives having different pH on primary and permanent teeth dentin.

PubMed

Ozmen, Bilal; Koyuturk, Alp Erdin; Tokay, Ugur; Cortcu, Murat; Sari, Mustafa Erhan

2015-10-16

The purpose of this in vitro study was to evaluate the dentin shear bond strength of 4 self-etching adhesives having a different pH on primary and permanent teeth dentin. The occlusal enamel was removed from 60 freshly extracted third molar and 60 primary second molar human teeth, which were randomly separated into 4 groups (n = 15). Four adhesive systems were applied: G-Bond (GC Corporation, Tokyo, Japan, pH: 1.5), Futura Bond M (Voco, Cuxhaver, Germany, pH: 1.4), Adper Prompt L-Pop (3M/ESPE, St Paul, MN, USA, pH: 0.8), and Clearfil S(3) Bond (Kuraray Medical, Tokyo, Japan, pH: 2.7) according to the manufacturer's instructions. After the application of dentin bonding agents, a composite resin material (Z250 Restorative A2, 3M ESPE, St. Paul, MN, USA) for permanent teeth and a compomer resin material (Dyract Extra A2, Dentsply, Konstanz, Germany) for primary teeth was applied onto the prepared dentin surfaces. The data were obtained by using a universal test machine at a crosshead speed of 1 mm/min. The mean values were compared using Tukey's multiple comparison test. Although there was no difference between adhesives on the permanent teeth, Clearfil S3 adhesive showed higher bond (18.07 ± 0.58 MPa) (P>0.05). Lower bond strength values were obtained from primary teeth and especially G-Bond adhesive (9.36 ± 0.48 MPa) (P<0.05). Self-etching adhesives with different pH and solvent types can be used successfully for permanent teeth dentin but adhesives with low pH did not provide greater shear bond strength values.

Significantly shorter Fe–S bond in cytochrome P450-I is consistent with greater reactivity relative to chloroperoxidase

DOE PAGES

Krest, Courtney M.; Silakov, Alexey; Rittle, Jonathan; ...

2015-08-03

Cytochrome P450 (P450) and chloroperoxidase (CPO) are thiolate-ligated haem proteins that catalyse the activation of carbon hydrogen bonds. The principal intermediate in these reactions is a ferryl radical species called compound I. P450 compound I (P450-I) is significantly more reactive than CPO-I, which only cleaves activated C–H bonds. In this paper, to provide insight into the differing reactivities of these intermediates, we examined CPO-I and P450-I using variable-temperature Mössbauer and X-ray absorption spectroscopies. These measurements indicate that the Fe–S bond is significantly shorter in P450-I than in CPO-I. This difference in Fe–S bond lengths can be understood in terms ofmore » variations in the hydrogen-bonding patterns within the ‘cys-pocket’ (a portion of the proximal helix that encircles the thiolate ligand). Weaker hydrogen bonding in P450-I results in a shorter Fe–S bond, which enables greater electron donation from the axial thiolate ligand. Finally, this observation may in part explain P450's greater propensity for C–H bond activation.« less

Activation of CH4 by Th(+) as studied by guided ion beam mass spectrometry and quantum chemistry.

PubMed

Cox, Richard M; Armentrout, P B; de Jong, Wibe A

2015-04-06

The reaction of atomic thorium cations with CH4 (CD4) and the collision-induced dissociation (CID) of ThCH4(+) with Xe are studied using guided ion beam tandem mass spectrometry. In the methane reactions at low energies, ThCH2(+) (ThCD2(+)) is the only product; however, the energy dependence of the cross-section is inconsistent with a barrierless exothermic reaction as previously assumed on the basis of ion cyclotron resonance mass spectrometry results. The dominant product at higher energies is ThH(+) (ThD(+)), with ThCH3(+) (ThCD3(+)) having a similar threshold energy. The latter product subsequently decomposes at still higher energies to ThCH(+) (ThCD(+)). CID of ThCH4(+) yields atomic Th(+) as the exclusive product. The cross-sections of all product ions are modeled to provide 0 K bond dissociation energies (in eV) of D0(Th(+)-H) ≥ 2.25 ± 0.18, D0(Th(+)-CH) = 6.19 ± 0.16, D0(Th(+)-CH2) ≥ 4.54 ± 0.09, D0(Th(+)-CH3) = 2.60 ± 0.30, and D0(Th(+)-CH4) = 0.47 ± 0.05. Quantum chemical calculations at several levels of theory are used to explore the potential energy surfaces for activation of methane by Th(+), and the effects of spin-orbit coupling are carefully considered. When spin-orbit coupling is explicitly considered, a barrier for C-H bond activation that is consistent with the threshold measured for ThCH2(+) formation (0.17 ± 0.02 eV) is found at all levels of theory, whereas this barrier is observed only at the BHLYP and CCSD(T) levels otherwise. The observation that the CID of the ThCH4(+) complex produces Th(+) as the only product with a threshold of 0.47 eV indicates that this species has a Th(+)(CH4) structure, which is also consistent with a barrier for C-H bond activation. This barrier is thought to exist as a result of the mixed ((4)F,(2)D) electronic character of the Th(+) J = (3)/2 ground level combined with extensive spin-orbit effects.

Thermodynamics of GaN(s)-NH3(v)+N2(v)+H2(v) system - Electronic aspects of the processes at GaN(0001) surface

NASA Astrophysics Data System (ADS)

Kempisty, Pawel; Strak, Pawel; Sakowski, Konrad; Krukowski, Stanislaw

2017-08-01

Comprehensive analysis of GaN(0001) surface in equilibrium with ammonia/hydrogen mixture was undertaken using results of ab initio calculations. Adsorption energies of the species derived from ammonia and molecular hydrogen and their stable sites were obtained. It was shown that the adsorption process type and energy depend on the position of Fermi level at the surface. Hydrogen decomposes into two separate H atoms, always adsorbed in the positions on top of the surface Ga atoms (On-top). Ammonia adsorption at GaN(0001) surface proceeds molecularly to ammonia in the On-top position or dissociatively into NH2 radicals in bridge (NH2-bridge) or On-top positions or into NH radicals in H3 (NH-H3) site. Presence of these species affects Fermi level pinning at the surface due to creation of new surface states. The Fermi level pinning in function of the surface attached species concentration was determined using extended electron counting rule (EECR). Results of ab initio calculations fully proved validity of the EECR predictions. Thermodynamic analysis of the surface in equilibrium with molecular hydrogen and ammonia vapor mixture is made giving the range of ammonia and hydrogen pressures, corresponding to Fermi level pinned at Ga-broken bond state for NH-H3&H and NH3&H and NH2-bridge&H coverage and at VBM for NH3 & H coverage. As the region of Fermi level pinned at Ga broken bond state corresponds to very low pressures, at pressures close to normal, GaN(0001) surface is almost totally covered by H, NH3 and NH2 located in On-top positions. It is also shown however that dominant portion of the hydrogen and ammonia pressures corresponds to Fermi level not pinned. Among them are these corresponding to MOVPE and HVPE growth conditions in which the surface is almost fully covered by NH3, NH2 and H species in On-top positions.

Choice of Bond Dissociation Enthalpies on which to Base the Stabilization Energies of Simple Radicals: DH(R-H)is Preferred because DH(R-Me) is Perturbed by Changes in Chain Branching

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

Poutsma, Marvin L

2008-01-01

The relative stabilization energies of radicals, SE(R ), along the simple series methyl/ethyl/i-propyl/t-butyl are known to vary in spread and even direction dependent on which dissociation enthalpies, DH(R-X), they are based on. Using a highly electronegative X is recognized as unwise, but it is not clear whether a choice of X = Me or X = R might not be preferred over the almost universal use of R = H. The enthalpies of isomerization of C4 radical pairs that vary only in the substitution pattern at the radical center but not in carbon skeleton illustrate that R = H ismore » indeed the better choice. Comparisons in the context of recent predictive models for alkane and radical stability indicate that, while relative DH(R-H) values highlight the desired difference in substitution pattern at the radical center, relative DH(R-Me) values are perturbed by differences in skeletal branching or protobranching which are well-known to affect thermochemistry. As a result, SE(R ) values derived from relative DH(R-Me) values are consistently too small. The same pattern is illustrated for prim, sec, and tert allylic and benzylic radicals (larger SE(R )) and for the parent vinyl, phenyl, and ethynyl radicals (negative SE(R )).« less

Structural and Spectroscopic Characterization of 17- and 18-Electron Piano-Stool Complexes of Chromium. Thermochemical Analyses of Weak Cr–H Bonds

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

van der Eide, Edwin F.; Helm, Monte L.; Walter, Eric D.

2013-02-04

The 17-electron radical CpCr(CO)2(IMe)• (IMe = 1,3-dimethylimidazol-2-ylidene) was synthesized by the reaction of IMe with [CpCr(CO)3]2, and characterized by single crystal X-ray diffraction and by EPR, IR and variable temperature 1H NMR spectroscopy. The metal-centered radical is monomeric under all conditions and exhibits Curie paramagnetic behavior in solution. An electrochemically reversible reduction to 18-electron CpCr(CO)2(IMe)- takes place at E½ = -1.89(1) V vs Cp2Fe+•/0 in MeCN, and was accomplished chemically with KC8 in THF. The salts K+(18-crown-6)[CpCr(CO)2(IMe)]- • ½THF and K+[CpCr(CO)2(IMe)]- • ¾THF were crystallographically characterized. Monomeric ion pairs are found in the former, whereas the latter has a polymericmore » structure due to a network of K∙∙∙O(CO) interactions. Protonation of K+(18-crown-6)[CpCr(CO)2(IMe)]- • ½THF gives the hydride CpCr(CO)2(IMe)H, which could not be isolated, but was characterized in solution; a pKa of 27.2(4) was determined in MeCN. A thermochemical analysis provides the Cr-H bond dissociation free energy (BDFE) for CpCr(CO)2(IMe)H in MeCN solution as 47.3(6) kcal mol-1. This value is exceptionally low for a transition metal hydride, and implies that the reaction 2 [Cr-H] → 2 [Cr•] + H2 is exergonic (ΔG = -9.0(8) kcal mol-1). This analysis explains the experimental observation that generated solutions of the hydride produce CpCr(CO)2(IMe)• (typically on the timescale of days). By contrast, CpCr(CO)2(PCy3)H has a higher Cr-H BDFE (52.9(4) kcal mol-1), is more stable with respect to H2 loss, and is isolable. 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. M.L.H. carried out the crystallographic studies and 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. The EPR studies were performed at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL. Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Effect of Spin Multiplicity in O2 Adsorption and Dissociation on Small Bimetallic AuAg Clusters.

PubMed

García-Cruz, Raúl; Poulain, Enrique; Hernández-Pérez, Isaías; Reyes-Nava, Juan A; González-Torres, Julio C; Rubio-Ponce, A; Olvera-Neria, Oscar

2017-08-17

To dispose of atomic oxygen, it is necessary the O 2 activation; however, an energy barrier must be overcome to break the O-O bond. This work presents theoretical calculations of the O 2 adsorption and dissociation on small pure Au n and Ag m and bimetallic Au n Ag m (n + m ≤ 6) clusters using the density functional theory (DFT) and the zeroth-order regular approximation (ZORA) to explicitly include scalar relativistic effects. The most stable Au n Ag m clusters contain a higher concentration of Au with Ag atoms located in the center of the cluster. The O 2 adsorption energy on pure and bimetallic clusters and the ensuing geometries depend on the spin multiplicity of the system. For a doublet multiplicity, O 2 is adsorbed in a bridge configuration, whereas for a triplet only one O-metal bond is formed. The charge transfer from metal toward O 2 occupies the σ* O-O antibonding natural bond orbital, which weakens the oxygen bond. The Au 3 ( 2 A) cluster presents the lowest activation energy to dissociate O 2 , whereas the opposite applies to the AuAg ( 3 A) system. In the O 2 activation, bimetallic clusters are not as active as pure Au n clusters due to the charge donated by Ag atoms being shared between O 2 and Au atoms.