Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

PubMed

Kurbanov, Elbek K; Leverentz, Hannah R; Truhlar, Donald G; Amin, Elizabeth A

2012-01-10

The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.

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.

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

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.

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.

Theoretical dissociation energies for the alkali and alkaline-earth monofluorides and monochlorides

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

1986-01-01

Spectroscopic parameters are accurately determined for the alkali and alkaline-earth monofluorides and monochlorides by means of ab initio self-consistent field and correlated wave function calculations. Numerical Hartree-Fock calculations are performed on selected systems to ensure that the extended Slater basis sets employed are near the Hartree-Fock limit. Since the bonding is predominantly electrostatic in origin, a strong correlation exists between the dissociation energy (to ions) and the spectroscopic parameter r(e). By dissociating to the ionic limits, most of the differential correlation effects can be embedded in the accurate experimental electron affinities and ionization potentials.

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.

First principle study of AlX (X=3d, 4d, 5d elements and Lu) dimer.

PubMed

Ouyang, Yifang; Wang, Jianchuan; Hou, Yuhua; Zhong, Xiaping; Du, Yong; Feng, Yuanping

2008-02-21

The ground state equilibrium bond length, harmonic vibrational frequency, and dissociation energy of AlX (X=3d,4d,5d elements and Lu) dimers are investigated by density functional method B3LYP. The present results are in good agreement with the available experimental and other theoretical values except the dissociation energy of AlCr. The present calculations show that the late transition metal can combine strongly with aluminum compared with the former transition metal. The present calculation also indicates that it is more reasonable to replace La with Lu in the Periodic Table and that the bonding strengths of zinc, cadmium, and mercury with aluminum are very weak.

A multivariate relationship for the impact sensitivities of energetic N-nitrocompounds based on bond dissociation energy.

PubMed

Li, Jinshan

2010-02-15

The ZPE-corrected N-NO(2) bond dissociation energies (BDEs(ZPE)) of a series of model N-nitrocompounds and typical energetic N-nitrocompounds have been calculated using density functional theory methods. Computed results show that using the 6-31G** basis set the UB3LYP calculated BDE(ZPE) is similar to the B3PW91 but is less than the UB3P86 and that for both UB3P86 and UB3PW91 methods the 6-31G(**) calculated BDE(ZPE) is close to the 6-31++G(**). For the series of model N-nitrocompounds it is drawn from the NBO analysis that at the UB3LYP/6-31G(**) level the order of BDE(ZPE) is not only in line with that of bond order but also with that of the energy gap between N-NO(2) bond and antibond orbitals. For the typical energetic N-nitrocompounds the impact sensitivity is strongly related to the BDE(ZPE) indeed, and based on the BDEs(ZPE) calculated at different density functional theory levels this work has established a good multivariate correlation of impact sensitivity with molecular parameters, which provides a method to address the sensitivity problem.

The effect of anatase TiO2 surface structure on the behavior of ethanol adsorption and its initial dissociation step: A DFT study

NASA Astrophysics Data System (ADS)

Zhang, Riguang; Liu, Zhixue; Ling, Lixia; Wang, Baojun

2015-10-01

The perfect and defective surfaces of anatase TiO2 including (1 0 1) and (0 0 1) surfaces have been chosen to probe into the effect of anatase TiO2 surface structure on the behavior of ethanol adsorption and initial dissociation step. Here, the results are obtained by density functional theory (DFT) calculation together with the periodic slab model. Our results show that the surface structure of anatase TiO2 can obviously affect the behavior of ethanol adsorption and the catalytic activity of its initial dissociation step; firstly, on the perfect and defective surfaces of anatase (1 0 1), ethanol dominantly exists in the form of molecule adsorption; however, ethanol is the dissociative adsorption on the hydroxylated anatase (0 0 1), and the coexistences of molecular and dissociation adsorption modes on the perfect anatase (0 0 1). On the other hand, the initial dissociation step of ethanol with molecule adsorption prefers to begin with its O-H bond cleavage leading to CH3CH2O and H species rather than the cleavage of its α-C-H, β-C-H, C-C and C-O bonds, namely, the preferable O-H bond cleavage for the initial dissociation step of ethanol is independent of the surface structure of anatase TiO2; however, the corresponding catalytic activity of ethanol initial dissociation step with the O-H bond cleavage on different anatase TiO2 surfaces is in the following order: hydroxylated (0 0 1) > perfect (0 0 1) > defective (1 0 1) > perfect (1 0 1), suggesting that the catalytic activity for the initial dissociation step of ethanol is sensitive to the surface structure of anatase TiO2, and the hydroxylated (0 0 1) is the most favorable surface. Among these surfaces, the most favorable product for the initial dissociation step of ethanol is CH3CH2O species.

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.

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.

Anchoring the Gas-Phase Acidity Scale from Hydrogen Sulfide to Pyrrole. Experimental Bond Dissociation Energies of Nitromethane, Ethanethiol, and Cyclopentadiene.

PubMed

Ervin, Kent M; Nickel, Alex A; Lanorio, Jerry G; Ghale, Surja B

2015-07-16

A meta-analysis of experimental information from a variety of sources is combined with statistical thermodynamics calculations to refine the gas-phase acidity scale from hydrogen sulfide to pyrrole. The absolute acidities of hydrogen sulfide, methanethiol, and pyrrole are evaluated from literature R-H bond energies and radical electron affinities to anchor the scale. Relative acidities from proton-transfer equilibrium experiments are used in a local thermochemical network optimized by least-squares analysis to obtain absolute acidities of 14 additional acids in the region. Thermal enthalpy and entropy corrections are applied using molecular parameters from density functional theory, with explicit calculation of hindered rotor energy levels for torsional modes. The analysis reduces the uncertainties of the absolute acidities of the 14 acids to within ±1.2 to ±3.3 kJ/mol, expressed as estimates of the 95% confidence level. The experimental gas-phase acidities are compared with calculations, with generally good agreement. For nitromethane, ethanethiol, and cyclopentadiene, the refined acidities can be combined with electron affinities of the corresponding radicals from photoelectron spectroscopy to obtain improved values of the C-H or S-H bond dissociation energies, yielding D298(H-CH2NO2) = 423.5 ± 2.2 kJ mol(-1), D298(C2H5S-H) = 364.7 ± 2.2 kJ mol(-1), and D298(C5H5-H) = 347.4 ± 2.2 kJ mol(-1). These values represent the best-available experimental bond dissociation energies for these species.

A quantitative relationship for the shock sensitivities of energetic compounds based on X-NO(2) (X=C, N, O) bond dissociation energy.

PubMed

Li, Jinshan

2010-08-15

The ZPE-corrected X-NO(2) (X=C, N, O) bond dissociation energies (BDEs(ZPE)) of 11 energetic nitrocompounds of different types have been calculated employing density functional theory methods. Computed results show that using the 6-31G** basis set the UB3LYP calculated BDE(ZPE) is less than the UB3P86. For these typical energetic nitrocompounds the shock-initiated pressure (P(98)) is strongly related to the BDE(ZPE) indeed, and a polynomial correlation of ln(P(98)) with the BDE(ZPE) has been established successfully at different density functional theory levels, which provides a method to address the shock sensitivity problem. Copyright 2010 Elsevier B.V. All rights reserved.

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.

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.

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.

A First Principles Study of H2 Adsorption on LaNiO3(001) Surfaces

PubMed Central

Pan, Changchang; Chen, Yuhong; Wu, Na; Zhang, Meiling; Yuan, Lihua; Zhang, Cairong

2017-01-01

The adsorption of H2 on LaNiO3 was investigated using density functional theory (DFT) calculations. The adsorption sites, adsorption energy, and electronic structure of LaNiO3(001)/H2 systems were calculated and indicated through the calculated surface energy that the (001) surface was the most stable surface. By looking at optimized structure, adsorption energy and dissociation energy, we found that there were three types of adsorption on the surface. First, H2 molecules completely dissociate and then tend to bind with the O atoms, forming two –OH bonds. Second, H2 molecules partially dissociate with the H atoms bonding to the same O atom to form one H2O molecule. These two types are chemical adsorption modes; however, the physical adsorption of H2 molecules can also occur. When analyzing the electron structure of the H2O molecule formed by the partial dissociation of the H2 molecule and the surface O atom, we found that the interaction between H2O and the (001) surface was weaker, thus, H2O was easier to separate from the surface to create an O vacancy. On the (001) surface, a supercell was constructed to accurately study the most stable adsorption site. The results from analyses of the charge population; electron localization function; and density of the states indicated that the dissociated H and O atoms form a typical covalent bond and that the interaction between the H2 molecule and surface is mainly due to the overlap-hybridization among the H 1s, O 2s, and O 2p states. Therefore, the conductivity of LaNiO3(001)/H2 is stronger after adsorption and furthermore, the conductivity of the LaNiO3 surface is better than that of the LaFeO3 surface. PMID:28772396

Density function theory study of the adsorption and dissociation of carbon monoxide on tungsten nanoparticles.

PubMed

Weng, Meng-Hsiung; Ju, Shin-Pon; Chen, Hsin-Tsung; Chen, Hui-Lung; Lu, Jian-Ming; Lin, Ken-Huang; Lin, Jenn-Sen; Hsieh, Jin-Yuan; Yang, Hsi-Wen

2013-02-01

The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk.

Site-Specific Imaging of Elemental Steps in Dehydration of Diols on TiO 2(110)

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

Acharya, Danda P.; Yoon, Yeohoon; Li, Zhenjun

2013-11-26

The conversion of diols on partially reduced TiO 2(110) at low coverage was studied using variable-temperature scanning tunneling microscopy, temperature programmed desorption and density functional theory calculations. We find, that below ~230 K, ethane-1,2-diol and propane-1,3-diol molecules adsorb predominantly on five-fold coordinated Ti5c atoms. The dynamic equilibrium between molecularly bound and dissociated species resulting from O-H bond scission and reformation is observed. As the diols start to diffuse on the Ti5c rows above ~230 K, they dissociate irreversibly upon encountering bridging oxygen (O b) vacancy (VO’s) defects. Two dissociation pathways, one via O-H and the other via C-O bond scissionmore » leading to identical surface intermediates, hydroxyalkoxy, O b-(CH 2)n-OH (n = 2, 3) and bridging hydroxyl, HO b, are seen. For O-H bond scission, the O b-(CH 2)n-OH is found on the position of the original VO, while for C-O scission it is found on the adjacent Ob site. Theoretical calculations suggest that the observed mixture of C-O/O-H bond breaking processes are a result of the steric factors enforced upon the diols by the second OH group that is bound to a Ti5c site. At room temperature, rich dissociation/reformation dynamics of the second, Ti5c-bound O-H leads to the formation of dioxo, Ob-(CH 2)n-OTi, species. Above ~400 K, both O b-(CH 2)n-OH and Ob-(CH 2)n-OTi species convert into a new intermediate, that is centered on Ob row. Combined experimental and theoretical evidence shows that this intermediate is most likely a new dioxo, O b-(CH 2) 2-Ob, species. Further annealing leads to sequential C-Ob bond cleavage and alkene desorption above ~ 500 K. Simulations find that the sequential C-O bond breaking process follows a homolytic diradical pathway with the first C-O bond breaking event accompanied by a non-adiabatic electron transfer within the TiO 2(110) substrate.« less

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice–Ramsperger–Kassel theory

PubMed Central

Bao, Junwei Lucas; Zhang, Xin

2016-01-01

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice–Ramsperger–Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements. PMID:27834727

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

PubMed

Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

2016-11-29

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C 2 F 4 ), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.

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.

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%).

Accurate prediction of bond dissociation energies of large n-alkanes using ONIOM-CCSD(T)/CBS methods

NASA Astrophysics Data System (ADS)

Wu, Junjun; Ning, Hongbo; Ma, Liuhao; Ren, Wei

2018-05-01

Accurate determination of the bond dissociation energies (BDEs) of large alkanes is desirable but practically impossible due to the expensive cost of high-level ab initio methods. We developed a two-layer ONIOM-CCSD(T)/CBS method which treats the high layer with CCSD(T) method and the low layer with DFT method, respectively. The accuracy of this method was validated by comparing the calculated BDEs of n-hexane with that obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory. On this basis, the C-C BDEs of C6-C20 n-alkanes were calculated systematically using the ONIOM [CCSD(T)/CBS(D-T):M06-2x/6-311++G(d,p)] method, showing a good agreement with the data available in the literature.

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

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).

Predicting Bond Dissociation Energies of Transition-Metal Compounds by Multiconfiguration Pair-Density Functional Theory and Second-Order Perturbation Theory Based on Correlated Participating Orbitals and Separated Pairs.

PubMed

Bao, Junwei Lucas; Odoh, Samuel O; Gagliardi, Laura; Truhlar, Donald G

2017-02-14

We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.

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.

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.

Dissociation energies of the hydrogen-bonded dimers RCN-HF (R = CH3, HCC) determined by rotational spectroscopy

NASA Astrophysics Data System (ADS)

Legon, A. C.; Millen, D. J.; North, Hazel M.

1987-03-01

The zero-point and equilibrium dissociation energies (D0 and De) of the hydrogen-bonded dimers CH3CN-HF and HCCCN-HF are determined experimentally on the basis of absolute intensity measurements of selected rotational transitions. A Stark-modulated microwave spectrometer is employed with the cooled absorption cell described by Legon et al. (1980). The results are presented in tables and analyzed. Energies determined are D0 = 26.1(0.6) kJ/mol and De = 29.0(0.9) kJ/mol for CH3CN-HF and D0 = 20.4(0.7) kJ/mol and De = 23.4(0.9) kJ/mol for HCCCN-HF. Theoretical De values calculated using the Morse potential function are found to be in much better agreement with the experimental results than those calculated with the Lennard-Jones potential function.

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

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.

A theoretical study of bond selective photochemistry in CH2BrI

NASA Astrophysics Data System (ADS)

Liu, Kun; Zhao, Hongmei; Wang, Caixia; Zhang, Aihua; Ma, Siyu; Li, Zonghe

2005-01-01

Bromoiodomethane photodissociation in the low-lying excited states has been characterized using unrestricted Hartree-Fock, configuration-interaction-singles, and complete active space self-consistent field calculations with the SDB-aug-cc-pVTZ, aug-cc-pVTZ, and 3-21g** basis sets. According to the results of the vertical excited energies and oscillator strengths of these low-lying excited states, bond selectivity is predicted. Subsequently, the minimum energy paths of the first excited singlet state and the third excited state for the dissociation reactions were calculated using the complete active space self-consistent field method with 3-21g** basis set. Good agreement is found between the calculations and experimental data. The relationships of excitations, the electronic structures at Franck-Condon points, and bond selectivity are discussed.

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.

Platinum-catalyzed hydrolysis etching of SiC in water: A density functional theory study

NASA Astrophysics Data System (ADS)

Van Bui, Pho; Toh, Daisetsu; Isohashi, Ai; Matsuyama, Satoshi; Inagaki, Kouji; Sano, Yasuhisa; Yamauchi, Kazuto; Morikawa, Yoshitada

2018-05-01

A comprehensive study of the physicochemical interactions and the reaction mechanism of SiC etching with water by Pt catalysts can reveal key details about the surface treatment and catalytic phenomena at interfaces. Therefore, density functional theory simulations were performed to study the kinetics of Pt-assisted water dissociation and breaking of a Si–C bond compared to the HF-assisted mechanism. These calculations carefully considered the elastic and chemical interaction energies at the Pt–SiC interface, activation barriers of Si–C bond dissociation, and the catalytic role of Pt. It was found that the Pt-catalyzed etching of SiC in water is initiated via hydrolysis reactions that break the topmost Si–C bonds. The activation barrier strongly depends on the elastic and chemical interactions. However, chemical interactions are a dominant factor and mainly contribute to the lowering of the activation barrier, resulting in an increased rate of reaction.

Mechanisms of catalytic cleavage of benzyl phenyl ether in aqueous and apolar phases

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

He, Jiayue; Lu, Lu; Zhao, Chen

2014-03-01

Catalytic pathways for the cleavage of ether bonds in benzyl phenyl ether (BPE) in liquid phase using Ni- and zeolite-based catalysts are explored. In the absence of catalysts, the C-O bond is selectively cleaved in water by hydrolysis, forming phenol and benzyl alcohol as intermediates, followed by alkylation. The hydronium ions catalyzing the reactions are provided by the dissociation of water at 523 K. Upon addition of HZSM-5, rates of hydrolysis and alkylation are markedly increased in relation to proton concentrations. In the presence of Ni/SiO 2, the selective hydrogenolysis dominates for cleaving the C aliphatic-O bond. Catalyzed by themore » dual-functional Ni/HZSM-5, hydrogenolysis occurs as the major route rather than hydrolysis (minor route). In apolar undecane, the non-catalytic thermal pyrolysis route dominates. Hydrogenolysis of BPE appears to be the major reaction pathway in undecane in the presence of Ni/SiO 2 or Ni/HZSM-5, almost completely suppressing radical reactions. Density functional theory (DFT) calculations strongly support the proposed C-O bond cleavage mechanisms on BPE in aqueous and apolar phases. These calculations show that BPE is initially protonated and subsequently hydrolyzed in the aqueous phase. Finally, DFT calculations suggest that the radical reactions in non-polar solvents lead to primary benzyl and phenoxy radicals in undecane, which leads to heavier condensation products as long as metals are absent for providing dissociated hydrogen.« less

DFT study on the interaction of TiO2 (001) surface with HCHO molecules

NASA Astrophysics Data System (ADS)

Wu, Guofei; Zhao, Cuihua; Guo, Changqing; Chen, Jianhua; Zhang, Yibing; Li, Yuqiong

2018-01-01

The interactions of formaldehyde (HCHO) molecule with TiO2 (001) surface were studied using density functional theory calculations. HCHO molecules are dissociated by the cleavage of Csbnd H bonds after adsorption on TiO2 surface. The strong interactions between HCHO melecules and TiO2 surface are largely attributed to the bonding of hydrogen of HCHO and oxygen of TiO2 surface, which is mainly from the hybridization of the H 1s, O 2p and O 2s. The newly formed Hsbnd O bonds cause the structure changes of TiO2 surface, and lead to the cleavage of Osbnd Ti bond of TiO2 surface. The Csbnd O bond that the dissociated remains of HCHO and newly formed Hsbnd O bond can be oxidized to form carbon dioxide and water in subsequent action by oxygen from the atomosphere. The charges transfer from HCHO to TiO2 surface, and the sum amount of the charges transferred from four HCHO molecules to TiO2 surface is bigger than that from one HCHO molecule to TiO2 surface due to the combined interaction of four HCHO molecules with TiO2 surface.

Controllable dissociations of PH3 molecules on Si(001)

NASA Astrophysics Data System (ADS)

Liu, Qin; Lei, Yanhua; Shao, Xiji; Ming, Fangfei; Xu, Hu; Wang, Kedong; Xiao, Xudong

2016-04-01

We demonstrate for the first time to our knowledge that controllable dissociation of PH3 adsorption products PH x (x = 2, 1) can be realized by STM (scanning tunneling microscope) manipulation techniques at room temperature. Five dissociative products and their geometric structures are identified via combining STM experiments and first-principle calculations and simulations. In total we realize nine kinds of controllable dissociations by applying a voltage pulse among the PH3-related structures on Si(001). The dissociation rates of the five most common reactions are measured by the I-t spectrum method as a function of voltage. The suddenly increased dissociation rate at 3.3 V indicates a transition from multivibrational excitation to single-step excitation induced by inelastic tunneling electrons. Our studies prove that selectively breaking the chemical bonds of a single molecule on semiconductor surface by STM manipulation technique is feasible.

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.

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.

The Dissociation Energies of CH4 and C2H2 Revisited

NASA Technical Reports Server (NTRS)

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

1995-01-01

The bond dissociation energies of CH4 and C2H2 and their fragments are investigated using basis set extrapolations and high levels of correlation. The computed bond dissociation energies (D(sub e)) are accurate to within 0.2 kcal/mol. The agreement with the experimental (D(sub 0)) values is excellent if we assume that the zero-point energy of C2H is 9.18 kcal/mol. The effect of core (1s) correlation on the bond dissociation energies of C-H bonds is shown to vary from 0.2 to 0.7 kcal/mol and that for C-C bonds varies from 0.4 to 2.2 kcal/mol.

Electron-hole pair effects in methane dissociative chemisorption on Ni(111)

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

Luo, Xuan; Jiang, Bin, E-mail: bjiangch@ustc.edu.cn; Juaristi, J. Iñaki

The dissociative chemisorption of methane on metal surfaces has attracted much attention in recent years as a prototype of gas-surface reactions in understanding the mode specific and bond selective chemistry. In this work, we systematically investigate the influence of electron-hole pair excitations on the dissociative chemisorption of CH{sub 4}/CH{sub 3}D/CHD{sub 3} on Ni(111). The energy dissipation induced by surface electron-hole pair excitations is modeled as a friction force introduced in the generalized Langevin equation, in which the independent atomic friction coefficients are determined within the local-density friction approximation. Quasi-classical trajectory calculations for CH{sub 4}/CH{sub 3}D/CHD{sub 3} have been carried outmore » on a recently developed twelve-dimensional potential energy surface. Comparing the dissociation probabilities obtained with and without friction, our results clearly indicate that the electron-hole pair effects are generally small, both on absolute reactivity of each vibrational state and on the mode specificity and bond selectivity. Given similar observations in both water and methane dissociation processes, we conclude that electron-hole pair excitations would not play an important role as long as the reaction is direct and the interaction time between the molecule and metal electrons is relatively short.« less

Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

NASA Astrophysics Data System (ADS)

Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Wang, Yangang; Hupalo, Myron; McDougall, Dan; Tringides, Michael; Ho, Kaiming

2013-12-01

The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H2 molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H2 molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

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.

Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

NASA Astrophysics Data System (ADS)

Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

2017-06-01

We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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.

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

Liu Kun; Zhao Hongmei; Wang Caixia

Bromoiodomethane photodissociation in the low-lying excited states has been characterized using unrestricted Hartree-Fock, configuration-interaction-singles, and complete active space self-consistent field calculations with the SDB-aug-cc-pVTZ, aug-cc-pVTZ, and 3-21g** basis sets. According to the results of the vertical excited energies and oscillator strengths of these low-lying excited states, bond selectivity is predicted. Subsequently, the minimum energy paths of the first excited singlet state and the third excited state for the dissociation reactions were calculated using the complete active space self-consistent field method with 3-21g** basis set. Good agreement is found between the calculations and experimental data. The relationships of excitations, the electronicmore » structures at Franck-Condon points, and bond selectivity are discussed.« less

Theoretical Study on Vibrational Spectra, Detonation Properties and Pyrolysis Mechanism for Cyclic 2-Diazo-4,6-dinitrophenol

NASA Astrophysics Data System (ADS)

Li, Xiao-hong; Yin, Geng-xin; Zhang, Xian-zhou

2012-10-01

Based on the full optimized molecular geometrical structures at the DFT-B3LYP/6-311+G** level, there exists intramolecular hydrogen bond interaction for cyclic 2-diazo-4,6-dinitrophenol. The assigned infrared spectrum is obtained and used to compute the thermodynamic properties. The results show that there are four main characteristic regions in the calculated IR spectra of the title compound. The detonation velocities and pressures are also evaluated by using Kamlet-Jacobs equations based on the calculated density and condensed phase heat of formation. Thermal stability and the pyrolysis mechanism of 2-diazo-4,6-dinitrophenol are investigated by calculating the bond dissociation energies at the B3LYP/6-311+G** level.

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.

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

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

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

A simple model for metal cation-phosphate interactions in nucleic acids in the gas phase: alkali metal cations and trimethyl phosphate.

PubMed

Ruan, Chunhai; Huang, Hai; Rodgers, M T

2008-02-01

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations to trimethyl phosphate, TMP. Endothermic loss of the intact TMP ligand is the only dissociation pathway observed for all complexes. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TMP and the M+(TMP) complexes. Theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between theory and experiment is reasonably good for all complexes except Li+(TMP). The absolute M+-(TMP) BDEs are found to decrease monotonically as the size of the alkali metal cation increases. No activated dissociation was observed for alkali metal cation binding to TMP. The binding of alkali metal cations to TMP is compared with that to acetone and methanol.

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.

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.

An ab initio study of Fe(CO)n, n = 1,5, and Cr(CO)6

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Rosi, Marzio; Bauschlicher, Charles W., Jr.

1991-01-01

Ab initio calculations have been performed for Cr(CO)6 and Fe(CO)n, n = 1,5. Basis sets of better than double zeta quality are used, and correlation is included using the modified coupler-pair functional method. The computed geometries and force constants are in reasonable agreement with experiment. The sequential bond dissociation energies of CO from Fe(CO)5 are estimated to be: 39, 31, 25, 22, and greater than 5 kcal/mol. It is noted that the first bond dissociation energy is relative to the singlet ground state of Fe(CO)5 and the lowest singlet state of Fe(CO)4, whereas the second is relative to the ground triplet states of Fe(CO)4 and Fe(CO)3. In addition, the binding energy for Fe-CO would be modified to 18 kcal/mol if dissociation occurred to the Fe(5F) excited state asymptote. The CO binding energies for Fe and Cr are found to be in poorer agreement with experiment than those found in a previous study on Ni(CO)4. The origins of this difference are discussed.

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

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.)

Theoretical study on adsorption and dissociation of NO2 molecules on BNNT surface

NASA Astrophysics Data System (ADS)

Singla, Preeti; Singhal, Sonal; Goel, Neetu

2013-10-01

The adsorption of NO2 molecules on (8,0) zigzag single-walled boron nitride nanotube surface is investigated using density functional theory calculations. Two interaction modes, nitro (interacting atom is N) and nitrite (O interacts with BNNT) have been studied with increase in number of NO2 molecules. The adsorption of single NO2 molecule in both configurations is observed to be exothermic and physical in nature. However, in nitrite configuration, NO2 molecules are chemisorbed on the surface leading to the dissociation of NO2 molecules into NO and O. The density of states, natural bond orbital analysis and frontier orbital pictures provide rational understanding of the charge transfer involved in the process and predict significant enhancement in the conductivity of the BNNT after NO2 adsorption. The DFT calculations show that NO2 adsorption introduces new impurity states in the band gap of bare BNNT and expand their applications as NO2 molecule gas sensor and catalytic surface for Nsbnd O dissociation depending upon the mode of adsorption.

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.

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).

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

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

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.

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

NASA Technical Reports Server (NTRS)

Dzegilenko, Fedor N.; Saini, Subhash (Technical Monitor)

1998-01-01

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Dispersion forces play a role in (Me 2 IPr)Fe(NAd)R 2 (Ad = adamantyl; R = neo Pe, 1-nor) insertions and Fe–R bond dissociation enthalpies (BDEs)

DOE PAGES

Cundari, Thomas R.; Jacobs, Brian P.; MacMillan, Samantha N.; ...

2018-01-01

Calculations show that dispersion forces in four-coordinate (Me 2 IPr)Fe(NAd)(1-nor) 2 ( 2b ) contribute to greater D(FeR) and subtly slow its migratory insertion relative to the neopentyl analogue.

Dispersion forces play a role in (Me 2 IPr)Fe(NAd)R 2 (Ad = adamantyl; R = neo Pe, 1-nor) insertions and Fe–R bond dissociation enthalpies (BDEs)

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

Cundari, Thomas R.; Jacobs, Brian P.; MacMillan, Samantha N.

Calculations show that dispersion forces in four-coordinate (Me 2 IPr)Fe(NAd)(1-nor) 2 ( 2b ) contribute to greater D(FeR) and subtly slow its migratory insertion relative to the neopentyl analogue.

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.

Extreme population inversion in the fragments formed by UV photoinduced S-H bond fission in 2-thiophenethiol.

PubMed

Ingle, Rebecca A; Karsili, Tolga N V; Dennis, Gregg J; Staniforth, Michael; Stavros, Vasilios G; Ashfold, Michael N R

2016-04-28

H atom loss following near ultraviolet photoexcitation of gas phase 2-thiophenethiol molecules has been studied experimentally, by photofragment translational spectroscopy (PTS) methods, and computationally, by ab initio electronic structure calculations. The long wavelength (277.5 ≥ λ(phot) ≥ 240 nm) PTS data are consistent with S-H bond fission after population of the first (1)πσ* state. The partner thiophenethiyl (R) radicals are formed predominantly in their first excited Ã(2)A' state, but assignment of a weak signal attributable to H + R(X˜(2)A'') products allows determination of the S-H bond strength, D0 = 27,800 ± 100 cm(-1) and the Ã-X˜ state splitting in the thiophenethiyl radical (ΔE = 3580 ± 100 cm(-1)). The deduced population inversion between the à and X˜ states of the radical reflects the non-planar ground state geometry (wherein the S-H bond is directed near orthogonal to the ring plane) which, post-photoexcitation, is unable to planarise sufficiently prior to bond fission. This dictates that the dissociating molecules follow the adiabatic fragmentation pathway to electronically excited radical products. π* ← π absorption dominates at shorter excitation wavelengths. Coupling to the same (1)πσ* potential energy surface (PES) remains the dominant dissociation route, but a minor yield of H atoms attributable to a rival fragmentation pathway is identified. These products are deduced to arise via unimolecular decay following internal conversion to the ground (S0) state PES via a conical intersection accessed by intra-ring C-S bond extension. The measured translational energy disposal shows a more striking change once λ(phot) ≤ 220 nm. Once again, however, the dominant decay pathway is deduced to be S-H bond fission following coupling to the (1)πσ* PES but, in this case, many of the evolving molecules are deduced to have sufficiently near-planar geometries to allow passage through the conical intersection at extended S-H bond lengths and dissociation to ground (X˜) state radical products. The present data provide no definitive evidence that complete ring opening can compete with fast S-H bond fission following near UV photoexcitation of 2-thiophenethiol.

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.

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.

Studies of protonated and anionic artemisinin in the gas-phase by infrared multi-photon dissociation and by negative ion photoelectron spectroscopies

NASA Astrophysics Data System (ADS)

Seydou, M.; Gillet, J. C.; Li, X.; Wang, H.; Posner, G. H.; Grégoire, G.; Schermann, J. P.; Bowen, K. H.; Desfrançois, C.

2007-12-01

Protonated and anionic artemisinin in the gas phase have respectively been studied by infrared multi-photon dissociation (IRMPD) spectroscopy and by anion photoelectron spectroscopy. Comparison of the measured IRMPD spectrum with calculated spectra of various conformations showed that the two lowest-energy protonated structures, both corresponding to protonation at the C dbnd O 14 carbonyl site, were observed experimentally. The calculations also indicated that the peroxide bridge in artemisinin is only slightly modified by protonation. Additionally, stable, intact (parent) artemisinin radical anions have been obtained for the first time in the gas phase and the photoelectron spectrum supports the computational finding that the excess electron is mainly localized on the σ ∗ orbital of the peroxide bond. The vertical detachment energy and adiabatic electron affinity, calculated at the MP2/6-31+G ∗ level, are in good agreement with the experimental data and the O-O distance is calculated to be stretched by more than 50% in the anion.

Molecular and Dissociative Adsorption of Water on (TiO 2 ) n Clusters, n = 1–4

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

Chen, Mingyang; Straatsma, Tjerk P.; Dixon, David A.

In the low energy structures of the (TiO 2) n(H 2O) m (n ≤ 4, m ≤ 2n) and (TiO 2) 8(H 2O) m (m = 3, 7, 8) clusters were predicted using a global geometry optimization approach, with a number of new lowest energy isomers being found. Water can molecularly or dissociatively adsorb on pure and hydrated TiO 2 clusters. Dissociative adsorption is the dominant reaction for the first two H 2O adsorption reactions for n = 1, 2, and 4, for the first three H 2O adsorption reactions for n = 3, and for the first four Hmore » 2O adsorption reactions for n = 8. As more H 2O’s are added to the hydrated (TiO 2)n cluster, dissociative adsorption becomes less exothermic as all the Ti centers become 4-coordinate. Furthermore two types of bonds can be formed between the molecularly adsorbed water and TiO 2 clusters: a Lewis acid–base Ti–O(H 2) bond or an O···H hydrogen bond. The coupled cluster CCSD(T) results show that at 0 K the H 2O adsorption energy at a 4-coordinate Ti center is ~15 kcal/mol for the Lewis acid–base molecular adsorption and ~7 kcal/mol for the H-bond molecular adsorption, in comparison to that of 8–10 kcal/mol for the dissociative adsorption. The cluster size and geometry independent dehydration reaction energy, ED, for the general reaction 2(-TiOH) → -TiOTi– + H 2O at 4-coordinate Ti centers was estimated from the aggregation reaction of nTi(OH) 4 to form the monocyclic ring cluster (TiO 3H 2) n + nH 2O. E D is estimated to be -8 kcal/mol, showing that intramolecular and intermolecular dehydration reactions are intrinsically thermodynamically allowed for the hydrated (TiO 2) n clusters with all of the Ti centers 4-coordinate, which can be hindered by cluster geometry changes caused by such processes. Finally by bending force constants for the TiOTi and OTiO bonds are determined to be 7.4 and 56.0 kcal/(mol·rad 2). Infrared vibrational spectra were calculated using density functional theory, and the new bands appearing upon water adsorption were assigned.« less

Molecular and Dissociative Adsorption of Water on (TiO 2 ) n Clusters, n = 1–4

DOE PAGES

Chen, Mingyang; Straatsma, Tjerk P.; Dixon, David A.

2015-10-20

In the low energy structures of the (TiO 2) n(H 2O) m (n ≤ 4, m ≤ 2n) and (TiO 2) 8(H 2O) m (m = 3, 7, 8) clusters were predicted using a global geometry optimization approach, with a number of new lowest energy isomers being found. Water can molecularly or dissociatively adsorb on pure and hydrated TiO 2 clusters. Dissociative adsorption is the dominant reaction for the first two H 2O adsorption reactions for n = 1, 2, and 4, for the first three H 2O adsorption reactions for n = 3, and for the first four Hmore » 2O adsorption reactions for n = 8. As more H 2O’s are added to the hydrated (TiO 2)n cluster, dissociative adsorption becomes less exothermic as all the Ti centers become 4-coordinate. Furthermore two types of bonds can be formed between the molecularly adsorbed water and TiO 2 clusters: a Lewis acid–base Ti–O(H 2) bond or an O···H hydrogen bond. The coupled cluster CCSD(T) results show that at 0 K the H 2O adsorption energy at a 4-coordinate Ti center is ~15 kcal/mol for the Lewis acid–base molecular adsorption and ~7 kcal/mol for the H-bond molecular adsorption, in comparison to that of 8–10 kcal/mol for the dissociative adsorption. The cluster size and geometry independent dehydration reaction energy, ED, for the general reaction 2(-TiOH) → -TiOTi– + H 2O at 4-coordinate Ti centers was estimated from the aggregation reaction of nTi(OH) 4 to form the monocyclic ring cluster (TiO 3H 2) n + nH 2O. E D is estimated to be -8 kcal/mol, showing that intramolecular and intermolecular dehydration reactions are intrinsically thermodynamically allowed for the hydrated (TiO 2) n clusters with all of the Ti centers 4-coordinate, which can be hindered by cluster geometry changes caused by such processes. Finally by bending force constants for the TiOTi and OTiO bonds are determined to be 7.4 and 56.0 kcal/(mol·rad 2). Infrared vibrational spectra were calculated using density functional theory, and the new bands appearing upon water adsorption were assigned.« less

A promising tool to achieve chemical accuracy for density functional theory calculations on Y-NO homolysis bond dissociation energies.

PubMed

Li, Hong Zhi; Hu, Li Hong; Tao, Wei; Gao, Ting; Li, Hui; Lu, Ying Hua; Su, Zhong Min

2012-01-01

A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol(-1)) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol(-1) to 0.15 and 0.18 kcal·mol(-1), respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol(-1). This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules.

A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies

PubMed Central

Li, Hong Zhi; Hu, Li Hong; Tao, Wei; Gao, Ting; Li, Hui; Lu, Ying Hua; Su, Zhong Min

2012-01-01

A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol−1) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol−1 to 0.15 and 0.18 kcal·mol−1, respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol−1. This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules. PMID:22942689

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.

A density functional theory study on the adsorption and decomposition of methanol on B12N12 fullerene-like nanocage

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Nurazar, Roghaye

2014-03-01

The adsorption and dissociative reaction of methanol on B12N12 fullerene-like nanocage is investigated by using density functional calculations. Equilibrium geometries, adsorption energies, and electronic properties of CH3OH adsorption on the surface of the B12N12 were identified. The calculated adsorption energies range from -1.3 to -34.9 kcal/mol. It is found that the electrical conductivity of the nanocage can be modified upon the adsorption of CH3OH. The mechanism of methanol decomposition via CO and OH bond scissions is also studied. The results indicate that OH bond scission is the most favorable pathway on the B12N12 surface.

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.

Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

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

Bhaskaran, Renjith; Sarma, Manabendra, E-mail: msarma@iitg.ernet.in

2014-09-14

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed aftermore » impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.« less

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

2014-03-01

Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

Aromatic aldehyde-catalyzed gas-phase decarboxylation of amino acid anion via imine intermediate: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Xiang, Zhang

2013-10-01

It is generally appreciated that carbonyl compound can promote the decarboxylation of the amino acid. In this paper, we have performed the experimental and theoretical investigation into the gas-phase decarboxylation of the amino acid anion catalyzed by the aromatic aldehyde via the imine intermediate on the basis of the tandem mass spectrometry (MS/MS) technique and density functional theory (DFT) calculation. The results show that the aromatic aldehyde can achieve a remarkable catalytic effect. Moreover, the catalytic mechanism varies according to the type of amino acid: (i) The decarboxylation of α-amino acid anion is determined by the direct dissociation of the Csbnd C bond adjacent to the carboxylate, for the resulting carbanion can be well stabilized by the conjugation between α-carbon, Cdbnd N bond and benzene ring. (ii) The decarboxylation of non-α-amino acid anion proceeds via a SN2-like transition state, in which the dissociation of the Csbnd C bond adjacent to the carboxylate and attacking of the resulting carbanion to the Cdbnd N bond or benzene ring take place at the same time. Specifically, for β-alanine, the resulting carbanion preferentially attacks the benzene ring leading to the benzene anion, because attacking the Cdbnd N bond in the decarboxylation can produce the unstable three or four-membered ring anion. For the other non-α-amino acid anion, the Cdbnd N bond preferentially participates in the decarboxylation, which leads to the pediocratic nitrogen anion.

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.

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.

Potential energy surfaces and reaction dynamics of polyatomic molecules

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

Chang, Yan-Tyng

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogenmore » atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.« less

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

Electric dipole moments and chemical bonding of diatomic alkali-alkaline earth molecules.

PubMed

Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2016-02-17

We investigate the properties of alkali-alkaline earth diatomic molecules in the lowest Σ(+) states of the doublet and quartet multiplicity by ab initio calculations. In all sixteen cases studied, the permanent electric dipole moment points in opposite directions for the two spin states. This peculiarity can be explained by molecular orbital theory. We further discuss dissociation energies and bond distances. We analyze trends and provide an empirically motivated model for the prediction of the permanent electric dipole moment for combinations of alkali and alkaline earth atoms not studied in this work.

First-principles study of the stability of free-standing germanene in oxygen atmosphere

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

Liu, G.; College of Physics and Communication Electronics, Jiangxi Normal University, Nanchang 330022; Liu, S. B., E-mail: sbliu@bjut.edu.cn

2015-09-28

The O{sub 2} dissociation and O atoms adsorption on free-standing germanene are studied by using first-principles calculations in this paper. Compared with the extremely active silicene in oxygen atmosphere, germanene is found to be less active due to an energy barrier for dissociation of about 0.57 eV. Moreover, the dissociated oxygen atom follows two opposite migration pathways on the germanene surface, which is quite different from the case of silicene. Furthermore, the migration and desorption of O atoms at room temperature are relatively difficult due to the strong Ge-O bonding, resulting in the formation of germanium oxides. Our results reveal themore » interplay between germanene and O{sub 2} and suggest the enhanced stability of germanene in oxygen atmosphere compared with silicene.« less

Ab initio study of the positronation of the CaO and SrO molecules including calculation of annihilation rates.

PubMed

Buenker, Robert J; Liebermann, Heinz-Peter

2012-07-15

Ab initio multireference single- and double-excitation configuration interaction calculations have been performed to compute potential curves for ground and excited states of the CaO and SrO molecules and their positronic complexes, e(+)CaO, and e(+)SrO. The adiabatic dissociation limit for the (2)Σ(+) lowest states of the latter systems consists of the positive metal ion ground state (M(+)) and the OPs complex (e(+)O(-)), although the lowest energy limit is thought to be e(+)M + O. Good agreement is found between the calculated and experimental spectroscopic constants for the neutral diatomics wherever available. The positron affinity of the closed-shell X (1)Σ(+) ground states of both systems is found to lie in the 0.16-0.19 eV range, less than half the corresponding values for the lighter members of the alkaline earth monoxide series, BeO and MgO. Annihilation rates (ARs) have been calculated for all four positronated systems for the first time. The variation with bond distance is generally similar to what has been found earlier for the alkali monoxide series of positronic complexes, falling off gradually from the OPs AR value at their respective dissociation limits. The e(+)SrO system shows some exceptional behavior, however, with its AR value reaching a minimum at a relatively large bond distance and then rising to more than twice the OPs value close to its equilibrium distance. Copyright © 2012 Wiley Periodicals, Inc.

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.

Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas-phase peptide cation-radicals.

PubMed

Shaffer, Christopher J; Pepin, Robert; Tureček, František

2015-12-01

We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas-phase peptide cation-radicals produced by electron transfer dissociation. z-Type fragment ions (●) Gly-Gly-Lys(+), coordinated to 18-crown-6-ether (CE), are generated, selected by mass and photodissociated in the 200-400 nm region. The UVPD action spectra indicate the presence of valence-bond isomers differing in the position of the Cα radical defect, (α-Gly)-Gly-Lys(+) (CE), Gly-(α-Gly)-Lys(+) (CE) and Gly-Gly-(α-Lys(+))(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time-dependent density functional theory (TD-DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion-electron reactions. Specifically, z-type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd.

"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.

The adsorption and dissociation of oxygen on Ag (111) supported χ3 borophene

NASA Astrophysics Data System (ADS)

Luo, W. W.; Liu, G.; Wang, X.; Lei, X. L.; Ouyang, C. Y.; Liu, S. Q.

2018-05-01

The superstructure of χ3 borophene on Ag (111) has recently been synthesized in experiment. In this work, we investigate its structural, electronic properties and the oxidation mechanism through first-principles calculations. We find the superstructure of χ3 borophene on Ag (111) maintain the planar characteristics, like its free-standing form, owing to the weakly interaction between adsorbate and substrate. Moreover, oxygen molecule can be spontaneously adsorbed on its superstructure in a manner of chemical adsorption. Importantly, the energy barrier of ∼0.35 eV for oxygen dissociation indicates its relative stability in ambient conditions compared with the active silicene. Furthermore, the mobility of O2-dissociation-induced O atom is poor at room temperature, implying the difficult migration of O atom on borophene surface. On the other hand, due to the strong Bsbnd O bonding, desorption of O2-dissociation-induced O atoms on superstructure of χ3 borophene becomes impossible, ultimately leading to form the boron oxides.

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.

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.

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.

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

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

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.

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

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 Central

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, O2), where larger clusters with n≥4 were not detected. The mechanisms for the formation of the HF, F−(HF)n, and O2−(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 (ECM). These ECM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O2(HF)n]− (n=1–4) was discussed on the basis of the bond lengths of O2H–F−(HF)n and O2−H–F(HF)n obtained by ab initio calculations. The calculations indicated that [O2(HF)4]− separated into O2H and F−(HF)3. PMID:28966900

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 .

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

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)].

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.

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

Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes

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

Rios, Daniel; Schoendorff, George E.; Van Stipdonk, Michael J.

2012-12-03

Combined collision-induced dissociation mass-spectrometry experiments and DFT calculations were employed to elucidate the molecular structure of "hypercoordinated" species and the energetics of water-elimination reactions of uranyl acetone complexes observed in earlier work (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). It is shown that the "hypercoordinated" species contain diacetone alcohol ligands bonded in either bidentate or monodentate fashion, which are indistinguishable from (acetone)2 in mass spectrometry. Calculations confirm that four diacetone ligands can form stable complexes, but that the effective number of atoms coordinating with uranium in the equatorial plane doesmore » not exceed five. Diacetone alcohol ligands are shown to form mesityl oxide ligands and alkoxide species through the elimination of water, providing an explanation for the observed water-elimination reactions.« less

Adsorption and dissociation of molecular oxygen on α-Pu (0 2 0) surface: A density functional study

NASA Astrophysics Data System (ADS)

Wang, Jianguang; Ray, Asok K.

2011-09-01

Molecular and dissociative oxygen adsorptions on the α-Pu (0 2 0) surface have been systematically studied using the full-potential linearized augmented-plane-wave plus local orbitals (FP-LAPW+lo) basis method and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. Chemisorption energies have been optimized for the distance of the admolecule from the Pu surface and the bond length of O-O atoms for four adsorption sites and three approaches of O 2 admolecule to the (0 2 0) surface. Chemisorption energies have been calculated at the scalar relativistic level with no spin-orbit coupling (NSOC) and at the fully relativistic level with spin-orbit coupling (SOC). Dissociative adsorptions are found at the two horizontal approaches (O 2 is parallel to the surface and perpendicular/parallel to a lattice vector). Hor2 (O 2 is parallel to the surface and perpendicular to a lattice vector) approach at the one-fold top site is the most stable adsorption site, with chemisorption energies of 8.048 and 8.415 eV for the NSOC and SOC cases, respectively, and an OO separation of 3.70 Å. Molecular adsorption occurs at the Vert (O 2 is vertical to the surface) approach of each adsorption site. The calculated work functions and net spin magnetic moments, respectively, increase and decrease in all cases upon chemisorption compared to the clean surface. The partial charges inside the muffin-tins, the difference charge density distributions, and the local density of states have been used to investigate the Pu-admolecule electronic structures and bonding mechanisms.

Structural and spectroscopic investigation of glycinium oxalurate

NASA Astrophysics Data System (ADS)

Kavitha, T.; Pasupathi, G.; Marchewka, M. K.; Anbalagan, G.; Kanagathara, N.

2017-09-01

Glycinium oxalurate (GO) single crystals has been synthesized and grown by the slow solvent evaporation method at room temperature. Single crystal X-ray diffraction study confirms that GO crystal crystallizes in the monoclinic system with centrosymmetric space group P121/c1. The grown crystals are built up from single protonated glycinium residues and single dissociated oxalurate anions. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the glycine and oxaluric acid residues forms a three-dimensional network. Hydrogen bonded network present in the crystal gives notable vibrational effect. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on HF and density functional theory B3LYP methods with 6-311++G(d,p) basis set. Frontier molecular orbital energies and other related electronic properties are calculated. The natural bonding orbital (NBO) charges have been calculated and interpreted. The molecular electrostatic potential map has been constructed and discussed in detail.

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

FT-IR and FT-Raman characterization and investigation of reactive properties of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide by molecular dynamics simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Ranjith, P. K.; Al-Abdullah, Ebtehal S.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Anto, P. L.; Sheena, Mary Y.; Armaković, Stevan; Armaković, Sanja J.; Zitko, Jan; Dolezal, Martin; Van Alsenoy, C.

2017-05-01

The FT-IR and FT-Raman spectra of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide were recorded and the experimentally observed wavenumbers are compared with the theoretically obtained wavenumbers. The redshift of the Nsbnd H stretching mode in the IR spectrum from the computed value indicated the weakening of the Nsbnd H bond. The ring breathing modes of the phenyl ring and pyrazine ring are assigned at 819 and 952 cm-1 theoretically. Using natural bond orbital analysis, the stability of the molecule arising from hyperconjugative interaction and charge delocalization has been analyzed. The most reactive sites in the molecule were identified by molecular electrostatic potential map. The calculations of the average local ionization energy (ALIE) were used for visualization and determination of molecule sites possibly prone to electrophilic attacks. Further information on possible reactive centers of title molecule has been obtained by calculations of Fukui functions. Vulnerability of title molecule towards autoxidation mechanism was investigated by calculations of bond dissociation energies (BDE), while vulnerability towards hydrolysis was investigated by calculations of radial distribution functions (RDF) as obtained after molecular dynamics (MD) simulations. Molecular docking studies suggest that the compound might exhibit inhibitory activity against mGluRs.

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Roonasi, Payman; Assle taghipour, Khatoon; van der Spoel, David; Manzetti, Sergio

2015-07-01

The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including EHOMO, ELUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.

A theoretical study of the decomposition of gold (I) complexes

NASA Astrophysics Data System (ADS)

Tossell, J. A.

1998-04-01

Structures, energetics and excitation energies are calculated for the gold (I) complexes CH 3Au, (CH 3) 2Au -, CH 3AuOH 2, CH 3AuPH 3 and PH 3AuCl at the Hartree-Fock and MP2 levels of theory, and for CH 3AuP(CH 3) 3, CH 3AuP(OH) 3 and Au 3Cl 3 at the HF level. The lowest-energy neutral triplet state of each 2-coordinate compound dissociates into either two or three radical species (always including the CH 3 radical), with the exception of (CH 3) 2Au - which shows only slight Au-C bond elongation. In contrast, the doublet anion states dissociate neutral ligands, like PH 3, but do not dissociate CH 3. These results indicate that gold (I) chemical vapor deposition processes must involve excited states of the neutrals rather than their anions.

Excess charge driven dissociative hydrogen adsorption on Ti2O4.

PubMed

Song, Xiaowei; Fagiani, Matias R; Debnath, Sreekanta; Gao, Min; Maeda, Satoshi; Taketsugu, Tetsuya; Gewinner, Sandy; Schöllkopf, Wieland; Asmis, Knut R; Lyalin, Andrey

2017-08-30

The mechanism of dissociative D 2 adsorption on Ti 2 O 4 - , which serves as a model for an oxygen vacancy on a titania surface, is studied using infrared photodissociation spectroscopy in combination with density functional theory calculations and a recently developed single-component artificial force induced reaction method. Ti 2 O 4 - readily reacts with D 2 under multiple collision conditions in a gas-filled ion trap held at 16 K forming a global minimum-energy structure (DO-Ti-(O) 2 -Ti(D)-O) - . The highly exergonic reaction proceeds quasi barrier-free via several intermediate species, involving heterolytic D 2 -bond cleavage followed by D-atom migration. We show that, compared to neutral Ti 2 O 4 , the excess negative charge in Ti 2 O 4 - is responsible for the substantial lowering of the D 2 dissociation barrier, but does not affect the molecular D 2 adsorption energy in the initial physisorption step.

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

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

PubMed

Velez-Vega, Camilo; Gilson, Michael K

2012-03-13

The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella sampling simulations and used to compute time-averaged mechanical stresses along the dissociation pathways. The stress calculations proved to be informative regarding the key interactions determining the length-force profiles and rupture forces. In particular, the unbinding transition of one complex is found to be a stepwise process, which is initially dominated by electrostatic interactions between the guest's ammoniums and the host's carbonyl groups, and subsequently limited by the extraction of the guest's bulky bicyclooctane moiety; the latter step requires some bond stretching at the cucurbituril's extraction portal. Conversely, the dissociation of a second complex with a more slender guest is mainly driven by successive electrostatic interactions between the different guest's ammoniums and the host's carbonyl groups. The calculations also provide information on the origins of thermodynamic irreversibilities in these forced dissociation processes.

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.

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.

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.

Reductive Elimination from Phosphine-Ligated Alkylpalladium(II) Amido Complexes To Form sp3 Carbon-Nitrogen Bonds.

PubMed

Peacock, D Matthew; Jiang, Quan; Hanley, Patrick S; Cundari, Thomas R; Hartwig, John F

2018-04-11

We report the formation of phosphine-ligated alkylpalladium(II) amido complexes that undergo reductive elimination to form alkyl-nitrogen bonds and a combined experimental and computational investigation of the factors controlling the rates of these reactions. The free-energy barriers to reductive elimination from t-Bu 3 P-ligated complexes were significantly lower (ca. 3 kcal/mol) than those previously reported from NHC-ligated complexes. The rates of reactions from complexes containing a series of electronically and sterically varied anilido ligands showed that the reductive elimination is slower from complexes of less electron-rich or more sterically hindered anilido ligands than from those containing more electron-rich and less hindered anilido ligands. Reductive elimination of alkylamines also occurred from complexes bearing bidentate P,O ligands. The rates of reactions of these four-coordinate complexes were slower than those for reactions of the three-coordinate, t-Bu 3 P-ligated complexes. The calculated pathway for reductive elimination from rigid, 2-methoxyarylphosphine-ligated complexes does not involve initial dissociation of the oxygen. Instead, reductive elimination is calculated to occur directly from the four-coordinate complex in concert with a lengthening of the Pd-O bond. To investigate this effect experimentally, a four-coordinate Pd(II) anilido complex containing a flexible, aliphatic linker between the P and O atoms was synthesized. Reductive elimination from this complex was faster than that from the analogous complex containing the more rigid, aryl linker. The flexible linker enables full dissociation of the ether ligand during reductive elimination, leading to the faster reaction of this complex.

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.

Absolute photoionization cross sections of furanic fuels: 2-ethylfuran, 2-acetylfuran and furfural.

PubMed

Smith, Audrey R; Meloni, Giovanni

2015-11-01

Absolute photoionization cross sections of the molecules 2-ethylfuran, 2-acetylfuran and furfural, including partial ionization cross sections for the dissociative ionized fragments, are measured for the first time. These measurements are important because they allow fuel quantification via photoionization mass spectrometry and the development of quantitative kinetic modeling for the complex combustion of potential fuels. The experiments are carried out using synchrotron photoionization mass spectrometry with an orthogonal time-of-flight spectrometer used for mass analysis at the Advanced Light Source of Lawrence Berkeley National Laboratory. The CBS-QB3 calculations of adiabatic ionization energies and appearance energies agree well with the experimental results. Several bond dissociation energies are also derived and presented. Copyright © 2015 John Wiley & Sons, Ltd.

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.

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.

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

Unimolecular Thermal Fragmentation of Ortho-Benzyne

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

Zhang, X.; Maccarone, A. T.; Nimlos, M. R.

2007-01-01

The ortho-benzyne diradical, o-C{sub 6}H{sub 4} has been produced with a supersonic nozzle and its subsequent thermal decomposition has been studied. As the temperature of the nozzle is increased, the benzyne molecule fragments: o-C{sub 6}H{sub 4} + {Delta} {yields} products. The thermal dissociation products were identified by three experimental methods: (i) time-of-flight photoionization mass spectrometry, (ii) matrix-isolation Fourier transform infrared absorption spectroscopy, and (iii) chemical ionization mass spectrometry. At the threshold dissociation temperature, o-benzyne cleanly decomposes into acetylene and diacetylene via an apparent retro-Diels-Alder process: o-C{sub 6}H{sub 4} + {Delta} {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH. The experimentalmore » {Delta}{sub rxn}H{sub 298}(o-C{sub 6}H{sub 4} {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH) is found to be 57 {+-} 3 kcal mol{sup -1}. Further experiments with the substituted benzyne, 3,6-(CH{sub 3}){sub 2}-o-C{sub 6}H{sub 2}, are consistent with a retro-Diels-Alder fragmentation. But at higher nozzle temperatures, the cracking pattern becomes more complicated. To interpret these experiments, the retro-Diels-Alder fragmentation of o-benzyne has been investigated by rigorous ab initio electronic structure computations. These calculations used basis sets as large as [C(7s6p5d4f3g2h1i)/H(6s5p4d3f2g1h)] (cc-pV6Z) and electron correlation treatments as extensive as full coupled cluster through triple excitations (CCSDT), in cases with a perturbative term for connected quadruples [CCSDT(Q)]. Focal point extrapolations of the computational data yield a 0 K barrier for the concerted, C{sub 2v}-symmetric decomposition of o-benzyne, E{sub b}(o-C{sub 6}H{sub 4} {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH) = 88.0 {+-} 0.5 kcal mol{sup -1}. A barrier of this magnitude is consistent with the experimental results. A careful assessment of the thermochemistry for the high temperature fragmentation of benzene is presented: C{sub 6}H{sub 6} {yields} H+[C{sub 6}H{sub 5}] {yields} H+[o-C{sub 6}H{sub 4}] {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH. Benzyne may be an important intermediate in the thermal decomposition of many alkylbenzenes (arenes). High engine temperatures above 1500 K may crack these alkylbenzenes to a mixture of alkyl radicals and phenyl radicals. The phenyl radicals will then dissociate first to benzyne and then to acetylene and diacetylene.« less

Unimolecular thermal fragmentation of ortho-benzene.

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

Zhang, X.; Maccarone, A. T.; Nimlos, M. R.

2007-01-01

The ortho-benzyne diradical, o-C{sub 6}H{sub 4} has been produced with a supersonic nozzle and its subsequent thermal decomposition has been studied. As the temperature of the nozzle is increased, the benzyne molecule fragments o-C{sub 6}H{sub 4}{sup +} {Delta} {yields} products. The thermal dissociation products were identified by three experimental methods: (i) time-of-flight photoionization mass spectrometry, (ii) matrix-isolation Fourier transform infrared absorption spectroscopy, and (iii) chemical ionization mass spectrometry. At the threshold dissociation temperature, o-benzyne cleanly decomposes into acetylene and diacetylene via an apparent retro-Diels-Alder process: o-C{sub 6}H{sub 4}{sup +}{Delta}{yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH. The experimental {Delta}{sub rxn}H{submore » 298}(o-C{sub 6}H{sub 4} {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH) is found to be 57 {+-} 3 kcal mol{sup -1}. Further experiments with the substituted benzyne, 3,6-(CH{sub 3}){sub 2}-o-C{sub 6}H{sub 2}, are consistent with a retro-Diels-Alder fragmentation. But at higher nozzle temperatures, the cracking pattern becomes more complicated. To interpret these experiments, the retro-Diels-Alder fragmentation of o-benzyne has been investigated by rigorous ab initio electronic structure computations. These calculations used basis sets as large as [C(7s6p5d4f3g2h1i)/H(6s5p4d3f2g1h)] (cc-pV6Z) and electron correlation treatments as extensive as full coupled cluster through triple excitations (CCSDT), in cases with a perturbative term for connected quadruples [CCSDT(Q)]. Focal point extrapolations of the computational data yield a 0 K barrier for the concerted, C{sub 2v}-symmetric decomposition of o-benzyne, E{sub b}(o-C{sub 6}H{sub 4} {yields} HC {triple_bond} CH+HC {triple_bond} C-C {triple_bond} CH) = 88.0 {+-} 0.5 kcal mol{sup -1}. A barrier of this magnitude is consistent with the experimental results. A careful assessment of the thermochemistry for the high temperature fragmentation of benzene is presented: C{sub 6}H{sub 6} {yields} H+[C{sub 6}H{sub 5}] {yields} H+[o-C{sub 6}H{sub 4}] {yields} HC {triple_bond} CH-HC {triple_bond} C-C {triple_bond} CH. Benzyne may be an important intermediate in the thermal decomposition of many alkylbenzenes (arenes). High engine temperatures above 1500 K may crack these alkylbenzenes to a mixture of alkyl radicals and phenyl radicals. The phenyl radicals will then dissociate first to benzyne and then to acetylene and diacetylene.« less

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...

Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.

2017-02-01

IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

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.

How Hot are Your Ions Really? A Threshold Collision-Induced Dissociation Study of Substituted Benzylpyridinium "Thermometer" Ions

NASA Astrophysics Data System (ADS)

Carpenter, John E.; McNary, Christopher P.; Furin, April; Sweeney, Andrew F.; Armentrout, P. B.

2017-09-01

The first absolute experimental bond dissociation energies (BDEs) for the main heterolytic bond cleavages of four benzylpyridinium "thermometer" ions are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. In this experiment, substituted benzylpyridinium ions are introduced into the apparatus using an electrospray ionization source, thermalized, and collided with Xe at varied kinetic energies to determine absolute cross-sections for these reactions. Various effects are accounted for, including kinetic shifts, multiple collisions, and internal and kinetic energy distributions. These experimentally measured 0 K BDEs are compared with computationally predicted values at the B3LYP-GD3BJ, M06-GD3, and MP2(full) levels of theory with a 6-311+G(2d,2p) basis set using vibrational frequencies and geometries determined at the B3LYP/6-311+G(d,p) level. Additional dissociation pathways are observed for nitrobenzylpyridinium experimentally and investigated using these same levels of theory. Experimental BDEs are also compared against values in the literature at the AM1, HF, B3LYP, B3P86, and CCSD(T) levels of theory. Of the calculated values obtained in this work, the MP2(full) level of theory with counterpoise corrections best reproduces the experimental results, as do the similar literature CCSD(T) values. Lastly, the survival yield method is used to determine the characteristic temperature (Tchar) of the electrospray source prior to the thermalization region and to confirm efficient thermalization. [Figure not available: see fulltext.

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.

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

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.

Communication: Infrared spectroscopy of protonated allyl-trimethylsilane: Evidence for the β-silyl effect

NASA Astrophysics Data System (ADS)

Chiavarino, Barbara; Crestoni, Maria Elisa; Lemaire, Joel; Maitre, Philippe; Fornarini, Simonetta

2013-08-01

β-trimethylsilyl-2-propyl cation has been formed by the gas phase protonation of allyl-trimethylsilane and characterized by infrared multiple photon dissociation spectroscopy. The experimental Cβ-Cα+ stretching feature at 1586 cm-1, remarkably blue-shifted with respect to a C-C single bond stretching mode, is indicative of high double bond character, a signature of β-stabilizing effect due to hyperconjugation of the trimethylsilyl group in the β-position with respect to the positively charged carbon. Density functional theory calculations at the B3LYP/6-311++G(2df,2p) level yield the optimized geometries and IR spectra for candidate isomeric cations and for neutral and charged reference species.

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.

Significance of β-dehydrogenation in ethanol electro-oxidation on platinum doped with Ru, Rh, Pd, Os and Ir.

PubMed

Sheng, Tian; Lin, Wen-Feng; Hardacre, Christopher; Hu, P

2014-07-14

In the exploration of highly efficient direct ethanol fuel cells (DEFCs), how to promote the CO2 selectivity is a key issue which remains to be solved. Some advances have been made, for example, using bimetallic electrocatalysts, Rh has been found to be an efficient additive to platinum to obtain high CO2 selectivity experimentally. In this work, the mechanism of ethanol electrooxidation is investigated using the first principles method. It is found that CH3CHOH* is the key intermediate during ethanol electrooxidation and the activity of β-dehydrogenation is the rate determining factor that affects the completeness of ethanol oxidation. In addition, a series of transition metals (Ru, Rh, Pd, Os and Ir) are alloyed on the top layer of Pt(111) in order to analyze their effects. The elementary steps, α-, β-C-H bond and C-C bond dissociations, are calculated on these bimetallic M/Pt(111) surfaces and the formation potential of OH* from water dissociation is also calculated. We find that the active metals increase the activity of β-dehydrogenation but lower the OH* formation potential resulting in the active site being blocked. By considering both β-dehydrogenation and OH* formation, Ru, Os and Ir are identified to be unsuitable for the promotion of CO2 selectivity and only Rh is able to increase the selectivity of CO2 in DEFCs.

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.

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.

Structural elucidation of direct analysis in real time ionized nerve agent simulants with infrared multiple photon dissociation spectroscopy.

PubMed

Rummel, Julia L; Steill, Jeffrey D; Oomens, Jos; Contreras, Cesar S; Pearson, Wright L; Szczepanski, Jan; Powell, David H; Eyler, John R

2011-06-01

Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds.

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.

Structure of a Water Monolayer on the Anatase TiO2(101) Surface

NASA Astrophysics Data System (ADS)

Patrick, Christopher E.; Giustino, Feliciano

2014-07-01

Titanium dioxide (TiO2) plays a central role in the study of artificial photosynthesis, owing to its ability to perform photocatalytic water splitting. Despite over four decades of intense research efforts in this area, there is still some debate over the nature of the first water monolayer on the technologically relevant anatase TiO2(101) surface. In this work, we use first-principles calculations to reverse engineer the experimental high-resolution x-ray photoelectron spectra measured for this surface by Walle et al. [J. Phys. Chem. C 115, 9545 (2011)] and find evidence supporting the existence of a mix of dissociated and molecular water in the first monolayer. Using both semilocal and hybrid functional calculations, we revise the current understanding of the adsorption energetics by showing that the energetic cost of water dissociation is reduced via the formation of a hydrogen-bonded hydroxyl-water complex. We also show that such a complex can provide an explanation of an unusual superstructure observed in high-resolution scanning tunneling microscopy experiments.

Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-01-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

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.

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.

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.

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

Koch, D.; Fertitta, E.; Paulus, B.

Due to the importance of both static and dynamical correlation in the bond formation, low-dimensional beryllium systems constitute interesting case studies to test correlation methods. Aiming to describe the whole dissociation curve of extended Be systems we chose to apply the method of increments (MoI) in its multireference (MR) formalism. To gain insight into the main characteristics of the wave function, we started by focusing on the description of small Be chains using standard quantum chemical methods. In a next step we applied the MoI to larger beryllium systems, starting from the Be{sub 6} ring. The complete active space formalismmore » was employed and the results were used as reference for local MR calculations of the whole dissociation curve. Although this is a well-established approach for systems with limited multireference character, its application regarding the description of whole dissociation curves requires further testing. Subsequent to the discussion of the role of the basis set, the method was finally applied to larger rings and extrapolated to an infinite chain.« less

Dissociation and reconstruction of double-decker bis(phthalocyaninato) terbium(III) complex (TbPc2) on Pd(001): A theoretical investigation

NASA Astrophysics Data System (ADS)

Liu, Heng; Hu, Yujie; Wang, Hao; Jiang, Bo; Xu, Xuechun; Cai, Yingxiang

2017-01-01

The study of molecule dissociation is helpful to disclose the nature of chemical bonds and to extend molecular functions. The double-decker bis(phthalocyaninato) terbium(III) complex (TbPc2) is a promising single-molecule magnet (SMM) which exhibits potential applications in spin-devices. In this study, we investigate the dissociation and reconstruction of TbPc2 on Pd(001) surface. The results show that a single TbPc2 adsorbed on Pd(001) tends to split into Pc/Pd(001)+TbPc. However, the TbPc/Pd(001)+Pc might also be observed in an experimental study due to only a slight difference in their dissociation energy. The TbPc2 molecules on Pd(001) will form a (5×3) reconstruction which is different from the (3×4) reconstruction of PbPc on Pd(001). If the TbPc2 molecules with (5×3) reconstruction is dissociated, this reconstruction will be inherited by its daughter molecules due to strong molecule-substrate interaction. In addition, nudged elastic band (NEB) calculation shows that Tb-down is the stable state of TbPc/Pd(001) and Tb-up is a metastable state. The transition between two states might be utilized to realize TbPc's switch or storage functions.

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.

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.

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

Orbital-free bond breaking via machine learning

NASA Astrophysics Data System (ADS)

Snyder, John C.; Rupp, Matthias; Hansen, Katja; Blooston, Leo; Müller, Klaus-Robert; Burke, Kieron

2013-12-01

Using a one-dimensional model, we explore the ability of machine learning to approximate the non-interacting kinetic energy density functional of diatomics. This nonlinear interpolation between Kohn-Sham reference calculations can (i) accurately dissociate a diatomic, (ii) be systematically improved with increased reference data and (iii) generate accurate self-consistent densities via a projection method that avoids directions with no data. With relatively few densities, the error due to the interpolation is smaller than typical errors in standard exchange-correlation functionals.

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

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

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

Bonding of Alkali-Alkaline Earth Molecules in the Lowest Σ^+ States of Doublet and Quartet Multiplicity

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Hauser, Andreas W.; Ernst, Wolfgang E.

2016-06-01

n the present study the ground state as well as the lowest ^4Σ^+ state were determined for 16 AK-AKE molecules. Multireference configuration interaction calculations were carried out in order to understand the bonding of diatomic alkali-alkaline earth (AK-AKE) molecules. The correlations between molecular properties (disociation energy, bond distances, electric dipole moment) and atomic properties (electronegativity, polarizability) will be discussed. A correlation between the dissociation energy and the dipole moment of the lowest ^4Σ^+ state was observed, while the dipole moment of the lowest ^2Σ^+ state does not show such a simple dependency. In this case an empirical relation could be established. The class of AK-AKE molecules was selected for this investigation due to their possible applications in ultracold molecular physics. J. V. Pototschnig, A. W. Hauser and W. E. Ernst, Phys. Chem. Chem. Phys., 2016,18, 5964-5973

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.

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.

Curcumin derivatives as metal-chelating agents with potential multifunctional activity for pharmaceutical applications.

PubMed

Ferrari, Erika; Benassi, Rois; Sacchi, Stefania; Pignedoli, Francesca; Asti, Mattia; Saladini, Monica

2014-10-01

Curcuminoids represent new perspectives for the development of novel therapeutics for Alzheimer's disease (AD), one probable mechanism of action is related to their metal complexing ability. In this work we examined the metal complexing ability of substituted curcuminoids to propose new chelating molecules with biological properties comparable with curcumin but with improved stability as new potential AD therapeutic agents. The K2T derivatives originate from the insertion of a -CH2COOC(CH3)3 group on the central atom of the diketonic moiety of curcumin. They retain the diketo-ketoenol tautomerism which is solvent dependent. In aqueous solution the prevalent form is the diketo one but the addition of metal ion (Ga(3+), Cu(2+)) causes the dissociation of the enolic proton creating chelate complexes and shifting the tautomeric equilibrium towards the keto-enol form. The formation of metal complexes is followed by both NMR and UV-vis spectroscopy. The density functional theory (DFT) calculations on K2T21 complexes with Ga(3+) and Cu(2+) are performed and compared with those on curcumin complexes. [Ga(K2T21)2(H2O)2](+) was found more stable than curcumin one. Good agreement is detected between calculated and experimental (1)H and (13)C NMR data. The calculated OH bond dissociation energy (BDE) and the OH proton dissociation enthalpy (PDE), allowed to predict the radical scavenging ability of the metal ion complexed with K2T21, while the calculated electronic affinity (EA) and ionization potential (IP) represent yardsticks of antioxidant properties. Eventually theoretical calculations suggest that the proton-transfer-associated superoxide-scavenging activity is enhanced after binding metal ions, and that Ga(3+) complexes display possible superoxide dismutase (SOD)-like activity. Copyright © 2014 Elsevier Inc. All rights reserved.

Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.

2016-01-01

We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

Magnetic behavior of Si-Ge bond in SixGe4-x nano-clusters

NASA Astrophysics Data System (ADS)

Nahali, Masoud; Mehri, Ali

2018-06-01

The structure of SixGe4-x nano-clusters were optimized by MPW1B95 level of theory using MG3S and SDB-aug-cc-PVTZ basis set. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. Since the Si-Si bond is stronger than Si-Ge and Ge-Ge bonds, the Si-Si, Si-Ge, and Ge-Ge diagonal bonds determine the precedence of the stability in these nano-clusters. The hybrid meta density functional calculations were carried out to investigate the adsorption of CO on all possible SixGe4-x nano-clusters. It was found that the silicon atom generally makes a stronger bond with CO than germanium and thereby preferentially affects the shape of structures having higher multiplicity. In Si-Ge structures with higher spin more than 95% of spins accumulate on positions with less bonds to other atoms of the cluster. Through CO adsorption on these clusters bridge structures are made that behave as spin bridge which conduct the spin from the nano-cluster surface to the adsorbate atoms. A better understanding of bridged structures was achieved upon introducing the 'spin bridge' concept. Based on exhaustive spin density analysis, it was found that the reason for the extra negative charge on oxygen in the bridged structures is the relocation of spin from the surface through the bridge.

Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

NASA Astrophysics Data System (ADS)

Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay

2017-02-01

FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.

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

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.

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.

Assessing the distinguishable cluster approximation based on the triple bond-breaking in the nitrogen molecule

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

Rishi, Varun; Perera, Ajith; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

2016-03-28

Obtaining the correct potential energy curves for the dissociation of multiple bonds is a challenging problem for ab initio methods which are affected by the choice of a spin-restricted reference function. Coupled cluster (CC) methods such as CCSD (coupled cluster singles and doubles model) and CCSD(T) (CCSD + perturbative triples) correctly predict the geometry and properties at equilibrium but the process of bond dissociation, particularly when more than one bond is simultaneously broken, is much more complicated. New modifications of CC theory suggest that the deleterious role of the reference function can be diminished, provided a particular subset of termsmore » is retained in the CC equations. The Distinguishable Cluster (DC) approach of Kats and Manby [J. Chem. Phys. 139, 021102 (2013)], seemingly overcomes the deficiencies for some bond-dissociation problems and might be of use in quasi-degenerate situations in general. DC along with other approximate coupled cluster methods such as ACCD (approximate coupled cluster doubles), ACP-D45, ACP-D14, 2CC, and pCCSD(α, β) (all defined in text) falls under a category of methods that are basically obtained by the deletion of some quadratic terms in the double excitation amplitude equation for CCD/CCSD (coupled cluster doubles model/coupled cluster singles and doubles model). Here these approximate methods, particularly those based on the DC approach, are studied in detail for the nitrogen molecule bond-breaking. The N{sub 2} problem is further addressed with conventional single reference methods but based on spatial symmetry-broken restricted Hartree–Fock (HF) solutions to assess the use of these references for correlated calculations in the situation where CC methods using fully symmetry adapted SCF solutions fail. The distinguishable cluster method is generalized: 1) to different orbitals for different spins (unrestricted HF based DCD and DCSD), 2) by adding triples correction perturbatively (DCSD(T)) and iteratively (DCSDT-n), and 3) via an excited state approximation through the equation of motion (EOM) approach (EOM-DCD, EOM-DCSD). The EOM-CC method is used to identify lower-energy CC solutions to overcome singularities in the CC potential energy curves. It is also shown that UHF based CC and DC methods behave very similarly in bond-breaking of N{sub 2}, and that using spatially broken but spin preserving SCF references makes the CCSD solutions better than those for DCSD.« less

Investigations on the fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene by certain flavonoids.

PubMed

Anbazhagan, V; Kalaiselvan, A; Jaccob, M; Venuvanalingam, P; Renganathan, R

2008-05-29

The fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) by seven flavonoids namely flavone, flavanone, quercetin, rutin, genistein, diadzein and chrysin has been investigated in acetonitrile and dichloromethane solvents. The bimolecular quenching rate constants lie in the range of 0.09-5.75 x 10(9)M(-1)s(-1) and are explained in terms of structure of the flavonoids studied. The reactivity of flavonoids are in the order: quercetin>rutin>genistein>diadzein>chrysin>flavone>flavanone. The quenching rate constants (k(q)) increase with increase in the number of -OH groups. The endergonic thermodynamic values of DeltaG(et) reveal that electron transfer quenching mechanism can be ruled out. Bond dissociation enthalpy calculations reveal that the position of -OH is important. Further in vitro-antioxidant activities of flavonoids were evaluated with rat liver catalase by gel electrophoresis. The deuterium isotope effect thus observed in this work provides evidence for hydrogen abstraction involved in the quenching process of singlet excited DBO by flavonoids. The data suggest the involvement of direct hydrogen atom transfer (radical scavenging) in the fluorescence quenching of DBO. Bond dissociation enthalpy calculation performed at B3LYP/6-31G(p')//B3LYP/3-21G level are in excellent agreement with the above observations and further reveal that the number OH groups and position of them decide the quenching ability of the flavonoids.

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).

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

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.

Ground and excited state dissociation dynamics of ionized 1,1-difluoroethene.

PubMed

Gridelet, E; Dehareng, D; Locht, R; Lorquet, A J; Lorquet, J C; Leyh, B

2005-09-22

The kinetic energy release distributions (KERDs) for the fluorine atom loss from the 1,1-difluoroethene cation have been recorded with two spectrometers in two different energy ranges. A first experiment uses dissociative photoionization with the He(I) and Ne(I) resonance lines, providing the ions with a broad internal energy range, up to 7 eV above the dissociation threshold. The second experiment samples the metastable range, and the average ion internal energy is limited to about 0.2 eV above the threshold. In both energy domains, KERDs are found to be bimodal. Each component has been analyzed by the maximum entropy method. The narrow, low kinetic energy components display for both experiments the characteristics of a statistical, simple bond cleavage reaction: constraint equal to the square root of the fragment kinetic energy and ergodicity index higher than 90%. Furthermore, this component is satisfactorily accounted for in the metastable time scale by the orbiting transition state theory. Potential energy surfaces corresponding to the five lowest electronic states of the dissociating 1,1-C2H2F2+ ion have been investigated by ab initio calculations at various levels. The equilibrium geometry of these states, their dissociation energies, and their vibrational wavenumbers have been calculated, and a few conical intersections between these surfaces have been identified. It comes out that the ionic ground state X2B1 is adiabatically correlated with the lowest dissociation asymptote. Its potential energy curve increases in a monotonic way along the reaction coordinate, giving rise to the narrow KERD component. Two states embedded in the third photoelectron band (B2A1 at 15.95 eV and C2B2 at 16.17 eV) also correlate with the lowest asymptote at 14.24 eV. We suggest that their repulsive behavior along the reaction coordinate be responsible for the KERD high kinetic energy contribution.

Water dissociation on Ni(100), Ni(110), and Ni(111) surfaces: Reaction path approach to mode selectivity

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

Seenivasan, H.; Jackson, Bret; Tiwari, Ashwani K.

We performed a comparative study of mode-selectivity of water dissociation on Ni(100), Ni(110), and Ni(111) surfaces at the same level of theory using a fully quantum approach based on the reaction path Hamiltonian. Calculations show that the barrier to water dissociation on the Ni(110) surface is significantly lower compared to its close-packed counterparts. Transition states for this reaction on all three surfaces involve the elongation of one of the O–H bonds. Furthermore, a significant decrease in the symmetric stretching and bending mode frequencies near the transition state is observed in all three cases and in the vibrational adiabatic approximation, excitationmore » of these softened modes results in a significant enhancement in reactivity. Inclusion of non-adiabatic couplings between modes results in the asymmetric stretching mode showing a similar enhancement of reactivity as the symmetric stretching mode. Dissociation probabilities calculated at a surface temperature of 300 K showed higher reactivity at lower collision energies compared to that of the static surface case, underlining the importance of lattice motion in enhancing reactivity. Mode selective behavior is similar on all the surfaces. Molecules with one-quantum of vibrational excitation in the symmetric stretch, at lower energies (up to 0.45 eV), are more reactive on Ni(110) than the Ni(100) and Ni(111) surfaces. But, the dissociation probabilities approach saturation on all the surfaces at higher incident energy values. Ultimately, Ni(110) is found to be highly reactive toward water dissociation among the low-index nickel surfaces owing to a low reaction barrier resulting from the openness and corrugation of the surface. These results show that the mode-selective behavior does not vary with different crystal facets of Ni qualitatively, but there is a significant quantitative effect.« less

Water dissociation on Ni(100), Ni(110), and Ni(111) surfaces: Reaction path approach to mode selectivity

DOE PAGES

Seenivasan, H.; Jackson, Bret; Tiwari, Ashwani K.

2017-02-17

We performed a comparative study of mode-selectivity of water dissociation on Ni(100), Ni(110), and Ni(111) surfaces at the same level of theory using a fully quantum approach based on the reaction path Hamiltonian. Calculations show that the barrier to water dissociation on the Ni(110) surface is significantly lower compared to its close-packed counterparts. Transition states for this reaction on all three surfaces involve the elongation of one of the O–H bonds. Furthermore, a significant decrease in the symmetric stretching and bending mode frequencies near the transition state is observed in all three cases and in the vibrational adiabatic approximation, excitationmore » of these softened modes results in a significant enhancement in reactivity. Inclusion of non-adiabatic couplings between modes results in the asymmetric stretching mode showing a similar enhancement of reactivity as the symmetric stretching mode. Dissociation probabilities calculated at a surface temperature of 300 K showed higher reactivity at lower collision energies compared to that of the static surface case, underlining the importance of lattice motion in enhancing reactivity. Mode selective behavior is similar on all the surfaces. Molecules with one-quantum of vibrational excitation in the symmetric stretch, at lower energies (up to 0.45 eV), are more reactive on Ni(110) than the Ni(100) and Ni(111) surfaces. But, the dissociation probabilities approach saturation on all the surfaces at higher incident energy values. Ultimately, Ni(110) is found to be highly reactive toward water dissociation among the low-index nickel surfaces owing to a low reaction barrier resulting from the openness and corrugation of the surface. These results show that the mode-selective behavior does not vary with different crystal facets of Ni qualitatively, but there is a significant quantitative effect.« less

Pyridine adsorption and diffusion on Pt(111) investigated with density functional theory

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

Kolsbjerg, Esben L.; Groves, Michael N.; Hammer, Bjørk, E-mail: hammer@phys.au.dk

2016-04-28

The adsorption, diffusion, and dissociation of pyridine, C{sub 5}H{sub 5}N, on Pt(111) are investigated with van der Waals-corrected density functional theory. An elaborate search for local minima in the adsorption potential energy landscape reveals that the intact pyridine adsorbs with the aromatic ring parallel to the surface. Piecewise interconnections of the local minima in the energy landscape reveal that the most favourable diffusion path for pyridine has a barrier of 0.53 eV. In the preferred path, the pyridine remains parallel to the surface while performing small single rotational steps with a carbon-carbon double bond hinged above a single Pt atom.more » The origin of the diffusion pathway is discussed in terms of the C{sub 2}–Pt π-bond being stronger than the corresponding CN–Pt π-bond. The energy barrier and reaction enthalpy for dehydrogenation of adsorbed pyridine into an adsorbed, upright bound α-pyridyl species are calculated to 0.71 eV and 0.18 eV, respectively (both zero-point energy corrected). The calculations are used to rationalize previous experimental observations from the literature for pyridine on Pt(111).« less

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

NASA Astrophysics Data System (ADS)

Sørensen, L. K.; Fleig, T.; Olsen, J.

2009-08-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Theoretical study on the ground state of the polar alkali-metal-barium molecules: Potential energy curve and permanent dipole moment

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

Gou, Dezhi; Kuang, Xiaoyu, E-mail: scu-kuang@163.com; Gao, Yufeng

2015-01-21

In this paper, we systematically investigate the electronic structure for the {sup 2}Σ{sup +} ground state of the polar alkali-metal-alkaline-earth-metal molecules BaAlk (Alk = Li, Na, K, Rb, and Cs). Potential energy curves and permanent dipole moments (PDMs) are determined using power quantum chemistry complete active space self-consistent field and multi-reference configuration interaction methods. Basic spectroscopic constants are derived from ro-vibrational bound state calculation. From the calculations, it is shown that BaK, BaRb, and BaCs molecules have moderate values of PDM at the equilibrium bond distance (BaK:1.62 D, BaRb:3.32 D, and BaCs:4.02 D). Besides, the equilibrium bond length (4.93 Åmore » and 5.19 Å) and dissociation energy (0.1825 eV and 0.1817 eV) for the BaRb and BaCs are also obtained.« less

Oxidation of InP nanowires: a first principles molecular dynamics study.

PubMed

Berwanger, Mailing; Schoenhalz, Aline L; Dos Santos, Cláudia L; Piquini, Paulo

2016-11-16

InP nanowires are candidates for optoelectronic applications, and as protective capping layers of III-V core-shell nanowires. Their surfaces are oxidized under ambient conditions which affects the nanowire physical properties. The majority of theoretical studies of InP nanowires, however, do not take into account the oxide layer at their surfaces. In this work we use first principles molecular dynamics electronic structure calculations to study the first steps in the oxidation process of a non-saturated InP nanowire surface as well as the properties of an already oxidized surface of an InP nanowire. Our calculations show that the O 2 molecules dissociate through several mechanisms, resulting in incorporation of O atoms into the surface layers. The results confirm the experimental observation that the oxidized layers become amorphous but the non-oxidized core layers remain crystalline. Oxygen related bonds at the oxidized layers introduce defective levels at the band gap region, with greater contributions from defects involving In-O and P-O bonds.

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

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.

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.

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.

Enhanced role of Al or Ga-doped graphene on the adsorption and dissociation of N2O under electric field.

PubMed

Lv, Yong-an; Zhuang, Gui-lin; Wang, Jian-guo; Jia, Ya-bo; Xie, Qin

2011-07-21

To find an effective strategy for the capture and decomposition of nitrous oxide (N(2)O) is very important in order to protect the ozone layer and control the effects of global warming. Based on first-principles calculations, such a strategy is proposed by the systemic study of N(2)O interaction with pristine and Al (or Ga)-doped graphene, and N(2)O dissociation on the surface of Al (or Ga)-doped graphene in an applied electric field. The calculated adsorption energy value shows the N(2)O molecule more firmly adsorbs on the surface of Al (or Ga)-doped graphene than that of pristine graphene, deriving from a stronger covalent bond between the N(2)O molecule and the Al (or Ga) atom. Furthermore, our study suggests that N(2)O molecules can be easily decomposed to N(2) and O(2) with the appropriate electric field, which reveals that Al-doped graphene may be a new candidate for control of N(2)O. This journal is © the Owner Societies 2011

A theoretical study of the structure and thermochemical properties of alkali metal fluoroplumbates MPbF3.

PubMed

Boltalin, A I; Korenev, Yu M; Sipachev, V A

2007-07-19

Molecular constants of MPbF3 (M=Li, Na, K, Rb, and Cs) were calculated theoretically at the MP2(full) and B3LYP levels with the SDD (Pb, K, Rb, and Cs) and cc-aug-pVQZ (F, Li, and Na) basis sets to determine the thermochemical characteristics of the substances. Satisfactory agreement with experiment was obtained, including the unexpected nonmonotonic dependence of substance dissociation energies on the alkali metal atomic number. The bond lengths of the theoretical CsPbF3 model were substantially elongated compared with experimental estimates, likely because of errors in both theoretical calculations and electron diffraction data processing.

Hugoniot equation of state of Si-doped glow discharge polymer and scaling to other plastic ablators

NASA Astrophysics Data System (ADS)

Huser, G.; Ozaki, N.; Colin-Lalu, P.; Recoules, V.; Sano, T.; Sakawa, Y.; Miyanishi, K.; Kodama, R.

2018-05-01

Pressure, density, and temperature were measured along the principal Hugoniot of the Si-doped Glow Discharge Polymer used in Inertial Confinement Fusion (ICF) capsules up to 5 Mbar, covering conditions beyond the first shock in a full-scale Inertial Confinement Fusion (ICF) capsule. The experiments were performed using the GEKKOXII laser at the Institute of Laser Engineering at Osaka University in Japan. Results are in good agreement with predictions obtained from ab initio Hugoniot calculations, but softer than the quotidian equation of state average atom model. Ab initio calculations show that dissociation of carbon bonds need to be taken into account in order to explain Hugoniot compressibility.

Role of Au-C Interactions on the Catalytic Activity of Au Nanoparticles Supported on TiC(001) Towards Molecular Oxygen Dissociation

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

Rodriguez, J.A.; Feria, L.; Jirsak, T.

2010-03-10

High-resolution photoemission and density functional calculations on realistic slab surface models were used to study the interaction and subsequent dissociation of O{sub 2} with Au nanoparticles supported on TiC(001). The photoemission results indicate that at 150 K O{sub 2} adsorbs molecularly on the supported gold nanoparticles, and upon heating to temperatures above 200 K the O{sub 2} {yields} 2O reaction takes place with migration of atomic oxygen to the TiC(001) substrate. The addition of Au to TiC(001) substantially enhances the rate of O{sub 2} dissociation at room temperature. The reactivity of Au nanoparticles supported on TiC(001) toward O{sub 2} dissociationmore » is much larger than that of similar nanoparticles supported either on TiO{sub 2}(110) or MgO(001) surfaces, where the cleavage of O-O bonds is very difficult. Density functional calculations carried out on large supercells show that the contact of Au with TiC(001) is essential for charge polarization and an enhancement in the chemical activity of Au. Small two-dimensional particles which expose Au atoms in contact with TiC(001) are the most reactive. While O{sub 2} prefers binding to Au sites, the O atoms interact more strongly with the TiC(001) surface. The oxygen species active during the low-temperature (<200 K) oxidation of carbon monoxide on Au/TiC(001) is chemisorbed O{sub 2}. Once atomic O binds to TiC(001), the chemisorption bond is so strong that temperatures well above 400 K are necessary to remove the O adatoms from the TiC(001) substrate by direct reaction with CO. The high reactivity of Au/TiC(001) toward O{sub 2} at low-temperature opens the route for the transformation of alcohols and amines on the supported Au nanoparticles.« less

Role of Au-C Interactions on the Catalytic Activity of Au Nanoparticles Supported on TiC(001) toward Molecular Oxygen Dissociation

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

Rodriguez, J.; Feria, L; Jirsak, T

2010-01-01

High-resolution photoemission and density functional calculations on realistic slab surface models were used to study the interaction and subsequent dissociation of O{sub 2} with Au nanoparticles supported on TiC(001). The photoemission results indicate that at 150 K O{sub 2} adsorbs molecularly on the supported gold nanoparticles, and upon heating to temperatures above 200 K the O{sub 2} {yields} 2O reaction takes place with migration of atomic oxygen to the TiC(001) substrate. The addition of Au to TiC(001) substantially enhances the rate of O{sub 2} dissociation at room temperature. The reactivity of Au nanoparticles supported on TiC(001) toward O{sub 2} dissociationmore » is much larger than that of similar nanoparticles supported either on TiO{sub 2}(110) or MgO(001) surfaces, where the cleavage of O-O bonds is very difficult. Density functional calculations carried out on large supercells show that the contact of Au with TiC(001) is essential for charge polarization and an enhancement in the chemical activity of Au. Small two-dimensional particles which expose Au atoms in contact with TiC(001) are the most reactive. While O{sub 2} prefers binding to Au sites, the O atoms interact more strongly with the TiC(001) surface. The oxygen species active during the low-temperature (<200 K) oxidation of carbon monoxide on Au/TiC(001) is chemisorbed O{sub 2}. Once atomic O binds to TiC(001), the chemisorption bond is so strong that temperatures well above 400 K are necessary to remove the O adatoms from the TiC(001) substrate by direct reaction with CO. The high reactivity of Au/TiC(001) toward O{sub 2} at low-temperature opens the route for the transformation of alcohols and amines on the supported Au nanoparticles.« less

X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond

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

de Serrano, V.S.; Davis, M.F.; Gaff, J.F.

X-ray crystal structures of the metcyano form of dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata (DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN{sup -}) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocketmore » of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN{sup -} or O{sub 2} in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN{sup -} or O{sub 2} in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S-O{sub 2} form of DHP [de Serrano et al. (2007), Acta Cryst. D63, 1094-1101], it is concluded that CN{sup -} is gradually replaced by O{sub 2} as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHP A compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN{sup -} at 100 K suggests that the distal pocket of DHP A has greater flexibility than most other hemoglobins.« less

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.

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.

A DFT and ab initio benchmarking study of metal-alkane interactions and the activation of carbon-hydrogen bonds.

PubMed

Flener-Lovitt, Charity; Woon, David E; Dunning, Thom H; Girolami, Gregory S

2010-02-04

Density functional theory and ab initio methods have been used to calculate the structures and energies of minima and transition states for the reactions of methane coordinated to a transition metal. The reactions studied are reversible C-H bond activation of the coordinated methane ligand to form a transition metal methyl hydride complex and dissociation of the coordinated methane ligand. The reaction sequence can be summarized as L(x)M(CH(3))H <==> L(x)M(CH(4)) <==> L(x)M + CH(4), where L(x)M is the osmium-containing fragment (C(5)H(5))Os(R(2)PCH(2)PR(2))(+) and R is H or CH(3). Three-center metal-carbon-hydrogen interactions play an important role in this system. Both basis sets and functionals have been benchmarked in this work, including new correlation consistent basis sets for a third transition series element, osmium. Double zeta quality correlation consistent basis sets yield energies close to those from calculations with quadruple-zeta basis sets, with variations that are smaller than the differences between functionals. The energies of important species on the potential energy surface, calculated by using 10 DFT functionals, are compared both to experimental values and to CCSD(T) single point calculations. Kohn-Sham natural bond orbital descriptions are used to understand the differences between functionals. Older functionals favor electrostatic interactions over weak donor-acceptor interactions and, therefore, are not particularly well suited for describing systems--such as sigma-complexes--in which the latter are dominant. Newer kinetic and dispersion-corrected functionals such as MPW1K and M05-2X provide significantly better descriptions of the bonding interactions, as judged by their ability to predict energies closer to CCSD(T) values. Kohn-Sham and natural bond orbitals are used to differentiate between bonding descriptions. Our evaluations of these basis sets and DFT functionals lead us to recommend the use of dispersion corrected functionals in conjunction with double-zeta or larger basis sets with polarization functions for calculations involving weak interactions, such as those found in sigma-complexes with transition metals.

A new quasi-relativistic approach for density functional theory based on the normalized elimination of the small component

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2002-01-01

A recently developed variationally stable quasi-relativistic method, which is based on the low-order approximation to the method of normalized elimination of the small component, was incorporated into density functional theory (DFT). The new method was tested for diatomic molecules involving Ag, Cd, Au, and Hg by calculating equilibrium bond lengths, vibrational frequencies, and dissociation energies. The method is easy to implement into standard quantum chemical programs and leads to accurate results for the benchmark systems studied.

Single ricin detection by atomic force microscopy chemomechanical mapping

NASA Astrophysics Data System (ADS)

Chen, Guojun; Zhou, Jianfeng; Park, Bosoon; Xu, Bingqian

2009-07-01

The authors report on a study of detecting ricin molecules immobilized on chemically modified Au (111) surface by chemomechanically mapping the molecular interactions with a chemically modified atomic force microscopy (AFM) tip. AFM images resolved the different fold-up conformations of single ricin molecule as well as their intramolecule structure of A- and B-chains. AFM force spectroscopy study of the interaction indicates that the unbinding force has a linear relation with the logarithmic force loading rate, which agrees well with calculations using one-barrier bond dissociation model.

Accurate multireference calculations of the electronic structure of TiF 2 and TiCl 2

NASA Astrophysics Data System (ADS)

Vogel, M.; Wenzel, W.

2005-09-01

We report a systematic study of the electronic structure of two members of the transition metal dihalide family, TiF 2 and TiCl 2. Using the configuration interaction method in large basis sets we investigated the lowest 15 states of TiF 2 and TiCl 2. We report bond lengths, frequencies and dissociation energies of both molecules. For TiF 2 we found a near degeneracy of the ground and the first excited state with a possible breakdown of the Born-Oppenheimer approximation.

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.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

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

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.

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.

Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 - A new method of calculation.

PubMed

Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I

2015-12-01

Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin. Copyright © 2015 Elsevier B.V. All rights reserved.

Theoretical studies on the crystal structure, thermodynamic properties, detonation performance and thermal stability of cage-tetranitrotetraazabicyclooctane as a novel high energy density compound.

PubMed

Zhao, Guo-zheng; Lu, Ming

2013-01-01

The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet-Jacobs equations. Thermal stability of 3,5,7,10,12,14,15,16-octanitro- 3,5,7,10,12,14,15,16-octaaza-heptacyclo[7.5.1.1(2,8).0(1,11).0(2,6).0(4,13).0(6,11)]hexadecane (cage-tetranitrotetraazabicyclooctane) was investigated by calculating the bond dissociation energy (BDE) at unrestricted B3LYP/6-31G (d) level. The calculated results show that the N-NO2 bond is a trigger bond during thermolysis initiation process. The crystal structure obtained by molecular mechanics (MM) methods belongs to Pna2(1) space group, with cell parameters a=12.840 Å, b=9.129 Å, c=14.346 Å, Z=6 and ρ=2.292 g·cm(-3). Both the detonation velocity of 9.96 km·s(-1) and the detonation pressure of 47.47 GPa are better than those of CL-20. According to the quantitative standard of energetics and stability, as a high energy density compound (HEDC), cage-tetranitrotetraazabicyclooctane essentially satisfies this requirement.

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

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.

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.

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)).

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.

Nature and kinetic analysis of carbon-carbon bond fragmentation reactions of cation radicals derived from SET-oxidation of lignin model compounds.

PubMed

Cho, Dae Won; Parthasarathi, Ramakrishnan; Pimentel, Adam S; Maestas, Gabriel D; Park, Hea Jung; Yoon, Ung Chan; Dunaway-Mariano, Debra; Gnanakaran, S; Langan, Paul; Mariano, Patrick S

2010-10-01

Features of the oxidative cleavage reactions of diastereomers of dimeric lignin model compounds, which are models of the major types of structural units found in the lignin backbone, were examined. Cation radicals of these substances were generated by using SET-sensitized photochemical and Ce(IV) and lignin peroxidase promoted oxidative processes, and the nature and kinetics of their C-C bond cleavage reactions were determined. The results show that significant differences exist between the rates of cation radical C1-C2 bond cleavage reactions of 1,2-diaryl-(β-1) and 1-aryl-2-aryloxy-(β-O-4) propan-1,3-diol structural units found in lignins. Specifically, under all conditions C1-C2 bond cleavage reactions of cation radicals of the β-1 models take place more rapidly than those of the β-O-4 counterparts. The results of DFT calculations on cation radicals of the model compounds show that the C1-C2 bond dissociation energies of the β-1 lignin model compounds are significantly lower than those of the β-O-4 models, providing clear evidence for the source of the rate differences.

Alkali Metal-Glucose Interaction Probed with Infrared Pre-Dissociation Spectroscopy

NASA Astrophysics Data System (ADS)

Kregel, Steven J.; Marsh, Brett; Zhou, Jia; Garand, Etienne

2015-06-01

The efficient extraction of cellulose from biomass and its subsequent conversion to glucose derivatives is an attractive goal in the field of energy science. However, current industrial methods require high ionic strength and harsh conditions. Ionic liquids (IL's) are a class of "green" compounds that have been shown to dissolve cellulose in concentrations of up to 25 wt%. In order to understand IL's extraordinary cellulose dissolving power, a molecular level understanding of the IL-cellulose interaction is needed. Toward that end, we have acquired infrared pre-dissociation spectra of M+-glucose, where M+=Li+, Na+, or K+. Through comparisons with density functional theory calculations, we have determined the relative abundances of various M+-glucose binding motifs in both the thermodynamic and kinetic limits. These results provide insight on the hydrogen bonding dynamics of glucose and are a step towards a fuller understanding of cellulose interactions with ionic liquids.

Replace with abstract title

NASA Astrophysics Data System (ADS)

Coho, Aleksander; Kioussis, Nicholas

2003-03-01

We use the semidiscrete variational generelized Peierls-Nabarro model to study the effect of Cu alloying on the dislocation properties of Al. First-principles density functional theory (DFT) is used to calculate the generalized-stacking-fault (GSF) energy surface when a <111> plane, on which one in four Al atoms has been replaced with a Cu atom, slips over a pure Al <111> plane. Various dislocation core properties (core width, energy, Peierls stress, dissociation tendency) are investigated and compared with the pure Al case. Cu alloying lowers the intrinsic stacking fault (ISF) energy, which makes dislocations more likely to dissociate into partials. We also try to understand the lowering of ISF energy in terms of Al-Cu and Al-Al bond formation and braking during shearing along the <112> direction. From the above we draw conclusions about the effects of Cu alloying on the mechanical properties of Al.

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.

Structures and Energetics of (MgCO 3 ) n Clusters ( n ≤ 16)

DOE PAGES

Chen, Mingyang; Jackson, Virgil E.; Felmy, Andrew R.; ...

2015-03-13

There is significant interest in the role of carbonate minerals for the storage of CO 2 and the role of prenucleation dusters in their formation. Global minima for (MgCO 3) n (n ≤ 16) structures were optimized using a tree growth-hybrid genetic algorithm in conjunction with MNDO/MNDO/d semiempirical molecular orbital calculations followed by density functional theory geometry optimizations with the B3LYP functional. The most stable isomers for (MgCO 3) n (n < 5) are approximately 2-dimensional. Mg can be bonded to one or two 0 atoms of a CO 3 2-, and the 1-O bonding scheme is more favored asmore » the cluster becomes larger. The average C-Mg coordination number increases as the cluster size increases, and at n = 16, the average C-Mg coordination number was calculated to be 5.2. The normalized dissociation energy to form monomers increases as n increases. At n = 16, the normalized dissociation energy is calculated to be 116.2 kcal/mol, as compared to the bulk value of 153.9 kcal/mol. The adiabatic reaction energies for the recombination reactions of (MgO) nclusters and CO 2 to form (MgCO 3) n were calculated. The exothermicity of the normalized recombination energy < RE >(CO 2) decreases as n increases and converged to the experimental bulk limit rapidly. The normalized recombination energy < RE >(CO 2) was calculated to be -52.2 kcal/mol for the monomer and -30.7 kcal/mol for n = 16, as compared to the experimental value of -27.9 kcal/mol for the solid phase reaction. Infrared spectra for the lowest energy isomers were calculated, and absorption bands in the previous experimental infrared studies were assigned with our density functional theory predictions. The 13C, 17O, and 25Mg NMR chemical shifts for the clusters were predicted. We found that the results provide insights into the structural and energetic transitions from nanoclusters of (MgCO 3) n to the bulk and the spectroscopic properties of clusters for their experimental identification.« less

Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

NASA Astrophysics Data System (ADS)

Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

2018-03-01

A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

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.

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.

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

Density Functional Theory Study of Spirodienone Stereoisomers in Lignin

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

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.

The spirodienone structure in lignin is a relatively recent discovery, and it has been found to occur in lignin of various plant species at concentrations of ~3%, which is sufficiently high to be important for better understanding of its properties and reactivity. The cyclic structure, with a ..beta..-1 bond, has been proposed to be a precursor for acyclic ..beta..-1 linkages in lignin. Previous analytical work has revealed the presence, but not the absolute configuration, of two stereoisomeric forms of spirodienone. The objective of the current work was to determine if there are thermodynamic differences that could help identify the experimentallymore » observed stereoisomers. Results from density functional theory calculations reveal the presence of clusters of stereoisomers with varying stability that may be of use in narrowing the list of possible structures. Furthermore, the bond dissociation enthalpy of the cyclic ring exhibited a particularly high value for the C-O cleavage reaction relative to more conventional ether bonds in lignin, perhaps due to limited electron delocalization possibilities.« less

Density Functional Theory Study of Spirodienone Stereoisomers in Lignin

DOE PAGES

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.; ...

2017-06-28

The spirodienone structure in lignin is a relatively recent discovery, and it has been found to occur in lignin of various plant species at concentrations of ~3%, which is sufficiently high to be important for better understanding of its properties and reactivity. The cyclic structure, with a ..beta..-1 bond, has been proposed to be a precursor for acyclic ..beta..-1 linkages in lignin. Previous analytical work has revealed the presence, but not the absolute configuration, of two stereoisomeric forms of spirodienone. The objective of the current work was to determine if there are thermodynamic differences that could help identify the experimentallymore » observed stereoisomers. Results from density functional theory calculations reveal the presence of clusters of stereoisomers with varying stability that may be of use in narrowing the list of possible structures. Furthermore, the bond dissociation enthalpy of the cyclic ring exhibited a particularly high value for the C-O cleavage reaction relative to more conventional ether bonds in lignin, perhaps due to limited electron delocalization possibilities.« less

Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network.

PubMed

Takahashi, Masae; Okamura, Nubuyuki; Fan, Xinyi; Shirakawa, Hitoshi; Minamide, Hiroaki

2017-04-06

We have investigated the terahertz-spectral property of nicotinamide focusing on the temperature dependence in the range of 14-300 K. We observed that almost all peaks in the terahertz spectrum of the nicotinamide crystal showed a remarkable shift with temperature, whereas the lowest-frequency peak at 34.8 cm -1 showed a negligible shift with temperature. By analyzing the terahertz spectrum with the dispersion-corrected density functional theory calculations, we found that the difference in the temperature dependence of the peak shift is well understood in terms of the presence/absence of stretching vibration of the intermolecular hydrogen bond in the mode and the change of cell parameters. The anharmonicity in the dissociation potential energy of very weak intermolecular hydrogen bonding causes the remarkable peak shift with temperature in the terahertz spectrum of nicotinamide. This finding suggests that the assignment and identification of peaks in the terahertz spectrum are systematically enabled by temperature-dependent measurements.

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.

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.

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.

The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

NASA Astrophysics Data System (ADS)

Zhang, Jiaheng; He, Xin; Gao, Haixiang

2011-10-01

In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.

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.

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.

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

Difluorophosphoryl nitrene F2P(O)N: matrix isolation and unexpected rearrangement to F2PNO.

PubMed

Zeng, Xiaoqing; Beckers, Helmut; Willner, Helge; Neuhaus, Patrik; Grote, Dirk; Sander, Wolfram

2009-12-14

Triplet difluorophosphoryl nitrene F(2)P(O)N (X(3)A'') was generated on ArF excimer laser irradiation (lambda=193 nm) of F(2)P(O)N(3) in solid argon matrix at 16 K, and characterized by its matrix IR, UV/Vis, and EPR spectra, in combination with DFT and CBS-QB3 calculations. On visible light irradiation (lambda>420 nm) at 16 K F(2)P(O)N reacts with molecular nitrogen and some of the azide is regenerated. UV irradiation (lambda=255 nm) of F(2)P(O)N (X(3)A'') induced a Curtius-type rearrangement, but instead of a 1,3-fluorine shift, nitrogen migration to give F(2)PON is proposed to be the first step of the photoisomerization of F(2)P(O)N into F(2)PNO (difluoronitrosophosphine). Formation of novel F(2)PNO was confirmed with (15)N- and (18)O-enriched isotopomers by IR spectroscopy and DFT calculations. Theoretical calculations predict a rather long P-N bond of 1.922 A [B3LYP/6-311+G(3df)] and low bond-dissociation energy of 76.3 kJ mol(-1) (CBS-QB3) for F(2)PNO.

Synthesis, XRD crystal structure, spectroscopic characterization, local reactive properties using DFT and molecular dynamics simulations and molecular docking study of (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Raveendran Pillai, Renjith; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Renjith, Rishikesh; Panicker, C. Yohannan; Van Alsenoy, C.

2017-06-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed to fit the title compound into the binding site of MOA-B enzyme.

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.

Importance of electronegativity differences and surface structure in molecular dissociation reactions at transition metal surfaces.

PubMed

Crawford, Paul; Hu, P

2006-12-14

The dissociative adsorption of N2 has been studied at both monatomic steps and flat regions on the surfaces of the 4d transition metals from Zr to Pd. Using density functional theory (DFT) calculations, we have determined and analyzed the trends in both straight reactivity and structure sensitivity across the periodic table. With regards to reactivity, we find that the trend in activation energy (Ea) is determined mainly by a charge transfer from the surface metal atoms to the N atoms during transition state formation, namely, the degree of ionicity of the N-surface bond at the transition state. Indeed, we find that the strength of the metal-N bond at the transition state (and therefore the trend in Ea) can be predicted by the difference in Mulliken electronegativity between the metal and N. Structure sensitivity is analyzed in terms of geometric and electronic effects. We find that the lowering of Ea due to steps is more pronounced on the right-hand side of the periodic table. It is found that for the early transition metals the geometric and electronic effects work in opposition when going from terrace to step active site. In the case of the late 4d metals, however, these effects work in combination, producing a more marked reduction in Ea.

ab initio calculation of the rate of vibrational relaxation and thermal dissociation of hydrogen by helium at high temperatures

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

Dove, J.E.; Raynor, S.

The master equation for the thermal dissociation of para-H/sub 2/ infinitely dilute in He, was solved for temperatures of 1000 to 10,000/sup 0/K. Transition probabilities, used in the master equation, were obtained, in the case of energy transfer transitions, from distorted wave and quasi-classical trajectory calculations and, for dissociative processes, from trajectory calculations alone. An ab initio potential was used. From the solution, values of the dissociation rate constant, vibrational relaxation times, and incubation times for dissociation and vibrational relaxation were calculated. The sensitivity of the calculated results to variations in the transition probabilities was examined. Vibrational relaxation is mostmore » sensitive to simultaneous transitions in vibration and rotation (VRT processes); pure rotational (RT) transitions also have a substantial effect. Dissociation is most strongly affected by RT processes, but changes in VRT and groups of dissociative transitions also have a significant effect. However complete suppression of all dissociative transitions except those from levels immediately next to the continuum lowers the dissociation rates only by a factor of about 2. The location of the dissociation ''bottleneck'' is discussed. 5 figures, 3 tables.« less

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)

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.

Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals.

PubMed

Sayfutyarova, Elvira R; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald

2017-09-12

We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multiconfiguration and multireference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a coordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wave function (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calculate the excitation energies for various transition-metal complexes in typical application scenarios. Additionally, we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not a universal solution to the active space problem, its premises are fulfilled in many application scenarios of transition-metal chemistry and bond dissociation processes. In these cases the technique makes MR calculations easier to execute, easier to reproduce by any user, and simplifies the determination of the appropriate size of the active space required for accurate results.

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.

Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue

2015-03-01

The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and layered structures are formed at the confinement of the GRA bilayer induced by the van der Waals attractions of NM with GRA and the dipole-dipole interactions of NM, which is strongly dependent on the confinement size, i.e., the GRA bilayer distance. These unique intermolecular arrangements and preferred orientations of confined NM lead to higher stabilities than bulk NM revealed by bond dissociation energy calculations.

Spin Transfer in Polymer Degradation of Abnormal Linkage

NASA Astrophysics Data System (ADS)

Yu, Tianrong; Tian, Chuanjin; Liu, Xizhe; Wang, Jia; Gao, Yang; Wang, Zhigang

2017-07-01

The degradation of polymer materials plays an important role in production and life. In this work, the degradation mechanism of poly-α-methylstyrene (PAMS) tetramers with abnormal linkage was investigated by using density functional theory (DFT). Calculated results indicate that the head-to-head and the tail-to-tail reactions needed to overcome the energy barriers are about 0.15 eV and about 1.26 eV, respectively. The broken C-C bond at the unsaturated end of the chain leads to the dissociation of alpha-methylstyrene (AMS) monomers one by one. Furthermore, the analyses of bond characteristics are in good agreement with the results of energy barriers. In addition, the spin population analysis presents an interesting net spin transfer process in depolymerization reactions. We hope that the current theoretical results provide useful help to understand the degradation mechanism of polymers.

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.

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.

Dissociative Photoionization of the Elusive Vinoxy Radical.

PubMed

Adams, Jonathan D; Scrape, Preston G; Lee, Shih-Huang; Butler, Laurie J

2017-08-24

These experiments report the dissociative photoionization of vinoxy radicals to m/z = 15 and 29. In a crossed laser-molecular beam scattering apparatus, we induce C-Cl bond fission in 2-chloroacetaldehyde by photoexcitation at 157 nm. Our velocity measurements, combined with conservation of angular momentum, show that 21% of the C-Cl photofission events form vinoxy radicals that are stable to subsequent dissociation to CH 3 + CO or H + ketene. Photoionization of these stable vinoxy radicals, identified by their velocities, which are momentum-matched with the higher-kinetic-energy Cl atom photofragments, shows that the vinoxy radicals dissociatively photoionize to give signal at m/z = 15 and 29. We calibrated the partial photoionization cross section of vinoxy to CH 3 + relative to the bandwidth-averaged photoionization cross section of the Cl atom at 13.68 eV to put the partial photoionization cross sections on an absolute scale. The resulting bandwidth-averaged partial cross sections are 0.63 and 1.3 Mb at 10.5 and 11.44 eV, respectively. These values are consistent with the upper limit to the cross section estimated from a study by Savee et al. on the O( 3 P) + propene bimolecular reaction. We note that the uncertainty in these values is primarily dependent on the signal attributed to C-Cl primary photofission in the m/z = 35 (Cl + ) time-of-flight data. While the value is a rough estimate, the bandwidth-averaged partial photoionization cross section of vinoxy to HCO + calculated from the signal at m/z = 29 at 11.53 eV is approximately half that of vinoxy to CH 3 + . We also present critical points on the potential energy surface of the vinoxy cation calculated at the G4//B3LYP/6-311++G(3df,2p) level of theory to support the observation of dissociative ionization of vinoxy to both CH 3 + and HCO + .

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.

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).

Interaction of Al with O2 exposed Mo2BC

NASA Astrophysics Data System (ADS)

Bolvardi, Hamid; Music, Denis; Schneider, Jochen M.

2015-03-01

A Mo2BC(0 4 0) surface was exposed to O2. The gas interaction was investigated using ab initio molecular dynamics and X-ray photoelectron spectroscopy (XPS) of air exposed surfaces. The calculations suggest that the most dominating physical mechanism is dissociative O2 adsorption whereby Mosbnd O, Osbnd Mosbnd O and Mo2sbnd Csbnd O bond formation is observed. To validate these results, Mo2BC thin films were synthesized utilizing high power pulsed magnetron sputtering and air exposed surfaces were probed by XPS. MoO2 and MoO3 bond formation is observed and is consistent with here obtained ab initio data. Additionally, the interfacial interactions of O2 exposed Mo2BC(0 4 0) surface with an Al nonamer is studied with ab initio molecular dynamics to describe on the atomic scale the interaction between this surface and Al to mimic the interface present during cold forming processes of Al based alloys. The Al nonamer was disrupted and Al forms chemical bonds with oxygen contained in the O2 exposed Mo2BC(0 4 0) surface. Based on the comparison of here calculated adsorption energy with literature data, Alsbnd Al bonds are shown to be significantly weaker than the Alsbnd O bonds formed across the interface. Hence, Alsbnd Al bond rupture is expected for a mechanically loaded interface. Therefore the adhesion of a residual Al on the native oxide layer is predicted. This is consistent with experimental observations. The data presented here may also be relevant for other oxygen containing surfaces in a contact with Al or Al based alloys for example during forming operations.

Comparing Ullmann Coupling on Noble Metal Surfaces: On-Surface Polymerization of 1,3,6,8-Tetrabromopyrene on Cu(111) and Au(111).

PubMed

Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Li, Zheshen; Studener, Florian; Stöhr, Meike

2016-04-18

The on-surface polymerization of 1,3,6,8-tetrabromopyrene (Br4 Py) on Cu(111) and Au(111) surfaces under ultrahigh vacuum conditions was investigated by a combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) calculations. Deposition of Br4 Py on Cu(111) held at 300 K resulted in a spontaneous debromination reaction, generating the formation of a branched coordination polymer network stabilized by C-Cu-C bonds. After annealing at 473 K, the C-Cu-C bonds were converted to covalent C-C bonds, leading to the formation of a covalently linked molecular network of short oligomers. In contrast, highly ordered self-assembled two-dimensional (2D) patterns stabilized by both Br-Br halogen and Br-H hydrogen bonds were observed upon deposition of Br4 Py on Au(111) held at 300 K. Subsequent annealing of the sample at 473 K led to a dissociation of the C-Br bonds and the formation of disordered metal-coordinated molecular networks. Further annealing at 573 K resulted in the formation of covalently linked disordered networks. Importantly, we found that the chosen substrate not only plays an important role as catalyst for the Ullmann reaction, but also influences the formation of different types of intermolecular bonds and thus, determines the final polymer network morphology. DFT calculations further support our experimental findings obtained by STM and XPS and add complementary information on the reaction pathway of Br4 Py on the different substrates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parameterized cross sections for Coulomb dissociation in heavy-ion collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.; Cucinotta, F. A.; Townsend, L. W.; Badavi, F. F.

1988-01-01

Simple parameterizations of Coulomb dissociation cross sections for use in heavy-ion transport calculations are presented and compared to available experimental dissociation data. The agreement between calculation and experiment is satisfactory considering the simplicity of the calculations.

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.

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.

Theory of Cooperative Activated Structural Relaxation in Polymer Nanocomposites Composed of Small and Sticky Particles

NASA Astrophysics Data System (ADS)

Xie, Shijie; Schweizer, Kenneth

Recently, Cheng, Sokolov and coworkers have discovered qualitatively new dynamic behavior (exceptionally large Tg and fragility increases, unusual thermal and viscoelastic responses) in polymer nanocomposites composed of nanoparticles comparable in size to a polymer segment which form physical bonds with both themselves and segments. We generalize the Elastically Collective Nonlinear Langevin Equation theory of deeply supercooled molecular and polymer liquids to study the cooperative activated hopping dynamics of this system based on the dynamic free energy surface concept. The theoretical calculations are consistent with segmental relaxation time measurements as a function of temperature and nanoparticle volume fraction, and also the nearly linear growth of Tg with NP loading; predictions are made for the influence of nonuniversal chemical effects. The theory suggests the alpha process involves strongly coupled activated motion of segments and nanoparticles, consistent with the observed negligible change of the heat capacity jump with filler loading. Based on cohesive energy calculations and transient network ideas, full structural relaxation is suggested to involve a second, slower bond dissociation process with distinctive features and implications.

Modelling fragmentations of aminoacids after resonant electron attachment: quantum evidence of possible direct -OH detachment

NASA Astrophysics Data System (ADS)

Panosetti, C.; Baccarelli, I.; Sebastianelli, F.; Gianturco, F. A.

2010-10-01

We investigate some aspects of the radiation damage mechanisms in biomolecules, focusing on the modelling of resonant fragmentation caused by the attachment of low-energy electrons (LEEs) initially ejected by biological tissues when exposed to ionizing radiation. Scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical model of exchange and correlation effects developped in our group. We present total elastic scattering cross-sections and resonance features obtained for the equilibrium geometries of glycine, alanine, proline and valine. Our results at those geometries of the target molecules are briefly shown to qualitatively explain some of the fragmentation patterns obtained in experiments. We further carry out a one-dimensional (1D) modeling for the dynamics of intramolecular energy transfers mediated by the vibrational activation of selected bonds: our calculations indicate that resonant electron attachment to glycine can trigger direct, dissociative evolution of the complex into (Gly-OH)- and -OH losses, while they also find that the same process does not occur via a direct, 1D dissociative path in the larger aminoacids of the present study.

DFT simulations of water adsorption and activation on low-index α-Ga2O3 surfaces.

PubMed

Zhou, Xin; Hensen, Emiel J M; van Santen, Rutger A; Li, Can

2014-06-02

Density functional theory (DFT) calculations are used to explore water adsorption and activation on different α-Ga2O3 surfaces, namely (001), (100), (110), and (012). The geometries and binding energies of molecular and dissociative adsorption are studied as a function of coverage. The simulations reveal that dissociative water adsorption on all the studied low-index surfaces are thermodynamically favorable. Analysis of surface energies suggests that the most preferentially exposed surface is (012). The contribution of surface relaxation to the respective surface energies is significant. Calculations of electron local density of states indicate that the electron-energy band gaps for the four investigated surfaces appears to be less related to the difference in coordinative unsaturation of the surface atoms, but rather to changes in the ionicity of the surface chemical bonds. The electrochemical computation is used to investigate the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) on α-Ga2O3 surfaces. Our results indicate that the (100) and (110) surfaces, which have low stability, are the most favorable ones for HER and OER, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Muoniated acyl and thioacyl radicals

NASA Astrophysics Data System (ADS)

McKenzie, Iain; Brodovitch, Jean-Claude; Ghandi, Khashayar; Percival, Paul W.

2006-03-01

The product of the reaction of muonium with tert-butylisocyanate was previously assigned as the muoniated tert-butylaminyl radical (I. McKenzie, J.-C. Brodovitch, K. Ghandi, S. Kecman, P. W. Percival, Physica B 326 (2003) 76). This assignment is incorrect since the muon and 14N hyperfine-coupling constants (hfcc) of this radical would have the opposite sign, which is in conflict with the experimental results. The radical is now reassigned as the muoniated N-tert-butylcarbamoyl radical, based on the similarities between the experimental muon and 14N hfcc and hfcc calculated at the UB3LYP/6-311G(d,p)//UB3LYP/EPR-III level. The large zero-point energy in the N-Mu bond results in the dissociation barrier of the muoniated N-tert-butylcarbamoyl radical being above the combined energy of the reactants, in contrast to the N-tert-butylcarbamoyl radical where the dissociation barrier lies below the combined energy of the reactants. The reaction of muonium with tert-butylisothiocyanate produced both conformers of the muoniated N-tert-butylthiocarbamoyl radical and their assignment was based on the similarities between the experimental and calculated muon hfcc. These are the first acyl and thioacyl radicals to be directly detected by muon spin spectroscopy.

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.

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.

Precursor anion states in dissociative electron attachment to chlorophenol isomers.

PubMed

Kossoski, F; Varella, M T do N

2016-07-28

We report a theoretical study on low-energy (<10 eV) elastic electron scattering from chlorophenol isomers, namely, para-chlorophenol (pCP), meta-chlorophenol (mCP), and ortho-chlorophenol (oCP). The calculations were performed with the Schwinger multichannel method with pseudopotentials, and analysis of the computed integral cross sections and virtual orbitals revealed one σCCl (∗), one σOH (∗), and three π(∗) shape resonances. We show that electron capture into the two lower lying π(∗) orbitals initiates dissociative processes that lead to the elimination of the chloride ion, accounting for the two overlapping peaks where this fragment was observed. Despite the relatively small differences on the energetics of the π(∗) resonances, a major isomeric effect was found on their corresponding autodetachment lifetimes, which accounts for the observed increasing cross sections in the progression pCP < mCP < oCP. In particular, dissociation from the π1 (∗) anion of pCP is largely suppressed because of the unfavorable mixing with the σCCl (∗) state. We found the intramolecular hydrogen bond present in oCP to have the opposite effects of stabilizing the σCCl (∗) resonance and destabilizing the σOH (∗) resonance. We also suggest that the hydrogen abstraction observed in chlorophenols and phenol actually takes place by a mechanism in which the incoming electron is directly attached to the dissociative σOH (∗) orbital.

Precursor anion states in dissociative electron attachment to chlorophenol isomers

NASA Astrophysics Data System (ADS)

Kossoski, F.; Varella, M. T. do N.

2016-07-01

We report a theoretical study on low-energy (<10 eV) elastic electron scattering from chlorophenol isomers, namely, para-chlorophenol (pCP), meta-chlorophenol (mCP), and ortho-chlorophenol (oCP). The calculations were performed with the Schwinger multichannel method with pseudopotentials, and analysis of the computed integral cross sections and virtual orbitals revealed one σCCl ∗ , one σOH ∗ , and three π∗ shape resonances. We show that electron capture into the two lower lying π∗ orbitals initiates dissociative processes that lead to the elimination of the chloride ion, accounting for the two overlapping peaks where this fragment was observed. Despite the relatively small differences on the energetics of the π∗ resonances, a major isomeric effect was found on their corresponding autodetachment lifetimes, which accounts for the observed increasing cross sections in the progression pCP < mCP < oCP. In particular, dissociation from the π1 ∗ anion of pCP is largely suppressed because of the unfavorable mixing with the σCCl ∗ state. We found the intramolecular hydrogen bond present in oCP to have the opposite effects of stabilizing the σCCl ∗ resonance and destabilizing the σOH ∗ resonance. We also suggest that the hydrogen abstraction observed in chlorophenols and phenol actually takes place by a mechanism in which the incoming electron is directly attached to the dissociative σOH ∗ orbital.

n-Dopants Based on Dimers of Benzimidazoline Radicals: Structures and Mechanism of Redox Reactions.

PubMed

Zhang, Siyuan; Naab, Benjamin D; Jucov, Evgheni V; Parkin, Sean; Evans, Eric G B; Millhauser, Glenn L; Timofeeva, Tatiana V; Risko, Chad; Brédas, Jean-Luc; Bao, Zhenan; Barlow, Stephen; Marder, Seth R

2015-07-20

Dimers of 2-substituted N,N'-dimethylbenzimidazoline radicals, (2-Y-DMBI)2 (Y=cyclohexyl (Cyc), ferrocenyl (Fc), ruthenocenyl (Rc)), have recently been reported as n-dopants for organic semiconductors. Here their structural and energetic characteristics are reported, along with the mechanisms by which they react with acceptors, A (PCBM, TIPS-pentacene), in solution. X-ray data and DFT calculations both indicate a longer C-C bond for (2-Cyc-DMBI)2 than (2-Fc-DMBI)2 , yet DFT and ESR data show that the latter dissociates more readily due to stabilization of the radical by Fc. Depending on the energetics of dimer (D2 ) dissociation and of D2 -to-A electron transfer, D2 reacts with A to form D(+) and A(-) by either of two mechanisms, differing in whether the first step is endergonic dissociation or endergonic electron transfer. However, the D(+) /0.5 D2 redox potentials-the effective reducing strengths of the dimers-vary little within the series (ca. -1.9 V vs. FeCp2 (+/0) ) (Cp=cyclopentadienyl) due to cancelation of trends in the D(+/0) potential and D2 dissociation energy. The implications of these findings for use of these dimers as n-dopants, and for future dopant design, are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Excited-state dissociation dynamics of phenol studied by a new time-resolved technique

NASA Astrophysics Data System (ADS)

Lin, Yen-Cheng; Lee, Chin; Lee, Shih-Huang; Lee, Yin-Yu; Lee, Yuan T.; Tseng, Chien-Ming; Ni, Chi-Kung

2018-02-01

Phenol is an important model molecule for the theoretical and experimental investigation of dissociation in the multistate potential energy surfaces. Recent theoretical calculations [X. Xu et al., J. Am. Chem. Soc. 136, 16378 (2014)] suggest that the phenoxyl radical produced in both the X and A states from the O-H bond fission in phenol can contribute substantially to the slow component of photofragment translational energy distribution. However, current experimental techniques struggle to separate the contributions from different dissociation pathways. A new type of time-resolved pump-probe experiment is described that enables the selection of the products generated from a specific time window after molecules are excited by a pump laser pulse and can quantitatively characterize the translational energy distribution and branching ratio of each dissociation pathway. This method modifies conventional photofragment translational spectroscopy by reducing the acceptance angles of the detection region and changing the interaction region of the pump laser beam and the molecular beam along the molecular beam axis. The translational energy distributions and branching ratios of the phenoxyl radicals produced in the X, A, and B states from the photodissociation of phenol at 213 and 193 nm are reported. Unlike other techniques, this method has no interference from the undissociated hot molecules. It can ultimately become a standard pump-probe technique for the study of large molecule photodissociation in multistates.

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.

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.

Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

NASA Astrophysics Data System (ADS)

Sheena Mary, Y.; Al-Shehri, Mona M.; Jalaja, K.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

2017-04-01

Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

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.

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.

Theoretical studies on 2-diazo-4,6-dinitrophenol derivatives aimed at finding superior propellants.

PubMed

Liu, Yan; Wang, Lianjun; Wang, Guixiang; Du, Hongchen; Gong, Xuedong

2012-04-01

In an attempt to find superior propellants, 2-diazo-4,6-dinitrophenol (DDNP) and its -NO(2), -NH(2), -CN, -NC, -ONO(2), and -NF(2) derivatives were studied at the B3LYP/6-311++G level of density functional theory (DFT). Sensitivity was evaluated using bond dissociation enthalpies (BDEs) and molecular surface electrostatic potentials. The C-NO(2) bond appears to be the trigger bond during the thermolysis process for these compounds, except for the -ONO(2) and -NF(2) derivatives. Electrostatic potential results show that electron-withdrawing substituents make the charge imbalance more anomalous, which may change the strength of the bond, especially the weakest trigger bond. Most of the DDNP derivatives have the impact sensitivities that are higher than that of DDNP, making them favorable for use as solid propellants in micro-rockets. The theoretical densities (ρ), heats of formation (HOFs), detonation energies (Q), detonation pressures (P), and detonation velocities (D) of the compounds were estimated. The effects of various substituent groups on ρ, HOF, Q, D, and P were investigated. Some derivatives exhibit perfect detonation properties. The calculated relative specific impulses (I (r,sp)) of all compounds except for -NH(2) derivatives were higher than that of DDNP, and also meet the requirements of propellants.

Radicals and molecular products from the gas-phase pyrolysis of lignin model compounds. Cinnamyl alcohol

PubMed Central

Khachatryan, Lavrent; Xu, Meng-xia; Wu, Ang-jian; Pechagin, Mikhail; Asatryan, Rubik

2016-01-01

The experimental results on detection and identification of intermediate radicals and molecular products from gas-phase pyrolysis of cinnamyl alcohol (CnA), the simplest non-phenolic lignin model compound, over the temperature range of 400–800 °C are reported. The low temperature matrix isolation – electron paramagnetic resonance (LTMI-EPR) experiments along with the theoretical calculations, provided evidences on the generation of the intermediate carbon and oxygen centered as well as oxygen-linked, conjugated radicals. A mechanistic analysis is performed based on density functional theory to explain formation of the major products from CnA pyrolysis; cinnamaldehyde, indene, styrene, benzaldehyde, 1-propynyl benzene, and 2-propenyl benzene. The evaluated bond dissociation patterns and unimolecular decomposition pathways involve dehydrogenation, dehydration, 1,3-sigmatropic H-migration, 1,2-hydrogen shift, C—O and C—C bond cleavage processes. PMID:28344372

Thermochemical factors affecting the dehalogenation of aromatics.

PubMed

Sadowsky, Daniel; McNeill, Kristopher; Cramer, Christopher J

2013-12-17

Halogenated aromatics are one of the largest chemical classes of environmental contaminants, and dehalogenation remains one of the most important processes by which these compounds are degraded and detoxified. The thermodynamic constraints of aromatic dehalogenation reactions are thus important for understanding the feasibility of such reactions and the redox conditions necessary for promoting them. Accordingly, the thermochemical properties of the (poly)fluoro-, (poly)chloro-, and (poly)bromobenzenes, including standard enthalpies of formation, bond dissociation enthalpies, free energies of reaction, and the redox potentials of Ar-X/Ar-H couples, were investigated using a validated density functional protocol combined with continuum solvation calculations when appropriate. The results highlight the fact that fluorinated aromatics stand distinct from their chloro- and bromo- counterparts in terms of both their relative thermodynamic stability toward dehalogenation and how different substitution patterns give rise to relevant properties, such as bond strengths and reduction potentials.

Theoretical study of the alkaline-earth metal superoxides BeO2 through SrO2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Sodupe, Mariona; Langhoff, Stephen R.

1992-01-01

Three competing bonding mechanisms have been identified for the alkaline-earth metal superoxides: these result in a change in the optimal structure and ground state as the alkaline-earth metal becomes heavier. For example, BeO2 has a linear 3Sigma(-)g ground-state structure, whereas both CaO2 and SrO2 have C(2v)1A1 structures. For MgO2, the theoretical calculations are less definitive, as the 3A2 C(2v) structure is computed to lie only about 3 kcal/mol above the 3Sigma(-)g linear structure. The bond dissociation energies for the alkaline-earth metal superoxides have been computed using extensive Gaussian basis sets and treating electron correlation at the modified coupled-pair functional or coupled-cluster singles and doubles level with a perturbational estimate of the triple excitations.

Efficient and accurate treatment of electron correlations with correlation matrix renormalization theory

DOE PAGES

Yao, Y. X.; Liu, J.; Liu, C.; ...

2015-08-28

We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We alsomore » show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.« less

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces.

PubMed

Kharche, Neerav; Muckerman, James T; Hybertsen, Mark S

2014-10-24

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The  GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.

Thermal Dissociation and Roaming Isomerization of Nitromethane: Experiment and Theory.

PubMed

Annesley, Christopher J; Randazzo, John B; Klippenstein, Stephen J; Harding, Lawrence B; Jasper, Ahren W; Georgievskii, Yuri; Ruscic, Branko; Tranter, Robert S

2015-07-16

The thermal decomposition of nitromethane provides a classic example of the competition between roaming mediated isomerization and simple bond fission. A recent theoretical analysis suggests that as the pressure is increased from 2 to 200 Torr the product distribution undergoes a sharp transition from roaming dominated to bond-fission dominated. Laser schlieren densitometry is used to explore the variation in the effect of roaming on the density gradients for CH3NO2 decomposition in a shock tube for pressures of 30, 60, and 120 Torr at temperatures ranging from 1200 to 1860 K. A complementary theoretical analysis provides a novel exploration of the effects of roaming on the thermal decomposition kinetics. The analysis focuses on the roaming dynamics in a reduced dimensional space consisting of the rigid-body motions of the CH3 and NO2 radicals. A high-level reduced-dimensionality potential energy surface is developed from fits to large-scale multireference ab initio calculations. Rigid body trajectory simulations coupled with master equation kinetics calculations provide high-level a priori predictions for the thermal branching between roaming and dissociation. A statistical model provides a qualitative/semiquantitative interpretation of the results. Modeling efforts explore the relation between the predicted roaming branching and the observed gradients. Overall, the experiments are found to be fairly consistent with the theoretically proposed branching ratio, but they are also consistent with a no-roaming scenario and the underlying reasons are discussed. The theoretical predictions are also compared with prior theoretical predictions, with a related statistical model, and with the extant experimental data for the decomposition of CH3NO2, and for the reaction of CH3 with NO2.

Dissociative photoionization of methyl chloride studied with threshold photoelectron-photoion coincidence velocity imaging

NASA Astrophysics Data System (ADS)

Tang, Xiaofeng; Zhou, Xiaoguo; Wu, Manman; Liu, Shilin; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi

2012-01-01

Utilizing threshold photoelectron-photoion coincidence (TPEPICO) velocity imaging, dissociation of state-selected CH3Cl+ ions was investigated in the excitation energy range of 11.0-18.5 eV. TPEPICO time-of-flight mass spectra and three-dimensional time-sliced velocity images of CH3+ dissociated from CH3Cl+(A2A1 and B2E) ions were recorded. CH3+ was kept as the most dominant fragment ion in the present energy range, while the branching ratio of CH2Cl+ fragment was very low. For dissociation of CH3Cl+(A2A1) ions, a series of homocentric rings was clearly observed in the CH3+ image, which was assigned as the excitation of umbrella vibration of CH3+ ions. Moreover, a dependence of anisotropic parameters on the vibrational states of CH3+(11A') provided a direct experimental evidence of a shallow potential well along the C-Cl bond rupture. For CH3Cl+(B2E) ions, total kinetic energy released distribution for CH3+ fragmentation showed a near Maxwell-Boltzmann profile, indicating that the Cl-loss pathway from the B2E state was statistical predissociation. With the aid of calculated Cl-loss potential energy curves of CH3Cl+, CH3+ formation from CH3Cl+(A2A1) ions was a rapid direct fragmentation, while CH3Cl+(B2E) ions statistically dissociated to CH3+ + Cl via internal conversion to the high vibrational states of X2E.

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.

High-temperature mass spectrometry - Vaporization of group 4-B metal carbides. [using Knudsen effusion

NASA Technical Reports Server (NTRS)

Stearns, C. A.; Kohl, F. J.

1974-01-01

The high temperature vaporization of the metal-carbon systems TiC, ZrC, HfC, and ThC was studied by the Knudsen effusion - mass spectrometric method. For each system the metal dicarbide and tetracarbide molecular species were identified in the gas phase. Relative ion currents of the carbides and metals were measured as a function of temperature. Second- and third-law methods were used to determine enthalpies. Maximum values were established for the dissociation energies of the metal monocarbide molecules TiC, ZrC, HfC, and ThC. Thermodynamic functions used in the calculations are discussed in terms of assumed molecular structures and electronic contributions to the partition functions. The trends shown by the dissociation energies of the carbides of Group 4B are compared with those of neighboring groups and discussed in relation to the corresponding oxides and chemical bonding. The high temperature molecular beam inlet system and double focusing mass spectrometer are described.

A modeling study of methane hydrate decomposition in contact with the external surface of zeolites.

PubMed

Smirnov, Konstantin S

2017-08-30

The behavior of methane hydrate (MH) enclosed between the (010) surfaces of the silicalite-1 zeolite was studied by means of molecular dynamics simulations at temperatures of 150 and 250 K. Calculations reveal that the interaction with the hydrophilic surface OH groups destabilizes the clathrate structure of hydrate. While MH mostly conserves the structure in the simulation at the low temperature, thermal motion at the high temperature breaks the fragilized cages of H-bonded water molecules, thus leading to the release of methane. The dissociation proceeds in a layer-by-layer manner starting from the outer parts of the MH slab until complete hydrate decomposition. The released CH 4 molecules are absorbed by the microporous solid, whereas water is retained at the surfaces of hydrophobic silicalite and forms a meniscus in the interlayer space. Methane uptake reaches 70% of the silicalite sorption capacity. The energy necessary for the endothermic MH dissociation is supplied by the exothermic methane absorption by the zeolite.

Six-dimensional quantum dynamics study for the dissociative adsorption of DCl on Au(111) surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Fu, Bina; Zhang, Dong H.

2014-04-01

We carried out six-dimensional quantum dynamics calculations for the dissociative adsorption of deuterium chloride (DCl) on Au(111) surface using the initial state-selected time-dependent wave packet approach. The four-dimensional dissociation probabilities are also obtained with the center of mass of DCl fixed at various sites. These calculations were all performed based on an accurate potential energy surface recently constructed by neural network fitting to density function theory energy points. The origin of the extremely small dissociation probability for DCl/HCl (v = 0, j = 0) fixed at the top site compared to other fixed sites is elucidated in this study. The influence of vibrational excitation and rotational orientation of DCl on the reactivity was investigated by calculating six-dimensional dissociation probabilities. The vibrational excitation of DCl enhances the reactivity substantially and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. The site-averaged dissociation probability over 25 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability.

Six-dimensional quantum dynamics study for the dissociative adsorption of DCl on Au(111) surface

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

Liu, Tianhui; Fu, Bina, E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H., E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

We carried out six-dimensional quantum dynamics calculations for the dissociative adsorption of deuterium chloride (DCl) on Au(111) surface using the initial state-selected time-dependent wave packet approach. The four-dimensional dissociation probabilities are also obtained with the center of mass of DCl fixed at various sites. These calculations were all performed based on an accurate potential energy surface recently constructed by neural network fitting to density function theory energy points. The origin of the extremely small dissociation probability for DCl/HCl (v = 0, j = 0) fixed at the top site compared to other fixed sites is elucidated in this study. The influence of vibrational excitationmore » and rotational orientation of DCl on the reactivity was investigated by calculating six-dimensional dissociation probabilities. The vibrational excitation of DCl enhances the reactivity substantially and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. The site-averaged dissociation probability over 25 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability.« less

Cysteine and cystine adsorption on FeS2(100)

NASA Astrophysics Data System (ADS)

Suzuki, Teppei; Yano, Taka-aki; Hara, Masahiko; Ebisuzaki, Toshikazu

2018-08-01

Iron pyrite (FeS2) is the most abundant metal sulfide on Earth. Owing to its reactivity and catalytic activity, pyrite has been studied in various research fields such as surface science, geochemistry, and prebiotic chemistry. Importantly, native iron-sulfur clusters are typically coordinated by cysteinyl ligands of iron-sulfur proteins. In the present paper, we study the adsorption of L-cysteine and its oxidized dimer, L-cystine, on the FeS2 surface, using electronic structure calculations based density functional theory and Raman spectroscopy measurements. Our calculations suggest that sulfur-deficient surfaces play an important role in the adsorption of cysteine and cystine. In the thiol headgroup adsorption on the sulfur-vacancy site, dissociative adsorption is found to be energetically favorable compared with molecular adsorption. In addition, the calculations indicate that, in the cystine adsorption on the defective surface under vacuum conditions, the formation of the S-Fe bond is energetically favorable compared with molecular adsorption. Raman spectroscopic measurements suggest the formation of cystine molecules through the S-S bond on the pyrite surface in aqueous solution. Our results might have implications for chemical evolution at mineral surfaces on the early Earth and the origin of iron-sulfur proteins, which are believed to be one of the most ancient families of proteins.

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

Marchetti, Barbara; Karsili, Tolga N. V.; Ashfold, Michael N. R., E-mail: mike.ashfold@bristol.ac.uk

Velocity map imaging methods, with a new and improved ion optics design, have been used to explore the near ultraviolet photodissociation dynamics of gas phase 2-bromo- and 2-iodothiophene molecules. In both cases, the ground (X) and spin-orbit excited (X*) (where X = Br, I) atom products formed at the longest excitation wavelengths are found to recoil with fast, anisotropic velocity distributions, consistent with prompt C–X bond fission following excitation via a transition whose dipole moment is aligned parallel to the breaking bond. Upon tuning to shorter wavelengths, this fast component fades and is progressively replaced by a slower, isotropic recoilmore » distribution. Complementary electronic structure calculations provide a plausible explanation for this switch in fragmentation behaviour—namely, the opening of a rival C–S bond extension pathway to a region of conical intersection with the ground state potential energy surface. The resulting ground state molecules are formed with more than sufficient internal energy to sample the configuration space associated with several parent isomers and to dissociate to yield X atom products in tandem with both cyclic and ring-opened partner fragments.« less

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.

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.

Studies on the synthesis, spectroscopic analysis, molecular docking and DFT calculations on 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazol 3-oxide

NASA Astrophysics Data System (ADS)

Benzon, K. B.; Sheena, Mary Y.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Pradhan, Kiran; Nanda, Ashis Kumar; Van Alsenoy, C.

2017-02-01

In this work we have investigated in details the spectroscopic and reactive properties of newly synthesized imidazole derivative, namely the 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide (HHPDI). FT-IR and NMR spectra were measured and compared with theoretically obtained data provided by calculations of potential energy distribution and chemical shifts, respectively. Insight into the global reactivity properties has been obtained by analysis of frontier molecular orbitals, while local reactivity properties have been investigated by analysis of charge distribution, ionization energies and Fukui functions. NBO analysis was also employed to understand the stability of molecule, while hyperpolarizability has been calculated in order to assess the nonlinear optical properties of title molecule. Sensitivity towards autoxidation and hydrolysis mechanisms has been investigated by calculations of bond dissociation energies and radial distribution functions, respectively. Molecular docking study was also performed, in order to determine the pharmaceutical potential of the investigated molecule.

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.

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

Molecular dynamics studies of the thermal decomposition of 2,3-diazabicyclo(2.2.1)hept-2-ene

NASA Astrophysics Data System (ADS)

Sorescu, Dan C.; Thompson, Donald L.; Raff, Lionel M.

1995-05-01

The reaction dynamics of the thermal gas-phase decomposition of 2,3-diazabicyclo (2.2.1)hept-2-ene-exo, exo-5,6-d2 have been investigated using classical trajectory methods on a semiempirical potential-energy surface. The global potential is written as a superposition of different reaction channel potentials containing bond stretching, bending and torsional terms, connected by parametrized switching functions. Reaction channels for stepwise and concerted cleavage of the two C-N bonds of the reactant have both been considered in construction of the potential. The geometries of 2,3-diazabicyclo(2.2.1)hept-2-ene, the diazenyl biradical and of the transition state corresponding to breaking of the remaining C-N bond of diazenyl biradical have been determined at the second order Möller-Plesset perturbation theory (MP2/6-31G*) and at Hartree-Fock (HF/6-31G*) levels, respectively. The bond dissociation energies have been estimated using the available thermochemical data and previously reported results for bicyclo(2.1.0)pentane [J. Chem. Phys. 101, 3729 (1994)]. The equilibrium geometries predicted by the semiempirical potential for reactants and products, the barrier height for thermal nitrogen extrusion from 2,3-diazabicyclo(2.2.1)hept-2-ene and the fundamental vibrational frequencies are in good to excellent agreement with the measured or ab initio calculated values. Using a projection method of the instantaneous Cartesian velocities onto the normal mode vectors and classical trajectory calculations, the dissociation dynamics of 2,3-diazabicyclo(2.2.1)hept-2-ene-exo, exo-5,6-d2 are investigated at several excitation energies in the range 60-175 kcal/mol. The results show the following: (1) The thermal reaction takes place with a preference for inversion of configuration in the reaction products, the exo-labeled bicyclo(2.1.0) pentane being the major product. The exo/endo ratio of bicyclo(2.1.0) pentane isomers is found to vary between 1.8-2.2 for the energy range considered. (2) For random energization of the vibrational modes, the energy dependence of the rate coefficients can be described by a RRK expression. (3) The significant broadening and overlapping of the power spectral bands, together with the disappearance of characteristic features in the power spectra of the internal coordinates calculated at different energies, indicate high intramolecular vibrational redistribution rates and global statistical behavior. (4) The energy partitioning among products shows that the internal energy is preferentially distributed into the vibrational degrees of freedom in BCP, while N2 is formed with small amounts of rotational and vibrational energies. Overall, the distribution of energy among the product degrees of freedom follows statistical predictions in the internal energy range investigated. (5) Stepwise dissociation of the C-N bonds is the predominant mechanism which characterizes the N2 elimination from the parent molecule. (6) Although statistical theories of reaction rates, such as Rice-Ramsperger-Kassel-Marcus (RRKM) theory, are unable to predict the product exo/endo ratio, this is not a result of the breakdown of the statistical assumption inherent in these theories, but rather to the fact that statistical theory does not address mechanistic questions related to post transition-state events. Although the results show that there is a near microcanonical distribution of energy in the 1,3-cyclopentanediyl radical, the system does not have sufficient time to explore all of the energetically accessible configuration space prior to the closure of the 1-3 bridgehead bond. The result is a nonstatistical exo/endo product ratio that deviates from the statistically expected result of unity.

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.

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.

Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Hutchins, Patrick M.; Murphy, Robert C.

2011-05-01

Oxidative modification of polyunsaturated fatty acids, which occurs through enzymatic and nonenzymatic processes, is typically initiated by the attachment of molecular oxygen to an unsaturated fatty acyl chain forming a lipid hydroperoxide (LOOH). Enzymatic pathways are critical for cellular homeostasis but aberrant lipid peroxidation has been implicated in important pathologies. Analysis of primary oxidation products such as hydroperoxides has proven to be challenging for a variety of reasons. While negative ion electrospray ionization has been used for the specific detection of some LOOH species, hydroperoxide dehydration in the ion source has been a significant drawback. Here we describe positive ion electrospray ionization of ammoniated 13-hydroperoxy-9Z, 11E-octadecadienoyl cholesterol and 9-hydroperoxy-10E, 12Z-octadecadienoyl cholesterol, [M + NH4]+, following normal phase high-pressure liquid-chromatography. Dehydration in the ion source was not prevalent and the ammoniated molecular ion was the major species observed. Collisionally induced dissociation of the two positional isomers yielded unique product ion spectra resulting from carbon-carbon cleavages along their acyl chains. Further investigation of this behavior revealed that complex collision induced dissociations were initiated by scission of the hydroperoxide bond that drove subsequent acyl chain cleavages. Interestingly, some of the product ions retained the ammonium nitrogen through the formation of covalent carbon-nitrogen or oxygen-nitrogen bonds. These studies were carried out using hydroperoxy-octadecadienoate cholesteryl esters as model compounds, however the observed mechanisms of [LOOH + NH4]+ ionization and dissociation are likely applicable to the analysis of other lipid hydroperoxides and may serve as the basis for selective LOOH detection as well as aid in the identification of unknown lipid hydroperoxides.

Transport governs flow-enhanced cell tethering through L-selectin at threshold shear.

PubMed

Yago, Tadayuki; Zarnitsyna, Veronika I; Klopocki, Arkadiusz G; McEver, Rodger P; Zhu, Cheng

2007-01-01

Flow-enhanced cell adhesion is a counterintuitive phenomenon that has been observed in several biological systems. Flow augments L-selectin-dependent adhesion by increasing the initial tethering of leukocytes to vascular surfaces and by strengthening their subsequent rolling interactions. Tethering or rolling might be influenced by physical factors that affect the formation or dissociation of selectin-ligand bonds. We recently demonstrated that flow enhanced rolling of L-selectin-bearing microspheres or neutrophils on P-selectin glycoprotein ligand-1 by force decreased bond dissociation. Here, we show that flow augmented tethering of these microspheres or cells to P-selectin glycoprotein ligand-1 by three transport mechanisms that increased bond formation: sliding of the sphere bottom on the surface, Brownian motion, and molecular diffusion. These results elucidate the mechanisms for flow-enhanced tethering through L-selectin.

Components of the Bond Energy in Polar Diatomic Molecules, Radicals, and Ions Formed by Group-1 and Group-2 Metal Atoms.

PubMed

Yu, Haoyu; Truhlar, Donald G

2015-07-14

Although many transition metal complexes are known to have high multireference character, the multireference character of main-group closed-shell singlet diatomic molecules like BeF, CaO, and MgO has been less studied. However, many group-1 and group-2 diatomic molecules do have multireference character, and they provide informative systems for studying multireference character because they are simpler than transition metal compounds. The goal of the present work is to understand these multireference systems better so that, ultimately, we can apply what we learn to more complicated multireference systems and to the design of new exchange-correlation functionals for treating multireference systems more adequately. Fourteen main-group diatomic molecules and one triatomic molecule (including radicals, cations, and anions, as well as neutral closed-shell species) have been studied for this article. Eight of these molecules contain a group-1 element, and six contain a group-2 element. Seven of these molecules are multireference systems, and eight of them are single-reference systems. Fifty-three exchange-correlation functionals of 11 types [local spin-density approximation (LSDA), generalized gradient approximation (GGA), nonseparable gradient approximation (NGA), global-hybrid GGA, meta-GGA, meta-NGA, global-hybrid meta GGA, range-separated hybrid GGA, range-separated hybrid meta-GGA, range-separated hybrid meta-NGA, and DFT augmented with molecular mechanics damped dispersion (DFT-D)] and the Hartree-Fock method have been applied to calculate the bond distance, bond dissociation energy (BDE), and dipole moment of these molecules. All of the calculations are converged to a stable solution by allowing the symmetry of the Slater determinant to be broken. A reliable functional should not only predict an accurate BDE but also predict accurate components of the BDE, so each bond dissociation energy has been decomposed into ionization potential (IP) of the electropositive element, electron affinity of the electronegative bonding partner (EA), atomic excitation energy (EE) to prepare the valence states of the interacting partners, and interaction energy (IE) of the valence-prepared states. Adding Hartree-Fock exchange helps to obtain better results for atomic excitation energy, and this leads to improvements in getting the right answer for the right reason. The following functionals are singled out for reasonably good performance on all three of bond distance, BDE, and dipole moment: B97-1, B97-3, MPW1B95, M05, M06, M06-2X, M08-SO, N12-SX, O3LYP, TPSS, τ-HCTHhyb, and GAM; all but two (TPSS and GAM) of these functionals are hybrid functionals.

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.

Surface-induced dissociation: a unique tool for studying energetics and kinetics of the gas-phase fragmentation of large ions

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

Laskin, Julia

2015-01-01

Surface-induced dissociation (SID) is valuable tool for investigating activation and dissociation of large ions in tandem mass spectrometry. This account summarizes key findings from studies of the energetics and mechanisms of complex ion dissociation, in which SID experiments were combined with Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data. These studies used time- and collision-energy-resolved SID experiments and SID combined with resonant ejection of selected fragment ions on a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Fast ion activation by collision with a surface combined with the long and variable timescale of a FT-ICR MS is perfectlymore » suited for studying the energetics and dynamics of complex ion dissociation in the gas phase. Modeling of time- and collision-energy-resolved SID enables accurate determination of energy and entropy effects in the dissociation process. It has been demonstrated that entropy effects play an important role in determining the dissociation rates of both covalent and non-covalent bonds in large gaseous ions. SID studies have provided important insights on the competition between charge-directed and charge-remote fragmentation in even-electron peptide ions and the role of charge and radical site on the energetics of the dissociation of odd-electron peptide ions. Furthermore, this work examined factors that affect the strength of non-covalent binding, as well as the competition between covalent and non-covalent bond cleavages and between proton and electron transfer in model systems. Finally, SID studies have been used to understand the factors affecting nucleation and growth of clusters in solution and the gas phase.« less

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

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).

Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson–Crick Base Pairing in Vacuo

PubMed Central

Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams*, Evan R.

2005-01-01

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)23−, (CCGG)23−, (AATTAAT)23−, (CCGGCCG)23−, A7·T73−, A7·A73−, T7·T73−, and A7·C73− 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 1013 to 1019 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, A7·T73−, to the single strands is significantly higher than that for the related noncomplementary A7·A73− and T7·T73− dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A7·A73− and A7·C73− but not for A7·T73− 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 (−ΔHd) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A7·T73− 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. PMID:16498487

H2S adsorption and dissociation on NH-decorated graphene: A first principles study

NASA Astrophysics Data System (ADS)

Faye, Omar; Eduok, Ubong; Szpunar, Jerzy; Samoura, Almoustapha; Beye, Aboubaker

2018-02-01

The removal of H2S gas poses an emerging environmental concern because of the lack of knowledge of an efficient adsorbent. A detailed theoretical study of H2S adsorption and dissociation on NH-doped graphene (GNH) has been carried out by means of density theory calculations. Our results reveal that the adsorption of H2S molecule on GNH composite is enhanced by the presence of active site such as the NH radicals. These NH radical sites formed NHsbnd H bonds and increase the charge transfer from H2S to GNH. The dissociation of the adsorbed H2S molecule leads the chemisorption of SH radical via H-transfer to GNH, while the formation of GNH2 at a weight percent of 3.76 wt% of NH radical is an endothermic process with an energy of 0.299 eV and 0.358 eV for ortho and para-position respectively. However, at 7.25 wt% NH radical, we observed a complete dissociation of H2S molecule with an energy released of 0.711 eV for the chemisorbed S atom on GN2H4. Moreover, the H-transfer of the second H atom of H2S molecule at 3.76 wt% was energetic unfavorable. The trend of predicted results within this study reveals that NH-doped graphene (GNH) successfully adsorbed and eliminated of H2S molecule; this work unveils definitive theoretical procedures which can be tested and validated experimentally.

Biomechanics of leukocyte rolling

PubMed Central

Sundd, Prithu; Pospieszalska, Maria K.; Cheung, Luthur Siu-Lun; Konstantopoulos, Konstantinos; Ley, Klaus

2011-01-01

Leukocyte rolling on endothelial cells and other P-selectin substrates is mediated by P-selectin binding to P-selectin glycoprotein ligand-1 expressed on the tips of leukocyte microvilli. Leukocyte rolling is a result of rapid, yet balanced formation and dissociation of selectin-ligand bonds in the presence of hydrodynamic shear forces. The hydrodynamic forces acting on the bonds may either increase (catch bonds) or decrease (slip-bonds) their lifetimes. The force-dependent ‘catch-slip’ bond kinetics are explained using the ‘two pathway model’ for bond dissociation. Both the ‘sliding-rebinding’ and the ‘allosteric’ mechanisms attribute ‘catch-slip’ bond behavior to the force-induced conformational changes in the lectin-EGF domain hinge of selectins. Below a threshold shear stress, selectins cannot mediate rolling. This ‘shear-threshold’ phenomenon is a consequence of shear-enhanced tethering and catch-bond enhanced rolling. Quantitative dynamic footprinting microscopy has revealed that leukocytes rolling at venular shear stresses (> 0.6 Pa) undergo cellular deformation (large footprint) and form long tethers. The hydrodynamic shear force and torque acting on the rolling cell are thought to be synergistically balanced by the forces acting on tethers and stressed microvilli, however, their relative contribution remains to be determined. Thus, improvement beyond the current understanding requires in silico models that can predict both cellular and microvillus deformation and experiments that allow measurement of forces acting on individual microvilli and tethers. PMID:21515934

Ab initio spectroscopy and ionic conductivity of water under Earth mantle conditions.

PubMed

Rozsa, Viktor; Pan, Ding; Giberti, Federico; Galli, Giulia

2018-06-18

The phase diagram of water at extreme conditions plays a critical role in Earth and planetary science, yet remains poorly understood. Here we report a first-principles investigation of the liquid at high temperature, between 11 GPa and 20 GPa-a region where numerous controversial results have been reported over the past three decades. Our results are consistent with the recent estimates of the water melting line below 1,000 K and show that on the 1,000-K isotherm the liquid is rapidly dissociating and recombining through a bimolecular mechanism. We found that short-lived ionic species act as charge carriers, giving rise to an ionic conductivity that at 11 GPa and 20 GPa is six and seven orders of magnitude larger, respectively, than at ambient conditions. Conductivity calculations were performed entirely from first principles, with no a priori assumptions on the nature of charge carriers. Despite frequent dissociative events, we observed that hydrogen bonding persists at high pressure, up to at least 20 GPa. Our computed Raman spectra, which are in excellent agreement with experiment, show no distinctive signatures of the hydronium and hydroxide ions present in our simulations. Instead, we found that infrared spectra are sensitive probes of molecular dissociation, exhibiting a broad band below the OH stretching mode ascribable to vibrations of complex ions.

Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

2010-10-14

A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low excitation energies largely below the dissociation limit as well as a negligible IVR contribution.

Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation.

PubMed

Lioe, Hadi; Laskin, Julia; Reid, Gavin E; O'Hair, Richard A J

2007-10-25

The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.

Hydrogen bonding Part 53. Correlation of differential scanning calorimetric data with IR and dissociation vapor pressure studies of transitions of hexamethonium chloride and bromide dihydrates and hexamethonium bromide monohydrate

NASA Astrophysics Data System (ADS)

Snider, Barbara L.; Harmon, Kenneth M.

1994-03-01

Differential scanning calorimetry of hexamethonium chloride dihydrate shows an endothermic transition of 2.70 kcal mol -1 at 36.81°C. This correlates well with the temperatures observed by IR spectra (36°C) and equilibrium dissociation vapor pressure studies (37°C) for the transition between Type I planar cluster and Type II extended linear HOH⋯Cl - hydrogen bonding, and with the value of 2.77 kcal mol -1 for this transition derived by Hess' law treatment of dissociation vapor pressure data. Differential scanning calorimetry of hexamethonium bromide shows a rapid endothermic transition of 2.38 kcal mol -1 at 35.15°C and a very slow endothermic transition of about 12-13 kcal mol -1 centered near 50°C. This latter endotherm corresponds to the transition between Type I and Type II HOH⋯Br - hydrogen bonding observed by IR and vapor pressure studies at 49°C. The nature of the 35.15°C endotherm is not known. Hexamethonium bromide also shows a third endotherm at 142.91°C, which presumably results from melting of hydrate in the sealed DSC cell. Combined analysis of differential scanning calorimetry and dissociation vapor pressure data predicts a value of about -13 kcal mol -1 for an exothermic disproportionation at 52°C of two hexamethonium bromide monohydrate to Type II dihydrate and anhydrous bromide.

A complete computational and spectroscopic study of 2-bromo-1, 4-dichlorobenzene - A frequently used benzene derivative

NASA Astrophysics Data System (ADS)

Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.; Mary, Y. Sheena; Panicker, C. Yohannan; Kaya, S.; Armaković, Stevan; Armaković, Sanja J.

2018-01-01

The coupled experimental and theoretical vibrational investigation of 2-bromo-1, 4-dichlorobenzene (BDB) molecule has been carried out and they have been duly compared with standard values in order to produce the reliability of the results. Results of DFT analysis carried out using B3LYP functional with 6-31 + G/6-311++G (d,p) basis set revealed that BDB has higher electronic density. The molecular geometry, 13C &1H Nuclear Magnetic Resonance (NMR), Natural Bond Orbital (NBO) and Natural Atomic Charge analyses have been obtained by DFT calculations. Nonlinear optical (NLO) properties, quantum chemical descriptors and first order hyperpolarizability have been calculated. In addition, Local reactivity properties reflected through average local ionization energies (ALIE), Fukui functions and bond dissociation energies have also been investigated. Besides investigation of docking properties, molecular dynamics simulations were also taken in account with a view to identify atoms that have relatively important interactions with water molecules. The title compound forms a stable complex with isopentenylpyrophosphate transferase with a binding affinity value as -4.6 kCal./Mol. and shows inhibitory activity against isopentenylpyrophosphate transferase.

Continuous Sound Velocity Measurements along the Shock Hugoniot Curve of Quartz

NASA Astrophysics Data System (ADS)

Li, Mu; Zhang, Shuai; Zhang, Hongping; Zhang, Gongmu; Wang, Feng; Zhao, Jianheng; Sun, Chengwei; Jeanloz, Raymond

2018-05-01

We report continuous measurements of the sound velocity along the principal Hugoniot curve of α quartz between 0.25 and 1.45 TPa, as determined from lateral release waves intersecting the shock front as a function of time in decaying-shock experiments. The measured sound velocities are lower than predicted by prior models, based on the properties of stishovite at densities below ˜7 g /cm3 , but agree with density functional theory molecular dynamics calculations and an empirical wide-regime equation of state presented here. The Grüneisen parameter calculated from the sound velocity decreases from γ ˜1 .3 at 0.25 TPa to 0.66 at 1.45 TPa. In combination with evidence for increased (configurational) specific heat and decreased bulk modulus, the values of γ suggest a high thermal expansion coefficient at ˜0. 25 - 0 .65 TPa , where SiO2 is thought to be a bonded liquid. From our measurements, dissociation of the molecular bonds persists to ˜0. 65 - 1 .0 TPa , consistent with estimates by other methods. At higher densities, the sound velocity is close to predictions from previous models, and the Grüneisen parameter approaches the ideal gas value.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

DOE PAGES

Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

2014-10-21

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1 b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation andmore » the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

Experimental and computational study on the molecular energetics of indoline and indole.

PubMed

da Silva, Manuel A V Ribeiro; Cabral, Joana I T A; Gomes, José R B

2008-11-27

Static bomb calorimetry, Calvet microcalorimetry and the Knudsen effusion technique were used to determine the standard molar enthalpy of formation in the gas phase, at T = 298.15 K, of the indole and indoline heterocyclic compounds. The values obtained were 164.3 +/- 1.3 kJ x mol(-1) and 120.0 +/- 2.9 kJ x mol(-1), respectively. Several different computational approaches and different working reactions were used to estimate the gas-phase enthalpies of formation for indole and indoline. The computational approaches support the experimental results reported. The calculations were further extended to the determination of other properties such as bond dissociation enthalpies, gas-phase acidities, proton and electron affinities and ionization energies. The agreement between theoretical and experimental data for indole is very good supporting the data calculated for indoline.

PdnCO (n = 1,2): accurate Ab initio bond energies, geometries, and dipole moments and the applicability of density functional theory for fuel cell modeling.

PubMed

Schultz, Nathan E; Gherman, Benjamin F; Cramer, Christopher J; Truhlar, Donald G

2006-11-30

Electrode poisoning by CO is a major concern in fuel cells. As interest in applying computational methods to electrochemistry is increasing, it is important to understand the levels of theory required for reliable treatments of metal-CO interactions. In this paper we justify the use of relativistic effective core potentials for the treatment of PdCO and hence, by inference, for metal-CO interactions where the predominant bonding mechanism is charge transfer. We also sort out key issues involving basis sets and we recommend that bond energies of 17.2, 43.3, and 69.4 kcal/mol be used as the benchmark bond energy for dissociation of Pd2 into Pd atoms, PdCO into Pd and CO, and Pd2CO into Pd2 and CO, respectively. We calculated the dipole moments of PdCO and Pd2CO, and we recommend benchmark values of 2.49 and 2.81 D, respectively. Furthermore, we tested 27 density functionals for this system and found that only hybrid density functionals can qualitatively and quantitatively predict the nature of the sigma-donation/pi-back-donation mechanism that is associated with the Pd-CO and Pd2-CO bonds. The most accurate density functionals for the systems tested in this paper are O3LYP, OLYP, PW6B95, and PBEh.

High-Level ab Initio Predictions for the Ionization Energies, Bond Dissociation Energies, and Heats of Formation of Titanium Oxides and Their Cations (TiOn/TiOn+, n = 1 and 2).

PubMed

Pan, Yi; Luo, Zhihong; Chang, Yih-Chung; Lau, Kai-Chung; Ng, C Y

2017-01-26

The ionization energies (IEs) of TiO and TiO 2 and the 0 K bond dissociation energies (D 0 ) and the heats of formation at 0 K (ΔH° f0 ) and 298 K (ΔH° f298 ) for TiO/TiO + and TiO 2 /TiO 2 + are predicted by the wave-function-based CCSDTQ/CBS approach. The CCSDTQ/CBS calculations involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation (HOC), core-valence (CV) electronic, spin-orbit (SO) coupling, and scalar relativistic (SR) effect corrections. The present calculations yield IE(TiO) = 6.815 eV and are in good agreement with the experimental IE value of 6.819 80 ± 0.000 10 eV determined in a two-color laser-pulsed field ionization-photoelectron (PFI-PE) study. The CCSDT and MRCI+Q methods give the best predictions to the harmonic frequencies: ω e (ω e + ) = 1013 (1069) and 1027 (1059) cm -1 and the bond lengths r e (r e + ) = 1.625 (1.587) and 1.621 (1.588) Å, for TiO (TiO + ) compared with the experimental values. Two nearly degenerate, stable structures are found for TiO 2 cation: TiO 2 + (C 2v ) structure has two equivalent TiO bonds, while the TiO 2 + (C s ) structure features a long and a short TiO bond. The IEs for the TiO 2 + (C 2v )←TiO 2 and TiO 2 + (C s )←TiO 2 ionization transitions are calculated to be 9.515 and 9.525 eV, respectively, giving the theoretical adiabatic IE value in good agreement with the experiment IE(TiO 2 ) = 9.573 55 ± 0.000 15 eV obtained in the previous vacuum ultraviolet (VUV)-PFI-PE study of TiO 2 . The potential energy surface of TiO 2 + along the normal vibrational coordinates of asymmetric stretching mode (ω 3 + ) is nearly flat and exhibits a double-well potential with the well of TiO 2 + (C s ) situated around the central well of TiO 2 + (C 2v ). This makes the theoretical calculation of ω 3 + infeasible. For the symmetric stretching (ω 1 + ), the current theoretical predictions overestimate the experimental value of 829.1 ± 2.0 cm -1 by more than 100 cm -1 . This work together with the previous experimental and theoretical investigations supports the conclusion that the CCSDTQ/CBS approach is capable of providing reliable IE and D 0 predictions for TiO/TiO + and TiO 2 /TiO 2 + with error limits less than or equal to 60 meV. The CCSDTQ/CBS calculations give the predictions of D 0 (Ti + -O) - D 0 (Ti-O) = 0.004 eV and D 0 (O-TiO) - D 0 (O-TiO + ) = 2.699 eV, which are also consistent with the respective experimental determination of 0.008 32 ± 0.000 10 and 2.753 75 ± 0.000 18 eV.

Chemistry at molecular junctions: Rotation and dissociation of O2 on the Ag(110) surface induced by a scanning tunneling microscope.

PubMed

Roy, Sharani; Mujica, Vladimiro; Ratner, Mark A

2013-08-21

The scanning tunneling microscope (STM) is a fascinating tool used to perform chemical processes at the single-molecule level, including bond formation, bond breaking, and even chemical reactions. Hahn and Ho [J. Chem. Phys. 123, 214702 (2005)] performed controlled rotations and dissociations of single O2 molecules chemisorbed on the Ag(110) surface at precise bias voltages using STM. These threshold voltages were dependent on the direction of the bias voltage and the initial orientation of the chemisorbed molecule. They also observed an interesting voltage-direction-dependent and orientation-dependent pathway selectivity suggestive of mode-selective chemistry at molecular junctions, such that in one case the molecule underwent direct dissociation, whereas in the other case it underwent rotation-mediated dissociation. We present a detailed, first-principles-based theoretical study to investigate the mechanism of the tunneling-induced O2 dynamics, including the origin of the observed threshold voltages, the pathway dependence, and the rate of O2 dissociation. Results show a direct correspondence between the observed threshold voltage for a process and the activation energy for that process. The pathway selectivity arises from a competition between the voltage-modified barrier heights for rotation and dissociation, and the coupling strength of the tunneling electrons to the rotational and vibrational modes of the adsorbed molecule. Finally, we explore the "dipole" and "resonance" mechanisms of inelastic electron tunneling to elucidate the energy transfer between the tunneling electrons and chemisorbed O2.

First-principles study of molecular NO dissociation on Ir(100) surface

NASA Astrophysics Data System (ADS)

Erikat, I. A.; Hamad, B. A.; Khalifeh, J. M.

2014-02-01

The dissociation of NO on Ir(100) surface is investigated using density functional theory (DFT). The pathway and transition state (TS) of the dissociation of NO molecule are determined using climbing image nudge elastic band (CI-NEB). The prerequisite state of NO dissociation is determining the most stable sites of the reactant and products. We found that the most energetically stable sites are the hollow for N atom and the bridge for NO molecule as well as O atom. We found that the bending of NO is the first step of the dissociation reaction due to the increase of the back-donation from the d-band of Ir to 2 π ∗ orbital of NO, which causes the weakening of NO bond. The dissociation energy barrier of NO molecule on Ir(100) surface is 0.49 eV.

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations.

PubMed

Chen, Ying; Bylaska, Eric J; Weare, John H

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+ . The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH 2 distances in the DFT calculations it was proposed that the surface Fe 3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination. Graphical abstract All first principle calculations, at all practically achievable levels, for the goethite 100 aqueous interface support a long bond and weak interaction between the exposed surface Fe 3+ and water molecules capping the surface. This result is supported by bond valence theory calculations and is indicative that each surface Fe 3+ is coordinated with only 5 neighbors.

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.

Strong correlation in incremental full configuration interaction

NASA Astrophysics Data System (ADS)

Zimmerman, Paul M.

2017-06-01

Incremental Full Configuration Interaction (iFCI) reaches high accuracy electronic energies via a many-body expansion of the correlation energy. In this work, the Perfect Pairing (PP) ansatz replaces the Hartree-Fock reference of the original iFCI method. This substitution captures a large amount of correlation at zero-order, which allows iFCI to recover the remaining correlation energy with low-order increments. The resulting approach, PP-iFCI, is size consistent, size extensive, and systematically improvable with increasing order of incremental expansion. Tests on multiple single bond, multiple double bond, and triple bond dissociations of main group polyatomics using double and triple zeta basis sets demonstrate the power of the method for handling strong correlation. The smooth dissociation profiles that result from PP-iFCI show that FCI-quality ground state computations are now within reach for systems with up to about 10 heavy atoms.

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

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.

DFT and AIM study of the protonation of nitrous acid and the pKa of nitrous acidium ion.

PubMed

Crugeiras, Juan; Ríos, Ana; Maskill, Howard

2011-11-10

The gas phase and aqueous thermochemistry, NMR chemical shifts, and the topology of chemical bonding of nitrous acid (HONO) and nitrous acidium ion (H(2)ONO(+)) have been investigated by ab initio methods using density functional theory. By the same methods, the dissociation of H(2)ONO(+) to give the nitrosonium ion (NO(+)) and water has also been investigated. We have used Becke's hybrid functional (B3LYP), and geometry optimizations were performed with the 6-311++G(d,p) basis set. In addition, highly accurate ab initio composite methods (G3 and CBS-Q) were used. Solvation energies were calculated using the conductor-like polarizable continuum model, CPCM, at the B3LYP/6-311++G(d,p) level of theory, with the UAKS cavity model. The pK(a) value of H(2)ONO(+) was calculated using two different schemes: the direct method and the proton exchange method. The calculated pK(a) values at different levels of theory range from -9.4 to -15.6, showing that H(2)ONO(+) is a strong acid (i.e., HONO is only a weak base). The equilibrium constant, K(R), for protonation of nitrous acid followed by dissociation to give NO(+) and H(2)O has also been calculated using the same methodologies. The pK(R) value calculated by the G3 and CBS-QB3 methods is in best (and satisfactory) agreement with experimental results, which allows us to narrow down the likely value of the pK(a) of H(2)ONO(+) to about -10, a value appreciably more acidic than literature values.

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.

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

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.

Effects of defects on thermal decomposition of HMX via ReaxFF molecular dynamics simulations.

PubMed

Zhou, Ting-Ting; Huang, Feng-Lei

2011-01-20

Effects of molecular vacancies on the decomposition mechanisms and reaction dynamics of condensed-phase β-HMX at various temperatures were studied using ReaxFF molecular dynamics simulations. Results show that three primary initial decomposition mechanisms, namely, N-NO(2) bond dissociation, HONO elimination, and concerted ring fission, exist at both high and lower temperatures. The contribution of the three mechanisms to the initial decomposition of HMX is influenced by molecular vacancies, and the effects vary with temperature. At high temperature (2500 K), molecular vacancies remarkably promote N-N bond cleavage and concerted ring breaking but hinder HONO formation. N-N bond dissociation and HONO elimination are two primary competing reaction mechanisms, and the former is dominant in the initial decomposition. Concerted ring breaking of condensed-phase HMX is not favored at high temperature. At lower temperature (1500 K), the most preferential initial decomposition pathway is N-N bond dissociation followed by the formation of NO(3) (O migration), although all three mechanisms are promoted by molecular vacancies. The promotion effect on concerted ring breaking is considerable at lower temperature. Products resulting from concerted ring breaking appear in the defective system but not in the perfect crystal. The mechanism of HONO elimination is less important at lower temperature. We also estimated the reaction rate constant and activation barriers of initial decomposition with different vacancy concentrations. Molecular vacancies accelerate the decomposition of condensed-phase HMX by increasing the reaction rate constant and reducing activation barriers.

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.

PubMed

Carrasco, Javier; López-Durán, David; Liu, Zongyuan; Duchoň, Tomáš; Evans, Jaime; Senanayake, Sanjaya D; Crumlin, Ethan J; Matolín, Vladimir; Rodríguez, José A; Ganduglia-Pirovano, M Verónica

2015-03-23

Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Supported by experimental and density-functional theory results, the effect of the support on OH bond cleavage activity is elucidated for nickel/ceria systems. Ambient-pressure O 1s photoemission spectra at low Ni loadings on CeO2 (111) reveal a substantially larger amount of OH groups as compared to the bare support. 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 this support effect is the ability of ceria to stabilize oxidized Ni(2+) 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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

First-principles prediction of the effects of temperature and solvent selection on the dimerization of benzoic acid.

PubMed

Pham, Hieu H; Taylor, Christopher D; Henson, Neil J

2013-01-24

We introduce a procedure of quantum chemical calculations (B3P86/6-31G**) to study carboxylic acid dimerization and its correlation with temperature and properties of the solvent. Benzoic acid is chosen as a model system for studying dimerization via hydrogen bonding. Organic solvents are simulated using the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The cyclic dimer is the most stable structure both in gas phase and solution. Dimer mono- and dihydrates could be found in the gas phase if acid molecules are in contact with water vapor. However, the formation of these hydrated conformers is very limited and cyclic dimer is the principal conformer to coexist with monomer acid in solution. Solvation of the cyclic dimer is more favorable compared to other complexes, partially due to the diminishing of hydrogen bonding capability and annihilation of dipole moments. Solvents have a strong effect on inducing dimer dissociation and this dependence is more pronounced at low dielectric constants. By accounting for selected terms in the total free energy of solvation, the solvation entropy could be incorporated to predict the dimer behavior at elevated temperatures. The temperature dependence of benzoic acid dimerization obtained by this technique is in good agreement with available experimental measurements, in which a tendency of dimer to dissociate is observed with increased temperatures. In addition, dimer breakup is more sensitive to temperature in low dielectric environments rather than in solvents with a higher dielectric constant.

Structure-activity relationships in defensin dimers: a novel link between beta-defensin tertiary structure and antimicrobial activity.

PubMed

Campopiano, Dominic J; Clarke, David J; Polfer, Nick C; Barran, Perdita E; Langley, Ross J; Govan, John R W; Maxwell, Alison; Dorin, Julia R

2004-11-19

Defensins are cationic antimicrobial peptides that have a characteristic six-cysteine motif and are important components of the innate immune system. We recently described a beta-defensin-related peptide (Defr1) that had potent antimicrobial activity despite having only five cysteines. Here we report a relationship between the structure and activity of Defr1 through a comparative study with its six cysteine-containing analogue (Defr1 Y5C). Against a panel of pathogens, we found that oxidized Defr1 had significantly higher activity than its reduced form and the oxidized and reduced forms of Defr1 Y5C. Furthermore, Defr1 displayed activity against Pseudomonas aeruginosa in the presence of 150 mm NaCl, whereas Defr1 Y5C was inactive. By using nondenaturing gel electrophoresis and Fourier transform ion cyclotron resonance mass spectrometry, we observed Defr1 and Defr1 Y5C dimers. Two complementary fragmentation techniques (collision-induced dissociation and electron capture dissociation) revealed that Defr1 Y5C dimers form by noncovalent, weak association of monomers that contain three intramolecular disulfide bonds. In contrast, Defr1 dimers are resistant to collision-induced dissociation and are only dissociated into monomers by reduction using electron capture. This is indicative of Defr1 dimerization being mediated by an intermolecular disulfide bond. Proteolysis and peptide mass mapping revealed that Defr1 Y5C monomers have beta-defensin disulfide bond connectivity, whereas oxidized Defr1 is a complex mixture of dimeric isoforms with as yet unknown inter- and intramolecular connectivities. Each isoform contains one intermolecular and four intramolecular disulfide bonds, but because we were unable to resolve the isoforms by reverse phase chromatography, we could not assign each isoform with a specific antimicrobial activity. We conclude that the enhanced activity and stability of this mixture of Defr1 dimeric isoforms are due to the presence of an intermolecular disulfide bond. This first description of a covalently cross-linked member of the defensin family provides further evidence that the antimicrobial activity of a defensin is linked to its ability to form stable higher order structures.

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

Cucurbit[6]uril: A Possible Host for Noble Gas Atoms.

PubMed

Pan, Sudip; Mandal, Subhajit; Chattaraj, Pratim K

2015-08-27

Density functional and ab initio molecular dynamics studies are carried out to investigate the stability of noble gas encapsulated cucurbit[6]uril (CB[6]) systems. Interaction energy, dissociation energy and dissociation enthalpy are calculated to understand the efficacy of CB[6] in encapsulating noble gas atoms. CB[6] could encapsulate up to three Ne atoms having dissociation energy (zero-point energy corrected) in the range of 3.4-4.1 kcal/mol, whereas due to larger size, only one Ar or Kr atom encapsulated analogues would be viable. The dissociation energy value for the second Ar atom is only 1.0 kcal/mol. On the other hand, the same for the second Kr is -0.5 kcal/mol, implying the instability of the system. The noble gas dissociation processes are endothermic in nature, which increases gradually along Ne to Kr. Kr encapsulated analogue is found to be viable at room temperature. However, low temperature is needed for Ne and Ar encapsulated analogues. The temperature-pressure phase diagram highlights the region in which association and dissociation processes of Kr@CB[6] would be favorable. At ambient temperature and pressure, CB[6] may be used as an effective noble gas carrier. Wiberg bond indices, noncovalent interaction indices, electron density, and energy decomposition analyses are used to explore the nature of interaction between noble gas atoms and CB[6]. Dispersion interaction is found to be the most important term in the attraction energy. Ne and Ar atoms in one Ng entrapped analogue are found to stay inside the cavity of CB[6] throughout the simulation at 298 K. However, during simulation Ng2 units in Ng2@CB[6] flip toward the open faces of CB[6]. After 1 ps, one Ne atom of Ne3@CB[6] almost reaches the open face keeping other two Ne atoms inside. At lower temperature (77 K), all the Ng atoms in Ngn@CB[6] remain well inside the cavity of CB[6] throughout the simulation time (1 ps).

Connecting Interface Structure to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

Understanding structure-function relationships at aqueous semiconductor interfaces presents fundamental challenges, including the discovery of the key interface structure motifs themselves. Important examples include the alignment of electrochemical redox levels with the semiconductor band edges and the identification of catalytic active sites. We have developed a multistep approach, initially demonstrated for GaN, ZnO and their alloys, motivated by measured high efficiency for photocatalytic water oxidation. The interface structure is simulated using ab initio molecular dynamics (AIMD). The calculated, average interface dipole is combined with the GW approach from many-body perturbation theory to calculate the energy level alignment between the semiconductor band edges and the centroid of the occupied 1b1 energy level of water and thus, the electrochemical levels. Cluster models are used to study reaction pathways. The emergent interface motif is the full (GaN) or partial (ZnO) dissociated interface water layer. Here I will focus on the aqueous interfaces to the stable TiO2 anatase (101) and rutile (110) facets. The AIMD calculations reveal interface water dissociation and reassociation processes through distinct pathways: one direct at the interface and the other via a spectator water molecule from the hydration layer. Comparisons between the two interfaces shows that the energy landscape for these pathways depends on the local hydrogen bonding patterns and the interplay with the interface template. Combined results from different initial conditions and AIMD temperatures demonstrate a partially dissociated interface water layer in both cases. Specifically for rutile, structure and the GW-based analysis of the interface energy level alignment agree with experiment. Finally, hole localization at different interface structure motifs will be discussed. Work performed in collaboration with J. Lyons, N. Kharche, M. Ertem and J. Muckerman, done in part at the CFN, which is a U.S. DOE Office of Science Facility, at BNL under Contract No. DE-SC0012704 and with resources from NERSC under Contract No. DE-AC02-05CH11231.

Ethylene dissociation on flat and stepped Ni(1 1 1): A combined STM and DFT study

NASA Astrophysics Data System (ADS)

Vang, Ronnie T.; Honkala, Karoliina; Dahl, Søren; Vestergaard, Ebbe K.; Schnadt, Joachim; Lægsgaard, Erik; Clausen, Bjerne S.; Nørskov, Jens K.; Besenbacher, Flemming

2006-01-01

The dissociative adsorption of ethylene (C 2H 4) on Ni(1 1 1) was studied by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The STM studies reveal that ethylene decomposes exclusively at the step edges at room temperature. However, the step edge sites are poisoned by the reaction products and thus only a small brim of decomposed ethylene is formed. At 500 K decomposition on the (1 1 1) facets leads to a continuous growth of carbidic islands, which nucleate along the step edges. DFT calculations were performed for several intermediate steps in the decomposition of ethylene on both Ni(1 1 1) and the stepped Ni(2 1 1) surface. In general the Ni(2 1 1) surface is found to have a higher reactivity than the Ni(1 1 1) surface. Furthermore, the calculations show that the influence of step edge atoms is very different for the different reaction pathways. In particular the barrier for dissociation is lowered significantly more than the barrier for dehydrogenation, and this is of great importance for the bond-breaking selectivity of Ni surfaces. The influence of step edges was also probed by evaporating Ag onto the Ni(1 1 1) surface. STM shows that the room temperature evaporation leads to a step flow growth of Ag islands, and a subsequent annealing at 800 K causes the Ag atoms to completely wet the step edges of Ni(1 1 1). The blocking of the step edges is shown to prevent all decomposition of ethylene at room temperature, whereas the terrace site decomposition at 500 K is confirmed to be unaffected by the Ag atoms. Finally a high surface area NiAg alloy catalyst supported on MgAl 2O 4 was synthesized and tested in flow reactor measurements. The NiAg catalyst has a much lower activity for ethane hydrogenolysis than a similar Ni catalyst, which can be rationalized by the STM and DFT results.

ADSORPTION AND DISSOCIATION OF O2 ON Ti3Al (0001) STUDIED BY FIRST-PRINCIPLES

NASA Astrophysics Data System (ADS)

Wei, Li-Jing; Guo, Jian-Xin; Dai, Xiu-Hong; Wang, Ying-Long; Liu, Bao-Ting

2015-05-01

The adsorption and dissociation of oxygen molecule on Ti3Al (0001) surface have been investigated by density functional theory (DFT) with the generalized gradient approximation (GGA). All possible adsorption sites including nine vertical and fifteen parallel sites of O2 are considered on Ti3Al (0001) surface. It is found that all oxygen molecules dissociate except for three vertical adsorption sites after structure optimization. This indicates that oxygen molecules prefer to dissociate on the junction site between Ti and Al atoms. Oxygen atoms coming from dissociation of oxygen molecule tend to occupy the most stable adsorption sites of the Ti3Al (0001) surface. The distance of O-O is related to the surface dissociation distance of Ti3Al (0001) surface. The valence electron localization function (ELF) and projected density of states (DOS) show that the bonds of O-O are breakaway at parallel adsorption end structures.

Deuterium enrichment by selective photo-induced dissociation of an organic carbonyl compound

DOEpatents

Marling, John B.

1981-01-01

A method for producing a deuterium enriched material by photoinduced dissociation which uses as the working material a gas phase photolytically dissociable organic carbonyl compound containing at least one hydrogen atom bonded to an atom which is adjacent to a carbonyl group and consisting of molecules wherein said hydrogen atom is present as deuterium and molecules wherein said hydrogen atom is present as another isotope of hydrogen. The organic carbonyl compound is subjected to intense infrared radiation at a preselected wavelength to selectively excite and thereby induce dissociation of the deuterium containing species to yield a deuterium enriched stable molecular product. Undissociated carbonyl compound, depleted in deuterium, is preferably redeuterated for reuse.

Ethane-xenon mixtures under shock conditions

DOE PAGES

Magyar, Rudolph J.; Root, Seth; Mattsson, Thomas; ...

2015-04-22

Mixtures of light elements with heavy elements are important in inertial confinement fusion. We explore the physics of molecular scale mixing through a validation study of equation of state (EOS) properties. Density functional theory molecular dynamics (DFT-MD) at elevated temperature and pressure is used to obtain the thermodynamic state properties of pure xenon, ethane, and various compressed mixture compositions along their principal Hugoniots. In order to validate these simulations, we have performed shock compression experiments using the Sandia Z-Machine. A bond tracking analysis correlates the sharp rise in the Hugoniot curve with the completion of dissociation in ethane. Furthermore, themore » DFT-based simulation results compare well with the experimental data along the principal Hugoniots and are used to provide insight into the dissociation and temperature along the Hugoniots as a function of mixture composition. Interestingly, we find that the compression ratio for complete dissociation is similar for several compositions suggesting a limiting compression for C-C bonded systems.« less

Optimized norm-conserving Hartree-Fock pseudopotentials for plane-wave calculations

NASA Astrophysics Data System (ADS)

Al-Saidi, W. A.; Walter, E. J.; Rappe, A. M.

2008-02-01

We report Hartree-Fock (HF)-based pseudopotentials suitable for plane-wave calculations. Unlike typical effective core potentials, the present pseudopotentials are finite at the origin and exhibit rapid convergence in a plane-wave basis; the optimized pseudopotential method [A. M. Rappe , Phys. Rev. B 41, 1227 (1990)] improves plane-wave convergence. Norm-conserving HF pseudopotentials are found to develop long-range non-Coulombic behavior which does not decay faster than 1/r , and is nonlocal. This behavior, which stems from the nonlocality of the exchange potential, is remedied using a recently developed self-consistent procedure [J. R. Trail and R. J. Needs, J. Chem. Phys. 122, 014112 (2005)]. The resulting pseudopotentials slightly violate the norm conservation of the core charge. We calculated several atomic properties using these pseudopotentials, and the results are in good agreement with all-electron HF values. The dissociation energies, equilibrium bond lengths, and frequencies of vibration of several dimers obtained with these HF pseudopotentials and plane waves are also in good agreement with all-electron results.

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

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

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

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.

a Theoretical Search for AN Electronic Spectrum of the He-BeO Complex

NASA Astrophysics Data System (ADS)

Gardner, Adrian; Heaven, Michael

2014-06-01

The surprisingly high dissociation energy of the He-Be bond in the He-BeO complex was first reported 25 years ago. Following which, a number of theoretical studies have investigated similar closed shell helium containing complexes. However, despite these investigations, a complex containing a strong He-X bond has thus far eluded experimental detection. In this work, potential energy surfaces of electronically excited states of the He-BeO complex have been calculated employing high level CASSCF+MRCI+Q methodologies and utilizing extended basis sets. Several excited states show strong interactions between helium and BeO lying in Franck-Condon accessible windows of electronic transitions arising from the vibrationless electronic ground state. It is hoped that the conclusions of this study will result in the observation an electronic spectrum of this long hypothesized strongly bound complex in the near future. W. Koch, J. R. Collins and G. Frenking, Chem. Phys. Lett. 1986, 132 330-333.

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.

Myricetin, rosmarinic and carnosic acids as superior natural antioxidant alternatives to α-tocopherol for the preservation of omega-3 oils.

PubMed

Guitard, Romain; Paul, Jean-François; Nardello-Rataj, Véronique; Aubry, Jean-Marie

2016-12-15

22 natural polyphenols are compared to 7 synthetic antioxidants including BHT, BHA, TBHQ and PG with regard to their ability to protect omega-3 oils from autoxidation. The antioxidant efficiency of phenols is assessed using the DPPH test and the measurement of oxygen consumption during the autoxidation of oils rich in omega-3 fatty acids. Also, the bond dissociation enthalpies (BDE) of the Ar-OH bonds are calculated and excellent correlations between thermodynamic, kinetic and oxidation data are obtained. It is shown that kinetic rates of hydrogen transfer, number of radicals scavenged per antioxidant molecule, BDE and formation of antioxidant dimers from the primary radicals play an important role regarding the antioxidant activity of phenols. Based on this, it is finally shown that myricetin, rosmarinic and carnosic acids are more efficient than α-tocopherol and synthetic antioxidants for the preservation of omega-3 oils. Copyright © 2016 Elsevier Ltd. All rights reserved.

The structures and properties of proton- and alkali-bound cysteine dimers.

PubMed

Ieritano, Christian; Carr, Patrick J J; Hasan, Moaraj; Burt, Michael; Marta, Rick A; Steinmetz, Vincent; Fillion, Eric; McMahon, Terrance B; Scott Hopkins, W

2016-02-14

The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm(-1) region show that protonation is localized on an amine group, and that intermolecular hydrogen bonding occurs between the protonated amine and the carbonyl oxygen of the neutral Cys moiety. Alkali-bound dimers adopt structures reminiscent of those observed for the monomeric Cys·Li(+) and Cys·Na(+) species. Calculations of the heavier Cys2·M(+) (M = K, Rb or Cs) species suggest that these are significantly less strongly bound than the lighter (M = H, Li, or Na) dimers.

Segmented all-electron Gaussian basis sets of double and triple zeta qualities for Fr, Ra, and Ac

NASA Astrophysics Data System (ADS)

Campos, C. T.; de Oliveira, A. Z.; Ferreira, I. B.; Jorge, F. E.; Martins, L. S. C.

2017-05-01

Segmented all-electron basis sets of valence double and triple zeta qualities plus polarization functions for the elements Fr, Ra, and Ac are generated using non-relativistic and Douglas-Kroll-Hess (DKH) Hamiltonians. The sets are augmented with diffuse functions with the purpose to describe appropriately the electrons far from the nuclei. At the DKH-B3LYP level, first atomic ionization energies and bond lengths, dissociation energies, and polarizabilities of a sample of diatomics are calculated. Comparison with theoretical and experimental data available in the literature is carried out. It is verified that despite the small sizes of the basis sets, they are yet reliable.

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

K.-F. Braun, V. Iancu, N. Pertaya, K.-H. Rieder and S.-W. Hla

Deviating from the common growth mode of molecular films of organic molecules where the adsorbates remain intact, we observe an essentially different growth behavior for metalocenes with a low temperature scanning tunneling microscope. Ferrocene molecules adsorb dissociatively and form a two layer structure after being decomposed into fragments. The toplayer unit cell is composed of two tilted cyclopentadienyl rings, while the first layer consists of the remaining fragments. Surprisingly a fourfold symmetry is observed for the top layer while the first layer displays threefold symmetry elements. It is this symmetry mismatch which induces an incommensurability between these layers in allmore » except one surface direction. The toplayer is weakly bonded and has an antiferromagnetic groundstate as calculated by local spin density functional approximation.« less

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.

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

Temperature dependence of dissociative electron attachment to bromo-chlorotoluene isomers: Competition between detachment of Cl- and Br-

NASA Astrophysics Data System (ADS)

Mahmoodi-Darian, Masoomeh; Huber, Stefan E.; Mauracher, Andreas; Probst, Michael; Denifl, Stephan; Scheier, Paul; Märk, Tilmann D.

2018-02-01

Dissociative electron attachment to three isomers of bromo-chlorotoluene was investigated in the electron energy range from 0 to 2 eV for gas temperatures in the range of 392-520 K using a crossed electron-molecular beam apparatus with a temperature regulated effusive molecular beam source. For all three molecules, both Cl- and Br- are formed. The ion yields of both halogenides show a pronounced temperature effect. In the case of Cl- and Br-, the influence of the gas temperature can be observed at the threshold peak close to 0 eV. The population of molecules that have some of their out-of-plane modes excited varies strongly in the temperature range investigated, indicating that such vibrations might play a role in the energy transfer towards bond breaking. Potential energy curves for the abstraction of Cl- and Br- were calculated and extrapolated into the metastable domain. The barriers in the diabatic curves approximated in this way agree well with the ones derived from the temperature dependence observed in the experiments.

Load-dependent ADP binding to myosins V and VI: Implications for subunit coordination and function

PubMed Central

Oguchi, Yusuke; Mikhailenko, Sergey V.; Ohki, Takashi; Olivares, Adrian O.; De La Cruz, Enrique M.; Ishiwata, Shin'ichi

2008-01-01

Dimeric myosins V and VI travel long distances in opposite directions along actin filaments in cells, taking multiple steps in a “hand-over-hand” fashion. The catalytic cycles of both myosins are limited by ADP dissociation, which is considered a key step in the walking mechanism of these motors. Here, we demonstrate that external loads applied to individual actomyosin V or VI bonds asymmetrically affect ADP affinity, such that ADP binds weaker under loads assisting motility. Model-based analysis reveals that forward and backward loads modulate the kinetics of ADP binding to both myosins, although the effect is less pronounced for myosin VI. ADP dissociation is modestly accelerated by forward loads and inhibited by backward loads. Loads applied in either direction slow ADP binding to myosin V but accelerate binding to myosin VI. We calculate that the intramolecular load generated during processive stepping is ≈2 pN for both myosin V and myosin VI. The distinct load dependence of ADP binding allows these motors to perform different cellular functions. PMID:18509050

Electrochemical and theoretical analysis of the reactivity of shikonin derivatives: dissociative electron transfer in esterified compounds.

PubMed

Armendáriz-Vidales, Georgina; Frontana, Carlos

2014-09-07

An electrochemical and theoretical analysis of a series of shikonin derivatives in aprotic media is presented. Results showed that the first electrochemical reduction signal is a reversible monoelectronic transfer, generating a stable semiquinone intermediate; the corresponding E(I)⁰ values were correlated with calculated values of electroaccepting power (ω(+)) and adiabatic electron affinities (A(Ad)), obtained with BH and HLYP/6-311++G(2d,2p) and considering the solvent effect, revealing the influence of intramolecular hydrogen bonding and the substituting group at position C-2 in the experimental reduction potential. For the second reduction step, esterified compounds isobutyryl and isovalerylshikonin presented a coupled chemical reaction following dianion formation. Analysis of the variation of the dimensionless cathodic peak potential values (ξ(p)) as a function of the scan rate (v) functions and complementary experiments in benzonitrile suggested that this process follows a dissociative electron transfer, in which the rate of heterogeneous electron transfer is slow (~0.2 cm s(-1)), and the rate constant of the chemical process is at least 10(5) larger.

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

Metal cation dependence of interactions with amino acids: bond dissociation energies of Rb(+) and Cs(+) to the acidic amino acids and their amide derivatives.

PubMed

Armentrout, P B; Yang, Bo; Rodgers, M T

2014-04-24

Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu < Asn < Gln.

Benchmarking lithium amide versus amine bonding by charge density and energy decomposition analysis arguments.

PubMed

Engelhardt, Felix; Maaß, Christian; Andrada, Diego M; Herbst-Irmer, Regine; Stalke, Dietmar

2018-03-28

Lithium amides are versatile C-H metallation reagents with vast industrial demand because of their high basicity combined with their weak nucleophilicity, and they are applied in kilotons worldwide annually. The nuclearity of lithium amides, however, modifies and steers reactivity, region- and stereo-selectivity and product diversification in organic syntheses. In this regard, it is vital to understand Li-N bonding as it causes the aggregation of lithium amides to form cubes or ladders from the polar Li-N covalent metal amide bond along the ring stacking and laddering principle. Deaggregation, however, is more governed by the Li←N donor bond to form amine adducts. The geometry of the solid state structures already suggests that there is σ- and π-contribution to the covalent bond. To quantify the mutual influence, we investigated [{(Me 2 NCH 2 ) 2 (C 4 H 2 N)}Li] 2 ( 1 ) by means of experimental charge density calculations based on the quantum theory of atoms in molecules (QTAIM) and DFT calculations using energy decomposition analysis (EDA). This new approach allows for the grading of electrostatic Li + N - , covalent Li-N and donating Li←N bonding, and provides a way to modify traditional widely-used heuristic concepts such as the -I and +I inductive effects. The electron density ρ ( r ) and its second derivative, the Laplacian ∇ 2 ρ ( r ), mirror the various types of bonding. Most remarkably, from the topological descriptors, there is no clear separation of the lithium amide bonds from the lithium amine donor bonds. The computed natural partial charges for lithium are only +0.58, indicating an optimal density supply from the four nitrogen atoms, while the Wiberg bond orders of about 0.14 au suggest very weak bonding. The interaction energy between the two pincer molecules, (C 4 H 2 N) 2 2- , with the Li 2 2+ moiety is very strong ( ca. -628 kcal mol -1 ), followed by the bond dissociation energy (-420.9 kcal mol -1 ). Partitioning the interaction energy into the Pauli (Δ E Pauli ), dispersion (Δ E disp ), electrostatic (Δ E elstat ) and orbital (Δ E orb ) terms gives a 71-72% ionic and 25-26% covalent character of the Li-N bond, different to the old dichotomy of 95 to 5%. In this regard, there is much more potential to steer the reactivity with various substituents and donor solvents than has been anticipated so far.

Li-Decorated β12-Borophene as Potential Candidates for Hydrogen Storage: A First-Principle Study.

PubMed

Liu, Tingting; Chen, Yuhong; Wang, Haifeng; Zhang, Meiling; Yuan, Lihua; Zhang, Cairong

2017-12-07

The hydrogen storage properties of pristine β 12 -borophene and Li-decorated β 12 -borophene are systemically investigated by means of first-principles calculations based on density functional theory. The adsorption sites, adsorption energies, electronic structures, and hydrogen storage performance of pristine β 12 -borophene/H₂ and Li- β 12 -borophene/H₂ systems are discussed in detail. The results show that H₂ is dissociated into Two H atoms that are then chemisorbed on β 12 -borophene via strong covalent bonds. Then, we use Li atom to improve the hydrogen storage performance and modify the hydrogen storage capacity of β 12 -borophene. Our numerical calculation shows that Li- β 12 -borophene system can adsorb up to 7 H₂ molecules; while 2Li- β 12 -borophene system can adsorb up to 14 H₂ molecules and the hydrogen storage capacity up to 10.85 wt %.

Methanol partial oxidation on Ag(111) from first principles

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

Aljama, Hassan; Yoo, Jong Suk; Nørskov, Jens K.

In this work, we examine the thermochemistry and kinetics of the partial oxidation of methanol to formaldehyde on silver surfaces. Periodic density functional theory calculations employing the BEEF-vdW functional are used to identify the most stable phases of the silver surface under relevant reaction conditions and the reaction energetics are obtained on these surfaces. The calculated binding energies and transition state energies are used as input in a mean-field microkinetic model providing the reaction kinetics on silver surfaces under different reaction conditions. Our results show that, under conditions pertaining to methanol partial oxidation, oxygen is present at low concentrations andmore » it plays a critical role in the catalytic reaction. Surface oxygen promotes the reaction by activating the OH bond in methanol, thus forming a methoxy intermediate, which can react further to form formaldehyde. Finally, the dissociation of molecular oxygen is identified as the most critical step.« less

Methanol partial oxidation on Ag(111) from first principles

DOE PAGES

Aljama, Hassan; Yoo, Jong Suk; Nørskov, Jens K.; ...

2016-10-26

In this work, we examine the thermochemistry and kinetics of the partial oxidation of methanol to formaldehyde on silver surfaces. Periodic density functional theory calculations employing the BEEF-vdW functional are used to identify the most stable phases of the silver surface under relevant reaction conditions and the reaction energetics are obtained on these surfaces. The calculated binding energies and transition state energies are used as input in a mean-field microkinetic model providing the reaction kinetics on silver surfaces under different reaction conditions. Our results show that, under conditions pertaining to methanol partial oxidation, oxygen is present at low concentrations andmore » it plays a critical role in the catalytic reaction. Surface oxygen promotes the reaction by activating the OH bond in methanol, thus forming a methoxy intermediate, which can react further to form formaldehyde. Finally, the dissociation of molecular oxygen is identified as the most critical step.« less

Calculation of smooth potential energy surfaces using local electron correlation methods

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

Mata, Ricardo A.; Werner, Hans-Joachim

2006-11-14

The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl{sup -} with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barriermore » heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.« less

Prediction of metastable metal-rare gas fluorides: FMRgF (M=Be and Mg; Rg=Ar, Kr and Xe).

PubMed

Jayasekharan, T; Ghanty, T K

2008-04-14

The structure, stability, charge redistribution, bonding, and harmonic vibrational frequencies of rare gas containing group II-A fluorides with the general formula FMRgF (where M=Be and Mg; Rg=Ar, Kr, and Xe) have been investigated using second order Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory [CCSD(T)] methods. The species, FMRgF show a quasilinear structure at the minima and a bent structure at the transition state. The predicted species are unstable with respect to the two-body dissociation channel, leading to the global minima (MF2+Rg) on the singlet potential energy surface. However, with respect to other two-body dissociation channel (FM+RgF), they are found to be stable and have high positive energies on the same surface. The computed binding energy for the two-body dissociation channels are 94.0, 164.7, and 199.7 kJ mol(-1) for FBeArF, FBeKrF, FBeXeF, respectively, at CCSD(T) method. The corresponding energy values are 83.4, 130.7, and 180.1 kJ mol(-1) for FMgArF, FMgKrF, and FMgXeF, respectively, at the same level of theory. With respect to the three-body dissociation (FM+Rg+F) channel as well as dissociation into atomic constituent, they are also found to be stable and have high positive energies. The dissociation of the predicted species typically proceeds via MRgF bending mode at the transition state. The computed barrier heights for the transition states are 11.4, 32.2, and 57.6 kJ mol(-1) for FBeArF, FBeKrF, and FBeXeF, respectively, at the CCSD(T) method. The corresponding barrier heights for the Mg containing species are 2.1, 9.2, and 32.1 kJ mol(-1) along the series Ar--Kr--Xe, respectively. The M--Rg bond energies of the FMRgF species is significantly higher than the corresponding bond energies of the M+--Rg species ( approximately 53 and approximately 15 kJ mol(-1) for Be+--Ar and Mg+--Ar, respectively). The computed energy diagram as well as the geometrical parameters along with the AIM results suggest that the species are metastable with partial covalent character in the M--Rg bonding. Thus, it may be possible to prepare and to characterize these species using low temperature matrix isolation technique.

Prediction of metastable metal-rare gas fluorides: FMRgF (M =Be and Mg; Rg =Ar, Kr and Xe)

NASA Astrophysics Data System (ADS)

Jayasekharan, T.; Ghanty, T. K.

2008-04-01

The structure, stability, charge redistribution, bonding, and harmonic vibrational frequencies of rare gas containing group II-A fluorides with the general formula FMRgF (where M =Be and Mg; Rg =Ar, Kr, and Xe) have been investigated using second order Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory [CCSD(T)] methods. The species, FMRgF show a quasilinear structure at the minima and a bent structure at the transition state. The predicted species are unstable with respect to the two-body dissociation channel, leading to the global minima (MF2+Rg) on the singlet potential energy surface. However, with respect to other two-body dissociation channel (FM+RgF), they are found to be stable and have high positive energies on the same surface. The computed binding energy for the two-body dissociation channels are 94.0, 164.7, and 199.7kJmol-1 for FBeArF, FBeKrF, FBeXeF, respectively, at CCSD(T) method. The corresponding energy values are 83.4, 130.7, and 180.1kJmol-1 for FMgArF, FMgKrF, and FMgXeF, respectively, at the same level of theory. With respect to the three-body dissociation (FM+Rg+F) channel as well as dissociation into atomic constituent, they are also found to be stable and have high positive energies. The dissociation of the predicted species typically proceeds via MRgF bending mode at the transition state. The computed barrier heights for the transition states are 11.4, 32.2, and 57.6kJmol-1 for FBeArF, FBeKrF, and FBeXeF, respectively, at the CCSD(T) method. The corresponding barrier heights for the Mg containing species are 2.1, 9.2, and 32.1kJmol-1 along the series Ar KrXe, respectively. The M Rg bond energies of the FMRgF species is significantly higher than the corresponding bond energies of the M+Rg species (˜53 and ˜15kJmol-1 for Be+Ar and Mg+Ar, respectively). The computed energy diagram as well as the geometrical parameters along with the AIM results suggest that the species are metastable with partial covalent character in the M Rg bonding. Thus, it may be possible to prepare and to characterize these species using low temperature matrix isolation technique.

Energetics using the single point IMOMO (integrated molecular orbital+molecular orbital) calculations: Choices of computational levels and model system

NASA Astrophysics Data System (ADS)

Svensson, Mats; Humbel, Stéphane; Morokuma, Keiji

1996-09-01

The integrated MO+MO (IMOMO) method, recently proposed for geometry optimization, is tested for accurate single point calculations. The principle idea of the IMOMO method is to reproduce results of a high level MO calculation for a large ``real'' system by dividing it into a small ``model'' system and the rest and applying different levels of MO theory for the two parts. Test examples are the activation barrier of the SN2 reaction of Cl-+alkyl chlorides, the C=C double bond dissociation of olefins and the energy of reaction for epoxidation of benzene. The effects of basis set and method in the lower level calculation as well as the effects of the choice of model system are investigated in detail. The IMOMO method gives an approximation to the high level MO energetics on the real system, in most cases with very small errors, with a small additional cost over the low level calculation. For instance, when the MP2 (Møller-Plesset second-order perturbation) method is used as the lower level method, the IMOMO method reproduces the results of very high level MO method within 2 kcal/mol, with less than 50% of additional computer time, for the first two test examples. When the HF (Hartree-Fock) method is used as the lower level method, it is less accurate and depends more on the choice of model system, though the improvement over the HF energy is still very significant. Thus the IMOMO single point calculation provides a method for obtaining reliable local energetics such as bond energies and activation barriers for a large molecular system.

Periodic density functional theory calculations of bulk and the (010) surface of goethite

PubMed Central

Kubicki, James D; Paul, Kristian W; Sparks, Donald L

2008-01-01

Background Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP). Results Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former. Conclusion Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces. PMID:18477389

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction.

PubMed

Bilić, Ante; Reimers, Jeffrey R; Hush, Noel S

2005-03-01

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Chen, Jun; Zhang, Zhaojun; Shen, Xiangjian; Fu, Bina; Zhang, Dong H.

2018-04-01

We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

Four-Component Relativistic State-Specific Multireference Perturbation Theory with a Simplified Treatment of Static Correlation.

PubMed

Ghosh, Anirban; Sinha Ray, Suvonil; Chaudhuri, Rajat K; Chattopadhyay, Sudip

2017-02-23

The relativistic multireference (MR) perturbative approach is one of the most successful tools for the description of computationally demanding molecular systems of heavy elements. We present here the ground state dissociation energy surfaces, equilibrium bond lengths, harmonic frequencies, and dissociation energies of Ag 2 , Cu 2 , Au 2 , and I 2 computed using the four-component (4c) relativistic spinors based state-specific MR perturbation theory (SSMRPT) with improved virtual orbital complete active space configuration interaction (IVO-CASCI) functions. The IVO-CASCI method is a simple, robust, useful and lower cost alternative to the complete active space self-consistent field approach for treating quasidegenerate situations. The redeeming features of the resulting method, termed as 4c-IVO-SSMRPT, lies in (i) manifestly size-extensivity, (ii) exemption from intruder problems, (iii) the freedom of convenient multipartitionings of the Hamiltonian, (iv) flexibility of the relaxed and unrelaxed descriptions of the reference coefficients, and (v) manageable cost/accuracy ratio. The present method delivers accurate descriptions of dissociation processes of heavy element systems. Close agreement with reference values has been found for the calculated molecular constants indicating that our 4c-IVOSSMRPT provides a robust and economic protocol for determining the structural properties for the ground state of heavy element molecules with eloquent MR character as it treats correlation and relativity on equal footing.

Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

PubMed

Nose, Holliness; Chen, Yu; Rodgers, M T

2013-05-23

The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

Chemistry in acetone complexes of metal dications: a remarkable ethylene production pathway.

PubMed

Wu, Jianhua; Liu, Dan; Zhou, Jian-Ge; Hagelberg, Frank; Park, Sung Soo; Shvartsburg, Alexandre A

2007-06-07

Electrospray ionization can generate microsolvated multiply charged metal ions for various metals and ligands, allowing exploration of chemistry within such clusters. The finite size of these systems permits comparing experimental results with accurate calculations, creating a natural laboratory to research ion solvation. Mass spectrometry has provided much insight into the stability and dissociation of ligated metal cations. While solvated singly charged ions tend to shrink by ligand evaporation, solvated polycations below a certain size exhibit charge reduction and/or ligand fragmentation due to organometallic reactions. Here we investigate the acetone complexes of representative divalent metals (Ca, Mn, Co, Ni, and Cu), comparing the results of collision-induced dissociation with the predictions of density functional theory. As for other solvated dications, channels involving proton or electron transfer compete with ligand loss and become dominant for smaller complexes. The heterolytic C-C bond cleavage is common, like in DMSO and acetonitrile complexes. Of primary interest is the unanticipated neutral ethylene loss, found for all metals studied except Cu and particularly intense for Ca and Mn. We focus on understanding that process in the context of competing dissociation pathways, as a function of metal identity and number of ligands. According to first-principles modeling, ethylene elimination proceeds along a complex path involving two intermediates. These results suggest that chemistry in microsolvated multiply charged ions may still hold major surprises.

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.

Photodissociation dynamics of nitromethane and methyl nitrite by infrared multiphoton dissociation imaging with quasiclassical trajectory calculations: signatures of the roaming pathway.

PubMed

Dey, Arghya; Fernando, Ravin; Abeysekera, Chamara; Homayoon, Zahra; Bowman, Joel M; Suits, Arthur G

2014-02-07

We combine the techniques of infrared multiphoton dissociation (IRMPD) with state selective ion imaging to probe roaming dynamics in the unimolecular dissociation of nitromethane and methyl nitrite. Recent theoretical calculations suggest a "roaming-mediated isomerization" pathway of nitromethane to methyl nitrite prior to decomposition. State-resolved imaging of the NO product coupled with infrared multiphoton dissociation was carried out to examine this unimolecular decomposition near threshold. The IRMPD images for the NO product from nitromethane are consistent with the earlier IRMPD studies that first suggested the importance of an isomerization pathway. A significant Λ-doublet propensity is seen in nitromethane IRMPD but not methyl nitrite. The experimental observations are augmented by quasiclassical trajectory calculations for nitromethane and methyl nitrite near threshold for each dissociation pathway. The observation of distinct methoxy vibrational excitation for trajectories from nitromethane and methyl nitrite dissociation at the same total energy show that the nitromethane dissociation bears a nonstatistical signature of the roaming isomerization pathway, and this is possibly responsible for the nitromethane Λ-doublet propensity as well.

Photodissociation Studies of Metal-Containing Clusters and Complexes

NASA Astrophysics Data System (ADS)

Pilgrim, Jeffrey Scott

1995-01-01

There have been two major areas of investigation for researchers working with laser ablation in molecular beams. The first area is the study of weakly-bound complexes. These complexes are bound by electrostatic interactions. In the present study the weakly bound interactions of the rare gases with the magnesium ion are investigated with electronic spectroscopy. The second major area is the study of metal and metal-containing clusters. Examples of previous investigations are the alkali metal clusters and the fullerenes. The present investigation is on metal -carbon clusters. The so-called metallo-carbohedrenes and metal-carbon nanocrystals are studied. Resonance enhanced photodissociation spectroscopy is used to obtain electronic excitation spectra of the Mg^+-rare gas species in the ultraviolet region. This investigation is facilitated by a reflectron time-of-flight mass spectrometer. The interaction of the rare gas with the metal ion is attributed to a "solvation" of the atomic ion transition. Simple bonding arguments predict that the excited state is more bound than the ground state for these complexes. This will result in a shift of the complex vibronic origin to lower energy from the atomic ion transition. This is exactly what is observed in the experiment with progressively larger shifts for the heavier rare gases. The electronic excitation spectra allow the vibrational frequencies and anharmonicities for these complexes to be obtained for the excited state. In turn, the excited state bond dissociation energies can be determined. Finally, conservation of energy allows calculation of the ground state bond dissociation energies. In the metal-carbon systems the stability of the metallo-carbohedrene, met-car, stoichiometry is shown to extend into the transition period at least to the iron group. Photodissociation with a 532 nm laser causes a loss of metal atoms for met-cars formed with first row transition metals and a loss of metal-carbon units for met-cars formed from second-row transition metal atoms. Larger metal-carbon clusters are found to be face-centered-cubic nanocrystals. Photodissociation of these nanocrystals causes fragmentation into smaller nanocrystals. In addition, nanocrystals also dissociatively rearrange into the met -car structure. Two of the metal-carbon nanocrystals ( rm Ti_{14}C_{13 }^+ and rm V_{14 }C_{13}^+) fragment into the met-car with a trapped carbon atom.

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.

Effects of molecular dissociation on the hydrogen equation of state

NASA Astrophysics Data System (ADS)

Bonev, Stanimir; Schwegler, Eric; Galli, Giulia; Gygi, Francois

2002-03-01

It has been suggested recently(François Gygi and G. Galli, submitted to Phys. Rev. Lett.) that the physical mechanism behind the larger compressibility of liquid deuterium observed in laser shock experiments as compared to ab initio simulations may be related to shock-induced electronic excitations. A possible result of such non-adiabatic processes is hindering of the molecular dissociation. This has motivated us to study the importance of molecular dissociation on the hydrogen equation of state. To this end, we have carried out ab initio molecular dynamics simulations of liquid deuterium where intramolecular dissociation is prevented by the use of bond length contraints. Simulations at both fixed thermodynamic conditions and dynamical simulations of shocked deuterium will be discussed.

Theoretical study of dissociative recombination of Cl{sub 2}{sup +}

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

Zhang Mingwu; Graduate School of Chinese Academy of Sciences, Beijing 100039; Department of Physics, Stockholm University, S-106 91 Stockholm

Theoretical studies of low-energy electron collisions with Cl{sub 2}{sup +} leading to direct dissociative recombination are presented. The relevant potential energy curves and autoionization widths are calculated by combining electron scattering calculations using the complex Kohn variational method with multireference configuration interaction structure calculations. The dynamics on the four lowest resonant states of all symmetries is studied by the solution of a driven Schroedinger equation. The thermal rate coefficient for dissociative recombination of Cl{sub 2}{sup +} is calculated and the influence on the thermal rate coefficient from vibrational excited target ions is investigated.

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.

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Fu, Bina; Zhang, Dong H.

2013-11-01

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the title molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.

Density functional theory study on the ionization potentials and electron affinities of thymine-formamide complexes

NASA Astrophysics Data System (ADS)

Sun, Haitao; Tang, Ke; Li, Yanmin; Su, Chunfang; Zhou, Zhengyu; Wang, Zhizhong

The effect of hydrogen bond interactions on ionization potentials (IPs) and electron affinities (EAs) of thymine-formamide complexes (T-F) have been investigated employing the density functional theory B3LYP at 6-311++G(d, p) basis set level. All complexes experience a geometrical change on either electron detachment or attachment, and the change might be facilitated or hindered according to the strength of the hydrogen-bonding interaction involved. The strength of hydrogen bonds presents an opposite changing trend on the two processes. A more important role that H-bonding interaction plays in the process of electron attachment than in the process of electron detachment can be seen by a comparison of the IPs and EAs of complexes with that of isolated thymine. Futhermore, the EAs of isolated thymine are in good agreement with the experimental values (AEA is 0.79 eV, VEA is -0.29 eV [Wetmore et al., Chem Phys Lett 2000, 322, 129]). The calculated total NPA charge distributions reveal that nearly all the negative charges locate on thymine monomer in the anions and even in the cationic states, there are a few negative charges on thymine monomer. An analysis of dissociation energies predicts the processes T-F+→ T++ F and T-F- → T- + F to be the most energetically favorable for T-F+ and T-F-, respectively. Content:text/plain; charset="UTF-8"

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.

Study of molecular carbon-hydrogen bond dissociation during shock compression

NASA Astrophysics Data System (ADS)

Hammel, Ben; Hawreliak, James

2017-06-01

Advancements in theory and experiment show that chemical interactions in warm dense mixtures play a non-negligible role in the high-temperature and high-pressure properties of a molecular compound. For example, recent work on polystyrene has observed features suggestive of molecular dissociation - non-linear ``kinks'' are evident in the material's Hugoniot, consistent with CH bond breaking. The assumption used in linear mixing models, that species are chemically inert, breaks down in warm dense mixtures. At the Institute for Shock Physics, we are developing the necessary capabilities to perform high-repetition-rate experiments needed to map out chemical-reaction features along a material's Hugoniot. Initially, we plan to benchmark our work to the data taken by Barrios et al., by reproducing the observed kink in the polystyrene Hugoniot. We then extend this capability to explore polypropylene, CH2, where we expect to observe multiple kink features - representative of the disassociation of multiple CH bonds. Work supported by DOE/NNSA, DOE/SC-OFES and Murdock Charitable Trust.

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

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.

Rate coefficients for dissociative attachment and resonant electron-impact dissociation involving vibrationally excited O{sub 2} molecules

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

Laporta, V.; Celiberto, R.; Tennyson, J.

Rate coefficients for dissociative electron attachment and electron-impact dissociation processes, involving vibrationally excited molecular oxygen, are presented. Analytical fits of the calculated numerical data, useful in the applications, are also provided.

Infrared Multiple-Photon Dissociation Action Spectroscopy of the b2 + Ion from PPG: Evidence of Third Residue Affecting b2 + Fragment Structure

NASA Astrophysics Data System (ADS)

Poutsma, John C.; Martens, Jonathan; Oomens, Jos; Maitre, Phillipe; Steinmetz, Vincent; Bernier, Matthew; Jia, Mengxuan; Wysocki, Vicki

2017-07-01

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2 + fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2 + ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2 + ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation.

Ab initio state-specific N2 + O dissociation and exchange modeling for molecular simulations

NASA Astrophysics Data System (ADS)

Luo, Han; Kulakhmetov, Marat; Alexeenko, Alina

2017-02-01

Quasi-classical trajectory (QCT) calculations are used in this work to calculate state-specific N2(X1Σ ) +O(3P ) →2 N(4S ) +O(3P ) dissociation and N2(X1Σ ) +O(3P ) →NO(X2Π ) +N(4S ) exchange cross sections and rates based on the 13A″ and 13A' ab initio potential energy surface by Gamallo et al. [J. Chem. Phys. 119, 2545-2556 (2003)]. The calculations consider translational energies up to 23 eV and temperatures between 1000 K and 20 000 K. Vibrational favoring is observed for dissociation reaction at the whole range of collision energies and for exchange reaction around the dissociation limit. For the same collision energy, cross sections for v = 30 are 4 to 6 times larger than those for the ground state. The exchange reaction has an effective activation energy that is dependent on the initial rovibrational level, which is different from dissociation reaction. In addition, the exchange cross sections have a maximum when the total collision energy (TCE) approaches dissociation energy. The calculations are used to generate compact QCT-derived state-specific dissociation (QCT-SSD) and QCT-derived state-specific exchange (QCT-SSE) models, which describe over 1 × 106 cross sections with about 150 model parameters. The models can be used directly within direct simulation Monte Carlo and computational fluid dynamics simulations. Rate constants predicted by the new models are compared to the experimental measurements, direct QCT calculations and predictions by other models that include: TCE model, Bose-Candler QCT-based exchange model, Macheret-Fridman dissociation model, Macheret's exchange model, and Park's two-temperature model. The new models match QCT-calculated and experimental rates within 30% under nonequilibrium conditions while other models under predict by over an order of magnitude under vibrationally-cold conditions.

Calculation of rates of exciton dissociation into hot charge-transfer states in model organic photovoltaic interfaces

NASA Astrophysics Data System (ADS)

Vázquez, Héctor; Troisi, Alessandro

2013-11-01

We investigate the process of exciton dissociation in ordered and disordered model donor/acceptor systems and describe a method to calculate exciton dissociation rates. We consider a one-dimensional system with Frenkel states in the donor material and states where charge transfer has taken place between donor and acceptor. We introduce a Green's function approach to calculate the generation rates of charge-transfer states. For disorder in the Frenkel states we find a clear exponential dependence of charge dissociation rates with exciton-interface distance, with a distance decay constant β that increases linearly with the amount of disorder. Disorder in the parameters that describe (final) charge-transfer states has little effect on the rates. Exciton dissociation invariably leads to partially separated charges. In all cases final states are “hot” charge-transfer states, with electron and hole located far from the interface.

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

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than being a function of the spin-up and spin-down densities. In work carried out so far, the multiconfigurational wave function is a multiconfiguration self-consistent-field wave function. The new formulation has the advantage that the reference wave function has the correct spatial and spin symmetry and can describe bond dissociation (of both single and multiple bonds) and electronic excitations in a formally and physically correct way. We then review the formulation of density functionals in terms of the on-top pair density. Finally we review successful applications of the theory to bond energies and bond dissociation potential energy curves of main-group and transition metal bonds, to barrier heights (including pericyclic reactions), to proton affinities, to the hydrogen bond energy of water dimer, to ground- and excited-state charge transfer, to valence and Rydberg excitations of molecules, and to singlet-triplet splittings of radicals. We find that that MC-PDFT can give accurate results not only with complete-active-space multiconfiguration wave functions but also with generalized-active-space multiconfiguration wave functions, which are practical for larger numbers of active electrons and active orbitals than are complete-active-space wave functions. The separated-pair approximation, which is a special case of generalized active space self-consistent-field theory, is especially promising. MC-PDFT, because it requires much less computer time and storage than pure WFT methods, has the potential to open larger and more complex strongly correlated systems to accurate simulation.

Algorithm for Calculating the Dissociation Constants of Ampholytes in Nonbuffer Systems

NASA Astrophysics Data System (ADS)

Lysova, S. S.; Skripnikova, T. A.; Zevatskii, Yu. E.

2018-05-01

An algorithm for calculating the dissociation constants of ampholytes in aqueous solutions is developed on the basis of spectrophotometric data in the UV and visible ranges without pH measurements of a medium and without buffer solutions. The proposed algorithm has been experimentally tested for five ampholytes of different strengths. The relative error of measuring dissociation constants is less than 5%.

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

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

Corona discharge ionization of paracetamol molecule: Peak assignment

NASA Astrophysics Data System (ADS)

Bahrami, H.; Farrokhpour, H.

2015-01-01

Ionization of paracetamol was investigated using ion mobility spectrometry equipped with a corona discharge ionization source. The measurements were performed in the positive ion mode and three peaks were observed in the ion mobility spectrum. Experimental evidence and theoretical calculations were used to correlate the peaks to related ionic species of paracetamol. Two peaks were attributed to protonated isomers of paracetamol and the other peak was attributed to paracetamol fragment ions formed by dissociation of the N-C bond after protonation of the nitrogen atom. It was observed that three sites of paracetamol compete for protonation and their relative intensities, depending on the sample concentration. The ratio of ion products could be predicted from the internal proton affinity of the protonation sites at each concentration.

Gas-phase study of new organozinc reagents by IRMPD-spectroscopy, computational modelling and tandem-MS.

PubMed

Massah, Ahmad R; Dreiocker, Frank; Jackson, Richard F W; Pickup, Barry T; Oomens, Jos; Meijer, Anthony J H M; Schäfer, Mathias

2011-08-07

An extensive set of organozinc iodides, useful for Negishi-type cross-coupling reactions, are investigated as respective cations after formal loss of iodide in the gas phase. Firstly, two new alkylzinc compounds derived from Tyrosine (Tyr) and Tryptophan (Trp) are closely examined. Secondly, the influence of specific protecting groups on the subtle balance between intra- and intermolecular coordination of zinc in these reagents is probed through trifluoroacetyl (TFA)-derivatized alkylzinc compounds. Finally, the influence of the strongly coordinating bidentate ligand N,N,N',N'-tetramethylethylenediamine (TMEDA) on the structure of alkylzinc cations is further explored in order to better understand the stability of the respective complexes towards water. A combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, infrared multiple-photon dissociation (IRMPD) spectroscopy and computational modelling allowed the full characterisation of all dimethylformamide (DMF)-solvated and TMEDA-coordinated alkylzinc cations in the gas phase. The calculations indicate that the zinc cation in gas-phase alkylzinc-DMF or TMEDA-complex ions preferentially adopts a tetrahedral coordination sphere with four ligands. Additionally, conformers with only three binding partners bound to zinc but with effectively combined hydrogen-bond interactions are also found. Collision induced dissociation (CID) patterns demonstrate that the zinc-DMF interaction in tetrahedral four-coordinate mono-DMF-zinc complex ions as well as the interaction between TMEDA and zinc in the corresponding complex ions is even stronger than typical covalent bonds. In most cases, all major features of the IRMPD spectra are consistent with only a single major isomer, allowing secured identification and assignment. This journal is © the Owner Societies 2011

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

Ethane-xenon mixtures under shock conditions

NASA Astrophysics Data System (ADS)

Flicker, Dawn; Magyar, Rudolph; Root, Seth; Cochrane, Kyle; Mattsson, Thomas

2015-06-01

Mixtures of light and heavy elements arise in inertial confinement fusion and planetary science. We present results on the physics of molecular scale mixing through a validation study of equation of state (EOS) properties. Density functional theory molecular dynamics (DFT/QMD) at elevated-temperature and pressure is used to obtain the properties of pure xenon, ethane, and various compressed mixture compositions along their principal Hugoniots. To validate the QMD simulations, we performed high-precision shock compression experiments using Sandia's Z-Machine. A bond tracking analysis of the simulations correlates the sharp rise in the Hugoniot curve with completion of dissociation in ethane. DFT-based simulation results compare well with experimental data and are used to provide insight into the dissociation as a function of mixture composition. Interestingly, we find that the compression ratio for complete dissociation is similar for ethane, Xe-ethane, polymethyl-pentene, and polystyrene, suggesting that a limiting compression exists for C-C bonded systems. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, Security Administration under contract DE-AC04-94AL85000.

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

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

Liu, Tianhui; Fu, Bina; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the titlemore » molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.« less

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.

Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-05-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

Use of density functional theory orbitals in the GVVPT2 variant of second-order multistate multireference perturbation theory.

PubMed

Hoffmann, Mark R; Helgaker, Trygve

2015-03-05

A new variation of the second-order generalized van Vleck perturbation theory (GVVPT2) for molecular electronic structure is suggested. In contrast to the established procedure, in which CASSCF or MCSCF orbitals are first obtained and subsequently used to define a many-electron model (or reference) space, the use of an orbital space obtained from the local density approximation (LDA) variant of density functional theory is considered. Through a final, noniterative diagonalization of an average Fock matrix within orbital subspaces, quasicanonical orbitals that are otherwise indistinguishable from quasicanonical orbitals obtained from a CASSCF or MCSCF calculation are obtained. Consequently, all advantages of the GVVPT2 method are retained, including use of macroconfigurations to define incomplete active spaces and rigorous avoidance of intruder states. The suggested variant is vetted on three well-known model problems: the symmetric stretching of the O-H bonds in water, the dissociation of N2, and the stretching of ground and excited states C2 to more than twice the equilibrium bond length of the ground state. It is observed that the LDA-based GVVPT2 calculations yield good results, of comparable quality to conventional CASSCF-based calculations. This is true even for the C2 model problem, in which the orbital space for each state was defined by the LDA orbitals. These results suggest that GVVPT2 can be applied to much larger problems than previously accessible.

Theoretical study on the dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides

NASA Astrophysics Data System (ADS)

Cheng, Li; Shen, Zuochun; Lu, Jianye; Gao, Huide; Lü, Zhiwei

2005-11-01

Dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides, CF 3I, C 2F 5I, and i-C 3F 7I are calculated accurately with B3LYP, MP n ( n = 2-4), QCISD, QCISD(T), CCSD, and CCSD(T) methods. Calculations are performed by using large-core correlation-consistent pseudopotential basis set (SDB-aug-cc-pVTZ) for iodine atom. In all energy calculations, the zero point vibration energy is corrected. And the basis set superposition error is corrected by counterpoise method in the calculation of dissociation energy. Theoretical results are compared with the experimental values.

The Contribution of Art Therapy to the Dissociative Disorders.

ERIC Educational Resources Information Center

Murphy, Patricia S.

1994-01-01

Explored concepts of brain hemispheric lateralization and distinct right brain functioning in extensive dissociation by administering Dissociative Experiences Scale to 114 engineering students and 92 university drawing students. Chi-square calculation found differences in dissociative scoring levels between groups that approached significance at…

Low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl.

PubMed

Bayat, Parisa; Lesage, Denis; Cole, Richard B

2018-05-29

The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using three techniques shows that, generally, when working with mono-lithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with di-lithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a non-resonant activation technique and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of mono-lithiated and di-lithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages (rearrangement) vs. direct glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on di-lithiated and tri-lithiated sugars reveal that intensities of product ions containing two Li + or three Li + , respectively, are higher than those bearing only one Li + . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl adducted lithiated sugar and NaCl adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system. This article is protected by copyright. All rights reserved.

Dissociation from beloved unhealthy brands decreases preference for and consumption of vegetables.

PubMed

Trump, Rebecca K; Connell, Paul M; Finkelstein, Stacey R

2015-09-01

Many people form strong bonds with brands, including those for unhealthy foods. Thus, prompting people to dissociate from beloved but unhealthy food brands is an intuitively appealing means to shift consumption away from unhealthy options and toward healthy options. Contrary to this position, we demonstrate that dissociating from unhealthy but beloved brands diminishes people's interest in consuming vegetables because the dissociation depletes self-regulatory resources. Across three experimental studies, we manipulate dissociation from two beloved brands both implicitly (studies 1-2) and explicitly (study 3) and observe effects on both preference for vegetables (studies 2-3) and actual vegetable consumption (study 1). In study 1, participants consumed fewer vegetables following dissociation from (vs. association with) a beloved candy brand. Study 2 demonstrates that the effect of depletion on preference for vegetables is more pronounced for those who strongly identify with the brand, as these individuals are most depleted by the dissociation attempt. Finally, study 3 illustrates that the difficulty experienced when trying to dissociate from beloved brands drives the observed effects on vegetable preference and consumption for those who strongly (vs. weakly) identify with the brand. Copyright © 2015 Elsevier Ltd. All rights reserved.

Tandem Mass Spectrometry of Heparan Sulfate Negative Ions: Sulfate Loss Patterns and Chemical Modification Methods for Improvement of Product Ion Profiles

NASA Astrophysics Data System (ADS)

Shi, Xiaofeng; Huang, Yu; Mao, Yang; Naimy, Hicham; Zaia, Joseph

2012-09-01

Heparan sulfate (HS) is a polysaccharide modified with sulfation, acetylation, and epimerization that enable its binding with protein ligands and regulation of important biological processes. Tandem mass spectrometry has been employed to sequence linear biomolecules e.g., proteins and peptides. However, its application in structural characterization of HS is limited due to the neutral loss of sulfate (SO3) during collisional induced dissociation (CID). In this report, we studied the dissociation patterns of HS disaccharides and demonstrate that the N-sulfate (N-S) bond is especially facile during CID. We identified factors that influence the propensities of such losses from precursor ions and proposed a Free Proton Index (FPI) to help select ions that are able to produce meaningful backbone dissociations. We then investigated the thermodynamics and kinetics of SO3 loss from sulfates that are protonated, deprotonated, and metal-adducted using density functional theory computations. The calculations showed that sulfate loss from a protonated site was much more facile than that from a deprotonated or metal-adducted site. Further, the loss of SO3 from N-sulfate was energetically favored by 3-8 kcal/mol in transition states relative to O-sulfates, making it more prone to this process by a substantial factor. In order to reduce the FPI, representing the number of labile sulfates in HS native chains and oligosaccharides, we developed a series of chemical modifications to selectively replace the N-sulfates of the glucosamine with deuterated acetyl group. These modifications effectively reduced the sulfate density on the HS oligosaccharides and generated considerably more backbone dissociation using on-line LC/tandem MS.

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

Dissociative photoionization of isoprene: experiments and calculations.

PubMed

Liu, Xianyun; Zhang, Weijun; Wang, Zhenya; Huang, Mingqiang; Yang, Xibin; Tao, Ling; Sun, Yue; Xu, Yuntao; Shan, Xiaobin; Liu, Fuyi; Sheng, Liusi

2009-03-01

Vacuum ultraviolet (VUV) dissociative photoionization of isoprene in the energy region 8.5-18 eV was investigated with photoionization mass spectroscopy (PIMS) using synchrotron radiation (SR). The ionization energy (IE) of isoprene as well as the appearance energies (AEs) of its fragment ions C(5)H(7) (+), C(5)H(5) (+), C(4)H(5) (+), C(3)H(6) (+), C(3)H(5) (+), C(3)H(4) (+), C(3)H(3) (+) and C(2)H(3) (+) were determined with photoionization efficiency (PIE) curves. The dissociation energies of some possible dissociation channels to produce those fragment ions were also determined experimentally. The total energies of C(5)H(8) and its main fragments were calculated using the Gaussian 03 program and the Gaussian-2 method. The IE of C(5)H(8), the AEs for its fragment ions, and the dissociation energies to produce them were predicted using the high-accuracy energy model. According to our results, the experimental dissociation energies were in reasonable agreement with the calculated values of the proposed photodissociation channels of C(5)H(8). Copyright (c) 2009 John Wiley & Sons, Ltd.

Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen.

PubMed

Marek, Aleš; Tureček, František

2014-05-01

Gas-phase dissociations were investigated for several peptide ions containing the Gly-Leu* N-terminal motif where Leu* was a modified norleucine residue containing the photolabile diazirine ring. Collisional activation of gas-phase peptide cations resulted in facile N₂ elimination that competed with backbone dissociations. A free lysine ammonium group can act as a Brønsted acid to facilitate N₂ elimination. This dissociation was accompanied by insertion of a lysine proton in the side chain of the photoleucine residue, as established by deuterium labeling and gas-phase sequencing of the products. Electron structure calculations were used to provide structures and energies of reactants, intermediates, and transition states for Gly-Leu*-Gly-Gly-Lys amide ions that were combined with RRKM calculations of unimolecular rate constants. The calculations indicated that Brønsted acid-catalyzed eliminations were kinetically preferred over direct loss of N₂ from the diazirine ring. Mechanisms are proposed to explain the proton-initiated reactions and discuss the reaction products. The non-catalyzed diazirine ring cleavage and N₂ loss is proposed as a thermometer dissociation for peptide ion dissociations.

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.

Mechanical response of transient telechelic networks with many-part stickers

NASA Astrophysics Data System (ADS)

Sing, Michelle K.; Ramírez, Jorge; Olsen, Bradley D.

2017-11-01

A central question in soft matter is understanding how several individual, weak bonds act together to produce collective interactions. Here, gel-forming telechelic polymers with multiple stickers at each chain end are studied through Brownian dynamics simulations to understand how collective interaction of the bonds affects mechanical response of the gels. These polymers are modeled as finitely extensible dumbbells using an explicit tau-leap algorithm and the binding energy of these associations was kept constant regardless of the number of stickers. The addition of multiple bonds to the associating ends of telechelic polymers increases or decreases the network relaxation time depending on the relative kinetics of association but increases both shear stress and extensional viscosity. The relationship between the rate of association and the Rouse time of dangling chains results in two different regimes for the equilibrium stress relaxation of associating physical networks. In case I, a dissociated dangling chain is able to fully relax before re-associating to the network, resulting in two characteristic relaxation times and a non-monotonic terminal relaxation time with increasing number of bonds per polymer endgroup. In case II, the dissociated dangling chain is only able to relax a fraction of the way before it re-attaches to the network, and increasing the number of bonds per endgroup monotonically increases the terminal relaxation time. In flow, increasing the number of stickers increases the steady-state shear and extensional viscosities even though the overall bond kinetics and equilibrium constant remain unchanged. Increased dissipation in the simulations is primarily due to higher average chain extension with increasing bond number. These results indicate that toughness and dissipation in physically associating networks can both be increased by breaking single, strong bonds into smaller components.

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.

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.

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

Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions.

PubMed

Soydaş, Emine; Bozkaya, Uğur

2015-04-14

An assessment of orbital-optimized MP2.5 (OMP2.5) [ Bozkaya, U.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 204105 ] for thermochemistry and kinetics is presented. The OMP2.5 method is applied to closed- and open-shell reaction energies, barrier heights, and aromatic bond dissociation energies. The performance of OMP2.5 is compared with that of the MP2, OMP2, MP2.5, MP3, OMP3, CCSD, and CCSD(T) methods. For most of the test sets, the OMP2.5 method performs better than MP2.5 and CCSD, and provides accurate results. For barrier heights of radical reactions and aromatic bond dissociation energies OMP2.5-MP2.5, OMP2-MP2, and OMP3-MP3 differences become obvious. Especially, for aromatic bond dissociation energies, standard perturbation theory (MP) approaches dramatically fail, providing mean absolute errors (MAEs) of 22.5 (MP2), 17.7 (MP2.5), and 12.8 (MP3) kcal mol(-1), while the MAE values of the orbital-optimized counterparts are 2.7, 2.4, and 2.4 kcal mol(-1), respectively. Hence, there are 5-8-folds reductions in errors when optimized orbitals are employed. Our results demonstrate that standard MP approaches dramatically fail when the reference wave function suffers from the spin-contamination problem. On the other hand, the OMP2.5 method can reduce spin-contamination in the unrestricted Hartree-Fock (UHF) initial guess orbitals. For overall evaluation, we conclude that the OMP2.5 method is very helpful not only for challenging open-shell systems and transition-states but also for closed-shell molecules. Hence, one may prefer OMP2.5 over MP2.5 and CCSD as an O(N(6)) method, where N is the number of basis functions, for thermochemistry and kinetics. The cost of the OMP2.5 method is comparable with that of CCSD for energy computations. However, for analytic gradient computations, the OMP2.5 method is only half as expensive as CCSD.

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.

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

PubMed

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

2015-09-01

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

OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

PubMed

He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

2017-08-15

Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

Destruction of Peptides and Nucleosides in Reactions with Low-Energy Electrons

NASA Astrophysics Data System (ADS)

Muftakhov, M. V.; Shchukin, P. V.

2018-05-01

Mass-spectrometry of negative ions is used to study dissociative electron capture by molecules of several nucleosides, simplest di- and tripeptides, and modified dipeptides. Energy domains and efficiencies of dissociative capture are determined for the objects under study, and threshold energies of several fragmentation processes are estimated. It is shown that cytidine and peptides are stable against fragmentation due to simple bond breaking at electron energies ranging from 0 to 1 eV.

Photodissociation spectroscopy of the dysprosium monochloride molecular ion

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

Dunning, Alexander, E-mail: alexander.dunning@gmail.com; Schowalter, Steven J.; Puri, Prateek

2015-09-28

We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl{sup +}. The photodissociation cross section for the photon energy range 35 500 cm{sup −1} to 47 500 cm{sup −1} is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm{sup −1}. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl{sup +} is extremely complex due to the presence of multiple open electronic shells,more » including the 4f{sup 10} configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy{sup +} ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.« less

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

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.

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

Impact of steam explosion on the wheat straw lignin structure studied by solution-state nuclear magnetic resonance and density functional methods.

PubMed

Heikkinen, Harri; Elder, Thomas; Maaheimo, Hannu; Rovio, Stella; Rahikainen, Jenni; Kruus, Kristiina; Tamminen, Tarja

2014-10-29

Chemical changes of lignin induced by the steam explosion (SE) process were elucidated. Wheat straw was studied as the raw material, and lignins were isolated by the enzymatic mild acidolysis lignin (EMAL) procedure before and after the SE treatment for analyses mainly by two-dimensional (2D) [heteronuclear single-quantum coherence (HSQC) and heteronuclear multiple-bond correlation (HMBC)] and (31)P nuclear magnetic resonance (NMR). The β-O-4 structures were found to be homolytically cleaved, followed by recoupling to β-5 linkages. The homolytic cleavage/recoupling reactions were also studied by computational methods, which verified their thermodynamic feasibility. The presence of the tricin bound to wheat straw lignin was confirmed, and it was shown to participate in lignin reactions during the SE treatment. The preferred homolytic β-O-4 cleavage reaction was calculated to follow bond dissociation energies: G-O-G (guaiacyl) (69.7 kcal/mol) > G-O-S (syringyl) (68.4 kcal/mol) > G-O-T (tricin) (67.0 kcal/mol).

Interaction of SO2 with Cu/TiC(0 0 1) and Au/TiC(0 0 1): Toward a New Family of DeSOx Catalysts

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

L Feria; J Rodriguez; T Jirsak

2011-12-31

Experiments carried out under well-controlled conditions and density functional theory (DFT)-based calculations evidence that Cu and Au nanoparticles supported on a TiC(0 0 1) surface are quite active for the dissociation of the SO{sub 2} molecule. The Cu/TiC(0 0 1) and Au/TiC(0 0 1) systems cleave both S-O bonds of SO{sub 2} at a temperature of 150 K, displaying a reactivity much larger than that of TiC(0 0 1) or extended surfaces of bulk copper and gold. The origin of the high activity of the Cu/TiC(0 0 1) and Au/TiC(0 0 1) systems lies on the interaction between the Cmore » atoms of the substrate and the metal atoms of the supported particle, which results in a large polarization of its electron density. Experiments and theory consistently indicate that the Cu/TiC system is more active toward SO{sub 2} dissociation than the Au/TiC system. This type of systems may provide alternative and efficient DeSO{sub x} catalysts.« less

Interaction of SO2 with Cu/TiC(001) and Au/TiC(001): Towards a New Family of DeSOx Catalysts

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

Rodriguez, J.A.; Feria, L.; Jirsak, T.

2011-04-25

Experiments carried out under well-controlled conditions and density functional theory (DFT)-based calculations evidence that Cu and Au nanoparticles supported on a TiC(0 0 1) surface are quite active for the dissociation of the SO{sub 2} molecule. The Cu/TiC(0 0 1) and Au/TiC(0 0 1) systems cleave both S-O bonds of SO{sub 2} at a temperature of 150 K, displaying a reactivity much larger than that of TiC(0 0 1) or extended surfaces of bulk copper and gold. The origin of the high activity of the Cu/TiC(0 0 1) and Au/TiC(0 0 1) systems lies on the interaction between the Cmore » atoms of the substrate and the metal atoms of the supported particle, which results in a large polarization of its electron density. Experiments and theory consistently indicate that the Cu/TiC system is more active toward SO{sub 2} dissociation than the Au/TiC system. This type of systems may provide alternative and efficient DeSO{sub x} catalysts.« less

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.

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

Equations for calculating the properties of dissociated steam

NASA Astrophysics Data System (ADS)

Aminov, R. Z.; Gudym, A. A.

2017-08-01

The equations of state for dissociated steam have been developed in the temperature and pressure ranges of 1250-2300 K and 0.01-10.00 MPa for calculating thermodynamic processes in thermal power units operating on high-temperature steam. These equations are based on the property tables for dissociated steam derived at a reference temperature of 0 K. It is assumed that the initial substance is steam, the dissociation of which—in accordance with the most likely chemical reactions—results in formation of molecules of hydrogen, oxygen, steam, hydroxyl, and atoms of oxygen and hydrogen. Differential thermodynamic correlations, considering a change in the chemical potential and the composition of the mixture, during the steam dissociation are used. A reference temperature of 0.01°C used in the calculation of parameters of nondissociated steam has been adopted to predict processes in thermal power units without matching the reference temperatures and to account for transformation of dissociated steam into its usual form for which there is the international system of equations with the water triple point of 0.01°C taken as the reference. In the investigated region, the deviation of dissociated steam properties from those of nondissociated steam, which increases with decreasing the pressure or increasing the temperature, was determined. For a pressure of 0.02 MPa and a temperature of 2200 K, these deviations are 512 kJ/kg for the enthalpy, 0.2574 kJ/(kg K) for the entropy, and 3.431 kJ/(kg K) for the heat capacity at constant pressure. The maximum deviation of the dissociated steam properties calculated by the developed equations from the handbook values that these equations are based on does not exceed 0.03-0.05%.

Photodissociation of Non-Covalent Peptide-Crown Ether Complexes

PubMed Central

Wilson, Jeffrey J.; Kirkovits, Gregory J.; Sessler, Jonathan L.; Brodbelt, Jennifer S.

2008-01-01

Highly chromogenic 18-crown-6-dipyrrolylquinoxaline coordinates primary amines of peptides, forming non-covalent complexes that can be transferred to the gas phase by electrospray ionization. The appended chromogenic crown ether facilitates efficient energy transfer to the peptide upon ultraviolet irradiation in the gas phase, resulting in diagnostic peptide fragmentation. Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) of these non-covalent complexes results only in their disassembly with the charge retained on either the peptide or crown ether, yielding no sequence ions. Upon UV photon absorption the intermolecular energy transfer is facilitated by the fast activation time scale of UVPD (< 10 ns) and by the collectively strong hydrogen bonding between the crown ether and peptide, thus allowing effective transfer of energy to the peptide moiety prior to disruption of the intermolecular hydrogen bonds. PMID:18077179

Linking photochemistry in the gas and solution phase: S-H bond fission in p-methylthiophenol following UV photoexcitation.

PubMed

Oliver, Thomas A A; Zhang, Yuyuan; Ashfold, Michael N R; Bradforth, Stephen E

2011-01-01

Gas-phase H (Rydberg) atom photofragment translational spectroscopy and solution-phase femtosecond-pump dispersed-probe transient absorption techniques are applied to explore the excited state dynamics of p-methylthiophenol connecting the short time reactive dynamics in the two phases. The molecule is excited at a range of UV wavelengths from 286 to 193 nm. The experiments clearly demonstrate that photoexcitation results in S-H bond fission--both in the gas phase and in ethanol solution-and that the resulting p-methythiophenoxyl radical fragments are formed with significant vibrational excitation. In the gas phase, the recoil anisotropy of the H atom and the vibrational energy disposal in the p-MePhS radical products formed at the longer excitation wavelengths reveal the operation of two excited state dissociation mechanisms. The prompt excited state dissociation motif appears to map into the condensed phase also. In both phases, radicals are produced in both their ground and first excited electronic states; characteristic signatures for both sets of radical products are already apparent in the condensed phase studies after 50 fs. No evidence is seen for either solute ionisation or proton coupled electron transfer--two alternate mechanisms that have been proposed for similar heteroaromatics in solution. Therefore, at least for prompt S-H bond fissions, the direct observation of the dissociation process in solution confirms that the gas phase photofragmentation studies indeed provide important insights into the early time dynamics that transfer to the condensed phase.

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

The problem of hole localization in inner-shell states of N2 and CO2 revisited with complete active space self-consistent field approach.

PubMed

Rocha, Alexandre B; de Moura, Carlos E V

2011-12-14

Potential energy curves for inner-shell states of nitrogen and carbon dioxide molecules are calculated by inner-shell complete active space self-consistent field (CASSCF) method, which is a protocol, recently proposed, to obtain specifically converged inner-shell states at multiconfigurational level. This is possible since the collapse of the wave function to a low-lying state is avoided by a sequence of constrained optimization in the orbital mixing step. The problem of localization of K-shell states is revisited by calculating their energies at CASSCF level based on both localized and delocalized orbitals. The localized basis presents the best results at this level of calculation. Transition energies are also calculated by perturbation theory, by taking the above mentioned MCSCF function as zeroth order wave function. Values for transition energy are in fairly good agreement with experimental ones. Bond dissociation energies for N(2) are considerably high, which means that these states are strongly bound. Potential curves along ground state normal modes of CO(2) indicate the occurrence of Renner-Teller effect in inner-shell states. © 2011 American Institute of Physics

Production of neutral species in Titan's ionosphere through dissociative recombination of ions

NASA Astrophysics Data System (ADS)

Plessis, Sylvain; Carrasco, Nathalie; Dobrijevic, Michel; Pernot, Pascal

2012-05-01

The production rates of neutral species by dissociative recombination (DR) of molecular ions with electrons in the ionosphere of Titan are quantified by a new model, including, for the first time, all the available kinetic data on this process. The calculation is based on the ion densities measured by the INMS instrument on Cassini orbiter during flyby T19 at 1100 km altitude. These production rates are compared with those predicted by photochemical models: we calculate that for many neutral species, DR has larger production rates than neutral chemistry. Concerning molecular growth in Titan's ionosphere, DR is shown to have two antagonistic effects: (1) a global chemical lysis of ions through C-C and C-N bond breaking (missed by the "H-loss" DR paradigm); and (2) an enhancement of the neutral chemistry by production of reactive radicals, such as C2H or NH2. Further exploration of this chemistry requires the development of ionospheric coupled models taking explicitly into account the richness of the DR process and the strong impact of ions on the budget of neutral species. This study emphasizes also the urgent need of additional experimental studies about DR of molecular ions, with two priorities: evaluation of the impact of the temperature of ions on the rates and fragmentation patterns, and the systematic study of the fragmentation patterns of CxHyNz+ ions with more than four heavy atoms (m/z > 60 u).

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Quantitative analysis of desorption and decomposition kinetics of formic acid on Cu(111): The importance of hydrogen bonding between adsorbed species

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

Shiozawa, Yuichiro; Koitaya, Takanori; Mukai, Kozo

2015-12-21

Quantitative analysis of desorption and decomposition kinetics of formic acid (HCOOH) on Cu(111) was performed by temperature programmed desorption (TPD), X-ray photoelectron spectroscopy, and time-resolved infrared reflection absorption spectroscopy. The activation energy for desorption is estimated to be 53–75 kJ/mol by the threshold TPD method as a function of coverage. Vibrational spectra of the first layer HCOOH at 155.3 K show that adsorbed molecules form a polymeric structure via the hydrogen bonding network. Adsorbed HCOOH molecules are dissociated gradually into monodentate formate species. The activation energy for the dissociation into monodentate formate species is estimated to be 65.0 kJ/mol atmore » a submonolayer coverage (0.26 molecules/surface Cu atom). The hydrogen bonding between adsorbed HCOOH species plays an important role in the stabilization of HCOOH on Cu(111). The monodentate formate species are stabilized at higher coverages, because of the lack of vacant sites for the bidentate formation.« less

Cleaving Off Uranyl Oxygens through Chelation: A Mechanistic Study in the Gas Phase

DOE PAGES

Abergel, Rebecca J.; de Jong, Wibe A.; Deblonde, Gauthier J. -P.; ...

2017-10-11

Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U 6+ chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidence d by CID, using deuterium and 18O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy. Density functional theorymore » (DFT) computations predict that the overall reaction requires only 132 kJ/mol, with the first oxygen activation entailing about 107 kJ/mol. Here, combined with analysis of similar, but unreactive ligands, these results shed light on the chelation-driven mechanism of uranyl oxo bond cleavage, demonstrating its dependence on the presence of ligand hydroxyl protons available for direct interactions with the uranyl oxygens.« less

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

Meaning and consequence of the coexistence of competitive hydrogen bond/salt forms on the dissociation orientation of non-covalent complexes.

PubMed

Darii, Ekaterina; Alves, Sandra; Gimbert, Yves; Perret, Alain; Tabet, Jean-Claude

2017-03-15

Non-covalent complexes (NCC) between hexose monophosphates (HexP) and arginine (R) were analyzed using ESI MS and MS/MS in negative mode under different (hard, HC and soft, SC) desolvation conditions. High resolution mass spectrometry (HRMS) revealed the presence of different ionic species, namely, homo- and heteromultimers of R and HexP. Deprotonated heterodimers and corresponding sodiated species were enhanced under HC likely due to a decrease in available charge number associated with the reduction of H + /Na + exchange. The quantum calculations showed that the formation of covalent systems is very little exothermic, therefore, such systems are disfavored. Desolvation dependent CID spectra of deprotonated [(HexP+R)‒H] - complexes demonstrated that they can exist within the hydrogen bond (HB) and salt bridge (SB) forms, yielding either NCC separation or covalent bond cleavages, respectively. Although HB forms are the main species, they cannot survive under HC; therefore, the minor SB forms became detectable. Energy-resolved mass spectrometry (ERMS) experiments revealed diagnostic fragment ions from both SB and HB forms, providing evidence that these isomeric forms are inconvertible. SB formation should result from the ionic interactions of highly acidic group of HexP with strongly basic guanidine group of arginine and thus requires an arginine zwitterion (ZW) form. This was confirmed by quantum calculations. Ion-ion interactions are significantly affected by the presence of sodium cation as demonstrated by the fragmentation patterns of sodiated complex species. Regarding CID data, only SB between protonated amino group of R and deprotonated phosphate group of HexP could be suggested, but the primary amine is not enough basic then, the SB must be fleeting. Nevertheless, the observation of the covalent bond cleavages suggests the presence of structures with a free negative charge able to induce fragmentations. Indeed, according to quantum calculations, solvated salt (SS) systems involving Na + /COO - salt solvated by neutral phosphate and negative charge on sugar ring are preferentially formed. Copyright © 2016 Elsevier B.V. All rights reserved.

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)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 Cs and C2h 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 Cs configuration of (CH2O)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 D0 of this global potential energy minimum.

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.

Validity of the site-averaging approximation for modeling the dissociative chemisorption of H{sub 2} on Cu(111) surface: A quantum dynamics study on two potential energy surfaces

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

Liu, Tianhui; Fu, Bina, E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H., E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

A new finding of the site-averaging approximation was recently reported on the dissociative chemisorption of the HCl/DCl+Au(111) surface reaction [T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 139, 184705 (2013); T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 140, 144701 (2014)]. Here, in order to investigate the dependence of new site-averaging approximation on the initial vibrational state of H{sub 2} as well as the PES for the dissociative chemisorption of H{sub 2} on Cu(111) surface at normal incidence, we carried out six-dimensional quantum dynamics calculations using the initial state-selected time-dependent wave packet approach, withmore » H{sub 2} initially in its ground vibrational state and the first vibrational excited state. The corresponding four-dimensional site-specific dissociation probabilities are also calculated with H{sub 2} fixed at bridge, center, and top sites. These calculations are all performed based on two different potential energy surfaces (PESs). It is found that the site-averaging dissociation probability over 15 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability for H{sub 2} (v = 0) and (v = 1) on the two PESs.« less

Electronic Structure Calculations of Ammonia Adsorption on Graphene and Graphene Oxide with Epoxide and Hydroxyl Groups

NASA Astrophysics Data System (ADS)

Nancy Anna Anasthasiya, A.; Khaneja, Mamta; Jeyaprakash, B. G.

2017-10-01

Ammonia adsorption on graphene (G) and graphene oxide (GO) was investigated through density functional theory calculations. In the GO system, the obtained binding energy, band gap, charge transfer and electronic structure revealed that the epoxide (GO-O) and hydroxyl groups (GO-OH) in GO enhance the NH3 adsorption, which leads to the chemisorption of NH3 on GO. The dissociation of NH3 to NH2 and formation of OH was also observed when the O and H atoms were separated at 0.985 Å, 1.019 Å, 1.035 Å, and 1.044 Å for various GO systems. The maximum charge transfer value was found to be 0.054 |e| with the binding energy of 1.143 eV for GO with a single epoxide (GO-1O) group. The charge transfer from NH3 to G or GO and the bond formation in this study agree with the reported experimental results.

A computational fluid dynamics simulation of a supersonic chemical oxygen-iodine laser

NASA Astrophysics Data System (ADS)

Waichman, K.; Rybalkin, V.; Katz, A.; Dahan, Z.; Barmashenko, B. D.; Rosenwaks, S.

2007-05-01

The dissociation of I II molecules at the optical axis of a supersonic chemical oxygen-iodine laser (COIL) was studied via detailed measurements and three dimensional computational fluid dynamics calculations. Comparing the measurements and the calculations enabled critical examination of previously proposed dissociation mechanisms and suggestion of a mechanism consistent with the experimental and theoretical results. The gain, I II dissociation fraction and temperature at the optical axis, calculated using Heidner's model (R.F. Heidner III et al., J. Phys. Chem. 87, 2348 (1983)), are much lower than those measured experimentally. Agreement with the experimental results was reached by using Heidner's model supplemented by Azyazov-Heaven's model (V.N. Azyazov and M.C. Heaven, AIAA J. 44, 1593 (2006)) where I II(A') and vibrationally excited O II(a1Δ) are significant dissociation intermediates.

Adsorption and desorption of hydrogen at nonpolar GaN (1 1 ¯ 00 ) surfaces: Kinetics and impact on surface vibrational and electronic properties

NASA Astrophysics Data System (ADS)

Lymperakis, L.; Neugebauer, J.; Himmerlich, M.; Krischok, S.; Rink, M.; Kröger, J.; Polyakov, V. M.

2017-05-01

The adsorption of hydrogen at nonpolar GaN (1 1 ¯00 ) surfaces and its impact on the electronic and vibrational properties is investigated using surface electron spectroscopy in combination with density functional theory (DFT) calculations. For the surface mediated dissociation of H2 and the subsequent adsorption of H, an energy barrier of 0.55 eV has to be overcome. The calculated kinetic surface phase diagram indicates that the reaction is kinetically hindered at low pressures and low temperatures. At higher temperatures ab initio thermodynamics show, that the H-free surface is energetically favored. To validate these theoretical predictions experiments at room temperature and under ultrahigh vacuum conditions were performed. They reveal that molecular hydrogen does not dissociatively adsorb at the GaN (1 1 ¯00 ) surface. Only activated atomic hydrogen atoms attach to the surface. At temperatures above 820 K, the attached hydrogen gets desorbed. The adsorbed hydrogen atoms saturate the dangling bonds of the gallium and nitrogen surface atoms and result in an inversion of the Ga-N surface dimer buckling. The signatures of the Ga-H and N-H vibrational modes on the H-covered surface have experimentally been identified and are in good agreement with the DFT calculations of the surface phonon modes. Both theory and experiment show that H adsorption results in a removal of occupied and unoccupied intragap electron states of the clean GaN (1 1 ¯00 ) surface and a reduction of the surface upward band bending by 0.4 eV. The latter mechanism largely reduces surface electron depletion.

Dissociative recombination of HCl+

NASA Astrophysics Data System (ADS)

Larson, Åsa; Fonseca dos Santos, Samantha; E. Orel, Ann

2017-08-01

The dissociative recombination of HCl+, including both the direct and indirect mechanisms, is studied. For the direct process, the relevant electronic states are calculated ab initio by combining electron scattering calculations to obtain resonance positions and autoionization widths with multi-reference configuration interaction calculations of the ion and Rydberg states. The cross section for the direct dissociation along electronic resonant states is computed by solution of the time-dependent Schrödinger equation. For the indirect process, an upper bound value for the cross section is obtained using a vibrational frame transformation of the elements of the scattering matrix at energies just above the ionization threshold. Vibrational excitations of the ionic core from the ground vibrational state, v = 0 , to the first three excited vibrational states, v = 1 , v = 2 , and v = 3 , are considered. Autoionization is neglected and the effect of the spin-orbit splitting of the ionic potential energy upon the indirect dissociative recombination cross section is considered. The calculated cross sections are compared to measurements.

Dissociative recombination of HCl.

PubMed

Larson, Åsa; Fonseca Dos Santos, Samantha; E Orel, Ann

2017-08-28

The dissociative recombination of HCl + , including both the direct and indirect mechanisms, is studied. For the direct process, the relevant electronic states are calculated ab initio by combining electron scattering calculations to obtain resonance positions and autoionization widths with multi-reference configuration interaction calculations of the ion and Rydberg states. The cross section for the direct dissociation along electronic resonant states is computed by solution of the time-dependent Schrödinger equation. For the indirect process, an upper bound value for the cross section is obtained using a vibrational frame transformation of the elements of the scattering matrix at energies just above the ionization threshold. Vibrational excitations of the ionic core from the ground vibrational state, v = 0, to the first three excited vibrational states, v = 1, v = 2, and  v = 3, are considered. Autoionization is neglected and the effect of the spin-orbit splitting of the ionic potential energy upon the indirect dissociative recombination cross section is considered. The calculated cross sections are compared to measurements.

Reactive, spectroscopic and antimicrobial assessments of 5-[(4-methylphenyl) acetamido]-2-(4-tert-butylphenyl)benzoxazole: Combined experimental and computational study

NASA Astrophysics Data System (ADS)

Mary, Y. Sheena; Alzoman, Nourah Z.; Menon, Vidya V.; Al-Abdullah, Ebtehal S.; El-Emam, Ali A.; Panicker, C. Yohannan; Temiz-Arpaci, Ozlem; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.

2017-01-01

The synthesis, FT-IR, FT-Raman and NMR spectral analysis of an antimicrobial active benzoxazole derivative, 5-[(4-methylphenyl)acetamido]-2-(4-tert-butylphenyl) benzoxazole (MPATB) is reported. The localization of HOMO, LUMO plots in the title compound over the title molecule shows the charge transfer in the molecular system through the conjugated paths.The electrophilic and nucleophilic sites are revealed from the molecular electrostatic potential map. The first hyperpolarizability of the title compound is greater than that of the standard nonlinear optical material urea and the title compound and its derivatives are good objects for further research in nonlinear optical analysis. Molecule sites prone to electrophilic attacks have been detected by calculation of average local ionization energies, while calculations of Fukui functions have provided additional information about the local reactivity properties. Bond dissociation energies have been calculated in order to investigate autoxidation possibilities of the title molecule, as well as to determine the weakest bonds and therefore the sites where process of degradation could start. Reactive properties with water have been investigated by molecular dynamics simulations and calculations of radial distribution functions. The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations ranging between 8 and 128 μg/ml. The compound exhibited significant antifungal activity (64 μg/ml) against Candida krusei, at same potency with the compared standard drugs fluconazole. The docked title compound forms a stable complex with thymidylate synthase and got a binding affinity value of -8.5 kcal/mol and the title compound can be a lead compound for developing new anti-cancerous drug.

Corona discharge ionization of paracetamol molecule: peak assignment.

PubMed

Bahrami, H; Farrokhpour, H

2015-01-25

Ionization of paracetamol was investigated using ion mobility spectrometry equipped with a corona discharge ionization source. The measurements were performed in the positive ion mode and three peaks were observed in the ion mobility spectrum. Experimental evidence and theoretical calculations were used to correlate the peaks to related ionic species of paracetamol. Two peaks were attributed to protonated isomers of paracetamol and the other peak was attributed to paracetamol fragment ions formed by dissociation of the N-C bond after protonation of the nitrogen atom. It was observed that three sites of paracetamol compete for protonation and their relative intensities, depending on the sample concentration. The ratio of ion products could be predicted from the internal proton affinity of the protonation sites at each concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab initio calculations on the positive ions of the alkaline-earth oxides, fluorides, and hydroxides

NASA Technical Reports Server (NTRS)

Partridge, H.; Langhoff, S. R.; Bauschlicher, C. W., Jr.

1986-01-01

Theoretical dissociation energies are presented for the alkaline-earth fluoride, hydroxide, and oxide positive ions that are considered to be accurate to 0.1-0.2 eV. The r(e) for the positive ions are found to be consistently shorter than the corresponding neutrals by 0.07 + or -0.02 A. The bonding in the ground states is demonstrated to be of predominantly M + 2 X - character. The a 3 Pi and A 1 Pi are found to lie considerably above the X 1 Sigma + ground states of the alkaline-earth fluoride and hydroxide positive ions. The overall agreement of the theoretical ionization potentials with the available experimental appearance potentials is satisfactory; these values should represent the most accurate and consistent set available.

Lignin-derived oak phenolics: a theoretical examination of additional potential health benefits of red wine.

PubMed

Setzer, William N

2011-08-01

Lignin-derived phenolic compounds can be extracted from oak barrels during the aging of red wine, and it is hypothesized that these compounds may contribute to the health benefits of red wine by their antioxidant, radical-scavenging, or chemopreventive activities. Density functional calculations (B3LYP/6-311++G) support the radical-scavenging abilities of the oak phenolics. Sinapaldehyde, syringaldehyde, syringol, and syringylacetone all have bond dissociation energies that are lower than resveratrol and comparable to the flavonoid catechin. Molecular docking studies of the oak phenolics with known resveratrol protein targets also show that these compounds dock favorably to the protein targets. Thus, lignin-derived oak phenolics, although found in small concentrations, may contribute to the beneficial antioxidant, chemopreventive, and cardioprotective effects of red wine.

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

Theoretical and experimental insights into the origin of the catalytic activity of subnanometric gold clusters: attempts to predict reactivity with clusters and nanoparticles of gold.

PubMed

Boronat, Mercedes; Leyva-Pérez, Antonio; Corma, Avelino

2014-03-18

Particle size is one of the key parameters determining the unexpected catalytic activity of gold, with reactivity improving as the particle gets smaller. While this is valid in the 1-5 nm range, chemists are now investigating the influence of particle size in the subnanometer regime. This is due to recent advances in both characterization techniques and synthetic routes capable of stabilizing these size-controlled gold clusters. Researchers reported in early studies that small clusters or aggregates of a few atoms can be extremely active in some reactions, while 1-2 nm nanoparticles are catalytically more efficient for other reactions. Furthermore, the possibility that small gold clusters generated in situ from gold salts or complexes could be the real active species in homogeneous gold-catalyzed organic reactions should be considered. In this Account, we address two questions. First, what is the origin of the enhanced reactivity of gold clusters on the subnanometer scale? And second, how can we predict the reactions where small clusters should work better than larger nanoparticles? Both geometric factors and electronic or quantum size effects become important in the subnanometer regime. Geometric reasons play a key role in hydrogenation reactions, where only accessible low coordinated neutral Au atoms are needed to dissociate H2. The quantum size effects of gold clusters are important as well, as clusters formed by only a few atoms have discrete molecule-like electronic states and their chemical reactivity is related to interactions between the cluster's frontier molecular orbitals and those of the reactant molecules. From first principles calculations, we predict an enhanced reactivity of small planar clusters for reactions involving activation of CC multiple bonds in alkenes and alkynes through Lewis acid-base interactions, and a better catalytic performance of 3D gold nanoparticles in redox reactions involving bond dissociation by oxidative addition and new bond formation by reductive elimination. In oxidation reactions with molecular O2, initial dissociation of O2 into basic oxygen atoms would be more effectively catalyzed by gold nanoparticles of ∼1 nm diameter. In contrast, small planar clusters should be more active for reactions following a radical pathway involving peroxo or hydroperoxo intermediates. We have experimentally confirmed these predictions for a series of Lewis acid and oxidation reactions catalyzed by gold clusters and nanoparticles either in solution or supported on solid carriers.

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.

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

Chen, Mingyang; Serna, Pedro; Lu, Jing

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

Ab initio studies of dissociative recombination

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1989-01-01

Quantum chemical calculations of the dissociative recombination of O2(+) and N2(+) are reported. An approach for calculating autoionization widths from high-principal-quantum-number Rydberg states is summarized, and an example is presented for the lowest dissociative state of O2. For O2(+), the 1Sigma(+)u state is the sole source of O(1S) from the lowest 10 vibrational levels of the ion. Rate coefficients for generating O(1S) and O(1D) at ionospheric temperatures are reported.

The production of O(1S) from dissociative recombination of O2(+). [in earth upper atmosphere

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1987-01-01

The first theoretical calculations of the rate coefficient alpha for dissociative recombination of O2(+) leading to O(1S) are reported for a wide range of temperatures. The findings are discussed in terms of the potential energy curves for the ground state of O2(+) and for the dissociative 1Sigma(u) state calculated here. Values of alpha for the equilibrium case in which the electron and vibrational temperatures are identical are shown.

Computational investigation of structural and electronic properties of aqueous interfaces of GaN, ZnO, and a GaN/ZnO alloy.

PubMed

Kharche, Neerav; Hybertsen, Mark S; Muckerman, James T

2014-06-28

The GaN/ZnO alloy functions as a visible-light photocatalyst for splitting water into hydrogen and oxygen. As a first step toward understanding the mechanism and energetics of water-splitting reactions, we investigate the microscopic structure of the aqueous interfaces of the GaN/ZnO alloy and compare them with the aqueous interfaces of pure GaN and ZnO. Specifically, we have studied the (101̄0) surface of GaN and ZnO and the (101̄0) and (12̄10) surfaces of the 1 : 1 GaN/ZnO alloy. The calculations are carried out using first-principles density functional theory based molecular dynamics (DFT-MD). The structure of water within a 3 Å distance from the semiconductor surface is significantly altered by the acid/base chemistry of the aqueous interface. Water adsorption on all surfaces is substantially dissociative such that the surface anions (N or O) act as bases accepting protons from dissociated water molecules while the corresponding hydroxide ions bond with surface cations (Ga or Zn). Additionally, the hard-wall interface presented by the semiconductor imparts ripples in the density of water. Beyond a 3 Å distance from the semiconductor surface, water exhibits a bulk-like hydrogen bond network and oxygen-oxygen radial distribution function. Taken together, these characteristics represent the resting (or "dark") state of the catalytic interface. The electronic structure analysis of the aqueous GaN/ZnO interface suggests that the photogenerated holes may get trapped on interface species other than the adsorbed OH(-) ions. This suggests additional dynamical steps in the water oxidation process.

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.

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.

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

Yan, Hao; Yang, Fan; Pan, Ding

Mechanical stimuli can modify the energy landscape of chemical reactions and enable reaction pathways, offering a synthetic strategy that complements conventional chemistry. These mechanochemical mechanisms have been studied extensively in one-dimensional polymers under tensile stress using ring-opening and reorganization, polymer unzipping and disulfide reduction as model reactions. In these systems, the pulling force stretches chemical bonds, initiating the reaction. Additionally, it has been shown that forces orthogonal to the chemical bonds can alter the rate of bond dissociation. Furthermore, these bond activation mechanisms have not been possible under isotropic, compressive stress (that is, hydrostatic pressure). Here we show that mechanochemistrymore » through isotropic compression is possible by molecularly engineering structures that can translate macroscopic isotropic stress into molecular-level anisotropic strain.« less

Nanomanufacturing of silicon surface with a single atomic layer precision via mechanochemical reactions.

PubMed

Chen, Lei; Wen, Jialin; Zhang, Peng; Yu, Bingjun; Chen, Cheng; Ma, Tianbao; Lu, Xinchun; Kim, Seong H; Qian, Linmao

2018-04-18

Topographic nanomanufacturing with a depth precision down to atomic dimension is of importance for advancement of nanoelectronics with new functionalities. Here we demonstrate a mask-less and chemical-free nanolithography process for regio-specific removal of atomic layers on a single crystalline silicon surface via shear-induced mechanochemical reactions. Since chemical reactions involve only the topmost atomic layer exposed at the interface, the removal of a single atomic layer is possible and the crystalline lattice beneath the processed area remains intact without subsurface structural damages. Molecular dynamics simulations depict the atom-by-atom removal process, where the first atomic layer is removed preferentially through the formation and dissociation of interfacial bridge bonds. Based on the parametric thresholds needed for single atomic layer removal, the critical energy barrier for water-assisted mechanochemical dissociation of Si-Si bonds was determined. The mechanochemical nanolithography method demonstrated here could be extended to nanofabrication of other crystalline materials.

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.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

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.

Simulations of dissociation constants in low pressure supercritical water

NASA Astrophysics Data System (ADS)

Halstead, S. J.; An, P.; Zhang, S.

2014-09-01

This article reports molecular dynamics simulations of the dissociation of hydrochloric acid and sodium hydroxide in water from ambient to supercritical temperatures at a fixed pressure of 250 atm. Corrosion of reaction vessels is known to be a serious problem of supercritical water, and acid/base dissociation can be a significant contributing factor to this. The SPC/e model was used in conjunction with solute models determined from density functional calculations and OPLSAA Lennard-Jones parameters. Radial distribution functions were calculated, and these show a significant increase in solute-solvent ordering upon forming the product ions at all temperatures. For both dissociations, rapidly decreasing entropy of reaction was found to be the controlling thermodynamic factor, and this is thought to arise due to the ions produced from dissociation maintaining a relatively high density and ordered solvation shell compared to the reactants. The change in entropy of reaction reaches a minimum at the critical temperature. The values of pKa and pKb were calculated and both increased with temperature, in qualitative agreement with other work, until a maximum value at 748 K, after which there was a slight decrease.

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