Gerber, B. R. ; Sebek, J. Dynamics simulations of atmospherically relevant molecular reactions. INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY 2009, 28, 207-222.Abstract
This article offers an overview of the recent progress in theoretical modelling of molecular reactions of atmospheric interest. The review covers processes in isolated molecules, e. g. vibrational overtone-induced processes in HNO(3) and H(2)SO(4). Another focal topic is thermally, as well as overtone-induced processes of NO(x), HNO(x) and other atmospherically relevant species in water clusters, the latter serving as models for water surfaces, aerosols and other water environments. Among the processes examined in water clusters are separations of NO(x) and HNO(x) into ion pairs in contact with water, and the reverse processes of anion/cation recombination to form neutral molecules. Physical insights into the mechanisms and properties of the processes, as extracted from theoretical simulations, are analysed. The methodology discussed in the review is mostly classical molecular dynamics simulations, using potentials directly from electronic structure methods. The merits and limitations of different electronic structure methods for the systems of interest are discussed. Limitations and open problems with regard to the classical dynamics approximation are also briefly examined. Concluding remarks are presented on the usefulness of classical dynamics with ab initio potentials for reactions of atmospheric chemistry. Possible directions for future progress are suggested.
Khriachtchev, L. ; Raesaenen, M. ; Gerber, B. R. Noble-Gas Hydrides: New Chemistry at Low Temperatures. ACCOUNTS OF CHEMICAL RESEARCH 2009, 42, 183-191.Abstract
Noble-gas chemistry has been undergoing a renaissance in recent years, due in large part to noble-gas hydrides, HNgY, where Ng noble-gas atom and Y = electronegative fragment. These molecules are exceptional because of their relatively weak bonding and large dipole moments, which lead to strongly enhanced effects of the environment, complexation, and reactions. In this Account, we discuss the matrix-isolation synthesis of noble-gas hydrides, their spectroscopic and structural properties, and their stabilities. This family of species was discovered in 1995 and now has 23 members that are prepared in noble-gas matrices (HXeBr, HKrCl, HXeH, HXeOH, HXeO, etc.). The preparations of the first neutral argon molecule, HArF, and halogen-free organic noble-gas molecules (HXeCCH, HXeCC, HKrCCH, etc.) are important highlights of the field. These molecules are formed by the neutral H + Ng + Y channel. The first addition reaction involving HNgY molecules was HXeCC + Xe + H -> HXeCCXeH, and this led to the first hydride with two noble-gas atoms (recently extended by HXeOXeH). The experimental synthesis of HNgY molecules starts with production of H and Y fragments in solid noble gas via the UV photolysis of suitable precursors. The HNgY molecules mainly form upon thermal mobilization of the fragments. One of the unusual properties of these molecules is the hindered rotation of some HNgY molecules in solid matrices; this has been theoretically modeled. HNgY molecules also have unusual solvation effects, and the H-Xe stretching mode shifts to higher frequencies (up to about 150 cm(-1)) upon interaction with other species. The noble hydrides have a new bonding motif: HNgY molecules can be represented in the form (H-Ng)(+)Y(-), where (H-Ng)+ is mainly covalent, whereas the interaction between (HNg)(+) and Y(-) is predominantly ionic. The HNgY molecules are highly metastable species representing high-energy materials. The decomposition process HNgY -> Ng + HY is always strongly exoergic; however, the decomposition is prevented by high barriers, for instance, about 2 eV for HXeCCH. The other decomposition channel HNgY - H + Ng + Y is endothermic for all prepared molecules. Areas that appear promising for further study include the extension of argon chemistry, preparation of new bonds with noble-gas atoms (such as Xe-Si bond), and studies of radon compounds. The calculations suggest the existence of related polymers, aggregates, and even HNgY crystals, and their experimental preparation is a major challenge. Another interesting task, still in its early stages, is the preparation of HNgY molecules in the gas phase.
Njegic, B. ; Raff, J. D. ; Chang, W. L. ; Dabdub, D. ; Finlayson-Pitts, B. J. ; Gordon, M. S. ; Gerber, B. R. PHYS 470-Unraveling of a new mechanism of atmospheric chemistry reactions: Formation of ClNO. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2009, 237.
Raff, J. D. ; Njegic, B. ; Gerber, B. R. ; Finlayson-Pitts, B. J. PHYS 471-Heterogeneous chlorine activation from NOx-HCl reactions on surfaces. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2009, 237.
Finlayson-Pitts, B. J. ; Raff, J. D. ; Njegic, B. ; Kamboures, M. A. ; Chang, W. ; Dabdub, D. ; Gerber, B. R. Surface reactions of oxides of nitrogen in the atmosphere. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2009, 237, 177.
Sukharev, M. ; Cohen, A. ; Gerber, R. B. ; Seideman, T. Ultrafast nonadiabatic photodissociation dynamics of F-2 in solid Ar. LASER PHYSICS 2009, 19, 1651-1659.Abstract
We explore the ultrafast spin-flip dynamics in a diatomic molecule imbedded in a rare gas matrix using the combination of a quantum mechanical and a semiclassical surface hopping method. Specifically, we investigate (1) the extent to which the phenomenon of electronically-localized eigenstates in strongly-coupled manifolds survives in the presence of rapid decay and a multitude of electronically coupled states; (2) the ability of the surface hopping method to predict the short time dynamics; and (3) the time range over which frozen lattice models are valid. Our results point to the active role played by a large number of coupled electronic states in the F-2/Ar dynamics while substantiating our confidence in the validity of the popular surface hopping approach for the system considered.
Link, O. ; Voehringer-Martinez, E. ; Lugovoj, E. ; Liu, Y. ; Siefermann, K. ; Faubel, M. ; Grubmueller, H. ; Gerber, B. R. ; Miller, Y. ; Abel, B. Ultrafast phase transitions in metastable water near liquid interfaces. FARADAY DISCUSSIONS 2009, 141, 67-79.Abstract
Electron spectroscopy for chemical analysis (ESCA) is a powerful tool for the quantitative analysis of the composition and the chemical environment of molecular systems. Due to the lack of compatibiltiy of liquids and vacuum, liquid-phase ESCA is much less well established. The chemical shift in the static ESCA approach is a particularly powerful observable quantity for probing electron orbital energies in molecules in different molecular environments. Employing high harmonics of 800nm (40 eV). near-infrared femtosecond pulses and liquid-water microbeams in vacuum we were able to add the dimension of time to the liquid interface ESCA technique. Tracing time-dependent chemical shifts and energies of valence electrons in liquid interfacial water in time, we have investigated the timescale and molecular signatures of laser-induced liquid-gas phase transitions on a picosecond timescale.
Raff, J. D. ; Njegic, B. ; Chang, W. L. ; Gordon, M. S. ; Dabdub, D. ; Gerber, B. R. ; Finlayson-Pitts, B. J. Chlorine activation indoors and outdoors via surface-mediated reactions of nitrogen oxides with hydrogen chloride (vol 106, pg 13647, 2009). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2009, 106, 16889.
Feldman, V. I. ; Kobzarenko, A. V. ; Baranova, I. A. ; Danchenko, A. V. ; Sukhov, F. F. ; Tsivion, E. ; Gerber, B. R. Direct visualization of the H-Xe bond in xenon hydrides: Xenon isotopic shift in the IR spectra. JOURNAL OF CHEMICAL PHYSICS 2009, 131.Abstract
IR spectra of xenon hydrides (HXeCCH, HXeCC, and HXeH) obtained from different xenon isotopes ((129)Xe and (136)Xe) exhibit a small but detectable and reproducible isotopic shift in the absorptions assigned to H-Xe stretching (by 0.17-0.38 cm(-1)). To our knowledge, it is the first direct experimental evidence for the H-Xe bond in HXeY type compounds. The shift magnitude is in good agreement with quantum-chemical calculations. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3250426]
Miller, Y. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Ionization of N2O4 in Contact with Water: Mechanism, Time Scales and Atmospheric Implications. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2009, 131, 12180-12185.Abstract
Ionization of N2O4 in and on thin water films on surfaces is believed to be a key step in the hydrolysis of NO2 which generates HONO, a significant precursor to the OH free radical in the lower atmosphere. Molecular dynamics simulations using ``on the fly'' high-level MP2 potentials are carried out for ONONO2 center dot(H2O)(n) clusters, n <= 8, used to mimic the surface reaction, in order to investigate the ionization process and determine its time-scale and mechanism around room temperature. The results are (i) the isolated molecule does not convert to the NO(+)NO3(-) ion pair, even for long times; (ii) for ONONO2 center dot(H2O)(n) with n = 1 and 2, ionization takes place in several picoseconds; (iii) for n >= 3, ionization is essentially immediate, implying that the neutral species does not have sufficient lifetime to be considered a significant intermediate in the reaction; and (iv) even at ice temperatures, T <= 250 K, ionization for n >= 3 is immediate. The implications for hydrolysis of oxides of nitrogen on surfaces in the atmosphere are discussed.
Tsivion, E. ; Gerber, B. R. Lifetimes of compounds made of noble-gas atoms with water. CHEMICAL PHYSICS LETTERS 2009, 482, 30-33.Abstract
The kinetic stability of the HXeOH and HXeOXeH molecules, chemically bound compounds made of Xe atoms and water, is studied by multi-reference ab initio methods. The decomposition paths, the transition states and the rates of dissociation as a function of temperature, are calculated. HXeOH and HXeOXeH are found to be protected by an energy barriers of 0.59 and 0.4 eV, respectively. Applying transition state theory, HXeOH and HXeOXeH have intrinsic half-lives of 1 h at 170 and 120 K, respectively. Implications of the results for the kinetic stability of these species are discussed. (C) 2009 Elsevier B. V. All rights reserved.
Domanskaya, A. ; Kobzarenko, A. V. ; Tsivion, E. ; Khriachtchev, L. ; Feldman, V. I. ; Gerber, B. R. ; Rasanen, M. Matrix-isolation and ab initio study of HXeCCH complexed with acetylene. CHEMICAL PHYSICS LETTERS 2009, 481, 83-87.Abstract
The HXeCCH center dot center dot center dot H(2)C(2) complex has been characterized by IR spectroscopy in a xenon matrix and ab initio calculations. This species exhibits a blue shift of the H-Xe stretching mode (19-28 cm(-1)) in comparison with the HXeCCH monomer, which indicates stabilization of the H-Xe bond upon complexation. The complex results from annealing-induced diffusion of acetylene molecules above 50 K to isolated HXeCCH formed at lower temperature. In addition, a weak absorption with a blue shift of +51 cm(-1) was tentatively assigned to the HXeCCH complex with two acetylene molecules. These experimental observations are supported by ab initio calculations. (C) 2009 Elsevier B.V. All rights reserved.
Miller, Y. ; Thomas, J. L. ; Kemp, D. D. ; Finlayson-Pitts, B. J. ; Gordon, M. S. ; Tobias, D. J. ; Gerber, B. R. Structure of Large Nitrate-Water Clusters at Ambient Temperatures: Simulations with Effective Fragment Potentials and Force Fields with Implications for Atmospheric Chemistry. JOURNAL OF PHYSICAL CHEMISTRY A 2009, 113, 12805-12814.Abstract
Structural properties of large NO(3)(-)center dot(H(2)O)(n) (n = 15-500) clusters are studied by Monte Carlo simulations using effective fragment potentials (EFPs) and by classical molecular dynamics simulations using a polarizable empirical force field. The simulation results are analyzed with a focus on the description of hydrogen bonding and solvation in the clusters. In addition, a comparison between the electronic structure based EFP and the classical force field description of the 32 water cluster system is presented. The EFP simulations, which focused on the cases of n = 15 and 32, show an internal, fully solvated structure and a ``surface adsorbed'' structure for the 32 water cluster at 300 K, with the latter configuration being more probable. The internal solvated structure and the ``surface adsorbed'' structure differ considerably in their hydrogen bonding coordination numbers. The force field based simulations agree qualitatively with these results, and the local geometry of NO(3)(-) and solvation at the surface-adsorbed site in the force field simulations are similar to those predicted using EFPs. Differences and similarities between the description of hydrogen bonding of the anion in the two approaches are discussed. Extensive classical force field based simulations at 250 K predict that long time scale stability of ``internal'' NO(3)(-), which is characteristic of extended bulk aqueous interfaces, emerges only for n > 300. Ab initio Moller-Plesset perturbation theory is used to test the geometries of selected surface and interior anions for n = 32, and the results are compared to the EFP and MD simulations. Qualitatively, all approaches agree that surface structures are preferred over the interior structures for clusters of this size. The relatively large aqueous clusters of NO(3)(-) studied here are of comparable size to clusters that lead to new particle formation in air. Nitrate ions on the Surface of such clusters may have significantly different photochemistry than the internal species. The possible implications of surface-adsorbed nitrate ions for atmospheric chemistry are discussed.
Kamboures, M. A. ; Raff, J. D. ; Miller, Y. ; Phillips, L. F. ; Finlayson-Pitts, B. J. ; Gerber, B. R. Complexes of HNO(3) and NO(3)(-) with NO(2) and N(2)O(4), and their potential role in atmospheric HONO formation. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2008, 10, 6019-6032.Abstract
Calculations were performed to determine the structures, energetics, and spectroscopy of the atmospherically relevant complexes (HNO(3))center dot(NO(2)),(HNO(3))center dot(N(2)O(4)),(NO(3)(-))center dot(NO(2)),and(NO(3)(-))center dot(N(2)O(4)). The binding energies indicate that three of the four complexes are quite stable, with the most stable (NO(3)(-))center dot(N(2)O(4)) possessing binding energy of almost -14 kcal mol(-1). Vibrational frequencies were calculated for use in detecting the complexes by infrared and Raman spectroscopy. An ATR-FTIR experiment showed features at 1632 and 1602 cm(-1) that are attributed to NO(2) complexed to NO(3)(-) and HNO(3), respectively. The electronic states of (HNO(3))center dot (N(2)O(4)) and (NO(3)(-))center dot(N(2)O(4)) were investigated using an excited state method and it was determined that both complexes possess one low-lying excited state that is accessible through absorption of visible radiation. Evidence for the existence of (NO(3)(-))center dot(N(2)O(4)) was obtained from UV/vis absorption spectra of N(2)O(4) in concentrated HNO(3), which show a band at 320 nm that is blue shifted by 20 nm relative to what is observed for N(2)O(4) dissolved in organic solvents. Finally, hydrogen transfer reactions within the (HNO(3))center dot(NO(2)) and (HNO(3))center dot(N(2)O(4)) complexes leading to the formation of HONO, were investigated. In both systems the calculated potential profiles rule out a thermal mechanism, but indicate the reaction could take place following the absorption of visible radiation. We propose that these complexes are potentially important in the thermal and photochemical production of HONO observed in previous laboratory and field studies.
Segev, E. ; Wyttenbach, T. ; Bowers, M. T. ; Gerber, B. R. Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2008, 10, 3077-3082.Abstract
Evidence from cross section data indicates that ubiquitin + 13 ions lose their secondary and tertiary structure in mass spectrometric experiments. These transitions from the folded state into the near linear final structure occur at the experimental temperatures on time scales that are far too long for conventional molecular dynamics simulations. In this study, an approach to mass spectrometric unfolding processes is developed and a detailed application to an ubiquitin + 13 ion system is presented. The approach involves a sequence of molecular dynamics simulations at gradually increasing temperatures leading to identification of major intermediate states, and the unfolding pathway. The unfolding rate at any temperature can then be calculated by a Rice-Ramsperger-Kassel (RRK) approach. For ubiquitin + 13, three interesting intermediate states were found and the final near linear geometry was computed. The several relevant energy barriers calculated for the process are in the range of 7 to 15 kcal mol(-1). The unfolding time scale at 300 K was computed to be 2 ms. Cross section calculations using a hard sphere scattering model were carried out for the final structure and found to be in good accord with the results of electrospray experiments supporting the theoretical model used. The approach employed here should be applicable to any other solvent-free protein system.
Wolf, I. ; Shapira, A. ; Giniger, R. ; Miller, Y. ; Gerber, B. R. ; Cheshnovsky, O. Critical size for intracluster proton transfer from water to an anion. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2008, 47, 6272-6274.
Cohen, A. ; Gerber, R. B. Dynamical u <-> g electronic state transitions in matrix photochemistry: Photodissociation of F-2 in solid Ar. CHEMICAL PHYSICS LETTERS 2008, 453, 173-177.Abstract
The photodissociation of F-2 in a lattice model of 255 argon atoms is studied using Tully's semiclassical `surface hopping' approach. The DIM method is used to model the 36 relevant potential energy surfaces and the nonadiabatic couplings between them. The photoexcitation is modeled by vertical promotion of the F-2 into the (1)Pi(u) state. It is found that early dynamics following excitation leads to rapid build-up of the g states population, and around t approximate to 50 fs the (total) g and u populations are roughly equal. Matrix-induced nonadiabatic transitions between u and g states cause the effect, and are briefly discussed. (C) 2008 Elsevier B.V. All rights reserved.
Miller, Y. ; Gerber, B. R. Dynamics of proton recombination with NO3- anion in water clusters. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2008, 10, 1091-1093.Abstract
Recombination events of a proton with NO3- at (H2O)(8) clusters are studied by molecular dynamics, using ``on-the-fly'' reliable ab initio MP2 potentials. The main findings are: (1) the lifetime of the ions is less than 1.2 picoseconds; (2) the recombination step invariably involves H3O+, not H5O2+; and (3) an essentially unique transition-state structure of H3O+/NO3- for recombination is found in all cases. Proton migration involves both H3O+ and H5O2+ species: Grotthuss and other mechanisms contribute.
von Helden, G. ; Compagnon, I. ; Blom, M. N. ; Frankowski, M. ; Erlekam, U. ; Oomens, J. ; Brauer, B. ; Gerber, R. B. ; Meijer, G. Mid-IR spectra of different conformers of phenylalanine in the gas phase. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2008, 10, 1248-1256.Abstract
The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.
Kamboures, M. A. ; van der Veer, W. ; Gerber, B. R. ; Phillips, L. F. Raman spectra of complexes of HNO(3) and NO(3)(-) with NO(2) at surfaces and with N(2)O(4) in solution. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2008, 10, 4748-4753.Abstract
Raman spectra of HNO(3)center dot NO(2) have been detected on liquid and solid surfaces in the presence of concentrated HNO(3) and NO(2) gas. The Raman spectrum of HNO(3) solutions containing N(2)O(4) has been partly reinterpreted in terms of contributions from HNO(3)center dot N(2)O(4) and N(2)O(4)center dot NO(3)(-) complexes.