Bargheer, M. ; Cohen, A. ; Gerber, R. B. ; Guehr, M. ; Korolkov, M. V. ; Manz, J. ; Niv, M. Y. ; Schroeder, M. ; Schwentner, N. Dynamics of electronic states and spin-flip for photodissociation of dihalogens in matrices: Experiment and semiclassical surface-hopping and quantum model Simulations for F-2 and CIF in solid Ar. JOURNAL OF PHYSICAL CHEMISTRY A 2007, 111, 9573-9585.Abstract
Three approaches are combined to study the electronic states' dynamics in the photodissociation of F-2 and OF in solid argon. These include (a) semiclassical surface-hopping simulations of the nonadiabatic processes involved. These simulations are carried out for the F-2 molecule in a slab of 255 argon atoms with periodic boundary conditions at the ends. The full manifold of 36 electronic states relevant to the process is included. (b) The second approach involves quantum mechanical reduced-dimensionality models for the initial processes induced by a pump laser pulse, which involve wavepacket propagation for the preoriented OF in the frozen argon lattice and incorporate the important electronic states. The focus is on the study of quantum coherence effects. (c) The final approach is femtosecond laser pump-probe experiments for OF in Ar. The combined results for the different systems shed light on general properties of the nonadiabatic processes involved, including the singlet to triplet and intertriplet transition dynamics. The main findings are (1) that the system remains in the initially excited-state only for a very brief, subpicosecond, time period. Thereafter, most of the population is transferred by nonadiabatic transitions to other states, with different time constants depending on the systems. (2) Another finding is that the dynamics is selective with regard to the electronic quantum numbers, including the A and Q quantum numbers, and the spin of the states. (3) The semiclassical simulations show that prior to the first ``collision'' of the photodissociated F atom with an Ar atom, the argon atoms can be held frozen, without affecting the process. This justifies the rigid-lattice reduced-dimensionality quantum model for a brief initial time interval. (4) Finally, degeneracies between triplets and singlets are fairly localized, but intertriplet degeneracies and near degeneracies can span an extensive range. The importance of quantum effects in photochemistry of matrix-isolated molecules is discussed in light of the results.
Gerber, R. B. ; Gonzdlez, L. ; Kohn, O. Molecular wave packet dynamics (in honour of Jorn Manz). CHEMICAL PHYSICS 2007, 338, 79-80.
Cohen, A. ; Gerber, R. B. Photodissociation of F-2 in solid Ar: Electronic state distribution in cage-exit. CHEMICAL PHYSICS 2007, 338, 200-206.Abstract
The role of different electronic states in cage-exit of F atoms for F-2 photodissociation in solid Ar is investigated by nonadiabatic molecular dynamics simulations, using Tully's ``Surface-Hopping'' approach. The 36 potential surfaces involved are treated by the diatomics-in-molecules (DIM) method. A simulation of 255 Ar atoms in an FCC structure with periodic boundary conditions is used. The results are: (I) Direct cage-exit events are not observed. At least two collisions of the F atoms with the Ar cage are necessary for cage-exit. (II) The total singlet to triplet population ratio at the instant of cage-exit is approximately the statistical one. (III) Some cage-exit events occur for the attractive states (1)Sigma(+)(g), (3)pi(u) but their role is much smaller than for the caged species. (IV) The Lambda quantum number distribution at cage-exit is more uniform than for the caged species. Thus, the electronic state distribution for cage-exit differs greatly from that of the caged species. (c) 2007 Elsevier B.V. All rights reserved.
Gerber, B. R. ; Miller, Y. Dynamics of chemical processes in overtone - Excited HNO3, HNO3-H2O, H2SO4, H2SO4-H2O. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2006, 231.
Segev, E. ; Grumbach, M. ; Gerber, R. B. Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2006, 8 4915-4923.Abstract
The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the beta hairpin to alpha helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.
Ansbacher, T. ; Gerber, B. R. New organic noble gas molecules: energetics, stability and potential energy surfaces of HCCXeCCH and HCCKrCCH. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2006, 8 4175-4181.Abstract
The diacetylides of Xe and Kr, HCCXeCCH and HCCKrCCH, are predicted to exist as metastable, chemically-bound compounds. The electronic structure, properties of the potential energy surfaces and decomposition paths are computed and analyzed. MP2, MCSCF and CASPT2 ab initio methods are used, as appropriate for each of the properties studied. Using transition state theory and the computed barrier for decomposition, the lifetime of HCCXeCCH is calculated as a function of temperature. The molecule is predicted to be stable well above the cryogenic range, with a lifetime of 24 h at 200 K. The implications for organic chemistry of the noble gases are discussed.
Shemesh, D. ; Gerber, B. R. Classical trajectory simulations of photoionization dynamics of tryptophan: Intramolecular energy flow, hydrogen-transfer processes and conformational transitions. JOURNAL OF PHYSICAL CHEMISTRY A 2006, 110, 8401-8408.Abstract
One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in ``on the fly'' calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.
D'Auria, R. ; Tobias, D. J. ; Gerber, B. R. ; Miller, Y. ; Xantheas, S. S. COLL 187-On the interfacial reaction mechanism between OH and Cl-: A detailed description of the mechanism leading to release of gaseous Cl2 from marine aerosols. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2006, 232.
Miller, Y. ; Gerber, B. R. Dynamics of vibrational overtone excitations of H(2)SO(4), H(2)SO(4)-H(2)O: Hydrogen-hopping and photodissociation processes. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006, 128, 9594-9595.
Sheng, L. ; Gerber, R. B. High coordination chemically bound compounds of noble gases with hydrocarbons: Ng(CCH)(4) and Ng(CCH)(6), (Ng=Xe or Kr). JOURNAL OF CHEMICAL PHYSICS 2006, 124.Abstract
Ab initio calculations predict the existence of the compounds Ng(- C CH)(4) and Ng(- C CH)(6), where Ng=Xe or Kr. Presently known organic noble gas compounds have a coordination number of two at most. The Ng(- C CH)(4) molecules have D-4h symmetry, and Ng(- C CH)(6) molecules have O-h symmetry. The bonding in all these compounds is partly ionic and partly covalent, with significant contributions from both types of bonding. The relatively high vibrational frequencies and the substantial Ng-(C CH) binding energy in these species indicate that these compounds should be fairly stable, at least in cryogenic conditions. These compounds could be a very interesting addition to the range of known organic noble gas compounds. Suggestions are made on possible approaches to their preparation. (c) 2006 American Institute of Physics.
Ramazan, K. A. ; Wingen, L. M. ; Miller, Y. ; Chaban, G. M. ; Gerber, R. B. ; Xantheas, S. S. ; Finlayson-Pitts, B. J. New experimental and theoretical approach to the heterogeneous hydrolysis of NO2: Key role of molecular nitric acid and its complexes. JOURNAL OF PHYSICAL CHEMISTRY A 2006, 110, 6886-6897.Abstract
Although heterogeneous chemistry on surfaces in the troposphere is known to be important, there are currently only a few techniques available for studying the nature of surface-adsorbed species as well as their chemistry and photochemistry under atmospheric conditions of 1 atm pressure and in the presence of water vapor. We report here a new laboratory approach using a combination of long path Fourier transform infrared spectroscopy ( FTIR) and attenuated total reflectance (ATR) FTIR that allows the simultaneous observation and measurement of gases and surface species. Theory is used to identify the surface-adsorbed intermediates and products, and to estimate their relative concentrations. At intermediate relative humidities typical of the tropospheric boundary layer, the nitric acid formed during NO2 heterogeneous hydrolysis is shown to exist both as nitrate ions from the dissociation of nitric acid formed on the surface and as molecular nitric acid. In both cases, the ions and HNO3 are complexed to water molecules. Upon pumping, water is selectively removed, shifting the NO3-HNO3(H2O)(y) equilibria toward more dehydrated forms of HNO3 and ultimately to nitric acid dimers. Irradiation of the nitric acid-water film using 300-400 nm radiation generates gaseous NO, while irradiation at 254 nm generates both NO and HONO, resulting in conversion of surface-adsorbed nitrogen oxides into photochemically active NOx. These studies suggest that the assumption that deposition or formation of nitric acid provides a permanent removal mechanism from the atmosphere may not be correct. Furthermore, a potential role of surface-adsorbed nitric acid and other species formed during the heterogeneous hydrolysis of NO2 in the oxidation of organics on surfaces, and in the generation of gas-phase HONO on local to global scales, should be considered.
Miller, Y. ; Chaban, G. M. ; Finlayson-Pitts, B. J. ; Gerber, R. B. Photochemical processes induced by vibrational overtone excitations: Dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O. JOURNAL OF PHYSICAL CHEMISTRY A 2006, 110, 5342-5354.Abstract
Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in ``on-the-fly'' simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO. isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these CH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNOx species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.
Mullin, J. M. ; Shemesh, D. ; Gerber, B. R. ; Gordon, M. S. PHYS 579-Si(100): When glycine attacks. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2006, 232.
Eshet, H. ; Ratner, M. A. ; Gerber, R. B. Selective energy and phase transfer in the photodissociation of I-2 in argon clusters: Quantum dynamics simulations. CHEMICAL PHYSICS LETTERS 2006, 431, 199-203.Abstract
Photodissociation of I-2 in the I2Ar17 cluster is studied by quantum wavepacket simulations, using time-dependent mean-field potentials. It is found that: (a) Initial energy transfer from the 12 is Mostly to three cluster modes, which undergo multiquantum excitation. Several other modes undergo single-quantum excitation. (b) Coherent phase transfer from the 12 to specific cluster modes is found. (c) Energy transfer from initially-excited modes to the other modes becomes large after 0.6 ps. Phase space interpretation is provided by computed Wigner distributions in time. (c) 2006 Elsevier B.V. All rights reserved.
Sheng, L. ; Gerber, B. R. Stability and structure of oligomers and polymers made of xenon and hydrocarbons: Theoretical predictions. JOURNAL OF CHEMICAL PHYSICS 2006, 125.Abstract
Calculations at B3LYP level predict the existence of three carbon chain oligomers containing HXeC C - branches: C7H8Xe2, C11H12Xe3, and C15H16Xe4. The geometries and NBO charges of the HXeC C - groups in the species are similar to those of the experimental known HXeC CH molecule, and are insensitive to the length of the carbon chain. The structures of the xenon oligomers are very similar to their hydrocarbon precursors. The energetics for C11H12Xe3 is calculated to assess the stability of these polymers. Similar to HXeCCH, C11H12Xe3 is kinetically stable and protected by a high barrier of 2.47 eV against dissociation to C11H12Xe2+Xe, and is energetically more stable by 1.30 eV than the C11H11Xe2+Xe+H products, which strongly supports the existence of the molecule. Extrapolation of the results for the oligomers suggests the existence of an extended [-CH2CH(C CXeH)-](n) polymer. A strategy for preparation is proposed. (c) 2006 American Institute of Physics.
Sheng, L. ; Cohen, A. ; Gerber, R. B. Theoretical prediction of chemically bound compounds made of argon and hydrocarbons. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006, 128, 7156-7157.
Brindle, C. A. ; Chaban, G. M. ; Gerber, R. B. ; Janda, K. C. Anharmonic vibrational spectroscopy calculations for (NH3)(HF) and (NH3)(DF): fundamental, overtone, and combination transitions. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2005, 7 945-954.Abstract
In order to study the effects of hydrogen bonding on the spectroscopic properties of (NH3)(HF) and (NH3)(DF) complexes, vibrational spectra ( including fundamental, overtone and combination transitions) were calculated using the vibrational self consistent field (VSCF) method. This ab initio VSCF method accounts for both one-dimensional anharmonicity and pair-wise mode-mode couplings for all vibrational modes of the molecule, using points on the potential energy surface (at the MP2/TZP level of theory in this study). An analysis of the coupling strength shows surprisingly important coupling effects from pair-wise interactions not expected to be major. This indicates the benefits of including all pair- wise mode-mode couplings for weakly bound systems. Hydrogen bonding induces similar to20% red shifts for the HF and DF stretch frequencies. The corrections due to anharmonicity for these modes are -6% and -5%, respectively. The anharmonic corrections for the intermolecular stretch of (NH3)(HF) and (NH3)( DF) are each about -5%. The NH3 umbrella motion has virtually no anharmonic correction in the complex, whereas free ammonia experiences a -15% correction. Also, the closing motion as well as the opening motion is restricted. The 1 + 1 combination transition of the proton stretching and intermolecular stretching modes has remarkably large intensity, larger even than the intensities for the first overtone of the proton stretching modes. The anharmonic frequency for the fundamental HF stretch, 3268 cm(-1), is in good agreement with the experimental gas phase result, 3215 cm(-1). A comparison to solid rare-gas matrix data shows that the VSCF frequencies are a consistent improvement over the harmonic approximation. The experimental data also support the use of the MP2 level of theory for the associated electronic structure calculations.
Miller, Y. ; Chaban, G. M. ; Gerber, R. B. Ab initio vibrational calculations for H(2)SO(4) and H(2)SO(4)center dot H(2)O: Spectroscopy and the nature of the anharmonic couplings. JOURNAL OF PHYSICAL CHEMISTRY A 2005, 109, 6565-6574.Abstract
Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H(2)SO(4)) and of sulfuric acid monohydrate cluster (H(2)SO(4)(.)H(2)O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H(2)SO(4) and H(2)SO(4)(.) H(2)O.
Adesokan, A. A. ; Fredj, E. ; Brown, E. C. ; Gerber, R. B. Anharmonic vibrational frequency calculations of 5,6-dihydrouracil and its complex with water: testing improved semiempirical potentials for biological molecules. MOLECULAR PHYSICS 2005, 103, 1505-1520.Abstract
The anharmonic vibrational spectra of the mutant nucleobase 5,6 dihydrouracil (DHU) and its complex with water are computed and the results are analysed with focus on the properties of the anharmonic coupling between different modes. A recently proposed potential surface is used, based on improving the potential from semiempirical PM3 electronic structure theory. This improved potential energy surface is obtained by a coordinate scaling that yields agreement for harmonic frequencies obtained through ab initio (MP2) or DFT methods. The improved PM3 potentials implemented herein give anharmonic frequencies that are in good agreement with experiment for isolated DHU. Similarly anharmonic frequencies for the DHU-water complex give good agreement when compared to experiments carried out on a remarkably similar model system; uracil-water. This supports the use of the improved PM3 potentials for the spectrochemical description of nucleobases and related molecules. The anharmonic frequencies for the scaled PM3 potential are computed by the vibrational self-consistent field (VSCF) method. The anharmonic coupling interaction between different vibrational modes are analyzed and characterized. For example, the CO out of plane bending mode in isolated DHU was observed to couple most strongly with the NH stretch mode at 3478 cm(-1). In the case of the DHU-H2O complex, strong coupling was observed between the O-3H water stretch and the CO out of plane bending modes of DHU at 759 cm(-1). The results suggest insights into patterns of intramolecular vibrational energy transfer in DHU and DHU-H2O.
Shemesh, D. ; Gerber, R. B. Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine. JOURNAL OF CHEMICAL PHYSICS 2005, 122.Abstract
Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in ``on the fly'' calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier. (c) 2005 American Institute of Physics.