Publications

2001
Gerber, R. B. ; Kavuru, M. . Does Salmeterol Increase In Patients With Copd?. CLEVELAND CLINIC JOURNAL OF MEDICINE 2001, 68, 600-601.
Wright, N. J. ; Gerber, R. B. . Extending The Vibrational Self-Consistent Method: Using A Partially Separable Wave Function For Calculating Anharmonic Vibrational States Of Polyatomic Molecules. JOURNAL OF CHEMICAL PHYSICS 2001, 114, 8763-8768.Abstract
A new method for the treatment of correlation effects between modes in vibrational self-consistent-field (VSCF) calculations is introduced. It is based upon using a partially separable form for the wave function. As a result, some of the modes are treated as mutually fully correlated, while the rest are separable. The modes which are explicitly coupled together in the calculation are chosen on physical grounds. Trial calculations are performed upon H2O, H3O+, and CH3NH2 and indicate that the method performs well. The agreement with experiment for the explicitly coupled modes is improved when compared to both the vibrational self-consistent-field method and its correlation-corrected extension. When interfaced with an electronic structure code this method opens the way for the accurate first-principles prediction of vibrational frequencies of strongly coupled modes. If only a few modes are mutually strongly coupled, the method has a very favorable scaling with system size, as does VSCF itself. (C) 2001 American Institute of Physics.
Cohen, A. ; Niv, M. Y. ; Gerber, R. B. . Formation Of Novel Rare-Gas-Containing Molecules By Molecular Photodissociation In Clusters. FARADAY DISCUSSIONS 2001, 118, 269-280.Abstract
Recent work by Rasanen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg . . . HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rg(n)(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are : (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl –> Xe . . . HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with ‘‘on the fly’’ calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe-54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.
Chaban, G. M. ; Lundell, J. ; Gerber, R. B. . Lifetime And Decomposition Pathways Of A Chemically Bound Helium Compound. JOURNAL OF CHEMICAL PHYSICS 2001, 115, 7341-7343.Abstract
HHeF, a first predicted chemically-bound helium compound, is a metastable species that disintegrates by tunneling through energy barriers into He+HF and H+He+F. The reaction paths for these decomposition processes are calculated with single-configurational Moller-Plesset (MP2) and multiconfigurational quasidegenerate MCQDPT2/MCSCF(10,6) electronic structure methods. The lifetime of HHeF, estimated using a one-dimensional model along the minimum energy path and the semiclassical WKB approximation, is more than 120 ps, that of DHeF is 14 ns. The relatively long lifetimes are encouraging for the preparation prospects of this helium compound. (C) 2001 American Institute of Physics.
2000
Chaban, G. M. ; Jung, J. O. ; Gerber, R. B. . Anharmonic Vibrational Spectroscopy Of Glycine: Testing Of Ab Initio And Empirical Potentials. JOURNAL OF PHYSICAL CHEMISTRY A 2000, 104, 10035-10044.Abstract
The second-order Moller-Plesset ab initio electronic structure method is used to compute points on the potential energy surface of glycine. Some 50 000 points are computed, covering the spectroscopically relevant regions, in the vicinity of the equilibrium structures of the three lowest-lying conformers of glycine. The vibrational states and spectroscopy are computed directly from the potential surface points using the correlation corrected vibrational self-consistent field (CC-VSCF) method, and the results are compared with experiment. Anharmonic effects and couplings between different vibrational modes that are included in the treatment are essential for satisfactory accuracy. The following are found: (1) The spectroscopic predictions from the ab initio potential are in very good accord with matrix experiments. (2) Theory agrees even more closely with spectroscopic data for glycine in He droplets, where environmental effects are much weaker than in the matrix. This suggests that errors in the ab initio potential are smaller than rare-gas matrix effects. (3) The accuracy of the ab initio potential is. by this spectroscopic test, much superior to that of OPLS-AA, a state-of-the-cut empirical potential. The relative failure of the empirical potential is due to its inability to describe: details of the hydrogen-bonded interactions, and is most critical in one of the glycine conformers where such interactions play an especially important role.
Chase, D. ; Manning, M. ; Morgan, J. A. ; Nathanson, G. M. ; Gerber, R. B. . Argon Scattering From Liquid Indium: Simulations With Embedded Atom Potentials And Experiment. JOURNAL OF CHEMICAL PHYSICS 2000, 113, 9279-9287.Abstract
An embedded-atom type potential for liquid indium is developed by fitting bulk liquid thermodynamic and structural data. An empirical pairwise Ar-In interaction is also proposed. Molecular-dynamics simulations of argon scattering from liquid indium are carried out and compared with molecular beam scattering data. Very good agreement is found between the experimental and theoretical angular and energy scattering distributions. This supports the potential functions used. Implications for the atomic-scale structure of liquid In and for gas-surface energy transfer are briefly discussed. (C) 2000 American Institute of Physics. [S0021-9606(00)70733-1].
Lundell, J. ; Chaban, G. M. ; Gerber, R. B. . Combined Ab Initio And Anharmonic Vibrational Spectroscopy Calculations For Rare Gas Containing Fluorohydrides, Hrgf. CHEMICAL PHYSICS LETTERS 2000, 331, 308-316.Abstract
MP2 and CCSD(T) calculations are used to analyse the structures and vibrational spectra of HRgF molecules, where the rare gas atom is He, Ne, Ar, Rr, Xe or Rn. We extend the analysis of the vibrational spectra of these molecules to include anharmonic corrections for the most likely candidates for experimental detection, i.e., HArF, HKrF, HXeF, and their deuterated isotopomers. The anharmonic correlation-corrected vibrational self-consistent-field (CC-VSCF) calculations are used for this, and fundamental, overtone and combination frequencies and their absorption intensities are computed. (C) 2000 Elsevier Science B.V. All rights reserved.
Wright, N. J. ; Gerber, R. B. ; Tozer, D. J. . Direct Calculation Of Anharmonic Vibrational States Of Polyatomic Molecules Using Density Functional Theory: Spectroscopic Tests Of Recently Developed Functionals. CHEMICAL PHYSICS LETTERS 2000, 324, 206-212.Abstract
The anharmonic vibrational frequencies of H2O, Cl-H2O and (H2O)(2) are calculated using potential energy surfaces computed from DFT, specifically the generalized-gradient approximation (GGA) functional HCTH and the hybrid functional B97(2c). HCTH gives reasonable agreement with experiment and can be recommended in situations where the use of a hybrid functional would be difficult. B97(2c) is found to be superior in accuracy to all other functionals tested and should be the functional of choice when the anharmonic potential energy surfaces of polyatomic systems are required for spectroscopic or similar applications. This point is illustrated by the excellent agreement with experiment obtained in calculations on formic and acetic acid using the B97(2c) functional. (C) 2000 Elsevier Science B.V. All rights reserved.
Lundell, J. ; Pettersson, M. ; Khriachtchev, L. ; Räsänen, M. ; Chaban, G. M. ; Gerber, R. B. . Infrared Spectrum Of Hxei Revisited: Anharmonic Vibrational Calculations And Matrix Isolation Experiments (Vol 322, Pg 389, 2000). CHEMICAL PHYSICS LETTERS 2000, 326, 191.
Niv, M. Y. ; Bargheer, M. ; Gerber, R. B. . Photodissociation And Recombination Of F-2 Molecule In Ar-54 Cluster: Nonadiabatic Molecular Dynamics Simulations. JOURNAL OF CHEMICAL PHYSICS 2000, 113, 6660-6672.Abstract
Photodissociation and recombination of an F-2 molecule embedded in an Ar cluster is investigated. The electronic states involved are described by the valence bond approach for the F(P-2)+F(P-2) interaction, with spin-orbit coupling included and the anisotropic interactions between F and Ar atoms described by the diatomics-in-molecules (DIM) approach. The potential energy surfaces for 36 electronic states and the nonadiabatic couplings between them are constructed in this basis. The surface hopping method is used for dynamical simulations. The main results are: (i) Spin nonconserving transitions play a crucial role both in the dissociation and in the recombination dynamics. (ii) The ratio between the population of the triplet states and the population of the singlet states reaches the statistical equilibrium value of 3:1 60 fs after the photoexcitation, but the population of specific singlet and triplet states remains nonstatistical for at least 1.5 ps. (iii) Recombination on the only bound excited state ((3)Pi (u)) becomes significant within 100 fs and builds up to 40% of the trajectories within 1 ps after excitation of the cluster with 4.6 eV. This is in accord with recent experiments on ClF/Ar solid, where strong emission from this state was found. (iv) 3% of recombination on the ground (1)Sigma (g) state is found as well. (v) For excitation energy of 4.6 eV, the dissociation can be direct or delayed. In delayed dissociation the F photofragments hit the Ar cage more than once before escaping the cage. (vi) For excitation energy of 6.53 eV the yield of dissociation was found to be 100%, and the dissociation is direct only. (C) 2000 American Institute of Physics. [S0021-9606(00)01240-X].
Baumfalk, R. ; Nahler, N. H. ; Buck, U. ; Niv, M. Y. ; Gerber, R. B. . Photodissociation Of Hbr Adsorbed On The Surface And Embedded In Large Ar-N Clusters. JOURNAL OF CHEMICAL PHYSICS 2000, 113, 329-338.Abstract
Ultraviolet (UV) photodissociation experiments are carried out for Ar-n(HBr) clusters in which the HBr is adsorbed on the surface of the Ar-n, and also on isomers of these systems in which HBr is embedded within the rare-gas cluster. The mean size of the cluster distribution in the experiments is around (n) over bar=130. The kinetic energy distribution (KED) of the hydrogen atoms that left the clusters is measured. Molecular dynamics (MD) simulations of the photodissociation of the chemically similar clusters Ar-n(HCl) are used to provide a qualitative interpretation of the experimental results. The clusters with embedded HBr give a very cold H-atom KED. The clusters with the surface-adsorbed HBr give a KED with two peaks, one corresponding to very low energy H atoms and the other pertaining to high energies, of the order of 1.35 eV. The theoretical simulations show that already for n=54, there is a strong cage effect for the ‘‘embedded’’ molecule case, resulting in slow H atoms. The surface-adsorbed case is interpreted as due to two types of possible adsorption sites of HX on Ar-55: for a locally smooth adsorption site, the cage effect is relatively weak, and hot H atoms emerge. Sites where the HBr is adsorbed at a vacancy of Ar-n lead to ‘‘encapsulation’’ of the H atom produced, with a strong cage effect. A weak tail of H atoms with energies well above the HBr monomer excess energy is observed for the embedded case. Simulations support that this is due to a second photon absorption by recombined, but still vibrationally hot, HBr. The results throw light on the differences between the cage effect inside bulk structure and at surfaces. (C) 2000 American Institute of Physics. [S0021-9606(00)00925-9].
Gerber, R. B. ; Korolkov, M. V. ; Manz, J. ; Niv, M. Y. ; Schmidt, B. . A Reflection Principle For The Control Of Molecular Photodissociation In Solids: Model Simulation For F-2 In Ar. CHEMICAL PHYSICS LETTERS 2000, 327, 76-84.Abstract
Laser pulse-induced photodissociation of molecules in rare-gas solids is investigated by representative quantum wavepackets or classical trajectories which are directed towards, or away from, cage exits, yielding dominant photodissociation into different neighbouring cages. The directionality is determined by a sequence of reflections inside the relief provided by the slopes of the potential energy surface of the excited system, which in turn depend on the initial preparation of the matrix isolated system, e.g, by laser pulses with different frequencies or by vibrational pre-excitation of the cage atoms. This reflection principle is demonstrated for a simple, two-dimensional model of F-2 in Ar. (C) 2000 Elsevier Science B.V. All rights reserved.
Lundell, J. ; Chaban, G. M. ; Gerber, R. B. . Anharmonic Vibrational Spectroscopy Calculations For Novel Rare-Gas-Containing Compounds: Hxeh, Hxecl, Hxebr, And Hxeoh. JOURNAL OF PHYSICAL CHEMISTRY A 2000, 104, 7944-7949.Abstract
A first-principles calculation of vibrational spectroscopy of HXeH, HXeCl, HXeBr, and HXeOH molecules is performed by combining ab initio codes with the vibrational self-consistent field (VSCF) method, and with its extension by perturbation theory (CC-VSCF). The MP2/CC-VSCF method is anharmonic, and it is able to reproduce the experimentally observed spectral features of HXeH, HXeCl, HXeBr, and HXeOH. The most intense bands of the HXeY molecules, the Xe-H stretching modes, are found to be highly anharmonic. In general, the other fundamental modes presented anharmonic effects to a lesser extent. New predictions of overtone and combination vibrations are made to help experimental investigations of these molecules. It is shown that vibrational spectroscopy calculations are reliable and useful for analyzing the spectral features of rare-gas-containing molecules. While the results of the MP2/CC-VSCF calculations are in much better agreement with experiments than the corresponding harmonic frequencies, substantial discrepancies remain. These are mostly due to the large electronic correlation effects in these systems, which are not sufficiently well presented at the MP2 level.
Chaban, G. M. ; Jung, J. O. ; Gerber, R. B. . Anharmonic Vibrational Spectroscopy Of Hydrogen-Bonded Systems Directly Computed From Ab Initio Potential Surfaces: (H(2)O)(N). JOURNAL OF PHYSICAL CHEMISTRY A 2000, 104, 2772-2779.Abstract
Vibrational energy levels and infrared absorption intensities of several neutral and ionic hydrogen-bonded clusters are computed directly from ab initio potential energy surfaces, and the results are compared with experiment. The electronic structure method used to compute the potential surfaces is MP2, with Dunning’s triple-zeta + polarization basis set. The calculation of the vibrational states from the potential surface points is carried out using the correlation corrected vibrational self-consistent field (CC-VSCF) method. This method includes anharmonicity and the coupling between different vibrational modes. The combined electronic structure/vibrational algorithm thus provides first-principles calculations of vibrational spectroscopy at a fairly accurate anharmonic level and can be useful for testing the accuracy of electronic structure methods by comparing with experimental vibrational spectroscopy. Systems treated here are (H(2)O)(n)
Wright, N. J. ; Gerber, R. B. . Direct Calculation Of Anharmonic Vibrational States Of Polyatomic Molecules Using Potential Energy Surfaces Calculated From Density Functional Theory. JOURNAL OF CHEMICAL PHYSICS 2000, 112, 2598-2604.Abstract
Potential energy surface points computed from variants of density functional theory (DFT) are used to calculate directly the anharmonic vibrational frequencies of H2O, Cl-H2O, and (H2O)(2). The method is an adaptation to DFT of a recent algorithm for direct calculations of anharmonic vibrational frequencies using ab initio electronic structure codes. The DFT calculations are performed using the BLYP and the B3LYP functionals and the results are compared with experiment, and also with those calculated directly from a potential energy surface obtained using ab initio Moller-Plesset second-order perturbation theory (MP2). The direct calculation of the vibrational states from the potential energy points is performed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method. This method includes anharmonicity and correlations between different vibrational modes. The accuracy of this method is examined and it is shown that for the experimentally measured transitions the errors in the CC-VSCF calculations are much less than the errors due to the potential energy surface. By comparison with the experimentally measured frequencies the CC-VSCF method thus provides a test for the quality of the potential energy surfaces. The results obtained with the B3LYP functional, in contrast to those of the BLYP functional, are of comparable quality to those obtained with MP2. The B3LYP anharmonic frequencies are in good agreement with experiment, showing this DFT method describes well the anharmonic part of the potential energy surface. The BLYP results systematically underestimate both the harmonic and anharmonic frequencies and indicate that using this functional for the description of hydrogen-bonded systems may cause significant errors. (C) 2000 American Institute of Physics. [S0021-9606(00)30105-2].
Knipping, E. M. ; Lakin, M. J. ; Foster, K. L. ; Jungwirth, P. ; Tobias, D. J. ; Gerber, R. B. ; Dabdub, D. ; Finlayson-Pitts, B. J. . Experiments And Simulations Of Ion-Enhanced Interfacial Chemistry On Aqueous Nacl Aerosols. SCIENCE 2000, 288, 301-306.Abstract
A combination of experimental, molecular dynamics, and kinetics modeling studies is applied to a system of concentrated aqueous sodium chloride particles suspended in air at room temperature with ozone. irradiated at 254 nanometers to generate hydroxyl radicals. Measurements of the observed gaseous molecular chlorine product are explainable only if reactions at the air-water interface are dominant. Molecular dynamics simulations show the availability of substantial amounts of chloride ions for reaction at the interface, and quantum chemical calculations predict that in the gas phase chloride ions will strongly attract hydroxl radicals. Model extrapolation to the marine boundary Layer yields daytime chlorine atom concentrations that are in good agreement with estimates based on field measurements of the decay of selected organics over the Southern Ocean and the North Atlantic. Thus, ion-enhanced interactions with gases at aqueous interfaces may play a more generalized and important role in the chemistry of concentrated inorganic salt solutions than was previously recognized.
Lundell, J. ; Pettersson, M. ; Khriachtchev, L. ; Räsänen, M. ; Chaban, G. M. ; Gerber, R. B. . Infrared Spectrum Of Hxei Revisited: Anharmonic Vibrational Calculations And Matrix Isolation Experiments. CHEMICAL PHYSICS LETTERS 2000, 322, 389-394.Abstract
Anharmonic correlation-corrected vibrational self-consistent-field (CC-VSCF) calculations are reported for the neutral HXeI molecule. Fundamental, overtone and combination frequencies and their absorption intensities are computed, and compared with previous and new experimental data from FTIR matrix isolation measurements. Agreement between experiment and calculations extend the identification of the HXeI molecule, and the calculations prove useful in aiding assignment of new observed transitions. The results show that especially the Xe-H bond of HXeI is highly anharmonic. While the agreement between theory and experiment is useful for assignment, quantitative discrepancies still remain due to the deficiency of MP2 theory to describe the highly anharmonic surface. (C) 2000 Elsevier Science B.V. All rights reserved.
Altshuler, E. S. ; Mills, D. L. ; Gerber, R. B. . Simulations Of Hydrogen Diffusion On Bcc Metal (110) Surfaces; Coverage And Temperature Dependence. SURFACE SCIENCE 2000, 452, 95-107.Abstract
We study the coverage and temperature dependences of the tracer diffusion coefficient for a chemisorbed layer of interacting hydrogen atoms on a model of a bcc metal (110) surface. The surface is rigid, and the short bridge barriers between adjacent chemisorption wells are sufficiently low that hydrogen atoms diffuse actively across the surface, on a time scale compatible with our molecular dynamics simulations. We deduce the coverage dependence of the effective activation barrier and the prefactor. We also examine, as a function of coverage, the percentage of jumps from singly occupied to either empty or occupied chemisorption wells, and from doubly occupied wells to empty or singly occupied wells. Although the effective activation barrier deduced from the numerical data exhibits a weak dependence on coverage, as found in data on H diffusion on the W(110) surface, the percentage of jumps of the types mentioned varies dramatically. The prefactor in the diffusion constant extracted from the simulations agrees well with elementary expectations for the rigid surface, but is much larger than that found experimentally. Finally, the low coverage tracer diffusivity is found to be appreciably anisotropic. The anisotropy decreases substantially as coverage increases. (C) 2000 Elsevier Science B.V. All rights reserved.
1999
Chaban, G. M. ; Jung, J. O. ; Gerber, R. B. . Ab Initio Calculation Of Anharmonic Vibrational States Of Polyatomic Systems: Electronic Structure Combined With Vibrational Self-Consistent Field. JOURNAL OF CHEMICAL PHYSICS 1999, 111, 1823-1829.Abstract
An algorithm for first-principles calculation of vibrational spectroscopy of polyatomic molecules is proposed, which combines electronic ab initio codes with the vibrational self-consistent field (VSCF) method, and with a perturbation-theoretic extension of VSCF. The integrated method directly uses points on the potential energy surface, computed from the electronic ab initio code, in the VSCF part. No fitting of an analytic potential function is involved. A key element in the approach is the approximation that only interactions between pairs of normal modes are important, while interactions of triples or more can be neglected. This assumption was found to hold well in applications. The new algorithm was applied to the fundamental vibrational excitations of H(2)O, Cl(-)(H(2)O), and (H(2)O)(2), using the Moller-Plesset method for the electronic structure. The vibrational frequencies found are in very good accord with experiments. Estimates suggest that this electronic ab initio/VSCF approach should be feasible, with reasonable computational resources, for all-mode calculations of vibrational energies and wave functions for systems of up to 10-15 atoms. The new method can be also very useful for testing the accuracy of electronic structure codes by comparing with experimental vibrational spectroscopy. (C) 1999 American Institute of Physics. [S0021-9606(99)01928-5].
Gregurick, S. K. ; Liu, J. H. Y. ; Brant, D. A. ; Gerber, R. B. . Anharmonic Vibrational Self-Consistent Field Calculations As An Approach To Improving Force Fields For Monosaccharides. JOURNAL OF PHYSICAL CHEMISTRY B 1999, 103, 3476-3488.Abstract
An Amber-type of force field, based on experimental vibrational frequencies which is suitable for monosaccharides. is presented. In the present force field, the atomic partial charges and some torsional parameters are derived from a fit of calculated vibrational energy levels to known experimental spectra for alpha-D-glucose. The vibrational spectra were calculated using the vibrational self-consistent field (VSCF) method, which includes contributions from both anharmonic and mode-coupled terms. We find that with a reparametrization of the force field the agreement between the experimental and calculated vibrational spectra is +/-3.3 cm(-1) for alpha-glucose and +/-5.1 cm(-1) for beta-glucose. Using the VSCF method, we an also able to lend support to the idea that the COH bending motion is strongly coupled to the methylene and methine modes, as well as the other internal modes. We then test our spectroscopically derived force field by calculating the anomeric effect for alpha –> beta glucose. Molecular dynamics simulations are performed separately for both anomers (alpha and beta) in order to evaluate configurational entropy, and hence free energy. We find that out of six simulations. half correctly predict the anomeric free energy Delta G(alpha–>beta) = -0.3 kcal/mol, while two simulations yield a Delta G(alpha–>beta) = +0.2 kcal/mol, and in one simulation Delta G(alpha–>beta) similar to 0.0 kcal/mol. We also calculate the atomic pair distribution function, g(r), and show that in most simulations, the beta-conformer is slightly more adept at structuring the surrounding water molecules, resulting in better hydrogen bonding fur this anomer. However, we believe that our force field, which is static, is unable to represent adequately the dynamic interactions between the pyranose sugar and the surrounding water molecules. This resulted in a large fluctuation about the average calculated anomeric free energy of Delta G(alpha–>beta) similar to -0.1 kcal/mol. Thus, while the current all atom force field is well suited for spectroscopic studies of monosaccharides, it is not yet well suited for dynamical studies.