Chaban, G. M. ; Gerber, B. R. Anharmonic vibrational spectroscopy calculations with electronic structure potentials: comparison of MP2 and DFT for organic molecules. THEORETICAL CHEMISTRY ACCOUNTS 2008, 120, 273-279.Abstract
Density functional theory (DFT) technique is the most commonly used approach when it comes to computation of vibrational spectra of molecular species. In this study, we compare anharmonic spectra of several organic molecules such as allene, propyne, glycine, and imidazole, computed from ab initio MP2 potentials and DFT potentials based on commonly used BLYP and B3LYP functionals. Anharmonic spectra are obtained using the direct vibrational self-consistent field (VSCF) method and its correlation-corrected extension (CC-VSCF). The results of computations are compared with available experimental data. It is shown that the most accurate vibrational frequencies are obtained with the MP2 method, followed by the DFT/B3LYP method, while DFT/BLYP results are often unsatisfactory.
Kjaergaard, H. G. ; Garden, A. L. ; Chaban, G. M. ; Gerber, B. R. ; Matthews, D. A. ; Stanton, J. F. Calculation of vibrational transition frequencies and intensities in water dimer: Comparison of different vibrational approaches. JOURNAL OF PHYSICAL CHEMISTRY A 2008, 112, 4324-4335.Abstract
We have calculated frequencies and intensities of fundamental and overtone vibrational transitions in water and water dimer with use of different vibrational methods. We have compared results obtained with correlation-corrected vibrational self-consistent-field theory and vibrational second-order perturbation theory both using normal modes and finally with a harmonically coupled anharmonic oscillator local mode model including CH-stretching and HOH-bending local modes. The coupled cluster with singles, doubles, and perturbative triples ab initio method with augmented correlation-consistent triple-zeta Dunning and atomic natural orbital basis sets has been used to obtain the necessary potential energy and dipole moment surfaces. We identify the strengths and weaknesses of these different vibrational approaches and compare our results to the available experimental results.
Steinberg, M. Z. ; Elber, R. ; McLafferty, F. W. ; Gerber, B. R. ; Breuker, K. Early Structural Evolution of Native Cytochrome c after Solvent Removal. CHEMBIOCHEM 2008, 9 2417-2423.Abstract
Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations.
Pele, L. ; Gerber, B. R. On the number of significant mode-mode anharmonic couplings in vibrational calculations: Correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides. JOURNAL OF CHEMICAL PHYSICS 2008, 128.Abstract
A computational study is made of the number of important anharmonic mode-mode couplings in the context of vibrational calculations for di-, tri-, and tetrapeptides. The method employed is the correlation-corrected vibrational self-consistent field (CC-VSCF) algorithm, which includes correlation effects between different vibrational modes. It is found that results of good accuracy can be obtained in calculations that include only N log N mode-mode coupling terms, where N is the number of modes. This simplification significantly accelerates CC-VSCF calculations for large molecules. A criterion based on the characteristics of the normal-mode displacements is employed to predict a priori unimportant coupling terms. The criterion is tested statistically using Spearman's rank correlation coefficient. The results are illustrated by calculations for several di-, tri-, and tetrapeptides using semiempirical PM3 potential surfaces. These results are analyzed and a statistical model for error estimation is given. The decrease in the number of included coupling from N(2) to N log N opens possibilities of anharmonic vibrational calculations for large peptides. (c) 2008 American Institute of Physics.
Gerber, R. B. ; Miller, Y. PHYS 572-Vibrational energy flow and charge transfer processes in water clusters. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2008, 236.
Kamboures, M. A. ; Miller, Y. ; Gerber, B. R. PHYS 638-Understanding the photochemistry of NOx complexes on urban surfaces through computational chemistry. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2008, 235.
Tsivion, E. ; Zilberg, S. ; Gerber, B. R. Predicted stability of the organo-xenon compound HXeCCH above the cryogenic range. CHEMICAL PHYSICS LETTERS 2008, 460, 23-26.Abstract
The kinetic stability of the HXeCCH molecule, a chemically bound compound made of Xe and acetylene was studied by multi-reference ab-initio methods. The decomposition paths, transition states and the rates of dissociation as a function of temperature, for the dominant dissociation reactions were calculated. The HXeCCH molecule is found to be protected by an energy barrier of 0.96 eV. Utilizing transition state theory, HXeCCH is predicted to have a half-life of 3 h at 0 degrees C and to be indefinitely stable under -20 degrees C. The results are very encouraging in the search for noble-gas hydrocarbons with room temperature stability. (C) 2008 Elsevier B. V. All rights reserved.
Khriachtchev, L. ; Isokoski, K. ; Cohen, A. ; Rasanen, M. ; Gerber, B. R. A small neutral molecule with two noble-gas atoms: HXeOXeH. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2008, 130, 6114-6118.Abstract
A novel noble-gas compound, HXeOXeH, is identified using IR spectroscopy, and it seems to be the smallest known neutral molecule with two noble-gas atoms'. HXeOXeH is prepared using, for example, UV photolysis of water in solid xenon and subsequent annealing at 40-45 K. The experimental observations are fully supported by extensive quantum chemical calculations. A large energy release of 8.3 eV is computationally predicted for the decomposition of HXeOXeH into the 2Xe + H2O global energy minimum. HXeOXeH may represent a first step toward the possible preparation of (Xe-O)(n) chains and it may be relevant to the terrestrial ``missing xenon'' problem.
Shemesh, D. ; Mullin, J. ; Gordon, M. S. ; Gerber, B. R. Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(100)-2 x 1 surface. CHEMICAL PHYSICS 2008, 347, 218-228.Abstract
The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 00)-2 x 1. The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and ``phonon'' (cluster) modes. Implications of the results for surface vibrational spectroscopy are discussed. (c) 2007 Elsevier B.V. All rights reserved.
Brauer, B. ; Dubnikova, F. ; Zeiri, Y. ; Kosloff, R. ; Gerber, B. R. Vibrational spectroscopy of triacetone triperoxide (TATP): Anharmonic fundamentals, overtones and combination bands. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008, 71, 1438-1445.Abstract
The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed. (c) 2008 Elsevier B.V. All rights reserved.
Cohen, A. ; Gerber, R. B. A 1 fs spin-flip in a chemical reaction: Photodissociation of HF in solid Ar. CHEMICAL PHYSICS LETTERS 2007, 441, 48-52.Abstract
The photodissociation of HF in solid argon is studied by nonadiabatic molecular dynamics simulations, using Tully's `surface hopping' method. The model includes 12 electronic states, described by DIM method. An extremely fast `spin-flip' transition is found corresponding to a population buildup in the (3)Pi state, already within about 1 fs after a vertical Frank-Condon excitation into the (1)Pi state. The effect is particularly striking in view of the relatively weak spin-orbit coupling in HE. The mechanism of this exceptionally fast spin-flip is discussed and a physical interpretation is provided. Comparison is made to the slower spin-flip computed previously for F-2/Ar, and found both theoretically and experimentally for ClF/Ar. (C) 2007 Elsevier B.V. All rights reserved.
Pele, L. ; Brauer, B. ; Gerber, B. R. Acceleration of correlation-corrected vibrational self-consistent field calculation times for large polyatomic molecules. THEORETICAL CHEMISTRY ACCOUNTS 2007, 117, 69-72.Abstract
Acceleration of the correlation-corrected Vibrational self-consistent field (CC-VSCF) method for anharmonic calculations of vibrational states of polyatomic molecules is described. The acceleration assumes pairwise additive interactions between different normal modes, and employs orthogonality of the single-mode vibrational wave functions. This greatly reduces the effort in computing correlation effects between different vibrational modes, which is treated by second order perturbation theory in CC-VSCF. The acceleration can improve the scaling of the overall computational effort from N(6) to N(4), where N is the number of vibrational modes. Sample calculation times, using semiempirical potential surfaces (PM3), ire given for a series of glycine peptides. Large Computational acceleration, and significant reduction of the scaling of the effort with system size, is found and discussed.
Adesokan, A. A. ; Pan, D. ; Fredj, E. ; Mathies, R. A. ; Gerber, B. R. Anharmonic vibrational calculations modeling the Raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2007, 129, 4584-4594.Abstract
The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C-8-C-9 stretching mode nu(29) (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C-9-O-2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.
Gerber, B. R. ; Miller, Y. ; Kamboures, M. A. Atmospheric reactions in water clusters: Mechanisms, dynamics and rates. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2007, 234.
Steinberg, M. Z. ; Breuker, K. ; Elber, R. ; Gerber, B. R. The dynamics of water evaporation from partially solvated cytochrome c in the gas phase. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2007, 9 4690-4697.Abstract
The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the mass spectrometer. In this work the dynamics of water evaporation from native cytochrome c covered by a monolayer of water is studied by molecular dynamics (MD) simulations at constant energy. A model of the initial conditions of the process is introduced. The temperature of the protein drops by about 100 K during the 400 picoseconds of the simulations. This sharp drop in temperature causes the water evaporation rate to decrease by about an order of magnitude, leaving the protein with 50% to 90% of the original water molecules, depending on the initial temperature of the simulation. The structural changes of the protein upon desolvation were considered through calculations of the radius of gyration and the root mean square (RMS) of the protein. A variation of 0.4 angstrom in the radius of gyration, together with an RMS value of less than 3 angstrom, indicates only minor changes in the overall shape of the protein structure. The water coordination number of the solvation shell is much smaller than that for bulk water. The mobility of water is high at the beginning of the simulations and drops as the simulation progresses and the temperature decreases. Incomplete desolvation of protein ions was also observed in recent experiments.
Miller, Y. ; Gerber, R. B. ; Vaida, V. Photodissociation yields for vibrationally excited states of sulfuric acid under atmospheric conditions. GEOPHYSICAL RESEARCH LETTERS 2007, 34.Abstract
Theoretical investigations of the dynamics of the sunlight initiated dehydration of sulfuric acid are performed under atmospheric conditions. The relevant time scales for collisional deactivation and for vibrational fluorescence, which may compete with sulfuric acid dehydration in the upper stratosphere and the mesosphere are evaluated to provide a realistic quantum yield consistent with spectroscopic and theoretical results. The results obtained allow evaluation of the J values for this photochemical reaction in the atmosphere. At the higher altitudes of the upper stratosphere and the mesosphere the J values obtained are sufficiently large to satisfy model requirements and explain field observations of SO2 vertical profiles and the concentration of condensation nuclei in the stratosphere for air of recent polar origin.
Sheng, L. ; Gerber, B. R. Predicted stability and structure of (HXeCCH)(n) (n=2 or 4) clusters and of crystalline HXeCCH. JOURNAL OF CHEMICAL PHYSICS 2007, 126.Abstract
Ab initio calculations predict the existence of the dimer and tetramer of HXeCCH. The interaction energies are -6.66 and -19.40 kcal mol(-1) for the dimer and tetramer, respectively. For both complexes, larger blue shifts of the Xe-H stretching mode are found, while the Xe-C stretching modes are slightly redshifted. The stability and structure of HXeCCH crystals is predicted by density functional theory calculations with periodic boundary conditions. Strong electrostatic interactions are found between the monomers in the crystal. The results are first evidence for the existence of crystalline materials made of a novel class of noble gas molecules. (c) 2007 American Institute of Physics.
Schweke, D. ; Brauer, B. ; Gerber, R. B. ; Haas, Y. The vibrational spectra of N-phenylpyrrole in the gas phase, in argon matrices and in single crystals. CHEMICAL PHYSICS 2007, 333, 168-178.Abstract
The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for some bands, indicating the presence of two major trapping sites, in agreement with previous predictions. The spectra are analyzed with the help of harmonic calculations on the free molecule and on its adduct with one or two argon atoms, and anharmonic frequency calculations on the free molecule. Harmonic frequencies were obtained at the MP2/cc-pVDZ and DFT-B3LYP/cc-pVDZ levels. Anharmonic frequencies were obtained by the correlation-corrected vibrational self-consistent field (CC-VSCF) method with a variant of the PM3 semiempirical electronic structure method, calibrated for much improved spectroscopic accuracy. The potential surfaces used in the CC-VSCF calculation obtained by adjusting standard PM3 surfaces so that they provide harmonic frequencies that are comparable to those obtained at the DFT-B3LYP/cc-pVDZ level. Agreement between the experimental and theoretical results is in general very good, allowing the assignments of most bands. The harmonic frequency calculations of PP-Ar clusters, at the MP2/cc-pVDZ level show that the environment can greatly affect the intensities of some of the transitions, which is in accord with experiment. (c) 2007 Elsevier B.V. All rights reserved.
Adesokan, A. A. ; Chaban, G. M. ; Dopfer, O. ; Gerber, B. R. Vibrational spectroscopy of protonated imidazole and its complexes with water molecules: Ab initio anharmonic calculations and experiments. JOURNAL OF PHYSICAL CHEMISTRY A 2007, 111, 7374-7381.Abstract
The results of anharmonic frequency calculations on neutral imidazole (C3N2H4, Im), protonated imidazole (ImH(+)), and its complexes with water (ImH(+))(H2O)(n), are presented and compared to gas phase infrared photodissociation spectroscopy (IRPD) data. Anharmonic frequencies are obtained via ab initio vibrational self-consistent field (VSCF) calculations taking into account pairwise interactions between the normal modes. The key results are: (1) Prediction of anharmonic vibrational frequencies on an MP2 ab initio potential energy surface show excellent agreement with experiment and outstanding improvement over the harmonic frequencies. For example, the ab initio calculated anharmonic frequency for (ImH(+))(H2O)N-2 exhibits an overall average percentage error of 0.6% from experiment. (2) Anharmonic vibrational frequencies calculated on a semiempirical potential energy surface fitted to ab initio harmonic data represents spectroscopy well, particularly for water complexes. As an example, anharmonic frequencies for (ImH(+))H2O and (ImH(+))(H2O)(2) show an overall average deviation of 1.02% and 1.05% from experiment, respectively. This agreement between theory and experiment also supports the validity and use of the pairwise approximation used in the calculations. (3) Anharmonic coupling due to hydration effects is found to significantly reduce the vibrational frequencies for the NH stretch modes. The frequency of the NH stretch is observed to increase with the removal of a water molecule or replacement of water with N-2. This result also indicates the ability of the VSCF method to predict accurate frequencies in a matrix environment. The calculation provides insights into the nature of anharmonic effects in the potential surface. Analysis of percentage anharmoncity in neutral Im and ImH(+) shows a higher percentage anharmonicity in the NH and CH stretch modes of neutral Im. Also, we observe that anharmonicity in the NH stretch modes of ImH(+) have some contribution from coupling effects, while that of neutral Im has no contribution whatsoever from mode-mode coupling. It is concluded that the incorporation of anharmonic effects in the calculation brings theory and experiment into much closer agreement for these systems.
Miller, Y. ; Chaban, G. M. ; Zhou, J. ; Asmis, K. R. ; Neumark, D. M. ; Gerber, B. R. {{Vibrational spectroscopy of (SO(4)(2-))center dot(H(2)O)(n) clusters. JOURNAL OF CHEMICAL PHYSICS 2007, 127.Abstract
The vibrational spectroscopy of (SO(4)(2-))center dot(H(2)O)(n) is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H(2)O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO(4)(2-))center dot(H(2)O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C(2v), in accordance with experiment. (6) No stable structures were found for (OH(-))center dot(HSO(4)(-))center dot(H(2)O)(n), for n <= 5. (C) 2007 American Institute of Physics.