# Publications

2002

Yang, H. S. ; Wright, N. J. ; Gagnon, A. M. ; Gerber, R. B. ; Finlayson-Pitts, B. J. An upper limit to the concentration of an SO2 complex at the air water interface at 298 K: infrared experiments and ab initio calculations. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2002, 4 1832-1838.Abstract

Unique reactions occurring at the interface between air and aqueous solutions are increasingly recognized to be of potential importance in atmospheric processes. Sulfur dioxide was one of the first species for which experimental evidence for the existence of a surface complex was obtained by several different groups, based on the kinetics of SO2 uptake into aqueous solutions, large decreases in surface tension and second harmonic generation spectroscopic studies. The uptake has been proposed to involve an uncharged surface complex which subsequently converts into ionic species. We report here the results of a search for an uncharged SO2 complex at or near the surface using attenuated total reflectance Fourier transform infrared spectrometry (ATR-FTIR) at 298 K guided by ab initio calculations of a 1:1 SO2-H2O complex. No infrared absorption bands attributable to such a complex of SO2 were observed experimentally in the expected region, giving an upper bound of 4 x 10(14) SO2 cm(-2) to the concentration of neutral SO2 molecules weakly sorbed to the surface in equilibrium with similar to1 atm SO2(g). The implications for the nature of the surface species and previous observations are discussed.

Gregurick, S. K. ; Chaban, G. M. ; Gerber, R. B. Ab initio and improved empirical potentials for the calculation of the anharmonic vibrational states and intramolecular mode coupling of N-methylacetamide. JOURNAL OF PHYSICAL CHEMISTRY A 2002, 106, 8696-8707.Abstract

The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans,, configuration, including all degrees of freedom. The anharmonic vibrational states and the spectroscopy are directly computed from this potential surface using the correlation corrected vibrational self-consistent field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low-temperature experimental matrix data. Analysis of our calculated spectroscopic results show that (1) the excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality. (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field. (3) The improved empirical force field in particular overestimates anharmonic couplings for the amide 11 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions. (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution. (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide I and other internal modes. The implication of this is that the intramolecular energy flow between the amide I and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.

Chaban, G. M. ; Gerber, R. B. Ab initio calculations of anharmonic vibrational spectroscopy for hydrogen fluoride (HF)(n) (n=3, 4) and mixed hydrogen fluoride/water (HF)(n)(H(2)O)(n) (n=1, 2, 4) clusters. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002, 58, 887-898.Abstract

Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)(n) with n = 3, 4 and mixed clusters of hydrogen fluoride with water (HF)(n)(H(2)O)(n) where n = 1, 2. For the (HF)(4)(H(2)O)(4) complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)(n), good agreement is found with experimental data. This agreement shows that the Moller-Plesset (MP2) potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)(n)(H(2)O)(n) experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments. Published by Elsevier Science B.V.

Gerber, R. B. ; Brauer, B. ; Gregurick, S. K. ; Chaban, G. M. Calculation of anharmonic vibrational spectroscopy of small biological molecules. PHYSCHEMCOMM 2002, 5 142-150.Abstract

The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and their 1:1 complexes with water is discussed. The strengths and limitations of the vibrational self-consistent field (VSCF) method and its extensions as a computational tool for this purpose are examined. Anharmonic coupling between different vibrational modes is found to be very important for these systems, even for fundamental transitions, and incorporation of these effects seems essential for quantitative interpretation of experimental data. Both analytical, empirical force fields, and potential surfaces computed from electronic structure methods are used in VSCF calculations of several benchmark systems and compared with experimental spectroscopic data. Glycine in several conformers, the glycine water complex, and N-methylacetamide are among the systems discussed. The main conclusions are: (1) Electronic structure methods such as MP2/DZP and density functional B97, give very good agreement with experimental data. Thus, MP2 and B97 clearly provide an accurate description of the anharmonic interactions. VSCF calculations, including all modes, with MP2, B97 and other successful methods are presently feasible for molecules with up to 15-20 atoms. (2) The electronic structure methods seem to give spectroscopic predictions in much better accord with experiment than standard empirical force fields such as AMBER or OPLS. The anharmonic couplings provided by these methods differ greatly, in the cases tested to date, from the ab initio ones. The implications of these results for future modeling of small biomolecules are discussed. Comments are provided on future directions in this subject, including extensions to large biomolecules.

Matsunaga, N. ; Chaban, G. M. ; Gerber, R. B. Degenerate perturbation theory corrections for the vibrational self-consistent field approximation: Method and applications. JOURNAL OF CHEMICAL PHYSICS 2002, 117, 3541-3547.Abstract

A new algorithm for computing anharmonic vibrational states for polyatomic molecules is proposed. The algorithm starts with the vibrational self-consistent field (VSCF) method and uses degenerate perturbation theory to correct for effects of correlation between different vibrational modes. The algorithm is developed in a version that computes the anharmonic vibrational spectroscopy directly from potential energy surface points calculated by using ab initio codes. The method is applied to several molecules where near degeneracies occur for excited vibrational states, including HOOH, HSSH, and HOOOH. The method yields results in very good accordance with experiments and generally provides improvements over nondegenerate perturbation corrections for VSCF. (C) 2002 American Institute of Physics.

Pettersson, M. ; Khriachtchev, L. ; Lignell, A. ; Rasanen, M. ; Bihary, Z. ; Gerber, R. B. HKrF in solid krypton. JOURNAL OF CHEMICAL PHYSICS 2002, 116, 2508-2515.Abstract

A new krypton-containing compound, HKrF, has been prepared in a low-temperature Kr matrix via VUV photolysis of the HF precursor and posterior thermal mobilization of H and F atoms. All three fundamental vibrations have been observed in the FTIR spectra at similar to1950 cm(-1) (H-Kr stretch), similar to650 cm(-1) (bending), and similar to415 cm(-1) (Kr-F stretch). Two distinct sites of HKrF have been identified. The energy difference between the H-Kr stretching vibrations for the two sites is remarkably large (26 cm(-1)), indicating a strong influence of the environment. In annealing after the photolysis of the precursor, HKrF is formed in two different stages: at 13-16 K from closely trapped H+F pairs and at T>24 K due to more extensive mobility of H and F atoms in the matrix. HKrF in a less stable site decreases at temperatures above 32 K, the other site being stable up to the sublimation temperature of the matrix. The photodecomposition cross section for HKrF has been measured between 193 and 350 nm and compared with the cross sections of the previously reported HArF and HKrCl molecules. The condensed-phase VSCF (vibrational self-consistent field) calculations suggest that the more stable form is a single-substitutional site and the less stable form is a double-substitutional site of HKrF in solid Kr. The gas to matrix shifts for these sites are predicted to be +(9-26) cm(-1) for the H-Kr stretching and the bending vibrations and -(7-10) cm(-1) for the Kr-F stretching vibrations. (C) 2002 American Institute of Physics.

Gerber, R. B. ; Mazzone, P. ; Arroliga, A. C. Paraneoplastic syndromes associated with bronchogenic carcinoma. CLINICS IN CHEST MEDICINE 2002, 23, 257+.Abstract

Paraneoplastic syndromes associated with lung cancer are diverse in their presentation, pathophysiology, and implications. They can be seen as a diagnostic and therapeutic challenge or as an opportunity to detect an otherwise asymptomatic malignancy. Unraveling the mechanisms that produce these syndromes will lead to insight into tumor biology that will be translated into novel approaches for early detection and therapy.

Jungwirth, P. ; Gerber, R. B. ; Ratner, M. A. Quantum simulations of vibrational dephasing of molecules in a cryogenic environment: HArF in an argon cluster. ISRAEL JOURNAL OF CHEMISTRY 2002, 42, 157-162.Abstract

The Classical Separable Potential (CSP) method, which is a mean-field approximation to multidimensional quantum dynamics, is applied to the dephasing process of a vibrationally excited HArF molecule in an argon cluster at low temperatures. Dephasing timescales of the order of 1 ps are estimated for dynamics following fundamental excitation of either the H-Ar or the Ar-F stretching mode of HArF. The CSP approach is valid over such timescales, and it is thus a viable approach to quantum simulations of dephasing at low temperatures. Vibrational relaxation is much slower: Quasi-classical molecular dynamics simulations yield a relaxation time around 100 ps for the initial v = 1 Ar-F stretching excitation. Such timescales are beyond the validity range of CSP; therefore, this or similar separable methods are inapplicable for vibrational energy decay.

Bihary, Z. ; Chaban, G. M. ; Gerber, R. B. Stability of a chemically bound helium compound in high-pressure solid helium. JOURNAL OF CHEMICAL PHYSICS 2002, 117, 5105-5108.Abstract

HHeF, a chemically-bound helium compound, has been predicted to be metastable in the gas phase. It decays by tunneling through energy barriers in picosecond timescales into He+HF and H+He+F. This paper studies the stability of HHeF in pressurized solid helium. Using realistic potentials for the HHeF/He interaction, the potential energy along the minimum energy paths for decomposition is evaluated, and tunneling decay times are computed by the WKB approximation. It is found that for pressures above 500 MPa, decomposition into H+He+F is completely suppressed. At 23 GPa, the highest pressure studied, the timescale for HHeF–>He+HF is in the millisecond range. At pressures well above 23 GPa, HHeF is thus expected to remain stable indefinitely. (C) 2002 American Institute of Physics.

Bargheer, M. ; Niv, M. Y. ; Gerber, R. B. ; Schwentner, N. Ultrafast solvent-induced spin-flip and nonadiabatic coupling: ClF in argon solids. PHYSICAL REVIEW LETTERS 2002, 89.Abstract

Femtosecond pump-probe spectra show direct evidence for ultrafast solvent-induced spin flip in photodissociation-recombination events of ClF, a light diatomic molecule, for which the spin-orbit coupling is weak. The bound triplet states ((3)Pi) of ClF are probed and the dynamics for excitation to the singlet state ((1)Pi(1)) is compared with excitation to the triplet state B((3)Pi(0)). The population initially excited to the singlet state (1)Pi(1) is transferred to the bound triplet states (3)Pi within tau(f)=0.5 ps. Oscillations in the spectra indicate wave packet dynamics with the triplet state period of 300 to 400 fs in both cases. According to simulations of F-2/Ar, most of the initially excited singlet state population is converted to repulsive and weakly bound triplet states within approximately 60 fs. In the first ps, 40% of the triplet population accumulates in the weakly bound (3)Pi states, in good accord with the experiment.

Bihary, Z. ; Chaban, G. M. ; Gerber, R. B. Vibrational spectroscopy and matrix-site geometries of HArF, HKrF, HXeCl, and HXeI in rare-gas solids. JOURNAL OF CHEMICAL PHYSICS 2002, 116, 5521-5529.Abstract

The vibrational spectroscopy and the matrix-site geometries of several novel rare-gas compounds in the matrix environment were computed theoretically, and compared with experiment. Ab initio calculations are used in the fitting of analytical potential surfaces for the HRgY molecules and for the interactions between HRgY and the matrix atoms Rg. With these potentials, matrix-site geometries for the molecule in the solid are computed. Finally, the vibrational spectroscopy of HRgY in the Rg matrix is computed using the vibrational self-consistent field (VSCF) method. The VSCF includes anharmonic effects, that are essential in this case. The version of VSCF used here includes coupling between HRgY and the vibrations of the solid atoms. The vibrations of 72 matrix atoms are treated. The main results are: (1) The matrix shifts are considerably greater than typically found for neutral, strongly bond molecules, but are much smaller than discrepancies between theory and experiment. This can be attributed to the insufficient accuracy of the potentials used for the HRgY molecules. This calls for better future description of the electronic structure of HRgY. (2) The matrix shifts and splitting effects are interpreted by the calculations in terms of the site geometries involved. These effects are very different for HArF, HKrF than for HXeCl, HXeI. (3) The computed matrix-site splittings are in semiquantitative accord with experiment. This supports the interaction potentials used between HRgY and the matrix. The results provide insights on the effects of the matrix on the rare-gas molecules. (C) 2002 American Institute of Physics.

Lundell, J. ; Cohen, A. ; Gerber, R. B. Quantum chemical calculations on novel molecules from xenon insertion into hydrocarbons. JOURNAL OF PHYSICAL CHEMISTRY A 2002, 106, 11950-11955.Abstract

Ab initio calculations have been performed on novel compounds that may greatly expand the scope of rare gas chemistry. These molecules are insertion compounds of xenon into unsaturated hydrocarbons, including acetylene, benzene, and phenol. We present computational evidence that molecules such as H-Xe-C2H, H-Xe-C6H5, and H-Xe-OC6H5 exist. Computational results suggest also the existence of a series of xenon-insertion compounds for larger hydrocarbons of these types. The predictions are not restricted to molecules p with only one xenon atom inserted in them but molecules such as H-Xe-C-2-Xe-H and H-Xe-C-2-XeC2-Xe-H are computationally stable as well. This suggests the existence of linear polymers H-(Xe-C-2)(n)-H for arbitrary large n. All predicted xenon-insertion molecules form a new class of possible precursors and intermediates for synthetic organic and organoelement chemistry.

Bargheer, M. ; Gerber, R. B. ; Korolkov, M. V. ; Kuhn, O. ; Manz, J. ; Schroder, M. ; Schwentner, N. Subpicosecond spin-flip induced by the photodissociation dynamics of ClF in an Ar matrix. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 2002, 4 5554-5562.Abstract

Ultrafast spin-flip is used to monitor the subpicosecond intersystem crossing dynamics from the (1)Pi to the (3)Pi state following photodissociation of ClF isolated in an Ar matrix by means of pump-probe spectroscopy. After photoexcitation of the (1)Pi state analysis of the populations of triplet states shows that about 50 percent of the spin-flip occurs during the first bond stretch which takes about 250 fs. The early time dynamics of the Cl-F bond in an Ar matrix is investigated theoretically by selecting representative singlet and triplet excited states from a diatomics-in-molecules Hamiltonian. In a one-dimensional model, wave-packet simulations for the first excursion are performed which give a lower limit of about 60 fs for the spin-flip process. The ultrafast spin flip is supported by the caging of the wave packet by the neighboring Ar atoms. Already before collision of the F and Ar atoms the rather large energy gap between the (1)Pi and (3)Pi states in the Franck-Condon region is reduced rapidly to near degeneracy. As a consequence the spin-orbit interaction becomes dominant, inducing more than 40% admixture of the triplet character in the (1)Pi state. Subsequent kinetic energy transfer from ClF to Ar, not yet included in the model, should slow down the Cl and F atoms on their way back toward shorter bond distances, implying stabilization of the wave packet in the (3)Pi state, where it is monitored by the probe laser pulse.

Chaban, G. M. ; Lundell, J. ; Gerber, R. B. Theoretical study of decomposition pathways for HArF and HKrF. CHEMICAL PHYSICS LETTERS 2002, 364, 628-633.Abstract

To provide theoretical insights into the stability and dynamics of the new rare gas compounds HArF and HKrF, reaction paths for decomposition processes HRgF –> Rg + HF and HRgF –> H + Rg + F (Rg = Ar, Kr) are calculated using ab initio electronic structure methods. The bending channels, HRgF –> Rg + HF, are described by single-configurational MP2 and CCSD(T) electronic structure methods, while the linear decomposition paths, HRgF –> H + Rg + F, require the use of multi-configurational wave functions that include dynamic correlation and are size extensive. HArF and HKrF molecules are found to be energetically stable with respect to atomic dissociation products (H + Rg + F) and separated by substantial energy barriers from Rg + HF products, which ensure their kinetic stability. The results are compatible with experimental data on these systems. (C) 2002 Elsevier Science B.V. All rights reserved.

2001

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. ; Gerber, R. B. ; Jung, J. O. ; Gregurick, S. K. Anharmonic vibrational spectroscopy of biological molecules: Use of ab initio, empirical, and hybrid (QM/MM) potentials. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 2001, 221, U284-U285.

Chaban, G. M. ; Gerber, R. B. Anharmonic vibrational spectroscopy of the glycine-water complex: Calculations for ab initio, empirical, and hybrid quantum mechanics/molecular mechanics potentials. JOURNAL OF CHEMICAL PHYSICS 2001, 115, 1340-1348.Abstract

Effects of intermolecular hydrogen bonding between glycine and one water molecule on the vibrational spectrum are investigated, using ab initio (at the level of second order Moller-Plesset perturbation theory), empirical (OPLS-AA), and mixed ab initio/empirical quantum mechanics/molecular mechanics (QM/MM) potentials. Vibrational spectroscopy is calculated using the correlation corrected vibrational self-consistent field method that accounts for anharmonicities and couplings between different vibrational normal modes. The intermolecular hydrogen bonding interactions are found to be very strong and to affect vibrational frequencies and infrared intensities of both the glycine and the water molecule to a very large extent. The predicted ab initio anharmonic spectra can be used to identify amino acids in complexes with water in experimental studies. The OPLS-AA potential is found to describe hydrogen bonding between glycine and water incorrectly, and to predict erroneous vibrational spectra. Hybrid (QM/MM) techniques can, however, be used to calculate more reliable vibrational spectra, in agreement with full ab initio treatment of the whole system, provided that the regions that contain hydrogen bonds are described by ab initio potentials. (C) 2001 American Institute of Physics.

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.

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.