R. Benny Gerber

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A new algorithm is presented for finding the global minimum, and other low-lying minima, of a potential energy surface (PES) of biological molecules. The algorithm synergetically combines three well-known global optimization methods: the diffusion equation method (DEM), which involves smoothing the PES; a simulated annealing (SA) algorithm; and evolutionary(More)
The harmonic approximation for the potential energy of proteins is known to be inadequate for the calculation of many protein properties. To study the effect of anharmonic terms on protein vibrations, the anharmonic wave functions for the ground state and low-lying excited states of the bovine pancreatic trypsin inhibitor (BPTI) were calculated. The results(More)
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(More)
Methyl peroxide (CH(3)OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH(3)OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood. We(More)
Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations(More)
The dynamics of Cl͑ 2 P͒ atoms in a solid Ar matrix is studied, with emphasis on electronic energy relaxation of excited states, and on p-orbital reorientation effects. The method used follows Tully's approach for nonadiabatic molecular dynamics simulations, which treats the electronic degrees of freedom quantum-mechanically, and the atomic motions(More)
The information content and properties of the cross section for atom scattering from a defect on a flat surface are investigated. Using the Sudden approximation, a simple expression is obtained that relates the cross section to the underlying atom/defect interaction potential. An approximate inversion formula is given, that determines the shape function of(More)
The reaction of (NO(+))(NO3(-)) with water is modelled in ONONO2·(H2O)4 clusters. Molecular Dynamics simulations using second-order Møller-Plesset perturbation (MP2) theory support the feasibility of the reaction of a charge-separated species to produce HONO and nitric acid.
The interaction of OH(-) with the sugar β-D-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-D-G)(-). (2) This reaction can be reversed when two(More)
A theoretical study is made on He scattering from three basic classes of disordered adlayers: (a) Translationally random adsorbates, (b) disordered compact islands and (c) fractal submonolayers. The implications of the results to experimental studies of He scattering from disordered surfaces are discussed, and a combined experimental-theoretical study is(More)