Bradley J. Gertner

Nonequilibrium solvation effects on reaction rates for model SN2 reactions in water

Molecular dynamics (MD) simulations of the model SN2 reaction Cl−+CH3Cl→ClCH3+Cl− in water, and variants thereof, are presented. The resulting transmission coefficients κ, that measure the deviations of the rates from the transition state theory (TST) rate predictions due to solvent‐induced recrossings, are used to assess the validity of the generalized Langevin equation (GLE)‐based Grote–Hynes (GH) theory. The GH predictions are found to agree with the MD results to within the error bars of the calculations for each of the 12 cases examined. This agreement extends from the nonadiabatic regime, where solvent molecule motions are unimportant and κ is determined by static solvent configurations at the transition state, into the polarization caging regime, where solvent motion is critical in determining κ. In contrast, the Kramers theory predictions for κ fall well below the simulation results. The friction kernel in the GLE used to evaluate the GH κ values is determined, from MD simulation, by a fixed‐parti...

Molecular dynamics of a modelSN2 reaction in water

Molecular dynamics are computed for a model SN2 reaction Cl−+CH3Cl→ClCH3+Cl− in water and are found to be strongly dependent on the instantaneous local configuration of the solvent at the transition state barrier. There are significant deviations from the simple picture of passage over a free energy barrier in the reaction coordinate, and thus, a marked departure from transition state theory occurs in the form of barrier recrossings. Factors controlling the dynamics are discussed, and, in particular, the rate of change of atomic charge distribution along the reaction coordinate is found to have a major effect on the dynamics. A simple frozen solvent theory involving nonadiabatic solvation is presented which can predict the outcome of a particular reaction trajectory by considering only the interaction with the solvent of the reaction system at the gas‐phase transition barrier. The frozen solvent theory also gives the transmission coefficient κ needed to make the transition state theory rate agree with the...

Molecular Dynamics Simulation of Hydrochloric Acid Ionization at the Surface of Stratospheric Ice

Molecular dynamics simulations were used to study the acid ionization of hydrochloric acid (HCl) at the basal plane surface of ice at 190 kelvin, as a model for the acid ionization process in Antarctic polar stratospheric clouds (PSCs). Initial conditions for HCl placement within the top bilayer of the ice lattice were selected on the basis of relevant dynamic equilibrium adsorption-desorption conditions. Free energy changes calculated for the first step in the stepwise acid ionization mechanism ranged from −5.8 to −6.7 kilocalories per mole for various likely initial conditions. These results indicate that acid ionization is thermodynamically favorable and that this process has important implications for ozone depletion mechanisms involving PSCs.

Nonadiabatic solvation model for SN2 reactions in polar solvents

An analytic theory for SN2 reactions in polar solvents in the nonadiabatic solvation limit is presented and used to interpret the computer simulation results of the preceding paper by Bergsma et al. The theory is based on the nonadiabatic solvation limit of previous studies by van der Zwan and Hynes and incorporates the solvent approximately but explicitly via a coordinate additional to the intrinsic reaction coordinate. Central results include: an explicit expression for the reaction transmission coefficient κ, the dependence of reaction probability on kinetic energy, the interpretation of κ in terms of nonequilibrium solvation entropy effects, and the deviation of the reaction coordinate from that assumed in the standard equilibrium solvation transition state theory view of the reaction.

Activation to the transition state : reactant and solvent energy flow for a model SN2 reaction in water

We have performed molecular dynamics calculations on a model Cl − +CH 3 ClS N 2 reaction in water in order to elucidate how the reactants obtain sufficient energy from the solvent to climb the potential energy barrier to reaction. This system, consisting of ionic and dipolar reagents in a polar solvent, is representative of a large class of chemical reactions with strong Coulombic reagent-solvent coupling. We find that the change in internal energy of the reactants during the barrier-climbing process involves three distinct epochs: (i) vibrational activation of the methyl chloride in the initial Cl − CH 3 Cl ion-dipole complex, (ii) gradual increase in kinetic and potential energies of the reactants, and (iii) fast dumping of reactant kinetic energy into reactant potential energy resulting in the reactants reaching the top of the potential energy barrier, with the symmetric structure Clδ − CH 3 δ + Clδ −

Model molecular dynamics simulation of hydrochloric acid ionization at the surface of stratospheric ice

The issue of the acid ionization of HCl at the surface of stratospheric ice particles, which is relevant in connection with Antarctic stratospheric ozone depletion, is studied theoretically. This study extends that of Gertner and Hynes (Science, 1996, 271, 1563) by examination of 12 new sites and by quantization of the transferring protons nuclear motion. Fourteen initial adsorption sites for the HCl are selected via arguments based on HCl incorporation mechanisms for a dynamic ice surface, for the basal-plane and prism face surfaces of ice. Acid ionization at 190 K in those sites is examined via combined electronic structure and classical molecular dynamics methodologies to estimate the reaction Gibbs energies and barriers. In each case examined, the acid ionization step of proton transfer from the HCl to a neighboring water molecule is estimated to be thermodynamically feasible and kinetically rapid.

Bihalide ion combination reactions in solution: electronic structure and solvation aspects

Abstract The Kim—Hynes theory for electronic structure for reaction systems in solution is applied to the reaction class of the title, focusing on the I - +I → I 2 - reaction in acetonitrile solvent from a valence bond perspective. The transition between a delocalized electronic structure at small internuclear separations r to localized structures at large r is described in terms of a two-dimensional nonequilibrium free energy surface; the second coordinate is a solvent coordinate gauging the state of the solvent orientational polarization. The reaction path on this surface is described, and is contrasted with an equilibrium solvation perspective. An important focus is the polarization force, defined as the force on the diatomic ion coordinate r due to the solvent, which arises from the charge shifting, or electronic structure change, in the solute system along the reaction coordinate. It is argued that this force should play a significant role in the vibrational relaxation of the I 2 - ion.

Dynamics of the A + BC reaction in solution

Abstract Molecular dynamics are computed for A+BC → AB+C in a rare gas solvent. Transition state theory is valid. For ± 0.02 ps about the barrier, reaction dynamics are essentially the same as without solvent. Reactive trajectories are translationally special over ≈ ± 0.02 ps, rotationally over ≈ ± 0.5 ps, and vibrationally over > 100ps.

A GENERALIZED LANGEVIN EQUATION APPROACH TO REORIENTATIONAL DYNAMICS IN NEMATIC LIQUID CRYSTALS

A new model of reorientational dynamics in nematic liquid crystals, based on a linear generalized Langevin equation (GLE) representation of the dynamics of a probe molecule, is developed. Derived in the limit of high order, the linearized angular motion of a probe molecule under the influence of director fluctuations is analyzed when the time scale of rotational relaxation is comparable to that of the cooperative modes of the liquid crystal solvent. This model allows negative total solvent contributions (director fluctuations plus a negative cross term) to the spectral density J1(ω) relative to the rotational diffusion contribution, a result predicted experimentally by least‐squares data fits. This result cannot be justified in terms of existing theories that assume a separation of time scales between the probe molecule motion and relaxation of the cooperative modes of the solvent. Results from the GLE‐based model (and the standard model) are compared to measured spectral densities of a highly ordered spi...

Fast space-filling molecular graphics using dynamic partitioning among parallel processors

We present a novel algorithm for the efficient generation of high-quality space-filling molecular graphics that is particularly appropriate for the creation of the large number of images needed in the animation of molecular dynamics. Each atom of the molecule is represented by a sphere of an appropriate radius, and the image of the sphere is constructed pixel-by-pixel using a generalization of the lighting model proposed by Porter (Comp. Graphics 1978, 12, 282). The edges of the spheres are antialiased, and intersections between spheres are handled through a simple blending algorithm that provides very smooth edges. We have implemented this algorithm on a multiprocessor computer using a procedure that dynamically repartitions the effort among the processors based on the CPU time used by each processor to create the previous image. This dynamic reallocation among processors automatically maximizes efficiency in the face of both the changing nature of the image from frame to frame and the shifting demands of the other programs running simultaneously on the same processors. We present data showing the efficiency of this multiprocessing algorithm as the number of processors is increased. The combination of the graphics and multiprocessor algorithms allows the fast generation of many high-quality images.