John P. Bergsma

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...

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.

Molecular dynamics of the A+BC reaction in rare gas solution

Molecular dynamics are computed for model atom transfers A+BC→AB+C in rare gas solvents at liquid densities. We find that the reaction dynamics can be understood in terms of a simple picture which consists of three stages: (1) activation of reactants, (2) barrier crossing, and (3) deactivation of products. The effects seen in stages (1) and (3) can be largely interpreted in terms of existing models of energy and phase decay in solution, while the effects seen in stage (2) can be largely interpreted in terms of gas phase A+BC barrier crossing dynamics. We find that transition state theory is in perfect agreement with the simulations for the 20 and 10 kcal/mol barrier reactions and is a very good description for a 5 kcal/mol reaction barrier. At low barrier curvature, dynamical effects due to the solvent are shown to induce some recrossings of the transition state barrier, thus causing rate constants calculated by simple transition state theory to be slightly too high. The Grote–Hynes modification of transi...

Transient x‐ray scattering calculated from molecular dynamics

With the continued development of pulsed x‐ray sources, it may in time be possible to use transient x‐ray diffraction to follow the molecular dynamics of chemical reactions in the liquid and solid states. To explore this possibility from the theoretical side, we have calculated, using classical molecular dynamics, the picosecond time‐resolved x‐ray scattering of a simplified model for a liquid state chemical reaction of substantial interest: the photodissociation of I2 molecules in rare gas and hexane solvents. The time scale of the separation of the I atoms and the effect of the solvent on their motion are observed in the computed transient x‐ray diffraction patterns, and such effects might also be observed in a suitably designed experiment. This illustrates that transient x‐ray diffraction might be an experimental tool for discovering the molecular dynamics of chemical reactions, with the advantage over transient optical spectroscopies such as infrared, electronic, and Raman that the connections between...

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.

Molecular Dynamics of Chemical Reactions in Solution

We hope to answer one of the most fundamental and important unsolved questions in chemistry: how, from a molecular perspective, do chemical reactions in solution actually occur. The key to solving this long-standing problem is to understand the molecular dynamics, i.e., the motions of the atoms and the forces that drive them. We have already developed theoretical techniques and computational procedures involving specialized computer hardware needed to calculate the molecular dynamics for many chemical reactions in solution. From the dynamics we have derived the interface for experimental verification, namely transient electronic, infrared, and Raman spectra as well as X-ray diffraction, all of which are potentially observable manifestations of the atomic motions during the reaction. We have tested our approach on the simple inorganic I2 photodissociation and solvent caging reaction. The agreement between molecular dynamics based theory and experimental picosecond transient electronic absorption spectrum as a function of solvent, time, and wavelength is sufficiently close as to indicate that for the first time we are discovering at least part of the molecular dynamics by which a real solution chemical reaction takes place.

Picosecond Dynamics of I 2 Photodissociation

While liquid solution reactions are much more important in chemistry, gas phase reactions are much better understood. Given the central importance of solution reactions to inorganic, organic, industrial and biochemistry, it is rather surprising that, as yet, there is not a single such reaction whose molecular dynamics are understood in detail. Theoretical and experimental evidence already makes clear that much of the important molecular dynamic action in solution reactions occurs on the picosecond and subpicosecond time scales. The dihalogen photodissociation and recombination reactions, X 2 + hv→X + X→X 2, involving the simplest possible molecular reactants and products, diatomics, and in rare gas solution involving only two elements, seem excellent candidates for study.

Molecular Dynamics of I2 Photodissociation in Cyclohexane: Experimental Picosecond Transient Electronic Absorption

Experimental and theoretical studies of the wavelength dependence of the transient electronic absorption of I2 in cyclohexane following photodissociation at 680 nm indicate a role for the vibrational decay of the already recombined I2 molecules.

Spectra from Molecular Dynamics.

Abstract : It has been shown, for systems for which the potential energy and the appropriate connection to the radiation field (dipole moment or polarizability) are known sufficiently accurately, that infrared, electronic, and nonresonance Raman spectra can be computed from classical molecular dynamics followed by simple quantum corrections to the spectra. Note that no adjustable parameters are needed for any of the spectra presented here. These essentially classical spectra can be compared to experimentally measured spectra to check that the underlying computed dynamics are correct, and the agreement illustrated here indicated that a basically classical view of the atomic motions involved in these spectra is a useful one, in harmony with our well calibrated physical intuition.