Francois Amar

We discuss simulation studies of cluster evaporation dynamics for several systems which can be considered typical of two limiting regimes: a statistical regime and a mode-specific regime. At the statistical limit, we compare the results of molecular dynamics (MD) simulations of the evaporation of small neutral argon clusters with both approximate statistical theories and exact classical phase space theory. In the limit of mode-specific excitation we discuss the photoexcitation and caging of diatomic molecules and ions in rare-gas and molecular clusters. Special attention is given to the I2(CO2)1 system. We compare simulation results with existing experimental data and discuss the transition from non-statistical to statistical evaporation as a function of cluster size.

QM/MM studies were performed to explore the energetics of exchange reactions of glutathione disulfide (GSSG) and the active site of thioredoxin [Cys32-Gly33-Pro34-Cys35] with and without zinc(ii), in vacuum and solvated models. The activation energy for exchange, in the absence of zinc, is 29.7 kcal mol(-1) for the solvated model. This is 3.3 kcal mol(-1) higher than the activation energy for exchange in the gas phase, due to ground state stabilization of the active site Cys-32 thiolate in a polar environment. In the presence of zinc, the activation energy for exchange is 4.9 kcal mol(-1) lower than in the absence of zinc (solvated models). The decrease in activation energy is attributed to stabilization of the charge-separated transition state, which has a 4-centered, cyclic arrangement of Zn-S-S-S with an estimated dipole moment of 4.2 D. A difference of 4.9 kcal mol(-1) in activation energy would translate to an increase in rate by a factor of about 4000 for zinc-assisted thiol-disulfide exchange. The calculations are consistent with previously reported experimental results, which indicate that metal-thiolate, disulfide exchange rates increase as a function of solvent dielectric. This trend is opposite to that observed for the influence of the dielectric environment on the rate of thiol-disulfide exchange in the absence of metal. The results suggest a dynamic role for zinc in thiol-disulfide exchange reactions, involving accessible cysteine sites on proteins, which may contribute to redox regulation and mechanistic pathways during oxidative stress.

We present results of molecular dynamics calculations of the recombination dynamics of a model system intended to mimic the main features of Br−2 in clusters of argon and CO2. The calculation displays a number of novel features, most notably, a consistent treatment of the asymptotic localization of the ‘‘extra’’ negative charge on one of the bromine atoms at large rBr–Br.

We have simulated the cluster dissociation reaction Ar→ Ar+ Ar (12≤ n≤ 14) using molecular dynamics (MD) with well defined internal energy and total angular momentum. Reaction rates and kinetic energy release distributions are compared to the predictions of ...

Motivated by the recent experiments of the Swedish group [M. Tchaplyguine, R. R. Marinho, M. Gisselbrecht et al., J. Chem. Phys. 120, 345 (2004)], we simulate the photoelectron spectra of pure xenon and argon clusters. The clusters are modeled using molecular dynamics with Hartree-Fock-dispersion type pair potentials while the spectrum is calculated as the sum of final state energy shifts of the atoms ionized within the cluster relative to the isolated gas phase ion. A self-consistent polarization formalism is used. Since signal electrons must travel through the cluster to reach the detector, we have accounted for the attenuation of the signal intensity by integrating an exponentially decaying scattering expression over the geometry of the cluster. Several different approaches to determining the required electron mean free paths (as a function of electron kinetic energy) are considered. Our simulated spectra are compared to the experimental results.

Using realistic pair potentials, we investigate the structures of mixed clusters of argon and nitrogen in order to interpret the experimental electron diffraction patterns reported by the Torchet group. Simulations of small clusters indicate that argon tends to segregate at the center of the clusters. For larger clusters, in the range of 50 to 200 molecules, MC methods have been used to simulate structures that are likely to be generated in the molecular beam. By comparing predicted electron diffraction patterns with those recorded in the experiments, our models allow us to estimate the average size and composition of the mixed clusters for a given set of experimental conditions (nozzle stagnation pressure and Ar partial pressure).

We have simulated the dissociation reactionA n →A n−1+A for small clusters (L-J argon) with well defined internal energy and total angular momentum. Reaction rates and kinetic energy release distributions are compared to the predictions of several statistical theories, including RRK, the “Engelking” model, and phase space theory (PST). We have applied classical phase space theory in an essentially exact formulation using accurate anharmonic vibrational densities of states (and no adjustable parameters). We present a critical evaluation of the different theories and sensitivity of the results to the underlying assumptions.