My Trajectory in Molecular Reaction Dynamics and Spectroscopy.

This is the story of a career in theoretical chemistry during a time of dramatic changes in the field due to phenomenal growth in the availability of computational power. It is likewise the story of the highly gifted graduate students and postdoctoral fellows that I was fortunate to mentor throughout my career. It includes reminiscences of the great mentors that I had and of the exciting collaborations with both experimentalists and theorists on which I built much of my research. This is an account of the developments of exciting scientific disciplines in which I was involved: vibrational spectroscopy, molecular reaction mechanisms and dynamics, e.g., in atmospheric chemistry, and the prediction of new, exotic molecules, in particular noble gas molecules. From my very first project to my current work, my career in science has brought me the excitement and fascination of research. What a wonderful pursuit!

A Noble-Gas Hydride in a Nitrogen Medium: Structure, Spectroscopy, and Intermolecular Vibrations of HXeBr@(N2)22.

Noble-gas hydrides have been extensively studied in noble gas matrices. However, little is known on their stability and properties in molecular hosts. Here, HXeBr in the N2 environment is modeled at the B3LYP-D level of theory in a complete single shell of 22 N2 molecules. The system is compared to similar models of HXeBr in CO2 and Xe clusters. The optimized structure of (HXeBr)@(N2)22 is of low symmetry and is highly anisotropic. None of the N2 molecules are freely rotating, and the host molecules are not symmetrically positioned with respect to the HXeBr axis. The axes of the N2 molecules are nonuniformly distributed. The computed anharmonic H-Xe stretching frequency of HXeBr in the N2 cluster is in good accord with the experimental value. The soft-mode frequencies of the cluster including both intermolecular vibrations and librations, have a broad distribution that ranges from 8.7 to 107 cm(-1). It is expected that these findings and specifically, the single-shell model, may shed light also on the local structure and vibrations of other impurities in a molecular media.

Sugar-salt and sugar-salt-water complexes: structure and dynamics of glucose-KNO3-(H2O)n.

Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and for complexes of the type glucose-KNO(3)-(H(2)O)(n), for n < or = 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO(3) leads to an "inverse anomeric effect", with the beta-glucose complex more stable than the alpha-glucose by approximately 1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO(3) remains undissociated in the 1 : 1 complex, with the K(+) hooked to the equilibrium site, and the NO(3)(-) bound to it, undergoing large-amplitude bending/torsional motions; (3) for n > or = 3 water molecules added to the system, charge separation into K(+) and NO(3)(-) ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.

Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach.

The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide; a multiple reaction path study of the blocked valine tripeptide; and the evolution in time from the beta hairpin to alpha helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.