Classical Trajectory Simulations of Photoionization Dynamics of Tryptophan: Intramolecular Energy Flow, Hydrogen-Transfer Processes and Conformational Transitions

Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment

The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.

Photochemistry of aldehyde clusters: cross-molecular versus unimolecular reaction dynamics

Semi-empirical on-the-fly dynamics simulations reveal the importance of cross-molecular reactions in the photochemistry of aldehyde clusters.

Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters

Recent progress in “on-the-fly” trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available.

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.

Ab initio photoionization dynamics of β-alanine

Photoionization dynamics of beta-alanine is studied by the trajectory simulations using the ab initio potential energy surface. Vertical photoionization in the spirit of the Franck-Condon principle is assumed both for the adiabatic and thermostatic simulations. Both intramolecular proton transfer and fragmentation while only the proton transfer are found in the thermostatic and adiabatic simulations, respectively, for the conformer having the intramolecular hydrogen bond N...H-O. The theoretical predictions are in line with the experimental observations available in the literatures. It is reported for the first time that the thermostatic temperatures strongly affect the fragmentation processes induced by photoionization.