Theoretical study of the dynamics of multi-dimensional systems: Vibrationally excited chemical reaction and the denaturation of DNA

Many chemical dynamical processes involve the behavior of a large number of coupled degrees of freedom. It has been a challenge to describe them accurately using theory. By developing practical methodologies to simplify the systems and the processes, we have studied two kinds of interesting systems: vibrationally excited chemical reaction dynamics and the denaturation of double helix DNA.; First we studied the chemical reaction dynamics between an atom and a tri-atomic molecule, using a quasiclassical trajectory method. The equations of motion are solved by classical mechanics, with the potential energy surface fit from ab initio calculations, and the initial and final vibrational-rotational states of the diatomic and tri-atomic molecules quantized by a semi-classical method. We have studied the dynamics of two benchmark systems, the reactions H + H₂O → H₂ + OH and H + HCN → H₂ + CN in detail, with focus on the enhancement of reactivity from vibrational excitation of the tri-atomic reactant. Most of our results are in very good agreement with state-of-art experimental data. For the reaction between H and H₂O, we discovered that with different OH stretching excitation of H₂O there is a transition in the reaction dynamics from activated to activationless behavior.; The thermal denaturation (melting) of double helix DNA is one of the most important physiological processes. When DNA molecules are attached to gold nanoparticles, the melting temperature becomes higher and the melting curve becomes much sharper than with DNA in solution. In order to study this complicated process, we have developed a reduced model, with each nucleotide simplified as one backbone site and one hydrogen bonding site, and used empirical potential functions to simulate the denaturation by Langevin dynamics. Our results on the melting of some short length DNA molecules, including the melting temperature and width agree well with experimental data. In addition, we found that for the melting of nanoparticle linked DNA, multiple melting steps may be involved. A cooperative thermodynamical model can be developed which fits the experimental results accurately.