| Three major projects are studied in this thesis.; Maximally Localized Wannier Functions (MLWFs) have been implemented within the Car-Parrinello molecular dynamics (CPMD) formalism. MLWFs provide straightforward pictures that jibe with chemical intuition, such as covalent bonds and lone pairs of electrons. Therefore, the movement of electrons, which plays a critical role in chemical reactions, can be quantitatively tracked during atomistic molecular dynamics. As an example, we study the electronic movement during the reaction of DNA bases with OH radicals. Concerted proton-electron loss is identified by monitoring the displacement of MLWFs in the processes of be used as a general tool to unveil mechanisms of chemical reactions.; CPMD has been used to study the oxidation of carbon nanotubes (CNTs), including the chemisorption of oxygen molecules and their subsequent dissociation. The results suggest a new mechanism to understand the dramatic change of CNT transport properties upon exposure to ambient oxygen. Some topological defects present on CNTs may be crucial to facilitate the chemisorption of oxygen molecules.; A very recently proposed systematic approach to deal with “rare events” has been implemented to map potential energy surfaces (PESs). In this approach, microscopic molecular dynamics is guided by a coarse-grained dynamics to explore a large region of the accessible configuration space. The efficiency of this approach is further improved by introducing a post-processing procedure that dramatically increases the accuracy of the reconstructed PES. This scheme is implemented using empirical force fields and tested by studying the conformational changes in small organic molecules, many of which are candidates for ligand-based drug design. Using this scheme, we have been able to reconstruct the whole PES of protonated trans-nicotine. This scheme is further combined with CPMD to very effectively study activated processes at the level of Density Functional Theory. As an example, we study the cope rearrangement in the gas phase and located products, transition states and intermediates. This scheme can be used as a general tool to study thermal-activated chemical reactions. |
