Developments and Applications of Chemical Dynamics Simulations; Surface-Induced Dissociation, Organic Reaction Mechanisms, and Non-Adiabatic Dynamics.



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Chemical dynamics simulations are an important tool to investigate atomic-level mechanisms of various chemical reactions. This dissertation includes developments and applications for different major areas of chemical dynamics simulations. The three topics investigated : 1) surface-induced dissociation (SID) of polypeptide ions; 2) reaction of molecular oxygen and ethylene; and 3) an algorithm for microcanonical sampling at a conical intersection. The collision dynamics of protonated octaglycine with the diamond {111} surface was studied to investigate energy transfer between the ion and surface, and fragmentation mechanisms of the peptide ion. The simulations mainly focused on representing mass spectrometry SID experiments. The results of the simulations provided an atomic level understanding of a new fragmentation mechanism, shattering, which is highly non-statistical process. As a part of efforts to understand combustion processes and stabilities of hydrocarbon fuels, the reaction of molecular oxygen and ethylene was studied using various electronic structure theories. The initial reaction paths were characterized for both the lowest lying triplet and singlet surfaces. Crossing and coupling between these surfaces were also characterized for possible non-adiabatic transitions. Chemical dynamics simulations involve numerical integrations of classical equation of motion. An ensemble of initial conditions must be chosen for the simulations that can be compared with experiments and/or statistical theories. An algorithm was developed to represent a microcanonical ensemble at a minimum energy conical intersection.



Chemical dynamics, SID, Non-adiabatic