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Open Access Dissertation

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First Advisor

H. B. Schlegel


In this dissertation, ab initio classical trajectory calculations have been carried out to study the dissociation of acetone radical cation, pentane-2,4-dione radical cation, and 1,3-cyclobutanedione radical cation. For acetone radical cation and pentane-2,4-dione radical cation, MP2 with bond additivity corrections generates a better potential energy surface at low cost and is thus used for molecular dynamics calculations. The dissociation of acetone radical cation is found to favor the loss of the newly formed methyl group in agreement with the experiments. The branching ratios of methyl loss were also calculated with different amount of excess energy and of specific mode excitation. Dissociation of pentane-2,4-dione radical cation and 1,3-cyclobutanedione radical cation has not been investigated experimentally, and the present trajectory calculations provide the first theoretical description of the dissociation dynamics.

The dissociations of the methanimine neutral, monocation and dication have been studied by ab initio classical trajectory calculations. Many of the trajectories dissociate directly to produce H+, H atom or H2. However, for a fraction of the cases, substantial migration of the hydrogen occurs within the molecule before dissociation. The preferred dissociation product for the neutral and the monocation is hydrogen atom. Dissociations of the dication and trication produced H+ rather than H atom.

The gas phase reaction of Th+ with H2O to produce HThO+ + H and ThO+ + H2 has been investigated using density functional theory and coupled cluster methods. Ab initio classical trajectory calculations have been carried out to obtain a better model of the molecular dynamics. The molecular dynamics simulations yield a branching ratio of ca 80% for the H2 elimination channel to 20% for the H atomic elimination channel in qualitative agreement with the observed ratio of 65% to 35%.

Complexes of the form An2(C8H8)2 (An = Th, Pa, U and Np) have been studied using density functional theory with scalar-relativistic effective core potentials. For uranium, a coaxial isomer with D8h symmetry is found to be more stable than a Cs isomer in which the dimetal unit is perpendicular to the C8 ring axis. Similar coaxial structures are predicted for Pa2(C8H8)2 and Np2(C8H8)2, while in Th2(C8H8)2 the C8H8 rings tilt away from the An-An axis. Further thermodynamic calculations suggest that it may be possible to generate these new complexes experimentally.

SB-3CT, (4 phenoxyphenylsulfonyl)methylthiirane, is a potent, mechanism-based inhibitor of the gelatinase sub-class of the matrix metalloproteinase (MMP) family of zinc proteases. The gelatinase MMPs are unusual in that there are several examples where both enantiomers of a racemic inhibitor have comparable inhibitory abilities. SB-3CT is one such example. The inhibition mechanism of the MMP2 gelatinase by the (S)-SB-3CT enantiomer and its oxirane analogue is examined computationally by QM/MM method, and compared to the mechanism of (R)-SB-3CT.

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