Physical insight into the quandaries of quantum chemistry
Jaeger, Heather Marie
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Four research pro jects and supporting information on the electronic and vibrational structure methods employed in this work are presented. The equilibrium structures of the two lowest-energy conformers of α-L-alanine are determined by removing vibrational eﬀects from experimental rotational constants and ﬁtting structural parameters, i.e. bond distances, bond angles, to the corrected set of rotational constants. It is shown that our structures are accurate, which gives merit to application of the semi-experimental method for large, less rigid molecules. Furthermore, high-level electronic structure methods show that the relative energy (including ZPVE) of the two lowest conformers, Ala-I and Ala-IIA 0.53(7) kcal mol−1. Two pro jects concerning gas-phase structures of non-bonded molecules are presented. Benzene interacts weakly with both acetylene and N2 (< 1000 cm−1 ). The equilibrium structure of the clusters exhibit a strong dependence on the interactions of molecular quadrupoles, such that a favorable quadrupole-quadrupole interaction exists at the global minimum. The intermolecular potential energy surface of the benzene-N2 complex is further investigated to reveal both internal rotation and sliding of N2 across the top plane of benzene, which leads to a tethered-top-like depiction of the vibrationally-averaged structure in the ground vibrational state. Infrared spectra of the benzene-benzenium (protonated-benzene) shows that protonated benzene hovers over the top of benzene with the sp3 C-H group pointed into the π cloud. The interaction energy is a much larger 10.5 kcal mol−1 than the benzene-acetylene and benzene-N2 dimers. Despite the interaction strength, an inherent ﬂoppiness to the complex is evidenced via peak broadening in the spectra and is justiﬁed by ﬂat region of the potential energy surface where two nearly isoenergetic isomers lie. Finally, a project on the primary oxidation products of DNA is presented. Electron loss occurs on the guanine base. The presence of surrounding water molecules and the Watson-Crick complement, cytosine, help to neutralize long-range damage by providing a low-energy pathway for distonic deprotonation.