| The computational work presented here consists of primary studies on inositol phosphates and Old Yellow Enzyme (OYE), and a secondary study on 1-(isopropylideneaminomethyl)pyrene.; The thermally accessible optimum geometries of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) were found at various levels of deprotonation, and were then used for further calculations of both theoretical coupling constants and qualitative energy barriers to ring inversion. Quantum and molecular mechanical calculations predicted the exclusive presence of the equatorial conformation at low pH and the axial conformation at high pH, which agree with experimental results. The theoretical coupling constants were determined using MacroModel, and again compared well with experimental values.; The electronic transitions that are the origin of the long-wavelength charge-transfer (CT) bands in complexes of OYE were described computationally, in addition to the reduction of OYE by reduced nicotinamide adenine dinucleotide (NADPH). The charge-transfer was confirmed quantum mechanically by examining the relative locations of the HOMO and LUMO molecular orbital plots, on the ligand and substrate. Additionally, the CT wavelength maximum for each substituted phenol compared well with the experimental values at the CIS/STO-3G level. Perturbation of the hydrogen bonding residues around the active site increased the CT maximum, an effect also observed experimentally. Molecular orbital plot analysis coupled with an atomic population analysis confirmed the expected reduction reaction between NADPH and FMN with a resultant charge of +0.846 and -0.846 respectively, and that a hydride transfer was occurring. Additionally, using a relaxed PES scan a preliminary activation energy of 73.3 kcal/mol was determined for the reduction of FMN to the semi-quinone state.; The lowest energy stacking and rotational energy barrier of 1-(isopropylideneaminomethyl)pyrene molecules were computationally determined. Using a relaxed PES scan at the HF/STO-3G level it was determined that the lowest energy stacking of the molecules occurred in a planar stacking configuration, in agreement with experiment, with a predicted rotational energy barrier of approximately 18.8 kcal/mol.; In each case, these computational problems arose as collaborative efforts to describe molecular interactions on an electronic level for the compounds currently being studied experimentally. |
