| The sequestering of alkali and alkaline earth cations by host structures (ethylenediamine tetraacetate, 18-crown-6, and hexaaza[18]annulene) was accomplished using density functional theory and either all electron or model core potential basis sets. The sequestering of alkali and alkaline earth cations by host structures (ethylenediamine tetraacetate, 18-crown-6, and hexaaza[18]annulene) was accomplished using density functional theory and either all electron or model core potential basis sets. These calculations allow for an understanding of the geometric position in which the cation bind to the host structure and the stabilization energy gained when forming the host/guest structures. Some solvation effects were taken into account for these calculations by either using polarizable continuum model or theDeltaDeltaE equation described in Chapter 4. The knowledge gained from these types of studies could aid in choosing the correct host molecule to remove specific cation(s) in industrial, commercial, and/or laboratory procedures.;Calculating a slice of the potential energy surface for noscapine was accomplished using quantum mechanics using semi-empirical method and rotating the molecule along a dihedral angle. Energetic barriers in the rotation along this dihedral angle can provide an understanding of the possible binding conformations.;A matrix of binding affinities of different isotypes of tubulin (ten isotypes or mutants and 1TUB from the PDB) to derivatives of peloruside (twenty five derivatives) and laulimalide (eighteen derivatives) was created. The binding affinity calculations were accomplished using molecular mechanics, molecular dynamics, and quantum mechanics methods. Several de novo drug designs have predicted improvement in tubulin binding affinities. |
