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Host/guest chemistry: from rings and metals to proteins and drugs

  • Author / Creator
    Gajewski, Melissa May
  • 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 the ΔΔE 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.

  • Subjects / Keywords
  • Graduation date
    2011-11
  • Type of Item
    Thesis
  • Degree
    Doctor of Philosophy
  • DOI
    https://doi.org/10.7939/R3Z06T
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Doctoral
  • Department
    • Department of Chemistry
  • Supervisor / co-supervisor and their department(s)
    • Klobukowski, Mariusz (Department of Chemistry)
    • Tuszynski, Jack (Department of Oncology)
  • Examining committee members and their departments
    • Marsh, Sharon (Faculty of Pharmacy and Pharmaceutical Sciences)
    • Weaver, Don (Department of Chemistry)
    • Veinot, Jonathan (Department of Chemistry)
    • Brown, Alexander (Department of Chemistry)
    • Gibbs-Davis, Julianne (Department of Chemistry)