Vibration Analysis of Heme Porphyrin

Table of Contents

  1. Title Page
  2. Abstract
  3. Introduction
    1. Myoglobin
    2. Spiro Group's Arguments
    3. Kitagawa Group's Argument
    4. Molecular Dynamics
    5. Molecular Models
    6. Molecular Dynamics
    7. Other Heme Force Fields
    8. Goals
  4. Methods and Materials
    1. General
    2. AMBER 4.1
    3. Molecular Mechanics Force Fields
      1. Bond and Angle Parameters
        1. Sundar/Sontum_old Modeling Method
        2. Sundar/Sontum_new Modeling Approach
      2. Dihedral Parameters (Bond torsion)
      3. Non-bonded Parameters
    4. Normal Mode Analysis
      1. NMODE
      2. NMANAL
    5. Consistent Force Fields
      1. Optimization Procedures
      2. Symmetry
      3. Potential Energy Distribution (nfit algorithm)
      4. Calc. File
      5. Observed File
      6. Matching Algorithm (NFIT_12)
      7. Orbital Visualization
        1. NMODE_P and RUN.VIS
    6. Force Constant Optimization
      1. Ravine Algorithm
      2. SIMPLEX Algorithm
    7. Force Field Selection
    8. IBELLY OPTION
  5. Chapter 3- Results Small Molecules
    1. Results and Discussion
    2. Relaxation of United Ethyl Approximation
    3. Non-United Nickel Octaethyl Porphyrin
    4. Force Field Development for Benzene, Toluene and Ethylbenzene.
      1. Deuterated Benzene
      2. Toluene
      3. Ethylbenzene
    5. Improper Torsion Terms.
    6. Conclusion Transferred over to NiOEP.
  6. Chapter 4- Results Old Force Field
    1. Nickel Octaethyl Porphyrin
    2. Vibration Features
      1. Nickel Nitrogen Constant
      2. Angle Bending Constants
    3. Structural Fits
    4. Dihedral (Proper and Improper) Parameters
      1. Proper Torsion Parameters
      2. IMPROPER Torsion
    5. Force Constants vs. Bond Lengths
    6. Transferability
    7. Conclusion
  7. Chapter 5 New Approach to Modeling
    1. Vibrational Fit
    2. .
        Sundar/Sontum_old vs. Sundar/Sontum_new Angle Force Constants
      1. Nickel-Nitrogen Force Constant
    3. Bond length vs. Force Constants
    4. Geometric Fit
    5. Transferability:
  8. Chapter 6 Heme Porphyrin Analysis
    1. Introduction
      1. Fe-N Force Constant
      2. Peripheral Heme groups
    2. Spiro/Kitagawa Controversy
      1. Isolated Heme Calculations:
      2. Myoglobin Protein Effects
  9. Chapter 7- Conclusions and Future Work
    1. Conclusions
    2. Future Work
  10. References
  11. Appendix A: Prep Files
    1. Benzene Prep File
    2. Ethyl Benzene Prep File
    3. Heme-Histidine Prep File
    4. Nickel octaethyl porphine Prep File
    5. Nickel porphine Prep File
  12. Appendix B: PDB Files
    1. Benzene PDB File
    2. Ethyl Benzene PDB File
    3. Ethyl Benzene PDB File
    4. Nickel octa ethyl porphine PDB File
    5. Nickel porphine PDB File
  13. Appendix C: Scale
  14. Appendix D: Obs Files
    1. Benzene Obs File
    2. Ethyl Benzene Obs File
    3. Nickel Octa Ethyl Porphine Obs File
    4. Nickel Octa Ethyl Porphine D4h Obs File
    5. Toluene Obs File
    6. Sample Run Nmode Script
  15. Appendix E: Symmetry Files
    1. Benzene Symmetry File
    2. Ethyl Benzene Symmetry File
    3. Nickel Octa Ethyl Porphine Symmetry File
    4. Nickel Octa Ethyl Porphine D4h Symmetry File
    5. Toluene Symmetry File
  16. Appendix F: Potential Files
    1. Benzene Potential File
    2. Ethyl Benzene Potential File
    3. Heme Potential File
    4. Heme Sundar New Potential File
    5. Heme Sundar Old Potential File
    6. Toluene Potential File