Investigation of bioenergetical processes with multiple-length-scale approaches / Michael Hoffmann. 2006
Content
- Abstract
- Kurzfassung
- Contents
- 1 Introduction
- 1.1 Bioenergetics
- 1.2 Rhodopsins and the Problem of Color Tuning
- 1.3 Aquaporins and the Problem of Proton Blockage
- 1.4 The Investigation of Bioenergetical Processes with Multiple-Length-Scale Approaches in this Work
- 1.5 Overview over this Work
- 2 Theoretical Foundations
- 2.1 Electronic Structure Methods
- 2.1.1 The quantum mechanical many-body problem
- 2.1.2 Density Functional Theory
- 2.1.3 The Density Functional Theory Based Tight Binding Method
- 2.1.4 Hartree-Fock Theory
- 2.1.5 The Orthogonalization Model
- 2.2 Configuration Interaction
- 2.3 Molecular Force Field
- 2.4 Free Energy Simulations
- 3 Multiple-Length-Scale Approaches
- 3.1 The Quantum Mechanical / Molecular Mechanical Method (QM/MM)
- 3.2 Electrostatic Interactions and Solvation in QM/MM Simulations
- 4 Long-Range Proton Transfer in Biomolecular Channels: Developments and a Model System
- 4.1 Reaction Coordinates for Long-Range Proton Transfer
- 4.1.1 Previous Suggestions
- 4.1.2 A New Reaction Coordinate
- 4.1.3 Comparison of Different Coordinates for a Linear Proton Wire
- 4.2 A Model Proton Channel
- 4.3 Concluding Remarks
- 5 Proton Exclusion in the Glycerol Facilitator GlpF
- 5.1 Structure and Glycerol Conductance of GlpF
- 5.2 Proton Blockage in Aquaporins - Current State of Knowledge
- 5.3 The Mechanism of Proton Exclusion in GlpF
- 5.3.1 Computational Details
- 5.3.2 Water Structure in GlpF
- 5.3.3 Potential of Mean Force Calculations
- 5.4 Discussion
- 6 Color Tuning in Archaeal Rhodopsins: Bacteriorhodopsin vs Phoborhodopsin
- 6.1 Structure and Photocycle of Bacteriorhodopsin
- 6.2 Structure and Photocycle of pharaonis Phoborhodopsin
- 6.3 Color Regulation - Current State of Knowledge
- 6.4 Computational Strategy and Methods
- 6.5 Color Tuning between Bacteriorhodopsin and Phoborhodopsin
- 6.5.1 Computational Details
- 6.5.2 Comparison of Structures
- 6.5.3 Excitation Energies and Dipole Moments of bR and ppR
- 6.5.4 Perturbation Analysis
- 6.5.5 Mutation Experiments in ppR
- 6.5.6 Vibrational Analysis
- 6.5.7 Dynamics
- 6.6 Discussion
- 7 Summary
- References
- Acknowledgements
- Colophon