1. Introduction 5632. Obtaining rate constants from molecular-dynamics simulations 5642.1 General relationships between quantum electronic structures and reaction rates 5642.2 The transition-state theory (TST) 5692.3 The transmission coefficient 5723. Simulating biological electron-transfer reactions 5753.1 Semi-classical surface-hopping and the Marcus equation 5753.2 Treating quantum mechanical nuclear tunneling by the dispersed-polaron/spin-boson method 5803.3 Density-matrix treatments 5833.4 Charge separation in photosynthetic bacterial reaction centers 5844. Light-induced photoisomerizations in rhodopsin and bacteriorhodopsin 5965. Energetics and dynamics of enzyme reactions 6145.1 The empirical-valence-bond treatment and free-energy perturbation methods 6145.2 Activation energies are decreased in enzymes relative to solution, often by electrostatic effects
that stabilize the transition state 6205.3 Entropic effects in enzyme catalysis 6275.4 What is meant by dynamical contributions to catalysis? 6345.5 Transmission coefficients are similar for corresponding reactions in enzymes and water 6365.6 Non-equilibrium solvation effects contribute to catalysis mainly through Δg[Dagger], not the
transmission coefficient 6415.7 Vibrationally assisted nuclear tunneling in enzyme catalysis 6485.8 Diffusive processes in enzyme reactions and transmembrane channels 6516. Concluding remarks 6587. Acknowledgements 6588. References 658Obtaining a detailed understanding of the dynamics of a biochemical reaction is a formidable
challenge. Indeed, it might appear at first sight that reactions in proteins are too complex to
analyze microscopically. At room temperature, even a relatively small protein can have as
many as 1034 accessible conformational states (Dill, 1985). In many cases, however, we have
detailed structural information about the active site of an enzyme, whereas such information
is missing for corresponding chemical systems in solution. The atomic coordinates of the
chromophore in bacteriorhodopsin, for example, are known to a resolution of 1–2 Å.
In addition, experimental studies of biological processes such as photoisomerization and
electron transfer have provided a wealth of detailed information that eventually may make
some of these processes classical problems in chemical physics as well as biology.
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