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Interplay of theory and computations in science - Examples drawn from theoretical/experimental studies of Reaction rates On-water catalysiorganic reactions Isotope fractionation Single-molecule fluctuations. Rudolph Marcus
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Interplay of theory and computations in science - Examples drawn from theoretical/experimental studies of Reaction rates On-water catalysiorganic reactions Isotope fractionation Single-molecule fluctuations Rudolph Marcus California Institute of Technology KITPC Workshop on Dynamics of Biomolecular Machinery Beijing August 6, 2009
ELECTRON TRANSFER MECHANISM Free Energy Reaction Coordinate
Time-dependent Stokes Shift Free Energy Reaction Coordinate
Time-dependent Stokes Shift Calculated from Solvent Dielectric dispersion Hsu, Song &RAM JPC 1997
Time-dependent Stokes Shift. Coumarin 343 in Water .… Experiment ----- Theory, no adjustable parameters Hsu, Song & RAM JPC B 1997
Free Energy Surfaces Protein Reorganization
Thermophilic Alcohol Dehydrogenase - Oxidation of Benzyl Alcohol AH~ 1017/s at low T Klinman et al. 1999, 2004 RAM 2008/2009
Fluctuations in Catalysis Rate & Spectral Diffusion Chloresterol oxidase oxidation of FAD Using data of Xie et al., Science 1998. Prakash & RAM PNAS 2007
Equation relating Correlation Functions: Electrostatic Fluctuations at Active Site Prakash & RAM PNAS 2007
Fluctuations and Dielectric Dispersion Prakash & RAM JPC B 2008
Fluctuations in Enzyme Catalysis & Dielectric Dispersion Lipase catalyzed ester hydrolysis Prakash & RAM PNAS 2007
Fluctuations for galactosidase Prakash & RAM 2008
Enzymes - Summary • When is the kinetic isotope effect H/D T- independent? • What does the breakpoint and pre-exponential factors of rate constants for a thermophilic enzyme tell us about flexibility? • When do different single molecule time-correlation functions agree for the same enzyme and why? • When does one expect “normal” Arrhenius preexponential factors A for H transfer? • Does one expect a small A for proton-coupled electron transfer?
An On-Water Cycloaddition Reaction Sharpless et al. 2005
Reaction Time Data Sharpless and co-workers, Angew. Chem. Int. Ed. 44, 3275 (2005)
Ice Surface http://www.lsbu.ac.uk/water/ice1h.html
TSTRate Constants Compared with Experimental Rates Interfacial H-Bond formation is the key to the on-water rate acceleration
Interaction of Theory, Computation & Experiment • Not Discussed Here • Mass-independent isotope effect in stratosphere • Combustion/atmospheric reactions and RRKM • Fluorescence blinking of semiconductor QDs • Vibrational adiabaticty, born of computatiom