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Theoretical and Computational Studies in Science: Reaction Rates and On-Water Catalysis

Explore the interplay of theory and computations in scientific research, focusing on examples from theoretical and experimental studies on reaction rates, on-water catalysis, isotope fractionation, and single-molecule fluctuations. This workshop showcases the work of Rudolph Marcus and others at the California Institute of Technology. Discover electron transfer mechanisms, free energy reactions, protein reorganization, fluctuation in catalysis, and more.

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Theoretical and Computational Studies in Science: Reaction Rates and On-Water Catalysis

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  1. 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

  2. ELECTRON TRANSFER MECHANISM Free Energy Reaction Coordinate

  3. Rate Constant for Electron Transfer

  4. Time-dependent Stokes Shift Free Energy Reaction Coordinate

  5. Time-dependent Stokes Shift Calculated from Solvent Dielectric dispersion Hsu, Song &RAM JPC 1997

  6. Time-dependent Stokes Shift. Coumarin 343 in Water .… Experiment ----- Theory, no adjustable parameters Hsu, Song & RAM JPC B 1997

  7. Free Energy Surfaces Protein Reorganization

  8. Thermophilic Alcohol Dehydrogenase - Oxidation of Benzyl Alcohol AH~ 1017/s at low T Klinman et al. 1999, 2004 RAM 2008/2009

  9. Fluctuations in Catalysis Rate & Spectral Diffusion Chloresterol oxidase oxidation of FAD Using data of Xie et al., Science 1998. Prakash & RAM PNAS 2007

  10. Equation relating Correlation Functions: Electrostatic Fluctuations at Active Site Prakash & RAM PNAS 2007

  11. Fluctuations and Dielectric Dispersion Prakash & RAM JPC B 2008

  12. Fluctuations in Enzyme Catalysis & Dielectric Dispersion Lipase catalyzed ester hydrolysis Prakash & RAM PNAS 2007

  13. Fluctuations for galactosidase Prakash & RAM 2008

  14. 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?

  15. An On-Water Cycloaddition Reaction Sharpless et al. 2005 

  16. Reaction Time Data Sharpless and co-workers, Angew. Chem. Int. Ed. 44, 3275 (2005)

  17. Ice Surface http://www.lsbu.ac.uk/water/ice1h.html

  18. TSTRate Constants Compared with Experimental Rates Interfacial H-Bond formation is the key to the on-water rate acceleration

  19. 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

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