Bases free energy

Kobrak, M. N., Systematic and statistical error in histogram-based free energy calculations, J. Comput. Chem. 2003, 24, 1437-1446... 

More recent measurements related to carbocation stabilities in strongly acidic media have involved rates of reaction rather than equilibria.52,54,72 75 Application of the X0 function to the correlation of reaction rates as well as equilibria mirrors the use of structure-based free energy relationships. Of interest is the access this gives to rate constants for (a) protonation of weakly basic alkenes and (b) acid-catalyzed ionization of alcohols to relatively unstable... 

Enzyme-Inhibitor Complexes Using a Preference-Based Free-Energy Surface. 

Based Free Energy Parameterization of Enzyme-Inhibitor Binding. Application to FDV-1-Protease Inhibitor Design. 

Woods, C.J., Essex, J.W., King, M.A. The development of replica-exchange-based free-energy methods. J. Phys. Chem. B 2003,107,13703-10. 

A. Wallqvist and D. G. Covell. Docking enzyme-inhibitor complexes using a preference-based free-energy surface. PROTEINS Structure, Function and Genetics, 25 403-419,... 

Wallqvist, A., Jernigan, R. L. Covell, D. G. (1995). A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-l-protease inhibitor design. Protein Science 4, 1881-1903. 

Similarly, a choice had to be made regarding the topics covered in this volume. For example, molecular dynamics (MD) based free-energy changes in solution calculations are not treated, because these are not yet a day-to-day practice in actual ligand design due to the very high computational demands for the long MD simulations required. 

A. Wallqvist, R. L. Jernigan, and D. G. Covell, Protein Sei., 4, 1881 (1995). A Preference-Based Free-Energy Parameterization of Enzyme Inhibitor Binding. Applications to HIV-1 Protease Inhibitor Design. 

In contrast to MD, relatively few MC based free energy simulation packages are in wide use. By far the most widely used MC-based package is BOSS. ... 

Figure 4.5 Specific acid-base free energy distributions of studied HA powder as observed for selected wetting probes. Square acetone diamond acetonitrile triangle ethanol...

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