Free energy perturbation simulations

Ding YB, Bernardo DN, Kroghjespersen K, Levy RM (1995) Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem 99(29) 11575—11583... 

Riccardi D, Schaefer P, Cui Q (2005) pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations A Quantitative Test of QM/MM Protocols. J Phys Chem B 109 17715-17733. 

K. M. Merz, and P. A. Kollman, Free energy perturbation simulations of the inhibition of... 

Molecular dynamics free-energy perturbation simulations utilizing the empirical valence bond model have been used to study the catalytic action of -cyclodextrin in ester hydrolysis. Reaction routes for nucleophilic attack on m-f-butylphenyl acetate (225) by the secondary alkoxide ions 0(2) and 0(3) of cyclodextrin giving the R and S stereoisomers of ester tetrahedral intermediate were examined. Only the reaction path leading to the S isomer at 0(2) shows an activation barrier that is lower (by about 3kcal mol ) than the barrier for the corresponding reference reaction in water. The calculated rate acceleration was in excellent agreement with experimental data. ... 

Aqvist, J. (1990), Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations,... 

Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials. 

J. Aqvist, Ion-water interaction potentials derived from free energy perturbation simulations, J. Phys. Chem., 94 (1990) 8021-8024. 

Riccardi, D., Schaefer, R, Cui, Q. pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations A quantitative test of QM/MM protocols. J. Phys. Chem. A 2005, 109,17715-33. 

A molecular dynamics free-energy perturbation simulation (121) comparing the phosphonamidate and phosphonate in solution and in the enzyme... 

Merz K M Jr and P A Kollman 1989 Free Energy Perturbation Simulations of the Inhibition of Thermolysin Prediction of the Free Energy of Bmdmg of a New Inhibitor. Journal of the American Chemical Society lll 5649-5658... 

Validation of the OPLS2.0 force field includes comparison to quantum mechanical energy profiles and experimental solvation free energies. For the latter, we performed explicit solvent molecular dynamics free energy perturbation simulations on a set of 239 diverse small molecules [80]. Compared with other popular force fields... 

P. Auffinger and G. Wipff,/. Chim. Phys., 88,2525 (1991). Quantitative Studies on Molecular Recognition Free Energy Perturbation Simulations on M c222 Cryptates in Water and in Methanol. 

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