Dynamical free energy

S. Miyamoto and P. A. Kollman. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 16 226-245, 1993. 

Miyamoto S and P A Kollman 1993a. Absolute and Relative Binding Tree Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Using Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16 226-245. 

S Hirono, PA Kollman. Calculation of the relative binding free energy of 2 -GMP and 2 -AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol 212 197-209, 1990. 

Beutler, T. C., Van Gunsteren, W. F. Molecular dynamics free energy calculation in four dimensions. J. Chtm. Phys. 1994, 101, 1417-1422. 

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... 

Chipot, C. Millot, C. Maigret, B. Kollman, P. A., Molecular dynamics free energy perturbation calculations. Influence of nonbonded parameters on the free energy of hydration of charged and neutral species, J. Phys. Chem. 1994, 98,11362-11372... 

Nina, M. Beglov, D. Roux, B., Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations, J. Phys. Chem. B 1997, 101, 5239-5248... 

These examples show that for difficult cases, and especially when a prediction is being made, a large number of simulations may be necessary. Today, the continuing increase in computer power has made such multiple simulations possible in a reasonable time frame. Several other recent studies illustrate the scope of molecular dynamics free energy for molecular recognition problems they include studies of nucleic acids [13], proteins [14-16], and methodological studies of convergence and precision [17, 18]. Several recent reviews provide additional examples [19, 20]. 

Molecular Dynamics Free Energy Yields Structures and Free Energy Components... 

Rozanska, X. Chipot, C., Modeling ion-ion interaction in proteins a molecular dynamics free energy calculation of the guanidinium-acetate association, J. Chem. Phys. 2000, 112, 9691-9694. 

C. Chipot, C. Millot, B. Maigret, and P. A. Kollman, Molecular dynamics free energy... 

Dynamics Free Energy Calculation in Four Dimensions. 

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. ... 

Here a is the elastic stress which arises from the change in the (dynamic) free energy in the macroscopic flow, while o(V) and a(S) are the viscous stresses produced by the polymer-solvent friction and the solvent-solvent friction, respectively. In concentrated isotropic polymer solutions, the elastic stress overwhelms the viscous stresses, so the latter are often neglected. However, it should be noticed that the viscous stresses may become significant in more dilute solutions as well as in nematic solutions where the elastic stress diminishes. 

Here the dynamic free energy AF is calculated from the static free energy by replacing the equilibrium orientational distribution function by the time-dependent distribution function. The calculation of 8(AF) for a rodlike polymer solution goes through the following three steps. 

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

Hirono, S. and Kollman, P.A. (1991) Relative binding free energy calculations of inhibitors to two mutants (Glu46 — Ala/Gin) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches, Prot. Eng. 4, 233-243. 

Knight, J.L., Brooks, C.L., III A-Dynamics free energy simulation methods. J. Comput. Chem. 2009, 30,1692-700. 

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

S. J. Hughes, J. A. Tanner, A. D. Hindley, A. D. Miller and I. R. Gould, Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment, BMC Structural Biology, 2003, 3, 5. 

Donnini, S., Mark, A.E., Juffer, A.H., Vflla, A. Molecular dynamics free energy calculaHon in four dimensions, J. Comp. Chem. 2005,26(2), 115-22. 

Roux, B., Nina, M., Pomes, R., Smith, J.C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel a molecular dynamics free energy perturbation study, Biophys. J. 1996, 71(2), 670-81. 

Deng, Y., Roux, B. Hydration of amino add side chains Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules, J. Chem. Phys. 2004,108,16567-76. 

C. Chipot, C. Millot, B. Maigret, and P. A. Kollman, y. Chem. Phys., 101, 7953 (1994). Molecular Dynamics Free Energy Simulations Influence of the Truncation of Long Range Non-bonded Electrostatic Interactions on Free Energy Calculations of Polar Molecules. 

P. L. Cummins, K. Ramnarayan, U. C. Singh, andj. E. Gready,/. Am. Ghem. Soc., 113,8247 (1991). Molecular Dynamics Free Energy Perturbation Study on the Relative Affinities of Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase. 

---