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Free energy perturbation
About: Free energy perturbation is a research topic. Over the lifetime, 1119 publications have been published within this topic receiving 64637 citations.
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TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.
Abstract: The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, a...
12,024 citations
TL;DR: In this article, a perturbation theory is developed, by which the thermodynamic properties of one system may be related to those of a slightly different system and to the difference in the intermolecular potentials of the two systems.
Abstract: A theoretical study is made of the equations of state of argon and nitrogen, at high temperatures and densities. The intermolecular potential used is of the Lennard‐Jones form, with an adjustable rigid sphere cutoff. A perturbation theory is developed, by which the thermodynamic properties of one system may be related to those of a slightly different system and to the difference in the intermolecular potentials of the two systems. In this article, the unperturbed system is a rigid sphere fluid, and the Lennard‐Jones potential is the perturbation. The results are in fair agreement with experiment, and also lead to an experimental test of the theoretical rigid sphere equation of state.
2,683 citations
TL;DR: In this article, the authors review the applications of free energy calculations employing molecular dynamics or Monte Carlo methods to a variety of chemical and biochemical phenomena, including molecular solvation, molecular association, macromolecular stability, and enzyme catalysis.
Abstract: The author will review the applications of free energy calculations employing molecular dynamics or Monte Carlo methods to a variety of chemical and biochemical phenomena. The focus is on the applications of such calculations to molecular solvation, molecular association, macromolecular stability, and enzyme catalysis. The molecules discussed range from monovalent ions and small molecules to proteins and nucleic acids.
1,960 citations
1,551 citations
TL;DR: This work uses explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules and shows that predictions can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.
Abstract: The accurate prediction of protein−ligand binding free energies is a primary objective in computer-aided drug design. The solvation free energy of a small molecule provides a surrogate to the desolvation of the ligand in the thermodynamic process of protein−ligand binding. Here, we use explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules. We also compare the performance of absolute solvation free energies obtained using the OPLS_2005 force field with two other commonly used small molecule force fields—general AMBER force field (GAFF) with AM1-BCC charges and CHARMm-MSI with CHelpG charges. Using the OPLS_2005 force field, we obtain high correlation with experimental solvation free energies (R2 = 0.94) and low average unsigned errors for a majority of the functional groups compared to AM1-BCC/GAFF or CHelpG/CHARMm-MSI. However, ...
1,229 citations