Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria.

Journal of Chemical Theory and Computation
William L Jorgensen, Laura L Thomas

Abstract

An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 - 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes.

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Citations

May 29, 2010·Journal of Computer-aided Molecular Design·Julien Michel, Jonathan W Essex
Sep 25, 2012·Journal of Chemical Information and Modeling·Lin LiTingjun Hou
Aug 23, 2011·Journal of the American Chemical Society·William L JorgensenKaren S Anderson
Oct 25, 2013·Journal of the American Chemical Society·Won-Gil LeeWilliam L Jorgensen
Sep 26, 2009·Journal of the American Chemical Society·Julien MichelWilliam L Jorgensen
Nov 16, 2011·Journal of Medicinal Chemistry·Mariela BolliniWilliam L Jorgensen
Apr 17, 2012·Journal of Medicinal Chemistry·Cheryl S LeungWilliam L Jorgensen
Sep 8, 2009·Nature Medicine·Charlotte Schubert
Apr 14, 2011·Physical Chemistry Chemical Physics : PCCP·Nuno M GarridoIoannis G Economou
Aug 21, 2012·PloS One·Muhammad Imtiaz ShafiqRalf Schmid
Nov 18, 2011·The Journal of Chemical Physics·Ryan P Steele, John C Tully
Jan 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shuang ZhouIgor S Aranson
Mar 12, 2013·Annual Review of Physical Chemistry·Riccardo Baron, J Andrew McCammon
Jan 26, 2016·Journal of Medicinal Chemistry·Marco De VivoAndrea Cavalli
Feb 14, 2015·The Journal of Physical Chemistry. B·Žofie SovováPetr Jurečka
Feb 24, 2016·The Journal of Physical Chemistry. B·Xin Cindy YanWilliam L Jorgensen
Aug 17, 2010·Current Opinion in Structural Biology·Robert J Woods, Matthew B Tessier
May 8, 2014·Journal of Chemical Theory and Computation·Daniel J ColeWilliam L Jorgensen
Jul 26, 2014·Journal of Chemical Theory and Computation·Jonah Z VilseckWilliam L Jorgensen
Feb 26, 2016·Journal of Medicinal Chemistry·John J Irwin, Brian K Shoichet
Nov 29, 2014·Wiley Interdisciplinary Reviews. Computational Molecular Science·Orlando Acevedo, Wiliiam L Jorgensen
Nov 19, 2015·International Journal of Molecular Sciences·Yunhui PengEmil Alexov
Nov 18, 2015·Journal of Chemical Theory and Computation·Leela S DoddaWilliam L Jorgensen
Jul 5, 2015·Journal of Computer-aided Molecular Design·Heloisa dos Santos Muniz, Alessandro S Nascimento
Sep 10, 2014·Biochimica Et Biophysica Acta·Daniel J ColeWilliam L Jorgensen
Nov 18, 2015·Journal of Chemical Theory and Computation·Mazen AhmadOlga V Kalinina
Nov 18, 2015·Journal of Chemical Theory and Computation·Mazen AhmadOlga V Kalinina
Apr 19, 2016·Journal of Chemical Information and Modeling·Xiao LiuJohn Z H Zhang
May 7, 2016·Journal of Chemical Theory and Computation·Song-Ho Chong, Sihyun Ham
Aug 10, 2016·Journal of Computer-aided Molecular Design·Stefano BosisioJulien Michel
Nov 30, 2011·Journal of Chemical Theory and Computation·Yilin MengAdrian E Roitberg
Jan 19, 2013·Journal of Chemical Theory and Computation·William L Jorgensen, Patric Schyman

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