Communication: Accurate hydration free energies at a wide range of temperatures from 3D-RISM

The Journal of Chemical Physics
Maksim MisinDavid S Palmer

Abstract

We present a new model for computing hydration free energies by 3D reference interaction site model (3D-RISM) that uses an appropriate initial state of the system (as suggested by Sergiievskyi et al.). The new adjustment to 3D-RISM theory significantly improves hydration free energy predictions for various classes of organic molecules at both ambient and non-ambient temperatures. An extensive benchmarking against experimental data shows that the accuracy of the model is comparable to (much more computationally expensive) molecular dynamics simulations. The calculations can be readily performed with a standard 3D-RISM algorithm. In our work, we used an open source package AmberTools; a script to automate the whole procedure is available on the web (https://github.com/MTS-Strathclyde/ISc).

References

Oct 24, 2002·Journal of Computational Chemistry·Araz JakalianChristopher I Bayly
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jun 9, 2004·Journal of Computational Chemistry·Gennady N Chuev, Maxim V Fedorov
Oct 8, 2005·Journal of Computational Chemistry·Jay L BanksRonald M Levy
Jan 19, 2006·Journal of Computational Chemistry·Norio Yoshida, Fumio Hirata
Mar 17, 2006·The Journal of Physical Chemistry. B·Adam C ChamberlinDonald G Truhlar
Feb 23, 2008·Molecular Pharmaceutics·David S PalmerJohn B O Mitchell
Mar 11, 2008·Chemistry Central Journal·Noel M O'BoyleGeoffrey R Hutchison
Mar 18, 2008·The Journal of Physical Chemistry. B·Thomas KlossStefan M Kast
Dec 24, 2008·The Journal of Chemical Physics·Stefan M Kast, Thomas Kloss
Feb 13, 2010·Journal of Chemical Theory and Computation·David L MobleyKen A Dill
May 5, 2010·Journal of Chemical Theory and Computation·Tyler LuchkoAndriy Kovalenko
Mar 17, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·David S PalmerMaxim V Fedorov
Apr 15, 2011·The Journal of Physical Chemistry. B·Andrey I FrolovMaxim V Fedorov
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Oct 5, 2012·Methods in Molecular Biology·Michael R Shirts, David L Mobley
Feb 25, 2014·Biophysical Journal·George M GiambaşuDavid A Case
Mar 19, 2014·Journal of Chemical Theory and Computation·Jean-François TruchonPaul Labute
Mar 26, 2014·Journal of Molecular Modeling·Jochen HeilStefan M Kast
Apr 29, 2014·Journal of Computational Chemistry·Yutaka MaruyamaFumio Hirata
Nov 12, 2013·Journal of Chemical Theory and Computation·Franziska HoffgaardStefan M Kast
Jul 8, 2014·Journal of Chemical Theory and Computation·Niels Hansen, Wilfred F van Gunsteren
Jun 12, 2012·Journal of Chemical Theory and Computation·Volodymyr P Sergiievskyi, Maxim V Fedorov
Sep 11, 2012·Journal of Chemical Theory and Computation·David S PalmerMaxim V Fedorov
Sep 8, 2009·Journal of Chemical Theory and Computation·Nuno M GarridoIoannis G Economou

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Citations

Jan 13, 2016·The Journal of Physical Chemistry. B·Maksim MisinDavid S Palmer
Nov 17, 2015·The Journal of Chemical Physics·Volodymyr SergiievskyiDaniel Borgis
May 24, 2016·Drug Discovery Today·Michael S Bodnarchuk
Jun 9, 2016·The Journal of Physical Chemistry. B·Maksim MisinMaxim V Fedorov
Sep 3, 2016·Journal of Computer-aided Molecular Design·Tyler LuchkoAndriy Kovalenko
Apr 4, 2017·Journal of Chemical Information and Modeling·Sereina Riniker
Jul 12, 2017·The Journal of Physical Chemistry. B·Shijie ShengJianzhong Wu
Jul 3, 2018·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Sergey SosninMaxim V Fedorov
Nov 19, 2015·Journal of Computational Chemistry·Hiraku Oshima, Masahiro Kinoshita
Nov 24, 2016·The Journal of Chemical Physics·Maksim MisinDavid S Palmer
Jul 10, 2017·The Journal of Chemical Physics·Takatoshi Fujita, Takeshi Yamamoto
Apr 20, 2019·Physical Review. E·Tsogbayar Tsednee, Tyler Luchko
Mar 15, 2020·Physical Review. E·Nathaniel Rupprecht, Dervis Can Vural
Jul 2, 2016·Journal of Physics. Condensed Matter : an Institute of Physics Journal·J JohnsonT Luchko
Jul 2, 2016·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Tomohiko HayashiMasahiro Kinoshita
Oct 23, 2019·Journal of Computer-aided Molecular Design·Dipankar Roy, Andriy Kovalenko
Aug 24, 2016·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Alexander E KobrynAndriy Kovalenko
Mar 10, 2021·The Journal of Chemical Physics·Anton RobertMaximilien Levesque
May 15, 2021·Journal of Chemical Theory and Computation·Daniel J FowlesJohn B O Mitchell
Aug 14, 2019·Journal of Chemical Information and Modeling·Shoichi TanimotoHaruyuki Nakano
Mar 16, 2018·Journal of Chemical Information and Modeling·Samiul M Ansari, David S Palmer
Apr 21, 2020·Journal of Chemical Information and Modeling·Vigneshwari SubramanianAntonio Llinas
Sep 28, 2017·Chemical Reviews·Emiliano BriniKen A Dill
May 5, 2016·Journal of Chemical Information and Modeling·Daniel RobinsonWoody Sherman
Oct 19, 2017·Journal of Chemical Information and Modeling·Haiyang ZhangChunhua Yin
Apr 13, 2019·The Journal of Physical Chemistry. a·Ádám GanyeczJózsef Csontos
Nov 15, 2017·The Journal of Physical Chemistry. B·Alexander B KuhnLars V Schäfer

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