Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization

Journal of Chemical Theory and Computation
Esther HeidAlexander D MacKerell

Abstract

The derivation of atomic polarizabilities for polarizable force field development has been a long-standing problem. Atomic polarizabilities were often refined manually starting from tabulated values, rendering an automated assignment of parameters difficult and hampering reproducibility and transferability of the obtained values. To overcome this, we trained both a linear increment scheme and a multilayer perceptron neural network on a large number of high-quality quantum mechanical atomic polarizabilities and partial atomic charges, where only the type of each atom and its connectivity were used as input. The predicted atomic polarizabilities and charges had average errors of 0.023 Å3 and 0.019 e using the neural net and 0.063 Å3 and 0.069 e using the simple increment scheme. As the algorithm relies only on the connectivities of the atoms within a molecule, thus omitting dependencies on the three-dimensional conformation, the approach naturally assigns like charges and polarizabilities to symmetrical groups. Accordingly, a convenient utility is presented for generating the partial atomic charges and atomic polarizabilities for organic molecules as needed in polarizable force field development.

References

Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·William L Jorgensen, Julian Tirado-Rives
Jul 19, 2005·Drug Discovery Today·Robin A E CarrDavid C Rees
Jan 21, 2006·The Journal of Chemical Physics·Alston J Misquitta, Anthony J Stone
Jun 7, 2011·Physical Chemistry Chemical Physics : PCCP·Christian SchröderOthmar Steinhauser
Apr 17, 2012·Theoretical Chemistry Accounts·Johnny C WuPengyu Ren
Nov 14, 2012·Journal of Chemical Information and Modeling·K VanommeslaegheA D MacKerell
Nov 14, 2012·Journal of Chemical Information and Modeling·K Vanommeslaeghe, A D MacKerell
May 9, 2013·Journal of Computational Chemistry·Brajesh K Rai, Gregory A Bakken
Nov 14, 2013·Journal of Chemical Theory and Computation·Lei Huang, Benoît Roux
Jan 30, 2014·Journal of Medicinal Chemistry·Richard D TaylorAlastair D G Lawson
Jun 15, 2014·Journal of Computer-aided Molecular Design·David L Mobley, J Peter Guthrie
Aug 21, 2014·Biophysical Journal·Jing Huang, Alexander D MacKerell
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Jan 13, 2015·The Journal of Physical Chemistry Letters·Alexey Savelyev, Alexander D MacKerell
Feb 5, 2015·The Journal of Physical Chemistry. a·Maxim V IvanovQadir K Timerghazin
May 10, 2011·Journal of Chemical Theory and Computation·Pär SöderhjelmUlf Ryde
Nov 1, 2005·Journal of Chemical Theory and Computation·Anthony J Stone
May 11, 2017·Journal of Chemical Theory and Computation·Robert M ParrishC David Sherrill
Feb 6, 2018·Physical Chemistry Chemical Physics : PCCP·Esther Heid, Christian Schröder
Feb 21, 2018·Journal of Chemical Information and Modeling·Patrick BleizifferSereina Riniker
Mar 16, 2018·Physical Chemistry Chemical Physics : PCCP·Esther HeidChristian Schröder
Apr 13, 2018·Physical Chemistry Chemical Physics : PCCP·Esther HeidChristian Schröder
Apr 26, 2018·Journal of Chemical Theory and Computation·Eliot BoulangerBenoît Roux
May 29, 2018·Physical Chemistry Chemical Physics : PCCP·Esther HeidChristian Schröder
Aug 3, 2018·The Journal of Chemical Physics·Esther HeidChristian Schröder

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Citations

Jan 8, 2021·Physical Chemistry Chemical Physics : PCCP·Nadine WeißStefan Spange
May 30, 2019·Chemical Reviews·Dmitry BedrovChristian Schröder
Sep 17, 2021·Chemical Reviews·Teo LombardoAlejandro A Franco
Oct 6, 2021·Journal of Chemical Theory and Computation·Chetan R RupakhetiBenoît Roux
Dec 8, 2021·Journal of Computational Chemistry·Abhishek A KognoleWonpil Im
Jan 18, 2022·The Journal of Physical Chemistry. B·Barbara KirchnerOldamur Hollóczki

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