Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model

Journal of Computational Chemistry
Hyun Woo Kim, Young Min Rhee

Abstract

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of ...Continue Reading

References

Sep 15, 1988·Physical Review A: General Physics·A D Becke
Aug 5, 1997·Chemical Reviews·Jennifer C. Ma, Dennis A. Dougherty
Oct 24, 2002·Journal of Computational Chemistry·Pengyu Ren, Jay W Ponder
Nov 25, 2003·Advances in Protein Chemistry·Jay W Ponder, David A Case
Nov 25, 2003·Journal of Computational Chemistry·Sandeep Patel, Charles L Brooks
Aug 31, 2004·The Journal of Chemical Physics·Laura GagliardiGunnar Karlström
Jan 21, 2006·The Journal of Chemical Physics·Alston J Misquitta, Anthony J Stone
Jul 21, 2006·The Journal of Physical Chemistry. B·Francesca IngrossoJacopo Tomasi
Aug 12, 2006·Physical Chemistry Chemical Physics : PCCP·Yihan ShaoMartin Head-Gordon
Feb 15, 2007·Journal of Computational Chemistry·Dennis ElkingRobert J Woods
Jul 28, 2007·The Journal of Physical Chemistry. a·Rustam Z KhaliullinMartin Head-Gordon
Feb 15, 2008·The Journal of Physical Chemistry. B·Kristina E FurseSteven A Corcelli
Apr 25, 2008·Journal of Computational Chemistry·Asbjørn Holt, Gunnar Karlström
Jun 6, 2008·The Journal of Chemical Physics·Marco Masia
Sep 5, 2008·Journal of the American Chemical Society·Kristina E Furse, Steven A Corcelli
Sep 20, 2008·Journal of Chemical Theory and Computation·Victor M AnisimovAlexander D Mackerell
Oct 30, 2008·Journal of Chemical Theory and Computation·Wangshen XieJiali Gao
Dec 19, 2008·Journal of Computational Chemistry·Pedro E M LopesAlexander D Mackerell
Feb 9, 2010·The Journal of Physical Chemistry. B·Jay W PonderTeresa Head-Gordon
Jun 26, 2010·Theoretical Chemistry Accounts·Pedro E M LopesAlexander D Mackerell
Oct 7, 2010·Journal of Computational Chemistry·Yue ShiPengyu Ren
Dec 21, 2010·The Journal of Physical Chemistry. B·Christopher M BakerAlexander D MacKerell
Dec 24, 2010·Journal of the American Chemical Society·Kristina E Furse, Steven A Corcelli
Dec 29, 2010·The Journal of Chemical Physics·Jonàs SalaMarco Masia
Aug 19, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Piotr CieplakJunmei Wang
Oct 25, 2011·Journal of Chemical Theory and Computation·Pengyu RenJay W Ponder
Jan 28, 2012·The Journal of Chemical Physics·Felix O Kannemann, Axel D Becke
Sep 9, 2008·Journal of Chemical Theory and Computation·Jean-François TruchonChristopher I Bayly
Jul 12, 2011·Journal of Chemical Theory and Computation·Ana Rute NevesMaria João Ramos
May 10, 2011·Journal of Chemical Theory and Computation·Pär SöderhjelmUlf Ryde
Aug 11, 2009·Journal of Chemical Theory and Computation·Kristina E Furse, Steven A Corcelli
Nov 1, 2005·Journal of Chemical Theory and Computation·Anthony J Stone
Nov 1, 2007·Journal of Chemical Theory and Computation·Ignacio SoterasF Javier Luque
Nov 1, 2007·Journal of Chemical Theory and Computation·François DehezChristophe Chipot
Jan 1, 2005·Journal of Chemical Theory and Computation·Victor M AnisimovAlexander D MacKerell
Apr 1, 1986·Journal of Computational Chemistry·Scott J WeinerDavid A Case

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Citations

Aug 9, 2013·The Journal of Physical Chemistry. B·Kay AnsorgBernd Engels
May 28, 2019·Journal of Chemical Information and Modeling·Seung Soo Kim, Young Min Rhee
Nov 20, 2015·Journal of Chemical Theory and Computation·Jae Woo Park, Young Min Rhee

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