Acidity constants from vertical energy gaps: density functional theory based molecular dynamics implementation

Physical Chemistry Chemical Physics : PCCP
Marialore Sulpizi, Michiel Sprik

Abstract

The question of how to compute acidity constants (pKa) treating solvent and solute at the same level of theory remains of some interest, for example in the case of high or low pH conditions. We have developed a density functional theory based molecular dynamics implementation of such a method. The method is based on a half reaction scheme computing free energies of dissociation from the vertical energy gaps for insertion or removal of protons. Finite system size effects are important, but largely cancel when half reactions are combined to full reactions. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pKa values (20 units). We find that the response of the aqueous solvent to vertical protonation/deprotonation is almost always asymmetric and correlated with the strength of the hydrogen bonding of the deprotonated base. We interpret these observations in analogy with the picture of solvent response to electronic ionization.

References

Sep 15, 1988·Physical Review A: General Physics·A D Becke
Jul 15, 1996·Physical Review. B, Condensed Matter·S GoedeckerJ Hutter
Nov 25, 1985·Physical Review Letters·R Car, M Parrinello
Mar 17, 2001·Science·P L GeisslerM Parrinello
Apr 20, 2001·Accounts of Chemical Research·S Hammes-Schiffer
Feb 19, 2002·Chemical Reviews·Christopher J. Cramer, Donald G. Truhlar
May 30, 2002·Journal of the American Chemical Society·Matthew D LiptakGeorge C Shields
Jun 6, 2002·Journal of the American Chemical Society·J E DaviesM Sprik
Jun 28, 2002·Nature·Mark E TuckermanMichele Parrinello
Nov 7, 2002·Journal of the American Chemical Society·Ivaylo Ivanov, Michael L Klein
Feb 8, 2003·Annual Review of Biophysics and Biomolecular Structure·Arieh Warshel
Apr 1, 2004·Journal of the American Chemical Society·Thomas SimonsonDavid A Case
Jul 23, 2004·The Journal of Chemical Physics·Wei YangMartin Karplus
Jan 11, 2005·The Journal of Chemical Physics·Joost VandeVondeleMichele Parrinello
Apr 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·D AsthagiriJ D Kress
Apr 20, 2005·Current Opinion in Structural Biology·John Mongan, David A Case
Jul 13, 2005·The Journal of Chemical Physics·Yoshitaka TateyamaIvano Tavernelli
Aug 3, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Patricia Hunt, Michiel Sprik
Sep 17, 2005·The Journal of Chemical Physics·Hideaki FujitaniVijay S Pande
Oct 20, 2005·Journal of Computational Chemistry·Frank Eckert, Andreas Klamt
Mar 24, 2006·The Journal of Physical Chemistry. B·Ivaylo IvanovMichael L Klein
Mar 29, 2007·The Journal of Physical Chemistry. B·Marialore SulpiziMichiel Sprik
Apr 14, 2007·The Journal of Physical Chemistry. B·Jessica M J SwansonGregory A Voth
Aug 19, 2007·The Journal of Physical Chemistry. B·Haiting LuChang-Guo Zhan
Aug 28, 2007·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Christian SimonMichael L Klein

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Citations

Mar 2, 2011·Physical Chemistry Chemical Physics : PCCP·Mathieu SalannePaul A Madden
Jul 19, 2012·Physical Chemistry Chemical Physics : PCCP·Jun Cheng, Michiel Sprik
Apr 24, 2013·Physical Chemistry Chemical Physics : PCCP·Hirofumi Sato
Jul 5, 2011·The Journal of Chemical Physics·Francesca CostanzoMichiel Sprik
Nov 10, 2009·The Journal of Chemical Physics·O Anatole von Lilienfeld
Feb 12, 2014·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Ali A HassanaliMichele Parrinello
Jun 24, 2010·The Journal of Chemical Physics·Jun ChengMichiel Sprik
Feb 2, 2016·The Journal of Physical Chemistry. B·Andrew C MengMichiel Sprik
Nov 10, 2015·The Journal of Physical Chemistry. B·Anil Kumar Tummanapelli, Sukumaran Vasudevan
Sep 4, 2015·The Journal of Physical Chemistry. B·Anil Kumar Tummanapelli, Sukumaran Vasudevan
Jun 17, 2016·Journal of Chemical Theory and Computation·Emanuele RossiniErnst-Walter Knapp
Mar 3, 2017·Journal of Chemical Theory and Computation·Assil Bouzid, Alfredo Pasquarello
Aug 30, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Thierry De MeyerVeronique Van Speybroeck
Apr 10, 2009·Journal of the American Chemical Society·Christopher AdriaanseMichiel Sprik
May 18, 2016·Physical Chemistry Chemical Physics : PCCP·Xiandong LiuRucheng Wang
Aug 6, 2014·Physical Chemistry Chemical Physics : PCCP·Murat Kiliç, Bernd Ensing
Jul 6, 2017·Physical Chemistry Chemical Physics : PCCP·Xiandong LiuRucheng Wang
Jun 22, 2017·Journal of Chemical Theory and Computation·Johannes FrenzelDominik Marx
Oct 7, 2016·Physical Chemistry Chemical Physics : PCCP·Xiandong LiuRucheng Wang
Jun 4, 2014·Journal of Computational Chemistry·Hao Hu, Lin Shen
Apr 18, 2019·Physical Chemistry Chemical Physics : PCCP·Vaishali ArunachalamSukumaran Vasudevan
Mar 8, 2012·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Kevin Leung, Louise J Criscenti
Nov 8, 2014·Physical Chemistry Chemical Physics : PCCP·Xiandong LiuRucheng Wang
Jan 22, 2020·Physical Chemistry Chemical Physics : PCCP·Guido Falk von Rudorff, O Anatole von Lilienfeld
Mar 8, 2012·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Marie-Pierre GaigeotMarialore Sulpizi
Jun 17, 2018·The Journal of Chemical Physics·Marialore Sulpizi, Johannes Lützenkirchen
May 1, 2020·Physical Chemistry Chemical Physics : PCCP·J BlumbergerR Vuilleumier
Jul 8, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Kevin Leung, Louise J Criscenti
Mar 15, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Marialore Sulpizi, Michiel Sprik
Mar 9, 2010·Journal of Chemical Theory and Computation·Jun Cheng, Michiel Sprik
Jul 29, 2021·The Journal of Physical Chemistry. B·Shuji OgataTomoya Kishi
Oct 18, 2012·The Journal of Physical Chemistry Letters·Yu-Lin ChenDave J Barlow
Nov 5, 2014·Accounts of Chemical Research·Jun ChengMichiel Sprik
Sep 13, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Manuel Corral ValeroGrégory Lefèvre

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