QM/MM calculations with deMon2k

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Dennis R SalahubAurélien de la Lande

Abstract

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.

References

Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Jul 21, 2004·The Journal of Chemical Physics·Andreas M KösterJ Ulises Reveles
Aug 12, 2004·The Journal of Chemical Physics·Andreas M KösterJorge M del Campo
Sep 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Henrik MouritsenReto Weiler
Mar 3, 2005·The Journal of Chemical Physics·Gino A DiLabioErin R Johnson
Jan 26, 2006·Journal of Computational Chemistry·Gerald GeudtnerPatrizia Calaminici
Feb 16, 2006·Journal of Computational Chemistry·Håkan W HugossonUrsula Rothlisberger
Feb 24, 2006·The Journal of Physical Chemistry. B·Guillaume Lamoureux, Benoît Roux
Apr 22, 2006·Journal of Computational Chemistry·Roberto Flores-MorenoAndreas M Köster
Feb 9, 2007·The Journal of Chemical Physics·Patrizia CalaminiciBernardo Zuniga-Gutierrez
Mar 6, 2007·Journal of Computational Chemistry·H Lee WoodcockBernard R Brooks
Oct 28, 2008·The Journal of Physical Chemistry. B·Demian RiccardiQiang Cui
Mar 1, 2007·Journal of Chemical Theory and Computation·Hao HuWeitao Yang
Jan 29, 2009·Angewandte Chemie·Hans Martin Senn, Walter Thiel
Mar 26, 2009·The Journal of Chemical Physics·Andreas M KösterBernardo Zuniga-Gutierrez
Sep 15, 2009·Structure·Mee Whi KimIlya Bezprozvanny
Sep 17, 2009·Journal of the American Chemical Society·Thomas LangenbacherTilman Kottke
Aug 27, 2010·Journal of Computational Chemistry·Oscar BertranJuan Torras
Oct 21, 2011·The Journal of Chemical Physics·Róbert Izsák, Frank Neese
Dec 16, 2011·Inorganic Chemistry·Johan Mähler, Ingmar Persson
Apr 13, 2012·The Journal of Physical Chemistry. B·Benoît Roux
Aug 4, 2012·Physical Chemistry Chemical Physics : PCCP·Harald Oberhofer, Jochen Blumberger
Jan 10, 2013·The Journal of Chemical Physics·Arindam BankuraMichael L Klein
Feb 23, 2013·The Journal of Biological Chemistry·Till BiskupErik Schleicher
Jul 19, 2013·The Journal of Chemical Physics·A Alvarez-Ibarra, A M Köster
Nov 22, 2013·Chemistry : a European Journal·Conchín MeliáAurélien de la Lande
Jan 25, 2014·Journal of Chemical Theory and Computation·Pedro E M LopesAlexander D Mackerell
Aug 27, 2014·Journal of the American Chemical Society·Fabien CailliezAurélien de la Lande
Oct 3, 2014·The Journal of Chemical Physics·Daniel Mejía-Rodríguez, Andreas M Köster
Jan 13, 2015·The Journal of Physical Chemistry. B·Hui LiSergei Yu Noskov
Sep 10, 2013·Journal of Chemical Theory and Computation·Bogdan LevSergei Yu Noskov
Oct 9, 2012·Journal of Chemical Theory and Computation·Christopher N Rowley, Benoıt Roux
Feb 14, 2012·Journal of Chemical Theory and Computation·Jan ŘezáčAurélien de la Lande
Nov 13, 2012·Journal of Chemical Theory and Computation·Aurelio Alvarez-IbarraDennis R Salahub
Feb 10, 2009·Journal of Chemical Theory and Computation·Ulla PentikäinenAdrian J Mulholland

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Citations

Feb 4, 2016·Journal of Computational Chemistry·Jan Řezáč
Jul 25, 2017·Journal of Chemical Theory and Computation·Xiaojing WuAurélien de la Lande
Mar 4, 2017·Journal of Molecular Modeling·Aurélien de la LandeAndreas Köster
May 10, 2019·The Journal of Chemical Physics·Daniel Mejía-Rodríguez, Aurélien de la Lande
May 1, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Aurélien de la LandeAndreas M Köster
Feb 8, 2019·Journal of Chemical Theory and Computation·Kiyoshi YagiYuji Sugita

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Methods Mentioned

BETA
Nuclear
Density-Fitting
X-ray

Software Mentioned

CHARMM
In
CINVESTAV
deMon2k Density Functional
CUBY
WIRES
PUPIL
Chem
AMBER
ChemShell

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