TY - JOUR
T1 - QM/MM calculations with deMon2k
AU - Salahub, Dennis R.
AU - Noskov, Sergei Yu
AU - Lev, Bogdan
AU - Zhang, Rui
AU - Ngo, Van
AU - Goursot, Annick
AU - Calaminici, Patrizia
AU - Köster, Andreas M.
AU - Alvarez-Ibarra, Aurelio
AU - Mejía-Rodríguez, Daniel
AU - Řezáč, Jan
AU - Cailliez, Fabien
AU - De La Lande, Aurélien
N1 - Publisher Copyright:
© 2015 by the authors; licensee MDPI.
PY - 2015/3/1
Y1 - 2015/3/1
N2 - 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.
AB - 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.
KW - Auxiliary DFT
KW - Biomolecular modeling
KW - Constrained DFT
KW - Density functional theory
KW - Double asymptotic expansion
KW - QM/MM
KW - Quantum Mechanical/Molecular Mechanical
KW - deMon2k software
UR - http://www.scopus.com/inward/record.url?scp=84929600896&partnerID=8YFLogxK
U2 - 10.3390/molecules20034780
DO - 10.3390/molecules20034780
M3 - Review article
C2 - 25786164
AN - SCOPUS:84929600896
SN - 1420-3049
VL - 20
SP - 4780
EP - 4812
JO - Molecules
JF - Molecules
IS - 3
ER -