In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.
REFERENCES
1.
E.
Harder
, W.
Damm
, J.
Maple
, C.
Wu
, M.
Reboul
, J. Y.
Xiang
, L.
Wang
, D.
Lupyan
, M. K.
Dahlgren
, J. L.
Knight
, J. W.
Kaus
, D. S.
Cerutti
, G.
Krilov
, W. L.
Jorgensen
, R.
Abel
, and R. A.
Friesner
, J. Chem. Theory Comput.
12
, 281
(2016
).2.
S.
Belsare
, A.
Esser
, D.
Marx
, and T.
Head-Gordon
, Biophys. J.
112
, 497a
(2017
).3.
S.
Grimme
, J. Chem. Theory Comput.
10
, 4497
(2014
).4.
G.
Jindal
and A.
Warshel
, J. Phys. Chem. B
120
, 9913
(2016
).5.
M. W.
van der Kamp
and A. J.
Mulholland
, Biochemistry
52
, 2708
(2013
).6.
E.
Boulanger
and W.
Thiel
, J. Chem. Theory Comput.
10
, 1795
(2014
).7.
J. C.
Richley
, J. N.
Harvey
, and M. N. R.
Ashfold
, J. Phys. Chem. C
116
, 18300
(2012
).8.
D.
Golze
, M.
Iannuzzi
, M.-T.
Nguyen
, D.
Passerone
, and J.
Hutter
, J. Chem. Theory Comput.
9
, 5086
(2013
).9.
D.
Golze
, J.
Hutter
, and M.
Iannuzzi
, Phys. Chem. Chem. Phys.
17
, 14307
(2015
).10.
O.
Andreussi
, I. G.
Prandi
, M.
Campetella
, G.
Prampolini
, and B.
Mennucci
, J. Chem. Theory Comput.
13
, 4636
(2017
).11.
A.
Klamt
and G.
Schüürmann
, J. Chem. Soc., Perkin Trans. 2
1993
, 799
.12.
S.
Miertuš
, E.
Scrocco
, and J.
Tomasi
, Chem. Phys.
55
, 117
(1981
).13.
A. V.
Marenich
, C. J.
Cramer
, and D. G.
Truhlar
, J. Phys. Chem. B
113
, 6378
(2009
).14.
A.
Klamt
, J. Phys. Chem.
99
, 2224
(1995
).15.
D.
Beglov
and B.
Roux
, J. Phys. Chem. B
101
, 7821
(1997
).16.
A.
Kovalenko
and F.
Hirata
, Chem. Phys. Lett.
290
, 237
(1998
).17.
P. H.
Fries
and G. N.
Patey
, J. Chem. Phys.
82
, 429
(1985
).18.
F.
Hirata
and P. J.
Rossky
, Chem. Phys. Lett.
83
, 329
(1981
).19.
A.
Kovalenko
and F.
Hirata
, J. Chem. Phys.
110
, 10095
(1999
).20.
J.
Heil
and S. M.
Kast
, J. Chem. Phys.
142
, 114107
(2015
).21.
A.
Kovalenko
and T. N.
Truong
, J. Chem. Phys.
113
, 7458
(2000
).22.
T.
Schlick
, Innovations in Biomolecular Modeling and Simulations
(Royal Society of Chemistry
, 2012
).23.
T. N.
Truong
and E. V.
Stefanovich
, Chem. Phys. Lett.
256
, 348
(1996
).24.
S.
Miranda
, J.
Feldt
, F.
Pratas
, R. A.
Mata
, N.
Roma
, and P.
Tomás
, Int. J. High Perform. Comput. Appl.
31
, 499
(2017
).25.
E.
Cubero
, F. J.
Luque
, M.
Orozco
, and J.
Gao
, J. Phys. Chem. B
107
, 1664
(2003
).26.
C. J.
Fennell
and J. D.
Gezelter
, J. Chem. Phys.
124
, 234104
(2006
).27.
M. E.
Mura
and P. J.
Knowles
, J. Chem. Phys.
104
, 9848
(1996
).28.
A. D.
Becke
, J. Chem. Phys.
88
, 2547
(1988
).29.
V.
Lebedev
, USSR Comput. Math. Math. Phys.
15
, 251
(1975
).30.
H.-J.
Werner
, P. J.
Knowles
, G.
Knizia
, F. R.
Manby
, M.
Schütz
, molpro, version 2012.1, a package of ab initio programs, 2012, see www.molpro.net.31.
F.
Weigend
and R.
Ahlrichs
, Phys. Chem. Chem. Phys.
7
, 3297
(2005
).32.
S.
Grimme
, J.
Antony
, S.
Ehrlich
, and H.
Krieg
, J. Chem. Phys.
132
, 154104
(2010
).33.
S.
Grimme
, S.
Ehrlich
, and L.
Goerigk
, J. Comput. Chem.
32
, 1456
(2011
).34.
E. R.
Johnson
and A. D.
Becke
, J. Chem. Phys.
123
, 024101
(2005
).35.
R.
Polly
, H.-J.
Werner
, F. R.
Manby
, and P. J.
Knowles
, Mol. Phys.
102
, 2311
(2004
).36.
J. P.
Perdew
, K.
Burke
, and M.
Ernzerhof
, Phys. Rev. Lett.
77
, 3865
(1996
).37.
C. H.
Bennett
, J. Comput. Phys.
22
, 245
(1976
).38.
J. D.
Chodera
, W. C.
Swope
, J. W.
Pitera
, C.
Seok
, and K. A.
Dill
, J. Chem. Theory Comput.
3
, 26
(2006
).39.
M. R.
Shirts
and J. D.
Chodera
, J. Chem. Phys.
129
, 124105
(2008
).40.
B.
Ensing
, E. J.
Meijer
, P. E.
Blöchl
, and E. J.
Baerends
, J. Phys. Chem. A
105
, 3300
(2001
).41.
M.
Cossi
, C.
Adamo
, and V.
Barone
, Chem. Phys. Lett.
297
, 1
(1998
).42.
C. K.
Regan
, S. L.
Craig
, and J. I.
Brauman
, Science
295
, 2245
(2002
).43.
T. N.
Truong
and E. V.
Stefanovich
, J. Phys. Chem.
99
, 14700
(1995
).44.
M.
Pagliai
, S.
Raugei
, G.
Cardini
, and V.
Schettino
, J. Mol. Struct.: THEOCHEM
630
, 141
(2003
).45.
K.
Senthilkumar
, J. I.
Mujika
, K. E.
Ranaghan
, F. R.
Manby
, A. J.
Mulholland
, and J. N.
Harvey
, J. R. Soc. Interface
5
, 207
(2008
).46.
D.
Shivakumar
, J.
Williams
, Y.
Wu
, W.
Damm
, J.
Shelley
, and W.
Sherman
, J. Chem. Theory Comput.
6
, 1509
(2010
).47.
P. F. B.
Gonçalves
and H.
Stassen
, Pure Appl. Chem.
76
, 231
(2004
).48.
J. W.
Pitera
and W. F.
van Gunsteren
, Mol. Simul.
28
, 45
(2002
).49.
G. D.
Hawkins
, C. J.
Cramer
, and D. G.
Truhlar
, J. Phys. Chem. B
102
, 3257
(1998
).50.
M.
Wang
, P.
Li
, X.
Jia
, W.
Liu
, Y.
Shao
, W.
Hu
, J.
Zheng
, B. R.
Brooks
, and Y.
Mei
, J. Chem. Inf. Model.
57
, 2476
(2017
).51.
D. G.
Fedorov
, Y.
Sugita
, and C. H.
Choi
, J. Phys. Chem. B
117
, 7996
(2013
).52.
M. T. C.
Martins-Costa
and M. F.
Ruiz-López
, Chem. Phys.
332
, 341
(2007
).53.
B. J. C.
Cabral
, J. Chem. Phys.
146
, 234502
(2017
).54.
M. C.
Caputo
, P. F.
Provasi
, L.
Benitez
, H. C.
Georg
, S.
Canuto
, and K.
Coutinho
, J. Phys. Chem. A
118
, 6239
(2014
).© 2017 Author(s).
2017
Author(s)
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