This paper assesses the ability of molecular density functional theory to predict efficiently and accurately the hydration free energies of molecular solutes and the surrounding microscopic water structure. A wide range of solutes were investigated, including hydrophobes, water as a solute, and the FreeSolv database containing 642 drug-like molecules having a variety of shapes and sizes. The usual second-order approximation of the theory is corrected by a third-order, angular-independent bridge functional. The overall functional is parameter-free in the sense that the only inputs are bulk water properties, independent of the solutes considered. These inputs are the direct correlation function, compressibility, liquid–gas surface tension, and excess chemical potential of the solvent. Compared to molecular simulations with the same force field and the same fixed solute geometries, the present theory is shown to describe accurately the solvation free energy and structure of both hydrophobic and hydrophilic solutes. Overall, the method yields a precision of order 0.5 kBT for the hydration free energies of the FreeSolv database, with a computer speedup of 3 orders of magnitude. The theory remains to be improved for a better description of the H-bonding structure and the hydration free energy of charged solutes.

1.
B.
Roux
and
T.
Simonson
,
Biophys. Chem.
78
,
1
(
1999
).
2.
J.
Mongan
,
C.
Simmerling
,
J. A.
McCammon
,
D. A.
Case
, and
A.
Onufriev
,
J. Chem. Theory Comput.
3
,
156
(
2007
).
3.
J.
Dzubiella
,
J. M. J.
Swanson
, and
J. A.
McCammon
,
Phys. Rev. Lett.
96
,
087802
(
2006
).
4.
R. W.
Zwanzig
,
J. Chem. Phys.
22
,
1420
(
1954
).
5.
C. H.
Bennett
,
J. Phys. Chem. Lett.
22
,
245
(
1976
).
6.
S.
Kumar
,
J. M.
Rosenberg
,
D.
Bouzida
,
R. H.
Swendsen
, and
P. A.
Kollman
,
J. Comput. Chem.
13
,
1011
(
1992
).
7.
M. R.
Shirts
and
J. D.
Chodera
,
J. Chem. Phys.
129
,
124105
(
2008
).
8.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
117
,
3605
(
2002
).
9.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
119
,
9686
(
2003
).
10.
R.
Roth
,
Y.
Harano
, and
M.
Kinoshita
,
Phys. Rev. Lett.
97
,
078101
(
2006
).
11.
S.
Chiba
,
Y.
Harano
,
R.
Roth
,
M.
Kinoshita
, and
M.
Sakurai
,
J. Comput. Chem.
33
,
550
(
2012
).
12.
Y.
Harano
,
R.
Roth
, and
S.
Chiba
,
J. Comput. Chem.
34
,
1969
(
2013
).
13.
H. S.
Ashbaugh
and
L. R.
Pratt
,
Rev. Mod. Phys.
78
,
159
(
2006
).
14.
R.
Roth
,
J. Phys.: Condens. Matter
22
,
063102
(
2010
).
15.
J.
Eller
,
T.
Matzerath
,
T.
van Westen
,and
J.
Gross
,
J. Chem. Phys.
154
,
244106
(
2021
).
16.
P.
Koehl
and
M.
Delarue
,
J. Chem. Phys.
132
,
064101
(
2010
).
17.
R.
Ramirez
,
R.
Gebauer
,
M.
Mareschal
, and
D.
Borgis
,
Phys. Rev. E
66
,
031206
(
2002
).
18.
R.
Ramirez
and
D.
Borgis
,
J. Phys. Chem. B
109
,
6754
(
2005
).
19.
F.
Hirata
and
P. J.
Rossky
,
Chem. Phys. Lett.
83
,
329
(
1981
).
20.
D.
Beglov
and
B.
Roux
,
J. Phys. Chem. B
101
,
7821
(
1997
).
21.
A.
Kovalenko
and
F.
Hirata
,
Chem. Phys. Lett.
290
,
237
(
1998
).
22.
A.
Kovalenko
and
F.
Hirata
,
J. Chem. Phys.
113
,
2793
(
2000
).
23.
A.
Kovalenko
and
F.
Hirata
,
J. Phys. Chem. B
103
,
7942
(
1999
).
24.
Y.
Maruyama
,
N.
Yoshida
,
H.
Tadano
,
D.
Takahashi
,
M.
Sato
, and
F.
Hirata
,
J. Comput. Chem.
35
,
1347
(
2014
).
25.
F.
Hoffgaard
,
J.
Heil
, and
S. M.
Kast
,
J. Chem. Theory Comput.
9
,
4718
(
2013
).
26.
J.
Heil
and
S. M.
Kast
,
J. Chem. Phys.
142
,
114107
(
2015
).
27.
Y.
Liu
,
J.
Fu
, and
J.
Wu
,
J. Phys. Chem. Lett.
4
,
3687
(
2013
).
28.
G. N.
Chuev
,
M. V.
Fedorov
, and
J.
Crain
,
Chem. Phys. Lett.
448
,
198
(
2007
).
29.
D. S.
Palmer
,
A. I.
Frolov
,
E. L.
Ratkova
, and
M. V.
Fedorov
,
Mol. Pharm.
8
,
1423
(
2011
).
30.
J.-F.
Truchon
,
B. M.
Pettitt
, and
P.
Labute
,
J. Chem. Theory Comput.
10
,
934
(
2014
).
31.
M.
Misin
,
D. S.
Palmer
, and
M. V.
Fedorov
,
J. Phys. Chem. B
120
,
5724
(
2016
).
32.
T.
Luchko
,
N.
Blinov
,
G. C.
Limon
,
K. P.
Joyce
, and
A.
Kovalenko
,
J. Comput.-Aided Mol. Des.
30
,
1115
(
2016
).
33.
J.
Johnson
,
D. A.
Case
,
T.
Yamazaki
,
S.
Gusarov
,
A.
Kovalenko
, and
T.
Luchko
,
J. Phys.: Condens. Matter
28
,
344002
(
2016
).
34.
D.
Roy
and
A.
Kovalenko
,
J. Phys. Chem. A
123
,
4087
(
2019
).
35.
N.
Tielker
,
D.
Tomazic
,
L.
Eberlein
,
S.
Güssregen
, and
S. M.
Kast
,
J. Comput.-Aided Mol. Des.
34
,
453
(
2020
).
36.
N.
Yoshida
,
T.
Imai
,
S.
Phongphanphanee
,
A.
Kovalenko
, and
F.
Hirata
,
J. Phys. Chem. B
113
,
873
(
2009
).
37.
T.
Luchko
,
S.
Gusarov
,
D. R.
Roe
,
C.
Simmerling
,
A.
David
,
J.
Tuszynski
, and
A.
Kovalenko
,
J. Chem. Theory Comput.
6
,
607
(
2011
).
38.
M. C.
Stumpe
,
N.
Blinov
,
D.
Wishart
,
A.
Kovalenko
, and
V. S.
Pande
,
J. Phys. Chem. B
115
,
319
(
2011
).
39.
D. J.
Sindhikara
and
F.
Hirata
,
J. Phys. Chem. B
117
,
6718
(
2013
).
40.
C.
Nguyen
,
T.
Yamazaki
,
A.
Kovalenko
,
D. A.
Case
,
M. K.
Gilson
,
T.
Kurtzman
, and
T.
Luchko
,
PLoS One
14
,
e0219473
(
2019
).
41.
G. M.
Giambaşu
,
D. A.
Case
, and
D. M.
York
,
J. Am. Chem. Soc.
141
,
2435
(
2019
).
42.
J.
Richardi
,
C.
Millot
, and
P. H.
Fries
,
J. Chem. Phys.
110
,
1138
(
1999
).
43.
M.
Lombardero
,
C.
Martín
,
S.
Jorge
,
F.
Lado
, and
E.
Lomba
,
J. Chem. Phys.
110
,
1148
(
1999
).
44.
L.
Belloni
and
I.
Chikina
,
Mol. Phys.
112
,
1246
(
2014
).
45.
L.
Gendre
,
R.
Ramirez
, and
D.
Borgis
,
Chem. Phys. Lett.
474
,
366
(
2009
).
46.
D.
Borgis
,
L.
Gendre
, and
R.
Ramirez
,
J. Phys. Chem. B
116
,
2504
(
2012
).
47.
S.
Zhao
,
R.
Ramirez
,
R.
Vuilleumier
, and
D.
Borgis
,
J. Chem. Phys.
134
,
194102
(
2011
).
48.
G.
Jeanmairet
,
M.
Levesque
,
R.
Vuilleumier
, and
D.
Borgis
,
J. Phys. Chem. Lett.
4
,
619
(
2013
).
49.
L.
Blum
and
A. J.
Torruella
,
J. Chem. Phys.
56
,
303
(
1972
).
50.
L.
Blum
,
J. Chem. Phys.
57
,
1862
(
1972
).
51.
L.
Ding
,
M.
Levesque
,
D.
Borgis
, and
L.
Belloni
,
J. Chem. Phys.
147
,
094107
(
2017
).
52.
M.
Levesque
,
R.
Vuilleumier
, and
D.
Borgis
,
J. Chem. Phys.
137
,
034115
(
2012
).
53.
G.
Jeanmairet
,
M.
Levesque
, and
D.
Borgis
,
J. Chem. Phys.
139
,
154101
(
2013
).
54.
G.
Jeanmairet
,
M.
Levesque
,
V.
Sergiievskyi
, and
D.
Borgis
,
J. Chem. Phys.
142
,
154112
(
2015
).
55.
C.
Gageat
,
L.
Belloni
,
D.
Borgis
, and
M.
Levesque
, arXiv:1709.10139 (
2017
).
56.
S.
Zhao
,
Z.
Jin
, and
J.
Wu
,
J. Phys. Chem. B
115
,
6971
(
2011
).
57.
S.
Zhao
,
Z.
Jin
, and
J.
Wu
,
J. Phys. Chem. B
115
,
15445
(
2011
).
58.
Y.
Liu
,
S.
Zhao
, and
J.
Wu
,
J. Chem. Theory Comput.
9
,
1896
(
2013
).
59.
S.
Luukkonen
,
M.
Levesque
,
L.
Belloni
, and
D.
Borgis
,
J. Chem. Phys.
152
,
064110
(
2020
).
60.
D.
Borgis
,
S.
Luukkonen
,
L.
Belloni
, and
G.
Jeanmairet
,
J. Phys. Chem. B
124
,
6885
(
2020
).
62.
W. L.
Jorgensen
,
J.
Chandrasekhar
,
J. D.
Madura
, and
M. L.
Klein
,
J. Chem. Phys.
79
,
926
(
1983
).
63.
H. J. C.
Berendsen
,
J. R.
Grigera
, and
T. P.
Straatsma
,
J. Phys. Chem.
91
,
6269
(
1987
).
64.
L.
Belloni
,
J. Chem. Phys.
147
,
164121
(
2017
).
65.
66.
E.
Kierlik
and
M. L.
Rosinberg
,
Phys. Rev. A
42
,
3382
(
1990
).
67.
R.
Roth
,
R.
Evans
,
A.
Lang
, and
G.
Kahl
,
J. Phys.: Condens. Matter
14
,
12063
(
2002
).
68.
Y.-X.
Yu
and
J.
Wu
,
J. Chem. Phys.
117
,
10156
(
2002
).
69.
Y.
Rosenfeld
,
J. Chem. Phys.
98
,
8126
(
1993
).
70.
S.
Nordholm
,
M.
Johnson
, and
B. C.
Freasier
,
Aust. J. Chem.
33
,
2139
(
1980
).
71.
P.
Tarazona
,
Phys. Rev. A
31
,
2672
(
1985
).
72.
W. A.
Curtin
and
N. W.
Ashcroft
,
Phys. Rev. A
32
,
2909
(
1985
).
73.
J.-P.
Hansen
and
I. R.
McDonald
,
Theory of Simple Liquids: With Applications to Soft Matter
, 4th ed. (
Academic Press
,
Amstersdam
,
2013
).
74.
L.
Belloni
,
J. Chem. Phys.
151
,
021101
(
2019
).
75.
S.
Luukkonen
, “
Hydration of drug-like molecules with molecular density functional theory and the hybrid-4th-dimension Monte-Carlo approach
,” Ph.D. thesis,
Université Paris-Saclay
,
2020
.
76.
F. M.
Floris
,
M.
Selmi
,
A.
Tani
, and
J.
Tomasi
,
J. Chem. Phys.
107
,
6353
(
1997
).
77.
D. M.
Huang
,
P. L.
Geissler
, and
D.
Chandler
,
J. Phys. Chem. B
105
,
6704
(
2001
).
78.
D. M.
Huang
and
D.
Chandler
,
J. Phys. Chem. B
106
,
2047
(
2002
).
79.
G.
Hummer
,
S.
Garde
,
A. E.
García
,
A.
Pohorille
, and
L. R.
Pratt
,
Proc. Natl. Acad. Sci. U. S. A.
93
,
8951
(
1996
).
80.
V. P.
Sergiievskyi
,
G.
Jeanmairet
,
M.
Levesque
, and
D.
Borgis
,
J. Phys. Chem. Lett.
5
,
1935
(
2014
).
81.
V.
Sergiievskyi
,
G.
Jeanmairet
,
M.
Levesque
, and
D.
Borgis
,
J. Chem. Phys.
143
,
184116
(
2015
).
82.
T. Y.
Hsu
and
G.
Jeanmairet
,
J. Chem. Phys.
154
,
131102
(
2021
).
83.
T.
Fujita
and
T.
Yamamoto
,
J. Chem. Phys.
147
,
014110
(
2017
).
84.
D. L.
Mobley
,
C. I.
Bayly
,
M. D.
Cooper
,
M. R.
Shirts
, and
K. A.
Dill
,
J. Chem. Theory Comput.
5
,
350
(
2009
).
85.
G. D. R.
Matos
,
D. Y.
Kyu
,
H. H.
Loeffler
,
J. D.
Chodera
,
M. R.
Shirts
, and
D. L.
Mobley
,
J. Chem. Eng. Data
62
,
1559
(
2017
).
86.
G.
Jeanmairet
,
M.
Levesque
, and
D.
Borgis
,
J. Chem. Theory Comput.
16
,
7123
(
2020
).
87.
T.
Kloss
,
J.
Heil
, and
S. M.
Kast
,
J. Phys. Chem. B
112
,
4337
(
2008
).
88.
H.
Sato
and
S.
Sakaki
,
J. Phys. Chem. A
108
,
1629
(
2004
).

Supplementary Material

You do not currently have access to this content.