A summary of the development of Monte Carlo statistical mechanics simulations for the computation of free energies of hydration of organic molecules is followed by presentation of results with the latest version of the optimized potentials for liquid simulations–all atom force field and the TIP4P water model. Scaling of the Lennard-Jones interactions between water, oxygen, and carbon atoms by a factor of 1.25 is found to improve the accuracy of free energies of hydration for 50 prototypical organic molecules from a mean unsigned error of 1.0–1.2 to 0.4 kcal/mol.

1.
E.
Wilhelm
and
R.
Battino
, “
Thermodynamic functions of the solubilities of gases in liquids at 25°
,”
Chem. Rev.
73
,
1
9
(
1973
).
2.
E.
Wilhelm
,
R.
Battino
, and
R. J.
Wilcock
, “
Low-pressure solubility of gases in liquid water
,”
Chem. Rev.
77
,
219
262
(
1977
).
3.
N.
Metropolis
,
A. W.
Rosenbluth
,
M. N.
Rosenbluth
,
A. H.
Teller
, and
E.
Teller
, “
Equation of state calculations by fast computing machines
,”
J. Chem. Phys.
21
,
1087
1092
(
1953
).
4.
W. L.
Jorgensen
, “
Perspective on equation of state calculations by fast computing machines
,”
Theor. Chem. Acc.
103
,
225
227
(
2000
).
5.
J.
Peddie
, “
Developing the computer
,” in
The History of Visual Magic in Computers
(
Springer
,
London
,
2013
).
6.
J. A.
Barker
and
R. O.
Watts
, “
Structure of water; a Monte Carlo calculation
,”
Chem. Phys. Lett.
3
,
144
145
(
1969
).
7.
F. H.
Stillinger
and
A.
Rahman
, “
Improved simulation of liquid water by molecular dynamics
,”
J. Chem. Phys.
60
,
1545
1557
(
1974
).
8.
G. C.
Lie
,
E.
Clementi
, and
M.
Yoshimine
, “
Study of the structure of molecular complexes. XIII. Monte Carlo simulation of liquid water with a configuration interaction pair potential
,”
J. Chem. Phys.
64
,
2314
2323
(
1976
).
9.
S.
Swaminathan
,
S. W.
Harrison
, and
D. L.
Beveridge
, “
Monte Carlo studies on the structure of a dilute aqueous solution of methane
,”
J. Am. Chem. Soc.
100
,
5705
5712
(
1978
).
10.
W. L.
Jorgensen
, “
Quantum and statistical mechanical studies of liquids. 2. Monte-Carlo simulations of liquid hydrogen fluoride
,”
J. Am. Chem. Soc.
100
,
7824
7831
(
1978
).
11.
W. L.
Jorgensen
, “
Minimal basis set description of the structure and properties of liquid water
,”
J. Am. Chem. Soc.
101
,
2016
2021
(
1979
).
12.
W. L.
Jorgensen
, “
Quantum and statistical mechanical studies of liquids. 7. Structure and properties of liquid methanol
,”
J. Am. Chem. Soc.
102
,
543
549
(
1980
).
13.
S.
Lifson
,
A. T.
Hagler
, and
P.
Dauber
, “
Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C=O⋯H– hydrogen bonds
,”
J. Am. Chem. Soc.
101
,
5111
5121
(
1979
).
14.
W. L.
Jorgensen
, “
Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
,”
J. Am. Chem. Soc.
103
,
335
340
(
1981
).
15.
I. R.
McDonald
, “
NPT-ensemble Monte Carlo calculations for binary liquid mixtures
,”
Mol. Phys.
23
,
41
58
(
1972
).
16.
J. C.
Owicki
and
H. A.
Scheraga
, “
Monte Carlo calculations in the isothermal-isobaric ensemble. 1. Liquid water
,”
J. Am. Chem. Soc.
99
,
7403
7412
(
1977
).
17.
H. J. C.
Berendsen
,
J. P. M.
Postma
,
W. F.
van Gunsteren
, and
J.
Hermans
, “
Interaction models for water in relation to protein hydration
,” in
Intermolecular Forces
,
The Jerusalem Symposia on Quantum Chemistry and Biochemistry
, edited by
B.
Pullman
(
Springer
,
1981
), Vol.
14
, pp.
331
342
.
18.
W. L.
Jorgensen
,
J.
Chandrasekhar
,
J. D.
Madura
,
R. W.
Impey
, and
M. L.
Klein
, “
Comparison of simple potential functions for simulating liquid water
,”
J. Chem. Phys.
79
,
926
935
(
1983
).
19.
W. D.
Cornell
,
P.
Cieplak
,
C. I.
Bayly
,
I. R.
Gould
,
K. M.
Merz
,
D. M.
Ferguson
,
D. C.
Spellmeyer
,
T.
Fox
,
J. W.
Caldwell
, and
P. A.
Kollman
, “
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
,”
J. Am. Chem. Soc.
117
,
5179
5197
(
1995
).
20.
A. D.
MacKerell
, Jr
,
D.
Bashford
,
M.
Bellott
,
R. L.
Dunbrack
, Jr.
,
J. D.
Evanseck
,
M. J.
Field
,
S.
Fischer
,
J.
Gao
,
H.
Guo
,
S.
Ha
,
D.
Joseph-McCarthy
,
L.
Kuchnir
,
K.
Kuczera
,
F. T. K.
Lau
,
C.
Mattos
,
S.
Michnick
,
T.
Ngo
,
D. T.
Nguyen
,
B.
Prodhom
,
W. E.
Reiher
III
,
B.
Roux
,
M.
Schlenkrich
,
J. C.
Smith
,
R.
Stote
,
J.
Straub
,
M.
Watanabe
,
J.
Wiórkiewicz-Kuczera
,
D.
Yin
, and
M.
Karplus
,
J. Phys. Chem. B
102
,
3586
3616
(
1998
).
21.
G. N.
Patey
and
J. P.
Valleau
, “
A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution
,”
J. Chem. Phys.
63
,
2334
2339
(
1975
).
22.
D. W.
Rebertus
,
B. J.
Berne
, and
D.
Chandler
, “
A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n-butane in CCl4
,”
J. Chem. Phys.
70
,
3395
3400
(
1979
).
23.
B.
Bigot
and
W. L.
Jorgensen
, “
Sampling methods for Monte Carlo simulations of n-butane in dilute solution
,”
J. Chem. Phys.
75
,
1944
(
1981
).
24.
R. O.
Rosenberg
,
R.
Mikkilineni
, and
B. J.
Berne
, “
Hydrophobic effect on chain folding. The trans to gauche isomerization of n-butane in water
,”
J. Am. Chem. Soc.
104
,
7647
7649
(
1982
).
25.
W. L.
Jorgensen
, “
Monte Carlo simulation of n-butane in water. Conformational evidence for the hydrophobic effect
,”
J. Chem. Phys.
77
,
5757
(
1982
).
26.
J.
Chandrasekhar
,
S. F.
Smith
, and
W. L.
Jorgensen
, “
SN2 reaction profiles in the gas phase and aqueous solution
,”
J. Am. Chem. Soc.
106
,
3049
3050
(
1984
).
27.
R. W.
Zwanzig
, “
High-temperature equation of state by a perturbation method. I. Nonpolar gases
,”
J. Chem. Phys.
22
,
1420
1426
(
1954
).
28.
W. L.
Jorgensen
and
C.
Ravimohan
, “
Monte Carlo simulation of differences in free energies of hydration
,”
J. Chem. Phys.
83
,
3050
3054
(
1985
).
29.
J. G.
Kirkwood
, “
Statistical mechanics of fluid mixtures
,”
J. Chem. Phys.
3
,
300
313
(
1935
).
30.
W. L.
Jorgensen
and
J.
Tirado-Rives
, “
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO
,”
J. Comput. Chem.
26
,
1689
1700
(
2005
).
31.
W. L.
Jorgensen
, “
Free energy calculations: A breakthrough for modeling organic chemistry in solution
,”
Acc. Chem. Res.
22
,
184
189
(
1989
).
32.
P. A.
Kollman
, “
Free energy calculations: Applications to chemical and biochemical phenomena
,”
Chem. Rev.
93
,
2395
2417
(
1993
).
33.
C.
Chipot
, “
Free energy methods for the description of molecular processes
,”
Annu. Rev. Biophys.
52
,
113
138
(
2023
).
34.
P. A.
Bash
,
U. C.
Singh
,
R.
Langridge
, and
P. A.
Kollman
, “
Free energy calculations by computer simulation
,”
Science
236
,
564
568
(
1987
).
35.
P.
Cieplak
and
P. A.
Kollman
, “
Calculation of the free energy of association of nucleic acid bases in vacuo and water solution
,”
J. Am. Chem. Soc.
110
,
3734
3739
(
1988
).
36.
J.
Hermans
,
A.
Pathiaseril
, and
A.
Anderson
, “
Excess free energy of liquids from molecular dynamics simulations. Application to water models
,”
J. Am. Chem. Soc.
110
,
5982
5986
(
1988
).
37.
W. L.
Jorgensen
,
J. F.
Blake
, and
J. K.
Buckner
, “
Free energy of TIP4P water and free energies of hydration of CH4 and Cl from statistical perturbation theory
,”
Chem. Phys.
129
,
193
200
(
1989
).
38.
J.
Åqvist
, “
Ion-water interaction potentials derived from free energy perturbation simulations
,”
J. Phys. Chem.
94
,
8021
8024
(
1990
).
39.
W. L.
Jorgensen
and
J.
Tirado-Rives
, “
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
,”
Proc. Natl. Acad. Sci. U. S. A.
102
,
6665
6670
(
2005
).
40.
D. L.
Mobley
,
C. I.
Bayly
,
M. D.
Cooper
,
M. R.
Shirts
, and
K. A.
Dill
, “
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
,”
J. Chem. Theory Comput.
5
,
350
358
(
2009
).
41.
E.
Harder
,
W.
Damm
,
J.
Maple
,
C.
Wu
,
M.
Reboul
,
J. Y.
Xiang
,
L.
Wang
,
D.
Lupyan
,
M.
Dahlgren
,
J. L.
Knight
,
J. W.
Kaus
,
D. S.
Cerutti
,
G.
Krilov
,
W. L.
Jorgensen
,
R.
Abel
, and
R. A.
Friesner
, “
OPLS3: A force field providing broad coverage of drug-like small molecules and proteins
,”
J. Chem. Theory Comput.
12
,
281
296
(
2016
).
42.
L. S.
Dodda
,
J. Z.
Vilseck
,
J.
Tirado-Rives
, and
W. L.
Jorgensen
, “
1.14*CM1A-LBCC: Localized bond-charge corrected CM1A charges for condensed-phase simulations
,”
J. Phys. Chem. B
121
,
3864
3870
(
2017
).
43.
C. R.
Rupakheti
,
A. D.
MacKerell
, Jr.
, and
B.
Roux
, “
Global optimization of the Lennard-Jones parameters for the Drude polarizable force field
,”
J. Chem. Theory Comput.
17
,
7085
7095
(
2021
).
44.
W. L.
Jorgensen
,
M.
Ghahremanpour
,
A.
Saar
, and
J.
Tirado-Rives
, “
OPLS/2020 force field for unsaturated hydrocarbons, alcohols, and ethers
,”
J. Phys. Chem. B
128
,
250
262
(
2024
).
45.
C.
Lu
,
C.
Wu
,
D.
Ghoreishi
,
W.
Chen
,
L.
Wang
,
W.
Damm
,
G. A.
Ross
,
M. K.
Dahlgren
,
E.
Russell
,
C. D.
Von Bargen
,
R.
Abel
,
R. A.
Friesner
, and
E. D.
Harder
, “
OPLS4: Improving force field accuracy on challenging regimes of chemical space
,”
J. Chem. Theory Comput.
17
,
4291
4300
(
2021
).
46.
J. W.
Ponder
and
D. A.
Case
, “
Force fields for protein simulations
,”
Protein Simul.
66
,
27
85
(
2003
).
47.
S.
Riniker
, “
Fixed-charge atomistic force fields for molecular dynamics simulations in the condensed phase: An overview
,”
J. Chem. Inf. Model.
58
,
565
578
(
2018
).
48.
P. S.
Nerenberg
and
T.
Head-Gordon
, “
New developments in force fields for biomolecular simulations
,”
Curr. Opin. Struct. Biol.
49
,
129
138
(
2018
).
49.
X.
He
,
B.
Walker
,
V. H.
Man
,
P.
Ren
, and
J.
Wang
, “
Recent progress in general force fields of small molecules
,”
Curr. Opin. Struct. Biol.
72
,
187
193
(
2022
).
50.
H. S.
Ashbaugh
,
L.
Liu
, and
L. N.
Surampudi
, “
Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration
,”
J. Chem. Phys.
135
,
054510
(
2011
).
51.
D.
Ballal
,
P.
Venkataraman
,
W. A.
Fouad
,
K. R.
Cox
, and
W. G.
Chapman
, “
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions
,”
J. Chem. Phys.
141
,
064905
(
2014
).
52.
B.
Xue
,
D. B.
Harwood
,
J. L.
Chen
, and
J. I.
Siepmann
, “
Monte Carlo simulations of fluid phase equilibria and interfacial properties for water/alkane mixtures: An assessment of nonpolarizable water models and of departures from the Lorentz–Berthelot combining rules
,”
J. Chem. Eng. Data
63
,
4256
4268
(
2018
).
53.
R. B.
Best
,
W.
Zheng
, and
J.
Mittal
, “
Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association
,”
J. Chem. Theory Comput.
10
,
5113
5124
(
2014
).
54.
I.
Cabeza de Vaca
,
R.
Zarzuela
,
J.
Tirado-Rives
, and
W. L.
Jorgensen
, “
Robust free energy perturbation protocols for creating molecules in solution
,”
J. Chem. Theory Comput.
15
,
3941
3948
(
2019
).
55.
A.
Ben-Naim
and
Y.
Marcus
, “
Solvation thermodynamics of nonionic solutes
,”
J. Chem. Phys.
81
,
2016
2027
(
1984
).
56.
M. H.
Abraham
, “
Thermodynamics of solution of homologous series of solutes in water
,”
J. Chem. Soc., Faraday Trans. 1
80
,
153
181
(
1984
).
57.
W. L.
Jorgensen
, “
Enthalpies and entropies of hydration from Monte Carlo simulations
,”
Phys. Chem. Chem. Phys.
26
,
8141
8147
(
2024
).
58.
M. W.
Mahoney
and
W. L.
Jorgensen
, “
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
,”
J. Chem. Phys.
112
,
8910
8922
(
2000
).
59.
C. M.
Baker
and
A. D.
MacKerell
, Jr.
, “
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers
,”
J. Mol. Model.
16
,
567
576
(
2010
).
60.
W. L.
Jorgensen
and
P.
Schyman
, “
Treatment of halogen bonding in the OPLS-AA force field: Application to potent anti-HIV agents
,”
J. Chem. Theory Comput.
8
,
3895
3901
(
2012
).
61.
X. C.
Yan
,
M. J.
Robertson
,
J.
Tirado-Rives
, and
W. L.
Jorgensen
, “
Improved description of sulfur charge anisotropy in OPLS force fields: Model development and parameterization
,”
J. Phys. Chem. B
121
,
6626
6636
(
2017
).
62.
G.
Karlström
,
P.
Linse
,
A.
Wallqvist
, and
B.
Jönsson
, “
Intermolecular potentials of the H2O-C6H6 and C6H6-C6H6 systems calculated in an ab initio SCFCI approximation
,”
J. Am. Chem. Soc.
105
,
3777
3782
(
1983
).
63.
W. L.
Jorgensen
and
D. L.
Severance
, “
Aromatic-aromatic interactions: Free energy profiles for the benzene dimer in water, chloroform, and liquid benzene
,”
J. Am. Chem. Soc.
112
,
4768
4774
(
1990
).
64.
J.
Tirado-Rives
and
W. L.
Jorgensen
, “
Viability of molecular modeling with Pentium-based PCs
,”
J. Comput. Chem.
17
,
1385
1386
(
1996
).
You do not currently have access to this content.