The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX2), where M = Mg2+, Ca2+, Sr2+, Ba2+ and X = Cl−, Br−, I−, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.
REFERENCES
1.
J. J. R.
Frausto da Silva
and R. J. P.
William
, The Biological Chemistry of the Elements: The Inorganic Chemistry of Life
, 2nd ed. (Oxford University Press
, 1991
).2.
Y.
Jiang
, A.
Lee
, J.
Chen
, V.
Ruta
, M.
Cadene
, B. T.
Chait
, and R.
MacKinnon
, Nature
423
, 33
–41
(2003
).3.
S. X.
Wang
, E.
Hur
, C. A.
Sousa
, L.
Brinen
, E. J.
Slivka
, and R. J.
Fletterick
, Biochemistry
42
(26
), 7959
–7966
(2003
).4.
T.
Dudev
and C.
Lim
, J. Am. Chem. Soc.
135
, 17200
–17208
(2013
).5.
J. A.
Cowan
, Chem. Rev.
98
, 1067
–1088
(1998
).6.
I.
Leontyev
and A.
Stuchebrukhov
, Phys. Chem. Chem. Phys.
13
(7
), 2613
(2011
).7.
8.
S.
Weerasinghe
and P. E.
Smith
, J. Chem. Phys.
119
, 11342
(2003
).9.
M. B.
Gee
, N. R.
Cox
, Y.
Jiao
, N.
Bentenitis
, S.
Weerasinghe
, and P. E.
Smith
, J. Chem. Theory Comput.
7
(5
), 1369
–1380
(2011
).10.
J.
Šponer
, M.
Otyepka
, P.
Banáš
, K.
Réblová
, and N. G.
Walter
, Innovations in Biomolecular Modeling and Simulations
(Royal Society of Chemistry
, 2012
), Vol. 2, pp. 129
–155
.11.
H. I.
Okur
, J.
Hladílková
, K. B.
Rembert
, Y.
Cho
, J.
Heyda
, J.
Dzubiella
, P. S.
Cremer
, and P.
Jungwirth
, J. Phys. Chem. B
121
(9
), 1997
–2014
(2017
).12.
A.
Kubíčková
, T.
Křížek
, P.
Coufal
, M.
Vazdar
, E.
Wernersson
, J.
Heyda
, and P.
Jungwirth
, Phys. Rev. Lett.
108
(18
), 186101
(2012
).13.
H.
Yu
, T. W.
Whitfield
, E.
Harder
, G.
Lamoureux
, I.
Vorobyov
, V. M.
Anisimov
, A. D.
MacKerell
, and B.
Roux
, J. Chem. Theory Comput.
6
(3
), 774
–786
(2010
).14.
J.
Huang
, P. E. M.
Lopes
, B.
Roux
, and A. D.
MacKerell
, J. Phys. Chem. Lett.
5
(18
), 3144
–3150
(2014
).15.
I. V.
Leontyev
and A. A.
Stuchebrukhov
, J. Chem. Theory Comput.
8
, 3207
–3216
(2012
).16.
I. V.
Leontyev
and A. A.
Stuchebrukhov
, J. Chem. Phys.
141
, 014103
(2014
).17.
I. V.
Leontyev
and A. A.
Stuchebrukhov
, J. Chem. Phys.
130
, 085102
(2009
).18.
Y.
Luo
and B.
Roux
, J. Phys. Chem. Lett.
1
(1
), 183
–189
(2010
).19.
Y.
Hashem
, E.
Westhof
, and P.
Auffinger
, Computational Structural Biology
(World Scientific
, 2008
), pp. 363
–399
.20.
H.
Ohtaki
, Monatsh. Chem.
132
(11
), 1237
–1268
(2002
).21.
S.
Kirmizialtin
and R.
Elber
, J. Phys. Chem. B
114
, 8207
–8220
(2010
).22.
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
, J. Am. Chem. Soc.
117
, 5179
–5197
(1995
).23.
B. R.
Brooks
, R. E.
Bruccoleri
, B. D.
Olafson
, D. J.
States
, S.
Swaminathan
, and M.
Karplus
, J. Comput. Chem.
4
, 187
–217
(1983
).24.
J.
Yoo
and A.
Aksimentiev
, J. Phys. Chem. Lett.
3
, 45
–50
(2012
).25.
P.
Auffinger
, RNA 3D Structure Analysis and Prediction
(Springer Berlin Heidelberg
, 2012
), Vol. 27, pp. 299
–318
.26.
P.
Auffinger
, N.
Grover
, and E.
Westhof
, Structural and Catalytic Roles of Metal Ions in RNA
(The Royal Society of Chemistry
, 2011
), Vol. 9, pp. 1
–36
.27.
J.
Yoo
, J.
Wilson
, and A.
Aksimentiev
, Biopolymers
105
, 752
–763
(2016
).28.
D. C.
Rau
, B.
Lee
, and V. A.
Parsegian
, Proc. Natl. Acad. Sci. U. S. A.
81
(9
), 2621
–2625
(1984
).29.
A. A.
Kornyshev
and S.
Leikin
, Phys. Rev. Lett.
82
(20
), 4138
–4141
(1999
).30.
E.
Raspaud
, M.
Olvera de la Cruz
, J. L.
Sikorav
, and F.
Livolant
, Biophys. J.
74
(1
), 381
–393
(1998
).31.
Y.
Jiang
, H.
Zhang
, W.
Feng
, and T.
Tan
, J. Chem. Inf. Model.
55
(12
), 2575
–2586
(2015
).32.
A.
Saxena
and D.
Sept
, J. Chem. Theory Comput.
9
, 3538
–3542
(2013
).33.
A.
Saxena
and A. E.
García
, J. Phys. Chem. B
119
, 219
–227
(2015
).34.
J.
Åqvist
, J. Phys. Chem.
94
, 8021
–8024
(1990
).35.
S.
Marchand
and B.
Roux
, Proteins: Struct., Funct., Genet.
33
, 265
–284
(1998
).36.
C. S.
Babu
and C.
Lim
, J. Phys. Chem. A
110
, 691
–699
(2006
).37.
S.
Mamatkulov
, M.
Fyta
, and R. R.
Netz
, J. Chem. Phys.
138
, 024505
(2013
).38.
W. F.
Van Gunsteren
and H. J. C.
Berendsen
, Groningen Molecular Simulation (GROMOS) Library Manual
(BIOMOS
, Groningen, The Netherlands
, 1987
), pp. 1
–221
.39.
J. G.
Kirkwood
and F. P.
Buff
, J. Chem. Phys.
19
, 774
(1951
).40.
41.
P. G.
Kusalik
and G. N.
Patey
, J. Chem. Phys.
86
(9
), 5110
–5116
(1987
).42.
P. E.
Smith
, J. Chem. Phys.
129
, 124509
(2008
).43.
O.
Söhnel
and P.
Novotný
, Densities of Aqueous Solutions of Inorganic Substances
(Elsevier
, Amsterdam
, 1985
).44.
45.
K. S.
Pitzer
, J. Phys. Chem.
77
, 268
–277
(1973
).46.
K. S.
Pitzer
, P.
Wang
, J. A.
Rard
, and S. L.
Clegg
, J. Solution Chem.
28
, 265
–282
(1999
).47.
F.
Deyhimi
and M.
Abedi
, J. Chem. Eng. Data
57
(2
), 324
–329
(2012
).48.
R. A.
Fine
and F. J.
Millero
, J. Chem. Phys.
59
(10
), 5529
–5536
(1973
).49.
S.
Weerasinghe
and P. E.
Smith
, J. Phys. Chem. B
107
, 3891
–3898
(2003
).50.
H. J. C.
Berendsen
, J. R.
Grigera
, and T. P.
Straatsma
, J. Phys. Chem.
91
, 6269
–6271
(1987
).51.
52.
S.
Gražulis
, D.
Chateigner
, R. T.
Downs
, A. F. T.
Yokochi
, M.
Quirós
, L.
Lutterotti
, E.
Manakova
, J.
Butkus
, P.
Moeck
, and A.
Le Bail
, J. Appl. Crystallogr.
42
, 726
–729
(2009
).53.
H. J. C.
Berendsen
, D.
van der Spoel
, and R.
van Drunen
, Comput. Phys. Commun.
91
, 43
–56
(1995
).54.
H. J. C.
Berendsen
, J. P. M.
Postma
, W. F.
van Gunsteren
, A.
DiNola
, and J. R.
Haak
, J. Chem. Phys.
81
, 3684
(1984
).55.
S.
Miyamoto
and P. A.
Kollman
, J. Comput. Chem.
13
(8
), 952
–962
(1992
).56.
T.
Darden
, D.
York
, and L.
Pedersen
, J. Chem. Phys.
98
(12
), 10089
–10092
(1993
).57.
P. E.
Smith
, E.
Matteoli
, and J. P.
O’Connell
, Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering and Biophysics
(CRC Press
, Boca Raton
, 2013
).58.
S.
Chandrasekhar
, Rev. Mod. Phys.
15
(1
), 1
–89
(1943
).59.
R.
Chitra
and P. E.
Smith
, J. Phys. Chem. B
104
(24
), 5854
–5864
(2000
).60.
M. P.
Allen
and D. J.
Tildesley
, Computer Simulation of Liquids
(Oxford University Press
, USA
, 1987
).61.
P. E.
Smith
and W. F. v.
Gunsteren
, J. Chem. Phys.
100
(1
), 577
–585
(1994
).62.
R. W.
Impey
, P. A.
Madden
, and I. R.
McDonald
, J. Phys. Chem.
87
(25
), 5071
–5083
(1983
).63.
M.
Kang
and P. E.
Smith
, J. Comput. Chem.
27
(13
), 1477
–1485
(2006
).64.
K.
Han
, R. M.
Venable
, A.-M.
Bryant
, C. J.
Legacy
, R.
Shen
, H.
Li
, B.
Roux
, A.
Gericke
, and R. W.
Pastor
, J. Phys. Chem. B
122
, 1484
–1494
(2018
).65.
J.
Wang
, P.
Cieplak
, and P. A.
Kollman
, J. Comput. Chem.
21
(12
), 1049
–1074
(2000
).66.
P.
Bjelkmar
, P.
Larsson
, M. A.
Cuendet
, B.
Hess
, and E.
Lindahl
, J. Chem. Theory Comput.
6
(2
), 459
–466
(2010
).67.
W. L.
Jorgensen
, D. S.
Maxwell
, and J.
Tirado-Rives
, J. Am. Chem. Soc.
118
(45
), 11225
–11236
(1996
).68.
K. M.
Callahan
, N. N.
Casillas-Ituarte
, M.
Roeselová
, H. C.
Allen
, and D. J.
Tobias
, J. Phys. Chem. A
114
(15
), 5141
–5148
(2010
).69.
R.
Caminiti
, G.
Licheri
, G.
Piccaluga
, and G.
Pinna
, Chem. Phys. Lett.
47
, 275
–278
(1977
).70.
H.
Ohtaki
and T.
Radnai
, Chem. Rev.
93
, 1157
–1204
(1993
).71.
J. P.
Piquemal
, L.
Perera
, G. A.
Cisneros
, P.
Ren
, L. G.
Pedersen
, and T. A.
Darden
, J. Chem. Phys.
125
, 054511
(2006
).72.
D.
Jiao
, C.
King
, A.
Grossfield
, T. A.
Darden
, and P.
Ren
, J. Phys. Chem. B
110
, 18553
–18559
(2006
).73.
J. P.
Larentzos
and L. J.
Criscenti
, J. Phys. Chem. B
112
, 14243
–14250
(2008
).74.
R.
Caminiti
, P.
Cucca
, M.
Monduzzi
, G.
Saba
, and G.
Crisponi
, J. Chem. Phys.
81
(1
), 543
–551
(1984
).75.
F.
Jalilehvand
, D.
Spångberg
, P.
Lindqvist-Reis
, K.
Hermansson
, I.
Persson
, and M.
Sandström
, J. Am. Chem. Soc.
123
, 431
–441
(2001
).76.
Y. S.
Badyal
, A. C.
Barnes
, G. J.
Cuello
, and J. M.
Simonson
, J. Phys. Chem. A
108
, 11819
–11827
(2004
).77.
J. L.
Fulton
, S. M.
Heald
, Y. S.
Badyal
, and J. M.
Simonson
, J. Phys. Chem. A
107
, 4688
–4696
(2003
).78.
V.-T.
Pham
and J. L.
Fulton
, J. Chem. Phys.
138
, 044201
(2013
).79.
G. W.
Neilson
and R. D.
Broadbent
, Chem. Phys. Lett.
167
, 429
–431
(1990
).80.
L. X.
Dang
, G. K.
Schenter
, and J. L.
Fulton
, J. Phys. Chem. B
107
, 14119
–14123
(2003
).81.
S.
Ramos
, G. W.
Neilson
, A. C.
Barnes
and M. J.
Capitán
, J. Chem. Phys.
118
, 5542
(2003
).82.
P.
D’Angelo
, V.
Migliorati
, F.
Sessa
, G.
Mancini
, and I.
Persson
, J. Phys. Chem. B
120
, 4114
–4124
(2016
).83.
G.
Perron
, A.
Roux
, and J. E.
Desnoyers
, Can. J. Chem.
59
(21
), 3049
–3054
(1981
).84.
S.
Obst
and H.
Bradaczek
, J. Phys. Chem.
100
, 15677
–15687
(1996
).85.
S.
Koneshan
, J. C.
Rasaiah
, R. M.
Lynden-Bell
, and S. H.
Lee
, J. Phys. Chem. B
102
, 4193
–4204
(1998
).86.
R. R.
Mills
and V. M. M.
Lobo
, Self-Diffusion in Electrolyte Solutions: A Critical Examination of Data Compiled From the Literature
(Elsevier
, 1989
).87.
J.
Barthel
, R.
Buchner
, and M.
Munsterer
, Electrolyte Data Collection, Part 2: Dielectric Properties of Water and Aqueous Electrolyte Solutions
(Wiley-VCH Verlag GmbH & Co. KGaA
, 1996
).88.
P. E.
Smith
and W. F.
van Gunsteren
, J. Chem. Phys.
100
, 3169
(1994
).89.
G.
Beggerow
, Heats of Mixing and Solution/Mischungs- Und Losungswarmen
(Springer-Verlag Berlin and Heidelberg GmbH & Co. KG Berlin
, Germany
, 1976
).90.
A.
Bleuzen
, P.-A.
Pittet
, L.
Helm
, and A. E.
Merbach
, Magn. Reson. Chem.
35
(11
), 765
–773
(1997
).91.
L.
Helm
and A. E.
Merbach
, Chem. Rev.
105
(6
), 1923
–1960
(2005
).92.
M.
Li
, Z.
Duan
, Z.
Zhang
, C.
Zhang
, and J.
Weare
, Mol. Phys.
106
(24
), 2685
–2697
(2008
).93.
D.
Di Tommaso
, E.
Ruiz-Agudo
, N. H.
de Leeuw
, A.
Putnis
, and C. V.
Putnis
, Phys. Chem. Chem. Phys.
16
(17
), 7772
–7785
(2014
).94.
A. Y.
Mehandzhiyski
, E.
Riccardi
, T. S.
van Erp
, T. T.
Trinh
, and B. A.
Grimes
, J. Phys. Chem. B
119
(33
), 10710
–10719
(2015
).© 2018 Author(s).
2018
Author(s)
You do not currently have access to this content.