-
1
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
DOI 10.1021/cr990052a
-
M. Orozco and F. Luque, J. Chem. Rev. 100, 4187 (2000). 10.1021/cr990052a (Pubitemid 32067769)
-
(2000)
Chemical Reviews
, vol.100
, Issue.11
, pp. 4187-4225
-
-
Orozco, M.1
Luque, F.J.2
-
2
-
-
17444404197
-
Density functional theory of solvation and its relation to implicit solvent models
-
DOI 10.1021/jp045453v
-
R. Ramirez and D. Borgis, J. Phys. Chem. B 109, 6754 (2005). 10.1021/jp045453v (Pubitemid 40538444)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.14
, pp. 6754-6763
-
-
Ramirez, R.1
Borgis, D.2
-
3
-
-
41349089274
-
Density functional theory of solvation in a polar solvent: Extracting the functional from homogeneous solvent simulations
-
DOI 10.1103/PhysRevE.66.031206, 031206
-
R. Ramirez, R. Gebauer, M. Mareschal, Phys. Rev. E 66, 031206 (2002). 10.1103/PhysRevE.66.031206 (Pubitemid 40606372)
-
(2002)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.66
, Issue.3
-
-
Ramirez, R.1
Gebauer, R.2
Mareschal, M.3
Borgis, D.4
-
4
-
-
28644443214
-
Direct correlation functions and the density functional theory of polar solvents
-
DOI 10.1016/j.chemphys.2005.07.038, PII S0301010405002831
-
R. Ramirez, M. Mareschal, and D. Borgis, Chem. Phys. 319, 261 (2005). 10.1016/j.chemphys.2005.07.038 (Pubitemid 41750493)
-
(2005)
Chemical Physics
, vol.319
, Issue.1-3
, pp. 261-272
-
-
Ramirez, R.1
Mareschal, M.2
Borgis, D.3
-
6
-
-
0004016501
-
-
10.1063/1.445869
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Phys. Chem. 79, 926 (1983). 10.1063/1.445869
-
(1983)
J. Phys. Chem.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
11
-
-
0023779259
-
-
10.1002/prot.340040104
-
M. Gilson and B. Honig, Proteins 4, 7 (1988). 10.1002/prot.340040104
-
(1988)
Proteins
, vol.4
, pp. 7
-
-
Gilson, M.1
Honig, B.2
-
14
-
-
0023338543
-
-
10.1073/pnas.84.10.3086
-
T. Ooi, M. Oobatake, and G. Nemethy, and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 84, 3086 (1987). 10.1073/pnas.84.10.3086
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 3086
-
-
Ooi, T.1
Oobatake, M.2
Nemethy, G.3
Scheraga, H.A.4
-
15
-
-
0344778061
-
-
10.1021/ja00172a038
-
W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127 (1990). 10.1021/ja00172a038
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
18
-
-
4043171970
-
-
10.1021/jp961992r
-
D. Qiu, P. S. Shenkin, F. P. Hollinger, and W. C. Still, J. Phys. Chem. A 101, 3005 (1997). 10.1021/jp961992r
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3005
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
19
-
-
0348189638
-
-
10.1021/j100588a008
-
G. L. Amidon, S. H. Yalkowsky, S. T. Anik, and S. C. Valvani, J. Phys. Chem. 79, 2239 (1975). 10.1021/j100588a008
-
(1975)
J. Phys. Chem.
, vol.79
, pp. 2239
-
-
Amidon, G.L.1
Yalkowsky, S.H.2
Anik, S.T.3
Valvani, S.C.4
-
21
-
-
0011930746
-
-
10.1021/j100663a023
-
R. B. Hermann, J. Phys. Chem. 76, 2754 (1972). 10.1021/j100663a023
-
(1972)
J. Phys. Chem.
, vol.76
, pp. 2754
-
-
Hermann, R.B.1
-
22
-
-
84962424501
-
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model
-
DOI 10.1002/jcc.20480
-
C. Curutchet, M. Orozco, F. J. Luque, B. Mennucci, and J. Tomasi, J. Comput. Chem. 27, 1769 (2006). 10.1002/jcc.20480 (Pubitemid 44672560)
-
(2006)
Journal of Computational Chemistry
, vol.27
, Issue.15
, pp. 1769-1780
-
-
Curutchet, C.1
Orozco, M.2
Luque, F.J.3
Mennucci, B.4
Tomasi, J.5
-
23
-
-
0015222647
-
-
10.1016/0022-2836(71)90324-X
-
B. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971). 10.1016/0022-2836(71)90324-X
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379
-
-
Lee, B.1
Richards, F.M.2
-
24
-
-
0037149093
-
A generalized-born solvation model for macromolecular hybrid-potential calculations
-
DOI 10.1021/jp0135050
-
E. Pellegrini and M. J. Field, J. Phys. Chem. A 106, 1316 (2002). 10.1021/jp0135050 (Pubitemid 35264278)
-
(2002)
Journal of Physical Chemistry A
, vol.106
, Issue.7
, pp. 1316-1326
-
-
Pellegrini, E.1
Field, M.J.2
-
25
-
-
0017429069
-
-
10.1146/annurev.bb.06.060177.001055
-
F. M. Richards, Annu. Rev. Biophys. Bioeng. 6, 151 (1977). 10.1146/annurev.bb.06.060177.001055
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151
-
-
Richards, F.M.1
-
26
-
-
0028222670
-
-
10.1002/prot.340180304
-
M. Holst, R. E. Kozack, F. Saied, and S. Subramaniam, Proteins:Struct., Funct., Genet. 18, 231 (1994). 10.1002/prot.340180304
-
(1994)
Proteins:Struct., Funct., Genet.
, vol.18
, pp. 231
-
-
Holst, M.1
Kozack, R.E.2
Saied, F.3
Subramaniam, S.4
-
27
-
-
0002334742
-
-
10.1016/0021-9991(91)90043-K
-
A. H. Juffer, E. F. F. Botta, B. A. M. van Keulen, A. van der Ploeg, and H. J. C. Berendsen, J. Comput. Phys. 97, 144 (1991). 10.1016/0021-9991(91)90043- K
-
(1991)
J. Comput. Phys.
, vol.97
, pp. 144
-
-
Juffer, A.H.1
Botta, E.F.F.2
Van Keulen, B.A.M.3
Ploeg, A.V.D.4
Berendsen, H.J.C.5
-
28
-
-
0022964504
-
Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
-
DOI 10.1002/prot.340010109
-
I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, Proteins: Struct., Funct., Genet. 1, 47 (1986). 10.1002/prot.340010109 (Pubitemid 17073401)
-
(1986)
Proteins: Structure, Function and Genetics
, vol.1
, Issue.1
, pp. 47-59
-
-
Klapper, I.1
Hagstrom, R.2
Fine, R.3
-
30
-
-
35048817417
-
-
10.1021/ct600216k
-
J. M. J. Swanson, J. A. Wagoner, N. A. Baker, and J. A. McCammon, J. Chem. Theory. Comput. 3, 170 (2007). 10.1021/ct600216k
-
(2007)
J. Chem. Theory. Comput.
, vol.3
, pp. 170
-
-
Swanson, J.M.J.1
Wagoner, J.A.2
Baker, N.A.3
McCammon, J.A.4
-
34
-
-
84947145359
-
-
10.1080/00268977500101341
-
H. L. Friedman, Mol. Phys. 29, 1533 (1975). 10.1080/00268977500101341
-
(1975)
Mol. Phys.
, vol.29
, pp. 1533
-
-
Friedman, H.L.1
-
35
-
-
0001585447
-
-
10.1021/j100116a025
-
M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon, J. Phys. Chem. 97, 3591 (1993). 10.1021/j100116a025
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 3591
-
-
Gilson, M.K.1
Davis, M.E.2
Luty, B.A.3
McCammon, J.A.4
-
38
-
-
0000709802
-
-
10.1063/1.467179
-
M. E. Davis, J. Chem. Phys. 100, 5149 (1994). 10.1063/1.467179
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 5149
-
-
Davis, M.E.1
-
39
-
-
0032556243
-
Free energy analysis of the conformational preferences of A and B forms of DNA in solution
-
DOI 10.1021/ja981307p
-
B. Jayaram, D. Sprous, M. A. Young, and D. L. Beveridge, J. Am. Chem. Soc. 120, 10629 (1998). 10.1021/ja981307p (Pubitemid 28498806)
-
(1998)
Journal of the American Chemical Society
, vol.120
, Issue.41
, pp. 10629-10633
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
41
-
-
0037196341
-
-
10.1002/jcc.1167
-
O. Guverch, J. Weiser, P. S. Shenkin, I. Kolossvry, and W. C. Still, J. Comput. Chem. 23, 214 (2001). 10.1002/jcc.1167
-
(2001)
J. Comput. Chem.
, vol.23
, pp. 214
-
-
Guverch, O.1
Weiser, J.2
Shenkin, P.S.3
Kolossvry, I.4
Still, W.C.5
-
43
-
-
0346971105
-
-
10.1002/jcc.10378
-
M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks III, J. Comput. Chem. 25, 265 (2004). 10.1002/jcc.10378
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 265
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
-
44
-
-
0034351511
-
GB/SA water model for the Merck molecular force field (MMFF)
-
DOI 10.1016/S1093-3263(00)00038-3, PII S1093326300000383
-
A. Cheng, S. A. Best, J. K. M. Merz, and C. H. Reynolds, J. Mol. Graphics. Modell. 18, 273 (2000). 10.1016/S1093-3263(00)00038-3 (Pubitemid 32250653)
-
(2000)
Journal of Molecular Graphics and Modelling
, vol.18
, Issue.3
, pp. 273-282
-
-
Cheng, A.1
Best, S.A.2
Merz Jr., K.M.3
Reynolds, C.H.4
-
45
-
-
0043197126
-
-
10.1021/jp034613k
-
W. Zhang, T. J. Hou, X. B. Qiao, and X. J. Xu, J. Phys. Chem. B 107, 9071 (2003). 10.1021/jp034613k
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 9071
-
-
Zhang, W.1
Hou, T.J.2
Qiao, X.B.3
Xu, X.J.4
-
48
-
-
84962433811
-
-
10.1063/1.3077917
-
P. Su and H. Li, J. Chem. Phys. 130, 074109 (2009). 10.1063/1.3077917
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 074109
-
-
Su, P.1
Li, H.2
-
52
-
-
84962433811
-
-
10.1063/1.3077917
-
P. F. Su and H. Li, J. Chem. Phys. 130, 074109 (2009). 10.1063/1.3077917
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 074109
-
-
Su, P.F.1
Li, H.2
-
54
-
-
36649035714
-
-
10.1021/ct7001539
-
A. V. Marenich, R. M. Olson, A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2055 (2007). 10.1021/ct7001539
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2055
-
-
Marenich, A.V.1
Olson, R.M.2
Chamberlin, A.C.3
Cramer, C.J.4
Truhlar, D.G.5
-
55
-
-
84962385262
-
-
10.1021/ct7001418
-
A. V. Marenich, R. M. Olson, C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2011 (2007). 10.1021/ct7001418
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2011
-
-
Marenich, A.V.1
Olson, R.M.2
Kelly, C.P.3
Cramer, C.J.4
Truhlar, D.G.5
-
56
-
-
36649020262
-
-
10.1021/ct7001607
-
R. M. Olson, A. V. Marenich, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2046 (2007). 10.1021/ct7001607
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2046
-
-
Olson, R.M.1
Marenich, A.V.2
Cramer, C.J.3
Truhlar, D.G.4
-
57
-
-
0037693073
-
-
10.1002/jcc.10236
-
J. G. ngyn, C. Chipot, F. Dehez, C. Httig, G. Jansen, and C. Millot, J. Comput. Chem. 24, 997 (2003). 10.1002/jcc.10236
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 997
-
-
Ngyn, J.G.1
Chipot, C.2
Dehez, F.3
Httig, C.4
Jansen, G.5
Millot, C.6
-
58
-
-
36649022872
-
-
10.1021/ct700156a
-
F. Dehez, J. G. ngyn, I. S. Gutiérrez, F. J. Luque, K. Schulten, and C. Chipot, J. Chem. Theory Comput. 3, 1914 (2007). 10.1021/ct700156a
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1914
-
-
Dehez, F.1
Ngyn, J.G.2
Gutiérrez, I.S.3
Luque, F.J.4
Schulten, K.5
Chipot, C.6
-
59
-
-
52149086369
-
-
10.1080/00268970802317496
-
F. Dehez, F. Archambault, I. Soteras, F. J. Luque, and C. Chipot, Mol. Phys. 106, 1685 (2008). 10.1080/00268970802317496
-
(2008)
Mol. Phys.
, vol.106
, pp. 1685
-
-
Dehez, F.1
Archambault, F.2
Soteras, I.3
Luque, F.J.4
Chipot, C.5
-
64
-
-
0038792211
-
-
10.1002/jcc.10272
-
M. S. Lee, M. Feig, F. R. J. Salsbury, and C. L. Brooks III, J. Comput. Chem. 24, 1348 (2003). 10.1002/jcc.10272
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1348
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.J.3
Brooks III, C.L.4
-
67
-
-
0037046727
-
Parametrization of a generalized Born/solvent-accessible surface area model and applications to the simulation of protein dynamics
-
DOI 10.1021/jp020058v
-
J. Zhu, Y. Y. Shi, and H. Y. Liu, J. Phys. Chem. B 106, 4844 (2002). 10.1021/jp020058v (Pubitemid 35281997)
-
(2002)
Journal of Physical Chemistry B
, vol.106
, Issue.18
, pp. 4844-4853
-
-
Zhu, J.1
Shi, Y.2
Liu, H.3
-
68
-
-
0000122439
-
-
10.1002/(SICI)1096-987X(199805)19:7769::AID-JCC73.0.CO;2-O
-
M. R. Reddy, M. D. Erion, A. Agarwal, V. N. Viswanadhan, D. Q. McDonald, and W. C. Still, J. Comput. Chem. 19, 769 (1998). 10.1002/(SICI)1096- 987X(199805)19:7769::AID-JCC73.0.CO;2-O
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 769
-
-
Reddy, M.R.1
Erion, M.D.2
Agarwal, A.3
Viswanadhan, V.N.4
McDonald, D.Q.5
Still, W.C.6
-
69
-
-
0000741414
-
A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
-
DOI 10.1063/1.476697, PII S002196069850325X
-
B. Jayaram, Y. Liu, and D. L. Beveridge, J. Chem. Phys. 109, 1465 (1998). 10.1063/1.476697 (Pubitemid 128678564)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.4
, pp. 1465-1471
-
-
Jayaram, B.1
Liu, Y.2
Beveridge, D.L.3
-
71
-
-
33746347382
-
New-generation Amber united-atom force field
-
DOI 10.1021/jp060163v
-
L. J. Yang, C. H. Tan, M. J. Hsieh, J. M. Wang, Y. Duan, P. Cieplak, J. Caidwell, P. A. Kollman, and R. Luo, J. Phys. Chem. B 110, 13166 (2006). 10.1021/jp060163v (Pubitemid 44115654)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.26
, pp. 13166-13176
-
-
Yang, L.1
Tan, C.-H.2
Hsieh, M.-J.3
Wang, J.4
Duan, Y.5
Cieplak, P.6
Caldwell, J.7
Kollman, P.A.8
Luo, R.9
-
72
-
-
77749298172
-
-
10.1021/jp910674d
-
J. W. Ponder, C. Wu, P. Ren, V. S. Pande, J. D. Chodera, M. J. Schnieders, I. Haque, D. L. Molbey, D. S. Lambrecht, R. A. DiStasio, M. Head-Gordon, G. N. I. Clark, M. B. Johnson, and T. Head-Gordon, J. Phys. Chem. B 114, 2549 (2010). 10.1021/jp910674d
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2549
-
-
Ponder, J.W.1
Wu, C.2
Ren, P.3
Pande, V.S.4
Chodera, J.D.5
Schnieders, M.J.6
Haque, I.7
Molbey, D.L.8
Lambrecht, D.S.9
Distasio, R.A.10
Head-Gordon, M.11
Clark, G.N.I.12
Johnson, M.B.13
Head-Gordon, T.14
-
73
-
-
33750899801
-
-
10.1021/ct050097l
-
R. C. Rizzo, T. Aynechi, D. A. Case, and I. D. Kuntz, J. Chem. Theory. Comput. 2, 128 (2006). 10.1021/ct050097l
-
(2006)
J. Chem. Theory. Comput.
, vol.2
, pp. 128
-
-
Rizzo, R.C.1
Aynechi, T.2
Case, D.A.3
Kuntz, I.D.4
-
75
-
-
84962463447
-
Thirty years of continuum solvation chemistry: A review, and prospects for the near future
-
DOI 10.1007/s00214-004-0582-3
-
J. Tomasi, Theor. Chem. Acc. 112, 184 (2004). 10.1007/s00214-004-0582-3 (Pubitemid 39329340)
-
(2004)
Theoretical Chemistry Accounts
, vol.112
, Issue.4
, pp. 184-203
-
-
Tomasi, J.1
-
77
-
-
33751157086
-
-
10.1021/j100007a062
-
A. Klamt, J. Phys. Chem. 99, 2224 (1995). 10.1021/j100007a062
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 2224
-
-
Klamt, A.1
-
78
-
-
84961976178
-
-
10.1063/1.473662
-
A. Klamt, J. Chem. Phys. 106, 6622 (1997). 10.1063/1.473662
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 6622
-
-
Klamt, A.1
-
83
-
-
84961976132
-
Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton
-
DOI 10.1021/jp063552y
-
C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B 110, 16066 (2006). 10.1021/jp063552y (Pubitemid 44366386)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.32
, pp. 16066-16081
-
-
Kelly, C.P.1
Cramer, C.J.2
Truhlar, D.G.3
-
86
-
-
0033269427
-
-
10.1007/s002140050513
-
J. B. Li, T. H. Zhu, G. D. Hawkins, P. Winger, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, Theor. Chem. Acc. 103, 9 (1999). 10.1007/ s002140050513
-
(1999)
Theor. Chem. Acc.
, vol.103
, pp. 9
-
-
Li, J.B.1
Zhu, T.H.2
Hawkins, G.D.3
Winger, P.4
Liotard, D.A.5
Cramer, C.J.6
Truhlar, D.G.7
-
87
-
-
0032557286
-
-
10.1016/S0009-2614(98)00194-8
-
J. B. Li, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Chem. Phys. Lett. 288, 293 (1998). 10.1016/S0009-2614(98)00194-8
-
(1998)
Chem. Phys. Lett.
, vol.288
, pp. 293
-
-
Li, J.B.1
Hawkins, G.D.2
Cramer, C.J.3
Truhlar, D.G.4
-
88
-
-
0001440875
-
Density functional solvation model based on CM2 atomic charges
-
DOI 10.1063/1.476521, PII S0021960698508446
-
T. H. Zhu, B. J. Li, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, J. Chem. Phys. 109, 9117 (1998). 10.1063/1.476521 (Pubitemid 128672492)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.20
, pp. 9117-9133
-
-
Zhu, T.1
Li, J.2
Hawkins, G.D.3
Cramer, C.J.4
Truhlar, D.G.5
-
89
-
-
3342936878
-
-
10.1126/science.256.5054.213
-
C. J. Cramer and D. G. Truhlar, Science 256, 213 (1992). 10.1126/science.256.5054.213
-
(1992)
Science
, vol.256
, pp. 213
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
91
-
-
84962415061
-
-
10.1039/b306954k
-
F. J. Luque, C. Curutchet, J. Muoz-Muriedas, A. Bidon-Chanal, I. Soteras, A. Morreale, J. L. Gelp, and M. Orozco, Phys. Chem. Chem. Phys. 5, 3827 (2003). 10.1039/b306954k
-
(2003)
Phys. Chem. Chem. Phys.
, vol.5
, pp. 3827
-
-
Luque, F.J.1
Curutchet, C.2
Muoz-Muriedas, J.3
Bidon-Chanal, A.4
Soteras, I.5
Morreale, A.6
Gelp, J.L.7
Orozco, M.8
-
95
-
-
34047168032
-
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
-
DOI 10.1063/1.2714528
-
M. J. Schnieders, N. A. Baker, P. Ren, and J. W. Ponder, J. Chem. Phys. 126, 124114 (2007). 10.1063/1.2714528 (Pubitemid 46517127)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.12
, pp. 124114
-
-
Schnieders, M.J.1
Baker, N.A.2
Ren, P.3
Ponder, J.W.4
-
97
-
-
0242443693
-
Force fields for protein simulations
-
DOI 10.1016/S0065-3233(03)66002-X
-
J. W. Ponder and D. A. Case, Adv. Protein. Chem. 66, 27 (2003). 10.1016/S0065-3233(03)66002-X (Pubitemid 37392314)
-
(2003)
Advances in Protein Chemistry
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
98
-
-
0346850017
-
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field
-
DOI 10.1021/ja037005r
-
A. Grossfield, P. Ren, and J. W. Ponder, J. Am. Chem. Soc. 125, 15671 (2003). 10.1021/ja037005r (Pubitemid 37532213)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.50
, pp. 15671-15682
-
-
Grossfield, A.1
Ren, P.2
Ponder, J.W.3
-
99
-
-
33947591301
-
Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization
-
DOI 10.1002/qua.21278
-
T. S. Rasmussen, P. Ren, J. W. Ponder, and F. Jensen, Int. J. Quantum Chem. 107, 1390 (2007). 10.1002/qua.21278 (Pubitemid 46480209)
-
(2007)
International Journal of Quantum Chemistry
, vol.107
, Issue.6
, pp. 1390-1395
-
-
Rasmussen, T.D.1
Ren, P.2
Ponder, J.W.3
Jensen, F.4
-
107
-
-
0034831674
-
Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model
-
DOI 10.1063/1.1336805
-
S. W. Rick, J. Chem. Phys. 114, 2276 (2001). 10.1063/1.1336805 (Pubitemid 32873150)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.5
, pp. 2276-2283
-
-
Rick, S.W.1
-
110
-
-
37049070447
-
-
10.1039/ft9949002881
-
A. C. T. van Duin, J. M. A. Baas, and B. van de Graaf, J. Chem. Soc., Faraday Trans. 90, 2881 (1994). 10.1039/ft9949002881
-
(1994)
J. Chem. Soc., Faraday Trans.
, vol.90
, pp. 2881
-
-
Van Duin, A.C.T.1
Baas, J.M.A.2
Van De Graaf, B.3
-
111
-
-
0001586289
-
-
10.1039/ft9969200353
-
A. C. T. van Duin, J. M. A. Baas, and B. van de Graaf, J. Chem. Soc., Faraday Trans. 92, 353 (1996). 10.1039/ft9969200353
-
(1996)
J. Chem. Soc., Faraday Trans.
, vol.92
, pp. 353
-
-
Van Duin, A.C.T.1
Baas, J.M.A.2
Van De Graaf, B.3
-
112
-
-
0042041206
-
-
10.1021/ja00051a040
-
A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. I. Goddard, and W. M. Skiff, J. Am. Chem. Soc. 114, 10024 (1992). 10.1021/ja00051a040
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 10024
-
-
Rappé, A.K.1
Casewit, C.J.2
Colwell, K.S.3
Goddard, W.A.I.4
Skiff, W.M.5
-
116
-
-
0036532208
-
Towards a polarizable force field for molecular liquids
-
DOI 10.1016/S0167-7322(01)00329-4, PII S0167732201003294
-
R. Chelli, R. Righini, S. Califano, and P. Procacci, J. Mol. Liq. 96, 87 (2002). 10.1016/S0167-7322(01)00329-4 (Pubitemid 34221241)
-
(2002)
Journal of Molecular Liquids
, vol.96-97
, pp. 87-100
-
-
Chelli, R.1
Righini, R.2
Califano, S.3
Procacci, P.4
-
120
-
-
0009008928
-
-
10.1016/S0009-2614(99)01289-0
-
Y. Cong and Z. Z. Yang, Chem. Phys. Lett. 316, 324 (2000). 10.1016/S0009-2614(99)01289-0
-
(2000)
Chem. Phys. Lett.
, vol.316
, pp. 324
-
-
Cong, Y.1
Yang, Z.Z.2
-
123
-
-
19944374774
-
Study of lithium cation in water clusters: Based on atom-bond electronegativity equalization method fused into molecular mechanics
-
DOI 10.1021/jp0458093
-
X. Li and Z. Z. Yang, J. Phys. Chem. A 109, 4102 (2005). 10.1021/jp0458093 (Pubitemid 40750865)
-
(2005)
Journal of Physical Chemistry A
, vol.109
, Issue.18
, pp. 4102-4111
-
-
Li, X.1
Yang, Z.-Z.2
-
124
-
-
22944470523
-
+-ion in atom-bond electronegativity equalization method-7P water: A molecular dynamics simulation study
-
DOI 10.1063/1.1853372, 084514
-
X. Li and Z. Z. Yang, J. Chem. Phys. 122, 084514 (2005). 10.1063/1.1853372 (Pubitemid 41047496)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.8
, pp. 1-15
-
-
Li, X.1
Yang, Z.-Z.2
-
125
-
-
18444413236
-
Ion solvation in water from molecular dynamics simulation with the ABEEM/MM force field
-
DOI 10.1021/jp051106p
-
Z. Z. Yang and X. Li, J. Phys. Chem. A 109, 3517 (2005). 10.1021/jp051106p (Pubitemid 40643940)
-
(2005)
Journal of Physical Chemistry A
, vol.109
, Issue.16
, pp. 3517-3520
-
-
Yang, Z.-Z.1
Li, X.2
-
126
-
-
13444282048
-
An investigation of alkane conformations based on the ABEEM/MM model
-
DOI 10.1016/j.cplett.2005.01.011, PII S0009261405000266
-
Q. Zhang and Z. Z. Yang, Chem. Phys. Lett. 403, 242 (2005). 10.1016/j.cplett.2005.01.011 (Pubitemid 40208391)
-
(2005)
Chemical Physics Letters
, vol.403
, Issue.4-6
, pp. 242-247
-
-
Zhang, Q.1
Yang, Z.-Z.2
-
127
-
-
33747241976
-
-
10.1063/1.2210940
-
Z. Z. Yang and P. Qian, J. Chem. Phys. 125, 064311 (2006). 10.1063/1.2210940
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 064311
-
-
Yang, Z.Z.1
Qian, P.2
-
129
-
-
77950131426
-
-
10.1021/ct9006647
-
D. X. Zhao, C. Liu, F. F. Wang, C. Y. Yu, L. D. Gong, S. B. Liu, and Z. Z. Yang, J. Chem. Theory Comput. 6, 795 (2010). 10.1021/ct9006647
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 795
-
-
Zhao, D.X.1
Liu, C.2
Wang, F.F.3
Yu, C.Y.4
Gong, L.D.5
Liu, S.B.6
Yang, Z.Z.7
-
131
-
-
33746868580
-
Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics
-
DOI 10.1063/1.2000245, 094507
-
Z.-Z. Yang and X. Li, J. Chem. Phys. 123, 094507 (2005). 10.1063/1.2000245 (Pubitemid 41329946)
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.9
, pp. 1-10
-
-
Yang, Z.-Z.1
Li, X.2
-
133
-
-
36749117171
-
-
10.1063/1.436185
-
R. G. Parr, R. A. Donnelly, M. Levy, and W. E. Palke, J. Chem. Phys. 68, 3801 (1978). 10.1063/1.436185
-
(1978)
J. Chem. Phys.
, vol.68
, pp. 3801
-
-
Parr, R.G.1
Donnelly, R.A.2
Levy, M.3
Palke, W.E.4
-
134
-
-
15744375697
-
-
Gaussian, Inc., Wallingford CT.
-
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, GAUSSIAN 03, Revision C.02; Gaussian, Inc., Wallingford CT 2004.
-
(2004)
GAUSSIAN 03, Revision C.02
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Montgomery Jr., J.A.7
Vreven, T.8
Kudin, K.N.9
Burant, J.C.10
Millam, J.M.11
Iyengar, S.S.12
Tomasi, J.13
Barone, V.14
Mennucci, B.15
Cossi, M.16
Scalmani, G.17
Rega, N.18
Petersson, G.A.19
Nakatsuji, H.20
Hada, M.21
Ehara, M.22
Toyota, K.23
Fukuda, R.24
Hasegawa, J.25
Ishida, M.26
Nakajima, T.27
Honda, Y.28
Kitao, O.29
Nakai, H.30
Klene, M.31
Li, X.32
Knox, J.E.33
Hratchian, H.P.34
Cross, J.B.35
Bakken, V.36
Adamo, C.37
Jaramillo, J.38
Gomperts, R.39
Stratmann, R.E.40
Yazyev, O.41
Austin, A.J.42
Cammi, R.43
Pomelli, C.44
Ochterski, J.W.45
Ayala, P.Y.46
Morokuma, K.47
Voth, G.A.48
Salvador, P.49
Dannenberg, J.J.50
Zakrzewski, V.G.51
Dapprich, S.52
Daniels, A.D.53
Strain, M.C.54
Farkas, O.55
Malick, D.K.56
Rabuck, A.D.57
Raghavachari, K.58
Foresman, J.B.59
Ortiz, J.V.60
Cui, Q.61
Baboul, A.G.62
Clifford, S.63
Cioslowski, J.64
Stefanov, B.B.65
Liu, G.66
Liashenko, A.67
Piskorz, P.68
Komaromi, I.69
Martin, R.L.70
Fox, D.J.71
Keith, T.72
Al-Laham, M.A.73
Peng, C.Y.74
Nanayakkara, A.75
Challacombe, M.76
Gill, P.M.W.77
Johnson, B.78
Chen, W.79
Wong, M.W.80
Gonzalez, C.81
Pople, J.A.82
more..
-
135
-
-
0020475449
-
-
10.1016/0022-2836(82)90515-0
-
J. Dyte and R. F. Doolittle, J. Mol. Biol. 157, 105 (1982). 10.1016/0022-2836(82)90515-0
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105
-
-
Dyte, J.1
Doolittle, R.F.2
-
136
-
-
0026076664
-
-
10.1021/bi00104a017
-
K. Sharp, A. Nicholls, R. Fredman, and B. Honig, Biochemistry 30, 9686 (1991). 10.1021/bi00104a017
-
(1991)
Biochemistry
, vol.30
, pp. 9686
-
-
Sharp, K.1
Nicholls, A.2
Fredman, R.3
Honig, B.4
-
139
-
-
0000304948
-
-
10.1021/ja00105a030
-
D. J. Tannor, B. Marten, R. Murphy, R. A. Friesner, D. Sitkoff, A. Nicholls, M. Ringnalda, W. A. I. Goddard, and B. Honig, J. Am. Chem. Soc. 116, 11875 (1994). 10.1021/ja00105a030
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 11875
-
-
Tannor, D.J.1
Marten, B.2
Murphy, R.3
Friesner, R.A.4
Sitkoff, D.5
Nicholls, A.6
Ringnalda, M.7
Goddard, W.A.I.8
Honig, B.9
-
140
-
-
4143090195
-
-
10.1007/BF00643580
-
S. Cabani, P. Gianni, V. Mollica, and L. Lepori, J. Solution Chem. 7, 721 (1978). 10.1007/BF00643580
-
(1978)
J. Solution Chem.
, vol.7
, pp. 721
-
-
Cabani, S.1
Gianni, P.2
Mollica, V.3
Lepori, L.4
-
141
-
-
0019883174
-
-
10.1021/bi00507a030
-
R. Wolfenden, L. Andersson, P. M. Cullis, and C. C. B. Southgate, Biochemistry 20, 849 (1981). 10.1021/bi00507a030
-
(1981)
Biochemistry
, vol.20
, pp. 849
-
-
Wolfenden, R.1
Andersson, L.2
Cullis, P.M.3
Southgate, C.C.B.4
-
142
-
-
0017855698
-
-
10.1021/bi00594a030
-
R. Wolfenden, Biochemistry 17, 201 (1978). 10.1021/bi00594a030
-
(1978)
Biochemistry
, vol.17
, pp. 201
-
-
Wolfenden, R.1
-
146
-
-
84986512474
-
-
10.1002/jcc.540040211
-
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983). 10.1002/jcc.540040211
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
147
-
-
84988053694
-
-
10.1002/jcc.540070216
-
S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem. 7, 230 (1986). 10.1002/jcc.540070216
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 230
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
149
-
-
0013271660
-
-
10.1021/j100204a034
-
C. Chipot, B. Maigret, J. L. Rivail, and H. A. Scheraga, J. Phys. Chem. 96, 10276 (1992). 10.1021/j100204a034
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 10276
-
-
Chipot, C.1
Maigret, B.2
Rivail, J.L.3
Scheraga, H.A.4
-
150
-
-
84962334359
-
-
See supplementary material at E-JCPSA6-134-047119 for solvation energies of small molecules.
-
See supplementary material at http://dx.doi.org/10.1063/1.3590718 E-JCPSA6-134-047119 for solvation energies of small molecules.
-
-
-
|