-
1
-
-
0142025560
-
Structure and Dynamics of Hydrated Ions
-
Ohtaki, H.; Radnai, T. Structure and Dynamics of Hydrated Ions Chem. Rev. 1993, 93, 1157-1204
-
(1993)
Chem. Rev.
, vol.93
, pp. 1157-1204
-
-
Ohtaki, H.1
Radnai, T.2
-
2
-
-
0028133296
-
A Simple Empirical-Model Describing the Thermodynamics of Hydration of Ions of Widely Varying Charges, Sizes, and Shapes
-
Marcus, Y. A Simple Empirical-Model Describing the Thermodynamics of Hydration of Ions of Widely Varying Charges, Sizes, and Shapes Biophys. Chem. 1994, 51, 111-127
-
(1994)
Biophys. Chem.
, vol.51
, pp. 111-127
-
-
Marcus, Y.1
-
3
-
-
79955711882
-
Ion Selectivity in Channels and Transporters
-
Roux, B.; Bernèche, S.; Egwolf, B.; Lev, B.; Noskov, S. Y.; Rowley, C. N.; Yu, H. Ion Selectivity in Channels and Transporters J. Gen. Physiol. 2011, 137, 415-426
-
(2011)
J. Gen. Physiol.
, vol.137
, pp. 415-426
-
-
Roux, B.1
Bernèche, S.2
Egwolf, B.3
Lev, B.4
Noskov, S.Y.5
Rowley, C.N.6
Yu, H.7
-
4
-
-
82755194890
-
Functionalized graphene sheets for arsenic removal and desalination of sea water
-
Mishra, A. K.; Ramaprabhu, S. Functionalized graphene sheets for arsenic removal and desalination of sea water Desalination 2011, 282, 39-45
-
(2011)
Desalination
, vol.282
, pp. 39-45
-
-
Mishra, A.K.1
Ramaprabhu, S.2
-
5
-
-
57549101676
-
Selective Ion Passage through Functionalized Graphene Nanopores
-
Sint, K.; Wang, B.; Kral, P. Selective Ion Passage through Functionalized Graphene Nanopores J. Am. Chem. Soc. 2008, 130, 16448-16449
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 16448-16449
-
-
Sint, K.1
Wang, B.2
Kral, P.3
-
6
-
-
79954578079
-
Biomimetic smart nanopores and nanochannels
-
Hou, X.; Guo, Y.; Jiang, L. Biomimetic smart nanopores and nanochannels Chem. Soc. Rev. 2011, 40, 2385-2401
-
(2011)
Chem. Soc. Rev.
, vol.40
, pp. 2385-2401
-
-
Hou, X.1
Guo, Y.2
Jiang, L.3
-
7
-
-
84862284389
-
Ion Binding Sites and Their Representations by Reduced Models
-
Roux, B. Ion Binding Sites and Their Representations by Reduced Models J. Phys. Chem. B 2012, 116, 6966-6979
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 6966-6979
-
-
Roux, B.1
-
8
-
-
0344796204
-
Ion Water Interaction Potential Derived from Free Energy Perturbation Simulations
-
Åqvist, J. Ion Water Interaction Potential Derived from Free Energy Perturbation Simulations J. Phys. Chem. 1990, 94, 8021-8024
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8021-8024
-
-
Åqvist, J.1
-
9
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins and Nucleic Acids
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; K. M., M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins and Nucleic Acids J. Am. Chem. Soc. 1995, 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, Jr.I.R.K.M.M.4
Ferguson, D.M.5
Spellmeyer, D.C.6
Fox, T.7
Caldwell, J.W.8
Kollman, P.A.9
-
10
-
-
0003396304
-
-
In; John Wiley & Sons: Chichester.
-
MacKerell, A. D.; Brooks, B.; C. L., B., III; Nilsson, L.; Won, Y.; Roux, B.; Karplus, M. In The Encyclopedia of Computational Chemistry; John Wiley & Sons: Chichester, 1998.
-
(1998)
The Encyclopedia of Computational Chemistry
-
-
Mackerell, A.D.1
Brooks III, B.C.L.B.2
Nilsson, L.3
Won, Y.4
Roux, B.5
Karplus, M.6
-
11
-
-
77950544751
-
Principles of Conduction and Hydrophobic Gating in K+ Channels
-
Jensen, M. O.; Borhani, D. W.; Lindorff-Larsen, K.; Maragakis, P.; Jogini, V.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Principles of Conduction and Hydrophobic Gating in K+ Channels Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5833-8
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 5833-5838
-
-
Jensen, M.O.1
Borhani, D.W.2
Lindorff-Larsen, K.3
Maragakis, P.4
Jogini, V.5
Eastwood, M.P.6
Dror, R.O.7
Shaw, D.E.8
-
12
-
-
77957131188
-
Selective Complexation of K+ and Na+ in Simple Polarizable Ion-Ligating Systems
-
Bostick, D. L.; Brooks, C. L. Selective Complexation of K+ and Na+ in Simple Polarizable Ion-Ligating Systems J. Am. Chem. Soc. 2010, 132, 13185-13187
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 13185-13187
-
-
Bostick, D.L.1
Brooks, C.L.2
-
13
-
-
80455174602
-
Protonation of Key Acidic Residues Is Critical for the K+-Selectivity of the Na/K Pump
-
Yu, H. B.; Ratheal, I. M.; Artigas, P.; Roux, B. Protonation of Key Acidic Residues Is Critical for the K+-Selectivity of the Na/K Pump Nat. Struct. Mol. Biol. 2011, 18, 1159-1163
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1159-1163
-
-
Yu, H.B.1
Ratheal, I.M.2
Artigas, P.3
Roux, B.4
-
14
-
-
78650546908
-
Two Mechanisms of Ion Selectivity in Protein Binding Sites
-
Yu, H. B.; Noskov, S. Y.; Roux, B. Two Mechanisms of Ion Selectivity in Protein Binding Sites Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 20329-20334
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 20329-20334
-
-
Yu, H.B.1
Noskov, S.Y.2
Roux, B.3
-
15
-
-
84873029441
-
Role of the Protein Matrix Rigidity and Local Polarization Effects in the Monovalent Cation Selectivity of Crystallographic Sites in the Na-Coupled Aspartate Transporter
-
Lev, B.; Noskov, S. Y. Role of the Protein Matrix Rigidity and Local Polarization Effects in the Monovalent Cation Selectivity of Crystallographic Sites in the Na-Coupled Aspartate Transporter Phys. Chem. Chem. Phys. 2013, 15, 2397-2404
-
(2013)
Phys. Chem. Chem. Phys.
, vol.15
, pp. 2397-2404
-
-
Lev, B.1
Noskov, S.Y.2
-
16
-
-
0346850017
-
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field
-
Grossfield, A.; Ren, P.; Ponder, J. W. Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field J. Am. Chem. Soc. 2003, 125, 15671-15682
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 15671-15682
-
-
Grossfield, A.1
Ren, P.2
Ponder, J.W.3
-
17
-
-
4043057278
-
CHARMM Fluctuating Charge Force Field for Proteins: II Protein/Solvent Properties from Molecular Dynamics Simulations Using a Nonadditive Electrostatic Model
-
Patel, S.; Mackerell, A. D., Jr.; Brooks, C. L., 3rd CHARMM Fluctuating Charge Force Field for Proteins: II Protein/Solvent Properties from Molecular Dynamics Simulations Using a Nonadditive Electrostatic Model J. Comput. Chem. 2004, 25, 1504-14
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1504-1514
-
-
Patel, S.1
Mackerell Jr., A.D.2
Brooks III, C.L.3
-
18
-
-
30344482264
-
A Polarizable Model of Water for Molecular Dynamics Simulations of Biomolecules
-
Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. A Polarizable Model of Water for Molecular Dynamics Simulations of Biomolecules Chem. Phys. Lett. 2006, 418, 245-249
-
(2006)
Chem. Phys. Lett.
, vol.418
, pp. 245-249
-
-
Lamoureux, G.1
Harder, E.2
Vorobyov, I.V.3
Roux, B.4
Mackerell, A.D.5
-
19
-
-
36649014917
-
Theoretical Study of Aqueous Solvation of K+ Comparing Ab Initio, Polarizable, and Fixed-Charge Models
-
Whitfield, T. W.; Varma, S.; Harder, E.; Lamoureux, G.; Rempe, S. B.; Roux, B. Theoretical Study of Aqueous Solvation of K+ Comparing Ab Initio, Polarizable, and Fixed-Charge Models J. Chem. Theor. Comp. 2007, 3, 2068-2082
-
(2007)
J. Chem. Theor. Comp.
, vol.3
, pp. 2068-2082
-
-
Whitfield, T.W.1
Varma, S.2
Harder, E.3
Lamoureux, G.4
Rempe, S.B.5
Roux, B.6
-
20
-
-
77950132714
-
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field
-
Yu, H. B.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V. M.; MacKerell, A. D.; Roux, B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field J. Chem. Theor. Comp. 2010, 6, 774-786
-
(2010)
J. Chem. Theor. Comp.
, vol.6
, pp. 774-786
-
-
Yu, H.B.1
Whitfield, T.W.2
Harder, E.3
Lamoureux, G.4
Vorobyov, I.5
Anisimov, V.M.6
Mackerell, A.D.7
Roux, B.8
-
21
-
-
17444426103
-
Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field
-
Noskov, S. Y.; Lamoureux, G.; Roux, B. Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field J. Phys. Chem. B 2005, 109, 6705-13
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6705-6713
-
-
Noskov, S.Y.1
Lamoureux, G.2
Roux, B.3
-
22
-
-
58149400921
-
A Novel Polarizable Model of Chloroform Based on Classical Drude Oscillators
-
Lamoureux, G.; Faraldo-Gomez, J.; Krupin, S. V.; S.Yu., N. A Novel Polarizable Model of Chloroform Based on Classical Drude Oscillators Chem. Phys. Lett. 2009, 268, 270-274
-
(2009)
Chem. Phys. Lett.
, vol.268
, pp. 270-274
-
-
Lamoureux, G.1
Faraldo-Gomez, J.2
Krupin, S.V.3
Yu, N.4
-
23
-
-
84857080087
-
The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers
-
Vorobyov, I.; Bennett, W. F. D.; Tieleman, D. P.; Allen, T. W.; Noskov, S. Y. The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers J. Chem. Theory Comput. 2012, 8, 618-628
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 618-628
-
-
Vorobyov, I.1
Bennett, W.F.D.2
Tieleman, D.P.3
Allen, T.W.4
Noskov, S.Y.5
-
24
-
-
33644879448
-
Absolute Hydration Free Energy Scale for Alkali and Halide Ions Established from Simulations with a Polarizable Force Field
-
Lamoureux, G.; Roux, B. Absolute Hydration Free Energy Scale for Alkali and Halide Ions Established from Simulations with a Polarizable Force Field J. Phys. Chem. B 2006, 110, 3308-3322
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3308-3322
-
-
Lamoureux, G.1
Roux, B.2
-
25
-
-
77955368256
-
A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide
-
Yu, H.; Mazzanti, C. L.; Whitfield, T. W.; Koeppe, R. E.; Andersen, O. S.; Roux, B. A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide J. Am. Chem. Soc. 2010, 132, 10847-10856
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 10847-10856
-
-
Yu, H.1
Mazzanti, C.L.2
Whitfield, T.W.3
Koeppe, R.E.4
Andersen, O.S.5
Roux, B.6
-
26
-
-
33846891132
-
Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics
-
Kuhne, T. D.; Krack, M.; Mohamed, F. R.; Parrinello, M. Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics Phys. Rev. Lett. 2007, 98, 066401
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 066401
-
-
Kuhne, T.D.1
Krack, M.2
Mohamed, F.R.3
Parrinello, M.4
-
27
-
-
18744373081
-
Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics
-
Schlegel, H. B.; Iyengar, S. S.; Li, X.; Milliam, J. M.; Voth, G. A.; Scuseria, G. E.; Frisch, M. J. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics J. Chem. Phys. 2002, 117, 8694-8703
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 8694-8703
-
-
Schlegel, H.B.1
Iyengar, S.S.2
Li, X.3
Milliam, J.M.4
Voth, G.A.5
Scuseria, G.E.6
Frisch, M.J.7
-
28
-
-
0000381544
-
Ab Initio Molecular-Dynamics Simulation of K+ Solvation in Water
-
Ramaniah, L.; Bernasconi, M.; Parrinello, M. Ab Initio Molecular-Dynamics Simulation of K+ Solvation in Water J. Chem. Phys. 1999, 111, 1587-1592
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 1587-1592
-
-
Ramaniah, L.1
Bernasconi, M.2
Parrinello, M.3
-
29
-
-
0034269312
-
The Solvation of Na+ in Water: First-Principles Simulations
-
White, J.; Schwegler, E.; Galli, G.; Gygi, F. The Solvation of Na+ in Water: First-Principles Simulations J. Chem. Phys. 2000, 113, 4668-4674
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 4668-4674
-
-
White, J.1
Schwegler, E.2
Galli, G.3
Gygi, F.4
-
30
-
-
0035392380
-
The Hydration Number of Na+ in Liquid Water
-
Rempe, S.; Pratt, L. The Hydration Number of Na+ in Liquid Water Fluid. Phas. Equil. 2001, 183, 121-132
-
(2001)
Fluid. Phas. Equil.
, vol.183
, pp. 121-132
-
-
Rempe, S.1
Pratt, L.2
-
31
-
-
2342608969
-
Inner Shell Definition and Absolute Hydration Free Energy of K+(aq) on the Basis of Quasi-chemical Theory and Ab Initio Molecular Dynamics
-
Rempe, S.; Asthagiri, D.; Pratt, L. Inner Shell Definition and Absolute Hydration Free Energy of K+(aq) on the Basis of Quasi-chemical Theory and Ab Initio Molecular Dynamics Phys. Chem. Chem. Phys. 2004, 6, 1966-1969
-
(2004)
Phys. Chem. Chem. Phys.
, vol.6
, pp. 1966-1969
-
-
Rempe, S.1
Asthagiri, D.2
Pratt, L.3
-
32
-
-
77950391024
-
Hydration and Coordination of K+ Solvation in Water from Ab Initio Molecular-Dynamics Simulation
-
Liu, Y.; Lu, H.; Wu, Y.; Hu, T.; Li, Q. Hydration and Coordination of K+ Solvation in Water from Ab Initio Molecular-Dynamics Simulation J. Chem. Phys. 2010, 132, 124503
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 124503
-
-
Liu, Y.1
Lu, H.2
Wu, Y.3
Hu, T.4
Li, Q.5
-
33
-
-
63849309828
-
Hydration of Sodium(I) and Potassium(I) Revisited: A Comparative QM/MM and QMCF MD Simulation Study of Weakly Hydrated Ions
-
Azam, S. S.; Hofer, T. S.; Randolf, B. R.; Rode, B. M. Hydration of Sodium(I) and Potassium(I) Revisited: A Comparative QM/MM and QMCF MD Simulation Study of Weakly Hydrated Ions J. Phys. Chem. A 2009, 113, 1827-1834
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 1827-1834
-
-
Azam, S.S.1
Hofer, T.S.2
Randolf, B.R.3
Rode, B.M.4
-
34
-
-
33644750286
-
Ab Initio Quantum Mechanical Charge Field (QMCF) Molecular Dynamics: A QM/MM MD Procedure for Accurate Simulations of Ions and Complexes
-
Rode, B.; Hofer, T.; Randolf, B.; Schwenk, C.; Xenides, D.; Vchirawongkwin, V. Ab Initio Quantum Mechanical Charge Field (QMCF) Molecular Dynamics: A QM/MM MD Procedure for Accurate Simulations of Ions and Complexes Theor. Chem. Acc. 2006, 115, 77-85
-
(2006)
Theor. Chem. Acc.
, vol.115
, pp. 77-85
-
-
Rode, B.1
Hofer, T.2
Randolf, B.3
Schwenk, C.4
Xenides, D.5
Vchirawongkwin, V.6
-
35
-
-
77951591762
-
Hydration Properties of the Bromide Aqua Ion: The Interplay of First Principle and Classical Molecular Dynamics, and X-ray Absorption Spectroscopy
-
D'Angelo, P.; Migliorati, V.; Guidoni, L. Hydration Properties of the Bromide Aqua Ion: The Interplay of First Principle and Classical Molecular Dynamics, and X-ray Absorption Spectroscopy Inorg. Chem. 2010, 49, 4224-4231
-
(2010)
Inorg. Chem.
, vol.49
, pp. 4224-4231
-
-
D'Angelo, P.1
Migliorati, V.2
Guidoni, L.3
-
36
-
-
66749185225
-
Ab Initio Molecular Dynamics Calculations of Ion Hydration Free Energies
-
Leung, K.; Rempe, S. B.; von Lilienfeld, O. A. Ab Initio Molecular Dynamics Calculations of Ion Hydration Free Energies J. Chem. Phys. 2009, 130, 204507-204511
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 204507-204511
-
-
Leung, K.1
Rempe, S.B.2
Von Lilienfeld, O.A.3
-
37
-
-
81855185381
-
Real-World Predictions from Ab Initio Molecular Dynamics Simulations
-
Kirchner, B.; di Dio, P. J.; Hutter, J. Real-World Predictions from Ab Initio Molecular Dynamics Simulations Top. Curr. Chem. 2012, 307, 109-153
-
(2012)
Top. Curr. Chem.
, vol.307
, pp. 109-153
-
-
Kirchner, B.1
Di Dio, P.J.2
Hutter, J.3
-
38
-
-
2342580710
-
Ultrafast Vibrational Dynamics of Hydrogen Bonds in the Condensed Phase
-
Nibbering, E. T.; Elsaesser, T. Ultrafast Vibrational Dynamics of Hydrogen Bonds in the Condensed Phase Chem. Rev. 2004, 104, 1887-914
-
(2004)
Chem. Rev.
, vol.104
, pp. 1887-1914
-
-
Nibbering, E.T.1
Elsaesser, T.2
-
39
-
-
77951245193
-
Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton
-
Marx, D.; Chandra, A.; Tuckerman, M. E. Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton Chem. Rev. 2010, 110, 2174-216
-
(2010)
Chem. Rev.
, vol.110
, pp. 2174-2216
-
-
Marx, D.1
Chandra, A.2
Tuckerman, M.E.3
-
40
-
-
33748633480
-
Electrostatic Basis for Enzyme Reaction
-
Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H. B.; Olsson, M. H. M. Electrostatic Basis for Enzyme Reaction Chem. Rev. 2006, 106, 3210-3235
-
(2006)
Chem. Rev.
, vol.106
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.B.5
Olsson, M.H.M.6
-
41
-
-
0041876227
-
Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights
-
Warshel, A. Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights Ann. Rev. Biophys. Biomolec. Struct. 2003, 32, 425-443
-
(2003)
Ann. Rev. Biophys. Biomolec. Struct.
, vol.32
, pp. 425-443
-
-
Warshel, A.1
-
42
-
-
0347051645
-
Density Functional Theory Based Molecular-Dynamics Study of Aqueous Chloride Solvation
-
Heuft, J. M.; Meijer, E. J. Density Functional Theory Based Molecular-Dynamics Study of Aqueous Chloride Solvation J. Chem. Phys. 2003, 119, 11788-11791
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 11788-11791
-
-
Heuft, J.M.1
Meijer, E.J.2
-
43
-
-
33646356998
-
Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
-
Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H. B.; Ghosh, P.; Prat-Resina, X.; Konig, P.; Li, G. H.; Xu, D. G.; Guo, H.; Elstner, M.; Cui, Q. C. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes J. Phys. Chem. B 2006, 110, 6458-6469
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 6458-6469
-
-
Riccardi, D.1
Schaefer, P.2
Yang, Y.3
Yu, H.B.4
Ghosh, P.5
Prat-Resina, X.6
Konig, P.7
Li, G.H.8
Xu, D.G.9
Guo, H.10
Elstner, M.11
Cui, Q.C.12
-
44
-
-
58149161538
-
QM/MM Modeling of Benzene Hydroxulation in Human Cytochrome P450 2C9
-
Bathelt, C. M.; Mulholland, A. J.; Harvey, J. N. QM/MM Modeling of Benzene Hydroxulation in Human Cytochrome P450 2C9 J. Phys. Chem. B 2008, 112, 13149-13156
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13149-13156
-
-
Bathelt, C.M.1
Mulholland, A.J.2
Harvey, J.N.3
-
45
-
-
33646508010
-
Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol o-Methyltransferase
-
Rod, T. H.; Ryde, U. Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol o-Methyltransferase J. Chem. Theory Comput. 2005, 1, 1240-1251
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 1240-1251
-
-
Rod, T.H.1
Ryde, U.2
-
46
-
-
43949083733
-
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
-
Hu, H.; Yang, W. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.2
-
47
-
-
62149122220
-
a, Redox Reactions, and Solvation Free Energies
-
a, Redox Reactions, and Solvation Free Energies J. Phys. Chem. B 2009, 113, 1253-1272
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1253-1272
-
-
Kamerlin, S.C.L.1
Haranczyk, M.2
Warshel, A.3
-
48
-
-
0038056330
-
Exploring the Quantum Mechanical/Molecular Mechanical Replica Path Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate Mutase
-
Woodcock, H. L.; Hodoscek, M.; Sherwood, P.; Lee, Y. S.; Schaefer, H. F.; Brooks, B. R. Exploring the Quantum Mechanical/Molecular Mechanical Replica Path Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate Mutase Theor. Chem. Acc. 2009, 109, 140-148
-
(2009)
Theor. Chem. Acc.
, vol.109
, pp. 140-148
-
-
Woodcock, H.L.1
Hodoscek, M.2
Sherwood, P.3
Lee, Y.S.4
Schaefer, H.F.5
Brooks, B.R.6
-
49
-
-
34249785686
-
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
-
Woodcock, H. L.; Hodošček, M.; Gilbert, A. T. B.; Gill, P. M. W.; Schaefer, H. F.; Brooks, B. R. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations J. Comput. Chem. 2007, 28, 1485-1502
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1485-1502
-
-
Woodcock, H.L.1
Hodošček, M.2
Gilbert, A.T.B.3
Gill, P.M.W.4
Schaefer, H.F.5
Brooks, B.R.6
-
50
-
-
33745294923
-
QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction
-
Kästner, J.; Senn, H. M.; Thiel, S.; Otte, S.; Thiel, W. QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction J. Chem. Theor. Comp. 2006, 2, 452-461
-
(2006)
J. Chem. Theor. Comp.
, vol.2
, pp. 452-461
-
-
Kästner, J.1
Senn, H.M.2
Thiel, S.3
Otte, S.4
Thiel, W.5
-
51
-
-
60349127442
-
QM/MM Methods for Biomolecular Systems
-
Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem. Intl. Ed. 2009, 48, 1198-1229
-
(2009)
Angew. Chem. Intl. Ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
52
-
-
84865066112
-
The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level Ab Initio Molecular Dynamics Simulations
-
Rowley, C. N.; Roux, B. The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level Ab Initio Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 3526-3535
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3526-3535
-
-
Rowley, C.N.1
Roux, B.2
-
53
-
-
85018193144
-
A Guide to QM/MM Methodology and Applications
-
Zhang, R.; Lev, B.; Cuervo, J. E.; Noskov, S. Y.; Salahub, D. R. A Guide to QM/MM Methodology and Applications Adv. Quantum Chem. 2010, 59, 353-400
-
(2010)
Adv. Quantum Chem.
, vol.59
, pp. 353-400
-
-
Zhang, R.1
Lev, B.2
Cuervo, J.E.3
Noskov, S.Y.4
Salahub, D.R.5
-
54
-
-
84859153494
-
A Practical Guide to Modelling Enzyme-Catalyzed Reactions
-
Lonsdale, R.; Harvey, J. N.; Mullholland, A. J. A Practical Guide to Modelling Enzyme-Catalyzed Reactions Chem. Soc. Rev. 2012, 41, 3025-3038
-
(2012)
Chem. Soc. Rev.
, vol.41
, pp. 3025-3038
-
-
Lonsdale, R.1
Harvey, J.N.2
Mullholland, A.J.3
-
55
-
-
33746382178
-
Geometry Optimization with QM/MM Methods II: Explicit Quadratic Coupling
-
Vreven, T.; Frisch, M. J.; Kudin, K. N.; Schlegel, H. B.; Morokuma, K. Geometry Optimization with QM/MM Methods II: Explicit Quadratic Coupling Mol. Phys. 2006, 104, 701-714
-
(2006)
Mol. Phys.
, vol.104
, pp. 701-714
-
-
Vreven, T.1
Frisch, M.J.2
Kudin, K.N.3
Schlegel, H.B.4
Morokuma, K.5
-
56
-
-
65249162238
-
Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases
-
Pentikainen, U.; Shaw, K. E.; Senthilkumar, K.; Woods, C. J.; Mulholland, A. J. Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases J. Chem. Theor. Comp. 2009, 5, 396-410
-
(2009)
J. Chem. Theor. Comp.
, vol.5
, pp. 396-410
-
-
Pentikainen, U.1
Shaw, K.E.2
Senthilkumar, K.3
Woods, C.J.4
Mulholland, A.J.5
-
57
-
-
77149168226
-
Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations
-
Shaw, K. E.; Woods, C. J.; Mulholland, A. J. Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations J. Phys. Chem. Lett. 2010, 1, 219-223
-
(2010)
J. Phys. Chem. Lett.
, vol.1
, pp. 219-223
-
-
Shaw, K.E.1
Woods, C.J.2
Mulholland, A.J.3
-
58
-
-
77953062855
-
The QM-MM Interface for CHARMM-deMon
-
Lev, B.; Zhang, R.; De la Lande, A.; Salahub, D.; Noskov, S. Y. The QM-MM Interface for CHARMM-deMon J. Comput. Chem. 2010, 31, 1015-1023
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1015-1023
-
-
Lev, B.1
Zhang, R.2
De La Lande, A.3
Salahub, D.4
Noskov, S.Y.5
-
59
-
-
0037115887
-
Optimization of Quantum Mechanical Molecular Mechanical Partitioning Schemes: Gaussian Delocalization of Molecular Mechanical Charges and the Double Link Atom Method
-
Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chatfield, D. C.; Hodoscek, M.; Brooks, B. R. Optimization of Quantum Mechanical Molecular Mechanical Partitioning Schemes: Gaussian Delocalization of Molecular Mechanical Charges and the Double Link Atom Method J. Chem. Phys. 2002, 117, 10534-10547
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 10534-10547
-
-
Das, D.1
Eurenius, K.P.2
Billings, E.M.3
Sherwood, P.4
Chatfield, D.C.5
Hodoscek, M.6
Brooks, B.R.7
-
60
-
-
34547314279
-
Characterization of Conformational Equilibria through Hamiltonian and Temperature Replica-Exchange Simulations: Assessing Entropic and Environmental Effects
-
Faraldo-Gomez, J. D.; Roux, B. Characterization of Conformational Equilibria through Hamiltonian and Temperature Replica-Exchange Simulations: Assessing Entropic and Environmental Effects J. Comput. Chem. 2007, 28, 1634-1647
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1634-1647
-
-
Faraldo-Gomez, J.D.1
Roux, B.2
-
61
-
-
84879379897
-
QM/MM Molecular Dynamics Simulations of the Hydration of Mg(II) and Zn(II) Ions
-
Riahi, S.; Rowley, C. N.; Roux, B. QM/MM Molecular Dynamics Simulations of the Hydration of Mg(II) and Zn(II) Ions Can. J. Chem. 2013, 91, 552-558
-
(2013)
Can. J. Chem.
, vol.91
, pp. 552-558
-
-
Riahi, S.1
Rowley, C.N.2
Roux, B.3
-
62
-
-
0001655657
-
Finite Representation of an Infinite Bulk System - Solvent Boundary Potential for Computer Simulations
-
Beglov, D.; Roux, B. Finite Representation of an Infinite Bulk System-Solvent Boundary Potential for Computer Simulations J. Chem. Phys. 1994, 100, 9050-9063
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
63
-
-
0000301294
-
The Proton'S Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster Ion Solvation Data
-
Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Tuttle, T. R.; Coe, J. V. The Proton'S Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster Ion Solvation Data J. Phys. Chem. A 1998, 102, 7791-7798
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 7791-7798
-
-
Tissandier, M.D.1
Cowen, K.A.2
Feng, W.Y.3
Gundlach, E.4
Cohen, M.H.5
Earhart, A.D.6
Tuttle, T.R.7
Coe, J.V.8
-
64
-
-
0442310716
-
Experimental-Determination of Absolute Half-Cell Emfs and Single Ion Free-Energies of Solvation
-
Gomer, R.; Tryson, G. Experimental-Determination of Absolute Half-Cell Emfs and Single Ion Free-Energies of Solvation J. Chem. Phys. 1977, 66, 4413-4424
-
(1977)
J. Chem. Phys.
, vol.66
, pp. 4413-4424
-
-
Gomer, R.1
Tryson, G.2
-
65
-
-
0033984826
-
A New Table of the Thermodynamic Quantities of Ionic Hydration: Values and Some Applications (Enthalpy-Entropy Compensation and Born Radii)
-
Schmid, R.; Miah, A. M.; Sapunov, V. N. A New Table of the Thermodynamic Quantities of Ionic Hydration: Values and Some Applications (Enthalpy-Entropy Compensation and Born Radii) Phys. Chem. Chem. Phys. 2000, 2, 97-102
-
(2000)
Phys. Chem. Chem. Phys.
, vol.2
, pp. 97-102
-
-
Schmid, R.1
Miah, A.M.2
Sapunov, V.N.3
-
66
-
-
0000610069
-
Solubility of Protons in Water
-
Klots, C. E. Solubility of Protons in Water J. Phys. Chem. 1981, 85, 3585-3588
-
(1981)
J. Phys. Chem.
, vol.85
, pp. 3585-3588
-
-
Klots, C.E.1
-
67
-
-
77749298172
-
Current Status of the AMOEBA Polarizable Force Field
-
Ponder, J. W.; Wu, C. J.; Ren, P. Y.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A.; Head-Gordon, M.; Clark, G. N. I.; Johnson, M. E.; Head-Gordon, T. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114, 2549-2564
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2549-2564
-
-
Ponder, J.W.1
Wu, C.J.2
Ren, P.Y.3
Pande, V.S.4
Chodera, J.D.5
Schnieders, M.J.6
Haque, I.7
Mobley, D.L.8
Lambrecht, D.S.9
Distasio, R.A.10
Head-Gordon, M.11
Clark, G.N.I.12
Johnson, M.E.13
Head-Gordon, T.14
-
68
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I. S.; Cheatham, T. E. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
69
-
-
84872074297
-
Hydration Structure of Salt Solutions from Ab Initio Molecular Dynamics
-
Bankura, A.; Carnevale, V.; Klein, M. L. Hydration Structure of Salt Solutions from Ab Initio Molecular Dynamics J. Chem. Phys. 2013, 138, 014501
-
(2013)
J. Chem. Phys.
, vol.138
, pp. 014501
-
-
Bankura, A.1
Carnevale, V.2
Klein, M.L.3
-
70
-
-
36149036746
-
X-Ray and Neutron-Diffraction Studies on Concentrated Aqueous-Solutions of Sodium-Nitrate and Silver-Nitrate
-
Skipper, N. T.; Neilson, G. W. X-Ray and Neutron-Diffraction Studies on Concentrated Aqueous-Solutions of Sodium-Nitrate and Silver-Nitrate J. Phys. Cond. Matt. 1989, 1, 4141-4154
-
(1989)
J. Phys. Cond. Matt.
, vol.1
, pp. 4141-4154
-
-
Skipper, N.T.1
Neilson, G.W.2
-
71
-
-
84855389998
-
A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution
-
Mähler, J.; Persson, I. A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution Inorg. Chem. 2012, 51, 425-438
-
(2012)
Inorg. Chem.
, vol.51
, pp. 425-438
-
-
Mähler, J.1
Persson, I.2
-
72
-
-
33644745177
-
Electronic Structure, Statistical Mechanical Simulations, and EXAFS Spectroscopy of Aqueous Potassium
-
Glezakou, V.-A.; Chen, Y.; Fulton, J.; Schenter, G.; Dang, L. Electronic Structure, Statistical Mechanical Simulations, and EXAFS Spectroscopy of Aqueous Potassium Theor. Chem. Acc. 2006, 115, 86-99
-
(2006)
Theor. Chem. Acc.
, vol.115
, pp. 86-99
-
-
Glezakou, V.-A.1
Chen, Y.2
Fulton, J.3
Schenter, G.4
Dang, L.5
-
73
-
-
33750625357
-
Ion Solvation and Water Structure in Potassium Halide Aqueous Solutions
-
Soper, A. K.; Weckström, K. Ion Solvation and Water Structure in Potassium Halide Aqueous Solutions Biophys. Chem. 2006, 124, 180-191
-
(2006)
Biophys. Chem.
, vol.124
, pp. 180-191
-
-
Soper, A.K.1
Weckström, K.2
-
74
-
-
0037242358
-
The Hydration Structures of F and Cl Investigated by Ab Initio QM/MM Molecular Dynamics Simulations
-
Tongraar, A.; Rode, B. M. The Hydration Structures of F and Cl Investigated by Ab Initio QM/MM Molecular Dynamics Simulations Phys. Chem. Chem. Phys. 2003, 5, 357-362
-
(2003)
Phys. Chem. Chem. Phys.
, vol.5
, pp. 357-362
-
-
Tongraar, A.1
Rode, B.M.2
-
76
-
-
0001635115
-
An Extended X-Ray-Absorption Fine-Structure Study of Aqueous-Solutions by Employing Molecular-Dynamics Simulations
-
D'Angelo, P.; Dinola, A.; Filipponi, A.; Pavel, N. V.; Roccatano, D. An Extended X-Ray-Absorption Fine-Structure Study of Aqueous-Solutions by Employing Molecular-Dynamics Simulations J. Chem. Phys. 1994, 100, 985-994
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 985-994
-
-
D'Angelo, P.1
Dinola, A.2
Filipponi, A.3
Pavel, N.V.4
Roccatano, D.5
-
77
-
-
0031360045
-
Hydration of Bromide Ion in Supercritical Water: An X-ray Absorption Fine Structure and Molecular Dynamics Study
-
Wallen, S. L.; Palmer, B. J.; Pfund, D. M.; Fulton, J. L.; Newville, M.; Ma, Y. J.; Stern, E. A. Hydration of Bromide Ion in Supercritical Water: An X-ray Absorption Fine Structure and Molecular Dynamics Study J. Phys. Chem. A 1997, 101, 9632-9640
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 9632-9640
-
-
Wallen, S.L.1
Palmer, B.J.2
Pfund, D.M.3
Fulton, J.L.4
Newville, M.5
Ma, Y.J.6
Stern, E.A.7
-
78
-
-
0000599205
-
Ion-Ion and Ion-Water Interactions in an Aqueous Solution of Erbium Bromide (ErBr3). A Differential Anomalous X-ray Scattering Study
-
Beudert, R.; Bertagnolli, H.; Zeller, M. Ion-Ion and Ion-Water Interactions in an Aqueous Solution of Erbium Bromide (ErBr3). A Differential Anomalous X-ray Scattering Study J. Chem. Phys. 1997, 106, 8841-8848
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 8841-8848
-
-
Beudert, R.1
Bertagnolli, H.2
Zeller, M.3
-
79
-
-
0036140587
-
An Ab Initio Study of Water Molecules in the Bromide Ion Solvation Shell
-
Raugei, S.; Klein, M. L. An Ab Initio Study of Water Molecules in the Bromide Ion Solvation Shell J. Chem. Phys. 2002, 116, 196-202
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 196-202
-
-
Raugei, S.1
Klein, M.L.2
|