-
3
-
-
60349127442
-
QM/MM Methods for Biomolecular Systems
-
Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
-
(2009)
Angew. Chem., Int. Ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
4
-
-
43949083733
-
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio QM/MM Methods
-
Hu, H.; Yang, W. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio QM/MM Methods Annu. Rev. Phys. Chem. 2008, 59, 573
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573
-
-
Hu, H.1
Yang, W.2
-
5
-
-
0038615889
-
Contributions of Conformational Compression and Preferential Transition State Stabilization to the Rate Enhancement by Chorismate Mutase
-
Guimarães, C. R. W.; Repasky, M. P.; Chandrasekhar, J.; Tirado-Rives, J.; Jorgensen, W. L. Contributions of Conformational Compression and Preferential Transition State Stabilization to the Rate Enhancement by Chorismate Mutase J. Am. Chem. Soc. 2003, 125, 6892-6899
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 6892-6899
-
-
Guimarães, C.R.W.1
Repasky, M.P.2
Chandrasekhar, J.3
Tirado-Rives, J.4
Jorgensen, W.L.5
-
6
-
-
36949037942
-
Catalysis of the Claisen Rearrangement
-
Majumdar, K. C.; Alam, S.; Chattopadhyay, B. Catalysis of the Claisen Rearrangement Tetrahedron 2008, 64, 597-643
-
(2008)
Tetrahedron
, vol.64
, pp. 597-643
-
-
Majumdar, K.C.1
Alam, S.2
Chattopadhyay, B.3
-
7
-
-
0000753381
-
Effect of Solvent on the Claisen Rearrangement of Allyl Vinyl Ether Using Ab Initio Continuum Methods
-
Davidson, M. M.; Hillier, I. H.; Hall, R. J.; Burton, N. A. Effect of Solvent on the Claisen Rearrangement of Allyl Vinyl Ether Using Ab Initio Continuum Methods J. Am. Chem. Soc. 1994, 116, 9294-9297
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 9294-9297
-
-
Davidson, M.M.1
Hillier, I.H.2
Hall, R.J.3
Burton, N.A.4
-
8
-
-
0000703656
-
Combined QM/MM Simulation Study of the Claisen Rearrangement of Allyl Vinyl Ether in Aqueous Solution
-
Gao, J. Combined QM/MM Simulation Study of the Claisen Rearrangement of Allyl Vinyl Ether in Aqueous Solution J. Am. Chem. Soc. 1994, 116, 1563-1564
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 1563-1564
-
-
Gao, J.1
-
9
-
-
0001718717
-
Transition Structure and Substituent Effects on Aqueous Acceleration of the Claisen Rearrangement
-
Sehgal, A.; Shao, L.; Gao, J. Transition Structure and Substituent Effects on Aqueous Acceleration of the Claisen Rearrangement J. Am. Chem. Soc. 1995, 117, 11337-11340
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11337-11340
-
-
Sehgal, A.1
Shao, L.2
Gao, J.3
-
10
-
-
77249146442
-
Claisen Rearrangements: Insight into Solvent Effects and "on Water" Reactivity from QM/MM Simulations
-
Acevedo, O.; Armacost, K. Claisen Rearrangements: Insight into Solvent Effects and "on Water" Reactivity from QM/MM Simulations J. Am. Chem. Soc. 2010, 132, 1966-1975
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 1966-1975
-
-
Acevedo, O.1
Armacost, K.2
-
11
-
-
84973100605
-
Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations
-
Severance, D. L.; Jorgensen, W. L. Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations J. Am. Chem. Soc. 1992, 114, 10966-10968
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 10966-10968
-
-
Severance, D.L.1
Jorgensen, W.L.2
-
12
-
-
0001423835
-
The Claisen Rearrangement. Response to Solvents and Substituents: The Case for Both Hydrophobic and Hydrogen Bond Acceleration in Water and for a Variable Transition State
-
Gajewski, J. J. The Claisen Rearrangement. Response to Solvents and Substituents: The Case for Both Hydrophobic and Hydrogen Bond Acceleration in Water and for a Variable Transition State Acc. Chem. Res. 1997, 30, 219-225
-
(1997)
Acc. Chem. Res.
, vol.30
, pp. 219-225
-
-
Gajewski, J.J.1
-
13
-
-
0039920133
-
Solvation Modeling in Aqueous and Nonaqueous Solvents
-
American Chemical Society: Washington, DC
-
Storer, J. W.; Giesen, D. J.; Hawkins, G. D.; Lynch, G. C.; Cramer, C. J.; Truhlar, D. G.; Liotard, D. A. Solvation Modeling in Aqueous and Nonaqueous Solvents. Structure and Reactivity in Aqueous Solution; American Chemical Society: Washington, DC, 1994; pp 24-49.
-
(1994)
Structure and Reactivity in Aqueous Solution
, pp. 24-49
-
-
Storer, J.W.1
Giesen, D.J.2
Hawkins, G.D.3
Lynch, G.C.4
Cramer, C.J.5
Truhlar, D.G.6
Liotard, D.A.7
-
14
-
-
0031648813
-
Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy
-
Bartels, C.; Karplus, M. Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy J. Phys. Chem. B 1998, 102, 865-880
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 865-880
-
-
Bartels, C.1
Karplus, M.2
-
15
-
-
33644772083
-
Equilibrium Free Energies from Nonequilibrium Metadynamics
-
Bussi, G.; Laio, A.; Parrinello, M. Equilibrium Free Energies from Nonequilibrium Metadynamics Phys. Rev. Lett. 2006, 96, 090601
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 090601
-
-
Bussi, G.1
Laio, A.2
Parrinello, M.3
-
16
-
-
84875760613
-
Metadynamics
-
Barducci, A.; Bonomi, M.; Parrinello, M. Metadynamics Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 826-843
-
(2011)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.1
, pp. 826-843
-
-
Barducci, A.1
Bonomi, M.2
Parrinello, M.3
-
17
-
-
0342929614
-
Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
-
Torrie, G. M.; Valleau, J. P. Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling J. Comput. Phys. 1977, 23, 187-199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
18
-
-
72049100419
-
A Selective Integrated Tempering Method
-
Yang, L.; Gao, Y. Q. A Selective Integrated Tempering Method J. Chem. Phys. 2009, 131, 214109
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 214109
-
-
Yang, L.1
Gao, Y.Q.2
-
19
-
-
39349096750
-
Selective Sampling of Transition Paths
-
Fu, X.; Yang, L.; Gao, Y. Q. Selective Sampling of Transition Paths J. Chem. Phys. 2007, 127, 154106
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 154106
-
-
Fu, X.1
Yang, L.2
Gao, Y.Q.3
-
20
-
-
33748374124
-
Statistical Mechanics of Isomerization Dynamics in Liquids and the Transition State Approximation
-
Chandler, D. Statistical Mechanics of Isomerization Dynamics in Liquids and the Transition State Approximation J. Chem. Phys. 1978, 68, 2959-2970
-
(1978)
J. Chem. Phys.
, vol.68
, pp. 2959-2970
-
-
Chandler, D.1
-
21
-
-
0022182829
-
Chemical Reaction Dynamics in Solution
-
Hynes, J. T. Chemical Reaction Dynamics in Solution Annu. Rev. Phys. Chem. 1985, 36, 573-597
-
(1985)
Annu. Rev. Phys. Chem.
, vol.36
, pp. 573-597
-
-
Hynes, J.T.1
-
22
-
-
2342448523
-
Rate-Promoting Vibrations and Coupled Hydrogen-Electron Transfer Reactions in the Condensed Phase: A Model for Enzymatic Catalysis
-
Mincer, J. S.; Schwartz, S. D. Rate-Promoting Vibrations and Coupled Hydrogen-Electron Transfer Reactions in the Condensed Phase: A Model for Enzymatic Catalysis J. Chem. Phys. 2004, 120, 7755-7760
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 7755-7760
-
-
Mincer, J.S.1
Schwartz, S.D.2
-
23
-
-
0002513670
-
Claisen Rearrangement of Allyl Vinyl Ether
-
American Chemical Society: Washington, DC, Vol.
-
Daniel, L. S.; William, L. J. Claisen Rearrangement of Allyl Vinyl Ether. Structure and Reactivity in Aqueous Solution; American Chemical Society: Washington, DC, 1994; Vol. 568, pp 243-259.
-
(1994)
Structure and Reactivity in Aqueous Solution
, vol.568
, pp. 243-259
-
-
Daniel, L.S.1
William, L.J.2
-
24
-
-
0034317160
-
A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution
-
Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution J. Phys. Chem. B 2000, 104, 11308-11315
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 11308-11315
-
-
Martí, S.1
Andrés, J.2
Moliner, V.3
Silla, E.4
Tuñón, I.5
Bertrán, J.6
-
25
-
-
0242558164
-
Conformational Equilibrium of Chorismate. A QM/MM Theoretical Study Combining Statistical Simulations and Geometry Optimisations in Gas Phase and in Aqueous Solution
-
Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Conformational Equilibrium of Chorismate. A QM/MM Theoretical Study Combining Statistical Simulations and Geometry Optimisations in Gas Phase and in Aqueous Solution J. Mol. Struct.: THEOCHEM 2003, 632, 197-206
-
(2003)
J. Mol. Struct.: THEOCHEM
, vol.632
, pp. 197-206
-
-
Martí, S.1
Andrés, J.2
Moliner, V.3
Silla, E.4
Tuñón, I.5
Bertrán, J.6
-
26
-
-
0029790271
-
Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement
-
Carlson, H. A.; Jorgensen, W. L. Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement J. Am. Chem. Soc. 1996, 118, 8475-8484
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 8475-8484
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
27
-
-
0029278692
-
New Insight into the Catalytic Mechanism of Chorismate Mutases from Structural Studies
-
Lee, A.; Stewart, J. D.; Clardy, J.; Ganem, B. New Insight into the Catalytic Mechanism of Chorismate Mutases from Structural Studies Chem. Biol. 1995, 2, 195-203
-
(1995)
Chem. Biol.
, vol.2
, pp. 195-203
-
-
Lee, A.1
Stewart, J.D.2
Clardy, J.3
Ganem, B.4
-
28
-
-
27644492410
-
Multiple High-Level QM/MM Reaction Paths Demonstrate Transition-State Stabilization in Chorismate Mutase: Correlation of Barrier Height with Transition-State Stabilization
-
Claeyssens, F.; Ranaghan, K. E.; Manby, F. R.; Harvey, J. N.; Mulholland, A. J. Multiple High-Level QM/MM Reaction Paths Demonstrate Transition-State Stabilization in Chorismate Mutase: Correlation of Barrier Height with Transition-State Stabilization Chem. Commun. 2005, 5068-5070
-
(2005)
Chem. Commun.
, pp. 5068-5070
-
-
Claeyssens, F.1
Ranaghan, K.E.2
Manby, F.R.3
Harvey, J.N.4
Mulholland, A.J.5
-
29
-
-
0001193489
-
Synthesis and Claisen Rearrangement of Alkoxyallyl Enol Ethers. Evidence for a Dipolar Transition State
-
Coates, R. M.; Rogers, B. D.; Hobbs, S. J.; Curran, D. P.; Peck, D. R. Synthesis and Claisen Rearrangement of Alkoxyallyl Enol Ethers. Evidence for a Dipolar Transition State J. Am. Chem. Soc. 1987, 109, 1160-1170
-
(1987)
J. Am. Chem. Soc.
, vol.109
, pp. 1160-1170
-
-
Coates, R.M.1
Rogers, B.D.2
Hobbs, S.J.3
Curran, D.P.4
Peck, D.R.5
-
30
-
-
64549117824
-
Organic Synthesis "on Water"
-
Chanda, A.; Fokin, V. V. Organic Synthesis "on Water" Chem. Rev. 2009, 109, 725-748
-
(2009)
Chem. Rev.
, vol.109
, pp. 725-748
-
-
Chanda, A.1
Fokin, V.V.2
-
32
-
-
58049201323
-
-
University of California.
-
Case, D.; Darden, T.; Cheatham, T.; Simmerling, C.; Wang, J.; Duke, R.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W. Amber 10; University of California: 2008.
-
(2008)
Amber 10
-
-
Case, D.1
Darden, T.2
Cheatham, T.3
Simmerling, C.4
Wang, J.5
Duke, R.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
-
33
-
-
1542779956
-
Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties
-
Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties Phys. Rev. B 1998, 58, 7260
-
(1998)
Phys. Rev. B
, vol.58
, pp. 7260
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seifert, G.8
-
34
-
-
0034225123
-
Hybrid SCC-DFTB/Molecular Mechanical Studies of H-Bonded Systems and of N-Acetyl-(L-Ala)-Methylamide Helices in Water Solution
-
Han, W. G.; Elstner, M.; Jalkanen, K.; Frauenheim, T.; Suhai, S. Hybrid SCC-DFTB/Molecular Mechanical Studies of H-Bonded Systems and of N-Acetyl-(L-Ala)-Methylamide Helices in Water Solution Int. J. Quantum Chem. 2000, 78, 459-479
-
(2000)
Int. J. Quantum Chem.
, vol.78
, pp. 459-479
-
-
Han, W.G.1
Elstner, M.2
Jalkanen, K.3
Frauenheim, T.4
Suhai, S.5
-
35
-
-
34547428921
-
Looking at Self-Consistent-Charge Density Functional Tight Binding from a Semiempirical Perspective
-
Otte, N.; Scholten, M.; Thiel, W. Looking at Self-Consistent-Charge Density Functional Tight Binding from a Semiempirical Perspective J. Phys. Chem. A 2007, 111, 5751-5755
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 5751-5755
-
-
Otte, N.1
Scholten, M.2
Thiel, W.3
-
36
-
-
0035863003
-
Energetics and Structure of Glycine and Alanine Based Model Peptides: Approximate SCC-DFTB, AM1 and PM3 Methods in Comparison with Dft, Hf and Mp2 Calculations
-
Elstner, M.; Jalkanen, K. J.; Knapp-Mohammady, M.; Frauenheim, T.; Suhai, S. Energetics and Structure of Glycine and Alanine Based Model Peptides: Approximate SCC-DFTB, AM1 and PM3 Methods in Comparison with Dft, Hf and Mp2 Calculations Chem. Phys. 2001, 263, 203-219
-
(2001)
Chem. Phys.
, vol.263
, pp. 203-219
-
-
Elstner, M.1
Jalkanen, K.J.2
Knapp-Mohammady, M.3
Frauenheim, T.4
Suhai, S.5
-
37
-
-
84890789306
-
Density Functional Tight Binding: Application to Organic and Biological Molecules
-
Gaus, M.; Cui, Q.; Elstner, M. Density Functional Tight Binding: Application to Organic and Biological Molecules Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 49-61
-
(2014)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.4
, pp. 49-61
-
-
Gaus, M.1
Cui, Q.2
Elstner, M.3
-
38
-
-
84859926841
-
Density-Functional Tight Binding -an Approximate Density-Functional Theory Method
-
Seifert, G.; Joswig, J. O. Density-Functional Tight Binding -an Approximate Density-Functional Theory Method Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 456-465
-
(2012)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.2
, pp. 456-465
-
-
Seifert, G.1
Joswig, J.O.2
-
39
-
-
0031651724
-
Tight-Binding Approach to Computational Materials Science
-
Elstner, M.; Porezag, D.; Jungnickel, G.; Frauenheim, T.; Suhai, S.; Seifert, G. Tight-Binding Approach to Computational Materials Science Mater. Res. Soc. Symp. Proc. 1998, 491, 131
-
(1998)
Mater. Res. Soc. Symp. Proc.
, vol.491
, pp. 131
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Frauenheim, T.4
Suhai, S.5
Seifert, G.6
-
40
-
-
2542444258
-
A Theoretical Study of Structures and Electron Affinities of Radical Anions of Guanine-Cytosine, Adenine-Thymine, and Hypoxanthine-Cytosine Base Pairs
-
Kumar, A.; Knapp-Mohammady, M.; Mishra, P.; Suhai, S. A Theoretical Study of Structures and Electron Affinities of Radical Anions of Guanine-Cytosine, Adenine-Thymine, and Hypoxanthine-Cytosine Base Pairs J. Comput. Chem. 2004, 25, 1047-1059
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1047-1059
-
-
Kumar, A.1
Knapp-Mohammady, M.2
Mishra, P.3
Suhai, S.4
-
41
-
-
39349109496
-
An Integrate-overerature Approach for Enhanced Sampling
-
Gao, Y. Q. An Integrate-overerature Approach for Enhanced Sampling J. Chem. Phys. 2008, 128, 064105
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 064105
-
-
Gao, Y.Q.1
-
42
-
-
41849124534
-
Self-Adaptive Enhanced Sampling in the Energy and Trajectory Spaces: Accelerated Thermodynamics and Kinetic Calculations
-
Gao, Y. Q. Self-Adaptive Enhanced Sampling in the Energy and Trajectory Spaces: Accelerated Thermodynamics and Kinetic Calculations J. Chem. Phys. 2008, 128, 134111
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 134111
-
-
Gao, Y.Q.1
-
43
-
-
1242346370
-
The Missing Term in Effective Pair Potentials
-
Berendsen, H.; Grigera, J.; Straatsma, T. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.1
Grigera, J.2
Straatsma, T.3
-
44
-
-
11344284526
-
Tables of Bond Lengths Determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds
-
Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. Tables of Bond Lengths Determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds J. Chem. Soc., Perkin Trans. 2 1987, S1-S19
-
(1987)
J. Chem. Soc., Perkin Trans. 2
, pp. 1-S19
-
-
Allen, F.H.1
Kennard, O.2
Watson, D.G.3
Brammer, L.4
Orpen, A.G.5
Taylor, R.6
-
45
-
-
70450206724
-
-
revision A.02; Gaussian, Inc. Wallingford, CT.
-
Frisch, M.; Trucks, G.; Schlegel, H. B.; Scuseria, G.; Robb, M.; Cheeseman, J.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. Gaussian 09, revision A.02; Gaussian, Inc.: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.1
Trucks, G.2
Schlegel, H.B.3
Scuseria, G.4
Robb, M.5
Cheeseman, J.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.10
-
46
-
-
3042524904
-
A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The Resp Model
-
Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The Resp Model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
47
-
-
79959999377
-
Red Server: A Web Service for Deriving Resp and Esp Charges and Building Force Field Libraries for New Molecules and Molecular Fragments
-
Vanquelef, E.; Simon, S.; Marquant, G.; Garcia, E.; Klimerak, G.; Delepine, J. C.; Cieplak, P.; Dupradeau, F.-Y. Red Server: A Web Service for Deriving Resp and Esp Charges and Building Force Field Libraries for New Molecules and Molecular Fragments Nucleic Acids Res. 2011, 39, W511-W517
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 511-W517
-
-
Vanquelef, E.1
Simon, S.2
Marquant, G.3
Garcia, E.4
Klimerak, G.5
Delepine, J.C.6
Cieplak, P.7
Dupradeau, F.-Y.8
-
48
-
-
77954566051
-
The Red. Tools: Advances in Resp and Esp Charge Derivation and Force Field Library Building
-
Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. The Red. Tools: Advances in Resp and Esp Charge Derivation and Force Field Library Building Phys. Chem. Chem. Phys. 2010, 12, 7821-7839
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.-Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
49
-
-
0037149093
-
A Generalized-Born Solvation Model for Macromolecular Hybrid-Potential Calculations
-
Pellegrini, E.; Field, M. J. A Generalized-Born Solvation Model for Macromolecular Hybrid-Potential Calculations J. Phys. Chem. A 2002, 106, 1316-1326
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 1316-1326
-
-
Pellegrini, E.1
Field, M.J.2
-
50
-
-
19944369519
-
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations
-
Nam, K.; Gao, J.; York, D. M. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations J. Chem. Theory Comput. 2005, 1, 2-13
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 2-13
-
-
Nam, K.1
Gao, J.2
York, D.M.3
-
51
-
-
42149100111
-
The Implementation of a Fast and Accurate QM/MM Potential Method in Amber
-
Walker, R. C.; Crowley, M. F.; Case, D. A. The Implementation of a Fast and Accurate QM/MM Potential Method in Amber J. Comput. Chem. 2008, 29, 1019-1031
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1019-1031
-
-
Walker, R.C.1
Crowley, M.F.2
Case, D.A.3
-
52
-
-
34547511107
-
Implementation of the Scc-Dftb Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package
-
Seabra, G. d. M.; Walker, R. C.; Elstner, M.; Case, D. A.; Roitberg, A. E. Implementation of the Scc-Dftb Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package J. Phys. Chem. A 2007, 111, 5655-5664
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 5655-5664
-
-
Seabra, D.G.M.1
Walker, R.C.2
Elstner, M.3
Case, D.A.4
Roitberg, A.E.5
-
53
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.3
-
54
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.5
-
56
-
-
84901830287
-
Dynamics of Spontaneous Flipping of a Mismatched Base in DNA Duplex
-
Yin, Y.; Yang, L.; Zheng, G.; Gu, C.; Yi, C.; He, C.; Gao, Y. Q.; Zhao, X. S. Dynamics of Spontaneous Flipping of a Mismatched Base in DNA Duplex Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 8043-8048
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
, vol.111
, pp. 8043-8048
-
-
Yin, Y.1
Yang, L.2
Zheng, G.3
Gu, C.4
Yi, C.5
He, C.6
Gao, Y.Q.7
Zhao, X.S.8
-
57
-
-
78651323641
-
Temperature Dependence of Hydrogen-Bond Stability in B-Hairpin Structures
-
Shao, Q.; Gao, Y. Q. Temperature Dependence of Hydrogen-Bond Stability in B-Hairpin Structures J. Chem. Theory Comput. 2010, 6, 3750-3760
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3750-3760
-
-
Shao, Q.1
Gao, Y.Q.2
-
58
-
-
84893080175
-
Stable Salt-Water Cluster Structures Reflect the Delicate Competition between Ion-Water and Water-Water Interactions
-
Liu, C.-W.; Wang, F.; Yang, L.; Li, X.-Z.; Zheng, W.-J.; Gao, Y. Q. Stable Salt-Water Cluster Structures Reflect the Delicate Competition between Ion-Water and Water-Water Interactions J. Phys. Chem. B 2014, 118, 743-751
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 743-751
-
-
Liu, C.-W.1
Wang, F.2
Yang, L.3
Li, X.-Z.4
Zheng, W.-J.5
Gao, Y.Q.6
-
59
-
-
33847541123
-
The Kinetics of the Rearrangement of Vinyl Allyl Ether1
-
Schuler, F. W.; Murphy, G. W. The Kinetics of the Rearrangement of Vinyl Allyl Ether1 J. Am. Chem. Soc. 1950, 72, 3155-3159
-
(1950)
J. Am. Chem. Soc.
, vol.72
, pp. 3155-3159
-
-
Schuler, F.W.1
Murphy, G.W.2
-
60
-
-
0013261892
-
The Volume Change of Activation in the Claisen and Curtius Rearrangements
-
Brower, K. R. The Volume Change of Activation in the Claisen and Curtius Rearrangements J. Am. Chem. Soc. 1961, 83, 4370-4372
-
(1961)
J. Am. Chem. Soc.
, vol.83
, pp. 4370-4372
-
-
Brower, K.R.1
-
61
-
-
26944481188
-
Interfaces and the Driving Force of Hydrophobic Assembly
-
Chandler, D. Interfaces and the Driving Force of Hydrophobic Assembly Nature 2005, 437, 640-647
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
-
62
-
-
34247897075
-
On the Theory of Organic Catalysis "on Water"
-
Jung, Y.; Marcus, R. On the Theory of Organic Catalysis "on Water" J. Am. Chem. Soc. 2007, 129, 5492-5502
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 5492-5502
-
-
Jung, Y.1
Marcus, R.2
-
63
-
-
0029789767
-
The Mechanism of the Claisen Rearrangement: Déjà Vu All over Again
-
Ganem, B. The Mechanism of the Claisen Rearrangement: Déjà Vu All over Again Angew. Chem., Int. Ed. Engl. 1996, 35, 936-945
-
(1996)
Angew. Chem., Int. Ed. Engl.
, vol.35
, pp. 936-945
-
-
Ganem, B.1
-
64
-
-
0001138032
-
The Conformational Equilibrium of Chorismate in Solution: Implications for the Mechanism of the Non-Enzymic and the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate
-
Copley, S. D.; Knowles, J. R. The Conformational Equilibrium of Chorismate in Solution: Implications for the Mechanism of the Non-Enzymic and the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate J. Am. Chem. Soc. 1987, 109, 5008-5013
-
(1987)
J. Am. Chem. Soc.
, vol.109
, pp. 5008-5013
-
-
Copley, S.D.1
Knowles, J.R.2
-
65
-
-
0142091405
-
The near Attack Conformation Approach to the Study of the Chorismate to Prephenate Reaction
-
Hur, S.; Bruice, T. C. The near Attack Conformation Approach to the Study of the Chorismate to Prephenate Reaction Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12015-12020
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 12015-12020
-
-
Hur, S.1
Bruice, T.C.2
-
66
-
-
0035979270
-
Substrate Conformational Transitions in the Active Site of Chorismate Mutase: Their Role in the Catalytic Mechanism
-
Guo, H.; Cui, Q.; Lipscomb, W. N.; Karplus, M. Substrate Conformational Transitions in the Active Site of Chorismate Mutase: Their Role in the Catalytic Mechanism Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 9032-9037
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 9032-9037
-
-
Guo, H.1
Cui, Q.2
Lipscomb, W.N.3
Karplus, M.4
-
67
-
-
0027267671
-
Binding of a High-Energy Substrate Conformer in Antibody Catalysis
-
Campbell, A. P.; Tarasow, T. M.; Massefski, W.; Wright, P. E.; Hilvert, D. Binding of a High-Energy Substrate Conformer in Antibody Catalysis Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8663-8667
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 8663-8667
-
-
Campbell, A.P.1
Tarasow, T.M.2
Massefski, W.3
Wright, P.E.4
Hilvert, D.5
-
68
-
-
0001694036
-
Substituent Effects on the Aliphatic Claisen Rearrangement. 1. Synthesis and Rearrangement of Cyano-Substituted Allyl Vinyl Ethers
-
Burrows, C. J.; Carpenter, B. K. Substituent Effects on the Aliphatic Claisen Rearrangement. 1. Synthesis and Rearrangement of Cyano-Substituted Allyl Vinyl Ethers J. Am. Chem. Soc. 1981, 103, 6983-6984
-
(1981)
J. Am. Chem. Soc.
, vol.103
, pp. 6983-6984
-
-
Burrows, C.J.1
Carpenter, B.K.2
-
69
-
-
0036424048
-
Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark
-
Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark Annu. Rev. Phys. Chem. 2002, 53, 291-318
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
70
-
-
33845282891
-
The Mechanism of Rearrangement of Chorismic Acid and Related Compounds
-
Gajewski, J. J.; Jurayj, J.; Kimbrough, D. R.; Gande, M. E.; Ganem, B.; Carpenter, B. K. The Mechanism of Rearrangement of Chorismic Acid and Related Compounds J. Am. Chem. Soc. 1987, 109, 1170-1186
-
(1987)
J. Am. Chem. Soc.
, vol.109
, pp. 1170-1186
-
-
Gajewski, J.J.1
Jurayj, J.2
Kimbrough, D.R.3
Gande, M.E.4
Ganem, B.5
Carpenter, B.K.6
-
71
-
-
0002075454
-
The Claisen and Cope Rearrangements
-
Rhoads, S. J.; Raulins, N. R. The Claisen and Cope Rearrangements Org. React. 1975, 22, 1-252
-
(1975)
Org. React.
, vol.22
, pp. 1-252
-
-
Rhoads, S.J.1
Raulins, N.R.2
-
72
-
-
0000518212
-
Effect of Polar Solvents on the Rates of Claisen Rearrangements: Assessment of Ionic Character
-
Brandes, E.; Grieco, P.; Gajewski, J. Effect of Polar Solvents on the Rates of Claisen Rearrangements: Assessment of Ionic Character J. Org. Chem. 1989, 54, 515-516
-
(1989)
J. Org. Chem.
, vol.54
, pp. 515-516
-
-
Brandes, E.1
Grieco, P.2
Gajewski, J.3
-
73
-
-
0000593549
-
A Semitheoretical Multiparameter Approach to Correlate Solvent Effects on Reactions and Equilibria
-
Gajewski, J. J. A Semitheoretical Multiparameter Approach to Correlate Solvent Effects on Reactions and Equilibria J. Org. Chem. 1992, 57, 5500-5506
-
(1992)
J. Org. Chem.
, vol.57
, pp. 5500-5506
-
-
Gajewski, J.J.1
-
74
-
-
0010421423
-
Factor Analysis of Solvent Effects on Reactions
-
American Chemical Society: Washington, DC, Vol.
-
Joseph, J. G.; Nancy, L. B. Factor Analysis of Solvent Effects on Reactions. Structure and Reactivity in Aqueous Solution; American Chemical Society: Washington, DC, 1994; Vol. 568, pp 229-242.
-
(1994)
Structure and Reactivity in Aqueous Solution
, vol.568
, pp. 229-242
-
-
Joseph, J.G.1
Nancy, L.B.2
-
75
-
-
37049067913
-
Water-Promoted Organic Synthesis Using Glyco-Organic Substrates: The Claisen Rearrangement
-
Lubineau, A.; Augé, J.; Bellanger, N.; Caillebourdin, S. Water-Promoted Organic Synthesis Using Glyco-Organic Substrates: The Claisen Rearrangement J. Chem. Soc., Perkin Trans. 1 1992, 1631-1636
-
(1992)
J. Chem. Soc., Perkin Trans. 1
, pp. 1631-1636
-
-
Lubineau, A.1
Augé, J.2
Bellanger, N.3
Caillebourdin, S.4
-
76
-
-
0033596304
-
Mechanism of Chorismate Mutase: Contribution of Conformational Restriction to Catalysis in the Claisen Rearrangement
-
Khanjin, N. A.; Snyder, J. P.; Menger, F. Mechanism of Chorismate Mutase: Contribution of Conformational Restriction to Catalysis in the Claisen Rearrangement J. Am. Chem. Soc. 1999, 121, 11831-11846
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 11831-11846
-
-
Khanjin, N.A.1
Snyder, J.P.2
Menger, F.3
-
77
-
-
0028842603
-
Location of the Active Site of Allosteric Chorismate Mutase from Saccharomyces Cerevisiae, and Comments on the Catalytic and Regulatory Mechanisms
-
Xue, Y.; Lipscomb, W. N. Location of the Active Site of Allosteric Chorismate Mutase from Saccharomyces Cerevisiae, and Comments on the Catalytic and Regulatory Mechanisms Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 10595-10598
-
(1995)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 10595-10598
-
-
Xue, Y.1
Lipscomb, W.N.2
|