-
1
-
-
84988053595
-
3Cl + Cl- Exchange Reaction and Gas Phase Protonation of Polyethers
-
3Cl + Cl- Exchange Reaction and Gas Phase Protonation of Polyethers J. Comput. Chem. 1986, 7, 718-730
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 718-730
-
-
Singh, U.C.1
Kollman, P.A.2
-
2
-
-
84986513644
-
A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations
-
Field, M. J.; Bash, P. A.; Karplus, M. A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations J. Comput. Chem. 1990, 11, 700-733
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
3
-
-
0027125907
-
A Priori Evaluation of Aqueous Polarization Effects Through Monte Carlo QM-MM Simulations
-
Gao, J.; Xia, X. A Priori Evaluation of Aqueous Polarization Effects Through Monte Carlo QM-MM Simulations Science 1992, 258, 631-635
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
4
-
-
84962367344
-
Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials
-
Gao, J. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials Rev. Comput. Chem. 1995, 7, 119
-
(1995)
Rev. Comput. Chem.
, vol.7
, pp. 119
-
-
Gao, J.1
-
5
-
-
0001491955
-
Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
-
Gao, J. Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry Acc. Chem. Res. 1996, 29, 298-305
-
(1996)
Acc. Chem. Res.
, vol.29
, pp. 298-305
-
-
Gao, J.1
-
6
-
-
0345713551
-
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
-
Bakowies, D.; Thiel, W. Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches J. Phys. Chem. 1996, 100, 10580-10594
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 10580-10594
-
-
Bakowies, D.1
Thiel, W.2
-
7
-
-
0345913527
-
Quantum Mechanical-Molecular Mechanical Coupled Potentials
-
Merz, K. M., Jr. Quantum Mechanical-Molecular Mechanical Coupled Potentials ACS Symp. Ser. 1998, 712, 2-15
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 2-15
-
-
Merz, Jr.K.M.1
-
8
-
-
0042354356
-
On the Treatment of Link Atoms in Hybrid Methods
-
Antes, I.; Thiel, W. On the Treatment of Link Atoms in Hybrid Methods ACS Symp. Ser. 1998, 712, 50-65
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 50-65
-
-
Antes, I.1
Thiel, W.2
-
9
-
-
0000049872
-
Enzyme Mechanisms with Hybrid Quantum and Molecular Mechanical Potentials. I. Theoretical Considerations. Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
-
Eurenius, K. P.; Chatfield, D. C.; Brooks, B. R.; Hodoscek, M. Enzyme Mechanisms with Hybrid Quantum and Molecular Mechanical Potentials. I. Theoretical Considerations. Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry Int. J. Quantum Chem. 1996, 60, 1189-1200
-
(1996)
Int. J. Quantum Chem.
, vol.60
, pp. 1189-1200
-
-
Eurenius, K.P.1
Chatfield, D.C.2
Brooks, B.R.3
Hodoscek, M.4
-
10
-
-
0347174868
-
A Methodology for Quantum Mechanical Modeling of Structure and Reactivity at Solid-Liquid Interfaces
-
Stefanovich, E. V.; Truong, T. N. A Methodology for Quantum Mechanical Modeling of Structure and Reactivity at Solid-Liquid Interfaces ACS Symp. Ser. 1998, 712, 92-104
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 92-104
-
-
Stefanovich, E.V.1
Truong, T.N.2
-
12
-
-
0000928098
-
A Hybrid Method for Solutes in Complex Solvents: Density Functional Theory Combined with Empirical Force Fields
-
Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M. A Hybrid Method for Solutes in Complex Solvents: Density Functional Theory Combined with Empirical Force Fields J. Chem. Phys. 1999, 110, 10452-10467
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 10452-10467
-
-
Eichinger, M.1
Tavan, P.2
Hutter, J.3
Parrinello, M.4
-
13
-
-
0041853291
-
A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation for Ab Iniitio Molecular Dynamics Simulations of Extended Systems
-
Woo, T. K.; Marrgl, P.; Diem, l; Ziegler, T. A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation for Ab Iniitio Molecular Dynamics Simulations of Extended Systems ACS Symp. Ser. 1998, 712, 128-147
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 128-147
-
-
Woo, T.K.1
Marrgl, P.2
Diem, L.3
Ziegler, T.4
-
14
-
-
0001615334
-
Monomer Capture in Brookhart's Ni(II) Diimine Olefin Polymerization Catalyst: Static and Dynamic Quantum Mechanics/Molecular Mechanics Study
-
Woo, T. K.; Blöchl, P. E.; Ziegler, T. Monomer Capture in Brookhart's Ni(II) Diimine Olefin Polymerization Catalyst: Static and Dynamic Quantum Mechanics/Molecular Mechanics Study J. Phys. Chem. A 2000, 104, 121-129
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 121-129
-
-
Woo, T.K.1
Blöchl, P.E.2
Ziegler, T.3
-
15
-
-
0345913518
-
Quantum Mechanical Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solutions
-
Bentzien, Florian, J.; Glennon, T. M.; Warshel, A. Quantum Mechanical Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solutions ACS Symp. Ser. 1998, 712, 16-34
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 16-34
-
-
Bentzien Florian, J.1
Glennon, T.M.2
Warshel, A.3
-
16
-
-
0041853283
-
The Local Self-Consistent Field: Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems
-
Assfeld, X.; Ferré, N.; Rivail, J.-L. The Local Self-Consistent Field: Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems ACS Symp. Ser. 1998, 712, 234-249
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 234-249
-
-
Assfeld, X.1
Ferré, N.2
Rivail, J.-L.3
-
17
-
-
0041853282
-
Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations
-
Cummins, P. L.; Gready, J. E. Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations ACS Symp. Ser. 1998, 712, 250-263
-
(1998)
ACS Symp. Ser.
, vol.712
, pp. 250-263
-
-
Cummins, P.L.1
Gready, J.E.2
-
18
-
-
0001763714
-
Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches
-
Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches J. Phys. Chem. A 2000, 104, 1720-1735
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 1720-1735
-
-
Reuter, N.1
Dejaegere, A.2
Maigret, B.3
Karplus, M.4
-
19
-
-
0035605891
-
Transition Structure Selectivity in Enzyme Catalysis: A QM/MM Study of Chorismate Mutase
-
Martí, S.; Andrés, J.; Moliner, V.; Silla, E.; Tuñón, I.; Bertrán, J. Transition Structure Selectivity in Enzyme Catalysis: A QM/MM Study of Chorismate Mutase Theor. Chem. Acc. 2001, 105, 207-212
-
(2001)
Theor. Chem. Acc.
, vol.105
, pp. 207-212
-
-
Martí, S.1
Andrés, J.2
Moliner, V.3
Silla, E.4
Tuñón, I.5
Bertrán, J.6
-
20
-
-
0036025446
-
Quantum Mechanical Methods for Enzyme Kinetics
-
Gao, J.; Truhlar, D. G. Quantum Mechanical Methods for Enzyme Kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-505
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 467-505
-
-
Gao, J.1
Truhlar, D.G.2
-
21
-
-
0036282937
-
The Incorporation of Quantum Effects in Enzyme Kinetics Modeling
-
Truhlar, D. G.; Gao, J.; Alhambra, C.; Garcia-Viloca, M.; Corchado, J.; Sánchez, M. L.; VillaÌ, J. The Incorporation of Quantum Effects in Enzyme Kinetics Modeling Acc. Chem. Res. 2002, 35, 341-349
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 341-349
-
-
Truhlar, D.G.1
Gao, J.2
Alhambra, C.3
Garcia-Viloca, M.4
Corchado, J.5
Sánchez, M.L.6
Villaì, J.7
-
22
-
-
33845956263
-
Catalytic Mechanism of Glycosyltransferases: Hybrid Quantum Mechanical/Molecular Mechanical Study of the Inverting N - Acetylglucosaminyltransferase i
-
Kozmon, S.; Tvaroska, I. Catalytic Mechanism of Glycosyltransferases: Hybrid Quantum Mechanical/Molecular Mechanical Study of the Inverting N-Acetylglucosaminyltransferase I J. Am. Chem. Soc. 2006, 128, 16921-16927
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 16921-16927
-
-
Kozmon, S.1
Tvaroska, I.2
-
23
-
-
33846570818
-
QM/MM: What Have We Learned, Where are We, and Where Do We Go from Here?
-
Lin, H.; Truhlar, D. G. QM/MM: What Have We Learned, Where are We, and Where Do We Go from Here? Theor. Chem. Acc. 2007, 117, 185-199
-
(2007)
Theor. Chem. Acc.
, vol.117
, pp. 185-199
-
-
Lin, H.1
Truhlar, D.G.2
-
25
-
-
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
-
26
-
-
0001582558
-
A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods
-
Zhang, Y.; Lee, T.-S.; Yang, W. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods J. Chem. Phys. 1999, 110, 46-54
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 46-54
-
-
Zhang, Y.1
Lee, T.-S.2
Yang, W.3
-
27
-
-
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
-
28
-
-
33646356998
-
Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
-
Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; König, P.; Li, G.; Xu, D.; Guo, H.; Elstner, M.; Cui, Q. 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.4
Ghosh, N.5
Prat-Resina, X.6
König, P.7
Li, G.8
Xu, D.9
Guo, H.10
Elstner, M.11
Cui, Q.12
-
29
-
-
80054704511
-
Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems
-
Brunk, E.; Ashari, N.; Athri, P.; Campomanes, P.; de Carvalho, F. F.; Curchod, B. F.E.; Diamantis, P.; Doemer, M.; Garrec, J.; Laktionov, A.; Micciarelli, M.; Neri, M.; Palermo, G.; Penfold, T. J.; Vanni, S.; Tavernelli, I.; Rothlisberger, U. Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems Chimia 2011, 65, 667-671
-
(2011)
Chimia
, vol.65
, pp. 667-671
-
-
Brunk, E.1
Ashari, N.2
Athri, P.3
Campomanes, P.4
De Carvalho, F.F.5
Curchod, B.F.E.6
Diamantis, P.7
Doemer, M.8
Garrec, J.9
Laktionov, A.10
Micciarelli, M.11
Neri, M.12
Palermo, G.13
Penfold, T.J.14
Vanni, S.15
Tavernelli, I.16
Rothlisberger, U.17
-
30
-
-
56349103811
-
Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method
-
Higashi, M.; Truhlar, D. G. Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method J. Chem. Theor. Comput. 2008, 4, 790-803
-
(2008)
J. Chem. Theor. Comput.
, vol.4
, pp. 790-803
-
-
Higashi, M.1
Truhlar, D.G.2
-
31
-
-
58149252285
-
Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory
-
Higashi, M.; Truhlar, D. G. Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory J. Chem. Theor. Comput. 2008, 4, 1032-1039
-
(2008)
J. Chem. Theor. Comput.
, vol.4
, pp. 1032-1039
-
-
Higashi, M.1
Truhlar, D.G.2
-
32
-
-
73949147308
-
Efficient Approach to Reactive Molecular Dynamics with Accurate Forces
-
Higashi, M.; Truhlar, D. G. Efficient Approach to Reactive Molecular Dynamics with Accurate Forces J. Chem. Theor. Comput. 2009, 5, 2925-2929
-
(2009)
J. Chem. Theor. Comput.
, vol.5
, pp. 2925-2929
-
-
Higashi, M.1
Truhlar, D.G.2
-
33
-
-
80052864531
-
Direct Simulation of Excited-State Intramolecular Proton Transfer and Vibrational Coherence of 10-Hydroxybenzo[h]quinoline in Solution
-
Higashi, M.; Saito, S. Direct Simulation of Excited-State Intramolecular Proton Transfer and Vibrational Coherence of 10-Hydroxybenzo[h]quinoline in Solution J. Phys. Chem. Lett. 2011, 2, 2366-2371
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 2366-2371
-
-
Higashi, M.1
Saito, S.2
-
34
-
-
11144332565
-
Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1
-
Shi, Y.; Lan, F.; Matson, C.; Mulligan, P.; Whetstine, J. R.; Cole, P. A.; Casero, R. A. Histone Demethylation Mediated By The Nuclear Amine Oxidase Homolog LSD1 Cell 2004, 119, 941-953
-
(2004)
Cell
, vol.119
, pp. 941-953
-
-
Shi, Y.1
Lan, F.2
Matson, C.3
Mulligan, P.4
Whetstine, J.R.5
Cole, P.A.6
Casero, R.A.7
-
35
-
-
24144462170
-
LSD1 Demethylates Repressive Histone Marks to Promote Androgen-Receptor-Dependent Transcription
-
Metzger, E.; Wissmann, M.; Yin, N.; Muller, J. M.; Schneider, R.; Peters, A. H. F. M.; Gunther, T.; Buettner, R.; Schule, R. LSD1 Demethylates Repressive Histone Marks to Promote Androgen-Receptor-Dependent Transcription Nature 2005, 437, 436-439
-
(2005)
Nature
, vol.437
, pp. 436-439
-
-
Metzger, E.1
Wissmann, M.2
Yin, N.3
Muller, J.M.4
Schneider, R.5
Peters, A.H.F.M.6
Gunther, T.7
Buettner, R.8
Schule, R.9
-
36
-
-
16344368814
-
Histone Demethylation Catalysed by LSD1 is a Flavin-Dependent Oxidative Process
-
Forneris, F.; Binda, C.; Vanoni, M. A.; Mattevi, A.; Battaglioli, E. Histone Demethylation Catalysed by LSD1 is a Flavin-Dependent Oxidative Process FEBS Lett. 2005, 579, 2203-2207
-
(2005)
FEBS Lett.
, vol.579
, pp. 2203-2207
-
-
Forneris, F.1
Binda, C.2
Vanoni, M.A.3
Mattevi, A.4
Battaglioli, E.5
-
37
-
-
29244455626
-
Human Histone Demethylase LSD1 Reads the Histone Code
-
Forneris, F.; Binda, C.; Vanoni, M. A.; Battaglioli, E.; Mattevi, A. Human Histone Demethylase LSD1 Reads the Histone Code J. Biol. Chem. 2005, 280, 41360-41365
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 41360-41365
-
-
Forneris, F.1
Binda, C.2
Vanoni, M.A.3
Battaglioli, E.4
Mattevi, A.5
-
38
-
-
33845935787
-
A Highly Specific Mechanism of Histone H3-K4 Recognition by Histone Demethylase LSD1
-
Forneris, F.; Binda, C.; Dall'Aglio, A.; Fraajie, M. W.; Battaglioli, E.; Mattevi, A. A Highly Specific Mechanism of Histone H3-K4 Recognition by Histone Demethylase LSD1 J. Biol. Chem. 2006, 281, 35289-35295
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 35289-35295
-
-
Forneris, F.1
Binda, C.2
Dall'Aglio, A.3
Fraajie, M.W.4
Battaglioli, E.5
Mattevi, A.6
-
39
-
-
41549132495
-
LSD1: Oxidative Chemistry for Multifaceted Functions in Chromatin Regulation
-
Forneris, F.; Binda, C.; Battaglioli, E.; Mattevi, A. LSD1: Oxidative Chemistry for Multifaceted Functions in Chromatin Regulation Trends Biochem. Sci. 2008, 33, 181-189
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 181-189
-
-
Forneris, F.1
Binda, C.2
Battaglioli, E.3
Mattevi, A.4
-
40
-
-
33646061354
-
A Mechanism-Based Inactivator for Histone Demethylase LSD1
-
Culhane, J. C.; Szewczuk, L. M.; Liu, X.; Da, G.; Marmorstein; Cole, P. A. A Mechanism-Based Inactivator for Histone Demethylase LSD1 J. Am. Chem. Soc. 2006, 128, 4536-4537
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 4536-4537
-
-
Culhane, J.C.1
Szewczuk, L.M.2
Liu, X.3
Da, G.4
Marmorstein5
Cole, P.A.6
-
41
-
-
33846025127
-
Dynamic Regulation of Histone Lysine Methylation by Demethylases
-
Shi, Y.; Whetstine, J. R. Dynamic Regulation of Histone Lysine Methylation by Demethylases Mol. Cell 2007, 25, 1-14
-
(2007)
Mol. Cell
, vol.25
, pp. 1-14
-
-
Shi, Y.1
Whetstine, J.R.2
-
42
-
-
34147173308
-
Trans -2-Phenylcyclopropylamine is a Mechanism-Based Inactivator of the Histone Demethylase LSD1
-
Schmidt, D. M. Z.; McCafferty, D. G. trans -2-Phenylcyclopropylamine is a Mechanism-Based Inactivator of the Histone Demethylase LSD1 Biochemistry 2007, 46, 4408-4416
-
(2007)
Biochemistry
, vol.46
, pp. 4408-4416
-
-
Schmidt, D.M.Z.1
McCafferty, D.G.2
-
43
-
-
59449087016
-
Histone Modifying Enzymes: Structures, Mechanisms, and Specificities
-
Marmorstein, R.; Trievel, R. C. Histone Modifying Enzymes: Structures, Mechanisms, and Specificities Biochim. Biophys. Acta, Gene Regul. Mech. 2009, 1789, 58-68
-
(2009)
Biochim. Biophys. Acta, Gene Regul. Mech.
, vol.1789
, pp. 58-68
-
-
Marmorstein, R.1
Trievel, R.C.2
-
44
-
-
78751610660
-
Structure and Function of Histone H3 Lysine 9 Methyltransferases and Demethylases
-
Krishnan, S.; Horowitz, S.; Trievel, R. C. Structure and Function of Histone H3 Lysine 9 Methyltransferases and Demethylases ChemBioChem 2011, 12, 254-263
-
(2011)
ChemBioChem
, vol.12
, pp. 254-263
-
-
Krishnan, S.1
Horowitz, S.2
Trievel, R.C.3
-
45
-
-
0034161331
-
Flavoenzymes: Diverse Catalysts with Recurrent Features
-
Fraaije, M. W.; Mattevi, A. Flavoenzymes: Diverse Catalysts with Recurrent Features Trends Biochem. Sci. 2000, 25, 126-132
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 126-132
-
-
Fraaije, M.W.1
Mattevi, A.2
-
46
-
-
0034860788
-
Substrate Dehydrogenation by Flavoproteins
-
Fitzpatrick, P. F. Substrate Dehydrogenation by Flavoproteins Acc. Chem. Res. 2001, 34, 299-307
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 299-307
-
-
Fitzpatrick, P.F.1
-
47
-
-
67049098986
-
Use of pH and Kinetic Isotope Effects to Establish Chemistry as Rate-Limiting in Oxidation of a Peptide Substrate by LSD1
-
Gaweska, H.; Pozzi, M. H.; Schmidt, D. M. Z.; McCafferty, D. G.; Fitzpatrick, P. F. Use of pH and Kinetic Isotope Effects to Establish Chemistry as Rate-Limiting in Oxidation of a Peptide Substrate by LSD1 Biochemistry 2009, 48, 5440-5445
-
(2009)
Biochemistry
, vol.48
, pp. 5440-5445
-
-
Gaweska, H.1
Pozzi, M.H.2
Schmidt, D.M.Z.3
McCafferty, D.G.4
Fitzpatrick, P.F.5
-
48
-
-
0033731344
-
Adiabatic Connection for Kinetics
-
Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. Adiabatic Connection for Kinetics J. Phys. Chem. A 2000, 104, 4811-4815
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 4811-4815
-
-
Lynch, B.J.1
Fast, P.L.2
Harris, M.3
Truhlar, D.G.4
-
49
-
-
43049141516
-
The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals
-
Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chem. Acc. 2008, 120, 215-241
-
(2008)
Theor. Chem. Acc.
, vol.120
, pp. 215-241
-
-
Zhao, Y.1
Truhlar, D.G.2
-
50
-
-
58149236927
-
Exploring the Limit of Accuracy of the Global Hybrid Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions
-
Zhao, Y.; Truhlar, D. G. Exploring the Limit of Accuracy of the Global Hybrid Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions J. Chem. Theor. Comput. 2008, 4, 1849-1868
-
(2008)
J. Chem. Theor. Comput.
, vol.4
, pp. 1849-1868
-
-
Zhao, Y.1
Truhlar, D.G.2
-
52
-
-
0035879976
-
6-31G* Basis Set for Third-Row Atoms
-
Rassolov, V.; Pople, J. A.; Ratner, M.; Redfern, P. C.; Curtiss, L. A. 6-31G* Basis Set for Third-Row Atoms J. Comput. Chem. 2001, 22, 976-984
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 976-984
-
-
Rassolov, V.1
Pople, J.A.2
Ratner, M.3
Redfern, P.C.4
Curtiss, L.A.5
-
53
-
-
15544366274
-
Benchmark Database of Barrier Heights for Heavy Atom Transfer, Nucleophilic Substitution, Association, and Unimolecular Reactions and Its Use to Test Theoretical Methods
-
Zhao, Y.; González-García, N.; Truhlar, D. G. Benchmark Database of Barrier Heights for Heavy Atom Transfer, Nucleophilic Substitution, Association, and Unimolecular Reactions and Its Use to Test Theoretical Methods J. Phys. Chem. A 2005, 109, 2012-2018
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 2012-2018
-
-
Zhao, Y.1
González-García, N.2
Truhlar, D.G.3
-
54
-
-
84894675774
-
-
Erratum. 2006, 110, 4942.
-
(2006)
Erratum
, vol.110
, pp. 4942
-
-
-
55
-
-
65249096094
-
The DBH24/08 Database and Its Use to Assess Electronic Structure Model Chemistries for Chemical Reaction Barrier Heights
-
Zheng, J.; Zhao, Y.; Truhlar, D. G. The DBH24/08 Database and Its Use to Assess Electronic Structure Model Chemistries for Chemical Reaction Barrier Heights J. Chem. Theory and Comput. 2009, 5, 808-821
-
(2009)
J. Chem. Theory and Comput.
, vol.5
, pp. 808-821
-
-
Zheng, J.1
Zhao, Y.2
Truhlar, D.G.3
-
56
-
-
84927937274
-
The Quest for a Universal Density Functional: The Accuracy of Density Functionals Across a Broad Spectrum of Databases in Chemistry and Physics
-
Peverati, R.; Truhlar, D. G. The Quest for a Universal Density Functional: The Accuracy of Density Functionals Across a Broad Spectrum of Databases in Chemistry and Physics Philos. Trans. Roy. Soc. A 2013, arxiv.org/abs/1212.0944
-
(2013)
Philos. Trans. Roy. Soc. A
-
-
Peverati, R.1
Truhlar, D.G.2
-
57
-
-
70450206724
-
-
revision A.02; Gaussian, Inc. Wallingford, CT
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision A.02; Gaussian, Inc.: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
-
58
-
-
70350406958
-
-
version 5.0; University of Minnesota: Minneapolis, MN
-
Yang, K.; Zhao, Y.; Truhlar, D. G. MN-GFM: Minnesota Gaussian Functional Module, version 5.0; University of Minnesota: Minneapolis, MN, 2011.
-
(2011)
MN-GFM: Minnesota Gaussian Functional Module
-
-
Yang, K.1
Zhao, Y.2
Truhlar, D.G.3
-
59
-
-
14844366310
-
The 6-31B(d) Basis Set and the BMC-QCISD and BMC-CCSD Multi-Coefficient Correlation Methods
-
Lynch, B. J.; Zhao, Y.; Truhlar, D. G. The 6-31B(d) Basis Set and the BMC-QCISD and BMC-CCSD Multi-Coefficient Correlation Methods J. Phys. Chem. A 2005, 109, 1643-1649
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 1643-1649
-
-
Lynch, B.J.1
Zhao, Y.2
Truhlar, D.G.3
-
60
-
-
0035147937
-
Gaussian-3X (G3X) Theory: Use of Improved Geometries, Zero-Point Energies, and Hartree-Fock Basis Sets
-
Curtiss, L. A.; Redfern, P. C.; Raghavachari, K.; Pople, J. A. Gaussian-3X (G3X) Theory: Use of Improved Geometries, Zero-Point Energies, and Hartree-Fock Basis Sets J. Chem. Phys. 2001, 114, 108-117
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 108-117
-
-
Curtiss, L.A.1
Redfern, P.C.2
Raghavachari, K.3
Pople, J.A.4
-
62
-
-
34547132094
-
Structural Basis of LSD1-CoREST Selectivity in Histone H3 Recognition
-
Forneris, F.; Binda, C.; Adamo, A.; Battaglioli, E.; Mattevi, A. Structural Basis of LSD1-CoREST Selectivity in Histone H3 Recognition J. Biol. Chem. 2007, 282, 20070-20074
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 20070-20074
-
-
Forneris, F.1
Binda, C.2
Adamo, A.3
Battaglioli, E.4
Mattevi, A.5
-
64
-
-
84986512474
-
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations J. Comput. Chem. 2004, 4, 187-217
-
(2004)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
65
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
66
-
-
0242663237
-
A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
67
-
-
84962345519
-
SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters
-
Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters J. Chem. Theor. Comput. 2005, 1, 1133-1152
-
(2005)
J. Chem. Theor. Comput.
, vol.1
, pp. 1133-1152
-
-
Kelly, C.P.1
Cramer, C.J.2
Truhlar, D.G.3
-
68
-
-
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. D.; 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.D.3
Kollman, P.A.4
-
69
-
-
18844410543
-
Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations
-
Lin, H.; Truhlar, D. G. Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations J. Phys. Chem. A 2005, 109, 3991-4404
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 3991-4404
-
-
Lin, H.1
Truhlar, D.G.2
-
70
-
-
77950101392
-
Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm
-
B. Wang, B.; Truhlar, D. G. Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm J. Chem. Theory Comput. 2010, 6, 359-369
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 359-369
-
-
Wang B, B.1
Truhlar, D.G.2
-
71
-
-
65249101955
-
-
version 2008-2; University of Minnesota: Minneapolis, MN
-
Higashi, M.; Marenich, A. V.; Olson, R. M.; Chamberlin, A. C.; Pu, J.; Kelly, C. P.; Thompson, J. D.; Xidos, J. D.; Li, J.; Zhu, T.; GAMESSPLUS, version 2008-2; University of Minnesota: Minneapolis, MN, 2008.
-
(2008)
GAMESSPLUS
-
-
Higashi, M.1
Marenich, A.V.2
Olson, R.M.3
Chamberlin, A.C.4
Pu, J.5
Kelly, C.P.6
Thompson, J.D.7
Xidos, J.D.8
Li, J.9
Zhu, T.10
-
72
-
-
84893169025
-
General Atomic and Molecular Electronic Structure System
-
Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J. General Atomic and Molecular Electronic Structure System J. Comput. Chem. 1993, 14, 1347-1363
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.J.10
-
73
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
74
-
-
33846823909
-
Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
75
-
-
2942532422
-
Development and Testing of a General AMBER Force Field
-
Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General AMBER Force Field J. Comput. Chem. 2004, 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.M.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
76
-
-
0001477037
-
Multiconfiguration Molecular Mechanics Algorithm for Potential Energy Surfaces of Chemical Reactions
-
Kim, Y.; Corchado, J. C.; VillaÌ, J.; Xing, J.; Truhlar, D. G. Multiconfiguration Molecular Mechanics Algorithm for Potential Energy Surfaces of Chemical Reactions J. Chem. Phys. 2000, 112, 2718-2735
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 2718-2735
-
-
Kim, Y.1
Corchado, J.C.2
Villaì, J.3
Xing, J.4
Truhlar, D.G.5
-
77
-
-
0035922555
-
Molecular Mechanics for Chemical Reactions. A Standard Strategy for Using Multi-Configuration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling
-
Albu, T.; Corchado, J. C.; Truhlar, D. G. Molecular Mechanics for Chemical Reactions. A Standard Strategy for Using Multi-Configuration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling J. Phys. Chem. A 2001, 105, 8465-8487
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 8465-8487
-
-
Albu, T.1
Corchado, J.C.2
Truhlar, D.G.3
-
78
-
-
33846309628
-
Multi-configuration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations
-
Lin, H.; Zhao, Y.; Tishchenko, O.; Truhlar, D. G. Multi-configuration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations J. Chem. Theory Comput. 2006, 2, 1237-1254
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1237-1254
-
-
Lin, H.1
Zhao, Y.2
Tishchenko, O.3
Truhlar, D.G.4
-
79
-
-
33846683874
-
Optimizing the Performance of the Multiconfiguration Molecular Mechanics Method
-
Tishchenko, O.; Truhlar, D. G. Optimizing the Performance of the Multiconfiguration Molecular Mechanics Method J. Phys. Chem. A 2006, 110, 13530-13536
-
(2006)
J. Phys. Chem. A
, vol.110
, pp. 13530-13536
-
-
Tishchenko, O.1
Truhlar, D.G.2
-
80
-
-
58449097905
-
Efficient Global Representations of Potential Energy Functions: Trajectory Calculations of Bimolecular Gas-Phase Reactions by Multiconfiguration Molecular Mechanics
-
Tishchenko, O.; Truhlar, D. G. Efficient Global Representations of Potential Energy Functions: Trajectory Calculations of Bimolecular Gas-Phase Reactions by Multiconfiguration Molecular Mechanics J. Chem. Phys. 2009, 130, 024105/1-15
-
(2009)
J. Chem. Phys.
, vol.130
-
-
Tishchenko, O.1
Truhlar, D.G.2
-
81
-
-
67650072440
-
Non-Hermitian Multiconfiguration Molecular Mechanics
-
Tishchenko, O.; Truhlar, D. G. Non-Hermitian Multiconfiguration Molecular Mechanics J. Chem. Theory Comput. 2009, 5, 1454-1461
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1454-1461
-
-
Tishchenko, O.1
Truhlar, D.G.2
-
82
-
-
77749328054
-
Gradient-Based Multiconfiguration Shepard Interpolation for Generating Potential Energy Surfaces for Polyatomic Reactions
-
Tishchenko, O.; Truhlar, D. G. Gradient-Based Multiconfiguration Shepard Interpolation for Generating Potential Energy Surfaces for Polyatomic Reactions J. Chem. Phys. 2010, 132, 084109/1-6
-
(2010)
J. Chem. Phys.
, vol.132
-
-
Tishchenko, O.1
Truhlar, D.G.2
-
83
-
-
30344440627
-
-
version 10; University of California: San Francisco, CA
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; AMBER, version 10; University of California: San Francisco, CA, 2008.
-
(2008)
AMBER
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
-
84
-
-
84876746946
-
-
version; University of Minnesota: Minneapolis, MN
-
Higashi, M.; Truhlar, D. G. AMBERPLUS, version 2010; University of Minnesota: Minneapolis, MN.
-
(2010)
AMBERPLUS
-
-
Higashi, M.1
Truhlar, D.G.2
-
85
-
-
69349093069
-
-
version 2.0.2; University of Rochester: Rochester, NY
-
Grossfield, A. WHAM, version 2.0.2; University of Rochester: Rochester, NY, 2008.
-
(2008)
WHAM
-
-
Grossfield, A.1
-
86
-
-
77955578037
-
A Non-orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions
-
Cembran, A.; Payaka, A.; Lin, Y.-L.; Xie, W.; Mo, Y.; Song, L.; Gao, J. A Non-orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions J. Chem. Theory Comput. 2010, 6, 2242-2251
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2242-2251
-
-
Cembran, A.1
Payaka, A.2
Lin, Y.-L.3
Xie, W.4
Mo, Y.5
Song, L.6
Gao, J.7
-
87
-
-
85056406805
-
Variational Transition State Theory and Multidimensional Tunneling for Simple and Complex Reactions in the Gas Phase, Solids, Liquids, and Enzymes. in Isotope
-
Kohen, A. Limbach, H.-H. Marcel Dekker: New York - 619
-
Truhlar, D. G. Variational Transition State Theory and Multidimensional Tunneling for Simple and Complex Reactions in the Gas Phase, Solids, Liquids, and Enzymes. In Isotope Effects in Chemistry and Biology, Kohen, A.; Limbach, H.-H. Marcel Dekker: New York, 2006; pp 579-619.
-
(2006)
Effects in Chemistry and Biology
, pp. 579
-
-
Truhlar, D.G.1
-
88
-
-
84879337691
-
Variational Transition State Theory
-
Dykstra, C. E. Frenking, G. Kim, K. S. Scuseria, G. E. Elsevier: Amsterdam - 87
-
Garrett, B. C.; Truhlar, D. G. Variational Transition State Theory. In Theory and Applications of Computational Chemistry: The First Forty Years; Dykstra, C. E.; Frenking, G.; Kim, K. S.; Scuseria, G. E., Eds.; Elsevier: Amsterdam, 2005; pp 67-87.
-
(2005)
Theory and Applications of Computational Chemistry: The First Forty Years
, pp. 67
-
-
Garrett, B.C.1
Truhlar, D.G.2
-
89
-
-
17644400195
-
Ensemble-Averaged Variational Transition State Theory with Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions
-
Truhlar, D. G.; Gao, J.; Garcia-Viloca, M.; Alhambra, C.; Corchado, J.; Sanchez, M. L.; Poulsen, T. D. Ensemble-Averaged Variational Transition State Theory with Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions Int. J. Quantum Chem. 2004, 100, 1136-1152
-
(2004)
Int. J. Quantum Chem.
, vol.100
, pp. 1136-1152
-
-
Truhlar, D.G.1
Gao, J.2
Garcia-Viloca, M.3
Alhambra, C.4
Corchado, J.5
Sanchez, M.L.6
Poulsen, T.D.7
|