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A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion
被引:74
作者
:
Ensing, B
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
Ensing, B
Laio, A
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
Laio, A
Gervasio, FL
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
Gervasio, FL
Parrinello, M
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
Parrinello, M
Klein, ML
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
Klein, ML
机构
:
[1]
Univ Penn, Ctr Mol Modeling, Philadelphia, PA 19104 USA
[2]
Univ Penn, Dept Chem, Philadelphia, PA 19104 USA
[3]
ETH, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland
来源
:
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
|
2004年
/ 126卷
/ 31期
关键词
:
D O I
:
10.1021/ja048285t
中图分类号
:
O6 [化学];
学科分类号
:
0703 ;
摘要
:
The prototype binuclear elimination (E2) reaction illustrates the mechanism of a large number of biochemical and industrial applied processes but has received surprisingly little attention in theoretical studies compared to, for example, the substitution (SN2) reaction. This is due to its concerted mechanism, which requires an independent description of the three bonds that are being formed or broken. In this work, we have taken the advantage of a new and promising methodology to efficiently sample intrinsically multidimensional free-energy surfaces. We locate the lowest free-energy reaction path in the 3D configurational space and use this finite-temperature intrinsic reaction coordinate in an umbrella sampling scheme to access the temperature contributions to high accuracy. The small increase of the barrier and the decrease of the overall endothermicity for the E2 reaction due to entropic contributions is non-trivial. Moreover, our strategy to efficiently handle multiple reaction coordinates could be a great benefit to many chemistry-related fields, such as enzyme catalysis, reactions in solution, and nucleation processes. Copyright © 2004 American Chemical Society.
引用
收藏
页码:9492 / 9493
页数:2
相关论文
共 18 条
[1]
Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunneling dynamics.: Theory and application to liver alcohol dehydrogenase
Alhambra, C
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Alhambra, C
Corchado, J
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Corchado, J
Sánchez, ML
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Sánchez, ML
Garcia-Viloca, M
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Garcia-Viloca, M
Gao, J
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Gao, J
Truhlar, DG
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Truhlar, DG
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BICKELHAUPT, FM
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0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
BICKELHAUPT, FM
BAERENDS, EJ
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0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
BAERENDS, EJ
NIBBERING, NMM
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0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
NIBBERING, NMM
ZIEGLER, T
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0
引用数:
0
h-index:
0
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FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
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FUKUI, K
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Garcia-Viloca, M
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0
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0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Garcia-Viloca, M
Gao, J
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Gao, J
Karplus, M
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Karplus, M
Truhlar, DG
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Truhlar, DG
[J].
SCIENCE,
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Kinetic isotope effects and transition state geometries. A theoretical investigation of E2 model systems
Glad, SS
论文数:
0
引用数:
0
h-index:
0
机构:
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
Glad, SS
Jensen, F
论文数:
0
引用数:
0
h-index:
0
机构:
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
Jensen, F
[J].
JOURNAL OF ORGANIC CHEMISTRY,
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A climbing image nudged elastic band method for finding saddle points and minimum energy paths
Henkelman, G
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Henkelman, G
Uberuaga, BP
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0
引用数:
0
h-index:
0
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Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Uberuaga, BP
Jónsson, H
论文数:
0
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0
h-index:
0
机构:
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Jónsson, H
[J].
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Factors affecting competitive ion-molecule reactions: ClO-+C2H5Cl and C2D5Cl via E2 and S(N)2 channels
Hu, WP
论文数:
0
引用数:
0
h-index:
0
机构:
UNIV MINNESOTA,DEPT CHEM,MINNEAPOLIS,MN 55455
Hu, WP
Truhlar, DG
论文数:
0
引用数:
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h-index:
0
机构:
UNIV MINNESOTA,DEPT CHEM,MINNEAPOLIS,MN 55455
Truhlar, DG
[J].
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
1996,
118
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←
1
2
→
共 18 条
[1]
Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunneling dynamics.: Theory and application to liver alcohol dehydrogenase
Alhambra, C
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Alhambra, C
Corchado, J
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Corchado, J
Sánchez, ML
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Sánchez, ML
Garcia-Viloca, M
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Garcia-Viloca, M
Gao, J
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Gao, J
Truhlar, DG
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
Truhlar, DG
[J].
JOURNAL OF PHYSICAL CHEMISTRY B,
2001,
105
(45)
: 11326
-
11340
[2]
[Anonymous], 2002, PHYS REV B
[3]
THEORETICAL INVESTIGATION ON BASE-INDUCED 1,2-ELIMINATIONS IN THE MODEL SYSTEM F-+CH3CH2F - THE ROLE OF THE BASE AS A CATALYST
BICKELHAUPT, FM
论文数:
0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
BICKELHAUPT, FM
BAERENDS, EJ
论文数:
0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
BAERENDS, EJ
NIBBERING, NMM
论文数:
0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
NIBBERING, NMM
ZIEGLER, T
论文数:
0
引用数:
0
h-index:
0
机构:
FREE UNIV AMSTERDAM,SCHEIKUNDIG LAB,SECTIE THEORET CHEM,DEBOELELAAN 1083,1081 HV AMSTERDAM,NETHERLANDS
ZIEGLER, T
[J].
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
1993,
115
(20)
: 9160
-
9173
[4]
Frisch M.J., 1998, GAUSSIAN 98
[5]
THE PATH OF CHEMICAL-REACTIONS - THE IRC APPROACH
FUKUI, K
论文数:
0
引用数:
0
h-index:
0
FUKUI, K
[J].
ACCOUNTS OF CHEMICAL RESEARCH,
1981,
14
(12)
: 363
-
368
[6]
FUKUI K, 1970, J AM CHEM SOC, V74, P4160
[7]
How enzymes work: Analysis by modern rate theory and computer simulations
Garcia-Viloca, M
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Garcia-Viloca, M
Gao, J
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Gao, J
Karplus, M
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Karplus, M
Truhlar, DG
论文数:
0
引用数:
0
h-index:
0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
Truhlar, DG
[J].
SCIENCE,
2004,
303
(5655)
: 186
-
195
[8]
Kinetic isotope effects and transition state geometries. A theoretical investigation of E2 model systems
Glad, SS
论文数:
0
引用数:
0
h-index:
0
机构:
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
Glad, SS
Jensen, F
论文数:
0
引用数:
0
h-index:
0
机构:
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
ODENSE UNIV,DEPT CHEM,DK-5230 ODENSE M,DENMARK
Jensen, F
[J].
JOURNAL OF ORGANIC CHEMISTRY,
1997,
62
(02)
: 253
-
260
[9]
A climbing image nudged elastic band method for finding saddle points and minimum energy paths
Henkelman, G
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Henkelman, G
Uberuaga, BP
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Uberuaga, BP
Jónsson, H
论文数:
0
引用数:
0
h-index:
0
机构:
Univ Washington, Dept Chem 351700, Seattle, WA 98195 USA
Jónsson, H
[J].
JOURNAL OF CHEMICAL PHYSICS,
2000,
113
(22)
: 9901
-
9904
[10]
Factors affecting competitive ion-molecule reactions: ClO-+C2H5Cl and C2D5Cl via E2 and S(N)2 channels
Hu, WP
论文数:
0
引用数:
0
h-index:
0
机构:
UNIV MINNESOTA,DEPT CHEM,MINNEAPOLIS,MN 55455
Hu, WP
Truhlar, DG
论文数:
0
引用数:
0
h-index:
0
机构:
UNIV MINNESOTA,DEPT CHEM,MINNEAPOLIS,MN 55455
Truhlar, DG
[J].
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY,
1996,
118
(04)
: 860
-
869
←
1
2
→