The Energy Gap as a Universal Reaction Coordinate for the
Simulation of Chemical Reactions

J 2009

The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions

MONES, Letif; Petr KULHÁNEK; Istvan SIMON; Alessandro LAIO; Monika FUXREITER et al.

Základní údaje

Originální název

The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions

Autoři

MONES, Letif; Petr KULHÁNEK; Istvan SIMON; Alessandro LAIO a Monika FUXREITER

Vydání

Journal of Physical Chemistry B, New York, American Chemical Society, 2009, 1520-6106

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10402 Inorganic and nuclear chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 3.471

Označené pro přenos do RIV

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000266545500019

Klíčová slova anglicky

free energy; energy gap; empirical valence bond

Příznaky

Recenzováno

Změněno: 23. 3. 2010 16:43, RNDr. Petr Kulhánek, Ph.D.

Anotace

V originále

The selection of a proper reaction coordinate is a major bottleneck in simulations of chemical reactions in complex systems. Increasing the number of variables that are used to bias the reaction largely affects the convergence and leads to an unbearable increase in computational price. This problem can be overcome by employing a complex reaction coordinate that depends on many geometrical variables of the system, such as the energy gap (E-GAP) in the empirical valence bond (EVB) method. E-GAP depends on all of the coordinates of the system, and its robustness has been demonstrated for a variety of enzymatic reactions. In this work, we demonstrate that E-GAP, derived from a classical representation, can be used as a reaction coordinate in systems described with any quantum chemistry Hamiltonian. Benefits of using E-GAP as a reaction coordinate as compared to a traditional geometrical variable are illustrated in the case of a symmetric nucleophilic substitution reaction in water solution. E-GAP is shown to provide a significantly more efficient sampling and allows a better localization of the transition state as compared to a geometrical reaction coordinate.

Citovat

MONES, Letif; Petr KULHÁNEK; Istvan SIMON; Alessandro LAIO a Monika FUXREITER. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. Journal of Physical Chemistry B. New York: American Chemical Society, 2009, roč. 2009, 113(22), s. 7867-7873, 6 s. ISSN 1520-6106.

@article{839387,
   author = {Mones, Letif and Kulhánek, Petr and Simon, Istvan and Laio, Alessandro and Fuxreiter, Monika},
   article_location = {New York},
   article_number = {113(22)},
   keywords = {free energy; energy gap; empirical valence bond},
   language = {eng},
   issn = {1520-6106},
   journal = {Journal of Physical Chemistry B},
   title = {The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions},
   volume = {2009},
   year = {2009}
}

TY  - JOUR
ID  - 839387
AU  - Mones, Letif - Kulhánek, Petr - Simon, Istvan - Laio, Alessandro - Fuxreiter, Monika
PY  - 2009
TI  - The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions
JF  - Journal of Physical Chemistry B
VL  - 2009
IS  - 113(22)
SP  - 7867-7873
EP  - 7867-7873
PB  - American Chemical Society
SN  - 15206106
KW  - free energy
KW  - energy gap
KW  - empirical valence bond
N2  - The selection of a proper reaction coordinate is a major bottleneck in simulations of chemical reactions in complex systems. Increasing the number of variables that are used to bias the reaction largely affects the convergence and leads to an unbearable increase in computational price. This problem can be overcome by employing a complex reaction coordinate that depends on many geometrical variables of the system, such as the energy gap (E-GAP) in the empirical valence bond (EVB) method. E-GAP depends on all of the coordinates of the system, and its robustness has been demonstrated for a variety of enzymatic reactions. In this work, we demonstrate that E-GAP, derived from a classical representation, can be used as a reaction coordinate in systems described with any quantum chemistry Hamiltonian. Benefits of using E-GAP as a reaction coordinate as compared to a traditional geometrical variable are illustrated in the case of a symmetric nucleophilic substitution reaction in water solution. E-GAP is shown to provide a significantly more efficient sampling and allows a better localization of the transition state as compared to a geometrical reaction coordinate.
ER  -

MONES, Letif; Petr KULHÁNEK; Istvan SIMON; Alessandro LAIO a Monika FUXREITER. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. \textit{Journal of Physical Chemistry B}. New York: American Chemical Society, 2009, roč.~2009, 113(22), s.~7867-7873, 6 s. ISSN~1520-6106.

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