Literature DB >> 15291524

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

Bernd Ensing1, Alessandro Laio, Francesco L Gervasio, Michele Parrinello, Michael L Klein.   

Abstract

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.

Entities:  

Year:  2004        PMID: 15291524     DOI: 10.1021/ja048285t

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  8 in total

1.  Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.

Authors:  Bernd Ensing; Michael L Klein
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-29       Impact factor: 11.205

2.  The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections.

Authors:  Volodymyr Babin; Christopher Roland; Thomas A Darden; Celeste Sagui
Journal:  J Chem Phys       Date:  2006-11-28       Impact factor: 3.488

3.  Insight into the folding inhibition of the HIV-1 protease by a small peptide.

Authors:  Massimiliano Bonomi; Francesco L Gervasio; Guido Tiana; Davide Provasi; Ricardo A Broglia; Michele Parrinello
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

4.  Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface.

Authors:  Sangwook Wu; Chang Jun Lee; Lee G Pedersen
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-04-08

5.  Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail.

Authors:  G Fiorin; A Pastore; P Carloni; M Parrinello
Journal:  Biophys J       Date:  2006-07-28       Impact factor: 4.033

6.  Dissociation of minor groove binders from DNA: insights from metadynamics simulations.

Authors:  Attilio Vittorio Vargiu; Paolo Ruggerone; Alessandra Magistrato; Paolo Carloni
Journal:  Nucleic Acids Res       Date:  2008-09-18       Impact factor: 16.971

7.  Pathways for the formation of ice polymorphs from water predicted by a metadynamics method.

Authors:  Hiroki Nada
Journal:  Sci Rep       Date:  2020-03-13       Impact factor: 4.379

8.  A Unified Framework for Understanding Nucleophilicity and Protophilicity in the SN 2/E2 Competition.

Authors:  Pascal Vermeeren; Thomas Hansen; Paul Jansen; Marcel Swart; Trevor A Hamlin; F Matthias Bickelhaupt
Journal:  Chemistry       Date:  2020-10-22       Impact factor: 5.236

  8 in total

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