Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution

The Journal of Physical Chemistry. B
Norio TakenakaMasataka Nagaoka

Abstract

In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

References

Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
May 28, 2005·The Journal of Chemical Physics·Kevin Leung, Susan B Rempe
Aug 12, 2005·Chemical Reviews·Jacopo TomasiRoberto Cammi
Oct 29, 2008·Physical Chemistry Chemical Physics : PCCP·Nasséra BenbrahimManuel F Ruiz-López
Aug 17, 2010·The Journal of Chemical Physics·Marius ReteganManuel F Ruiz-López
Oct 16, 2010·Journal of Computational Chemistry·Takuya OkamotoMasataka Nagaoka
Apr 10, 2012·The Journal of Chemical Physics·Hiroshi Nakano, Takeshi Yamamoto
Aug 17, 2012·The Journal of Physical Chemistry. B·Herbert C Georg, Sylvio Canuto
Oct 8, 2013·The Journal of Physical Chemistry. B·Marilia T C Martins-Costa, Manuel F Ruiz-Lopez
Oct 21, 2014·Journal of Chemical Theory and Computation·Peng TaoBernard R Brooks
Aug 12, 2014·Journal of Chemical Theory and Computation·Yukichi KitamuraMasataka Nagaoka

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antibodies: Agglutination

Antibody-mediated agglutination is the clumping of cells in the presence of antibody, which binds multiple cells together. This enhances the clearance of pathogens. Find the latest research on antibody-mediated agglutination here.