Literature DB >> 26878566

Calculating Free Energy Changes in Continuum Solvation Models.

Junming Ho1,2, Mehmed Z Ertem3.   

Abstract

We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment.

Entities:  

Year:  2016        PMID: 26878566     DOI: 10.1021/acs.jpcb.6b00164

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  18 in total

1.  How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?

Authors:  Junbo Chen; Bun Chan; Yihan Shao; Junming Ho
Journal:  Phys Chem Chem Phys       Date:  2020-02-19       Impact factor: 3.676

Review 2.  Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.

Authors:  Fernando Luís Barroso daSilva; Luis Gustavo Dias
Journal:  Biophys Rev       Date:  2017-09-18

3.  Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge.

Authors:  Qiao Zeng; Michael R Jones; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-08-20       Impact factor: 3.686

4.  Relative Order of Acidity among Hydroxyl Groups of Oxyluciferin and Emission Light Colors in Aqueous Solution.

Authors:  Jian-Ge Zhou; Shan Yang; Zhen-Yan Deng; Jerzy Leszczynski
Journal:  J Photochem Photobiol A Chem       Date:  2020-04-02       Impact factor: 4.291

5.  Cephalexin degradation initiated by OH radicals: theoretical prediction of the mechanisms and the toxicity of byproducts.

Authors:  R Masmoudi; S Khettaf; A Soltani; A Dibi; L Messaadia; M Benamira
Journal:  J Mol Model       Date:  2022-05-10       Impact factor: 1.810

6.  An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.

Authors:  Samarjeet Prasad; Jing Huang; Qiao Zeng; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-01       Impact factor: 3.686

7.  Towards a converged strategy for including microsolvation in reaction mechanism calculations.

Authors:  Rebecca Sure; Moad El Mahdali; Alex Plajer; Peter Deglmann
Journal:  J Comput Aided Mol Des       Date:  2021-01-09       Impact factor: 3.686

8.  A DFT investigation of the blue bottle experiment: Ehalf-cell analysis of autoxidation catalysed by redox indicators.

Authors:  Taweetham Limpanuparb; Pakpong Roongruangsree; Cherprang Areekul
Journal:  R Soc Open Sci       Date:  2017-11-08       Impact factor: 2.963

9.  Tropylium-promoted carbonyl-olefin metathesis reactions.

Authors:  Uyen P N Tran; Giulia Oss; Domenic P Pace; Junming Ho; Thanh V Nguyen
Journal:  Chem Sci       Date:  2018-05-04       Impact factor: 9.825

10.  One-Electron Reduction Potentials: Calibration of Theoretical Protocols for Morita⁻Baylis⁻Hillman Nitroaromatic Compounds in Aprotic Media.

Authors:  Amauri Francisco da Silva; Antonio João da Silva Filho; Mário L A A Vasconcellos; Otávio Luís de Santana
Journal:  Molecules       Date:  2018-08-24       Impact factor: 4.411

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.