Literature DB >> 20503993

New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision.

Matthew A Wyczalkowski1, Andreas Vitalis, Rohit V Pappu.   

Abstract

We present two new methods for estimating the entropy and enthalpy decomposition of free energy calculations. These methods are based on temperature derivatives of the Bennett Acceptance Ratio and the Multistate Bennett Acceptance Ratio estimators, respectively. We test the accuracy of these new estimators using a simple one-dimensional model. A detailed assessment of their performance is reported by studying the solvation of N-methylacetamide. Finally, we quantify the free energies of solvation for 11 model compounds using the OPLS-AA force field and a variation of this force field. Thermodynamic decompositions of these calculated free energies are obtained to highlight the utility of these quantities for refining force field parameters by comparing computed free energies and their decompositions to their experimental counterparts.

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Year:  2010        PMID: 20503993     DOI: 10.1021/jp103050u

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


  7 in total

1.  Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Authors:  Amanda Li; Michael K Gilson
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

2.  Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations.

Authors:  Yue Shi; Crystal Z Zhu; Stephen F Martin; Pengyu Ren
Journal:  J Phys Chem B       Date:  2012-01-31       Impact factor: 2.991

3.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

4.  Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

Authors:  David R Bell; Rui Qi; Zhifeng Jing; Jin Yu Xiang; Christopher Mejias; Michael J Schnieders; Jay W Ponder; Pengyu Ren
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

5.  Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.

Authors:  Niel M Henriksen; Andrew T Fenley; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2015-09-08       Impact factor: 6.006

6.  Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies.

Authors:  Andrew T Fenley; Niel M Henriksen; Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2014-07-23       Impact factor: 6.006

7.  Explanation of the Formation of Complexes between Representatives of Oxazolidinones and HDAS-β-CD Using Molecular Modeling as a Complementary Technique to cEKC and NMR.

Authors:  Wojciech Bocian; Elżbieta Bednarek; Katarzyna Michalska
Journal:  Int J Mol Sci       Date:  2021-07-01       Impact factor: 5.923

  7 in total

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