Literature DB >> 20352296

Prediction of tautomer ratios by embedded-cluster integral equation theory.

Stefan M Kast1, Jochen Heil, Stefan Güssregen, K Friedemann Schmidt.   

Abstract

The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol(-1)) as well as for the full set of quantitative reaction data (2.0 kcal mol(-1)) among the SAMPL2 participants.

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Year:  2010        PMID: 20352296     DOI: 10.1007/s10822-010-9340-x

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  3 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Quantum chemistry in solution by combining 3D integral equation theory with a cluster embedding approach.

Authors:  Thomas Kloss; Jochen Heil; Stefan M Kast
Journal:  J Phys Chem B       Date:  2008-03-15       Impact factor: 2.991

3.  Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions.

Authors:  Stefan M Kast; Thomas Kloss
Journal:  J Chem Phys       Date:  2008-12-21       Impact factor: 3.488

  3 in total
  11 in total

1.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

2.  The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory.

Authors:  Nicolas Tielker; Lukas Eberlein; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2018-08-02       Impact factor: 3.686

3.  The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.

Authors:  Nicolas Tielker; Daniel Tomazic; Jochen Heil; Thomas Kloss; Sebastian Ehrhart; Stefan Güssregen; K Friedemann Schmidt; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2016-08-23       Impact factor: 3.686

4.  Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.

Authors:  Lukas Eberlein; Frank R Beierlein; Nico J R van Eikema Hommes; Ashish Radadiya; Jochen Heil; Steven A Benner; Timothy Clark; Stefan M Kast; Nigel G J Richards
Journal:  J Chem Theory Comput       Date:  2020-03-20       Impact factor: 6.006

5.  Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint.

Authors:  Sedat Karabulut; Hilmi Namli; Jerzy Leszczynski
Journal:  J Comput Aided Mol Des       Date:  2013-08-07       Impact factor: 3.686

6.  Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

Authors:  Jochen Heil; Daniel Tomazic; Simon Egbers; Stefan M Kast
Journal:  J Mol Model       Date:  2014-03-25       Impact factor: 1.810

7.  Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations.

Authors:  Rasmus A X Persson; Viren Pattni; Anurag Singh; Stefan M Kast; Matthias Heyden
Journal:  J Chem Theory Comput       Date:  2017-08-25       Impact factor: 6.006

8.  Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution.

Authors:  Marcus Wieder; Josh Fass; John D Chodera
Journal:  Chem Sci       Date:  2021-07-19       Impact factor: 9.825

9.  Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?

Authors:  Nicolas Tielker; Lukas Eberlein; Gerhard Hessler; K Friedemann Schmidt; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2020-10-20       Impact factor: 3.686

10.  SAMPL7 physical property prediction from EC-RISM theory.

Authors:  Nicolas Tielker; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2021-07-19       Impact factor: 3.686

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