Literature DB >> 20432055

Analysis of SM8 and Zap TK calculations and their geometric sensitivity.

Benjamin A Ellingson1, A Geoffrey Skillman, Anthony Nicholls.   

Abstract

A prospective study of aqueous solvation energies was done using the SM8 and Zap TK models for a variety of geometries. CM4M charges calculated with M06 and M06-2X were found to yield similar results for the SM8 model. Zap TK calculations were primarily done with AM1BCC charges but limited attempts to use charges derived from DFT showed promise. The OMEGA application quickly generated conformations that performed well with both solvation models, while the use of computationally expensive DFT optimized geometries yielded increased RMSE and MSE. It is shown that increasing levels of gas phase geometry optimization yield increasingly unfavorable solvation energy for single conformer models.

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Year:  2010        PMID: 20432055     DOI: 10.1007/s10822-010-9355-3

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


  10 in total

1.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

2.  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

3.  SAMPL2 and continuum modeling.

Authors:  Anthony Nicholls; Stanislaw Wlodek; J Andrew Grant
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

4.  Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

Authors:  Raphael F Ribeiro; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Comput Aided Mol Des       Date:  2010-04-01       Impact factor: 3.686

5.  Treating entropy and conformational changes in implicit solvent simulations of small molecules.

Authors:  David L Mobley; Ken A Dill; John D Chodera
Journal:  J Phys Chem B       Date:  2008-01-03       Impact factor: 2.991

6.  Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies.

Authors:  Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

7.  The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization.

Authors:  Anthony Nicholls; Stanislaw Wlodek; J Andrew Grant
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

8.  A universal approach to solvation modeling.

Authors:  Christopher J Cramer; Donald G Truhlar
Journal:  Acc Chem Res       Date:  2008-06       Impact factor: 22.384

9.  Charge Model 4 and Intramolecular Charge Polarization.

Authors:  Ryan M Olson; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

10.  Performance of SM8 on a test to predict small-molecule solvation free energies.

Authors:  Adam C Chamberlin; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2008-06-26       Impact factor: 2.991

  10 in total
  5 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.  SAMPL2 and continuum modeling.

Authors:  Anthony Nicholls; Stanislaw Wlodek; J Andrew Grant
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

3.  Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

Authors:  Benjamin A Ellingson; Matthew T Geballe; Stanislaw Wlodek; Christopher I Bayly; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2014-03-16       Impact factor: 3.686

4.  SAMPL4 & DOCK3.7: lessons for automated docking procedures.

Authors:  Ryan G Coleman; Teague Sterling; Dahlia R Weiss
Journal:  J Comput Aided Mol Des       Date:  2014-02-11       Impact factor: 3.686

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

  5 in total

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