Literature DB >> 20358259

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

Raphael F Ribeiro1, Aleksandr V Marenich, Christopher J Cramer, Donald G Truhlar.   

Abstract

We applied the solvation models SM8, SM8AD, and SMD in combination with the Minnesota M06-2X density functional to predict vacuum-water transfer free energies (Task 1) and tautomeric ratios in aqueous solution (Task 2) for the SAMPL2 test set. The bulk-electrostatic contribution to the free energy of solvation is treated as follows: SM8 employs the generalized Born model with the Coulomb field approximation, SM8AD employs the generalized Born approximation with asymmetric descreening, and SMD solves the nonhomogeneous Poisson equation. The non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell is treated as a sum of terms that are products of geometry-dependent atomic surface tensions and solvent-accessible surface areas of the individual atoms of the solute. On average, three models tested in the present work perform similarly. In particular, we achieved mean unsigned errors of 1.3 (SM8), 2.0 (SM8AD), and 2.6 kcal/mol (SMD) for the aqueous free energies of 30 out of 31 compounds with known reference data involved in Task 1 and mean unsigned errors of 2.7 (SM8), 1.8 (SM8AD), and 2.4 kcal/mol (SMD) in the free energy differences (tautomeric ratios) for 21 tautomeric pairs in aqueous solution involved in Task 2.

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Year:  2010        PMID: 20358259     DOI: 10.1007/s10822-010-9333-9

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


  16 in total

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

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Review 6.  Modeling protein-ligand complexes.

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8.  Class IV charge models: a new semiempirical approach in quantum chemistry.

Authors:  J W Storer; D J Giesen; C J Cramer; D G Truhlar
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9.  SM6:  A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

10.  Charge Model 4 and Intramolecular Charge Polarization.

Authors:  Ryan M Olson; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
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  24 in total

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

Authors:  Benjamin A Ellingson; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-30       Impact factor: 3.686

3.  Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

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5.  λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy.

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6.  Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4.

Authors:  Gerhard König; Frank C Pickard; Ye Mei; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2014-02-07       Impact factor: 3.686

7.  Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

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8.  Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Andrew C Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O Dral; Samarjeet Prasad; Michael Jones; Yihan Shao; Walter Thiel; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-08-30       Impact factor: 3.686

9.  Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections.

Authors:  Frank C Pickard; Gerhard König; Florentina Tofoleanu; Juyong Lee; Andrew C Simmonett; Yihan Shao; Jay W Ponder; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-19       Impact factor: 3.686

10.  An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Authors:  Frank C Pickard; Gerhard König; Andrew C Simmonett; Yihan Shao; Bernard R Brooks
Journal:  Bioorg Med Chem       Date:  2016-08-22       Impact factor: 3.641

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