Literature DB >> 26616625

Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening.

Aleksandr V Marenich1, Christopher J Cramer1, Donald G Truhlar1.   

Abstract

We present a new self-consistent reaction field continuum solvation model based on the generalized Born (GB) approximation for the bulk electrostatic contribution to the free energy of solvation. The new model improves on the earlier SM8 model by using the asymmetric descreening algorithm of Grycuk to treat dielectric descreening effects rather than the Coulomb field approximation; it will be called Solvation Model 8 with asymmetric descreening (SM8AD). The SM8AD model is applicable to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known, in particular dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters. It does not require the user to assign molecular mechanics types to an atom or a group; all parameters are unique and continuous functions of geometry. This model employs a single set of parameters (solvent acidity-dependent intrinsic Coulomb radii for the treatment of bulk electrostatics and solvent description-dependent atomic surface tensions coefficients for the treatment of nonelectrostatic and short-range electrostatic effects). The SM8AD model was optimized over 26 combinations of theoretical levels including various basis sets (MIDI!, 6-31G*, 6-31+G*, 6-31+G**, 6-31G**, cc-pVDZ, DZVP, 6-31B*) and electronic structure methods (M05-2X, M05, M06-2X, M06, M06-HF, M06-L, mPW1PW, mPWPW, B3LYP, HF). It may be used with confidence with any level of electronic structure theory as long as self-consistently polarized Charge Model 4 or other self-consistently polarized charges compatible with CM4 charges are used, for example, CM4M charges can be used. With M05-2X/6-31G*, the SM8AD model achieves a mean unsigned error of 0.6 kcal/mol on average over 2 560 solvation free energies of tested aqueous and nonaqueous neutral solutes and a mean unsigned error of 3.9 kcal/mol on average over 332 solvation free energies of aqueous and nonaqueous ions.

Entities:  

Year:  2009        PMID: 26616625     DOI: 10.1021/ct900312z

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  18 in total

1.  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

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

Authors:  Jiří Šponer; Judit E Šponer; Anton I Petrov; Neocles B Leontis
Journal:  J Phys Chem B       Date:  2010-11-04       Impact factor: 2.991

3.  Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Authors:  Jaydeep P Bardhan; Pavel Jungwirth; Lee Makowski
Journal:  J Chem Phys       Date:  2012-09-28       Impact factor: 3.488

Review 4.  Generalized Born Implicit Solvent Models for Biomolecules.

Authors:  Alexey V Onufriev; David A Case
Journal:  Annu Rev Biophys       Date:  2019-03-11       Impact factor: 12.981

5.  Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Authors:  Zhenli Xu; Wei Cai
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2011-11-07       Impact factor: 10.780

6.  Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.

Authors:  Maximiliano Riquelme; Alejandro Lara; David L Mobley; Toon Verstraelen; Adelio R Matamala; Esteban Vöhringer-Martinez
Journal:  J Chem Inf Model       Date:  2018-08-31       Impact factor: 4.956

7.  Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.

Authors:  Ignacio Soteras; Modesto Orozco; F Javier Luque
Journal:  J Comput Aided Mol Des       Date:  2010-03-19       Impact factor: 3.686

8.  SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges.

Authors:  Maximiliano Riquelme; Esteban Vöhringer-Martinez
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

9.  H2 activation by hydrogenase-inspired NiFe catalyst using frustrated Lewis pair: effect of buffer and halide ion in the heterolytic H-H bond cleavage.

Authors:  Miho Isegawa; Takahiro Matsumoto; Seiji Ogo
Journal:  RSC Adv       Date:  2021-08-23       Impact factor: 3.361

10.  Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.

Authors:  Gerhard König; Phillip S Hudson; Stefan Boresch; H Lee Woodcock
Journal:  J Chem Theory Comput       Date:  2014-02-11       Impact factor: 6.006

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