Journal ArticleDOI
Extension of the platform of applicability of the SM5.42R universal solvation model
Jiabo Li,Tianhai Zhu,Gregory D. Hawkins,Paul Winget,Daniel Liotard,Christopher J. Cramer,Donald G. Truhlar +6 more
TLDR
In this paper, the authors presented eight new parameterizations of the SM5.42R solvation model: B3LYP/MIDI!, B3PVDZ, AM1, PM3, BPW91/MidI!, and AM1/PM3, with mean unsigned errors in the range 0.43-0.46-kcal/mol.Abstract:
We present eight new parameterizations of the SM5.42R solvation model: in particular we present parameterizations for HF/MIDI!, HF/6-31G*, HF/6-31+G*, HF/cc-pVDZ, AM1, PM3, BPW91/MIDI!, and B3LYP/MIDI!. Two of the new cases are parameterized using the reaction-field operator presented previously, and six of the new cases are parameterized with a simplified reaction-field operator; results obtained by the two methods are compared for selected examples. For a training set of 2135 data for 275 neutral solutes containing H, C, N, O, F, S, P, Cl, Br, and I in 91 solvents (water and 90 nonaqueous solvents), seven of the eight new parameterizations give mean unsigned errors in the range 0.43–0.46 kcal/mol, and the eighth – for a basis set containing diffuse functions – gives a mean unsigned error of 0.53 kcal/mol. The mean unsigned error for 49 ionic solutes (containing the same elements) in water is 3.5–3.9 kcal/mol for the Hartree–Fock, Becke–Perdew–Wang-1991 and Becke three-parameter Lee–Yang–Parr cases and 4.1 and 4.0 kcal/mol for parameterized model 3 and Austin model 1, respectively. The methods are tested for sensitivity of solvation free energies to geometry and for predicting partition coefficients of carbonates, which were not included in the training set.read more
Citations
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Journal ArticleDOI
Quantum mechanical continuum solvation models.
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Journal ArticleDOI
Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
TL;DR: The SMD model may be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space, including, for example, the conductor-like screening algorithm.
Journal ArticleDOI
Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton.
TL;DR: Using the same set of ions that was recently used to develop the SM6 continuum solvation model, SM6 retains its previously determined high accuracy; indeed, in most cases the mean unsigned error improves when it is tested against the more accurate reference data.
Journal ArticleDOI
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
TL;DR: A new ansatz is presented that combines molecular dynamics simulations with MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) to rank the binding affinities of 12 TIBO-like HIV-1 RT inhibitors, and it is found that this approach can be reliably applied in ranking the ligands from the databases for this important target.
Journal ArticleDOI
A Universal Approach to Solvation Modeling
TL;DR: The SM8 continuum model, the culmination of a series of SMx models, permits the modeling of such diverse media as aqueous and organic solvents, soils, lipid bilayers, and air-water interfaces and is useful for predicting the significant influence of condensed phases on processes associated with a change in molecular charge.
References
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Book
AB INITIO Molecular Orbital Theory
TL;DR: In this paper, the use of theoretical models as an alternative to experiment in making accurate predictions of chemical phenomena is discussed, and the formulation of theoretical molecular orbital models starting from quantum mechanics is discussed.
Book
Quantum Theory of Chemical Reactions
TL;DR: Theoretical study of a homogeneous Catalytic reaction: The Chlorotris-(Triphenylphosphine)Rhodium(I)-Catalyzed Hydrogenation of Olefins.
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