scholarly journals Effects of generalized-Born implicit solvent models in NMR structure refinement

2013 ◽  
Vol 17 (1) ◽  
pp. 11-18 ◽  
Author(s):  
Jun-Goo Jee
Keyword(s):  
Structure Refinement ◽  
Nmr Structure ◽  
Implicit Solvent ◽  
Generalized Born ◽  
Solvent Models ◽  
Implicit Solvent Models

Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

scholarly journals Generalized Born Implicit Solvent Models for Biomolecules

2019 ◽  
Vol 48 (1) ◽  
pp. 275-296 ◽  
Author(s):  
Alexey V. Onufriev ◽  
David A. Case
Keyword(s):  
Md Simulations ◽  
Implicit Solvent ◽  
Molecular Mechanics Calculations ◽  
Generalized Born ◽  
Solvent Models ◽  
Explicit Consideration ◽  
Aqueous Solvation ◽  
Solvent Molecules ◽  
The Individual ◽  
Implicit Solvent Models

It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.

scholarly journals Simulations of Surfactant and Lipid Assemblies with Generalized Born Implicit Solvent Models

2010 ◽  
Vol 98 (3) ◽  
pp. 486a ◽  
Author(s):  
Jana K. Shen ◽  
Yuhang Wang ◽  
Jason A. Wallace ◽  
Peter Koenig
Keyword(s):  
Implicit Solvent ◽  
Generalized Born ◽  
Solvent Models ◽  
Lipid Assemblies ◽  
Implicit Solvent Models

VERIFICATION OF THE GENERALIZED BORN MODEL AT SHORT DISTANCES

2013 ◽  
Vol 13 (06) ◽  
pp. 1340020
Author(s):  
XIAOCHUAN TANG ◽  
YONG DUAN
Keyword(s):  
Analytical Solutions ◽  
Md Simulations ◽  
Solvation Energy ◽  
Implicit Solvent ◽  
Generalized Born ◽  
Simple Description ◽  
Born Model ◽  
Solvent Models ◽  
Potential Methods ◽  
Gb Model

The generalized Born (GB) model, one of the implicit solvent models, is widely applied in molecular dynamics (MD) simulations as a simple description of the solvation effect. In the GB model, an empirical function called the Still's formula, with the algorithmic simplicity, is utilized to calculate the solvation energy due to the polarization, termed as ΔG pol . Applications of the GB model have exhibited reasonable accuracy and high computational efficiency. However, there is still room for improvements. Most of the attempts to improve the GB model focus on optimizing effective Born radii. Contrarily, limited researches have been performed to improve the feasibility of the Still's formula. In this paper, analytical methods was applied to investigate the validity of the Still's formula at short distance. Taking advantage of the toroidal coordinates and Mehler–Fock transform, the analytical solutions of the GB model at short distances was derived explicitly for the first time. Additionally, the solvation energy was numerically computed using proper algorithms based on the analytical solutions and compared with ΔG pol calculated in the GB model. With the analysis on the deficiencies of the Still's formula at short distances, potential methods to improve the validity of the GB model were discussed.

scholarly journals The validation of quantum chemical lipophilicity prediction of alcohols

2016 ◽  
Vol 9 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Martin Michalík ◽  
Vladimír Lukeš
Keyword(s):  
Linear Correlation ◽  
Quantum Chemical ◽  
Partition Coefficients ◽  
The Other ◽  
Basis Set ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Lipophilicity Prediction ◽  
Triple Zeta ◽  
Implicit Solvent Models

AbstractThe validation of octanol-water partition coefficients (logP) quantum chemical calculations is presented for 27 alkane alcohols. The chemical accuracy of predicted logPvalues was estimated for six DFT functionals (B3LYP, PBE0, M06-2X, ωB97X-D, B97-D3, M11) and three implicit solvent models. Triple-zeta basis set 6-311++G(d,p) was employed. The best linear correlation with the experimental logPvalues was achieved for the B3LYP and B97-D3 functionals combined with the SMD model. On the other hand, no linearity was found when IEF-PCM or C-PCM implicit models were employed.

First-Shell Solvation of Ion Pairs:  Correction of Systematic Errors in Implicit Solvent Models†

2004 ◽  
Vol 108 (21) ◽  
pp. 6643-6654 ◽  
Author(s):  
Zhiyun Yu ◽  
Matthew P. Jacobson ◽  
Julia Josovitz ◽  
Chaya S. Rapp ◽  
Richard A. Friesner
Keyword(s):  
Ion Pairs ◽  
Systematic Errors ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Implicit Solvent Models
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