scholarly journals Short solvent model for ion correlations and hydrophobic association

2020 ◽  
Vol 117 (3) ◽  
pp. 1293-1302 ◽  
Author(s):  
Ang Gao ◽  
Richard C. Remsing ◽  
John D. Weeks
Keyword(s):  
Computer Simulations ◽  
Potential Of Mean Force ◽  
Implicit Solvent ◽  
Coulomb Interactions ◽  
Solvent Models ◽  
Solvent Model ◽  
Dilute Aqueous Solutions ◽  
Hydrophobic Solutes ◽  
Local Molecular Field Theory ◽  
Implicit Solvent Models

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent–solvent and solute–solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

scholarly journals Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ifat Shub ◽  
Ehud Schreiber ◽  
Yossef Kliger
Keyword(s):  
Elevated Temperatures ◽  
Md Simulations ◽  
Implicit Solvent ◽  
Dynamic Simulations ◽  
Implicit Solvent Model ◽  
Solvent Models ◽  
Solvent Model ◽  
Wide Range ◽  
Implicit Solvent Models ◽  
Computer Power

Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications.

scholarly journals Predicting Octanol–Water Partition Coefficients of Fluorinated Drug-Like Molecules: A Combined Experimental and Theoretical Study

2020 ◽  
Vol 73 (8) ◽  
pp. 677
Author(s):  
Ying Min Wu ◽  
Yuvixza Lizarme Salas ◽  
Yun Cheuk Leung ◽  
Luke Hunter ◽  
Junming Ho
Keyword(s):  
Partition Coefficients ◽  
Theoretical Study ◽  
Log P ◽  
Implicit Solvent ◽  
Mean Absolute Deviation ◽  
Empirical Methods ◽  
Absolute Deviation ◽  
Solvent Models ◽  
Solvent Model ◽  
Implicit Solvent Models

In this paper, a dataset of 11 fluorinated compounds containing a variety of functional groups (amides, esters, indoles, and ethers) as well as mono, gem-difluoro, erythro-difluoro, and threo-difluoro patterns were synthesised and their octanol–water partition coefficients (log P) were measured using a shake-flask method. The resulting data was used to assess the performance of several popular empirical fragment-based methods as well as quantum chemical implicit solvent models (SMD and SM12). Overall, the empirical miLOGP, ALOGPS, and ALOGP methods performed the best with a mean absolute deviation (MAD) of ~0.25 log units, while the best performing implicit solvent model SMD has a slightly higher MAD of 0.36 log units. Based on the present work and previous studies, the miLOGP and ALOGP empirical methods are recommended for fast and moderately accurate prediction of log P for neutral organic solutes.

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.

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.

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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