scholarly journals Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study

2020 ◽  
Vol 16 (7) ◽  
pp. 4755-4755
Author(s):  
Gabriel Bramley ◽  
Manh-Thuong Nguyen ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Chris-Kriton Skylaris
Keyword(s):  
Implicit Solvent ◽  
Water Interface ◽  
Solvent Models ◽  
Work Functions ◽  
Implicit Solvent Models

scholarly journals Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study

2020 ◽  
Vol 16 (4) ◽  
pp. 2703-2715 ◽  
Author(s):  
Gabriel Bramley ◽  
Manh-Thuong Nguyen ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Chris-Kriton Skylaris
Keyword(s):  
Implicit Solvent ◽  
Water Interface ◽  
Solvent Models ◽  
Work Functions ◽  
Implicit Solvent Models

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

scholarly journals Computational studies of peptide-induced membrane pore formation

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160219 ◽  
Author(s):  
Richard Lipkin ◽  
Themis Lazaridis
Keyword(s):  
Pore Formation ◽  
Coarse Grained ◽  
Future Research ◽  
Implicit Solvent ◽  
Computational Studies ◽  
Membrane Pore ◽  
Membrane Pores ◽  
Solvent Models ◽  
Future Research Directions ◽  
Implicit Solvent Models

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

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