Faculty Opinions recommendation of Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

2008 ◽  
Author(s):  
Richard Henchman
Keyword(s):  
Computational Chemistry ◽  
Small Molecule ◽  
Free Energies ◽  
Blind Test ◽  
Solvation Free Energies

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

2008 ◽  
Vol 51 (4) ◽  
pp. 769-779 ◽  
Author(s):  
Anthony Nicholls ◽  
David L. Mobley ◽  
J. Peter Guthrie ◽  
John D. Chodera ◽  
Christopher I. Bayly ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
Small Molecule ◽  
Free Energies ◽  
Blind Test ◽  
Solvation Free Energies

scholarly journals Performance of SM8 on a Test To Predict Small-Molecule Solvation Free Energies

2008 ◽  
Vol 112 (29) ◽  
pp. 8651-8655 ◽  
Author(s):  
Adam C. Chamberlin ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Small Molecule ◽  
Free Energies ◽  
Solvation Free Energies

scholarly journals Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

2009 ◽  
Vol 113 (14) ◽  
pp. 4538-4543 ◽  
Author(s):  
Aleksandr V. Marenich ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Small Molecule ◽  
Free Energies ◽  
Test Set ◽  
Solvation Free Energies

scholarly journals Fast and Accurate Calculation of Small Molecule Solvation Free Energies using Replica Exchange Accelerated Molecular Dynamics

2012 ◽  
Vol 102 (3) ◽  
pp. 447a
Author(s):  
Mehrnoosh Arrar ◽  
William Sinko ◽  
Mikolai Fajer ◽  
Cesar Agusto ◽  
F. de Oliveira ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Small Molecule ◽  
Replica Exchange ◽  
Free Energies ◽  
Accurate Calculation ◽  
Accelerated Molecular Dynamics ◽  
Solvation Free Energies

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution

2006 ◽  
Vol 419 (1-3) ◽  
pp. 240-244 ◽  
Author(s):  
Takumi Hori ◽  
Hideaki Takahashi ◽  
Masayoshi Nakano ◽  
Tomoshige Nitta ◽  
Weitao Yang
Keyword(s):  
Aqueous Solution ◽  
Free Energies ◽  
Solvation Free Energies ◽  
Acetic Acids

scholarly journals Blind prediction of solvation free energies from the SAMPL4 challenge

2014 ◽  
Vol 28 (3) ◽  
pp. 135-150 ◽  
Author(s):  
David L. Mobley ◽  
Karisa L. Wymer ◽  
Nathan M. Lim ◽  
J. Peter Guthrie
Keyword(s):  
Free Energies ◽  
Blind Prediction ◽  
Solvation Free Energies
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