Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules

2013 ◽  
Vol 34 (15) ◽  
pp. 1354-1362 ◽  
Author(s):  
Silvia A. Martins ◽  
Sergio F. Sousa
Keyword(s):  
Computational Methods ◽  
Comparative Assessment ◽  
Free Energies ◽  
Solvation Free Energies

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics

2004 ◽  
Vol 120 (8) ◽  
pp. 3770-3776 ◽  
Author(s):  
K. Magnus Åberg ◽  
Alexander P. Lyubartsev ◽  
Sven P. Jacobsson ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Free Energies ◽  
Solvation Free Energies ◽  
Expanded Ensemble

Comparative assessment of informational content of the equations of F.P. Hadlock and the computer program of V.N. Demidov in determination of term of gestation and fetal weight in the III trimester of gestation

2017 ◽  
Author(s):  
E.A. Derkach , O.I. Guseva
Keyword(s):  
Computer Program ◽  
High Precision ◽  
Gestational Age ◽  
Computer Programs ◽  
Comparative Assessment ◽  
Fetal Weight ◽  
Informational Content ◽  
Third Trimester ◽  
The Third

Objectives: to compare the accuracy of equations F.P. Hadlock and computer programs by V.N. Demidov in determining gestational age and fetal weight in the third trimester of gestation. Materials: 328 patients in terms 36–42 weeks of gestation are examined. Ultrasonography was performed in 0–5 days prior to childbirth. Results: it is established that the average mistake in determination of term of pregnancy when using the equation of F.P. Hadlock made 12,5 days, the computer program of V.N. Demidov – 4,4 days (distinction 2,8 times). The mistake within 4 days, when using the equation of F.P. Hadlock has met on average in 23,1 % of observations, the computer program of V.N. Demidov — 65,9 % (difference in 2,9 times). The mistake more than 10 days, took place respectively in 51,7 and 8,2 % (distinction by 6,3 times). At a comparative assessment of size of a mistake in determination of fetal mass it is established that when using the equation of F.P. Hadlock it has averaged 281,0 g, at application of the computer program of V.N. Demidov — 182,5 g (distinction of 54 %). The small mistake in the mass of a fetus which isn't exceeding 200 g at application of the equation of F.P. Hadlock has met in 48,1 % of cases and the computer program of V.N. Demidov — 64,0 % (distinction of 33,1 %). The mistake exceeding 500 g has been stated in 18 % (F.P. Hadlock) and 4,3 % (V.N. Demidov) respectively (distinction 4,2 times). Conclusions: the computer program of V.N. Demidov has high precision in determination of term of a gestation and mass of a fetus in the III pregnancy.

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

Determination of Relative Configuration in Organic Compounds by NMR Spectroscopy and Computational Methods

ChemInform ◽  
2007 ◽  
Vol 38 (50) ◽  
Author(s):  
Giuseppe Bifulco ◽  
Paolo Dambruoso ◽  
Luigi Gomez-Paloma ◽  
Raffaele Riccio
Keyword(s):  
Nmr Spectroscopy ◽  
Organic Compounds ◽  
Computational Methods ◽  
Relative Configuration

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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