scholarly journals Resolving solvophobic interactions inferred from experimental solvation free energies and evaluated from molecular simulations

2017 ◽  
Vol 667 ◽  
pp. 62-67 ◽  
Author(s):  
J. Wesley Barnett ◽  
Amna Bhutta ◽  
Sarah C. Bierbrier ◽  
Natalia da Silva Moura ◽  
Henry S. Ashbaugh
Keyword(s):  
Molecular Simulations ◽  
Free Energies ◽  
Solvophobic Interactions ◽  
Solvation Free Energies

scholarly journals Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

2017 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Daisy Y. Kyu ◽  
Hannes H. Loeffler ◽  
John D. Chodera ◽  
Michael R. Shirts ◽  
...  
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Molecular Simulations ◽  
General Purpose ◽  
Free Energies ◽  
Energy Functions ◽  
Neutral Compounds ◽  
Aqueous Solvation ◽  
Solvation Free Energies

AbstractSolvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.

scholarly journals 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies

2009 ◽  
Vol 5 (9) ◽  
pp. 2436-2446 ◽  
Author(s):  
Nuno M. Garrido ◽  
António J. Queimada ◽  
Miguel Jorge ◽  
Eugénia A. Macedo ◽  
Ioannis G. Economou
Keyword(s):  
Partition Coefficients ◽  
Molecular Simulations ◽  
Free Energies ◽  
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.

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