Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular–continuum approach

2003 ◽  
Vol 119 (15) ◽  
pp. 8038-8046 ◽  
Author(s):  
M. V. Vener ◽  
I. V. Leontyev ◽  
M. V. Basilevsky
Keyword(s):  
Free Energies ◽  
Continuum Approach ◽  
Polyatomic Ions ◽  
Solvation Free Energies

scholarly journals Machine Learning Guided Approach for Studying Solvation Environments

2019 ◽  
Author(s):  
Yasemin Basdogan ◽  
Mitchell C. Groenenboom ◽  
Ethan Henderson ◽  
Sandip De ◽  
Susan Rempe ◽  
...  
Keyword(s):  
A Priori ◽  
Optimization Procedure ◽  
Low Energy ◽  
Free Energies ◽  
Continuum Approach ◽  
Explicit Solvent ◽  
Linear Dimensionality Reduction ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Solvation Free Energies

<div><div><div><p>Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics based cluster-continuum approach for calculating single ion solvation free energies. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs the Smooth Overlap for Atomic Positions (SOAP) kernel to quantify the similarity between different low energy solute environments. From these data, we use sketch-map, a non-linear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies with errors within five percent of experimental measurements for most cases.</p></div></div></div>

scholarly journals Machine Learning Guided Approach for Studying Solvation Environments

2019 ◽  
Author(s):  
Yasemin Basdogan ◽  
Mitchell C. Groenenboom ◽  
Ethan Henderson ◽  
Sandip De ◽  
Susan Rempe ◽  
...  
Keyword(s):  
A Priori ◽  
Optimization Procedure ◽  
Low Energy ◽  
Free Energies ◽  
Continuum Approach ◽  
Explicit Solvent ◽  
Linear Dimensionality Reduction ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Solvation Free Energies

<div><div><div><p>Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics based cluster-continuum approach for calculating single ion solvation free energies. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs the Smooth Overlap for Atomic Positions (SOAP) kernel to quantify the similarity between different low energy solute environments. From these data, we use sketch-map, a non-linear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies with errors within five percent of experimental measurements for most cases.</p></div></div></div>

scholarly journals Solvation energies of ions with ensemble cluster-continuum approach

2020 ◽  
Vol 22 (39) ◽  
pp. 22357-22368
Author(s):  
Lukáš Tomaník ◽  
Eva Muchová ◽  
Petr Slavíček
Keyword(s):  
Free Energies ◽  
Continuum Approach ◽  
Ensemble Cluster ◽  
Solvation Energies ◽  
Solvation Free Energies

An alternative cluster-continuum approach for the calculation of solvation free energies of ions.

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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