Accuracy of the microsolvation–continuum approach in computing the pKa and the free energies of formation of phosphate species in aqueous solution

2010 ◽  
Vol 12 (41) ◽  
pp. 13804 ◽  
Author(s):  
Emilia Tang ◽  
Devis Di Tommaso ◽  
Nora H. de Leeuw
Keyword(s):  
Aqueous Solution ◽  
Free Energies ◽  
Continuum Approach ◽  
Phosphate Species

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 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>

General parameterized SCF model for free energies of solvation in aqueous solution

1991 ◽  
Vol 113 (22) ◽  
pp. 8305-8311 ◽  
Author(s):  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Aqueous Solution ◽  
Free Energies

scholarly journals Carbonyl Addition Reactions: Factors Affecting the Hydrate–Hemiacetal and Hemiacetal–Acetal Equilibrium Constants

1975 ◽  
Vol 53 (6) ◽  
pp. 898-906 ◽  
Author(s):  
J. Peter Guthrie
Keyword(s):  
Aqueous Solution ◽  
Carbonyl Compounds ◽  
Equilibrium Constants ◽  
Substituent Effects ◽  
Steric Effects ◽  
Addition Reactions ◽  
Free Energies ◽  
Electronic Effects ◽  
Factors Affecting ◽  
Analogous Formula

Equilibrium constants for hydrate–hemiacetal interconversion in aqueous solution at 25° have been measured for four fluorinated carbonyl compounds: compound, alcohol, K4 (M−1): CF3CHO, C2H5OH, 2.3; CF3COCH3, CH3OH, 1.0; CF3COPh, CH3OH, 3.5; CF3COCF3, CH3OH, 0.14. These values, combined with values from the literature, permit an examination of substituent effects upon the equilibrium constant for[Formula: see text]The free energy change for this process, corrected for symmetry and steric effects, follows the equation[Formula: see text]Thus electronic effects upon this equilibrium are generally small and in fact are often smaller than steric effects.This analysis permits and justifies the calculation of free energies of formation of [Formula: see text] compounds from the (more generally measurable) free energies of formation of the analogous [Formula: see text] compounds.

Acid Ionizations of Nitroalkanes in Aqueous Solution

1973 ◽  
Vol 51 (12) ◽  
pp. 1941-1944 ◽  
Author(s):  
Takeki Matsui ◽  
Loren G. Hepler
Keyword(s):  
Aqueous Solution ◽  
Carboxylic Acids ◽  
Equilibrium Constants ◽  
Free Energies ◽  
Methyl Substitution ◽  
Calorimetric Measurements ◽  
Acid Ionizations

Calorimetric measurements have led to ΔH0 values for ionization of nitromethane, nitroethane, 1-nitropropane, and 2-nitropropane in aqueous solution at 298°K. Combinations of these enthalpies with free energies from equilibrium constants for ionization have led to ΔS0 values for the ionization reactions. It is noted that the trend toward decreasing pK with methyl substitution in nitroalkanes is unusual compared to phenols and carboxylic acids. Similarly, correlations of ΔS0 with ΔG0 and ΔH0 are different for nitroalkanes than for other acids.

A group equivalents scheme for free energies of formation of organic compounds in aqueous solution

1992 ◽  
Vol 70 (4) ◽  
pp. 1042-1054 ◽  
Author(s):  
J. Peter Guthrie
Keyword(s):  
Aqueous Solution ◽  
Organic Compounds ◽  
Group Contributions ◽  
Free Energies

Group contributions have been determined allowing the calculation of free energies of formation in aqueous solution for organic compounds containing carbon, hydrogen, and oxygen. The system works well for monofunctional compounds. The available literature data for 198 compounds can be accommodated using 79 parameters with an rms deviation of 0.74 kcal/mol.

Na+ and K+ Binding by Fulvic Acid

1973 ◽  
Vol 51 (19) ◽  
pp. 3217-3222 ◽  
Author(s):  
Donald S. Gamble
Keyword(s):  
Aqueous Solution ◽  
Fulvic Acid ◽  
Free Energies ◽  
Acid Base ◽  
Titration Curves ◽  
Electrostatic Binding ◽  
Binding Regions

The electrostatic binding of Na+ and K+ by fulvic acid in aqueous solution has been measured with cation electrodes at 25.00 °C ± 0.05. The binding equilibria were followed during the course of acid–base titrations, and have revealed distinct binding regions in the titration curves. In one of these regions Na+ is more strongly bound than is K+. The standard free energies of binding were 11.7 × 103 to 20.5 × 103 J/mol ± 2% for Na+, and 11.5 × 103 to 17.8 × 103 J/mol ± 1%, for K+.

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