Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

2017 ◽  
Vol 146 (24) ◽  
pp. 244113 ◽  
Author(s):  
Raffaele Fiorentini ◽  
Kurt Kremer ◽  
Raffaello Potestio ◽  
Aoife C. Fogarty
Keyword(s):  
Amino Acid ◽  
Free Energies ◽  
Adaptive Resolution ◽  
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.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

2021 ◽  
Author(s):  
Monika Michaelis ◽  
Massimo Delle Piane ◽  
Dirk Rothenstein ◽  
Carole C. Perry ◽  
Lucio Colombi Ciacchi
Keyword(s):  
Amino Acid ◽  
Free Energies
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