Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale

1992 ◽  
Vol 114 (17) ◽  
pp. 6798-6801 ◽  
Author(s):  
Yaxiong Sun ◽  
David Spellmeyer ◽  
David A. Pearlman ◽  
Peter Kollman
Keyword(s):  
Amino Acid ◽  
Gas Phase ◽  
Free Energies ◽  
Critical Test ◽  
Hydrophobicity Scale ◽  
Phase Water ◽  
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.

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

scholarly journals Nanostructures of PAMAM Dendrimers in Drug Delivery System for 5-Fluorouracil

2020 ◽  
pp. 309-323
Author(s):  
Fatemeh Haghighi ◽  
Ali Morsali ◽  
Mohammad R. Bozorgmehr ◽  
S. Ali Beyramabadi
Keyword(s):  
Gas Phase ◽  
Molecular Descriptors ◽  
Pamam Dendrimers ◽  
Stable Configuration ◽  
Free Energies ◽  
Quantum Molecular Descriptors ◽  
Solvation Energies ◽  
Reduced Toxicity ◽  
Solvation Free Energies ◽  
Binding Free Energies

In this article, we studied five noncovalent structures for adsorption of 5 fluorouracil drug (5 FL) on poly(amidoamine) G0 generation dendrimer (PAMAMG0) carrier using M06-2X and B3LYPfunctionals. We investigate the quantum molecular descriptors and the binding and solvation energies in gas phase and aqueous solution. The energetic stability of non-bonded species (PAMAMG0/5-FL1-5) was shown through evaluation of binding free energies. The solvation free energies of PAMAMG0/5-FL1-5 are negative, indicating that the solvation process is spontaneous. We considered quantum molecular descriptors such as electrophilicity power and global hardness and found reduced toxicity of 5-FL drug near PAMAMG0 carrier as well as facilitated drug release. The AIM (Atoms In Molecule) analysis for all PAMAMG0/5-FL1-5 structures demonstrated that the pseudo-hydrogen and hydrogen bonds are essential in the functionalization of PAMAMG0 with 5-FL drug. We found thatthe structure in which 5-FL drug interacts with CO functional groups of PAMAMG0 is the most stable configuration

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