Solvation energies of the proton in methanol revisited and temperature effects

2018 ◽  
Vol 20 (46) ◽  
pp. 29184-29206 ◽  
Author(s):  
Alhadji Malloum ◽  
Jean Jules Fifen ◽  
Jeanet Conradie
Keyword(s):  
Temperature Effects ◽  
Free Energies ◽  
Solvation Energies ◽  
Solvation Free Energies

Various functionals assessing solvation free energies and enthalpies of the proton in methanol.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

scholarly journals Solvation free energies for periodic surfaces: comparison of implicit and explicit solvation models

2016 ◽  
Vol 18 (46) ◽  
pp. 31850-31861 ◽  
Author(s):  
Stephan N. Steinmann ◽  
Philippe Sautet ◽  
Carine Michel
Keyword(s):  
Free Energy ◽  
Liquid Interfaces ◽  
Free Energies ◽  
Periodic Surfaces ◽  
Solvation Energies ◽  
Solvation Models ◽  
Implicit And Explicit ◽  
Solvation Free Energies ◽  
Solid Liquid ◽  
Explicit Solvation

A strategy based on molecular mechanics free energy of perturbation, seeded by quantum mechanics, is presented to take solvation energies into account in the context of periodic, solid–liquid interfaces.

scholarly journals Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

2020 ◽  
Author(s):  
Lieyang Chen ◽  
Anthony Cruz ◽  
Daniel R. Roe ◽  
Andrew Simmonett ◽  
Lauren Wickstrom ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Long Range ◽  
Free Energies ◽  
Particle Mesh Ewald ◽  
Lennard Jones ◽  
Current Implementation ◽  
Solvation Energies ◽  
Solvation Free Energies ◽  
Solvation Theory

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.

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.

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

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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