Comparison of two simulation methods to compute solvation free energies and partition coefficients

Yang, Li; Ahmed, Alauddin; Sandler, Stanley I.

doi:10.1002/jcc.23127

Cited by 31 publications

(23 citation statements)

References 91 publications

(179 reference statements)

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“…This force field has been validated with both experimental data and ab initio calculations [68]–[70]. Additionally, previous studies [25], [28], [79] have used OPLS to calculate solvation energies and phase behavior for systems involving water/chloroform and octanol/water. The solutes in these studies consisted of n-alkane, polar, nonpolar, alcohol, aromatic, and polychlorinated biphenyl molecules.…”

Section: Methodsmentioning

confidence: 86%

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

2013

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The odorant partition coefficient is a physicochemical property that has been shown to dramatically influence odorant deposition patterns in the mammalian nose, leading to a chromatographic separation of odorants along the sensory epithelium. It is unknown whether a similar phenomenon occurs in fish. Here we utilize molecular dynamics simulations, based on a simplified molecular model of olfactory mucus, to calculate water/mucus partition coefficients for amino acid odorants (alanine, glycine, cysteine, and valine) that are known to elicit feeding behavior in fish. Both fresh water and salt water environments are considered. In fresh water, all four amino acids prefer the olfactory mucus phase to water, and the partition coefficient is shown to correlate with amino acid hydrophobicity. In salt water, a reversal in odorant partitioning is found, where each of the feeding stimulants (except glycine) prefer the water phase to olfactory mucus. This is due to the interactions between the salt ions and the odorant molecules (in the water phase), and between the salt and simplified mucin (in the olfactory mucus phase). Thus, slightly different odorant deposition patterns may occur in the fish olfactory organ in fresh and salt water environments. However, in both underwater environments we found that the variation of the water/mucus odorant partition coefficient is approximately one order of magnitude, in stark contrast to air/mucus odorant partition coefficients that can span up to six orders of magnitude. We therefore anticipate relatively similar deposition patterns for most amino acid odorants in the fish olfactory chamber. Thus, in contrast to terrestrial species, living in an underwater environment may preclude appreciable chromatographic odorant separation that may be used for spatial coding of odor identity across the olfactory epithelium. This is consistent with the reported lack of spatial organization of olfactory receptor neurons in the fish olfactory epithelium.

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Section: Methodsmentioning

confidence: 86%

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

2013

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“…As shown in Fig. 7, 94% of the computational tasks could be finished within 40 min for each compound, while a typical explicit-solvent simulation method requires hundreds of CPU hours even for a relative small molecule [127]. By contrast, the average computation time is 27 min based on the MDFT calculation on a desktop PC with single Intel E-1230CPU core.…”

Section: Resultsmentioning

confidence: 97%

Toward high-throughput predictions of the hydration free energies of small organic molecules from first principles

Jia

2016

Fluid Phase Equilibria

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“…Particularly, molecular simulations begin with a description of the energy and forces in a physical system as a function of the coordinates -what is known as a "force field" -and allow calculation of numerous physical properties from simulations of such systems 28 . In addition to potentially providing predictions of various quantities like host-guest and protein-ligand binding affinities, [29][30][31][32][33] distribution and partition coefficients, 34,35 solvation free energies [36][37][38] or other physical properties for design applications, comparison of such results to experiment provides a quantitative test of the underlying physical model or force field.…”

Section: Introductionmentioning

confidence: 99%

Infinite Dilution Activity Coefficients as Constraints for Force Field Parameterization and Method Development

Matos¹,

Calabró²,

Mobley³

2018

Preprint

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<p>Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD) simulations, begin with a underlying energy model or force field and then, based on this model, use simulations to compute properties of interest. However, one of the most significant challenges in molecular dynamics and modeling studies is ensuring that the force field is a good enough approximation of the underlying physics that computed quantities can be used to reproduce experimental properties with the desired level of accuracy. Parameterization of force fields depend on various experimental properties including as much of the chemistry of interest as possible. Physicochemical properties measurable in a relatively straightforward manner are particularly interesting for developers. Such properties can be measured for a relatively diverse chemical set and used to expand the parameterization dataset as needed. Here, we examine infinite dilution activity coefficients (IDACs) which are experimental quantities that can play this role. We retrieved 237 empirical IDACs from NIST's ThermoML, a database of measured thermodynamic properties, and we estimated the corresponding values using solvation free energy calculations. We found that calculated IDAC values correlate strongly with experiment. Specifically, the natural logarithm of calculated and experimental IDAC values shows a Pearson correlation coefficient of 0.85+/-0.02. The calculated IDAC values allow us to identify strengths and potential weaknesses of force field parameters for specific functional groups in solutes and solvents, suggesting these may be a valuable source of data for force field parameterization, capturing some of the same type of information as hydration and solvation free energies and thus potentially providing a useful new source of experimental data.</p>

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Comparison of two simulation methods to compute solvation free energies and partition coefficients

Cited by 31 publications

References 91 publications

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

Toward high-throughput predictions of the hydration free energies of small organic molecules from first principles

Infinite Dilution Activity Coefficients as Constraints for Force Field Parameterization and Method Development

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