Dataset Information

Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

ABSTRACT: The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar aromatic compounds. To investigate a cause of error, we employed a novel systematic framework of quantum-mechanical/molecular-mechanical (QM/MM) coupling protocol in explicit solvation manner, termed DFT-CES, based on the grid-based mean-field treatment. With the aid of DFT-CES, we delved into multiple energy parts, thereby comparing DFT-CES and PB models component-by-component. By applying the modified PB model to estimate the hydration free energies of non-polar solutes, we find a possibility to improve the predictability of PB models. We expect that this study could shed light on providing an accurate route to study the hydration thermodynamics for various solute compounds.

SUBMITTER: Lee H

PROVIDER: S-EPMC6278349 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

Lee Hankyul H Lim Hyung-Kyu HK Kim Hyungjun H

Molecules (Basel, Switzerland) 20181109 11

The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar arom ...[more]

PMID: 30423973

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Project description:Accurate yet efficient computational models of solvent environment are central for most calculations that rely on atomistic modeling, such as prediction of protein-ligand binding affinities. In this study, we evaluate the accuracy of a recently developed generalized Born implicit solvent model, GBNSR6 (Aguilar et al. J. Chem. Theory Comput. 2010, 6, 3613-3639), in estimating the electrostatic solvation free energies (ΔG(pol)) and binding free energies (ΔΔG(pol)) for small protein-ligand complexes. We also compare estimates based on three different explicit solvent models (TIP3P, TIP4PEw, and OPC). The two main findings are as follows. First, the deviation (RMSD = 7.04 kcal/mol) of GBNSR6 binding affinities from commonly used TIP3P reference values is comparable to the deviations between explicit models themselves, e.g. TIP4PEw vs TIP3P (RMSD = 5.30 kcal/mol). A simple uniform adjustment of the atomic radii by a single scaling factor reduces the RMS deviation of GBNSR6 from TIP3P to within the above "error margin" - differences between ΔΔG(pol) estimated by different common explicit solvent models. The simple radii scaling virtually eliminates the systematic deviation (ΔΔG(pol)) between GBNSR6 and two out of the three explicit water models and significantly reduces the deviation from the third explicit model. Second, the differences between electrostatic binding energy estimates from different explicit models is disturbingly large; for example, the deviation between TIP4PEw and TIP3P estimates of ΔΔG(pol) values can be up to ∼50% or ∼9 kcal/mol, which is significantly larger than the "chemical accuracy" goal of ∼1 kcal/mol. The absolute ΔG(pol) calculated with different explicit models could differ by tens of kcal/mol. These discrepancies point to unacceptably high sensitivity of binding affinity estimates to the choice of common explicit water models. The absence of a clear "gold standard" among these models strengthens the case for the use of accurate implicit solvation models for binding energetics, which may be orders of magnitude faster.

Project description:The adsorption of helium on charged hexabenzocoronene (Hbc, C42H18), a planar polycyclic aromatic hydrocarbon (PAH) molecule of D6h symmetry, was investigated by a combination of high-resolution mass spectrometry and classical and quantum computational methods. The ion abundance of HenHbc+ complexes versus size n features prominent local anomalies at n = 14, 38, 68, 82, and a weak one at 26, indicating that for these "magic" sizes, the helium evaporation energies are relatively large. Surprisingly, the mass spectra of anionic HenHbc- complexes feature a different set of anomalies, namely at n = 14, 26, 60, and 62, suggesting that the preferred arrangement of the adsorbate atoms depends on the charge of the substrate. The results of our quantum calculations show that the adsorbate layer grows by successive filling of concentric rings that surround the central benzene ring, which is occupied by one helium atom each on either side of the substrate. The helium atoms are fairly localized in filled rings and they approximately preserve the D6h symmetry of the substrate, but helium atoms in partially filled rings are rather delocalized. The first three rings contain six atoms each; they account for magic numbers at n = 14, 26, and 38. The size of the first ring shrinks as atoms are filled into the second ring, and the position of atoms in the second ring changes from hollow sites to bridge sites as atoms are filled into the third ring. Beyond n = 38, however, the arrangement of helium atoms in the first three rings remains essentially frozen. Presumably, another ring is filled at n = 68 for cations and n = 62 for anions. The calculated structures and energies do not account for the difference between charge states, although they agree with the measurements for the cations and show that the first solvation shell of Hbc± is complete at n = 68. Beyond that size, the adsorbate layer becomes three-dimensional, and the circular arrangement of helium changes to hexagonal.

Dataset Information

Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

Publications

Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

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