Hydration/Dehydration Behavior of Polyalcoholic Compounds Governed by Development of Intramolecular Hydrogen Bonds

Interaction-Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG⁺G⁺TG⁺G⁺g^-)-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as "preparation energy" or "reorganization energy". We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme's efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 3₁₀-polyglycine and H⁺GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction-deletion in 2-nitrobenzene-1,3-diol.

Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects

Background

The formation of intramolecular hydrogen bonds (IHBs) may induce the remarkable changes in molecular physicochemical properties. Within the framework of the extended solvent-contact model, we investigate the effect of implementing the IHB interactions on the accuracy in estimating the molecular hydration free energies.

Results

The performances of hydration free energy functions including and excluding the IHB parameters are compared using the molecules distributed for SAMPL4 blind prediction challenge and those in Free Solvation Database (FSD). The calculated hydration free energies with IHB effects are found to be in considerably better agreement with the experimental data than those without them. For example, the root mean square error of the estimation decreases from 2.56 to 1.66 and from 1.73 to 1.54 kcal/mol for SAMPL4 and FSD molecules, respectively, due to the extension of atomic parameter space to cope with IHBs.

Conclusions

These improvements are made possible by reducing the overestimation of attractive interactions between water and the solute molecules involving IHBs. The modified hydration free energy function is thus anticipated to be useful for estimating the desolvation cost for various organic molecules.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-015-0106-2) contains supplementary material, which is available to authorized users.

Are all polar molecules hydrophilic? Hydration numbers of nitro compounds and nitriles in aqueous solution

Typical highly polar nitro compounds and nitriles should be classified ashydroneutralcompounds because of their hydration numbers of zero.

Are all polar molecules hydrophilic? Hydration numbers of ketones and esters in aqueous solution

Hydration numbers of typical polar compounds like ketones and esters in aqueous solution were precisely determined using high-frequency dielectric relaxation techniques up to a frequency of 50 GHz at 25 °C. Because the hydration number is one of the most quantitative parameters to demonstrate how much are molecules hydrophilic, it is a critical parameter to determine the hydrophilicity of compounds. Hydration numbers of some ketones bearing carbonyl groups were determined to be ca. 0 irrespective of the species of molecules. Moreover, hydration numbers of some esters were also evaluated to be ca. 0 as well as the ketones. These findings suggested that there is no hydrogen bond formation between the ester group and water molecules, nor is there the hydrogen bond formation between the carbonyl group and water molecules. Consequently, esters and ketones bearing typical polar groups are not classified into hydrophilic compounds, but into "hydroneutral" compounds positioned between hydrophilic and hydrophobic ones. Molecular motions of the examined polar molecules in aqueous solution were well described with single Debye-type rotational relaxation modes without strong interaction between solute and water molecules, and also between solute molecules because of the obtained Kirkwood factor close to unity. This independent rotational mode for the polar compounds results from the hydroneutral characteristics caused by the relationship n(H) = 0.