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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.

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