Ekaterina L. Ratkova

An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors.

In this work, we report a novel method for the estimation of the hydration free energy of organic molecules, the structural descriptors correction (SDC) model. The method is based on a combination of the reference interaction site model (RISM) with several empirical corrections. The model requires only a small number of chemical descriptors associated with the main features of the chemical structure of solutes: excluded volume, branch, double bond, benzene ring, hydroxyl group, halogen atom, aldehyde group, ketone group, ether group, and phenol fragment. The optimum model was selected after testing of different RISM free energy expressions on a training set of 65 molecules. We show that the correction parameters of the SDC model are transferable between different chemical classes, which allows one to cover a wide range of organic solutes. The new model substantially increases the accuracy of calculated HFEs by RISM giving the standard deviation of the error for a test set of 120 organic molecules around 1.2 kcal/mol.

Solvation thermodynamics of organic molecules by the molecular integral equation theory : approaching chemical accuracy

The integral equation theory (IET) of molecular liquids has been an active area of academic research in theoretical and computational physical chemistry for over 40 years because it provides a consistent theoretical framework to describe the structural and thermodynamic properties of liquid-phase solutions. The theory can describe pure and mixed solvent systems (including anisotropic and nonequilibrium systems) and has already been used for theoretical studies of a vast range of problems in chemical physics / physical chemistry, molecular biology, colloids, soft matter, and electrochemistry. A consider- able advantage of IET is that it can be used to study speci fi c solute − solvent interactions, unlike continuum solvent models, but yet it requires considerably less computational expense than explicit solvent simulations.

Hydration Thermodynamics Using the Reference Interaction Site Model: Speed or Accuracy?

We report a method to dramatically improve the accuracy of hydration free energies (HFE) calculated by the 1D and 3D reference interaction site models (RISM) of molecular integral equation theory. It is shown that the errors in HFEs calculated by RISM approaches using the Gaussian fluctuations (GF) free energy functional are not random, but can be decomposed into linear combination of contributions from different structural elements of molecules (number of double bonds, number of OH groups, etc.). Therefore, by combining RISM/GF with cheminformatics, one can develop an accurate method for HFE prediction. We call this approach the structural description correction model (SDC) ( Ratkova et al. J. Phys. Chem. B 2010 , 114 , 12068 ). In this work, we investigated the prediction quality of the SDC model combined with 1D and 3D RISM approaches. In parallel, we analyzed the computational performance of these two methods. The SDC model parameters were obtained by fitting against a training set of 53 simple organic molecules. To demonstrate that the values of these parameters were transferable between different classes of molecules, the models were tested against 98 more complex molecules (including 38 polyfragment compounds). The results show that the 3D RISM/SDC model predicts the HFEs with very good accuracy (RMSE of 0.47 kcal/mol), while the 1D RISM approach provides only moderate accuracy (RMSE of 1.96 kcal/mol). However, a single 1D RISM/SDC calculation takes only a few seconds on a PC, whereas a single 3D RISM/SDC HFE calculation is approximately 100 times more computationally expensive. Therefore, we suggest that one should use the 1D RISM/SDC model for large-scale high-throughput screening of molecular hydration properties, while further refinement of these properties for selected compounds should be carried out with the more computationally expensive but more accurate 3D RISM/SDC model.

Toward a Universal Model To Calculate the Solvation Thermodynamics of Druglike Molecules: The Importance of New Experimental Databases

We demonstrate that a new free energy functional in the integral equation theory of molecular liquids gives accurate calculations of hydration thermodynamics for druglike molecules. The functional provides an improved description of excluded volume effects by incorporating two free coefficients. When the values of these coefficients are obtained from experimental data for simple organic molecules, the hydration free energies of an external test set of druglike molecules can be calculated with an accuracy of about 1 kcal/mol. The 3D RISM/UC method proposed here is easily implemented using existing computational software and allows in silico screening of the solvation thermodynamics of potential pharmaceutical molecules at significantly lower computational expense than explicit solvent simulations.

Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants.

Here, we discuss a new method for predicting the hydration free energy (HFE) of organic pollutants and illustrate the efficiency of the method on a set of 220 chlorinated aromatic hydrocarbons. The new model is computationally inexpensive, with one HFE calculation taking less than a minute on a PC. The method is based on a combination of a molecular integral equations theory, one-dimensional reference interaction site model (1D RISM), with the cheminformatics approach. We correct HFEs obtained by the 1D RISM with a set of empirical corrections. The corrections are associated with the partial molar volume and structural descriptors of the molecules. We show that the introduced corrections can significantly improve the quality of the 1D RISM HFE predictions obtained by the partial wave free energy expression [ Ten-no , S. J. Chem. Phys. 2001 , 115 , 3724 ] and the Kovalenko-Hirata closure [ Kovalenko , A. ; Hirata , F. J. Chem. Phys. 1999 , 110 , 10095 ]. We also show that the quality of the model can be further improved by the reparametrization using QM-derived partial charges instead of the originally used OPLS-AA partial charges. The final model gives good results for polychlorinated benzenes (the mean and standard deviation of the error are 0.02 and 0.36 kcal/mol, correspondingly). At the same time, the model gives somewhat worse results for polychlorobiphenyls (PCBs) with a systematic bias of -0.72 kcal/mol but a small standard deviation equal to 0.55 kcal/mol. We note that the error remains the same for the whole set of PCBs, whereas errors of HFEs predicted with continuum solvation models (data were taken from Phillips , K. L. et al. Environ. Sci. Technol. 2008 , 42 , 8412 ) increase significantly for higher chlorinated PCB congeners. In conclusion, we discuss potential future applications of the model and several avenues for its further improvement.

In silico screening of bioactive and biomimetic solutes using Integral Equation Theory

The Integral Equation Theory (IET) of Molecular Liquids is a theoretical framework for modelling solution phase behaviour that has recently found new applications in computational drug design. IET allows calculation of solvation thermodynamic parameters at significantly lower computational expense than explicit solvent simulations, but also provides information about the microscopic solvent structure that is not accessible by implicit continuum models. In this review we focus on recent advances in two fields of research using these methods: (i) calculation of the hydration free energies of bioactive molecules; (ii) modelling the aggregation of biomimetic molecules. In addition, we discuss sources of experimental solvation data for druglike molecules.

On a relationship between molecular polarizability and partial molar volume in water.

We reveal a universal relationship between molecular polarizability (a single-molecule property) and partial molar volume in water that is an ensemble property characterizing solute-solvent systems. Since both of these quantities are of the key importance to describe solvation behavior of dissolved molecular species in aqueous solutions, the obtained relationship should have a high impact in chemistry, pharmaceutical, and life sciences as well as in environments. We demonstrated that the obtained relationship between the partial molar volume in water and the molecular polarizability has in general a non-homogeneous character. We performed a detailed analysis of this relationship on a set of ~200 organic molecules from various chemical classes and revealed its fine well-organized structure. We found that this structure strongly depends on the chemical nature of the solutes and can be rationalized in terms of specific solute-solvent interactions. Efficiency and universality of the proposed approach was demonstrated on an external test set containing several dozens of polyfunctional and druglike molecules.