Computation of hydration free energies of organic solutes with an implicit water model

Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein-ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies

The SM6, SM8, and SMD quantum mechanical aqueous continuum solvation models are applied to predict free energies of aqueous solvation for 61 molecules in the SAMPL1 test set described elsewhere (Guthrie. J. Phys. Chem. B 2009, 113, 4501-4507). For direct comparison to other models, frozen geometries, provided by Guthrie, were used together with the M06-2X density functional and the 6-31G(d) basis set. For the bulk electrostatic component of the solvation free energy, SM6 and SM8 employ a generalized Born model that uses polarized discrete partial atomic charges to model the electron density, with these charges being calculated by the CM4 and CM4M class IV charge models, respectively; SMD uses the polarized continuous quantum mechanical charge density. If five sulfonylureas are removed from the SAMPL1 set, the root-mean-square deviations (RMSDs) of SM6, SM8, and SMD on the remaining 56 molecules are 2.4, 2.6, and 2.5 kcal mol(-1), respectively. The SM6, SM8, and SMD RMSDs on the five sulfonylureas are 14.2, 12.6, and 11.1 kcal mol(-1), respectively; however, we suggest that the uncertainty in the target solvation free energies for these molecules may be quite large.

I-SOLV: A new surface-based empirical model for computing solvation free energies

We have developed a new empirical model, I-SOLV, for computing solvation free energies of neutral organic molecules. It computes the solvation free energy of a solute molecule by summing up the contributions from its component atoms. The contribution from a certain atom is determined by the solvent-accessible surface area as well as the surface tension of this atom. A total of 49 atom types are implemented in our model for classifying C, N, O, S, P, F, Cl, Br and I in common organic molecules. Their surface tensions are parameterized by using a data set of 532 neutral organic molecules with experimentally measured solvation free energies. A head-to-head comparison of our model with several other solvation models was performed on a test set of 82 molecules. Our model outperformed other solvation models, including widely used PB/SA and GB/SA models, with a mean unsigned error as low as 0.39 kcal/mol. Our study has demonstrated again that well-developed empirical solvation models are not necessarily less accurate than more sophisticated theoretical models. Empirical models may serve as appealing alternatives due to their simplicity and accuracy.