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Norio Yoshida

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Aug 2026

Accurate Atomic Decomposition Method in 3D-RISM Theory via Multi-Input Linear Correction: Application to the Protein Hydrophobic Core

Solvation free energy (SFE) is a fundamental thermodynamic quantity governing biomolecular processes in solution. Although the atomic decomposition method derived from the Kirkwood charging formula enables site-resolved evaluation of SFE contributions, its application within the three-dimensional reference interaction site model (3D-RISM) theory suffers from systematic overestimation relative to benchmark values. Here, we developed the Multi-Input Linear Correction for Atomic Decomposition (MILC-AD) framework by extending the original MILC approach to the atomic decomposition scheme within 3D-RISM theory. Unlike the original MILC framework, which relies on the nondecomposable partial molar volume (PMV), the proposed method uses atomically decomposable solute–solvent interaction energies as descriptors. Validated against 628 molecules from the benchmark FreeSolv database, the framework achieves a mean absolute deviation (MAD) of 0.57 kcal/mol relative to the Bennett acceptance ratio (BAR) calculations using ensemble-averaged predictions over ten conformations per molecule. As a representative application, the method is applied to the 36-residue villin headpiece subdomain HP36, revealing the site-resolved balance between intramolecular packing, SFE, and solvation entropy underlying the cooperative assembly of its hydrophobic core. These results demonstrate the potential of the MILC-AD framework as a practical tool for quantitative, site-resolved thermodynamic analyses of complex biomacromolecular systems.

Yutaka Maruyama, Norio Yoshida · 0 citations
Aug 2026

A Gradient-Corrected Polarizable Continuum Model for Improved Reaction Fields at the SCF Level

We propose an improved model, termed the gradient-corrected PCM (GCPCM), for improving the energy accuracy of the polarizable continuum model (PCM). Our previous study revealed deficiencies of PCM in describing the reaction field, i.e., the electrostatic potential generated by the solvent. These deficiencies can be partially alleviated by introducing an empirical correction to the solvent charges. As a result, solute–solvent interactions are improved at the self-consistent field level, leading to enhanced energy accuracy. The performance of GCPCM was evaluated through single-point calculations and geometry optimizations of phenol and phenolate, calculations of the free energy profile for proton transfer in glycine, and analysis of solvent responses of the HOMO and LUMO orbital energies of Brooker’s merocyanine. The results demonstrate that the characteristic destabilization of charged solutes observed in conventional PCM is effectively resolved. Furthermore, despite having a computational cost comparable to that of PCM, GCPCM shows the potential to achieve an energy accuracy similar to that of 3D-RISM-SCF. The development of GCPCM enables more convenient and accurate treatment of solvation effects, which is expected to allow researchers to focus on other important challenges, such as the accurate description of electronic states.

Y. Kanamaru, Norio Yoshida, Toru Matsui · 0 citations