Jul 2026· Journal of Chemical Theory and Computation· Vol 22, pp. 7362-7369· 0 citations· 19 references
Medicine
Abstract
Interatomic potentials which accurately describe long-range electrostatics require atom-centered charges. One such method to determine these atom-centered charges from density functional theory (DFT) calculations is the density-derived atomic point (DDAP) charge method. DDAP fits atom-centered Gaussians to the ground-state DFT charge density and preserves the multipole moments that govern long-range electrostatics. While these charges accurately predict long-range behavior, in practice, they are limited by their reliance on fixed, heuristic parameters and a constrained solver that becomes numerically unstable for complex or covalent systems. In this work, we present opt-DDAP, which solves this limitation by reformulating the algorithm as a differentiable computational graph. This reformulation allows for the optimization of Gaussian basis parameters and the reciprocal-space cutoff using automatic differentiation. To ensure numerical robustness through this automatic differentiation process, we replace the conventional Lagrange-multiplier approach with a pseudoinverse solution followed by charge renormalization, maintaining stability even in the presence of ill-conditioned matrices. We validate the framework on NaCl vacancy supercells and on MoS2, demonstrating faithful reconstruction of both absolute and difference charge densities. The optimized charges are intended to serve as inputs to effective electrostatic models in machine learning and empirical interatomic potentials that incorporate long-range interactions.
Alchemical free energy perturbation (FEP) is one of the most rigorous methods for predicting protein-ligand binding affinities, yet charged-ligand calculations suffer from finite-size electrostatic artifacts introduced by periodic boundary conditions, which can bias results by several kcal·mol-1. Existing approaches ea...
Runduo Liu, Wanyi Huang, Yufen Yao et al.· Journal of Chemical Theory a...· 0 citations
This review presents a concise overview of the theoretical foundations of DFT and the major approximations used in modern calculations, as well as the practical workflow from structural preparation and convergence testing to geometry optimization, electronic-structure calculations and property analysis.
Hariharan Vaiyapuri Manemaran, Girija Kesavan· International Journal of Mul...· 0 citations
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 par...
Y. Kanamaru, Norio Yoshida, Toru Matsui· Journal of Chemical Theory a...· 0 citations
We present an efficient plane-wave implementation of analytical nuclear forces for electronic excited states described by the Bethe-Salpeter equation (BSE). The formulation combines density-matrix perturbation theory with a Lagrangian approach, and avoids both explicit empty-state summations and the response calculatio...
Yu-Ming Jin, V. Yu, M. Govoni et al.· 2 citations· ⚡1
The generalized PB theory is validated using a perturbed two-atom system and a diverse set of proteins with different structures in vacuum and water, demonstrating its accuracy and robustness, regardless of the choice of sharp-interface and diffuse-interface PB models and different numerical solvers.
Matthias Dogbatsey, Yuanzhen Shao, Emil Alexov et al.· 0 citations
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