The ion-dipole correction of the 3DRISM solvation model to accurately compute water distributions around negatively charged biomolecules

S Cao, Y Qiu, IC Unarta, EC Goonetilleke… - The Journal of …, 2022 - ACS Publications
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation
model to compute the structural and thermodynamic properties of biomolecules in aqueous …

3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic …

S Cao, L Zhu, X Huang - Molecular Physics, 2018 - Taylor & Francis
The 3D reference interaction site model (3DRISM) is a powerful tool to study the
thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the …

3DRISM multigrid algorithm for fast solvation free energy calculations

VP Sergiievskyi, MV Fedorov - Journal of chemical theory and …, 2012 - ACS Publications
In this paper we present a fast and accurate method for modeling solvation properties of
organic molecules in water with a main focus on predicting solvation (hydration) free …

Recent developments in integral equation theory for solvation to treat density inhomogeneity at solute–solvent interface

S Cao, KA Konovalov, IC Unarta… - Advanced Theory and …, 2019 - Wiley Online Library
The integration equation theory (IET) provides highly efficient tools for the calculation of
structural and thermodynamic properties of molecular liquids. In recent years, the 3D …

A highly parallelizable integral equation theory for three dimensional solvent distribution function: Application to biomolecules

D Yokogawa, H Sato, T Imai, S Sakaki - The Journal of chemical …, 2009 - pubs.aip.org
Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated
waters around a protein. We develop a new approach to calculate 3D solvation structure …

High-throughput prediction of the hydration free energies of small molecules from a classical density functional theory

Y Liu, J Fu, J Wu - The Journal of Physical Chemistry Letters, 2013 - ACS Publications
The classical density functional theory (DFT) is proposed as an efficient computational tool
for high-throughput prediction of the solvation free energies of small molecules in liquid …

A solvation‐free‐energy functional: A reference‐modified density functional formulation

T Sumi, A Mitsutake, Y Maruyama - Journal of computational …, 2015 - Wiley Online Library
The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of
the most applicable integral equation theories for molecular liquids, overestimates the …

Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods

T Kalvoda, T Martinek, P Jungwirth… - The Journal of Chemical …, 2024 - pubs.aip.org
Hydration and, in particular, the coordination number of a metal ion is of paramount
importance as it defines many of its (bio) physicochemical properties. It is not only essential …

[HTML][HTML] Hybrid method for representing ions in implicit solvation calculations

S Sun, C Karki, Y Xie, Y Xian, W Guo, BZ Gao… - Computational and …, 2021 - Elsevier
Fast and accurate calculations of the electrostatic features of highly charged biomolecules
such as DNA, RNA, and highly charged proteins are crucial and challenging tasks …

Accurate prediction of hydration free energies and solvation structures using molecular density functional theory with a simple bridge functional

D Borgis, S Luukkonen, L Belloni… - The Journal of Chemical …, 2021 - pubs.aip.org
This paper assesses the ability of molecular density functional theory to predict efficiently
and accurately the hydration free energies of molecular solutes and the surrounding …