The ion-dipole correction of the 3DRISM solvation model to accurately compute water distributions around negatively charged biomolecules
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 …
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 …
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 …
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 …
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
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 …
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 …
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
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 …
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 …
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 …
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
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 …
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 …
and accurately the hydration free energies of molecular solutes and the surrounding …