CDFTPY: A python package for performing classical density functional theory calculations for molecular liquids

M Valiev, GN Chuev, MV Fedotova - Computer Physics Communications, 2022 - Elsevier
Classical density functional theory (CDFT) provides a rigorous theoretical framework for the
statistical mechanics based analysis of many-body systems. This approach has proven to be …

Unified framework of multiscale density functional theories and its recent applications

S Zhao, Y Liu, X Chen, Y Lu, H Liu, Y Hu - Advances in Chemical …, 2015 - Elsevier
Most chemical engineering processes involve complex multiphase fluid systems, and their
evolution depends on the mechanism by which the inhomogeneous subsystems exchange …

Molecular insight on hydration of protein tyrosine phosphatase 1B and its complexes with ligands

SE Kruchinin, GN Chuev, MV Fedotova - Journal of Molecular Liquids, 2023 - Elsevier
Abstract Knowledge of hydration and the role of solvent in protein–ligand (PL) binding is
essential for rational drug design. In this direction, a complete description of PL binding …

Evaluation of an efficient 3D-RISM-SCF implementation as a tool for computational spectroscopy in solution

M Reimann, M Kaupp - The Journal of Physical Chemistry A, 2020 - ACS Publications
The 3D-RISM-SCF solvent-model implementation of Gusarov et al.[J. Phys. Chem. A 2006,
110, 6083− 6090] in the Amsterdam density functional program has been improved and …

Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model

DS Palmer, VP Sergiievskyi, F Jensen… - The Journal of chemical …, 2010 - pubs.aip.org
We report on the results of testing the reference interaction site model (RISM) for the
estimation of the hydration free energy of druglike molecules. The optimum model was …

Reaction Entropies in Solution from Analytical Three-Dimensional Reference Interaction Site Model Derivatives with Application to Redox and Spin-Crossover …

M Reimann, M Kaupp - The Journal of Physical Chemistry A, 2022 - ACS Publications
An analytical approach to compute the excess entropy of solvation at constant pressure in
three-dimensional reference interaction site model (3D-RISM) calculations is presented. It …

Combinations of simulation and integral equation theory

SM Kast - Physical Chemistry Chemical Physics, 2001 - pubs.rsc.org
Much work has been done to accelerate the prediction of structure and thermodynamics,
particularly of the chemical potential of condensed phases by means of molecular …

3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction

S Sosnin, M Misin, DS Palmer… - Journal of Physics …, 2018 - iopscience.iop.org
In this work, we present a new method for predicting complex physical-chemical properties
of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) …

[PDF][PDF] The contribution of interchain salt bridges to triple-helical stability in collagen

T Gurry, PS Nerenberg, CM Stultz - Biophysical journal, 2010 - cell.com
Studies on collagen and collagen-like peptides suggest that triple-helical stability can vary
along the amino acid chain. In this regard, it has been shown that lysine residues in the Y …

Renormalized site density functional theory for models of ion hydration

GN Chuev, MV Fedotova, M Valiev - The Journal of Chemical Physics, 2021 - pubs.aip.org
The development of accurate statistical mechanics models of molecular liquid systems is a
problem of great practical and fundamental importance. Site-density functional theory …