QM/MM/3D-RISM study of an electronic structure change of benzimidazole derivative induced by molecular recognition of cucurbit[7]uril

IOP Conference Series Materials Science and Engineering, Journal Year: 2025, Volume and Issue: 1325(1), P. 012008 - 012008

Published: Feb. 1, 2025

Abstract The quantum mechanics/molecular mechanics three-dimensional reference interaction site model (QM/MM/3D-RISM) method is a three-layer hybrid approach designed to calculate the electronic structure of complex molecules in solution. In this study, QM/MM/3D-RISM was employed investigate changes ligand upon molecular recognition by macrocyclic host molecule cucurbit[7]uril (CB7). Thiabendazole (TBZ), benzimidazole derivative, selected as ligand, which known for its significant alterations properties such p K a, solubility, photostability, and fluorescence intensity binding CB7. calculations elucidated mechanism underlying induced encapsulation, well role solvation these transformations.

Language: Английский

Influence of Water/Ethanol Mixing Ratio on Gemcitabine Binding to Cucurbit-7-uril Based on Molecular Dynamics Simulations and Three-Dimensional Reference Interaction Site Model

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Accurate binding affinities of the cucurbit-7-uril-gemcitabine (CB7-GEM) complex in pure water and ethanol/water-mixed solvents were obtained by combining molecular dynamics simulations three-dimensional reference interaction site model (3D-RISM) calculations. Point charges CB7 GEM molecules, depending on solvent mixture ratios, determined using 3D-RISM self-consistent field (3D-RISM-SCF) The calculated reveal that most preferable CB7-GEM forms system. complexes mixed show lower stability at higher ethanol ratios. Stable conformations different concentrations appear to be a key factor trend affinity enhancement. Conformations high-water fractions, associated with stability, exhibit internal energies than those high-methanol fractions. Disruption hydrogen-bonding formation also plays crucial role solvation free energies. An explicit is for accurate calculations these binary mixtures, providing results comparable experiments.

Language: Английский

Why is Dimeric 3D Domain Swapping in Antibody Light Chains Missing from the Solution? Atomistic Insights Mechanisms

The Journal of Physical Chemistry B, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 13, 2024

Misfolding of antibody light chains can lead to systemic chain amyloidosis, which is associated with misfolding and aggregation. The may engage in 3D domain swapping within the variable region (#4V

Language: Английский