Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages DOI Creative Commons
Keith G. Andrews

Beilstein Journal of Organic Chemistry, Journal Year: 2025, Volume and Issue: 21, P. 421 - 443

Published: Feb. 24, 2025

The bespoke environments in enzyme active sites can selectively accelerate chemical reactions by as much 1019. Macromolecular and supramolecular chemists have been inspired to understand mimic these accelerations selectivities for applications catalysis sustainable synthesis. Over the past 60+ years, mimicry strategies evolved with changing interests, understanding, synthetic advances but, ubiquitously, research has focused on use of a molecular "cavity". activities different cavities vary subset features available particular cavity type. Unsurprisingly, without access mimics able encompass more/all functional sites, examples cavity-catalyzed processes demonstrating enzyme-like rate remain rare. This perspective will briefly highlight some key traditional catalysis, type, order contextualize recent development robust organic cage catalysts, which exploit stability, functionality, reduced symmetry enable promising catalytic modes.

Language: Английский

easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms DOI
Abdelazim M. A. Abdelgawwad, Antonio Francés‐Monerris

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

The dynamics of metal centers are challenging to describe due the vast variety ligands, metals, and coordination spheres, hampering existence general databases transferable force field parameters for classical molecular simulations. Here, we present easyPARM, a Python-based tool that can calculate wide range complexes from routine frequency calculations with electronic structure methods. approach is based on unique labeling strategy, in which each ligand atom coordinates receives type. This design prevents parameter shortage, duplication, necessity post-process output files, even very complicated whose parametrization process remain automatic. program requires Cartesian Hessian matrix, geometry xyz file, atomic charges provide reliable force-field extensively benchmarked against density functional theory both gas condensed phases. procedure allows description at low computational cost an accuracy as good quality matrix obtained by quantum chemistry easyPARM v2.00 reads vibrational frequencies Gaussian (version 09 or 16) ORCA 5 6) format provides refined Amber format. These be directly used NAMD engines converted other formats. available free charge GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).

Language: Английский

Citations

0
Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages DOI Creative Commons
Keith G. Andrews

Beilstein Journal of Organic Chemistry, Journal Year: 2025, Volume and Issue: 21, P. 421 - 443

Published: Feb. 24, 2025

The bespoke environments in enzyme active sites can selectively accelerate chemical reactions by as much 1019. Macromolecular and supramolecular chemists have been inspired to understand mimic these accelerations selectivities for applications catalysis sustainable synthesis. Over the past 60+ years, mimicry strategies evolved with changing interests, understanding, synthetic advances but, ubiquitously, research has focused on use of a molecular "cavity". activities different cavities vary subset features available particular cavity type. Unsurprisingly, without access mimics able encompass more/all functional sites, examples cavity-catalyzed processes demonstrating enzyme-like rate remain rare. This perspective will briefly highlight some key traditional catalysis, type, order contextualize recent development robust organic cage catalysts, which exploit stability, functionality, reduced symmetry enable promising catalytic modes.

Language: Английский

Citations

0