Related Experiment Video
Updated: Feb 10, 2026

Gradient Echo Quantum Memory in Warm Atomic Vapor
Published on: November 11, 2013
Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and
Joseph C R Thacker1,2, Mark A Vincent1,2, Paul L A Popelier1,2
1Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK.
Abstract:
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor. Chem. Acc. 2017, 136, 86], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here, the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17 689 individual IQA terms to be calculated). When REG and IQA work together it is possible to determine a reaction mechanism at atomistic resolution from data directly derived from quantum calculations, without arbitrary parameters. Moreover, the mechanism determined by this novel method gives concrete insight into how the active site residues catalyse peptide hydrolysis.
More Related Videos
14:44Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
08:40Synthesis of Metal Nanoparticles Supported on Carbon Nanotube with Doped Co and N Atoms and its Catalytic Applications in Hydrogen Production
Published on: December 6, 2021
Related Concept Videos
The Quantum-Mechanical Model of an Atom
The Energies of Atomic Orbitals
SN1 Reaction: Mechanism
Firstly, the haloalkane ionizes to generate a carbocation intermediate and a halide ion. This heterolytic cleavage is highly endothermic with large activation energy. The ionization of the substrate, facilitated by a...
Atomic Radii and Effective Nuclear Charge
Reaction Mechanisms
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
Determining Order of Reaction