Related Experiment Video
Updated: Jan 31, 2026

Chemical Modification of the Tryptophan Residue in a Recombinant Ca2+-ATPase N-domain for Studying Tryptophan-ANS FRET
Published on: October 9, 2021
Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field
Hanif M Khan1,2, Alexander D MacKerell3, Nathalie Reuter2,4
1Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway.
Abstract:
Cation-π interactions between tryptophan and choline or trimethylated lysines are vital for many biological processes. The performance of the additive CHARMM36 force field against target quantum mechanical data is shown to reproduce QM equilibrium geometries but required modified Lennard-Jones potentials to accurately reproduce the QM interaction energies. The modified parameter set allows accurate modeling, including free energies, of cation-π indole-choline and indole-trimethylated lysines interactions relevant for protein-ligand, protein-membrane, and protein-protein interfaces.
Related Concept Videos
π Molecular Orbitals of the Allyl Cation and Anion
Vector Addition of Forces
To understand the concept of vector addition, consider the scenario of a ship being pulled by two small tugboats. The two forces, F1 and F2, act concurrently on the ship in different directions. The parallelogram law can be used to calculate the net force...
Intermolecular Forces
Force On A Current Loop In A Magnetic Field
Conjugate Addition (1,4-Addition) vs Direct Addition (1,2-Addition)
Conjugate addition results in a thermodynamically stable product. The reaction retains the stronger C=O bond at the expense of the weaker C=C π bond. The process is slow as the β carbon is less electrophilic than the carbonyl carbon.
Direct addition products are...
Intermolecular vs Intramolecular Forces

