Papers › Understanding the role of intramolecular ion-pair interactions in conformational...
Understanding the role of intramolecular ion-pair interactions in conformational stability using an ab initio thermodynamic cycle
Sabyasachi Chakraborty, Kalyaneswar Mandal, Raghunathan Ramakrishnan
The archive published only this paper's code-link row. Authors, date and abstract are from arXiv's metadata (CC0), read from the Kaggle arXiv metadata snapshot of 2026-09-12 where its title matched the archive's; the title is the archive's.
Intramolecular ion-pair interactions yield shape and functionality to many molecules. With proper orientation, these interactions overcome steric factors and are responsible for the compact structures of several peptides. In this study, we present a thermodynamic cycle based on isoelectronic and alchemical mutation to estimate intramolecular ion-pair interaction energy. We determine these energies for 26 benchmark molecules with common ion-pair combinations and compare them with results obtained using intramolecular symmetry-adapted perturbation theory. For systems with long linkers, the ion-pair energies evaluated using both approaches deviate by less than 2.5% in vacuum phase. The thermodynamic cycle based on density functional theory facilitates calculations of salt-bridge interactions in model tripeptides with continuum/microsolvation modeling, and four large peptides: 1EJG (crambin), 1BDK (bradykinin), 1L2Y (a mini-protein with a tryptophan cage), and 1SCO (a toxin from the scorpion venom).
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections