Login / Signup

Understanding the Role of Intramolecular Ion-Pair Interactions in Conformational Stability Using an Ab Initio Thermodynamic Cycle.

Sabyasachi ChakrabortyKalyaneswar MandalRaghunathan Ramakrishnan
Published in: The journal of physical chemistry. B (2023)
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 the 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 the 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).
Keyphrases
  • density functional theory
  • molecular dynamics
  • energy transfer
  • escherichia coli
  • molecular dynamics simulations
  • amino acid
  • high resolution
  • aqueous solution
  • small molecule
  • binding protein
  • low cost
  • monte carlo