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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).<\/jats:p>","DOI":"10.1021\/acs.jpcb.2c06803","type":"journal-article","created":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T17:23:03Z","timestamp":1673630583000},"page":"648-660","source":"Crossref","is-referenced-by-count":1,"title":["Understanding the Role of Intramolecular Ion-Pair\nInteractions in Conformational Stability Using an\n                    <i>Ab Initio<\/i>\n                    Thermodynamic Cycle"],"prefix":"10.1021","volume":"127","author":[{"given":"Sabyasachi","family":"Chakraborty","sequence":"first","affiliation":[{"name":"Tata Institute of Fundamental Research Hyderabad , ,","place":["Hyderabad, India, 500046"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3194-1378","authenticated-orcid":true,"given":"Kalyaneswar","family":"Mandal","sequence":"additional","affiliation":[{"name":"Tata Institute of Fundamental Research Hyderabad , ,","place":["Hyderabad, India, 500046"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7288-9238","authenticated-orcid":true,"given":"Raghunathan","family":"Ramakrishnan","sequence":"additional","affiliation":[{"name":"Tata Institute of Fundamental Research Hyderabad , ,","place":["Hyderabad, India, 500046"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,1,13]]},"reference":[{"key":"2026081804430944200_cit1","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1039\/C7MD00381A","article-title":"A systematic analysis of atomic protein-ligand\ninteractions in the PDB","volume":"8","author":"Ferreira\nde Freitas","year":"2017","journal-title":"MedChemComm"},{"key":"2026081804430944200_cit2","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1002\/1439-7633(20020703)3:7&lt;604::AID-CBIC604&gt;3.0.CO;2-X","article-title":"Close-range electrostatic\ninteractions in proteins","volume":"3","author":"Kumar","year":"2002","journal-title":"ChemBioChem."},{"key":"2026081804430944200_cit3","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/j.molstruc.2007.05.014","article-title":"PA\/pKa equalization\nand the prediction\nof the hydrogen-bond strength: a synergism of classical thermodynamics\nand structural crystallography","volume":"844-845","author":"Gilli","year":"2007","journal-title":"J. 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