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With the goal of a more universal understanding and translatability of collision-induced dissociation and unfolding (CID\/U) experiments, we recently introduced software (\u201cIonSPA\u201d) for simulating ion heating, cooling, and kinetic energy damping during collisional activation. A key parameter in IonSPA is the \u201cpseudo-atom mass\u201d, which controls the efficiency of energy transfer between an ion\u2019s vibrational modes and the gas particle on a collision-by-collision basis. Here, we use molecular dynamic (MD) simulations to study energy transfer efficiency for native charge states of three different protein ions. Energy transfer efficiency is found to depend primarily on the collision gas type, relative speed of the collision, and total vibrational energy of the ion. Efficiency trends toward unity (completely inelastic and thermalizing) at zero collision speed, decreases to a minimum at a moderate collision speed, and increases again toward highly inelastic at high collision speeds. Dependence on collision geometry and the role of the centrifugal barrier and interaction potential are also explored. A pseudo-atom mass function based on gas type, ion vibrational temperature, and collision speed is derived from these MD simulations and implemented into IonSPA to calculate thermochemical barrier values in CID and CIU.<\/jats:p>","DOI":"10.1021\/jasms.6c00292","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T15:01:57Z","timestamp":1788879717000},"page":"2552-2564","source":"Crossref","is-referenced-by-count":0,"title":["Modeling Energy Transfer\nEfficiency in Collision-Induced\nDissociation and Unfolding Using Molecular Dynamics Simulations"],"prefix":"10.1021","volume":"37","author":[{"given":"Austin W.","family":"Green","sequence":"first","affiliation":[{"name":"1253 University of Oregon , , , ,","place":["Eugene, Oregon, United States, 97403-1253"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7505-9168","authenticated-orcid":true,"given":"James S.","family":"Prell","sequence":"additional","affiliation":[{"name":"1253 University of Oregon , , , ,","place":["Eugene, Oregon, United States, 97403-1253"]},{"name":"1252 University of Oregon , , , ,","place":["Eugene, Oregon, United States, 97403-1252"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"2026100710070520700_cit1","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1126\/science.1124619","article-title":"Mass Spectrometry and Protein Analysis","volume":"312","author":"Domon","year":"2006","journal-title":"Science"},{"key":"2026100710070520700_cit2","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/s43586-023-00203-4","article-title":"Mass spectrometry\nusing electrospray ionization","volume":"3","author":"Prabhu","year":"2023","journal-title":"Nat. Rev. Methods\nPrimers"},{"key":"2026100710070520700_cit3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/(SICI)1098-2787(1997)16:1&lt;1::AID-MAS1&gt;3.0.CO;2-L","article-title":"Studying\nnoncovalent protein complexes by electrospray ionization mass spectrometry","volume":"16","author":"Loo","year":"1997","journal-title":"Mass Spectrom. Rev."},{"key":"2026100710070520700_cit4","doi-asserted-by":"publisher","first-page":"116655","DOI":"10.1016\/j.ijms.2021.116655","article-title":"Native mass spectrometry\nfor structural biology: A\nperspective","volume":"468","author":"Ruotolo","year":"2021","journal-title":"Int. J. Mass Spectrom."},{"key":"2026100710070520700_cit5","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.1016\/j.jasms.2007.02.015","article-title":"Sizing\nlarge proteins\nand protein complexes by electrospray ionization mass spectrometry\nand ion mobility","volume":"18","author":"Kaddis","year":"2007","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2026100710070520700_cit6","doi-asserted-by":"publisher","first-page":"117290","DOI":"10.1016\/j.ijms.2024.117290","article-title":"Modeling\ncollisional kinetic energy damping, heating, and cooling of ions in\nmass spectrometers: A tutorial perspective","volume":"504","author":"Prell","year":"2024","journal-title":"Int. J. Mass Spectrom."},{"key":"2026100710070520700_cit7","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1016\/j.jasms.2009.04.023","article-title":"Comparison of CID\nversus ETD based MS\/MS fragmentation\nfor the analysis of protein ubiquitination","volume":"20","author":"Sobott","year":"2009","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2026100710070520700_cit8","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1021\/jasms.9b00055","article-title":"Rapid Determination of Activation\nEnergies for Gas-Phase Protein Unfolding and Dissociation in a Q-IM-ToF\nMass Spectrometer","volume":"31","author":"Donor","year":"2020","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2026100710070520700_cit9","doi-asserted-by":"publisher","first-page":"46854","DOI":"10.1021\/jacs.5c07327","article-title":"Determination of Thermochemical Barriers\nin Multiple-Collision-Induced\nDissociation Experiments on Gas-Phase Protein Complexes","volume":"147","author":"Shepherd","year":"2025","journal-title":"J. Am. Chem. 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Soc."},{"key":"2026100710070520700_cit30","first-page":"921","article-title":"Mechanisms of\ncollision-induced dissociation of fast ions","volume-title":"Recent Developments in Mass Spectrometry","author":"Durup","year":"1970"},{"key":"2026100710070520700_cit31","doi-asserted-by":"publisher","first-page":"5530","DOI":"10.1063\/1.1457438","article-title":"Collision-induced dissociation of\nformaldehyde cations: The effects of vibrational mode, collision energy,\nand impact parameter","volume":"116","author":"Liu","year":"2002","journal-title":"J. Chem. Phys."},{"key":"2026100710070520700_cit32","doi-asserted-by":"publisher","first-page":"4302","DOI":"10.1063\/1.1450544","article-title":"On the efficiency of energy transfer in collisional\nactivation of small peptides","volume":"116","author":"Laskin","year":"2002","journal-title":"J. Chem. Phys."},{"key":"2026100710070520700_cit33","doi-asserted-by":"publisher","first-page":"16082","DOI":"10.1021\/jp961623v","article-title":"Structural\ninformation from ion mobility measurements: Effects of the long-range\npotential","volume":"100","author":"Mesleh","year":"1996","journal-title":"J. Phys. Chem."},{"key":"2026100710070520700_cit34","doi-asserted-by":"publisher","first-page":"3887","DOI":"10.1021\/jp312432z","article-title":"Ion Mobilities in Diatomic Gases: Measurement versus\nPrediction with Non-Specular Scattering Models","volume":"117","author":"Larriba","year":"2013","journal-title":"J. Phys. Chem. A"},{"key":"2026100710070520700_cit35","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/j.jcp.2013.05.038","article-title":"Free molecular collision\ncross section calculation\nmethods for nanoparticles and complex ions with energy accommodation","volume":"251","author":"Larriba","year":"2013","journal-title":"J. Comput. Phys."},{"key":"2026100710070520700_cit36","doi-asserted-by":"publisher","first-page":"15019","DOI":"10.1039\/C5CP01017A","article-title":"Gas molecule\nscattering & ion mobility measurements for organic macro-ions\nin He versus N-2 environments","volume":"17","author":"Larriba-Andaluz","year":"2015","journal-title":"Phys. Chem. Chem.\nPhys."},{"key":"2026100710070520700_cit37","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/0009-2614(96)00941-4","article-title":"An exact hard-spheres\nscattering model for the mobilities\nof polyatomic ions","volume":"261","author":"Shvartsburg","year":"1996","journal-title":"Chem. Phys. Lett."},{"key":"2026100710070520700_cit38","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1002\/jms.142","article-title":"MassKinetics: a theoretical\nmodel of mass spectra incorporating physical\nprocesses, reaction kinetics and mathematical descriptions","volume":"36","author":"Drahos","year":"2001","journal-title":"J. Mass Spectrom."},{"key":"2026100710070520700_cit39","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1002\/oms.1210260507","article-title":"Collision-Induced\ndecomposition of peptides. An investigation\ninto the effect of collision gas pressure on translational energy\nlosses","volume":"26","author":"Bradley","year":"1991","journal-title":"Org. Mass Spectrom."},{"key":"2026100710070520700_cit40","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1021\/ed051p308","article-title":"Collinear\nCollision Chemistry: A simple model for inelastic and reactive collision\ndynamics","volume":"51","author":"Mahan","year":"1974","journal-title":"J. Chem. Educ."},{"key":"2026100710070520700_cit41","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/S1044-0305(97)00246-8","article-title":"Applications\nof Collision Dynamics in Quadrupole Mass Spectrometry","volume":"9","author":"Douglas","year":"1998","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2026100710070520700_cit42","doi-asserted-by":"publisher","first-page":"1430","DOI":"10.1021\/j100156a073","article-title":"Theory of collisional activation\nof macromolecules.\nImpulsive collisions of organic ions","volume":"95","author":"Uggerud","year":"1991","journal-title":"J. Phys.\nChem."},{"key":"2026100710070520700_cit43","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1021\/jasms.5c00008","article-title":"Computed\nVibrational Heat Capacitites\nfor Gas-Phase Biomolecular Ions","volume":"36","author":"Paris","year":"2025","journal-title":"J. Am. Soc.\nMass Spectrom."},{"key":"2026100710070520700_cit44","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1007\/s13361-017-1594-2","article-title":"Collidoscope: An\nImproved Tool for Computing Collisional Cross-Sections with the Trajectory\nMethod","volume":"28","author":"Ewing","year":"2017","journal-title":"J. Am. Soc. 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Mass Spectrom."},{"key":"2026100710070520700_cit53","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1021\/ac960804q","article-title":"Effects of Charge\nState on Fragmentation\nPathways, Dynamics, and Activation Energies of Ubiquitin Ions Measured\nby Blackbody Infrared Radiative Dissociation","volume":"69","author":"Jockusch","year":"1997","journal-title":"Anal. Chem."},{"key":"2026100710070520700_cit54","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1063\/1.1371958","article-title":"Guided\nion beam study of collision-induced dissociation\ndynamics: integral and differential cross sections","volume":"115","author":"Muntean","year":"2001","journal-title":"J. Chem. Phys."},{"key":"2026100710070520700_cit55","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1103\/PhysRev.23.710","article-title":"On the\nResistance Experienced by Spheres in their Motion through Gases","volume":"23","author":"Epstein","year":"1924","journal-title":"Phys. Rev."},{"key":"2026100710070520700_cit56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1103\/PhysRev.22.1","article-title":"The General\nLaw of Fall of a Small Spherical Body through a Gas, and its Bearing\nupon the Nature of Molecular Reflection from Surfaces","volume":"22","author":"Millikan","year":"1923","journal-title":"Phys. Rev."},{"key":"2026100710070520700_cit57","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1002\/rcm.5013","article-title":"Enhancements\nin travelling wave ion\nmobility resolution","volume":"25","author":"Giles","year":"2011","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2026100710070520700_cit58","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1080\/0144235X.2020.1826708","article-title":"Fundamentals of ion mobility in the free molecular\nregime. Interlacing the past, present and future of ion mobility calculations","volume":"39","author":"Larriba-Andaluz","year":"2020","journal-title":"Int. Rev. Phys. Chem."},{"key":"2026100710070520700_cit59","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1021\/jp9628702","article-title":"Binding\nEnergies of the Proton-Bound\nAmino Acid Dimers Gly\u00b7Gly, Ala\u00b7Ala, Gly\u00b7Ala, and Lys\u00b7Lys\nMeasured by Blackbody Infrared Radiative Dissociation","volume":"101","author":"Price","year":"1997","journal-title":"J. Phys. Chem. B"},{"key":"2026100710070520700_cit60","unstructured":"COMSOL Multiphysics\n(R) v. 6.2; COMSOL AB, 2023. www.comsol.com (accessed 2026-7-17)."},{"key":"2026100710070520700_cit61","unstructured":"Manura, D.\n          \n          SIMION (R)\n8.1 User Manual, 2008. 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