Encapsulation of Greenhouse Gases in Clathrate Hydrates: Structural Insights, Energetics, Chemical Interactions, and Environmental Implications

Encapsulation of Greenhouse Gases in Clathrate Hydrates: Structural Insights, Energetics, Chemical Interactions, and Environmental Implications | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Encapsulation of Greenhouse Gases in Clathrate Hydrates: Structural Insights, Energetics, Chemical Interactions, and Environmental Implications Arun Ramamurthy, Giridhar Baburao, Jahnavi Abburi, Gopi Ragupathy This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6099632/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 05 Jul, 2025 Read the published version in Scientific Reports → Version 1 posted 10 You are reading this latest preprint version Abstract The encapsulation of greenhouse gases (GHGs), such as CCl4, CF2Cl2, CH3Br, CH3Cl, CH4, CO, CO2, H2S, CH3F, N2O, NF3, O3, CF4, SF6, and SO2, within 512, 51262, and 51264 clathrate hydrate cages is being investigated in our study using Density Functional Theory (DFT). The smaller cages introduce steric constraints, leading to bond distortions and significant vibrational blue-shifts, while larger cages offer greater flexibility, resulting in red-shifts or minimal vibrational alterations. Intermediate-sized cages provide a nuanced balance between spatial limitations and structural stabilization. Natural Bonding Orbital (NBO) analysis reveals systematic changes in orbital contributions, occupancies, and anti-bonding interactions upon encapsulation, highlighting enhanced bond stabilization and a reduction in environmental reactivity. Atoms in Molecules (AIM) analysis further corroborates that encapsulated molecules exhibit strong bonding, remaining securely trapped and exhibiting minimal reactivity. Energy Decomposition Analysis (EDA) indicates that while smaller cages amplify interaction energies, they can also introduce substantial steric strain. In contrast, Non-Covalent Interaction (NCI) analysis highlights that the stability of hydrate cages is enhanced by stronger H-bonds and weaker van der Waals interactions as cage size increases. This underscores the potential of clathrate hydrates in stabilizing reactive molecules and GHGs, offering key insights for addressing ecological challenges and mitigating climate change. Physical sciences/Chemistry/Environmental chemistry Physical sciences/Chemistry/Physical chemistry Physical sciences/Chemistry/Theoretical chemistry Earth and environmental sciences/Environmental sciences Full Text Additional Declarations No competing interests reported. Supplementary Files SupportingInformationScientificreports.pdf Cite Share Download PDF Status: Published Journal Publication published 05 Jul, 2025 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 14 Apr, 2025 Reviews received at journal 11 Apr, 2025 Reviews received at journal 27 Mar, 2025 Reviewers agreed at journal 20 Mar, 2025 Reviewers agreed at journal 19 Mar, 2025 Reviewers invited by journal 19 Mar, 2025 Editor assigned by journal 19 Mar, 2025 Editor invited by journal 04 Mar, 2025 Submission checks completed at journal 03 Mar, 2025 First submitted to journal 24 Feb, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6099632","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":423883151,"identity":"c562906d-724e-432f-8aa7-b34ba99d8123","order_by":0,"name":"Arun Ramamurthy","email":"","orcid":"","institution":"Vellore Institute of Technology University","correspondingAuthor":false,"prefix":"","firstName":"Arun","middleName":"","lastName":"Ramamurthy","suffix":""},{"id":423883152,"identity":"fd922e66-c4ab-4e20-abe6-fdb159ef089d","order_by":1,"name":"Giridhar Baburao","email":"","orcid":"","institution":"Vellore Institute of Technology University","correspondingAuthor":false,"prefix":"","firstName":"Giridhar","middleName":"","lastName":"Baburao","suffix":""},{"id":423883153,"identity":"d75fc6d3-cb12-4c7b-b9d1-e2759aeefd3e","order_by":2,"name":"Jahnavi Abburi","email":"","orcid":"","institution":"Vellore Institute of Technology University","correspondingAuthor":false,"prefix":"","firstName":"Jahnavi","middleName":"","lastName":"Abburi","suffix":""},{"id":423883154,"identity":"a281091a-b713-45a5-af03-b8506d5bd7c7","order_by":3,"name":"Gopi Ragupathy","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAtUlEQVRIiWNgGAWjYNACAxsGNghLgmgtaQxsbKRpYTjMALOGMDBvYL/4uKDgfGKffAPjhx8MFnkEtcgc4Ck2nmFwO7GNjYFZsodBopigFgkGnjRpHoPbxiC/SAP5iQ1EajkH0sL8m0gt7MeAWg7IAbWwEWkLMw8z0C/JQC2JbZY9BsRoYW9/+Ljgjx2PfPPhwzd+VNQR1sLAzGPADGExAhUbEFQPAuwPmIlSNwpGwSgYBSMXAAAZfCokTV2TrAAAAABJRU5ErkJggg==","orcid":"","institution":"Vellore Institute of Technology University","correspondingAuthor":true,"prefix":"","firstName":"Gopi","middleName":"","lastName":"Ragupathy","suffix":""}],"badges":[],"createdAt":"2025-02-24 20:08:11","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6099632/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6099632/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41598-025-08202-z","type":"published","date":"2025-07-05T15:58:41+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":86179653,"identity":"912332ca-616b-41af-9a6f-71a890158418","added_by":"auto","created_at":"2025-07-07 16:18:07","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2460548,"visible":true,"origin":"","legend":"","description":"","filename":"EncapsulationofGreenhouseGasesinClathrateHydratesStructuralInsightsEnergeticsChemicalInteractionsandEnvironmentalImplications.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6099632/v1_covered_e878e4ad-895a-4e15-b04c-b338a23cbc1c.pdf"},{"id":77801935,"identity":"c1863206-d109-4140-b261-13b6def05feb","added_by":"auto","created_at":"2025-03-05 16:42:28","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":17058670,"visible":true,"origin":"","legend":"","description":"","filename":"SupportingInformationScientificreports.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6099632/v1/f5f6b0befefe076c36509e76.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Encapsulation of Greenhouse Gases in Clathrate Hydrates: Structural Insights, Energetics, Chemical Interactions, and Environmental Implications","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-6099632/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6099632/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"The encapsulation of greenhouse gases (GHGs), such as CCl4, CF2Cl2, CH3Br, CH3Cl, CH4, CO, CO2, H2S, CH3F, N2O, NF3, O3, CF4, SF6, and SO2, within 512, 51262, and 51264 clathrate hydrate cages is being investigated in our study using Density Functional Theory (DFT). The smaller cages introduce steric constraints, leading to bond distortions and significant vibrational blue-shifts, while larger cages offer greater flexibility, resulting in red-shifts or minimal vibrational alterations. Intermediate-sized cages provide a nuanced balance between spatial limitations and structural stabilization. Natural Bonding Orbital (NBO) analysis reveals systematic changes in orbital contributions, occupancies, and anti-bonding interactions upon encapsulation, highlighting enhanced bond stabilization and a reduction in environmental reactivity. Atoms in Molecules (AIM) analysis further corroborates that encapsulated molecules exhibit strong bonding, remaining securely trapped and exhibiting minimal reactivity. Energy Decomposition Analysis (EDA) indicates that while smaller cages amplify interaction energies, they can also introduce substantial steric strain. In contrast, Non-Covalent Interaction (NCI) analysis highlights that the stability of hydrate cages is enhanced by stronger H-bonds and weaker van der Waals interactions as cage size increases. This underscores the potential of clathrate hydrates in stabilizing reactive molecules and GHGs, offering key insights for addressing ecological challenges and mitigating climate change.","manuscriptTitle":"Encapsulation of Greenhouse Gases in Clathrate Hydrates: Structural Insights, Energetics, Chemical Interactions, and Environmental Implications","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-05 16:42:17","doi":"10.21203/rs.3.rs-6099632/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-04-14T05:23:53+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-11T21:11:47+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-03-27T11:31:06+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"275078831304408691554394374340100345714","date":"2025-03-20T04:18:59+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"127379457997874290453685253974137242630","date":"2025-03-19T17:30:38+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-19T14:08:40+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-03-19T13:53:23+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-03-04T09:47:34+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-03-03T09:49:22+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-02-24T19:58:44+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"6908f55a-a004-4451-8930-b1c620fc5286","owner":[],"postedDate":"March 5th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":45169399,"name":"Physical sciences/Chemistry/Environmental chemistry"},{"id":45169400,"name":"Physical sciences/Chemistry/Physical chemistry"},{"id":45169401,"name":"Physical sciences/Chemistry/Theoretical chemistry"},{"id":45169402,"name":"Earth and environmental sciences/Environmental sciences"}],"tags":[],"updatedAt":"2025-07-07T16:08:58+00:00","versionOfRecord":{"articleIdentity":"rs-6099632","link":"https://doi.org/10.1038/s41598-025-08202-z","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2025-07-05 15:58:41","publishedOnDateReadable":"July 5th, 2025"},"versionCreatedAt":"2025-03-05 16:42:17","video":"","vorDoi":"10.1038/s41598-025-08202-z","vorDoiUrl":"https://doi.org/10.1038/s41598-025-08202-z","workflowStages":[]},"version":"v1","identity":"rs-6099632","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6099632","identity":"rs-6099632","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}