Synthesis and Characterizations of Novel Pentacoordinate Iron(II) Porphyrin: Insights from X-ray Crystallography, Interactions Mechanisms, DFT Modeling, QTAIM Analysis and Molecular Docking Investigations

Synthesis and Characterizations of Novel Pentacoordinate Iron(II) Porphyrin: Insights from X-ray Crystallography, Interactions Mechanisms, DFT Modeling, QTAIM Analysis and Molecular Docking Investigations | 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 Research Article Synthesis and Characterizations of Novel Pentacoordinate Iron(II) Porphyrin: Insights from X-ray Crystallography, Interactions Mechanisms, DFT Modeling, QTAIM Analysis and Molecular Docking Investigations Mondher Dhifet, Bouzid Gassoumi This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8855772/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The reaction of four-coordinate picket fence iron(II) porphyrin complex [Fe II (TpivPP)] with cryptand-222 solubilized C 5 H 10 NNaS 2 in organic solvents, yelds the five-coordinate porphyrin species [Fe II (TpivPP)(SH)] − . The five-coordinate, high-spin (S = 2) (hydrogensulfido)(α,α,α,α-tetrakis( o -pivalamidophenyl)porphinato)iron(II) “picket fence” porphyrin derivative [Na(2,2,2-crypt)][Fe II (TpivPP)(SH)] ( I ) has been synthesized and characterized by UV-vis and IR spectroscopies as well as single-crystal structure determinations. The average equatorial iron-pyrrole nitrogens [Fe-N p = 2.106(4) Å] bond length and the distance between the iron and the 24-atom core of the porphyrin ring [Fe-P C = 0.610(2) Å] are longer than those of all other similar five-coordinate iron(II) high-spin porphyrinates. The iron atom is pentacoordinated by the four nitrogen atoms of the pyrrole rings and the sulfur atom of the SH − group. The Fe-S(SH) bond length is 2.3225(17) Å. This compound crystallizes in the orthorhombic system with the space group Pbca . A computational modelling study has been conducted utilizing density functional theory (DFT), Hirshfled surface (HS), HOMO/LUMO analyses, and QTAIM-NCI-RDG iso-surfaces were employed to elucidate the mechanisms of interactions, chemical reactivity properties, and the nature and types of forces contributing to the stability of the complex. Molecular docking analyses have been employed to investigate the potential antibacterial of our material, demonstrating its efficacy against Escherichia coli. Iron(II) porphyrin complexes Hydrogensulfido iron(II) porphyrin X-ray diffraction UV-visible Hirshfeld surface analysis DFT-calculations NCI and RDG analyses Full Text Additional Declarations No competing interests reported. Supplementary Files SupportingInformation.doc Cite Share Download PDF Status: Posted Version 1 posted 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-8855772","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":592975484,"identity":"d2dabbf2-0d24-47fa-8760-d54d93a625e0","order_by":0,"name":"Mondher Dhifet","email":"","orcid":"","institution":"University of Monastir","correspondingAuthor":false,"prefix":"","firstName":"Mondher","middleName":"","lastName":"Dhifet","suffix":""},{"id":592975486,"identity":"392696dc-1770-4d67-a77d-680f2cbcda9d","order_by":1,"name":"Bouzid Gassoumi","email":"data:image/png;base64,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","orcid":"","institution":"University of Monastir","correspondingAuthor":true,"prefix":"","firstName":"Bouzid","middleName":"","lastName":"Gassoumi","suffix":""}],"badges":[],"createdAt":"2026-02-11 21:53:20","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8855772/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8855772/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104163056,"identity":"49f8591e-c796-4b1a-abc2-5d181f935e5f","added_by":"auto","created_at":"2026-03-08 12:09:56","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1952150,"visible":true,"origin":"","legend":"","description":"","filename":"RevisedManuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8855772/v1_covered_c0f3d41a-786b-4738-8e84-511ed468f321.pdf"},{"id":102892799,"identity":"52403ee7-78f8-42ac-857a-08e5fba74710","added_by":"auto","created_at":"2026-02-18 05:32:51","extension":"doc","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":549888,"visible":true,"origin":"","legend":"","description":"","filename":"SupportingInformation.doc","url":"https://assets-eu.researchsquare.com/files/rs-8855772/v1/e2551bc8a6aa4adc1f509866.doc"}],"financialInterests":"No competing interests reported.","formattedTitle":"Synthesis and Characterizations of Novel Pentacoordinate Iron(II) Porphyrin: Insights from X-ray Crystallography, Interactions Mechanisms, DFT Modeling, QTAIM Analysis and Molecular Docking Investigations","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Iron(II) porphyrin complexes, Hydrogensulfido iron(II) porphyrin, X-ray diffraction, UV-visible, Hirshfeld surface analysis, DFT-calculations, NCI and RDG analyses","lastPublishedDoi":"10.21203/rs.3.rs-8855772/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8855772/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe reaction of four-coordinate picket fence iron(II) porphyrin complex [Fe\u003csup\u003eII\u003c/sup\u003e(TpivPP)] with cryptand-222 solubilized C\u003csub\u003e5\u003c/sub\u003eH\u003csub\u003e10\u003c/sub\u003eNNaS\u003csub\u003e2\u003c/sub\u003e in organic solvents, yelds the five-coordinate porphyrin species [Fe\u003csup\u003eII\u003c/sup\u003e(TpivPP)(SH)]\u003csup\u003e\u0026minus;\u003c/sup\u003e. The five-coordinate, high-spin (S\u0026thinsp;=\u0026thinsp;2) (hydrogensulfido)(α,α,α,α-tetrakis(\u003cem\u003eo\u003c/em\u003e-pivalamidophenyl)porphinato)iron(II) \u0026ldquo;picket fence\u0026rdquo; porphyrin derivative [Na(2,2,2-crypt)][Fe\u003csup\u003eII\u003c/sup\u003e(TpivPP)(SH)] (\u003cb\u003eI\u003c/b\u003e) has been synthesized and characterized by UV-vis and IR spectroscopies as well as single-crystal structure determinations. The average equatorial iron-pyrrole nitrogens [Fe-N\u003csub\u003ep\u003c/sub\u003e= 2.106(4) \u0026Aring;] bond length and the distance between the iron and the 24-atom core of the porphyrin ring [Fe-P\u003csub\u003eC\u003c/sub\u003e = 0.610(2) \u0026Aring;] are longer than those of all other similar five-coordinate iron(II) high-spin porphyrinates. The iron atom is pentacoordinated by the four nitrogen atoms of the pyrrole rings and the sulfur atom of the SH\u003csup\u003e\u0026minus;\u003c/sup\u003e group. The Fe-S(SH) bond length is 2.3225(17) \u0026Aring;. This compound crystallizes in the orthorhombic system with the space group \u003cem\u003ePbca\u003c/em\u003e. A computational modelling study has been conducted utilizing density functional theory (DFT), Hirshfled surface (HS), HOMO/LUMO analyses, and QTAIM-NCI-RDG iso-surfaces were employed to elucidate the mechanisms of interactions, chemical reactivity properties, and the nature and types of forces contributing to the stability of the complex. Molecular docking analyses have been employed to investigate the potential antibacterial of our material, demonstrating its efficacy against Escherichia coli.\u003c/p\u003e","manuscriptTitle":"Synthesis and Characterizations of Novel Pentacoordinate Iron(II) Porphyrin: Insights from X-ray Crystallography, Interactions Mechanisms, DFT Modeling, QTAIM Analysis and Molecular Docking Investigations","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-18 05:32:46","doi":"10.21203/rs.3.rs-8855772/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"11fb9893-f9bb-4299-b310-8b4bab49f1bd","owner":[],"postedDate":"February 18th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-03-08T12:09:37+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-18 05:32:46","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8855772","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8855772","identity":"rs-8855772","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}