New chlorophylls designed by theoretical spectroscopy and machine learning

New chlorophylls designed by theoretical spectroscopy and machine learning | 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 New chlorophylls designed by theoretical spectroscopy and machine learning Fabian Weber, Simon Petry, Dennis J. Nürnberg, Jan P. Götze This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7423883/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 11 Dec, 2025 Read the published version in Photosynthesis Research → Version 1 posted 9 You are reading this latest preprint version Abstract The main pigment for oxygenic photosynthesis, chlorophyll (Chl) a , is structurally related to several other Chl variants, naturally occurring mostly with mono-oxidized substitutions. These include Chl b , Chl d and Chl f , divinyl chlorophyll (DVChl) a and b , and 8 1 -hydroxy-Chl and (the artificial) 3-acetyl-Chl a . In this contribution, we computationally explore an expanded set of over 250,000 Chl variants, looking for potentially interesting targets for synthetic biology. We focus on optical properties, employing a machine learning (ML) approach and subsequently verifying the corresponding predictions using time-dependent density functional theory (TD-DFT) and multireference DFT (DFT/MRCI). We find that (i) Chl f is the best monosubstituted red-shifted Chl, as no other Chl in our set exceeds Chl f in terms of both red shift and absorption intensity, (ii) Chl b is not the best Chl to harvest photons from the green region of the optical spectrum, as several other Chls with the same or better green absorbance were identified (most notably DVChl b ) and (iii) the T 1 energy of Chls can be slightly adapted. The latter would enable experiments to check if it is beneficial to have the T 1 transition energy located between the two lowest O 2 singlet state transitions, as it is found for Chl a ; this might be a prerequisite for stable, efficient oxygen generation. Our ML approach thus provides a thorough overview on an extensive subset of potential Chl modifications which could be used for tuning oxygenic photosynthesis, if suitable synthesis pathways can be found. Full Text Additional Declarations No competing interests reported. Supplementary Files chlmlSI.pdf Cite Share Download PDF Status: Published Journal Publication published 11 Dec, 2025 Read the published version in Photosynthesis Research → Version 1 posted Editorial decision: Revision requested 10 Oct, 2025 Reviews received at journal 02 Oct, 2025 Reviews received at journal 12 Sep, 2025 Reviewers agreed at journal 12 Sep, 2025 Reviewers agreed at journal 30 Aug, 2025 Reviewers invited by journal 29 Aug, 2025 Editor assigned by journal 25 Aug, 2025 Submission checks completed at journal 23 Aug, 2025 First submitted to journal 21 Aug, 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. 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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-7423883","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":508130951,"identity":"53a2c6b6-49b9-4569-b65f-04e249e3a995","order_by":0,"name":"Fabian Weber","email":"","orcid":"","institution":"Freie Universität Berlin","correspondingAuthor":false,"prefix":"","firstName":"Fabian","middleName":"","lastName":"Weber","suffix":""},{"id":508130952,"identity":"3d09c3fd-f594-44b8-99be-25bfbe9a5794","order_by":1,"name":"Simon Petry","email":"","orcid":"","institution":"Freie Universität Berlin","correspondingAuthor":false,"prefix":"","firstName":"Simon","middleName":"","lastName":"Petry","suffix":""},{"id":508130953,"identity":"3e2d3db0-03ee-4c62-84f2-478e91ab3334","order_by":2,"name":"Dennis J. 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These include Chl \u003cem\u003eb\u003c/em\u003e, Chl \u003cem\u003ed\u003c/em\u003e and Chl \u003cem\u003ef\u003c/em\u003e, divinyl chlorophyll (DVChl) \u003cem\u003ea\u003c/em\u003e and \u003cem\u003eb\u003c/em\u003e, and 8\u003csup\u003e1\u003c/sup\u003e-hydroxy-Chl and (the artificial) 3-acetyl-Chl \u003cem\u003ea\u003c/em\u003e. In this contribution, we computationally explore an expanded set of over 250,000 Chl variants, looking for potentially interesting targets for synthetic biology. We focus on optical properties, employing a machine learning (ML) approach and subsequently verifying the corresponding predictions using time-dependent density functional theory (TD-DFT) and multireference DFT (DFT/MRCI). We find that (i) Chl \u003cem\u003ef\u003c/em\u003e is the best monosubstituted red-shifted Chl, as no other Chl in our set exceeds Chl \u003cem\u003ef\u003c/em\u003e in terms of both red shift and absorption intensity, (ii) Chl \u003cem\u003eb\u003c/em\u003e is not the best Chl to harvest photons from the green region of the optical spectrum, as several other Chls with the same or better green absorbance were identified (most notably DVChl \u003cem\u003eb\u003c/em\u003e) and (iii) the T\u003csub\u003e1\u003c/sub\u003e energy of Chls can be slightly adapted. The latter would enable experiments to check if it is beneficial to have the T\u003csub\u003e1\u003c/sub\u003e transition energy located between the two lowest O\u003csub\u003e2\u003c/sub\u003e singlet state transitions, as it is found for Chl \u003cem\u003ea\u003c/em\u003e; this might be a prerequisite for stable, efficient oxygen generation. Our ML approach thus provides a thorough overview on an extensive subset of potential Chl modifications which could be used for tuning oxygenic photosynthesis, if suitable synthesis pathways can be found.\u003c/p\u003e","manuscriptTitle":"New chlorophylls designed by theoretical spectroscopy and machine learning","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-05 15:21:24","doi":"10.21203/rs.3.rs-7423883/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-10T12:55:04+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-02T09:43:35+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-12T22:04:49+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"18001994189901898633150463923631426442","date":"2025-09-12T07:31:31+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"329720399042251862424375010790633394334","date":"2025-08-30T09:38:04+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-29T17:20:59+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-25T06:14:45+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-23T06:17:41+00:00","index":"","fulltext":""},{"type":"submitted","content":"Photosynthesis Research","date":"2025-08-21T08:13:54+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"photosynthesis-research","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pres","sideBox":"Learn more about [Photosynthesis Research](http://link.springer.com/journal/11120)","snPcode":"11120","submissionUrl":"https://submission.nature.com/new-submission/11120/3","title":"Photosynthesis Research","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"e6fae450-9148-478a-bc6e-a304ad7af168","owner":[],"postedDate":"September 5th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-15T16:15:25+00:00","versionOfRecord":{"articleIdentity":"rs-7423883","link":"https://doi.org/10.1007/s11120-025-01183-0","journal":{"identity":"photosynthesis-research","isVorOnly":false,"title":"Photosynthesis Research"},"publishedOn":"2025-12-11 15:59:40","publishedOnDateReadable":"December 11th, 2025"},"versionCreatedAt":"2025-09-05 15:21:24","video":"","vorDoi":"10.1007/s11120-025-01183-0","vorDoiUrl":"https://doi.org/10.1007/s11120-025-01183-0","workflowStages":[]},"version":"v1","identity":"rs-7423883","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7423883","identity":"rs-7423883","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}