Quantum Dynamics of DNA Excited State Relaxation Driven by Base Stacking and Pairing Interactions

Quantum Dynamics of DNA Excited State Relaxation Driven by Base Stacking and Pairing Interactions | 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 Quantum Dynamics of DNA Excited State Relaxation Driven by Base Stacking and Pairing Interactions Hong-Guang Duan, Jinwen Li, Tianrui Chen, Fulu Zheng, RJ Dwayne Miller, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7578032/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 DNA exhibits remarkable photostability, largely attributed to ultrafast internal conversion pathways that dissipate absorbed UV photon energy through conical intersections (CIs). While isolated nucleobases undergo rapid deactivation on sub-picosecond timescales, their incorporation into stacked and paired DNA architectures introduces significant alterations to excited-state dynamics. Base stacking and Watson-Crick pairing give rise to delocalized excitonic and charge-transfer (CT) states that display extended lifetimes and complex relaxation behavior. In this work, we combine a linear vibronic coupling (LVC) Hamiltonian with an effective transformation to a structured system-bath representation, enabling explicit inclusion of key vibrational modes that drive nonadiabatic transitions. The hierarchical equations of motion (HEOM) method is employed to simulate population dynamics in systems ranging from adenine monomers to stacked heptamers, as well as A–T paired motifs and a combined (A–A)–T trimer. Our simulations show that increasing the number of stacked bases accelerates the initial decay rate (lifetimes decreasing from ∼300 fs in dimers to ∼230 fs in heptamers) but reduces the overall recovery to the ground state by up to ∼40%, indicating population trapping in long-lived excitonic states. Base-pairing effects are modeled via proton-coupled electron transfer (PCET) using a double Morse potential representation. For both A–T and C–G pairs, PCET was found to suppress direct ground-state recovery, further stabilizing excited-state populations. In the combined stacking–pairing configuration, PCET-mediated pairing reduced deactivation more effectively than stacking alone, especially in short oligomers. This vibrationally resolved framework captures the quantitative interplay between excitonic coupling, CIs, and PCET, providing mechanistic insight into how DNA structural motifs govern the fate and lifetime of photoexcited states. Physical sciences/Physics/Atomic and molecular physics/Atomic and molecular interactions with photons Physical sciences/Physics/Chemical physics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SI.pdf Quantum Dynamics of DNA Excited State Relaxation Driven by Base Stacking and Pairing Interactions 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-7578032","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":517637287,"identity":"69cce369-ea36-47b3-9182-1e691efe89db","order_by":0,"name":"Hong-Guang 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While isolated nucleobases undergo rapid deactivation on sub-picosecond timescales, their incorporation into stacked and paired DNA architectures introduces significant alterations to excited-state dynamics. Base stacking and Watson-Crick pairing give rise to delocalized excitonic and charge-transfer (CT) states that display extended lifetimes and complex relaxation behavior. In this work, we combine a linear vibronic coupling (LVC) Hamiltonian with an effective transformation to a structured system-bath representation, enabling explicit inclusion of key vibrational modes that drive nonadiabatic transitions. The hierarchical equations of motion (HEOM) method is employed to simulate population dynamics in systems ranging from adenine monomers to stacked heptamers, as well as A–T paired motifs and a combined (A–A)–T trimer. 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