Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy

Erickson, Blake A.; Heim, Zachary N.; Pieri, Elisa; Liu, Erica; Martı́nez, Todd J.; Neumark, Daniel M.

doi:10.26434/chemrxiv.9750872.v1

Cited by 4 publications

(8 citation statements)

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“…S40). Moreover, it agrees with recent photoelectron spectroscopy experiments on thymine and 5mUrd which also did not nd evidence for the involvement of the nπ* state 28,37 .…”

Section: Involvement Of the Np* State In The Deactivation Of Uridine supporting

confidence: 92%

“…In particular, in pyrimidines, the time scale of IC and the involvement of intermediate dark states are still disputed. Experimental transient absorption (TA), photo-electron spectroscopy and uorescence up-conversion measurements on pyrimidines and their nucleosides in aqueous solution agree on the early fate of the initially excited (ππ*) singlet state, that decays with one or two sub-picosecond components 12,14,[22][23][24][25][26][27][28][29] and a further component of several picoseconds [12][13][14][22][23][24][25][26][27][30][31][32][33] . The sub-picosecond decay has been assigned to direct IC to the ground state and/or to a dark (nπ*) singlet excited state, whereas the long component has been attributed to various mechanisms including ground state vibrational cooling, intersystem crossing (ISC) to triplet states, IC of dark states to the ground state or population trapping in the ππ* state.…”

Section: Introductionmentioning

confidence: 82%

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Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

Cerullo

Borrego-Varillas

Nenov

et al. 2020

Preprint

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DNA owes its remarkable photostability to the ability of its building blocks – the nucleosides – to efficiently dissipate the excess electronic energy acquired upon photoexcitation with ultraviolet light. The exact mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy with broad spectral coverage and state-of-the-art quantum dynamics simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. For both nucleosides we track the wave packet motion from the Franck-Condon region to the conical intersection (CI) with to the ground state and observe a direct spectral signature of an excited-state vibrational mode leading to the CI. We find that 5mUrd exhibits an order of magnitude longer excited state lifetime with respect to Urd and assign it to the larger inertia of the methyl group involved in the ring puckering mode leading to the CI. We argue that this longer lifetime enables the activation of potentially lesion-inducing coordinates such as ring opening, elucidating the origin of the susceptibility of thymine-containing DNA strands to photodamage.

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“…S40). Moreover, it agrees with recent photoelectron spectroscopy experiments on thymine and 5mUrd which also did not nd evidence for the involvement of the nπ* state 28,37 .…”

Section: Involvement Of the Np* State In The Deactivation Of Uridine supporting

confidence: 92%

Section: Introductionmentioning

confidence: 82%

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

Cerullo

Borrego-Varillas

Nenov

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Contrasting to the slow S 0 population increase in gas phase, abrupt changes are seen in solution reaching 50% to 70% of the total population in 300 fs, regardless of the initial excitation to S 2 or S 1 . This QM/MM-NAMD result is consistent with recent liquid jet time-resolved photoelectron spectroscopy, 58 where the lower lying ππ* (S 1 ) state is found to decay in ∼400 fs independent of pump photon energy.…”

Section: Analytic Excited State Energysupporting

confidence: 89%

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

Huix‐Rotllant

Schwinn

Pomogaev

et al. 2022

J. Chem. Theory Comput.

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The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6−4 photoproducts.

show abstract

“…Contrasting to the slow S 0 population increase in gas phase, an abrupt changes are seen in solution reaching 50% ∼ 70% of the total population in 300 fs, regardless of initial excitation of S 2 or S 1 . This QM/MM-NAMD result is consistent with recent liquid jet time-resolved photoelectron spectroscopy, 58 where the lower lying ππ * (S 1 ) state is found to decay in ∼ 400 fs independent of pump photon energy.…”

Section: Photochemistry Of Solvated Thyminesupporting

confidence: 89%

Photochemistry of thymine in solution and DNA revealed by an electrostatic embedding QM/MM combined with mixed-reference spin-flip TDDFT

Huix‐Rotllant

Schwinn

Pomogaev

et al. 2022

Preprint

View full text Add to dashboard Cite

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density-functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fitting (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) non-adiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed the accelerated deactivation decay pathways, which is consistent with the experimental decay time of ~ 400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

show abstract

Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy

Cited by 4 publications

References 0 publications

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

Photochemistry of thymine in solution and DNA revealed by an electrostatic embedding QM/MM combined with mixed-reference spin-flip TDDFT

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