Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

Huix‐Rotllant, Miquel

doi:10.3390/molecules26196021

Cited by 2 publications

(3 citation statements)

References 42 publications

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“…The S 2 undergo a rapid internal conversion to the lower S 1 state of nπ * character after reaching the S 1 /S 2 conical intersection that is accessed in a barrierless reaction. 63 As discussed in the previous section, this ultrafast ππ * → nπ * population transfer completes within about 100 fs in both gas and aqueous condition leading to the metastable S 1 (nπ * ) state. From the S 1 minimum, there exist several conical intersections (CI 10 ) with the ground state.…”

Section: Photochemistry Of Solvated Thyminementioning

confidence: 68%

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

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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 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

Section: Photochemistry Of Solvated Thyminementioning

confidence: 68%

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

show abstract

“…The S 2 states undergo a rapid internal conversion to the lower S 1 state of nπ* character after reaching the S 1 /S 2 conical intersection that is accessed in a barrierless reaction. 63 As discussed in the previous section, this ultrafast ππ* → nπ* population transfer completes within about 100 fs in both gas and aqueous conditions leading to the metastable S 1 (nπ*) state. From the S 1 minimum, there exist several conical intersections (CI 10 ) with the ground state.…”

Section: Photochemical Mechanism Of Thymine Dimer Formation In Dnamentioning

confidence: 69%

“…At the Franck–Condon (FC) with S 0 minimum geometry, the S 1 (ππ*) and S 2 (nπ*) states are almost degenerate. The S 2 states undergo a rapid internal conversion to the lower S 1 state of nπ* character after reaching the S 1 /S 2 conical intersection that is accessed in a barrierless reaction . As discussed in the previous section, this ultrafast ππ* → nπ* population transfer completes within about 100 fs in both gas and aqueous conditions leading to the metastable S 1 (nπ*) state.…”

Section: Resultsmentioning

confidence: 87%

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.

Self Cite

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 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

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

Cited by 2 publications

References 42 publications

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

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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