3-Methylation alters excited state decay in photoionised uracil

Segarra‐Martí, Javier; Tran, Thierry; Bearpark, Michael J.

doi:10.1039/d2cp03460c

Cited by 5 publications

(9 citation statements)

References 85 publications

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“…This suggests that pyrimidine and purine DNA/RNA nucleobases have different conical intersection topographies underpinning their ultrafast decay channel, despite featuring similar lifetimes . A more thorough report will be presented soon covering this and other important aspects related to the effects of dynamic electron correlation at the intersection seam in DNA/RNA species. , …”

Section: Discussionmentioning

confidence: 99%

“…As CASSCF does not add contributions toward electron correlation beyond those orbitals directly included in the active space (i.e., due to strong/static correlation), and due to their localized nature, expanding the basis set has a relatively small effect that is likely more discernible in purine-based species due to their larger molecular frames (and larger amount of correlating orbitals included therein). We expect a (potentially) more prominent role of basis set size when including also dynamic electron correlation, 98 which we plan to look at in future work.…”

Section: Discussionmentioning

confidence: 99%

“… 125 A more thorough report will be presented soon covering this and other important aspects related to the effects of dynamic electron correlation at the intersection seam in DNA/RNA species. 98 , 126 …”

Section: Discussionmentioning

confidence: 99%

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Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Cuéllar-Zuquin,

Pepino,

Fdez. Galván

et al. 2023

J. Chem. Theory Comput.

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We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1 n O/N π* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Cuéllar-Zuquin,

Pepino,

Fdez. Galván

et al. 2023

J. Chem. Theory Comput.

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“…The CMS-PDFT method gives the correct topology of closely spaced PESs at and near conical intersections. CMS-PDFT may be compared to extended multistate complete active space second-order perturbation theory (XMS-CASPT2), , which has been demonstrated to be a highly accurate quantum chemical method that can describe important dynamic correlation effects at and near the conical intersections that control quenching and other electronically nonadiabatic processes. − Although CMS-PDFT gives results of comparable quality, including near conical intersections, it is advantageous as it is much less expensive.…”

Section: Introductionmentioning

confidence: 99%

Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory

Calio,

Hermes,

Bao

et al. 2024

J. Phys. Chem. A

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Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. In this work, we develop interstate coupling vectors (ISCs) for CMS-PDFT in the OpenMolcas and PySCF/mrh electronic structure packages. Yet, the main focus of this work is using ISCs to calculate minimum-energy conical intersections (MECIs) by CMS-PDFT. This is performed using the projected constrained optimization method in OpenMolcas, which uses ISCs to restrain the iterations to the conical intersection seam. We optimize the S 1 /S 0 MECIs for ethylene, butadiene, and benzene and show that CMS-PDFT gives smooth PESs in the vicinities of the MECIs. Furthermore, the CMS-PDFT MECIs are in good agreement with the MECI calculated by the more expensive XMS-CASPT2 method.

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“…Application of RT-TD-WF made possible computing HHG spectra of organic and biological molecules, such as uracil. ,, Optical properties of uracil were extensively studied, with special attention to the photophysics of electronic states and ,− Raman , and photoelectron spectra. − Interest was also focused on electron attachment to study possible pathways leading to radiation damage. − Much less is known on HHG of gas-phase uracil, mainly due to the difficulty of vaporizing the sample. Indeed, HHG spectra of gas-phase uracil, and its fragments, were recorded by means of plasma ablation. , Interpretation of those results was made complicated by the presence of the uracil cation and its fragments, other than the bare uracil.…”

Section: Introductionmentioning

confidence: 99%

Role of Inner Molecular Orbitals in High-Harmonic Generation Spectra of Aligned Uracil

Luppi,

Coccia

2023

J. Phys. Chem. A

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3-Methylation alters excited state decay in photoionised uracil

Abstract: UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in...

Cited by 5 publications

References 85 publications

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory

Role of Inner Molecular Orbitals in High-Harmonic Generation Spectra of Aligned Uracil

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