Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models

Martínez‐Fernández, Lara; Pepino, Ana Julieta; Segarra‐Martí, Javier; Bányász, Ákos; Garavelli, Marco; Improta, Roberto

doi:10.1021/acs.jctc.6b00518

Cited by 45 publications

(43 citation statements)

References 99 publications

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“…Due to the planarity of the surface, and depending on the threshold employed during the optimization procedure, the presence of a given minimum may be warranted or not. This particularly flat topology of the PEH is not intrinsic to CASSCF/CASPT2, having been reported with other methods [24,73], and is in agreement with the broad emission band recorded and with its small fluorescence quantum yield [62].…”

Section: Caspt2//casscfsupporting

confidence: 89%

“…Figure 1) [17,34,63]. The conclusions derived from those studies seem to be dependent on the strategy used, highlighting the additional insights provided by more sophisticated MEP techniques to map PEHs, while stressing the need for computing experimental observables derived from accurate PEHs to be able to unambiguously compare face-to-face with the experiment [17,73].…”

Section: Caspt2//casscfmentioning

confidence: 99%

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Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

et al. 2016

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Abstract:The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1 (ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

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Section: Caspt2//casscfsupporting

confidence: 89%

Section: Caspt2//casscfmentioning

confidence: 99%

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

et al. 2016

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“…Another molecule related to 2tCyt and recently investigated theoretically is 5-methylcytidine, for which the first ππ * and nπ * states were shown 59 to blue-shift when going from THF/ACN to water, which is in line with the behavior of 2tCyt and Cyt.…”

Section: Discussionsupporting

confidence: 60%

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

et al. 2017

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The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents.

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“…This is more obvious in cluster K, where the 1 L a traces (consisting of two close-lying traces due to the 1 L a states of the two adenine moieties) along Ω 1 are slightly split but strongly red-shifted with respect to the other clusters due to the presence of close-lying water molecules pointing to the C4-C5 bond, not featured for the other conformations, which seems to strongly red-shift these excitations. Despite treating the neighbouring water molecules at the MM level, their inclusion at this lower level has been recently shown to reproduce the qualitative features for related systems of the low-lying electronic excitations, 63 such as 1 L a , and is expected to qualitatively reproduce the solvatochromic shift for the states on the high-energy window like HL…”

Section: Resultsmentioning

confidence: 99%

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

et al. 2018

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A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards a study of the highly flexible water-solvated adenine-adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display various intermolecular arrangements, known to deeply affect their photochemical outcome. Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the complexity of the flexible ApA conformational space. By using our sum-over-states (SOS) approach to obtain the 2DES spectra for each of these selected conformations, we can discern spectral changes and relate them to specific nuclear arrangements: close lying π-stacked bases exhibit a splitting of their respective 1La signal traces; T-stacked bases exhibit the appearance of charge transfer states in the low-energy Vis probing window while displaying no 1La splitting, being particularly favoured when promoting amino to 5-ring interactions; unstacked and distant adenine moieties exhibit signals similar to those of the adenine monomer, as is expected for non-interacting nucleobases. 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. This is expected to aid the understanding of how nucleobase aggregation controls and modulates the photostability and photo-damage of extended DNA/RNA systems.

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Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models

Cited by 45 publications

References 99 publications

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

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