# Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

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## Abstract

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## 1. Introduction

## 2. Materials and Methods

#### 2.1. Diabatisation and Linear Vibronic Coupling Model

#### 2.2. Absorption Spectra

## 3. Computational Details

## 4. Results

#### 4.1. Pyrimidines

#### 4.1.1. Uracil and Thymine

#### 4.1.2. Cytosine

#### 4.2. Purines

#### 4.2.1. Adenine

#### 4.2.2. Guanine

## 5. Concluding Remarks

## Supplementary Materials

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Conflicts of Interest

## References

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Sample Availability: Samples of the compounds are not available from the authors. |

**Figure 1.**Schematic description (and atom labeling) of the five nucleobases: (

**a**) Uracil, (

**b**) Thymine, (

**c**) Cytosine, (

**d**) Adenine and (

**e**) 9H-Guanine. In the 7H tautomer the hydrogen atom is bonded to the N7 Nitrogen atom rather than N9.

**Figure 2.**Absorption spectra of Uracil from the LVC model (red), without inter-state coupling (green), TD-DFT calculations with stick spectra (blue), and experimental data (black) [52]. Cusp in experimental spectrum at 5.75 eV due to gap in data from 5.5 eV to 5.75 eV as separate spectra obtained for lower energy and upper energy bands, recorded at different temperatures (501 K and 439 K, respectively). Low energy peak from experiment and LVC spectra normalised to 1, with other calculated spectra normalised with the same value as LVC spectra. CAM-B3LYP spectra red-shifted by 0.3 eV, PBE0 by 0.15 eV. LVC spectra broadened with Gaussian HWHM 0.04 eV, TD-DFT with HWHM 0.25 eV.

**Figure 3.**Absorption spectra of Thymine from the LVC model (red), without inter-state coupling (green), TD-DFT calculations with stick spectra (blue), and experimental data of 1-methylthymine (black) [52]. Low energy peak from experiment and LVC spectra normalised to 1, with other calculated spectra normalised with the same value as LVC spectra. CAM-B3LYP spectra red-shifted by 0.3 eV, PBE0 by 0.15 eV. LVC spectra broadened with Gaussian HWHM 0.04 eV, TD-DFT with HWHM 0.25 eV.

**Figure 4.**Nonadiabatic dynamics of electronic populations of Uracil in the gas phase, as predicted by an LVC Hamiltonian parameterised with calculations at the FC point using CAM-B3LYP (

**top**) and PBE0 (

**bottom**) functionals with a 6-311+G(d,p) basis set.

**Figure 5.**Nonadiabatic dynamics of electronic populations of Thymine in the gas phase, as predicted by an LVC Hamiltonian parameterised with calculations at the FC point using CAM-B3LYP (

**top**) and PBE0 (

**bottom**) functionals with 6-311+G(d,p) basis set.

**Figure 6.**Absorption spectra of Cytosine from the LVC model (red), without inter-state coupling (green), and TD-DFT calculations with stick spectra (blue). Most intense peaks from LVC spectra normalised to 1, with other calculated spectra normalised with the same value. All calculated spectra unshifted. LVC spectra broadened with Gaussian HWHM 0.04 eV, TD-DFT with HWHM 0.25 eV.

**Figure 7.**Absorption spectra of Adenine from the LVC model (red), without inter-state coupling (green), TD-DFT calculations with stick spectra (blue), and experimental data (black) [52]. Main peak from experiment and LVC spectra normalised to 1, with other calculated spectra normalised with the same value as LVC spectra. CAM-B3LYP spectra red-shifted by 0.25 eV, PBE0 by 0.08 eV. LVC spectra broadened with Gaussian HWHM 0.04 eV, TD-DFT with HWHM 0.25 eV.

**Figure 8.**Nonadiabatic dynamics of electronic populations of Adenine in the gas phase, as predicted by an LVC Hamiltonian parameterised with calculations at C${}_{s}$ minimum using CAM-B3LYP (

**top**) and PBE0 (

**bottom**) functionals with 6-311+G(d,p) basis set.

**Figure 9.**Absorption spectra of (

**a**) 9H-Guanine and (

**b**) 7H-Guanine from the LVC model (red), without inter-state coupling (green), TD-DFT calculations with stick spectra (blue), and experimental data (black) [53]. Most intense peak from experiment and LVC spectra normalised to 1, with other calculated spectra normalised with the same value as LVC spectra. Panel (

**c**) shows the combination (pink) of 9H (purple) and 7H (orange) LVC spectra compared to experiment (black). Most intense peak from experiment and 7H-9H combination normalised to 1. Individual 7H and 9H spectra normalised with same value as 7H-9H combination. For all panels CAM-B3LYP spectra on the left red-shifted by 0.3 eV, PBE0 spectra on the right red-shifted by 0.08 eV. LVC spectra broadened with Gaussian HWHM 0.04 eV, TD-DFT with HWHM 0.25 eV.

**Figure 10.**Nonadiabatic dynamics of electronic populations of 9H-Guanine in the gas phase, as predicted by an LVC Hamiltonian parameterised with calculations using CAM-B3LYP (

**top**) and PBE0 (

**bottom**) functionals with 6-311+G(d,p) basis set.

**Figure 11.**Nonadiabatic dynamics of electronic populations of 7H-Guanine in the gas phase, as predicted by an LVC Hamiltonian parameterised with calculations using CAM-B3LYP (

**top**) and PBE0 (

**bottom**) functionals with 6-311+G(d,p) basis set.

**Table 1.**Energies (${E}_{i}^{0}$), oscillator strengths ${f}_{i}$, and electronic characters for the predominant excited states of the pyrimidine bases involved in the dynamics, calculated at the ground-state minimum (FC point, ${C}_{\mathrm{s}}$ symmetry). CAM-B3LYP and PBE0 calculations with 6-311+G(d,p) basis set in gas phase. Energies in eV.

Uracil | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 5.10 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 | S${}_{1}$ | 4.82 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 |

S${}_{2}$ | 5.50 | 0.190 | $\pi {\pi}^{*}$1 | S${}_{2}$ | 5.33 | 0.150 | $\pi {\pi}^{*}$1 |

S${}_{3}$ | 6.18 | 0.003 | $\pi $Ry${}_{\sigma}$1 | S${}_{4}$ | 6.05 | 0.002 | $\pi $Ry${}_{\sigma}$1 |

S${}_{5}$ | 6.62 | 0.045 | $\pi {\pi}^{*}$2 | S${}_{5}$ | 6.14 | 0.039 | $\pi {\pi}^{*}$2 |

S${}_{6}$ | 6.88 | 0.170 | $\pi {\pi}^{*}$3 | S${}_{7}$ | 6.63 | 0.130 | $\pi {\pi}^{*}$3 |

Thymine | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 5.14 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}1$ | S${}_{1}$ | 4.89 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}1$ |

S${}_{2}$ | 5.31 | 0.192 | $\pi {\pi}^{*}1$ | S${}_{2}$ | 5.13 | 0.154 | $\pi {\pi}^{*}1$ |

S${}_{3}$ | 5.94 | 0.001 | $\pi R{y}_{\sigma}1$ | S${}_{3}$ | 5.80 | 0.000 | $\pi R{y}_{\sigma}1$ |

S${}_{4}$ | 6.47 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}2$ | S${}_{4}$ | 6.10 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}2$ |

S${}_{5}$ | 6.67 | 0.055 | $\pi {\pi}^{*}2$ | S${}_{5}$ | 6.23 | 0.071 | $\pi {\pi}^{*}2$ |

S${}_{6}$ | 6.73 | 0.218 | $\pi {\pi}^{*}3$ | S${}_{6}$ | 6.45 | 0.155 | $\pi {\pi}^{*}3$ |

Cytosine | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 5.01 | 0.067 | $\pi {\pi}^{*}1$ | S${}_{1}$ | 4.79 | 0.047 | $\pi {\pi}^{*}1$ |

S${}_{2}$ | 5.29 | 0.002 | n${}_{\mathrm{N}}{\pi}^{*}1$ | S${}_{2}$ | 4.97 | 0.001 | n${}_{\mathrm{N}}{\pi}^{*}1$ + n${}_{\mathrm{O}}{\pi}^{*}1$ |

S${}_{4}$ | 5.91 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}1$ | S${}_{3}$ | 5.36 | 0.001 | n${}_{\mathrm{N}}{\pi}^{*}1$ − n${}_{\mathrm{O}}{\pi}^{*}1$ |

S${}_{5}$ | 5.94 | 0.134 | $\pi {\pi}^{*}2$ | S${}_{4}$ | 5.61 | 0.099 | $\pi {\pi}^{*}2$ |

S${}_{6}$ | 6.13 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}2$ | S${}_{6}$ | 5.84 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}2$ |

**Table 2.**Energies (${E}_{i}^{0}$), oscillator strengths ${f}_{i}$, and electronic characters for the predominant excited states of the purine bases involved in the dynamics, calculated at the ground-state minimum (FC point, ${C}_{\mathrm{s}}$ symmetry). CAM-B3LYP and PBE0 calculations with 6-311+G(d,p) basis set in gas phase. Energies in eV.

Adenine | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 5.37 | 0.000 | n${}_{\mathrm{N}}{\pi}^{*}1$ | S${}_{1}$ | 5.11 | 0.001 | n${}_{\mathrm{N}}{\pi}^{*}1$ |

S${}_{2}$ | 5.39 | 0.286 | L${}_{\mathrm{a}}$ | S${}_{2}$ | 5.16 | 0.231 | L${}_{\mathrm{a}}$ |

S${}_{3}$ | 5.52 | 0.015 | L${}_{\mathrm{b}}$ | S${}_{3}$ | 5.41 | 0.037 | L${}_{\mathrm{b}}$ |

S${}_{4}$ | 5.87 | 0.009 | $\pi $Ry${}_{\sigma}$1 | S${}_{4}$ | 5.65 | 0.007 | $\pi $Ry${}_{\sigma}$1 |

9H-Guanine | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 5.18 | 0.173 | L${}_{\mathrm{a}}$ | S${}_{1}$ | 4.86 | 0.002 | $\pi $Ry${}_{\sigma}$1 |

S${}_{2}$ | 5.22 | 0.003 | $\pi $Ry${}_{\sigma}$1 | S${}_{2}$ | 5.04 | 0.153 | L${}_{\mathrm{a}}$ |

S${}_{3}$ | 5.61 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 | S${}_{3}$ | 5.36 | 0.282 | L${}_{\mathrm{b}}$ |

S${}_{4}$ | 5.63 | 0.336 | L${}_{\mathrm{b}}$ | S${}_{5}$ | 5.47 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 |

7H-Guanine | |||||||

CAM-B3LYP | PBE0 | ||||||

State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. | State | ${\mathit{E}}_{\mathit{i}}^{\mathbf{0}}$ | ${\mathit{f}}_{\mathit{i}}$ | Char. |

S${}_{1}$ | 4.91 | 0.151 | L${}_{\mathrm{a}}$ | S${}_{1}$ | 4.72 | 0.127 | L${}_{\mathrm{a}}$ |

S${}_{2}$ | 5.30 | 0.004 | $\pi $Ry${}_{\sigma}$1 | S${}_{2}$ | 4.98 | 0.003 | $\pi $Ry${}_{\sigma}$1 |

S${}_{3}$ | 5.51 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 (+n${}_{\mathrm{N}9}{\pi}^{*}$) | S${}_{3}$ | 5.25 | 0.000 | n${}_{\mathrm{O}}{\pi}^{*}$1 (+n${}_{\mathrm{N}9}{\pi}^{*}$) |

S${}_{5}$ | 5.87 | 0.158 | L${}_{\mathrm{b}}$ | S${}_{5}$ | 5.59 | 0.122 | L${}_{\mathrm{b}}$ |

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**MDPI and ACS Style**

Green, J.A.; Jouybari, M.Y.; Aranda, D.; Improta, R.; Santoro, F.
Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. *Molecules* **2021**, *26*, 1743.
https://doi.org/10.3390/molecules26061743

**AMA Style**

Green JA, Jouybari MY, Aranda D, Improta R, Santoro F.
Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. *Molecules*. 2021; 26(6):1743.
https://doi.org/10.3390/molecules26061743

**Chicago/Turabian Style**

Green, James A., Martha Yaghoubi Jouybari, Daniel Aranda, Roberto Improta, and Fabrizio Santoro.
2021. "Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases" *Molecules* 26, no. 6: 1743.
https://doi.org/10.3390/molecules26061743