Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

Fedotov, Daniil; Paul, Alexander C.; Koch, Henrik; Santoro, Fabrizio; Coriani, Sonia; Improta, Roberto

doi:10.1039/d1cp04340d

Cited by 7 publications

(7 citation statements)

References 64 publications

(123 reference statements)

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“…We have applied our method to thymine, a prototypical heteroatomic ring, whose photophysical behavior is the focus of ongoing experimental and computational studies. ,,− The vRR spectra computed in the gas phase are in good agreement with the experimental ones, measured in water, for what concerns both the position and the relative intensity of the different peaks. The only significant discrepancy between the two sets of data concerns the high energy region (>1600 cm –1 ), where three peaks are present in the computed spectra, to be compared with the single experimental peak.…”

Section: Discussionmentioning

confidence: 81%

Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine

Aranda

Jouybari

et al. 2022

J. Phys. Chem. A

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We present a viable protocol to compute vibrational resonance Raman (vRR) spectra for systems with several closelying and potentially coupled electronic states. It is based on the parametrization of linear vibronic coupling (LVC) models from time-dependent density functional theory (TD-DFT) calculations and quantum dynamics propagations of vibronic wavepackets with the multilayer version of the multiconfiguration time-dependent Hartree (ML-MCTDH) method. Our approach is applied to thymine considering seven coupled electronic states, comprising the three lowest bright states, and all vibrational coordinates. Computed vRR at different excitation wavelengths are in good agreement with the available experimental data. Up to 250 nm the signal is dominated by the lowest HOMO → LUMO transition, whereas at 233 nm, in the valley between the two lowest energy absorption bands, the contributions of all the three bright states, and their interferences and couplings, are important. Inclusion of solvent (water) effects improves the agreement with experiment, reproducing the coalescence of vibrational bands due to CC and C�O stretchings. With our approach we disentangle and assess the effect of interferences between the contribution of different quasi-resonant states to the transition polarizability and the effect of interstate couplings. Our findings strongly suggest that in cases of close-lying and potentially coupled states a simple inclusion of interference effects is not sufficient, and a fully nonadiabatic computation should instead be performed. We also document that for systems with strong couplings and quasi-degenerate states, the use of HT perturbative approach, not designed for these cases, may lead to large artifacts.

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Section: Discussionmentioning

confidence: 81%

Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine

Aranda

Jouybari

et al. 2022

J. Phys. Chem. A

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“…Studying the electronic excited states of nucleobases is of great interest as they are responsible for the light absorption of nucleic acids in the middle ultraviolet region, which further leads to rich photochemical processes . Accurately predicting these excited states is theoretically challenging because several states of diverse characters (π → π*, n → π*, and Rydberg) appear close in energy. ,,− Herein, we predict vertical excitation energies of isolated gas-phase nucleobase molecules using SA-DSRG.…”

Section: Resultsmentioning

confidence: 99%

“…127 For the molecules in Figure 1, the geometries, active spaces, and the number of averaged states were directly taken from QUESTDB. 41,99,101 For nucleobases, we followed the recent theoretical work 124,128 and optimized the geometries using CAM-B3LYP/6-311+G(d,p) 129,130 under C s point group. We note that the planar guanine tautomers considered here possess one imaginary mode on the pyramidalization of the amino group.…”

Section: Computational Detailsmentioning

confidence: 99%

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Assessment of State-Averaged Driven Similarity Renormalization Group on Vertical Excitation Energies: Optimal Flow Parameters and Applications to Nucleobases

Wang

Fang

2022

J. Chem. Theory Comput.

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“…65 Although this is not possible for the linear response formulation of TD-DFT, the most used in computational spectroscopy, several developing and applicative works have been done in this direction. [66][67][68] However, the TDMs can be obtained in an approximate way from the one-electron transition density matrix between two excited states. The transition density matrix is expressed as:…”

Section: Evaluation Of Excited States Transition Dipole Momentmentioning

confidence: 99%

Automatized protocol and interface to simulate QM/MM time‐resolved transient absorption at TD‐DFT level with COBRAMM

et al. 2022

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We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.

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Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

Abstract: We report a benchmark of excited state absorption of the four DNA bases using ab initio (EOM-CCSD, EOM-CC3) and TD-CAM-B3LYP methods, in the gas phase and in chloroform, a step towards the interpretation of time-resolved absorption spectra in solution.

Cited by 7 publications

References 64 publications

Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine

Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine

Assessment of State-Averaged Driven Similarity Renormalization Group on Vertical Excitation Energies: Optimal Flow Parameters and Applications to Nucleobases

Automatized protocol and interface to simulate QM/MM time‐resolved transient absorption at TD‐DFT level with COBRAMM

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