Calculation of vibrationally resolved absorption spectra of acenes and pyrene

Benkyi, Isaac; Tapavicza, Enrico; Fliegl, Heike; Sundholm, Dage

doi:10.1039/c9cp04178h

Cited by 56 publications

(69 citation statements)

References 81 publications

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“…The RADLESS module was used for the simulation of vibronic absorption and fluorescence spectra. 20,21 The resolution of the calculated spectra can be raised by increasing the integration time. An integration time of 2.42 ps was found to be proficient for the comparison with the experimental spectra.…”

Section: Methodsmentioning

confidence: 99%

“…19 The geometric displacement and the Duschinsky rotation matrix are used to construct a generating function that allows the simulation of absorption and fluorescence spectra within the zerotemperature approximation. This method has been developed and implemented by Tapavicza et al 20,21 The simulated spectra can be compared with ultraviolet-visible (UV-Vis) absorption and fluorescence spectra measured by matrix isolation spectroscopy. Absorption spectra for the perylene, terrylene and quaterrylene molecules have been recorded by Halasinski et al 22 The absorption and fluorescence spectra of perylene have been recorded by Joblin et al 23 As with all DFT methods the choice of the correct functional is significant for the accuracy of the calculated results.…”

Section: Introductionmentioning

confidence: 99%

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Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes

Greiner

Sundholm

2020

Phys. Chem. Chem. Phys.

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A generating function method was used to simulate the vibrationally resolved absorption and emission spectra of perylene, terrylene and quaterrylene. This method operates on the basis of adiabatic excitation energies and electronic ground and excited state vibrational frequencies. These parameters were calculated using density functional theory with the PBE0 functional for perylene and terrylene and with the BH-LYP functional for quaterrylene. The vertical excitation energies of the lower excited states were calculated using functionals with differing amounts of Hartree-Fock exchange. The optimal functional for each molecule was chosen by comparing these energies to literature excitation energies. Using this technique the calculated absorption spectra and the calculated emission spectrum of perylene were found to be in excellent agreement with the literature experimental spectra after introducing a shift and a scaling factor. The most prominent bands of the absorption spectra were assigned to their respective vibronic transitions. † Electronic supplementary information (ESI) available: The Cartesian ground and excited state coordinates of the optimized molecular structures, the oscillator strengths of the vertical excitations and the calculated ground and excited state harmonic frequencies of the studied molecules are given as supporting information. All assigned bands in the calculated absorption spectra with a relative intensity of above 2%. See

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes

Greiner

Sundholm

2020

Phys. Chem. Chem. Phys.

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“…This represents a significantly greater challenge since, in addition to the excitation energies and transition dipole moments, it requires the vibrational frequencies and normal modes of the ground and excited states to be described accurately. Simulated vibrationally resolved spectra for neutral acenes, including naphthalene, and pyrene have been reported [42,43]. Dierksen and Grimme reported calculations of the vibronic structure in electronic spectra for the low-energy bands of range of organic molecules, including pyrene, with the Franck-Condon (FC) and Franck-Condon-Herzberg-Teller (FCHT) approximations based upon TDDFT calculations with the B3LYP exchange-correlation functional [42].…”

Section: Introductionmentioning

confidence: 99%

“…The calculations provided a good description of the vibrational structure although an energy shift needed to be applied to the vertical excitation energy. More recently, the calculation of vibrationally resolved absorption spectra of acenes and pyrene has been reported using a real-time generating function method in combination with TDDFT and the PBE0 functional [43].…”

Section: Introductionmentioning

confidence: 99%

Simulation of vibrationally resolved absorption spectra of neutral and cationic polyaromatic hydrocarbons

2020

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The identification of the carriers of the absorption features associated with the diffuse interstellar bands (DIBs) is a long-standing problem in astronomical spectroscopy. Computational simulations can contribute to the assignment of the carriers of DIBs since variations in molecular structure and charge state can be studied more readily than through experimental measurements. Polyaromatic hydrocarbons have been proposed as potential carriers of these bands, and it is shown that simulations based upon density functional theory and time-dependent density functional theory calculations can describe the vibrational structure observed in experiment for neutral and cationic naphthalene and pyrene. The vibrational structure arises from a small number of vibrational modes involving in-plane atomic motions, and the Franck–Condon–Herzberg–Teller approximation improves the predicted spectra in comparison with the Franck–Condon approximation. The study also highlights the challenges for the calculations to enable the assignment in the absence of experimental data, namely prediction of the energy separation between the different electronic states to a sufficient level of accuracy and performing vibrational analysis for higher-lying electronic states.

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“…The intramolecular excimer ( 1 SPy 2 * ) can be formed by two processes when two SPys are end‐linked to ssDNA: 1) excitation of the non‐oxidized cofacial SPy dimer (the ground state dimer); 2) dynamical formation by the excited state of SPy ( 1 SPy * ) associating with its neutral counterpart ( SPy ) within the short lifetime of 1 SPy* . The population of the ground‐state conformation of the doubly SPy ‐modified ssDNA with the two end‐linked SPys forming a non‐oxidized cofacial SPy dimer can be deciphered through the absorbance ratio of the absorption band at 345 nm (14A g transition of S 0 →S 2 ) to the absorption band at 360 nm (0–0 transition of S 0 →S 2 ) . In the case of SPy‐T 4 ‐SPy , the ratio exceeds unity, and this suggests that a large population of SPy‐T 4 ‐SPy molecules are in such a ground‐state conformation with the two end‐linked SPys in cofacial contact in the non‐oxidized state.…”

Section: Resultsmentioning

confidence: 99%

Sulfonated Pyrene as a Photoregulator for Single‐Stranded DNA Looping

Miyamoto

Tojo

et al. 2020

Chemistry A European J

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Controlling the conformationa nd functiono fb iomolecules through photoregulators holds great promise as a spatiotemporally controllable tool for disease control.I na ddition, introducing photoregulators into biomoleculesh as also found applicationsi nc onstructings martn anomaterials. In spite of the astonishing advances that have been made in the past few years, realizing highly controllable and efficient regulation over the conformation and functiono fb iomolecules under physiological conditionsi ss till challenging. Herein,s ulfonated pyrene SPy was synthesized and used as ap hotoregulator to control the looping of single-stranded DNAs (ssDNAs) in aqueous solution.Due to its water solubility, SPy merits use in the study of biomolecules in aqueous solution.T he looping of the doubly SPy-modified ssDNAs is stimulated by irradiation and regulated by SPy.P hotoionization generatest he radicalc ation of SPy (SPyC + ). The association of SPyC + + with its neutralc ounterpart, SPy,g ives rise to the dimer radicalc ation of SPy (SPy 2 C + + ). During the association process, the stabilization energy released to form SPy 2 C + + provides ad riving force for the looping of ssDNAs. Conversely,t he formed loop conformationsw ere trapped by the formation of SPy 2 C + + ,a nd this allowed the looping dynamics to be investigated. The results reported herein suggest potential of SPy as ap hotoregulator for controlling the conformationa nd function of biomolecules under physiological conditions.[a] J.[a] Immediately formed SPy 2 C + + component. P static = DOD t = 10 ns /DOD max .

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Calculation of vibrationally resolved absorption spectra of acenes and pyrene

Abstract: Absorption spectra of polycyclic aromatic hydrocarbons have been simulated by using a real-time generating function method that combines adiabatic electronic excitation energies with vibrational energies of the excited states.

Cited by 56 publications

References 81 publications

Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes

Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes

Simulation of vibrationally resolved absorption spectra of neutral and cationic polyaromatic hydrocarbons

Sulfonated Pyrene as a Photoregulator for Single‐Stranded DNA Looping

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