Vibronic Absorption Spectra Research Articles

Internal Conversion Cascade in a Carbon Nanobelt: A Multiconfigurational Quantum Dynamical Study.

Carbon nanobelts feature intriguing photophysical properties, due to their high symmetry and structural rigidity. Here, we consider a (6,6) armchair carbon nanobelt, i.e., the very first carbon nanobelt to be synthesized [Povie et al., Science 2017, 356, 172] and characterize the internal conversion dynamics using multiconfigurational quantum dynamics via the multi-layer multiconfiguration time-dependent Hartree (ML-MCTDH) method. A symmetry-adapted linear vibronic coupling Hamiltonian for 26 electronic states and 210 vibrational modes is employed. Electronic excitations are found to decay through a dense manifold of excited states, which interact via multiple conical intersections, while inducing minimal geometry change. It is shown that a rapid coherent decay, exhibiting a nonvanishing quantum flux on a time scale of less than 50 fs, transitions toward a slower, decoherent decay at longer times. As previously suggested in the literature, electronic relaxation is hindered by phonon bottlenecks such that a stepwise internal conversion cascade is observed. The computed vibronic absorption spectrum is shown to be in good agreement with the experimental spectrum.

Theoretical study of vibronic absorption spectra and Franck-Condon factors of copper and silver hydrides

The electronic absorption spectra of CuH and AgH molecules are calculated using the analytical expression for the spectral density related to the thermal dipole time correlation function. In addition, the vibronic transition probabilities between the initial and final states are determined by calculating the transition dipole moments and the Franck-Condon factors using the LEVEL program. The spectroscopic constants recently obtained from MRCI + SOC calculations are used to calculate the absorption spectral line shapes of CuH and AgH molecules and plotted in the time and frequency domains for the vibronic transitions from the ground state Ω = 0+(I) to the excited states Ω = 0+(II), 0+(III), 1(I), 1(II), 1(III), and 1(IV) for CuH and to the excited states Ω = 0+(II), 0+(III), 0+(IV), 1(II), 1(III), 1(IV), 1(V), and 1(VI) for AgH.

Calculation of quasi-diabatic states within the DFT/MRCI(2) framework: The QD-DFT/MRCI(2) method.

We describe a procedure for the calculation of quasi-diabatic states within the recently introduced DFT/MRCI(2) framework [S. P. Neville and M. S. Schuurman, J. Chem. Phys. 157, 164103 (2022)]. Based on an effective Hamiltonian formalism, the proposed procedure, which we term QD-DFT/MRCI(2), has the advantageous characteristics of being simultaneously highly efficient and effectively black box in nature while directly yielding both quasi-diabatic potentials and wave functions of high quality. The accuracy and efficiency of the QD-DFT/MRCI(2) formalism are demonstrated via the simulation of the vibronic absorption spectra of furan and chlorophyll a.

TD‐DFT analysis of the excitation of H‐dimers of cationic dyes in an aqueous solution using functionals without additional dispersion correction

AbstractThis work is a development and extension of the previous one (DOI: 10.1039/d3cp00882g). Here, H‐dimers of acridine (acridine orange—AO and proflavine—PF), thiazine (methylene blue—MB and thionine—TH), and oxazine (brilliant cresyl blue—BCB and Nile blue—NB) dyes were modeled using hybrid functionals with a large proportion of exact Hartree–Fock exchange and long‐range correction. It turned out that nine functionals (LC‐ωHPBE, M06HF, M052X, M062X, M08HX, M11, MN15, SOGGA11X, and ωB97XD) reliably stabilize these molecular aggregates in both the ground and excited states. In addition, these functionals ensure that the conditions for transition moments (M(dimer) ≈ M(monomer) from strong coupling theory for H‐aggregates) and absorption maxima (λmax(dimer) < λmax(monomer) from Kasha exciton theory) are met. The S2 excited state stabilizes the H‐dimers more strongly than the ground state, while the S1 state stabilizes even more than S2. This is due to the large overlap between the corresponding molecular orbitals (LUMO > HOMO−1 > HOMO). When calculating the vibronic absorption spectra, the best agreement with the experiment for AO2, PF2, and NB2 showed the M08HX functional, and M11—for MB2 and BCB2. For dye monomers, these functionals gave the worst agreement, and MN15 demonstrated the closest similarity to the experiment. Vibronic absorption spectra for AO2, MB2, BCB2, and NB2 were calculated for the first time. The exciton splitting is calculated, which for MB2 is in good agreement with the experimental value.

Nitrile Imines as Peptide and Oligonucleotide Photo-Cross-Linkers in Gas-Phase Ions.

Nitrile imines produced by photodissociation of 2,5-diaryltetrazoles undergo cross-linking reactions with amide groups in peptide-tetrazole (tet-peptide) conjugates and a tet-peptide-dinucleotide complex. Tetrazole photodissociation in gas-phase ions is efficient, achieving ca. 50% conversion with 2 laser pulses at 250 nm. The formation of cross-links was detected by CID-MS3 that showed structure-significant dissociations by loss of side-chain groups and internal peptide segments. The structure and composition of cross-linking products were established by a combination of UV-vis action spectroscopy and cyclic ion mobility mass spectrometry (c-IMS). The experimental absorption bands were found to match the bands calculated for vibronic absorption spectra of nitrile imines and cross-linked hydrazone isomers. The calculated collision cross sections (CCSth) for these ions were related to the matching experimental CCSexp from multipass c-IMS measurements. Loss of N2 from tet-peptide conjugates was calculated to be a mildly endothermic reaction with ΔH0 = 80 kJ mol-1 in the gas phase. The excess energy in the photolytically formed nitrile imine is thought to drive endothermic proton transfer, followed by exothermic cyclization to a sterically accessible peptide amide group. The exothermic nitrile imine reaction with peptide amides is promoted by proton transfer and may involve an initial [3 + 2] cycloaddition followed by cleavage of the oxadiazole intermediate. Nucleophilic groups, such as cysteine thiol, did not compete with the amide cyclization. Nitrile imine cross-linking to 2'-deoxycytidylguanosine was found to be >80% efficient and highly specific in targeting guanine. The further potential for exploring nitrile-imine cross-linking for biomolecular structure analysis is discussed.

TD-DFT analysis of excitation of the closed-form spironaphthopyran in methanol solution: The contribution of vibronic transitions and intermolecular hydrogen bonds

A set of forty hybrid functionals, combined with a 6–31++G(d,p) basis set and an IEFPCM solvent description, was applied to calculate the S0→S1 excitation of the spironaphthopyran (SNP) photochromic compound. None of the hybrid functionals resulted in Cspiro-O bond cleavage upon optimization of the S1 excited state of the SNP, in contrast to the spiropyran BIPS which we studied earlier. At the same time, the deformations of the SNP during excitation turned out to be very small (in contrast to those for BIPS) which made it possible to calculate its vibronic absorption spectrum. The best agreement between the calculated and experimental absorption bands was demonstrated by the SOGGA11X functional. The main result of this work is confirmation of the vibration participation in the breaking of the Cspiro-O bond in the S1 excited state of the SNP. This assumption based on experimental data was previously put forward by other authors. Strong H-bonds between the SNP and two methanol molecules enhance the photoinduced distortions of the latter and are slightly weakened upon excitation.

Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry.

We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.

Photoexcitation of Nile blue dye in aqueous solution: TD-DFT study

The vibronic absorption spectra of Nile blue (NB) oxazine dye in an aqueous solution using 13 hybrid functionals, the 6-31++G(d,p) basis set, and the IEFPCM solvent model were calculated. It turned out that the O3LYP functional provided the best agreement with the experiment. Various parameters of the NB cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were obtained. Maps of the distribution of electron density and electrostatic potential have been built. The influence of four strong hydrogen bonds of the dye with water molecules on the absorption spectrum was analyzed. It has been shown that two from these bonds were strengthened upon NB excitation and two ones were weakened. It was found that explicit assignment of water molecules strongly bound to the dye leads to a redshift of the spectrum as a whole and worsened its shape.

Coumarin 337 in aqueous solution: interplay between excitation and hydration

Excitation of the C337, highly fluorescent dye in an aqueous solution was studied by the TD-DFT. Through the B3PW91/6-311++G(d, p)/IEFPCM theory level, we obtained the C337 vibronic absorption spectrum which exactly reproduces the experimental maximum. Significant differences are shown between the results of calculating the transition energies using the models of vertical and vibronic transitions. Upon excitation, the main shift of the electron density occurs from C10 to C4 neighboring atom. Thus, large-scale ICT not occur. The effect of excitation on the vibrational spectra of C337 was analyzed. A single C337 molecule and its five different hydration complexes with strongly bound water molecules have been analyzed. Various hydrate complexes of the dye have been studied, and the effect of hydration on its excitation vibrational properties has been elucidated. It was taken into account that a water molecule can attach to the nitrogen atom N1 ("A" type) and the C=O carbonyl ("B" type), and cyano C≡N ("C" type) groups of the dye.

TD-DFT STUDY OF TOLUIDINE BLUE O IN AQUEOUS SOLUTION: VIBRONIC TRANSITIONS AND ELECTRONIC PROPERTIES

The vibronic absorption spectrum of Toluidine blue O (TBO) dye in an aqueous solution was calculated using the time-dependent density functional theory (TD-DFT). The calculations were performed using all hybrid functionals supported by Gaussian16 software and 6-31++G(d,p) basis set with IEFPCM and SMD solvent models. The IEFPCM gave underestimated values of λmax in comparison with the experiment, what is a manifestation of the TD-DFT "cyanine failure". However, the SMD made it possible to obtain good agreement between calculated and experimental spectra. The best fit was achieved using the X3LYP functional. The dipole moments and atomic charges of the ground and excited states of the TBO molecule were calculated. Photoexcitation leads to an increase in the dipole moment of the dye molecule. An insignificant photoinduced electron transfer was found in the central ring of the chromophore of the TBO molecule. Vibronic transitions play a significant role in the absorption spectrum of the dye.

Electron-phonon coupling and vibrational properties of size-selected linear carbon chains by resonance Raman scattering

UV resonance Raman spectroscopy of size-selected linear sp-carbon chains unveils vibrational overtones and combinations up to the fifth order. Thanks to the tunability of the synchrotron source, we excited each H-terminated polyyne (HCnH with n = 8,10,12) to the maxima of its vibronic absorption spectrum allowing us to precisely determine the electronic and vibrational structure of the ground and excited states for the main observed vibrational mode. Selected transitions are shown to enhance specific overtone orders in the Raman spectrum in a specific way that can be explained by a simple analytical model based on Albrecht’s theory of resonance Raman scattering. The determined Huang–Rhys factors indicate a strong and size-dependent electron-phonon coupling increasing with the sp-carbon chain length.

Comparison of Linear Response Theory, Projected Initial Maximum Overlap Method, and Molecular Dynamics-Based Vibronic Spectra: The Case of Methylene Blue.

The simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited electronic states. In this report, we show that the utilization of such a procedure within an adiabatic linear response (LR) theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent field method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical gradient and molecular dynamics (MD) trajectory-based approaches. For the methylene blue chromophore, we compare vibronic absorption spectra computed with the following: an adiabatic Hessian approach with LR theory-optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method-optimized structures, and excitation energy time-correlation functions generated from an MD trajectory. Because of mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with LR theory and time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in LR theory strongly couples to the optical excitation while showing S1/S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited-state adiabatic Hessian of LR theory-optimized structures and also showcases three alternatives that are less sensitive to adiabatic state mixing effects.

Coumarin 343 in aqueous solution: theoretical analysis of absorption.

Vibronic coupling and hydration were taken into account when describing the absorption of coumarin C343 (both neutral and anionic forms) in an aqueous media. It was shown that the B3LYP functional with the 6-31 + + G(d,p) basis set and the IEFPCM solvent continuum model give theoretical vibronic absorption spectra, which are coincide with the experimental ones. Of the structural differences between C3430 and C343-, there is a different twisting of the carboxyl group additionally changing due to excitation. Upon excitation, a significant shift in the electron density occurs from the C10 atom to the C4 atom only. Thus, a charge transfer on the scale of the entire molecule does not occur. Different hydration complexes with strongly bound water molecules have been analyzed.

Coumarin 314 excitation in aqueous media: Contributions of vibronic coupling and hydration

Vibronic coupling and hydrogen bonding were considered when analyzing the excitation of coumarin C314. It was found that the B3PW91 functional in combination with the 6–31++G(d,p) basis set and the IEFPCM solvent model gives a calculated vibronic absorption spectrum, which is in good agreement with the experimental one both in the position of the maximum and in shape. Significant differences are shown between the results of calculating the transition energies using the models of vertical and vibronic transitions. Both a single C314 molecule and its five different hydration complexes with strongly bound water molecules have been analyzed. It was taken into account that a water molecule can attach both to the nitrogen atom N1 (“A” type) and the C=O carbonyl groups of the dye (“B” type). The vibronic emission spectra of a single C314 molecule and its hydrate complexes were also calculated and analyzed.

How the Interplay among Conformational Disorder, Solvation, Local, and Charge-Transfer Excitations Affects the Absorption Spectrum and Photoinduced Dynamics of Perylene Diimide Dimers: A Molecular Dynamics/Quantum Vibronic Approach.

In this contribution we present a mixed quantum-classical dynamical approach for the computation of vibronic absorption spectra of molecular aggregates and their nonadiabatic dynamics, taking into account the coupling between local excitations (LE) and charge-transfer (CT) states. The approach is based on an adiabatic (Ad) separation between the soft degrees of freedom (DoFs) of the system and the stiff vibrations, which are described by the quantum dynamics (QD) of wave packets (WPs) moving on the coupled potential energy surfaces (PESs) of the LE and CT states. These PESs are described with a linear vibronic coupling (LVC) Hamiltonian, parameterized by an overlap-based diabatization on the grounds of time-dependent density functional theory computations. The WPs time evolution is computed with the multiconfiguration time-dependent Hartree method, using effective modes defined through a hierarchical representation of the LVC Hamiltonian. The soft DoFs are sampled with classical molecular dynamics (MD), and the coupling between the slow and fast DoFs is included by recomputing the key parameters of the LVC Hamiltonians, specifically for each MD configuration. This method, named Ad-MD|gLVC, is applied to a perylene diimide (PDI) dimer in acetonitrile and water solutions, and it is shown to accurately reproduce the change in the vibronic features of the absorption spectrum upon aggregation. Moreover, the microscopic insight offered by the MD trajectories allows for a detailed understanding of the role played by the fluctuation of the aggregate structure on the shape of the vibronic spectrum and on the population of LE and CT states. The nonadiabatic QD predicts an extremely fast (∼50 fs) energy transfer between the two LEs. CT states have only a moderate effect on the absorption spectrum, despite the fact that after photoexcitation they are shown to acquire a fast and non-negligible population, highlighting their relevance in dictating the charge separation and transport in PDI-based optical devices.

Photoexcitation of oxazine 4 dye in aqueous solution: TD-DFT study

The vibronic absorption spectra of oxazine 4 (OX4) dye in an aqueous solution using 40 hybrid functionals, the 6–31++G(d,p) basis set, and the SMD solvent model were calculated. It turned out that the X3LYP functional provided the best agreement with the experiment in the positions of the main maximum and the short-wavelength shoulder. Our calculations showed that this shoulder is vibronic and is not caused by a separate electronic transition. At the same time, the shoulder intensity in the calculated spectrum turned out to be lower than in the experimental one. Various parameters of the OX4 cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were calculated. Maps of the distribution of electron density and electrostatic potential have been built. The influence of four strong hydrogen bonds of the dye with water molecules on the absorption spectrum was analyzed. It has been shown that these bonds were strengthened upon OX4 excitation. It was found that explicit assignment of water molecules strongly bound to the dye leads to a redshift of the spectrum as a whole, but does not change its shape. Photoexcitation of the dye leads to a noticeable polarization of only one of the four considered water molecules (associated with the endocyclic nitrogen atom in the central ring of the chromophore, the electron density on which increases the most).

Vibronic absorption spectra and excited states of acridine red dye in aqueous solution: TD-DFT/DFT study

Abstract The vibronic absorption spectra of acridine red (AR) xanthene dye in an aqueous solution using 40 hybrid functionals, the 6-31++G(d,p) basis set, and the IEFPCM solvent model were calculated. It turned out that the O3LYP functional provided the best agreement with the experiment in the positions of the main maximum and the short-wavelength subband (shoulder). The calculations showed that this shoulder is vibronic. At the same time, the shoulder intensity in the calculated spectrum turned out to be lower than in the experimental one. Apparently, insignificant dimerization, which occurs even at low concentrations of the dye in solution, contributes to the shoulder of the experimental absorption spectrum. Various parameters of the AR cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were calculated. Maps of the distribution of electron density and electrostatic potential have been built. The influence of the strong hydrogen bonds of the dye with three water molecules on the absorption spectrum was analyzed. It has been shown that these bonds are strengthened upon AR excitation. The strengthening of two hydrogen bonds with water upon excitation leads to a lowering of the potential energy surface of the excited state, which causes a decrease in the excitation energy (i.e., an increase in the wavelength of the absorbed photon) as compared to a purely implicit specification of the water environment. Therefore, explicit assignment of waters strongly bound to the dye leads to spectrum redshift.

Photoexcitation of brilliant cresyl blue dye in aqueous solution: TD-DFT study

The vibronic absorption spectra of brilliant cresyl blue (BCB) oxazine dye in an aqueous solution using 40 hybrid functionals, the 6-31++G(d,p) basis set, and the SMD solvent model were calculated. It turned out that the X3LYP functional provided the best agreement with the experiment in the positions of the main maximum and the short-wavelength shoulder. Our calculations showed that this shoulder is vibronic and is not caused by a separate electronic transition. At the same time, the shoulder intensity in the calculated spectrum turned out to be lower than in the experimental one. Various parameters of the BCB cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were calculated. Maps of the distribution of electron density and electrostatic potential have been built. The influence of four strong hydrogen bonds of the dye with water molecules on the absorption spectrum was analyzed. It has been shown that these bonds are strengthened upon BCB excitation. It was found that explicit assignment of water molecules strongly bound to the dye leads to a redshift of the spectrum. Photoexcitation of the dye leads to a noticeable polarization of only one of the four considered water molecules.

Photoexcitation of methylene green dye in aqueous solution: TD-DFT study

The vibronic absorption spectra of methylene green (MG) thiazine dye in an aqueous solution using X3LYP hybrid functional, the 6-31++G(d,p) basis set, and the SMD solvent model were calculated. It turned out that this theory level the choice of which is based on previous theoretical studies of thiazine dyes provided excellent agreement with the experiment in the positions of the main maximum and the short-wavelength shoulder. Our calculations showed that this shoulder is vibronic and is not caused by a separate electronic transition. At the same time, the shoulder intensity in the calculated spectrum turned out to be lower than in the experimental one. Various parameters of the MG cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were calculated. The dipole moment of the dye molecule in the ground state turned out to be the same as in the excited one, contrary to previous studies, where the dipole moment of a thiazine dyes without a nitro group increases upon excitation. This could be explained by the influence of the MG nitro group in position 6, due to which electron density increases on both diametrically opposite N10 and S5 atoms of the central ring. At the same time, in other thiazine dyes (without a nitro group), photoexcitation leads to a one-sided increase in the electron density at the N10 atom, and as a result, the projection of the dipole moment directed across the chromophore increases significantly. Maps of the distribution of electron density and electrostatic potential have been built. The influence of the strong hydrogen bonds of the dye with three water molecules on the absorption spectrum was analyzed. It has been shown that these bonds are strengthened upon MG excitation. It was found that explicit assignment of water molecules strongly bound to the dye leads to a redshift of the spectrum as a whole and worsened its shape.

Theoretical analysis of lactone and carboxylate forms of camptothecin in aqueous solution: Electronic states, absorption spectra, and hydration

The vibronic absorption spectra of the camptothecin drug in an aqueous solution have been calculated for the first time. The calculations were carried out by the TD-DFT method. It was shown that both for lactone and carboxylate forms an excellent agreement with the experimental spectrum gives the BMK/6-31++G(d,p)/IEFPCM theory level. It was demonstrated that absorption spectra of both forms in the 300–400 nm wavelength range are due to single HOMO → LUMO (S0 → S1) electronic transition, and the short-wavelength smaller peak and shoulder are of vibronic origin. This result is at odds with the previous conclusions of other authors that this peak has a dimeric nature or is caused by interaction with an aqueous medium, and the shoulder is due to a separate electronic transition. According to my calculations, strong hydrogen bonds of the lactone and carboxylate forms with water molecules do not affect their absorption spectra. This is because some of these H-bonds were enhanced by photoexcitation of alkaloid molecules, while others were weakened. The opening of the lactone ring does not affect the position of the vibronic absorption bands but only leads to their significant broadening. Therefore, two separate maxima of the lactone form of the alkaloid merge into one broad peak. The absence of the influence of the lactone E ring on the absorption of the alkaloid is since the frontier orbitals are localized on other rings of the chromophore. Calculations have shown that the dipole moment of both forms of the alkaloid decreases significantly upon excitation. In combination with the practically zero contribution of specific interactions with an aqueous environment, this result indicates the n → π* type of the considered electronic transition. It agrees with both the experimental and theoretical results of some authors. Various characteristics of excited states of both drug forms (IR spectra, atomic charges, electron density, and electrostatic potential distributions) were obtained.