Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.

As in the case of cytosine [Phys. Chem. Chem.

Computational analysis of the vibrational spectra and structure of aqueous cytosine.

The recently developed efficient protocol for the explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [Katsyuba , , 2020, , 6664-6670] is used to describe aqueous solutions of cytosine. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was shown to be sufficient to reproduce experimental vibrational frequencies and relative IR and Raman intensities. An equally good quality of Raman spectra was provided by B3LYP-D3/def2-TZVP and B3LYP-D3/aug-cc-pVDZ simulations.

Characterization of Conjugation Effects in the Series of Quinoxaline-2-ones by Means of Vibrational Raman Spectroscopy.

A broad series of quinoxalinone-based π-conjugated donor-acceptor fluoro- and NLO-phores is characterized by means of Raman spectroscopy and single-crystal X-ray analysis supported by quantum chemical computations. Intense Raman spectroscopic markers that allow the differentiation of even closely related structures are identified. The intensities of these bands are shown to be related to the conjugation of the different molecular moieties, and they can provide an estimation of its extent.

2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra.

We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case.

Benzimidazolylquinoxalines: novel fluorophores with tuneable sensitivity to solvent effects.

We report on the photophysical properties, conjugation, conformational behavior, intra- and intermolecular hydrogen bonds (HBs) of a series of novel fluorophores, consisting of 3-arylquinoxaline and benzimidazole moieties linked by a single CC bond. Computations employing density functional theory (DFT) reveal that conjugation between these moieties stabilizes syn-conformers with two HB centers located on the same side of the molecule. Anti-conformers form stronger intermolecular HBs with DMSO and DMF than syn-conformers, and this influences the energy gap between syn- and anti-forms, especially upon excitation of the molecules to the S state.

Conjugation in and optical properties of 1-R-1,2-diphospholes and 1-R-phospholes.

The strength of conjugation between the diene moieties of 1-R-1,2-diphospholes and 1-R-phospholes and exocyclic phenyl groups of these P-heteroles has been quantitatively characterized by the use of Raman activities of the bands of the phenyl substituents. It is shown that conjugation in both types of phospholes is very similar to the conjugation of phenyl groups with the diene system of cyclopentadiene. Introduction of substituents (-OMe, -C(═O)H, -NO2, -NMe2, and -CH═CH2) in the para-position of the phenyl groups of 1-R-1,2-diphospholes extends π-delocalization of exocyclic groups into the electronic system of the 1,2-diphosphole ring, producing bathochromic shifts of the absorption bands up to 63 nm.

Application of time-dependent density functional theory and optical spectroscopy toward the rational design of novel 3,4,5-triaryl-1-R-1,2-diphospholes.

Twenty 3,4,5-triaryl-1-R-1,2-diphospholes were studied within the framework of density functional theory (DFT) and experimentally by UV/vis spectroscopy to check their suitability for opto-electronic applications. Time-dependent DFT (TD-DFT) calculations employing the PBE0 hybrid density functional combined with moderately sized def-TZVP basis set were shown to excellently reproduce the experimental absorption spectra of various 1,2-diphospholes. Frontier molecular orbital analysis reveals that HOMO and LUMO are mainly localized on the diphosphole ring and, to some extent, on the aryl moieties.

Is there a simple way to reliable simulations of infrared spectra of organic compounds?

To assess the ability of the quantum-chemical computations to reproduce the experimental relative intensities in the infrared (IR) spectra of both the gas- and condensed-phase systems, the hybrid DFT functional B3LYP has been applied to simulation of IR spectra for species containing from three to twelve first- or second-row atoms, both in the gas phase and in CCl4 solutions. The results demonstrate that B3LYP, combined with the highly compact double-ζ basis set 6-31+G* and "scaled quantum mechanics" techniques, offers excellent quantitative performance in the calculations of relative IR intensities and frequencies (ν ≤ 2200 cm(-1)) for the bands of vibrations of medium-size isolated molecules, whereas it produces unsatisfactory results for the solutions of the same species. Neither larger basis sets nor implicit treatment of the media effects improve the agreement of the simulated spectra with the condensed-phase experiment.