Predicting the UV-vis spectra of oxazine dyes

The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines

Oxazine dyes act as reporters of their near environment by the response of their fluorescence spectra. At the same time, their fluorescence spectra exhibit a pronounced vibrational progression. In this work, we computationally investigate the impact of near-environment models consisting of aggregated water as well as betaine molecules on the vibrational profile of fluorescence spectra of different oxazine derivatives. For aggregated betaine and a water molecule located above the plane of the dyes, we observe a distinct modification of the vibrational profile, which is more pronounced than the effect of a continuum description of a solvent environment. Our analysis shows that this effect cannot be explained by a pure change in the electronic structure, but that also vibrational degrees of freedom of the environment can be decisive for the vibrational profile and should, hence, not generally be neglected.

Oligomerization Mechanism of Methylglyoxal Regulated by the Methyl Groups in Reduced Nitrogen Species: Implications for Brown Carbon Formation

Uncertain chemical mechanisms leading to brown carbon (BrC) formation affect the drivers of the radiative effects of aerosols in current climate predictions. Herein, the aqueous-phase reactions of methylglyoxal (MG) and typical reduced nitrogen species (RNSs) are systematically investigated by using combined quantum chemical calculations and laboratory experiments. Imines and diimines are identified from the mixtures of methylamine (MA) and ammonia (AM) with MG, but not from dimethylamine (DA) with the MG mixture under acidic conditions, because deprotonation of DA cationic intermediates is hindered by the amino groups occupied by two methyl groups. It leads to N-heterocycle (NHC) formation in the MG + MA (MGM) and MG + AM (MGA) reaction systems but to N-containing chain oligomer formation in the MG + DA (MGD) reaction system. Distinct product formation is attributed to electrostatic attraction and steric hindrance, which are regulated by the methyl groups of RNSs. The light absorption and adverse effects of NHCs are also strongly related to the methyl groups of RNSs. Our finding reveals that BrC formation is mainly contributed from MG reaction with RNSs with less methyl groups, which have more abundant and broad sources in the urban environments.

Cryogenic fluorescence spectroscopy of oxazine ions isolated in vacuo

Recent developments in fluorescence spectroscopy have made it possible to measure both absorption and dispersed fluorescence spectra of isolated molecular ions at liquid-nitrogen temperatures. Absorption is here obtained from fluorescence-excitation experiments and does not rely on ion dissociation. One large advantage of reduced temperature compared to room-temperature spectroscopy is that spectra are narrow, and they provide information on vibronic features that can better be assigned from theoretical simulations. We report on the intrinsic spectroscopic properties of oxazine dyes cooled to about 100 K. They include six cations (crystal violet, darrow red, oxazine-1, oxazine-4, oxazine-170 and nile blue) and one anion (resorufin). Experiments were done with a home-built setup (LUNA2) where ions are stored, mass-selected, cooled, and photoexcited in a cylindrical ion trap. We find that the Stokes shifts are small (14-50 cm-1), which is ascribed to rigid geometries, that is, there are only small geometrical changes between the electronic ground and excited states. However, both the absorption and the emission spectra of darrow-red cations are broader than those of the other ionic dyes, which is likely associated with a less symmetric electronic structure and more non-zero Franck-Condon factors for the vibrational progressions. In the case of resorufin, the smallest ion under study, vibrational features are assigned based on calculated spectra.

Hypochlorous acid triggered fluorescent probes for in situ imaging of a psoriasis model

Psoriasis is a common skin disease with complex pathogenesis that lacks diagnostic methods. Typically, psoriasis is an inflammation-related disease accompanied by high expression of reactive oxygen species (ROS) in the infected part. However, due to the lack of suitable tools, it is difficult to identify the ROS, especially certain types of ROS (e.g., HOCl) in the psoriasis model. Here, two HOCl-specific fluorescent probes, G1 and G2, were designed and synthesized based on oxazine 1. Both probes could react with HOCl with high selectivity among other ROS under physiological conditions. The selected probe G2 could detect HOCl in HL-60 cells without special stimulation and detect endogenously produced HOCl in the mouse model of arthritis. Thus, G2 was used to identify and image HOCl in situ in the imiquimod induced psoriasis model. The result showed that HOCl was a potential pathological marker of psoriasis.

Photoexcitation of oxazine 170 dye in aqueous solution: TD-DFT study

The vibronic absorption spectra of OX170 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 long-range corrected ωB97XD functional provided the best agreement with the experiment in the positions of the main maximum and the short-wavelength shoulder. 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 OX170 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 was shown that these bonds are strengthened upon OX170 excitation. It was found that explicit assignment of water molecules strongly bound to the dye leads to a redshift of the calculated spectrum by ≈15 nm as a whole, and worsened 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).

Theoretical insights into the structural, photophysical and nonlinear optical properties of phenoxazin-3-one dyes

Here we investigate the structural, photophysical and nonlinear optical (NLO) properties of phenoxazin-3-one dyes, resazurin (Rz) and resorufin (Rf), by performing quantum chemical calculations using the DFT and TDDFT methods.

Luminescence spectroscopy of oxazine dye cations isolated in vacuo

Gas-phase luminescence spectroscopy reveals transition energies of oxazine dye cations with no disturbance from counter ions or solvent molecules.

Acetophenone Mannich bases: study of ionic liquid catalysed synthesis and antioxidative potential of products

Three-component Mannich reaction of acetophenone or 4-iodoacetophenone with a variety of substituted anilines and benzaldehyde, catalysed with diethanolammonium chloroacetate, was performed under mild conditions. Mannich bases (MBs), of which five are new, were obtained in good to excellent yields. All compounds were characterized using elemental analysis, NMR and IR. In addition, detailed experimental and simulated UV-Vis spectral characterization of these compounds is presented here for the first time. In vitro antioxidative potential of synthetized MBs was evaluated using 2,2-diphenyl-1-picryl-hydrazyl radical and density functional theory (DFT) thermodynamical study. It was shown that compounds with anisidine moiety express moderate antioxidative activity. Mechanism of the organocatalysed Mannich reaction was thoroughly inspected by means of DFT. The reaction undergoes the hydrogen bonding-assisted mechanism. Moreover, the proposed rate determining step of the overall reaction is water elimination in the process of iminium ion formation. To the extent of our knowledge, this is the first detailed report on the influence of this type of catalyst on the formation of iminium ion, as a crucial intermediate for the whole reaction.

A DFT investigation of the blue bottle experiment: E∘half-cell analysis of autoxidation catalysed by redox indicators

The blue bottle experiment is a collective term for autoxidation reactions catalysed by redox indicators. The reactions are characterized by their repeatable cycle of colour changes when shaken/left to stand and intricate chemical pattern formation. The blue bottle experiment is studied based on calculated solution-phase half-cell reduction potential of related reactions. Our investigation confirms that the reaction in various versions of the blue bottle experiment published to date is mainly the oxidation of an acyloin to a 1,2-dicarbonyl structure. In the light of the calculations, we also propose new non-acyloin reducing agents for the experiment. These results can help guide future experimental studies on the blue bottle experiment.

Hydroxylated Fluorescent Dyes for Live-Cell Labeling: Synthesis, Spectra and Super-Resolution STED

Hydroxylated rhodamines, carbopyronines, silico‐ and germanorhodamines with absorption maxima in the range of 530–640 nm were prepared and applied in specific labeling of living cells. The direct and high‐yielding entry to germa‐ and silaxanthones tolerates the presence of protected heteroatoms and may be considered for the syntheses of various sila‐ and germafluoresceins, as well as ‐rhodols. Application in stimulated emission depletion (STED) fluorescence microscopy revealed a resolution of 50–75 nm in one‐ and two‐color imaging of vimentin‐HaloTag fused protein and native tubulin. The established structure–property relationships allow for prediction of the spectral properties and the positions of spirolactone/zwitterion equilibria for the new analogues of rhodamines, carbo‐, silico‐, and germanorhodamines using simple additive schemes.

Multiconfigurational and DFT analyses of the electromeric formulation and UV-vis absorption spectra of the superoxide adduct of ferrous superoxide reductase

The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer. In an attempt to clarify the electromeric formulation of this adduct, we report a computational study using a multiconfigurational complete active space self-consistent field (MC-CASSCF) wave function approach as well as modelling the UV-vis absorption spectra with time-dependent density functional theory (TD-DFT). The MC-CASSCF calculations disclose a weak interaction between iron and the dioxygenic ligand and a dominant configuration with an essentially ferrous-superoxo character. The computed UV-vis absorption spectra reveal a marked dependence on the choice of density functional - both in terms of location of bands and in terms of orbital contributors. For the main band in the visible region, besides the recently reported thiolate-to-superoxide charge transfer, a more salient, and less functional-dependent, feature is a thiolate-to-ferric iron charge transfer, consistent with a ferric-peroxo electromer. By contrast, the computed UV-vis spectra of a ferric-hydroperoxo SOR model match distinctly better (and with no qualitative dependence on the DFT methodology) the 600-nm band as due to a mainly thiolate-to-ferric character - supporting the assignment of the SOR "600-nm intermediate" as a S=5/2 ferric-hydroperoxo species.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

Accuracy of color prediction of anthraquinone dyes in methanol solution estimated from first principle quantum chemistry computations

The electronic spectrum of four different anthraquinones (1,2-dihydroxyanthraquinone, 1-aminoanthraquinone, 2-aminoanthraquinone and 1-amino-2-methylanthraquinone) in methanol solution was measured and used as reference data for theoretical color prediction. The visible part of the spectrum was modeled according to TD-DFT framework with a broad range of DFT functionals. The convoluted theoretical spectra were validated against experimental data by a direct color comparison in terms of CIE XYZ and CIE Lab tristimulus model color. It was found, that the 6-31G** basis set provides the most accurate color prediction and there is no need to extend the basis set since it does not improve the prediction of color. Although different functionals were found to give the most accurate color prediction for different anthraquinones, it is possible to apply the same DFT approach for the whole set of analyzed dyes. Especially three functionals seem to be valuable, namely mPW1LYP, B1LYP and PBE0 due to very similar spectra predictions. The major source of discrepancies between theoretical and experimental spectra comes from L values, representing the lightness, and the a parameter, depicting the position on green→magenta axis. Fortunately, the agreement between computed and observed blue→yellow axis (parameter b) is very precise in the case of studied anthraquinone dyes in methanol solution. Despite discussed shortcomings, color prediction from first principle quantum chemistry computations can lead to quite satisfactory results, expressed in terms of color space parameters.

Excited state electric dipole moment of nile blue and brilliant cresyl blue: a comparative study

A solvatochromic study on the photophysical properties of two cationic oxazine dyes (brilliant cresyl blue and nile blue) was carried out. The electronic absorption and emission spectra of the dyes were recorded in various organic solvents with different polarity. The ground and the excited state dipole moments of the dyes were estimated from solvatochromic shift method. The solvent dependent spectral shifts in absorption and fluorescence spectra were analyzed by the Katritzky and Kamlet-Taft multi-parameter scales. This work is characterized by detailed quantitative studies on the nature and extent of solvent-solute interactions.

Nanoporous anodic alumina barcodes: toward smart optical biosensors

Toward a smart optical biosensor based on nanoporous anodic alumina (NAA): by modifying the pore geometry in nanoporous anodic alumina we are able to change the effective medium at will and tune the photoluminescence of NAA. The oscillations in the PL spectrum are converted into exclusive barcodes, which are useful for developing optical biomedical sensors in the UV-Visible region.