Water-soluble organic luminophores based on 3-(1,3-benzothiazol-2-yl)-4-hydroxybenzenesulfonic acid were studied both experimentally and by density functional theory for the first time. Because of peculiarities in chemical structure, one of them has a large Stokes shift, which results from excited state intramolecular proton transfer.

Aptamers, short oligonucleotides, are capable of high-affinity binding to targets due to their unique structure. Shortening the aptamer while maintaining the active site will increase the affinity and reduce the cost of synthesis. Using the example of the aptamer LC-224, a method for rational optimization of its length and verification of the validity of the developed approach is tested. The use of computer modeling and small-angle X‑ray scattering shows the possibility of optimizing the aptamer structure by removing nucleotides that do not participate in binding to the target. It is shown that truncation of the aptamer does not reduce the affinity and specificity of the DNA aptamer. Thus, theoretical and experimental studies demonstrate successful experience in optimizing the structure of a DNA aptamer by shortening it without compromising its affinity and specificity for its target.

Gadolinium (Gd)-containing fullerenols are perspective agents for magnetic resonance imaging and cancer research. They combine the unique paramagnetic properties of Gd with solubility in water, low toxicity and antiradical activity of fullerenols. We compared the bioeffects of two Gd-containing fullerenols with a different number of oxygen groups—20 and 42: Gd@C82O20H14 and Gd@C82O42H32. The bioluminescent bacteria-based assay was applied to monitor the toxicity of fullerenols, bioluminescence was applied as a signal physiological parameter, and bacterial enzyme-based assay was used to evaluate the fullerenol effects on enzymatic intracellular processes. Chemiluminescence luminol assay was applied to monitor the content of reactive oxygen species (ROS) in bacterial and enzymatic media. It was shown that Gd@C82O42H32 and Gd@C82O20H14 inhibited bacterial bioluminescence at >10−1 and >10−2 gL−1, respectively, revealing a lower toxicity of Gd@C82O42H32. Low-concentration (10−3–10−1 gL−1) bacterial bioluminescence activation by Gd@C82O42H32 was observed, while this activation was not found under exposure to Gd@C82O20H14. Additional carboxyl groups in the structure of Gd@C82O42H32 were determined by infrared spectroscopy and confirmed by quantum chemical calculations. The groups were supposed to endow Gd@C82O42H32 with higher penetration ability through the cellular membrane, activation ability, lower toxicity, balancing of the ROS content in the bacterial suspensions, and lower aggregation in aqueous media.

The photoluminescence and UV-Vis absorption spectra of copolyamides containing 1,9-anthrazoline with paraand meta-[(substituted carbonyl)amino]phenyl-1-ene moieties in a polymer backbone were studied by a combination of experimental and theoretical approaches. The investigation was accomplished through timedependent density functional theory electronic structure calculations of small-molecule models mimicking a polymer chain. Theoretical absorption and luminescence spectra of ten atomistic models were compared with corresponding experimental data, and the optical properties of two new luminescent molecules with bromine auxochrome were predicted. An analysis of the optical properties demonstrate an identical effect of the type and position of a substituent on the spectra for para- and meta-[(substituted carbonyl)amino]phenyl-1-ene moieties. It was found that the absorption and luminescence spectra of theoretical para-models demonstrate red shifts relative to the corresponding meta-ones. The same phenomenon was observed in experimental spectra of lowmolecular-mass compounds and corresponding copolyamides in solution and bulk. Unique optical properties allow anthrazoline-based polymer compounds to be used in numerous advanced optoelectronic applications with desired optical and electronic characteristics.

Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy. This involved characterizing the previously selected aptamer for vaccinia virus (VACV), evaluating the aggregation and molecular interaction of the optimized aptamers with the recombinant oncolytic virus VV-GMCSF-Lact, and estimating their immunoshielding properties in the presence of human blood serum. We chose one optimized aptamer, NV14t_56, with the highest affinity to the virus from the pool of several truncated aptamers and built its 3D model. The NV14t_56 remained stable in human blood serum for 1 h and bound to VV-GMCSF-Lact in the micromolar range (Kd ≈ 0.35 μM). Based on dynamic light scattering data, it has been demonstrated that aptamers surround viral particles and inhibit aggregate formation. In the presence of serum, the hydrodynamic diameter (by intensity) of the aptamer–virus complex did not change. Microscale thermophoresis (MST) experiments showed that NV14t_56 binds with virus (EC50 = 1.487 × 109 PFU/mL). The analysis of the amplitudes of MST curves reveals that the components of the serum bind to the aptamer–virus complex without disrupting it. In vitro experiments demonstrated the efficacy of VV-GMCSF-Lact in conjunction with the aptamer when exposed to human blood serum in the absence of neutralizing antibodies (Nabs). Thus, NV14t_56 has the ability to inhibit virus aggregation, allowing VV-GMCSF-Lact to maintain its effectiveness throughout the storage period and subsequent use. When employing aptamers as protective agents for oncolytic viruses, the presence of neutralizing antibodies should be taken into account.

Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering "character".

The functionalization of copolyfluorenes containing dicyanophenanthrene units by closo-decaborate anion is described. Target copolyfluorenes were analyzed using SEM, UV-vis, luminescence, NMR, and Fourier-transform infrared (FTIR) spectroscopy. The effect of complexation with the closo-decaborate anion on the photophysical properties was studied both experimentally and theoretically. The PL data indicate an efficient charge transfer from fluorene to the dicyanophenanthrene units coordinated to the closo-decaborate. The coordination of closo-decaborate clusters to the nitrile groups of copolyfluorenes provides an important route to new materials for sensors and light-emitting devices while, at the same time, serving as a platform for further study of the nature of boron clusters.

Gd@C82OxHy endohedral complexes for advanced biomedical applications (computer tomography, cancer treatment, etc.) were synthesized using high-frequency arc plasma discharge through a mixture of graphite and Gd2O3 oxide. The Gd@C82 endohedral complex was isolated by high-efficiency liquid chromatography and consequently oxidized with the formation of a family of Gd endohedral fullerenols with gross formula Gd@C82O8(OH)20. Fourier-transformed infrared (FTIR) spectroscopy was used to study the structure and spectroscopic properties of the complexes in combination with the DFTB3 electronic structure calculations and infrared spectra simulations. It was shown that the main IR spectral features are formed by a fullerenole C82 cage that allows one to consider the force constants at the DFTB3 level of theory without consideration of gadolinium endohedral ions inside the carbon cage. Based on the comparison of experimental FTIR and theoretical DFTB3 IR spectra, it was found that oxidation of the C82 cage causes the formation of Gd@C82O28H20, with a breakdown of the integrity of the parent C82 cage with the formation of pores between neighboring carbonyl and carboxyl groups. The Gd@C82O6(OOH)2(OH)18 endohedral complex with epoxy, carbonyl and carboxyl groups was considered the most reliable fullerenole structural model.

Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460–470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein–substrate complex was optimized using a linear scaling quantum–mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified.

Recently, there has been an increased interest in natural polysaccharides, in particular, chitosan, which are widely used in medicine and industry. Chitosan labeled with fluorescein dyes acquires additional optical properties that can be used in sensing and delivery systems. Mechanism of binding of a polymer to a label largely determines the field of its possible applications. The quantum chemical calculation using the B3LYP/aug-cc-pVDZ theory level has been made in order to contribute to the understanding of intermolecular interactions. The geometry of fluorescein, eosin Y, and erythrosin B in the dianionic, monoanionic, and neutral quinoid forms interacting with chitosan has been optimized and the absorption spectra have been calculated using the time-dependent density functional theory taking into account the solvent. The comparison of the calculated absorption spectra with the experimental data has shown a major role of the electrostatic mechanism in binding of anionic dyes to the protonated chitosan groups.

Multistage dissociation of fluoroscein dyes, widely used in biological labeling, yields a variety of ionic and tautomeric forms in a wide range of pH values. In contrast to well-studied absorption spectra, the emission spectra are not quite readily interpreted due to their strong overlapping and proton transfer in electronically excited states. The least studied are the fluorescent properties of eosin and erythrosin dyes containing heavy atoms (Br, I), in which the characteristics of the dianionic form only are reliably determined. In the framework of the density functional theory using the B3LYP-functional including nonequilibrium solvation, the geometries of the series of ionic forms of eosin and erythrosin in the ground and excited states are found, and the electronic spectra are calculated. Based on the identified linear regression of the calculated and experimental data for the earlier resolved electronic spectra, for the first time, the emission spectrum maxima of the monoanionic, neutral quinoid, and cationic forms of the dyes are determined. The spectral peculiarities (Stokes shifts) are discussed in terms of variation of the molecule and ion geometries in the ground and excited states.

Fluorescein and its halogenated derivatives representing a family of homologous dyes with the gradual substitution of halogen atoms for hydrogen ones are widely used in biomedicine as fluorescent probes. This stimulates the intense experimental and theoretical studies of their fluorescent properties in aqueous solutions. However, the theoretical calculations are complicated by the necessity of taking into account the effect of a solvent (water) in the explicit form and the need for effective basic sets. This is especially important for the dyes that contain heavy atoms. In this study, the quantum-chemical investigations of the dianionic form of fluorescein and its Br- and I-substituted derivatives (eosin Y and erythrosin B) have been carried out using the time-dependent density functional theory (B3LYP functional) implemented in the GAMESS software suite. The effect of a solvent has been considered in the framework of the modified Thomas polarizable continuum model. The calculations have been made for vertical (absorption and emission) excitations in the adiabatic approximation and at the nonequilibrium solvation. The results obtained for the nonequilibrium solvation are in excellent agreement with the experimental data for fluorescein and its halogenated derivatives.