Sergey P. Ivanov

Spectroscopic Studies of the Supramolecular Interactions Between Uracil and 5-Hydroxy-6-Methyluracil with Bovine Serum Albumin and its Bilirubin Complex

Using fluorescence and absorption spectroscopy the interaction of bovine serum albumin and its bilirubin complex with uracil and 5-hydroxy-6-methyluracil in phosphate buffer at pH 7.4 was investigated. The parameters of forming intermolecular complexes (binding constants, quenching rate constants, the radius of the quenching sphere and etc.) were determined. The interaction between serum albumin and uracils is carried out by the static quenching of protein fluorescence and has predominantly hydrophobic character. Using synchronous fluorescence spectroscopy the influence of uracil and 5-hydroxy-6-methyluracil on the conformational changes of the protein molecule was studied. Uracils effectively binds to bilirubin-albumin complex compared to free protein, which is caused by the interaction with tetrapyrrolic pigment in macromolecular complex. Molecular docking calculations also being presented.

Porous polymer adsorbents modified with uracil

The possibility of using supramolecular uracil structures as surface modifiers of porous polymer adsorbents is studied. The properties of adsorbent samples obtained are found to depend on the amount of modifier applied and the specific surface of the original polymer. The formation of a net uracil structure, which affects thermodynamic adsorption functions of organic molecules, requires a higher surface concentration of the modifier than in the case of other supramolecular structures.

Properties of the surface of a porous polymer modified with 5-fluorouracil, according to data of gas chromatography

The effect or modification with 5-fluorouracil on the sorption activity of porous polymeric adsorbent is studied. It is demonstrated that the supramolecular structure formed on the surface is able to addition-ally contribute to the values of the specific retention volumes. It is found that the structure of 5-fluorouracil is capable of size effects corresponding to a molecular window of approximately 7–8 Å. It is concluded that surface polarity diminishes after modification, due to the shielding effect of four fluorine atoms present in the cavity.

Erratum to: “Quantum-Chemical Calculations of the Relative Stability of the Keto-Enol Tautomers of 5-Chlorouracyl”

Relative energies (by MP4(SQTQ)/def2-TZVPP) for 13 tautomeric conformers of 5-chlorouracyl in the gas phase and in solution with consideration of nonspecific solvation in water are calculated. The geometrical parameters of the calculated conformers are analyzed. A stability series of tautomers with respect to the diketo form is obtained. It is shown that nonspecific solvation leads to changes in the stability series.

Aza-Michael reaction of 12-N-carboxamide of (–)-cytisine under high pressure conditions

The first example of aza-Michael reaction of 12-N-carboxamide of quinolizidine alkaloid (–)-cytisine with α,β-unsaturated ketones, dimethyl acetylenedicarboxylate and β-nitrostyrene under high pressure condition has been described. It has been shown that the [4+2]-cycloaddition takes place in the case with N-phenylmaleimide.

Theoretical Models for Quantitative Description of the Acid-Base Equilibria of the 5,6-Substituted Uracils

The acidities of 18 5,6-substituted uracils have been numerically estimated as pKa values in terms of three theoretical models. The first scheme includes the calculation of the gas-phase acidity of uracil with the G3MP2B3 method and taking into account the solvent effect using the polarizable continuum approximation PCM(SMD)-TPSS/aug-cc-pVTZ. The second model is one step and implies calculation of the free Gibbs energies of the hydrate complex of uracil (and its anion) with 5 water molecules by the TPSS/aug-cc-pVTZ method. This model accounts for the solvent effect corresponding to both specific and nonspecific solvation. The third scheme required high time and computational resources and includes the strong features of the two previous schemes. Here, the theoretical estimation of pKa is performed by the CBS-QB3 composite method. As in the second approach, both specific (as pentahydrate) and nonspecific solvent effects are determined. We have analyzed the advantages and model restrictions of the considered schemes for the pKa calculations. All models have systematic errors, which have been corrected with the linear empirical regression relations. In the presented model, the absolute mean deviations of the pKa values of uracils dissociating via the N1-H bonds diminish to 0.25, 0.28, and 0.23 pKa units (respectively, for I, II, and III models), which corresponds to ∼0.3 kcal/mol on the energy scale. The applicability of our computational schemes to uracils dissociating via N3-H, O-H (orotic acids) and C-H bonds is discussed.

Analysis of binding ability of two tetramethylpyridylporphyrins to albumin and its complex with bilirubin

An interaction between 5,10,15,20-tetrakis-(N-methyl-x-pyridyl)porphyrins, x=2; 4 (TMPyPs) with bovine serum albumin (BSA) and its bilirubin (BR) complex was investigated by UV-Viz and fluorescence spectroscopy under imitated physiological conditions involving molecular docking studies. The parameters of forming intermolecular complexes (binding constants, quenching rate constants, quenching sphere radius etc.) were determined. It was showed that the interaction between proteins and TMPyPs occurs via static quenching of protein fluorescence and has predominantly hydrophobic and electrostatic character. It was revealed that obtained complexes are relatively stable, but in the case of TMPyP4 binding with proteins occurs better than TMPyP2. Nevertheless, both TMPyPs have better binding ability with free protein compared to BRBSA at the same time. The influence of TMPyPs on the conformational changes in protein molecules was studied using synchronous fluorescence spectroscopy. It was found that there is no competition of BR with TMPyPs for binging sites on protein molecule and BR displacement does not occur. Molecular docking calculations have showed that TMPyPs can bind with albumin via tryptophan residue in the hydrophilic binding site of protein molecule but it is not one possible interaction way.

Cyclopentene-fused [C60]-fullerenes: synthesis and electrochemical properties

New cyclopentene-fused [C60]-fullerene derivatives containing terpene moieties have been synthesized by [3 + 2]-addition to fullerene C60. All obtained products were fully characterized by 1H- and 13C-NMR, IR, and MS. The electrochemical properties have been studied by cyclic voltammograms (CV), combined with absorption spectra, which are consistent with those obtained from density functional theory (DFT) calculations. It was found that all fulleropyrrolidines showed very similar absorption spectra, orbital energies, in which electron densities in both the LUMO and HOMO are mainly located on the fullerene cage, suggesting that C60 act as the acceptor. All the compounds exhibited good thermal stability. All determined characteristics of fullerene conjugates were compared to [6,6]-phenyl-C61-butyric acid methyl ester ([60]PCBM), a popular fullerene-containing compound.Graphical abstract

Thermodynamics of the Adsorption of Organic Molecules on Graphitized Carbon Black Modified with a Monolayer of 5-Hydroxy-6-methyluracil

Thermodynamic characteristics of the adsorption of alkanes, alcohols, arenes, and esters on graphitized carbon black with a deposited monolayer (0.17%) of 5-hydroxy-6-methyluracil are studied by means of inverse gas chromatography at infinite dilution. It is established that size effects (violation of the additivity of molar changes in internal energy and the entropy of adsorption for pairs of molecules of one homologous series that differ by one methyl group) are observed when organic molecules are adsorbed on the surface of the resulting adsorbent. The size effects are similar to those observed when 1% 5-hydroxy-6-methyluracil is deposited on graphitized carbon black. It is concluded that the observed violation of additivity is associated with cavities in the supramolecular structure.

Molecular complexation of uracil with bovine serum albumin and its complex with bilirubin studied by spectroscopic methods

The interactions of uracil (U) with bovine serum albumin (BSA) and its complex with bilirubin (BR·BSA) in phosphate buffer at pH 7.4 were studied by fluorescence and electronic spectroscopy. The parameters of the resulting intermolecular complexes (binding constants, quenching rate constants, the radius of the quenching sphere-of-action, etc.) were determined. The interaction of BSA with U occurs through a static quenching of protein fluorescence and has a predominantly hydrophobic character. The effect of U on the conformational changes of the protein molecule was analyzed by synchronous fluorescence spectroscopy. Uracil binds to BR·BSA more efficiently than to the free protein due to the interaction of U with the tetrapyrrole pigment incorporated in the macromolecular complex.