Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations.

The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand-receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug's experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of 'Atoms in Molecules', and their contributions to the total crystal energy or ligand-receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand-receptor complexes (320.1-394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.

Reaction of Picolinamides with Ketones Producing a New Type of Heterocyclic Salts with an Imidazolidin-4-One Ring.

Reactions of picolinamides with 1,3-propanesultone in methanol followed by the treatment with ketones led to a series of previously unknown chemical transformations, yielding first pyridinium salts (2a-f), with a protonated endocyclic nitrogen atom, and then heterocyclic salts (3a-j) containing an imidazolidin-4-one ring. The structures of intermediate and final products were determined by IR and 1H, 13C NMR spectroscopy, and X-ray study. The effects of the ketone and alcohol structures on the product yield were studied by quantum-chemical calculations. The stability of salts 3a-j towards hydrolysis and alcoholysis makes them excellent candidates for the search for new types of biologically active compounds.

Developing a Chemical and Structural Understanding of the Surface Oxide in a Niobium Superconducting Qubit.

Superconducting thin films of niobium have been extensively employed in transmon qubit architectures. Although these architectures have demonstrated improvements in recent years, further improvements in performance through materials engineering will aid in large-scale deployment. Here, we use information retrieved from secondary ion mass spectrometry and electron microscopy to conduct a detailed assessment of the surface oxide that forms in ambient conditions for transmon test qubit devices patterned from a niobium film. We observe that this oxide exhibits a varying stoichiometry with NbO and NbO2 found closer to the niobium film/oxide interface and Nb2O5 found closer to the surface. In terms of structural analysis, we find that the Nb2O5 region is semicrystalline in nature and exhibits randomly oriented grains on the order of 1-3 nm corresponding to monoclinic N-Nb2O5 that are dispersed throughout an amorphous matrix. Using fluctuation electron microscopy, we are able to map the relative crystallinity in the Nb2O5 region with nanometer spatial resolution. Through this correlative method, we observe that the highly disordered regions are more likely to contain oxygen vacancies and exhibit weaker bonds between the niobium and oxygen atoms. Based on these findings, we expect that oxygen vacancies likely serve as a decoherence mechanism in quantum systems.

Stable and reactive diacetyliminoxyl radical in oxidative C-O coupling with ß-dicarbonyl compounds and their complexes.

As a rule, reactive free radicals used in organic synthesis are too labile to be isolated, whereas persistent radicals are inert and find limited synthetic application. In the present study, the unusually stable diacetyliminoxyl radical was presented as a "golden mean" between transient and stable unreactive radicals. It was successfully employed as a reagent for oxidative C-O coupling with ß-dicarbonyl compounds. Using this model radical the catalytic activity of acids, bases and transition metal ions in free-radical coupling was revealed.