Visualization and substructure retrieval tools in the MOGADOC database (molecular gasphase documentation)

Over the years the MOGADOC database, which covers the literature for gas-phase electron diffraction, microwave spectroscopy, and molecular radio astronomy from the inception of each method, has been developed. Recently visualization and substructure retrieval tools have been implemented. New features are described by means of typical database applications.     

Use of imaging plates (IPs) in the gas-phase electron diffraction (GED) experiments on the EG-100 M apparatus. The tetrachloromethane molecule as a test object

The gas-phase electron diffraction (GED) experiment at the Moscow State University was carried out for the first time using imaging plates (IPs). The response of the Fuji BAS-MP IPs calibrated by means of ¹⁴C standard sources was found to be linear in a broad dynamic interval (larger than 10⁴). The GED study of tetrachloromethane was carried out in order to test the applied technique (IP reader FLA7000) and the developed software. The determined structural parameters of the CCl₄ molecule are in excellent agreement with those obtained in experiments with photographic registration.     

Accurate equilibrium structures of fluoro- and chloroderivatives of methane

This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF₄, CClF₃, CCl₂F₂, CCl₃F, CHClF₂, CHCl₂F, CH₂F₂, CH₂ClF, CH₂Cl₂, and CCl₄) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH₂F₂, CH₂Cl₂, CH₂ClF, CHClF₂, and CCl₂F₂, accurate semi-experimental equilibrium (r^SE_e) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration–rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the r^SE_e structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon–halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH₃Li, CF₃CCH, and CF₃CN, are also computed.     

Theoretical Study of Sulfines and Sulfenes. Similarities and Differences in Structure and Reactivity. A New View

Abstract.

Sulfenes and sulfines contrary to usual opinion can not be considered as structure-similar compounds.     

Aqueous photocatalytic oxidation of prednisolone

The research into the aqueous photocatalytic oxidation of the anti-inflammatory drug prednisolone was undertaken with P25 titanium dioxide (Evonik) and visible light-sensitive sol-gel synthesized titania-based photocatalysts containing carbon, sulphur, and iron. Possible prednisolone photocatalytic oxidation reaction pathways were proposed based on a number of oxidation by-products determined in the present study. The prednisolone adsorption properties, effects of initial prednisolone concentration, pH, usual wastewater matrix admixtures, like carbamide and sucrose, were studied. The nontoxicity of doped catalysts towards Tetrahymena thermophila, a ciliate protozoa present in the activated sludge, indicated their lower oxidative ability compared to P25, but also implied their potential application in pre-treatment of toxic hazardous materials under VIS or solar radiation before the biological degradation stage.      

Vanadium‐Catalyzed Solvent‐Free Synthesis of Quaternary α‐Trifluoromethyl Nitriles by Electrophilic Trifluoromethylation

The direct electrophilic trifluoromethylation of silyl ketene imines (SKIs) with hypervalent iodine reagents leads to the formation of quaternary α‐trifluoromethyl nitriles in good yields. This new reaction has been carried out with a variety of substituted SKIs under solvent‐free conditions using a vanadium(IV) catalyst (5 mol %). The corresponding products may be transformed into useful organofluorine building blocks.     

The molecular structure of N-methylsuccinimide studied by gas-phase electron diffraction (GED) and quantum-chemical methods

The molecular structure of N-methylsuccinimide was studied by the GED method at a nozzle temperature of 69–73°C. Anharmonic vibrational corrections to thermal-average r _a bond lengths, Δ(r _a − r _e), were calculated using the quadratic and cubic force constants from B3LYP/6-31G(df, p) calculations. The molecular skeleton was found to be planar within measurement errors. Some structural effects were likely caused by the conjugation of the N atom with two C=O bonds. The equilibrium geometric parameters derived from the experimental data and those from MP2/cc-pVTZ(seg-opt) calculations were in close agreement.     

Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.     

Molecular structure of 1,5-diazabicyclo[3.1.0]hexane as determined by gas electron diffraction and quantum-chemical calculations

The equilibrium molecular structure and conformation of 1,5-diazabicyclo[3.1.0]hexane (DABH) has been studied by the gas-phase electron-diffraction method at 20 degrees C and quantum-chemical calculations. Three possible conformations of DABH were considered: boat, chair, and twist. According to the experimental and theoretical results, DABH exists exclusively as a boat conformation of C s symmetry at the temperature of the experiment. The MP2 calculations predict the stable chair and twist conformations to be 3.8 and 49.5 kcal mol(-1) above the boat form, respectively. The most important semi-experimental geometrical parameters of DABH (r(e), A and angle)e), deg) are (N1-N5) = 1.506(13), (N1-C6) = 1.442(2), (N1-C2) = 1.469(4), (C2-C3) = 1.524(7), (C6-N1-C2) = 114.8(8), (N5-N1-C2) = 107.7(4), (N1-C2-C3) = 106.5(9), and (C2-C3-C4) = 104.0(10). The natural bond orbital (NBO) analysis has shown that the most important stabilization factor in the boat conformation is the n(N) --> sigma*(C-C) anomeric effect. The geometry calculations and NBO analysis have been performed also for the bicyclohexane molecule.