QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Thermal desorption/gas chromatography/mass spectrometry approach for characterization of the volatile fraction from amber specimens: A possibility of tracking geological origins

Research on the chemical composition of fossil resins has evolved during the last decades as a multidisciplinary field and is strongly oriented toward the correlation with their geological and botanical origin. Various extraction procedures and chromatographic techniques have been used together for identifying the volatile compounds contained in the fossil resin matrix. Hyphenation between thermal desorption (TD), gas chromatography (GC) and mass spectrometry detection (MS) has been chosen to investigate the volatile compounds fraction from ambers with a focus on Romanite (Romanian amber) and Baltic amber species. A data analysis procedure was developed for the main purpose of fingerprinting ambers based on the MS identity of the peaks generated by the volatile fraction, together with their relative percentual area within the chromatogram. Chromatographic data analysis was based entirely on Automated Mass Spectral Deconvolution & Identification System (AMDIS) software to produce deconvoluted mass spectra which were used to build-up a mixed mass spectra and relative retention scale library. Multivariate data analysis was further applied on AMDIS results with successful discrimination between Romanite and Baltic ambers. A special trial was conducted to generate pyrolysis “like” macromolecular structure breakdown to volatile compounds by gamma irradiation with a high absorbed dose of 500 kGy. Contrary to our expectations the volatile fraction fingerprints were not modified after irradiation experiments. A complementary non-destructive new approach by ESR spectroscopy was also proposed for discriminating between Romanite and Baltic ambers.     

The Landau–Hall problem on canal surfaces

In this note we study the Landau–Hall problem on a generalized canal surface and classify all uniform magnetic trajectories of a charged particle moving on such a surface under the action of a uniform magnetic field.     

A Variational Characterization of the Effective Yield Set for Ionic Polycrystals

The effective yield set of ionic polycrystals is characterized by means of variational principles in $L^\infty $ associated to supremal functionals acting on matrix-valued divergence-free fields.     

Thermal stability of piroxicam

The application of thermal method is of great importance regarding the pharmaceutical problems such as the control of raw materials, the determination of purity, the qualitative and quantitative analysis of drug formulation, tests of thermal stability and compatibility and the determination of kinetic parameters etc. The purpose of a kinetic investigation is to calculate the kinetic parameters and the determination of the kinetic model for the studied process. The results are further used to predict the system’s behaviour in various circumstances. A kinetic study regarding the piroxicam—active substance’s thermal decomposition was performed under isothermal conditions and nitrogen atmosphere, for the temperature steps: 200, 205, 210, 215 and 220 °C. The TG/DTG data were processed by three differential methods: isothermal—isoconversional, Friedman’s isothermal isoconversional and isothermal model-fitting. The obtained results are in good accord between them, as well as with those obtained under non-isothermal conditions from a previous work and confirm the necessity of the kinetic parameters determining in different thermal conditions, by the adequate calculation methods.     

Stereocontrolled synthesis of enantiopure anticancer cyclopentenone prostaglandin analogues: (−)- and (+)-TEI-9826

The synthesis of both enantiomers of TEI-9826 has been accomplished in seven steps with an overall yield of 44% starting from diastereomeric camphor protected 3-[(dimethoxyphosphoryl)methyl]-4,5-dihydroxycyclopent-2-enones. The key steps include a fully diastereoselective hydrogenation of the endocyclic carbon–carbon double bond in the cyclopentenone ring controlled with a chiral diol moiety and the conversion of the latter into a new transposed olefinic bond.     

Self-collimation of light in disordered left-handed metamaterials

Transmission of light through a left-handed slab is studied theoretically. The slab consists of randomly distributed electric and magnetic scatterers. In a practical realization these could be wire and split ring resonators forming a disordered metamaterial. Enhanced transmission close to the middle of the slab is demonstrated. It is explained canalization of source image through self-collimated channels. Existence of self-collimated channels localized on the surface of the slab is demonstrated and a possibility of sub-wavelength imaging by such a system is discussed.     

The Cubical Cohomology Ring: An Algorithmic Approach

A cohomology ring algorithm in a dimension-independent framework of combinatorial cubical complexes is developed with the aim of applying it to the topological analysis of high-dimensional data. This approach is convenient in the cup-product computation and motivated, among others, by interpreting pixels or voxels in digital images as cubes. The S-complex theory and so called co-reductions are adopted to build a cohomology ring algorithm speeding up the algebraic computations.     

1,3-Dipolar cycloadditions of new 2,5-bifunctionalized five-membered cyclic nitrones

A new family of five-membered cyclic nitrones bearing functional groups at positions 2 and 5 were tested in 1,3-cycloadditions with various dipolarophiles. These reactions gave the corresponding cycloadducts as single diastereomers in high yields. The reaction scope was examined, 23 compounds were isolated and fully characterized. The comparison of the reactivity was carried out by a study of reaction conversions while different nitrones or dipolarophiles were used. In addition, the exceptional reactivity of nitrone bearing benzylamino group in position 2 was studied. The formation of the nitrone complex and evaluation of its reactivity in 1,3-DC is presented.