Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Laser Ablation Molecular Isotopic Spectrometry: Parameter influence on boron isotope measurements

Laser Ablation Molecular Isotopic Spectrometry (LAMIS) was recently reported for optical isotopic analysis of condensed samples in ambient air and at ambient pressure. LAMIS utilizes molecular emissions which exhibit larger isotopic spectral shits than in atomic transitions. For boron monoxide ¹⁰BO and ¹¹BO, the isotopic shifts extend from 114 cm⁻¹ (0.74 nm) to 145–238 cm⁻¹ (5–8 nm) at the B²Σ⁺ (v = 0) → X²Σ⁺ (v = 2) and A²Π_i (v = 0) → X²Σ⁺ (v = 3) transitions, respectively. These molecular isotopic shifts are over two orders of magnitude larger than the maximum isotopic shift of approximately 0.6 cm⁻¹ in atomic boron. This paper describes how boron isotope abundance can be quantitatively determined using LAMIS and how atomic, ionic, and molecular optical emission develops in a plasma emanating from laser ablation of solid samples with various boron isotopic composition. We demonstrate that requirements for spectral resolution of the measurement system can be significantly relaxed when the isotopic abundance ratio is determined using chemometric analysis of spectra. Sensitivity can be improved by using a second slightly delayed laser pulse arriving into an expanding plume created by the first ablation pulse.     

Study of the vibrational spectra of SO2, H2O and D2O using the U(4) algebraic model

Using the U(4) algebraic model, in this work we report a study of the vibrational spectra of SO₂, H₂0¹⁸ and D₂O¹⁶. The inclusion of intermode couplings in algebraic models has been stated to give a deep insight into detailed spectroscopy for these bent XY₂ molecules. Improved set of algebraic parameters has been reported to provide improved RMS deviations for these molecules.     

Raman spectroscopic characteristics of octa-substituted bis(phthalocyaninato) rare earth complexes peripherally substituted with (4-methoxy)phenoxy derivatives

The Raman spectroscopic data in the range 500-1800 cm⁻¹ for a series of 15 rare earth double-deckers with tervalent rare earths M^III[Pc(MeOPhO)₈]₂ (M = Y, La, …, Lu, except Ce, Pr and Pm), reduced state HPr[Pc(MeOPhO)₈]₂ and intermediate-valent cerium Ce[Pc(MeOPhO)₈]₂ have been collected using laser excitation source emitting at 632.8 nm. With excitation at 632.8 nm, which is in close resonance with the main Q absorption band of the phthalocyanine ligand, typical Raman marker bands of the monoanion radical [Pc(MeOPhO)₈]⁻ were observed at 1500-1528 cm⁻¹ as very strong bands resulting from the coupling of pyrrole CC and aza CN stretchings. For Ce[Pc(MeOPhO)₈]₂ and HPr[Pc(MeOPhO)₈]₂, a very strong band at 1499 cm⁻¹ with contributions from both pyrrole CC and aza CN stretchings and also isoindole stretching was the marker Raman band of [Pc(MeOPhO)₈]²⁻. In addition, the influence of ionic radius of the rare earth metal and substituent species on the Raman scatting characteristics of sandwich-type compounds has also been tentatively studied.     

Solute-solvent interactions in formamide and zinc chloride solutions: An investigation by Raman spectroscopy

Raman experiments of formamide and zinc chloride solutions in a wide concentration range (0.1-5.0 mol kg⁻¹) have been carried out. The spectral changes were interpreted on three different ways: (i) the rupture of the H-bonds of FA was evidenced by the trend observed in the ν_CO, δ_HNH and restricted (translation or libration) modes; (ii) the appearance of a new band in the ν_CN region (∼1338 cm⁻¹) was assigned to FA coordinated to Zn (II) through nitrogen atom; (iii) the electronic delocalization in the FA structure upon complexation provided the appearance of new features in the δ_CH and ν_CH regions. The quantitative treatment performed at the ν_CN region of FA allowed the determination of an average number of 3 FA molecules per Zn (II) in the first solvation shell. This value is supported by the appearance of features assigned to ZnCl⁺ and ZnCl₂ entities that also occupy vertices of the tetrahedron at higher salt concentrations. The present study may be useful for a better understanding on electrochemical processes employed in the production of dendritic zinc films as well as FA hydrolysis catalyzed by this metal.     

Comment on the assignments of some vibrational bands of oxalyl fluoride

In view of existing contradictory assignments of the symmetrical stretching vibrations associated with the formal C-C and C-F bonds of trans/cis oxalyl fluoride, an additional theoretical analysis of the corresponding calculated wavenumbers was preformed on trans-C₂O₂F₂ and cis-C₂O₂F₂ based on previously calculated ab initio scaled force fields at the HF/6-31G computational level and new force fields calculated at the MP2/aug-cc-pVTZ level. This novel analysis included computational data from the isotopic shifts brought about by incorporating ¹³C and ¹⁴C atoms into the structure. A detailed examination of the calculated wavenumbers made it possible to validate the assignments of the ν₂ and ν₃ wavenumbers in the trans-C₂O₂F₂ and cis-C₂O₂F₂ molecules as the formal C-C bond stretching and the formal C-F bond symmetrical stretching vibrations, respectively.     

A novel biological strategy for morphology control of PbWO4 crystals in tomato extract

PbWO(4) crystals were readily synthesized by reacting lead oxide (PbO(2)) with sodium tungstate (Na(2)WO(4)·2H(2)O) at room temperature in the presence of tomato extract. Biomolecules such as vitamins, proteins in the extract played both the roles of reductant and template. The size and morphology of the PbWO(4) crystals could be controlled by adjusting the concentration of the reactants. When the concentration ratio of PbO(2) and Na(2)WO(4) was increased, the morphologies of the products varied from spherical to fusiform. Room-temperature fluorescence spectra indicated the products had a slight blue shift compared to the solid structure, which may be due to the structure defects in the crystals. The possible mechanism of PbWO(4) crystal growth in tomato extract was discussed.     

Novel tricarbonyl rhenium complexes of 5,8-quinolinedione derivatives - Synthesis, spectroscopic characterisation, X-ray structure and DFT calculations

The molecular structure of 7-acetamido-2-methyl-quinoline-5,8-dione has been determined and the reactivity of 7-acetamido-2-methyl-quinoline-5,8-dione (1) and 6-acetamido-2-methyl-quinoline-5,8-dione (2) towards Re(CO)₅Cl has been examined. Two novel tricarbonyl rhenium complexes, fac-[Re(CO)₃(7-acetamido-2-methyl-quinoline-5,8-dione)Cl]·CHCl₃ (3·CHCl₃) and fac-[Re(CO)₃(6-acetamido-2-methyl-quinoline-5,8-dione)Cl]₂·CHCl₃ (4·CHCl₃), have been synthesized and characterized spectroscopically and structurally. The electronic spectrum of 3 was investigated at the TDDFT level employing B3LYP functional in combination with LANL2DZ.     

Syntheses,Crystal Structures and Property Studies on Cu（Ⅱ） and Co（Ⅱ） Complexes with 1,8-Naphthalimid Schiff Base

The ligand of N-(2-hydroxybenzylideneamino)-1,8-naphthalimide (HL) and its metal complexes of CuL2 (1) and CoL2 (2) have been synthesized. Elemental analysis, IR and X-ray single-crystal diffraction characterizations for 1 and 2 have been carried out. In the complexes of 1 and 2, the central metallic ions of Cu2+ and Co2+ coordinate with two deprotonated ligands of L-, respectively and adopt distorted square planar geometries. The thermal analysis result shows that the two complexes undergo two similar decomposition processes because of their similar geometric configurations. For the two complexes, fluorescence spectra measurements indicate that complex CoL2 emits stronger blue fluorescence than HL and the complex CuL2 does not emit fluorescence at all.     

Glass transition of hydrated wheat gliadin powders

Modulated-temperature differential scanning calorimetric and dynamic mechanical analyses and dielectric spectroscopy were used to investigate the glass transition of hydrated wheat gliadin powders with moisture absorption ranged from 2.30 db%to 18.21 db%.Glass transition temperature(I_g)of dry wheat gliadin was estimated according to the Gordon Taylor equation.Structural heterogeneity at high degrees of hydration was revealed in dielectric temperature and frequency spectra.The activation energies(E_a)of the two relaxations were calculated from Arrhenius equation.