Interplay of thermochemistry and Structural Chemistry, the journal (volume 23, 2012, issues 1–3) and the discipline

In the current review of the journal Structural Chemistry, the contents of the issues 1–3 for the calendar year 2012 are related to thermochemistry. A brief thermochemical commentary is added to the summary of each article.     

Biphenyl-type sensing system in proton-rich environment by fluorescence and quantum-chemical calculations

Biphenyl derivative N-allyl-N′-(4′-nitro[1,1′-biphenyl]-4-yl)thiourea (BP1) was synthesized as a functional fluorescent sensor for protons and their photophysical properties were studied. The influence of environment protonation on photophysical properties of the biphenyls in solutions was investigated using UV absorption, steady-state and time-resolved fluorescence spectroscopy. Semi-empirical and DFT calculations and optimization of the molecular structure of the biphenyl derivatives in vacuum, in polar solvents and in a proton-rich environment were conducted using the HyperChem, Amsol and Gaussian3 software package. Fluorescence quenching with addition of acidic acid was observed and the Stern-Volmer quenching rate constant was about 3.0×10⁹ M⁻¹ s⁻¹. Intermolecular hydrogen bonds formations by the protons with the sulphur being substituted to the biphenyls generate charge movement and strong increase (×5) of the dipole moment of the fluorophore.     

Abatement of waste-water biorefractory organics via electro-oxidative treatment

The electrochemical oxidation of coumaric acid, a biorefractory compound present in several industrial waste waters, has been investigated by use of Pt-Ti anodes and at electrolyte concentration (0.02 N NaCl or Na2SO4) low enough to allow direct dischargeability of the waste water into superficial water basins according to the Italian law (DL 152/11-5-99). Particularly, the role of the electrolyte over the conversion rate has been assessed. The obtained results show that the oxidation process should take place both at the electrode surface and in the bulk of the solution, via electrochemically-generated oxidising species (H2O2, persulfates, Cl2, NaClO). The faster coumaric acid abatement rates were found with chloride based electrolytes, which, however, lead to the formation of non-biodegradable small-molecular-weight chlorinated hydrocarbons.     

Bis­(tetra­methyl­ammonium) hexa­molyb­date hydrate, [(CH3)4N]2[Mo6O19]·H2O

The crystal and molecular structure of the title compound, (C₄H₁₂N)₂[Mo₆O₁₉]·H₂O, has been determined from X‐ray diffraction data. The poly­oxo­anion [Mo₆O₁₉]^2? is built up from six distorted MoO₆ octa­hedra sharing common edges and one common vertex at the central O atom, and has crystallographic m3m (O_h) symmetry. The cation has crystallographic 3m symmetry.     

Simultaneous LC Analysis of Food Dyes in Soft Drinks

Liquid chromatography with diode-array detection has been used for simultaneous analysis of eight water-soluble synthetic colorants (E102, E104, E110, E122, E124, E129, E131, and E133) in non-alcoholic beverages. The colors were separated in 15 min on a C₁₈ reversed-phase column with a linear mobile phase gradient prepared from tetrabutylammonium hydrogen sulfate, methanol, and deionized water. The analytical characteristics of the separation were evaluated. Good linearity (r ² = 0.9988–0.9999), adequate limits of quantification, and high recovery (from 96.3 to 98.5%) were achieved. The method was used for analysis of 57 samples of soft drinks. The experimental results showed the colorants were present in 34 of the samples, and confirmed the method is sensitive, rapid, precise, and suitable for routine analysis of synthetic organic dyes.

     

Macromolecular nature of nanosheets of quasi‐TiO2 from (tetra‐isopropyl)orthotitanate modified by methacrylic acid

In this paper we concentrate on the general behavior of oxotitanium hydrosol, which was earlier developed by us as a precursor of the TiO₂ nanoparticles and nanocomposite. The oxotitanium hydrosol was synthesized by the chemical decomposition of a molecular complex of the methacrylic acid/(tetra‐isopropyl)orthotitanate (MAA/TIPT) by means of the hydrogen peroxide. The raw product chemical decomposition of MAA/TIPT is the colloidal suspension of the oxotitanium compound in the water. The oxotitanium compound was separated from hydrosol and identified on the basis of X‐ray and Raman spectroscopy investigations. The status of water in the hydrosol was also investigated by the Raman spectroscopy. The photophysical behaviors of the oxotitanium hydrosol on the basis of the light absorption and photoluminescence (PL) investigations are presented. The light absorption (260 nm) and PL emission (313 nm) allow us to identify the inorganic phase of hydrosol as nanosheets' crystallites of quasi‐TiO₂. Macromolecular nature of nanosheets of quasi‐TiO₂ was revealed only for a higher concentration solution of nanosheets' crystallites of quasi‐TiO₂ at the hydrosol. A macromolecular nature of nanosheets of quasi‐TiO₂ by the red shift of absorption edge and PL wavelength with increase in the concentration of the oxotitanium hydrosol as well as the formation of hydrogels and birefringence developed under an influence of mechanical shearing is evidenced. Copyright © 2009 John Wiley & Sons, Ltd.     

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     

Comparative analysis of CE‐SSCP to standard RFLP‐CE‐FLA method in quantification of known viral variants within an RNA virus quasispecies

RNA viruses display the highest replication error rate in our biosphere, leading to highly diverse viral populations termed quasispecies. The gold standard method for detection and quantification of variants in a quasispecies is cloning and sequencing, but it is expensive, laborious and time consuming. Therefore, other mutation detection approaches, including SSCP, are often used. In this study, we demonstrate development and the usage of a CE‐SSCP method for quantification of two nearly identical viral variants in heterogenic population of a mumps virus strain and its comparison to RFLP‐CE‐fragment length analysis (RFLP‐CE‐FLA). Analyzed PCR fragments were of the same size (245 bp) with one difference in their nucleotide sequence. The limit of detection of both methods was at 5% of the minor variant. When PCR amplicons of the two variants were pooled, methods' results were very similar. On the contrary, the quantification results of samples in which variants were mixed prior to PCR showed substantial difference between the two methods. Our results indicate that although both methods can be used for detection and monitoring of a specific mutation within a viral population, caution should be taken when quantitative analysis of complex samples is based solely on results of one method.     

A Non‐Heme Iron Photocatalyst for Light‐Driven Aerobic Oxidation of Methanol

Non‐heme (L)Fe^III and (L)Fe^III‐O‐Fe^III(L) complexes (L=1,1‐di(pyridin‐2‐yl)‐N,N‐bis(pyridin‐2‐ylmethyl)ethan‐1‐amine) underwent reduction under irradiation to the Fe^II state with concomitant oxidation of methanol to methanal, without the need for a secondary photosensitizer. Spectroscopic and DFT studies support a mechanism in which irradiation results in charge‐transfer excitation of a Fe^III?μ‐O?Fe^III complex to generate [(L)Fe^IV=O]²⁺ (observed transiently during irradiation in acetonitrile), and an equivalent of (L)Fe^II. Under aerobic conditions, irradiation accelerates reoxidation from the Fe^II to the Fe^III state with O₂, thus closing the cycle of methanol oxidation to methanal.