Formation of organoxenon dications in the reactions of xenon with dications derived from toluene

The bimolecular reactivity of xenon with C₇H_n²⁺ dications (n=6–8), generated by double ionization of toluene using both electrons and synchrotron radiation, is studied by means of a triple‐quadrupole mass spectrometer. Under these experimental conditions, the formation of the organoxenon dications C₇H₆Xe²⁺ and C₇H₇Xe²⁺ is observed to occur by termolecular collisional stabilization. Detailed experimental and theoretical studies show that the formation of C₇H₆Xe²⁺+H₂ from doubly ionized toluene (C₇H₈²⁺) and xenon occurs as a slightly endothermic, direct substitution of dihydrogen by the rare gas with an expansion to a seven‐membered ring structure as the crucial step. For the most stable isomer of C₇H₆Xe²⁺, an adduct between the cycloheptatrienyldiene dication and xenon, the computed binding energy of 1.36 eV reaches the strength of (weak) covalent bonds. Accordingly, electrophiles derived from carbenes might be particularly promising candidates in the search for new rare‐gas compounds.     

Investigation of multi-layered silicate ceramics using laser ablation optical emission spectrometry,laser ablation inductively coupled plasma mass spectrometry,and electron microprobe analysis

The applicability of laser ablation (LA) inductively coupled plasma (ICP) spectrometry for assessing elemental distributions in layered ceramics was investigated and compared with electron probe microanalysis (EPMA). Ordinary glazed wall tiles were employed as model specimens due to their defined structure and composition. They were used for calibration in the analysis of ancient pottery. A qualitative depth profile was acquired by single-spot laser drilling perpendicular to coatings with a Nd:YAG (1064 nm) laser coupled with an ICP optical emission spectrometer (OES). The lower lateral resolution associated with the laser spot diameter of 1.0 mm led to smoothing of the depth profile due to the averaging of local irregularities. In addition, transverse line scans by ablation across the tile section using an ArF* (193 nm) laser coupled with an ICP mass spectrometer (MS) were performed. LA-ICP-OES depth profiles and LA-ICP-MS transverse scans were validated by EPMA section scans and 2D back-scattered electrons images. The LA-ICP-OES acquisition was less dependent on sample surface and layer irregularities, whereas the transverse line scan over the tile section with the small-spot beam offered insight into the micromorphology of the individual layer. The combined approach revealed the occurrence of individual mineral grains, micro-heterogeneities and the character of interfaces between layers.     

Interaction of hydrated protons with octyl-phenyl-N,N-diisobutylcarbamoylmethyl phosphine oxide (CMPO): NMR and theoretical study

Interaction of octyl-phenyl-N,N-diisobutylcarbamoylmethylphosphine oxide (CMPO, the 'classical' rare metal extraction agent) with fully ionized hydrated protons (HP) was studied in acetonitrile-d(3) using (1)H, (13)C, (31)P NMR, PFG NMR and magnetic relaxation. The experimental results were confronted with high-precision ab initio DFT calculations. Relative chemical shifts of NMR signals of CMPO (0.01 mol/L) under the presence of HP in the molar ratio β = 0-2.0 mol/mol show binding between CMPO and HP. Self-diffusion measurements using (1)H PFG NMR demonstrate that larger complexes with higher content of CMPO are generally formed at β < 0.75. Analyzing the collective dependence of (13)C and (31)P NMR chemical shifts on β by the use of program LETAGROP, we obtained very good fitting for the assumed coexistence of two complexes (CMPO)(2)·HP (C(2)) and CMPO.HP (C(1)). The logarithms of the respective stabilization constants log K(i) were found to be 7.518 (C(2)) and 4.581 (C(1)). The system dynamics was studied by measuring the transverse (1)H NMR relaxation using CPMG sequence with varying delays t(p) between the π pulses in the mixtures with β = 0.4-0.8. The following exchange correlation times were obtained: τ(10) = 2.35 × 10(-5), τ(20) = 0.82 × 10(-4), τ(21) = 0.45 × 10(-3) s. The DFT calculations support the conclusion that the complexes C(1) and C(2) are the main species in the mixtures of CMPO with HP. They also agree with the NMR and FTIR observation that the main site to which H(3) O(+) is bound is the P=O group, whereas the amide group does not form a strong bond with the ion when excess water molecules are present.     

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

A semiempirical quantum mechanical PM6-DH2 method accurately covering the dispersion interaction and H-bonding was used to score fifteen structurally diverse CDK2 inhibitors. The geometries of all the complexes were taken from the X-ray structures and were reoptimised by the PM6-DH2 method in continuum water. The total scoring function was constructed as an estimate of the binding free energy, i.e., as a sum of the interaction enthalpy, interaction entropy and the corrections for the inhibitor desolvation and deformation energies. The applied scoring function contains a clear thermodynamical terms and does not involve any adjustable empirical parameter. The best correlations with the experimental inhibition constants (ln K _i) were found for bare interaction enthalpy (r ² = 0.87) and interaction enthalpy corrected for ligand desolvation and deformation energies (r ² = 0.77); when the entropic term was considered, however, the correlation becomes worse but still acceptable (r ² = 0.52). The resulting correlation based on the PM6-DH2 scoring function is better than previously published function based on various docking/scoring, SAR studies or advanced QM/MM approach, however, the robustness is limited by number of available experimental data used in the correlation. Since a very similar correlation between the experimental and theoretical results was found also for a different system of the HIV-1 protease, the suggested scoring function based on the PM6-DH2 method seems to be applicable in drug design, even if diverse protein–ligand complexes have to be ranked.     

Computational and experimental evidence of through-space NMR spectroscopic J coupling of hydrogen atoms

J coupling in NMR spectroscopy is conventionally associated with covalent bonds. A noncovalent contribution often called through-space coupling (TSC) has been observed for heavy atoms. In this study, the TSC was detected and analyzed for the more common (1)H-(1)H coupling as well. In synthesized model molecules the hydrogen positions could be well controlled. For several coupling constants the through-space mechanism was even found to be the predominant factor. The nature and magnitude of the phenomenon were also analyzed by density functional computations. Calculated carbon- and hydrogen-coupling maps and perturbed electronic densities suggest that the aromatic system strongly participates in the noncovalent contribution. Unlike covalent coupling, which is usually governed by the Fermi contact, TSC is dominated by the diamagnetic term comprising interactions of nuclei with the electron orbital angular momentum. The computations further revealed a strong distance and conformational dependence of TSC. This suggests that the through-space coupling can be explored in molecular structural studies in the same way as the covalent one.     

Secondary processes in atmospheric pressure chemical ionization–ion trap mass spectrometry: a case study of orotic acid

Atmospheric pressure chemical ionization is known for producing unusual artifacts of the ionization process in some cases. In this work, processes occuring in atmospheric pressure chemical ionization/MS of orotic acid that afforded ions accompanying protonated and deprotonated orotic acid molecules in the spectra were studied. Two processes ran in parallel in the ion source: decarboxylation of neutral orotic acid and collision‐induced dissociation of its protonated or deprotonated form. A procedure discerning pre‐ionization decomposition and post‐ionization dissociation by manipulating ion source parameters was proposed. Experiments with isotopically labeled solvents confirmed ion–molecule reactions of the product of collision‐induced dissociation of protonated orotic acid with solvent molecules in the ion source and even under vacuum in the ion trap. Copyright © 2012 John Wiley & Sons, Ltd.     

Electrophoretic and chromatographic evaluation of transgenic barley expressing a bacterial dihydrodipicolinate synthase

Nutritional quality of human and animal foodstuffs is determined by the content of essential amino acids. Barley is the fourth most important cereal of the world and the second most important cereal grown in the Czech Republic. Cereal grains such as barley contain insufficient levels of some essential amino acids, especially lysine. Dihydrodipicolinate synthase is the key enzyme involved in the regulatory step for lysine biosynthesis. Two constructs pBract214::sTPdapA and pBract214::mdapA containing the dapA gene from Escherichia coli coding for the bacterial dihydrodipicolinate synthase were used for transformation of barley. An Agrobacterium-mediated technique was used for transformation of immature embryos of spring barley cv. Golden Promise. Transgenic barley plants of the T0 and T1 generations were evaluated by PCR, real-time PCR, gel electrophoresis, and Western blot. Amino acid content was analyzed by HPLC after HCl hydrolysis. The lysine content in leaves of the T1 generation plant no. 5/5 was 50% higher than in wild-type plants; the lysine content in seeds of T2 generation plant no. 5/16 was 30% higher than in wild-type seeds of spring barley cv. Golden Promise.     

A hint on the correlation between cellulose fibers polymerization degree and their thermal and thermo-oxidative degradation

The degree of polymerization is one of the main parameters reflecting cellulose ageing. Viscometry is a method frequently used for determination of cellulose fibers polymerization degree, however, sample preparation and viscosity measurement are demanding, time consuming and do not provide reproducible results. In this study, the relationship between polymerization degree of cellulose fibers obtained by viscosity measurement and their degradation parameters obtained by thermal analysis were investigated. Differential scanning calorimetry provided values of effective combustion heat and thermogravimetry (TG) was used for the determination of temperatures and associated mass losses during the cellulose degradation. Effective combustion heat did not show any correlation with degree of polymerization of investigated cotton fabrics. In contrast, results from TG suggested several promising nonlinear correlations which could be used as a hint to develop a method useful for quick determination of cotton fabrics polymerization degree. The most promising correlations with cellulose polymerization degree were found for both rates of thermal and thermo-oxidative degradations.