Structural and spectroscopic properties of the peroxodiferric intermediate of Ricinus communis soluble Δ9 desaturase

Large-scale quantum and molecular mechanical methods (QM/MM) and QM calculations were carried out on the soluble Δ(9) desaturase (Δ(9)D) to investigate various structural models of the spectroscopically defined peroxodiferric (P) intermediate. This allowed us to formulate a consistent mechanistic picture for the initial stages of the reaction mechanism of Δ(9)D, an important diferrous nonheme iron enzyme that cleaves the C-H bonds in alkane chains resulting in the highly specific insertion of double bonds. The methods (density functional theory (DFT), time-dependent DFT (TD-DFT), QM(DFT)/MM, and TD-DFT with electrostatic embedding) were benchmarked by demonstrating that the known spectroscopic effects and structural perturbation caused by substrate binding to diferrous Δ(9)D can be qualitatively reproduced. We show that structural models whose spectroscopic (absorption, circular dichroism (CD), vibrational and M?ssbauer) characteristics correlate best with experimental data for the P intermediate correspond to the μ-1,2-O(2)(2-) binding mode. Coordination of Glu196 to one of the iron centers (Fe(B)) is demonstrated to be flexible, with the monodentate binding providing better agreement with spectroscopic data, and the bidentate structure being slightly favored energetically (1-10 kJ mol(-1)). Further possible structures, containing an additional proton or water molecule are also evaluated in connection with the possible activation of the P intermediate. Specifically, we suggest that protonation of the peroxide moiety, possibly preceded by water binding in the Fe(A) coordination sphere, could be responsible for the conversion of the P intermediate in Δ(9)D into a form capable of hydrogen abstraction. Finally, results are compared with recent findings on the related ribonucleotide reductase and toluene/methane monooxygenase enzymes.     

Highly efficient thermal cyclization reactions of alkylidene esters in continuous flow to give aromatic/heteroaromatic derivatives

Intramolecular thermal cyclization and benzannulation reactions of the Gould–Jacobs and Conrad–Limpach types were performed in a designed continuous flow reactor system at temperatures in the range of 300–360 °C and under high pressure conditions (100–160 bar) with very short residence times (0.45–4.5 min) in tetrahydrofuran as a low-boiling point solvent. Substituted heteroaromatic compounds including pyridopyrimidinones and hydroxyquinolines were synthesized in moderate to high yields. Application of the reaction conditions also allows the synthesis of naphthol and biphenyl derivatives. The procedure involves an easy work-up and the non-batchwise preparative synthesis method is suitable for automation.     

The s-monotone index selection rules for pivot algorithms of linear programming

In this paper we introduce the concept of s-monotone index selection rule for linear programming problems. We show that several known anti-cycling pivot rules like the minimal index, Last-In–First-Out and the most-often-selected-variable pivot rules are s-monotone index selection rules. Furthermore, we show a possible way to define new s-monotone pivot rules. We prove that several known algorithms like the primal (dual) simplex, MBU-simplex algorithms and criss-cross algorithm with s-monotone pivot rules are finite methods.     

Rate constant for the reaction of CH3C(O)CH2 radical with HBr and its thermochemical implication

The fast flow method with laser induced fluorescence detection of CH₃C(O)CH₂ was employed to obtain the rate constant of k₁ (298 K) = (1.83 ± 0.12 (1σ)) × 10¹⁰ cm³ mol^?1 s^?1 for the reaction CH₃C(O)CH₂ + HBr ? CH₃C(O)CH₃ + Br (1, ?1). The observed reduced reactivity compared with n‐alkyl or alkoxyl radicals can be attributed to the partial resonance stabilization of the acetonyl radical. An application of k₁ in a third law estimation provides Δ_fH(CH₃C(O)CH₂) values of ?24 kJ mol^?1 and ?28 kJ mol^?1 depending on the rate constants available for reaction ( ‐1 ) from the literature. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 38: 32–37, 2006     

Detection of new fumonisin mycotoxins and fumonisin-like compounds by reversed-phase high-performance liquid chromatography/electrospray ionization ion trap mass spectrometry

Fumonisins were produced in a rice culture infected with Fusarium verticillioides. To decrease the possibility of the formation of artifacts, the fumonisins were analyzed by reversed-phase high-performance liquid chromatography with electrospray ionization ion trap tandem mass spectrometry (RP-HPLC/ESI-IT-MS2) immediately after the extraction of the culture material without any sample clean-up. In addition to already known fumonisins, numerous new fumonisin mycotoxins and fumonisin-like compounds were detected. On the basis of the IT-MS2 data, detailed fragmentation pathways including new mechanisms were proposed for the different series of fumonisins. The retention times, the masses of the protonated molecules and of the product ions including the backbones and the characteristic neutral mass losses from the protonated molecules of the new compounds suggested their structures (applying the well-known designation): iso-FA1a,b, iso-FB1a-d, iso-FB2,3a-e, PHFB2a-c, PHFB4a-d, FB5/iso-FB5a-d, FBK1 2TCA, FBK4 2TCA, FC2, iso-FC2,3, PHFC4, FD and FBX series. The relative quantities of fumonisins and fumonisin-like compounds found in the sample extract were expressed as percentages of FB1 (0.02-100%). The backbone of the compound denoted FD contained fewer carbon atoms than the well-known fumonisins with the C19 or C20 backbone and may well be a precursor of the longer compounds. For the compounds denoted FBX (12 compounds), one or two OH groups attached to the fumonisin backbone were esterified by carboxylic acids other than tricarballylic acid, such as cis-aconitic acid, oxalylsuccinic acid and oxalylfumaric acid.     

Determination of ergosterol in Fusarium-infected wheat by liquid chromatography-atmospheric pressure photoionization mass spectrometry

A rapid liquid chromatography-atmospheric pressure photoionization mass spectrometry (LC-APPI-MS) method was developed for the determination of ergosterol in wheat grains. The effects of the dopants acetone, toluene and anisole on the ionization efficiency were studied. To identify the predominant ions, APPI-MS-MS studies were performed. Different LC and MS parameters were optimized to obtain maximum sensitivity. The effects of the mobile phase composition and of the flow rate were investigated. Additionally, the effects of the nebulizer gas pressure, the drying gas flow, the vaporizer temperature, the fragmentor voltage and the capillary voltage on the ionization efficiency were evaluated. The calibration curve exhibited good linearity and reproducibility. The detection limit (S/N=3) was 0.15 ng on column, which allows the determination of ergosterol in wheat at a concentration as low as 0.12 microg/g. Twenty wheat varieties artificially infected with Fusarium graminearum were investigated by this method.     

Adsorption of poly(ethylene oxide) at the air/water interface: a dynamic and static surface tension study

The adsorption of polyethylene oxide (PEO) homologues in a wide range of molecular weight (from M(PEO)=200 to 10(6)) at the air/aqueous solution interface was investigated by dynamic and static surface tension measurements. An approximate estimate for the lower limit of PEO concentration was given at which reliable equilibrium surface tension can be determined from static surface tension measurements. It was shown that the observed jump in the earlier published sigma-lg(c(PEO)) curves is attributable to the nonequilibrium surface tension values at low PEO concentrations. The adsorption behavior of short chain PEO molecules (M(PEO)1000) is similar to that of the ordinary surfactants. The estimated standard free energy of PEO adsorption, DeltaG(0), increases linearly with the PEO molecular weight until M(PEO)=1000. In this molecular weight range, DeltaG(0) was found to be approximately the fifth of the hydrophobic driving force related to the adsorption of a surfactant with the same number of methylene groups. In the case of the longer chain PEOs the driving force of adsorption is so high that the adsorption isotherm is near saturation in the experimentally available polymer concentration range. Above a critical molecular weight the PEO adsorption reveals universal features, e.g., the surface tension and the surface density of segments do not depend on the polymer molecular weight.     

Formal synthesis of (+)-varitriol. Application of Pd(II)/Cu(II)-catalysed bicyclisation of unsaturated polyols

A formal and improved synthesis of natural (+)-varitriol from d-glucose and dimethyl l-tartrate, respectively, are reported. The key steps are the Pd(II)/Cu(II)-catalysed bicyclisation of O-benzyl protected triols l-xylo-15 and l-xylo-15/l-lyxo-15, respectively, followed by ring opening of intermediate dianhydro-l-gulitol 16. The syntheses of key intermediate of the furanoside portion 17 proceed in 13 steps with 5% (from bisacetone-d-glucose), and in 12 steps with 7.6% over-all yield from dimethyl l-tartrate, respectively.     

Investigation of genetic variants of α-1 acid glycoprotein by ultra-performance liquid chromatography–mass spectrometry

Genetic variants of human plasma alpha-1 acid glycoprotein (AGP) have been studied in cancer, compared with a group of healthy control. AGP has four genetic variants: AGP F1, F2, and S variants correspond to the ORM1 gene whereas AGP A corresponds to the ORM2 gene. The proportion of ORM1 and ORM2 variants were studied in plasma using a novel UPLC–MS method. Plasma total AGP level was 0.5 ± 0.2 g L⁻¹ and the proportions of the ORM1 and ORM2 variants were 76.3 ± 8.2% and 23.7 ± 8.2%, respectively. In cancer plasma AGP levels increased fourfold and the proportion of ORM1 variants increased to 88.7 ± 6.8%. Changes in the proportion of genetic variants due to cancer were clearly significant, as shown by statistical analysis. Three different cancer types have been studied, lymphoma, melanoma, and ovarian cancer. The results did not show any difference depending on cancer type. The results indicate that, in accordance with prior expectations, the ORM1 variant is predominantly responsible for the acute-phase property of AGP.     

Gas-Phase Transformation of Fluorinated Benzoporphyrins to Porphyrin-Embedded Conical Nanocarbons

Geodesic nitrogen-containing graphene fragments are interesting candidates for various material applications, but the available synthetic protocols, which need to overcome intrinsic strain energy during the formation of the bowl-shaped skeletons, are often incompatible with heteroatom-embedded structures. Through this mass spectrometry-based gas-phase study, we show by means of collision-induced dissociation experiments and supported by density functional theory calculations, the first evidence for the formation of a porphyrin-embedded conical nanocarbon. The influences of metalation and functionalization of the used tetrabenzoporphyrins have been investigated, which revealed different cyclization efficiencies, different ionization possibilities, and a variation of the dissociation pathway. Our results suggest a stepwise process for HF elimination from the fjord region, which supports a selective pathway towards bent nitrogen-containing graphene fragments.