A nickel hydride complex in the active site of methyl-coenzyme m reductase: implications for the catalytic cycle

Methanogenic archaea utilize a specific pathway in their metabolism, converting C1 substrates (i.e., CO2) or acetate to methane and thereby providing energy for the cell. Methyl-coenzyme M reductase (MCR) catalyzes the key step in the process, namely methyl-coenzyme M (CH3-S-CoM) plus coenzyme B (HS-CoB) to methane and CoM-S-S-CoB. The active site of MCR contains the nickel porphinoid F430. We report here on the coordinated ligands of the two paramagnetic MCR red2 states, induced when HS-CoM (a reversible competitive inhibitor) and the second substrate HS-CoB or its analogue CH3-S-CoB are added to the enzyme in the active MCR red1 state (Ni(I)F430). Continuous wave and pulse EPR spectroscopy are used to show that the MCR red2a state exhibits a very large proton hyperfine interaction with principal values A((1)H) = [-43,-42,-5] MHz and thus represents formally a Ni(III)F430 hydride complex formed by oxidative addition to Ni(I). In view of the known ability of nickel hydrides to activate methane, and the growing body of evidence for the involvement of MCR in "reverse" methanogenesis (anaerobic oxidation of methane), we believe that the nickel hydride complex reported here could play a key role in helping to understand both the mechanism of "reverse" and "forward" methanogenesis.     

Scoring Unusual Words with Varying Mismatch Errors

Patterns consisting of strings with a bounded number of mismatches are central to coding theory and find multiple applications in text processing and computational biology. In this latter field, the presence of over-represented patterns of this kind has been linked, for instance, to modeling regulatory regions in biosequences. The study and computation of expected number of occurrences and related scores for these patterns is made difficult by the sheer explosion of the roster of candidates that need to be evaluated. In recent work, properties of pattern saturation and score monotonicity have proved capable to mitigate this problem. In such a context, expectation and score monotonicity has been established within the i.i.d. model for all cases of interest except that of a fixed word length with a varying number of mismatches. The present paper completes this investigation by showing that the expected number of occurrences in a textstring for such a word is bi-tonic, that is, behaves as a unimodal function of the number of errors. This extends to this case the time and space savings brought about by discovery algorithms based on pattern saturation. Work Supported in part by the Italian Ministry of University and Research under the Bi-National Project FIRB RBIN04BYZ7, and by the Research Program of Georgia Tech. An extended abstract related to this work was presented at the Dagstuhl Seminar Dagstuhl on “Combinatorial and Algorithmic Foundations of Pattern and Association Discovery”, May 14-19, 2006 [3].     

In Situ Observation of C−C Coupling and Step Poisoning During the Growth of Hydrocarbon Chains on Ni(111)

The synthesis of high-value fuels and plastics starting from small hydrocarbon molecules plays a central role in the current transition towards renewable energy. However, the detailed mechanisms driving the growth of hydrocarbon chains remain to a large extent unknown. Here we investigated the formation of hydrocarbon chains resulting from acetylene polymerization on a Ni(111) model catalyst surface. Exploiting X-ray photoelectron spectroscopy up to near-ambient pressures, the intermediate species and reaction products have been identified. Complementary in situ scanning tunneling microscopy observations shed light onto the C−C coupling mechanism. While the step edges of the metal catalyst are commonly assumed to be the active sites for the C−C coupling, we showed that the polymerization occurs instead on the flat terraces of the metallic surface.     

Structural Modifications of cis‐Glycofused Benzopyran Compounds and Their Influence on the Binding to Amyloid‐β Peptide

A small library of glycofused tricyclic compounds with a central pyran ring chemically modified in the position para to the ring oxygen has been synthesised. The influence of the chemical modification on the structural conformation of the compounds and on their ability to bind Aβ peptide has been evaluated respectively using molecular mechanics (MM) and molecular dynamics (MD) simulations, and STD NMR spectroscopy. The introduction of particularly polar/charged groups leads to the loss of binding ability, without a significant change in the conformation, whilst other substitutions does not significantly affect either the structural conformation or the binding.     

Butadienic building blocks from 2-nitrothiophene as precursors of nitrogen heterocycles: intriguing dichotomic behavior

With the goal of their exploitation for the synthesis of heterocycles, sulfides 10 and sulfones 11, derived from the initial ring-opening of 2-nitrothiophene (5) with pyrrolidine/AgNO3 in EtOH, were reacted with diazomethane. Interesting dichotomic behavior was found to yield pyrazolines 17 from 10 and isoxazolines 18 (as the main products) from 11. Intriguingly enough, in the latter case, an unexpected apparent C-C methylene insertion was also observed, leading to the homologous cyclopropanes 19 as secondary products.     

Development and validation of an HPLC-UV detection assay for the determination of rufinamide in human plasma and saliva

The development of a simple and rapid high-performance liquid chromatography (HPLC) method for the determination of the new antiepileptic drug rufinamide (RFN) in human plasma and saliva is reported. Samples (250 μl) are alkalinized with ammonium hydroxide (pH 9.25) and extracted with dichloromethane using metoclopramide as internal standard. Separation is achieved with a Spherisorb silica column (250 × 4.6 mm i.d., 5 μm) at 30 °C using as mobile phase a solution of methanol/dichloromethane/n-hexane 10/25/65 (vol/vol/vol) mixed with 6 ml ammonium hydroxide. The instrument used was a Shimadzu LC-10Av chromatograph and flow rate was 1.5 ml min^-1, with a LaChrom L-7400 UV detector set at 230 nm. Calibration curves are linear [r ² = 0.998 ± 0.002 for plasma (n = 10) and r ² = 0.999 ± 0.001 for saliva (n = 9)] over the range of 0.25–20.0 μg ml^-1, with a limit of quantification at 0.25 μg ml^-1. Precision and accuracy are within current acceptability standards. The assay is suitable for pharmacokinetic studies in humans and for therapeutic drug monitoring.     

Gadolinium-doped LipoCEST agents: a potential novel class of dual 1H-MRI probes

A novel class of paramagnetic liposome-based systems acting as dual T(1) and CEST (1)H-MRI contrast agents is described. The vesicles contain a shift reagent in the aqueous core and a Gd-complex on the external surface conjugated through a biodegradable linker. As such, the probe can generate T(1) contrast only, but after the cleavage and removal of the Gd-coating, the CEST contrast is switched on.     

Gold nanoparticles incarcerated in nanoporous syndiotactic polystyrene matrices as new and efficient catalysts for alcohol oxidations

The controlled synthesis of gold nanoparticles (AuNPs), incarcerated in a semicrystalline nanoporous polymer matrix that consisted of a syndiotactic polystyrene-co-cis-1,4-polybutadiene multi-block copolymer is described. This catalyst was successfully tested in the oxidation of primary and secondary alcohols, in which we used dioxygen as the oxidant under mild conditions. Accordingly, (±)-1-phenylethanol was oxidised to acetophenone in high yields (96%) in 1 h, at 35 °C, whereas benzyl alcohol was quantitatively oxidised to benzaldehyde with a selectivity of 96% in 6 h. The specific rate constants calculated from the corresponding kinetic plots were among the highest found for polymer-incarcerated AuNPs. Similar values in terms of reactivity and selectivity were found in the oxidation of primary alcohols, such as cinnamyl alcohol and 2-thiophenemethanol, and secondary alcohols, such as indanol and α-tetralol. The remarkable catalytic properties of this system were attributed to the formation, under these reaction conditions, of the nanoporous ε crystalline form of syndiotactic polystyrene, which ensures facile and selective accessibility for the substrates to the gold catalyst incarcerated in the polymer matrix. Moreover, the polymeric crystalline domains produced reversible physical cross-links that resulted in reduced gold leaching and also allowed the recovery and reuse of the catalyst. A comparison of catalytic performance between AuNPs and annealed AuNPs suggested that multiple twinned defective nanoparticles of about 9 nm in diameter constituted the active catalyst in these oxidation reactions.     

Is the Reduction in Tracer Diffusivity under Nanoscopic Confinement Related to a Frustrated Segmental Mobility?

We developed an experimental method for the determination of the tracer diffusivity D_tr in ultrathin polymer films, and the changes in the segmental mobility of tracer molecules while they diffuse through matrices of different thickness and get adsorbed onto a target substrate. D_tr starts decreasing already at 120–150 nm and drops to 1% of its bulk value in films as thin as 7.5 nm. We discuss the results highlighting a strong decoupling between the reduction in mass transport at the nanoscale and the increase in the glass transition temperature determined via capacitive dilatometry together with a breakdown of the Stokes–Einstein relation between orientational and translational degrees of freedom.

     

Wooden windows: Sound insulation evaluation by means of artificial neural networks

Windows are the weakest part of a façade in terms of acoustic performance: the weighted sound insulation index (R_w), measured according to ISO 140-3, is the fundamental parameter to evaluate the façade acoustic insulation.The paper aims at developing an artificial neural network (ANN) model to estimate the R_w value of wooden windows based on a limited number of windows parameters; this is a new approach because acoustic phenomena are non-linear and affected by a plurality of factors and, therefore, usually investigated through experimentation.Data set is taken from experimental campaigns carried out at the Laboratory of Acoustics, University of Perugia. A multilayer feed-forward approach was chosen and the model was implemented in MATLAB. On the basis of the results obtained by means of a preliminary training and test campaign of several ANN architectures, five main parameters were selected as network inputs: window typology, frame and shutters thickness, number of gaskets, R_w of glazing; R_w value of the window is the network output. Different ANN configurations were trained and a root mean-square error less than 3% was obtained, comparable to measurement uncertainty.This approach allows to develop a model which, with input parameters varying within appropriate ranges, can easily estimate the acoustic performance of wooden windows without experimental campaign on prototypes, saving both money and time. If the training data set is large enough, the presented approach could be very useful for design and optimization of acoustic performance of new products.