Oxidation of 13C-labeled methane in surface crusts of pig- and cattle slurry

Storage tanks for slurry from animal production constitute important point sources for emission of CH4 into the atmosphere. Recent investigations have demonstrated that surface crust formed on top of animal slurry provides a habitat for CH4 oxidation activity, a finding which may open for new opportunities to reduce greenhouse gas emissions during storage of animal wastes. In this work, 13C-labeled CH4 was used as a tracer to examine the absolute rates of CH4 oxidation and production in intact crust materials, collected from six different pig- and cattle slurry tanks in late autumn. Methane concentrations were generally reduced in the presence of surface crust samples, with the exception of a LECA-based (light expanded clay aggregates) crust from a pig slurry tank. In four samples, CH4 consumption was induced following a 2-4 days lag phase, whereas one cattle slurry crust consumed CH4 immediately and showed a 92% decline in CH4 concentration within the first week. Consumption of 13C-labeled CH4 was paralleled by the production of 13C-labeled CO2, thus providing direct evidence that microbial oxidation of CH4 to CO2 was taking place. Between 23% and 36% of the CH4-13C consumed in the active samples was accounted for in the gas phase CO2 indicating incomplete conversion of CH4 to CO2; however, comparable amounts of 13C was immobilized in the crust samples. Overall, the results showed that significant CH4 oxidation to CO2 in slurry crust samples occurs immediately or is inducible upon exposure to CH4.     

Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study

Human homogentisate dioxygenase is an Fe(II)-dependent enzyme responsible for aromatic ring cleavage. The mechanism of its catalytic reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode. It was found that binding of the substrate dianion with a vacant position trans to Glu341 is most favorable. The model was then truncated to include only the most relevant parts of the active-site residues involved in iron coordination and substrate binding. Thus, methylimidazole was used to model His292, His335, His365, and His371, while propionate modeled Glu341. The computational results suggest that the catalytic reaction of homogentisate dioxygenases involves three major chemical steps: formation of the peroxo intermediate, homolytic cleavage of the O-O bond leading to an arene oxide radical, and finally, cleavage of the six-membered ring. Calculated barriers for alternative reaction paths are markedly higher than for the proposed mechanism, and thus the computational results successfully explain the product specificity of the enzyme. Interestingly, the results indicate that the type of ring scission, intra or extra with respect to the substituents coordinating to iron, is controlled by the barrier heights for the decay of the arene oxide radical intermediate.     

An improved synthesis of Fmoc-N-methyl-alpha-amino acids

A highly efficient and environmentally more benign synthesis of Fmoc-N-methyl-alpha-amino acids from the corresponding Fmoc-amino acid, via intermediate 5-oxazolidinones, has been developed by using Lewis acid catalysis for the reductive opening of the oxazolidinone ring.     

Synthesis of a regioregular zwitterionic conjugated oligoelectrolyte, usable as an optical probe for detection of amyloid fibril formation at acidic pH

Changes of the optical properties of conjugated polyelectrolytes have been utilized to monitor noncovalent interactions between biomolecules and the conjugated polyelectrolytes in sensor applications. A regioregular, zwitterionic conjugated oligoelectrolyte was synthesized in order to create a probe with a defined set of optical properties and hereby facilitate interpretation of biomolecule-oligoelectrolyte interactions. The synthesized oligoelectrolyte was used at acidic pH as a novel optical probe to detect amyloid fibril formation of bovine insulin and chicken lysozyme. Interaction of the probe with formed amyloid fibrils results in changes of the geometry and the electronic structure of the oligoelectrolyte chains, which were monitored with absorption and emission spectroscopy.     

Line shapes in CP/MAS (13)C NMR spectra of cellulose I

The CP/MAS (13)C NMR line shape of cellulose I has been qualitatively analyzed by direct simulations using the Ornstein-Uhlenbeck stochastic process and the Kubo model. Both approaches describe a anhydroglucose C4 carbon as a oscillator with fluctuating Larmor frequency. The NMR resonance frequency is written omega=omega +omega(t), where the fluctuating part with zero mean was modelled as a stationary Markov diffusion process. The simulation results both motivates the use of multiple line shapes when fitting CP/MAS (13)C NMR spectra recorded on cellulose I and gives some insights into why signals from crystalline cellulose I give rise to Lorentzian line shapes.     

Comparing the performance of FLUFF-BALL to SEAL-CoMFA with a large diverse estrogen data set: from relevant superpositions to solid predictions

In this work a template-based molecular mechanistic superposition algorithm FLUFF (Flexible Ligand Unified Force Field) and an accompanying local coordinate QSAR method BALL (Boundless Adaptive Localized Ligand) are validated against the benchmark techniques SEAL (Steric and Electrostatic Alignment) and CoMFA (Comparative Molecular Field Analysis) using a large diverse set of 245 xenoestrogens extracted from the EDKB (Endocrine Disruptor Knowledge Base) maintained by NCTR (National Centre for Toxicological Research). The results indicate that FLUFF is capable of generating relevant superpositions not only for BALL but also for CoMFA, as both techniques give predictive QSAR models. When the BALL and CoMFA methods are compared, it is clear that the BALL algorithm met or even exceeded the results of the standard 3D-QSAR method CoMFA using alignments either from the tailor-made superposition technique FLUFF or the reference method SEAL. The FLUFF-BALL method can be easily automated, and it is computationally light, providing thus a good computational "sieve" capable of fast screening of large molecule libraries.     

A Theoretical Study of AtildeΠ MgCN

We use the RENNER program system (see, for example, P. Jensen, G. Osmann, and P. R. Bunker, in “Computational Molecular Spectroscopy” (P. Jensen and P. R. Bunker, Eds.), Wiley, Chichester, 2000, and references therein) to make a detailed calculation of the rovibronic energies in the first excited electronic state, òΠ, of the MgCN radical. This calculation is based on ab initio data computed at the MR-SDCI(+Q)/[TZ3P+f (Mg), aug-cc-pVQZ (N and C)] level of theory. We have also obtained the standard spectroscopic constants and have used these to calculate vibronic energies from perturbation expressions (J. T. Hougen and J. P. Jesson, J. Chem. Phys.38, 1524-1525 (1963)); these results are compared to those computed with RENNER. It is shown that for MgCN, the perturbation theory is dilapidated due to Fermi resonances. No spectra involving the Ã²Π electronic state of MgCN have been observed. To assist such observations, we have calculated Franck-Condon factors for some of the vibronic bands in the òΠ←Xtilde;²Σ⁺ electronic transition.     

Piezoelectrically actuated flextensional micromachined ultrasound transducers

This paper presents novel micromachined two-dimensional array piezoelectrically actuated flextensional transducers that can be used to generate sound in air or water. Micromachining techniques to fabricate these devices are also presented. Individual unimorph array elements consist of a thin piezoelectric annular disk and a thin, fully clamped, circular plate. We manufacture the transducer in two-dimensional arrays using planar silicon micromachining and demonstrate ultrasound transmission in air at 2.85 MHz with 0.15 microm/V peak displacement. The devices have a range of operating resonance frequencies starting from 450 kHz up to 4.5 MHz. Such an array could be combined with on-board driving and addressing circuitry for different applications.     

Quantum chemical study on the interaction of some bisphosphonates and Ca2+: The role of molecular electrostatic potentials in the prediction of binding geometry

Summary Molecular electrostatic potentials have been used to model the calcium binding properties of some bisphosphonate drugs, which are used to treat various bone diseases. The mechanism of action involves the binding of bisphosphonates to the bone surface, where calcium plays an important role. Electrostatic potential maps derived from ab initio partial charges have been compared with both the crystal structure and the fully optimized ab initio structure of (dichloro)methylenebisphosphonate-calcium ion complex. Molecular electrostatic potentials can correctly predict the calcium binding geometry of bisphosphonate-type compounds and this type of information can be used in the practical drug design work.