Detection of bar gene encoding phosphinothricin herbicide resistance in plants by electrochemical biosensor

An electrochemical biosensor for the detection of bar gene coding phosphinothricin herbicide resistance is presented. The detection was based on hybridization reaction between the specific to bar gene 19-mer probe immobilized on the electrode surface and complementary DNA in a sample. Single-stranded DNA probe specific to bar gene was covalently attached by 5'-phosphate end to the surface of carbon paste electrode. Outer layer of a conventional CPE was provided with carboxyl groups of stearic acid. ssDNA was coupled to the electrode through ethylenediamine with the use of water-soluble 1-ethyl-3(3'-dimethylaminopropyl)-carbodiimide and N-hydroxy-sulfosuccinimide as activating reagents. Hybridization reaction at the electrode surface was detected via Co(bpy)(3)(3+), which possess a much higher affinity to the resulting DNA duplex compared to ssDNA probe. Detection limit of the sensor was 0.1 microM of target DNA fragments and its response was linear from 5 to 20 microM. Hybridization event was also detected by measuring guanine peak but this approach presented distinctly higher detection limit (1 muM) and lower reproducibility. Complete time of one measurement with the use of the biosensor including covalent attachment of ethylenediamine (linker) and ssDNA probe to the electrode, hybridization with target and interaction with electroactive indicator was about 70 min.     

Binding of CO, NO, and O2 to heme by density functional and multireference ab initio calculations

Using the CASSCF/CASPT2 approach, along with several DFT methods (PBE0, B3LYP, BP86, OLYP), we have investigated the bonding of CO, NO, and O2 molecules to two model heme systems: an iron(II) porphyrin with and without an axial imidazole ligand. The experimentally available binding energies are best reproduced by the CASPT2 method and with the OLYP functional. The other functionals considered perform much worse, either severely overbinding (BP86) or underbinding (B3LYP, PBE0). Significant discrepancies between the different density functionals are observed, not only for the energetics but sometimes also for structure predictions. This confirms our viewpoint that a balanced treatment of the electronic exchange and correlation is vital to describe the weak metal-ligand bond between heme and CO, NO, or O2. The binding energies DeltaEb were split into two contributions: the so-called spin-pairing energy DeltaE sp and the "inherent" binding energy DeltaEb0, and both contributions were analyzed in terms of method and basis set effects. We have also investigated the spin density distributions resulting from the bonding of the NO molecule (a noninnocent ligand) to heme. Our analysis at the DFT and CASSCF level shows that, while various density functionals predict qualitatively very different spin distributions, the CASSCF spin populations most closely correspond to the results obtained with the pure BP86 or OLYP rather than with the hybrid functionals.     

Asymptotic Distributions of Empirical Interaction Information

Methodology and Computing in Applied Probability - Interaction Information is one of the most promising interaction strength measures with many desirable properties. However, its use for...     

Oligonuclear Molecular Models of Intermetallic Phases: A Case Study on [Pd2Zn6Ga2(Cp*)5(CH3)3]

The synthesis, characterization, and theoretical investigation by means of quantum‐chemical calculations of an oligonuclear metal‐rich compound are presented. The reaction of homoleptic dinuclear palladium compound [Pd₂(μ‐GaCp*)₃(GaCp*)₂] with ZnMe₂ resulted in the formation of unprecedented ternary Pd/Ga/Zn compound [Pd₂Zn₆Ga₂(Cp*)₅(CH₃)₃] ( 1 ), which was analyzed by ¹H and ¹³C NMR spectroscopy, MS, elemental analysis, and single‐crystal X‐ray diffraction. Compound 1 consisted of two C_s‐symmetric molecular isomers, as revealed by NMR spectroscopy, at which distinct site‐preferences related to the Ga and Zn positions were observed by quantum‐chemical calculations. Structural characterization of compound 1 showed significantly different coordination environments for both palladium centers. Whilst one Pd atom sat in the central of a bi‐capped trigonal prism, thereby resulting in a formal 18‐valence electron fragment, {Pd(ZnMe)₂(ZnCp*)₄(GaMe)}, the other Pd atom occupied one capping unit, thereby resulting in a highly unsaturated 12‐valence electron fragment, {Pd(GaCp*)}. The bonding situation, as determined by atoms‐in‐molecules analysis (AIM), NBO partial charges, and molecular orbital (MO) analysis, pointed out that significant Pd? Pd interactions had a large stake in the stabilization of this unusual molecule. The characterization and quantum‐chemical calculations of compound 1 revealed distinct similarities to related M/Zn/Ga Hume–Rothery intermetallic solid‐state compounds, such as Ga/Zn‐exchange reactions, the site‐preferences of the Zn/Ga positions, and direct M? M bonding, which contributes to the overall stability of the metal‐rich compound.     

Theoretical determination of the infrared spectra of amorphous polymers

The simple procedure of calculating the infrared spectra of polymers is presented. It is based on selecting the relevant, medium-size representative fragments of a polymer, for which the vibrational frequencies are computed within the harmonic approximation, in conjunction with the multiparameter scaling techniques. Scaling is necessary to predict the reliable fundamentals, which, along with the calculated intensities and properly chosen band widths, reproduce the observed band shapes with high accuracy. Applications to the three polymers: poly(methyl methacrylate), poly(vinyl acetate), and poly(isopropenyl acetate) are presented. The simulated spectra are in good agreement with the experiment. The assignment of bands is reported. The obtained results indicate strong delocalization of the vibrational modes within polymers, which is in accord with the most recent experimental finding [Macromolecules2008, 41, 2494-2501]. Good agreement between the observed and the calculated spectra of deuterated PMMA confirms the correctness of our approach. The preliminary results obtained for the highly irregular macromolecular compound (vinyl-functionalized silica) are also shown.     

Microextraction techniques in the analysis of food flavor compounds: A review

Food flavor compounds due to the complexity of food as a matrix, and usually their very low concentrations in a product, as well as their low odor thresholds, create a challenge in their extraction, separation and quantitation. Food flavor volatiles represent compounds of different polarity, volatility and chemical character, which determine method of extraction for their isolation from food. Microextraction techniques, mainly SPME and SBSE have been used for food flavor compounds analysis for two decades. Microextraction methods other than SPME and SBSE are seldom used despite their analytical potential. The review discusses the nature of food flavor compounds, and different approaches to food flavor analysis. It summarizes the use of microextraction methods in food flavor compounds analysis based on papers published in the last 5 years, and discusses the potential of microextraction methods in this field.     

Rigid, perdeuterated lanthanoid cryptates: extraordinarily bright near-IR luminophores

Near-IR emissive lanthanoid cryptates have been developed with the lanthanoids Yb, Nd, Er, and Pr by designing a fully deuterated ligand environment that greatly suppresses multiphonon nonradiative deactivation pathways through avoidance of high-energy oscillators and rigidification of the ligand backbone. Strong luminescence is observed in CD(3)CN for all four lanthanoids. Luminescence lifetimes in CD(3)CN are among the highest values for molecular complexes in solution reported so far (Yb, τ(obs) = 79 μs; Nd, τ(obs) = 3.3 μs). For the ytterbium cryptate, the highest luminescence lifetime can be obtained using CD(3)OD (τ(obs) = 91 μs) and even in nondeuterated CH(3)CN the lifetime is still unusually high (τ(obs) = 53 μs). X-ray crystallography and (1)H NMR analysis of the corresponding nondeuterated lutetium cryptate suggest that the inner coordination sphere in solution is completely saturated by the octadentate cryptand and one chloride counterion. All lanthanoid cryptates remarkably show complete stability during reversed-phase HPLC measurements under strongly acidic conditions.     

Thermal stability of hybrid materials based on epoxy functional (poly)siloxanes

Epoxy functional (poly)siloxanes are one of the most important classes of modified silicones. Due to high reactivity of epoxy group and specific features of siloxane chain, they can make an excellent raw material for synthesis of hybrid materials. Results obtained in this study have shown that both the modification of epoxy resins with epoxy functional disiloxanes as well as the application of polysiloxanes with long polysiloxane chains and a specified content of epoxy groups makes it possible to produce hybrid materials of very good thermal stability. Crosslinking reactions were carried out with use of four diamines of which the best one appeared to be 4,4??-diaminodiphenylmethane. The highest thermal stability was found in the case of hybrid materials obtained from epoxy functional polysiloxanes.     

Non-extinction of a Fleming-Viot particle model

We consider a branching particle model in which particles move inside a Euclidean domain according to the following rules. The particles move as independent Brownian motions until one of them hits the boundary. This particle is killed but another randomly chosen particle branches into two particles, to keep the population size constant. We prove that the particle population does not approach the boundary simultaneously in a finite time in some Lipschitz domains. This is used to prove a limit theorem for the empirical distribution of the particle family.