Thermal isomerization of cis,anti,cis-tricyclo[6.3.0.0(2,7)]undec-3-ene to endo-tricyclo[5.2.2.0(2,6)]undec-8-ene

[reaction: see text] The gas-phase thermal isomerization of cis,anti,cis-tricyclo[6.3.0.0(2,7)]undec-3-ene (1) to endo-tricyclo[5.2.2.0(2,6)]undec-8-ene (2) at 315 degrees C occurs cleanly through a symmetry-forbidden [1,3] suprafacial,retention (sr) pathway.     

Sequence-specific fluorescence detection of DNA by polyamide-thiazole orange conjugates

Fluorescent methods to detect specific double-stranded DNA sequences without the need for denaturation may be useful in the field of genetics. Three hairpin pyrrole-imidazole polyamides 2-4 that target their respective sequences 5'-WGGGWW-3', 5'-WGGCCW-3', and 5'-WGWWCW-3' (W = A or T) were conjugated to thiazole orange dye at the C-termini to examine their fluorescence properties in the presence and absence of match duplex DNA. The conjugates fluoresce weakly in the absence of DNA but showed significant enhancement (>1000-fold) upon the addition of 1 equiv of match DNA and only slight enhancement with the addition of mismatch DNA. The polyamide-dye conjugates bound specific DNA sequences with high affinity (Ka > 10(8) M(-1)) and unwound the DNA duplex through intercalation (unwinding angle, phi, approximately 8 degrees). This new class of polyamides provides a method to specifically detect DNA sequences without denaturation.     

Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins

The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.     

Effect of substituents at silicon on the oxidative addition of trisubstituted silanes to [RhCl(cod)PPh3]

Summary Trisubstituted silanes, HSiR_3–n X _n (R = Me, Et, Pr or Bu; X = Cl, OEt or Ph; and n = 0–3) readily undergo oxidative addition to complex [RhCl(cod)PPh₃] (where cod = cycloocta-1,5-diene).The quantitative correlation between rate constants, k ₁, of the reaction, followed spectrophotometrically at 20 °C in benzene solutions, and the structure of tri-substituted silanes represented by stereoelectronic parameters , and E of the substituents, was established: logk ₁ = a + b + c + dE. The reaction rate is accelerated by electron-withdrawing substituents at silicon and retarded by the bulk and pd donation of nonalkyl substituents.Author to whom all correspondence should be directed.     

Diffusion coefficients of the monomer and oligomers in hydroxyethyl methacrylate

The diffusion coefficients are reported of rubbery ternary systems consisting of the polymer, its monomer analogue (i.e., the saturated equivalent of the monomer), and trace quantities of oligomers (dimer, trimer, tetramer and hexamer) for 2‐hydroxyethyl methacrylate (HEMA). These have been obtained with pulsed‐field‐gradient NMR spectroscopy with a polymer weight fraction (f_p) of 0 ≤ f_p ≤ 0.4. The oligomers are macromonomers synthesized with a cobalt catalytic chain‐transfer agent. The diffusion coefficients are about an order of magnitude smaller than those for monomers such as methyl methacrylate; this effect is ascribed to hydrogen bonding in HEMA. The diffusion coefficient D_i of an i‐meric oligomer has been fitted with moderate accuracy by an empirical universal scaling relation, D_i(f_p)/D₁(f_p) ≈ i, previously found to provide an adequate fit to corresponding data for styrene and for methyl and butyl methacrylates. The approximate empirical scaling relation seems to hold for a remarkably wide range of types of monomer/polymer systems. These results are of use in modeling rates and molecular weight distributions in free‐radical polymerization, particularly for termination (which is chain‐length‐dependent and is controlled by the diffusion coefficient of chains of the low degrees of polymerization studied here). © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2491–2501, 2003     

P-polarized nonlinear surface polaritons near the surface of a saturable self-defocusing medium: Threshold case

We have obtained the solution of the stationary problem for P-polarized nonlinear surface polaritons (NLSP) near the interface of two media, one of which is optically linear and the other having an optical nonlinearity with saturation and a dielectric function of the form: =_xx=_zz=₀+a|E|²/(1+b|E|²), where E is the amplitude of the electric field. On this basis the NLSP energy and propagation properties, the polarization structure and the localization depth of the NLSP field as well as the physically allowed region in the parameter space have been investigated for the case in which the parameter ₀ is positive, b is non-negative, and a and ₁ are negative (₁ is the dielectric function of the linear medium); ₀>|₁|.     

A study of the anharmonic effects on the vibrational spectra of a realistic retinal chromophore model

Ab initio and vibrational self-consistent field (VSCF) computations are used to investigate the vibrational normal coordinates of the protonated Schiff base (PSB) 4-cis-gamma,eta-dimethyl-C9H9 NH2+. The ground and the first excited states are investigated. Both harmonic and anharmonic frequencies for the first three overtones of the ground and first excited states are reported. Special attention is payed to the discussion of the normal coordinates modes that involve the central C=C bond which plays a significant role in the isomerization process.     

Derivatisation in gas chromatographic determination of acidic herbicides in aqueous environmental samples

This paper reviews derivatisation processes applied in chromatographic determination of acidic herbicides (with carboxyl and phenol groups), mainly in aqueous environmental samples. The discussion focuses on the basic derivatisation reactions used to convert herbicides to derivatives to make them analysable by gas chromatography, and possibly to reduce detection limits and/or increase extraction recovery from aqueous samples. The reactions are transesterification, esterification, silylation, alkylation, and extractive and pyrolytic alkylation. The reagents used to conduct the reactions are numerous. Diazomethane is a very efficient methylation reagent but explosive and toxic. Methyl iodide also ensures rapid and efficient methylation. Benzyl bromide can be used directly in water but derivatisation yield is low and reproducibility is poor. Butyl chloroformate and dimethyl sulfite can also be used for derivatisation in water, and acetic anhydride can be used for in-situ derivatisation of phenolic herbicides. For increasing selectivity of GC detection pentafluorobenzyl bromide (for ECD) and (2-cyanethyl)dimethyl(diethylamino)silane (for NPD) have been applied. Very characteristic ions are produced in mass spectra if silyl groups are introduced, e.g. by using bis(trimethylsilyl)trifluoroacetamide. Tetramethylammonium, trimethylphenylammonium, tetraalkylammonium, and trimethylsulfonium hydroxides and salts can by used for derivatisation at elevated temperature in the GC injection port. Extractive alkylation is relatively efficient if tetraalkylammonium salts with long chain alkyl groups are used.     

Regioselective Synthesis of 5- and 3-Hydroxy-N-Aryl-1H-Pyrazole-4-Carboxylates and Their Evaluation as Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase

In silico evaluation of various regioisomeric 5- and 3-hydroxy-substituted alkyl 1-aryl-1H-pyrazole-4-carboxylates and their acyclic precursors yielded promising results with respect to their binding in the active site of dihydroorotate dehydrogenase of Plasmodium falciparum (PfDHODH). Consequently, four ethyl 1-aryl-5-hydroxy-1H-pyrazole-4-carboxylates and their 3-hydroxy regioisomers were prepared by two-step syntheses via enaminone-type reagents or key intermediates. The synthesis of 5-hydroxy-1H-pyrazoles was carried out using the literature protocol comprising acid-catalyzed transamination of diethyl [(dimethylamino)methylene]malonate with arylhydrazines followed by base-catalyzed cyclization of the intermediate hydrazones. For the synthesis of isomeric methyl 1-aryl-3-hydroxy-1H-pyrazole-4-carboxylates, a novel two-step synthesis was developed. It comprises acylation of hydrazines with methyl malonyl chloride followed by cyclization of the hydrazines with tert-butoxy-bis(dimethylamino)methane. Testing the pyrazole derivatives for the inhibition of PfDHODH showed that 1-(naphthalene-2-yl)-5-hydroxy-1H-pyrazole-4-carboxylate and 1-(naphthalene-2-yl)-, 1-(2,4,6-trichlorophenyl)-, and 1-[4-(trifluoromethyl)phenyl]-3-hydroxy-1H-pyrazole-4-carboxylates (~30% inhibition) were slightly more potent than a known inhibitor, diethyl α-{[(1H-indazol-5-yl)amino]methylidene}malonate (19% inhibition).     

Raman Method in Identification of Species and Varieties,Assessment of Plant Maturity and Crop Quality—A Review

The present review covers reports discussing potential applications of the specificity of Raman techniques in the advancement of digital farming, in line with an assumption of yield maximisation with minimum environmental impact of agriculture. Raman is an optical spectroscopy method which can be used to perform immediate, label-free detection and quantification of key compounds without destroying the sample. The authors particularly focused on the reports discussing the use of Raman spectroscopy in monitoring the physiological status of plants, assessing crop maturity and quality, plant pathology and ripening, and identifying plant species and their varieties. In recent years, research reports have presented evidence confirming the effectiveness of Raman spectroscopy in identifying biotic and abiotic stresses in plants as well as in phenotyping and digital selection of plants in farming. Raman techniques used in precision agriculture can significantly improve capacities for farming management, crop quality assessment, as well as biological and chemical contaminant detection, thereby contributing to food safety as well as the productivity and profitability of agriculture. This review aims to increase the awareness of the growing potential of Raman spectroscopy in agriculture among plant breeders, geneticists, farmers and engineers.