Synthesis and NMR spectroscopic analysis of 3-nitro-pyranoside, 3-nitro-septanoside and 4-nitro-septanoside derivatives by condensation of the anion of nitromethane with glycoside

The utility of the nitroaldol reaction for accessing 3-nitro-pyranoside, 3-nitro-septanoside or 4-nitro-septanoside derivatives, by reaction of the anion of nitromethane with glycoside dialdehydes is demonstrated. Initially, the feasibility of using unprotected glucoside dialdehydes was probed for the synthesis of the septanoside products, but this affoided pyranoside rather than septanoside targets. Subsequent studies utilised protected glycoside dialdehydes within the methodology, which allowed entry into a range of 3-nitro or 4-nitro-septanosides in good yield NMR spectroscopic analysis allowed determination of the stereochemistry of each of the products thus afforded.

Notations and conventions in molecular spectroscopy: part 1. General spectroscopic notation

The field of Molecular Spectroscopy was surveyed in order to determine a set of conventions and symbols which are in common use in the spectroscopic literature. This document, which is Part I in a series, establishes the notations and conventions used for general spectroscopic notations and deals with quantum mechanics, quantum numbers (vibrational states, angular momentum and energy levels), spectroscopic transitions, and miscellaneous notations (e.g. spectroscopic terms). Further parts will follow, dealing inter alia with symmetry notation, permutation and permutation-inversion symmetry notation, vibration-rotation spectroscopy and electronic spectroscopy.

Analytical potentials for triatomic molecules from spectroscopic data V. Application to HOX (X=F, Cl, Br, I)

Analytical potential energy functions are reported for HOX (X=F, Cl, Br, I). The surface for HOF predicts two metastable minima as well as the equilibrium configuration. These correspond to HFO (bent) and OHF (linear). Ab initio calculations performed for the HOF surface confirm these predictions. Comparisons are drawn between the two sets of results, and a vibrational analysis is undertaken for the hydrogen bonded OHF species. For HOCl, one further minimum is predicted, corresponding to HClO (bent), the parameters for which compare favourably with those reported from ab initio studies. In contrast, only the equilibrium configurations are predicted to be stable for HOBr and HOI.

Analytical potentials for triatomic molecules from spectroscopic data VI. On choosing internal coordinates to describe triatomic potential energy surfaces with more than one minimum

Orthogonal internal coordinates are defined which have useful properties for constructing the potential energy functions of triatomic molecules with two or three minima on the surface. The coordinates are used to obtain ground state potentials of ClOO and HOF, both of which have three minima.

The effect of environment on endosperm cell-wall development in Triticum aestivum during grain filling: an infrared spectroscopic imaging study

One of the major factors contributing to the failure of new wheat varieties is seasonal variability in end-use quality. Consequently, it is important to produce varieties which are robust and stable over a range of environmental conditions. Recently developed sample preparation methods have allowed the application of FT-IR spectroscopic imaging methods to the analysis of wheat endosperm cell wall composition, allowing the spatial distribution of structural components to be determined without the limitations of conventional chemical analysis. The advantages of the methods, described in this paper, are that they determine the composition of endosperm cell walls in situ and with minimal modification during preparation. Two bread-making wheat cultivars, Spark and Rialto, were selected to determine the impact of environmental conditions on the cell-wall composition of the starchy endosperm of the developing and mature grain, focusing on the period of grain filling (starting at about 14 days after anthesis). Studies carried out over two successive seasons show that the structure of the arabinoxylans in the endosperm cell walls changes from a highly branched form to a less branched form. Furthermore, during development the rate of restructuring was faster when the plants were grown at higher temperature with restricted water availability from 14 days after anthesis with differences in the rate of restructuring occurring between the two cultivars.

Mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in RNA binding by using surface plasmon resonance

Phosphorylation of the coronavirus nucleoprotein (N protein) has been predicted to play a role in RNA binding. To investigate this hypothesis, we examined the kinetics of RNA binding between nonphosphorylated and phosphorylated infectious bronchitis virus N protein with nonviral and viral RNA by surface plasmon resonance (Biacore). Mass spectroscopic analysis of N protein identified phosphorylation sites that were proximal to RNA binding domains. Kinetic analysis, by surface plasmon resonance, indicated that nonphospborylated N protein bound with the same affinity to viral RNA as phosphorylated N protein. However, phosphorylated N protein bound to viral RNA with a higher binding affinity than nonviral RNA, suggesting that phosphorylation of N protein determined the recognition of virus RNA. The data also indicated that a known N protein binding site (involved in transcriptional regulation) consisting of a conserved core sequence present near the 5' end of the genome (in the leader sequence) functioned by promoting high association rates of N protein binding. Further analysis of the leader sequence indicated that the core element was not the only binding site for N protein and that other regions functioned to promote high-affinity binding.

Spectroscopic imaging of arteries and atherosclerotic plaques

Fourier transform infrared (FTIR) spectroscopic imaging using a focal plane array detector has been used to study atherosclerotic arteries with a spatial resolution of 3-4 mum, i.e., at a level that is comparable with cellular dimensions. Such high spatial resolution is made possible using a micro-attenuated total reflection (ATR) germanium objective with a high refractive index and therefore high numerical aperture. This micro-ATR approach has enabled small structures within the vessel wall to be imaged for the first time by FTIR. Structures observed include the elastic lamellae of the tunica media and a heterogeneous distribution of small clusters of cholesterol esters within an atherosclerotic lesion, which may correspond to foam cells. A macro-ATR imaging method was also applied, which involves the use of a diamond macro-ATR accessory. This study of atherosclerosis is presented as an illustrative example of the wider potential of these A TR imaging approaches for cardiovascular medicine and biomedical applications. (C) 2004 Wiley Periodicals, Inc.

Malacosporean-like spores in urine of rainbow trout react with antibody and DNA probes to Tetracapsuloides bryosalmonae

Tetracapsuloides bryosalmonae is the myxozoan parasite causing proliferative kidney disease (PKD) of salmonid fishes in Europe and North America. The complete life cycle of the parasite remains unknown despite recent discoveries that the stages infectious for fish develop in freshwater bryozoans. During the course of examinations of the urine of rainbow trout (Oncorhynchus mykiss) with or recovering from PKD we identified spores with features similar to those of T. bryosalmonae found in the bryozoan host. Spores found in the urine were subspherical, with a width of 16 mum and height of 14 mum, and possessed two soft valves surrounding two spherical polar capsules (2 mum in diameter) and a single sporoplasm. The absence of hardened valves is a distinguishing characteristic of the newly established class Malacosporea that includes T. bryosalmonae as found in the bryozoan host. The parasite in the urine of rainbow trout possessed only two polar capsules and two valve cells compared to the four polar capsules and four valves observed in the spherical spores of 19 mum in diameter from T. bryosalmonae from the bryozoan host. Despite morphological differences, a relationship between the spores in the urine of rainbow trout and T. bryosalmonae was demonstrated by binding of monoclonal and polyclonal antibodies and DNA probes specific to T. bryosalmonae.

Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary

Sulphate-reducing bacteria (SRB) and methanogenic archaea (MA) are important anaerobic terminal oxidisers of organic matter. However, we have little knowledge about the distribution and types of SRB and MA in the environment or the functional role they play in situ. Here we have utilised sediment slurry microcosms amended with ecologically significant substrates, including acetate and hydrogen, and specific functional inhibitors, to identify the important SRB and MA groups in two contrasting sites on a UK estuary. Substrate and inhibitor additions had significant effects on methane production and on acetate and sulphate consumption in the slurries. By using specific 16S-targeted oligonucleotide probes we were able to link specific SRB and MA groups to the use of the added substrates. Acetate consumption in the freshwater-dominated sediments was mediated by Methanosarcinales under low-sulphate conditions and Desulfobacter under the high-sulphate conditions that simulated a tidal incursion. In the marine-dominated sediments, acetate consumption was linked to Desulfobacter. Addition of trimethylamine, a non-competitive substrate for methanogenesis, led to a large increase in Methanosarcinales signal in marine slurries. Desulfobulbus was linked to non-sulphate-dependent H-2 consumption in the freshwater sediments. The addition of sulphate to freshwater sediments inhibited methane production and reduced signal from probes targeted to Methanosarcinales and Methanomicrobiales, while the addition of molybdate to marine sediments inhibited Desulfobulbus and Desulfobacterium. These data complement our understanding of the ecophysiology of the organisms detected and make a firm connection between the capabilities of species, as observed in the laboratory, to their roles in the environment. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Dinuclear copper and zinc complexes of a hexaazamacrocycle containing p-xylyl spacers and bridging anions: theoretical and spectroscopic studies

The hexaazamacrocycle 7,22-dimethyl-3,7,11,18,22,26-hexaazatricyclo[26.2.2.2(13,16)] tetratriaconta-1(30), 13,15,28,31,33- hexaene (Me-2[30] pbz(2)N(6)) was synthesized and characterised by single crystal X-ray diffraction. The macrocycle adopts a conformation with the two aromatic rings almost parallel at a distance of ca. 4.24 Angstrom, but displaced relative to each other by ca. 1.51 Angstrom. The protonation constants of this compound and the stability constants of its complexes with Cu2+ and Zn2+, were determined in water - methanol (9 : 1 v/v) at 25 degreesC with ionic strength 0.10 mol dm(-3) in KCl. The potentiometric and spectroscopic studies (NMR of zinc, cadmium and lead complexes, and EPR of the copper complexes) indicate the formation of only dinuclear complexes. The association constants of the dinuclear copper complex with anions ( thiocyanate, terephthalate and glyphosate) and neutral molecules (1,4-benzenedimethanol, p-xylylenediamine and terephthalic acid) were determined at 20 degreesC in methanol. The structural preferences of this ligand and of its dinuclear copper(II) complex with a variety of bridging ligands were evaluated theoretically by molecular mechanics calculations (MM) and molecular dynamics (MD) using quenching techniques.

Facile synthesis of Cu(II) complexes of monocondensed N,N,N donor Schiff base ligands: crystal structure, spectroscopic and magnetic properties

Four new copper(II) complexes, [((CuLN3)-N-1)(2)](ClO4)(2) (1), [(CuL2 N-3)(2)](ClO4)(2) (2), [CuL3(N-3)ClO4)](n) (3) and [CuL4(mu-1,1-N-3)(mu-1,3-N-3)(ClO4)](n) (4) where L-1 = N-1-pyridin-2-yl-methylene-propane-1,3-diamine, L-2 = N-1-(1-pyridin-2-yl-ethylidene)propane-1,3-diamine, L-3 =N-1-(1-pyridin-2-yl-ethylidene)ethane-1,2-diamine and L-4=N-1-(1-pyridin-2-yl-ethylidene)propane-1,2-diamine are four tridentate N,N,N donor Schiff base ligands, have been derived and structurally characterized by X-ray crystallography. Compounds 1 and 2 consist of double basal-apical end-on (EO) azide bridged dinuclear Cu-II complexes with square-pyramidal geometry. In complex 3 the square planar mononuclear [CuL3 (N-3)] units are linked by weakly coordinated perchlorate ions in the axial positions of Cu-II to form a one-dimensional chain. Two such chains are connected by hydrogen bonds involving perchlorate ions and azide groups. Compound 4 consists of 1-D chains in which the Cu-II ions with a square-pyramidal geometry are alternately bridged by single EO and end-to-end (EE) azido ligands, both adopting a basal-apical disposition. Variable temperature (300-2 K) magnetic susceptibility measurements and magnetization measurements at 2 K have been performed. The results reveal that complexes 1 and 2 are antiferromagnetically coupled through azido bridges (J= -12.18 +/- 0.09 and -4.43 +/- 0.1 cm(-1) for 1 and 2, respectively). Complex 3 shows two different magnetic interactions through the two kinds of hydrogen bonds; one is antiferromagnetic (J(1) = - 9.69 +/- 0.03 cm(-1)) and the other is ferromagnetic (J(2) = 1.00 +/- 0.01 cm(-1)). From a magnetic point of view complex 4 is a ferromagnetic dinuclear complex (J= 1.91 +/- 0.01 cm(-1)) coupled through the EO bridge only. The coupling through the EE bridge is practically nil as the N(azido)-Cu-II (axial) distance (2.643 angstrom) is too long. (C) 2006 Elsevier Ltd. All rights reserved.

Low molecular weight organogelators from self-assembling synthetic tripeptides with coded amino acids: morphological, structural, thermodynamic and spectroscopic investigations

A series of self-assembling terminally blocked tripeptides (containing coded amino acids) form gels in various aromatic solvents including benzene, toluene, xylenes at low concentrations. However these tripeptides do not form gels in aliphatic hydrocarbons like n-hexane, cyclohexane, n-decane etc. Morphological studies of the dried gel indicate the presence of an entangled fibrous network, which is responsible for gelation. Differential scanning calorimetric (DSC) studies of the gels produced by peptide 1 clearly demonstrates thermoreversible nature of the gel and tripeptide-solvent complex may be produced during gel formation. FT-IR and H-1 NMR studies of the gels demonstrate that an intermolecular hydrogen-bonding network is formed during gelation. Single crystal X-ray diffraction studies for peptides 1, 2 and 3 have been performed to investigate the molecular arrangement that might be responsible for forming the fibrous network of these self-assembling peptide gelators. It has been found that the morph responsible for gelation of peptides 1, 2 and 3 in benzene is somewhat different from that of its xerogel.