Electronic structure of siloxene model compounds

The electronic structures of one-dimensional and two-dimensional siloxene (Si₆O₃H₆) model compounds have been examined theoretically, using the semiempirical tight-binding self-consistent field crystal orbital (SCF-CO) method. These compounds are formed by silicon-based chain and planar structures containing a regular array of oxygen atoms. Results show that the two-dimensional polysilane in which OH groups are substituted for H atoms possesses a relatively smaller direct gap than other siloxenes. It is assumed that the electronic structures of siloxenes are affected not only by the dimensionality of Si-Si -conjugational networks due to an array of oxygen atoms, but also by the diminishing of the electron population in the Si-Si bonding orbitals caused by oxygen atoms with large electronegativity.     

Electronic structure of polysilole and related compounds

The electronic structures, in the optimized geometries, of polysilacyclopentadiene (polysilole), polygermacyclopentadiene, and silole-thiophene alternating copolymer, have been studied theoretically using the one-dimensional tight-binding self-consistent field crystal orbital (SCF-CO) method. It has been found that the band gap values of these polymers are slightly smaller than those of the ordinary five-membered polyheterocycles such as polythiophene. The larger -polarized nature between the Group IV atom and the carbon atom might be expected to exhibit a different behaviour, compared with polythiophene, when they are doped with ann-type dopant.     

Retention mechanism of analytes in the solid-phase extraction process using molecularly imprinted polymers. Application to the extraction of triazines from complex matrices

The influence of sampling variables on the concentration of the dopamine metabolites 3-methoxytyramine (3MT), dihydroxyphenylacetic acid (DOPAC) and homovanilic acid (HVA) was examined in equine urine. A logarithmic transformation of the data for all horses gave distribution which approximated the normal distributions for each metabolite. The mean urinary concentration of 3 MT in horses was 214 ng/mL and the application of a threshold with a probability of 1 in 10,000 gave an actionable level of 4 microg/mL. Environmental variables were not forensically significant in determining the population distribution. HVA was not found to be a reliable indicator of dopamine or levodopa administration.     

Electronic structure and decomposition reaction mechanism of cyclopropenone, phenylcylopropenone and their sulfur analogues: a theoretical study

The electronic structure, the origin of the extraordinary stability and the reaction mechanisms of the decomposition reaction of the three-membered ring cyclopropenone (IO), its phenyl derivative (IIO) and its sulfur analogues (IS and IIS) have been investigated at the B3LYP/6-311?+?G** level of theory. All critical points on the reaction surface, reactants, transition states and intermediates were determined. Reaction rate constants and half-lives have been computed. Natural bond orbital (NBO) analysis has been used to investigate the type and extent of interaction in the studied species. Results indicate that the decomposition reaction occurs via a stepwise mechanism, with the formation of a short-lived intermediate. The characters of the intermediates for the decomposition of IIO and IIS are different. In case of IIO decomposition, the intermediate structure is of prevailing zwitterionic character, whereas that for the decomposition of IIS is of prevailing carbene character. Solvent effects are computed, analyzed and discussed.     

Electronic structure and molecular design of simplified polyimide systems

The electronic structures of newly designed polyimide systems (ethenetetracarboxylic 1,2:1,2-dianhydride-diaminoethyne (PI-A) and ethenetetracarboxylic 1,1:2,2-dianhydride-diaminoethyne(PI-B)) are studied in detail with respect to their optimized geometries on the basis of the one-dimensional tight-binding self-consistent field crystal-orbital method. The computational results have revealed that PI-B shows intriguing properties such as a very small band gap and a wide bandwidth near the frontier level, compared with PI-A and other polyimides. Since PI-B would be a promising candidate for a new electric conducting material, a reaction diagram for this polymer is also proposed.Also affiliated to Central Research Laboratories, Matsushita Electric Industrial Co., Moriguchi 570, Japan.     

Adherence of Pseudomonas aeruginosa to inanimate polymers including biomaterials

Cells of Pseudomonas aeruginosa were adhered to polymethyl methacrylate, polyvinyl acetate, polyvinyl chloride, polyhydroxyethyl methacrylate, mixed-acrylic, silicone, and natural latex materials. Planktonic bacteria and bacteria that adhered to the test materials were compared for their uptake of either L-[3,4,5-³H] leucine or [methyl-³H] thymidine during growth in a minimal medium. Leucine incorporation was reduced and thymidine uptake was negligible in adherent bacteria for up to 8 h following primary attachment by which time cells in the planktonic state showed active uptake of both substrates. These reduced uptake periods correlated with lag phases of growth of adherent cells as determined with a sonication-release plate count procedure and analyses of adenosine triphosphate (ATP). The extent of the lag phase of the adherent populations was dependent on initial densities of adhered cells and the nature of the substratum. Received 02 December 1998/ Accepted in revised form 25 April 1999     

The skull and jaw musculature as guides to the ancestry of salamanders

The fossil record provides no evidence supporting a unique common ancestry for frogs, salamanders and apodans. The ancestors of the modern orders may have diverged from one another as recently as 250 million years ago, or as long ago as 400 million years according to current theories of various authors. In order to evaluate the evolutionary patterns of the modern orders it is necessary to determine whether their last common ancestor was a rhipidistian fish, a very primitive amphibian, a labyrimhodom or a ‘lissamphibian’. The broad cranial similarities of frogs and salamanders, especially the dominance of the braincase as a supporting element, can be associated with the small size of the skull in their immediate ancestors. Hynobiids show the most primitive cranial pattern known among the living salamander families and “provide a model for determining the nature of the ancestors of the entire order. Features expected in ancestral salamanders include: (1) Emargination of the cheek; (2) Movable suspensorium formed by the quadrate, squamosal and pterygoid; (3) Occipital condyle posterior to jaw articulation; (4) Distinct prootic and opisthotic; (5) Absence ol otic notch; (6) Stapes forming a structural link between braincase and cheek. In the otic region, cheek and jaw suspension, the primitive salamander pattern (resembles most closely the microsaurs among known Paleozoic amphibians, and shows no significant features in common with either ancestral frogs or the majority of labyrinth odonts. The basic pattern of the adductor jaw musculature is consistent within both frogs and salamanders, but major differences are evident between the two groups. The dominance of the adductor mandibulae externus in salamanders can be associated with the open cheek in all members of that order, and the small size of this muscle in frogs can be associated with the large otic notch. The spread of different muscles over the otic capsule, the longus head ol the adductor mandibulae posterior in frogs and the superficial head of the adductor mandibulae internus in salamanders, indicates that fenestration of the skull posterodorsal to the orbit occurred separately in the ancestors of the two groups. Reconstruction of the probable pattern of the jaw musculature in Paleozoic amphibians indicates that frogs and salamanders might have evolved from a condition hypothesized for primitive labyrinthodonts, but the presence of a large otic notch in dissorophids suggests specialization toward the anuran, not the urodele condition. The presence of either an einarginated cheek or an embayment of the lateral surface of the dentary and the absence of an otic notch in microsaurs indicate a salamander-like distribution of die adductor jaw muscles. The ancestors of frogs and salamanders probably diverged from one another in the early Carboniferous, Frogs later evolved from small labyrinthodonts and salamanders from microsaurs. Features considered typical of lissamphibians evolved separately in the two groups in the late Permian andTriassic.     

X-ray structure and the reaction mechanism of bovine heart cytochrome c oxidase

X-ray structure of bovine heart cytochrome c oxidase in the fully oxidized state shows a peroxide bridging between Fe2+ and Cu2+ in the O2 reduction site. The bond distances for Fe-O and Cu-O are 2.52 and 2.16 A, respectively. The structure is consistent with antiferromagnetic coupling between the two metals, which has long been known and to recent redox titration results [J. Biol. Chem. 274 (1999) 33403]. The trigonal planer coordination of Cu1+ in the O2 reduction site is consistent with the very weak interaction between Cu1+ and O2 bound at Fe2+ revealed by time-resolved resonance Raman investigations. One of the three histidine imidazoles coordinated to the Cu ion in the O2 reduction site fixes a tyrosine phenol group near the O2 reduction site with the direct covalent link between the two groups. The structure suggests that the phenol group is the site for donating protons to the bound O2. Redox-coupled conformational change in an extramembrane loop indicates that an aspartate (Asp51) in the loop apart from the O2 reduction site is the site for proton pumping.     

Synthesis, crystal structure and luminescent properties of two cadmium thiocyanate coordination polymers with benzylpyridyl cations

Two luminescent Cd(II) complexes [RBzPy][Cd(SCN)₃] for R = Cl (1) and Br (2) have been synthesized and structurally characterized. The Cd atoms are all N3S3 hexa-coordinated with six bridging SCN⁻ and form infinite [Cd(SCN)₃]_∞ polymeric chains. The layer arrangement of the anionic chains was obtained using the larger halogenated benzylpyridyl cations. The luminescent properties of 1 and 2 in the solid state were investigated.     

Homo- and heterochiral coordination polymers of silver with diaminocyclohexane as bridging ligand: Trends in alkylbenzoates

Reaction of Ag₂CO₃ with four methyl-substituted derivatives of benzoic acid afforded silver benzoates; no additional anions are involved in these solids. One of the silver carboxylates was studied by X-ray diffraction: in the crystal, silver 3,5-dimethylbenzoate monohydrate consists of carboxylato-bridged discrete dinuclear molecules with a short Ag?Ag separation of 2.7719(5) Å and one weakly bonded hydrate water molecule per cation. The binary silver carboxylates were combined with either racemic or enantiopure trans-1,2-diaminocyclohexane and resulted in four homochiral and four heterochiral crystalline solids. All eight structures feature cationic chain polymers, carboxylate anions and hydrate water. In three of the solids derived from the racemic ligand, the individual cationic chains are homochiral. In all structures, the primary coordination of the Ag(I) centers by nitrogen is essentially linear. Despite the chemical similarity in the anions, the backbone of the polymers proved to be conformationally soft with variable Ag-N-C-C torsion angles. In the resulting structures, the diamine ligand may bridge two cations in a wide distance range between ca. 3.0 and ca. 7.2 Å. Both the chirality of the trans-1,2-diaminocyclohexane ligand and the substitution pattern of the benzoate anion have strong impact on the nature of secondary interactions perpendicular to the polymer strands: either weak coordination by carboxylato or hydrate water oxygen atoms or argentophilic interactions are encountered. The Ag?Ag contacts increase the dimensionality of the solids from chain polymers to layer structures.     

Sugar-linked biodegradable polymers: Regio-specific ester bonds of glucose hydroxyls in their reaction with maleic anhydride functionalized polystyrene and elucidation of the polymer structures formed

In the development of sugar-linked synthetic polymers as biodegradable polymers, it is imperative to know the variety of polymer structures formed by the reaction of a multi-functional sugar molecule with the functionalized synthetic polymer on which the sugar is to be anchored. Enzymes produced by the microorganisms causing the polymer to biodegrade can be sensitive to the particular type of sugar hydroxyl utilized (such as anomeric, primary, or secondary hydroxyl group) for getting anchored to the polymer. In this paper, we present synthesis of regio-specific ester derivatives of glucose with anhydride, functionalized polymers, i.e., ester formation specifically with the anomeric, primary or secondary hydroxyls of glucose. Characterization of these different esters groups was done using FTIR spectroscopy; each ester peak was further deconvoluted to yield its different components. For this purpose, we studied the reactions of d-glucose, 6-O-trityl glucose, methyl glucoside, 1,2-5,6-diisopropylidene-d-glucose, and 1,2,3,4-tetraacetyl-d-glucose with maleic anhydride functionalized polystyrene (PSMAH). In this study, the primary hydroxyl of glucose was found to be even more reactive than the anomeric hydroxyl. The peaks at 1716, 1725, and 1729–1737 cm⁻¹ were assigned to the ester carbonyl of the anomeric, primary, and secondary hydroxyls of glucose (C2, C3, and C4), respectively. An attempt was made to quantify the extent to which the different polymer structures are formed in a particular reaction by taking ratios of non-variable reference peaks (polystyrene peak at 1493 cm⁻¹) and variable peaks caused by the reaction (the residual anhydride carbonyl at 1780 cm⁻¹).     

Examination of the nickel site structure and reaction mechanism in Streptomyces seoulensis superoxide dismutase

Superoxide dismutases are metalloenzymes involved in protecting cells from oxidative damage arising from superoxide radical or reactive oxygen species produced from superoxide. Examples of enzymes containing Cu, Mn, and Fe as the redox-active metal have been characterized. Recently, a SOD containing one Ni atom per subunit was reported. The amino acid sequence of the NiSOD deduced from the nucleotide sequence of the structural gene sodN from Streptomyces seoulensis is reported and has no homology with other SODs. X-ray absorption spectroscopic studies coupled with EPR of the Ni center show that the Ni in the oxidized (as isolated) enzyme is in a five-coordinate site composed of three S-donor ligands, one N-donor, and one other O- or N-donor. This unique coordination environment is modified by the loss of one N- (or O-) donor ligand in the dithionite-reduced enzyme. The NiSOD activity was determined by pulse radiolysis, and a value of kcat = 1.3 x 10(9) M-1 s-1 per Ni was obtained. The rate is pH sensitive and drops off rapidly above pH 8. The results characterize a novel class of metal center active in catalyzing the redox chemistry of superoxide and, when placed in context with other nickel enzymes, suggest that thiolate ligation is a prerequisite for redox-active nickel sites in metalloenzymes.     

On the structure of molecularly imprinted polymers by modifying charge on functional groups through molecular dynamics simulations

Molecularly imprinted polymers (MIPs) have been widely applied in many fields owing to their advantages. The recognition mechanism between target molecules and MIPs and the influence of dominant factor on the recognition process are still poorly understood. In this paper, a cubic methacrylate-based MIP model was constructed, and the charge on carboxyl group atoms was changed artificially to investigate the recognition process. It is found that the diffusion coefficients of the target molecules (cholesterol) are not affected by polymer network structure. The recognition process is mainly determined by the mesh sizes of the polymer network. In addition, the structure of modified MIP systems was also discussed from the viewpoints of radial distribution function and hydrogen bonds system. These results suggest that the polymer matrix structure would be enhanced with an increase in charge. Thus, it influences the structure of the water molecules in the system a little.     

The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase

Escherichia coli 2,4-dienoyl-CoA reductase is an iron-sulfur flavoenzyme required for the metabolism of unsaturated fatty acids with double bonds at even carbon positions. The enzyme contains FMN, FAD, and a 4Fe-4S cluster and exhibits sequence homology to another iron-sulfur flavoprotein, trimethylamine dehydrogenase. It also requires NADPH as an electron source, resulting in reduction of the C4-C5 double bond of the acyl chain of the CoA thioester substrate. The structure presented here of a ternary complex of E. coli 2,4-dienoyl-CoA reductase with NADP+ and a fatty acyl-CoA substrate reveals a possible mechanism for substrate reduction and provides details of a plausible electron transfer mechanism involving both flavins and the iron-sulfur cluster. The reaction is initiated by hydride transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. In the final stages of the reaction, the fully reduced FMN provides a hydride ion to the C5 atom of substrate, and Tyr-166 and His-252 are proposed to form a catalytic dyad that protonates the C4 atom of the substrate and complete the reaction. Inspection of the substrate binding pocket explains the relative promiscuity of the enzyme, catalyzing reduction of both 2-trans,4-cis- and 2-trans,4-trans-dienoyl-CoA thioesters.     

Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans and catalytic reaction mechanism

Uridine-diphospho-N-acetylglucosamine (UDP-GlcNAc) is a precursor of the bacterial and fungal cell wall. It is also used in a component of N-linked glycosylation and the glycosylphosphoinositol anchor of eukaryotic proteins. It is synthesized from N-acetylglucosamine-1-phosphate (GlcNAc-1-P) and uridine-5'-triphosphate (UTP) by UDP-GlcNAc pyrophosphorylase (UAP). This is an S(N)2 reaction; the non-esterified oxygen atom of the GlcNAc-1-P phosphate group attacks the alpha-phosphate group of UTP. We determined crystal structures of UAP from Candida albicans (CaUAP1) without any ligands and also complexed with its substrate or with its product. The series of structures in different forms shows the induced fit movements of CaUAP1. Three loops approaching the ligand molecule close the active site when ligand is bound. In addition, Lys-421, instead of the metal ion in prokaryotic UAPs, is coordinated by both phosphate groups of UDP-Glc-NAc and acts as a cofactor. However, a magnesium ion enhances the enzymatic activity of CaUAP1, and thus we propose that the magnesium ion increases the affinity between UTP and the enzyme by coordinating to the alpha- and gamma-phosphate group of UTP.     

Anthochlors and other flavonoids as honey guides in the compositae

Anthochlor pigments have been recorded for the first time in three species of Helianthus and in Viguiera laciniata. Yellow flavonols based on quercetagetin or gossypetin have been found in yellow flowered species of Eriophyllum and Geraea. In Eriophyllum, all seven species studied contain quercetagetin and/or patuletin 7-glucosides. In those species containing UV honey guides, either yellow flavonoid or colourless quercetin glycosides can be responsible for producing strongly UV absorbent zones on the flowers. Thus in Helianthus, honey guides in some species result from UV absorbance by the chalcone coreopsin and the aurone sulphurein, whilst in H. annuus they result from absorbance by quercetin 3- and 7-glucosides. Furthermore, the occurrence of yellow flavonoids in flowers is not directly correlated with the presence of UV nectar guides. A detailed study of the distribution of chalcone in Coreopsis bigelovii flowers revealed that the anthochlor was present in epidermal cells on both upper and lower surfaces.     

Self-assembly of three novel mixed-ligand coordination polymers: Formation of 2-D grids, 1-D chains and ladders and crystal band structure

Hydrothermal reaction of the carboxylate-based ligands with metal salts (or oxide) and 4,4′-bipyridine as a second linker, afforded three new coordination polymers, namely, [Co(PCPA)₂(4,4′-bpy)]_n (1) with 2-D rectangle grids, Cu(PCPA)₂(4,4′-bpy)]_n (2) with a linear chain, [Ag(PCPA)(PCPAH)(4,4′-bpy) · H₂O]_n (3) with 1-D molecular ladder (4,4′-bpy = 4,4′-bipyridine; PCPA = p-chlorophenoxyacetate; PCPAH = p-chlorophenoxyacetic acid). It is noticeable that compound 3 is also a supramolecular framework built by coordination bonds, weak interactions between Ag ions, π-π stacking interactions and hydrogen-bonded interactions. The three compounds with different structure motifs have been characterized by elemental analyses, IR spectra, ultraviolet-visible diffuse reflection integral spectra, fluorescent spectra and single crystal X-ray diffraction analysis. Furthermore, the bonding properties of compound 3 were investigated in terms of the absorption spectrum, as well as the calculated band structures and density of states.     

A series of inorganic-organic hybrid compounds constructed from bis(undecatungstophosphate) lanthanates and copper-organic units

A series of inorganic-organic hybrid compounds built from bis(undecatungstophosphate) lanthanates and copper-complexes, namely, H₈[Cu(en)₂H₂O]₄[Cu(en)₂]{[Cu(en)₂][La(PW₁₁O₃₉)₂]}₂·18H₂O (1), H₆[Na₂(en)₂(H₂O)₅][Cu(en)₂H₂O]₄[Cu(en)₂]{[Cu(en)₂][Ce(PW₁₁O₃₉)₂]}₂·16H₂O (2), H₆[Na₂(en)₂(H₂O)₅][Cu(en)₂H₂O]₄[Cu(en)₂]{[Cu(en)₂][Pr(PW₁₁O₃₉)₂]}₂·18H₂O (3), H₆[Na₂(en)₂(H₂O)₄][Cu(en)₂H₂O]₄[Cu(en)₂]{[Cu(en)₂][Nd(PW₁₁O₃₉)₂]}₂·14H₂O (4), H₆[Na₂(en)₂(H₂O)₅][Cu(en)₂H₂O]₄[Cu(en)₂]{[Cu(en)₂][Sm(PW₁₁O₃₉)₂]}₂·20H₂O (5), and H₇[Cu(en)₂]₂[Sm(PW₁₁O₃₉)₂]·10H₂O (6) (where en = 1,2-ethylenediamine), have been prepared. In these compounds, two lacunary [PW₁₁O₃₉]⁷⁻ anions sandwich an eight-coordinated Ln(III) cation to yield [Ln(PW₁₁O₃₉)₂]¹¹⁻ anion in a twisted square anti-prismatic geometry, which is further bridged by [Cu(en)₂]²⁺ fragments to generate a 1D zigzag-like chain. In 1-6, the coordination bond interactions and weak interactions between adjacent 1D chains play an important role in the zigzagging distances and angles of different 1D chains. The magnetic studies indicate that antiferromagnetic interactions exist in compounds 1, 2 and 4.