Carbon Atom In Position Research Articles

Carbon-rich boron carbide in the eutectic product synthesized by resistance heating of B 2CN in graphite

Rhombohedral boron carbide has been synthesized by resistance heating of B 2CN in graphite. The boron carbide and graphite form a clad morphology in a eutectic product containing ∼39 wt.% of carbon. Graphite with different interlayer spacing has been observed. A wide range of carbon-rich concentration for the boron carbide indicating strong carbon segregation has been detected. Precise measurements of lattice parameters and composition analysis for the boron carbides suggest that more than 20 at.% of carbon may have dissolved into some sections of the rhombohedral boron carbide crystals. Positions of the extra carbon atoms in the rhombohedral structure are discussed.

CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation.

The first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to Pseudomonas putida GPo1 AlkB, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome P450s. Recently, a family of cytoplasmic P450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. One member of this family, CYP153A6 from Mycobacterium sp. HXN-1500, hydroxylates medium-chain-length alkanes (C6 to C11) to 1-alkanols with a maximal turnover number of 70 min(-1) and has a regiospecificity of > or =95% for the terminal carbon atom position. Spectroscopic binding studies showed that C6-to-C11 aliphatic alkanes bind in the active site with Kd values varying from approximately 20 nM to 3.7 microM. Longer alkanes bind more strongly than shorter alkanes, while the introduction of sterically hindering groups reduces the affinity. This suggests that the substrate-binding pocket is shaped such that linear alkanes are preferred. Electron paramagnetic resonance spectroscopy in the presence of the substrate showed the formation of an enzyme-substrate complex, which confirmed the binding of substrates observed in optical titrations. To rationalize the experimental observations on a molecular scale, homology modeling of CYP153A6 and docking of substrates were used to provide the first insight into structural features required for terminal alkane hydroxylation.

Structural Basis for the Function of Clostridium difficile Toxin B

Toxin B is a member of the family of large clostridial cytotoxins which are of great medical importance. Its catalytic fragment was crystallized in the presence of UDP-glucose and Mn2+. The structure was determined at 2.2 A resolution, showing that toxin B belongs to the glycosyltransferase type A family. However, toxin B contains as many as 309 residues in addition to the common chainfold, which most likely contribute to the target specificity. A superposition with other glycosyltransferases shows the expected positions of the acceptor oxygen atom during glucosyl transfer and indicates further that the reaction proceeds probably along a single-displacement pathway. The C1'' donor carbon atom position is defined by the bound UDP and glucose. It assigns the surface area of toxin B that forms the interface to the target protein during the modifying reaction. A docking attempt brought the known acceptor atom, Thr37 O(gamma1) of the switch I region of the RhoA:GDP target structure, near the expected position. The relative orientation of the two proteins was consistent with both being attached to a membrane. Sequence comparisons between toxin B variants revealed that the highest exchange rate occurs around the active center at the putative docking interface, presumably due to a continuous hit-and-evasion struggle between Clostridia and their eukaryotic hosts.

Methionine and derivatives: Exploring chirality at sulfur

AbstractChiral molecules, both small and large, play important roles in biochemistry, molecular biology, and related biosciences. The central position of carbon atoms in determining chirality has received considerable attention. Less well known is the fact that chirality is also possible for sulfur atoms in certain compounds. This article introduces the role of sulfur chirality in metabolic reactions by considering methionine derivatives with chiral sulfur atoms, S‐adenosylmethionine and its decarboxylated product, methionine S‐oxide, and methionine sulfoximine.

Computational Study of Structures and Properties of Metallaboranes: Cobalt Bis(dicarbollide)

A density functional study at the BP86/AE1 level is presented for the cobalt bis(dicarbollide) ion [3-Co-(1,2-C2B9H11)2]- (1) and selected isomers and rotamers thereof. Rotation of the two dicarbollide moieties with respect to each other is facile, as judged by the small energetic separation of the three rotamers located (within 11 kJ mol(-1)) and by the low barriers for their interconversion (at most 41 kJ mol(-1)). Among the isomers differing in carbon atom positions that contain two equivalent dicarbollide ligands, the 1,7 ("carbon apart") form [2-Co-(1,7-C2B9H11)2]- is the most stable, 121 kJ mol(-1) below 1. The electronic structure of 1 is characterized in terms of molecular orbitals, population analysis, and excitation energies from time-dependent density functional theory, relevant to UV/Vis spectroscopy. Experimental 11B NMR chemical shifts of 1 are reproduced to better than 5 ppm at the GIAO-B3LYP/II' level, and the computed delta(11B) values are only little affected by rotational averaging or the presence of a polarizable continuum. Larger such effects are found for the as-yet unknown 59Co chemical shift, for which a value in the range between -1800 and -2400 ppm is predicted. Even though the accuracy achieved for the theoretical delta(11B) values is somewhat lower than that for heteroboranes at conventional ab initio levels, the level of density functional employed can afford qualitatively reliable chemical shifts, which can be useful in assignments and structural refinements of heteroboranes containing transition metal.

Influence of germanium ad-dimers on carbon incorporation in the Si(001) surface

We present a theoretical study of the influence of germanium ad-dimers on carbon incorporation in the Si(001) surface. Our ab initio energetic calculations show that the presence of a germanium ad-dimer clearly improves the single-carbon-atom penetration in the Si(001) subsurface layers with respect to the defectless surface. The energetic barrier observed in the case of the defectless Si(001) surface has disappeared, and the third-layer $\ensuremath{\alpha}$ sites are largely favored. Comparing our results to those obtained in the presence of silicon ad-dimers, we notice roughly similar trends, but our study emphasizes the role of the chemical nature of the ad-dimer following its orientation. On the other hand, the size difference between the germanium and silicon atoms in the ad-dimers is found to be of less importance. We eventually show that parameters such as the chemical nature, orientation, and location of the ad-dimers can be adequately monitored to improve carbon penetration in the Si(001) surface and allow a better control of the carbon atom positions in the subsurface layers.

Crystal Structure of Arachidonic Acid Bound to a Mutant of Prostaglandin Endoperoxide H Synthase-1 That Forms Predominantly 11-Hydroperoxyeicosatetraenoic Acid

Kinetic studies and analysis of the products formed by native and mutant forms of ovine prostaglandin endoperoxide H synthase-1 (oPGHS-1) have suggested that arachidonic acid (AA) can exist in the cyclooxygenase active site of the enzyme in three different, catalytically competent conformations that lead to prostaglandin G2 (PGG2), 11R-hydroperoxyeicosatetraenoic acid (HPETE), and 15R,S-HPETE, respectively. We have identified an oPGHS-1 mutant (V349A/W387F) that forms predominantly 11R-HPETE. Thus, the preferred catalytically competent arrangement of AA in the cyclooxygenase site of this double mutant must be one that leads to 11-HPETE. The crystal structure of Co3+-protoporphyrin IX V349A/W387F oPGHS-1 in a complex with AA was determined to 3.1 A. Significant differences are observed in the positions of atoms C-3, C-4, C-5, C-6, C-10, C-11, and C-12 of bound AA between native and V349A/W387F oPGHS-1; in comparison, the positions of the side chains of cyclooxygenase active site residues are unchanged. The structure of the double mutant presented here provides structural insight as to how Val349 and Trp387 help position C-9 and C-11 of AA so that the incipient 11-peroxyl radical intermediate is able to add to C-9 to form the 9,11 endoperoxide group of PGG2. In the V349A/W387F oPGHS-1.AA complex the locations of C-9 and C-11 of AA with respect to one another make it difficult to form the endoperoxide group from the 11-hydroperoxyl radical. Therefore, the reaction apparently aborts yielding 11R-HPETE instead of PGG2. In addition, the observed differences in the positions of carbon atoms of AA bound to this mutant provides indirect support for the concept that the conformer of AA shown previously to be bound within the cyclooxygenase active site of native oPGHS-1 is the one that leads to PGG2.

Preparation, Crystal Structure at 298 and 90 K and Phase Transition in (C2H5NH3)2[SbBr5] Studied by the Single Crystal X-Ray Diffraction Method

The reaction of antimony(III) oxide with ethylamine, in molar ratios from 1:1 to 1:10, in concentrated hydrobromic acid leads to the formation of one product - bis(ethylammonium) pentabromoantimonate( III). The structure of (C2H5NH3)2[SbBr5] was determined at 298 and 90 K, below and above the phase transition that occurs at about 158.5 K. The orthorhombic system was found in both phases, space groups Cmca and Pbca at 298 and 90 K, respectively. At both temperatures the structure consists of [SbBr6]3− octahedra connected via cis bromine atoms forming one-dimensional zig-zag [{SbBr5}2−]n chains. The ethylammonium cations fill the space between polyanionic chains. The organic and inorganic substructures are held together by a system of N(-H)···Br interactions. Their influence on the deformation of [SbBr6]3− octahedra is well reflected in differences in the corresponding Sb-Br bond lengths and Br-Sb-Br angles in both phases. The phase transition is of the first order and the order-disorder type. It is related to changes in the molecular dynamics of the ethylammonium cations. In the low-temperature phase the organic cations are ordered, while at 298 K both crystallographically independent cations are disordered. The type of disorder is realized by the presence of two positions of the methyl carbon atoms

Origin of chemiluminescence accompanying the reaction of the 9-cyano-10-methylacridinium cation with hydrogen peroxide.

The 9-cyano-10-methylacridinium cation possesses an electrophilic center at the carbon atom in position (9) susceptible to the addition of anions. The addition of OOH(-) to this cation--in weakly acidic, neutral, or alkaline media--initiates processes leading to the formation of electronically excited 10-methyl-9-acridinone, which deactivates by light emission. The effect of changes in reactant concentrations and pH on emission decay with time, as well as other features of the accompanying chemiluminescence, were established. Calculations carried out at the semiempirical and density functional theory level demonstrated that initial addition of OOH(-) and subsequent processes lead either to the elimination of OCNH (in weakly acidic and neutral media) or OCN(-) (in alkaline media) and that their exothermicity is sufficiently high to generate electronically excited 10-methyl-9-acridinone. On the other hand, primary addition of OH(-) to C(9) in alkaline media initiates the conversion of the cation to the nonexcited 10-methyl-9-acridinone. This relatively rapid process influences to a substantial extent the intensity of the chemiluminescence. The prospects for the analytical application of 9-cyano-10-methylacridinium salts are briefly outlined.

Isotopic discrimination between D-[1- 13C]fructose and D-[2- 13C]fructose in rat liver cells

When liver cells from either normal or hereditarily diabetic rats are exposed to 13C-enriched D-fructose (10 mM) and unlabelled D-glucose (also 10 mM) in the presence of D 2O, the output of 13C-enriched D-glucose generated from D-[1- 13C]fructose is significantly lower than that from D-[2- 13C]fructose. This coincides with a higher generation of 13C-enriched L-lactate and L-alanine from D-[1- 13C]fructose, as compared to D-[2- 13C]fructose. In absolute terms, the mean paired difference in the output of 13C-enriched D-glucose generated from D-[1- 13C]fructose versus D-[2- 13C]fructose is not significantly different from the mean paired difference in the production of 13C-enriched L-lactate and L-alanine from the same precursors, with an overall mean value of 7.01 ± 1.59 μmol ( n = 8; P < 0.005). It is proposed that these findings indicate isotopic discrimination at the phosphoglucoisomerase level between 12C and 13C for the carbon atom in position 1 (as compared to that in position 2) of D-fructose 6-phosphate.

Arachidonate geometrical isomers generated by thiyl radicals: the relationship with trans lipids detected in biological samples.

The presence of trans fatty acids in mammalians is attributed to exogenous sources; nevertheless, trans isomers could be easily formed by free radical-catalyzed isomerization processes in vivo. The isomerization of methyl arachidonate (all-cis isomer) catalyzed by thiyl radical is proposed as a methodology applicable in biochemical laboratories, which produces mono- and di-trans isomers. Carbon-13 nuclear magnetic resonance spectroscopy shows that the carbon atom in position 15 is characteristic for each mono- and di-trans isomer. Antioxidants, such as alpha-tocopherol and all-trans-retinol acetate, inhibited the isomerization process. Trans phospholipids are formed in erythrocyte membranes by exposing blood to gamma-irradiation in the presence of thiols, which is in contradiction with the known role of these compounds as radioprotectors. Trans isomers are also analyzed in tissues harvested from breast cancer patients and compared to the adipose breast tissue taken a few centimeters from the edge of the tumor from the same patient. This work is generally aimed at contributing to the debate on trans fatty acids and stimulating a reconsideration of the current view on the exclusive presence of cis double bonds in cell membranes by studying radical processes that could affect or protect this natural configuration.

(13)C-NMR isotopomer distribution analysis: a method for measuring metabolic fluxes in condensation biosynthesis.

(13)C NMR spectroscopy associated with the use of (13)C-enriched substrates is a powerful tool to investigate intracellular metabolism because of the wealth of information contained in the distribution of isotopes in key metabolites. A new method of using (13)C label distribution measurements in carbon skeletons of metabolites to estimate metabolic fluxes through biochemical reaction networks is presented here. This method can be applied to metabolite synthesis occurring by condensation reactions of the type nA --> B, where n is the number of precursor A molecules needed to synthesize one molecule of product B. NMR isotopomer distribution analysis (NMR-IDA) involves the introduction of a (13)C-enriched precursor, and measurements of the (13)C positional enrichments at just one carbon atom position of the product B via (13)C NMR spectroscopy. Information on isotopomer distribution is obtained, and data are analyzed according to a mathematical model based on multinomial probability expressions to obtain the best fit between theoretical and experimental (13)C label distribution. The use of the NMR-IDA method allows for estimation of two key parameters representing the fractional flux of (13)C-enriched tracer A molecules to total precursor A pool and the fraction of product B synthesized in the presence of a (13)C-enriched source, respectively. A practical example of NMR-IDA application to fatty acid synthesis from [(1,2 (13)C(2))acetyl]-L-carnitine in cultured primary astrocytes is also presented.

Crystal Structure of a Metastable Anthracene Modification, Grown from the Vapor Phase

The crystal structure of a new monoclinic metastable phase of anthracene formed during vapor growth has been determined from single crystal X-ray data (DARCH-1 automatic diffractometer, Mo K α radiation). This metastable anthracene phase crystallizes in the monoclinic space group P2 1 /n with a =8.553(2), b =6.021(1), c =22.334(4), Å and β=124.54(3)°, and four molecules per unit cell. All carbon and hydrogen atom positions have been determined and refined to R=0.044 for 330 unique reflections.

Dimethyl Branching of Long n-Alkanes in the Range from Decane to Tetracosane on Pt/H–ZSM-22 Bifunctional Catalyst

Single long n-alkanes in the range n-C10 to n-C24 were hydroisomerized at 233°C in a fixed-bed down-flow vapor-phase reactor loaded with Pt/H–ZSM-22 zeolite catalyst. The multibranched isomer fractions obtained by skeletal isomerization of the different n-alkanes were analyzed in detail with GC-MS. The large majority of multibranched isomers were dimethyl branched. In the preferred isomers, the tertiary carbon atoms carrying the methyl branchings were separated by 3 up to 14 carbon atom positions. Further peculiarities were the preferential formation of isomers with symmetric methyl positions on the chain. Among this family of “symmetric” isomers, the formation of 2,x−3-dimethyl–Cx−2 isomer was favored in conversions of n-Cx alkanes with x equal to or smaller than 17 and disfavored with longer molecules. In the family of 3,n-dimethyl–Cx−2 isomers obtained from the longest alkanes studied (n-C20, n-C22, n-C24), the preferred n positions were from 8 to 12 and from 14 to 18. In the 4,n-dimethyl–Cx−2 isomers, the preferred n positions were from 8 to 17. It was also found that the formation of a dimethyl-branched isomer occurs preferentially through methyl branching of a monomethyl-branched isomer having already the more centrally positioned methyl group rather than the one close to the extremity of the chain. These peculiar positional selectivities and reaction paths can be explained by key-lock catalysis in pairs of micropore openings on the external surface of the ZSM-22 zeolite crystals.

The formation of chloride adducts in the detection of dinitro-compounds by ion mobility spectrometry

The formation of chloride adducts by dinitro-alkanes in the gas phase has been studied by ion mobility spectrometry. Special emphasis was placed on the association of chloride with 2,3-dimethyl-2,3-dinitrobutane (DMNB), a prospective taggant for plastic explosives, but the reactions of chloride with 1,4-dinitrobutane (DNB) and with 2,3-dimethyl-2,4-dinitropentane (DMDNP) were also studied briefly. The thermal stabilities of the chloride adducts as shown by the effect of temperature on the mobility spectra were found to decrease in the order DNB·Cl − > DMDNP·Cl − > DMNB·Cl −. The equilibrium Cl − + DMNB = DMNB·Cl − was set up in the drift tube and by monitoring the drift time of the single peak due to the equilibrium mixture of Cl − and DMNB·Cl − as the DMNB concentration was varied, the equilibrium constant was determined. Measurement of the equilibrium constant at a series of temperatures gave ΔH 0 = −92.1 ± 3.1 kJ mol −1 and ΔS 0 = −92.1 ± 7.4 J K −1 mol −1 for the association. The enthalpy change for the formation of the most stable of the dinitro adducts, DNB · Cl −, is estimated to be 20 kJ mol −1 more negative than that for the DMNB adduct. The order of the stabilities of the chloride complexes is consistent with the number of very acidic hydrogen atoms on the carbon atoms in positions α to the nitro groups viz. DNB, 4; DMDNP, 2; DMNB, 0. The determined vapor pressures of DMNB and DNB over the respective ranges −20 to +50 °C and −10 to +30 °C respectively, are described by the equations log P = 19.82 ± 0.09 − (4 878 ± 26)/T (K) and log P = 18.08 ± 0.29 − (4 274 ± 81)/T (K), where P is the vapor pressure in parts per billion by volume, T is temperature in kelvin, and the quoted uncertainties are the standard errors.

First-principles study of the atomic oxygen adsorption on the (0 0 0 1) graphite surface and dissolution

In the framework of the density-functional theory we studied the atomic oxygen adsorption on the basal graphite surface at three imposed oxygen coverages 50, 25, 5.5% for three different adsorption sites, and also the dissolution of the atomic oxygen in graphite at one fixed coverage. Independently of the concentration, the most stable position of oxygen atoms is directly above a carbon–carbon bond (bridge), followed by the directly above a carbon atom position (top), and the directly above a hexagonal hollow (hex) site. Intercalating oxygen just below the surface layer, shows that dissoluted oxygen is more stable than adsorbed one.

Synthesis, Spectral Characterisation and Crystal Structure of (1,24-Bicyclophthalocyaninato)bismuth(III)

A new orange bicyclophthalocyanine complex of bismuth(III), [Bi(C48H24N13)], has been synthesised by means of the template reaction of bismuth(III) acetate with phthalodinitrile. The ligand consists of the phthalocyanine skeleton, which is bridged by two additional isoindole units. The conjugation of the phthalocyanine ring is interrupted by the two bridgehead sp3-hybridised carbon atoms. The main difference between this new bicyclophthalocyanine and those previously reported in the literature lies in the position of the bridgehead carbon atoms. In order to differentiate between these bicyclophthalocyaninato complexes, we propose a nomenclature: [Bi(C48H24N13)] is named Bi(1,24-Pcc), and the other bicyclic ligands already reported in the literature are named (1,16-Pcc) and (1,17-Pcc). The molecular structure of Bi(1,24-Pcc) shows the coordination polyhedron around the bismuth atom, made up of the six isoindole nitrogen atoms of the macrocycle, as a strongly distorted trigonal prism. The two Bi−Niso bonds of the bridge and two of the four Bi−Niso bonds of the (Pc) ring have bond lengths between 2.40 and 2.47 A. One of the remaining bonds is longer (2.55 A), and the sixth has a very short length of 2.20 A. This new complex was fully characterised by UV/Vis and IR spectroscopy, also reported here.

POLYMERIC MOLECULAR PATTERN IN THE CRYSTALS OF A CALCIUM(II) COMPLEX WITH PYRIDINE-3,4-DICARBOXYLATE AND WATER LIGANDS

Crystals of triaquamono (μ-pyridine-3,4-dicarboxylato-O,O′,O,O′)(aqua-O)calcium(II) contain molecular ribbons in which two adjacent calcium ions are bridged via oxygen atoms donated by the carboxylate group attached to carbon atom “3” in the pyridine ring. Both oxygen atoms are bidentate, each being coordinated to two caloium ions. In addition, every second pair of calcium(II) ions is bridged by a water oxygen atom. The coordination polyhedron around the calcium(II) ion is pentagonal bipyramidal; its equatorial plane is composed of two bridging oxygen atoms each belonging to the carboxylate group of the adjacent ligands, the bridging water oxygen atom and two coordinated water molecules. Another coordinated water oxygen atom constitutes the apex of the pyramid on one side of the pentagon, while two bridging carboxylate oxygen atoms donated by the same carboxylate group make two apices on the other side of the pentagon. The pyridine hetero-ring nitrogen atom does not participate in coordination to the central ion. Both oxygen atoms of the carboxylate group attached to the carbon atom in position “4” of the pyridine ring are not directly coordinated to the calcium(II) ion and act only as acceptors in the hydrogen bond system.

Chemical Composition and Recrystallization of Epicuticular Waxes: Coiled Rodlets and Tubules

Abstract: Coiled rodlets characterize several non‐related taxa within the angiosperms. They often occur together with tubules but sometimes also with platelets or transitional forms between them. The ultrastructure chemistry, and recrystallization of epicuticular waxes of three species were investigated by high‐resolution scanning electron microscopy, gas chromatography, and mass spectrometry. Whereas Buxus sempervirens (Buxaceae) and Chrysanthemum segetum (Asteraceae) show coiled rodlets in combination with tubules, Leymus arenarius (Poaceae) exhibits tubules but no coiled rodlets. Chemical analyses reveal that the predominating β‐diketones of all species differ completely in their molecular structure. Those of the former two species are mainly substituted in carbon atom positions up to 12. In contrast, the wax of L. arenarius contains only hentriacontane‐14,16‐dione and 25‐hydroxy‐hentriacontane‐14,16‐dione. Standard solutions of the total waxes from B. sempervirens, C. segetum and L. arenarius, the purified β‐diketone fraction from C. segetum and hentriacontane‐14,16‐dione from Secale cereale were taken for recrystallization experiments under different conditions in relation to solvent and crystallization velocity. It was demonstrated that coiled rodlets grew exclusively from total waxes of B. sempervirens and C. segetum, and its β‐diketone fraction but never from L. arenarius wax or pure hentriacontane‐14,16‐dione. The recrystallization experiments pointed out that conditions, such as the chemical environment and physical factors, strongly influence the formation of coiled rodlets and tubules. It is concluded that coiled rodlets are formed by self‐assembly in close dependence on the position of β‐diketo substitution. The future role of β‐diketones in the classification of coiled rodlets within wax crystals is discussed.

Structure and electronic properties of nitrogen-containing carbon nanotubes

The structure and electronic properties of nitrogen-containing carbon nanotubes are investigated using self-consistent field crystal orbital method. The models of these tubes are constructed by substitution of some carbon atoms with nitrogen atoms in the armchair carbon nanotube. The calculated band structures show that these nanotubes can be metals or semiconductors depending on the relative position of nitrogen and carbon atoms. The most stable non-metallic tubes are narrow energy gap (EG) semiconductors. Metallic tubes have two overlapped partially filled bands. The influence of Fermi vector positions on metal–insulator phase transition is discussed in the metallic NC tubes.