Coatomer Research Articles

Structures and Properties of Cytosine…CO Complex

The calculations on the interaction between cytosine and carbon monoxide have been performed at B3LYP/6-311+G** level and six local minimum isomers have been found. Both C and O can combine with N—H bond of cytosine and then hydrogen bonds between them are formed. The carbon atom of CO has a privilege to bind with cytosine. The length of CO bond is diminished in C combined complexes and it is lengthened in O combined complexes. In addition, the frequencies of CO suffer blue shifts in the former and red shifts in the latter.

Electrostatic properties of small molecules by means of atomic multipoles from the quantum theory of atoms in molecules

AbstractAtomic multipoles from the Quantum Theory of Atoms in Molecules (QTAIM), up to quadrupoles, and CHELPG charges are employed in the description of electrostatic properties of some small linear molecules: H2, HF, HCl, HBr, HCN, HNC, and CO. A proton is placed on the molecular axis in distances within the range 3–8 Å from the terminal atoms. The polarization of molecular electronic densities induced by the proton is readily included by the calculation of atomic multipoles in each proton‐molecule arrangement. Electrostatic potentials at the proton position as given by QTAIM multipoles are always in better agreement with the reference results, calculated directly at the B3LYP/6‐311G(3d,3p) level, than those predicted with CHELPG charges, particularly for cases in which QTAIM multipoles showed that the contribution of atomic charges to these potentials is not clearly predominant over other contributions as in H2, HCl, HBr, HNC, and CO. The lone pair at the carbon atoms in CO and HNC, as described by QTAIM atomic dipoles, is indispensable in studies of electrostatic properties of these molecules. Moreover, QTAIM multipoles are also able to describe properly the large polarizations induced by the proton along the proton‐molecule distances studied. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Role of a Novel Mixed-Valence-Ligand on the Structures of Supramolecular Polymeric Complexes

The design of supramolecular polymer complexes of ruthenium, rhodium and uranium based on the homopolymer N-acryloyl-1-ethyl-2-thiourea (AETH) has been pursued. AETH shows three types of coordination behaviour. It acts as a neutral bidentate ligand coordinating through its thiocarbonyl sulphur and carbonyl oxygen atoms in both the mixed valence paramagnetic trinuclear polymer complexes ((1) and (2)) and mononuclear polymer complexes ((3)–(5)). On the other hand, it behaves as a monobasic bidentate ligand coordinating through CS and enolic (C–O) bonds in the mixed ligand poly-chelates (PAETH), which are obtained from the reaction of AETH with RuCl3 · x H2O in the presence of N-heterocyclic base consisting of polymer complexes ((7) and (8)). The mononuclear compound (6) acts as a monobasic and neutral bidentate ligand coordinating through CO and imino atoms. Monomeric distorted octahedral or trimeric chlorine-bridge pseudo-octahedral structures are proposed for these polymer complexes. The stoichiometries of the poly-chelates are 1:1, 1:2 and 3:2 (metal/homo-polymer) and exhibit six-coordinations. The amine homo-polymer exchange reactions of coordination poly-chelate in symmetrical and unsymmetrical bidentate homo-polymer complexes have been investigated and the ligand field parameters were also calculated. The homo-polymer and its polymer complexes have been characterized using a variety of physiochemical techniques.

Dry reforming of methane over LaNi1−yByO3±δ (B=Mg, Co) perovskites used as catalyst precursor

Abstract Perovskites LaNiO3, LaNi1−xMgxO3−δ and LaNi1−xCoxO3−δ were synthesized by auto combustion method. TPR analysis reveled that Mg or Co substituted perovskites were more difficult to reduce. The perovskites were evaluated as catalyst precursors in the dry reforming of methane. Catalysts obtained by reduction of LaNiO3 and LaNi1−xMgxO3−δ perovskite had the highest catalytic activity for CO2 reforming of CH4 at 700 °C using drastic reaction conditions (10 mg of catalyst, a mixture of CH4/CO2 without dilution gas). Methane and carbon dioxide conversions were 57% and 67%, respectively, with a H2/CO ratio equal to 0.47. The presence of cobalt leads to a decrease of the catalytic activity. This decreasing of activity may be attributed to the Co–Ni alloy formation. Computational calculations revealed that Ni atom cleaves the C–H atom while Co is not able to activate the CH4 molecule. The interaction energy of CH4 with the Ni and CO atom was 18 kcal/mol and 0.7 kcal/mol, respectively.The catalysts were characterized by TPR, TEM and in situ XRD.

Bat breath reveals metabolic substrate use in free-ranging vampires

We analysed the stable carbon isotope ratio in exhaled CO(2) (delta(13)C(breath)) of free-ranging vampires to assess the type of metabolized substrate (endogenous or exogenous substrate) and its origin, i.e. whether the carbon atoms came from a C(4) food web (grass and cattle) or the C(3) food web in which they were captured (a rainforest remnant and its mammals). For an improved understanding of factors influencing the delta(13)C(breath) of vampires, we conducted feeding experiments with captive animals. The mean delta(13)C(breath) of starved bats was depleted in (13)C in relation to the diet by 4.6 per thousand (n = 10). Once fed with blood, delta(13)C(breath )levelled off within a short time approximately 2.2 per thousand above the stable carbon isotope signature of the diet. The median time required to exchange 50% of the carbon atoms in exhaled CO(2) with carbon atoms from the ingested blood was 18.6 min (mean 29.5 +/- 19.0 min, n = 5). The average delta(13)C of wing membrane and fur in free-ranging vampire bats suggested that bats almost exclusively foraged for cattle blood during the past weeks. The delta(13)C(breath) of the same bats averaged -19.1 per thousand. Given that all free-ranging vampires were starving and that the delta(13)C of cattle was more in enriched in (13)C by 5-6 per thousand than the delta(13)C(breath) of vampires, we conclude that the vampire bats of our study metabolised fat that was predominantly built from carbon atoms originating from cattle blood. Since delta(13)C of wing membrane and fur integrates over weeks and months respectively and delta(13)C(breath) over hours and days, we also conclude that vampire bats of the studied population consistently ignored rainforest mammals and chose cattle as their prey during and prior to our study.

The Existence of Multiple Conformers of Interleukin-21 Directs Engineering of a Superpotent Analogue

The high resolution three-dimensional structure of human interleukin (hIL)-21 has been resolved by heteronuclear NMR spectroscopy. Overall, the hIL-21 structure is dominated by a well defined central four-helical bundle, arranged in an up-up-down-down topology, as observed for other cytokines. A segment of the hIL-21 molecule that includes the third helical segment, helix C, is observed to exist in two distinct and interchangeable states. In one conformer, the helix C segment is presented in a regular, alpha-helical conformation, whereas in the other conformer, this segment is largely disordered. A structure-based sequence alignment of hIL-21 with receptor complexes of the related cytokines, interleukin-2 and -4, implied that this particular segment is involved in receptor binding. An hIL-21 analog was designed to stabilize the region around helix C through the introduction of a segment grafted from hIL-4. This novel hIL-21 analog was demonstrated to exhibit a 10-fold increase in potency in a cellular assay.

Location and coordination of promoter atoms in Co- and Ni-promoted MoS2-based hydrotreating catalysts

In this study, we used scanning tunneling microscopy (STM) and density functional theory (DFT) to investigate the atomic-scale structure of the active Co- or Ni-promoted MoS2 nanoclusters in hydrotreating catalysts. Co-promoted MoS2 nanoclusters (Co–Mo–S) are found to adopt a hexagonal shape, with Co atoms preferentially located at (1¯010) edges with a 50% sulfur coverage. The first atom-resolved STM images of the Ni-promoted MoS2 nanoclusters (Ni–Mo–S) reveal that the addition of Ni also leads to truncated morphologies, but the degree of truncation and the Ni sites are observed to depend on the nanocluster size. Larger clusters (type A) are structurally similar to Co–Mo–S exposing fully Ni-substituted (1¯010) edges with a 50% S coverage. Smaller clusters (type B) show dodecagonal shapes terminated by three different edges, all of which contain Ni-promoter atoms fully or partially substituting the Mo atoms. The findings may shed more light on the different selectivities observed for the Co- and Ni-promoted hydrotreating catalysts.

Electrocatalytic oxidation of methyl tert-butyl ether (MTBE) in aqueous solution at a nickel electrode

This study utilized the electrocatalytic characteristics of nickel electrode to perform degradation of methyl tert-butyl ether (MTBE) in aqueous solution. Lab experiments were conducted in a spiltless bath type cell equipped with a nickel electrode as working electrode, a platinum wire as counter electrode, and an Ag/AgCl electrode as reference electrode. Effects of controlled potential, supporting electrolyte, and solution pH on the efficiency of MTBE removal were examined under the control of the constant-potential conditions. Experiment results showed that the optimum electrolytic condition was operated at 0.35 V in a 1 M KOH electrolyte solution, and the initial 20 mg l −1 MTBE was reduced by 73% within 180 min under the optimum control. As using 1 M Na 2SO 4 and 1 M KCl as electrolyte, the efficiency of MTBE removal dropped to 60% and 50% under the similar controls. Comparing with various pH controls, the strong basic condition is favorable for electrocatalytic oxidation of MTBE in the Ni-electrolytic system. The efficiency of MTBE removal showed a rising trend with increasing initial pH of the solution. The formation of a redox NiOOH/Ni(OH) 2 layer on the anode surface, which was observed on the SEM image, can explain that nickel plays a mediator role on improving electrocatalytic oxidation of MTBE at 0.35 V in a strong basic condition. The by-products of MTBE degradation were identified as acetone and CO 2 by GC/MS, and the distributions of carbon atoms in acetone, CO 2, and MTBE were found 22%, 51%, and 27% through the optimum control of electrochemical oxidation.

The role of F A1:Ag+ defects in laser light generation and coadsorption of CO and halogen atoms at the KCl and KBr surface sites. First principles calculations

AbstractFA1:Ag+ color center at the low coordination (100) and (110) surface sites of KCl and KBr thin films play an important role in providing tunable laser oscillation and adsorbatesubstrate interactions. Double-well potentials at this site are investigated using ab initio molecular electronic structure calculations. The calculated Stokes shifted (optical transition bands), opticaloptical conversion efficiencies, the probability of orientational destruction, exciton (energy) transfer and Glasner-Tompkins empirical rule suggest that laser light generation is sensitive to (i) the lattice anion, (ii) the coordination number of surface ions, and (iii) the choice of the basis set centered on the anion vacancy. The adsorbate-substrate interactions were found to be dependent on the electronegativity of the adatom and on the lattice anion. Optimised geometries and the coadsorption of CO and (F, Cl, Br, I) on KCl and KBr (100) crystals are presented. Calculated chemisorption energies for CO on the (halogen atom/defect free sites of KCl and KBr (100) crystals) showed that the coadsorption of halogen atom tends to block other adsorbate-substrate interactions at the nearest neighbour sites. Thus if halogen atom coverage increases, the CO prefers to be adsorbed on the K+ site of the KCl and KBr (100) surfaces and on KBr relative to KCl.

A density-functional theory study of the adsorption of CO molecules on Au/Ni(111)

The adsorption of carbon monoxide in the vicinity of an isolated Au adatom on a Ni(111)surface has been studied using ab initio density-functional theory (DFT). Our detailedinvestigations of the potential-energy surface for the binding of CO atoms show that forbonding sites in which the molecule binds at least to one Ni nearest neighbour of the Auadatom, the adsorption energy is reduced by up to 1.2 eV. At larger distances fromthe impurity, the adsorption energies are almost unchanged. On the other hand,binding to the Au adatom is much stronger than on a flat Au surface. These resultsare discussed in relation to the electronic structure of the Au-doped Ni surface.

Density Function Theory Study of CO Adsorption on Fe3O4(111) Surface

Density functional theory calculations have been carried out for CO adsorption on the Fe(oct2)- and Fe(tet1)-terminated Fe(3)O(4)(111) surfaces, which are considered as active catalysts in water-gas shift reaction. It is found that the on-top configurations are most stable on these two surfaces. Some bridge configurations are also stable in which the new C-O bond formed between the surface O atom and the C atom of CO. The adsorption on the Fe(oct2)-terminated surface is more stable than on the Fe(tet1)-terminated surface. The density of state reveals the binding mechanism of CO adsorption on the two surfaces. Our calculations have also shown that the absorbed CO can migrate from the on-top site to the bridge site or 3-fold site. The oxidation of CO via surface oxygen atoms is feasible, which is in good agreement with experimental results.

Atom–Molecule Interactions on Transition Metal Surfaces: A DFT Study of CO and Several Atoms on Rh(100), Pd(100) and Ir(100)

Density functional theory (DFT) calculations have been performed to determine the interaction energy between a CO probe molecule and all atoms from the first three rows of the periodic table coadsorbed on Rh(100), Pd(100) and Ir(100) metal surfaces. Varying the coverage of CO or the coadsorbed atom proved to have a profound effect on the strength of the interaction energy. The general trend, however, is the same in all cases: the interaction energy becomes more repulsive when moving towards the right along a row of elements, and reaches a maximum somewhere in the middle of a row of elements. The absolute value of the interaction energy between an atom-CO pair ranges from about -0.40 eV (39 kJ mol(-1)) attraction to +0.70 eV (68 kJ mol(-1)) repulsion, depending on the coadsorbate, the metal and the coverage. The general trend in interaction energies seems to be a common characteristic for several transition metals.

Investigation of phase miscibility of CoCrPt thin films using anomalous x-ray scattering and extended x-ray absorption fine structure

The phase miscibility of Co, Cr and Pt in oriented nanostructured CoCrPt magnetic thin films was investigated using anomalous x-ray scattering (AXS) from the (002) reflection and extended x-ray absorption fine structure (EXAFS) at CoK, CrK and PtLIII edges. The AXS measurements at CoK edge clearly showed the presence of Co in the crystalline region. However, Cr was not detected in the lattice. The EXAFS at CoK edge indicated that the nearest neighboring atoms of Co were mixed with 80% Co and 20% Pt, consistent with the results of EXAFS at PtLIII edge. Our observations suggested that only Pt and Co were at the Co (002) lattice of the nanotextured CoCrPt thin films. This indicated that the AXS alone may not be reliable to determine the phase miscibility in textured thin films. Complementary information from the EXAFS was useful to understand the phase miscibility of nanoscale materials.

Mössbauer spectroscopy of interphase boundaries of Co/CoO bilayers

Co films and Co/CoO bilayers that were deposited by the method of magnetron sputtering on the MgO(100) and Al2O3(110) single-crystal substrates have been studied using electron microscopy and Mossbauer spectroscopy. The surface, bulk, and interphase Mossbauer spectra of the layers and bilayers under examination have been investigated. It is shown that the 57Co(57Fe) atoms located in the region of a Co/CoO interphase boundary can be in different magnetic states and have different valences and chemical surroundings.

Direct observation of molecularly-aligned molecules in the second physisorbed layer-CO/Ag(1 1 0)

We report the direct observation of oriented second-layer physisorbed molecules on a single crystal surface by electron stimulated desorption. Experiments and simulations show that the orientation of the second-layer physisorbed CO molecules on Ag(1 1 0) is the result of both electrostatic and dispersion forces from the underlying chemisorbed CO and Ag atoms. At 25 K, the physisorbed C–O bond is tilted and azimuthally oriented with the C–O bond axis inclined in an azimuthal plane at 45° to the principal Ag(1 1 0) azimuthal crystallographic directions. The O atom in CO is directed outward, giving an O + beam at 43° to the normal.

Cobalt complexes with cinchonidine and quinidine: Effect of C8/C9 stereochemistry and 6′‐substitution on intermolecular interactions

The title compounds, (cinchonidinium)trichlorocobalt(II) [(C(19)H(23)ON(2))CoCl(3)] (CoCdn) and (quinidinium)trichlorocobalt(II) [(C(20)H(25)O(2)N(2))CoCl(3)] (CoQd), are zwitterions that differ in absolute configuration and conformation. In both complexes, the sp(3) nitrogen of quinuclidine is protonated, whereas the sp(2) nitrogen of quinoline is linked to the Co(II) atom, which coordinates three chlorine atoms in distorted tetrahedral geometry. The mutual orientations of the quinoline and quinuclidine moieties in CoCdn and CoQd differ significantly because of different hydrogen bonding involving the hydroxyl group. In both complexes, the quinuclidine NH groups and hydroxyl groups are hydrogen-bond donors to the chlorine atoms of Co(II) tetrahedra. In CoQd the hydrogen bonding leads to formation of a nine-membered ring consisting of Co, two chlorines, and a fragment of the quinidine molecule. A comparison of the crystal structures of four Cinchona alkaloid complexes with trichlorocobalt(II) shows that their space groups are determined by the absolute configuration of the alkaloid, whereas the hydrogen-bonding pattern is mainly affected by the substituent in the quinoline ring, i.e., by hydrogen or methoxyl group.

Interaction of Cobalt Atoms with an Oxidized Si(100)2 × 1 Surface

The initial stages of oxidation of a Si(100)2 × 1 surface and the interaction of cobalt atoms with it were studied by core-level photoelectron spectroscopy. The study was carried out with cobalt coverages of up to 8 ML. Computer modeling of the spectra of photoexcited electrons revealed Co atom penetration under the silicon oxide layer, an effect observed even at room temperature. This process was shown to give rise to the disappearance of silicon interface phases at the oxide-layer-silicon boundary and to the formation of a more complex phase involving atoms of Co, O, and Si. After completion of the process, a Co-Si solid solution forms at the interface.

Magnetism and structure on the atomic scale: Small cobalt clusters in Cu(001)

The interplay between structure and magnetic properties of small cobalt clusters embedded in a Cu(001) surface is studied performing ab initio and tight-binding calculations in a fully relaxed geometry. We reveal that, despite the small macroscopic mismatch between Co and Cu, the strain relaxations at the interface have a profound effect on the structure of the clusters and the substrate. The physical mechanism responsible for the strain relaxations in embedded clusters is related to the size-dependent mesoscopic mismatch which has been recently introduced to understand homo- and heteroepitaxial growth at the mesoscale [O. V. Lysenko et al., Phys. Rev. Lett. 89, 126102 (2002)]. We show that the atomic relaxations strongly reduce the magnetic anisotropy energy (MAE) and the orbital magnetic moments of embedded clusters. The largest MAE of about $1.8\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ is found for a single Co atom in the Cu(001) surface. A strong enhancement of the spin magnetic moments in embedded clusters as compared to a single atom of Co incorporated in the Cu(001) surface is found. Magnetic properties of embedded and supported clusters are compared. While in supported clusters the MAE is strongly enhanced at the edge atoms, the immersion of the cluster into the surface and atomic relaxations make the distribution of the local MAE contributions and orbital-moment values almost homogeneous.

STM-tip induced displacement of Co atoms embedded in a Cu(0 0 1) surface

We present experimental evidence for a controlled movement of single atoms of Co incorporated in a Cu(0 0 1) surface under the influence of a scanning tunnelling microscope (STM) tip. The Co atoms move preferentially along such [1 1 0] nearest neighbour directions in the Cu surface which lie in an acute angle to the vertical sweep direction of the STM tip. The induced motion of the Co atoms is controllable by the tip bias voltage. We propose that a tip mediated surface vacancy exchange process is responsible for the observed motion of the impurity atoms.

The interaction of formohydroxamic acid with carbon monoxide: FTIR matrix isolation and quantum chemistry studies

Abstract Argon matrix infrared spectra of the complexes formed between formohydroxamic acid (HCONHOH) and carbon monoxide have been recorded. The experimental results indicate formation of three isomeric complexes. In two complexes the NH or OH groups of formohydroxamic acid are attached to the carbon atom of the CO molecule and in the third complex the NH group interacts with the oxygen atom of CO. The formohydroxamic acid complex with two CO molecules is also trapped in the matrix. One of the two CO molecules interacts with the NH group and the second one with the OH group of HCONHOH, in both cases the site of interaction is the carbon atom of CO. Theoretical studies of the structure and spectral characteristics of the complexes were carried out on the DFT(B3LYP)/6-311++G(2d,2p) level. The calculated vibrational frequencies for the complexes present in the matrices are in good agreement with the experimental data. The calculations show also an additional potential energy minimum corresponding to the complex in which the OH group of formohydroxamic acid is attached to the oxygen atom of carbon monoxide.