Classical Valence Similarity in Fullerene Derivatives

Summary.  The generalized Pauling bond order was enumerated in the C₆₀ fullerene cage molecule (truncated icosahedral symmetry). This index measures chemical similarity in fullerene derivatives such as dihydrofullerene (C₆₀H₂), anionized monohydrofullerene (C₆₀H⁻), N-substituted monohydrofullerene (C₅₉NH), the fullerene dimer ((C₆₀)₂), and the dianionic fullerene dimer ((C₆₀)₂ ²⁻). It is also useful in judging the chemical stability of isomers. Received October 9, 2001. Accepted November 9, 2001     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

The Effects of M2O3 on Stabilizing Monocopper over the Surface of Cu-ZnO-M2O3 Catalysts for Mathanol Synthesis

The effects of M₃O₃ (M = Al, Sc etc.) in Cu-ZnO-M₂O₃ catalysts on methanol synthesis at low pressure were studied with ESR, XPS and TPR spectroscopy. The results of ESR showed that the generation of monovalent cationic defects was because the valence state and electronic charge on the ZnO lattice lost their balance as M³⁺ doped into ZnO. The induced effect by Sc³⁺ is stronger than that by Al³⁺. The results of XPS and TPR indicated that the amount and stabilization of Cu⁺ on the surface of reduced copper-based catalyst and its catalytic activity were affected by the monovalent cationic defects on the surface of ZnO.     

Preparation and crystal structure ofexo-2,exo-6-dihydroxy-2,6-dimethyl-9-oxabicyclo[3.3.1]nonane

In a further exploration of the structural factors causing alicyclic diols such asexo-2,exo-6-dihydroxy-2,6-dimethylbicyclo[3.3.1]nonane (1) to adopt the helical tubuland inclusion host structure, the title compound (8) has been synthesized and its crystal structure determined. This 9-oxa analogue of (1) has a totally different structure [C₁₀H₁₈O₃; orthorhombic;P2₁2₁2;a 18.989(4),b 19.064(3),c 14.256(3) Å;Z 20; with finalR 0.065] due to involvement of the ether oxygen atom in the hydrogen bonding network. The structure of the diol (8) approximatesP¯42₁ c symmetry, and 16 of the 20 molecules per cell create a hostlike structure of this symmetry, which consists of tightly bound hydrogen bonded pillars parallel toc. The remaining guestlike molecules occupy inequivalent pseudo ¯4 sites separated byc/2 to form weakly bound columns parallel toc. Hydrogen bonds also occur between the pillars and columns. An ordered structure with sensible intermolecular contacts can be formed inP2₁2₁2₁ with thec axis doubled. A difference betweena andb axial lengths correlates with a difference in occupancies of pseudo-¯4-related sites for the guest-like component of the structure.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

Spectroscopic properties of the photoproducts of pyridoxal-5′-P irradiation: Catalytic site recognition of ribonuclease A

Photoproducts of pyridoxal-5-P, i.e., 4-pyridoxic-5-P and bis-pyridoxal-5-P, have been studied by spectroscopic methods. The spectroscopic properties of bis-pyridoxal-5-P (bis-PLP) resemble those of pyridoxal-5-P (PLP) under similar experimental conditions. The coupling of methylen hydrogens to the phosphorus atom has been shown by NMR spectroscopy. The singlet in the³¹P-NMR spectra and the triplet in¹H-undecoupled experiments confirm the presence of the phosphate group in the 5 position of the structure of the vitamin. The effect of pH and solvent composition on the relative distribution of species of bis-pyridoxine-5-P (bis-PNP) has been investigated by absorption and fluorescence spectroscopy. The acid-base dissociation of the phosphate group is easily detected by emission spectroscopy. Bis-PNP and bis-PLP bind to the enzyme RNase A and they behave as competitive inhibitors with respect to the substrate cytidine-2-3-cyclic phosphate. The natural forms of vitamin B₆, pyridoxine, and pyridoxine-5-P have no effect on the catalytic activity of the protein. Experimental evidence derived from fluorescence and inhibition experiments is consistent with the hypothesis that bis-PNP recognizes the catalytic site of RNase A.     

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation

Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.     

Cellular automata approach to site percolation on ℤ2. A numerical study

We present a cellular automata model as a new approach to Bernoulli site percolation on the square lattice. A new macroscopic quantity is defined and numerically computed at each level step of the automata dynamics. Its limit manifests a critical behavior at a value of the site occupancy probability quite close to those obtained for site percolation on ² with the best-known numerical methods.     

Defect clusters and precipitation/oxidation of MgO-Co1−xO solid solution

MgO and Co_1−xO powders in 9:1 and 1:9 molar ratio (denoted as M₉C₁ and M₁C₉, respectively) were sintered and homogenized at 1600°C followed by annealing at 850°C and 800°C, respectively to form defect clusters and precipitates. Analytical electron microscopic observations indicated the protoxide remained as rock salt structure with complicated planar diffraction contrast for M₉C₁ sample, however with spinel paracrystal precipitated from the M₁C₉ sample due to the assembly of charge- and volume-compensating defects of the 4:1 type, i.e., four octahedral vacant sites surrounding one Co³⁺-filled tetrahedral interstitial site. The spacing of such defect clusters is 4.5 times the lattice spacing of the average spinel structure of Mg-doped Co_3−δO₄, indicating a higher defect cluster concentration than undoped Co_3−δO₄. The {111} faulting of Mg-doped Co_3−δO₄/Co_1−xO in the annealed M₁C₉ sample implies the possible presence of zinc blend-type defect clusters with cation vacancies assembled along oxygen close packed (111) plane.