Searching of chemical structure data bases with parallel computer hardware

The use of two types of parallel computer hardware for increasing the efficiency of processing in chemical structure data bases is discussed. The distributed array processor can be used for the clustering of 2-D chemical structure data bases by using the Jarvis—Patrick clustering method and for the ranking of output in an experimental system for substructure searching in the 3-D macromolecules in the Protein Data Bank. The Inmos transputer can be used in the construction of PC-based systems for 2-D substructure searching and in the identification of the maximal substructures common to pairs of 3-D molecules.     

Inorganic-organic interpenetrating frameworks: 4,4'-bipyridine N,N'-dioxide as a bridging hydrogen-bond acceptor

4,4'-Bipyridine N,N'-dioxide (L) acts as a hydrogen-bond acceptor in the compounds ([M(NO3)2(H2O)4].L2) (M = Co, Ni) to form doubly-interpenetrated framework materials with sixfold topological connectivity.     

Ab initio structure of 3p4p in Si I

Multiconfiguration calculations have been performed in order to estimate ab initio energies for the configuration 3p4p in Si I. A preliminary attempt has also been made to calculate E2 transition rates for transitions from levels of 3p ² to those of 3p4p. However, these rates show a gauge dependence, which indicates that further correlation needs to be included to obtain accurate rates and lifetimes.     

Electrochemical and spectroscopic characterization of surface sol-gel processes

(3-Mercaptopropyl)trimethoxysilane (MTS) forms a unique film on a platinum substrate by self-assembly and sol-gel cross-linking. The gelating and drying states of the self-assembled MTS sol-gel films were probed by use of electrochemical and spectroscopic methods. The thiol moiety was the only active group within the sol-gel network. Gold nanoparticles were employed to detect the availability of the thiol group and their interaction further indicated the physicochemical states of the sol-gel inner structure. It was found that the thiol groups in the open porous MTS aerogel matrix were accessible to the gold nanoparticles while thiol groups in the compact MTS xerogel network were not accessible to the gold nanoparticles. The characteristics of the sol-gel matrix change with time because of its own irreversible gelating and drying process. The present work provides direct evidence of gold nanoparticle binding with thiol groups within the sol-gel structures and explains the different permeability of "aerogel" and "xerogel" films of MTS on the basis of electrochemical and spectroscopic results. Two endogenous species, hydrogen peroxide and ascorbic acid, were used to test the permeability of the self-assembled sol-gel film in different states. The MTS xerogel film on the platinum electrode was extremely selective against ascorbic acid while maintaining high sensitivity to hydrogen peroxide in contrast to the relatively high permeability of ascorbic acid in the MTS aerogel film. This study showed the potential of the MTS sol-gel film as a nanoporous material in biosensor development.     

On the solid state structure of 4-iodobenzoic acid

The solid-state structure of 4-iodobenzoic acid has been confirmed by variable temperature X-ray diffraction, variable temperature solid-state NMR and differential scanning calorimetry. 4-iodobenzoic acid crystallizes in the space group P2(1)/n, and dimerizes in the solid state about a center of inversion. Using extensive X-ray crystallographic data collections, the placement of the carboxylate H atoms from the residual electron density in difference Fourier maps was determined. The position of the electron density associated with the proton is found to vary with temperature in that the population of the disordered sites changes with varying temperature. Determination of the crystal structure between the temperatures of 248 and 198 K was not possible due to a phase transition, an endothermic event occurring at 230.77 K. The phase transition is also indicated by a change in the relaxation time of the ring carbon atoms in the solid-state NMR data. Though the dominating force in the dimeric unit in the solid state is the presence of strong hydrogen bonds, there are also van der Waals forces present between the iodine atoms. In the layered structure, the iodine-iodine distance is within the van der Waals contact radii, an interaction which causes a deformation in the electron density of the iodine atoms.     

Intermolecular recognition and crystal packing in molybdenum and tungsten coordination polymers as deduced from powder X-ray diffraction data

The molecular conformations and packing of [(tBuCO2)3M2(mu-X)M2(O2CtBu)3], where M = Mo and W, and X = oxalate and perfluoroterephthalate, determined in the solid-state from powder X-ray diffraction analysis, reveal one-dimensional coordination polymers involving pivalate-oxygen to metal interactions (X = perfluoroterephthalate), and oxalate--as well as pivalate-oxygen to metal bonds (X = oxalate), and allows explanation of the unusual state-dependent chromic properties of these compounds.     

Distant-dipole field in liquids and diffusion: a perturbative approach

A perturbative approach is employed to solve the Bloch-Torrey equations in the presence of distant-dipole fields in nuclear magnetic resonance. The procedure, although only carried out to first order in the perturbation parameter a=1/k2Dtaud, could, in principle, be generalized to higher orders. Here D is the diffusivity, taud the dipolar demagnetization time, and k is the wave vector of the spatial modulation of magnetization produced by the magnetic field gradient. The results are especially interesting for dilute binary mixtures consisting of molecular species with different diffusivities. In this case the calculated two-dimensional correlation spectroscopy revamped by asymmetric Z-gradient echo detection spectra are shown to be free from some inadequacies resulting from a simplistic application of standard approximations.     

Palladium-Catalyzed Carbonylation and Coupling Reactions of Aryl Chlorides and Amines

The palladium-catalyzed amidation of electron-deficient aryl chlorides proceeds readily in the presence of low CO pressures and a slight excess of an iodide salt. The rates of amidation are accelerated over those without added salt, and iodide is preferred over bromide or chloride. More electron-rich aryl chlorides were not effectively amidated, either with or without added iodide. We postulate that an intermediate anionic palladium(0) iodide complex is responsible for the enhanced reactivity.     

Synergism in binary mixtures of Thermobifida fusca cellulases Cel6B,Cel9A,and Cel5A on BMCC and Avicel

In an earlier binding study conducted in our laboratory using Thermobifida fusca cellulases Cel6B, Cel9A, and Cel5A (formally Thermomonospora fusca E₃, E₄, and E₅), it was observed that binding capacities for these three cellulases were 18–30 times higher on BMCC than on Avicel. These results stimulated an interest in how the difference in accessibility between the two cellulosic substrates would affect synergism observed with cellulase mixtures. To explore the impact of substrate, accessibility on the extent of conversion and synergism, three binary T. fusca cellulase mixtures were tested over a range of cellulase ratios and total molar cellulase concentrations on Avicel and BMCC. Higher extents of conversion were observed for BMCC due to the higher enzyme to substrate ratio resulting from the higher binding The processive endoglucanase, Cel9A, had four times the extent of conversion of the end endocellulase Cel5A, while the exocellulase Cel6B had three times the extent of conversion of Cel5A. Approximately 500 nmol/g of the cel9A+Cel6B mixture was needed to obtain 80% conversion, while the Cel6B+Cel5A and Cel9A+Cel5A mixtures required 1500 and 1250 nmol/g, respectively, to obtain 80% conversion. Thus, it appears that the more accessible structure of BMCC, as reflected by its binding capacity, results in relative higher processive activity.     

Influence of the exchange‐correlation functional in all‐electron calculations of the vibrational frequencies of corundum (α‐Al2O3)

The equilibrium structural parameters, high‐ and low‐frequency dielectric tensors, Born effective charges, and Γ‐point vibrational frequencies of bulk Al₂O₃ corundum are calculated by using the periodic, ab initio program CRYSTAL, which adopts an all‐electron Gaussian‐type basis set. The effect of basis set and the performance of three different functionals, i.e., LDA, PW91, and B3LYP, are discussed. The mean absolute deviation from the measured frequencies is as small as 7 cm^?1 for both the LDA and B3LYP functionals, indicating that these functionals perform extremely well in this case. The mean absolute deviation increases to 18 cm^?1 when the PW91 functional is used. All three functionals reproduce the equilibrium geometry of corundum to a high level of accuracy, with LDA and B3LYP outperforming PW91 slightly. The comparison of the current all‐electron calculations with previous plane‐wave, pseudo‐potential calculations shows an overall similar performance. The results of isotopic substitution for both Al and O are also presented. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006