An irregular lattice model to simulate crack paths in bonded granular assemblies

Peer reviewed

An irregular lattice model to simulate crack paths in bonded granular assemblies

Peer reviewed

A comparison of calculated and experimental HRTEM images of twinned boron carbide

High resolution TEM images of boron carbide (B13C2) have been recorded and compared with images calculated using the multislice method as implemented by M. A. O'Keefe in the SHRLI programs. Images calculated for the [010] zone, using machine parameters for the JEOL 2000FX AEM operating at 200 keV, indicate that for the structure model of Will et al., the optimum defocus image can be interpreted such that white spots correspond to B12 icosahedra for thin specimens and to low density channels through the structure adjacent to the direct inter-icosahedral bonds for specimens of intermediate thickness (-40 > t > -100 nm). With this information, and from the symmetry observed in the TEM images, it is likely that the (101) twin plane passes through the center of icosahedron located at the origin. This model was tested using the method of periodic continuation. Resulting images compare favorably with experimental images, thus supporting the structural model. The introduction of a (101) twin plane through the origin creates distortions to the icosahedral linkages as well as to the intra-icosahedral bonding. This increases the inequivalence of adjacent icosahedral sites along the twin plane, and thereby increases the likelihood of bipolaron hopping.

FTIR study of poly(propylene carbonate)/bisphenol A blends

A systematic investigation by FTIR spectroscopy was undertaken on blends of poly(propylene carbonate) (PPC) and bisphenol A (BPA). It provided direct evidence of the hydrogen bond (H-bond) between BPA O-H groups and PPC C=O groups. Using a curve-fitting method, qualitative as well as quantitative information concerning this H-bond interaction was obtained. The inter-H-bond in PPC/BPA blends was weaker than the self-H-bond in BPA. The absorptivities of the free and the H-bonded C=O groups were nearly equal. The fraction of H-bonded C=O in the blends increased with BPA content and leveled off at a value close to 40%. Finally, FTIR-temperature measurements of pure PPC and a representative blend were reported: by monitoring the peak areas of C=O absorptions, the dissociation of the inter-H-bonds and the thermal degradation of PPC were observed. It revealed that the presence of BPA clearly retarded the thermal degradation of PPC.

Density functional/Monte Carlo study of ring-opening polymerization

Density functional calculations of the structure, potential energy surface and reactivity for organic systems closely related to bisphenol-A-polycarbonate (BPA-PC) provide the basis for a model describing the ring-opening polymerization of its cyclic oligomers by nucleophilic molecules. Monte Carlo simulations using this model show a strong tendency to polymerize that is increased by increasing density and temperature, and is greater in 3D than in 2D. Entropy in the distribution of inter-particle bonds is the driving force for chain formation. (C) 2002 Elsevier Science B.V. All rights reserved.

Granule-based knowledge representation for intra and inter transaction association mining

Abstract With the phenomenal growth of electronic data and information, there are many demands for the development of efficient and effective systems (tools) to perform the issue of data mining tasks on multidimensional databases. Association rules describe associations between items in the same transactions (intra) or in different transactions (inter). Association mining attempts to find interesting or useful association rules in databases: this is the crucial issue for the application of data mining in the real world. Association mining can be used in many application areas, such as the discovery of associations between customers’ locations and shopping behaviours in market basket analysis. Association mining includes two phases. The first phase, called pattern mining, is the discovery of frequent patterns. The second phase, called rule generation, is the discovery of interesting and useful association rules in the discovered patterns. The first phase, however, often takes a long time to find all frequent patterns; these also include much noise. The second phase is also a time consuming activity that can generate many redundant rules. To improve the quality of association mining in databases, this thesis provides an alternative technique, granule-based association mining, for knowledge discovery in databases, where a granule refers to a predicate that describes common features of a group of transactions. The new technique first transfers transaction databases into basic decision tables, then uses multi-tier structures to integrate pattern mining and rule generation in one phase for both intra and inter transaction association rule mining. To evaluate the proposed new technique, this research defines the concept of meaningless rules by considering the co-relations between data-dimensions for intratransaction-association rule mining. It also uses precision to evaluate the effectiveness of intertransaction association rules. The experimental results show that the proposed technique is promising.

Conformations of three heterocyclicperhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.

Conformations of three heterocyclic perhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2,3-b]p yrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.

Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.

DNA fragments with stretches of cytosine residues can fold into four-stranded structures in which two parallel duplexes, held together by hemiprotonated cytosine.cytosine+ (C.C+) base pairs, intercalate into each other with opposite polarity. The structural details of this intercalated DNA quadruplex have been assessed by solution NMR and single crystal x-ray diffraction studies of cytosine-rich sequences, including those present in metazoan telomeres. A conserved feature of these structures is the absence of stabilizing stacking interactions between the aromatic ring systems of adjacent C.C+ base pairs from intercalated duplexes. Effective stacking involves only the exocyclic keto groups and amino groups of the cytidine bases. The apparent absence of stability provided by stacking interactions between the bases in this intercalated DNA has prompted us to examine the available structures in detail, in particular with regard to unusual features that could compensate for the lack of base stacking. In addition to base-on-deoxyribose stacking and intra-cytidine C-H...O hydrogen bonds, this analysis reveals the presence of a hitherto unobserved, systematic intermolecular C-H...O hydrogen bonding network between the deoxyribose sugar moieties of antiparallel backbones in the four-stranded molecule.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Inter- and intramolecular enantioselective carbolithiation reactions

In this review we summarize recent developments in inter- and intramolecular enantioselective carbolithiation reactions carried out in the presence of a chiral ligand for lithium, such as (-)-sparteine, to promote facial selection on a C=C bond. This is an attractive approach for the construction of new carbon-carbon bonds in an asymmetric fashion, with the possibility of introducing further functionalization on the molecule by trapping the reactive organolithium intermediates with electrophiles.

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Morphological Alterations in Newly Born Dentate Gyrus Granule Cells That Emerge after Status Epilepticus Contribute to Make Them Less Excitable

Computer simulations of external current stimulations of dentate gyrus granule cells of rats with Status Epilepticus induced by pilocarpine and control rats were used to evaluate whether morphological differences alone between these cells have an impact on their electrophysiological behavior. The cell models were constructed using morphological information from tridimensional reconstructions with Neurolucida software. To evaluate the effect of morphology differences alone, ion channel conductances, densities and distributions over the dendritic trees of dentate gyrus granule cells were the same for all models. External simulated currents were injected in randomly chosen dendrites belonging to one of three different areas of dentate gyrus granule cell molecular layer: inner molecular layer, medial molecular layer and outer molecular layer. Somatic membrane potentials were recorded to determine firing frequencies and inter-spike intervals. The results show that morphologically altered granule cells from pilocarpine-induced epileptic rats are less excitable than control cells, especially when they are stimulated in the inner molecular layer, which is the target area for mossy fibers that sprout after pilocarpine-induced cell degeneration. This suggests that morphological alterations may act as a protective mechanism to allow dentate gyrus granule cells to cope with the increase of stimulation caused by mossy fiber sprouting.