Bond Pattern Research Articles

Crystal Structure of a Metallohybrid Acid of 1,3,5-Benzenetricarboxylic Acid of Copper(II)

The crystal structure of a metallohybrid carboxylic acid obtained from the reaction of 1,3,5-benzenetricarboxylic acid (TCAH3) with copper(II)acetate monohydrate in the presence of pyridine (py) having composition Cu(py)2(TCAH2)2(H2O)2 [1] is reported. It crystallizes in triclinic space group P-1 and with a = 7.0110(3)A, b = 8.9523(5)A, c = 11.5370(5) A, α = 79.776(3) °, β = 82.881(3)°, γ = 83.628(3)°, and V = 704.18(6)A3. The hydrogen bond in 1 is compared with the hydrogen bond pattern in the structure of 1,3-dicarbomethoxy 4,6-benzenedicarboxylic acid, which crystallizes in mononclinic space group P21/c and has unit cell parameters of a = 6.9549(16)A, b = 8.7676(15)A, c = 20.111(4)A; β = 92.585(17) ° and V = 1225.1(4) A3. Crystal structure of a metallohybrid carboxylic acid obtained from the reaction of 1,3,5-benzenetricarboxylic acid with copper(II)acetate monohydrate in the presence of pyridine is determined and compared with hydrogen bond pattern present in the structure of 1,3-dicarbomethoxy 4,6-benzenedicarboxylic acid. Crystal structure of a metallohybrid acid of 1,3,5-benzenetricarboxylic acid of copper(II). Kusum Bania, Nilotpal Barooah, Rupam Sarma, Jubaraj B. Baruah

A kinematic FE limit analysis model for thick English bond masonry walls

Two-wythes masonry walls arranged in English bond texture were often used in the past as bearing panels in seismic area. On the other hand, earthquake surveys have demonstrated that masonry strength under horizontal actions is usually insufficient, causing premature collapses of masonry buildings, often ascribed to out-of-plane actions. Furthermore, many codes of practice impose for new brickwork walls a minimal slenderness, which for instance is fixed by the Italian O.P.C.M. 3431 equal to 12 for artificial bricks and 10 for natural blocks masonry. For the above reasons, the analysis at failure of English bond brickwork walls under out-of-plane actions is a topic that deserves consideration, despite the fact that almost the totality of the studies of masonry at failure is devoted to running bond arrangements. Furthermore, it must be noted that an approach based on the analysis of running bond texture – in comparison with English bond pattern – is not suitable for the investigation of the behavior of bearing panels. In this framework, in the present paper, a Reissner–Mindlin kinematic limit analysis approach is presented for the derivation of the macroscopic failure surfaces of two-wythes masonry arranged in English bond texture. In particular, the behavior of a 3D system constituted by infinitely resistant bricks connected by joints reduced to interfaces with frictional behavior and limited tensile/compressive strength is identified with a 2D Reissner–Mindlin plate. In this way, assuming both an associated flow rule for the constituent materials and a finite subclass of possible deformation modes, an upper bound approximation of macroscopic English bond masonry failure surfaces is obtained as a function of macroscopic bending moments, torsion and shear forces. Several examples of technical relevance are treated both at a cell level and at a structural level, addressing the differences in terms of collapse loads and failure surfaces due to different textures and constituent laws for joints. Finally, two meaningful structural examples consisting of a panel in cylindrical flexion and a masonry slab constrained at three edges and out-of-plane loaded are discussed. A detailed comparison in terms of deformed shapes at collapse and failure loads between a 2D FE Reissner–Mindlin limit analysis approach and a full 3D heterogeneous FE model shows the reliability of the results obtained using the kinematic identification approach proposed.

Preparation and crystalline analysis of high‐grade bamboo dissolving pulp for cellulose acetate

AbstractHigh grade bamboo dissolving pulp for cellulose acetate (named as acetate bamboo pulp) was prepared from bamboo Cizhu (Dendrocalamus affinnis) by oxygen‐alkali pulping, xylanase and DMD (an intermediate product of the reaction of oxone with acetone) delignification treatments, and H2O2 bleaching. Its properties and structures were investigated by different analytical techniques, and compared with those of high grade hardwood dissolving pulp for cellulose acetate (named as acetate wood pulp), viscose bamboo pulp, and bamboo fiber for textile. Most of its properties are comparable with those of acetate wood pulp except ash contents and DCM (dichloromethane) extractive that are slightly high. Crystallinities and crystalline allomorphs of acetate bamboo pulp and the three samples were determined by FTIR spectroscopy, X‐ray diffraction and solid state 13C NMR spectroscopy, and the results obtained by the three methods were coincident. Bamboo cellulose crystalline allomorphs are classified as Iβ‐dominant type, and a higher lateral order index and a larger crystallite size for acetate bamboo pulp were found in spite of its crystallinity similar to acetate wood pulp. Different intermolecular hydrogen bond patterns are likely be responsible for the predominant crystalline fibrils in acetate bamboo pulp. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008

Modification of the Hydrogen Bonds Network in a Hydroxyl Functionalized Dithiolene Ligand by HgX2 Complexation

AbstractLigand L (4,5‐bis[(2′‐hydroxyethyl)thio]1,3‐dithiole‐2‐thione) which crystallizes in the monoclinic system (P21/n) displays a 1‐D network generated by a succession of intra‐molecular and inter‐molecular hydrogen bonds. Weak π‐π and S···S interactions are also observed in the supramolecular structure. Reaction of L with one equivalent of mercury(II) iodide affords the adduct [HgI2L] (1a). The crystal structure of this complex shows that coordination occurs exclusively via the sulfur atom of the thione function (C=S). The ligation on HgI2 induces a change of the hydrogen bond pattern generated by the hydroxyl substituents: only intermolecular hydrogen bonds are present, organizing the adduct 1a in form of centrosymmetrical dimers in the solid state. The propensity of HgI2 to build‐up chains via μ2‐iodo ligand may be at the origin of the modification of the hydrogen bond network.

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.

Heterodimer of tetraaryl- and tetratosylurea calix[4]arenes: first single crystal X-ray analysis and guest encapsulation properties in CDCl 3

The first single crystal X-ray analysis of the heterodimer of tetraaryl- and tetratosylurea calix[4]arenes was reported, which revealed the real pattern of the hydrogen bonds. Moreover, the heterodimer showed good encapsulation abilities for some organic molecules in CDCl 3.

Boron hydrogen in crystalline form

In a three-dimensional crystal two different orientations of boron hydrogen chains havebeen considered. The geometrical orientations of the chains are based on the space groupsP 21/a and P 21/n depending on whether the single bond–double bond pattern on the two chains in the unitcell is in phase or antiphase, respectively. Using the full potential linearized augmentedplane waves (FP-LAPW) density functional theory within the generalized gradientapproximation, the optimal volumes, the ground state energies, band structuresand the density of states of levels have been reported. Our results show that thein-phase pattern behaves as a poor conductor while the antiphase has a gap of0.5 eV.

Resilient Parenting: Overcoming Poor Parental Bonding

This study identified groups of mothers with varying patterns of adaptive functioning and bonds with their own parents. These patterns were related to mothers' parenting of their own children to understand how some mothers avoid repeating the cycle of poor parenting. Data from 210 new mothers were analyzed before hospital discharge about bonding with their caregivers during childhood and six to 12 months later about adaptive functioning, life circumstances, and parenting. Latent duster analysis identified four distinct groups of mothers with regard to parental bonds and adaptive functioning: positive-adaptive mothers (good bonding and good adaptive functioning), positive-maladaptive mothers (good bonding and poor adaptive functioning), resilient mothers (poor bonding and good adaptive functioning), and vulnerable mothers (poor bonding and poor adaptive functioning). Despite poor parental bonds, resilient mothers were coping as well as the positive-adaptive mothers and were significantly less likely to experience parenting stress related to the parenting role, unsatisfying interactions with their infants, and attributions of their children as difficult to care for. Some mothers were able to overcome poor bonds with their own caregivers to develop good adaptive functioning in adulthood and provide good parenting to their own children. KEY WORDS: infants; latent cluster analysis; parenting; resilience ********** It is widely accepted that parenting behaviors and styles are transmitted across generations (Belsky, Jaffee, Sligo, Woodward, & Silva, 2005). Child abuse and harsh discipline, for example, are frequently linked to parents' childhood experiences, and childhood abuse or harsh parenting is considered to be a risk factor for engaging in similar parenting (Dixon, Browne, & Hamilton-Giachritsis, 2005a, 2005b). Less research has examined continuity of positive parenting, but recent evidence has suggested that it, too, is transmitted from one generation to the next (Chen & Kaplan, 2001). Discontinuity of parenting styles and behavior has received less attention, but it has also been of interest in the study of abused children because a significant proportion of abused or harshly parented individuals grow up to be nonabusing parents (for example, Egeland, Jacobvitz, & Sroufe, 1988). Egeland and associates found that mothers who broke the cycle of abuse reported supportive relationships with nonparental adults during childhood and supportive relationships with their mates. Caliso and Milner (1992) also reported that having a supportive relationship with a partner predicted breaking the cycle of abuse and that parents who had been abused as children but did not abuse their own children had different parenting attitudes than those who continued the pattern of abusive parenting. Examining recollections of parenting received by mothers, some authors have found correlations with those mothers' parenting of their own children (Hammond, Landry, Swank, & Smith, 2000). In contrast, Adler and colleagues (1991) did not find such an association in a low-risk sample. They suggested that stress may mediate the relation between parental bonds and quality of parenting, so the absence of risk factors and high stress in their sample might explain their findings. Phelps and colleagues (1998) used the Adult Attachment Interview (AAI) (George, Kaplan, & Main, 1985) to investigate the role of stress, comparing the parenting of mothers who reported secure parental bonds, those who reported insecure bonds, and those described as secures, who reported insecure bonds but articulated resolution of their feelings about the relationships. Under both high and low stress, the parenting of earned secure mothers did not differ from that of continuously secure mothers. The parenting of mothers who reported insecure bonds, on the other hand, was dependent on stress level. …

Effect of ultrasonic power on wedge bonding strength and interface microstructure

During the aluminum wire wedge bonding, the ultrasonic power and bonding strength were obtained. Based on those data, the relationship between ultrasonic power and bonding strength was studied. The results show that: 1) ultrasonic power is affected by ultrasonic power ratio and other uncontrolled factors such as asymmetric substrate quality, unstable restriction on the interface between wedge tool and aluminum wire; 2) when ultrasonic power is less than 1.0 W, increasing ultrasonic power leads to increasing bonding strength and decreasing failure bonding; on the contrary, when ultrasonic power is greater than 1.6 W, increasing power leads to decreasing bonding strength and increasing failure bonding; 3) only when ultrasonic power is between 1.0 W and 1.6 W. can stable and high yield bonding be reached. Finally, the microstructure of bonding interface was observed, and a ring-shaped bond pattern is founded in the center and friction scrape besides the ring area.

An Experimental and Theoretical Study of the Formation of Nanostructures of Self-Assembled Cyanuric Acid through Hydrogen Bond Networks on Graphite

The self-assembly of cyanuric acid into ordered nanostructures on a crystalline substrate, highly ordered pyrolytic graphite (HOPG), has been investigated at low temperature under ultrahigh vacuum (UHV) conditions by means of scanning tunneling microscopy in conjunction with theoretical simulations. Many domains with different self-assembly patterns were observed. One such domain represents the formation of an open 2D rosette (cyclic) structure from the self-assembly process, the first observation of this type of structure for pure cyanuric acid on a graphite substrate. Each self-assembled domain exhibits characteristic superstructures formed through different hydrogen bond networks at low coverage and low deposition rate. Experimental observation of coexistent, two-dimensional crystalline structures with distinct hydrogen bond patterns is supported by energy minimizations and molecular dynamics calculations, which show multiple stable structures for this molecule when self-assembled on graphite.

Conformational Analysis of Heteroannularly Substituted Ferrocene Oligoamides

AbstractThe main conformer of symmetrical conjugates of ferrocene‐1,1′‐dicarboxylic acid with natural amino acids – Fn(CO–AA1–2–OMe)2 (type I, Fn = ferrocene‐1,1′‐diyl, AA = L‐α‐amino acid) – is supported by two hydrogen bonds between the peptide substituents. To compare intramolecular hydrogen bond patterns of type I conjugates with related asymmetrically substituted derivatives, type II (MeNHCO–Fn–CO–AA–OMe) and type III conjugates (MeNHCO–Fn–CO–AA–NHMe) were prepared in moderate‐to‐good yields in a few steps starting from 1′‐(methoxycarbonyl)ferrocene‐1‐carboxylic acid by using the HOBt/EDC method (AA = Gly, Ala, Val). 1H NMR spectroscopic variation ratio analysis suggests that an increase in the steric demand of the amino acid side chains favours conformations with hydrogen‐bonded FnCONHMe groups. CD spectroscopy of chiral derivatives reveals that (P)‐helical conformations predominate in solution. The experimental findings are in accordance with DFT calculations. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

Intra‐ and Intermolecular H···Cl–Ni Bonding Patterns in a Series of Highly Preorganized Dinuclear Nickel(II) Complexes

AbstractFour dinickel complexes [L1Ni2(μ‐Cl)(Cl)2]·2CH3OH (1a), [L1Ni2(μ‐Cl)(CH3OH)](ClO4)2 (1b), [L2Ni2(μ‐Cl)Cl2(H2O)2]·H2O (2) and [L3Ni2Cl2(CH3OH)2]Cl·2CH3OH (3) were synthesized and structurally characterized. The ligand scaffolds have a central pyrazolato bridge and N‐donor chelate arms that provide two proximate binding pockets for the nickel ions. While the longer ligand side arms in 1a, 1b and 2 induce Ni···Ni distances of around 4.0 Å and favour incorporation of a chlorido bridge within the dimetallic pocket, a stretched Ni···Ni separation of 4.6 Å with an unusual intramolecular Cl···H–O linkage is observed in 3. Various Cl···H–O hydrogen‐bonding motifs are identified in the solid‐state structures of 1–3, where either the H‐donor (MeOH or H2O) or the H‐acceptor (chlorido) or both are bound to a nickel ion, and their relative donor–acceptor distances are discussed. Magnetic coupling mediated through the pyrazolato and chlorido bridges is rather weak and antiferromagnetic, but it is even weaker for the Cl···H–O linkage. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

Expression of human acid ceramidase in insect cells. Analysis of processing, glycosylation and disulfide bond pattern.

Expression of human acid ceramidase in insect cells. Analysis of processing, glycosylation and disulfide bond pattern.

Experimental investigation on flexural performance of masonry walls reinforced with GFRP

This paper presents the results of a test program for flexure reinforcing characteristics of gless fiber-rein forced polymer(GFRP) sheets bonded to masonry beams. A total of eight specimens subjected to monotonic four-point bending were tested up to failure. These specimens were constructed with two different bond patterns. Six of these specimens were reinforced by using GFRP sheets prior to testing, and the remaining two were not reinforced. The test results indicate a significant increase in both load-bearing capacity and ductile performance of the reinforced walls over the unreinforced ones.

Protein–RNA contacts at crystal packing surfaces

The crystal packing surfaces comprising protein-RNA interactions were analyzed for 50 RNA-protein crystal structures in the Protein Data Bank database. Protein-RNA crystal contacts, which represent nonspecific protein-RNA interfaces, were investigated for their amino acid propensities, hydrogen bond patterns, and backbone and side chain interactions. When compared to biologically relevant interactions, the protein-RNA crystal contacts exhibit similarities as well as differences with respect to the principles of protein-RNA interactions. Similar to what was observed at cognate protein-RNA interfaces, positively charged amino acids have high propensities at noncognate protein-RNA interfaces and preferentially form hydrogen bonds with RNA phosphate groups. In contrast, nonpolar residues are less frequently associated with noncognate interactions. These results highlight the important roles of both electrostatic and hydrogen bonding interactions, facilitated by positively charged amino acids, in mediating both specific and nonspecific protein-RNA interactions.

Cloning of the cDNA for murine von Willebrand factor and identification of orthologous genes reveals the extent of conservation among diverse species

Interaction of von Willebrand factor (VWF) with circulating platelets promotes hemostasis when a blood vessel is injured. The A1 domain of VWF is responsible for the initial interaction with platelets and is well conserved among species. Knowledge of the cDNA and genomic DNA sequences for human VWF allowed us to predict the cDNA sequence for murine VWF in silico and amplify its entire coding region by RT–PCR. The murine VWF cDNA has an open reading frame of 8,442 bp, encoding a protein of 2,813 amino acid residues with 83% identity to human pre-pro-VWF. The same strategy was used to predict in silico the cDNA sequence for the ortholog of VWF in a further six species. Many of these predictions diverged substantially from the putative Reference Sequences derived by ab initio methods. Our predicted sequences indicated that the VWF gene has a conserved structure of 52 exons in all seven mammalian species examined, as well as in the chicken. There is a minor structural variation in the pufferfish Takifugu rubripes insofar as the VWF gene in this species has 53 exons. Comparison of the translated amino acid sequences also revealed a high degree of conservation. In particular, the cysteine residues are conserved precisely throughout both the pro-peptide and the mature VWF sequence in all species, with a minor exception in the pufferfish VWF ortholog where two adjacent cysteine residues are omitted. The marked conservation of cysteine residues emphasizes the importance of the intricate pattern of disulfide bonds in governing the structure of pro-VWF and regulating the function of the mature VWF protein. It should also be emphasized that many of the conserved features of the VWF gene and protein were obscured when the comparison among species was based on the putative Reference Sequences instead of our predicted cDNA sequences.

Oxo-anion binding by protonated (dimethylphenyl)(pyridyl)ureas

The anion coordination chemistry of two protonated urea-based ligands, N-(2,4-dimethylphenyl)-N′-(3-pyridy1)urea (1) and N-(2,6-dimethylphenyl)-N′-(3-pyridy1)urea (2) is reported. Reaction of 1 or 2 with inorganic oxo-acids such as perchloric, nitric or sulfuric acid affords the adducts (3–6) of the corresponding anions with protonated ligands (1H+ and 2H+). The solid-state structures of the anion complexes display a rich variety of hydrogen bond motifs involving the urea NH groups, carbonyl, protonated pyridyl NH+ fragment, water molecules, and the anions. While complexes with ligand 1 (3 and 4) crystallize as monohydrate, compounds with 2 (5 and 6) are solvent-free, which leads to notable differences in their hydrogen bond patterns. When crystallized from the acid mixture HClO4/HNO3 or HClO4/H2SO4 both 1 and 2 selectively bind the perchlorate anion.

Experimental electron density study of a complex between copper(ii) and the antibacterial quinolone family member ciprofloxacin

An experimental charge density study of a 1 : 1 complex of Cu-cfx (cfx = ciprofloxacin), 1 [Cu(cfx)(H(2)O)(3)]SO4.2H(2)O, has been performed using single-crystal X-ray diffraction data collected at 100 K using conventional Mo Kalpha radiation. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the electron density with the atoms in molecules (AIM) approach. The copper atom binds to two oxygen atoms in one end of the zwitterionic form of the cfx molecule, in addition to forming bonds with three water molecules, forming a square pyramidal coordination geometry. AIM decomposition of the experimental electron density establishes that the copper atom binds more strongly to the cfx molecule than to the water molecules, suggesting that the latter can be detached leaving behind a reactive, water-free Cu-cfx complex available for interaction with e.g. a macromolecular site. AIM analysis of the extensive hydrogen bond pattern reveals that the positively charged N-end of the zwitterionic cfx forms a relatively strong N-H-O hydrogen bond implying that this region of cfx may play an important role in the docking process in the active site. Visualisation and statistics of selected density derived properties on the molecular surface of the isolated cfx molecule vs its metal complexed counterpart points out regions of potential reactivity. The effect of the fluorine atom is to expand the negative region of the electrostatic potential, while the nitrogen end is heavily electropositive and willingly donates to--for molecular docking purposes--relatively strong hydrogen bonding. The Cu atom is highlighted as a potentially highly reactive site which is likely to interact strongly with any given negative ligand.

A Unique Loop Extension in the Serine Protease Domain of Haptoglobin Is Essential for CD163 Recognition of the Haptoglobin-Hemoglobin Complex

Haptoglobin and haptoglobin-related protein are homologous hemoglobin-binding proteins consisting of a complement control repeat (alpha-chain) and a serine protease domain (beta-chain). Haptoglobin-hemoglobin complex formation promotes high affinity binding of hemoglobin to the macrophage scavenger receptor CD163 leading to endocytosis and degradation of the haptoglobin-hemoglobin complex. In contrast, complex formation between haptoglobin-related protein and hemoglobin does not promote high affinity interaction with CD163. To define structural components of haptoglobin important for CD163 recognition, we exploited this functional difference to design and analyze recombinant haptoglobin/haptoglobin-related protein chimeras complexed to hemoglobin. These data revealed that only the beta-chain of haptoglobin is involved in receptor recognition. Substitution of 4 closely spaced amino acid residues of the haptoglobin beta-chain (valine 259, glutamate 261, lysine 262, and threonine 264) abrogated the high affinity receptor binding. The 4 residues are encompassed by a part of the primary structure not present in other serine protease domain proteins. Structural modeling based on the well characterized serine protease domain fold suggests that this sequence represents a loop extension unique for haptoglobin and haptoglobin-related protein. A synthetic peptide representing the haptoglobin loop sequence exhibited a pronounced inhibitory effect on receptor binding of haptoglobin-hemoglobin.

Importance of Molecular Shape for the Overall Stability of Hydrogen Bond Motifs in the Crystal Structures of Various Carbamazepine-Type Drug Molecules

Carbamazepine, a first generation anticonvulsant, is known to crystallize in various polymorphic forms, all of which exhibit an anti-carboxamide hydrogen bond dimer motif. Furthermore, unless cocrystallized with carboxylic acids, these dimers are also present in most crystal structures of the known carbamazepine solvates. On the other hand, two derivatives of the drug (oxcarbazepine and 10,11-dihydrocarbamazepine) have been reported to adopt hydrogen bond chain motifs in their crystal structures, whereas the epoxy derivative (10,11-epoxycarbamazepine) shows a third mode of hydrogen bonding, syn-dimers. In order to rationalize the differences in hydrogen bonding caused by the small changes in molecular structure, computational searches for the low-energy crystal structures of these drugs were performed and hydrogen bond patterns in both the hypothetical and experimentally determined crystal structures were analyzed. In addition, interaction energies between pairs of molecules were calculated using the SCDS...