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Bonding Network (bonding + network)
Kinds of Bonding Network Selected AbstractsDiastereopure Cationic NCN-Pincer Palladium Complexes with Square Planar ,4 - N,C,N,O CoordinationEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2006Silvia Gosiewska Abstract Neutral NCN-pincer palladium bromide complex 2 containing the monoanionic, enantiopure pincer ligand 2,6-bis{[(S)-2-hydroxymethyl-1-pyrrolidinyl]methyl}phenyl bromide (1) with bis- ortho -(S)-prolinol substituents was synthesized and isolated as a mixture of three stereoisomers [(SN,SN,SC,SC), (RN,SN,SC,SC), and (RN,RN,SC,SC)] in a 1:1:1 ratio. Upon abstraction of the bromide ion from the unresolved mixture of 2, single diastereoisomers of the cationic complexes [3]BF4 and [3]PF6, respectively, were formed with a unique,4 - N,C,N,O coordination mode of ligand 1. X-ray crystal structure determination established the intramolecular,4 - N,C,N,O coordination of 1 to palladium where the typical mer -,3 - N,C,N pincer coordination is accompanied by coordination of one of the hydroxy groups of the (S)-prolinol moieties. The water molecule that was cocrystallized in the crystal structure of [3]PF6 does not coordinate to palladium, but instead is involved in a hydrogen bonding network. The catalytic potential of both cationic complexes, [3]BF4 and [3]PF6, was tested in an aldol reaction of aldehydes with methyl isocyanoacetate to yield the oxazoline products as racemic mixtures.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Uniformly Nucleobase-Functionalized ,-Peptide Helices: Watson,Crick Pairing or Nonspecific AggregationEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2007Angelina Weiß Abstract The organization and architecture of helices is fundamental in folding of protein tertiary structures. Therefore, stable ,-peptide helices are used as models for the selective organization of secondary structures. Nucleobases are already established as recognition elements to organize two ,-peptide helices in antiparallel orientation. The investigation of ,-peptide helices uniformly functionalized with one type of nucleobases provided further insight in the recognition mode and requirements for specific interaction within the linear and very rigid helical backbone topology. Specific helix interaction based on base pair recognition is predominant as soon as Watson,Crick pairing is allowed. If the hydrogen bonding donor/acceptor pattern prohibits the Watson,Crick geometry, a quite stable nonspecific interaction was found based on aromatic interactions or on a nonspecific hydrogen bonding network. The latter aggregation was also confirmed with tyrosine side chains.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] High-Field Scanning Probe Lithography in Hexadecane: Transitioning from Field Induced Oxidation to Solvent Decomposition through Surface Modification,ADVANCED MATERIALS, Issue 21 2007I. Suez High field scanning probe lithography in hexadecane leads to two different chemical reactions depending on surface hydrophilicity. On a hydrophilic surface, oxidation of the sample occurs; a hydrophobic surface, results in solvent decomposition and nanoscale deposition of etch resistant material. The features are characterized with photoelectron emission microscopy and are carbonaceous in nature with a highly cross-linked bonding network. Tone reversal in a fluorinated etch is achieved. [source] Transforming powder mechanical properties by core/shell structure: Compressible sandJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2010Limin Shi Abstract Some active pharmaceutical ingredients possess poor mechanical properties and are not suitable for tableting. Using fine sand (silicon dioxide), we show that a core/shell structure, where a core particle (sand) is coated with a thin layer of polyvinylpyrrolidone (PVP), can profoundly improve powder compaction properties. Sand coated with 5% PVP could be compressed into intact tablets. Under a given compaction pressure, tablet tensile strength increases dramatically with the amount of coating. This is in sharp contrast to poor compaction properties of physical mixtures, where intact tablets cannot be made when PVP content is 20% or less. The profoundly improved tabletability of core/shell particles is attributed to the formation of a continuous three-dimensional bonding network in the tablet. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:4458,4462, 2010 [source] An examination of binding motifs associated with inter-particle interactions between facetted nano-crystals of acetylsalicylic acid and ascorbic acid through the application of molecular grid-based search methods,JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 12 2009R.B. Hammond Abstract Grid-based intermolecular search methods using atom,atom force fields are used to assess the structural nature of potential crystal,crystal interfacial binding associated with the examination of representative pharmaceutical formulation components, viz acetylsalicylic acid (aspirin) and ascorbic acid (vitamin C). Molecular models of nano-sized molecular clusters for these two compounds, shaped in accordance with an attachment energy model of the respective particle morphologies, are constructed and used together with a grid-based search method to model the likely inter-particle interactions. The most-stable, mutual alignments of the respective nano-clusters based on their interaction energies are identified in the expectation that these are indicative of the most likely inter-particle binding configurations. The stable inter-particle binding configurations identified reveal that the number of interfacial hydrogen bonds formed between the binding particles is, potentially, an important factor in terms of the stability of inter-particle cohesion. All preferred inter-particle alignments are found to involve either the (1,0,0) or the (1,1,0) face of aspirin crystals interacting with a number of the growth forms of ascorbic acid. Four main types of interfacial hydrogen bonds are found to be associated with inter-particle binding and involve acceptor,donor interactions between hydroxyl, carbonyl, ester and lactone acceptor groups and hydroxyl donor groups. This hydrogen bonding network is found to be consistent with the surface chemistry of the interacting habit faces with, in general, the number of hydrogen bonds increasing for the more stable alignments. The likely usefulness of this approach for predicting solid-state formulation properties is reviewed. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4589,4602, 2009 [source] Identification and characterisation of the E951 artificial food sweetener by vibrational spectroscopy and theoretical modellingJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2009Niculina Peica Abstract Aspartame (E951), a very well-known dipeptide sweetener, approximately 150,200 times sweeter than sugar, is widely used in a variety of applications, especially in soft drinks. A drawback of E951 is its relatively low stability at high pH values and at high temperatures, thereby limiting its use. The changes observed in the very strong bands from the 1600,1300 cm,1 spectral region, characteristic to the ,(CO) mode coupled with the NH bending mode, allows to establish the species present in the Raman and SERS solutions at different concentrations and pH values. More exactly, a molecule protonation at the amino group was detected on going from basic to acidic pH values. The DFT calculated geometry, harmonic vibrational modes and Raman scattering activities of E951 were in good agreement with the experimental data and helped establish its SERS behaviour on silver surfaces. According to the DFT calculations performed, E951 can give rise to an intramolecular hydrogen bonding network, with lengths in the same range as the hydrogen bonds in the peptide unit moieties. Copyright © 2009 John Wiley & Sons, Ltd. [source] Microstructure and Molecular Interaction in Glycerol Plasticized Chitosan/Poly(vinyl alcohol) Blending FilmsMACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 10 2009Songmiao Liang Abstract Exploring some basic interactions in blending systems is of great significance for designing a blend with controlled structure and properties. This work attempts to analyze microstructure and molecular interaction in glycerol plasticized chitosan/poly(vinyl alcohol) blends by atomic force microscopy, differential scanning calorimetry and ATR-FTIR spectroscopy. Our results show that the blending films are aggregated by spherical chitosan/poly(vinyl alcohol) blending nanoparticles. The size and aggregation behavior of these particles are closely related to glycerol content. The presence of glycerol gives rise to a continuous closing in Tg of poly(vinyl alcohol) and chitosan components, suggesting an improved miscibility of the blend. Strong hydrogen bonding interaction in the blend is observed and further distinguished by peak resolution. Moreover, more interesting evidence on the effect of glycerol in the blends is provided by monitoring the structure evolution of the blend at different blending steps using atomic force microscopy. The formation of strong hydrogen bonding network among glycerol molecules and polymer matrix was considered as the main driving force to result in the changes in the microstructure and miscibility of the blend. [source] Isofagomine Induced Stabilization of GlucocerebrosidaseCHEMBIOCHEM, Issue 16 2008Gregory J. Kornhaber Dr. Abstract Structurally destabilizing mutations in acid ,-glucosidase (GCase) can result in Gaucher disease (GD). The iminosugar isofagomine (IFG), a competitive inhibitor and a potential pharmacological chaperone of GCase, is currently undergoing clinical evaluation for the treatment of GD. An X-ray crystallographic study of the GCase-IFG complex revealed a hydrogen bonding network between IFG and certain active site residues. It was suggested that this network may translate into greater global stability. Here it is demonstrated that IFG does increase the global stability of wild-type GCase, shifting its melting curve by ,15,°C and that it enhances mutant GCase activity in pre-treated N370S/N370S and F213I/L444P patient fibroblasts. Additionally, amide hydrogen/deuterium exchange mass spectroscopy (H/D-Ex) was employed to identify regions within GCase that undergo stabilization upon IFG-binding. H/D-Ex data indicate that the binding of IFG not only restricts the local protein dynamics of the active site, but also propagates this effect into surrounding regions. [source] Synthesis and Electrochemical Properties of Tetrasubstituted TetraphenylethenesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 15 2006Alina Schreivogel Abstract Tetrakis(4-acetoxyphenyl and 4-benzoyloxyphenyl)ethenes 1f and 1g were obtained by acylation of tetrakis(4-hydroxyphenyl)ethene 1b. Ullmann etherification of 4,4,-dihydroxybenzophenone 2b and subsequent McMurry coupling yielded tetrakis(phenoxyphenyl)ethene 1i. The tetrakis(acetamidophenyl)ethene 1h was prepared in three steps from tetraphenylethene 1c by nitration, Raney-Ni reduction and subsequent acetylation. Alternatively, trifluoroacetamide 1j, 2-methylhexanamide 1k and 2,4-dimethylbenzamide 1l, with less tendency to form 2D hydrogen bonding networks and thus increased solubility as compared to 1h, were prepared by acylation of 4,4,-diaminobenzophenone 2a and subsequent McMurry coupling. Compounds 1f,l were investigated by cyclic voltammetry. While the phenyl ether derivative 1i displays single-electron processes during oxidation, a two-electron process was discovered for trifluoroacetamide 1j as was also supposed for the esters 1f and 1g. In addition, comproportionation constants were shown to be dependent on the solvent. In situ IR spectroelectrochemistry provided evidence for quinoidal type substructures in the dioxidized forms of tetraphenylethenes 1. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] 27 ps DFT molecular dynamics simulation of ,-maltose: A reduced basis set study,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Udo Schnupf Abstract DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as ,-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in ,-maltose. In previous studies, the gg,-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in ,20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1,···H4 distance of 2.28 Å confirms that the syn form is the primary glycosidic conformation, while the average C1,O1,C4 bond angle was 118.8°, in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Structures of the Chromophore Binding Sites in BLUF Domains as Studied by Molecular Dynamics and Quantum Chemical Calculations,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Kazuya Obanayama BLUF (blue-light sensing using FAD) domains constitute a new family of flavin-based blue light photoreceptors. The photocycle of BLUF is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes in the bound chromophore. The hydrogen bond rearrangements upon illumination have been inferred from spectral changes in the chromophore: ,10 nm redshift of the absorption maximum and ,16 cm,1 downshift of the C4=O stretching frequency. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. In particular, the orientation of a conserved Gln (Gln63 in AppA) is presently one of the most questioned topics in the field. Here we perform molecular dynamics simulations for the wild-type AppA, AppA1-124C20S, BlrB and T110078 and furthermore quantum chemical calculations to investigate their spectroscopic properties in the dark and signaling states. On the basis of these results, we reveal the dynamic aspect of hydrogen bonding networks at the active site and propose theoretically reasonable models for the dark and signaling states of the BLUF domains. [source] | |||||||||||||