Search results for "Models"
showing 10 items of 8211 documents
Self-Organization of 2-Acylaminopyridines in the Solid State and in Solution
2010
Aggregation of 2-acylaminopyridines and their 6-methyl derivatives in chloroform solution was studied by (1)H, (13)C, and (15)N NMR spectroscopies. The results were compared with (13)C and (15)N CPMAS NMR and IR spectral as well as with X-ray structural data. Intermolecular interactions in solution and in solid state were found to have a similar nature. Relatively strong N(amide)-H···N(pyridine) intermolecular hydrogen bonds enable dimerization to take place. Steric interactions in N-pivaloyl- and N-1-adamantylcarbonyl as well as that caused by the 6-methyl group hinder formation of the dimeric aggregates stabilized by the N(amide)-H···N(pyridine) intermolecular hydrogen bonds. In general, …
Self-Sorting Dimerization of Tetraurea Calix[4]arenes
2007
Calix[4]arenes substituted by four urea functions are self-complementary molecules that spontaneously combine in apolar solvents in the presence of an ammonium salt to form dimeric capsules held together by a belt of hydrogen bonds. In the presence of tetraethylammonium salts, the Et4N+ cation is included as a guest. The sorting between dimeric capsules formed in a mixture of calix[4]arenes directly depends on the steric crowding of the substituents grafted on the urea groups whether aromatic derivatives or aliphatic chains linking urea functions in mono-, di-, or tetraloop structures. Simple rules allow one to anticipate which capsules will be exclusively formed when calix[4]arenes are mix…
Reasons for the exclusive formation of heterodimeric capsules between tetra-tolyl and tetra-tosylurea calix[4]arenes
2007
The selective heterodimerization of tetra-tolyl (1a) and tetra-tosylurea (1b) calixarenes, serendipitously found by Rebek et al. (R. K. Castellano, B. H. Kim and J. Rebek, Jr., J. Am. Chem. Soc., 1997, 119, 12671–12672), has been used for the construction of highly sophisticated macrocycles and well-defined supramolecular assemblies. Regrettably, hitherto, neither the exact structure of these heterodimers nor the reason for their exclusive formation is known. We present molecular dynamics simulations using the AMBER force field in explicit chloroform solvent for the two homodimers, the heterodimer and the two uncomplexed tetra-urea calixarenes. The rigid rotation about the C–S–N–C bond of t…
High Pressure Enhances Hexacoordination in Neuroglobin and Other Globins
2005
The techniques of high applied pressure and flash photolysis have been combined to study ligand rebinding to neuroglobin (Ngb) and tomato Hb, globins that may display a His-Fe-His hexacoordination in the absence of external ligands. High pressure induces a moderate decrease in the His association rate and a large decrease in His dissociation rate, thus leading to an enhancement of the overall His affinity. The overall structural difference between penta- and hexacoordinated globins may be rather small and can be overcome by external modifications such as high pressure. Over the pressure range 0.1-700 MPa (7 kbar), the globins may show a loss of over a factor of 100 in the amplitude of the b…
Molecules with New Topologies Derived from Hydrogen-Bonded Dimers of Tetraurea Calix[4]arenes
2008
Tetraurea calix[4]arenes 2 have been synthesized in which two adjacent aryl urea residues are connected to a loop by an aliphatic chain -O-(CH(2))(n)-O-. The remaining urea residues have a bulky 3,5-di-tert-butylphenyl residue and an omega-alkenyloxyphenyl residue. Since this bulky residue cannot pass through the loop, only one homodimer (22) is formed in apolar solvents, for steric reasons, in which the two alkenyl residues penetrate the two macrocyclic loops. Covalent connection of these alkenyl groups by olefin metathesis followed by hydrogenation creates compounds 3, which consist of molecules with hitherto unknown topology. Their molecular structure was confirmed by (1)H NMR spectrosco…
The first unpaired electron placed inside a C3-symmetry P-chirogenic cluster
2010
The Pd(3)(dppm*)(3)(CO)(n+) enantiomers (n = 2 (2), 1 (3)) were prepared either from (R,R)- or (S,S)-P-chirogenic bis(phenyl-m-xylylphosphino)methane (dppm*; 1) and Pd(OAc)(2) in the presence of CF(3)CO(2)H, CO and water (n = 2), and then by reductive electrolysis (n = 1). The stable enantiomeric [Pd(3)((S,S)-dppm*)(3)(CO)](+)˙ (3), is the first C(3)-symmetry radical-cation M-M bonded cluster, therefore the odd electron is delocalized onto the Pd(3) frame within this symmetry. The novel chiral species have been characterized by circular dichroism (CD) of both enantiomers of the Pd(3)(dppm*)(3)(CO)(2+) clusters (2) and by EPR spectroscopy for the Pd(3)((S,S)-dppm*)(3)(CO)(+)˙ paramagnetic co…
Factors Dictating the Pseudocatalytic Efficiency of Avidins
2006
The hydrolysis of biotinyl p-nitrophenyl ester (BNP) by a series of avidin derivatives was examined. Surprisingly, a hyperthermostable avidin-related protein (AVR4) was shown to display extraordinary yet puzzling hydrolytic activity. In order to evaluate the molecular determinants that contribute to the reaction, the crystal structure of AVR4 was compared with those of avidin, streptavidin and key mutants of the two proteins in complex with biotinyl p-nitroanilide (BNA), the inert amide analogue of BNP. The structures revealed that a critical lysine residue contributes to the hydrolysis of BNP by avidin but has only a minor contribution to the AVR4-mediated reaction. Indeed, the respective …
Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin
2003
The protein chicken avidin is a commonly used tool in various applications. The avidin gene belongs to a gene family that also includes seven other members known as the avidin-related genes (AVR). We report here on the extremely high thermal stability and functional characteristics of avidin-related protein AVR4/5, a member of the avidin protein family. The thermal stability characteristics of AVR4/5 were examined using a differential scanning calorimeter, microparticle analysis, and a microplate assay. Its biotin-binding properties were studied using an isothermal calorimeter and IAsys optical biosensor. According to these analyses, in the absence of biotin AVR4/5 is clearly more stable (T…
Molecular Architecture of Strictosidine Glucosidase: The Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family[W]
2007
Abstract Strictosidine β-d-glucosidase (SG) follows strictosidine synthase (STR1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. This family is composed of ∼2000 structurally diverse compounds. SG plays an important role in the plant cell by activating the glucoside strictosidine and allowing it to enter the multiple indole alkaloid pathways. Here, we report detailed three-dimensional information describing both native SG and the complex of its inactive mutant Glu207Gln with the substrate strictosidine, thus providing a structural characterization of substrate binding and identifying the amino acids …
Meprins, membrane-bound and secreted astacin metalloproteinases
2008
The astacins are a subfamily of the metzincin superfamily of metalloproteinases. The first to be characterized was the crayfish enzyme astacin. To date more than 200 members of this family have been identified in species ranging from bacteria to humans. Astacins are involved in developmental morphogenesis, matrix assembly, tissue differentiation and digestion. Family members include the procollagen C-proteinase (BMP1, bone morphogenetic protein 1), tolloid and mammalian tolloid-like, HMP (Hydra vulgaris metalloproteinase), sea urchin BP10 (blastula protein) and SPAN (Strongylocentrotus purpuratus astacin), the 'hatching' subfamily comprising alveolin, ovastacin, LCE, HCE ('low' and 'high' c…