Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy

A series of G-rich oligonucleotides able to form tetraplexes has been studied by FTIR spectroscopy. Characteristic markers of the formation of guanine tetrads are given. Moreover, we propose a new marker discriminating between parallel and antiparallel tetraplexes: the position of the C6O6 guanine carbonyl stretching vibration. In intermolecular parallel tetrameric structures formed by four separate strands this absorption is observed at 1693 cm-1 while for antiparallel tetrameric structures, either intramolecular or formed by dimerization of hairpins, this vibrational mode is observed at 1682 cm-1. These shifts to higher wavenumbers, when compared to the position of a free guanine C6O6 carbonyl stretching vibration observed at 1666 cm-1(Deltanu=27 cm-1 for parallel tetraplexes and Deltanu=16 cm-1 for antiparallel tetraplexes) reflect different strand orientations in the structures. This marker has been used to evidence the possibility of an antiparallel-parallel tetraplex reorganization for Oxytricha nova d(G4T4G4) and d((G4T4)3G4) and human d(G3T2AG3) telomeric sequences induced by Na+/K+ or Na+/Ca2+ ion exchange. Formation of the guanine tetrads, characterization of the phosphate geometries and of the sugar conformations have also been obtained by FTIR for the different tetraplexes.     

Synthesis, crystal structures, and luminescent properties of two types of lanthanide phosphonates

Hydrothermal reactions of different lanthanide(III) salts with an amino-diphosphonate ligand (H₄L=C₆H₅CH₂N(CH₂PO₃H₂)₂) led to two series of lanthanide phosphonates, namely, Ln(H₂L)(H₃L) (Ln=La, 1; Pr, 2; Nd, 3; Sm, 4; Eu, 5; Gd, 6; Tb, 7). Compounds 1-5 feature a one-dimensional (1D) chain structure in which dimers of two edge-sharing LnO₈ polyhedra are interconnected by bridging phosphonate groups, such 1D arrays are further interlinked via strong hydrogen bonds between non-coordinated phosphonate oxygen atoms into a two-dimensional (2D) layer with the phenyl groups of the ligands orientated toward the interlayer space. Compounds 6 and 7 also show a different 1D array in which the LnO₆ octahedra are bridged by phosphonate groups via corner-sharing, such chains are also further interlinked by hydrogen bonds into a 2D supramolecular layer. Compounds 5 and 7 emit red and green light with a lifetime of 2.1 and 3.7 ms, respectively.     

A novel system for measurement of types and densities of sulfur crosslinks of a filled rubber vulcanizate

A novel system for measuring the crosslink densities of mono-, di- and polysulfides of a filled rubber vulcanizate was developed. The system included pre-swelling, cleavage of sulfur crosslinks by a chemical probe using thiol/n-hexylamine instead of thiol/piperidine, and two step swelling. A sample cage made of stainless steel mesh was used to measure multiple samples at the same time and to reduce experimental errors. The organic materials-extracted sample was pre-swollen in toluene to introduce the probe chemicals more rapidly and homogeneously into the whole network. Polysulfidic crosslinkages were cleaved by a chemical probe of propane-2-thiol/n-hexylamine in toluene, while di- and polysulfidic crosslinkages were dissociated by a chemical probe of n-hexanethiol/n-hexylamine in toluene. The experimental errors were lower than 2%. By using cubic apparent crosslink density, fractions of the crosslink types of an unknown rubber vulcanizate could be estimated even although the filler content and rubber composition are not analyzed.     

Supramolecular bidentate ligands by metal-directed in situ formation of antiparallel beta-sheet structures and application in asymmetric catalysis

The principles of protein structure design, molecular recognition, and supramolecular and combinatorial chemistry have been applied to develop a convergent metal-ion-assisted self-assembly approach that is a very simple and effective method for the de novo design and the construction of topologically predetermined antiparallel beta-sheet structures and self-assembled catalysts. A new concept of in situ generation of bidentate P-ligands for transition-metal catalysis, in which two complementary, monodentate, peptide-based ligands are brought together by employing peptide secondary structure motif as constructing tool to direct the self-assembly process, is achieved through formation of stable beta-sheet motifs and subsequent control of selectivity. The supramolecular structures were studied by (1)H, (31)P, and (13)C NMR spectroscopy, ESI mass spectrometry, X-ray structure analysis, and theoretical calculations. Our initial catalysis results confirm the close relationship between the self-assembled sheet conformations and the catalytic activity of these metallopeptides in the asymmetric rhodium-catalyzed hydroformylation. Good catalyst activity and moderate enantioselectivity were observed for the selected combination of catalyst and substrate, but most importantly the concept of this new methodology was successfully proven. This work presents a perspective interface between protein design and supramolecular catalysis for the design of beta-sheet mimetics and screening of libraries of self-organizing supramolecular catalysts.     

Quantum chemical DFT study of two types of stable structures of Ni(II) high-spin binuclear carboxylate complexes

Quantum chemical calculations of the electronic structure of [Ni₂(??-O₂CCH₃)₄(O-DMSO)₂] complex were performed using the DFT B3LYP method in the 6-31G(d,p) basis. The calculations made it possible to detect the existence of two types of stable structures of Ni(II) high-spin binuclear carboxylate complexes with different terminal ligands, i.e. with a relatively symmetrical metal-carboxylate Ni₂(??-O₂CR)₄ framework and with its significant distortion caused by the second-order Jahn-Teller effect.     

High-field 1H MAS and 15N CP-MAS NMR studies of alanine tripeptides and oligomers: distinction of antiparallel and parallel beta-sheet structures and two crystallographically independent molecules

beta-Strand peptides are known to assemble into either antiparallel (AP) or parallel (P) beta-sheet forms which are very important motifs for protein folding and fibril formations occurring in silk fibroin or amyloid proteins. Well-resolved 1H NMR signals including NH protons were observed for alanine tripeptides (Ala)3 with the AP and P structures as well as (Ala)n (n = 4-6) by high-field/fast magic-angle spinning NMR. Amide NH and amino NH3+ 1H signals of (Ala)3 with the P structure were well resonated at 7.5 and 8.9 ppm, respectively, whereas they were not resolved for the AP structure. Notably, NH 1H signals of (Ala)3 and (Ala)4 taking the P structure are resonated at higher field than those of the AP structure by 1.0 and 1.1 ppm, respectively. Further, NH 15N signals of (Ala)3 with the AP structure were resonated at lower field by 2 to 5 ppm than those of (Ala)3 with the P structure. These relative 1H and 15N hydrogen bond shifts of the P structure with respect to those of the AP structure are consistent with the relative hydrogen bond lengths of the interstrand N-H...O=C bonds. Distinction between the two crystallographically independent chains present in the AP and P structures was feasible by 15N chemical shifts but not by 1H chemical shifts because of insufficient spectral resolution in the latter. Calculated 1H and 15N shielding constants by density functional theory are generally consistent with the experimental data, although some discrepancies remain depending upon the models used.     

Biocompatible micropatterning of two different cell types

The spatial arrangement of individual cell types can now be routinely controlled using soft-lithography-based micropatterning of complementary cell-adhesive and cell-resistant patterns. However, the application of these tools in tissue engineering to recreate tissue complexity in vitro has been hampered by the challenge of finding noncytotoxic procedures for converting complementary cell-resistant regions that define the arrangement of the first cell type into cell-adhesive regions to allow for the attachment of other cell types. A polyelectrolyte assembly approach is presented here for the first time, which allows for this noncytotoxic conversion and, thus, micropatterning of two different cell types, for example, endothelial cells and fibroblasts, on biodegradable substrates. The flexibility of this approach is further demonstrated by inducing organized capillary formation by endothelial cells on micropatterned lines followed by subsequent assembly of fibroblasts.     

Crystal structures of two 4-phenylbenzophenones

Two 4-phenylbenzophenones (I) and (II) are synthesized via Friedel-Crafts reactions. There are four crystallographically independent molecules with different conformations in the crystal structure of [1,1′-biphenyl]-4-yl(2-chlorophenyl)methanone (I). Crystals are orthorhombic, Pca2₁, C₁₉H₁₃ClO, a = 13.699(3) Å, b = 8.9385(17) Å, c = 46.836(9) Å; V = 5735(2) ų, Z = 16, d _x = 1.356 g/cm³. Torsion angles between the biphenyl rings are between 28.5° and 30.8°. Several C-H…O and C-H…Cl hydrogen bonds and weak π-π stacking contacts consolidate the crystal. Crystals of [1,1′-biphenyl]-4-yl(3-methoxyphenyl)methanone (II) are orthorhombic, Pbca, C₂₀H₁₆O₂, a = 7.8179(15) Å, b = 16.003(3) Å, c = 23.345(5) Å; V = 2920.7(10) ų, Z = 8, d _x = 1.311 g/cm³. The torsion angle between the biphenyl rings is 28.1° and C-H…O hydrogen bonds are observed in compound (II).     

Protein separation with aqueous-aqueous polymer systems by two types of counter-current chromatographs.

Two different types of counter-current chromatographs, the cross-axis coil planet centrifuge (X-axis CPC) and horizontal flow-through coil planet centrifuge (horizontal CPC), were evaluated for protein separation with an aqueous-aqueous two-phase polymer system. The sample solution, containing 10-200 mg each of cytochrome c, myoglobin, ovalbumin and hemoglobin in 2 ml of each phase was eluted with the lower phase. In both instruments, the effects of the flow-rate, revolution speed, and parameter beta (helical diameters of the multilayer coil) on the protein separation were investigated. The best results were obtained from the X-axis CPC operated at 750 rpm and a flow-rate of 2.0 ml/min using a multilayer coil with a small helical diameter (beta = 0.25-0.60). Four protein samples were well resolved in less than 5 h.     

Thermal analysis of two types of dextran-coated magnetite

The thermal stability of two kinds of dextran-coated magnetite (dextran with molecular weight of 40,000 (Dex40) and 70,000 (Dex70)), obtained by dextran adsorption onto the magnetite surface is investigated in comparison with free dextran in air and argon atmosphere. The thermal behavior of the two free dextran types and corresponding coated magnetites is similar, but atmosphere dependent. The magnetite catalyzes the thermal decomposition of dextran, the adsorbed dextran displaying lower initial decomposition temperatures comparative with the free one in both working atmospheres. The dextran adsorbed onto the magnetite surface decomposes in air through a strong sharp exothermic process up to ~450 °C while in argon atmosphere two endothermic stages are identified, one in the temperature range 160–450 °C and the other at 530–800 °C.