Toward the supramolecular structure of collagen: a molecular dynamics approach

The structure, stability, and conformational dynamics of an assembly of two pentameric bundles made of collagen-like triple helical segments are explored using 1.2 ns molecular dynamics simulations in three environments: 8.0% (v/v) formaldehyde/water solution, 1.4% (v/v) gallic acid/water solution, and pure water. Stable supramolecular arrangements, where the two collagen units are very close to each other at interacting distances, are identified via docking and energy minimization procedures. Analysis of the interaction with formaldehyde and gallic acid suggests that they perturb the protein in a similar way depending on hydrogen-bonding capability, hydrophobic association properties, and the size and concentration of the compound.     

Treatment with lignin residue

Acid hydrolysis of lignocellulose to hydrolysates intended for production of fuel ethanol results in the formation of byproducts in addition to fermentable sugars. Some of the byproducts, such as phenolic compounds and furan aldehydes, are inhibitory to the fermenting microorganism. Detoxification of the hydrolysates may be necessary for production of ethanol at a satisfactory rate and yield. The lignin residue obtained after hydrolysis is a material with hydrophobic properties that is produced in large amounts as a byproduct within an ethanol production process based on lignocellulosic raw materials. We have explored the possibility of using this lignin residue for detoxification of spruce dilute-acid hydrolysates prior to fermentation with Saccharomyces cerevisiae. Three dilute-acid hydrolysates of spruce were treated with lignin residue, which in all cases resulted in improved fermentability in terms of productivity and yield of ethanol. The effect was improved by washing the lignin before treatment, by using larger amounts of lignin in the treatment, and by performing the treatment at low temperature. Treatment with the lignin residue removed up to 53% of the phenolic compounds and up to 68% of the furan aldehydes in a spruce dilute-acid hydrolysate. A larger fraction of furfural was removed compared to the less hydrophobic 5-hydroxymethylfurfural.     

Formation of heterotopic metallacalix[n]arenes (n=3, 4, 6) containing ethylenediaminepalladium(II) metal fragments and 4,7-phenanthroline and 2-pyrimidinolate bridges. Synthesis, structure and host-guest chemistry

A multicomponent reaction involving ethylenediaminepalladium(II), 2-pyrimidinol derivatives (L) [L=2-pyrimidinol (a); 4-methyl-2-pyrimidinol (b); 4,6-dimethyl-2-pyrimidinol (c)] and 4,7-phenanthroline (4,7-phen) leads to the formation of heterotopic cyclic metallamacrocycles of the type [Pdn(en)n(mu-N,N'-L)m(mu-N,N'-4,7-phen)n-m](2n-m)+ [n=3, m=1 (3); n=4, m=2 (4); n=6, m=4 (5)]. These species can be obtained by different reaction pathways, including: (i) reaction of ethylenediaminepalladium(ii), L and 4,7-phen building blocks and (ii) reaction of the homotopic species [Pd4(en)4(mu-N,N'-L)4]4+ (1) and [Pd3(en)3(mu-N,N'-4,7-phen)3]6+ (2). The resulting heterotopic metallamacrocycles have been characterised by 1D and 2D 1H NMR spectroscopy. Additionally, species 3c and 4a have been studied by X-ray crystallography. The former one contains almost isosceles triangles of [Pd3(en)3(mu-N,N'-4,6-dimethyl-2-pyrimidinolate)(mu-N,N[prime or minute]-4,7-phen)2]5+ formulation, exhibiting a pinched-cone conformation. 4a contains a tetranuclear parallelogram [Pd4(en)4(mu-N,N'-2-pyrimidinolate)2(mu-N,N'-4,7-phenanthroline)2]6+, exhibiting a 1,3-alternate conformation. The host-guest properties of the here reported species have been studied, showing that they are able to interact with cationic as well as with anionic species.     

Thermodynamics of beta-amyloid fibril formation

Amyloid fibers are aggregates of proteins. They are built out of a peptide called beta-amyloid (Abeta) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the amyloid precursor protein (APP). X-ray diffraction experiments have shown that these fibrils are rich in beta-structures, whereas the shape of the peptide displays an alpha-helix structure within the APP in its biologically active conformation. A realistic model of fibril formation is developed based on the 17 residues Abeta12-28 amyloid peptide, which has been shown to form fibrils structurally similar to those of the whole Abeta peptide. With the help of physical arguments and in keeping with experimental findings, the Abeta12-28 monomer is assumed to be in four possible states (i.e., native helix conformation, beta-hairpin, globular low-energy state, and unfolded state). Making use of these monomeric states, oligomers (dimers, tertramers, and octamers) were constructed. With the help of short, detailed molecular dynamics calculations of the three monomers and of a variety of oligomers, energies for these structures were obtained. Making use of these results within the framework of a simple yet realistic model to describe the entropic terms associated with the variety of amyloid conformations, a phase diagram can be calculated of the whole many-body system, leading to a thermodynamical picture in overall agreement with the experimental findings. In particular, the existence of micellar metastable states seem to be a key issue to determine the thermodynamical properties of the system.     

Coordination frameworks containing the pyrimidin-4-olate ligand. Synthesis, thermal, magnetic, and ab initio XRPD structural characterization of nickel and zinc derivatives

Extended coordination frameworks containing the pyrimidin-4-olate ligand (4-pymo) and Zn(II) and Ni(II) metal ions have been obtained by solid state reactions and have been fully characterized by spectroscopic, thermal, and magnetic measurements and by ab initio XRPD. The reaction of ZnO and 4-Hpymo at 140 degrees C gives a solid microcrystalline phase, Zn(4-pymo)(2) (1). Its 3D framework contains Zn(II) centers linked by 4-pymo ligands acting in two different coordination modes, namely, the N,N'- and the N,O-exo-bidentate ones, which result in a pseudotetrahedral ZnN(3)O chromophore. Thermal treatment of the "molecular" Ni(4-pymo)(2)(H(2)O)(4) complex (2) above 140 degrees C gives an anhydrous amorphous material analyzing as Ni(4-pymo)(2) (3a). Further heating of this material above 388 degrees C results in the formation of the microcrystalline layered Ni(4-pymo)(2) species (3b), in which Ni(II) centers are bridged by N,O-exo-bidentate 4-pymo ligands (assisted by longer Ni.N contacts). The thermal dependence of the magnetic susceptibility has been studied for the paramagnetic species 2 and 3a. 2 shows a weak antiferromagnetic interaction [J = -0.313(5) cm(-)(1)] transmitted through the multiple H-bonding interactions between the exocyclic pyrimidine and water oxygen atoms coordinated to the metal centers. 3a behaves as a 2D Heisenberg antiferromagnet with J = -4.11(3) cm(-)(1).     

Influence of membrane surface properties on the growth of neuronal cells isolated from hippocampus

Membranes have become of great interest for tissue engineering application, since they offer the advantage of developing neuronal tissue that may be used in implantable or in vitro hybrid systems for the simulation of brain function. The behaviour of neurons isolated from the hippocampus on membranes with different surface properties was investigated.     

Breakdown kinetics of aggregates from poly(ethylene glycol‐bl‐propylene sulfide) di‐ and triblock copolymers induced by a non‐ionic surfactant

We explored the effects of addition of the nonionic surfactant Triton X‐100 on the stability of aggregates of poly(ethylene glycol‐bl‐propylene sulfide) di‐ and triblock copolymers. Fluorescence spectra of pyrene, used as a probe molecule, elucidated the various stages of transformation from pure copolymeric micelles to surfactant‐rich micelles. Turbidity measurements yielded insight into the mechanism of the interaction, the hydrophobicity of the copolymer driving the process. Triton X‐100 tends to strongly interact with highly hydrophobic copolymers by inserting into the core of the micellar aggregates. On the other hand, Triton X‐100 tends to interact with the corona of micelles formed by less hydrophobic copolymers which, for this reason, are more stable upon addition of this destabilizing agent. Kinetic data give evidence that only monomers, not micelles of surfactant, interact with the copolymer micelles. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2477–2487, 2008     

Adsorption of d-alaninol on Cu(1 0 0)

Adsorption of d-alaninol on Cu(1 0 0) at room temperature has been investigated by photoelectron spectroscopy in the soft X-ray and VUV energy range and low energy electron diffraction (LEED). d-Alaninol was found by LEED to self-assemble at full coverage; core and valence photoemission spectra are presented at low and full coverage. Chemisorption occurs at room temperature. The bonding at low coverage takes place at the hydroxylic group; at full coverage there is evidence of bonding for both hydroxylic and amino groups.