Biopolymers for biocatalysis: Structure and catalytic mechanism of hydroxynitrile lyases

Hydroxynitrile lyases catalyze the reversible cleavage of α-cyanohydrins to yield hydrocyanic acid and the corresponding aldehyde or ketone. Besides its biological interest, this class of enzymes is also of relevance in industrial biocatalysis for the enantioselective condensation of HCN with a variety of aldehydes and ketones. Several distinctly different types of hydroxynitrile lyases (HNLs) are known, which must have originated through convergent evolution from different ancestral proteins. Three-dimensional structural data are known for three classes of hydroxynitrile lyases. Insights into the reaction mechanisms emerged from a combination of structural, enzyme kinetic, spectroscopic, and molecular modeling data. For all three types of HNLs, mechanisms involving acid–base catalysis were proposed. In members belonging to the α,β-hydrolase type, the amino acid residues of the catalytic triad presumably act as general acid/base, whereas for flavine adenine dinucleotide (FAD)-dependent HNLs a single histidine residue fulfills this function. In the third type of HNL—which is related to carboxypeptidase—acid–base catalysis involves the carboxylate of the C-terminal residue. The catalytic relevance of a positive electrostatic potential in the active site was suggested in some of the mechanistic proposals. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 479–486, 2004     

Loss without recovery of Gibbsianness during diffusion of continuous spins

We consider a specific continuous-spin Gibbs distribution μ_t=0 for a double-well potential that allows for ferromagnetic ordering. We study the time-evolution of this initial measure under independent diffusions. For `high temperature' initial measures we prove that the time-evoved measure μ<sub>t</sub> is Gibbsian for all t. For `low temperature' initial measures we prove that μ_t stays Gibbsian for small enough times t, but loses its Gibbsian character for large enough t. In contrast to the analogous situation for discrete-spin Gibbs measures, there is no recovery of the Gibbs property for large t in the presence of a non-vanishing external magnetic field. All of our results hold for any dimension d≥2. This example suggests more generally that time-evolved continuous-spin models tend to be non-Gibbsian more easily than their discrete-spin counterparts. Research carried out at EURANDOM and supported by Deutsche Forschungsgemeinschaft     

Über Sesquiselenide der Lanthanoide: Einkristalle von Ce2Se3 im C‐, Gd2Se3 im U‐ und Lu2Se3 im Z‐Typ

On Sesquiselenides of the Lanthanoids: Single Crystals of C‐type Ce₂Se₃, U‐type Gd₂Se₃, and Z‐type Lu₂Se₃ Single crystals of lanthanoid sesquiselenides (M₂Se₃; here: M = Ce, Gd, Lu) are accessible through conversion of the elements (lanthanoid and selenium) in molar ratios of 2:3 within seven days at 850 °C from evacuated silica ampoules if equimolar amounts of NaCl serve as a flux. In the case of Ce₂Se₃ (a = 897.74(6) pm) und Gd₂Se₃ (a = 872.56(5) pm) the cubic C‐type (I4¯3d, Z = 5.333) forms as dark red beads, whereas the orthorhombic Z‐type (Fddd, Z = 16) emerges for Lu₂Se₃ (a = 1125.1(1), b = 798.06(8), c = 2387.7(2) pm) as orange‐yellow bricks. Upon oxidation of monochloride hydrides (MClH_x or A_yMClH_x; M = Ce, Gd, Lu; x = 1; A = Li, Na; y = 0.5) with selenium in arc‐welded tantalum ampoules the same main products appear with C‐Ce₂Se₃ and Z‐Lu₂Se₃, even with a surplus of NaCl or LiCl as fluxing agent. In the case of Gd₂Se₃, however, black‐red needles of the orthorhombic U‐type (Pnma, Z = 4; a = 1118.2(1), b = 403.48(4); c = 1097.1(1) pm) are yielded instead of C‐Gd₂Se₃. C‐Ce₂Se₃ crystallizes in a cation‐deficient Th₃P₄‐type structure (Ce₂S₃ type) according to Ce_2.667□_0.333Se₄ (Z = 4) or with Z = 5.333 for the empirical formula Ce₂Se₃. Here, Ce³⁺ is coordinated by eight Se^2— anions trigon‐dodecahedrally. In U‐Gd₂Se₃ (U₂S₃ type) two crystallographically independent Gd³⁺ cations with coordination numbers of 7 (Gd1) and 7+1 (Gd2), respectively, are present, exhibiting mono‐ or bicapped trigonal prisms as coordination polyhedra. The crystal structure of Z‐Lu₂Se₃ (Sc₂S₃ type) shows two different Lu³⁺ cations as well, which now both reside in octahedral coordination of six Se^2— anions each.     

Heat conductivity of three periodic Hard Disks via nonequilibrium molecular dynamics

We use a driving field, of the type first suggested by Evans, to generate a steady heat current in the simplest possible system, a two-dimensional periodic fluid of three hard disks. Hard-disk motion equations can be conveniently derived from repulsive constant-force or linear-force potentials by considering the infinitely repulsive limit of these potentials. We show that the isoenergetic and isokinetic forms of the nonequilibrium equations of motion generate steady-state heat conductivities differing by terms of order 1/N, whereN is the number of particles. The resulting conductivities appear to vary as the logarithm of the driving field strength. Even at low fields, the three-body periodic-system results lie well below Enskog's infinite-system prediction.     

Microarray-based in vitro evaluation of DNA oligomer libraries designed in silico.

We report on the microarray-based in vitro evaluation of two libraries of DNA oligonucleotide sequences, designed in silico for applications in supramolecular self-assembly, such as DNA computing and DNA-based nanosciences. In this first study which is devoted to the comparison of sequence motif properties theoretically predicted with their performance in real-life, the DNA-directed immobilization (DDI) of proteins was used as an example of DNA-based self-assembly. Since DDI technologies, DNA computing, and DNA nanoconstruction essentially depend on similar prereguisites, in particular, large and uniform hybridization efficiencies combined with low nonspecific cross-reactivity between individual sequences, we anticipate that the microarray approach demonstrated here will enable rapid evaluation of other DNA sequence libraries.     

Tetramethylammonium-calcium-triazid. Darstellung und Kristallstruktur

[N(CH₃)₄]Ca(N₃)₃,M=240.29, was prepared from aqueous solutions of tetramethylammoniumazide with calciumazide at 298 K. The crystals are tetragonala=936.6(7) pm,c=694.7(5)pm, space group P4/nmm,Z=2, (x)=1.31Mgm^–3. The crystal structure was determined by single crystal x-ray diffraction (234 Mo-K-reflections, =0.469 mm^–1,R=0.064). Calcium is octahedrally coordinated to six azide groups. The octahedra are connected via azide groups to a threedimensional array with the complex ammonium ions between. The terminal nitrogen atoms of the azide groups and the methyl groups are considerably disordered.

     

Syntheses of bile pigments. Part 15. First unequivocal assignment of the absolute configuration of an urobilinoid bile pigment by X-ray diffraction analysis of its synthetic precursor

(?)-(4S,16S)-8, 12-bis[de(2-carboxyethyl)]mesourobilin-IIIα hydrochloride ( 8 ) has been synthesized from the enantiomerically pure 1,4,5,10-tetrahydro-1-oxodipyrrin-9-carboxylic-acid precursor 6a whose absolute configuration was determined by X-ray diffraction analysis of the N-[(S)-1-(1-naphthyl)ethyl] carboxamide 7b . The present results prove unequivocally that an (S,S)-configurated urobilin chromophore displays a negative Cotton effect in the VIS absorption range. However, the helicity of the inherently dissymmetric chromophore remains undetermined.     

Zur Stereochemie der Vitamin D3-Epoxide Röntgenstrukturanalyse einer 5,6-7,8-Diepoxidverbindung

Epoxidation of vitamin D₃ with benzonitrile ¦H₂O₂¦ KHCO₃ (Payne's reagent) yields exclusively the 5,6-mono-oxirane2. Further epoxidation with the same reagent gives the 5,6-7,8-bisepoxide3 a. Its stereochemistry and therefore the stereochemistry of2 was established by single crystal X-ray analysis of thep-Brbenzoate3b. Thereby for the first time a directive effect of a homoallylic hydroxyl group during thePayne-epoxidation was established.

Herrn Prof.Mihailovic (Universität Belgrad) mit den besten Wünschen zum 60. Geburtstag gewidmet.