Delamination of layered double hydroxides in polar monomers: new LDH-acrylate nanocomposites

The layered double hydroxide Mg2Al(OH)6(C12H25SO4) was delaminated to give high levels of inclusion in acrylate monomers; subsequent polymerisation of the monomers containing the LDH dispersion gave polyacrylates with the inorganic component still in the delaminated form.     

Light-directed radial combinatorial chemistry: orthogonal safety-catch protecting groups for the synthesis of small molecule microarrays

We describe the development of photolabile protecting groups based on the 3,4,5-trimethoxyphenacyl group (TMP). Orthogonal safety-catches were created by introducing an acid-activatible dimethyl ketal (AA-TMP) and an oxidatively activatible 1,3-dithiane (OA-TMP) into the photolabile TMP group. We demonstrate the application of these protecting groups in light-directed synthesis of small molecule microarrays with diversity elements radially attached to a hydroxyproline scaffold.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Helicity‐Encoded Molecular Strands: Efficient Access by the Hydrazone Route and Structural Features

Control over the folding of molecular strands may be achieved by appropriate choice of the constituting subunits, in particular for chains of specific heterocycles such as sequences of directly connected pyridine (py) and pyrimidine (pym) rings, which are known to fold into extended helical structures. Since the hydrazone (hyz) group represents an isomorphic analogue of a py site, the condensation of hydrazine and carboxaldehyde derivatives of pym offers a very efficient approach to strands incorporating hyz instead of py units and constituted by sequences of alternating hyz and pym groups. A series of such strands of different lengths, up to ten hyz units, i.e., 1 – 7 , were synthesized. Their spectral properties indicate that they fold indeed into helical shapes. Extensive characterization was performed in solution by ¹HNMR spectroscopy and in the solid state by determination of the crystal structures of eight such strands. They all display the expected helical geometry with up to 3 ¹/₃ turns and direct stacking contacts. The efficiency and flexibility of the synthetic approach as well as its wide potential for generation of diversity through lateral decoration make the (hyz? pym) subunit a particularly attractive helicity codon.     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

Synthesis of titanium(IV) guanidinate complexes and the formation of titanium carbonitride via low-pressure chemical vapor deposition

The mono(guanidinato) complex [Ti(NMe2)2Cl{i-PrNC[N(SiMe3)2]N-i-Pr}] (1) was prepared by reaction of [Ti(NMe2)2Cl2] with 1 or 2 equiv of the lithium guanidinate salt [Li{i-PrNC[N(SiMe3)2]N-i-Pr}]. Compound 1 has been characterized by X-ray crystallography. Treatment of TiCl4 with 2 equiv of [Li{i-PrNC[N(SiMe3)2]N-i-Pr}] resulted in the formation of dark red crystals. X-ray crystallography showed that these crystals consist of a 70:30 mixture of two bis(guanidinato) complexes, namely, [TiCl2{i-PrNC[N(SiMe3)2]N-i-Pr}{i-PrNC(N=CMe2)N-i-Pr}] (2) and [TiCl2{i-PrNC[N(SiMe3)2]N-i-Pr}{i-PrNC[N(H)-i-Pr]N-i-Pr}] (3). Both compounds 2 and 3 possess a transformed guanidinate ligand. Low-pressure chemical vapor deposition of either compound 1 or [TiCl2{i-PrNC(NMe2)N-i-Pr}] (4) at 600 degrees C results in thin films of titanium carbonitride.     

Structural and Spectroscopic Characterization of Iron(III) Dioxoporphodimethene Complexes and Their Autoreduction to an Iron(II) Complex in Pyridine

Three iron complexes of the meso-dioxo derivative of octaethylporphryin (trans-H(2)OEPO(2)) were characterized by X-ray diffraction. Green ClFe(III)(trans-OEPO(2)).1.5C(6)H(6) crystallizes in the monoclinic space group P2(1)/c with a = 13.766(3) ?, b = 19.075(3) ?, c = 15.217(3) ?, beta = 99.87(2) degrees at 123 K with Z = 4. Refinement of 2712 reflections with F > 6.0sigma(F) and 223 parameters yielded R = 0.0624, R(w) = 0.0596. The iron complex contains a domed dioxoporphodimethene macrocyclic ligand. The observation of a five-coordinate iron(III) ion with an axial Fe-Cl distance of 2.232(2) ? and in-plane Fe-N distances averaging 2.082 ? is consistent with its high-spin (S = (5)/(2)) character. This monomer is readily converted to the green {Fe(III)(trans-OEPO(2))}(2)O using aqueous hydroxide. {Fe(III)(trans-OEPO(2))}(2)O crystallizes in the monoclinic space group C2/c with a = 23.541(8) ?, b = 15.392(5) ?, c = 18.686(8) ?, and beta = 90.09(3) degrees at 294 K with Z = 8. Refinement of 3472 reflections with F > 6.0sigma(F) and 393 parameters yielded R = 0.0484, R(w) = 0.0527. The complex possesses a crystallographically imposed 2-fold symmetry axis that passes through the oxo ligand. The dioxoporphodimethene ligands within the molecule are roof-shaped and fold away from each other. The axial Fe-O distance is 1.749(1) ? with longer in-plane Fe-N distances (average 2.077 ?). The Fe-O-Fe angle of 165.4(2) degrees deviates significantly from linearity and is more acute than related porphyrin complexes. Pyridine solutions of either the iron(III) monomer or &mgr;-oxo dimer autoreduce over a period of days to give (py)(2)Fe(II)(trans-OEPO(2)). This red compound crystallizes in the space group P2(1) with a = 19.177(4) ?, b = 20.039(4) ?, c = 10.547(2) ?, and beta = 100.36(3) degrees at 130 K with Z = 2. Refinement of 5090 reflections with one restraint and 984 parameters yielded R1 = 0.0684, wR2 = 0.1763. The complex crystallizes with two distinct molecules in the asymmetric unit; each molecule contains a different degree of disorder with respect to the trans meso oxygen atoms (50/50, 71/29). Each independent molecule exhibits severe ruffling of the macrocycle. The six coordinate iron(II) center is diamagnetic. The axial Fe-N(pyridine) distances average 1.98 ?, and the in-plane Fe-N(pyrrole) distances average 1.95 ?. A common trend observed for the dioxoporphodimethene macrocycle in all of these structures is an elongation toward the trans oxidized meso carbons. These complexes were originally prepared as cis and trans isomeric mixtures that can be enriched in the trans isomer by fractional crystallization. This is evident in their distinctive (1)H NMR spectra. In addition, these compounds are characterized by electron impact mass spectrometry and UV-visible, ESR, and infrared spectroscopies.