Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.     

Conformational mobility of thianthrene-5-oxide

[reaction: see text] Data on the apparent dipole moment of thianthrene-5-oxide (1) and (1)H NMR spectra in different solvents support the conformational mobility of 1, which flaps between two limit boat conformations with the sulfinyl group in pseudoequatorial and pseudoaxial positions, respectively. The conformational equilibrium of 1 occurs too fast for the (1)H NMR (500 MHz) time-scale even at -130 degrees C, and the equilibrium constant has not been determined. The apparent dipole moments of 1 in n-hexane and 1,4-dioxane and the (1)H NMR spectra of 1 and the model compounds cis- and trans-thianthrene-5,10-dioxides (2) and thianthrene (5) in different solvents and at various temperatures confirm that the relative position of the conformational equilibrium of 1 is solvent-dependent, and more polar solvents favor the conformation with the sulfoxide group in the pseudoaxial position (1(')(ax)). Variable-temperature (1)H NMR spectra have established the interconversion barrier of trans-2 and confirmed that the conformational equilibrium of cis-2 is strongly displaced toward the conformation with both sulfinyl groups in the pseudoequatorial position. The (1)H NMR data support the transannular interaction of the functional groups in 1 and trans-2.     

The crystal structure of the inorganic surface films formed on Mg and Li intercalation compounds and the electrode performance

A crystallographic approach was applied to elucidate the influence of the nature of the surface films on the electrochemical behavior of Li and Mg intercalation compounds. This paper presents two examples: (1) protection of graphite electrodes by Li₂CO₃ surface films, and (2) the unique electrochemical behavior of Mg-containing Chevrel phases (MgCP) obtained by different synthetic routes. In the former case, the elucidation of the protection mechanism and the explanation of the high performance of such protected electrodes are based on the analysis of possible Li-ion motion in the carbonate crystal structure. In the latter case, a combination of synthesis, electrochemistry and XRD analysis was used to explain an unusual phenomenon: the difference between the excellent electrochemical behavior of the Chevrel phase (CP) based on Cu-leached Cu₂Mo₆S₈ (CuCP), and the poor electrochemical activity of the high-temperature synthesized MgCP, with the same phase composition. It is shown that this phenomenon is caused by MgO formation on the surface of the latter material. The different surface chemistry of the MgCPs obtained by the two different synthetic routes was substantiated by revealing the correlation between the electrochemical activity and the chemical stability of these materials under ambient atmosphere conditions. Dedicated to Prof. Mikhail A. Vorotyntsev on the occasion of his 60th birthday.     

Inclusion of Two PhP(O)(OH) 2 Guest Molecules into the Cavity of Macrocyclic Cavidand Cucurbit[8]uril

A new inclusion compound which is a supramolecular adduct of cucurbit[8]uril with two guest molecules of phenylphosphonic acid, PhP(O)(OH)₂, included into the cavity as ``two guests in host'' is reported. The guests match both size and hydrophilicity/hydrophobicity requirements. Two phenyl groups of molecules of PhP(O)(OH)₂ are directed toward the center of the large hydrophobic cavity whereas the PO(OH)₂ groups are outward-looking and bound with each hydrophilic portal of cucurbit[8]uril by a short hydrogen bond.     

Chemo-enzymatic synthesis of 4-methylumbelliferyl beta-(1-->4)-D-xylooligosides: new substrates for beta-D-xylanase assays

Transglycosylation catalyzed by a beta-D-xylosidase from Aspergillus sp. was used to synthesize a set of 4-methylumbelliferyl (MU) beta-1-->4-D-xylooligosides having the common structure [beta-D-Xyl-(1-->4)]2-5-beta-D-Xyl-MU. MU xylobioside synthesized chemically by the condensation of protected MU beta-D-xylopyranoside with ethyl 2,3,4-tri-O-acetyl-1-thio-beta-D-xylopyranoside was used as a substrate for transglycosylation with the beta-D-xylosidase from Aspergillus sp. to produce higher MU xylooligosides. The structures of oligosaccharides obtained were established by 1H and 13C NMR spectroscopy and electrospray tandem mass spectrometry. MU beta-D-xylooligosides synthesized were tested as fluorogenic substrates for the GH-10 family beta-D-xylanase from Aspergillus orizae and the GH-11 family beta-D-xylanase I from Trichoderma reesei. Both xylanases released the aglycone from MU xylobioside and the corresponding trioside. With substrates having d.p. 4 and 5, the enzymes manifested endolytic activities, splitting off MU, MUX, and MUX2 primarily.     

CdSe and CdSe/CdS nanorod solids

We demonstrate the self-organization of CdSe nanorods into nematic, smectic, and crystalline solids. Layered colloidal crystals of CdSe nanorods grow by slow destabilization of a nanocrystal solution upon allowing the diffusion of a nonsolvent into the colloidal solution of nanocrystals. The colloidal crystals of nanorods show characteristic birefringence, which we assign to specific spherulite-like texture of each nanorod assembly. To demonstrate the general character of nanorod self-assembly technique, CdSe/CdS heterostructure nanorods were organized into highly luminescent superlattices.     

Synthesis of a model system for the preparation of phloroglucinol containing natural products

A model system for the synthesis of phloroglucinol containing natural products was synthesized. Key steps include a manganic acetate-mediated cyclization and the facile conversion of an alkene into a β-bromoenone.     

Solid-phase synthesis of a tyrphostin ether library

The solid-phase synthesis of a 4500-member (30 x 15 x 10) tyrphostin library is demonstrated utilizing the Irori-directed sorting system. Fmoc-protected PL-Rink resin was used as the solid support. After Fmoc-deprotection, aryl aldehydes were attached to the resin through reductive amination. Acylation of the resulting secondary amines with cyanoacetic acid was followed by a Knoevenagel condensation with phenolic aldehydes. Mitsunobu coupling of primary alcohols to the resin-bound phenols yielded the final library of compounds 1.     

Di­chloro­bis(1‐propyl­imidazolidine‐2‐thione‐κS)­cobalt(II)

The crystal structure of the title compound, [CoCl₂(C₆H₁₂N₂S)₂], consists of monomer units of a Co^II atom coordinated to two 1‐propyl­imidazolidine‐2‐thione ligands and to two chloride ions. The heterocyclic thione ligand is monodentate and coordinated to the metal through the thione S atom. The environment around the Co^II atom is a slightly distorted tetrahedron. The Co—S bond lengths are 2.341 (2) and 2.330 (2) Å, and the Co—Cl bond lengths are 2.234 (2) and 2.238 (2) Å. The most important point of distortion is the S—Co—S bond angle of only 97.83 (8)°. Intramolecular classical hydrogen bonds are found between the chloride ions and the N—H groups. Additionally, intra‐ and intermolecular non‐classical hydrogen bonds are found.     

Synthesis,Spectroscopic and EPR Results and Crystal Structure of Copper(II) Formato Derivatives with Pyrazine and Dimethylpyrazines

The complexes of copper formato with pyrazine and dimethylpyrazines: Cu(HCOO)₂(pyrz) ( 1 ), Cu₂(HCOO)₄(pyrz) ( 2 ), Cu₂(HCOO)₄(2,3‐Me₂pyrz) ( 3 ), Cu₂(HCOO)₄(2,5‐Me₂pyrz) ( 4 ), and Cu₂(HCOO)₄(2,6‐Me₂pyrz)₂ ( 5 ) have been synthesized and characterized by chemical analysis and IR and electronic spectro scopies. The three‐dimensional structure of compound 1 consists of –Cu–pyrz–Cu–pyrz– chains joined by bridging formate groups coordinated, in configuration syn‐anti, to two copper atoms. The coordination around the copper atom is orthorhombic with two Cu–O distances of 2.374(1) Å, two Cu–O of 1.952 Å and two Cu–N of 2.080 Å. Compound 5 is formed by molecular dimers with the [Cu₂(μ‐HCOO)₄] unit, two copper atoms and four syn‐syn fomate groups, and two ligands coordinated to the copper atoms in the axial positions. In compounds 2 and 3 chains of [Cu₂(μ‐HCOO)₄] dimers with pyrz or 2,3‐Me₂pyrz as bridging ligands are formed. The EPR signal of 1 is orthorhombic (g = 2.23, 2.20 and 2.06). In the EPR spectra of 2 – 5 compounds the triplet (S = 1) signals are observed. The g_?, g_∥ and D values are been calculated.