Four-stranded DNA structures can be stabilized by two different types of minor groove G:C:G:C tetrads

Four-stranded nucleic acid structures are central to many processes in biology and in supramolecular chemistry. It has been shown recently that four-stranded DNA structures are not only limited to the classical guanine quadruplex but also can be formed by tetrads resulting from the association of Watson-Crick base pairs. Such an association may occur through the minor or the major groove side of the base pairs. Structures stabilized by minor groove tetrads present distinctive features, clearly different from the canonical guanine quadruplex, making these quadruplexes a unique structural motif. Within our efforts to study the sequence requirements for the formation of this unusual DNA motif, we have determined the solution structure of the cyclic oligonucleotide dpCCGTCCGT by two-dimensional NMR spectroscopy and restrained molecular dynamics. This molecule self-associates, forming a symmetric dimer stabilized by two G:C:G:C tetrads with intermolecular G-C base pairs. Interestingly, although the overall three-dimensional structure is similar to that found in other cyclic and linear oligonucleotides of related sequences, the tetrads that stabilize the structure of dpCCGTCCGT are different to other minor groove G:C:G:C tetrads found earlier. Whereas in previous cases the G-C base pairs aligned directly, in this new tetrad the relative position of the two base pairs is slipped along the axis defined by the base pairs. This is the first time that a quadruplex structure entirely stabilized by slipped minor groove G:C:G:C tetrads is observed in solution or in the solid state. However, an analogous arrangement of G-C base pairs occurs between the terminal residues of contiguous duplexes in some DNA crystals. This structural polymorphism between minor groove GC tetrads may be important in stabilization of higher order DNA structures.     

Zinc-zinc bonded zincocene structures. Synthesis and characterization of Zn2(eta5-C5Me5)2 and Zn2(eta5-C5Me4Et)2

While, in general, decamethylzincocene, Zn(C5Me5)2, and other zincocenes, Zn(C5Me4R)2 (R = H, But, SiMe3), react with dialkyl and diaryl derivatives, ZnR'2, to give the half-sandwich compounds (eta5-C5Me4R)ZnR', under certain conditions the reactions of Zn(C5Me5)2 with ZnEt2 or ZnPh2 produce unexpectedly the dizincocene Zn2(eta5-C5Me5)2 (1) in low yields, most likely as a result of the coupling of two (eta5-C5Me5)Zn* radicals. An improved, large scale (ca. 2 g) synthesis of 1 has been achieved by reduction of equimolar mixtures of Zn(C5Me5)2 and ZnCl2 with KH in tetrahydrofuran. The analogous reduction of Zn(C5Me4R)2 (R = H, SiMe3, But) yields only decomposition products, but the isotopically labeled dimetallocene 68Zn2(eta5-C5Me5)2 and the related compound Zn2(eta5-C5Me4Et)2 (2) have been obtained by this procedure. Compound 2 has lower thermal stability than 1, but it has been unequivocally characterized by low-temperature X-ray diffraction studies. As for 1 a combination of structural characterization techniques has provided unambiguous evidence for its formulation as the Zn-Zn bonded dimer Zn2(eta5-C5Me4Et)2, with a short Zn-Zn bond of 2.295(3) A indicative of a strong Zn-Zn bonding interaction. The electronic structure and the bonding properties of 1 and those of related dizincocenes Zn2(eta5-Cp')2 have been studied by DFT methods (B3LYP level), with computed bond distances and angles for dizincocene 1 very similar to the experimental values. The Zn-Zn bond is strong (ca. 62 kcal.mol-1 for 1) and resides in the HOMO-4, that has a contribution of Zn orbitals close to 60%, consisting mostly of the Zn 4s orbitals (more than 96%).     

Synthesis and catalytic properties of MIL-100(Fe), an iron(III) carboxylate with large pores

The large-pore iron(III) carboxylate MIL-100(Fe) with a zeotype architecture has been isolated under hydrothermal conditions, its structure solved from synchrotron X-ray powder diffraction data, while Friedel-Crafts benzylation catalytic tests indicate a high activity and selectivity for MIL-100(Fe).     

A new, efficient and stereoselective synthesis of tricyclic and tetracyclic compounds by samarium diiodide induced cyclisations of naphthyl-substituted arylketones--an easy access to steroid-like skeletons

In this report, we present the application of samarium diiodide induced cyclisations of naphthyl-substituted ketones towards an easy and stereoselective access to tri- and tetracyclic-functionalised compounds. Typical naphthalene derivatives were studied to investigate the scope and limitations of this novel cyclisation process. The model substrates studied demonstrate that the samarium ketyl cyclisations are essentially restricted to the formation of six-membered rings. The diastereoselectivity of these reactions is strongly influenced by the connection of the alkyl side chain to the naphthalene core. Gamma-naphth-1-yl-substituted ketones furnished cyclisation products, such as 17 or 22-26, as single diastereomers, whereas gamma-naphth-2-yl-substituted precursors gave mixtures of diastereomers--as demonstrated by the conversion of model compound 10 into tricyclic products 18 a/18 b, or that of cyclohexanone derivative 33 into tetracyclic diastereomers 34 a/34 b. Cyclic ketones as ketyl precursors furnished steroid-like tetracyclic skeletons; however, due to the cis/cis fusion of rings B/C and C/D these products have an "unnatural" bowl-like shape. Several of the cyclisation products have been identified by X-ray analyses, which not only proved the constitutions, but also the relative configurations and the preferred conformations. Steroid analogue 23 was subjected to subsequent transformations, which demonstrate that the styrene-like double bond of such compounds can be used for further structural diversification. First attempts to synthesise related azasteroids by incorporating nitrogen atoms into the ketone moiety are also reported. Thus, pyrrolidine derivatives 44 and 47 as well as piperidine derivatives 50 and 52 were subjected to samarium diiodide induced cyclisations. The expected tetracyclic products 48, 49 a/49 b, 51 and 53 a/53 b were obtained in moderate to good yields. The stereoselectivities observed follow the rules already established for the all-carbon precursors. The resulting products, bearing a nitrogen atom in ring D, are interesting azasteroid analogues with "unnatural" configuration.     

Preparation,crystal structures and spectroscopic characterization of oxalate copper(II) complexes containing the nitrogen ligands 4,4′-dimethyl-2,2′-bipyridine and di(2-pyridyl)sulfide

The preparation, crystal structures and spectroscopic characterization of four oxalate copper(II) complexes containing the 4,4′-dimethyl-2,2′-bipyridine (Mebpy) or di(2-pyridyl)sulfide (DPS) nitrogen ligands namely [μ-(ox){Cu(Mebpy)(NO₃)(H₂O)}₂] (1), [μ-(ox){Cu(Mebpy)(ClO₄)(H₂O)}₂] (2), [μ-(ox){Cu(DPS)(H₂O)}₂](ClO₄)₂ (3) and [Cu(DPS)(ox)(H₂O)] · 2H₂O (4) are described. X-ray diffraction measurements have shown that complexes 1–3 are binuclear, in which the oxalate anion bridges two Cu(II) centers, while the complex (4) is mononuclear and the oxalate anion adopts the terminal bidentate chelating coordination mode. In 1 and 2 the Cu(II) sites display a distorted octahedral geometry (4+2 environment) and in compounds 3 and 4 the Cu(II) centers exhibit a slightly distorted square pyramidal geometry. In addition, complexes 1 and 2 present a 2D supramolecular arrangement through hydrogen bonds between coordination water molecules and nitrate or perchlorate anions and π-stacking interaction between the pyridyl rings of Mebpy nitrogen ligands.     

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside–RNA recognition, glucose‐nucleobase pairs have been examined. Deoxyoligonucleotides with a 6‐deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6‐Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6‐deoxyglucose‐guanine pair closely resembles a purine‐pyrimidine geometry. Quantum chemical calculations indicate that glucose‐purine pairs are as stable as a natural T‐A pair.     

Ionic‐Liquid‐Based Polymer Electrolytes for Battery Applications

The advent of solid‐state polymer electrolytes for application in lithium batteries took place more than four decades ago when the ability of polyethylene oxide (PEO) to dissolve suitable lithium salts was demonstrated. Since then, many modifications of this basic system have been proposed and tested, involving the addition of conventional, carbonate‐based electrolytes, low molecular weight polymers, ceramic fillers, and others. This Review focuses on ternary polymer electrolytes, that is, ion‐conducting systems consisting of a polymer incorporating two salts, one bearing the lithium cation and the other introducing additional anions capable of plasticizing the polymer chains. Assessing the state of the research field of solid‐state, ternary polymer electrolytes, while giving background on the whole field of polymer electrolytes, this Review is expected to stimulate new thoughts and ideas on the challenges and opportunities of lithium‐metal batteries.     

Optimization of non-natural nucleotides for selective incorporation opposite damaged DNA

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the pi-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of shape and pi-electron density. In this report, we describe the synthesis and kinetic characterization of four novel nucleotide analogs, 5-cyanoindolyl-2'-deoxyriboside 5'-triphosphate (5-CyITP), 5-ethyleneindolyl-2'-deoxyriboside 5'-triphosphate (5-EyITP), 5-methylindolyl-2'-deoxyriboside 5'-triphosphate (5-MeITP), and 5-ethylindolyl-2'-deoxyriboside 5'-triphosphate (5-EtITP). Kinetic analyses indicate that the overall catalytic efficiencies of all four nucleotides are related to their base-stacking properties. In fact, the catalytic efficiency for nucleotide incorporation opposite an abasic site displays a parabolic trend in the overall pi-electron surface area of the non-natural nucleotide. In addition, each non-natural nucleotide is incorporated opposite templating DNA approximately 100-fold worse than opposite an abasic site. These data indicate that selectivity for incorporation opposite damaged DNA can be achieved through optimization of the base-stacking properties of the incoming nucleotide.     

Synthesis, crystal structure, and magnetic studies of oxo-centered trinuclear chromium(III) complexes: [Cr(3)(mu(3)-O)(mu(2)-PhCOO)(6)(H(2)O)(3)]NO(3). 4H(2)O.2CH(3)OH, a case of spin-frustrated system, and [Cr(3)(mu(3)-O)- (mu(2)-PhCOO)(2)(mu(2)-OCH(2)CH(3))(2)(bpy)(2)(NCS )(3)], a new type of [Cr(3)O] core

The synthesis, crystal structure, and magnetic properties of two trinuclear oxo-centered carboxylate complexes are reported and discussed: [Cr3(mu3-O)(mu2-PhCOO)6(H2O)3]NO3.4H2O.2CH3OH (1) and [Cr3(mu3-O)(mu2-PhCOO)2(mu2-OCH2CH3)2(bpy)2(NCS)3] (2). For both complexes the crystal system is monoclinic, with space group C2/c for 1 and P1/n for 2. The structure of complex 1 consists of discrete trinuclear cations, associated NO3- anions, and lattice methanol and water molecules. The structure of complex 2 is built only by neutral discrete trinuclear entities. The most important feature of 2 is the unusual skeleton of the [Cr3O] core due to the lack of peripheral bridging ligands along one side of the triangular core, which is unique among the structurally characterized (mu3-oxo)trichromium(III) complexes. Magnetic measurements were performed in the 2-300 K temperature range. For complex 1, in the high-temperature region (T > 8 K), experimental data could be satisfactorily reproduced by using an isotropic exchange model, H = -2J12S1S2 - 2J13S1S3 - 2J23S2S3 (J12 = J13 = J23) with Jij = -10.1 cm(-1), g = 1.97, and TIP = 550 x 10(-6) emu mol(-1). The antisymmetric exchange interaction plays an important role in the magnetic behavior of the system, so in order to fit the experimental magnetic data at low temperature, a new magnetic model was used where this kind of interaction was also considered. The resulting fitting parameters are the following: Gzz = 0.25 cm(-1), delta = 2.5 cm(-1), and TIP = 550 x 10(-6) emu mol(-1). For complex 2, the experimental data could be satisfactorily reproduced by using an isotropic exchange model, H = -2J1(S1S2 + S1S3) - 2J2(S2S3) with J1 = -7.44 cm(-1), J2 = -51.98 cm(-1), and g = 1.99. The magnetization data allows us to deduce the ground term of S = 1/2, characteristic of equilateral triangular chromium(III) for complex 1 and S = 3/2 for complex 2, which is confirmed by EPR measurements.     

Nonbonding orbitals in fullerenes: nuts and cores in singular polyhedral graphs

A zero eigenvalue in the spectrum of the adjacency matrix of the graph representing an unsaturated carbon framework indicates the presence of a nonbonding pi orbital (NBO). A graph with at least one zero in the spectrum is singular; nonzero entries in the corresponding zero-eigenvalue eigenvector(s) (kernel eigenvectors) identify the core vertices. A nut graph has a single zero in its adjacency spectrum with a corresponding eigenvector for which all vertices lie in the core. Balanced and uniform trivalent (cubic) nut graphs are defined in terms of (-2, +1, +1) patterns of eigenvector entries around all vertices. In balanced nut graphs all vertices have such a pattern up to a scale factor; uniform nut graphs are balanced with scale factor one for every vertex. Nut graphs are rare among small fullerenes (41 of the 10 190 782 fullerene isomers on up to 120 vertices) but common among the small trivalent polyhedra (62 043 of the 398 383 nonbipartite polyhedra on up to 24 vertices). Two constructions are described, one that is conjectured to yield an infinite series of uniform nut fullerenes, and another that is conjectured to yield an infinite series of cubic polyhedral nut graphs. All hypothetical nut fullerenes found so far have some pentagon adjacencies: it is proved that all uniform nut fullerenes must have such adjacencies and that the NBO is totally symmetric in all balanced nut fullerenes. A single electron placed in the NBO of a uniform nut fullerene gives a spin density distribution with the smallest possible (4:1) ratio between most and least populated sites for an NBO. It is observed that, in all nut-fullerene graphs found so far, occupation of the NBO would require the fullerene to carry at least 3 negative charges, whereas in most carbon cages based on small nut cubic polyhedra, the NBO would be the highest occupied molecular orbital (HOMO) for the uncharged system.