Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Folding of a Donor-Containing Ionene by Intercalation with an Acceptor

Cationic ionenes that bear electron-rich 1,5-dialkoxynaphthalene (DAN) units within the alkylene segment were allowed to interact with different types of electron-deficient, acceptor-containing molecules in an effort to realize intercalation-induced folding of the ionenes; the collapse of the chains was expected to occur in such a way that the donor and acceptor units become arranged in an alternating fashion. Several acceptor-bearing molecules were prepared by the derivatization of pyromellitic dianhydride and naphthalene tetracarboxylic dianhydride with two different oligoethylene glycol monomethyl ether monoamines. This yielded acceptor molecules with different water solubility and allowed the examination of solvophobic effects in the folding process. UV/Vis spectroscopic studies were carried out by using a 1:1 mixture of the DAN-ionenes and different acceptor molecules in water/DMSO solvent mixtures. The intensity of the charge-transfer (CT) band was seen to increase with the water content in the solvent mixture, thereby suggesting that the intercalation is indeed aided by solvophobic effects. The naphthalene diimide (NDI) bearing acceptor molecules consistently formed significantly stronger CT complexes when compared to the pyromellitic diimide (PDI) bearing acceptor molecules, which is a reflection of the stronger pi-stacking tendency of the former. AFM studies of drop-cast films of different ionene-acceptor combinations revealed that compact folded structures are formed most effectively under conditions in which the strongest CT complex is formed.

A simple equivalent circuit analysis of rectangular folded-waveguide slow-wave structure

A simple yet accurate equivalent circuit model was developed for the analysis of slow-wave properties (dispersion and interaction impedance characteristics) of a rectangular folded-waveguide slow-wave structure. Present formulation includes the effects of the presence of beam-hole in the circuit, which were ignored in existing approaches. The analysis was benchmarked against measurement as well as with 3D electromagnetic modeling using MAFIA for two typical slow-wave structures operating in Ka- and Q-bands, and close agreements were observed. The analysis was extended for demonstrating the effect of the variation of beam-hole radius on the RF interaction efficiency of the device. (C) 2009 Elsevier GmbH. All rights reserved.

Geometry and quadratic nonlinearity of charge transfer complexes in solution using depolarized hyper-Rayleigh scattering

We report large quadratic nonlinearity in a series of 1:1 molecular complexes between methyl substituted benzene donors and quinone acceptors in solution. The first hyperpolarizability, beta(HRS), which is very small for the individual components, becomes large by intermolecular charge transfer (CT) interaction between the donor and the acceptor in the complex. In addition, we have investigated the geometry of these CT complexes in solution using polarization resolved hyper-Rayleigh scattering (HRS). Using linearly (electric field vector along X direction) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I-2 omega,I-X,I-X/I-2 omega,I-Z,I-X and D' = I-2 omega,I-X,I-C/I-2 omega,I-Z,I-C in the laboratory fixed XYZ frame by detecting the second harmonic scattered light in a polarization resolved fashion. The experimentally obtained first hyperpolarizability, beta(HRS), and the value of macroscopic depolarization ratios, D and D', are then matched with the theoretically deduced values from single and double configuration interaction calculations performed using the Zerner's intermediate neglect of differential overlap self-consistent reaction field technique. In solution, since several geometries are possible, we have carried out calculations by rotating the acceptor moiety around three different axes keeping the donor molecule fixed at an optimized geometry. These rotations give us the theoretical beta(HRS), D and D' values as a function of the geometry of the complex. The calculated beta(HRS), D, and D' values that closely match with the experimental values, give the dominant equilibrium geometry in solution. All the CT complexes between methyl benzenes and chloranil or 1,2-dichloro-4,5-dicyano-p-benzoquinone investigated here are found to have a slipped parallel stacking of the donors and the acceptors. Furthermore, the geometries are staggered and in some pairs, a twist angle as high as 30 degrees is observed. Thus, we have demonstrated in this paper that the polarization resolved HRS technique along with theoretical calculations can unravel the geometry of CT complexes in solution. (C) 2011 American Institute of Physics. doi:10.1063/1.3514922]

Crystallography of solid-liquid interface and evolution of texture during directional solidification of Tb0.3Dy0.7Fe1.95 alloy

The effect of growth texture on the magnetostriction of ternary Tb0.3Dy0.7Fe1.95 was studied by conducting unidirectional solidification experiments using a zoning set-up. Detailed texture evolutions were studied using X-ray diffraction on samples obtained by varying growth rates from 18 to 72 cm/h, under a temperature gradient of 100 degrees C/cm. The estimated texture co-efficient and pole figures of the samples indicate that during the onset of the solidification, < 110 > and < 331 >/'rotated < 110 >' texture components nucleate and grow in all the samples. However, as the solidification progresses, < 112 > texture component becomes dominant at higher growth rate. This results in an improvement of magnetostriction from 1000 to 1300 microstrains for samples grown at growth rates of 18 and 72 cm/h respectively. The transition of preferred growth direction occurs through intermediate orientations < 123 >. An attempt has been made in this paper to explain the occurrence of different growth texture by considering the stability of growing interface, its planar packing fraction and atomic stacking sequence of several low index planes. (C) 2010 Elsevier Ltd. All rights reserved.

2-(4-Methylsulfanylphenyl)-1H-benzimidazol-3-ium bromide

In the cation of the title compound, C14H13N2S+center dot Br-, the essentially planar benzimidazole system (r.m.s. deviation = 0.0082 angstrom) is substituted with a 4-methylsulfanylphenyl ring. The dihedral angle between the benzimidazole system and the 4-methylsulfanylphenyl ring is 2.133 (2)degrees. The crystal structure is characterized by strong and highly directional intermolecular N-H center dot center dot center dot Br hydrogen bonds involving the bromide ion. Moreover, C-H center dot center dot center dot S interactions result in chains of molecules along the c axis. The supramolecular assembly is further stabilized by pi-pi stacking interactions between the benzimidazole system and 4-methylsulfanylphenyl rings centroid-centroid distance = 3.477 (4) angstrom].

Effects of halogen substitution in nucleic acid components. Structure of sodium 5-bromocytidine 5'-phosphate hydrate

The conformation of 5-bromocytidine 5'-monophosphate in the title compound, Na+.C9H11BrN3O8P-.1.25H2O, is anti, C(3')-endo and gauche-gauche, similar to that in analogous non-halogenated nucleosides/nucleotides. The Na ion coordinates directly with phosphate O atoms and base atoms. Br is not involved in any stacking interaction.

Study of Texture Evolution at High Strain Rates in FCC Materials

Evolution of crystallographic texture during high strain rate deformation in FCC materials with different stacking fault energy (Ni, Cu, and Cu-10Zn alloy) has been studied. The texture evolved in FCC materials at these strain rates show little dependence on the Stacking Fault Energy and the amount of deformation. Copper shows an anomalous behavior that is attributed to the ease of cross slip and continuous Dynamic Recrystallization that are operative under the experimental conditions.

Role of organic fluorine in crystal engineering

The design of compounds with novel and improved physico-chemical properties as advanced functional materials with a specific application spectrum requires the knowledge about possible supramolecular packing motifs and their experimental control in crystalline lattice. Besides the structure of the individual molecule, non-covalent interactions play a significant role in the determination of molecular conformation, along with the formation of three-dimensional supramolecular architecture in a crystal as a requirement for molecular recognition processes, and the related bioactivity. Involvement of functional groups will contribute to the formation of a predefined packing motif due to their well-defined interactions. The strength and directionality of these interactions create characteristic packing motifs, which can be used for the design of supramolecular arrangements by the development of appropriate strategies for the precise control of their topology. Most relevant of these non-covalent interactions are stacking interactions and hydrogen bonds, which have been subjects of extensive study in the last two decades. In recent literature, substantial efforts have been put in by various researchers towards the understanding of interactions involving organic fluorine and the role they play in generating different packing motifs which guides assembling of molecules in the crystal lattice.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.

Synthesis and x-ray crystal structure of a CuII-theophylline complex: [Cu(theo)2 (H2O)3]·2H2O

The complex [Cu-II (theo)(2)(H2O)(3)].2H(2)O (theo = theophylline) was obtained from aqueous solution. The crystals belong to the monoclinic system, space group P2(1)/n, and are reflection twins about the (001) face. The structure was solved using data from a twinned crystal and refined to final R and R(W) values of 0.069 and 0.064, respectively. Copper has a square-pyramidal coordination with two thee molecules coordinating through N(7) at equatorial positions. The remaining sites are occupied by water molecules. O(6) of one of the thee molecules is at the other axial site at a longer distance of 3.18 Angstrom. This could lead to an alternate (4+1+1) octahedral coordination geometry for Cu-II. The packing is stabilized by stacking interactions between the theophylline moieties at an average separation of 3.46 Angstrom.

Chemical and microstructural modifications in LiPON thin films exposed to atmospheric humidity

Lithium phosphorus oxynitride (LiPON), the widely used solid electrolyte for thin film microbatteries, is not compatible with the ambient humid temperatures. The reasons for reduction in ionic conductivity of LiPON thin films from 2.8 x 10(-6) Scm(-1) to 9.9 x 10(-10) Scm(-1) when exposed to air are analyzed with the aid of AC impedance measurements, SEM, XPS and stylus profilometry. Initially, particulate-free film surfaces obtained soon after rf sputter deposition in N-2 ambient conditions becomes covered with microstructures, forming pores in the film when exposed to air. LiPON films are deposited on Ti coated silicon in addition to bare silicon, ruling out the possibility of stress-related rupturing from the LiPON/Si interface. The reduction of nitrogen, phosphorus, and increased presence of lithium, oxygen and carbon over the film surface lowers the ionic conductivity of LiPON films when exposed to air. (c) 2011 Elsevier B.V. All rights reserved.

Constructions of 2D-Metallamacrocycles Using Half-Sandwich Ru-2(II) Precursors: Synthesis, Molecular Structures, and Self-Selection for a Single Linkage Isomer

Coordination-driven self-assembly of oxalato-bridged half-sandwich p-cymene ruthenium complex Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)] (O3SCF3)(2) (1a) with several ditopic donors (L-a-L-d) in methanol affords a series of bi- and tetranuclear metallamacrocycles (2a and 3-5). Similarly, the combination of 2,5-dihydroxy-1,4-benzoquinonato (dhbq)-bridged binuclear complex Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) with a flexible bidentate amide linker (L-a) in 1:1 molar ratio gave the corresponding tetranuclear complex 2b. All the macrocycles were isolated as their triflate salts in high yields and were fully characterized by various spectroscopic techniques. Finally, the molecular structures of all the assemblies were determined unambiguously by single-crystal X-diffraction analysis. Interestingly, the combination of acceptor 1a or 1b with an unsymmetrical linear ditopic donor L-a results in a self-sorted linkage isomeric (head-to-tail) macrocycle (2a or 2b) despite the possibility of formation of two different isomeric macrocycles (head-to-head or head-to-tail) due to different connectivity of the donor. Molecular structures of the complexes 2a and 2b showed tetranuclear rectangular geometry with dimensions of 5.51 angstrom x 13.29 angstrom for 2a and 7.91 angstrom x 13.46 angstrom for 2b. In both cases, two binuclear Ru-2(II) building blocks are connected by a mu-N-(4-pyridyl)isonicotinamide donor in a head-to-tail fashion. Surprisingly, the macrocycle 2a loses one counteranion and cocrystallizes with monodeprotonated 1,3,5-trihydroxybenzene via strong intermolecular pi-pi stacking and hydrogen bonding. The tweezer complex 3 showed strong fluorescence in solution, and it showed fluorescence sensing toward nitroaromatic compounds. A fluorescence study demonstrated a marked quenching of the initial fluorescence intensity of the macrocycle 3 upon gradual addition of trinitrotoluene and exhibits significant fluorescence quenching response only for nitroaromatic compounds compared to various other aromatic compounds tested.