The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N‐aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)₂, and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non‐modified PNA duplex adopts a P‐type helical structure similar to that of previously characterized PNAs. The atomic‐level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P‐type helical structure, its flexibility is relatively high. For example, the base‐pair rise in the bipyridine‐containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π‐stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl‐modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.     

The stuffed framework structure of SrP2N4: challenges to synthesis and crystal structure determination

SrP2N4 was obtained by high-pressure high-temperature synthesis utilizing the multianvil technique (5 GPa, 1400 degrees C) starting from mixtures of phosphorus(V) nitride and strontium azide. SrP2N4 turned out to be isotypic with BaGa(2)O(4) and is closely related to KGeAlO(4). The crystal structure (SrP2N4, a=17.1029(8), c=8.10318(5) A, space group P6(3) (no. 173), V=2052.70(2) A3, Z=24, R(F2)=0.0633) was solved from synchrotron powder diffraction data by applying a combination of direct methods, Patterson syntheses, and difference Fourier maps adding the unit cell information derived from electron diffraction and symmetry information obtained from 31P solid-state NMR spectroscopy. The structure of SrP2N4 was refined by the Rietveld method by utilizing both neutron and synchrotron X-ray powder diffraction data, and has been corroborated additionally by 31P solid-state NMR spectroscopy by employing through-bond connectivities and distance relations.     

Morphology and crystal structure of the poly(ethylene oxide)–hydroquinone molecular complex

The occurrence of a molecular complex between poly(ethylene oxide) (PEO) and p‐dihydroxybenzene (hydroquinone) has been determined using different experimental techniques such as differential scanning calorimetry (DSC), wide‐angle X‐ray diffraction (WAXD), and Fourier transform infrared spectroscopy (FTIR). From DSC investigations, an ethylene oxide/hydroquinone molar ratio of 2/1 was deduced. During the heating, the molecular complex undergoes a peritectic reaction and spontaneously transforms into a liquid phase and crystalline hydroquinone (incongruent melting). A triclinic unit cell (a = 1.17 nm, b = 1.20 nm, c = 1.06 nm, α = 78°, β = 64°, γ = 115°), containing eight ethylene oxide (EO) monomers and four hydroquinone molecules, has been determined from the analysis of the X‐ray diffraction fiber patterns of stretched and spherulitic films. The PEO chains adopt a helical conformation with four monomers per turn, which is very similar to the 7₂ helix of the pure polymer. A crystal structure is proposed on the basis of molecular packing considerations and X‐ray diffraction intensities. It consists of a layered structure with an alternation of PEO and small molecules layers, both layers being stabilized by an array of hydrogen bonds. The morphology of PEO–HYD crystals was studied by small angle X‐ray scattering and DSC. As previously shown for the PEO–resorcinol complex, PEO–HYD samples crystallize with a lamellar thickness corresponding to fully extended or integral folded chains. The relative proportion of lamellae with different thicknesses depends on the crystallization temperature and time. Finally, the observed morphologies are discussed in terms of intermolecular interactions and chain mobility. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1197–1208, 1999     

Synthesis,crystal structure solution and characterization of two organic–inorganic hybrid layered materials based on metal sulfates and 1,4‐phenylenediamine

Two organic–inorganic hybrid layered materials, namely poly[(μ‐1,4‐diaminobenzene‐κ²N:N′)[μ₃‐sulfato(VI)‐κ⁴O:O′:O′′,O′′′]manganese], [Mn(SO₄)(C₆H₈N₂)]_n, 1 , and poly[(μ‐1,4‐diaminobenzene‐κ²N:N′)[μ₃‐sulfato(VI)‐κ⁴O:O′:O′′,O′′′]copper], [Cu(SO₄)(C₆H₈N₂)]_n, 2 , have been synthesized using 1,4‐phenylenediamine (PPD) as an organic template and component (linker). Both materials form three‐dimensional frameworks. The crystal structures were determined using data from powder X‐ray diffraction measurements. The purity and morphology of the compounds were studied by elemental analyses and SEM investigations, and their thermal stabilities were determined by thermogravimetric and nonambient powder X‐ray diffraction measurements, which indicated that 1 is stable up to 537 K and 2 is stable up to 437 K.     

Formation of Thiosemicarbazone‐Functionalized Complexes with (GeS2)2 and (SnS2)2 Units

By reaction of organo‐functionalized germanium or tin sesquisulfides [(R¹T)₄S₆] (T = Ge, Sn; R¹ = CMe₂CH₂COMe) with thiosemicarbazide or its methyl or phenyl derivative, a series of four compounds were obtained and structurally characterized that are based on an inorganic (TS₂)₂ unit with an extended organic chelate ligand CMe₂CH₂CMeNNCSNHR′ (R′ = H, Me, Ph). The products combine a small, reactive metal chalcogenide moiety with a ligand system that allows for a variety of directed extensions at the terminal NHR′ group. Thus, this work represents the starting point to a multifaceted consecutive chemistry involving both the extension of the binary inorganic unit and further derivatization and/or coordination of the organic ligands.     

Synthesis, crystal structure, and properties of two modifications of MgB(12)C(2)

Single crystals of two modifications of the new magnesium boride carbide MgB(12)C(2) were synthesized from the elements in a metallic melt by using tantalum ampoules. Crystals were characterized by single-crystal X-ray diffraction and electron microprobe analysis (energy-dispersive (EDX) and wavelength-dispersive (WDX) X-ray spectroscopy). Orthorhombic MgB(12)C(2) is formed in a Cu/Mg melt at 1873 K. The crystal structure of o-MgB(12)C(2) (Imma, Z=4, a=5.6133(10), b=9.828(2), c=7.9329(15) A, 574 reflections, 42 variables, R(1)(F)=0.0208, wR(2)(I)=0.0540) consists of a hexagonal primitive array of B(12) icosahedra with Mg atoms and C(2) units in trigonal-prismatic voids. Each icosahedron has six exohedral B--B and six B--C bonds. Carbon is tetrahedrally coordinated by three boron atoms and one carbon atom with a remarkably long C--C distance of 1.727 A. Monoclinic MgB(12)C(2) is formed in an Al/Mg melt at 1573 K. The structure of m-MgB(12)C(2) (C2/c, Z=4, a=7.2736(11), b=8.7768(13), c=7.2817(11) A, beta=105.33(3) degrees , 1585 reflections, 71 variables, R(1)(F)=0.0228, wR(2)(I)=0.0610) may be described as a distorted cubic close arrangement of B(12) icosahedra. Tetrahedral voids are filled by C atoms and octahedral voids are occupied by Mg atoms. The icosahedra are interconnected by four exohedral B--B bonds to linear chains and by eight interstitial C atoms to form a three-dimensional covalent network. Both compounds fulfill the electron-counting rules of Wade and Longuet-Higgins.     

The crystal structure of anhydrous beta-caffeine as determined from X-ray powder-diffraction data

The crystal structure of the low-temperature form of anhydrous caffeine has been determined by using X-ray powder-diffraction data with a combined simulated-annealing/Rietveld method. Anhydrous caffeine crystallizes with five crystallographically independent molecules in a monoclinic C-centred unit cell with dimensions of a=43.0390(17), b=15.0676(6) and c=6.95314(14) A and a beta angle of 99.027(2) degrees.     

Crystallographic report: Crystal and molecular structure of tetramethylammoniumdiisothiocyanatotriphenyltin(IV), [NMe4SnPh3(NCS)2]

The structure of NMe₄SnPh₃(NCS)₂ is molecular, without any significant intermolecular contacts in the lattice. The trigonal plane around the tin atom is defined by three carbon atoms from the phenyl groups and the axial positions occupied by the NCS groups. Copyright © 2003 John Wiley & Sons, Ltd.     

Molecular dynamics (MD) simulations and large-angle X-ray scattering (LAXS) studies of the solid-state structure and assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl-)phosphazene in the bulk state and in the cast film

The intrachain conformation, molecular structure and interchain assembly of isotactic (R)-poly(2,2'-dioxy-1,1'-binaphthyl)phosphazene (P-DBNP) both in the bulk state (I) and in the cast film (II) were studied by molecular dynamics (MD) simulations of models, as implemented by a bias potential for the analysis of the radial distribution function (RDF) obtained from large-angle X-ray scattering (LAXS) data. The microscopic structure and order extension of the polymer changed from I to II, as qualitatively shown in the shapes of their experimentally measured RDF curves. With the use of a bias potential, the MD simulations provided a much more accurate analysis of the models, as seen in the reproduction of the RDFs. The chiral P-DBNP chain was found to be consistent with helix conformations in both the I and the II samples. The predominant interchain clustering motif was best reproduced with a seven-chain model. In the case of I, the maximum chain length was 18 monomeric -R(2)NP- units, while in the case of the cast film II the chain was more elongated, up to distances of approximately 100 A, equivalent to over 48 monomeric -R(2)NP- units. The seven-chain assembly was accounted for in terms of nonbonded interactions favouring the minimum voids area between the seven tubular structures of the material. The results validate our earlier finding that MD analysis with implementation of a biasing potential for the RDFs can provide quantitative information on the structural and conformational features of amorphous solids. The combined theoretical and experimental approach was found to be a useful tool to detect, locate and evaluate the intra- and intermolecular modifications of materials subsequent to their phase transformation and, as in the present case, changes in their microscopic structures or preparation methods.     

Two-component hydrogels comprising fatty acids and amines: structure, properties, and application as a template for the synthesis of metal nanoparticles

Stearic acid or eicosanoic acid mixed with di- or oligomeric amines in specific molar ratios form stable gels in water. The formation of such hydrogels depends on the hydrophobicity of the fatty acid, and also on the type of amine used. The gelation properties of these two-component systems were investigated using electron microscopy, FTIR spectroscopy, 1H NMR spectroscopy, differential scanning calorimetry (DSC), and both single-crystal and cast-film X-ray diffraction. Results of FTIR spectral analysis suggest salt formation during gelation. 1H NMR analysis of the gels indicates that the fatty acid chains are immobilized in the gel state and when the gel melts, these chains regain their mobility. Analysis of DSC data indicates that increase in the spacer length in the di-/oligomeric amine lowers the gel-melting temperature. Two of these gelator salts developed into crystals and structural details of such systems could be secured by single-crystal X-ray diffraction analysis. The structural information of the salts thus obtained was compared with the XRD data of the self-supporting films of those gels. Such analyses provided pertinent structural insight into the supramolecular interactions that prevail within these gelator assemblies. Analysis of the crystal structure confirmed that multilayered lamellar aggregates exist in the gel and it also showed that the three-dimensional ordering observed in the crystalline phase is retained in only one direction in the gel state. Finally, the hydrogel was used as a medium for the synthesis of silver nanoparticles. The nanoparticles were found to position themselves on the fibers and produced a long, ordered assembly of gel-nanoparticle composite.     

New Aquapentachlorochromate(III) Compounds: K2[CrCl5(H2O)] and (NH4)2[CrCl5(H2O)]

Synthesis and crystal structures of two new compounds, K₂[CrCl₅(H₂O)] ( I ) and (NH₄)₂[CrCl₅(H₂O)] ( II ) are reported. Both compounds were prepared from chromium(VI) salts by two different methods and reaction pathways of these syntheses are suggested. The crystal structures of these two aquapentachlorochromates(III) have been determined from three dimensional X‐ray data collected at low temperature, 173 K. The two structures are isomorphous and their unit cell dimensions are quite similar. They are orthorhombic, space groups Pnma, with Z = 4. Both structures are composed of [CrCl₅(H₂O)]^2? units held together by the counterion framework. The coordination around the chromium ion deviates from a regular octahedron due to the shorter equatorial chromium‐oxygen bond.     

Semiclathrates of the Ge-P-Te system: synthesis and crystal structures

Novel compounds [Ge_46?xP_x]Te_y (13.9≤x≤15.6, 5.92≤y≤7.75) with clathrate‐like structures have been prepared and structurally characterized. They crystallize in the space group Fm$\bar 3Novel compounds [Ge(46-x) P(x) ]Te(y) (13.9≤x≤15.6, 5.92≤y≤7.75) with clathrate-like structures have been prepared and structurally characterized. They crystallize in the space group Fm ?3 with the unit cell parameter changing from 20.544(2) to 20.698(2) ? (Z=8) on going from x=13.9 to x=15.6. Their crystal structure is composed of a covalently bonded Ge-P framework that hosts tellurium atoms in the guest positions and can be viewed as a peculiar variant of the type?I clathrate superstructure. In contrast to the conventional type I clathrates, [Ge(46-x) P(x) ]Te(y) contain tricoordinated (3b) atoms and no vacancies in the framework positions. As a consequence of the transformation of the framework, the majority of the guest tellurium atoms form a single covalent bond with the host framework and thus the title compounds are the first representative of semiclathrates with covalent bonding. A comparison is made with silicon clathrates and the evolution of the crystal structure upon changing the tellurium content is discussed.