Crystal structure of lansoprazole sulfone

The structure of 2-({[3-methyl-4-(2,2,2-trifluoroethoxy)-2-pyridinyl]methyl} sulfonyl)-1H-1,3-benzimidazole, C₁₆H₁₄N₃O₃F₃S, has been solved. The compound belongs to the monoclinic space group (P2₁/c) with cell parameters a = 8.8693(9) Å, b = 23.369(2) Å, c = 8.6141(8) Å, β = 104.68(1)°, V = 1727.2(3) ų, Z = 4. The final R and wR(F ²) values were 0.070 and 0.147, respectively. The title molecule has a ‘Z’ shape in the crystal structure. The fused benzimidazole moiety and the pyridine ring are nearly coplanar. The molecules are linked by N-H…N and C-H…O hydrogen bonds into chains of edge-fused R ₂ ² (14), R ₂ ² R ₂ ² (8), and R ₂ ² (18) rings along the c-axis. The crystal lattice is further strengthened by π-π stacking interactions.     

Synthesis and crystal structure of two derivatives of benzodiazepines

Two benzodiazepine derivatives, C₂₃H₂₂N₂O (I), 2-methyl-8-methoxy-2,4-diphenyl-2,3-dihydro-1H-1,5-benzodiazepine, and C₂₂H₁₇N₃O₂Br₂ (II), 2-methyl-7-nitro-2,4-bis(4′-bromophenyl)-2,3-dihydro-1H-1,5-benzodiazepine, were studied by single crystal X-ray diffraction method. Compound (I) crystallizes in the monoclinic system, space group P2₁/c, a = 13.1703(17) Å, b = 11.1990(14) Å, c = 12.9093(16) Å, β = 107.831(2)°, V = 1812.6(3) ų, Z = 4. Compound (II) crystallizes in the monoclinic system, space group P2₁/n, a = 11.7345(12) Å, b = 12.7477(13) Å, c = 13.5965(14) Å, β = 95.221(2)°, V = 2025.4(4) ų, Z = 4. The molecules of (I) and (II) have T-shape form with the diazepine ring at the junction point. The seven membered central benzodiazepine ring in both structures adopt a twist-boat conformation. The crystal packing is stabilized by C-H…π (in I) and C-H…O (in II) interactions.     

Elucidating 2D Charge-Density-Wave Atomic Structure in an MX–Chain by the 3D-ΔPair Distribution Function Method**

Many solids, particularly low-dimensional systems, exhibit charge density waves (CDWs). In one dimension, charge density waves are well understood, but in two dimensions, their structure and their origin are difficult to reveal. Herein, the 2D charge-density-wave atomic structure and stabilization mechanism in the bromide-bridged Pd compound [Pd(cptn)₂Br]Br₂ (cptn=1R,2R-diaminocyclopentane) is investigated by means of single-crystal X-ray diffraction employing the 3D-Δpair distribution function (3D-ΔPDF) method. Analysis of the diffuse scattering using 3D-ΔPDF shows that a 2D-CDW is stabilized by a hydrogen-bonding network between Br⁻ counteranion and the amine (NH₂) group of the cptn in-plane ligand, and that 3D ordering is prevented due to a weak plane to plane correlation. We extract the effective displacements of the atoms describing the atomic structure quantitatively and discuss the stabilization mechanism of the 2D-CDW. Our study provides a method to identify and measure the key interaction responsible for the dimensionality and stability of the CDW that can help further progress of rational design.     

Effect of High Pressure on the Polymorphs of Paracetamol

Effect of hydrostatic pressure on the two (I – monoclinic and II – orthorhombic) polymorphs of paracetamol was studied by X-ray diffraction in the diamond anvil cell at pressures up to 4.5 GPa (for the monoclinic form) and up to 5.5 GPa (for the orthorhombic form). The two groups of phenomena were studied: (i) the anisotropic structural distortion of the same polymorph, (ii) transitions between the polymorphs induced by pressure. The anisotropy of structural distortion of polymorphs I and II was well reproducible from sample to sample, also from powder samples to single crystals. The bulk compressibility of the two forms was shown to be practically the same. However, a noticeable qualitative difference in the anisotropy of structural distortion was observed: with increasing pressure the structure of polymorph II contracted in all the directions showing isotropic compression in the planes of hydrogen-bonded molecular layers, whereas the layers in the structure of the polymorph I expanded in some directions. Maximum compression in both polymorphs I and II was observed in the directions normal to the molecular layers. The transitions between the polymorphs induced by pressure were poorly reproducible and depended strongly on the sample and on the procedure of increasing/decreasing pressure. No phase transitions were induced in the single crystals of the monoclinic polymorph at pressures at least up to 4GPa, although a partial transformation of polymorph I into polymorph II was observed at increased pressure in powder samples. Polymorph II transformed partly into the polymorph I during grinding. The transformation could be hindered if grinding was carried out in CCl₄. This revised version was published online in August 2006 with corrections to the Cover Date.     

Giant deuteron migration during the isosymmetric phase transition in deuterated 3,5-pyridinedicarboxylic acid

Deuterated 3,5‐pyridinedicarboxylic acid exhibits reversible temperature‐induced deuteron migration of a magnitude unprecedented in this class of compounds. We used a combination of variable‐temperature powder and single‐crystal neutron diffraction and density functional theory (DFT)‐based computational methods to elucidate the origin of this remarkable behaviour. Single‐crystal neutron diffraction shows that between 15 and 300 K, the deuteron moves by 0.32(1) Å and the structure changes from a low‐temperature N? D???O form to a high‐temperature N???D? O form. Variable‐temperature powder neutron‐diffraction data, which was fitted by using parametric Rietveld refinement, show that this deuteron migration is due to an isosymmetric, first‐order phase transition that occurs by growth of the daughter phase in the parent‐phase matrix. Similar phase transitions are observed in two selectively deuterated forms of the material. DFT calculations demonstrate the role of phonons and show that vibrational free‐energy stabilisation, which plays a key role in the observed structural phase transitions, is more pronounced in the fully deuterated material and proportional to the mass of the molecule, that is, the level of deuteration. This is consistent with our experimental work, for which distinct crystallographic phase transitions were clearly observed for the three deuterated systems, but not for the fully protonated material.     

Structure and liquid crystalline properties of 2-hydroxyazobenzenes. X-ray diffraction, infra-red and DFT theoretical studies

The family of 2′-hydroxy-4′-alkyloxyazobenzenes containing in position 4 either CH₃ or Cl group with varying number of carbon atoms in alkyl group was analysed from the point of view of liquid crystalline properties and intramolecular OHN hydrogen bonding. The phase transition diagrams show that insertion of the OH group in 2′ position leads to a marked extention of mesophases as compared with parent azobenzenes and appearance in addition to nematic of the smectic SmA phase in the case of 4-chloro-derivatives. The role of chelate conjugating OHN hydrogen bonds in modification of mesophases is discussed based on DFT theoretical and X-ray as well as infrared studies. The importance of the molecule pairing is emphasized. Most important feature of mesophases and crystalline state of compounds under study is appearance of a continuous absorption down to 500 cm⁻¹ which is absent in solutions and Ar matrices.     

Introducing a Hydrogen‐Bond Donor into a Weakly Nucleophilic Brønsted Base: Alkali Metal Hexamethyldisilazides (MHMDS,M=Li,Na, K,Rb and Cs) with Ammonia

Alkali metal 1,1,1,3,3,3‐hexamethyldisilazide (MHMDSs) are one of the most utilised weakly nucleophilic Brønsted bases in synthetic chemistry and especially in natural product synthesis. Like lithium organics, they aggregate depending on the employed donor solvents. Thus, they show different reactivity and selectivity as a function of their aggregation and solvation state. To date, monomeric LiHMDS with monodentate donor bases was only characterised in solution. Since the first preparation of LiHMDS in 1959 by Wannagat and Niederprüm, all efforts to crystallise monomeric LiHMDS in the absence of chelating ligands failed. Herein, we present ammonia adducts of LiHMDS, NaHMDS, KHMDS, RbHMDS and CsHMDS with unprecedented aggregation motifs: 1) The hitherto missing monomeric key compound in the LiHMDS aggregation architectures. Monomeric crystal structures of trisolvated LiHMDS ( 1 ) and NaHMDS ( 2 ), showing unique intermolecular hydrogen bonds, 2) the unprecedented tetrasolvated KHMDS ( 3 ) and RbHMDS ( 4 ) dimers and 3) the disolvated CsHMDS ( 5 ) dimer with very close intermolecular Si?CH₃???Cs s‐block “agostic” interactions have been prepared and characterised by single‐crystal X‐ray structure analysis.     

The crystal structures at 80 K and IR spectra of the complex of 4-methylpyridine with pentachlorophenol and its deuterated analogue

The crystal structures of the complex of 4-methylpyridine with pentachlorophenol (MP-PCP) and its deuterated analogue (MP-PCP-d) were determined at 80 K by X-ray diffraction. The MP-PCP complex crystallizes in the space group P with a = 7.267(7), b = 8.966(9), c = 13.110(14)Å, = 99.70(8), β = 118.16(9), γ = 103.38(8)° and Z = 2 and the MP-PCP-d complex in the monoclinic Cc space group with a = 3.826(2), b = 27.54(2), c = 13.209(12)Å, β = 101.38(9)° and Z = 4. The O… H … N bridge bond distance of 2.515(4) Å is significantly shorter than that determined at room temperature (2.552(4) Å) and the O---D … N bond length of 2.628(6) Å is only slightly shorter than at room temperature (2.638(3) Å). The temperature dependence of the IR spectra confirms the symmetrization of the OHN hydrogen bond.     

The crystal structure of 3-methyluracil from X-ray powder diffraction data

The crystal structure of 3-methyluracil has been determined ab initio by conventional monochromatic X-ray powder diffraction data. The crystal data are: orthorombic, a=6.6294(1), b=13.1816(3), c=6.53938(9) (Å), V=571.45(3) (ų), space group Pbnm, Z=8. The structure was solved by direct methods and the final Rietveld refinement converged to R_p=0.0398, R_wp=0.0528, R_Bragg=0.0294. The crystal structure exhibits endless chains of planar molecules, connected via head-to-tail N-H?O hydrogen bonds.     

The crystal structures at 80 K and IR spectra of the complex of 4-methylpyridine with pentachlorophenol and its deuterated analogue

The crystal structures of the complex of 4-methylpyridine with pentachlorophenol (MP---PCP) and its deuterated analogue (MP---PCP-d) were determined at 80 K by X-ray diffraction. The MP---PCP complex crystallizes in the space group with a = 7.267(7), b = 8.966(9), c = 13.110(14) Å, = 99.70(8), β = 118.16(9), γ = 103.38(8)° and Z = 2 and the MP---PCP-d complex in the monoclinic Cc space group with a = 3.826(2), b = 27.54(2), c = 13.209(12) Å, β = 101.38(9)° and Z = 4. The O…H…N bridge bond distance of 2.515(4) Å is significantly shorter than that determined at room temperature (2.552(4) Å) and the O---D…N bond length of 2.628(6) Å is only slightly shorter than at room temperature (2.638(3) Å). The temperature dependence of the IR spectra confirms the symmetrization of the OHN hydrogen bond.