Intra- vs intermolecular hydrogen bonding. The crystal structure of 5-methyl-2-hydroxyacetophenone thiosemicarbazone monohydrate and salicylaldehyde-2-methylthiosemicarbazone monohydrate

The crystal structure of 5-methyl-acetophenonethiosemicarbazone monohydrate,A, and salicylaldehyde-2-methylthiosemicarbazone monohydrate,B, were determined using single crystal X-ray diffraction.A crystallizes in the monoclinic space groupC2/c, with lattice parametersa=14.161(2),b=15.753(1) ?,c=11.084(1) ?, β=112.59(1)° andZ=4, yielding a calculated density ofD _calc=1.352 mg/m³.B crystallizes in the triclinic space groupP1, witha=7.233(2) ?,b=7.371(2) ?,c=11.841(2) ?, α=82.77(2)°, β=78.33(2)°, γ=63.06(2)° andD _calc=1.371 mg/m³ forZ=2,. In bothA andB the immine nitrogen and the sulfur atom areanti with respect to N2-C8. WhileA presents the usual intramolecular six membered hydrogen bond ring,B has instead an intermolecular hydrogen bond between the hydroxy moiety of the salicyladehyde and a water molecule. AM1 calculations agree with the experimental conformations observed in both compounds. Contribution No. 1619 of the Instituto de Química, UNAM.     

Molecular and crystal structure of 3-(4-chlorophenylthio)-1-(2,4-dinitrophenylamino)-pyrrolidine-2,5-dione

3-(4-Chlorophenylthio)-1-(2,4-dinitrophenylamino)-pyrrolidine-2,5-dione, C₁₆H₁₁N₄C10₆S, was obtained in the addition reaction of 4-chlorobenzenethiol and 2,4-dinitrophenyl-aminomaleimide. It forms orthorhombic crystals; the finalR=0.048 for 1083 unique observed reflections. The molecule consists of three rigid rings connected by single bonds. A synclinal conformation of the terminal phenyl rings (A andC) with respect to the central pyrrolidine ring (B) is observed in the crystal, with ringsA andC close to one another. An intramolecular hydrogen bond N(2)O(4) of 2.593(7) Å is observed. The structure of the title compound was also investigated by IR,¹H-NMR and M.S.     

X-Ray Crystal Structure and Photo Chemistry of N-Methyl-N-(1-phenylvinyl)benzamide

Abstract  

N-methyl-N-(1-phenylvinyl)benzamide (I) has empirical formula C₁₆H₁₅NO, crystallizes in the monoclinic space group, P21/n, with unit cell parameters a = 8.9101(2) ?, b = 15.1416(4) ?, c = 9.7737(2) ?, α = 90°, β = 109.3320(10)°, γ = 90°, Z = 4. Interestingly, the Compound (I) undergoes photocyclization upon irradiation of light to give two cyclic lactams (A and B) below 3100 ?. Compound (I) can be cyclized at either of two equivalent ortho positions. The mechanism for formation of lactam A may involve electrocyclic ring closure reaction upon irradiation of light to give six-membered cyclic zwitterionic intermediate. The ring proton rearranges via [1, 5]-H shift to give isomerized product A. The minor photoproduct B is supposed to be formed via photocyclization process followed by a loss of proton and the tautomerized product undergoes oxidation for the revival of aromaticity.     

N,N′-(1,2-phenylene)bis(pyridoxal-hydrochlorideiminato)copper(II): crystallographic and spectroscopic studies

(C₂₂H₂₂CuN₄O₄Cl_{2 2}·7H₂O is triclinic,C _i– ¹ t-P1. Unit cell dimensions at 293 K area=12.028(3),b=20.378(6),c=11.387(3) Å, =113.10(2),=84.13(2), =95.99(2)°,V=2547.5 0A³,D _c =1.573 Mg. m^–3, andZ=2. The structure has been determined from single-crystal data collected with a four-circle diffractometer and refined from 3904 reflections down toR=0.054 andR _w =0.058. The asymmetric unit is built from two independent A and B molecules in which the copper atom has a square pyramidal environment in A and an octahedral one inB. Intermolecular Cu-O (hydroxymethyl groups) contacts observed in the solid state are partially present in aqueous solutions.     

Crystal structure of PbUO2(CH3COO)4(H2O)3

Single crystals of PbUO₂(CH₃COO)₄(H₂O)₃ have been investigated by X-ray diffraction (R = 0.029 for 3175 reflections). The structure of this compound is formed by [Pb(CH₃COO)(H₂O)₃]⁺ chains, which are oriented along the [100] axis and limited by one-core complexes [UO2(CH₃COO)₃]⁻. The coordination numbers of the Pb(II) and U(VI) atoms are 8, and the coordination polyhedron of uranium is a hexagonal bipyramid whose vertices contain oxygen atoms of three bidentate cyclic acetate groups and the uranyl group. Taking into account the different crystallographic roles of acetate ions, the crystal-chemical formula of [PbUO₂(CH₃COO)₄(H₂O)₃] chains can be written as AA′B ²¹ B ¹¹(B ⁰¹)₂ M ₃¹, where A = Pb; A′ = UO₂²⁺; M ¹ = H₂O; and B ²¹, B ¹¹, and B ⁰¹ are CH₃COO⁻ groups.     

Crystal structure and vibrational spectra of polyamine-copper(II) complexes

The structures of [Cu(en)(H₂O)₂]SO₄ (I), [Cu(en)₂](NO₃)₂ (II) and [Cu(trien)I]I (III) have been determined by single crystal X-ray diffraction. ComplexI is monoclinic, space group C2/c, with unit cell parametera=7.232(1),b=11.725(2),c=9.768(1), =105.50(1)°, andZ=4. ComplexII is also monoclinic, space group P2₁/a, witha=7.978(2),b=9.982(4),c=8.218(3), =111.11(2)°, andZ=2. ComplexIII is orthorhombic, space group P2₁2₁2₁, witha=8.098(1),b=11.902(1),c=13.682(2), andZ=4. The structures were solved by direct methods and refined by full-matrix least-squares to finalR values of 0.031, 0.043 and 0.036 for complexesI, II, andIII, respectively. ComplexesI andII show an octahedral coordination geometry. ComplexIII shows a square pyramidal coordination geometry. ComplexI forms infinite monodimensional chains where the SO ₄ ^2– ions acts as a bridge between two neighboringen molecules. The vibrational spectra of these complexes agree well with their crystal structures. Structure and stability of seven other related Cu(II) complexes of (trien), (dien)₂, (en)₂ and (en) are inferred in this study.     

Crystal and molecular structure of 1-phenyl-3-(2-hydroxyphenylamino)-2-buten-1-one,C16H15NO2

Orange, yellow, and colorless crystals were obtained for the title compound. The orange crystals are triclinic, space groupP¯1,a=9.181(2),b=10.734(2),c=15.245(3) Å,=73.06(2),=79.21(2), =67.83(2)°,V=1325.9(5) ų,Z=4. Two different symmetry-independent molecules (moleculeA andB) were determined in the crystal unit. The conformation ofA is stabilized by an intramolecular H bond from the amino NH to the keto and phenolic O atoms [1.89(2) and 2.38(2) Å, respectively]. The conformation ofB is stabilized by only one intramolecular H bond, from the amino NH to the keto O atom [1.925(2) Å]. The colorless crystals (moleculeC) are monoclinic, space groupP2₁/n,a=11.883(3),b=11.004(3),c=10.053(3) Å,=95.93(3)°,V=1307.5(6) ų,Z=4. This conformation is stabilized by one intramolecular H bond, the same as in B, with N-HO, 1.84(3) Å. An intermolecular H bond is observed forA,B, and C, O-HO, 2.634(2), 2.640(2), and 2.697(2) Å, respectively. The yellow crystals are adducts with ethanol (¹H NMR, infrared and GC measurements).     

Crystal structures of 4,11-pregnadiene-3,20-dione and 21-methyl-20-oxa-4-pregnene-3,20-dione

The structures of the title compounds were solved by direct methods and refined by anisotropic full-matrix least-squares methods. 4,11-Pregnadiene-3,20-dione, C₂₁H₂₈O₂(1) crystallizes in the monoclinic space groupP2₁ (Z=2). The unit cell parametersa, b, c (Å), and (°) were: 12.319(2), 7.700(2), 9.717(2), 109.41(2). TheA- andC-rings exhibit intermediate sofa-halfchair conformations. TheB-ring has a chair conformation and theD-ring assumes an intermediate envelope-half-chair conformation. The progesterone side chain has a typical conformation; the C16–C17–C20–O20 torsion angle is –15.1(4)°. 21-Methyl-20-oxa-4-pregnene-3,20-dione, C₂₁H₃₀O₃ (2) crystallizes in the orthorhombic space groupP2₁2₁2₁ (Z=4). The unit cell parametersa, b, c (Å) were: 12.926(2), 19.447(4), 7.313(1). The progesterone side chain has an unusual conformation; the C16–C17–C20–O20 torsion angle is 174.6(4)°. TheA-ring has a 1, 2-half-chair conformation, ringsB andC exhibit chair conformations and ringD is in a 13,14-half-chair conformation.     

EPR spectra of (L-aspartate)di(2-pyridyl)aminezinc(II) hydrate substitutionally copper(II) doped complex

The [(L-aspartate)di(2-pyridyl)aminezinc(II)]hydrate doped with traces of copper was prepared. Electron paramagnetic resonance spectra of the polycrystalline sample were recorded at room temperature by using the X-band of the EPR spectrometer. The observedg factors for the complex areg _‖=2.258 andg _⊥=2.066. TheA _‖ value is 165.10⁻⁴ cm⁻¹. The crystal and molecular structure of the complex are also reported. The complex crystallizes in the monoclinic system; space groupP2₁ witha=7.2053(11),b=10.447(2),c=10.812(2) Å, β=108.489(14)° andZ=2. The structure can be described in the crystal lattice as polymeric chains.     

EPR spectra of (L-aspartate)di(2-pyridyl)aminezinc(II) hydrate substitutionally copper(II) doped complex

The [(L-aspartate)di(2-pyridyl)aminezinc(II)]hydrate doped with traces of copper was prepared. Electron paramagnetic resonance spectra of the polycrystalline sample were recorded at room temperature by using the X-band of the EPR spectrometer. The observedg factors for the complex areg _‖=2.258 andg _⊥=2.066. TheA _‖ value is 165.10⁻⁴ cm⁻¹. The crystal and molecular structure of the complex are also reported. The complex crystallizes in the monoclinic system; space groupP2₁ witha=7.2053(11),b=10.447(2),c=10.812(2) Å, β=108.489(14)° andZ=2. The structure can be described in the crystal lattice as polymeric chains.     

Ligand-induced polyhedral opening in the mixed-metal cluster MeCCo2NiCp(CO)6 by 4,5-Bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd): X-ray structure of Co2NiCp(CO)4[μ2,η2,η1-C(Me)C=C(PPh2)C(O)CH2C(O)](μ2-PPh2)

The mixed-metal cluster MeCCo₂NiCp(CO)₆ (1) reacts with the diphosphine ligand 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd) in refluxing CH₂Cl₂ to afford the disubstituted cluster MeCCo₂NiCp(CO)₄(bpcd) (2), which exists as a 1:1 mixture of bridging and chelating bpcd isomers. VT ³¹P NMR spectroscopy confirms that the two bpcd isomers do not interconvert in solution over the temperature range of 182–298 K. Thermolysis of cluster 2 leads to bpcd/cluster activation and formation of the phosphido-bridged cluster Co₂NiCp(CO)₄[μ₂,η²,η¹-C(Me)C=C(PPh₂)C(O)CH₂C(O)](μ₂-PPh₂) (3). The ligand-induced polyhedral expansion that accompanies the formation of the title cluster was established by X-ray diffraction analysis. Co₂NiCp(CO)₄[μ₂,η²,η¹-C(Me)C=C(PPh₂)C(O)CH₂C(O)](μ₂-PPh₂) crystallizes in the triclinic space group P-1, a=9.679(2), b=11.691(2), c=16.653(3) ?, α=85.849(3)°, β=85.456(4)°, γ=66.453(3)°, V=1720.3(6) A³, Z=2, D _cacl=1.632 Mg/m³; R=0.0874, R _w=0.1998 for 7053 observed reflections with I > 2σ(I).     

Nickel(II) and cobalt(II) nitrate and chloride networks with 2-aminopyrimidine

The coordination chemistry of 2-aminopyrimidine (PymNH₂) with nickel(II) and cobalt(II) nitrate and chloride is reported, including seven new X-ray crystal structures. Two [Ni(NO₃)₂(PymNH₂)₂(OH₂)] isomers were found (A: C2/c, a=13.3006(5), b=7.9727(3), c=28.5453(11), β=101.758(2), V=2963.48(19), Z=8 and B·1/2 acetone: P2₁/c, a=7.66060(10), b=10.6792(2), c=20.6790(3), β=100.2970(10), 1664.48(5), Z=4). In both cases one nitrate is monodentate and the other is chelating and the PymNH₂ ligands coordinate through ring nitrogen atoms. Hydrogen bonding results in double sheet structure for isomer A, and a three dimensional channeled network for isomer B. [Co(NO₃)₂(PymNH₂)₂(OH₂)] (C2/c, a=13.3507(2), b=7.99520(10), c=28.6734(3), β=102.3540(10), V=2989.77(7), Z=8) is isostructural to Ni isomer A. [CoCl₂(PymNH₂)] (Cmcm, a=3.6139(2), b=14.3170(7), c=12.9986(7), V=672.55(6), Z=4) is a sheet coordination network, consisting of corner-sharing chains of Co₂(μ-Cl)₂ bridged by PymNH₂ through ring nitrogen atoms; [CoCl₂(PymNH₂)₂] (C2/c, a=11.2774(6), b=6.5947(4), c=16.5687(9), β=92.269(3), V=1231.27(12), Z=4) is a tetrahedral molecule knit into a ribbon structures through pairs of hydrogen bonds. Isostructural trans-[NiCl₂(PymNH₂)₄] (C2/c, a=7.67760(10), b=18.7224(3), c=15.0418(2), β=99.6740(10), V=2131.41(5), Z=4) and trans-[CoCl₂(PymNH₂)₄] (C2/c, a=7.69120(10), b=18.5957(2), c=15.1091(2), β=99.5280(10), V=2131.14(5), Z=4) are simple octahedral molecules, with hydrogen-bonding producing sheet structures.     

The role of X-ray crystallography in drug design: Identification of the two isomers 17β-hydroxy-17α-methyl-5(β andα)-androstano-(2,3-C)-1′, 2′, 5′-oxadiazole (HS804 and HS805) (steroids and related studies,Part 62)

Crystal structure analysis has distinguished between the two epimers 17-hydroxy-17-methyl-5( and)-androstano-(2, 3-C)-1, 2, 5-oxadiazole (HS804 and HS805). HS804 is trigonal,P3₂,a=14.820(4),c=7.177(3) Å,Z=3 and HS805 is orthorhombic,P2₁2₁2₁,a=9.507(4),b=18.528,c=10.048(4) Å,Z=4. The crystal structures were solved by direct methods and refined by full-matrix least squares toR=0.0376 for 1419 reflections (HS804) andR=for 1819 reflections (HS805), using diffractometer measured data with CuK radiation. The two molecules have different ring connections,A/B cis in HS804 andA/B trans in HS805, the planar oxadiazole ring beingcis fused to ringA in both molecules. RingA is strained in both molecules.     

Synthesis and Crystal Structures of Two Polymorphs of Trilanthanum Iridium Septaoxide (La<Subscript>3</Subscript>IrO<Subscript>7</Subscript>)

Abstract  

Two polymorphs of trilanthanum iridium septaoxide, La₃IrO₇, were prepared as single crystals using a molten cesium hydroxide flux and were structurally characterized using single-crystal X-ray diffraction. Polymorph A crystallizes in the orthorhombic space group Cmcm with unit cell dimensions of a = 11.2103(3) ?, b = 7.4982(2) ?, and c = 7.6110(2) ?. Polymorph B crystallizes into the monoclinic space group P2₁/n with the unit cell dimensions of a = 8.8512(5) ?, b = 5.7167(3) ?, c = 24.4454(13) ?, and β = 95.542(2)°. The crystal structure of polymorph A is isostructural to the family of compounds with formula Ln₃MO₇ (M = Nb⁵⁺, Mo⁵⁺, Ru⁵⁺, Ta⁵⁺, Re⁵⁺, Os⁵⁺, and Ir⁵⁺) while the crystal structure of polymorph B has no known corollaries.     

Crystal and molecular structures of trans-bis(acetonitrile)bis(bipyridine)ruthenium(II) perchlorate and trans-diamminebis(bipyridine)ruthenium(II) perchlorate

The structures of trans-[(MeCN)₂(bpy)₂Ru](ClO₄)₂(I) andtrans-[(NH₃)₂(bpy)₂Ru](ClO₄)₂(II) have been determined by single crystal X-ray diffraction methods. (I) forms monoclinic crystals in the space groupP2₁/c witha=8.399(2),b=10.406(2),c=15.590(3) Å,=93.78(2)° andZ=2 atT=293 K. The final refinement gaveR=0.040 for 2448 reflections withF _o ² >3(F _o ² ). (II) crystallizes in the triclinic space groupP¯1 witha=1.702(1),b=8.439(2),c=10.525(2) Å,=107.56(2),=104.63(1), =100.89(2)° andZ=1 atT=293 K. Refinement using 1878 reflections withF _o ² >3(F _o ² ) produced a finalR value of 0.036. Both of these structures have the ruthenium atom located on a crystallographic inversion center. The bipyridine ligands in both structures are in the bowed conformation as a means of circumventing the steric problems associated with the trans arrangement of the bipyridine ligands. The Ru-N(monodentate) distance is longer for the ammonia complex (2.106(3) Å) than for the acetonitrile complex (2.008(4) Å); there are no significant differences in the distances and angles of the two Ru(bpy)₂ frameworks.     

X-ray structural investigation of two optically active 1N-epimers of 2,5,7,10,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-dienenickel(II) diperchlorate. A novel conformation of the macrocyclic ligand

The structures oftrans-1NH,8NH- (I) andcis-1NH,8NH-(II)-2,5,7,10,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-dienenickel(II) diperchlorates have been investigated by X-ray diffractometric methods. CompoundI crystallizes in a monoclinic system, space groupP2₁,Z=4,a=11.225(1),b=13.710(1),c=15.898(2) Å,=109.22(1)°. CompoundII crystallizes in an orthorhombic system, space groupP2₁2₁2₁,Z=4,a=15.529(2),b=14.129(2),c=10.621(1) Å. The structures were solved by the heavy-atom method followed by a series of Fourier syntheses, and refined by full-matrix least squares to give forI andII R=0.051 (for 3787 independent reflections) andR=0.048 (for 1494 reflections), respectively. Conformational analysis of chelate rings and of the macrocyclic ring was performed forI andII, and the results were compared with those of some known 1,4,8,11-tetraazacyclotetradeca-4,11-dienenickel (II) complexes. A novel conformation of the macrocycle was found in cationI. Conformations of the methyl groups are forI andII 2(a),7(e),10(a),14(e) and 2(a),7(e),10(a),14(a), respectively, with a 1,3-syn-axial interaction of the 2,14-methyl groups inII. The absolute configuration of cationI is 1N(S), 2(R), 7(R), 8N(S), 10(R), 14(S), and differs from that of cationII by 1N(R) exclusively (1N-epimeric compounds).     

X-Ray Diffraction Studies of 4-n-Decyl(oxy)phenyl-4'-n'-butyl(oxy)benzoate and 4-n-Decyl(oxy)phenyl-4'-n'-hexyl(oxy)benzoate

Liquid crystal aromatic esters of compositions C₁₀H₂₁OC₆H₄C(O)OC₆H₄OC₄H₉ (1) and C₁₀H₂₁OC₆H₄C(O)OC₆H₄OC₆H₁₃ (2) have been investigated by X-ray structural analysis. On temperature rise, these compounds undergo phase transitions crystal-smectic (S_A)-nematic-isotropic (1) and crystal-smectic (S_C)-smectic(S_A)-nematic-isotropic (2) at temperatures 64.5, 80.7, 89.1°C and 62.0, 77.0, 82.5, 88.5°C, respectively. Crystal packing of the compounds consists of alternating loosely packed aliphatic and closely packed aromatic regions. The number of types of weak directional interactions in aromatic regions in both crystal packings was found to be equal to a number of phase transitions in crystal-mesophase-isotropic systems.     

Crystal and molecular structures oftrans-dichloro-(ethylene) (4-methylpyridine)platinum(II) andtrans-dichloro(ethylene) (2,4,6-trimethylpyridine)platinum(II)

The crystal and molecular structures oftrans-[PtCl₂(C₂H₄)(4-MeC₅H₄N)] (I) andtrans-[PtCl₂(C₂H₄)(2,4,6-Me₃C₅H₂N)] (II) have been determined by single-crystal x-ray methods.I crystallizes in space groupP2₁/c witha= 4.991(1), b=21.658(3), c=10.675(3) Å, =110.17(2) °,Z=4;II is orthorhombic (Pbca) witha=10.295(6),b=12.393(8),c=20.370(10) Å,Z=8.Full-matrix least-squares refinements have given finalR factors of 0.053 (1520 reflections) forI and 0.042. (1412 reflections) forII. The intensities were recorded by counter methods, and only those reflections havingI>3(I) were used in the analyses.In both complexes, platinum is four-coordinate with the two chlorine atoms, the double bond of the ethylene, and the nitrogen atom of the substituted pyridine. The two structures are discussed in terms of the arrangement of the pyridine ligand with respect to the PtCl₂(C₂H₄) moiety.     

Crystal and molecular structure of 2-(p-tolyl)-2-dehydrosparteine

The formula of the title compound is C₂₂H₃₀N₂,M _T =322.5; monoclinic:P2₁,a=7.569(3),b=9.381(1),c=13.684(4) Å,=105.81(2)°,Z=2,V _c =933.7 ų,D _x =1.15 g cm^–3,(CuK)=5.1 cm^–1. The sparteine skeleton (bis-quinolizidine system) has atrans-trans configuration. RingA has an intermediate form between the sofa and half-chair conformations, ringsB andD-chair, and ringC-boat conformations, respectively. The double bond C(2)=C(3) is equal to 1.343(9) Å. The phenyl ring is planar and makes an angle with a plane through N(1), C(2), C(3), and C(4) atoms equal to 43.9°.     

Intramolecular hydrogen bonding and tautomerism in N-(3-pyridil)-2-oxo-1-naphthylidenemethylamine

N-(3-pyridil)-2-oxo-1-naphthylidenemethylamine (C₁₆H₁₂N₂O) was studied by elemental analysis, IR, ¹H NMR, and UV–visible techniques and X-ray diffraction methods. The UV–visible spectrum of the compound was investigated in solutions effect polarity. The polarity of the some solvents was modifierly the additional (CF₃COOH) and [(C₂H₅)₃N]. The compound is in tautomeric equilibrium (phenol-imine O–H···N and keto-amine O···H–N forms) in polar and nonpolar solvents. The keto-amine form is observed in basic solutions of DMSO, ethanol, chloroform, benzene, cyclohexane, and in acidic solutions of chloroform and benzene, but not in acidic solutions of DMSO and ethanol. The compound crystallizes in the monoclinic, space group P2₁/a with a = 7.010(5) Å, b = 13.669(4) Å, c = 12.764(4) Å, = 101.23(4)°, V = 1199.6(10) ų, Z = 4, D _c = 1.375 g/cm³, (Mo K) = 0.088 mm^–1, R = 0.045 for 1658 reflections [I > 2(I)]. The title compound is not planar two Schiff base moieties A [C1–C11, O1] and B [N1, C12, C13, N2, C14, C15, C16] are inclined at an angle of 27.4(1)° reflecting mainly the twist about C12–N1 [C11–C12–N1–C13, 29.7(2)°]. There is a strong intramolecular hydrogen bond (O–H···N) of 2.529(2) Å.