X-ray mapping in heterocyclic design: II. Diffractometric study of crystalline 2-oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride

The crystal structure of 2-oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride, C₇H₇ClN₂O, is determined by X-ray diffraction. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0408. The alternation of bond lengths in the molecule is inconsiderable, but does not disappear completely, since no aromatization occurs upon formation of the bicycle from the molecule. This structural change is apparently due to the increased conjugation of the NH group with the pyridine residue of the bicycle. One of the specific structural features of the salt is the formation of the N⁺-HïCl^? hydrogen bond (N-H, 0.792 Å; H?Cl, 2.260 Å; and N-H?Cl, 171.2°).     

Crystal structure of <Emphasis Type="Italic">p</Emphasis>-carboxyphenylhydrazone benzoylacetone

The crystal structure of p-carboxyphenylhydrazone benzoylacetone is determined. The crystals are monoclinic, a = 13.614(4) Å, b = 11.388(2) Å, c = 20.029(6) Å, β = 104.82(2)°, V = 2339(9) ų, Z = 8, space group C2/c, and R = 0.038 for 1622 reflections with I > 2σ(I). The crystal is built of C₁₇H₁₄N₂O₄ neutral molecules that are linked by O-H?O hydrogen bonds between the carboxyl groups into centrosymmetric pseudodimers. The effect of carboxylation of the phenylhydrazone fragment and the position of the carboxyl group on the molecular packing in the crystal is determined. The N(1)-H(1N)?O(1) intramolecular hydrogen bond (N-H, 0.94 Å; H?O, 1.87 Å; N?O, 2.59 Å; and the N-H?O angle, 133°) is formed in the molecule.     

Crystal structure of aminoguanidinium hexahydro-closo-hexaborate dihydrate, (CN4H7)2B6H6 · 2H2O

The (HAgu)₂B₆H₆ · 2H₂O compound was synthesized and its crystal structure was determined [R = 0.0385 for 2018 reflections with I > 2σ(I)]. The structure consists of HAgu ⁺ cations, centrosymmetric B₆H ₆ ^2? anions, and water molecules. The anions have an almost regular octahedral structure. The bond lengths and angles lie within the following narrow ranges: B-B, 1.715–1.726(2) Å; B-H, 1.08–1.14(2) Å; B-B-B, 59.72°–60.29(9)° and 89.63°–90.20(11)°; and B-B-H, 133.2°–137.0(9)°. The HAgu ⁺ cations and water molecules are involved in the O-H?O, N-H?O, and N-N?N hydrogen bonds and participate in numerous (N, O)-H?H-B specific interactions with the B₆H ₆ ^2? anions, which results in splitting and high-frequency shift of the band of B-H stretching vibrations in the IR spectrum.     

Synthesis and crystal structure of a new organic compound: Bis(4,4′-diaminodiphenylmethane) (4,4′-diammoniodiphenylmethane) dichloride monohydrate

A new organic compound with the formula C₃₉H₄₆Cl₂N₆O was synthesized from aqueous solution of 4,4′-diaminodiphenylmethane and hydrochloric acid at room temperature. This compound crystallizes in the monoclinic space group C2: a = 25.6525(16), b = 5.7107(3), c = 13.7777(8) Å, β = 118.862(2)°, V = 1767.64(22) ų and Z = 2, giving D _x = 1.288 g cm^?3. The refinement converged to R ₁ = 0.027 and wR ₂ = 0.0649. The structural arrangement can be described as infinite layers parallel to bc plane. In these layers cations and non protonated molecules are linked with N-H...N hydrogen bonds building [C₃₉H₄₄N₆]²⁺ organic clusters. These clusters, in turn, are linked by N-H...Cl and O-H...Cl hydrogen bonds.     

Crystal structure of hydrazine 5-amino-1-benzyl-1,2,3-triazole-4-carboxylate hexafluorosilicate trihydrate

Hydrazine 5-amino-1-benzyl-1,2,3-triazole-4-carboxylate hexafluorosilicate trihydrate (I) is synthesized. The crystal structure of the compound synthesized is determined. Crystals I are monoclinic, a = 13.353(1) Å, b = 21.094(2) Å, c = 20.233(2) Å, β = 94.05(3)°, space group P2₁/c, and R = 0.0584 for 16 601 reflections with I > 2σ(I). In the asymmetric part of the unit cell, four organic cations protonated at the terminal hydrazine nitrogen atoms, two hexafluorosilicate anions, and six water molecules are linked into a three-dimensional framework through hydrogen bonds of the N-H?F, N-H?O, and O-H?F types.     

Crystal structure of [N-(2-carbamoylethyl)iminodiacetato]-aqua(1,10-phenanthroline)cobalt(III) chloride 3.5 hydrate

The crystal structure of [N-(2-carbamoylethyl)iminodiacetato]-aqua(1,10-phenanthroline) cobalt(III) chloride 3.5 hydrate [Co(Ceida)(H₂O)(Phen)Cl · 3.5H₂O (I) has been determined by ¹H NMR technique and X-ray diffraction analysis. The crystals are triclinic, a = 10.352(2) Å, b = 12.534(3) Å, c = 20.665(4) Å, α = 107.02(3)°, β = 92.22(3)°, γ = 111.63(3)°, Z = 4, space group $P\bar 1$ , andR = 0.0438. The unit cell involves two crystallographically nonequivalent but virtually identical cationic complexes [Co(Ceida)(H₂O)(Phen)]⁺. The tridentate chelate ligand Ceida ^2? (N + 2O) occupies the face in the coordination octahedron of the Co atom, and the propionamide group remains free. The mean bond lengths are as follows: Co-O_Ceida, 1.876 Å; Co-N_Ceida, 1.981 Å; Co-N_Phen, 1.945 Å; and Co-O_w, 1.915 Å. In the structure, the arrangement of cationic complexes and certain water molecules exhibits a pseudosymmetry (the 2₁ axis). The cations and water molecules are located in the layers, and the anions are arranged between the layers. The structural elements are linked by hydrogen bonds and van der Waals interactions.     

Crystal and molecular structure of 2-[(4-nitrophenyl)carbonyl]cyclohex-1-ene-1-yl 4-nitrobenzoate

The crystal structure of 2-[(4-nitrophenyl)carbonyl]cyclohex-1-ene-1-yl 4-nitrobenzoate is studied (T = 173 K, R1 = 0.0354 for 2713 observed reflections). This crystal is orthorhombic, a = 7.8367(8) Å, b = 9.6082(10) Å, c = 23.856(3) Å, V = 1796.3(3) ų, space group P2₁2₁2₁, and Z = 4. The molecule has a folded configuration, which is stabilized by π-π interactions between its two parts. A system of intermolecular C-H...O hydrogen bonds (H...O, 2.44–2.67 Å; CHO angles 122°–169°) and intramolecular C-H...O contacts closing five-membered cycles (H...O, 2.42–2.59 Å; CHO angles 96°–102°) are formed in the structure.     

Synthesis and Structure of Di(1,2,4,6-tetraphenylpyridinium) Octachlorodirhenate(III)

The (NC₅H₂(C₆H₅)₄)₂[Re₂Cl₈] · 2CH₃CN compound was prepared by the reaction of (n-Bu₄N)₂[Re₂Cl₈] with the 1,2,4,6-tetraphenylpyridinium tosylate in the acetonitrile; it crystallizes upon cooling of the solution at –15°C. The structure consists of the ((C₆H₅)₄C₅H₂N)⁺ cation and Re₂Cl ₈ ^2? anion with virtual D_4h symmetry. The average Re–Re and Re–Cl bond distances are 2.2205 and 2.3431 Å, respectively. In the structure, the Re₂Cl ₈ ^2? anions are disordered, such that 71.34% of the Re–Re units are aligned in one direction while 28.66% are aligned orthogonal to it. The principal crystallographic data are as follows: sp. gr. R?3; a = 26.554(1) Å, c = 23.666(1) Å; V = 14451.6(1) ų; Z = 9; D_x = 1.643 g cm^–3.     

Co-crystal structure and optical properties of 9-fluorenone and naphthalene-1, 5-diamine

The co-crystal of 9-fluorenone and naphthalene-1, 5-diamine has been prepared and its structure is characterized by single-crystal X-ray analysis. It belongs to monoclinic system, space group P2₁/c with a = 9.0421(7), b = 18.1114(14), c = 8.1444(6) Å; β = 104.7232(10)°; V = 1296.20(17) ų, Z = 4. The crystal packing is stabilized by N-H…O intermolecular hydrogen bonds, as well as π-π stacking. Optical studies showed that the co-crystal exhibited red shift in PMMA film. The hydrogen bonds were easily destroyed in solvent.     

Synthesis of spinacine and spinacine derivatives: crystal and molecular structures of Nπ-hydroxymethyl spinacine and Nα-methyl spinaceamine

The natural amino acid L-Spinacine (4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine-6-carboxylic acid) has been synthesized following a new pathway which gives a chemically and optically pure product with an excellent yield. The crystal structures of a synthetic intermediate, N^π-hydroxymethyl-spinacine, and a spinacine derivative, N^α-methyl-spinaceamine, have been investigated through X-ray diffraction: Spi(πMeOH)·H₂O, monoclinicP2 _i,a=8.571(1),b=6.682(1),c=8.588(1) Å, and β=94.67(1)^o. Spm(αMe)·2HCl·H₂O, triclinicP l,a=7.492(4),b=10.799(3),c=7.040(2) Å, α=91.88(2), β=98.36(3) and γ=73.34(3)^o. Spi(πMeOH) crystallizes with a water molecule and displays a zwitterionic character. The carboxylate group is in equatorial position and forms a short electrostatic interaction of 2.618(2) Å between one of its oxygens and the protonated nitrogen of the tetrahydropyridine ring. The crystal packing is assured by strong O?H???O, O?H???N, N?H???N intermolecular hydrogen bonds and C?H???O close contacts. The biprotonated compounds Spm(αMe) crystallizes with two Cl^? anions and a water molecule. The positive charge on the imidazole ring is delocalized on the conjugated moiety N=C?N. The crystal is built up by clusters formed by two biprotonated Spm(αMe) molecules, four Cl^? anions and two water molecules linked together by hydrogen bonds.     

(Imidazole)(3,3′-trimethylenedinitrilo bis (2-butanone oximate)) copper(II) perchlorate: Synthesis and crystal structure of a five-coordinate copper-protein model complex

The synthesis and crystal structure of the novel pentacoordinated complex [Cu(DOHPN)(IMI-DAZOLE)] (ClO4), (DOHPN=(3,3′-trimethylenedinitrilo bis 2-butanone oxime) are reported. The X-ray crystal structure (space groupP2₁/n, a=11.349(2) Å,b=14.241(3) Å,c= 12.635(3) Å; α=90°, β=100.21 (3)°, γ=90°) shows that the copper(II) ion occupies a distorted square-pyramidal geometry with the imidazole ligand occupying the axial position. The copper(II)-(N)imidazole distance is 2.125(3) Å and the copper(II)-tetraaza plane distance is 0.385/Å. The tetraaza ligand DOHPN adopts a “butterfly-like” geometry with a dihedral angle of 149.69°. The title complex is the first structurally characterized compound of the series [Cu(DOHPN)(axial ligand)]ⁿ⁺ where the axial ligand is a neutral N-heterocycle with known biological relevance. A comparison of the structural parameters with those observed when the axial ligand is H₂O or NCS^? (N-bonded) gives the following series with increasing metal-ligand interaction: H₂O>IMIDAZOLE>NCS^? (N-bonded).     

X-ray diffraction studies oncis-[Ru(bpy)2(PMe3)Cl+][ClO4 −] andcis-[Ru(bpy)2{PMe2(o-tol)}Cl+][ClO4 −]; two ordered structures in thecis-bis(bipyridyl)chloro(phosphine)-ruthenium(II) series

The complexcis-[Ru(bpy)₂(PMe₃)Cl⁺][ClO₄ ^?] crystallizes in space group P2₁/c andcis-[Ru(bpy)₂{PMe₂(o-tol)]Cl⁺][ClO₄ ^?] crystallizes in space group $P\bar 1$ ; each is present as a racemate and neither structure suffers from disorder. The Ru?PMe₂(o-tol) bond length of 2.324(2)Å is slightly longer than the simple Ru?PMe₃ bond length of 2.310(2) Å.     

1,3,5-trichlorotricyanobenzene complexes with mesitylene (1/1) and benzene (1/3)

Trichlorotricyanobenzene-mesitylene (1/1) is monoclinic, space group P2₁/n; at ?88°Ca=10.509(3),b=14.863(7),c=11.518(3) Å, β=99.38(2)⁰,V=1775(2) ų,D _x =1.409(2) g cm^?3,Z=4. Trichlorotricyanobenzene-benzene (1/3) is hexagonal, space group $P\bar 6$ ; at ?99°Ca=17.3914(3),c=7.2673(1) Å,V=1903.6(1) ų,D _x =1.2844(1) g cm^?3,Z=3. In both complexes there are stacks of alternating trichlorotricyanobenzene and hydrocarbon molecules. In both complexes there are sheets of molecules perpendicular to the stacks. In the mesitylene complex these sheets contain equal numbers of both kinds of molecules with the trichlorotricyanobenzene molecules arranged in tapes. In the benzene complex the sheets contain only one kind of molecule or the other. The sheets containing the trichlorotricyanobenzene molecules have approximately linear C?N...Cl?C intermolecular interactions with N...Cl distances about 3.02 å.     

Crystal structure of SrFe(<Emphasis Type="Italic">EDTA</Emphasis>)Cl · 5H<Subscript>2</Subscript>O

The crystal structure of the SrFe(Edta)Cl · 5H₂O (I) complex is determined. The crystals are monoclinic, a = 7.530(4) Å, b = 10.575(3) Å, c = 23.308(10) Å, β = 95.75(4)°, Z = 4, and space group P2₁/c. The structural units of I are infinite ribbons of the molecular type that are formed by tetranuclear fragments. A tetranuclear fragment involves the centrosymmetric positively charged dimer group [Sr(H₂O)₄Cl] ₂ ²⁺ at the center and the [Fe(Edta)(H₂O)]_? anionic complexes, which compensate for the positive charge of the dimer group, at the periphery. These constituents are bound via bridging oxygen atoms of the Edta ligands. The coordination number of the Sr atom is nine. The Sr-O bond lengths lie in the range between 2.552 and 2.766 Å, the Sr-Cl bond length is 3.216(3) Å, and the Sr?Sr distance is 4.371(1) Å. The parameters of the [Fe(Edta)(H₂O)]^? group are within the range of values observed in such complexes: Fe-O, 1.996–2.086(3) Å; Fe-O(w), 2.110(4) Å; and Fe-N, 2.289(4) and 2.327(4) Å. Separate ribbons are linked by hydrogen bonds involving all H₂O molecules and terminal oxygen atoms of the Edta ligand.     

Structure of (N-(2-hydroxyphenyl)-salicylaldiminopiperidino) Ni(II) complex

The crystal and molecular structure of the title complex, C₁₈H₁₉N₂O₂Ni, has been determined by direct methods. The compound crystallizes in the monoclinic crystal system witha=22.973(1),b=5.212(1),c=27.076(1)Å, β=106.46(1)°, space groupC2/c,V=3109.1(6)ų, Z=8, andD _x=1.51g cm^?3. The nickel atom is in a slightly distorted square-planar environment of two oxygens [Ni(1)?O(1) 1.824(3) and Ni(1)?O(2) 1.856(3)Å] and two nitrogens [Ni(1)?N(1) 1.849(3) and Ni(1)?N(2) 1.932(3)Å] with O?Ni?N angles between 85.7(1) and 97.1(1)°. The nickel atom is 0.006 Å out of the plane of its ligands.     

Crystal structure of the supramolecular system of indole-2,3-dione 1-(2-oxopropyl)-3-ethylene ketal and its thiosemicarbazone

The crystal structure of a supramolecular system consisting of indole-2,3-dione 1-(2-oxopropyl)-3-ethylene ketal (I) and indole-2,3-dione 1-(2-oxopropyl)-3-ethylene ketal thiosemicarbazone (II) molecules that are linked together by hydrogen bonds is determined using X-ray diffraction. The crystal is monoclinic, and the unit cell parameters are as follows: a = 12.8360(3) Å, b = 10.7330(3) Å, c = 19.4610(3) Å, β = 99.566(1)°, space group P2₁/c, and Z = 4 (C₂₇H₂₉N₅O₇S). In molecules I and II, the indole-2,3-dione 3-ethylene ketal fragments have a virtually identical structure. The pyrrole and dioxolane fragments are spiro-linked through the carbon atom with a dihedral angle close to 90°. The adjacent pyrrole and benzene rings are coplanar to within 4.4°. In molecule II, the oxygen atom of the dioxolane fragment and the terminal nitrogen atom of the thiosemicarbazide fragment are involved in the N-HïO intramolecular hydrogen bond [3.294(2) Å]. The key role in the formation of the crystal structure is played by intermolecular hydrogen bonds of the N-H?dO, C-H?O, C-H?N, and N-H?S types.     

Structural study of [(CH3)2NH2]2CoCl4 single crystals at room temperature

The structure of the crystals grown from a solution of dimethylammonium and cobalt chlorides is determined. It is found that the crystals have the composition [(CH₃)₂NH₂]₂CoCl₄. At room temperature, the crystals are monoclinic (space group P2₁/c, Z = 4) and the unit cell parameters are as follows: a = 8.545(2) Å, b = 11.447(2) Å, c = 13.313(3) Å, and β = 90.10°. Cations and anions form simple and bifurcated hydrogen bonds N-H?Cl.     

X-ray structure analysis of 5N-ethyl-8-carboxy-9-oxo-11-methyl-pyrido[2,1-b]quinazoline

The crystal structure of 5N-ethyl-8-carboxy-9-oxo-11-methyl-pyrido[2,1-b]quinazoline (C₁₆H₁₆N₂O₃) has been determined by X-ray diffraction analysis. The compound crystallizes in the monoclinic crystal system (space group P2₁/c) with the unit cell parameters a = 9.775(1) Å, b = 15.868(1) Å, c = 9.799(1) Å, β = 113.50(1)°, Z = 4. The benzene ring is planar, the pyrimidine ring exists in 11β-sofa conformation, and the pyridone ring deviates slightly from planarity. The crystal packing exhibits intra-and intermolecular interactions of the O-H?O, C-H?O, and C-H?N types.     

Crystal structure of strontium hilgardite

The crystal structure of strontium hilgardite, CaSr[B₅O₉]Cl ? H₂O, was established by the method of X-ray diffraction analysis (synchrotron radiation; diffractometer equipped with a position-sensitive detector; λ = 0.688 Å; 3191 reflections with F < 4σ(F); R = 0.045 in the anisotropic approximation). The triclinic unit-cell parameters are as follows: a = 6.5732(6) Å, b = 6.4445(6) Å, c = 6.3693(6) Å, α = 60.995(2)°, β = 61.257(2)°, γ = 77.191(2)°, sp. gr. P1; Z = 1. The Ca and Sr atoms were found to be disordered over two positions. The structures of strontium hilgardite and hilgardite-1A differ in the configurations of the seven-vertex Sr-and Ca(2)-polyhedra. The structure solved in this work is consistent with two series of borates studied previously. One of these groups involves pentaborates with different degrees of hydration of borate complexes, and the second group includes Sr-containing borates.     

The 1:1 crystal complex of salicylic acid and urea

The 1∶1 crystal complex of salicylic acid (C₇H₆O₃) and urea (CH₄N₂O), mp 121° C, is monoclinic, with space groupC2/c (C ₂ ⁶ h, No. 15) and unit cell dimensionsa=22.206(3),b=5.108(1),c=17.177(2) Å,β=106.18(1)°.d _calc=1.407 g cm^?3,d _meas=1.41 g cm^?3 forZ=8. The structure was determined by direct methods and refined by a full-matrix least-squares procedure to giveR=0.057 andR _w =0.050 for 1652 integrated intensities above 2σ(I). The structure contains a strong OH?O hydrogen bond with O?O distance 2.54 Å in which the carboxyl OH group is donor and urea oxygen atom is acceptor. There are two NH?O intermolecular hydrogen bonds with N?O distances of 2.90 and 2.96 Å. Additionally, the salicyclic acid contains an intramolecular OH?O hydrogen bond of 2.56 Å.