X-ray mapping in heterocyclic design: VII. Diffraction study of the structure of N-pyridoneacetic acid and the product of its intramolecular dehydration

The structure of pyridoneacetic acid C₇H₇N₁O₃(I) is determined by the single-crystal X-ray diffraction technique. The crystals of I are monoclinic, a = 7.4502(15) Å, b = 10.006(6) Å, c = 9.960(3) Å, β = 109.96(2)°, Z = 4, and space group P2₁/c. The structure of pyridoneacetic acid is solved by the direct method and refined by the least-squares procedure in the anisotropic approximation to R = 0.0387. The structure of the product of its intramolecular dehydration, C₇H₆N₁O₂B₁F₄(II), is determined by the grid search procedure and refined by the Reitveld method (R _p = 0.045, R _wp = 0.58, R _e = 0.026, and χ² = 4.69). The crystals of II are monoclinic, a = 10.4979(3) Å, b = 11.4467(3) Å, c = 7.6027(1) Å, β = 100.83(2)°, Z = 4, and space group P2₁/n. The system of two conjugated heterocycles is planar.     

X-ray mapping in heterocyclic design: VI. X-ray diffraction study of 3-(isonicotinoyl)-2-oxooxazolo[3,2-<Emphasis Type="Italic">a</Emphasis>]pyridine and the product of its hydrolysis

The structure of 3-(isonicotinoyl)-2-oxooxazolo[3,2-a]pyridine, C₁₃H₈N₂O₃, (I) is determined by X-ray powder diffraction analysis. Crystals I are orthorhombic, a = 16.610(2) Å, b = 3.853(1) Å, c = 16.431(2) Å, Z = 4, and space group Pna2₁. The structure is solved by the grid search procedure and refined by the Reitveld method (R_p = 0.086, R_wp = 0.115, R_e = 0.030, and χ² = 11.138). The structure of the product of hydrolysis of compound I, C₁₂H₁₀N₂O₂, (II) is determined by the single-crystal X-ray diffraction technique. Crystals II are orthorhombic, a = 8.755(4) Å, b = 10.526(17) Å, c = 23.088(6) Å, Z = 8, and space group Pc2₁b. The structure is solved by the direct method and refined by the full-matrix least-squares procedure to R = 0.0464. A fragment of two fused heterocycles in I is planar. The dihedral angle between the plane of the pyridine ring in the isonicotinoyl fragment and the plane of the bicyclic system is 51.2(2)°. Both exocyclic CO groups that are adjacent to the five-membered fragment contain double bonds. The structures of two crystallographically independent molecules II are almost identical to each other, and the isonicotinoyl fragment is nearly perpendicular to the plane of the pyridone fragment [84.3(1)° and 87.0(1)°].     

Crystal and molecular structure of a diradical, 1,3-dinitro-4,6-di[3-(2,2,5,5-tetramethyl)-pyrrolidinyl-N-oxide]aminobenzene monohydrate

The crystal structure of 1,3-dinitro-4,6-di[3-(2,2,5,5-tetramethyl)pyrrolidinyl-N-oxide] aminobenzene monohydrate has been determined by single-crystal X-ray diffraction methods using the 1793 unique reflections for which 3 ° < 2θ < 40 ° andI > 3σ(I), and refined to a conventionalR index of 0.032. Counter methods using MoKα radiation were employed. Crystals form in the triclinic space groupP¯1 (No. 2) witha = 16.160(10),b = 11.686(6),c = 7.211(5) Å, α = 95.87(5) °, β = 98.67(5) °, and γ = 107.74(4) °. All hydrogen atom positions were determined. Intramolecular hydrogen-bonding between the nitro and amino groups has, in part, caused the central 20 atoms of the molecule, counting hydrogen atoms, to lie in an approximate plane. The benzene ring is distorted by its substituents to the symmetrymm2(C _2v ). The internal angles of the benzene ring range from 116.1 ° to 124.7 ° (esd = 0.3 °), and its bonds are between 1.368 Å and 1.436 Å (esd = 0.004 Å) in length. Four of the five atoms in each pyrrolidine ring are nearly coplanar; the remaining atom, the carbon bonded to the amine nitrogen in each case, lies approximately 0.53 Å from the corresponding plane. The best four-atom planes of the two pyrrolidine rings are each near to perpendicular to the central plane, giving the molecule a lobster-like appearance; they are each rotated approximately 15 °, in opposite senses, from perpendicular. The intramolecular distance between the two pyrrolidine nitrogen atoms, to which the unpaired charges can be assigned, is 7.68 Å. One of the nitroso oxygen atoms is hydrogen-bonded by two symmetry-equivalent water molecules. The inversion center necessitates that the remaining hydrogen atoms of these water molecules both hydrogen-bond to a symmetry-equivalent nitroso oxygen atom to give a hydrogen-bonded four-oxygen ring.     

Molecular and crystal structures of N-methyl-N-nitro-2-chloroaniline

The crystal structure of N-methyl-N-nitro-2-chloroaniline is determined by X-ray diffraction [a = 9.218(2) Å, b = 12.593(3) Å, c = 14.510(2) Å, space group Pbca, and Z = 8]. The structure is solved by the direct method and refined in the anisotropic approximation to R = 0.0377. All hydrogen atoms are localized. The structural parameters obtained agree with the data of the ab initio quantum-chemical B3LYP/6-31G** calculations. The data obtained are compared with those for N-methyl-N-nitro-4-chloroaniline. Conclusions on the interaction of the functional groups in the molecule are drawn.     

X-ray mapping in heterocyclic design: XI. X-ray diffraction study of 1-benzoyl-3-(pyridin-2-yl)-thiocarbamide and the product of its reaction with oxidants

The structures of 1-benzoyl-3-(pyridin-2-yl)-thiocarbamide C₁₃H₁₁N₃O₁S₁ (I) and 2-benzoylimino-1,2,4-thiadiazole[2,3-a]pyridine C₁₃H₉N₃O₁S₁ (II) are studied by X-ray diffraction. Structures I [a = 5.342(4) Å, b = 20.428(5) Å, c = 11.784(4) Å, β = 90.55(2)°, Z = 4, space group P2₁/n) and II [a = 6.258(6) Å, b = 18.068(14) Å, c = 10.185(10) tA, β = 95.45(8)°, Z = 4, space group P2₁/n) are determined by direct methods and refined to R ₁ = 0.0673 and 0.0802, respectively. In structure I, both intramolecular (involving the O atom) and intermolecular (involving the N and S atoms) hydrogen bonds are observed. The latter bonds are responsible for the formation of centrosymmetric molecular dimers. In structure II, a short intramolecular contact (2.168 Å) is observed between the S and O atoms.     

Crystal and molecular structures of 2-amino-5-(m-nitrophenyl)-1,3,4-Thiadiazole

2-Amino-5-(m-nitrophenyl)-1,3,4-thiadiazole (C₈H₆N₄O₂S) is studied using IR and ¹H NMR spectroscopy and X-ray diffraction (CAD4 automated diffractometer, λMoK _α, graphite monochromator, 957 unique reflections, Patterson method, R = 0.0326). The crystals are monoclinic, a = 11.832 Å, b = 9.862 Å, c = 8.353 Å, β = 110.40(3)°, V = 913.6(3) ų, d _calcd = 1.212 g cm^?3, μ(MoK _α) = 0.253 mm^?1, Z = 4, and space group P2₁/c. In the crystal, the C₈H₆N₄O₂S molecules form infinite layers parallel to the xz plane. Each layer contains aromatic rings with nitro groups that deviate from the layer plane on either side of the layer. In the packing, the aromatic rings with nitro groups of one layer fill spaces between aromatic rings with nitro groups of the adjacent layers.     

Synthesis and structure of zinc iodide complex with thiocarbamide, [Zn(CH4N2S)2I2]

A complex compound of zinc iodide with thiocarbamide [Zn(CH₄N₂S)₂I₂] is obtained and its structure is studied by X-ray diffraction. Crystals are monoclinic, a = 10.494(2) Å, b = 7.473(2) Å, c = 14.871(4) Å, β = 91.354(18)°, V = 1165.9(5) ų, space group P2₁/c, Z = 4. The structural unit of the crystal is molecular complex [Zn(CH₄N₂S)₂I₂], in which the zinc atom is coordinated by sulfur atoms of two thiocarbamide molecules and two iodine atoms.     

Isomerization of 2-seleno-1,3,2-diazaphospholidine derivatives

For the first time the isomerization of 1,3,2-diazaphospholidine-2-selenide derivatives in refluxing benzene in the presence of trace water was observed, and the structure of isomerized product was determined by X-ray diffraction, IR, ¹H NMR, ³¹P NMR, and elemental analysis. The mechanism of isomerization was also proposed. The isomerized phosphoroheterocycle (C₂₆H₃₈N₃O₅PSe, Mr = 582.52) is orthorhombic with space group Pbca, a = 17.1010(9) Å, b = 16.6404(9) Å, c = 20.7517(11) Å, V = 5905.3(5) ų, Z = 8, Dr = 1.310 g/cm³, λ = 0.71073 Å, μ (Mo Kα) = 1.363 mm^?1, F(000) = 2432. The structure was refined to R1 = 0.0482, wR2 = 0.1204 for 5214 unique reflections with I > 2σ(I). Intramolecular and intermolecular hydrogen bonds are observed in the crystal packing.     

Structure determination of 3β-acetoxy-cholest-5-ene-7-one—A steroid

The crystal structure of 3β-acetoxy-cholest-5-ene-7-one (C₂₉H₄₆O₃) has been determined by X-ray diffraction methods. The compound crystallizes in the monoclinic crystal system (space group P2₁) with the unit cell parameters a = 9.632(1) Å, b = 12.280(1) Å, c = 23.099(2) Å, β = 99.52(1)°, and Z = 4. The structure has been solved by direct methods and refined to an R-value of 0.065 for 3927 observed reflections [F ₀ > 4σ(F ₀)]. Two crystallographically independent molecules (I and II) in the asymmetric unit have been observed. In both molecules, rings A and C of the steroid nucleus exist in a chair conformation. Ring B of molecule I adopts a 5α,6β half-chair conformation, and ring B of molecule II shows a 6α sofa conformation. Ring D adopts a 13α,14β half-chair conformation in molecule I and a 13α,14β half-chair conformation in molecule II. The crystal structure is stabilized by the intramolecular and intermolecular C-H?O interactions.     

Crystal and molecular structures of 4-N-morpholino-7-phenyl 1,3-isobenzofurandione

The crystal and molecular structures of 4-N-morpholino-7-phenyl-1,3-isobenzofurandione have been determined by X-ray diffraction analysis (Nicolet R3m automated diffractometer, MoK _α radiation, graphite monochromator, θ/2θ scan mode). It is found that the compound crystallizes in the orthorhombic system, space group Pbca. The unit cell parameters are as follows: a = 7.773(2) Å, b = 14.652(3) Å, c = 25.614(5) Å, and Z = 8. The structure is solved by the direct method and refined to R1 = 0.0504 [I > 2σ(I)]. The conformational and geometric characteristics of the studied compound and the molecular packing in the crystal are discussed.     

Synthesis and structure of oxovanadium(IV) complexes [VO(<Emphasis Type="Italic">Acac</Emphasis>)<Subscript>2</Subscript>] and [VO(<Emphasis Type="Italic">Sal</Emphasis>: <Emphasis Type="Italic">L</Emphasis>-alanine)(H<Subscript>2</Subscript>O)]

Bis(acetylacetonato)oxovanadium C₁₀H₁₄O₅V (I) and (S)-[2-(N-salicylidene)aminopropionate]oxovanadium monohydrate C₁₀H₉NO₅V (II) are synthesized. The crystal structures of compounds I and II are determined using single-crystal X-ray diffraction. Crystals of compound I are triclinic, a = 7.4997(19) Å, b = 8.2015(15) Å, c = 11.339(3) Å, α = 91.37(2)°, β = 110.36(2)°, γ = 113.33(2)°, Z = 2, and space group \(P\bar 1\). Crystals of compound II are monoclinic, a = 8.5106(16) Å, b = 7.373(2) Å, c = 9.1941(16) Å, β = 101.88(1)°, Z = 2, and space group P2₁. The structures of compounds I and II are solved by direct methods and refined to R₁ = 0.0382 and 0.0386, respectively. The oxovanadium complexes synthesized are investigated by vibrational spectroscopy.     

Crystal structures of molecular complexes of 18-crown-6 with 2-aminobenzoic and 5-amino-1-benzyl-1,2,3-triazole-4-carboxylic acid hydrazides

The crystal structures of two host-guest molecular complexes of 18-crown-6 with 2-aminobenzoic acid hydrazide monohydrate (the ratio host: guest: H₂O = 1: 2: 2) (complex I) and 5-amino-1-benzyl-1,2,3-triazole-4-carboxylic acid hydrazide (the host: guest ratio = 1: 2) (complex II) are determined by X-ray diffraction analysis. Crystals I are monoclinic, a = 8.468(2) Å, b = 17.378(3) Å, c = 10.517(2) Å, β = 96.88(3)°, space group P2₁/n, and R = 0.0393 for 6692 reflections. Crystals II are orthorhombic, a = 18.489(1) Å, b = 10.192(3) Å, c = 20.412(2) Å, space group Pbca, and R = 0.0540 for 3513 reflections. In both complexes, the centrosymmetric 18-crown-6 and guest molecules are joined together through the NH?O (crown) hydrogen bonds, which involve all the hydrogen atoms of the hydrazine group. The NH?O=C intramolecular hydrogen bond is observed in the guest molecule. In structure I, the water molecule serves as a bridge between the guest molecules related by the glide-reflection plane and combines the guest-host-guest complexes into layers. In structure II, the guest molecules are linked into chains through hydrogen bonds of the NH?O=C type; in turn, the chains composed of guest molecules and the crown ether molecules bonded to these chains form a layered structure.     

Crystal and molecular structure of the membrane-active antibiotic enniatin C

The crystal structure of the cyclic hexadepsipeptide antibiotic enniatin C c[-(L-MeLeu-D-Hyi)₃-], C₃₄H₅₉N₃O₉, was established by X-ray structure analysis (sp. gr. P2₁, a = 20.205(5) Å, b = 8.702(2) Å, c = 25.587(6) Å, γ = 97.0(5)°, V = 4465.3(18) ų, Z = 4, R = 0.089 for 3601 reflections with I > 2σ(I)). The unit cell contains two independent molecules of enniatin C, one ethanol molecule disordered over two positions, and approximately two water molecules occupying four positions and forming hydrogen bonds with each other. The independent antibiotic molecules adopt virtually identical conformations similar to those observed in the structures of enniatin B and its Na,Ni-complex. These conformations are characterized by alternating upward and downward orientations of the carbonyl groups and pseudoequatorial orientations of side radicals. The Leu residues have stretched conformations. The N-methylamide groups of the independent antibiotic molecules face each other, whereas the molecules are displaced by approximately 8.4 Å with respect to each other along the mean planes of the rings.     

Low-temperature study of the molecular and crystal structures of 2-(2′-tosylamino-5′-nitrophenyl)-4H-3,1-benzoxazin-4-one, an organic luminophore

The crystal structure of 2-(2′-tosylamino-5′-nitrophenyl)-4H-3,1-benzoxazin-4-one (I) is studied by X-ray diffraction at 100 K (C₂₁H₁₅N₃O₆S, a = 20.899(2) Å, b = 10.948(1) Å, c = 8.260(1) Å, V = 1889.3(1) ų, Z = 4, and space group Pbn2₁). The compound exhibits an anomalous Stokes shift. Upon cooling, the oxazineaminophenyl fragment of compound I acquires a quinoid structure and the linear parameters of the intramolecular N-H?N hydrogen bond increase (the distance between the heterocyclic nitrogen atom and the hydrogen atom of the tosylamino group becomes 1.92 Å). The complete optimization of the geometry of molecules in compound I and unsubstituted 2-(2′-tosylaminophenyl)-4H-3,1-benzoxazin-4-one in the ground singlet electronic state is performed by the semiempirical method with the MOPAC program. It is shown that the oxygen atoms in the sulfo group of molecule I are nonequivalent, because one of them is involved in the intermolecular C-H?O hydrogen bond.     

Molecular and crystal structures of 8,9-dimethoxy-5′,5′-dimethyl-1,2,3,5,6,10b-hexahydropyrrolo[2,1-a]isoquinoline-1-spiro-2′-cyclohexane-3,1′,3′-trione

The crystal and molecular structures of 8,9-dimethoxy-5′,5′-dimethyl-1,2,3,5,6,10b-hexahydropyr-rolo[2,1-a]isoquinoline-1-spiro-2′-cyclohexane-3,1′,3′-trione are studied by X-ray diffraction. The unit cell parameters are a = 9.478(2) Å, b = 9.844(3) Å, c = 11.663(3) Å, α = 111.17(2)°, β = 99.56(2)°, γ = 105.82(2)°, Z = 2, and space group P1ˉ. The structure is solved by the direct method and refined to R = 0.0411 [I > 4σ(I)]. Conformational and geometric characteristics of the compound studied and the molecular packing in the crystal are discussed. __________ Translated from Kristallografiya, Vol. 45, No. 2, 2000, pp. 286–288. Original Russian Text Copyright ? 2000 by Lyakhov, Ivashkevich, Govorova, Mikhal’chuk.     

The structures of N-(t-butoxycarbonyl)-3-methylbenz[f]indole and N-benzenesulfonyl-4-bromo-3-methylbenz[f]indole

N-(t-butoxycarbonyl)-3-methylbenz[f]indole,1, C₁₈H₁₉NO₂, crystallizes in orthorhombic space groupPna2₁ witha=6.0338(2),b=24.839(4),c=10.2481(7) Å,V=1535.9(3) ų,Z=4. The structure was refined toR=0.051 for 2007 observed reflections. The benz[f]indole ring system is nearly planar, exhibiting mean deviation of 0.048 Å. The ester plane of thet-butoxycarbonyl substituent is nearly coplanar with the benz[f]indole ring system, forming a C?N?C=O torsion angle with magnitude 10.6(5)⁰.N-benzenesulfonyl-4-bromo-3-methyl-benz[f]indole,2, C₁₉H₁₄BrNO₂S crystallizes in triclinic space groupP?1 witha=8.1400(5),b=10.0587(8),c=10.8863(7) Å, α=89.927(7), β=110.495(5), γ=96.846(6)⁰,V=828.2(3) ų,Z=2. The structure was refined toR=0.050 for 2653 observed reflections. The benz[f]indole ring system is nearly planar, with mean deviation 0.016 Å, and forms a dihedral angle of 80.93(9)⁰ with the phenyl plane.     

Crystal and molecular structure of 11,12-dihydroxydrim-8(9)-en-7-one

The crystal structure of 11,12-dihydroxydrim-8(9)-en-7-one was determined by X-ray diffraction. The unit cell parameters are a = 7.534(3), b = 12.192(5), c = 8.067(4) Å, β = 98.01(3) Å, space group P2₁, and Z = 2 for C₁₅H₂₄O_3. The structure was solved by direct methods and refined in the anisotropic approximation to R = 0.051 and R _w = 0.113. The intramolecular O-H?O hydrogen bond [2.892(6) Å] between the hydroxy groups closes an additional seven-membered H-ring in the molecule. In the crystal, the intermolecular O-H?O hydrogen bond [2.857(4) Å] between the hydroxyl group and the carbonyl oxygen atom links the molecules related by the translation along the c-axis to form infinite chains.     

Crystal structure of (2,2′-bipyrimidine)-dinitratopalladium(II) acetone solvate

(2,2′-bipyrimidine)dinitratopalladium(II) forms a triclinic crystal in space groupP?1 witha=7.605(5) Å,b=8.791(4) Å,c=12.632(5) Å, α=85.11(3)⁰, β=78.79(4)⁰, γ=77.45(4)⁰,V=807.7(7) ų, andZ=2. The Pd atom exhibits square planar coordination geometry with mean Pd?O=2.206(7) Å, Pd?N=1.990(5) Å, O?Pd?O=92.0(2)⁰, and N?Pd?N=81.0(2)⁰. The complexes associate across an inversion center with Pd...Pd=3.190(2) Å. The bipyrimidine ligand is bowed with a 5.9(2)⁰ dihedral angle between the C₄N₂ rings. The nitrate ions are on the same side of the N₂O₂ donor atoms plane and make 60.4(2)⁰ and 66.6(2)⁰ dihedral angles with that plane.     

Crystal structures of two platinum-bipyrimidine complexes: Pt(bpm)Cl2·dmf and Pt(bpm)(dmso)(SO4)·H2O

Red Pt(bpm)Cl₂·dmf forms a stacked structure which has Pt…Pt separations of 3.423(2) A and 3.447(2) Å with Pt…Pt…Pt angles of 155.39(3)^o. The unit cell isP-1, witha=6.712(4) A,b=10.0765(6) Å,c=11.551(3) Å, α=106.732(12)^o, β=103.65(4)^o, γ=90.46(3)^o, andZ=2. The structure refined to anR(F) of 0.046 using 181 parameter and 2165 reflections withI>1σ(I). The yellow complex Pt(bpm)(dmso)(SO₄)·H₂O does not stack in the solid state: the shortest Pt…Pt separation is 4.638(2) Å. The unit cell is alsoP-1, witha=8.060(3) A,b=9.560(3) A,c=9.7534(18) Å, α=90.62(2)^o, β=99.43(3)^o, γ=90.66(3)^o, andZ=2. The structure refined to anR(F) of 0.039 using 208 parameters and 3689 reflections withI>1σ(l).     

Clathrate formation of gossypol: The structure of the complex of gossypol with tropolone

The clathrate of gossypol with tropolone is prepared for the first time and studied by X-ray diffraction. The structure is determined and refined using 7307 reflections (Siemens SMART/CCD diffractometer). The crystals are monoclinic, C₃₀H₃₀O₈ · 2C₇H₆O₂, a = 35.5892(1) Å, b = 12.8893(2) Å, c = 18.5910(2) Å, β = 118.54(3)°, Z = 8, space group C2/c, and R = 0.058. Each gossypol molecule is linked to two tropolone molecules through hydrogen bonds. The host (gossypol) and guest (tropolone) molecules form separate bilayers that are parallel to the bc plane and alternate along the a-axis.