Mathematical simulation and X-ray diffraction investigation of the crystal structure of (R)-[(R)-o-(1-N,N-dimethylaminoethyl)phenyl]-2,5-dimethoxyphenyl(phenyl)methanol

The crystal structure of (R)-[(R)-o-(1-N,N-dimethylaminoethyl)phenyl]-2,5-dimethoxyphenyl(phenyl)methanol is mathematically simulated by the discrete modeling of molecular packings. A complete set of possible model variants is analyzed using the proposed algorithm with the aim of choosing the appropriate models that can serve as starting models for solving and refining the crystal structure from X-ray diffraction data. The crystals of the compound under investigation are monoclinic, a = 9.268(2) Å, b = 8.802(2) Å, c = 13.176(3) Å, β = 94.01(3)°, space group P2₁, and Z = 2. The structure is solved for a starting model calculated using the discrete modeling method and refined by the full-matrix least-squares procedure to R(F) = 0.037 and ωR(F ²) = 0.097.     

Crystal structure of (Z)-1-(sec-butyl)-3-(4-dimethylaminophenyl)-2-(1H-1,2,4-triazol-1-yl)propen-2-one

The crystal structure of the title compound is determined by X-ray diffraction studies. The structure is solved by the direct method. The experimental data are obtained on a DAR-UMB diffractometer by the θ-θ/2θ scan technique using MoK _α radiation. The crystal is monoclinic, a = 17.913(3) Å, b = 17.239(3) Å, c = 5.501(5) Å, γ = 74.4(3)°, space group P2₁/a, Z = 4 for C₁₇H₂₂N₄O, and ρ_calcd = 1.211 g/cm³. The molecule consists of the phenyl and triazole rings and the dimethylamino, carbonyl, and isopropyl groups attached to the rings. The dihedral angle between the rings is 67.4°. The carbonyl oxygen atom and the triazole ring are in the trans position relative to each other. The N-C-C-O torsion angle is 172.8°. The molecule is in the Z isomeric form.     

Molecular and crystal structures of 1R,4R-cis-2-(4-phenylbenzylidene)-n-menthan-3-one

The molecular and crystal structures of chiral 1R,4R-cis-2-(4-phenylbenzylidene)-n-menthan-3-one (I) have been determined by X-ray diffraction analysis. Crystals I are monoclinic, a = 6.755(3) Å, b = 9.860(3) Å, c = 14.103(6) Å, β = 98.95(1)°, space group P2₁, Z = 2, and R = 0.035 for 1031 reflections. A chair conformation of the cyclohexanone ring in the molecule is substantially distorted toward a “half-chair” conformation. The enone and benzylidene groupings are virtually planar (the torsion angles are equal to 13.0° and 4.9°, respectively). The benzene rings of the biphenyl fragment are rotated with respect to each other through an angle of 40°–43°. Among the compounds under consideration, the distortion of bond angles at the sp ² carbon atoms of the benzylidene grouping as a criterion for the steric stress of molecules is maximum in structure I.     

X-ray structure analysis of 3β-hydroxy-4-(1,4-oxazin-4-yl)-androstane (C31H54NO2)

The crystal structure of 3β-hydroxy-4-(1,4-oxazin-4-yl)-androstane (C₃₁H₅₄NO₂) has been determined by X-ray crystallographic techniques. The compound crystallizes in the orthorhombic space group P2₁2₁2 with the following unit-cell parameters: a = 7.124(1) Å, b = 10.127(1) Å, c = 40.660(1) Å, V = 2933.4(1) ų, and Z = 4. The structure has been solved by direct methods and refined to an R factor of 0.067. Three six-membered rings, A, C, and E, exist in the chair conformation, while the ring B adopts a distorted half-chair conformation. The five-membered ring, D, has a distorted envelope conformation. The crystal structure is stabilized by strong intermolecular O-H...O hydrogen bonds.     

Molecular and crystal structures of 1R,4R-cis-2-(4-hydroxybenzylidene)-p-menthan-3-one

The molecular and crystal structures of chiral 1R, 4R-cis-2-(4-hydroxybenzylidene)-p-menthan-3-one (I) are determined by X-ray diffraction analysis. Single crystals of I are orthorhombic, a = 8.997(2) Å, b = 11.314(2) Å, c = 14.847(3) Å, V = 1511.3(5) ų, Z = 4, and space group P2₁2₁2₁. The cyclohexanone ring in molecules of compound I has a chair-type conformation with the axial methyl and equatorial isopropyl groups. The enone and benzylidene groupings are nonplanar. The considerable distortion of bond angles at the sp ² carbon atoms of the benzylidene grouping and the puckering parameters of the cyclohexanone ring in the structure of I are close to those observed for the previously studied compound with the p-methoxy substituent. In the crystal, molecules I are linked by very short intermolecular hydrogen bonds .     

Crystal structure of the molecular complex of 3-[1-(4-nitrophenyl)-3-oxobutyl]-4-hydroxychromen-2-one with ethanol

The crystal structure of 2,3H-2-methyl-4-(4-nitrophenyl)-5-oxobenzopyrano[3,4-e]dihydropyran-2-ol is investigated using X-ray diffraction. The unit cell contains an ethanol molecule that forms hydrogen bonds with O-H and C-O groups of two molecules of the main compound and acts as a proton donor and a proton acceptor in these hydrogen bonds. Owing to these interactions, infinite chains are formed in the crystal. The crystallographic data for the structure of C₁₉H₁₅NO₆·C₂H₅OH (M = 399.39) are as follows: the crystals are triclinic, space group P1, a = 5.5340(3) Å, b = 8.0109(4) Å, c = 11.0112(5) Å, α = 88.773(2)°, β = 84.788(2)°, γ = 79.958(2)°, and Z = 1.     

Crystal and molecular structure of the 1: 1 molecular complex between 1e-benzyl-3e-hydroxy-3a-methyl-4a-tosylhydrazo-6e-phenylpiperidine-4e-carbonitrile and diethyl ether

The crystal and molecular structure of the 1: 1 complex between 1e-benzyl-3e-hydroxy-3a-methyl-4a-tosylhydrazo-6e-phenylpiperidine-4e-carbonitrile and diethyl ether is studied by X-ray diffraction (Nicolet R3m diffractometer, MoK _α radiation, ? /2? scan mode). The crystals are triclinic, space group $P\bar 1$ , a = 10.547(4) Å, b = 12.382(5) Å, c = 13.487(6) Å, α = 114.79(3)°, β = 97.28(3)°, γ = 98.40(3)°, and Z = 2. The structure is solved by the direct method and refined to R = 0.0605. Molecular structures and hydrogen bonds are discussed.     

Crystal structure of 1-methyl-3-([2,2-dimethyl-4,6-dioxo-1,3-dioxane-5-ylidene]methyl)urea

The crystal structure of 1-Methyl-3-([2,2-dimethyl-4,6-dioxo-1,3-dioxane-5-ylidene]methyl)urea (C₉H₁₂N₂O₅) has been determined by single crystal X-ray diffraction analysis. The crystals are monoclinic, a = 5.3179(2), b = 18.6394(6), c =10.8124(3) Å, β = 100.015(2)°, Z = 4, sp. gr. P2₁/c, R = 0.0381 for 2537 reflections with I > 2σ(I). Except for C(CH₃)₂ group, the molecule is planar. The structure is stabilized by inter- and intramolecular N-H...O hydrogen bonds and weak C-H...O interactions.     

Synthesis and crystal structure of bis[2-[N-(2-chlorophenyl)formimidayl]-1-naphtholato]-(6Cl)copper(II)

The title compound, bis[2-[N-(2-chlorophenyl)formimidayl]-1-naphtholato]-(6Cl) copper(II), [Cu(C₁₇H₁₁NOCl)₂] (1) was synthesized and its crystal structure was determined. The Compound 1 is monoclinic, space group P2 ₁/c with a = 9.146(3) Å, b = 18.724(3) Å, c = 16.230(2) Å, β = 96.46(1)°, V = 2761.8(11) ų, Z = 4, D _c = 1.503 g cm^?3, μ(Mo Kα) = 1.020 mm^?1, R = 0.0606 for 2361 reflections [I > 2σ(I)]. In the title compound, the Cu atom is coordinated by an N₂O₂ donor set from the imine-phenol ligand in a slightly distorted square planar coordination geometry, with the two phenolate O atoms being deprotonated. The Cu–O bond lengths are 1.878(4) and 1.889(4) Å, the Cu–N bond lengths are 1.980(5) and 1.985(5) Å. The angles O1–Cu–N1 and O2–Cu–N2 are 90.96(19) and 90.72(19)°, respectively.     

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.     

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.     

Molecular and crystal structures of 1R,4S-2-(4-carbomethoxy)benzylidene-n-menthan-3-one

The molecular and crystal structures of chiral 1R,4S-2-(4-carbomethoxy)benzylidene-n-menthan-3-one (I) are determined by X-ray diffraction analysis. Crystals I are orthorhombic; at 20°C: a = 11.961(3) Å, b = 26.453(8) Å, c = 5.400(2) Å, space group P2₁2₁2₁, and Z = 4 (C₁₉H₂₅O₃). In molecule I, the cyclohexanone ring with the axial methyl and isopropyl substituents adopts a chair conformation. It is found that the enone and arylidene fragments of compound I have a substantially nonplanar structure. The shortened intramolecular contacts between atoms of the arylidene grouping and the α fragment of the cyclohexanone ring and their associated distortions of bond angles at the sp ² carbon atoms are the common structural features of 2-arylidene-n-menthan-3-ones irrespective of the stereochemical configuration of the C(4) chiral center.     

Molecular and crystal structures of 2-amino-5-benzoyl-4-(2-nitrophenyl)-3-cyano-4,5-dihydrothiophene

The crystal structure of 2-amino-5-benzoyl-4-(2-nitrophenyl)-3-cyano-4,5-dihydrothiophene is determined by X-ray diffraction analysis. The unit cell parameters are as follows: a = 10.878(2) Å, b = 12.890(3) Å, c = 13.539(4) Å, α = 108.15(2)°, β = 99.26(2)°, γ = 107.13(2)°, V = 1656(2) ų, d _calcd = 1.410 g/cm³, Z = 4, and space group P1ˉ. The molecules occupy two systems of independent positions in the crystal. Similar to the compounds studied earlier in this series, the o-nitrophenyl substituent has a synperiplanar orientation relative to the hydrogen atom at the C(4) atom of the heterocycle. __________ Translated from Kristallografiya, Vol. 45, No. 2, 2000, pp. 282–285. Original Russian Text Copyright ? 2000 by Nesterov, Kuleshova, Samet, Shestopalov.     

Synthesis,spectroscopic characterization and crystal structure of 5-bromo-1-(2-cyano-pyridin-4-yl)-1H-indazole-3-carboxylic acid diethylamide

The title compound 5-bromo-1-(2-cyano-pyridin-4-yl)-1H-indazole-3-carboxylic acid diethylamide, C₁₈H₁₆BrN₅O, is prepared from 5-bromoindazole-3-carboxylic acid methylester. N ¹-arylation is carried out with 4-chloro-2-cyanopyridine and the resulting product is converted to diethylamide by reacting with thionyl chloride and diethylamine. The structure is identified from its FT-IR, ¹H NMR, ¹³C NMR spectroscopy, elemental analysis data and unambiguously confirmed by single crystal X-ray diffraction studies. There are two symmetry independent molecules in the asymmetric unit with no significant differences in bond lengths and angles. The title compound crystallizes in the triclinic system, space group \(P\bar 1\) , with a = 11.2330(2); b = 11.6130(2); c = 15.4710(3) Å, α = 92.515(1)°; β = 109.956(1)°; γ = 107.199(1)°; V = 1788.45(6)ų and z = 4. An intramolecular C-H…N hydrogen bond forms an S(6) ring motif in one of the unique molecules. In the crystal, two molecules are linked about a center of inversion by C-H…O hydrogen bonded dimers generating an R ₂ ² (16) ring motif. The crystal packing is stabilized by C-H…N, C-H…O hydrogen bonds and π…π stacking interactions.     

X-ray diffraction, spectroscopic and DFT studies of 1-(4-bromophenyl)-3,5-diphenylformazan

The crystal structure of 1-(4-bromophenyl)-3,5-diphenylformazan was determined by X-ray single crystal diffraction technique. The crystals are orthorhombic, a = 23.0788(9), b = 7.9606(3), c = 18.6340(12) Å, Z = 8, sp. gr. Pbca, R ₁ = 0.074. The structure was also examined using the density-functional theory. Its structure stability, and frontier molecular orbital components were discussed and the results were compared with X-ray and spectral results. The maximum absorbtion peaks of the UV-vis spectrum of the compound have been calculated using the time-dependent density-functional theory. It was found a good agreement between the calculated and experimental maximum absorption wavelength.     

X-ray mapping in heterocyclic design: VIII. Synthesis and X-ray diffraction study of dimethyl 3-(p-chlorobenzoyl)-5-chloroindolizine-1,2-dicarboxylate and the product of its cyclization 1,2-bis(carbomethoxy)-6-chloro-3H-isoquinolino[1,2,3-d,c]indolizine-3-one

Dimethyl 3-(p-chlorobenzoyl)-5-chloroindolizine-1,2-dicarboxylate, C₁₉H₁₃Cl₂NO₅, (2) and the product of its cyclization 1,2-bis(carbomethoxy)-6-chloro-3H-isoquinolino[1,2,3-d,c]indolizine-3-one, C₁₉H₁₂ClNO₅, (3) are synthesized, and their molecular and crystal structures are determined by the single-crystal X-ray diffraction technique. Crystals 2 are monoclinic, a = 9.627(3) Å, b = 6.646(2) Å, c = 28.500(9) Å, β = 98.72(2)°, Z = 4, and space group P2₁/c. Crystals 3 are monoclinic, a = 7.048(4) Å, b = 10.582(4) Å, c = 21.760(7) Å, β = 97.23(4)°, Z = 4, and space group P2₁/c. The structures are solved by the direct method and refined in the anisotropic approximation by the full-matrix least-squares procedure to R = 0.0504 and 0.0510 for 2 and 3, respectively. In both structures, the intramolecular and intermolecular contacts involving the C, H, and O atoms are observed.     

Crystal and molecular structure of 5,6-diphenyl-2-(α-formyl-benzyliden)-2H-thiopyranes

The crystal and molecular structure of the title compound has been determined by X-ray diffraction techniques. It crystallizes in the monoclinic space group P2₁/n with cell parameters a = 6.101(3) Å, b = 14.365(6) Å, c = 21.888(7) Å, β = 90.20(4)°, Z = 4. The structure was solved by direct methods and refined by least-squares calculations to an R value of 0.074. The molecule exists in solid state in the Z configuration. The very short intramolecular O S distance of 2.654(8) Å can be explained with polar interactions between the O and S atoms.     

Crystal structure of 3-amino-5-acetyl-4,7-dihydro-6-methyl-4-(2-nitrophenyl)-2-cyanothieno[2,3-b]-pyridine and specific features of its molecular packing in crystal

The molecular and crystal structures of 3-amino-5-acetyl-4,7-dihydro-6-methyl-4-(2-nitrophenyl)-2-cyanothieno[2,3-b]-pyridine is determined by X-ray diffraction. The unit-cell parameters are as follows: a = 14.68(1) Å, b = 8.704(5) Å, c = 25.36(1) Å, V = 3241(6) ų, d _calcd = 1.453 g/cm³, Z = 8(1,1), and space group Pna2₁. Theo-nitrophenyl substituent is synperiplanar relative to the hydrogen atom at the C(4) atom of the heterocycle. Two crystallographically independent reference molecules A and B in the structure can be considered a pair of the enantiomers related by an approximate noncrystallographic center of inversion. The degree of approximation of this pseudocenter is discussed. It is shown that the structure can be described as a combination of two systems of translationally equal layers. The pseudosymmetry of the crystal structure and the possibility of forming a similar molecular packing with a higher crystallographic symmetry are considered.     

Molecular and crystal structures of chiral 2-(4-phenylbenzylidene)-3-methyl-6-isopropylcyclohexanone 6-bromo derivative

The molecular and crystal structures of chiral 3R, 6S-2-(4-phenylbenzylidene)-3-methyl-6-bromo-6-isopropylcyclohexanone C₂₃H₂₅BrO (Ia) are determined by X-ray diffraction. Crystals Ia are monoclinic, a = 11.005(4) Å, b = 12.229(4) Å, c = 14.376(5) Å, β = 91.37(1)°, Z = 4, and space group P2₁. The geometric parameters of two crystallographically independent molecules are close to each other in magnitude. The cyclohexanone ring adopts a chair-type conformation with an equatorial isopropyl substituent and an axial orientation of the methyl group and the C-Br bond. The 3,6-alkyl groups are in the cis position with respect to the cyclohexanone ring. It is demonstrated that, in the series of 6-bromo substituted compounds, as in their analogues unsubstituted for bromine in the 6-position, the maximum flattening of the cinnamoyl fragment O=C-C=C-C₆H₄ X is observed in the structure with X = C₆H₅.     

Crystal structure analysis of 4-phenylquinolin-2-(1<Emphasis Type="Italic">H</Emphasis>)-one

The crystal structure of 4-phenylquinolin-2-(1H)-one (C₁₅H₁₁NO) is determined by X-ray diffraction. The compound crystallizes in the orthorhombic crystal system (space group Pbca) with the unit cell parameters a = 7.382(2) Å, b = 21.795(3) Å, c = 14.066(5) Å, and Z = 8. The structure is solved by direct methods and refined to an R-value of 0.0398 for 1360 observed reflections [F₀ > 4σ (F₀)]. The quinoline moiety and the substituted phenyl ring are nearly planar. The dihedral angle between these two moieties is 64.65(6)°. The crystal structure is stabilized by two intermolecular N-H?O and C-H?O interactions.