X-ray mapping in heterocyclic design: 16. X-ray diffraction study of 1-(4-chlorophenacyl)-4-methyl-1,5,6,7-tetrahydro-2<Emphasis Type="Italic">H</Emphasis>-cyclopenta[<Emphasis Type="Italic">b</Emphasis>]pyridin-2-one

The structure of 1-(4-chlorophenacyl)-4-methyl-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one is studied using single-crystal X-ray diffraction. The structure (a = 37.006(8) Å, b = 8.967(3) Å, c = 27.911(3) Å, β = 96.52(2)°, Z = 24, space group P2₁/c) is solved by direct methods and refined to R₁ = 0.0608 and wR₂ = 0.1170. Six crystallographically independent molecules differ in the dihedral angle between the phenyl and heterocycle planes. The formation of Cl?Cl aggregates is discussed.     

X-ray mapping in heterocyclic design: IV. Crystal structure determination of 3-(p-nitrobenzoyl)-2-oxooxazolo[3,2-a]pyridine from powder diffraction data

The structure of 3-(p-nitrobenzoyl)-2-oxooxazolo[3,2-a]pyridine is determined by the powder diffraction technique. The crystals are monoclinic, a = 13.642(2) Å, b = 22.278(3) Å, c = 3.917(1) Å, β = 90.63(2)°, Z = 4, and space group P2₁/n. The structure is solved by a modified Monte Carlo method and refined by the Reitveld method. The six-membered heterocycle is characterized by the alternation of partially single and partially double bonds. The system of two conjugated heterocycles is planar and forms a dihedral angle of 46.1(1)° with the plane of the phenyl ring. The nitro group is virtually coplanar with the phenyl fragment. An extensive system of intramolecular and intermolecular contacts involving hydrogen, oxygen, and nitrogen atoms is observed in the crystal.     

Crystal structure and spectral characteristics of 2-methyl-3-chloro-9-hydroxypyrido[1,2-<Emphasis Type="Italic">a</Emphasis>]pyrimidin-4-one and bis(2-methyl-3-chloro-9-hydroxypyrido[1,2-<Emphasis Type="Italic">a</Emphasis>]pyrimidin-4-onium) perchlorate

2-Methyl-3-chloro-9-hydroxypyrido[1,2-a]pyrimidin-4-one (I) and bis(2-methyl-3-chloro-9-hydroxypyrido[1,2-a]pyrimidin-4-onium) perchlorate (Ia) are synthesized and studied by X-ray diffraction and IR spectroscopy. It is shown that compound I exists in the molecular form in crystals and in the zwitterion form in solutions. The structural units of compound Ia are partially protonated centrosymmetric dimeric cations and perchlorate anions. The dimeric cation involves two molecules I in the zwitterion form. These molecules are linked together by a strong symmetric hydrogen bond formed with the participation of a proton located at the inversion center. The structures of a series of pyrido[1,2-a]pyrimidines are investigated and compared. It is demonstrated that the tautomeric equilibrium revealed in solutions of compounds of this class depends on the solvent type and pH of the medium.     

X-ray mapping in heterocyclic design: XV. Tricyclic heterocycles based on 2-oxo-2,5,6,7-tetrahydro-1<Emphasis Type="Italic">H</Emphasis>-cyclopenta[<Emphasis Type="Italic">b</Emphasis>]pyridine-3-carbonitrile

The structures of five compounds are studied using single-crystal X-ray diffraction: 2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 15.641(8) Å, b = 9.373(5) Å, c = 7.387(4) Å, β = 92.91(5)°, Z = 4, space group P2₁/c]; 1-[2-(4-chlorophenyl)-2-oxoethyl]-2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 4.728(4) Å, b = 28.035(11) Å, c = 11.184(3) Å, Z = 4, space group P2₁2₁2₁]; 2-[2-(4-chlorophenyl)-2-oxoethoxy]-6,7-dihydro-5H-cyclopenta[b]pyridine-3-carbonitrile [a = 10.1202(13) Å, b = 11.2484(18) Å, c = 13.4323(19) Å, β = 102.05(1)°, Z = 4, space group P2₁/c]; 2-(4-chlorophenyl)-3a, 6,7,8-tetrahydrocyclopenta[e][1.3]oxazolo[3.2-a]pyridine-4-carboxamide perchlorate [a = 7.702(2) Å, b = 9.599(3) Å, c = 23.798(5) Å, β = 93.44(2)°, Z = 4, space group P2₁/c]; and (3-amino-6,7-dihydro-5H-cyclopenta[b]furo[3.2-e]pyridin-2-yl)(4-chlorophenyl)methanone [a = 7.3273(2) Å, b = 13.390(3) Å, c = 28.792(8) Å, Z = 8, space group Pbca]. The structures are solved using direct methods and refined by the full-matrix least-squares procedure in the anisotropic approximation to R = 0.0580, 0.0724, 0.0469, 0.0477, and 0.0418, respectively.     

Electron diffraction study of 1<Emphasis Type="Italic">M</Emphasis> illites with interstratified <Emphasis Type="Italic">trans</Emphasis>- and <Emphasis Type="Italic">cis</Emphasis>-vacant 2 : 1 layers

Illites from the volcanogenic Zn-Au-Ag sulfide deposit Galkinskoe (Northern Urals) have been investigated using oblique-texture electron diffraction patterns in combination with the simulation of diffraction effects. Along with single-phase tv/cv1M illites, the structures of which are formed by statistically interstratified dioctahedral 2: 1 layers with vacant trans- or cis-octahedra, illites in the form of a mixture of two interstratified tv/cv1M phases, with the dominance of tv- or cv layers, are identified. It is shown that in the latter case the diffraction pattern can also be interpreted within the single-phase tv/cv model, provided that the tv- and cv layers are distributed with some tendency to segregate. The structural features indicating the preference of the two-phase model are analyzed.     

Experimental and Semi-Empirical and DFT Calculational Studies on (<Emphasis Type="Italic">E</Emphasis>)-2-[(2,4-Dichlorophenylimino) methyl]-<Emphasis Type="Italic">p</Emphasis>-cresol

Abstract  

The molecular and crystal structure of the title compound, C₁₄H₁₁Cl₂NO, has been determined by X-ray single crystal diffraction technique. The compound crystallizes in the orthorhombic, space group Pbca with unit cell dimensions a = 7.5537(10) ?, b = 11.5518(13) ?, c = 29.760(4) ?, M _r  = 280.14, V = 2596.8(6) ?³, Z = 8, R ₁ = 0.065 and wR ₂ = 0.191. The title compound exists in the enol–imine tautomeric form with a strong intramolecular O–H···N hydrogen bond. The dihedral angle between the two benzene rings is 37.66(15)°. The asymmetric unit in the crystal structure contains only one neutral molecule. Calculational studies were performed by using AM1, PM3, PM6 semi-empirical and DFT methods. Geometry optimizations of compound have been carried out by using three semi-empirical methods and DFT method and bond lengths, bond and torsion angles of title compound have been determined. Dipole moments (Debye) and the energy parameters of compound (kcal/mol) were calculated by using above mentioned calculation methods. Atomic charge distribution has been obtained from AM1, PM3, PM6 and DFT. In order to determine conformational flexibility on the molecule, molecular energy profile of the title compound was obtained with respect to the selected torsion angle T(N1–C7–C1–C2), which is varied from −180° to +180° in every 10 via PM3 semi-empirical method.     

Synthesis and structure of 7-methyl-5-phenyl-1<Emphasis Type="Italic">H</Emphasis>-pyrazolo[4,3-<Emphasis Type="Italic">e</Emphasis>]tetrazolo[4,5-<Emphasis Type="Italic">b</Emphasis>][1,2,4]triazine<Superscript>(1)</Superscript>

The synthesis of 5-azido-3-methyl-1-phenyl-1H-pyrazolo[4,3-e][1,2,4]triazine 2 and 7-methyl-5-phenyl-1H-pyrazolo[4,3-e]tetrazolo[4,5-b][1,2,4]triazine 3 is described and the crystal and molecular structure of the latter is reported. This compound crystallizes in the monoclinic system, space group P2₁/n, with cell constants a = 11.607(2) Å, b = 7.982(1) Å, c = 13.147(2) Å, = 110.60(1), Z = 4, T = 293 K and D_cal = 1.470 g cm^–3. The structure was solved by direct methods and refined to R value of 0.0368 for 1906 reflections. The X-ray analysis revealed that the linear form of the tetrazolo-fused ring system of 3 exists in the crystal. The molecule as a whole has an almost planar conformation stabilized by the short intramolecular NsH interaction. The molecular packing in the crystal is determined by the van der Waals forces only.Part 26 in 1,2,4-triazines in organic synthesis. For part 25 see Mojzych et al.¹     

Synthesis,Characterization and Crystal Structure of 2-Nitro-<Emphasis Type="Italic">N</Emphasis>-[2,4-dichlorophenyl]-<Emphasis Type="Italic">N</Emphasis>-(2-methylbenzoyl)benzamide

Abstract  

The title benzamide was synthesized in two steps by refluxing N-(2,4-dichlorophenyl)-2-nitrobenzamide with thionyl chloride in dry toluene to afford 2,4-dichloro-N-[chloro(2-nitrophenyl]methylene)benzenamine intermediate followed by treatment with 2-methyl benzoic acid in presence of triethyl amine. The structure was confirmed by spectroscopic and elemental analysis. The crystal structure was determined from single crystal X-ray diffraction data. It crystallizes in the monoclinic space group P 21/c with unit cell dimensions a = 10.4122(7), b = 12.9613(7) and c = 15.5518(10) ?. The dihedral angle between the two aromatic rings is 82.32(4)°. The N2 and N3 nitro groups are oriented with respect to their attached phenyl rings at dihedral angles of 1.97(3)° and 15.73(3)°, respectively.     

Crystal Structure and Conformational Analysis of 4-[(<Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylamino)Benzylidene]-2-Phenyloxazole-5-One

Abstract  

Molecular and crystal structure of 4-[(p-N,N-dimethylamino)benzylidene]-2-phenyloxazol-5-one, C₁₈H₁₆N₂O₂, have been determined by single crystal X-ray diffraction study. The title compound is monoclinic, with a = 12.1704(23) ?, b = 3.9810(5) ?, c = 30.9603(56) ?, β = 101.176(15)°, Z = 4, D _x = 1.32 g/cm³, μ(Mo Kα) = 0.087 mm⁻¹, and space group is P12₁/c1. The structure was solved by direct methods and refined to a final R = 0.047 for 3166 reflections with I > 2σ(I). The crystal structure is stabilized by C–H⋯O and C–H⋯N type intra-molecular, C–H⋯O type inter-molecular interactions. To enlighten the flexibility and the geometric isomerism (E or Z) of the title compound, the selected torsion angle is varied from −180 to 180° in every 10° separately and molecular energy profile is calculated and analyzed.     

Synthesis,redox properties,and X-ray diffraction structure of 2,3-<Emphasis Type="Italic">bis</Emphasis>(ethylthio)-<Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">p</Emphasis>-MeOC<Subscript>6</Subscript>H<Subscript>4</Subscript>)maleimide

Refluxing 2,3-dichloromaleic anhydride with p-anisidine in benzene with water removal gives the condensation product 2,3-dichloro-N-(p-MeOC₆H₄)maleimide (1) 75% yield. This new maleimide compound reacts with added ethanethiol in the presence of Et₃N or DBU to furnish the bidentate sulfide ligand 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) in 85% yield. Each product has been characterized in solution by IR, NMR, and UV-vis spectroscopies, and the solid-state structure of 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide was unequivocally established by single-crystal X-ray diffraction analysis. 2,3-bis(Ethylthio)-N-(p-MeOC₆H₄)maleimide crystallizes in the monoclinic space group C2/c, a = 20.035(3)Å, b = 9.188(1)Å, c = 16.887(2)Å, = 93.696(2)°, V = 3102.3(8)ų, Z = 8, and D_calcd = 1.385 mg/m³; R = 0.0268, R_w = 0.0676 for 2025 reflections with I > 2 (I). The nature of the LUMO in 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) has been determined by extended Hückel molecular orbital calculations, and these data are discussed relative to the cyclic voltammetry results and other structurally relevant compounds prepared in our labs.     

Co-crystal Structure of 11-Hydroxy-2,3,9-trimethoxy-6<Emphasis Type="Italic">H</Emphasis>-chromeno[3,4-<Emphasis Type="Italic">b</Emphasis>]chromen-12-one and 11-Hydroxy-2,3,9-trimethoxy-chromeno[3,4-<Emphasis Type="Italic">b</Emphasis>]chromene-6,12-dione

Abstract  

A 1:1 co-crystal structure of 11-hydroxy-2,3,9-trimethoxy-6H-chromeno[3,4-b]chromen-12-one and 11-hydroxy-2,3,9-trimethoxy-chromeno[3,4-b]chromene-6,12-dione (stemonone) was crystallized from the reaction mixture of 6-deoxyclitoriacetal and methanesulfonyl chloride, and its structure was characterized by X-ray diffraction. This co-crystal crystallizes in a triclinic crystal system, space group P(−1) with unit cell parameters of a = 8.1317(3) Å, b = 9.8224(4) Å, c = 10.7268(3) Å, α = 78.116(1)°, β = 77.463(1)°, γ = 77.140(1)°, Z = 2 and V = 804.11(3) Å³. The crystal structure was solved by direct methods and refined by full-matrix least-squares on F ² to final values of R ₁ = 0.0501 and wR ₂ = 0.1520.     

Structure of 1-(2,6-dimethylphenyl)-<Emphasis Type="Italic">N</Emphasis>-hydroxy-4,4-dimethyl-2,5-dioxo-<Emphasis Type="Italic">N</Emphasis>-phenyl-3-pyrrolidine carboxamide

The title compound is crystallized in the monoclinic space group P2₁/c with cell parameters a = 7.499, b = 13.336, c = 19.390 Å, β = 99.716°, V = 1911.4 ų, Z = 4, D _cal = 1.273 Mg/m³ at T = 120 K. The structure is refined by full-matrix least-squares procedures to final R ₁ = 0.0548 and wR ₂ = 0.1089 for 3424 reflections. Two phenyl rings are noncoplanar with regard to each other and pyrrolidine core. The structure contains intramolecular hydrogen bond.     

Synthesis and Crystal Structure of (5-Methyl-3-phenyl-1<Emphasis Type="Italic">H</Emphasis>-pyrazol-1-yl)-[5-(<Emphasis Type="Italic">p</Emphasis>-tolylamino)-2<Emphasis Type="Italic">H</Emphasis>-1,2,3-triazol-4-yl]methanone

Abstract  

(5-Methyl-3-phenyl-1H-pyrazol-1-yl)-[5-(p-tolylamino)-2H-1,2,3-triazol-4-yl]methanone was synthesized and characterized by ¹H NMR, MS and IR spectra data. The structure of title compound was identified by X-ray diffraction. Compound, C₂₀H₁₈N₆O, Mr = 358.40, crystallizes in the triclinic space group P-1 with unit cell parameters a = 10.303(6), b = 12.489(7), c = 15.305(9) ?, α = 108.489(12), β = 101.920(11), γ = 96.971(13)°, V = 1790.0(17) ?³, Z = 4, Dx = 1.330 mg/cm³. The final R was 0.0520.     

Crystal Structure of 2-(4,5-Bis(4-methoxyphenyl)-5<Emphasis Type="Italic">H</Emphasis>-chromeno[4,3-<Emphasis Type="Italic">b</Emphasis>]pyridin-2-yl)phenol

Abstract  

The title compound 2-(4,5-bis(4-methoxyphenyl)-5H-chromeno[4,3-b]pyridin-2-yl)- phenol (C₃₂H₂₅NO₄, Mr = 487.53) was synthesized and crystallized. The crystal belongs to monoclinic, space group P2(1)/c with a = 12.4170 (11), b = 18.313 (2), c = 11.7103 (10) ?, β = 111.569(2)°, V = 2476.4(4) ?³, Mr = 487.53, Z = 4, Dc = 1.308 g/cm³, μ(MoK _α ) = 0.086 mm⁻¹, F(000) = 1024, the final R ₁ = 0.0632 and wR ₂ = 0.1454. X-ray analysis reveals that the atoms of C(1), C(2), C(3), C(4), C(5) and N(1) form a planar six-membered ring, while the atoms of C(1), C(2), C(6), C(7), C(12) and O(1) form a six-membered ring of envelope conformation.     

Synthesis and Crystal Structure of Bis[<Emphasis Type="Italic">N</Emphasis>-{(<Emphasis Type="Italic">S</Emphasis>)-1-Phenylethyl}-<Emphasis Type="Italic">N</Emphasis>-{1-(2-Pyridinyl)Methyl}Amine] Zinc(II) Perchlorate

Abstract  

The reaction of N-[(S)-1-phenylethyl]-N-[1-(2-pyridinyl)methyl]amine (PEPMA) with Zn(ClO₄)₂ affords (PEPMA)₂Zn(ClO₄)₂ at room temperature. The complex is characterized by elemental analysis, ¹H-MNR and X-ray crystallography. The crystal system is orthorhombic with space group of P2₁2₁2₁ and unit cell parameters: a = 8.6911(4), b = 9.7755(7), c = 37.275(2) ?, V = 3166.9(3) ?³, Z = 4, D _x  = 1.445 Mg/m³. The crystal structure reveals that zinc metal is ligated by two PEPMA ligands in a distorted tetrahedral fashion. Interestingly, both nitrogen atoms of amine at PEPMA to the central zinc metal exhibit (R)-configuration.     

Synthesis,Characterization and Biological Activity Studies on 6-<Emphasis Type="Italic">p</Emphasis>-Dimethylaminophenyl-5,6-dihydrobenzoimidazo[1,2-<Emphasis Type="Italic">c</Emphasis>]quinazoline: Crystal Structure of the Title Compound and Comparative Study with Related Derivatives

Abstract  

Reaction of o-aminophenylbenzimidazole with p-dimethylaminobenzaldehyde yielded 6-p-dimethylaminophenyl-5,6-dihydrobenzoimidazo[1,2-c]quinazoline, which was characterized by elemental analysis, IR, UV–Vis, ¹H NMR, ¹³C NMR, mass spectral studies and X-ray crystal structure analysis. Studies on the antimicrobial activity of the compound revealed that it is active against fungus Yeast but not Bacillus subtilis. The compound crystallized in the space group P2₁/n with the unit cell parameters a = 10.652(2) ?, b = 11.002(2) ?, c = 15.753(2) ?, β = 109.29(2)° and the structure was refined to an R-factor of 0.0479. The hydropyrimidine ring in the quinazoline moiety is in skew-boat conformation. The dimethylamino group attached to phenyl ring is in conjugation with it. The structure was stabilized by intermolecular C–H–N interactions. A few of the related quinazolines (6-p-hydroxyphenyl-5,6-dihydrobenzoimidazo[1,2-c]quinazoline; 6-phenyl-5,6-dihydrobenzoimidazo[1,2-c]quinazoline; 6-pyridyl-5,6-dihydrobenzoimidazo[1,2-c]quinazoline; 6-furyl-5,6-dihydrobenzoimidazo[1,2-c]quinazoline) were also examined for their biological activity, in addition to their characterization by IR, UV–Vis, ¹H and ¹³C NMR spectral studies along with structural comparison.     

Solid-state structure of a 1:1 adduct of 2-<Emphasis Type="Italic">t</Emphasis>-butylphenol and 3-<Emphasis Type="Italic">t</Emphasis>-butylsalicylaldehyde

The co-crystal structure of 2-t-butylphenol with 3-t-butylsalicylaldehyde (1) was obtained by single-crystal X-ray diffraction. 2-t-Butylphenol was co-crystallized with 1 equivalent of 3-t-butylsalicylaldehyde. The phase crystallizes in the monoclinic system with P2₁/c space group. The unit cell dimensions are a = 12.351(3) Å, b = 15.253(3) Å, c = 10.377(2) Å, β = 97.58(3)^∘, V = 1937.8(7) ų and Z = 4. The structure of the crystal layered by nonpolar group includes strong intramolecular and weak intermolecular hydrogen bonds. The aldehyde oxygen O2 accepts a three-centered bond through intramolecular O1–H1A⋅sO2 and intermolecular O3–H3A⋅sO2 interactions. In addition, the crystal consists of right-handed helical (P) and left-handed helical (M) chains linked by hydrogen bonding.     

Crystal and molecular structures of benzo[4,5]imidazo[1,2-<Emphasis Type="Italic">c</Emphasis>]quinazolin-6-one and 10-carboxybenzo[4,5]imidazo[1,2-<Emphasis Type="Italic">c</Emphasis>]quinazolin-6-one: A quantum-chemical study of their tautomerism

Benzo[4,5]imidazo[1,2-c]quinazolin-6-one and 10-carboxybenzo[4,5]imidazo[1,2-c]quinazolin-6-one were isolated in the crystalline state and studied by X-ray diffraction. The crystal and molecular structures of these compounds were determined by X-ray diffraction. The energy characteristics of the tautomeric and ionic forms were calculated by the quantum-chemical PM3 method.     

An X-ray Crystallographic Study of 1,4-Di[(<Emphasis Type="Italic">E</Emphasis>)-2-(<Emphasis Type="Italic">p</Emphasis>-tolyl)-1-diazenyl]piperazine

Abstract  

The crystal structure of methyl 1,4-di[(E)-2-(p-tolyl)-1-diazenyl]piperazine (4) has been determined by single crystal X-ray diffraction analysis. The bis-triazene (4) adopts a normal chair conformation in the piperazine ring, with puckering parameters : φ₂ = −29(5)°, Q_T = 0.534(2) ? and θ₂ = 177.0(2)°. The crystal structure of 4 is compared with the structure of the triazene (2a) and the closely related bis-triazenes (3 and 5a). The piperazine ring of 2a and 4 adopt a typical chair conformation, whereas the piperazine ring of 3 adopts an unusual pseudo-boat conformation. Crystal data: 4 C₁₈H₂₂N₆, triclinic, space group P[`1] P\overline{1} , a = 6.8925(2) ?, b = 7.8574(3) ?, c = 16.8856(8) ?, α = 103.103(2)°, β = 90.528(2)°, γ = 101.776(2)° and V = 870.44 (6) ?³, for Z = 2.     

Mathematical simulation and X-ray diffraction investigation of the crystal structure of 1-phenyl-1-<Emphasis Type="Italic">tert</Emphasis>-butyl-3-methyl-1,3-dihydroisobenzofuran

An algorithm for using a priori generation of crystal structures by the discrete modeling method for the interpretation of data obtained from single-crystal X-ray diffraction experiments is considered. The crystal structure of 1-phenyl-1-tert-butyl-3-methyl-1,3-dihydroisobenzofuran is mathematically simulated using the discrete modeling of molecular packings and studied by X-ray diffraction. The simulation is performed for two isomers of the initial chemical compound that are possible from the viewpoint of the mechanism of the chemical reaction used in the synthesis of this compound. Appropriate models that can serve as starting models for solving and refining the crystal structure with the use of X-ray diffraction data are chosen from a complete set of calculated structural models in accordance with specific criteria. The structure is solved using a starting model calculated using the discrete modeling method and refined by the full-matrix least-squares procedure.