X-ray mapping in heterocyclic design: X. X-ray diffraction study of 4-methyl-6,7,8,9-tetrahydro-2-quinolone

The structure of 4-methyl-6,7,8,9-tetrahydro-2-quinolone is studied by the single-crystal X-ray diffraction technique (a = 6.6890(17) Å, b = 7.926(2) Å, c = 8.993(3) Å, α = 85.50(2)°, β = 68.22(2)°, γ = 82.89(2)°, Z = 2, and space group \(\bar P1\)). The structure is solved by direct methods and refined to R₁ = 0.0592 and wR₂ = 0.1206. In the crystal, intermolecular hydrogen bonds link molecules into centrosymmetric dimers.     

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)°].     

X-ray diffraction investigation of 1-phenyl-3-isopropyl-5-(benzothiazol-2-yl)formazan

The crystal structure of 1-phenyl-3-isopropyl-5-(benzothiazol-2-yl)formazan is investigated using X-ray diffraction. The compound crystallizes in the form of two crystallographically independent molecules (A and B) in identical conformations that are stabilized by intermolecular hydrogen bonds. The intermolecular hydrogen bonds N-H…N (N…N, 2.892 and 2.939 Å) link molecules into AB dimers. Both molecules have a flattened structure, except for the isopropyl fragment. The bonds in the formazan chains are delocalized. Molecules A and B have close geometric characteristics.     

X-ray mapping in heterocyclic design: XII. X-ray diffraction study of 2-pyridones containing cycloalkane fragments annelated to the C(5)-C(6) bond

The structures of 4,6-dimethyl-1H-pyridin-2-one [a = 6.125(2) Å, b = 15.153(4) Å, and c = 14.477(4) Å, Z = 8, space group Pbca], the 2: 1: 1 complex of 4-methyl-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one with phosphoric acid and methanol [a = 11.181(2) Å, b = 14.059(6) Å, c = 13.593(4) Å, β = 97.78(2)°, Z = 8, space group P2₁/n], 4-methyl-1,5,6,7,8,9-hexahydro-2H-cyclohepta[b]pyridin-2-one [a = 12.565(6) Å, b = 5.836(6) Å, c = 13.007(3) Å, β = 93.10(3)°, Z = 4, space group P2₁/n], and 4-methyl-5,6,7,8,9,10-hexahydrocycloocta[b]pyridin-2(1H)-one [a = 12.955(3) Å, b = 6.1595(15) Å, c = 13.038(3) Å, β = 95.50(2)°, Z = 4, space group P2₁/n] are determined by single-crystal X-ray diffraction. The structures are solved by direct methods and refined by the full-matrix least-squares procedure in the anisotropic approximation to R = 0.0755, 0.0644, 0.0754, and 0.0569, respectively. The structures of 4-methyl-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one [a = 7.353(4) Å, b = 8.176(4) Å, c = 13.00(1) Å, β = 105.64(2)°, Z = 4, space group P2₁/c] and 2-oxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile [a = 5.9870(2) Å, b = 16.5280(5) Å, c = 9.6540(3) Å, β = 111.52(4)°, Z = 4, space group P2₁/c] are studied by the powder diffraction technique. The structures are solved using the grid search procedure and refined by the Rietveld method to R _wp = 0.108 and 0.058, R_exp = 0.032 and 0.027, R _p = 0.076 and 0.043, R _b = 0.123 and 0.077, and χ² = 7.9 and 3.64, respectively. In all the structures, hydrogen bonds involving the N, H, and O atoms of the pyridone fragment are formed.     

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.     

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.     

X-ray mapping in heterocyclic design: 18. X-ray diffraction study of a series of derivatives of 3-cyanopyridine-2-one with annelated heptane and octane cycles

Seven new, previously unknown, bicyclic and tricyclic heterocycles based on derivatives of 3-cyanopyrid-2-ones are obtained: 2-oxo-2,5,6,7,8,9-hexahydro-1H-cyclohepta[b]pyridine-3-carbonitrile, C₁₁H₁₂N₂O (1a); 2-[2-(4-chlorophenyl)-2-oxoethoxy]-6,7,8,9-tetrahydro-5Н-cyclohepta[b]pyridine-3-carbonitrile, C₁₉H₁₇ClN₂O₂ (2a); (3-amino-6,7,8,9-tetrahydro-5H-cyclohepta[b]furo[3,2-e]pyridin-2-yl)(4- chlorophenyl)methanone, C₁₉H₁₇ClN₂O₂ (3); 2-oxo-1,2,5,6,7,8,9,10-octahydrocycloocta[b]pyridine-3-carboxamide, C₁₂H₁₆N₂O₂ (4); 2-[2-(4-chorophenyl)-2-oxoethoxy]-5,6,7,8,9,10-hexahydrocycloocta[b]pyridine-3-carboxamide, C₂₀H₂₁ClN₂O₃ (5a); 1-[2-(4-chlorophenyl)-2-oxoethyl]-2-oxo-1,2,5,6,7,8,9,10-octahydrocycloocta[b]pyridine-3-carboxamide, C₂₀H₂₁ClN₂O₃ (5b); and 2-[2-(4-chlorophenyl)-2-oxoethoxy]-5,6,7,8,9,10-hexahydrocycloocta[b]pyridine-3-carbonitrile, C₂₀H₁₉ClN₂O₂, (6). All compounds are characterized by ¹H NMR spectroscopy, and their crystal structures are determined by X-ray diffraction.     

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.     

Synthesis and X-ray diffraction study of palladium(II) 1,3-diphenyl-5-(benzothiazol-2-yl)formazanate

The behavior of 1,3-diphenyl-5-(benzothiazol-2-yl)formazan as a bidentate ligand in the synthesis of the mononuclear palladium complex was investigated using slow diffusion. According to the X-ray diffraction study, the PdN4 coordination unit has a distorted square structure. The ligands form two six-membered chelate rings formed through the N1 and N4 atoms of the formazan fragment.     

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: IX. X-ray structure investigation of conjugated aminodienes

The single-crystal structures of two aminodienes containing an oxazole fragment, namely, 1-pip-eridyl-4-[5-(4-nitrophenyl)-oxazol-2-yl]-buta-1,3-diene C 18 H 19 N 3 O 3 (IIa) and 1-hexamethyleneimine-4-[5-(4-nitrophenyl)-oxazol-2-yl]-buta-1,3-diene C₁₉H₂₁N₃O₃ (IIb), are studied by X-ray diffraction. Structures IIa [a = 16.181(6) Å, b = 5.939(3) Å, c = 17.337(9) Å, β = 96.13(2)°, Z = 4, and space group P2₁] and IIb [a = 7.4704(11) Å, b = 10.9904(19) Å, c = 43.434(6) Å, β = 91.24(1)°, Z = 8, and space group P2₁/_c] are solved by the direct method and refined to R = 0.060 and 0.238, respectively. Although the ring sizes of the cyclic amines in compounds IIa and IIb are different, the designs of two structures are identical. Each structure contains two topologically identical but crystallographically independent molecules. In structure IIa, the intramolecular hydrogen bonds between the N atoms of the oxazole fragments and the H atoms of the diene fragments are formed. In structure IIb, similar bonds are absent.     

X-ray mapping in heterocyclic design: XIV. Tricyclic heterocycles based on 2-Oxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile

The structures of four compounds are studied using single-crystal X-ray diffraction: 1-[2-(4-chlorophenyl)-2-oxoethyl]-2-oxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile [a = 4.908(4) Å, b = 11.644(10) Å, c = 13.587(2) Å, β = 94.31(5)°, Z = 2, space group P2₁]; 2-[2-(4-chlorophenyl)-2-oxoethoxy]-5,6,7,8-tetrahydroquinoline-3-carbonitrile [a = 7.6142(8) Å, b = 14.778(2) Å, c = 14.132(2) Å, β = 100.38(1)°, Z = 4, space group P2₁/c]; 4-(aminocarbonyl)-2-(chlorophenyl)-6,7,8,9-tetrahydro[1.3]oxazolo[3,2-a]quinolin-3-ium per-chlorate [a = 5.589(7) Å, b = 24.724(15) Å, c = 13.727(5) Å, β = 97.66(9)°, Z = 4, space group P2₁/n]; and (3-amino-5,6,7,8-tetrahydrofuro[2,3-b]quinolin-2-yl)-(4-chlorophenyl) methanone [a = 7.150(2) Å, b = 7.4288(10) Å, c = 15.314(3) Å, α = 98.030(10)°, β = 99.21(2)°, γ = 105.34(2)°, Z = 2, space group \(P\bar 1\)]. The structures are solved by direct methods and refined by the full-matrix least-squares procedure in the anisotropic approximation to R = 0.0728, 0.0439, 0.1228, and 0.0541, respectively. The structure of 1-(4-chlorophenyl)-4-piperidin-1-yl-8,9-dihydro-7H-pyrrolo[3.2.1-ij]quinoline-5-carboxamide [a = 23.9895(9) Å, b = 5.1557(3) Å, c = 17.0959(9) Å, β = 106.43°, Z = 4, space group P ₁/c] is investigated by X-ray powder diffraction. This structure is solved using the grid search procedure and refined by the Rietveld method to R _wp = 0.0773, R _exp = 0.0540, R _p = 0.0585, R _b = 0.1107, and χ ² = 1.78.     

X-ray mapping in heterocyclic design: XIII. Structure of substituted tetrahydroquinolines

The structures of 4-methyl-2-chloro-5,6,7,8-tetrahydroquinoline [a = 8.138(2) Å, b = 11.127(4) Å, c = 11.234(2) Å, β = 111.30(2)°, Z = 4, space group P2₁/c, 4-methyl-2-methoxy-5,6,7,8-tetrahydroquinoline [a = 5.7651(16) Å, b = 8.530(2) Å, c = 10.455(3) Å, α = 73.76(2)°, β = 86.95(2)°, γ = 83.97(2)°, Z = 2, space group P $\bar 1$ , 4-methyl-2-(4-chlorophenacyl)-5,6,7,8-tetrahydro-1H-quinolin-2-one [a = 8.873(2) Å, b = 17.137(2) Å, c = 24.515(4) Å, Z = 8, space group Pbn2₁], and 2-(4-chlorophenyl)-5-methyl-6,7,8,9-tetrahy-drooxazolo[3.2-a]quinolin-10-ylium perchlorate [a = 8.110(6) Å, b = 17.818(7) Å, c = 17.721(5) Å, β = 100.46(4)°, Z = 4, space group P2₁/c] are studied by single-crystal X-ray diffraction. The structures are solved by direct methods and refined by the full-matrix least-squares procedures in the anisotropic approximation to R = 0.0581, 0.0667, 0.0830, and 0.0607, respectively.     

X-ray diffraction study of the complex of the enzyme SAICAR synthase with the reaction product

The three-dimensional structure of the complex of the enzyme SAICAR synthase with the product of the enzymatic reaction, SAICAR, was solved and refined by methods of protein crystallography. The SAICAR-binding site in the active site of the enzyme was found. The amino-acid residues providing the binding of the reaction product with the protein were revealed. These residues were compared with those involved in the substrate binding in the complex with AICAR and succinic acid studied earlier.     

X-ray Structures of Pharmacologically Active 2-(3,5-Dimethyl-pyrazol-1-yl)-methylacetanilides

Abstract X-ray structures of three pharmacologically active lidocaine analogs, containing a common, substituted pyrazole moiety as the basic residue and variously substituted phenyl rings as the hydrophobic residue, have been determined. This isomeric series comprises 2-(3,5-dimethyl-pyrazol-1-yl)-2′-methylacetanilide (1), 2-(3,5-dimethyl-pyrazol-1-yl)-3′-methylacetanilide monohydrate (2), and 2-(3,5-dimethyl-pyrazol-1-yl)-4′-methylacetanilide (3). Crystal data are 1: space group P2 ₁ /c with a = 4.7617(2), b = 11.5638(4), c = 23.603(1) ?, β = 90.736(2)°, Z = 4; 2: P2 ₁ /c with a = 4.7260(1), b = 13.7001(4), c = 21.7006(6) ?, β = 93.425(1)°, Z = 4; 3: P2 ₁ /n with a = 6.4103(3), b = 24.584(1), c = 8.4449(4) ?, β = 100.273(3)°, Z = 4. In 1–3, the amide bond is trans-planar but the basic and hydrophobic residues adopt different orientations relative to this plane. Hydrogen bonding in 1 and 3 is based on C(4) linear arrays whereas in the monohydrate 2, the presence of water gives rise to R ₄ ⁴ (16) ring motifs. A summary of the local anesthetic and anti-arrhythmic properties of 1–3 is provided. Graphical abstract X-ray Structures of Pharmacologically Active 2-(3,5-Dimethyl-pyrazol-1-yl)-methylacetanilides Christina Zalaru, Mino R. Caira, Mircea Iovu, and Elena Cristea The title compounds are lidocaine analogs that display local anesthetic and anti-arrhythmic activities. X-ray analyses revealed a range of solid-state conformations among these isomeric compounds as well as variation in hydrogen bonding schemes, namely C(4) (R = o-, p-CH3) and R44(16) (R = m-CH3, monohydrate crystal). 1,1-Os3(CO)9(μ-CO)(phen)     

Single Crystal X-ray Study of 6-Phenyl-4-(p-tolyl)pyridin-2(1H)-one

Crystallography Reports - The title compound 6-phenyl-4-(p-tolyl)pyridin-2(1H)-one was synthesized via one-pot, three component reaction of (E)-1-phenyl-3-(p-tolyl)-2-propen-1-one, ethyl...     

X-ray mapping in heterocyclic design: III. Diffractometric study of the crystal structure of 1-methyl-2-oxo-2,3-dihydroimidazo[1,2-a]pyridinium bromide

The crystal structure of 1-methyl-2-oxo-2,3-dihydroimidazo[1,2-a]pyridinium bromide C₈H₉BrN₂O is determined by X-ray diffraction. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0599. The geometry of the pyridinium fragment observed in the molecule corresponds to the limited number of centers at which the positive charge can be delocalized. Apparently, this delocalization predominantly occurs in the NCN fragment of the imidazole ring and only slightly affects the pyridine moiety of the molecule.     

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°).     

X-Ray diffraction and vibrational spectroscopic study of 2-chloro-N-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]-thiazol-2-yl}-acetamide

The title compound C₁₈H₂₁ClN₂SO crystallizes with Z = 4 in space group P2₁/c. The structure of the title compound was characterized by ¹H-NMR, ¹³C-NMR, IR and single crystal diffraction. There are an intermolecular N-H…O hydrogen bond and a C-H…π interactions in crystal packing. In addition to the molecular geometry and packing obtained from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in ground state have been calculated using density functional theory method DFT (B3LYP) with 6-31G (d, p) basis set. Calculated frequencies, bond lengths, angles and dihedral angles are in good agreement with the corresponding experimental data.