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: 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.     

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 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: 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: V. Diffractometric study of the crystal structure of 2-hydroxy-3-trifluoracetylimidazo[1,2-a]pyridine hydrochloride at 180 K

The crystal structure of 2-hydroxy-3-trifluoracetylimidazo[1,2-a]pyridine hydrochloride C₉H₆F₃ClN₂O₂ is determined by X-ray diffraction at 180 K. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0296. The alternation of bond lengths in the six-membered fragment of the molecule is observed. One of the specific features of the crystal structure is the formation of a system of the N-H?Cl^? (N?Cl, 3.09 Å; N-H, 0.83 Å; H?Cl, 2.33 Å; and N-H?Cl, 153°) and O-H?Cl^? (O?Cl, 2.87 Å; O-H, 0.95 Å; H?Cl, 1.92 Å; and O-H?Cl, 178°) hydrogen bonds in which the chlorine atoms are related to the reference atom by different symmetry transformations.     

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: 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 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: 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 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: 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: 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.     

Molecular rearrangement of photoparthenin by BF3-etherate-acetic acid complex: X-ray crystal structure of a novel product

The structure of a novel compound,Iupac name: bicyclo [2.4.0]-octa-1,3-dimethyl-2,3-pentan-9-methylene-8, 10-butan-diolide, which resulted on treatment of photoparthenin with BF₃-etherate acetic acid, has been established uniquely by X-ray crystallography. C₁₅H₁₈O₄ is orthorhombic, space group P2₁2₁2₁, with the cell dimensionsa=8.444(1),b=9.964(2),c=16.239(2) Å,V=1366.3(2) ų,Z=4,M _r =262.3,D _o=1.29,D _x=1.28 g cm^–3, F(000)=560,T=293K,R=0.065 for 818 observed reflections. -lactone ring has a skew-boat, -lactone ring has an envelope, and the remaining six-membered ring has a distorted chair conformation. The four-membered ring is nonplanar. There are two intramolecular and one intermolecular short C-HO interactions 2.819, 2.834, and 3.259 Å, respectively, which stabilize the crystal structure.N.C.L. Communication No. 4583.     

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer of the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.     

Synthesis and X-ray structure analysis of 2-acetylamino-benzoic acid

The title compound crystallizes in the orthorhombic space group Fdd2 with unit cell parameters a = 10.848(1) Å, b = 30.264(1) Å and c = 10.577(1) Å, V = 3472.47(2) ų, and Z = 4. The final reliability index is 0.030 for 700 observed reflections. Nitrogen of the amide group and carbon atom of the acid group deviate significantly below and above the plane of the phenyl ring. The crystal cohesion is accentuated by N—HO and O—HO hydrogen bonds.     

Diffraction intensities and the structure of amorphous carbon

A model structure of amorphous carbon is investigated incorporating layered domains connected by means of a random network, the relative proportions of the two regions being a variable of the model. It is shown that for a certain relative proportion of the two regions there is good agreement between the predicted and experimentally observed electron and X-ray scattering intensities. The effects of covalent bonding are also studied and shown to be significant for small k.     

X-ray Diffraction Analysis and Electron Microscopy of the Carbon Fiber Structure

Crystallography Reports - A technique for studying the carbon-fiber structure using X-ray diffraction and electron microscopy has been developed. Average crystal-structure parameters are determined...     

On the Theory of X-ray Diffraction Interferometry in Single Crystals. Peculiarities of Effect and Possibilities of Application

Crystallography Reports - A new version of X-ray diffraction interferometer in a single crystal is studied theoretically. This device is similar to the Young interferometer with two slits, but,...     

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.