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: 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: 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: 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.     

New sulfur derivatives of 2,3-dichloropyrrolo[1,2-a] benzimidazol-1-one. Demonstration of regioselective thiolate addition and X-ray diffraction structures of 2-chloro-3-methylthiopyrrolo[1,2-a]benzimidazol-1-one and 2,3-di(benzylthio)pyrrolo[1,2-a]benzimidazol-1-one

The reaction of thiols with the heterocyclic compound 2,3-dichloropyrrolo[1,2-a] benzimidazol-1-one (1) has been investigated as a route to new redox-active, bidentate sulfur ligands. Treatment of 1 with either methylthiol or benzylthiol in the presence of pyridine affords monosulfide compounds 2-chloro-3-methylthiopyrrolo[1,2-a] benzimidazol-1-one (2) and 2-chloro-3-benzylthiopyrrolo[1,2-a]benzimidazol-1-one (3) and the disulfide derivatives 2,3-di(methylthio)pyrrolo[1,2-a]benzimidazol-1-one (4) and 2,3-di(benzylthio)pyrrolo[1,2-a]benzimidazol-1-one (5). The substitution of the first chlorine group in 2,3-dichloropyrrolo[1,2-a]benzimidazol-1-one (1) occurs regioselectively at C-3 to produce 2-chloro-3-methylthiopyrrolo[1,2-a]benzimidazol-1-one (2) and 2-chloro-3-benzylthiopyrrolo[1,2-a]benzimidazol-1-one (3), followed by replacement of the remaining chlorine group to furnish the disulfide compounds 4 and 5. The new thiols have been isolated by column chromatography and characterized in solution by spectroscopic methods. The molecular structures of 2-chloro-3-methylthiopyrrolo[1,2-a]benzimidazol-1-one and 2,3-di(benzylthio)pyrrolo[1,2-a]benzimidazol-1-one have been determined by X-ray crystallography. Compound 2 crystallizes as two independent molecules in the monoclinic space group P2₁/c, a = 13.221(2) Å, b = 18.478(2) Å, c = 8.948(1) Å, = 100.088(3)°, V = 2152.3(5) ų, Z = 8, and d_calc = 1.547 Mg/m³; R = 0.0354, R_w = 0.0739 for 2820 reflections with I > 2(I). Compound 5 crystallizes in the triclinic space group P-1, a = 5.180(1) Å, b = 11.494(2) Å, c = 17.243(3) Å, = 86.024(3)°, = 88.606(4)°, = 81.235(3)°, V = 1012.1(4) ų, Z = 2, and d_calc = 1.360 Mg/m³; R = 0.0354, R_w = 0.0692 for 2655 reflections with I > 2(I). The redox properties of the disulfide compounds 4 and 5 have been explored by cyclic voltammetry, where a one-electron reduction at ca. –1.10 V has been observed for each compound. The site of electron accession in has been established by carrying out molecular orbital calculations at the extended Hüuckel level on the model compound 2,3-di(thio)pyrrolo[1,2-a]benzimidazol-1-one.     

Synthesis and Crystal Structure of Compound 1,5-bis(4-methoxyphenyl)-3a-(2-phenyl-2H-1,2,3-triazol-4-yl)-4,5-dihydro-3aH-benzo[b][1,2,4]oxadiazolo[4,5-d][1,4]thiazepine

Abstract The crystal structure of title compound has been determined. The compound crystallizes in the triclinic system with space group P-1, lattice parameters; a = 9.2938 (5) ?, b = 11.9992 (7) ?, c = 25.5918 (13) ?, α = 91.343 (2)°, β = 95.8360 (10)°, γ = 101.005 (2)°, V = 2784.3 (3) ?³, Z = 4, X-Ray analysis reveals that the molecular backbone consists of tricyclic system with the central seven-membered ring in twisted chair-like conformation. Graphical abstract The crystal structure of 1,5-bis(4-methoxyphenyl)-3a-(2-phenyl-2H-1,2,3-triazol-4-yl)-4,5-dihydro-3aH-benzo[b][1,2,4]oxadiazolo[4,5-d][1,4]thiazepine was first determined by single-crystal X-ray diffraction which reveals that the molecular backbone consists of a tricyclic system with the central seven-membered ring in twisted chair-like conformation .     

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 diffraction and total 1H and 13C NMR assignment of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine)

The X-ray diffraction structure of (RS)-5,6-dihydro-7,8-dimethoxy-5-methyl-6-(2-oxopropyl)-(2,3-methylenedioxyphenyl)-[c]-phenanthridine ((RS)-6-acetonyldihydrochelerythrine), isolated as an artifact from Bocconia Arborea, is reported. This compound crystallizes as orthorhombic system, space group Pna2₁, with a = 13.216(2) Å, b = 7.6547(10) Å, c = 20.096(3) Å. The phenanthridine central ring presents a distorted boat conformation, which gives rise to two planes with 21.30° between them. The acetonyl group at the six position forms weak C — H O and C — H -ring interactions. The title compound was completely characterized in solution by ¹H and ¹³C and 2D NMR experiments.     

Chlorine-atom abstraction and cluster fragmentation in the reaction of H3Re3(CO)10(MeCN)2 with the diphosphine ligand 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd): X-ray diffraction structure of fac-ClRe(CO)3(bpcd)

Treatment of the activated trirhenium cluster H₃Re₃(CO)₁₀(MeCN)₂ with the diphosphine ligand 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd) in CH₂Cl₂ does not afford the expected cluster product H₃Re₃(CO)₁₀(bpcd) but rather the mononuclear complex fac-ClRe(CO)₃(bpcd). The identity of fac-ClRe(CO)₃(bpcd) was determined in solution by IR and NMR (¹H and ³¹P) spectroscopies and the solid-state structure was established by X-ray diffraction analysis. fac-ClRe(CO)₃(bpcd) crystallizes in the triclinic space P-1, a = 9.958(2) Å, b = 11.991(3) Å, c = 13.676(3) Å, α = 73.230(4)°, β = 73.806(4)°, γ = 77.409(4)°, V = 1484.6(6) ų, Z = 2, and d _calc = 1.723 Mg/m³; R = 0.0367, R _w  = 0.0857 for 4253 reflections with I > 2σ(l).     

X-ray crystal structure analysis of nitroxazepine: 10-(3-dimethylaminopropyl)-2-nitro-10,11-dihydrodibenz [b,f][l,4]oxazepin-11-one

The title compound, C₁₈H₁₉O₄N₃,M _r=341, the base (I) of the dibenzoxazepine anti-depressant drug Sintamil, crystallizes in the orthorhombic space group,Pbca withZ=8 in a cella=8.636(2),b=23.687(3),c=16.787(3)Å,V _c=3434 ų. The structure was solved by direct methods and refined toR=0.102 (R _w=0.093) with 1348 observed CuK reflections. The tricyclic framework takes up a saddle shape with the heterocyclic ring in boat conformation; the flanking planar aromatic rings make angles 148.2(3), 150.8(3)° with the central ring plane, compared with 143.5(5), 158.1(5)° in Sintamil monohydrate (II). BothI andII have extended-CNMe₂ side chains (with appreciable thermal motion); this conformation, and the distances of the -N(CH₃)₃ nitrogen to the centers of aromatic rings (6.4 and 7.8 Å inI), are consistent with inhibition of uptake mechanisms underlying the pharmacological action.     

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.     

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.     

Crystal and molecular structure of 2′,2′,4,4,5′,5′,6,6-octamethyl-2′,4,5′,6-tetrahydrofuro[3,4-d]-1, 3-oxathiol-2-spiro-3′-furan-4′-(3′H)-one

Crystals of the title compound are monoclinic,a = 13.966(4),b = 9.141(3),c= 15.901(6) Å, =123.0(7) °,Z = 4. The structure was established by direct methods based on 2827 reflections, using MoK radiation, refined to an ultimate coventionalR of 0.081. The furanone ring is closely similar to that found in a related spiro-connected molecule in this series.     

Ligand substitution in the halo-bridged diruthenium compound [Ru(CO)3Cl2]2 by 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd). Synthesis, spectral properties, and X-ray diffraction structures of cis(CO), trans(Cl)-RuCl2(CO)2 (bpcd) and cis(CO)-RuCl[C(O)Et](CO)2(bpcd)

The reaction between 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd) and the chlorobridged diruthenium complex [Ru(CO)₃Cl₂]₂ (1) proceeds readily at room temperature in CH₂Cl₂ to give the new ruthenium compounds cis(CO),trans(Cl)-RuCl₂(CO)₂(bpcd) (2) and cis(CO)-RuCl[C(O)Et](CO)₂(bpcd) (3) as the major and minor products, respectively. Compound 2 was isolated and fully characterized in solution, and the molecular structure was established by X-ray diffraction analysis. cis(CO),trans(Cl)-RuCl₂(CO)₂(bpcd) crystallizes in the triclinic space P-1, a = 9.931(5) Å, b = 12.093(7) Å, c = 13.529(7) Å, α = 72.886(9)°, β = 74.739(9)°, γ = 76.851(9)°, V = 1478.2(1) ų, Z = 2, and d _calc = 1.556 mg/m³; R = 0.0841, R _w = 0.1880 for 4137 reflections with I > 2σ(I). The chlorine atoms in 2 adopt a trans geometry at the octahedral ruthenium center, with the two CO groups exhibiting a cis orientation and trans to the bpcd ligand. cis(CO)–RuCl[C(O)Et](CO)₂(bpcd) crystallizes as two independent molecules in the unit cell in the triclinic space P-1, a = 9.941(2) Å, b = 14.867(2) Å, c = 22.414(3) Å, α = 80.257(3)°, β = 84.796(2)°, γ = 75.207(3)°, V = 3152.6(8) ų, Z = 4, and d _calc = 1.504 mg/m³; R = 0.0428, R _w = 0.0962 for 8242 reflections with I > 2σ(I). The two CO groups are situated cis to each and are opposite to chlorine and phosphine moieties. The production of the minor propionyl compound 3 is discussed with respect to the trace amount of EtOH that is present in the CHCl₃ solvent that is used in the preparation of [Ru(CO)₃Cl₂]₂.     

The Molecular and Crystal Structure of 1 Ref, 3trans-bis(4-chloro-phenyl)-2trans-nitro-5-oxoperhydropyrazolo[1,2-a] pyrazol,a “non-cisoid” 1,3-Dipol Adduct

The three-dimensional structure of the title compound has been established by means of an X-ray analysis. The product was formed by a thermal 1,3-dipolar cycloaddition. According to the concerted [_π4_s + _π2_s]-mechanism the formation of this stereoisomer should actually be forbidden. The structure determined by X-ray analysis confirms the chemical results.     

Reaction of 2,3-bis(diphenylphosphino)maleic acid-thioanhydride (bmata) with PhCCo3(CO)9. X-ray diffraction structure of {\text{Co}}_{\text{3}} ({\text{CO)}}_{\text{6}} [\mu _2 ,\eta ^2 ,\eta ^1 {\text{ - C(Ph)}}{\text{(O)](}}\mu _2 {\text{ - PPh}}_{\text{2}} )

The benzylidyne-capped cluster PhCCo₃(CO)₉ (1) reacts with the diphosphine ligand 2,3-bis(diphenylphosphino)maleic acid-thioanhydride (bmata) to afford ultimately the new cluster ${\text{Co}}_{\text{3}} ({\text{CO)}}_{\text{6}} [\mu _2 ,\eta ^2 ,\eta ^1 {\text{ - C(Ph)}}{\text{(O)](}}\mu _2 {\text{ - PPh}}_{\text{2}} )$ (3) in low yield under thermolysis conditions or by Me₃NO activation of PhCCo₃(CO)₉. The intermediate cluster compound PhCCo₃(CO)₇(bmata) (2) has been confirmed by IR spectroscopy and is shown to give ${\text{Co}}_{\text{3}} ({\text{CO)}}_{\text{6}} [\mu _2 ,\eta ^2 ,\eta ^1 {\text{ - C(Ph)}}{\text{(O)](}}\mu _2 {\text{ - PPh}}_{\text{2}} )$ upon heating. Cluster 3 has been isolated and characterized in solution by IR and ³¹P NMR spectroscopies, and the solid-state structure of 3 was established by X-ray diffraction analysis. ${\text{Co}}_{\text{3}} ({\text{CO)}}_{\text{6}} [\mu _2 ,\eta ^2 ,\eta ^1 {\text{ - C(Ph)}}{\text{(O)](}}\mu _2 {\text{ - PPh}}_{\text{2}} )$ crystallizes in the triclinic space group P ${\bar 1}$ , a = 11.6053(8) Å, b = 11.8438(8) Å, c = 15.099(1) Å, α = 105.169(5)^○, β = 90.530(5)^○, γ = 104.976(6)^○, V = 1928.5(2) ų, Z = 2, and d _calc = 1.578; R = 0.0442, R _w = 0.481 for 2591 observed reflections with I > 3σ (I). The cyclic voltammetric properties of 3 have been investigated and are contrasted with the related bma-derived cluster ${\text{Co}}_{\text{3}} ({\text{CO)}}_{\text{6}} [\mu _2 ,\eta ^2 ,\eta ^1 {\text{ - }}{\text{(O)OC(O)](}}\mu _2 {\text{ - PPh}}_{\text{2}} )$ .