Monothioindigo,determined by microcrystal structure analysis

Indigo and thioindigo pigments are used for a wide range of applications. The crystal structure of the mixed compound monothioindigo [systematic name: (E)‐2‐(3‐oxo‐2,3‐dihydro‐1‐benzothiophen‐2‐ylidene)‐2,3‐dihydro‐1H‐indol‐3‐one], C₁₆H₉NO₂S, has been determined by microcrystal structure analysis from a crystal with a size of just 1 × 2 × 10 µm. The crystal structure of monothioindigo resembles those of indigo and thioindigo. The molecules show orientational disorder, with site‐occupation factors of 0.962 (2) and 0.038 (2) for the major and minor disorder components, respectively. The indigo fragment donates an intermolecular hydrogen bond, leading to a criss‐cross arrangement of molecules similar to that in indigo, whereas the thioindigo fragment exhibits only van der Waals interactions and molecular stacking, similar to that in thioindigo.     

Benz[cd]indol‐2(1H)‐one at 298 and 100 K

Weakly diffracting crystals of benz[cd]indol‐2(1H)‐one (naphtholactam), C₁₁H₇NO, were unsuitable for data collection by early photographic methods. However, a diffractometer data set collected at room temperature in 1989 was solved and refined. The peak scans were broad, and the results indicated disorder or a satellite crystal. Recent data collection (on another crystal from the same sample) with an area detector at 100 K revealed the same disorder, and made it possible to refine two different, more complete, disorder models. Both models assume an occasional 180° rotation of the nearly planar centrosymmetric cis‐lactam dimer. The refinements differ, especially in the anisotropic displacement parameters for the –C(=O)—NH– portion of the molecule. Both models at 100 K give a C—N (`amide') bond distance of 1.38 Å, about 0.04 Å longer than the average distance in saturated γ‐lactams in the Cambridge Structural Database. Cohesive packing interactions between molecules include opposing‐dipole dimers; the packing may explain the 10:1 ratio favoring the major‐occupancy molecule.     

2‐(4‐Bromophenyl)‐1,2‐dihydropyrimido[1,2‐a]benzimidazol‐4(3H)‐one and 4‐(4‐methylphenyl)‐3,4‐dihydropyrimido[1,2‐a]benzimidazol‐2(1H)‐one form hydrogen‐bonded base‐paired dimers

The title compounds, 2‐(4‐bromo­phenyl)‐1,2‐di­hydro­pyrimido­[1,2‐a]­benzimidazol‐4‐(3H)‐one, C₁₆H₁₂Br­N₃O, (IVa), and 4‐(4‐methylphenyl)‐3,4‐dihydropyrimido[1,2‐a]benzimidazol‐2‐(1H)‐one, C₁₇H₁₅N₃O, (Vb), both form R(8) centrosymmetric dimers via N—H?N hydrogen bonds. The N?N distance is 2.943 (3) Å for (IVa) and 2.8481 (16) Å for (Vb), with the corresponding N—H?N angles being 129 and 167°, respectively. However, in other respects, the supra­molecular structures of the two compounds differ. Both compounds contain different C—H?π interactions, in which the C—H?π(centroid) distances are 2.59 and 2.47 Å for (IVa) and (Vb), respectively (the latter being a short distance), with C—H?π(centroid) angles of 158 and 159°, respectively. The supramolecular structures also differ, with a short Br?O distance of 3.117 (2) Å in bromo derivative (IVa), and a C—H?O interaction with a C?O distance of 3.2561 (19) Å and a C—H?O angle of 127° in tolyl system (Vb). The di­hydro­pyrimido part of (Vb) is disordered, with a ratio of the major and minor components of 0.9:0.1. The disorder consists of two non‐interchangeable envelope conformers, each with an equatorial tolyl group and an axial methine H atom.     

Hypervalent organoselenium compounds stabilized by intramolecular coordination: synthesis and crystal structures

Two novel hypervalent selenium(IV) compounds stabilized by intramolecular interactions, namely 6‐phenyl‐6,7‐dihydro‐5H‐2,3‐dioxa‐2aλ⁴‐selenacyclopenta[hi]indene, C₁₄H₁₂O₂Se, 14 , and 5‐phenyl‐5,6‐dihydro‐4H‐benzo[c][1,2]oxaselenole‐7‐carbaldehyde, C₁₄H₁₂OSe₂, 15 , have been synthesized by the reaction of 2‐chloro‐1‐formyl‐3‐(hydroxymethylene)cyclohexene with in‐situ‐generated disodium diselenide (Na₂Se₂). The title compounds were characterized by FT–IR spectroscopy, ESI–MS, and single‐crystal X‐ray diffraction studies. For 14 , there is whole‐molecule disorder, with occupancies of 0.605 (10) and 0.395 (10), a double bond between C and Se, and the five‐membered selenopentalene rings are coplanar. The packing is stabilized by π–π stacking interactions involving one of the five‐membered Se/C/C/C/O rings [centroid–centroid (Cg…Cg) distance = 3.6472 (18) Å and slippage = 1.361 Å], as well as C—H…π interactions involving a C—H group and the phenyl ring. In addition, there are bifurcated C—H…Se,O interactions which link the molecules into ribbons in the c direction. For 15 , the C—Se bond lengths are longer than those of 14 . The two five‐membered rings are coplanar. There are no π–π or C—H…π interactions; however, molecules are linked by C—H…O interactions into centrosymmetric dimers, with graph‐set notation R₂²(16).     

3,7‐Dibromohinokitiol: a redetermination

The structure of the title compound (systematic name: 3,7‐di­bromo‐2‐hydroxy‐6‐iso­propyl­cyclo­hepta‐2,4,6‐trien‐1‐one), C₁₀H₁₀Br₂O₂, previously described by Ito, Fukazawa & Iitaka [Tetrahedron Lett. (1972), 13 , 745–749], has been redetermined. Strong inter‐ and intramolecular hydrogen bonds, with H...O distances of 2.17 (9) and 2.06 (6) Å, respectively, are observed. There are also two short Br...Br and two short Br...(ring centroid) interactions. Important dimensions include C—O(carbonyl) = 1.252 (5) Å, C—O(hydroxyl) = 1.355 (5) Å, C—Br(3‐position) = 1.904 (4) Å and C—Br(7‐­position) = 1.905 (4) Å, and an O—C—C—O ring torsion angle of −6.7 (6)°.     

Improved Synthesis of Indirubin Derivatives by Sequential Build‐Up of the Indoxyl Unit: First Preparation of Fluorescent Indirubins

Indirubin, present in extracts of Isatis tinctoria and some other plant species, has promising cytotoxicity against a variety of cell lines by inhibition of cyclin‐dependent kinases. Chemical synthesis of its derivatives relies on the combination of isatins and 2,3‐dihydro‐1H‐indol‐3‐one (‘indoxyl’) derivatives and usually yields indigo as well as other by‐products. Inspection of the hydrolysis of the long‐known condensation products of 2‐thioxothiazolidin‐4‐one with isatins gave useful hints for an improved synthesis of indirubins: this reaction does not yield quinoline derivatives but 2‐(2,3‐dihydro‐2‐oxo‐1H‐indol‐3‐ylidene)‐2‐sulfanyl acetic acids. By substitution of the sulfanyl group in this oxindoles with anilines and straightforward cyclization under Nazarov conditions, a broad variety of indirubins substituted in the indoxyl ring system are thus available, usually in very good purity and yield. Use of naphthylamines in this reaction sequence yields various fluorescent substances with λ_fl at ca. 630 nm.     

Tetrameric triphenylsilanol, (Ph3SiOH)4, and the adduct (Ph3SiOH)2–di­methyl sulfoxide,both at 120 K,and the adduct (Ph3SiOH)4–1,4‐dioxan at 150 K: interplay of O—H⋯O and C—H⋯π(arene) interactions

The structure of tetrameric tri­phenyl­silanol, C₁₈H₁₆OSi, (I), has been re‐investigated at 120 (2) K. The hydroxyl H atoms were readily located and one of the arene rings is disordered over two closely positioned sets of sites. The mol­ecules are linked into cyclic tetramers, having approximate (S₄) symmetry, via O—H?O hydrogen bonds [H?O 1.81–1.85 Å, O?O 2.634 (3)–2.693 (3) Å and O—H?O 156–166°]. At ambient temperature, there are indications of multiple disorder of the phenyl‐ring sites. In bis­(tri­phenyl­silanol) di­methyl sulfoxide solvate, 2C₁₈H₁₆OSi·C₂H₆OS, (II), the di­methyl sulfoxide component is disordered across a twofold rotation axis in C2/c, and the molecular components are linked by a single O—H?O hydrogen bond [H?O 1.85 Å, O?O 2.732 (2) Å and O—H?O 172°] into three‐mol­ecule aggregates, which are themselves linked into a single three‐dimensional framework by two C—H?π(arene) interactions. In tetrakis­(tri­phenyl­silanol) 1,4‐dioxan solvate, 4C₁₈H₁₆OSi·C₄H₈O₂, (III), the 1,4‐dioxan component lies across an inversion centre in space group P and centrosymmetric five‐mol­ecule aggregates are linked by paired C—H?π(arene) interactions to form molecular ladders.     

Asymmetric Proline‐Catalyzed Addition of Aldehydes to 3H‐Indol‐3‐ones: Enantioselective Synthesis of 2,3‐Dihydro‐1H‐indol‐3‐ones with Quaternary Stereogenic Centers

The proline‐catalyzed addition of various aliphatic aldehydes to sterically hindered 2‐aryl‐substituted 3H‐indol‐3‐ones affords 2,2‐disubstituted 2,3‐dihydro‐1H‐indol‐3‐one derivatives with excellent enantioselectivities. In addition, the synthesis of a chiral derivative, (S)‐2‐(2‐bromophenyl)‐2,3‐dihydro‐2‐(2‐hydroxyethyl)‐1H‐indol‐3‐one, which can be used as an intermediate for the preparation of the natural product hinckdentine A was accomplished with a high level of enantioselectivity.     

Polymeric μ‐bromo‐μ‐pyridine‐3‐carboxyl­ato‐κ3O,O′:N‐mercury(II)

The asymmetric unit of the title polymeric complex, [HgBr(C₆H₄NO₂)]_n or HgBr(nic), contains mercury coordinated via two Br atoms [Hg—Br = 2.6528 (9) and 2.6468 (9) Å], two carboxyl­ate O atoms, which form a characteristic four‐membered chelate ring [Hg—O = 2.353 (6) and 2.478 (7) Å], and an N atom [Hg—N = 2.265 (5) Å], in the form of a very irregular (3+2)‐coordination polyhedron. The pronounced irregularity of the effective Hg (3+2)‐coordination is a result of the rigid stereochemistry of the nicotinate ligand. According to the covalent and van der Waals radii criteria, the strongest bonds are Hg—Br and Hg—N. These covalent interactions form a two‐dimensional poly­mer. The puckered planes are connected by van der Waals interactions, and there are only two intermolecular C—H⋯O hydrogen bonds [3.428 (10) and 3.170 (10) Å].     

A tetrabromo‐1,4‐ethanonaphthalene and related dibromo‐1,4‐ethenonaphthalene

(1RS,3RS,4RS,10SR)‐2,2,3,10‐Tetrabromo‐1,2,3,4‐tetrahydro‐1,4‐ethanonaphthalene, C₁₂H₁₀Br₄, (I), is the first structure to be reported with four Br atoms bound to a 1,4‐ethanonaphthalene framework and also the first which possesses three Br atoms in exo positions. Interactions between the Br atoms [three short intramolecular Br...Br distances of 3.1094 (4), 3.2669 (4) and 3.4415 (5) Å] have little effect on the C—C bond lengths but lead to significant twisting of the cage structure compared with the parent hydrocarbon, which is expected to be fully eclipsed at the two saturated C₂H₄ bridge positions. Chemically related (1SR,4RS)‐2,3‐dibromo‐1,4‐ethenonaphthalene, C₁₂H₈Br₂, (II), obtained by double dehydrobromination of (I), represents the first structure of any halogen‐substituted benzobarrelene. This cis‐dibromide shows little evidence of steric congestion at the double bond [Br...Br = 3.5276 (8) Å] as a consequence of the large C—C—Br angles [average C=C—Br angle = 126.15 (10)°].     

2,3,12,13‐Tetrabromo‐5,10,15,20‐tetrakis(4‐butoxyphenyl)porphyrin 1,2‐dichloroethane solvate

Nonmesogenic 2,3,12,13‐tetrabromo‐5,10,15,20‐tetrakis(4‐butoxyphenyl)porphyrin crystallizes as the title 1,2‐dichloroethane solvate, C₆₀H₅₈Br₄N₄O₄·C₂H₄Cl₂. The porphyrin ring shows a nonplanar conformation, with an average mean plane displacement of the β‐pyrrole C atoms from the 24‐atom (C₂₀N₄) core of ±0.50 (3) Å. The 1,2‐dichloroethane solvent is incorporated between the porphyrin units and induces the formation of one‐dimensional chains via interhalogen Cl...Br and butyl–aryl C—H...π interactions. These chains are oriented along the unit‐cell a axis, with the macrocyclic ring planes lying almost parallel to the (010) plane. The chains are arranged in an offset fashion by aligning the butoxy chains approximately above or below the faces of the adjacent porphyrin core, resulting in decreased interporphyrin π–π interactions, and they are held together by weak intermolecular (C—Br...π, C—H...π and C—H...Br) interactions. The nonplanar geometry of the macrocyclic ring is probably due to the weak interporphyrin interactions induced by the solvent molecule and the peripheral butoxy groups. The nonplanarity of the mesogens could influence the mesogenic behaviour differently relative to planar porphyrin mesogens.     

The seven‐membered nickelacycle [NiBr{o‐CH=C(CF3)C6H4CH2PPh2‐κ2C,P}{PPh(CH2Ph)2}]

The crystal and molecular structures of the title compound, 3‐bromo‐3‐(di­benzyl­phenyl­phospho­nio)‐2,2‐di­phenyl‐5‐trifluoromethyl‐1H‐benzo­[e][1,2]­phosphanickelepine, [NiBr(C₂₂H₁₇F₃P)(C₂₀H₁₉P)], which was obtained as the major regioisomer from insertion of HCCCF₃ into the Ni—C bond of the five‐membered phosphanickelacycle [NiBr(o‐C₆H₄CH₂PPh₂‐κ²C,P){PPh(CH₂Ph)₂}], have been determined. Principal geometric data include the Ni—X bond lengths Ni—Br 2.3343 (4) Å, Ni—P 2.1867 (7) and 2.2094 (7) Å, and Ni—C 1.882 (3) Å, and the two trans angles P—Ni—P 171.55 (3)° and Br—Ni—C 176.88 (9)°.     

(8‐Dimethylamino‐1‐naphthyl)dimethylammonium 3‐carboxy‐1,4,5,‐6,7,7‐hexachlorobicyclo[2.2.1]hept‐5‐ene‐2‐carboxylate hydrate

The structure of the title compound, C₁₄H₁₉N₂⁺·C₉H₃Cl₆O₄^?·H₂O, consists of singly ionized 1,4,5,6,7,7‐hexachlorobicyclo[2.2.1]hept‐5‐ene‐2,3‐dicarboxylic acid anions and protonated 1,8‐bis(dimethylamino)naphthalene cations. In the (8‐dimethylamino‐1‐napthyl)dimethylammonium cat­ion, a strong disordered intramolecular hydrogen bond is formed with N?N = 2.589 (3) Å. The geometry and occupancy obtained in the final restrained refinement suggest that the disordered hydrogen bond may be asymmetric. Water mol­ecules link the anion dimers into infinite chains via hydrogen bonding.     

4,8‐Di­methoxy‐1‐naphthalene­methanol

The title compound, C₁₃H₁₄O₃, crystallized in the centrosymmetric space group C2/c with one mol­ecule as the asymmetric unit. Each hydroxyl O atom is involved in hydrogen bonds with two other hydroxyl O atoms. The resulting chains of interactions propagate along [001]. In these interactions, the hydroxyl H atoms are disordered and the O?O distances are 2.648 (2) and 2.698 (2) Å. Two leading intermolecular C—H?O interactions have H?O distances of 2.80 and 2.84 Å and C—H?O angles of 136 and 144°; these interactions form chain and ring patterns. Taken together with the hydrogen bonds, they result in a three‐dimensional network.     

Different molecular conformations co‐exist in each of three 2‐aryl‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamides: hydrogen bonding in zero,one and two dimensions

4‐Antipyrine [4‐amino‐1,5‐dimethyl‐2‐phenyl‐1H‐pyrazol‐3(2H)‐one] and its derivatives exhibit a range of biological activities, including analgesic, antibacterial and anti‐inflammatory, and new examples are always of potential interest and value. 2‐(4‐Chlorophenyl)‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamide, C₁₉H₁₈ClN₃O₂, (I), crystallizes with Z′ = 2 in the space group P, whereas its positional isomer 2‐(2‐chlorophenyl)‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamide, (II), crystallizes with Z′ = 1 in the space group C2/c; the molecules of (II) are disordered over two sets of atomic sites having occupancies of 0.6020 (18) and 0.3980 (18). The two independent molecules of (I) adopt different molecular conformations, as do the two disorder components in (II), where the 2‐chlorophenyl substituents adopt different orientations. The molecules of (I) are linked by a combination of N—H…O and C—H…O hydrogen bonds to form centrosymmetric four‐molecule aggregates, while those of (II) are linked by the same types of hydrogen bonds forming sheets. The related compound N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)‐2‐(3‐methoxyphenyl)acetamide, C₂₀H₂₁N₃O₃, (III), is isomorphous with (I) but not strictly isostructural; again the two independent molecules adopt different molecular conformations, and the molecules are linked by N—H…O and C—H…O hydrogen bonds to form ribbons. Comparisons are made with some related structures, indicating that a hydrogen‐bonded R₂²(10) ring is the common structural motif.     

The 7‐bromo derivative of 2‐amino‐2′‐deoxytubercidin fluorinated at the sugar moiety

The title compound, 2,4‐diamino‐5‐bromo‐7‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabinofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine, C₁₁H₁₃BrFN₅O₃, shows two conformations of the exocyclic C4′—C5′ bond, with the torsion angle γ (O5′—C5′—C4′—C3′) being 170.1 (3)° for conformer 1 (occupancy 0.69) and 60.7 (7)° for conformer 2 (occupancy 0.31). The N‐glycosylic bond exhibits an anti conformation, with χ = −114.8 (4)°. The sugar pucker is N‐type (C3′‐endo; ³T₄), with P = 23.3 (4)° and τ_m = 36.5 (2)°. The compound forms a three‐dimensional network that is stabilized by several intermolecular hydrogen bonds (N—H...O, O—H...N and N—H...Br).     

Di­bromo­[(–)‐sparteine‐κ2N,N′]­zinc(II)

In the title compound, di­bromo­[(6R,7S,8S,14S)‐1,3,4,7,7a,8,9,10,11,13,14,14a‐dodeca­hydro‐7,14‐methano‐2H,6H‐dipyrido­[1,2‐a:1′,2′‐e][1,5]­diazo­cine‐κ²N,N′]­zinc(II), [ZnBr₂(C₁₅H₂₆N₂)], the chiral nitro­gen‐chelating alkaloid (?)‐l ‐sparteine acts as a bidentate ligand, with two bromide ligands occupying the remaining coordination sites, producing a slightly distorted tetrahedral structure. The dihedral angle between the N—Zn—N and Br—Zn—Br planes is 82.4 (1)°. The distortion of the tetrahedral coordination is demonstrated by the fact that the midpoint of the N?N line does not lie in the Br—Zn—Br plane, but is tilted towards one of the N atoms by 0.164 Å. Similarly, the midpoint of the Br?Br line is tilted towards one of the Br atoms by 0.117 Å.     

The sesquiterpenoid nootkatone and the absolute configuration of a di­bromo derivative

Nootkatone, or (4R,4aS,6R)‐4,4a,5,6,7,8‐hexa­hydro‐4,4a‐di­methyl‐6‐(1‐methyl­ethenyl)­naphthalen‐2(3H)‐one, C₁₅H₂₂O, a sesquiterpene with strong repellent properties against Formosan subterranean termites and other insects, has the valencene skeleton. The di­bromo derivative (1S,3R,4S,4aS,6R,8aR)‐1,3‐di­bromo‐6‐iso­propyl‐4,4a‐di­methyl‐1,2,3,4,5,6,7,8‐octa­hydro­naphthalen‐2‐one, C₁₅H₂₄Br₂O, has two independent mol­ecules in the asymmetric unit, which differ in the rotation of the iso­propyl group with respect to the main skeleton. The C—Br distances are in the range 1.950 (4)–1.960 (4) Å. Both independent molecules form zigzag chains, with very short intermolecular carbonyl–carbonyl interactions, having the perpendicular motif and O⋯C distances of 2.886 (6) and 2.898 (6) Å. These chains are flanked by intermolecular Br⋯Br interactions of distances in the range 4.067 (1)–4.218 (1) Å. The absolute configuration of the di­bromo derivative was determined, from which that of nootkatone was inferred.     

An analysis of C—H⋯O and C—H⋯π interactions in three substituted 4‐ketotetra­hydro­indoles

The crystal and molecular structures of the three 4‐ketotetrahydro­indoles 2‐(4‐chloro­phenyl)‐1‐(4‐fluoro­phenyl)‐6,6‐dimethyl‐4,5,6,7‐tetra­hydro‐1H‐indol‐4‐one (C₂₂H₁₉ClFNO), (I), 1‐(4‐fluoro­phenyl)‐2‐(4‐methoxy­phenyl)‐6,6‐di­methyl‐4,5,6,7‐tetra­hydro‐1H‐indol‐4‐one (C₂₃H₂₂FNO₂), (II), and 6,6‐dimethyl‐1,2‐di­phenyl‐4,5,6,7‐tetra­hydro‐1H‐indol‐4‐one (C₂₂H₂₁NO), (III), have been determined via single‐crystal X‐ray diffraction in order to study the intermolecular interactions therein. All three structures are stabilized via intermolecular C—H⋯O and C—H⋯π interactions, generating different molecular motifs.     

Seven 3‐methylidene‐1H‐indol‐2(3H)‐ones related to the multiple‐receptor tyrosine kinase inhibitor sunitinib

The solid‐state structures of a series of seven substituted 3‐methylidene‐1H‐indol‐2(3H)‐one derivatives have been determined by single‐crystal X‐ray diffraction and are compared in detail. Six of the structures {(3Z)‐3‐(1H‐pyrrol‐2‐ylmethylidene)‐1H‐indol‐2(3H)‐one, C₁₃H₁₀N₂O, (2a); (3Z)‐3‐(2‐thienylmethylidene)‐1H‐indol‐2(3H)‐one, C₁₃H₉NOS, (2b); (3E)‐3‐(2‐furylmethylidene)‐1H‐indol‐2(3H)‐one monohydrate, C₁₃H₉NO₂·H₂O, (3a); 3‐(1‐methylethylidene)‐1H‐indol‐2(3H)‐one, C₁₁H₁₁NO, (4a); 3‐cyclohexylidene‐1H‐indol‐2(3H)‐one, C₁₄H₁₅NO, (4c); and spiro[1,3‐dioxane‐2,3′‐indolin]‐2′‐one, C₁₁H₁₁NO₃, (5)} display, as expected, intermolecular hydrogen bonding (N—H...O=C) between the 1H‐indol‐2(3H)‐one units. However, methyl 3‐(1‐methylethylidene)‐2‐oxo‐2,3‐dihydro‐1H‐indole‐1‐carboxylate, C₁₃H₁₃NO₃, (4b), a carbamate analogue of (4a) lacking an N—H bond, displays no intermolecular hydrogen bonding. The structure of (4a) contains three molecules in the asymmetric unit, while (4b) and (4c) both contain two independent molecules.