Exploring the structural landscape of 2‐(thiophen‐2‐yl)‐1,3‐benzothiazole: high‐Z′ packing polymorphism and cocrystallization with calix[4]tube

We report here for the first time a cocrystal of the so‐called neutral calix[4]tube, which is two tail‐to‐tail‐arranged and partially deprotonated tetrakis(carboxymethoxy)calix[4]arenes, including three sodium ions, with 2‐(thiophen‐2‐yl)‐1,3‐benzothiazole, namely trisodium bis(carboxymethoxy)bis(carboxylatomethoxy)calix[4]arene tris(carboxymethoxy)(carboxylatomethoxy)calix[4]arene–2‐(thiophen‐2‐yl)‐1,3‐benzothiazole–dimethyl sulfoxide–water (1/1/2/2), 3Na⁺·C₃₆H₃₀O₁₂^2?·C₃₆H₃₁O₁₂^?·C₁₁H₇NS₂·2C₂H₆OS·2H₂O, which provides a new approach into the host–guest chemistry of inclusion complexes. Three packing polymorphs of the same benzothiazole with high Z′ (one with Z′ = 8 and two with Z′ = 4) were also discovered in the course of our desired cocrystallization. The inspection of these polymorphs and a previously known polymorph with Z′ = 2 revealed that Z′ increases as the strength of intermolecular contacts decreases. Also, these results expand the frontier of invoking calixarenes as a host for nonsolvent small molecules, besides providing knowledge on the rare formation of high‐Z′ packing polymorphs of simple molecules, such as the target benzothiazole.     

Wave‐like structure in 3‐(4,6‐diamino‐1,3,5‐triazin‐2‐yl)‐2‐naphthonitrile

In the title compound, C₁₄H₁₀N₆, which crystallizes with Z′ = 2 in the C2/c space group, the molecules are linked by N—H...N hydrogen bonds into chains, which are arranged in a wave‐like form stabilized by aromatic π–π stacking interactions. This work demonstrates the usefulness of aromatic triazine derivatives in crystal engineering.     

Two polymorphs,with Z′ = 1 and 2, of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine in P21/c,and 2‐amino‐4‐chloro‐6‐piperidino­pyrimidine,which is isomorphous and almost isostructural with the Z′ = 2 polymorph

Crystallization of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine, C₈H₁₁ClN₄O, (I), yields two polymorphs, both with space group P2₁/c, having Z′ = 1 (from diethyl ether solution) and Z′ = 2 (from di­chloro­methane solution), denoted (Ia) and (Ib), respectively. In polymorph (Ia), the mol­ecules are linked by an N—H⋯O and an N—H⋯N hydrogen bond into sheets built from alternating R(8) and R(40) rings. In polymorph (Ib), one mol­ecule acts as a triple acceptor of hydrogen bonds and the other acts as a single acceptor; one N—H⋯O and three N—H⋯N hydrogen bonds link the mol­ecules in a complex chain containing two types of R(8) and one type of R(18) ring. 2‐Amino‐4‐chloro‐6‐piperidino­pyrimidine, C₉H₁₃ClN₄, (II), which is isomorphous with polymorph (Ib), also has Z′ = 2 in P2₁/c, and the mol­ecules are linked by three N—­H⋯N hydrogen bonds into a centrosymmetric four‐mol­ecule aggregate containing three R(8) rings.     

Z/E‐Isomerism of 3‐[4‐(dimethylamino)phenyl]‐2‐(2,4,6‐tribromophenyl)acrylonitrile: crystal structures and secondary intermolecular interactions

The Z and E isomers of 3‐[4‐(dimethylamino)phenyl]‐2‐(2,4,6‐tribromophenyl)acrylonitrile, C₁₇H₁₃Br₃N₂, ( 1 ), were obtained simultaneously by a Knoevenagel condensation between 4‐(dimethylamino)benzaldehyde and 2‐(2,4,6‐tribromophenyl)acetonitrile, and were investigated by X‐ray diffraction and density functional theory (DFT) quantum‐chemical calculations. The (Z)‐( 1 ) isomer is monoclinic (space group P2₁/n, Z′ = 1), whereas the (E)‐( 1 ) isomer is triclinic (space group P, Z′ = 2). The two crystallographically‐independent molecules of (E)‐( 1 ) adopt similar geometries. The corresponding bond lengths and angles in the two isomers of ( 1 ) are very similar. The difference in the calculated total energies of isolated molecules of (Z)‐( 1 ) and (E)‐( 1 ) with DFT‐optimized geometries is ∼4.47 kJ mol⁻¹, with the minimum value corresponding to the Z isomer. The crystal structure of (Z)‐( 1 ) reveals strong intermolecular nonvalent Br…N [3.100 (2) and 3.216 (3) Å] interactions which link the molecules into layers parallel to (10). In contrast, molecules of (E)‐( 1 ) in the crystal are bound to each other by strong nonvalent Br…Br [3.5556 (10) Å] and weak Br…N [3.433 (4) Å] interactions, forming chains propagating along [110]. The crystal packing of (Z)‐( 1 ) is denser than that of (E)‐( 1 ), implying that the crystal structure realized for (Z)‐( 1 ) is more stable than that for (E)‐( 1 ).     

Hydrogen bonding in C‐substituted nitroanilines: molecular ladders in 2‐trifluoromethyl‐4‐nitroaniline and sheets of R(12) and R(32) rings in 3‐trifluoromethyl‐4‐nitroaniline

In 2‐tri­fluoro­methyl‐4‐nitro­aniline, C₇H₅F₃N₂O₂, (I), the mol­ecules lie across a mirror plane in space group Pnma. The mol­ecules are linked by paired N—H?O hydrogen bonds to form a C(8)[R(6)] chain of rings, pairs of which are linked into a molecular ladder by a single C—H?O hydrogen bond. The isomeric 3‐tri­fluoro­methyl‐4‐nitro­aniline, (II), has Z′ = 2 in space group P2₁/c. Each mol­ecule is linked to four others by N—H?O hydrogen bonds to form sheets built from alternating R(12) and R(32) rings.     

(Acetato‐κO)aqua(1H‐imidazole‐κN3)(picolinato‐κ2N,O)copper(II) 0.87‐hydrate: a Z′> 1 structure

The crystal structure of the title compound, [Cu(C₆H₄NO₂)(C₂H₃O₂)(C₃H₄N₂)(H₂O)]·0.87H₂O, has a square‐pyramidal‐coordinated Cu^II centre (the imidazole is trans to the picolinate N atom, the acetate is trans to the picolinate –CO₂ group and the aqua ligand is in a Jahn–Teller‐elongated apical position) and has two symmetry‐independent molecules in the unit cell (Z′ = 2), which are connected through complementary imidazole–picolinate N—H...O hydrogen bonding. The two partially occupied solvent water molecules are each disordered over two positions. The disordered solvent water molecules, together with pseudosymmetry elements, support the notion that a crystal structure with multiple identical chemical formula units in the structural asymmetric unit (Z′ > 1) can represent a crystal `on the way', that is, a kinetic intermediate form which has not yet reached its thermodynamic minimum. Neighbouring molecules form π–π stacks between their imidazole and picolinate N‐heterocycles, with centroid–centroid distances in the range 3.582 (2)–3.764 (2) Å.     

Preparation and structural analysis of (±)‐cis‐ethyl 2‐sulfanylidenedecahydro‐1,6‐naphthyridine‐6‐carboxylate and (±)‐trans‐ethyl 2‐oxooctahydro‐1H‐pyrrolo[3,2‐c]pyridine‐5‐carboxylate

Bicycle ring closure on a mixture of (4aS,8aR)‐ and (4aR,8aS)‐ethyl 2‐oxodecahydro‐1,6‐naphthyridine‐6‐carboxylate, followed by conversion of the separated cis and trans isomers to the corresponding thioamide derivatives, gave (4aSR,8aRS)‐ethyl 2‐sulfanylidenedecahydro‐1,6‐naphthyridine‐6‐carboxylate, C₁₁H₁₈N₂O₂S. Structural analysis of this thioamide revealed a structure with two crystallographically independent conformers per asymmetric unit (Z′ = 2). The reciprocal bicycle ring closure on (3aRS,7aRS)‐ethyl 2‐oxooctahydro‐1H‐pyrrolo[3,2‐c]pyridine‐5‐carboxylate, C₁₀H₁₆N₂O₃, was also accomplished in good overall yield. Here the five‐membered ring is disordered over two positions, so that both enantiomers are represented in the asymmetric unit. The compounds act as key intermediates towards the synthesis of potential new polycyclic medicinal chemical structures.     

trans‐(dl‐Isoleucinato‐N,O)[tris(2‐aminoethyl)amine‐κ4N]cobalt(III) diperchlorate

The racemic title compound, trans‐[N,N‐bis(2‐amino­ethyl)‐1,2‐ethanediamine‐κ⁴N]­(dl ‐isoleucinato‐N,O)­cobalt(III) di­per­chlor­ate, [Co(C₆H₁₈N₄)(C₆H₁₂NO₂)](ClO₄)₂, crystallizes in the enantiomorphous space group P2₁2₁2₁ with Z = 12 (Z′ = 3). Each of the three cations in the asymmetric unit represents a different chirality of the isoleucine ligand; two of them are R (or d ) and the third is the S (or l ) enantiomer. The mixture crystallizes in a so‐called unbalanced crystallization, in which the cations adopt a chiral array of composition RRS or SSR, depending on the crystal selected for data collection.     

Two enamines derived from 1‐n‐alkyl‐3‐methylpyrazol‐5‐ones

The first two crystal structures of en­amines derived from 1‐n‐alkyl‐3‐methyl‐5‐pyrazolones, namely 1‐(n‐hexyl)‐3‐methyl‐4‐[1‐(phenyl­amino)­propyl­idene]‐2‐pyrazolin‐5‐one, C₁₉H₂₇N₃O, (I), and N,N′‐bis{1‐[1‐(n‐hexyl)‐3‐methyl‐5‐oxo‐2‐pyrazolin‐4‐yl­idene]­ethyl}hexane‐1,6‐di­amine, C₃₀H₅₂N₆O₂, (II), are reported. The mol­ecule of (II) lies about an inversion centre. Both (I) and (II) are stabilized by intramolecular N—H⋯O hydrogen bonding. This confirms previous results based on spectroscopic evidence alone.     

3‐Benzyl‐2‐(4‐fluorophenyl)‐1,3‐thiazolidin‐4‐one

The title compound, C₁₆H₁₄FNOS, crystallizes with Z′ = 2 in the space group P2₁/c. In one of the two independent molecules, the heterocyclic ring is effectively planar, but in the other molecule this ring adopts an envelope conformation. The molecules are weakly linked by two C—H...O hydrogen bonds to form C₂²(14) chains. Comparisons are made with some symmetrically substituted 2‐aryl‐3‐benzyl‐1,3‐thiazolidin‐4‐ones.     

4‐Ethynyl‐4‐hydroxycyclohexan‐1‐one and 4‐ethynyl‐4‐hydroxy‐2,3,5,6‐tetramethylcyclohexa‐2,5‐dien‐1‐one

The title compounds, C₈H₁₀O₂, (I), and C₁₂H₁₄O₂, (II), occurred as by‐products in the controlled synthesis of a series of bis­(gem‐alkynols), prepared as part of an extensive study of synthon formation in simple gem‐alkynol derivatives. The two 4‐(gem‐alkynol)‐1‐ones crystallize in space group P2₁/c, (I) with Z′ = 1 and (II) with Z′ = 2. Both structures are dominated by O—H?O=C hydrogen bonds, which form simple chains in the cyclo­hexane derivative, (I), and centrosymmetric dimers, of both symmetry‐independent mol­ecules, in the cyclo­hexa‐2,5‐diene, (II). These strong synthons are further stabilized by C[triple‐bond]C—H?O=C, C_methylene—H?O(H) and C_methyl—H?O(H) interactions. The direct intermolecular interactions between donors and acceptors in the gem‐alkynol group, which characterize the bis­(gem‐alkynol) analogues of (I) and (II), are not present in the ketone derivatives studied here.     

3‐[5‐(4‐Chlorophenyl)‐1‐(4‐methoxyphenyl)‐1H‐pyrazol‐3‐yl]propionic acid and the corresponding methyl ester

The synthesis of 3‐[5‐(4‐chlorophenyl)‐1‐(4‐methoxyphenyl)‐1H‐pyrazol‐3‐yl]propionic acid, C₁₉H₁₇ClN₂O₃, (I), and its corresponding methyl ester, methyl 3‐[5‐(4‐chlorophenyl)‐1‐(4‐methoxyphenyl)‐1H‐pyrazol‐3‐yl]propionate, C₂₀H₁₉ClN₂O₃, (II), is regiospecific. However, correct identification of the regioisomer formed by spectroscopic techniques is not trivial and single‐crystal X‐ray analysis provided the only means of unambiguous structure determination. Compound (I) crystallizes with Z′ = 2. The propionic acid groups of the two crystallographically unique molecules form a hydrogen‐bonded dimer, as is typical of carboxylic acid groups in the solid state. Conformational differences between the methoxybenzene and pyrazole rings give rise to two unique molecules. The structure of (II) features just one molecule in the asymmetric unit and the crystal packing makes greater use than (I) of weak C—H...A interactions, despite the lack of any functional groups for classical hydrogen bonding.     

Synthesis and Cytotoxicity of Arene‐Ru Compounds Containing 4‐Nitroaniline or 2‐Halogenated 4‐Nitroaniline

The compounds [(η⁶‐p‐cymene)RuCl₂(4‐nitroaniline)] and [(η⁶‐p‐cymene)RuCl₂(2‐halogen‐4‐nitroaniline)] were synthesized and characterized by various means. The [(η⁶‐p‐cymene)RuCl₂(4‐nitroaniline)] and [(η⁶‐p‐cymene)RuCl₂(2‐fluoro‐4‐nitroaniline)] compounds were determined by X‐ray diffraction, appearing in a distorted piano‐stool type of arrangement with similar bond lengths and angles around the ruthenium. The compounds exhibited moderate to strong in vitro cytotoxicity against A549 and MCF‐7 human cancer cells. Substitution of heavy halogen atom on the ortho position of para‐nitroaniline weakened the cytotoxicity against both of MCF‐7 and A549, except the cases of fluorine substitution for hydrogen atom regarding A549 and bromine substitution for chlorine atom regarding MCF‐7, which showed minor deviation.     

Quervernetzung lamellarer Schichten mit Hilfe von (O–H…O)‐Wasserstoffbrücken: Strukturen von M⊕⊖N(SO2C6H4‐4‐COOH)2 (M⊕ = K⊕, Rb⊕, Cs⊕)

Structures of Ionic Di(arenesulfonyl)amides. 4. Cross‐Linking Lamellar Layers by O–H…O Hydrogen Bonds: Structures of M^⊕⊖N(SO₂C₆H₄‐4‐COOH)₂ (M^⊕ = K^⊕, Rb^⊕, Cs^⊕) Syntheses and low‐temperature X‐ray crystal structures are reported for M^IN(SO₂C₆H₄‐4‐COOH)₂, where M = K (monoclinic, space group P2₁/c, Z = 4, Z′ = 1), M = Rb (monoclinic, P2₁, Z = 4, Z′ = 2), or M = Cs (monoclinic, P2₁/c, Z = 4, Z′ = 1). The three compounds are examples of layered inorgano‐organic solids where the inorganic component is comprised of metal cations and N(SO₂)₂ groups and the outer regions are formed by the 4‐carboxy substituted phenyl rings of the folded anions. In the two‐dimensional coordination networks, K^⊕ and Cs^⊕ adopt irregular and chemically distinct [MN₁O₇] octacoordinations, whereas the independent Rb^⊕ cations attain irregular nonacoordinations of type [RbN₂O₇] or [RbO₉] respectively. The crystal packings of the compounds are governed by self‐assembly of parallel layers through exhaustive hydrogen bonding between carboxylic acid groups, resulting in a dense array of cyclic (COOH)₂ motifs within the interlamellar regions.     

Synthesis and tuberculostatic activity of novel N′‐methyl‐4‐(pyrrolidin‐1‐yl)picolinohydrazide and N′‐methylpyrimidine‐2‐carbohydrazide derivatives

The synthesis of N′‐methyl‐4‐(pyrrolidin‐1‐yl)picolinohydrazide and N′‐methyl‐pyrimidine‐2‐carbohydrazide derivatives ( 5a and 5b ) was carried out. These compounds were used as starting materials to obtain methyl N′‐methylhydrazinecarbodithioates 6a and 6b , which, on reaction with either triethylamine or hydrazine, gave corresponding 1,3,4‐oxadiazioles 7a and 7b or 1,2,4‐triazoles 9a and 9b with the free NH₂ group at the N‐4 position, respectively. Compounds 8a – e , particularly containing cyclic amines at N‐4 of the 1,2,4‐triazole ring, were also obtained. Synthesized compounds were tested in vitro for their activity against Mycobacterium tuberculosis. The structure–activity relationship analysis for obtained compounds was done. © 2012 Wiley Periodicals, Inc. Heteroatom Chem 23:223–230, 2012; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.21008     

4- (4,6-二甲基嘧啶-2-基)-3-硫代脲酸甲酯的合成晶体结构及量子化学研究

4-（4,6-Dimethylpyrimidin-2-yl）-3-thio-allophanic acid methyl ester was synthesized with mixing 2-amino-4,6- dimethylpyrimidine, potassium thiocyanate and methyl chloroformate in ethyl acetate. Single crystals suitable for X-ray diffraction measurement were obtained by recrystallization from dimethylformamide at room temperature. The crystal belongs to monoclinic symmetry with space group C2/m, and crystal parameters of a= 1.7537（5） nm, b= 0.6759（2） nm, c=1.1148（3） nm, β=118.557（4）°, V=1.1605（6） nm^3, Z=4, De= 1.375 g/cm^3,μ=0.271 mm^-1, F（000）=504, and 1519 [1〉2σ（I）] observable independent reflections were used for the determination and refmement of the crystal structures with final R1 of 0.0372 and wR2 of 0.0992. The theoretical investigation of the title compound was carried out with DRT-B3LYP/6-311G, HF/6-311G and MP2/6-311G methods, and the atomic net charges and the population were discussed.     

5,5′‐Bis(hydroxymethyl)‐3,3′‐dimethoxybiphenyl‐2,2′‐diol with a new three‐dimensional 3‐modal topology of synthons

The title lignin model compound, C₁₆H₁₈O₆, resides on a twofold axis parallel with the b axis, with the mid‐point of the internal C—C(−x + 1, y, −z + ) bond located on the twofold axis. The exo angles between the methoxy groups and the benzene rings deviate significantly from the expected value of 120° [125.15 (7) and 114.27 (6)°]. A 12‐coordinated 3‐modal three‐dimensional net with a new topology was identified on the synthon level. A comparison of the flexibility of related o,o′‐disubstituted biphenyl derivatives and biphenyl is presented, with the angles between the ring planes in substituted biphenyls found to be in the range 40–70°.     

Synthesis,crystal structure and magnetic properties of diaquabis(2,6‐diamino‐7H‐purin‐1‐ium‐κN9)bis(4,4′‐oxydibenzoato‐κO)cobalt(II) dihydrate

The title mononuclear Co^II complex, [Co(C₅H₇N₆)₂(C₁₄H₈O₅)₂(H₂O)₂]·2H₂O, has been synthesized and its crystal structure determined by X‐ray diffraction. The complex crystallizes in the triclinic space group P, with one formula unit per cell (Z = 1 and Z′ = ). It consists of a mononuclear unit with the Co^II ion on an inversion centre coordinated by two 2,6‐diamino‐7H‐purin‐1‐ium cations, two 4,4′‐oxydibenzoate anions (in a nonbridging κO‐monodentate coordination mode, which is less common for the anion in its Co^II complexes) and two water molecules, defining an octahedral environment around the metal atom. There is a rich assortment of nonbonding interactions, among which a strong N⁺—H…O⁻ bridge, with a short N…O distance of 2.5272 (18) Å, stands out, with the H atom ostensibly displaced away from its expected position at the donor side, towards the acceptor. The complex molecules assemble into a three‐dimensional hydrogen‐bonded network. A variable‐temperature magnetic study between 2 and 300 K reveals an orbital contribution to the magnetic moment and a weak antiferromagnetic interaction between Co^II centres as the temperature decreases. The model leads to the following values: A (crystal field strength) = 1.81, λ (spin‐orbit coupling) = −59.9 cm⁻¹, g (Landé factor) = 2.58 and zJ (exchange coupling) = −0.5 cm⁻¹.     

(±)‐(2,3,4,4a,5,6,7,8‐Octa­hydro‐2‐oxo­naphthalen‐1‐yl)acetic acid: hydrogen‐bonding pattern of the mono­hydrate of an unsaturated bicyclic γ‐keto acid

In the title compound, C₁₂H₁₆O₃·H₂O, the water of hydration accepts a hydrogen bond from the carboxyl group and donates hydrogen bonds to the carboxyl carbonyl and the ketone groups of two different neighbors, yielding a complex three‐dimensional hydrogen‐bonding array. There are two independent hydrated mol­ecules in the asymmetric unit (Z′ = 2) related by a pseudo‐translation.     

Four (E,Z,E)‐1‐(4‐alkoxy­phen­yl)‐6‐(4‐nitro­phen­yl)hexa‐1,3,5‐trienes

The crystal structures of the four E,Z,E isomers of 1‐(4‐alk­oxy­phen­yl)‐6‐(4‐nitro­phen­yl)hexa‐1,3,5‐triene, namely (E,Z,E)‐1‐(4‐methoxy­phen­yl)‐6‐(4‐nitro­phen­yl)hexa‐1,3,5‐triene, C₁₉H₁₇NO₃, (E,Z,E)‐1‐(4‐ethoxy­phen­yl)‐6‐(4‐nitro­phen­yl)hexa‐1,3,5‐triene, C₂₀H₁₉NO₃, (E,Z,E)‐1‐(4‐nitro­phen­yl)‐6‐(4‐n‐propoxyphen­yl)hexa‐1,3,5‐triene, C₂₁H₂₁NO₃, and (E,Z,E)‐1‐(4‐n‐butoxy­phen­yl)‐6‐(4‐nitro­phen­yl)hexa‐1,3,5‐triene, C₂₂H₂₃NO₃, have been determined. Inter­molecular N⋯O dipole inter­actions between the nitro groups are observed for the meth­oxy derivative, while for the eth­oxy derivative, two adjacent mol­ecules are linked at both ends through N⋯O dipole–dipole inter­actions between the N atom of the nitro group and the O atom of the eth­oxy group to form a supra­molecular ring‐like structure. In the crystal structures of the n‐prop­oxy and n‐but­oxy derivatives, the shortest inter­molecular distances are those between the two O atoms of the alk­oxy groups. Thus, the nearest two mol­ecules form an S‐shaped supra­molecular dimer in these crystal structures.