Comparison of the crystal structures of the potent anticancer and anti‐angiogenic agent regorafenib and its monohydrate

Regorafenib {systematic name: 4‐[4‐({[4‐chloro‐3‐(trifluoromethy)phenyl]carbamoyl}amino)‐3‐fluorophenoxy]‐1‐methylpyridine‐2‐carboxamide}, C₂₁H₁₅ClF₄N₄O₃, is a potent anticancer and anti‐angiogenic agent that possesses various activities on the VEGFR, PDGFR, raf and/or flt‐3 kinase signaling molecules. The compound has been crystallized as polymorphic form I and as the monohydrate, C₂₁H₁₅ClF₄N₄O₃·H₂O. The regorafenib molecule consists of biarylurea and pyridine‐2‐carboxamide units linked by an ether group. A comparison of both forms shows that they differ in the relative orientation of the biarylurea and pyridine‐2‐carboxamide units, due to different rotations around the ether group, as measured by the C—O—C bond angles [119.5 (3)° in regorafenib and 116.10 (15)° in the monohydrate]. Meanwhile, the conformational differences are reflected in different hydrogen‐bond networks. Polymorphic form I contains two intermolecular N—H…O hydrogen bonds, which link the regorafenib molecules into an infinite molecular chain along the b axis. In the monohydrate, the presence of the solvent water molecule results in more abundant hydrogen bonds. The water molecules act as donors and acceptors, forming N—H…O and O—H…O hydrogen‐bond interactions. Thus, R₄²(28) ring motifs are formed, which are fused to form continuous spiral ring motifs along the a axis. The (trifluoromethyl)phenyl rings protrude on the outside of these motifs and interdigitate with those of adjacent ring motifs, thereby forming columns populated by halogen atoms.     

The effect of Cl...π interactions on the conformations of 4‐chloro‐5‐(2‐phenoxyethoxy)phthalonitrile and 4‐chloro‐5‐[2‐(pentafluorophenoxy)ethoxy]phthalonitrile

4‐Chloro‐5‐(2‐phenoxyethoxy)phthalonitrile, C₁₆H₁₁ClN₂O₂, (I), and 4‐chloro‐5‐[2‐(pentafluorophenoxy)ethoxy]phthalonitrile, C₁₆H₆ClF₅N₂O₂, (II), show different types of electrostatic interaction. In (I), the phenoxy and phthalonitrile (benzene‐1,2‐dicarbonitrile) moieties are well separated in an open conformation and intermolecular C—H...π interactions are observed in the crystal packing. On the other hand, in (II), the pentafluorophenoxy moiety interacts closely with the Cl atom to form a folded conformation containing an intramolecular halogen–π interaction.     

Three trifluoro­methyl‐substituted protoporphyrinogen IX oxidase inhibitors

The structures of methyl 5‐[2‐chloro‐4‐(trifluoro­methyl)phenoxy]‐2‐nitro­benzoate, C₁₅H₉ClF₃N₃O₅, (I), methyl 2‐chloro‐5‐[3‐methyl‐2,6‐dioxo‐4‐(trifluoro­methyl)‐1,2,3,6‐tetrahydro­pyrimidin‐1‐yl]benzoate, C₁₄H₁₀ClF₃N₂O₄, (II), and 2‐[4‐chloro‐2‐fluoro‐5‐(prop‐2‐ynyloxy)phenyl]‐4‐(trifluoro­methyl)piperidine‐2,6‐dione, C₁₅H₁₀ClF₄NO₃, (III), are similar in their dihedral angles and in the distances between the farthest two atoms. There are two independent molecules in the structure of (I). The dihedral angles between the two aromatic rings in each molecule in (I), between the benzene and tetrahydro­pyrimidine rings in (II), and between the benzene ring and the five‐atom planar portion of the piperidine‐2,6‐dione ring in (III) are 80.78 (11)/89.75 (11), 89.13 (9) and 87.52 (13)°, respectively. The distances between the farthest two atoms, viz. O⋯F in the two molecules of (I), and Cl⋯F in (II) and (III), are 11.763 (7)/11.953 (6), 10.734 (10) and 10.889 (9) Å, respectively. In all three crystal structures, the molecules are linked to generate sheets of molecules via C—H⋯O interactions.     

N‐(X‐Chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide (with X = 2 and 4)

The structures of N‐(2‐chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide and N‐(4‐chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide, both C₁₆H₁₃ClN₂O₄S, are stabilized by extensive intramolecular hydrogen bonds. The 4‐chloro derivative forms dimeric pairs of molecules lying about inversion centres as a result of intermolecular N—H...O hydrogen bonds, forming 14‐membered rings representing an R₂²(14) motif; the 2‐chloro derivative is devoid of any such intermolecular hydrogen bonds. The heterocyclic thiazine rings in both structures adopt half‐chair conformations.     

The structures of 1,4‐diaryl‐5‐trifluoromethyl‐1H‐1,2,3‐triazoles related to J147, a drug for treating Alzheimer's disease

J147 [N‐(2,4‐dimethylphenyl)‐2,2,2‐trifluoro‐N′‐(3‐methoxybenzylidene)acetohydrazide] has recently been reported as a promising new drug for the treatment of Alzheimer's disease. The X‐ray structures of seven new 1,4‐diaryl‐5‐trifluoromethyl‐1H‐1,2,3‐triazoles, namely 1‐(3,4‐dimethylphenyl)‐4‐phenyl‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₇H₁₄F₃N₃, 1 ), 1‐(3,4‐dimethylphenyl)‐4‐(3‐methoxyphenyl)‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₈H₁₆F₃N₃O, 2 ), 1‐(3,4‐dimethylphenyl)‐4‐(4‐methoxyphenyl)‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₈H₁₆F₃N₃O, 3 ), 1‐(2,4‐dimethylphenyl)‐4‐(4‐methoxyphenyl)‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₈H₁₆F₃N₃O, 4 ), 1‐[2,4‐bis(trifluoromethyl)phenyl]‐4‐(3‐methoxyphenyl)‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₈H₁₀F₉N₃O, 5 ), 1‐(3,4‐dimethoxyphenyl)‐4‐(3,4‐dimethoxyphenyl)‐5‐trifluoromethyl‐1H‐1,2,3‐triazole (C₁₉H₁₈F₃N₃O₄, 6 ) and 3‐[4‐(3,4‐dimethoxyphenyl)‐5‐(trifluoromethyl)‐1H‐1,2,3‐triazol‐1‐yl]phenol (C₁₇H₁₄F₃N₃O₃, 7 ), have been determined and compared to that of J147 . B3LYP/6‐311++G(d,p) calculations have been performed to determine the potential surface and molecular electrostatic potential (MEP) of J147 , and to examine the correlation between hydrazone J147 and the 1,2,3‐triazoles, both bearing a CF₃ substituent. Using MEPs, it was found that the minimum‐energy conformation of 4 , which is nearly identical to its X‐ray structure, is closely related to one of the J147 seven minima.     

An unusual conformation of gabapentin (Gpn) in Pyr‐Gpn‐NH‐NH‐Pyr stabilized by weak interactions

The crystal structure of N‐[(1‐{2‐oxo‐2‐[2‐(pyrazin‐2‐ylcarbonyl)hydrazin‐1‐yl]ethyl}cyclohexyl)methyl]pyrazine‐2‐carboxamide monohydrate (Pyr‐Gpn‐NN‐NH‐Pyr·H₂O), C₁₉H₂₃N₇O₃·H₂O, reveals an unusual trans–gauche (tg⁻) conformation for the gabapentin (Gpn) residue around the C^γ—C^β (θ₁) and C^β—C^α (θ₂) bonds. The molecular conformation is stabilized by intramolecular N—H...N hydrogen bonds and weak C—H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N—H...O and O—H...O hydrogen bonds together with weak C—H...O and π–π inteactions.     

Two centrosymmetric dinuclear phenanthroline–copper(II) complexes with 3,5‐dichloro‐2‐hydroxybenzoic acid and 5‐chloro‐2‐hydroxybenzoic acid

The title compounds, bis(μ‐3,5‐dichloro‐2‐oxidobenzoato)‐κ³O¹,O²:O²;κ³O²:O¹,O²‐bis[(3,5‐dichloro‐2‐hydroxybenzoic acid‐κO¹)(1,10‐phenanthroline‐κ²N,N′)copper(II)], [Cu₂(C₇H₂Cl₂O₃)₂(C₇H₄Cl₂O₃)₂(C₁₂H₈N₂)₂], (I), and bis(μ‐5‐chloro‐2‐oxidobenzoato)‐κ³O¹,O²:O¹;κ³O¹:O¹,O²‐bis[(5‐chloro‐2‐hydroxybenzoic acid‐κO¹)(1,10‐phenanthroline‐κ²N,N′)copper(II)] ethanol monosolvate, [Cu₂(C₇H₃ClO₃)₂(C₇H₅ClO₃)₂(C₁₂H₈N₂)₂]·C₂H₆O, (II), contain centrosymmetric dinuclear complex molecules in which Cu²⁺ cations are surrounded by a chelating 1,10‐phenanthroline ligand, a chelating 3,5‐dichloro‐2‐oxidobenzoate or 5‐chloro‐2‐oxidobenzoate anionic ligand and a monodentate 3,5‐dichloro‐2‐hydroxybenzoic acid or 5‐chloro‐2‐hydroxybenzoic acid ligand. The chelating benzoate ligand also bridges to the other Cu²⁺ ion in the molecule, but the O atom involved in the bridge is different in the two complexes, being the phenolate O atom in (I) and a carboxylate O atom in (II). The bridge completes a 4+1+1 axially elongated tetragonal–bipyramidal arrangement about each Cu²⁺ cation. The complex molecules of both compounds are linked into one‐dimensional supramolecular chains through O—H...O hydrogen bonds.     

Granisetron,an antiemetic drug,and its cobalt complex

The crystal structures of granisetron [systematic name: 1‐methyl‐N‐(9‐methyl‐9‐azabicyclo[3.3.1]nonan‐7‐yl)indazole‐3‐carboxamide], C₁₈H₂₄N₄O, (I), an antinauseant and antiemetic agent, and its Co^II complex, diaqua[1‐methyl‐N‐(9‐methyl‐9‐azoniabicyclo[3.3.1]nonan‐7‐yl)indazole‐3‐carboxamide]cobalt(II) tetrachloride dodecahydrate, [Co(C₁₈H₂₅N₄O)₂(H₂O)₂]Cl₄·12H₂O, (II), have been determined by X‐ray diffraction. The granisetron molecule is in an extended conformation in both structures. Twisting of the central carboxamide group facilitates the Co^II coordination in (II). The Co^II atom is located on an inversion centre. The azabicyclononane ring adopts a chair–boat conformation in both structures. The molecules in (I) are linked into centrosymmetric dimers and form tetracyclic rings through C—H...O hydrogen‐bonding interactions. The simultaneous presence of free chloride ions in conjunction with a number of hydration water molecules in (II) provides interesting hydrogen‐bond patterns. This study can aid in the investigation of the properties of metal complexes with active pharmaceuticals in which the drug molecules play the role of a ligand.     

Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

4,1′,6′‐Trichloro‐4,1′,6′‐trideoxysucrose monohydrate

At 160 K, the gluco­pyran­osyl ring in 1,6‐di­chloro‐1,6‐di­deoxy‐β‐d ‐fructo­furan­osyl 4‐chloro‐4‐deoxy‐α‐d ‐gluco­pyran­oside monohydrate, C₁₂H₁₉Cl₃O₈·H₂O, has a near ideal ⁴C₁ chair conformation, while the fructo­furan­osyl ring has a ⁴T₃ conformation. The conformation of the sugar mol­ecule is quite different to that of sucralose, particularly in the conformation about the glycosidic linkage, which affects the observed pattern of intramolecular hydrogen bonds. A complex series of intermolecular hydrogen bonds links the sugar and water mol­ecules into an infinite three‐dimensional framework.     

Three oxo complexes with a tetra­nuclear [Cu4(μ2‐Cl)6(μ4‐O)] unit

The three title compounds, namely 4‐phenyl‐1H‐imidazolium hexa‐μ₂‐chloro‐chloro‐μ₄‐oxo‐tris­(4‐phenyl‐1H‐imidazole‐κN¹)­tetra­copper(II) monohydrate, (C₉H₉N₂)[Cu₄Cl₇O(C₉H₈N₂)₃]·H₂O, hexa‐μ₂‐chloro‐μ₄‐oxo‐tetra­kis­(pyridine N‐oxide‐κO)tetra­copper(II), [Cu₄Cl₆O(C₅H₅NO)₄], and hexa‐μ₂‐chloro‐tetra­kis(2‐methyl‐1H‐imidazole‐κN¹)‐μ₄‐oxo‐tetra­copper(II) methanol trisolvate, [Cu₄Cl₆O(C₄H₆N₂)₄]·3CH₄O, exhibit the same Cu₄OCl₆ framework, where the O atom at the centre of an almost regular tetra­hedron bridges four copper cations at the corners. This group is in turn surrounded by a Cl₆ octa­hedron, leading to a rather globular species. This special arrangement of the Cu^II cations results in a diversity of magnetic behaviours.     

The structures of three Hg2X4L2 macrocycles {X = Cl,Br and I,and L = 1,2‐bis[4‐(pyridin‐3‐yl)phenoxy]ethane} assembled from ether‐bridged dipyridyl ligands

The new ether‐bridged dipyridyl ligand 1,2‐bis[4‐(pyridin‐3‐yl)phenoxy]ethane (L) has been used to synthesize three isostructural centrosymmetric binuclear Hg^II macrocycles, namely bis{μ‐1,2‐bis[4‐(pyridin‐3‐yl)phenoxy]ethane‐κ²N:N′}bis[dichloridomercury(II)], [Hg₂Cl₄(C₂₄H₂₀N₂O₂)₂], and the bromido, [Hg₂Br₄(C₂₄H₂₀N₂O₂)₂], and iodido, [Hg₂I₄(C₂₄H₂₀N₂O₂)₂], analogues. The Hg atoms adopt a highly distorted tetrahedral coordination environment consisting of two halides and two pyridine N‐donor atoms from two bridging ligands. In the solid state, the macrocycles form two‐dimensional sheets in the bc plane through noncovalent Hg...X and X...X (X = Cl, Br and I) interactions.     

Conformational studies of hydantoin‐5‐acetic acid and orotic acid

Hydantoin‐5‐acetic acid [2‐(2,5‐dioxoimidazolidin‐4‐yl)acetic acid] and orotic acid (2,6‐dioxo‐1,2,3,6‐tetrahydropyrimidine‐4‐carboxylic acid) each contain one rigid acceptor–donor–acceptor hydrogen‐bonding site and a flexible side chain, which can adopt different conformations. Since both compounds may be used as coformers for supramolecular complexes, they have been crystallized in order to examine their conformational preferences, giving solvent‐free hydantoin‐5‐acetic acid, C₅H₆N₂O₄, (I), and three crystals containing orotic acid, namely, orotic acid dimethyl sulfoxide monosolvate, C₅H₄N₂O₄·C₂H₆OS, (IIa), dimethylammonium orotate–orotic acid (1/1), C₂H₈N⁺·C₅H₃N₂O₄⁻·C₅H₄N₂O₄, (IIb), and dimethylammonium orotate–orotic acid (3/1), 3C₂H₈N⁺·3C₅H₃N₂O₄⁻·C₅H₄N₂O₄, (IIc). The crystal structure of (I) shows a three‐dimensional network, with the acid function located perpendicular to the ring. Interestingly, the hydroxy O atom acts as an acceptor, even though the carbonyl O atom is not involved in any hydrogen bonds. However, in (IIa), (IIb) and (IIc), the acid functions are only slightly twisted out of the ring planes. All H atoms of the acidic functions are directed away from the rings and, with respect to the carbonyl O atoms, they show an antiperiplanar conformation in (I) and synperiplanar conformations in (IIa), (IIb) and (IIc). Furthermore, in (IIa), (IIb) and (IIc), different conformations of the acid O=C—C—N torsion angle are observed, leading to different hydrogen‐bonding arrangements depending on their conformation and composition.     

Orthorhombic modification of tri­phenyl­tin 3‐ureidopropionate

The Sn atom in catena‐poly­[tri­phenyl­tin(IV)‐μ‐(3‐ureidopropionato‐O¹:O³)], [Sn(C₆H₅)₃(C₄H₇N₂O₃)]_n, is five‐coordinate and has a trans‐C₃SnO₂ trigonal‐bipyrmidal geometry arising from bridging through the O atom of the ureido fragment of an adjacent carboxyl­ate group. Infinite chains propagate helically along the c axis and adjacent chains are linked by N—H?O [N?O 2.851 (4) Å] hydrogen bonds into layers.     

N‐Benzyl­tetra­hydro­pyrido‐anellated thio­phene derivatives: new anti­cholinesterases

The title compounds, tert‐butyl 6‐benzyl‐2‐(3,3‐diethyl­ureido)‐4,5,6,7‐tetra­hydro­thieno[2,3‐c]pyridine‐3‐carboxyl­ate, C₂₄H₃₃N₃O₃S, (I), 7‐benzyl‐2‐diethyl­amino‐5,6,7,8‐tetra­hydro‐3‐oxa‐9‐thia‐1,7‐diaza­fluoren‐4‐one, C₂₀H₂₃N₃O₂S, (II), and N‐(7‐benzyl‐4‐oxo‐5,6,7,8‐tetra­hydro‐4H‐3,9‐dithia‐1,7‐diaza­fluoren‐2‐yl)benzamide, C₂₃H₁₉N₃O₂S₂, (III), form monoclinic crystal systems. In (I) and (II), the mol­ecules are linked into a three‐dimensional framework by weak inter­molecular C—H⋯O=C hydrogen bonds, whereas in (III) stronger inter­molecular N—H⋯O=C inter­actions are observed. The conformation of (I) is further stabilized by an intra­molecular N—H⋯O=C hydrogen bond, which effects the planarity of the ureido­thio­phene­carboxyl­ate moiety.     

2‐Chloro‐4‐nitrobenzoic acid as a coformer with pharmaceutical cocrystals and molecular salts

A series of five binary complexes, i.e. three cocrystals and two molecular salts, using 2‐chloro‐4‐nitrobenzoic acid as a coformer have been produced with five commonly available compounds, some of pharmaceutical relevance, namely, 2‐chloro‐4‐nitrobenzoic acid–isonicotinamide (1/1), C₇H₄ClNO₄·C₆H₆N₂O, 2‐chloro‐4‐nitrobenzoic acid–3,3‐diethylpyridine‐2,4(1H,3H)‐dione (2/1), 2C₇H₄ClNO₄·C₉H₁₃NO₂, 2‐chloro‐4‐nitrobenzoic acid–pyrrolidin‐2‐one (1/1), C₇H₄ClNO₄·C₄H₇NO, 2‐carboxypiperidinium 2‐chloro‐4‐nitrobenzoate, C₆H₁₂NO₂^?·C₇H₃ClNO₄^?, and (2‐hydroxyethyl)ammonium 2‐chloro‐4‐nitrobenzoate, C₂H₈NO⁺·C₇H₃ClNO₄^?. The coformer falls under the classification of a `generally regarded as safe' compound. All five complexes make use of a number of different heteromeric hydrogen‐bonded interactions. Intermolecular potentials were evaluated using the CSD‐Materials module.     

A novel copper(II) complex with 1,10‐phenanthroline and ciprofloxacin

The X‐ray structure analysis of the title compound, chloro[1‐cyclopropyl‐6‐fluoro‐1,4‐dihydro‐4‐oxo‐7‐(piperazin‐4‐ium‐1‐yl)‐3‐quinolinecarboxylate‐κ²O³,O⁴](1,10‐phenanthroline‐κ²N,N′)copper chloride dihydrate, [CuCl(C₁₇H₁₈FN₃O₃)(C₁₂H₈N₂)]Cl·2H₂O or [CuCl(cfH)(phen)]Cl·2H₂O, where cfH is 1‐cyclopropyl‐6‐fluoro‐1,4‐dihydro‐4‐oxo‐7‐(piperazin‐4‐ium‐1‐yl)‐3‐quinolinecarboxylate and phen is 1,10‐phenanthroline, shows that the geometry around the Cu ion is a slightly distorted square pyramid. Two O atoms of the carbonyl and carboxyl groups of ciprofloxacin and two N atoms of 1,10‐phenanthroline are coordinated to the metal centre in the equatorial plane, and a Cl⁻ ion is coordinated at the apical position. Extensive intermolecular hydrogen bonding produces a supramolecular structure that consists of alternating six‐ and 12‐membered rings.     

Benzyl 5‐{2‐[2‐(diethoxy­phosphinoyl)­acetyl]‐3‐oxo‐7‐thia‐2,4‐di­aza­bi­cyclo­[3.3.0]­oct‐6‐yl}pentanoate,a novel biotin derivative

The title compound, C₂₃H₃₃N₂O₇PS, has its phospho­no­acetate carbonyl group rotated slightly out of the plane of the ureido ring, with a C—N—C—O torsion angle of ?6.9 (4)°. The sulfur‐containing ring has an envelope conformation, while the ureido ring is nearly planar.