Pseudo-inversion Centre Research Articles

2,4-Dibromo-6-[(2-hydroxy-5-methylanilino)methylidene]cyclohexa-2,4-dienone

The new bromo-substituted title compound, C14H11Br2NO2, was synthesized by the condensation of 3,5-dibromosalicylaldehyde and 2-amino-4-methyl phenol. The asymmetric unit consists of two crystallographically independent molecules (AandB), which are related to each other by a pseudo-inversion centre. Both molecules are almost planar; dihedral angles between the two benzene rings are 11.40 (11)° forAand 3.05 (12)° forB. In each molecule, there is an intramolecular N—H...O hydrogen bond with anS(6) ring motif. In the crystal, two independent molecules are linked by O—H...O hydrogen bonds, forming a pseudo-inversionA–Bdimer.

(E)-2-Benzoyl-3-[1-phenyl-3-(thiophen-2-yl)-1H-pyrazol-4-yl]acrylonitrile

The asymmetric unit of the title compound, C23H15N3OS, consists of two crystallographically independent molecules, which are related by a pseudo-inversion centre. In one molecule, the pyrazolyl ring makes dihedral angles of 35.7 (4), 19.1 (1) and 47.3 (1)°, respectively, with the thiophenyl ring, the attached phenyl ring and the phenyl ring of the benzoyl group. In the second molecule, the corresponding values are 37.4 (1), 16.1 (1) and 48.2 (1)°, respectively. In the crystal, the two independent molecules are linked to each otherviaa π–π interaction between the pyrazolyl rings [centroid–centroid distance = 3.578 (12) Å]. Weak intermolecular C—H...O interactions are also observed. The thiophenyl ring of one molecule is disordered over two orientations, with a refined occupancy ratio of 0.768 (3):0.232 (3).

Synthesis and crystal structures of two structurally related kryptoracemates.

Kryptoracemates are racemic compounds (pairs of enantiomers) that crystallize in Sohnke space groups (space groups that contain neither inversion centres nor mirror or glide planes nor rotoinversion axes). Thus, the two symmetry-independent molecules cannot be transformed into one another by any symmetry element present in the crystal structure. Usually, the conformation of the two enantiomers is rather similar if not identical. Sometimes, the two enantiomers are related by a pseudosymmetry element, which is often a pseudocentre of inversion, because inversion symmetry is thought to be favourable for crystal packing. We obtained crystals of two kryptoracemates of two very similar compounds differing in just one residue, namely rac-N-[(1S,2R,3S)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(pivalamido)propyl]benzamide, C27H32N2O3, (I), and rac-N-[(1S,2S,3R)-2-methyl-3-(5-methylfuran-2-yl)-1-phenyl-3-(propionamido)propyl]benzamide dichloromethane hemisolvate, C25H28N2O3·0.5CH2Cl2, (II). The crystals of both compounds contain both enantiomers of these chiral molecules. However, since the space groups [P212121 for (I) and P1 for (II)] contain neither inversion centres nor mirror or glide planes nor rotoinversion axes, there are both enantiomers in the asymmetric unit, which is a rather uncommon phenomenon. In addition, it is remarkable that (II) contains two pairs of enantiomers in the asymmetric unit. In the crystal, molecules are connected by intermolecular N-H...O hydrogen bonds to form chains or layered structures.

Ab initio structure determination of kidney stone potassium quadriurate from synchrotron powder diffraction data, a 150 year problem solved

Abstract The structure of potassium urate, co-crystallized with uric acid K(C5H3N4O3)(C5H4N4O3), from human kidney stones, is determined ab initio from synchrotron powder diffraction data, space group P21/c, a = 3.60504(9) A, b = 19.9293(7) A, c = 18.4841(6) A, β = 100.503(2)°, Z = 4. Each uric acid molecule is connected to a urate anion through three hydrogen bonds, both molecules are related by a pseudo-inversion center and are randomly distributed in the crystal. Two of the oxygen atoms of the uric acid molecule and two of the urate anions are involved in the potassium coordination forming KO7 monocapped trigonal prisms sharing their triangular bases, building infinite chains extending along the short a axis. Such a formulation, though controversial, has been claimed to exist since 1862 and named potassium quadriurate. The crystal structure is optimized by energy minimization (DFT) in the solid state, using a hybrid PBE0 functional. The capacity of the urate anion to connect by strong hydrogen bonds to a uric acid molecule has implications concerning the uric acid transport in biological media.

Crystal structure of 3-bromo-pyridine N-oxide.

In the title compound, C5H4BrNO, there are two mol­ecules in the asymmetric unit that are related by a pseudo-inversion center. The two independent mol­ecules are approximately planar, with an observed (ring–ring) angle of 5.49 (13)°. The crystal structure exhibits a herringbone pattern with the zigzag running along the b-axis direction. The least-squares plane containing the rings of both asymmetric molecules and the plane containing the symmetrically related mol­ecules make a plane–plane angle of 66.69 (10)°, which makes the bend of the herringbone pattern. The bromo group on one mol­ecule points to the bromo group on the neighboring mol­ecule, with a Br⋯Br inter­molecular distance of 4.0408 (16) Å. The herringbone layer-to-layer distance is 3.431 (4) Å with a shift of 1.742 (7) Å. There are no short contacts, hydrogen bonds, or π–π inter­actions.

Hydrogen bonding in 4-nitrobenzene-1,2-diamine and two hydrohalide salts.

The structures of 4-nitrobenzene-1,2-diamine [C6H7N3O2, (I)], 2-amino-5-nitroanilinium chloride [C6H8N3O2(+)·Cl(-), (II)] and 2-amino-5-nitroanilinium bromide monohydrate [C6H8N3O2(+)·Br(-)·H2O, (III)] are reported and their hydrogen-bonded structures described. The amine group para to the nitro group in (I) adopts an approximately planar geometry, whereas the meta amine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine group meta to the nitro group is protonated. Compound (I) displays a pleated-sheet hydrogen-bonded two-dimensional structure with R2(2)(14) and R4(4)(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three-dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo-inversion center. The dominant hydrogen-bonding interactions involve the chloride ion and result in R4(2)(8) rings linked to form a ladder-chain structure. The chains are joined by N-H···Cl and N-H···O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to form R4(2)(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternating R5(5)(15) and R6(4)(24) rings. Ammonium N-H···Br interactions join the sheets to form a three-dimensional extended structure. Energy-minimized structures obtained using DFT and MP2 calculations are consistent with the solid-state structures. Consistent with (II) and (III), calculations show that protonation of the amine group meta to the nitro group results in a structure that is about 1.5 kJ mol(-1) more stable than that obtained by protonation of the para-amine group. DFT calculations on single molecules and hydrogen-bonded pairs of molecules based on structural results obtained for (I) and for 3-nitrobenzene-1,2-diamine, (IV) [Betz & Gerber (2011). Acta Cryst. E67, o1359] were used to estimate the strength of the N-H···O(nitro) interactions for three observed motifs. The hydrogen-bonding interaction between the pairs of molecules examined was found to correspond to 20-30 kJ mol(-1).

Packing considerations of 10-oxa-9-boraphenanthrene derivatives.

The crystal structures of three products of the reaction of 2-phenylphenol and BCl3 have been determined. The structures show intriguing packing patterns and an interesting case of pseudosymmetry. In addition, one of the two polymorphs has a primitive monoclinic crystal system, but it is twinned and emulates an orthorhombic C-centred structure. Tris(biphenyl-2-yl) borate, C36H27BO3, (III), crystallizes with only one molecule in the asymmetric unit. The dihedral angles between the planes of the aromatic rings in the biphenyl moieties are 50.47 (13), 44.95 (13) and 42.60 (13)°. The boron centre is in a trigonal planar coordination with two of the biphenyl residues on one side of the BO3 plane and the remaining biphenyl residue on the other side. One polymorph of 10-oxa-9-boraphenanthren-9-ol, C12H9BO2, (Va), crystallizes with two almost identical molecules (r.m.s. deviation of all non-H atoms = 0.039 Å) in the asymmetric unit. All non-H atoms lie in a common plane (r.m.s. deviation = 0.015 Å for both molecules in the asymmetric unit). The two molecules in the asymmetric unit are connected into dimers via O-H···O hydrogen bonds. A second polymorph of 10-oxa-9-boraphenanthren-9-ol, (Vb), crystallizes as a pseudo-merohedral twin with two almost identical molecules (r.m.s. deviation of all non-H atoms = 0.035 Å) in the asymmetric unit. All non-H atoms lie in a common plane (r.m.s. deviation = 0.012 Å for molecule 1 and 0.014 Å for molecule A). Each of the two molecules in the asymmetric unit is connected into a centrosymmetric dimer via O-H···O hydrogen bonds. The main difference between the two polymorphic structures is that in (Va) the two molecules in the asymmetric unit are hydrogen bonded to each other, whereas in (Vb), each molecule in the asymmetric unit forms a hydrogen-bonded dimer with its centrosymmetric equivalent. 9-[(Biphenyl-2-yl)oxy]-10-oxa-9-boraphenanthrene, C24H17BO2, (VI), crystallizes with four molecules in the asymmetric unit. The main differences between them are the dihedral angles between the ring planes. Apart from the biphenyl moiety, all non-H atoms lie in a common plane (r.m.s. deviations = 0.026, 0.0231, 0.019 and 0.033 Å for molecules 1, A, B and C, respectively). This structure shows pseudosymmetry; molecules 1 and A, as well as molecules B and C, are related by a pseudo-translation of about 1/2 in the direction of the b axis. Molecules 1 and B, as well as molecules A and C, are related by a pseudo-inversion centre at 1/4,1/8,1/2. Neither between molecules 1 and C nor between molecules A and B can pseudosymmetry be found.

The pseudo-inversion symmetry of 9,90′ (1,3,4-oxadiazole-2,5-diyldi(1,1′-biphenyl)-2′,4- diyl)bis[9H-carbazole] in the light of OD theory

Abstract The crystal structure of 9,9′-(1,3,4-oxadiazole- 2,5-diyldi(1,1′-biphenyl)-2′,4-diyl)bis[9H-carbazole] [Pna21, Z = 4, a = 17.9874 (4) Å, b = 9.2989 (8) Å, c = 21.5822 (9) Å, Robs = 0.0395, 9239 F data, 496 parameters] features a pseudo-centre of inversion strictly valid only for isolated layers of the structure. It is an order-disorder (OD) structure made up of one kind of non-polar layers composed of (I) molecules connected to polar layer pairs. The major polytype is of a maximum degree of order. The magnitude of the intrinsic translation vectors of the glides and screws relating adjacent layers is a convenient quantification of the deviation from perfect centrosymmetry.

(Z)-N-[1-(Aziridin-1-yl)-2,2,2-tri-fluoro-ethyl-idene]-4-bromo-aniline.

The title compound, C10H8BrF3N2, crystallizes with two independent mol­ecules in the asymmetric unit, which can be considered as being related by a pseudo-inversion center, so their conformations are different; the corresponding N=C—N—C torsion angles are 54.6 (5) and −50.5 (5)°. In the crystal, mol­ecules related by translation in [001] inter­act through short inter­molecular Br⋯F contacts [3.276 (2) and 3.284 (2) Å], thus forming two types of crystallographically independent chains.

5-(4-Chlorophenyl)-7-(4-methylphenyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine

The title compound, C23H21ClN4, contains two molecules (A and B) in the asymmetric unit, which are related to one another by a pseudo-inversion center. The non-aromatic pyrrolidine ring in each independent mol­ecule adopts a half-chair conformation; the ring puckering parameters are θ = 0.407 (3) Å and ϕ = 270.5 (4)°, and the pseudo-rotation parameters are ρ = 72.5 (3)° and τ = 42.2 (2)° for an N—C bond of molecule A, and the corresponding values are 0.415 (3) Å, 271.6 (4)°, 73.6 (3)° and 42.6 (2)° for molecule B. The dihedral angles between the central fused-ring system and the substituted chlorophenyl and methylphenyl rings are 66.35 and 45.59°, respectively, for molecule A, and 64.51 and 41.89° for molecule B. The geometry of all four intramolecular C—H⋯π interactions are of type III. π–π interactions involving the centroids of symmetry-related pyrrole rings of molecule B are 4.390 Å, contributing further to the stability of the molecule.

Triphenylsilanol–4,4′-bipyridyl (4/1): theZ′ = 4 polymorph revisited

A fully ordered structure is reported for the polymorph of triphenylsilanol-4,4'-bipyridyl (4/1), 4C18H16OSi·C10H8N2, having Z' = 4. The asymmetric unit contains four similar but distinct five-molecule aggregates, in which the central bipyridyl unit is linked to two molecules of triphenylsilanol via O-H···N hydrogen bonds, with a further pair of triphenylsilanol molecules linked to the first pair via O-H···O hydrogen bonds. An extensive series of C-H···π(arene) hydrogen bonds links these aggregates into complex sheets. This structure is compared with a previously reported structure [Bowes, Ferguson, Lough & Glidewell (2003). Acta Cryst. B59, 277-286], which was based on an erroneous disordered structural model arising from a false direct-methods solution with reference to a strong pseudo-inversion centre.

Chirality Inversion Process of a Bulky Alkyl Group in the Crystalline State Photo‐Isomerization of Cobaloxime Complex Crystals

AbstractThe complex of [(R)‐tert‐(butoxycarbonyl)ethyl][(S)‐1‐cyclohexylethylamine]bis(dimethylglyoximato)cobalt(III), (R‐bce)(S‐cha)cobaloxime, 1, showed a racemization of the R‐bce group on exposure to a xenon lamp with retention of the single crystal form. A part of the R‐bce groups gradually inverted to the opposite configuration in the P212121 cell. However, the inversion of the R‐bce group converged when the R:S ratio became ca.75:25. The shape of the reaction cavity for the disordered bce group became symmetric at the ratio. For the related complex crystal with pyridine as an axial ligand, (R‐bce)(py)cobaloxime, 2, there are two crystallographically independent molecules, A and B, which are related by a pseudo inversion center in the P21 cell. When the crystal was exposed to the xenon lamp, the R‐bce group of the A molecule was gradually inverted to the opposite configuration without decomposition of the single crystal form, whereas the R‐bce group of B remained unchanged. Finally the pseudo inversion center became a crystallographic one and the space group became P21/c. The third complex crystal with water as an axial ligand, (R‐bce)(aqua)cobaloxime, 3, showed no changed on exposure to the xenon lamp. This is well explained by the size and shape of the reaction cavities for the R‐bce groups in the three crystals.

3-(Adamantan-1-yl)-4-methyl-1-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)-4,5-dihydro-1H-1,2,4-triazole-5-thione

In the title compound, C25H32F3N5S, two independent mol­ecules comprise the asymmetric unit and are related across a pseudo-centre of inversion. The piperazine rings have chair conformations with each N-bound substituent occupying an equatorial position so that the dihedral angles between the planes of the triazole and benzene ring are 78.20 (19) and 79.10 (19)° for the two independent mol­ecules, indicating that the mol­ecules have an L-shape. In the crystal, a three-dimensional architecture is stabilized by C—H⋯π inter­actions. The crystal studied was an inversion twin with the fractional contribution of the minor component being 0.27 (9).

3,4′,5-Trichlorobiphenyl-4-yl 2,2,2-trichloroethyl sulfate

Crystals of the title compound, C14H8Cl6O4S, are twinned by inversion, with unequal components [0.85 (3):0.15 (3)]. The asymmetric unit contains two independent mol­ecules that are related by a pseudo-inversion center. The Car—O [1.393 (9) and 1.397 (9) Å] and ester S—O bond lengths [1.600 (5) and 1.590 (5) Å] of both mol­ecules are comparable to the structurally related 2,3,5,5-trichloro­biphenyl-4-yl 2,2,2-trichloro­ethyl sulfate. The dihedral angles between the benzene rings in the two mol­ecules are 37.8 (2) and 35.0 (2)°.

Bis{(R)-1-(3-aminosulfonyl-4-methoxyphenyl)-N-[2-(2-ethoxyphenoxy)ethyl]propan-2-aminium} adipate tetrahydrate

The title compound, 2C20H29N2O5S+·C6H8O4 2−·4H2O, which was found to be optically active, is a relatively rare example of a chiral compound crystallizing in the triclinic crystal system. The dihedral angles between the phenyl rings of the cations are 60.03 (15) and 62.03 (16)°, while the C atoms of the anion are almost coplanar (r.m.s. deviation 0.085 Å) and all trans to each other. In the crystal, the components are connected by an extensive network of N—H⋯O and O—H⋯O hydrogen bonds. The sulfonamide groups link the cations into pairs via two N—H⋯O hydrogen bonds about the pseudo-inversion centre, leading to the formation of R 2 2(8) rings. The anions are stacked in between four cationic pairs. Pairs of water mol­ecules bridge the larger building units, forming hydrogen bonds with the remaining two O atoms of the anion.

Dicyclohexylammonium (S)-2-azido-3-phenylpropanoate

The asymmetric unit of the title compound, C12H24N+·C9H8N3O2 −, consists of two dicyclo­hexyl­ammonium cations linked to two (S)-2-azido-3-phenyl­propano­ate anions by four short N—H⋯O hydrogen bonds with N⋯O distances in the range 2.712 (3)–2.765 (3) Å. The dicyclo­hexyl­ammonium cations and the aryl and carboxyl­ate groups of the anion are related by a pseudo-inversion centre, with overall crystallographic inversion symmetry for the structure broken by the chirality of the α-C atoms of the anions.

Dibenzylazanium (oxalato-κ2 O,O′)triphenylstannate(IV)

The title compound, (C14H16N)[Sn(C6H5)3(C2O2)], was synthesised by allowing C2O4(Bz2NH2)2 (Bz = benzyl) to react with SnPh3Cl. The asymmetric unit is built up by four SnPh3C2O4 anions and four Bz2NH2 cations which are related by a pseudo-inversion centre. Each SnIV cation is five-coordinated by the three phenyl groups and two O atoms belonging to the chelating oxalate ligand; the coordination geometry is that of a distorted trigonal bipyramid. Anions and cations are linked through N—H⋯O hydrogen bonds into a layer structure parallel to (001). Moreover, the anion–cation pairs are associated by two bifurcated N—H⋯O hydrogen bonds, generating pseudo-dimers. One of the phenyl groups of one anion is disordered over two sets of sites in a 0.69:0.31 ratio. The Flack parameter value of 0.44 (1) indicates racemic twinning.

5-Nitro-1-(prop-2-yn-1-yl)-2,3-dihydro-1H-1,3-benzodiazol-2-one

In the two independent mol­ecules of the title compound, C10H7N3O3, the nitro substitutent is twisted slightly with respect to the benzodiazol fused-ring system [dihedral angles = 4.9 (3) and 8.5 (1)°]. The two independent mol­ecules are disposed about a pseudo inversion center and are held together by N—H⋯O hydrogen bonds. The supramolecular dimer is essentially planar [dihedral angle between the fused rings = 2.0 (1)°]. Adjacent dimers are linked by acetyl­ene–nitro C—H⋯O inter­actions, generating a ribbon motif along (110).

6-Bromoindigo dye

6-Bromoindigo (MBI) [systematic name: 6-bromo-2-(3-oxo-2,3-dihydro-1H-indol-2-ylidene)-2,3-dihydro-1H-indol-3-one], C(16)H(9)BrN(2)O(2), crystallizes with one disordered molecule in the asymmetric unit about a pseudo-inversion center, as shown by the Br-atom disorder of 0.682 (3):0.318 (3). The 18 indigo ring atoms occupy two sites which are displaced by 0.34 Å from each other as a result of this packing disorder. This difference in occupancy factors results in each atom in the reported model used to represent the two disordered sites being 0.08 Å from the higher-occupancy site and 0.26 Å from the lower-occupancy site. Thus, as a result of the disorder, the C-Br bond lengths in the disordered components are 0.08 and 0.26 Å shorter than those found in 6,6'-dibromoindigo (DBI) [Süsse & Krampe (1979). Naturwissenschaften, 66, 110], although the distances within the indigo ring are similar to those found in DBI. The crystals are also twinned by merohedry. Stacking interactions and hydrogen bonds are similar to those found in the structures of indigo and DBI. In MBI, an interaction of the type C-Br...C replaces the C-Br...Br interactions found in DBI. The interactions in MBI were calculated quantum mechanically using density functional theory and the quantum theory of atoms in molecules.

2,4-Di-tert-butyl-6-[(R/S)-1-(3,5-di-tert-butyl-2-hydroxyphenyl)ethyl]phenyl [(1R,4S)-7,7-dimethyl-2-oxobicyclo[2.2.1]heptan-1-yl]methanesulfonate

The asymmetric unit of the title compound, C40H60O5S, comprises two diastereomers related, except for the chiral camphor groups, by a pseudo-inversion centre. In both diasteromers, the camphor sulfate moiety maintained the absolute configuartion (R,S) of the precursor. However, the absolute configurations at the methine C atoms are of opposite chirality. Both mol­ecules reveal intra­molecular O—H⋯O hydrogen bonds, whereas van der Waals inter­actions define the crystal packing.