Barbara Wicher

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic.

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975). Acta Cryst. B 31, 1454-1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol -OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C(43)H(58)N(4)O(12)·5H(2)O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O-H···O and N-H···N hydrogen bonds. Four of the symmetry-independent water molecules are arranged via hydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interact via O-H···O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

A third polymorph of N,N′-bis­(pyridin-2-yl)benzene-1,4-diamine

A third polymorph of the title compound, C16H14N4, has been obtained. The molecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridylamine units. Like in the triclinic form [Bensemann et al. (2002 ▶). New J. Chem. 26, 448–456], the recognition process between 2-pyridylamine units takes place through formation of a cyclic R 2 2(8) hydrogen-bond motif, leading to the creation of tapes parallel to [001].

N,N'-Bis(pyridin-2-yl)benzene-1,4-diamine-quinoxaline (2/1).

The asymmetric unit of the title compound, 2C16H14N4·C8H6N2, consits of one molecule of N,N′-bis(pyridin-2-yl)benzene-1,4-diamine (PDAB) and one half-molecule of quinoxaline (QX) that is located around an inversion centre and disordered over two overlapping positions. The PDAB molecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridylamine units. In the crystal, these self-complementary units are N—H⋯N hydrogen bonded via a cyclic R 2 2(8) motif, creating tapes of PDAB molecules extending along [010]. Inversion-related tapes are arranged into pairs through π–π stacking interactions between the benzene rings [centroid–centroid distance = 3.818 (1) Å] and the two symmetry-independent pyridine groups [centroid–centroid distance = 3.760 (1) Å]. The QX molecules are enclosed in a cavity formed between six PDAB tapes.

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

N,N′-Bis(pyridin-2-yl)benzene-1,4-diamine–naphthalene (2/1)

The asymmetric unit of the title compound, C10H8·2C16H14N4, consists of one molecule of N,N′-bis(pyridin-2-yl)benzene-1,4-diamine (PDAB) and one half of the centrosymmetric naphthalene molecule. The PDAB molecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridylamine units. In the crystal, N—H⋯N hydrogen bonds between the PDAB molecules generate a cyclic R 2 2(8) motif, leading to the formation of PDAB tapes extending along [100]. The tapes are arranged into (010) layers and the naphthalene molecules are enclosed in cavities formed between the PDAB layers.

Bis(di-2-pyridylamine-κ2N2,N2')silver(I) trifluoromethanesulfonate: polar arrangement of trifluoromethanesulfonate anions in a pseudo-centrosymmetric framework of coordination cations.

The asymmetric unit of the title compound, [Ag(C(10)H(9)N(2))(2)]CF(3)SO(3) or [Ag(dpa)(2)]OTf (dpa is di-2-pyridylamine and OTf is the trifluoromethanesulfonate anion), contains two [Ag(dpa)(2)](+) coordination cations and two OTf anions. The coordination geometry of the Ag(I) atom is intermediate between square-planar and tetrahedral, with similar deformations at the two symmetry-independent metal centres. The dpa ligands coordinate in a bidentate chelating mode. The OTf anions are in the outer coordination sphere and bridge the coordination cations via N-H...O interactions to form two symmetry-independent hydrogen-bonded chains. The [Ag(dpa)(2)](+) cations are arranged via interactions involving the aromatic groups into a pseudo-centrosymmetric three-dimensional framework with two types of channels, each confining congeners of one of the symmetry-independent anions. The most interesting feature of this structure is its bulk polarity resulting from an approximately parallel alignment of the anions in the channels.

Lagoden dimethylformamide hemisolvate dihydrate: absolute configuration, dipolar interactions and hydrogen-bonding interactions.

Lagoden (L.3H2O, where L is Na+.C20H33O6-; sodium 3beta,16,18-trihydroxy-8,13-epi-9,13-epoxylabdan-15-oate trihydrate) is widely used as an effective haemostatic agent. It has been crystallized from dimethylformamide (DMF) as sodium 3beta,16,18-trihydroxy-8,13-epi-9,13-epoxylabdan-15-oate dimethylformamide hemisolvate dihydrate, Na+.C20H33O6-.0.5C3H7NO.2H2O or L2.DMF.4H2O, and the asymmetric unit contains two of the latter formulation. The four symmetry-independent Na+ cations and lagoden anions, one DMF molecule and six of the eight symmetry-independent water molecules assemble into a one-dimensional polymeric structure via dipolar and hydrogen-bonding interactions. The lagoden anions coordinate to the Na+ cations via the carboxylate groups and the two primary hydroxy groups, whereas the secondary OH groups are solely involved in hydrogen bonding. Two of the four symmetry-independent lagoden anions act in a chelating mode, forming seven-membered chelate rings. The absolute structure, based on anomalous dispersion data collected at 130 K with Cu Kalpha radiation, confirms an inverted configuration at chiral centres C8 and C13 (labdane numbering) relative to the labdane skeleton.

Cholic acid–quinoxaline (2/1)

In the title inclusion compound, 2C24H40O5·C8H6N2, the unit cell contains two molecules of cholic acid (3α,7α,12α-trihydroxy-5β-cholan-24-oic acid) and one molecule of quinoxaline which implies disorder of the quinoxaline in the space group P21. The amphiphilic molecules of cholic acid assemble, in an antiparallel arrangement, via O—H⋯O hydrogen bonds, into typical corrugated host bilayers which are lipophilic on the outside and lipophobic on the inside. The host framework belongs to the so called α-trans subtype. The quinoxaline molecules are accommodated in lipophilic channels formed between neighboring bilayers with only van der Waals interactions between host and guest. There is a crystallographic twofold screw axis directed along an empty channel in the host framework; however, neighboring guests in any one channel are related by a unit-cell translation along the b axis. Thus, the overall structure is a 1:1 superposition of two such channels related by the crystallographic twofold screw axis.