Molecular and supramolecular ionic aggregates H(x)O(y)(z) in organic and organometallic crystalline hydrates.

Ionic aggregates of the form H(x)O(y)(z) (z ≠ 0) have been characterized during an analysis of 245 crystal structures extracted from the Cambridge Structural Database [Allen (2002). Acta Cryst. B58, 380-388]. A systematic nomenclature is proposed for these species. Three modes of hydrogen bonding are described, characterized in part by the distance between contiguous O atoms: normal (NHB; O···O = 2.6-3.0 Å), charge assisted (CAHB; O···O = 2.5 Å) and molecular (MHB; O···O = 2.4 Å). The three modes are consistent with previous reports, our experimental results, and quantum-chemical-optimized geometries and energetics. No evidence is presented concerning the possible existence or stability of these aggregates in solution. Rather, emphasis is placed on the necessity in crystal structure analysis to develop thoroughly existing hydrogen-bonded networks, ignorance of which can lead to erroneous crystal structure models and other physico-chemical data associated with composition and charge balance.

Avoiding problems with hydrogen misplacement in reporting crystal structures.

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one-, two- or three-dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space-group symmetry. Yet some reported structures fail to include all possible donor­acceptor close contacts, or to seek H-atom electron densities associated with apparent D-H∙∙∙A trios, while some H-atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high-quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen-bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.

1-[3-(Naphthalen-1-yl)phen-yl]naphthal-ene.

The title compound, C(26)H(18), consists of a benzene ring with meta-substituted 1-naphthalene substituents, which are essentially planar (r.m.s. deviation = 0.039 and 0.027 Å). The conformation is mixed syn/anti, with equivalent torsion angles about the benzene-naphthalene bonds of 121.46 (11) and 51.58 (14)°.

2-[3-(Naphthalen-2-yl)phen-yl]naph-thal-ene.

The title compound, C(26)H(18), consists of a benzene ring with meta-substituted 2-naphthalene substituents, which are essentially planar [r.m.s. deviations = 0.022 (1) and 0.003 (1) Å]. The conformation is syn, with equivalent torsion angles about the benzene-naphthalene bonds of -36.04 (13) and +34.14 (13)°. The mol-ecule has quasi-C(s) mol-ecular symmetry.

µ(2)-m-Xylylenebis(salicylaldiminato)-bis-(η(4)-1,5-cyclo-octa-diene)dirhodium(I) dichloro-methane solvate.

In the title solvate, [Rh(2)(C(22)H(18)N(2)O(2))(C(8)H(12))(2)]·CH(2)Cl(2), each organometallic mol-ecule is composed of two Rh(I) cations, the tetra-dentate dianion α,α'-bis-(salicylaldiminato)-m-xylene and two 1,5-cyclo-octa-diene (COD) ligands. Each Rh(I) atom is coordinated by one O atom [Rh-O = 2.044 (2) and 2.026 (2) Å], one N atom [Rh-N = 2.083 (2) and 2.090 (2) Å], and one COD ligand via two η(2)-bonds, each directed toward the mid-point of a C=C bond (Cg): Rh-Cg = 2.007 (2), 2.013 (2), 2.000 (2) and 2.021 (2) Å. Each Rh(I) atom has a quasi-square-planar coordination geometry, with average r.m.s. deviations of 0.159 (1) and 0.204 (1) Šfrom the mean planes defined by Rh and the termini of its four coordinating bonds. The two COD ligands have quasi-C(2) symmetry, twisted from ideal C(2v) symmetry by 30.0 (3) and -33.1 (3)°, and are quasi-enanti-omers of one another. The intra-molecular Rh⋯Rh distance of 5.9432 (3) Šsuggests that there is no direct metal-metal inter-action.

N-[2-(Phenyl-sulfon-yl)eth-yl]benzyl-amine.

The title compound, C(15)H(17)NO(2)S, exhibits intra-molecular hydrogen bonding between the amine H atom and a sulfonyl O atom. The conformation of the mol-ecule is described by the four PhCH(2)-NH-CH(2)-CH(2)-SO(2)Ph torsion angles of 79.6 (2), -166.21 (14), -70.29 (17) and -58.93 (13)°.

(1R,4R,5aS,7S,9aS)-7,9a-Dimethyl-6-methyl-ene-3-oxo-1,3,4,5,5a,6,7,8,9,9a-deca-hydro-naphtho-[1,2-c]furan-1,4-diyl diacetate.

The title compound, C(19)H(24)O(6), is a sesquiterpene lactone isolated from the Kenyan plant Warburgia ugandensis. Ring A adopts a chair conformation, ring B is in a C(2) twist conformation and the lactone ring is nearly planar with maximum deviation 0.007 (1) Å. The reported absolute configuration is based on that of the similar compound bromo-parasiticolide A and is supported by analysis of Bijvoet differences from light atoms in Mo Kα radiation.

Monoclinic polymorph of 2,5-dide-oxy-2,5-epithio-1,3:4,6-bis-O-[(R)-phenyl-methyl-ene]-l-iditol.

The title compound C(20)H(20)O(4)S, is polymorphic. In the tetra-gonal form, the mol-ecule lies on a crystallographic twofold axis, while the monoclinic form has only approximate C(2) mol-ecular symmetry. The greatest excursion from C(2) symmetry is in the orientation of the two phenyl rings; at 100 K, one of the rings is rotated -37.2 (3)° and the other by 46.9 (3)° from their symmetric (tetra-gonal) positions. There are only minor differences in the three-ring nucleus; the best mol-ecular fit of the tetra-gonal and monoclinic forms, both at 100 K and excluding phenyl rings and H atoms, shows an r.m.s. deviation of 0.066 Å. Both forms have the same absolute configuration.

Ortho-rhom-bic polymorph of (2E)-2-(2,3-dihydro-1H-inden-1-yl-idene)-2,3-di-hydro-1H-inden-1-one.

The title compound, C(18)H(14)O, is polymorphic at 123 K. The ortho-rhom-bic form reported herein has two independent mol-ecules in the asymmetric unit, with mol-ecular volume 313.5 Å(3). The previously reported triclinic (P-1) form [Raston & Scott (2000 ▶). Green Chem., 2, 49-52] has mol-ecular volume 309.6 Å(3) at the same temperature. All three mol-ecules deviate significantly and systematically from the putative C(s) symmetry (δ(r.m.s.) = 0.0265, 0.0256, 0.0497 Å). Comparison of the two molecules in the orthorhombic polymorph shows that 16 of the 19 equivalent pairs of framework atoms have a mirror-image pattern of deviations (above/below plane), suggesting that the two are quasi-enanti-omorphs. The pattern of deviations in the triclinic form is nearly the same (13 of 19 atom pairs) as the ortho-rhom-bic form.

1,2-Bis{2-[2-(trimethyl-sil-yl)ethyn-yl]phen-yl}ethane-1,2-dione.

The title compound, C(24)H(26)O(2)Si(2), has C(2) crystallographic symmetry. The dihedral angle between the aromatic rings is 84.5 (2)°. The acetyl-ene group is slightly non-linear, with angles at the acetyl-ene C atoms of 175.7 (2) and 177.0 (2)°. In the crystal structure, only van de Waals interactions occur.

1-(Adamantan-1-yl)-3-(4-meth-oxy-phenyl)prop-2-en-1-one.

The title mol-ecule, C(20)H(24)O(2), is a chalconoid derivative in which the keto-enone group is slightly distorted from planarity; the O=C-C=C torsion angle is 12.24 (13)°.

1,2,3,4,5,6,7,8,13,13,14,14-Dodeca-chloro-1,4,4a,4b,5,8,8a,12b-octa-hydro-1,4:5,8-dimethano-triphenyl-ene at 90†K.

The previously reported room-temperature crystal structure [Jaud Baldy, Negrel, Poite & Chanon (1993 ▶). Z. Kristallogr.204, 289-291] of the title compound, C(20)H(8)Cl(12), is monoclinic with Z' = 1, whereas the 90 K structure reported herein is triclinic with Z' = 2 and shows a 2% volume contraction. The crystallographically independent unit chosen consists of both enanti-omers (Λ and Δ) of this propeller-like mol-ecule. Both enanti-omers display quasi-twofold symmetry, with average bond-length/bond-angle deviations of 0.0018 (4) Šand 0.41 (2)° for Λ, and 0.0026 (4) Šand 0.50 (2)° for Δ.

(S)-2-Oxotetra-hydro-furan-3-aminium bromide.

In the title HBr salt of (S)-homoserine lactone, C(4)H(8)NO(2) (+)·Br(-), the five-membered ring has an envelope conformation, with the -CH(2)- C atom adjacent to the N-substituted C atom at the flap position. The four-atom mean plane (r.m.s. deviation = 0.005 Å) of the envelope forms a dihedral angle of 32.12 (9)° with the three-atom flap plane. The distorted square-pyramidal coordination about the anion involves five surrounding cations, with the square base defined by three N-H⋯Br hydrogen bonds [Br⋯N = 3.3046 (10), 3.3407 (12) and 3.3644 (13) Å] and near-contact with an H atom attached to C [Br⋯C = 3.739 (1) Å]. Another Br⋯C contact of 3.427 (1) Šdefines the apex. There is also an N-H⋯O hydrogen bond present linking the cations.

Tetra-methyl anthracene-2,3,6,7-tetra-carboxyl-ate-tetra-methyl 9,10-dihydro-9,10-dioxoanthracene-2,3,6,7-tetra-carboxyl-ate (1/1).

In the title co-crystal, C(22)H(16)O(10)·C(22)H(18)O(8), the independent tetra-methyl 9,10-dihydro-9,10-dioxoanthracene-2,3,6,7-tetra-carboxyl-ate, (I), and tetra-methyl anthracene-2,3,6,7-tetra-carboxyl-ate, (II), components occupy separate crystallographic inversion centers. In (II), the dihedral angles between the mean aromatic plane and the two independent carboxyl-ate planes are 41.32 (10) and -38.35 (10)°. The methyl-carboxyl-ate groups of (I) are disordered, with each resolvable into two groups. In the least disordered carboxyl-ate, the apparent angles between the mean aromatic plane and the two partial carboxyl-ate planes [site occupations = 0.510 (3) and 0.490 (3)] are 16.8 (3) and 23.3 (3)°. In the highly disordered group, the apparent angles between the mean aromatic plane and the two partial carboxyl-ate planes [site occupations = 0.510 (3) and 0.490 (3)] are 78.3 (3) and -74.1 (3)°. In addition, this extreme disorder leads to an artificially elongated C(aromatic)-C(carbox-yl) bond.

(2R,4R)-4-(2-Eth-oxy-2-oxoeth-yl)-2,6,6-trimeth-yl-2-oxo-1,3,6,2λ(5)-dioxaza-phospho-can-6-ium iodide.

The title compound, C(11)H(23)NO(5)P(+)·I(-), consists of an eight-membered cationic heterocyclic ring in a boat-chair conformation. The ring features a tetra-alkyl-ammonium N and a methyl-phospho-nate P atom. A -CH(2)(CO)OC(2)H(5) ester side chain at the C adjacent to oxygen produces two chiral centers at that substituted C atom and the P atom, both of which were determined to have absolute R,R configurations. A previously determined racemic bromide analog has exactly the same ring but with a -C(15)H(31) side chain. In that structure, both chiral centers show the same relative R/S,R/S configurations, but the ring in the bromide analog is in a boat conformation.

syn-5,10,15-Tris(dichloro-meth-yl)-5,10,15-trihy-droxy-5H-diindeno-[1,2-a:1',2'-c]fluorene dichloro-methane 0.82-solvate.

The title compound, C(30)H(18)Cl(6)O(3)·0.82CH(2)Cl(2), consists of a slightly cup-shaped seven-ring truxene nucleus with hy-droxy and dichloro-methyl substituents at stereocenters 5R/S, 10R/S and 15R/S. C-Cl distances are in the range 1.759 (4)-1.783 (3) Å. Solvent channels parallel to the b axis appear to be partially occupied by highly disordered dichloro-methane solvent mol-ecules, the contribution of which were removed from the refinement with the SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155]. Only one of the OH groups forms a hydrogen bond, which is inter-molecular to another OH group, forming centrosymmetric dimers in the crystal.

(E)-3,3',4,4',7,7',8,8'-Octa-methyl-2H,2'H-1,1'-bi(cyclo-penta-[fg]acenaphthyl-enyl-idene)-2,2',5,5',6,6'-hexa-one dichloro-methane monosolvate.

The title compound, C(36)H(24)O(6)·CH(2)Cl(2), is a dimer of two essentially planar (r.m.s., deviations of fitted plane of 14 pyracene C atoms = 0.0539 and 0.0543 Å) tetra-cyclic pyracene frameworks (each with four methyl groups and three carbonyl groups on the peripheral carbon atoms) twisted along a central C=C bond with an angle of 50.78 (3)° at 90 K. There are notably long Csp(2)-Csp(2) bonds associated with the carbonyl groups, the longest being 1.601 (3) Šbetween two carbonyl C atoms. There are also intermolecular carbonyl⋯carbonyl interactions of both parallel and antiparallel types, with C⋯O distances in the range 3.041 (3) to 3.431 (2) Å. This compound is of inter-est with respect to the synthesis of fullerene fragments, such as corannulene and semibuckminsterfullerene derivatives (or 'buckybowls'), and is a side product of the previously reported oxidation reaction. Structural details, such as planarity analysis of fused rings, out-of-plane deviation of substituents, inter-molecular inter-actions, and longer than typical bond lengths, will be discussed as well as comparisons to structurally related compounds.

25,26-Bis(propan-2-yl-idene)hepta-cyclo[20.2.1.1(10,13).0(2,21).0(3,8).0(9,14).0(15,20)]hexa-cosa-2(21),3,5,7,9(14),11,15,17,19,23-deca-ene.

In the title compound, C(32)H(28), the central cyclo-octa-tetra-ene ring has a boat conformation, and the mol-ecule is saddle shaped. The seat is defined by the mean plane of the four-atom attachment points (r.m.s. deviation = 0.014 Å) of the two bicyclo-heptenyl substituents. These substituents comprise the pommel and cantle, with each mean plane defined by four atoms proximate to the seat (r.m.s. deviations = 0.002 and 0.004 Å). Relative to the seat, the pommel and cantle bend up 31.16 (4) and 29.40 (5)°, while the benzo units (flaps, r.m.s. deviations = 0.006 and 0.009 Å) bend down 36.75 (4) and 38.46 (4)°. The mean planes of the dimethyl-ethyl-idene units are almost perpendicular to the saddle seat, making dihedral angles 86.89 (4) and 88.01 (4)°.

Bis[2,3,4-trimethyl-5-[(3,4,5-trimethyl-2H-pyrrol-2-yl-idene-κN)meth-yl]-1H-pyrrolato-κN]copper(II).

In the title complex, [Cu(C(15)H(19)N(2))(2)] or [Cu(L(2))] (HL is 3,3',4,4',5,5'-hexa-methyl-pyrromethene), the Cu(II) atom is coordinated by four N atoms [Cu-N 1.939 (2)-1.976 (2) Å] from two L ligands in a distorted tetra-hedral geometry. The mean planes of the CuN(2)C(3) metallocyclic rings form a dihedral angle of 72.73 (6)°. In the L ligands, the pyrrole rings are inclined to each other at dihedral angles of 3.03 (7) and 9.83 (7)°. The crystal packing exhibits weak inter-molecular C-H⋯π inter-actions, which form chains in [100].

Di-µ-carbonyl-bis-[bis-(triphenyl-phos-phane)rhodium(0)](Rh-Rh) acetone disolvate.

The dirhodium complex, [Rh(2)(C(18)H(15)P)(4)(CO)(2)]·2(CH(3))(2)CO, has crystallographic twofold symmetry and the Rh-Rh distance is 2.6266 (8) Å. The four atoms proximate to each Rh atom [Rh-P = 2.3222 (7) and 2.3283 (8) Å, and Rh-C = 1.961 (3) and 2.045 (3) Å] form a distorted tetra-hedron with large deviations from the putative tetra-hedral angles [r.m.s. deviation = 23 (1)°]. The six angles more closely approximate those of a trigonal bipyramid [r.m.s. deviation = 14 (1)°] with one missing equatorial ligand. The two bridging carbonyl ligands are much more linearly coordinated to one Rh [Rh-C O = 151.0 (2)°] than to the other [127.0 (2)°], and the two Rh(2)CO planes form a dihedral angle of 45.43 (5)°. The two acetone solvent mol-ecules are disordered, and their estimated scattering contribution was subtracted from the observed diffraction data using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst.D65, 148-155].