Frank H. Herbstein

Some 60 new space-group corrections

Some 60 examples of crystal structures are presented which can be better described in space groups of higher symmetry than used in the original publications. These are divided into three categories: (A) incorrect Laue group (33 examples), (B) omission of a center of symmetry (22 examples), (C) omission of a center of symmetry coupled with a failure to recognize systematic absences (nine examples). Category A errors do not lead to significant errors in molecular geometry, but these do accompany the two other types of error. There are 19 of the current set of examples which have publication dates of 1996 or later. Critical scrutiny on the part of authors, editors and referees is needed to eliminate such errors in order not to impair the role of crystal structure analysis as the chemical court of last resort.

Catenated and non-catenated inclusion complexes of trimesic acid

Trimesic acid (benzene-1, 3,5-tri-carboxylic acid; TMA) can in principle form two-dimensional hydrogen-bonded hexagonal networks in which central holes of the network have net diameters of 14 Å. Although such holes would be expected to be natural locations for guest molecules, non-catenated single networks have not been found in any of the crystals containing TMA studied in the last sixteen years. Instead, anhydrous α-TMA, TMA pentaiodide (TMA.I5) and (so-called) γ-TMA have mutually triply-catenated structures in which triplets of networks are interlaced [3,4,5], while the hydrated complexes are based on non-catenated nets of composition TMA.H2O [6]. We have now found conditions under which single networks are preserved without catenation, the cavities being occupied by guests such as n-tetradecane, n-heptanol, n-octanol, n-decanol, octene, cyclooctane and isooctane. The structures of 2TMA. n-tetradecane and 2TMA. isooctane have been solved and refined to R=13.0% and R=11.3%, respectively, disorder of the guest molecules having prevented further refinement of the room-temperature data. Determination of the crystal structures of the other complexes, which are isostructural with 2TMA. n-tetradecane, is now in progress. We are also investigating other potential guests.

How precise are measurements of unit-cell ­dimensions from single crystals?

The results of single-site and many-site measurements of cell dimensions from single crystals are compared for Bond and four-circle diffractometers using samples of corundum (essentially pure rhombohedral alpha-Al2O3, aluminum oxide) of high diffraction quality, where the effects of small changes in temperature and composition (Cr2O3, chromium oxide, in solid solution) can be taken into account. Similar comparisons are made for four-circle diffractometer measurements on ruby (alpha-Al2O3, with 0.46 wt % Cr in solid solution). The precisions are some parts in 10(5). There is partial support for the Taylor-Kennard [Acta Cryst. (1986), B42, 112-120] dictum that standard uncertainties (s.u.s) of cell parameters from routine four-circle diffractometer measurements are less than those for many-site measurements by factors of 5 for cell lengths and 2.5 for cell angles. For organic crystals, independent repetitions of adequate quality for comparison and analysis of routine four-circle diffractometer measurements are available only for alpha-oxalic acid dihydrate and anthracene. The experimental standard uncertainties given for these two crystals agree reasonably well with the sample s.u.s at room temperature, but appreciably less well at approximately 100 K, again giving partial support to the Taylor-Kennard dictum. The relation between specimen characteristics and attainable precision is emphasized; the precisions for routine measurements on good quality organic crystals are some parts in 10(4). Area-detector measurements of cell dimensions have also been appraised; currently published s.u.s from such measurements appear to be highly unreliable, and this is supported by a recent analysis of the operation of such diffractometers [Paciorek et al. (1999). Acta Cryst. A55, 543-557]. Formulation of a standard protocol for such measurements is badly needed. The dangers inherent in high degrees of replication are illustrated by recounting Kapteyns Parable of the Chinese Emperor. Attention is drawn to the fact that there has been little improvement in claimed precisions over the past 40-60 years.

More Space-Group Corrections: From Triclinic to Centred Monoclinic and to Rhombohedral; Also From P1 to P-1 and From Cc to C2/c

We present 14 examples of crystal structures that were originally described as triclinic, but are properly described as either C-centred monoclinic (ten examples) or rhombohedral (four examples). There is also one example each of changes from P1 to P1 and from Cc to C2/c.

X-ray and neutron diffraction study of benzoylacetone in the temperature range 8–300 K: comparison with other cis-enol molecules

The crystal structure of benzoylacetone (1-phenyl-1,3-butanedione, C(10)H(10)O(2); P2(1)/c, Z = 4) has been determined at 300, 160 (both Mo Kalpha X-ray diffraction, XRD), 20 (lambda = 1.012 Å neutron diffraction, ND) and 8 K (Ag Kalpha XRD), to which should be added earlier structure determinations at 300 (Mo Kalpha XRD and ND, lambda = 0.983 Å) and 143 K (Mo Kalpha XRD). Cell dimensions have been measured over the temperature range 8-300 K; a first- or second-order phase change does not occur within this range. The atomic displacement parameters have been analyzed using the thermal motion analysis program THMA11. The most marked change in the molecular structure is in the disposition of the methyl group, which has a librational amplitude of approximately 20 degrees at 20 K and is rotationally disordered at 300 K. The lengths of the two C-O bonds in the cis-enol ring do not differ significantly, nor do those of the two C-C bonds, nor do these lengths change between 8 and 300 K. An ND difference synthesis (20 K) shows a single enol hydrogen trough (rather than two half H atoms), approximately centered between the O atoms; analogous results were obtained by XRD (8 K). It is inferred that the enol hydrogen is in a broad, flat-bottomed single-minimum potential well between the O atoms, with a libration amplitude of approximately 0.30 Å at 8 K. These results suggest that at 8 K the cis-enol ring in benzoylacetone has quasi-aromatic character, in agreement with the results of high-level ab initio calculations made for benzoylacetone [Schiøtt et al. (1998). J. Am. Chem. Soc. 120, 12117-12124]. Application [in a related paper by Madsen et al. (1998). J. Am. Chem. Soc. 120, 10040-10045] of multipolar analysis and topological methods to the charge density obtained from the combined lowest temperature X-ray and neutron data provides evidence for an intramolecular hydrogen bond with partly electrostatic and partly covalent character, and large p-delocalization in the cis-enol ring. This is in good agreement with what is expected from the observed bond lengths. Analysis of the total available (through the Cambridge Structural Database, CSD) population of cis-enol ring geometries confirms earlier reports of correlation between the degree of bond localization in the pairs of C-C and C-O bonds, but does not show the dependence of bond localization on d(O.O) that was reported earlier for a more restricted sample. It is suggested that the only reliable method of determining whether the enol hydrogen is found in a single or double potential well is by low-temperature X-ray or (preferably) neutron diffraction.

Classification of closed shell TCNQ salts into structural families and comparison of diffraction and spectroscopic methods of assigning charge states to TCNQ moieties1

More than 50 crystals containing 7,7,8,8-tetracyanoquinodimethane (TCNQ) in various guises are classified into a limited number of structural types and the possible assignment of charge states by diffraction and spectroscopic methods is compared. In the crystalline state the 7,7,8,8-tetracyanoquinodimethane (TCNQ) moiety is found in mixed stack π–π* molecular compounds with neutral TCNQ as acceptor and a variety of neutral donors, and as five types of salt, three of which contain only TCNQ1− and have either (i) segregated monad TCNQ stacks, (ii) mixed-stack {[cation+][TCNQ1−]} arrangements or (iii) isolated {2[cation+]  · [(TCNQ1−)2]} π-dimers, while the remaining two contain both TCNQ0 and TCNQ1− and have compositions (iv) {[cation+] ]} and (v) {[cation+]2  ·  }. Each family is found with a characteristic isostructural packing arrangement, there being differences of detail among the members; there are some exceptions to the overall rule, usually with combinations of standard packing elements forming a non-standard overall arrangement. Each structural group has been analysed in the same way. First, the crystal chemistry is described, then various probes of increasing sensitivity are applied to establish the charge state of the moieties and their relation to the packing arrangement. The several probes are (i) X-ray diffraction, giving moiety geometries (bond lengths and deviations from planarity) (ii) infra-red and resonance Raman spectroscopy for identification of charge states (iii) electron spin resonance and magnetic measurements (where applicable) to give further details of moiety structure. Bond lengths have been surveyed for the various types of TCNQ moiety. The differences are not large, the bond most sensitive to charge being the extra-ring double bond (c), while bond length differences for adjacent single-bond double-bond pairs (intra-ring (b  – a) and extra-ring (c  – d)) also provide a way of distinguishing different charge states. Although bond lengths have provided, for almost 40 years, a popular way to assess moiety charge, our present review suggests that much caution is required in the application of this method not only to individual structures determined at room temperature but even to those determined at very low temperatures. Resonance Raman spectroscopy provides an alternative method of assessing moiety charge and is determinative with singly charged TCNQ moieties but not with other TCNQ species; both methodology and correlation with diffraction results require further investigation. Most studies of electrical conductivity lack detail about orientation and temperature dependence and thus are difficult to relate to packing arrangements. ESR measurements generally confirm strong antiferromagnetic coupling within π-dimers. 1An abbreviated version was presented at the 2007 Salt Lake City Meeting of the American Crystallographic Association on the occasion of the Fankuchen Award to FHH.

Arrays with Local Centers of Symmetry in Space Groups Pca21 and Pna21

Of the several hundred structures in the Cambridge Structural Database [version 4.6 (1992), Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, England] having space groups Pca2_1 or Pna2_1 and more than one molecule in the asymmetric unit (Z > 4), approximately three-quarters contain local centers of symmetry. These local centers, which are not crystallographic centers, occur predominantly near x = 1/8, y = ¼ in Pca2_1 or near x = 1/8, y = 0 in Pna2_1; this also holds for the limited number of examples we have examined of pseudo-centrosymmetric molecules with Z = 4. Local centers at these points create unusual correlations between corresponding atoms in the two molecules.

The crystal structures of three isomorphous trimesic acid channel inclusion complexes of polyhalide ions. A second example of triple catenation in the solid state

The three polyhalide complexes of trim esic acid (benzene-1, 3, 5-tricarboxylic acid; TMA) with compositions TMA.0.7H2O. 0.09 HI5(I), TMA. 0.7H2O. 0.103 HBr5(II), TMA. 0.7H2O. 0.167 HIBr2(III) are isomorphous (for example, for I, a = 21.945(7), b = 17.917(6), c = 16.711(6) Å, the space group is 1222, Z = 24; II and III have very similar cell dimensions). Crystal structure analysis (four-circle diffractometer, graphite-monochro-mated MoKa: I, 2273reflexions, R = 12.2% ; III, 1747 reflexions, R = 12.4%) shows that all three have the same TMA fram ework, which consists of two mutually-perpendicular infinite hexagonal planar networks of hydrogen-bonded TMA molecules. The two networks are parallel to (110) and (11̄0) respectively and are mutually triply catenated. The arrangement is such as to leave channels of square cross section along the z-direction, which contain the linear polyhalide ions. I an d II have pentahalide ions incommensurable with the TMA framework; the diffuse scattering pattern from I allows the structure of the I-5 ion to be determined as consisting of strongly interacting . . . I2 - - - I- I2 . . . units and it is inferred that Br-5 has a similar structure. Compound III has IBr-2 ions commensurable with the TMA framework, but some difficulties remain in the interpretration of these results. The TMA framework has additional voids in the region about 1/2, 0, 1/2 and these are occupied by the water molecules (ca. sixteen per unit cell) in disordered fashion. The protons required to balance the charges of the polyhalide ions are presumably attached to some of these water molecules. The materials are characterized as crystalline acid-molecule complexes.

Pyridinium picrate – the structures of phases I and II. Correction of previous report for phase I. Study of the phase transformation

Pyridinium picrate, C 5 H 6 N + .C 6 H 2 N 3 O 7 , was reported [Kofler (1944). Z. Elektrochem. 50, 200-207] to exist in two crystalline phases, one (I) being stable below 343 K and the other (II) between 343 K and the melting point (∼438 K). The room-temperature structure of phase I, studied by two-dimensional methods, has been reported [Talukdar & Chaudhuri (1976). Acta Cryst. B32, 803-808]. We were led to reinvestigate the system by a number of unusual features in Koflers description of the phase behaviour. Single crystals of phase I were grown from solution and those of phase II from the melt. We have determined the structure of both phases, including analysis of the thermal motion of the picrate ions, which was found to be appreciably larger in phase II than in phase I

The polyiodide salts: Pyridinium pentaiodide;β-naphthylammonium pentaiodide; andN-methyl-γ-picolinium heptaiodide. Structures with channel inclusion features

The crystal structures of three polyiodode salts are reported (pyridinium pentaiodide, monoclinic,P21/m,a=9.221(5),b=12.918(5),c=6.026(4) Å, β=103.60(7)o,Z=2,RF=0.087 for 1187 intensities; β-naphthyl-ammonium pentaiodide, triclinic,173-1,a=10.390(5),b=9.502(5),c=4.462(3) Å, α=99.19(7), β=90.40(7),γ=108.49(8)o,Z=2,RF=0.059 for 1319 intensities;N-methyl-γ-picolinium heptaiodide, monoclinic,C2/c,a=19.315(7),b=12.714(5),c=8.442(4) Å, β=107.26(7)o,Z=4,RF=0.065 for 1336 intensities). All three structures can be described as having channel inclusion features; the cations are contained in channels in polyiodide frameworks based on different arrangements of I2 molecules and I3− anions. This structural type is the converse of the more widespread kind where polyiodide anions are contained in an organic matrix (e.g., cyclodextrin polyiodides).