Ian G. Dance

SUPRAMOLECULAR MOTIFS : CONCERTED MULTIPLE PHENYL EMBRACES BETWEEN PH4P+ CATIONS ARE ATTRACTIVE AND UBIQUITOUS

Examination of the Cambridge Structural Database reveals that Ph4P+ cations in crystals associate through phenyl-phenyl nonbonded interactions which are attractive, concerted, and widespread. Intermolecular phenyl-phenyl conformations, which are offset-face-to-face (off), edge-to-face (ef) or vertex-to face (vf), combine in five classes of supramolecular motifs for {Ph4P+}2 pairs, namely the sextuple phenyl embrace (SPE) with (ef)6 and offset sextuple phenyl embrace (OSPE) containing (off)1 (ef)2(ef/vf)2, the translational quadruple phenyl embrace (TQPE) with (ef)4, the parallel quadruple phenyl embrace (PQPE) with (off)1(vf)2, and the double phenyl embrace (DPE) with (off)1. Typical intermolecular attractive energies (kJ per mol of {Ph4P+}2) for these motifs are SPE 85, OSPE 57, TQPE 70, PQPE 41, DPE 34. There is strong interpenetration of the cations in these motifs: 489/770 structures in the CSD have P P≤7 A (spherical Ph4P+ has a van der Waals diameter of 13.6 A). Of the 812 instances of P P ≤7 A, 86% are SPE, 10% are OSPE, 2% are TQPE, and only 2% are unclassified, Average P P separations in the PQPE and DPE are 8.3 A. Centrosymmetry is prevalent in all except the TQPE, which has implications for the engineering of noncentric crystals.

Distance criteria for crystal packing analysis of supramolecular motifs

Supramolecular phenomena are determined by energies, but a different property, geometry, is commonly measured, and abundant data are available. The sum of van der Waals radii, the conventional distance criterion in assessing geometrical data, needs to be related to the relevant intermolecular potential, with cognisance of the chemistry of the molecular surface. The relationship between distance distributions in crystals and the distance scale of the intermolecular potential is evaluated, and the relevant concepts (and mis-concepts) are elaborated. The position of the minimum in the intermolecular potential, that is the most stabilising distance, is ca. 0.4 A larger than the van der Waals distance. In crystals a small number of destabilising contacts less than the van der Waals distance can be enforced by a much larger number of longer stabilising distances. Crystal packing analyses with cut-offs at the van der Waals distance are likely to miss key supramolecular features.

Crystal supramolecular motifs: two-dimensional grids of terpy embraces in [ML2]z complexes (L=terpy or aromatic N3-tridentate ligand)

By analysis of crystal packing we have identified a crystal supramolecular motif that is a two-dimensional net of terpy embraces formed by metal complexes [M(terpy)2]2+ (terpy=2,2′:6′,2″-terpyridyl) and similar meridional [M(N3-tridentate)2] complexes. The terpy embrace involves two complexes attracted by one offset-face-to-face (off) and two edge-to-face (ef) interactions by the outer pyridyl rings of the ligand. In many crystals containing small monoanions there is a two-dimensional net of these embraces, in which each complex forms eight ef and four off interactions with its neighbours. The principal axes of the complexes are normal to the layer, which is exactly or approximately planar, and can occur with high (tetragonal) or low crystal symmetry. Grooves that occur on the layer surfaces, formed between parallel central pyridyl rings of the ligands, run in orthogonal directions on the two surfaces of each layer. Anions and solvent molecules in the crystals are usually disordered, in or near the grooves. The net attractive energy of the terpy embrace for a pair of [M(terpy)2]2+ is calculated to be ca. 15 kJ mol-1: in the two-dimensional net the attractive cation···cation energy per cation is ca. 29 kJ mol-1. Inclusion of the anions associated with one layer increases the attractive energy per [M(terpy)2]2+ to the order of 130 kJ mol-1. A variety of ligands, which are minor or major modifications of terpy, also form this supramolecular motif. Hydrogen bonding involving NH functions of these ligands, solvent, and/or anions, does not in general disrupt the motif. In one instance where the [M(N3-tridentate)2] complex is uncharged there is mutual interpenetration of contiguous layers. These infinite two-dimensional nets of octahedral metal complex sites formed as crystal supramolecules are analogous to the two-dimensional gridlike supermolecules formed by extended oligo-chelating ligands. Opportunities for crystal engineering are discussed.

Engineering grids of metal complexes: development of the 2D M(terpy)2 embrace motif in crystals

The two-dimensional terpy embrace motif, a concert of multiple edge-to-face and offset-face-to-face interactions, assembles [M(terpy)2]2+ complexes into regular square grids, as layers that are stacked in crystals. The layers possess deep segmented grooves on their surfaces, with the cavities occupied by small anions and sometimes by solvent. In this paper we survey and analyse the crystal packing in all known cases of this motif, together with new crystal structures and crystal growth information for [Ni(terpy)2](PF6)2, [Ni(terpy)2](PF6)2·acetone, and [Ni(terpy)2](PF6)2·DMF. The main types of stacking patterns and interlayer domains are classified, in relation to absence or presence of solvation, and the resulting space-groups. The different structures of [Co(terpy)2](ClO4)2·xH2O, which can have strong influences on magnetic properties, are considered, and it is proposed that the subtle variations are due to a balance between optimal electrostatic stabilisation of the crystal when anions alone occupy the cavities, and hydrogen bonding (intra-layer and inter-layer) stabilisation when water is included. With larger anions and/or solvent molecules there is minor tilting of the M(terpy)2 complexes such that the two surfaces of the layer are different. The patterns and principles of crystal packing for 2D M(terpy)2 grids developed here are the foundation for subsequent descriptions and analyses of related crystal structures of derived compounds. The lack of published information about crystallisation conditions and processes is a limitation on the crystal engineering of these metal complex grids.

X-ray absorption spectroscopy of cadmium phytochelatin and model systems

Higher plants, algae and some yeasts respond to potentially toxic heavy metals such as cadmium by synthesizing phytochelatins and related cysteine-rich polypeptides. We have used X-ray absorption spectroscopy to study the nature of cadmium binding in such peptides isolated from maize (Zea mays) exposed to low levels of cadmium, and in two synthetic cadmium-peptide complexes, Cd-(gamma-Glu-Cys)3Gly and Cd-(alpha-Glu-Cys)3Gly. We have used the synthetic ions [Cd(SPh)4]2-, [Cd4(SPh)10]2- and [S4Cd10(SPh)16]4-as crystallographically defined models for the cadmium site. The Cd K-edge extended X-ray absorption fine structure (EXAFS) data, together with the Cd K, LI, LII and LIII near-edge spectra, reveal a predominantly tetrahedral coordination of cadmium by sulfur in both the phytochelatin and synthetic peptide complexes. In particular, the Cd LIII-edge lacks a peak at 3534.9 e V which was found to be prominent for oxygen- or nitrogen-coordinated species. The Cd-S distance in the phytochelatin complex is 2.54 A. The Cd K-edge EXAFS does not show any isolated, well-defined Cd-Cd interactions; however, contrary to the conclusion of previous work, their absence is not necessarily indicative of isolated cadmium-thiolate ligation. Evidence from other studies suggests that high static disorder, combined with a large vibrational component, serve to effectively wash out this contribution to the EXAFS. The sulfur K-edge, moreover, shows a low-energy feature both in the phytochelatin and in the synthetic cadmium-peptide complexes which is consistent with sulfide bound in a cluster with cadmium as found for [S4Cd10(SPh)16]4-. This feature strongly suggests the presence of a polynuclear cadmium cluster in maize phytochelatin.

Molecules embracing in crystals

We review the main types of intermolecular embrace motifs adopted by molecules with arylated surfaces, and draw attention to some recent interesting developments.

Supramolecular potentials and embraces for fluorous aromatic molecules

In order to understand better the supramolecular chemistry of fluorous molecules, and particularly coordination complexes and organometallic molecules with perfluoroaromatic substituents, the relevant intermolecular potentials have been parametrised. It is shown that density functional calculations using the Perdew–Wang PWC functional and numerical basis sets adequately describe weak intermolecular attractive energies [e.g. (C6H6)2], but that gradient corrected BP or BLYP functionals do not. Due to a dearth of experimental data on intermolecular energies for perfluoroaromatic systems, these density functional calculations of the supramolecular isomers of (C6F6)2 are used to parametrise the Lennard-Jones plus electrostatic potential for fluoroaromatic and derivative molecules. Intermolecular energies for local interactions in the crystal structures of C6F6, C6F6·C6D6, and octafluoronaphthalene are reported. Strong directionality is not observed in the supramolecular forces between fluoroaromatics and the electrostatic components of the intermolecular energies are small, <15% of the total; the polarisation of the C–F bond is also less than expected from electronegativity differences. Perfluorinated molecules and ions such as [B(C6F5)4]− engage in multiple phenyl embrace motifs, comparable to those of phenylated molecules, despite the reversed polarity of aromatic C–F relative to C–H bonds (and the opposite quadrupole moments of C6F6 and C6H6). Examples of the sixfold perfluorophenyl embrace (6PFE), the hexagonal array of sixfold perfluorophenyl embraces (HA6PFE), and fourfold perfluorophenyl embraces (4PFE) are described. The intermolecular attractive energies of some of these motifs comprised of concerted edge-to-face and offset-face-to-face interactions are in the range −5.5 to −11.7 kcal mol−1. It is concluded that there are no major differences between the supramolecular motifs and energies of perfluorinated- and hydroaromatics.

Inorganic intermolecular motifs, and their energies

This article focuses on materials containing inorganic molecules and coordination complexes, assembled via intermolecular interactions. For inorganic systems that can contain the full range of elements and exhibit the full diversity of chemistry, some clarification is needed for fundamental concepts about molecular and non-molecular structure. An underlying theme is the need for knowledge of intermolecular energy potentials as a prerequisite for reliable design and preparation of molecular materials. Relationships between intermolecular potentials, histograms of intermolecular distances, and van der Waals surfaces, are discussed. A density functional method for efficient calculation of intermolecular potentials is evaluated, and some results presented, particularly for compounds with high-Z atoms where the integrity of molecular surfaces is diminished. In the context of the higher ordering of molecular assemblies, the main types of concerted intermolecular embraces between arylated molecules and representative coordination complexes are reviewed. When charged polyatomic molecules are assembled, and homo-charged molecules are segregated, there are basic questions about the relative magnitudes and influences of electrostatic energies: this issue is considered in the context of observed embraces between homo-charged polyatomic molecules and coordination complexes.

The formation and crystal and molecular structures of hexa(μ-organothiolato)tetracuprate(I) cage dianions: bis-(tetramethylammonium)hexa-(μ-methanethiolato)tetracuprate(I) and two polymorphs of bis(tetramethylammonium)hexa-(μ-benzenethiolato)-tetracuprate(I)

Abstract X-Ray analysis shows that the crystalline compounds (Me4N)2[Cu4(SMe)6] (1), (Me4N)2[Cu4(SPh)6] (2) and (Me4N)2[Cu4(SPh)6]EtOH (3) all contain the [tetrahedro-CuI4-octahedro-(SR)6]2− molecular cage. Very well developed pale yellow crystals of (2) and (3) can be obtained directly from a mixture of copper(II) salt and excess benzenethiol with tertiary amine in alcohol. The substituents R of the [Cu4(SR)6]2− cage remove the high symmetry of the Cu4S6 core, and allow three configurational isomers for the cage. All known instances of this cage structure occur as the isomer which minimises the number of close contacts of substituents over the surface of the cage. Despite this, there remain intra-cage repulsive interactions between substituents, greater for RPh than for RMe, which cause distortions primarily in the SCuS angles which range from 105–144°. CuS distances are coupled, apparently electronically, to opposite SCuS angles. The stereo-chemical analysis is extended to all known Cu4(SR)6 cages, and to alternative cage structures.

Contrasting crystal supramolecularity for [Fe(phen)3]I8 and [Mn(phen)3]I8: complementary orthogonality and complementary helicity

The crystallisation, crystal structures, and analyses of crystal supramolecularity for [Fe(phen)3]I8 and [Mn(phen)3]I8 are reported. Crystalline [Fe(phen)3]I8 contains the first example of one-dimensionally extended sixfold aryl embraces (6AE) between [M(phen)3]2+ complexes. The interchain domains contain twisted I82– ions, which are translated along the axis of the domain to form polyiodide helices. Sections of the polyiodide helix slot into the grooves between the phen ligands in each [Fe(phen)3]2+ complex: these grooves are canted in helical fashion in each complex, even though the extended 6AE chain is not helical, and there is good local registry and geometrical complementarity between the polyiodide helices and the cation chains. The polyiodide helices are buttressed further by concerted C–H⋯I interactions. The crystal approaches trigonal symmetry. In contrast, crystalline [Mn(phen)3] (I3)(I5) contains neither 6AE nor the parallel fourfold aryl embraces (P4AE) characteristic of [M(phen)3]z complexes, but does display a relatively rare instance of a homo-chiral P4AE. The association of [Mn(phen)3]2+ complexes and the I3– and I5– ions is effective and close, and manifests well the complementary orthogonality of [M(phen)3]z complexes and polyiodides. There are two formula units in the asymmetric unit of [Mn(phen)3](I3)(I5), and the high-spin [Mn(phen)3]2+ cations are distorted from the octahedral stereochemistry of low-spin [Fe(phen)3]2+. The issues of whether these two structures could be regarded as substitutional polymorphs, and which is the more stable, and whether each could crystallise with the structure of the other, are discussed.