Showing papers in "CrystEngComm in 2004"

CH/π hydrogen bonds in crystals

Abstract: The nature and characteristics of the CH/π interaction are discussed by comparison with other weak molecular forces such as the CH/O and OH/π interaction. The CH/π interaction is a kind of hydrogen bond operating between a soft acid CH and a soft base π-system (double and triple bonds, C6 and C5 aromatic rings, heteroaromatics, convex surfaces of fullerenes and nanotubes). The consequences of CH/π hydrogen bonds in supramolecular chemistry are reviewed on grounds of recent crystallographic findings and database analyses. The topics include intramolecular interactions, crystal packing (organic and organometallic compounds), host/guest complexes (cavity-type inclusion compounds of cyclodextrins and synthetic macrocyclic hosts such as calixarenes, catenanes, rotaxanes and pseudorotaxanes), lattice-inclusion type clathrates (including liquid crystals, porphyrin derivatives, cyclopentadienyl compounds and C60 fullerenes), enantioselective clathrate formation, catalytic enantioface discriminating reactions and solid-state photoreaction. The implications of the CH/π concept for crystal engineering and drug design are evident.

Interpenetrating metal–organic and inorganic 3D networks: a computer-aided systematic investigation. Part I. Analysis of the Cambridge structural database

Abstract: The occurrence of interpenetration in metal–organic and inorganic networks has been investigated by a systematic analysis of the CSD and ICSD structural databases. For this purpose, a novel version of TOPOS (a program package for multipurpose crystallochemical analysis) has been employed, where the procedure of recognition of interpenetrating nets is based on the representation of a crystal structure as a finite reduced graph. In this paper we report a comprehensive list (301 Refcodes) of interpenetrating metal–organic 3D structures from CSD, that are analyzed on the basis of their topologies. Interesting trends and novel features have been observed and distinct classes of interpenetrating nets have been envisaged, depending on the relationships of the individual motifs.

Reflexion on molecular tectonics

Abstract: Molecular crystals are solid and periodic materials. These entities may be regarded as supramolecular architectures and thus be described as molecular networks, which are infinite molecular assemblies possessing translational symmetry and composed of complementary or self-complementary tectons capable of mutual interactions. This way of analysing structural features of crystalline materials called molecular tectonics not only permits crystals to be described as supramolecular architectures generated through molecular recognition processes but also allows molecular networks to be conceived with predicted connectivity and thus dimensionality through the design of tectons. A formal description and analysis of molecular networks is given.

A method for the prediction of the crystal structure of ionic organic compounds—the crystal structures of o-toluidinium chloride and bromide and polymorphism of bicifadine hydrochloride

Abstract: The crystal structures of o-toluidinium chloride (1), o-toluidinium bromide (2) and two polymorphs of bicifadine hydrochloride (3) have been determined. The polymorphs of 3 differ in their molecular conformation and in their mode of packing. Crystallisation studies and quantum mechanical calculations show that the more readily crystallisable polymorph grows from the thermodynamically most stable conformer. On heating, conversion to the second polymorph takes place just below the melting point. The crystal structures of 1, 2 and the first polymorph of 3 have been successfully predicted using a procedure that is suitable for simple ionic organics.

Questions for crystal engineering of halocuprate complexes: concepts for a difficult system

Abstract: We evaluate prospects for the crystal engineering of anionic halocuprate complexes [CunXm]z−, X = Cl, Br, I, crystallised with polyatomic cations that possess alkyl or aryl coated surfaces and do not form hydrogen bonds. In solution, halocuprate complexes are involved in kinetically fast dissociative and associative equilibria, as well as redox variation between Cu(I), mixed Cu(I)/Cu(II) and Cu(II), and so the species that crystallise need not be those that predominate in solution: we describe instances of this complication, and the trapping of complexes which are not evident in solution. Our survey includes the relationships between cation properties and the identity and structure of the crystallised halocuprate complex, and the occurrence of polymorphism and de-facto polymorphism. A key aspect is the packing arrangement of anions and cations in these crystals: we illustrate the primary influence of electrostatic energies in determination of crystal packing, and the secondary but significant influences of cation··cation motifs and embraces in controlling details of crystal structure. In the context of crystal engineering, for which fundamental understanding and control of the crystallisation process and of the crystal structure are prerequisites, we conclude that even a chemically simple coordination system such as [CunXm]z− needs additional knowledge and physico-chemical insight before there can be confident design and reliable fabrication of desired crystals. Progress will be aided by the publication (in crystal structure papers) of more information about crystallising solutions and the effects of crystallisation variables, as well as ability to repeat crystallisation.

The innovative momentum of crystal engineering

Abstract: Crystal engineering has become an established part in various segments of industrial research. The toolbox of crystal engineering not only offers design strategies for performance chemicals and characterization tools for active ingredients but also helps to provide fundamental concepts for understanding the principles behind the formation and properties of organic solids. In this highlight examples are given for the application of crystal engineering during different phases of development of various industrial products, e.g. pigments, dyes, agrochemicals and drugs. In addition, future needs and possible development trends in crystal engineering are discussed with a special emphasis on novel innovative materials.

High-pressure recrystallisation—a route to new polymorphs and solvates

Abstract: The recrystallisation of organic compounds from solution under high-pressure conditions is shown to be a versatile method for the formation of new polymorphs and solvates. The technique is illustrated by the crystallisation of a new polymorph of phenanthrene from dichloromethane at a pressure of 0.7 GPa, and the crystallisation of a novel dihydrate of paracetamol from water at a pressure of 1.1 GPa. These phases have been characterised by single crystal X-ray diffraction. We also demonstrate that the technique can be used to prepare a polymorph that is metastable under ambient conditions. Thus the orthorhombic form of paracetamol was crystallised from ethanol at a pressure of 1.1 GPa.

Metal–organic framework structures of Cu(II) with pyridine-2,6-dicarboxylate and different spacers: identification of a metal bound acyclic water tetramer

Abstract: The ligand pyridine-2,6-dicarboxylic acid (pdcH2) reacts under hydrothermal conditions, with Cu(NO3)2·6H2O in the presence of different N-heterocycles used as spacers to form 1D, 2D or 3D metal–organic framework structures depending on the nature of the spacer. These network structures are characterized by X-ray crystallography, variable temperature magnetic measurements, powder X-ray diffraction, infrared and thermal gravimetric analyses. With 4,4′-bipyridine spacer, a 2D network is formed where every alternate Cu(II) ion in the chain is coordinated terminally to an acyclic tetrameric water cluster.

Supramolecular isomers in the same crystal: a new case involving two different types of layers polycatenated in the 3D architecture of [Cu(bix)2(SO4)]·7.5H2O [bix = 1,4-bis(imidazol-1-ylmethyl)benzene]

Abstract: The reactions of copper(II) sulfate with the flexible ligand 1,4-bis(imidazol-1-ylmethyl)benzene (bix) in H2O/acetone solution have afforded two novel coordination polymers, i.e. the 1D species [Cu(bix)(H2O)3(SO4)]·H2O and the 3D networked array [Cu(bix)2(SO4)]·7.5H2O. The former polymer contains highly undulated chains that are joined into 2D layers via hydrogen bond bridges. The second species shows an unusual 3D architecture comprised of two interlocked sets of different 2D layers, giving inclined polycatenation. Both sets of layers display the same (4,4) topology but exhibit quite different tiling patterns (with ‘ideal’ plane symmetry c2mm and p4gm, respectively) because of the varied conformations of the bix ligands on passing from the first set to the second one. These two 2D motifs represent a new case of supramolecular isomerism in the same crystal. The sulfate anions form μ2-bridges between copper ions, that cross-link the two sets of layers, giving a single 3D self-penetrating 6-connected network. This shows channels (total free void ca. 27% of the cell volume) containing many solvated water molecules, that are lost upon thermal activation and regained with crystal modification. A brief analysis of the known examples of supramolecular isomers contained in the same crystal is also reported.

The co-crystallisation of pyridine with benzenepolycarboxylic acids: The interplay of strong and weak hydrogen bonding motifs

Abstract: Co-crystallisation of pyridine with terephthalic, trimesic, phthalic, isophthalic and pyromellitic acids has been investigated via single crystal X-ray diffraction and thermogravimetric analysis, concentrating on the nature of the intermolecular interactions. The five new compounds are terephthalic acid bis(pyridine) solvate, trimesic acid tris(pyridine) solvate, pyridinium hydrogen phthalate, isophthalic acid pyridine solvate and pyridinium trihydrogen pyromellitate. A variety of supramolecular hydrogen bonded motifs involving interactions between pyridine molecules and carboxylic acid groups are observed rather than just the R22(7) O–H⋯N/C–H⋯O motif; while the common carboxylic acid head-to-tail ring motif is absent in all of the examples investigated. TGA analysis of pyridine loss from two of the compounds has been shown to correlate with the strength of hydrogen bonds in the crystal structures.

Synthesis, crystal structure and magnetic properties of two-dimensional malonato-bridged cobalt(II) and nickel(II) compounds

Abstract: Two isostructural malonato-bridged complexes of formula {[M(H2O)2][M(mal)2(H2O)2]}n [M = Co(II) (1), Ni(II) (2); H2mal = malonic acid] have been synthesised and characterized by X-ray diffraction. Their structure consists of corrugated layers of trans-diaquabismalonatemetalate(II) and trans-diaquametal(II) units bridged by carboxylate–malonate groups in the anti–syn conformation. Two crystallographycally independent metal atoms occur in 1 and 2. The malonate anion acts simultaneously as a bidentate and bis-monodentate ligand. Variable-temperature (1.9–295 K) magnetic susceptibility measurements indicate the occurrence of weak antiferro- (1) and ferromagnetic (2) interactions between the cobalt(II) (1) and nickel(II) ions (2) through the anti–syn caboxylate–malonate bridge. A brief discussion on the structural diversity and crystal engineering possibilities of the malonate complexes with divalent first-row transition metal ions other than copper(II) is carried out.

Heteromeric intermolecular interactions as synthetic tools for the formation of binary co-crystals

Abstract: The crystal structure of 4-nitrobenzamide pyrazinecarboxamide (1 ∶ 1) contains two homomeric amide⋯amide dimers, which is in sharp contrast with the structural motifs displayed by the vast majority of binary co-crystals (illustrated here with five new examples), where the driving force for the supramolecular assembly is one or more strong heteromeric intermolecular interactions.

The R21(6) hydrogen-bonded synthon in neutral urea and metal-bound halide systems

Abstract: The recurrence of the R21(6) motif between urea and metal bound halides is explored through studies in the CSD, including examples of the closely related thiourea and guanidine-based structures. A series of compounds containing the isomeric pyridyl–urea ligands 1 and 2 attached to trans-dihalide metal units have been prepared and their X-ray crystal structures determined. A hydrogen-bonding motif between the metal-bound halide ligands and the urea groups on the pyridyl ligands is observed in most cases which takes the form of an R21(6) ring. Three copper(II) complexes, [Cu(2)2Cl2]·2MeOH 3, [Cu(2)2Br2(MeOH)] 4 and [Cu(2)2Cl2(EtOH)] 5 all retain this supramolecular synthon despite a changing coordination environment and alteration of the halide ligands. A series of solvates of the complex [Pd(1)2Cl2] (6–8) shows that the R21(6) synthon does not occur in the presence of strongly hydrogen-bond accepting solvents such as DMF (6) and MeCN (7) but is observed in the presence of the hydrogen bond donor solvent methanol (8). The motif also occurs within an octahedral cadmium system [Cd(1)4Cl2]·2H2O·2MeCN 9. In all cases in which the R21(6) synthon is observed chain-like structures form between the metal complexes. Two contrasting structures based around tetrahedral zinc(II) centres [Zn(1)2Cl2] (10) and [Zn(1)2I2]·0.5MeOH (11) do not display the bifurcated synthon, showing instead an R22(8) motif in the case of 10 or no ring-type halide interaction in 11.

Controlling molecular and supramolecular structure of hydrogen-bonded coordination compounds

Abstract: In order to organize and assemble a variety of octahedral coordination complexes into infinite 1-D chains of desired connectivity, dibenzoylmethane was used as a chelating, “blocking” ligand, and isonicotinamide and 4-(3-carboxamidophenyl)pyridine were employed as structure directing supramolecular reagents. Five M(II) complexes were prepared using this molecular/supramolecular synthetic strategy. The crystal structure determination of these compounds shows the same principal supramolecular motif; infinite 1-D chains. In addition, the presence of the relatively bulky phenyl groups in DBM reduces packing efficiency in this system and provides better opportunities for the construction of solvated host structures.

Crystal to crystal transformation in the solid state

Abstract: Either co-milling or simple mixing of benzoquinone (BQ) and diol crystals of varied melting point temperature produces adduct crystals through very slow and gradual molecular diffusion processes in the solid state. Their formation process was compared and discussed based on the crystal structures of the starting diols and the diol–BQ adducts.

A 1H NMR study of crystal nucleation in solution

Abstract: Solution NMR data can provide information about the interactions of molecules in the first stages of crystallisation, and 1H NMR complexation-induced changes in chemical shift can be used to determine high resolution three-dimensional structures of complexes in solution. The concentration-dependent changes in 1H NMR chemical shift of two different compounds have been used to make predictions about how these compounds pack in the crystalline state. The structures of dimer motifs characterised in solution agree very well with the structures of dimers found in the corresponding X-ray crystal structures. Solution NMR experiments therefore provide an experimental tool for probing the organisation of molecules in the solid state.

Synthetic crystallography: synthon mimicry and tecton elaboration in metallate anion salts

Abstract: The use of molecular tectons (building blocks) able to form cyano-based hydrogen bonded synthons (NH⋯NC) to synthesise a diverse range of crystal structures is described. Square planar dianionic metal complexes with 4 terminal cyano groups are shown to form salts with the dications [4,4′-H2bipy]2+ and [4,4′-H2bipip]2+ in which hydrogen bond networks of varying dimensionality are formed. The structures of new salts of these cations with [M(CN)4]2−, [M(SCN)4]2−, and [M(mnt)2]2− (M = Pt, and in one case Pd) are reported and compared with those of analogous [MCl4]2− and [M(dtox)2]2− salts. The consequences of the stereochemical preference of the cyano group for linear CN⋯H hydrogen bonding and the prospects for the elaboration of cyano-functionalised tectons to afford chemical and structural diversity in the structures synthesised are discussed.

Mechanochemical and solution preparation of the coordination polymers Ag[N(CH2CH2)3N]2[CH3COO]·5H2O and Zn[N(CH2CH2)3N]Cl2

Abstract: The coordination polymer Ag[N(CH2CH2)3N]2[CH3COO]·5H2O has been obtained by co-grinding in the solid state and in the air of a stoichiometric amount of silver acetate and of [N(CH2CH2)3N]. Single crystals suitable for X-ray diffraction have been obtained from a water–methanol solution and used to compare calculated and experimental X-ray powder diffractograms. When ZnCl2 is used instead of AgCH3COO in the equimolar reaction with [N(CH2CH2)3N], the solution and solid-state treatments afford different products. Single crystals of the Zn-based coordination polymer Zn[N(CH2CH2)3N]Cl2 have been obtained by layering a solution of ZnCl2 in methanol over a solution of [N(CH2CH2)3N] in CH2Cl2. The product of the co-grinding, identified only on the basis of X-ray powder diffraction, converts, on prolonged grinding, into the crystalline material obtained from the reaction in solution, namely anhydrous Zn[N(CH2CH2)3N]Cl2.

Designing neutral coordination networks using inorganic supramolecular synthons: Combination of coordination chemistry and C–H⋯Cl hydrogen bonding

Abstract: Crystal structure determination of two compounds, [(L3)MnIICl2(EtOH)] (1) and [(L6)FeIIICl3] (2) [L3 = 2-[3-(2′-pyridyl)pyrazol-1-ylmethyl]pyridine; L6 = methyl[2-(2-pyridyl)ethyl](2-pyridylmethyl)amine], the former one reported for the first time, demonstrates that these coordination units can be used effectively as supramolecular synthons in crystal engineering to construct neutral networks. In continuation of our recent contribution on inorganic crystal engineering from the standpoint of metal–ligand coordination chemistry and C–H⋯Cl2MII hydrogen-bonding, in this work we have investigated the potential of coordination modules present in 1 and 2 in bringing about generality and diversity of C–H⋯Cl hydrogen bonding interactions. Special attention has been directed to the influence of additional (i) coordinated solvent molecule, which can act as hydrogen bond donor/acceptor and (ii) chloride ion in the assembly of supramolecular architectures via noncovalent interactions. Inorganic supramolecular synthons 1 and 2 give rise to molecular staircase and zig-zag network, respectively. Re-examination of previously reported compound [(L6)ZnCl2] with extended limit of hydrogen bonding interaction reveals additional helical network.

Engineering polymers with variable topology – bipyridine adducts of cadmium dithiophosphates

Abstract: A series of 1∶1 adducts formed between Cd(S2P(OiPr)2)2 and the bifunctional ligands 4,4′-bipyridine (1), trans-1,2-bis(4-pyridyl)ethylene (2), 1,2-bis(4-pyridyl)ethane (3), trans-1,2-bis(2-pyridyl)ethylene (4), 1,2-bis(4-pyridyl)propane (5) and 4,4′-dipyridylsulfide (6) demonstrate variable polymer topology (linear, zigzag and arched) and cadmium atom coordination geometry (cis- and trans-N2S4) depending on the nature of the bridging ligand and steric influences of the ligands. Increasing the steric bulk of the Lewis acid, to Cd(S2P(OCy)2)2, results in comparable topologies with bipyridine ligands 1, 2, and 4 but, precludes polymer formation in the adduct formed with 5, a dimer being formed instead.

Steric control over polymer formation and topology in adducts of zinc dithiophosphates formed with bridging bipyridine ligands

Abstract: A series of Zn(S2P(OR)2)2, R = iPr and Cy, adducts with bridging bipyridine ligands, i.e. 4,4′-bipyridine, trans-1,2-bis(4-pyridyl)ethylene and 1,2-bis(4-pyridyl)ethane have been investigated. The topology of the polymeric structures, i.e. zig-zag versus straight chain, can be controlled by the nature of the bridging bipyridine ligand in the case of adducts formed by Zn(S2P(OCy)2)2, an effect that can be traced to the steric bulk of the cyclohexyl groups. Polymer formation is precluded in the case of the adduct formed between Zn(S2P(OCy)2)2 and 4,4′bipyridine, again a result that is directly ascribed to the steric bulk of the thiolate residue.

Two square grid coordination polymers with manganese(II) and 1,4-bis(imidazole-1-ylmethyl)benzene

Abstract: The reactions of the highly flexible ligand 1,4-bis(imidazol-1-ylmethyl)benzene (bix) with manganese(II) azide and dicyanamide (dca), respectively, have afforded two 2-D coordination polymers, [Mn(N3)2(bix)2]n (1) {[Mn(dca)2(bix)2]·CH3OH}n (2), which have been characterized crystallographically. In both complexes, the metal ion is octahedrally coordinated by two axial azido or dca− ions, which compensate the charge, and four equatorial bix ligands in the trans conformation, and the bix ligands serve as the spacers between metal ions, resulting in 2-D (4,4) square grid layers. Based on the known examples of metal–bix complexes, a brief analysis of the flexibility of the bix ligand and some comments on the assembly are also presented.

Quantifying intermolecular interactions and their use in computational crystal structure prediction

Abstract: Intermolecular interactions control the crystal structures adopted by rigid organic molecules. Methods of quantifying the intermolecular forces from the ab initio charge density of the molecule have been extended to organic molecules, albeit more approximately than for small polyatomics. This has led to some almost non-empirical models being used to study organic packing, including crystal structure prediction studies. These studies are highlighted, with particular emphasis on what they reveal about the transferability assumptions that underpin the use of empirical atom–atom intermolecular potentials and intuitive crystal design.

Supramolecular synthon competition in organic sulfonates: A CSD survey

Abstract: The hydrogen bonding motifs seen in sulfonate salts have been examined using the CSD. In a total sample of 1069 sulfonate salts, 594 structures contain NH-donors, and this subset of structures has been investigated in detail. Several robust hydrogen-bonding motifs have been identified. A particularly robust R(2,2)8 motif, here called the bidentate motif, has been investigated in more detail. This motif occurs with a probability of 75.4% in the CSD, and 78.6% in the sulfonate salts. A set of rules for the prediction of the occurrence of the bidentate motif in sulfonate salts has been developed.

A critical look on the nature of the intra-molecular interligand π,π-stacking interaction in mixed-ligand copper(II) complexes of aromatic side-chain amino acidates and α,α′-diimines

Abstract: The mixed ligand complexes {[Cu(4Cl-Phe)(bpy)(H2O)]Cl·[Cu(4Cl-Phe)(bpy)Cl]·2H2O} (1) and [Cu(4HPG)(bpy)]·2H2O (2) were synthesized and their crystal structures determined by X-ray crystallography (4Cl-Phe = D,L-4-chlorophenylalaninato, 4HPG = D-4-hydroxyphenylglycinato, bpy = 2,2′-bipyridine). The asymmetric unit of crystals of 1 consists of two slightly different Cu(II) complexes-one contains an axial water ligand, whereas the second one has a chloride anion at that position. By contrast, 2 exhibits two close similar molecules, both having axial chloride ligands, and non coordinated water. The geometrical parameters for π,π-stacking interactions were determined by an application of PLATON program. Intermolecular π,π-interaction between bpy ligands on adjacent Cu(II) moieties results in homo pairs of complexes in the case of 1. In addition, both species of compound 1 exhibit intramolecular interligand π,π-interaction between the 4Cl-phenyl ring of 4Cl-Phe and the metalloaromatic Cu–bpy chelate ring. In crystal 2, multi-stacked homo chains are formed. Analogous calculations for previously reported, related compounds, similar to those presented here, revealed that in most cases with intra-molecular interligand π,π-interaction there is an efficient “aryl–metal chelate ring” π,π-stacking instead of an aryl–aryl interligand π,π-interaction, which indeed is not observed. These findings let us to take a critical look at the nature of the intramolecular interligand π,π-stacking interaction in the referred copper(II) mixed-ligand complexes.

Supramolecular control of fluorinated benzophenones in the crystalline state

Abstract: Crystal structures of three fluorinated benzophenones were determined via single crystal X-ray diffraction. The occurrence of the C–F⋯H, F⋯F, C–F⋯πF interactions in these crystal structures indicates that a base limit of fluorine atoms in the molecule seems to be necessary for successful competition with the hydrogen type of interactions.

Probing helix formation in chains of vertex-linked octahedra

Abstract: The rational design of crystal structures based on the chemical nature of molecular components, a longstanding and exciting research topic in organic solid state chemistry, is an emerging theme of crystal engineering in inorganic solid state chemistry. In particular, noncentrosymmetric structures, or those lacking inversion symmetry, are important for future technologies that are based on piezoelectricity, pyroelectricity, ferroelectricity and second harmonic generation (SHG). Materials that exhibit these properties provide a large and new class of solids for studies in basic science associated with the noncentrosymmetric (chiral, polar, or chiral–polar) space groups. Structures comprised of vertex-linked octahedra are common in inorganic solids. The subject of our Highlight is the rational synthesis of linear, zigzag or helical chains when two vertices of an octahedron, which are either adjacent (cis) or opposite (trans), are linked.

3D Self-penetrating coordination network constructed by dicyanamide and 1,2-bis(4-pyridyl)ethane-N,N′-dioxide (bpeado)

Abstract: The complexes of formulae M(dca)2(bpeado) (M = Mn (1), Fe (2), Co (3), Ni (4), Cu (5); dca = dicyanamide; bpeado = 1,2-bis(4-pyridyl)ethane-N,N′-dioxide) have been synthesized and characterized by X-ray single crystal diffraction. Compounds 1–5 contain 3D self-penetrating networks, in which bidentate dca ligands bridge the octahedral metal ions to form square-grid like M(dca)2 sheets and these sheets are further connected by criss-crossing bpeado to give a 3D self-penetrating network. Variable temperature magnetic susceptibility studies have shown that these compounds generally display very weak antiferromagnetic coupling because of the long bpeado and μ1,5-dca pathways. Consequently, no magnetic ordering was found.

A novel 2D mixed valence copper(I/II) rectangular grid constructed with pyrazine and croconate

Abstract: A novel 2D rectangular grid coordination polymer with a mixed valence localized copper(I/II), [Cu2ICuII(pyz)2(C5O5)2 (H2O)2]n (pyz, pyrazine; C5O52−, croconate dianion) has been hydrothermally synthesized viain situ redox reaction of Cu(II), and characterized by X-ray diffraction analysis, magnetic and EPR study. The structure extends to a 3D supramolecular network through H-bonding.