Hydrogen Bond Synthons Research Articles

Hydrogen bond patterns in aromatic and aliphatic dioximes

Despite their established hydrogen bonding capability, oxime functional groups (–C(R′)NOH) have received far less attention in supramolecular chemistry than their carboxyl and amide counterparts. Here we report a series of dioximes (R′H, CH3, NH2) for which hydrogen bonding patterns have been examined in the solid state to establish the reliability of hydrogen-bonded synthons available for use in supramolecular syntheses using oximes. In all cases, network structures were formed, most frequently propagated through oxime–oxime O–H⋯N hydrogen-bonded dimer formation [R22(6) graph set] and less often using C(3) chain or R44(12) ring arrangements. Even in the systems where R′ = NH2, robust and dominant oxime–oxime hydrogen bonding prevails, with amino groups playing a supporting role in network construction primarily via weaker N–H⋯O hydrogen bonds. The compounds studied are aromatic dioximes 1,3-C6H4(C(R′)NOH)21–3 and 1,4-C6H4(C(R′)NOH)24–6 (R′ = H, CH3, NH2), and aliphatic dioximes fumaramide dioxime 7 (R′ = NH2) and succinamide dioxime 8 (R′ = NH2).

Supramolecular synthesis of brick wall and honeycomb networks from the T-shaped molecule 5-nitrosalicylic acid

The T-geometry of O–H⋯O and C–H⋯O hydrogen bonding groups in the title molecule (5-NSA) form a brick wall network that is modularly expanded and transformed to chair cyclohexane and honeycomb architectures in molecular complexes with trans-1,4-dithiane-1,4-dioxide and dioxane. The variation in hydrogen bond synthons results in different examples of topologically related (6,3) nets.

Porphyrin architectures bearing functionalized xanthene spacers.

A modular synthetic strategy for the construction of cofacial porphyrin architectures bearing hydrogen-bond synthons on a xanthene platform is presented. The convergent approach is based on a xanthene aldehyde-ester building block that is easily obtainable on a multigram scale with minimal purification. Treatment of this xanthene derivative with a variety of aryl aldehydes and pyrrole under standard Lindsey conditions affords a family of meso-substituted porphyrins bearing a single functionalized xanthene spacer. Direct modification of the hydrogen-bond synthon after macrocyclization proceeds smoothly to furnish porphyrin systems with a variety of cofacial functionalities (e.g., carboxylic acid, ester, amide). Porphyrins bearing two trans-functionalized xanthene spacers are prepared by the MacDonald [2 + 2] condensation of the xanthene aldehyde-ester with readily available 5-aryl-substituted dipyrromethanes such as 5-mesityldipyrromethane to afford the pure alpha,alpha- and alpha,beta-porphyrin atropisomers after chromatographic separation. The versatility of this synthetic method offers intriguing opportunities for the use of these and related templates for the study of proton-coupled activation of small molecules.

Hydrogen-bonded supramolecular synthons in complexes of copper(ii) halides with polymethylene-linked bis(amidino-O-alkylurea) ligands

Elegant supramolecular architectures are formed by copper(II) halide complexes of polymethylene-linked bis(amidino-O-alkylurea) ligands (L2m: C2-linked, alkyl = methyl; L3m: C3-linked, alkyl = methyl; L2e: C2-linked, alkyl = ethyl; L3e: C3-linked, alkyl = ethyl). The tetradentate ligands co-ordinate copper(II) to give square planar [CuL]2+ complex cations, which, owing to their versatile hydrogen-bonding capacity, form diverse hydrogen-bonded supramolecular synthons with the anions. Structural analysis of a series of four chlorides, [CuL2m]Cl2·2H2O 1, [CuL2e]Cl2·MeOH·3H2O 2a, [CuL3m]Cl2·MeOH·0.5H2O 5a and [CuL2m]4[CuCl4]Cl6·5H2O 9, and a single bromide, [CuL3m]Br2·MeOH·0.3H2O 7a, has revealed two conserved supramolecular synthons, one of which is present in four structures, the other of which is present in three structures. The basic building block in 2a, 5a, 7a and 9 is a hydrogen-bonded 1-D chain of alternating [CuL]2+ cations and halide anions. A slightly modified motif, including a water molecule, occurs in 1. The chains are linked into 2-D sheets by hydrogen-bonding contacts involving the anions and solvate (water and/or methanol) molecules, either directly (1) or via formation of ribbons (2a, 5a, 7a and 9). When linked directly the cations in adjacent chains are parallel, but when linked via ribbons they are alternating. 3-D frameworks result from a combination of elongated axial Cu⋯Cl contacts and complex hydrogen-bonding contacts involving the anions and solvate molecules.

Generation and structural characterisation of a difluorodimethoxyborate-mediated hydrogen-bonded supramolecular synthon

Recrystallisation of [CuL2e][BF4]2 [L2e = 1,2-bis(amidino-O-ethylurea)ethane] from methanol affords [CuL2e][BF2(OMe)2][BF4], the basic building block of which is a 1-D linear chain of [CuL2e]2+ cations linked by difluorodimethoxyborate-mediated hydrogen-bonded supramolecular synthons. Hydrogen-bonded [BF4]− anions link the chains to form a 2-D sheet structure; weak co-ordinate interactions between Cu(II) centres and [BF4]− anions in adjacent sheets generate a 3-D network. Recrystallisation of [CuL2m][BF4]2 [L2m = 1,2-bis(amidino-O-methylurea)ethane] from methanol leaves it unaltered. The [CuL2m]2+–[BF4]− system does not give rise to the same sort of supramolecular synthon and linear 1-D chain as the [CuL2e]2+–[BF2(OMe)2]− system. Instead the basic building block is a zigzag chain of [CuL2m]2+ cations linked through a different arrangement of hydrogen-bonded [BF4]− anions. The [BF4]− anions also act as hydrogen-bonding acceptors to connect the chains, firstly into 2-D sheets and ultimately into a 3-D network.

Database research in crystal engineering

The Cambridge Structural Database is a storehouse of over 250 000 small-molecule organic and organometallic crystal structures. Statistical analysis of structural data provides a better understanding of the nature of hydrogen bonds and intermolecular interactions and facilitates in the identification of frequently occurring interaction patterns and supramolecular synthons. With an enhanced knowledge of hydrogen bond synthons in crystals, novel strategies may be designed for the self-assembly of supramolecular architectures from multi-functional molecules. The twin phenomena of polymorphism and pseudopolymorphism have been studied by extracting information on molecular conformations and solvent inclusion from the database. The approach geometry of hydrogen bond donors to various functional groups derived from small-molecule crystal structures is used as a model in structure-based drug design and pharmacophore mapping. Thus, the implications of crystal engineering today go far beyond organic and metal–organic crystal design into supramolecular materials, nanotechnology, ligand–protein binding and crystal structure prediction. This Highlight surveys the importance of database research in some of these areas.

Structurally homologous beta- and meso-amidinium porphyrins.

A synthetic strategy has been developed to afford porphyrins site-derivatized with the same hydrogen-bond synthon attached directly to the macrocyclic ring. Porphyrin homologues derivatized at the β and meso positions with an amidinium group form 1:1 supramolecular complexes with benzoate acceptors and show notable differences in their excited-state properties that are dependent on the site of the salt bridge.

Racemic 1,2-diphenylbut-3-yn-2-ol.

Molecules of the title compound, C(16)H(14)O, are chiral and crystallize in space group P-4 with Z' = 2, and with one R and one S molecule in the asymmetric unit. The conformations of the phenyl rings in the two independent molecules differ slightly. Supramolecular organization in the crystal is via tetrameric O-H. H(O) hydrogen-bonded synthons formed separately by each conformer. These tetrameric synthons stack along the c axis via C[triple-bond]C-H.O(H) hydrogen bonds. The only link between the conformer stacks is provided by weaker C(methylene)-H and C(phenyl)-H interactions with pi(arene) density.

Organic–inorganic hybrid solids: control of perhalometallate solid state structures †

MX⋯HN+ hydrogen bond synthons have been exploited in preparation of crystalline salts [4,4′-H2bipy][MX4] [X = Cl, M = Pd, Pt, Co, Zn, Hg, Mn, Cd and Pb; X = Br, M = Pd, Co, Zn and Mn]. In these salts three structural forms for the halometallate species are observed: mononuclear square planar (M = Pd, Pt) or tetrahedral (M = Co, Zn, Hg) and polymeric cis edge-sharing octahedral (M = Mn, Cd, Pb). These correspond to three structural motifs which form the basis of the crystal structures formed in their [4,4′-H2bipy]2+ salts: ribbon polymer (M = Pt, Pd); herring-bone packing of cyclic dimers (M = Co, Zn, Hg); layer cross-linked polymers [{MX4}n]2n- (M = Mn, Cd, Pb). The factors controlling the structures adopted, the hierarchy of intermolecular interactions present in these crystals and the principles that may be inferred and exploited further are considered.

Cation-controlled formation of [{MCl4}n]2n− chains in [4,4′-H2bipy][MCl4] (M = Mn, Cd): an alternative to the A2MCl4 <100> layer perovskite structure†

The cis-MCl2‥HN+ chelated hydrogen bond synthon has been exploited in preparation of crystalline [4,4′- H2bipy][MCl4] (M = Mn 2 and Cd 3), which shows a one-dimensional substructure of the form [{MCl4}n]2n– consisting of a kinked chain of doubly edge sharing MCl6 octahedra. These chains are cross-linked by hydrogen bonding to the [4,4′-H2bipy]2+ ions.

Building organic assemblies with 2-pyridone and dicarboxylic acids: relating molecular conformation and synthon stability to crystal structure

The syntheses and crystal structures of five cocrystals; 2-pyridone oxalic acid (2/1), 2-pyridone succinic acid (2/1), 2-pyridone adipic acid (2/1) dihydrate, 2-pyridone suberic acid (2/1), and 2-pyridone sebacic acid (2/1), are reported. The competition between two similar self-complementary hydrogen-bonded synthons (carboxylic acid and 2-pyridone) are examined systematically in this series of cocrystals. In each case, the crystal structure contains planar dimers of 2-pyridone which are bridged by a dicarboxylic acid via a combination of C–H ⋯ O and O–H ⋯ O hydrogen bonds to generate infinite 1-D ribbons. The orientation of these ribbons is determined by changes in molecular shape and conformational flexibility of the dicarboxylic acid.