Supramolecular interactions in the solid state

Conformation-aggregation interplay in the simplest aliphatic ethers probed under high pressure

The structures of the simplest symmetric primary ethers [(CnH2n+1)2O, n = 1-3] determined under high pressure revealed their conformational preferences and intermolecular interactions. In three new polymorphs of diethyl ether (C2H5)2O, high pressure promotes intermolecular CH...O contacts and enforces a conversion from the trans-trans conformer present in the α, β and γ phases to the trans-gauche conformer, which is higher in energy by 6.4 kJ mol-1, in the δ phase. Two new polymorphs of dimethyl ether (CH3)2O display analogous transformations of the CH...O bonds. The crystal structure of di-n-propyl ether (C3H7)2O, determined for the first time, is remarkably stable over the whole pressure range investigated from 1.70 up to 5.30 GPa.

Controlling the Formation of Two Concomitant Polymorphs in Hg(II) Coordination Polymers

Controlling the formation of the desired product in the appropriate crystalline form is the fundamental breakthrough of crystal engineering. On that basis, the preferential formation between polymorphic forms, which are referred to as different assemblies achieved by changing the disposition or arrangement of the forming units within the crystalline structure, is one of the most challenging topics still to be understood. Herein, we have observed the formation of two concomitant polymorphs with general formula {[Hg(Pip)₂(4,4′-bipy)]·DMF}_n (P1A, P1B; Pip = piperonylic acid; 4,4′-bipy = 4,4′-bipyridine). Besides, [Hg(Pip)₂(4,4′-bipy)]_n (2) has been achieved during the attempts to isolate these polymorphs. The selective synthesis of P1A and P1B has been successfully achieved by changing the synthetic conditions. The formation of each polymorphic form has been ensured by unit cell measurements and decomposition temperature. The elucidation of their crystal structure revealed P1A and P1B as polymorphs, which originates from the Hg(II) cores and intermolecular associations, especially pinpointed by Hg···π and π···π interactions. Density functional theory (DFT) calculations suggest that P1B, which shows Hg(II) geometries that are further from ideality, is more stable than P1A by 13 kJ·mol^–1 per [Hg(Pip)₂(4,4′-bipy)]·DMF formula unit, and this larger stability of P1B arises mainly from metal···π and π···π interactions between chains. As a result, these structural modifications lead to significant variations of their solid-state photoluminescence.

We have successfully isolated two concomitant polymorphs with formula {[Hg(Pip)₂(4,4′-bipy)]·DMF}_n (P1A and P1B), as well as their desolvated form 2. Then, both polymorphs were selectively synthesized by temperature or anion-template formation. Their crystal structures revealed distorted pentagonal pyramidal geometries and show that differences arise from geometry and packing that led to different solid-state photoluminescence emissions. According to periodic-DFT calculations, distortions in P1B are counterbalanced leading to a more stable form by Hg(II)···π and π···π interactions.

Stochastic hydration of a high-nitro-gen-content molecular compound recrystallized under pressure

Partial hydration of organic compounds can be achieved by high-pressure crystallization. This has been demonstrated for the high-nitro-gen-content compound 6-chloro-1,2,3,4-tetrazolo[1,5-b]pyridazine (C4H2N5Cl), which becomes partly hydrated by isochoric crystallizations below 0.15 GPa. This hydrate, C4H2N5Cl·xH2O, is isostructural with the ambient-pressure phase α of C4H2N5Cl, but the crystal volume is somewhat larger than that of the anhydrate. At 0.20 GPa, the α-C4H2N5Cl anhydrate phase transforms abruptly into a new higher-symmetry phase, α'; the transformation is clearly visible due to a strong contraction of the crystals. The hydrate α-C4H2N5Cl·xH2O can also be isothermally compressed up to 0.30 GPa before transforming to the α'-C4H2N5Cl·xH2O phase. The isochoric recrystallization of C4H2N5Cl above 0.18 GPa yields a new anhydrous phase β, which, on releasing pressure, transforms back to the α phase below 0.15 GPa. The structural transition from the α to the β phase is destructive for the single crystal and involves a large volume drop and significant elongation of all the shortest intermolecular distances which are the CH⋯N and CH⋯Cl hydrogen bonds, as well as the N⋯N contacts. The α-to-α' phase transition increases the crystal symmetry in the subgroup relation; however, there are no structural nor symmetry relations between phases α and β.

Hydrogen Bonding Directed Self-Assembly of a Binuclear Ag(I) Metallacycle into a 1D Supramolecular Polymer

An Ag(I) metallacycle obtained unexpectedly during the preparation of Pd(II) complexes of the bifunctional ligand 5-([2,2′-bipyridin]-5-yl)pyrimidine-2-amine (L) has been characterized using X-ray structure determination as a binuclear, metallacyclic species [Ag₂L₂](SbF₆)₂, where both the bipyridine and pyrimidine-N donors of L are involved in coordination to the metal. The full coordination environment of the Ag(I) defines a case of highly irregular 4-coordination. In the crystal, the Ag-metallacycles assemble into one-dimensional supramolecular metalladynamers linked together by hydrogen-bonding interactions.

Structure-property relationships of molecular shape and orientation with compression and expansion of xylitol

Easy crystallization distinguishes xylitol from other sugars, which usually condense into a syrup from aqueous solution. Although two polymorphs, i.e. metastable monoclinic and high-density orthorhombic, have been reported for xylitol, only the latter is in practical use. Under high pressure, the same orthorhombic phase has been obtained by both isothermal and isochoric recrystallization. The stability of the orthorhombic xylitol phase to 5.0 GPa has been correlated with a uniform compression of all hydrogen bonds and some flexibility of the molecular conformation, which cushion the pressure-induced local strains. The anisotropic compressibility of xylitol and its thermal expansion are consistent with the rule of inverse effects of pressure and temperature. This inverse strain relationship has been correlated with the dimensions and orientation of xylitol molecules in the crystal structure.

Effect of pyridyl donors from organic ligands versus metalloligands on material design

This review illustrates designs and structures of various coordination frameworks constructed using assorted organic ligands and metalloligands offering pyridyl donors to evaluate the impact of flexibility versus rigidity on material design.

Post-synthetic modification of supramolecular assemblies of β-diketonato Cu(ii) complexes: comparing and contrasting the molecular topology by crystal structure and quantum computational studies

Solvent-induced structural transformations on the metal coordination sphere in homoleptic (1 and 2) and heteroleptic (3 and 4) Cu(ii) complexes were analyzed and investigated by crystallographic and quantum computational studies.

Crystal design by CH...N and N...N interactions: high-pressure structures of high-nitrogen-content azido-triazolopyridazines compounds

High-nitrogen-content compounds 6-azido-1,2,4-triazolo[4,3-b]pyridazine (C₅H₃N₇) and its 3-methyl derivative (C₆H₅N₇) have been in situ crystallized in a diamond-anvil cell and their structures determined by single-crystal X-ray diffraction. Under ambient and high-pressure conditions the crystallizations yield the same phases: the C₅H₃N₇ anhydrate and C₆H₅N₇ hydrated clathrate. In both the structures there are clearly distinguished regions of short CH...N and N...N intermolecular contacts, the latter involving exclusively the azide groups. High pressure initially increases the contents of water in the channel pores of the clathrate.

A Series of Manganese(III) Salen Complexes as a Result of Team-Based Inquiry in a Transnational Education Programme

The development of a team-based approach to research-led transnational practical chemistry teaching is described in which a team of five Chinese students on an articulated transnational degree programme, supported by a team of academic and technical staff, carried out a study examining the structural chemistry of a series of manganese(III) salen complexes. A series of four crystallographically characterized manganese(III) salen complexes with ancillary carboxylate ligands are reported here. The carboxylate coordination modes range from the bridging syn-anti μ² -κO : κO' mode observed in the predominant cyclohexanoate and isobutyrate species, to a capping terminal monodentate mode for the adamantanoate species, and an unusual mixture of bridging and terminal coordination modes observed in a second minor phase of the cyclohexanoate species. The variation on extended structures based on the weakly interacting aliphatic backbones may provide a useful basis for further structural studies.

Quasi-Isostructural Co(II) and Ni(II) Complexes with Mefenamato Ligand: Synthesis, Characterization, and Biological Activity

Three metal complexes of mefenamato ligand 1 were synthesized: [Co2(mef)4(EtOH)2(H2O)4]: 2; [Co(mef)2(MeOH)4]∙2MeOH: 3; and [Ni(mef)2(MeOH)4]∙2MeOH: 4. Their compositions and properties were investigated by elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). Crystal structures were determined by the single crystal X-ray diffraction technique. Additionally, their antioxidant and antimicrobial activity were established, thus proving good/moderate bioactivity against Gram-positive bacteria and yeasts. In the crystal structure of 2, an apical water molecule is shared between two adjacent cobalt(II) ions, resulting in the formation of a polymeric chain extending along the [100] direction. Meanwhile, structures 3 and 4 have strong intermolecular hydrogen bonds with diverse topologies that yield unique quasi-isostructural arrangements. The packing topology is reflected by the Hirshfeld surface analysis of intermolecular contacts.

The Volumetric Source Function: Looking Inside van der Waals Interactions

The study of van der Waals interactions plays a central role in the understanding of bonding across a range of biological, chemical and physical phenomena. The presence of van der Waals interactions can be identified through analysis of the reduced density gradient, a fundamental parameter at the core of Density Functional Theory. An extension of Bader’s Quantum Theory of Atoms in Molecules is developed here through combination with the analysis of the reduced density gradient. Through this development, a new quantum chemical topological tool is presented: the volumetric source function. This technique allows insight into the atomic composition of van der Waals interactions, offering the first route towards applying the highly successful source function to these disperse interactions. A new algorithm has been implemented in the open-source code, CRITIC2, and tested on acetone, adipic and maleic acids molecular crystals, each stabilized by van der Waals interactions. This novel technique for studying van der Waals interactions at an atomic level offers unprecedented opportunities in the fundamental study of intermolecular interactions and molecular design for crystal engineering, drug design and bio-macromolecular processes.

Xenon in oxide frameworks: at the crossroads between inorganic chemistry and planetary science

The chemistry of noble gases was for a long time dominated by fluoride-bearing compounds of xenon. However, the last two decades have brought new insights into the chemistry of xenon oxides and oxysalts, including insights involving a novel type of non-covalent interaction (aerogen bonding), discoveries of new xenon oxides, oxide perovskite frameworks and evidence for an abrupt increase of xenon reactivity under extreme pressure-temperature conditions. The complex implementation of these findings could facilitate the development of explanations for long-standing interdisciplinary problems, such as the depletion of heavy noble gases in contemporary planetary atmospheres - the cosmochemical enigma known as the "missing xenon" paradox.

Preorganization: A Powerful Tool in Intermolecular Halogen Bonding in Solution

Preorganization is a powerful tool in supramolecular chemistry which has been utilized successfully in intra- and intermolecular halogen bonding. In previous work, we had developed a bidentate bis(iodobenzimidazolium)-based halogen bond donor which featured a central trifluoromethyl substituent. This compound showed a markedly increased catalytic activity compared to unsubstituted bis(iodoimidazolium)-based Lewis acids, which could be explained either by electronic effects (the electron withdrawal by the fluorinated substituent) or by preorganization (the hindered rotation of the halogen bonding moieties). Herein, we systematically investigate the origin of this increased Lewis acidity via a comparison of the two types of compounds and their respective derivatives with or without the central trifluoromethyl group. Calorimetric measurements of halide complexations indicated that preorganization is the main reason for the higher halogen bonding strength. The performance of the catalysts in a series of benchmark reactions corroborates this finding.

Methylene spacer regulated variation in supramolecular assembly of zinc(ii) dicyanamide complexes with reduced Schiff base ligands: synthesis, structure and DFT study

Three tetranuclear zinc dicyanamide complexes with three potential hexadentate reduced Schiff base ligands have been synthesized and characterized. The DFT study is devoted to the analysis of the competition between C–H⋯π and π⋯π interactions.

Methods for easy recognition of isostructurality – lab jack-like crystal structures of halogenated 2-phenylbenzimidazoles

Easy recognition and numerical description of isostructurality; how different the similar structures can be; supramolecular aspects of isostructurality.

Binding motif of ebselen in solution: chalcogen and hydrogen bonds team up

Ebselen, a compound active against SARS-CoV-2, forms a bifurcated supramolecular synthon thanks to chalcogen bond and hydrogen bond cooperation.

Exploring and predicting intermolecular binding preferences in crystalline Cu(ii) coordination complexes

A simple model focusing on electrostatic contributions to interaction energies was found to be very effective for rationalizing the appearance of specific supramolecular interactions in a series of Cu(ii) coordination compounds. The experimental space was provided by a combination of Cu(ii) cations with acac-based anions (hexafluoracetylacetonato and trifluoracetylacetonato) and a series of pyridine-oxime ligands (3-pyridinealdoxime, methyl 3-pyridyl ketoxime, 4-pyridinealdoxime, methyl 4-pyridyl ketoxime, phenyl 4-pyridyl ketoxime). The calculated molecular electrostatic potential (MEP) values at competing hydrogen-bond acceptor sites, for ten structurally characterized complexes, provided guidelines for predicting supramolecular connectivity in cases when the MEP difference exceeded certain cut-off values, while two different and well-defined outcomes are possible within the so called 'grey zone', delineated by a range of MEP differences. It was also shown that the structural outcome within this region is determined by the influence of relatively weak, but distinct, auxillary interactions.

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

ortho-Fluoroazobenzenes are a remarkable example of bistable photoswitches, addressable by visible light. Symmetrical, highly fluorinated azobenzenes bearing an iodine substituent in para-position were shown to be suitable supramolecular building blocks both in solution and in the solid state in combination with neutral halogen bonding acceptors, such as lutidines. Therefore, we investigate the photochemistry of a series of azobenzene photoswitches. Upon introduction of iodoethynyl groups, the halogen bonding donor properties are significantly strengthened in solution. However, the bathochromic shift of the π→π* band leads to a partial overlap with the n→π* band, making it slightly more difficult to address. The introduction of iodine substituents is furthermore accompanied with a diminishing thermal half-life. A series of three azobenzenes with different halogen bonding donor properties are discussed in relation to their changing photophysical properties, rationalized by DFT calculations.

Exploiting Unsaturated Carbon-Iodine Compounds for the Preparation of Carbon-Rich Materials

Conjugated carbon-rich materials have drawn much academic and industrial attention in recent years, due to their intriguing electronic and optical properties and potential applications including organic photovoltaics, flexible and wearable electronics, and chemical and biological sensors. Unsaturated carbon-iodine compounds, mainly the derivatives of iodoalkenes and iodoalkynes, are a class of molecules in which iodine atoms are directly connected to unsaturated carbons. These compounds provide unique advantages in the pursuit of carbon-rich materials, largely due to the Lewis acidity of iodine atoms and the lability of the carbon-iodine bonds. The Lewis acidity and electrophilicity of iodine in unsaturated carbon-iodine compounds make them excellent donors of halogen bonding, which is an attractive interaction between the electrophilic halogen atoms and Lewis basic species. Halogen bonding has emerged as a reliable building block in crystal engineering and supramolecular architectures. In this Account, we illustrate examples of the controlled assembly of diiodopolyynes within host-guest cocrystals that contain oxalamide or urea hosts with appropriate Lewis basic end groups and diiodobutadiyne or diiodohexatriyne guests. Halogen bonding interactions between the host and guest result in an ordered alignment of the diiodopolyynes that allows for a solid-state topochemical polymerization. We have used this approach to prepare poly(diiododiacetylene), PIDA, and poly(iodoethynyliododiacetylene), PIEDA, two conjugated polymers composed only of carbon and iodine. In addition, the polarity of the carbon-iodine bond gives unsaturated carbon-iodine compounds an electron-rich π-system, permitting electrophilic addition reactions with molecular halogens. The halogenated products of these additions can then serve as precursors to other conjugated carbon-rich systems. The lability of the carbon-iodine bond, together with the polarizability of iodine and the higher electronegativity of sp- and sp²-hybridized carbons, open up further possibilities in pursuing novel carbon nanomaterials from unsaturated carbon-iodine compounds. For example, we have developed an iterative method for the synthesis of longer symmetric polyynes from shorter diiodopolyynes, using Stille coupling to the iodine-capped polyynes. The iodination/coupling cycle symmetrically lengthens the polyyne chain by two carbon-carbon triple bonds. This method is particularly helpful for preparing polyynes with an odd number of carbon-carbon triple bonds. In addition, the lability of the carbon-iodine bonds of PIDA leads to facile carbonization by pyrolysis or laser irradiation. More strikingly, diiodoalkenes undergo quantitative elimination of iodine in the presence of Lewis bases. This reaction can be used to eliminate iodine at room temperature from PIDA, in which the carbon-iodine bonds are much more easily broken than in the diiodopolyynes, resulting in graphitic carbon materials.

Origin of the isotropic motion in crystalline molecular rotors with carbazole stators

Herein we report two crystalline molecular rotors 1 and 4 that show extremely narrow signals in deuterium solid-state NMR spectroscopy. Although this line shape is typically associated with fast-moving molecular components, our VT 2H NMR experiments, along with X-ray diffraction analyses and periodic DFT computations show that this spectroscopic feature can also be originated from low-frequency intramolecular rotations of the central phenylene with a cone angle of 54.7° that is attained by the cooperative motion of the entire structure that distorts the molecular axis to rotation. In contrast, two isomeric structures (2 and 3) do not show a noticeable intramolecular rotation, because their crystallographic arrays showed very restricting close contacts. Our findings clearly indicate that the multiple components and phase transitions in crystalline molecular machines can work in concert to achieve the desired motion.

Effect of pressure on slit channels in guanine sodium salt hydrate: a link to nucleobase intermolecular interactions

The crystal structure of a hydrate of the sodium salt of guanine (2Na⁺·C₅H₃N₅O²⁻·7H₂O) was studied at high pressure by single-crystal X-ray diffraction and Raman spectroscopy.

High pressure: a complementary tool for probing solid-state processes

High pressure offers insight into the mechanisms of a wide range of solid-state phenomena occurring under atmospheric pressure conditions.

[2+2] Halogen-bonded boxes employing azobenzenes

Herein, we report the synthesis and crystal structures of three [2+2] supramolecular boxes assembled by halogen bonding.

Structural flexibility of halogen bonds showed in a single-crystal-to-single-crystal [2+2] photodimerization

Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N⋯I halogen bonding - a 'workhorse' interaction for the crystal engineer - to support a single-crystal-to-single-crystal [2+2] photodimerization. A comparison is provided of the geometric changes experienced by the halogen-bonded components in the single-crystal reaction to the current crystal landscape of N⋯I halogen bonds, as derived from the Cambridge Structural Database. Specifically, a linear-to-bent type of deformation of the halogen-bonded components was observed, which is expected to support the development of functional halogen-bonded materials containing molecules that can undergo movements in close-packed crystal environments.

Studying weak inter-actions in crystals at high pressures: when hardware matters

The quality of structural models for 1,2,4,5-tetra-bromo-benzene (TBB), C6H2Br4, based on data collected from a single crystal in a diamond anvil cell at 0.4 GPa in situ using two different diffractometers belonging to different generations have been compared, together with the effects of applying different data-processing strategies.

Halogen Bonding in Solution: Anion Recognition, Templated Self-Assembly, and Organocatalysis

The halogen bond is a supramolecular interaction between a Lewis-acidic region of a covalently bound halogen and a Lewis base. It has been studied widely in silico and experimentally in the solid state; however, solution-phase applications have attracted enormous interest in the last few years. This Minireview highlights selected recent developments in halogen bond interactions in solution, with a focus on the use of receptors based on halogen bonds in anion recognition and sensing, anion-templated self-assembly, as well as in organocatalysis.

Behavior of intermolecular interactions in α-glycine under high pressure

Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.

Halogen bonding two-point recognition with terphenyl derivatives

Neutral terphenyl-based halogen bond donors form two-point halogen bonding motifs with oxadiazoles in the solid state.

A new water stable zinc metal organic framework as an electrode material for hydrazine sensing

Metal–organic frameworks (MOFs) as direct electrode materials for electrochemical sensing can offer inherent advantages such as containing sensing element and redox mediator in a single molecule.

Polymorphism of a porous hydrogen bond-assisted ionic organic framework

The polymorphs of a cationic iHOF constructed by anion⋯pi interactions and the role of molecular inflexibility in framework construction are presented.