Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D-D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D-D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

Anion-assisted supramolecular assemblies of zinc(II) complexes with isonicotinamide

Five zinc(II) coordination compounds, [ZnCl₂(isn)₂] (1), [ZnBr₂(isn)₂] (2), [Zn(NO₃)₂(H₂O)(isn)₂] (3), [Zn(CH₃COO)₂(isn)]₂ (4) and [Zn(isn)₄(H₂O)₂](ClO₄)₂ (5) (isn = isonicotinamide), were prepared by the reactions of the isonicotinamide (pyridine-4-carboxamide, isn) and corresponding zinc(II) salts. Their crystal structures were determined by the single-crystal X-ray diffraction method. The coordination environment of zinc(II) is tetrahedral in the compounds containing small halide anions (chloride, bromide), 1 and 2. An expansion of the zinc(II) coordination environment to the octahedral is observed in the presence of the monodentate and bridging nitrate ions in 3. The coordination environments of both zinc(II) ions in dimeric acetate complex 4 is also enlarged in the comparison with 1 and 2, one zinc(II) ion being octahedrally coordinated and the other being pentacoordinated. The zinc(II) ion in 5 also reaches higher coordination environment (octahedral), which is enabled by binding of additional water molecules, since the perchlorate ion is uncoordinated. The supramolecular amide-amide homosynthon R 2 2 ( 8 ) is preserved in the presence of halide, nitrate and acetate ions (1-4), but it is completely disrupted in the crystal packing of 5 due to the presence of the bulky perchlorate anion. Spectroscopic analysis of compounds 1-5 was performed by IR spectroscopy in the solid state and by ¹³C NMR spectroscopy in the DMSO solutions. The NMR data support a complete decomposition of 3 in the DMSO solution, but 1, 2, 4 and 5 remain unchanged in the solution. Thermal properties of the coordination compounds were also investigated by TGA and DSC methods.

Ternary and quaternary cocrystals of 2,7-dihydroxynaphthalene: systematic design with a large synthon module

Ternary and quaternary cocrystals of 2,7-dihydroxynaphthalene are synthesized with N-bases and polyaromatic hydrocarbons.

Externally Regulated Specific Molecular Recognition Driven Pathway Selectivity in Supramolecular Polymerization

This article reveals 4-dimethylaminopyridine (DMAP) regulated pathway selectivity in the supramolecular polymerization of a naphthalene-diimide derivative (NDI-1), appended with a carboxylic acid group. In decane, NDI-1 produces ill-defined aggregate (Agg-1) due to different H-bonding motifs of the -COOH group. With one mole equivalent DMAP, the NDI-1/DMAP complex introduces new nucleation condition and exhibits a cooperative supramolecular polymerization producing J-aggregated fibrillar nanostructure (Agg-2). With 10 % DMAP and fast cooling (10 K/min), similar nucleation and open chain H-bonding with the free monomer in an anti-parallel arrangement produces identical J-aggregate (Agg-2a). With 2.5 % DMAP and slow cooling (1 K/min), a distinct nucleation and supramolecular polymerization pathway emerge leading to the thermodynamically controlled Agg-3 with face-to-face stacking and 2D-morphology. Slow cooling with 5-10 % DMAP produces a mixture of Agg-2a and Agg-3. Computational modelling studies provide valuable insights into the internal order and the pathway complexity.

Validation of the supramolecular synthon preference through DFT and physicochemical property investigations of pyridyl salts of organo-sulfonates

Understanding of the supramolecular synthon competition is sparse and the synthon hierarchy studies are limited. Herein, we validate the synthon preferences in multi-functional organic precursor through DFT and crystallographic studies.

Recurrent motifs in pharmaceutical cocrystals involving glycolic acid: X-ray characterization, Hirshfeld surface analysis and DFT calculations

Crystallization studies on some pyridinecarboxamides and methylated xanthines with glycolic acid as coformer, were carried out on formation of synthons and their influence on stability and solubility, the energy landscape and stabilization energies.

Isonicotinamide-Based Compounds: From Cocrystal to Polymer

The reaction between [Cu(μ-OAc)(μ-Pip)(MeOH)]₂ (1) (OAc = acetate; Pip = 1,3-benzodioxole-5-carboxylate) and isonicotinamide (Isn) in MeOH as solvent yielded two mixture pairs of three compounds: {(HPip)₂(Isn) (2), [Cu(Pip)₂(Isn)₂] (3)} and {(3), {[Cu₃(Pip)₂(OAc)₂(μ-Isn)₂(Isn)₂(μ-OCH₃)₂(MeOH)₂]·2MeOH}_n (4)}. Modifying the reaction conditions (t, T, molar ratio), 2 and 3 have been successfully isolated, whereas 3 and 4 had to be mechanically separated. The recrystallization of 3 in pentanol yielded single crystals of compound [Cu(Pip)₂(Isn)₂]·C₅H₁₁OH (3a). The X-ray crystal structure of 2, 3a, and 4 has been elucidated showing a cocrystal, a monomer, and an unusual coordination polymer, respectively. The Pip ligand exhibited a chelate (3a) or a monodentate (4) coordination mode, but the Isonicotinamide (Isn) ligand is the one that promoted the arrangement of different structures and also mainly directs the formation of the 2D and 3D supramolecular assemblies. All the structures have been analyzed by Hirshfeld surface. In addition, the energy frameworks and lattice energy values of 2 and 3a have been calculated.

Exploring short strong hydrogen bonds engineered in organic acid molecular crystals for temperature dependent proton migration behaviour using single crystal synchrotron X-ray diffraction (SCSXRD)

Short strong hydrogen bonds in multi-component organic acid molecular crystals exhibit temperature dependent proton migration for certain HB donor–acceptor distances.

Does stoichiometry matter? Cocrystals of aliphatic dicarboxylic acids with isonicotinamide: odd–even alternation in melting points

This study outlines the synthesis of four cocrystals of aliphatic dicarboxylic acids {pimelic acid to sebacic acid (HOOC–(CH₂)_n–COOH, n = 5, 6, 7 and 8)} and isonicotinamide in a ratio of 1 : 2.

Temperature-induced phase transition of isonicotinamide-malonic acid (2/1) and supramolecular construct analysis of isonicotinamide structures

The isonicotinamide-malonic acid (2/1) co-crystal salt (2IN·C3) exhibits a first-order displacive structural phase transition from low-temperature triclinic P1̅ crystal structure to high-temperature monoclinic C2/c crystal structure and vice versa at the transition temperatures of 298 (1) and 295 (1) K, respectively, as determined by variable-temperature SCXRD analysis and DSC measurements. The asymmetric unit of 2IN·C3 comprises three malonic acid molecules and six isonicotinamide molecules at the low-temperature phase, and this is reduced to a half-molecule of malonic acid and an isonicotinamide molecule in the high-temperature phase. The carboxyl and pyridinium H atoms are disordered at both phases. The observed phase transition near room temperature is triggered by the molecular displacement of the isonicotinamide molecule and the syn-anti conformational transformation of the malonic acid molecule with deviation angles of 10.4 and 11.7°, respectively, which induced an energy change of 19.1 kJ mol−1 in the molecular cluster comprising a central isonicotinamide molecule and eight neighboring molecules. However, the total interaction energy of the molecular cluster of a central malonic acid molecule and eight neighboring molecules does not change significantly upon the phase transition. The molecules of isonicotinamide structures except IN·IN+·triazole ‒ form zero-dimensional finite arrays or one-dimensional chains as the primary supramolecular construct by carboxyl···pyridyl (−35.9 to −56.7 kJ mol−1) and carboxamide···carboxamide (−53.6 to −68.7 kJ mol−1) or carboxyl···carboxamide (−52.6 to −67.1 kJ mol−1) synthons.

Probing the Crystal Structure Landscape by Doping: 4-Bromo, 4-Chloro, and 4-Methylcinnamic Acids

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of π⋅⋅⋅π interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen.

Exploring the structural landscape with ‘partial’ fluoro-substitution as a probe

The landscape of β-cinnamic acid is explored by an extension of the previously reported fluorosubstitution protocol.

Temperature-induced first-order displacive phase transition of isonicotinamide-4-methoxybenzoic acid co-crystal

Isonicotinamide–4-methoxybenzoic acid co-crystal (1), C6H6N2O·C8H8O3, is formed through slow evaporation from methanol solution and it undergoes a first-order isosymmetry (monoclinicI2/a↔ monoclinicI2/a) structural phase transition atTc= 142.5 (5) K, which has been confirmed by an abrupt jump of crystallographic interaxial angle β from variable-temperature single-crystal XRD and small heat hysteresis (6.25 K) in differential scanning calorimetry measurement. The three-dimensional X-ray crystal structures of (1) at the low-temperature phase (LTP) (100, 140 and 142 K) and the high-temperature phase (HTP) (143, 150, 200, 250 and 300 K) were solved and refined as a simple non-disordered model with finalR[F2> 2σ(F2)] ≃ 0.05. The asymmetric unit of (1) consists of crystallographically independent 4-methoxybenzoic acid (A) and isonicotinamide (B) molecules in both enantiotropic phases. MoleculeAadopts a `near-hydroxyl' conformation in which the hydroxyl and methoxy groups are positioned on the same side. Both `near-hydroxyl' and `near-carbonyl' molecular conformations possess minimum conformational energies with an energy difference of < 0.15 kJ mol−1from a potential energy surface scan. In the crystal, molecules are joined into linearABBAarrays by intermolecular N—H...O and O—H...N hydrogen bonds which were preserved in both phases. However, theseABBAarrays are displaced from planarity upon LTP-to-HTP transition and the changes in inter-array interactions are observed in two-dimensional fingerprint plots of their Hirshfeld surfaces. ThePIXELenergies of each molecular pair in both phases were calculated to investigate the difference in intermolecular interaction energies before and after the displacement ofABBAarrays from planarity, which directly leads to the single-crystal-to-single-crystal phase transition of (1).

Crystal structure of 4-carbamoylpyridinium chloride

The hydro-chloride salt of isonicotinamide, C6H7N2O(+)·Cl(-), has been synthesized from a dilute solution of hydro-chloric acid in aceto-nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro-chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol-ecule and a chloride anion. An array of hydrogen-bonding inter-actions, including a peculiar bifurcated pyridinium-chloride inter-action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented.

The hierarchies of hydrogen bonds in salts/cocrystals of isoniazid and its Schiff base – a case study

A series of two salts of isoniazid and two cocrystals of its Schiff base have been synthesized and well characterized. Further, the hydrogen bonding patterns have been studied and the correlation between the bond distances and corresponding pK_a's have been deduced.

A gallic acid–succinimide co-crystal landscape: polymorphism, pseudopolymorphism, variable stoichiometry co-crystals and concomitant growth of non-solvated and solvated co-crystals

A design aspect for selective formation of diverse solid forms such as solvates, hydrates and anhydrous forms has been successfully investigated in a gallic acid–succinimide co-crystal landscape.

Combinatorial crystal synthesis of ternary solids based on 2-methylresorcinol

Cocrystallization experiments of 2-methylresorcinol with several N-bases were performed to identify selective and preferred crystallization routes in relevant structural landscapes.

Crystal structure and prediction

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

Combinatorial crystal synthesis: structural landscape of phloroglucinol:1,2-bis(4-pyridyl)ethylene and phloroglucinol:phenazine

A large number of crystal forms, polymorphs and pseudopolymorphs, have been isolated in the phloroglucinol-dipyridylethylene (PGL:DPE) and phloroglucinol-phenazine (PGL:PHE) systems. An understanding of the intermolecular interactions and synthon preferences in these binary systems enables one to design a ternary molecular solid that consists of PGL, PHE, and DPE, and also others where DPE is replaced by other heterocycles. Clean isolation of these ternary cocrystals demonstrates synthon amplification during crystallization. These results point to the lesser likelihood of polymorphism in multicomponent crystals compared to single-component crystals. The appearance of several crystal forms during crystallization of a multicomponent system can be viewed as combinatorial crystal synthesis with synthon selection from a solution library. The resulting polymorphs and pseudopolymorphs that are obtained constitute a crystal structure landscape.

Proton location in acid⋯pyridine hydrogen bonds of multi-component crystals

Role of local crystal environment on proton location was modelled using DFT calculations. Alteration in the strength of the hydrogen bonding can convert a system from a salt to a co-crystal.

Why don't we find more polymorphs?

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Crystal engineering: from molecule to crystal

How do molecules aggregate in solution, and how do these aggregates consolidate themselves in crystals? What is the relationship between the structure of a molecule and the structure of the crystal it forms? Why do some molecules adopt more than one crystal structure? Why do some crystal structures contain solvent? How does one design a crystal structure with a specified topology of molecules, or a specified coordination of molecules and/or ions, or with a specified property? What are the relationships between crystal structures and properties for molecular crystals? These are some of the questions that are being addressed today by the crystal engineering community, a group that draws from the larger communities of organic, inorganic, and physical chemists, crystallographers, and solid state scientists. This Perspective provides a brief historical introduction to crystal engineering itself and an assessment of the importance and utility of the supramolecular synthon, which is one of the most important concepts in the practical use and implementation of crystal design. It also provides a look to the future from the viewpoint of the author, and indicates some directions in which this field might be moving.

Beyond crystals: the dialectic of materials and information

We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The complex structures now being studied in biology and produced in nanotechnology have outstripped the framework of classical crystallography, and a variety of organizing concepts are now taking shape into a more modern and dynamic science of structure, form and function. Absolute stability and equilibrium are replaced by metastable structures existing in a flux of energy-carrying information and moving within an energy landscape of complex topology. Structures give place to processes and processes to systems. The fundamental level is that of atoms. As smaller and smaller groups of atoms are used for their physical properties, quantum effects become important; already we see quantum computation taking shape. Concepts move towards those in life with the emergence of specifically informational structures. We now see the possibility of the artificial construction of a synthetic living system, different from biological life, but having many or all of the same properties. Interactions are essentially nonlinear and collective. Structures begin to have an evolutionary history with episodes of symbiosis. Underlying all the structures are constraints of time and space. Through hierarchization, a more general principle than the periodicity of crystals, structures may be found within structures on different scales. We must integrate unifying concepts from dynamical systems and information theory to form a coherent language and science of shape and structure beyond crystals. To this end, we discuss the idea of categorizing structures based on information according to the algorithmic complexity of their assembly.