Crystal engineering: a holistic view

Mining predicted crystal structure landscapes with high throughput crystallisation: old molecules, new insights

New crystal forms of two well-studied organic molecules are identified in a computationally targeted way, by combining structure prediction with a robotic crystallisation screen, including a ‘hidden’ porous polymorph of trimesic acid.

Organic molecules tend to close pack to form dense structures when they are crystallised from organic solvents. Porous molecular crystals defy this rule: they contain open space, which is typically stabilised by inclusion of solvent in the interconnected pores during crystallisation. The design and discovery of such structures is often challenging and time consuming, in part because it is difficult to predict solvent effects on crystal form stability. Here, we combine crystal structure prediction (CSP) with a robotic crystallisation screen to accelerate the discovery of stable hydrogen-bonded frameworks. We exemplify this strategy by finding new phases of two well-studied molecules in a computationally targeted way. Specifically, we find a new ‘hidden’ porous polymorph of trimesic acid, δ-TMA, that has a guest-free hexagonal pore structure, as well as three new solvent-stabilized diamondoid frameworks of adamantane-1,3,5,7-tetracarboxylic acid (ADTA). Beyond porous solids, this hybrid computational–experimental approach could be applied to a wide range of materials problems, such as organic electronics and drug formulation.

Chalcogen bonding of two ligands to hypervalent YF4 (Y = S, Se, Te, Po)

The ability of two NH₃ ligands to engage in simultaneous chalcogen bonds to a hypervalent YF₄ molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another in a pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y = S, while Te, and Po tend toward the trans structure; they are nearly equally stable for Se. In either case, the binding energy rises rapidly with the size of the Y atom, exceeding 30 kcal mol^-1 for PoF₄.

Triptycene End-Capped Quinoxalinophenanthrophenazines (QPPs): Influence of Substituents and Conditions on Aggregation in the Solid State

Triptycene end-capped quinoxalinophenanthrophenazine reveals a coplanar arrangement with a high overlap of the π planes. Four structurally related model compounds bearing electron-withdrawing or -donating groups were synthesized, and their optoelectronic properties were characterized by using cyclovoltammetry, absorption- and emission spectroscopy as well as theoretical calculations. The directional robustness of the triptycene end-capping of these compounds was tested by using single-crystal X-ray diffraction. The impact of solvents and crystallization conditions has also been investigated. In total, 17 single-crystal structures were obtained. Each structure was evaluated for its potential charge-transfer capability taking into account the overall molecular packing, solvent enclathration and the structural overlap of the π planes of adjacent molecules. For this purpose, charge-transfer integrals were also calculated for every π-stacked dimer.

Strategy and Methodology in the Synthesis of Multicomponent Molecular Solids: The Quest for Higher Cocrystals

Crystal engineering is the art and science of making crystals by design. Crystallization is inherently a purifying phenomenon. Bringing together more than one organic compound into the same crystal always needs deliberate action. Cocrystals are important because they offer a route to the controlled modulation of crystal properties. The route to cocrystal synthesis was opened up with the heterosynthon concept, which considers the complementary recognition of chemical groups from different molecules. Using this concept, binary cocrystals of enormous variety have been generated, even as crystal engineering has evolved into a form of solid-state supramolecular synthesis. Introducing a third component (a component is somewhat arbitrarily defined as an organic substance that is a solid at room temperature, mostly with the idea of excluding solvates) in a stoichiometric manner requires substantially greater effort and a careful balance of intermolecular interactions-their strengths, directional properties, and distance falloff characteristics. The first systematic ternary cocrystal synthesis was reported around 15 years ago. Drawing in a fourth component in stoichiometric amounts is exceedingly difficult, and we reported such syntheses in 2016. To date, a limited number of ternary cocrystals have been realized (around 120 in all, with a half from our group) and an even smaller number of quaternary cocrystals (around 30, all from our group, barring one). It is impressive that our experiments largely yielded the intended higher cocrystal (three- or four-component) with very small traces of contaminating binaries and pure compounds. A fifth or sixth component may be brought into the solid in the manner of a solid solution in that these components are situated at one of the sites of the quaternary cocrystal. To date, five components have not been included stoichiometrically within the same crystal. This is still an open challenge. The merit in synthesizing (higher) cocrystals is that one can systematically engineer property modularity: Each component is associated with a distinct property. This is important in the pharmaceutical industry, where each component can, in principle, confer a different, desirable property-drug action, solubility, or permeability. However, difficult synthetic targets are also addressed in chemistry simply because they are there. The intellectual satisfaction in making something that is very difficult to make renders the enterprise worthwhile in itself, and new chemistry usually gets uncovered in the process. The development of synthetic organic chemistry can undoubtedly be credited to various reliable methods for chemical transformations, and many difficult total syntheses were achieved by employing these methods over two centuries of research. In contrast, supramolecular synthesis (of multicomponent cocrystals and other assemblies) is in no way at a similar level of sophistication because the subject is still relatively young. Our group and others have reported the synthesis of many higher cocrystals with reliable, reproducible, and robust design strategies. There is a general perception that the isolation of some of these cocrystals is a matter of luck! The crux of this Account is that far from being a serendipitous matter, higher cocrystals may only be made with a judicious combination of strategy and methodology-the essence of synthesis.

Effect of solvent environment on excited state intramolecular proton transfer in 2-(4-(dimethylamino)phenyl)-3-hydroxy-6,7-dimethoxy-4h-chromen-4-one

The new ratiometric fluorescent probe 2-(4-(dimethylamino)phenyl)-3-hydroxy-6,7-dimethoxy-4h-chromen-4-one (HOF) monitoring of methanol in biodiesel was discovered experimentally (T. Y. Qin et al., Sens. Actuators, B, 2018, 277, 484-491). But the experimental study did not report the reaction mechanism in detail. In this study, density functional theory (DFT) and time-density functional theory (TDDFT) methods were used to theoretically study the excited-state intramolecular proton transfer (ESIPT) process of the HOF molecule. The molecular structure in the ground state and the excited state was optimized, and the infrared vibrational spectra, the frontier molecular orbitals, the charge transfer, the potential energy curves and the transition-state structures were calculated. The calculated results prove that the solvent polarity has a great influence on the ESIPT reaction of the HOF molecule. As the solvent polarity increased, the intensity of the intramolecular hydrogen bond decreased, and ESIPT was more difficult to occur. This work has studied the mechanism of the ESIPT reaction in more detail, and paved the way for future research on HOF molecules.

Influence of ligand positional isomerism on the molecular and supramolecular structures of cobalt(II)-phenylimidazole complexes

In a study to evaluate the impact of flexible positional isomeric ligands on the coordination geometry and self-assembly process of 3d metal complexes, the synthesis of eight new cobalt(II) complexes with the 2-phenylimidazole (LH) and 5-phenylimidazole (L'H) ligands has been carried out. A variety of parameters/conditions have been probed using the general Co^II/X^-/LH or L'H (X^- = Cl^-, Br^-, I^-, NO₃^-, NCS^-, ClO₄^-, SO₄^2-) reaction system. Interestingly, X-ray analyses reveal two distinct groups of complexes: reactions with LH only lead to tetrahedral or quasi-tetrahedral complexes {i.e. [CoCl₂(LH)₂] (1), [CoI₂(LH)₂] (2), [Co(NO₃)₂(LH)₂] (3), [Co(NCS)₂(LH)₂] (4)}, whereas L'H favours octahedral coordination {i.e. [Co(L'H)₄(MeCN)(H₂O)]I₂ (5), [Co(L'H)₄(MeCN)(H₂O)](NO₃)₂ (6) and [Co(NCS)₂(L'H)₄)]·2MeOH (7·2MeOH)}. A tetrahedral [Co(NCS)₂(L'H)₂)] (8) complex was also concurrently isolated with complex 7. The effects of the positional isomeric ligands LH and L'H and of the coordinated inorganic anions on the stoichiometry and packing arrangements of the complexes are thoroughly discussed. The supramolecular assembly is firmly directed, in all types of complexes, by robust N-H...X (X = Cl, I, O or S) motifs, leading to varying dimensionalities (1D, 2D or 3D) and packing arrangements. The formation of these motifs has been activated by choosing appropriate anions X, acting as terminal ligands or counterions. At a second level of organization, additional subordinate C-H...X (X = Cl, I, O or S), C-H...π and π...π intermolecular interactions complement the rigidity of the complexes' packing towards compact 3D assemblies. Hirshfeld surface analyses provided insight into the intermolecular interactions, allowed quantification of the individual contact types and comparison between the complexes.

Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY-X···X-Z(B)m] Type (X = Cl, Br, I)

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

Directed Polymorphism and Mechanofluorochromism of Conjugated Materials through Weak Non-Covalent Control

Understanding and manipulating crystal polymorphism can provide novel strategies for materials discovery in organic optoelectronics. In this paper, a series of seven ester-terminated three-ring phenylene ethynylenes (PEs) exhibit structure-dependent polymorphism wherein alkyl chain length modulates the propensity to form violet or green fluorescent solid phases, as well as tunable thermal and mechanofluorochromic (MFC) transitions. These compounds harness "soft" non-covalent control to achieve polymorphism: the electronic substituent effect of the ester groups weakens the fluoroarene-arene (ArF-ArH) interactions that typically direct crystal packing of this class of compounds, increasing competitiveness of other interactions. Small structural modifications tip this balance and shift the prevalence of violet- or green-emitting polymorphs. Compounds with short alkyl chain lengths show both violet and various green fluorescent polymorphs, while the violet fluorescent form dominates with alkyl lengths longer than butyl. Further, thermally induced green-to-violet fluorescent crystal-to-crystal transitions occur for single crystals of CO2-1 and CO2-3. Finally, the PEs show reversible violet-to-green mechanofluorochromism (MFC), with temperature required for reversion of this MFC decreasing with alkyl chain length. We therefore present this design of directional but weak interactions as a strategy to access polymorphs and tunable stimuli-responsive behavior in solids.

Supramolecular networks and Hirshfeld surfaces of oxydiacetic acid and iminodiacetic acid salts

Oxydiacetic acid (Oda) and iminodiacetic acid (Ida) have been combined with two diamines, namely ethylenediamine (en) and o-phenylenediamine (o-phen), to give three molecular crystals of compositions [(Oda^2-)(en²⁺)]·H₂O (Odaen), [(Ida^-)(0.5en⁺)] (Idaen) and [(Oda^-)(o-phen⁺)] (Odaophen). Single crystal X-ray structure determination of the three molecular salts revealed that the hydrogen bonding interactions form distinct supramolecular chains. In Odaen, water molecules and Oda^2- anions generate one-dimensional supramolecular chains where two chains overlap each other in zigzag form. In Odaophen, Oda^- anions generate a one-dimensional linear supramolecular chain. In Idaen, both intermolecular and intramolecular proton transfer occurs. Ida^- anions generate a one-dimensional zigzag chain. These one-dimensional supramolecular chains extend to form different two-dimensional supramolecular chains by the interaction of diaminium and monoaminium cations. Intermolecular close contacts are also examined using Hirshfeld analysis to reveal similarities and differences in the crystal structures.

Halogen Bonds of Halotetrafluoropyridines in Crystals and Co-crystals with Benzene and Pyridine

The structures of the three para-substituted halotetrafluoropyridines with chlorine, bromine, and iodine have been determined in the solid state (X-ray diffraction). The structures of these compounds and that of pentafluoropyridine were also determined in the gas phase (electron diffraction). Structures in the solid state of the bromine and iodine derivatives exhibit halogen bonding as a structure-determining motif. On the way to an investigation of halogen bond formation of halotetrafluoropyridines in the solid state with the stronger Lewis base pyridine, co-crystals of benzene adducts were investigated to gain an understanding of the influence of aryl-aryl interactions. These co-crystals showed halogen bonding only for the two heavier halotetrafluoropyridines. In the pyridine co-crystals halogen bonding was observed for all three para-halotetrafluoropyridines. The formation of homodimers and heterodimers with pyridine is also supported by quantum-chemical calculations of electron density topologies and natural bond orbitals.

Is Gelation Behavior Predictable through a Crystal Engineering Approach? A Case Study in Four Similar Coordination Compounds

In this paper, a detailed study on the gelation properties of a series of terpyridine and dipyrazine-pyridine ligands in the presence of metal salts is reported. To reveal the driving forces for the self-assembly of the metallogelators, their crystal structure is scrutinized. Inspired by the gelation of CuCl₂[Terpy- nCN], where "Terpy- nCN" is 4'-( n-cyanophenyl)-2,2',6',2″-terpyridine, to look into the aggregation behavior of the related analogues, synthesis of CuCl₂[Dipyz-py- nCN] derivatives, where "Dipyz-py- nCN" is 4-( n-cyanophenyl)-2,6-di-pyrazin-2-yl-pyridine, with the same cyano groups is performed. We then find that the Dipyz-py counterpart forms crystals when the molecules are stacked in an alternating way, instead of the unidirectional one required for gel formation. A crystal engineering approach is applied to determine the interactions that are favorable for fabricating a fiber network that is likely to be present in both crystalline and gel states and to find the interaction that disturbs this delicate balance between gelation and crystallization in coordination compounds; then, we conclude that the subtle balance between the molecular shape and intermolecular interactions is the origin of the gelation and crystallization of the current molecular system. This enables us to find the mutual connection among the structure of molecules, assembly behavior, and intermolecular interactions. With our experiments, a deep understanding of the balance among solution, gelation, and crystallization with subtle molecular diversions is provided.

Photoluminescence Properties of Two Closely Related Isostructural Series Based on Anderson-Evans Cluster Coordinated With Lanthanides [Ln(H2O)7{X(OH)6Mo6O18}]•yH2O, X = Al, Cr

The paper describes synthesis and structural characterization of the whole series of two closely related lanthanide coordinated chromium or aluminum hexamolybdates (Anderson-Evans cluster) including twelve new members hitherto unreported: [Ln(H₂O)₇{X(OH)₆Mo₆O₁₈}]·4H₂O and [Ln(H₂O)₇{X(OH)₆Mo₆O₁₈}Ln(H₂O)₇]{X(OH)₆Mo₆O₁₈}·16H₂O where X = Al or Cr and Ln = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, and Y. Crystal structures of all the solids were established by powder and single crystal X-ray diffraction techniques. The two series are dictated by a different aggregation of the same set of molecular species: Lighter lanthanides favor coordination interaction between lanthanide ions and molybdate cluster forming 1D chains (Series I) while the heavier lanthanides result in the stacking of a cation, a pair of lanthanide hydrates coordinating to the cluster, and an anion, the discrete cluster is further stabilized through a large number of water molecules (Series II). Crystallization with Er³⁺ and Tm³⁺ ions results in a concomitant mixture of Series I and II. Photoluminescence of single crystals of all the chromium molybdates was dominated by a ruby-like emission including those which contain optically active ions Pr, Sm, Eu, Tb, Dy, and Tm. In contrast, aluminum analogs showed photoluminescence corresponding to characteristic lanthanide emissions. Our results strongly suggest a possible energy transfer from f levels of lanthanide ions to d levels of chromium (III) causing the quenching of lanthanide emission when coordinated with chromium molybdates. Intensity measurements showed that the emission from chromium molybdates are almost two orders of magnitude lower than naturally occurring ruby with broader line widths at room temperature.

Investigating the solubilization effect of oxcarbazepine by forming cocrystals

Oxcarbazepine (OXCBZ) is a poorly soluble drug that can't form a salt. The apparent solubilities of the OXCBZ–OA and OXCBZ–2,5-DHBA cocrystals increased approximately 2.6 and 4.7 times of that of OXCBZ.

Recognition of the π-hole donor ability of iodopentafluorobenzene – a conventional σ-hole donor for crystal engineering involving halogen bonding

This study is the first recognition of iodopentafluorobenzene's π-hole donor ability.

Switching hydrogen bonds to readily interconvert two room-temperature long-term stable crystalline polymorphs in chiral molecular perovskites

Two room-temperature polymorphic forms could be long-term stable yet easily interconvertible by switching the inter-cationic H-bonds in chiral molecular perovskites.

Cocrystals and Salts of 3,5-Bis(pyridinylmethylene)piperidin-4-one with Aromatic Poly-Carboxylates and Resorcinols: Influence of Stacking Interactions on Solid-State Luminescence Properties

Two bis-pyridyl-substituted α,β-unsaturated ketones were shown to form complexes with carboxylic acids and resorcinol derivatives. The neutral acid–acid homosynthon was observed in only one complex out of the five acid-bis-pyridyl containing complexes studied here, while the –COO−⋯HOOC– synthon was found to be dominant as it was observed in four complexes. The carboxylates self-assembled to form discrete dimeric, anionic, 1D chains and also exhibited mixed ionic hydrogen bonds. On the other hand, resorcinol derivatives displayed O–H⋯N hydrogen bonding to form tetrameric aggregates of bis-pyridyl ketone molecules and respective co-formers, while 3,5-dihydroxy benzoic acid (DHBA) molecules formed 1D chains by clipping two molecules of ketones with three DHBA molecules. Such clipping by the resorcinol derivatives promoted continuous π–π stacking interactions. Consequently, these materials emitted at higher wavelengths compared with the parent bis-pyridyl-substituted α,β-unsaturated ketones.

The effect of different environments on excited-state intramolecular proton transfer in 4′-methoxy-3-hydroxyflavone

Excited state intramolecular proton transfer reaction occurs with increasing difficulty in the solvents tested in the order toluene → ACN → DMF.

Geometric H/D isotope effect in a series of organic salts involving short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups

Noticeable elongations of donor–acceptor distances upon deuteration are confirmed in short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups.

Lone pair⋯π interaction versus σ-hole appearance in metal-bonded halogens

Three complexes of N-(2,5-diluorophenyl)-2-pyrazine carboxamide and ZnX₂ have been synthesized. The crystal structures reveal that in all three coordination compounds, metal-bound halides have interacted with π systems through a negative electrostatic region.

A single-crystal-to-single-crystal transformation affording photochromic 3D MORF crystals

Metal–organic framework (MOF) type crystals in which rigid, viologen-based pillars are surrounded by cucurbit[7]uril (CB[7]) macrocycles are described.

Syntheses and structural aspects of six-membered palladacyclic complexes derived fromN,N′,N′′-triarylguanidines with N- or S-thiocyanate ligands

Linkage isomers8·2/3PhMe and9·MeOH were synthesized, isolated and structurally characterized by SCXRD and the role of solvent of crystallization in the formation of these linkage isomers identified.

A benzimidazole-based non-symmetrical tripodal receptor for the ratiometric fluorescence sensing of fluoride ions and solid state recognition of sulfate ions

A novel tripodal receptor has been reported as a fluorescent chemosensor for fluoride ions. Moreover, in solid state, seven units of the protonated receptors form a pseudo-capsular cavity to encapsulate two pairs of sulphate anions.

Stoichiometry mechanosynthesis and interconversion of metal salts containing [CuCl3(H2O)]− and [Cu2Cl8]4−

The mechanochemical interconversion of two salts was achieved by the addition of an appropriate amount of one of the corresponding components (HL or CuCl₂·2H₂O), and the progress of dynamic interconversion was revealed by PXRD, fluorescence and Raman spectroscopy.

Polymorphism and molecular conformations of nicosulfuron: structure, properties and desolvation process

Nine solid forms of nicosulfuron were found for the first time and their structures and properties were studied in detail.

Bottom-Up Construction and Reversible Structural Transformation of Supramolecular Isomers based on Large Truncated Tetrahedra

A rational synthetic strategy to construct two supramolecular isomers based on polyoxovanadate organic polyhedra with tetrahedral symmetries is presented. VMOP-α, a low-temperature product, has an extremely large cell volume (470 842 ų ), which is one of the top three for well-defined MOPs. The corner-to-corner packing of tetrahedra leads to a quite low density of 0.174 g cm^-3 with 1D channels (ca. 5.4 nm). The effective pore volume is up to 93.6 % of cell volume, nearly the largest found in MOPs. For the high-temperature outcome, VMOP-β, the cell volume is only 15 513 ų . The packing mode of tetrahedra is corner-to-face, giving rise to a high-density architecture (1.324 g cm^-3 ; channel 0.8 nm). Supramolecular structural transformation between VMOP-α and VMOP-β can be reversibly achieved by temperature-induced solvent-mediated transformation. These findings give a good opportunity for understanding 3D supramolecular aggregation and crystal growth based on large molecular tectonics.

Construction of Highly Efficient Carbazol-9-yl-Substituted Benzimidazole Bipolar Hosts for Blue Phosphorescent Light-Emitting Diodes: Isomer and Device Performance Relationships

Four isomers of carbazol-9-yl-substituted 1,2-diphenylbenzimidazole at 7, 6, 5, and 4 positions, named as 1-CbzBiz, 2-CbzBiz, 3-CbzBiz, and 4-CbzBiz, respectively, have been synthesized. Instead of having an identical molecular weight, the CbzBiz's have their glass transition temperatures ( T_g) spanning a large range from 53 to 90 °C. Their T_g and melting point ( T_m) basically obey the Boyer-Kauzmann rule ( T_g = g· T_m with g ≈ 0.7) on the absolute temperature scale (in kelvins). However, while 1-CbzBiz and 4-CbzBiz demonstrate a small g value of 0.66, which is significantly smaller than other common organic glass molecules, 3-CbzBiz shows an unexpectedly high g value of 0.73, implying higher intermolecular interactions in the glass. These CbzBiz's are suitable hosts for bis[2-(4,6-difluorophenyl)pyridinato- C², N](picolinato)iridium(III) (FIrpic) in phosphorescence organic light-emitting diodes (PhOLEDs). The optimized PhOLED of indium tin oxide/4,4'-cyclohexylidenebis[ N, N-bis(4-methylphenyl)benzenamine]/4Cbz/4-CbzBiz-FIrpic(15%)/diphenylbis(4-(pyridin-3-yl)phenyl)silane/LiF-Al shows a maximum brightness of 18 760 cd/m², a current efficiency of 64.1 cd/A, and the external quantum efficiency of 30.9%.

Switching of Monomer Fluorescence, Charge-Transfer Fluorescence, and Room-Temperature Phosphorescence Induced by Aromatic Guest Inclusion in a Supramolecular Host

Crystal engineering of three-component crystals with guest-dependent photoluminescence switching, including (i) crystallization-induced emission enhancement, (ii) intermolecular charge-transfer emission, and (iii) room-temperature phosphorescence under ultraviolet irradiation, was demonstrated. This strategy was based on the confinement of aromatic guests in a supramolecular host (denoted as EBPDI-TPFB) composed of 5,5'-(ethyne-1,2-diyl)bis(2-pyridin-3-yl-isoindoline-1,3-dione (EBPDI) with two tris(pentafluorophenyl)borane (TPFB) molecules linked by B-N dative bonds that acted as Lewis pairs. The single-crystal X-ray structures of complexes with eight different guests were collected, revealing that the size and/or shape of the supramolecular host EBPDI-TPFB was modulated by the included guest molecules. The excellent guest inclusion ability of EBPDI-TPFB allowed systematic photoluminescence regulation of the complexes, which exhibited multicolor emissions in the crystalline state. Photoluminescence switching characteristics of the complexes were observed upon removing the guests or mechanical grinding of the crystals. These results indicated that using the host-guest chemistry of multicomponent crystals not only facilitates crystallization, but also can reveal hidden optical functions by combining molecules of interest, which should contribute to the fields of physical chemistry and materials science.