X-ray Snapshot Observation of Palladium-Mediated Aromatic Bromination in a Porous Complex

Atomic-resolution structure analysis inside an adaptable porous framework

We introduce a versatile metal-organic framework (MOF) for encapsulation and immobilization of various guests using highly ordered internal water network. The unique water-mediated entrapment mechanism is applied for structural elucidation of 14 bioactive compounds, including 3 natural product intermediates whose 3D structures are clarified. The single-crystal X-ray diffraction analysis reveals that incorporated guests are surrounded by hydrogen-bonded water networks inside the pores, which uniquely adapt to each molecule, providing clearly defined crystallographic sites. The calculations of host-solvent-guest structures show that the guests are primarily interacting with the MOF through weak dispersion forces. In contrast, the coordination and hydrogen bonds contribute less to the total stabilization energy, however, they provide highly directional point interactions, which help align the guests inside the pore.

Highly Luminescent Crystalline Sponge: Sensing Properties and Direct X-ray Visualization of the Substrates

A phenomenon of crystalline sponge is represented by guest-dependent structural fluidity of the host polymeric lattice in highly crystalline sorbents, such as metal-organic frameworks, driven by multiple weak intermolecular interactions. Such induced fitting in MOFs is a valuable property in selective adsorption, guest determination by single-crystal XRD and in-situ structural analysis under external stimuli. In this work, a porous three-dimensional metal-organic framework [Eu₂(DMF)₄(ttdc)₃]·4.45DMF (1_DMF; DMF = N,N-dimethylformamide, ttdc^2- = trans-thienothiophenedicarboxylate anion) was applied as a crystalline sponge bearing luminescent functionality to couple its sensing properties with direct structural determination of the adsorbed molecules. As a result, the paper discusses crystal structures and luminescent properties for the successfully obtained new adducts with the crystallographic formulae [Eu₂(DMSO)₄(ttdc)₃]·2.5DMSO·2.2H₂O (1_DMSO; DMSO = dimethylsulfoxide), [Eu₂(DMF)₄(ttdc)₃]·3phet (1_phet; phet = phenylethanal) and [Eu₂(DMF)_3.5(cin)_0.5(ttdc)₃]·1.64cin (1_cin; cin = trans-cinnamaldehyde). As a result of inclusion of DMSO into 1, a slight increase in the quantum yield and excited state phosphorescence lifetime was observed, while the adsorption of phet leads to a considerable (up to three times) decrease in the corresponding values. The incorporation of cinnamal results in a full quenching of QY, from 20% down to zero, and a more than order of magnitude diminishing of the excited state lifetime compared to the initial 1_DMF. The effective sensing of cinnamal was explained from the structural point of view by its direct coordination to the Eu³⁺ emitter, as well as by multiple weak intermolecular interactions with ttdc antenna ligand, both capable of enhancing the non-radiative energy dissipation.

Catalysis in Single Crystalline Materials: From Discrete Molecules to Metal-Organic Frameworks

Catalysis is one of the key techniques for people's modern life. It has created numerous essential chemicals such as biomedicines, agricultural chemicals and unique materials. Heterogeneous catalysis is the new emerging method with reusable catalysts. Among heterogenous catalysis patterns developed so far, single crystalline catalysis has become the promising one owing to its high catalytic density and selectivity resulted by the inherent porosity, orderliness of the lattices and permeability. These crystalline catalysts could be used in various reactions such as photo-dimerization, Diels-Alder reaction, CO₂ transformation and so on. In this review, we highlighted the reported works about the single crystalline catalysts. Both discrete small molecules and metal-organic frameworks (MOFs) have been used to prepare single crystals for catalysis. For discrete molecules based crystalline catalysts, coordinated and covalent molecules have been used. There were more catalytic modes in crystalline MOF catalysts. Three patterns were identified in this review: single crystalline MOFs i) without catalytic sites, ii) with inherent catalytic features and iii) with introducing catalytic units by post synthetic modification. Based on these examples, this review committed to provide the inspirations for the further design and application of single crystalline materials.

Single-Crystal-to-Single-Crystal Transformations of Metal-Organic-Framework-Supported, Site-Isolated Trigonal-Planar Cu(I) Complexes with Labile Ligands

Transition-metal complexes bearing labile ligands can be difficult to isolate and study in solution because of unwanted dinucleation or ligand substitution reactions. Metal-organic frameworks (MOFs) provide a unique matrix that allows site isolation and stabilization of well-defined transition-metal complexes that may be of importance as moieties for gas adsorption or catalysis. Herein we report the development of an in situ anion metathesis strategy that facilitates the postsynthetic modification of Cu(I) complexes appended to a porous, crystalline MOF. By exchange of coordinated chloride for weakly coordinating anions in the presence of carbon monoxide (CO) or ethylene, a series of labile MOF-appended Cu(I) complexes featuring CO or ethylene ligands are prepared and structurally characterized using X-ray crystallography. These complexes have an uncommon trigonal planar geometry because of the absence of coordinating solvents. The porous host framework allows small and moderately sized molecules to access the isolated Cu(I) sites and displace the "place-holder" CO ligand, mirroring the ligand-exchange processes involved in Cu-centered catalysis.

Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies

This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI₂ )₃ (tpt)₂ ]⋅x(solvent)}_n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.

Applying the Crystalline Sponge Method to Agrochemicals: Obtaining X-ray Structures of the Fungicide Metalaxyl-M and Herbicide S-Metolachlor

The crystalline sponge method is a technique that provides the ability to elucidate the absolute structure of noncrystalline or hard to crystallize compounds through single-crystal X-ray diffraction by removing the need to obtain crystals of the target compound. In this study the crystalline sponges {[(ZnX₂)₃(2,4,6-tris(4-pyridyl)-1,3,5-trazine)₂].x(solvent)} _n (X = I, Br) were used to obtain X-ray structures of the agrochemical active ingredients metalaxyl-M and S-metolachlor. The effect of the temperature used during guest uptake and the influence of changing the host framework ZnX₂ nodes on guest encapsulation were investigated. Additionally, three compounds containing chemical fragments similar to those of metalaxyl-M and S-metolachlor (phenylacetaldehyde, N-ethyl-o-toluidine, and methyl phenylacetate) were also encapsulated. This allowed for the effect of guest size on the position that guests occupy within the host frameworks to be examined. The disorder experienced by the guest compounds was documented, and an analysis of the intermolecular host-guest interactions (CH···π and π ···π) used for guest ordering within the host frameworks was also undertaken in this study.

The chemistry of phosphines in constrained, well-defined microenvironments

Developments in the confinement of phosphines within micro- or nano-environments are explored. Phosphines are ubiquitous across metal coordination chemistry and underpin some of the most famous homogeneous transition metal catalysts. Constraining phosphines within confined environments influences not only their behaviour but also that of their metal complexes. Notable examples include the use of metal-organic frameworks (MOFs) or metal-organic cages (MOCs) to support phosphines which demonstrate how the microenvironment within such constructs leads to reactivity modification. The development of phosphine confinement is explored and parallels are drawn with related constrained macrocyclic systems and mechanically interlocked molecules. The review concludes by identifying areas that remain a challenge and those that will provide new avenues for research.

Application of Crystalline Matrices for the Structural Determination of Organic Molecules

While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.

X-ray Crystallographic Observation of Chiral Transformations within a Metal-Peptide Pore

Porous metal complexes enable single-crystal X-ray crystallographic observation of included guests or reaction intermediates through simple soaking with the guests/substrates. Previous studies on this technique have often encountered difficulties in the observation of chiral structures because the host frameworks had no chirality. We synthesized a new metal-peptide porous complex through a folding-and-assembly strategy and utilized the chiral pore for trapping chiral guests. Chiral alcohols and ketones were successfully included within the pore. Crystallographic analyses clearly revealed not only their chemical structures but also chiral transformation events within the pore such as fixed conformations or an unstable hemiacetal formation.

Enhancing catalytic alkane hydroxylation by tuning the outer coordination sphere in a heme-containing metal-organic framework

Catalytic heme active sites of enzymes are sequestered by the protein superstructure and are regulated by precisely defined outer coordination spheres. Here, we emulate these protective functions in the porphyrinic metal-organic framework PCN-224 by post-synthetic acetylation and subsequent hydroxylation of the Zr6 nodes. A suite of physical methods demonstrates that both transformations preserve framework structure, crystallinity, and porosity without modifying the inner coordination spheres of the iron sites. Single-crystal X-ray analyses establish that acetylation replaces the mixture of formate, benzoate, aqua, and terminal hydroxo ligands at the Zr6 nodes with acetate ligands, and hydroxylation affords nodes with seven-coordinate, hydroxo-terminated Zr4+ ions. The chemical influence of these reactions is probed with heme-catalyzed cyclohexane hydroxylation as a model reaction. By virtue of passivated reactive sites at the Zr6 nodes, the acetylated framework oxidizes cyclohexane with a yield of 68(8)%, 2.6-fold higher than in the hydroxylated framework, and an alcohol/ketone ratio of 5.6(3).

Hypervalent organoiodine(v) metal-organic frameworks: syntheses, thermal studies and stoichiometric oxidants

Iodinated analogues of the highly porous IRMOF-9 and UiO-67 frameworks were prepared and post-synthetically oxidised with dimethyldioxirane (DMDO). Analysis by X-ray photoelectron spectroscopy (XPS) confirmed promotion to the iodine(v) state and detailed differential scanning calorimetry-thermal gravimetric analysis (DSC-TGA) showed the hypervalent metal-organic frameworks (MOFs) undergo exothermic elimination at ∼200 °C with XPS showing hypervalency is maintained. The hypervalent MOFs are active heterogeneous reagents in sulfoxidation and alcohol oxidation reactions. The crystallinity and porosity of the MOFs were maintained following post-synthetic oxidation, thermolysis and after the heterogeneous reactions, as shown by powder X-ray diffraction (PXRD) and gas adsorption analyses. This work showcases the unique ability MOFs hold for studying chemical reactions and the potential for hypervalent organoiodine MOFs as reuseable oxidants.

Isolating reactive metal-based species in Metal-Organic Frameworks - viable strategies and opportunities

Structural insight into reactive species can be achieved via strategies such as matrix isolation in frozen glasses, whereby species are kinetically trapped, or by confinement within the cavities of host molecules. More recently, Metal-Organic Frameworks (MOFs) have been used as molecular scaffolds to isolate reactive metal-based species within their ordered pore networks. These studies have uncovered new reactivity, allowed observation of novel metal-based complexes and clusters, and elucidated the nature of metal-centred reactions responsible for catalysis. This perspective considers strategies by which metal species can be introduced into MOFs and highlights some of the advantages and limitations of each approach. Furthermore, the growing body of work whereby reactive species can be isolated and structurally characterised within a MOF matrix will be reviewed, including discussion of salient examples and the provision of useful guidelines for the design of new systems. Novel approaches that facilitate detailed structural analysis of reactive chemical moieties are of considerable interest as the knowledge garnered underpins our understanding of reactivity and thus guides the synthesis of materials with unprecedented functionality.

Novel Porous Crystals with Macrocycle-Based Well-Defined Molecular Recognition Sites

Molecular recognition is one of the fundamental events in biological systems, as typified by enzymes that enable highly efficient and selective catalytic reactions through precise recognition of substrate(s) and cofactor(s) in the binding pockets. Chemists therefore have long been inspired by such excellent molecular systems to develop various synthetic receptors with well-defined binding sites. Their effort is currently being devoted to the construction of not only molecular receptors but also self-assembled host compounds possessing connected cavities (pores) in the crystalline frameworks to rationally design functional porous materials capable of efficiently adsorbing molecules or ions at binding sites on the pore walls. However, it is still challenging to design multiple distinct binding sites that are precisely arranged in an identical framework, which is currently one of the most important targets in this field to realize elaborate molecular systems beyond natural enzymes.In this Account, we provide an overview of porous crystals with well-defined molecular recognition sites. We first show several strategies for arranging macrocyclic binding sites in crystalline frameworks such as metal-organic frameworks, porous molecular crystals, and covalent organic frameworks. Porous metal-macrocycle frameworks (MMFs) that we have recently developed are then described as a new type of porous crystals with well-defined multiple distinct binding sites. The MMF-1 crystal, which was developed first and is composed of four stereoisomers of helical Pd^II₃-macrocycle complexes, has one-dimensional channels with dimensions of 1.4 nm × 1.9 nm equipped with enantiomeric pairs of five distinct binding sites. This structural feature of MMF-1 therefore allows for site-selective and asymmetric arrangement of not only single but also multiple guest molecules in the crystalline channels based on molecular recognition between the guests and the multiple binding sites. This characteristic was also exploited to develop a heterogeneous catalyst by non-covalently immobilizing an organic acid on the pore surface of MMF-1 to conduct size-specific catalytic reactions. In addition, adsorption of a photoreactive substrate in MMF was found to switch the photoreaction pathway to cause another reaction with the aid of photoactivated Pd^II centers arranged on the pore walls. Furthermore, the dynamic, transient process of molecular arrangement incorporated in MMF-1 has been successfully visualized by single-crystal X-ray diffraction analysis. The formation of homochiral MMF-2 composed of only (P)- or (M)-helical Pd^II₃-macrocycle complexes is also described. Thus, macrocycle-based porous crystals with a complex structure such as MMFs are expected to serve as novel porous materials that have great potential to mimic or surpass enzymes by utilizing well-defined multiple binding sites capable of spatially arranging a catalyst, substrate, and effector for highly selective and allosterically tunable catalytic reactions, which can be also visualized by crystallographic analysis because of their crystalline nature.

Halogen Bonding in a Crystalline Sponge

Host-guest interactions are the key to the supramolecular chemistry and the further application of the receptors to study the structural details of the small guest molecules. Crystalline sponges as a kind of supramolecular receptor need to be investigated in terms of the binding ability with the guests. We found in this work that one guest with σ-hole donors and another with electron-donating species were separately entrapped in two distinct channels of the host framework via the crystalline sponge method. Halogen bonding and weak hydrogen bonding were detected between the host and the two guests, respectively. The ability of the crystalline sponge to absorb and sort guests of different types was unambiguously confirmed by X-ray crystallography.

Protecting-Group-Free Site-Selective Reactions in a Metal-Organic Framework Reaction Vessel

Site-selective organic transformations are commonly required in the synthesis of complex molecules. By employing a bespoke metal-organic framework (MOF, 1·[Mn(CO)₃N₃]), in which coordinated azide anions are precisely positioned within 1D channels, we present a strategy for the site-selective transformation of dialkynes into alkyne-functionalized triazoles. As an illustration of this approach, 1,7-octadiyne-3,6-dione stoichiometrically furnishes the mono-"click" product N-methyl-4-hex-5'-ynl-1',4'-dione-1,2,3-triazole with only trace bis-triazole side-product. Stepwise insights into conversions of the MOF reaction vessel were obtained by X-ray crystallography, demonstrating that the reactive sites are "isolated" from one another. Single-crystal to single-crystal transformations of the Mn(I)-metalated material 1·[Mn(CO)₃(H₂O)]Br to the corresponding azide species 1·[Mn(CO)₃N₃] with sodium azide, followed by a series of [3+2] azide-alkyne cycloaddition reactions, are reported. The final liberation of the "click" products from the porous material is achieved by N-alkylation with MeBr, which regenerates starting MOF 1·[Mn(CO)₃(H₂O)]Br and releases the organic products, as characterized by NMR spectroscopy and mass spectrometry. Once the dialkyne length exceeds the azide separation, site selectivity is lost, confirming the critical importance of isolated azide moieties for this strategy. We postulate that carefully designed MOFs can act as physical protecting groups to facilitate other site-selective and chemoselective transformations.

Co₂ and Co₃ Mixed Cluster Secondary Building Unit Approach toward a Three-Dimensional Metal-Organic Framework with Permanent Porosity

Large and permanent porosity is the primary concern when designing metal-organic frameworks (MOFs) for specific applications, such as catalysis and drug delivery. In this article, we report a MOF Co11(BTB)₆(NO₃)₄(DEF)₂(H₂O)14 (1, H₃BTB = 1,3,5-tris(4-carboxyphenyl)benzene; DEF = N,N-diethylformamide) via a mixed cluster secondary building unit (SBU) approach. MOF 1 is sustained by a rare combination of a linear trinuclear Co₃ and two types of dinuclear Co₂ SBUs in a 1:2:2 ratio. These SBUs are bridged by BTB ligands to yield a three-dimensional (3D) non-interpenetrated MOF as a result of the less effective packing due to the geometrically contrasting SBUs. The guest-free framework of 1 has an estimated density of 0.469 g cm-3 and exhibits a potential solvent accessible void of 69.6% of the total cell volume. The activated sample of 1 exhibits an estimated Brunauer-Emmett-Teller (BET) surface area of 155 m² g-1 and is capable of CO₂ uptake of 58.61 cm³ g-1 (2.63 mmol g-1, 11.6 wt % at standard temperature and pressure) in a reversible manner at 195 K, showcasing its permanent porosity.

Crystallography of encapsulated molecules

The crystallography of supramolecular host-guest complexes is reviewed and discussed as a part of small molecule crystallography. In these complexes, the host binds the guests through weak supramolecular interactions, such as hydrogen and halogen bonding, cation-π, anion-π, C-H-π, π-π, C-H-anion interactions and the hydrophobic effect. As the guest often shows severe disorder, large thermal motion and low occupancies, the reliable crystallographic determination of the guest can be very demanding. The analysis of host-guest interactions using tools such as Hirshfeld and cavity volume surface analysis will help to look closely at the most important host-guest interactions. The jewel in the crown of utilizing host-guest interactions in the solid-state is the recently developed Crystalline Sponge Method (CSM) by Makoto Fujita. This method, when successful, gives an accurate and unambiguous 3-D structure of the structurally unknown guest molecule from only micro- or nanogram amounts of the guest molecule. In the case of an optically pure enantiomer, its absolute configuration can be determined.

Structural and dynamic studies of substrate binding in porous metal-organic frameworks

Porous metal-organic frameworks (MOFs) are the subject of considerable research interest because of their high porosity and capability of specific binding to small molecules, thus underpinning a wide range of materials functions such as gas adsorption, separation, drug delivery, catalysis, and sensing. MOFs, constructed by the designed assembly of metal ions and functional organic linkers, are an emerging class of porous materials with extended porous structures containing periodic binding sites. MOFs thus provide a new platform for the study of the chemistry and reactivity of small molecules in confined pores using advanced diffraction and spectroscopic techniques. In this review, we focus on recent progress in experimental investigations on the crystallographic, dynamic and kinetic aspects of substrate binding within porous MOFs. In particular, we focus on studies on host-guest interactions involving open metal sites or pendant functional groups in the pore as the primary binding sites for guest molecules.

The growing importance of crystalline molecular flasks and the crystalline sponge method

This article showcases recent advancements made using crystalline molecular flasks and the widening list of prospective applications for the crystalline sponge method. This expansion has coincided with an increasing number of materials termed crystalline sponges, and a report of a predictive means of identifying candidates from crystallographic databases. The crystalline sponge method's primary application has been determination of absolute configuration, and this has evolved from the analysis of carefully chosen planar aromatic guests to more diverse identification of natural products, biological metabolites, and analysis of volatile chemical components. However with time-resolved X-ray crystallography providing arguably the most informative atomic scale insights of dynamic chemical processes, this application of the crystalline sponge method may soon eclipse structural determination in terms of importance.

Site-selective synthesis of functionalized dibenzo[f,h]quinolines and their derivatives involving cyclic diaryliodonium salts via a decarboxylative annulation strategy

An unprecedented site-selective synthesis of dibenzo[f,h]quinolines and their derivatives was reported via an acid directed decarboxylative annulation cascade.

The Crystalline Sponge Method: A Solvent-Based Strategy to Facilitate Noncovalent Ordered Trapping of Solid and Liquid Organic Compounds

A strategy that leverages solvent effects to noncovalently trap solid and unstable liquid organic compounds within a crystalline sponge ({[(ZnI2)3(tris(4-pyridyl)-1,3,5-triazine)2]·x(CHCl3)}n) in a simple, mild, and efficient fashion for target molecule structure determination via X-ray diffraction is disclosed. Host-guest structures were obtained using third-generation synchrotron radiation, and new beamline hardware allowed rapid data collection in ~5-24 minutes. This is 40-90% faster than previously reported crystalline sponge synchrotron datasets collected by us, and approximately a 150-720-fold decrease in time versus using a typical in-house diffractometer, effectively enabling the potential for high-throughput analysis. The new target molecule inclusion method using methyl tert-butyl ether (MTBE) solvent was demonstrated by trapping (E)-stilbene, vanillin, 4-(trifluoromethyl)phenyl azide, and (+)-artemisinin (an antimalarial drug). The potential of guests to maximize intermolecular interactions with the crystalline sponge framework at the expense of attenuating intramolecular interactions (e.g., π-conjugation) was observed for (E)-stilbene. Trapping of vanillin and (+)-artemisinin elicited single-crystal-to-single-crystal transformations where space group symmetry reduced from C2/c to P1̄ and C2, respectively, and the absolute configuration of (+)-artemisinin was determined through anomalous dispersion.

Isolation and evolution of labile sulfur allotropes via kinetic encapsulation in interactive porous networks

The isolation and characterization of small sulfur allotropes have long remained unachievable because of their extreme lability. This study reports the first direct observation of disulfur (S2) with X-ray crystallography. Sulfur gas was kinetically trapped and frozen into the pores of two Cu-based porous coordination networks containing interactive iodide sites. Stabilization of S2 was achieved either through physisorption or chemisorption on iodide anions. One of the networks displayed shape selectivity for linear molecules only, therefore S2 was trapped and remained stable within the material at room temperature and higher. In the second network, however, the S2 molecules reacted further to produce bent-S3 species as the temperature was increased. Following the thermal evolution of the S2 species in this network using X-ray diffraction and Raman spectroscopy unveiled the generation of a new reaction intermediate never observed before, the cyclo-tri-sulfur dication (cyclo-S3 (2+)). It is envisaged that kinetic guest trapping in interactive crystalline porous networks will be a promising method to investigate transient chemical species.

An Iodine-Vapor-Induced Cyclization in a Crystalline Molecular Flask

A vapor-induced cyclization has been observed in the host environment of a crystalline molecular flask (CMF), within which 1,8-bis(2-phenylethynyl)naphthalene (bpen), a diarenynyl system primed for cyclization, was exposed to iodine vapor to yield the corresponding indeno[2,1-α]phenalene species. The cyclization process, unique in its vapor-induced, solvent-free nature, was followed spectroscopically, and found to occur concurrently with the displacement of lattice solvent for molecular iodine in CMF⋅0.75 bpen⋅2.25 CHCl3 ⋅H2 O. The cyclization occurred under mild conditions and without the need to suspend the crystals in solvent. The ability of CMFs to host purely gas-induced reactions is further highlighted by the subsequent sequential oxidation reaction of cyclized 7-iodo-12-phenylindeno[2,1-α]phenalene (ipp) with molecular oxygen derived from air, yielding 12-hydroxy-7-iodo-2-phenylindeno[2,1-α]phenalen-1(12H)-one (hipp).

In Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge

A reversible Michael addition reaction between thiol nucleophiles and cyanoenones has been previously postulated to be the mechanism-of-action of a new family of reversible covalent drugs. However, the hypothetical Michael adducts in this mechanism have only been detected by spectroscopic methods in solution. Herein, the crystallographic observation of reversible Michael addition with a potent cyanoenone drug candidate by means of the crystalline-sponge method is reported. After inclusion of the cyanoenone substrate, the sponge crystal was treated with a thiol solution. Subsequent crystallographic analysis confirmed the single-crystal-to-single-crystal transformation of the substrate into the impermanent Michael adduct.

Emerging applications of metal–organic frameworks

Metal–organic frameworks are highly crystalline porous materials which present emerging opportunities in biotechnology, catalysis, microelectronics and photonics.

Copper coordination polymers from cavitand ligands: hierarchical spaces from cage and capsule motifs, and other topologies

Copper coordination polymers from cavitand ligands are reported including networked cage-motif structures, one of which takes up C₆₀ from solution.

The cyclotriveratrylene-type ligands (±)-tris(iso-nicotinoyl)cyclotriguaiacylene L1 (±)-tris(4-pyridylmethyl)cyclotriguaiacylene L2 and (±)-tris{4-(4-pyridyl)benzyl}cyclotriguaiacylene L3 all feature 4-pyridyl donor groups and all form coordination polymers with Cu^I and/or Cu^II cations that show a remarkable range of framework topologies and structures. Complex [Cu^I₄Cu^II_1.5(L1)₃(CN)₆]·CN·n(DMF) 1 features a novel 3,4-connected framework of cyano-linked hexagonal metallo-cages. In complexes [Cu₃(L2)₄(H₂O)₃]·6(OTf)·n(DMSO) 2 and [Cu₂(L3)₂Br₂(H₂O)(DMSO)]·2Br·n(DMSO) 3 capsule-like metallo-cryptophane motifs are formed which linked through their metal vertices into a hexagonal 2D network of (4³.12³)(4².12²) topology or a coordination chain. Complex [Cu₂(L1)₂(OTf)₂(NMP)₂(H₂O)₂]·2(OTf)·2NMP 4 has an interpenetrating 2D 3,4-connected framework of (4.6².8)(6².8)(4.6².8²) topology with tubular channels. Complex [Cu(L1)(NCMe)]·BF₄·2(CH₃CN)·H₂O 5 features a 2D network of 6³ topology while the Cu^II analogue [Cu₂(L1)₂(NMP)(H₂O)]·4BF₄·12NMP·1.5H₂O 6 has an interpenetrating (10,3)-b type structure and complex [Cu₂(L2)₂Br₃(DMSO)]·Br·n(DMSO) 7 has a 2D network of 4.8² topology. Strategies for formation of coordination polymers with hierarchical spaces emerge in this work and complex 2 is shown to absorb fullerene-C₆₀ through soaking the crystals in a toluene solution.

Coordination templated [2+2+2] cyclotrimerization in a porous coordination framework

Controlling chemical reactions by the supramolecular confinement effects of nanopores has attracted great attention. Here we show that open metal sites in porous coordination frameworks can constitute more powerful and strict templates for precision syntheses. A Fe(III) dicarboxylate framework functionalized with triangularly arranged metal sites is used to accomplish [2+2+2] cyclotrimerization reactions for organonitrile, alkyne and alkene monomers bearing a geometrically suitable pyridyl group. In situ single-crystal X-ray diffraction facilitates the direct observation of such a coordination templated reaction, before cylcotrimerization, the monomer coordinates at the Fe(III) centre by its pyridyl donor, which forces three unsaturated groups to gather around a position very similar with that of the desired covalent cyclic trimer. After the reaction, the trimers serve as tripodal ligands to perfectly fix the Fe(III) ions and the whole crystal to generate an exceptionally rigid and porous material with large surface area coupled with guest-proof zero thermal expansion.

X-ray Crystallography in Open-Framework Materials

Open-framework materials, such as metal-organic frameworks (MOFs) and coordination polymers have been widely investigated for their gas adsorption and separation properties. However, recent studies have demonstrated that their highly crystalline structures can be used to periodically organize guest molecules and non-structural metal compounds either within their pore voids or by anchoring to their framework architecture. Accordingly, the open framework can act as a matrix for isolating and elucidating the structures of these moieties by X-ray diffraction. This concept has broad scope for development as an analytical tool where obtaining single crystals of a target molecule presents a significant challenge and it additionally offers potential for obtaining insights into chemically reactive species that can be stabilized within the pore network. However, the technique does have limitations and as yet a general experimental method has not been realized. Herein we focus on recent examples in which framework materials have been utilized as a scaffold for ordering molecules for analysis by diffraction methods and canvass areas for future exploration.

Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to realign molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies.

Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method

A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal-organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.