The Crystalline Sponge Method in Water

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.

Crystal Engineering of a Chiral Crystalline Sponge That Enables Absolute Structure Determination and Enantiomeric Separation

Chiral metal-organic materials (CMOMs), can offer molecular binding sites that mimic the enantioselectivity exhibited by biomolecules and are amenable to systematic fine-tuning of structure and properties. Herein, we report that the reaction of Ni(NO₃)₂, S-indoline-2-carboxylic acid (S-IDECH), and 4,4'-bipyridine (bipy) afforded a homochiral cationic diamondoid, dia, network, [Ni(S-IDEC)(bipy)(H₂O)][NO₃], CMOM-5. Composed of rod building blocks (RBBs) cross-linked by bipy linkers, the activated form of CMOM-5 adapted its pore structure to bind four guest molecules, 1-phenyl-1-butanol (1P1B), 4-phenyl-2-butanol (4P2B), 1-(4-methoxyphenyl)ethanol (MPE), and methyl mandelate (MM), making it an example of a chiral crystalline sponge (CCS). Chiral resolution experiments revealed enantiomeric excess, ee, values of 36.2-93.5%. The structural adaptability of CMOM-5 enabled eight enantiomer@CMOM-5 crystal structures to be determined. The five ordered crystal structures revealed that host-guest hydrogen-bonding interactions are behind the observed enantioselectivity, three of which represent the first crystal structures determined of the ambient liquids R-4P2B, S-4P2B, and R-MPE.

The benefits of Cu Kβ radiation for the single-crystal X-ray structure determination of crystalline sponges

The crystalline sponge method facilitates the X-ray structure determination of samples that do not crystallize or are too sparsely available to afford viable crystallization. By including these materials in a metal-organic framework, the structure of the guest molecules can be determined. Some of the inherent difficulties of this method are discussed and the use of Cu Kβ radiation is presented as a simple and effective means to improve the quality of the diffraction data that can be obtained from a sponge crystal.

Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes

Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.

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.

Guest-protein incorporation into solvent channels of a protein host crystal (hostal)

Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.

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.

Tuning dimensionality between 2D and 1D MOFs by lanthanide contraction and ligand-to-metal ratio

2D/1D dimensionality tuning in LnMOFs is related to both (i) ligand-to-metal ratio and (ii) lanthanide contraction, this is only possible with Er/Tm, lighter lanthanides e.g. Pr only produced 2D MOFs, despite different ligand-to-metal ratios were used.

Elucidating pore chemistry within metal–organic frameworks via single crystal X-ray diffraction; from fundamental understanding to application

The application of metal–organic frameworks (MOFs) to diverse chemical sectors is aided by their crystallinity, which permits the use of X-ray crystallography to characterise their pore chemistry and provides invaluable insight into their properties.

An Expansion of Crystalline Sponge X-ray Analysis to Elucidate the Molecular Structure of Reactive Compounds via Ion Pair Formation

The crystalline sponge (CS) method allows structural elucidation of a target compound (guest) in solution by single crystal X-ray diffraction through trapping the guest into the CS framework. In principle, the CS method is inapplicable to reactive compounds that break the CS framework, such as acidic, basic, or nucleophilic ones. Here, a solution to this problem is disclosed wherein an ion pair of the guest compound is formed during the guest-soaking step by adding a suitable reagent. The ion pair can be observed and does not damage the CS framework. Using the developed method, amino, guanidino, and amidino compounds have been successfully analyzed as ion pairs with sulfonic acids. Practical utility has been shown because the absolute configurations of optically resolved amine derivatives were revealed with only a few micrograms. This demonstrates that the ion-pair-soaking method is simple and expands the range of compounds applicable to the CS method.