Determination of the absolute configuration of compounds bearing chiral quaternary carbon centers using the crystalline sponge method

Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation

Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.

Absolute configuration determination of pharmaceutical crystalline powders by MicroED via chiral salt formation

Microcrystal electron diffraction (MicroED) has established its complementary role alongside X-ray diffraction in crystal structure elucidation. Unfortunately, kinematical refinement of MicroED data lacks the differentiation power to assign the absolute structure solely based on the measured intensities. Here we report a method for absolute configuration determination via MicroED by employing salt formation with chiral counterions.

Crystalline Sponge Method by Three-Dimensional Electron Diffraction

The crystalline sponge method has shown to be a novel strategy for the structure determination of noncrystalline, oily, or trace amount of a compound. A target compound was absorbed and oriented orderly in the pregrown porous crystal for x-ray diffraction analysis. However, the diffusion in the micron-sized crystals is rather difficult. Lots of trial-and-error experiments are needed to optimize the guest-soaking process and to improve data quality. Nanocrystals are better in diffusion, yet it could not conduct a single crystal x-ray diffraction (SCXRD) analysis. Three-dimensional electron diffraction (3D-ED) is a powerful diffraction tool for the structure determination of small crystals. In this work, we successfully carried out the crystalline sponge method by 3D-ED technique using {(ZnI2)3-[2,4,6-tris(4-pyridyl)-1,3,5-triazine]2·x(guest)}n (1-Guest) porous complex nanocrystals. On account of the better diffuse ability of nanocrystals, the time needed for solvent exchange and guest soaking protocols are shortened 50-fold faster versus the original protocol. The crystal structure of the crystalline sponge incorporated with three different guests was fully resolved using a merged dataset. The structure model was identical to previously reported ones using x-ray, showing that the accuracy of the 3D-ED was comparable with SCXRD. The refinement results can also give the precise occupancy of the guest molecule soaked in the porous crystal. This work not only provides a new data collection strategy for crystalline sponge method but also demonstrates the potential of 3D-ED techniques to study host-guest interaction by solving the fine structure of porous material.

Comprehensive Structural Analysis of the Bitter Components in Beer by the HPLC-Assisted Crystalline Sponge Method

Trans-iso-α-acid is one of the main contributors to the bitter taste of fresh beer and is known to transform into various derivatives during beer aging. However, structural characterization of the derivatives has been a challenging task because of the formation of too many components. Herein, we report that most of the transformation products of trans-iso-α-acid, isolated in this study in only small quantities by HPLC, can be structurally analyzed with the crystalline sponge method. Thirteen compounds, including eight that were previously unreported, have been successfully isolated and analyzed with complete assignment of their absolute configuration. This provides an improved understanding of the chemical transformations that occur during beer aging.

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.

Absolute Configuration Determination from Low ee Compounds by the Crystalline Sponge Method. Unusual Conglomerate Formation in a Pre-Determined Crystalline Lattice

When chiral compounds with low enantiomeric excess (ee, R:S=m:n) were absorbed into the void of the crystalline sponge (CS), enantiomerically pure [(R)_m (S)_n ] chiral composites were formed, changing the centrosymmetric space group into non-centrosymmetric one. The absolute configuration of the analyte compounds was elucidated with a reasonable Flack (Parsons) parameter value. This phenomenon is characteristic to the "post-crystallization" in the pre-determined CS crystalline lattice, seldom found in common crystallization where the crystalline lattice is defined by an analyte itself. The results highlight the potential of the CS method for absolute configuration determination of low ee samples, an often encountered situation in asymmetric synthesis studies.

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.

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.

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.

Stepwise Evolution of Molecular Nanoaggregates Inside the Pores of a Highly Flexible Metal-Organic Framework

The crystalline sponge method (CSM) is primarily used for structural determination by single-crystal X-ray diffraction of a single analyte encapsulated inside a porous MOF. As the host-guest systems often show severe disorder, reliable crystallographic determination is demanding; thus the dynamics of the guest entering and the formation of nanoconfined molecular aggregates has not been in the spotlight. Now, the concept is investigated of the CSM for monitoring the structural evolution of nanoconfined supramolecular aggregates of eugenol guests with displacement of DMF inside the cavities of the flexible MOF, PUM168. The interpretation of the electron density provides a series of unique detailed snapshots depicting the supramolecular guest aggregation, thus showing the tight interplay between the host flexible skeleton and the molecular guests through the DMF-to-eugenol exchange process.

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.

Assigning the Absolute Configurations of Chiral Primary Amines Based on Experimental and DFT-Calculated 19F Nuclear Magnetic Resonance

In this work, a novel method for assigning the absolute configuration of a chiral primary amine has been developed based on the experimental and DFT-calculated 19F NMR chemical shift differences of its derived two fluorinated amides by reacting with two enantiomers of a chiral derivatizing agent FPP (α-fluorinated phenylacetic phenylselenoester) separately. Comparing the experimental chemical shift difference Δ δ α - F R , S of (R)-FPA-amide/(S)-FPA-amide with the calculated Δδα-F R,S of (R)-FPA-(R)-amide/(S)-FPA-(R)-amide, if the experimental Δδα-F R,S has the same symbol (positive or negative) as one of the theoretical Δδα-F R,S , the assigned configuration of the amine is considered to be consistent with the theoretical one. Our method could be applied to a broad substrate scope avoiding wrong conclusion due to empirical judgment.

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.

Enantioselective synthesis of tetrahydrocyclopenta[b]indole bearing a chiral quaternary carbon center via Pd(ii)–SPRIX-catalyzed C–H activation

Pd(ii)–SPRIX promotes the first highly enantioselective cyclization of 3-alkenylindoles into the corresponding indoles bearing a chiral quaternary carbon center via C–H activation and an assisting effect by the allyl substituent.