Where is the Oxygen? Structural Analysis of α-Humulene Oxidation Products by the Crystalline Sponge Method

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.

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 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 of Small Molecules by Co-Crystallization

The most reliable method to determine the absolute configuration of chiral molecules is X-ray crystallography, but small molecules can be difficult to crystallize. We report rapid co-crystallization of tetraaryladamantanes with small molecules as different as n-decane to nicotine to produce crystals for X-ray analysis and the assignment of absolute configuration when the molecules are chiral. A screen of 52 diverse compounds gave inclusion in co-crystals for 88 % of all cases and a high-resolution structure in 77 % of cases. Furthermore, starting from three milligrams of analyte, a combination of NMR spectroscopy and X-ray crystallography produced a full structure in less than three days using an adamantane crystallization chaperone that encapsulates the analyte at room temperature.

Microcrystal Electron Diffraction (MicroED) for Small-Molecule Structure Determination

The development of new methods to analyze and determine molecular structures parallels the ability to accelerate synthetic research. For many decades, single-crystal analysis by X-ray diffraction (SXRD) has been the definitive tool for structural analysis at the atomic level; the drawback, however, is that a suitable single crystal of the analyte needs to be grown. The recent innovation of the crystalline sponge (CS) method allows the microanalysis of compounds simply soaked in a readily prepared CS crystal, thus circumventing the need to screen crystallization conditions while also using only a trace amount of the sample. In this context, electron diffraction for the structure determination of small molecules is discussed as potentially the next big development in this field.

A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis

Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products. Here, we report the identification and biochemical characterization of LphTPS-A, a sesquiterpene synthase from the red macroalga Laurencia pacifica. Using the combination of transcriptomics, sesquiterpene synthase expression in yeast, and microgram-scale nuclear magnetic resonance-coupled crystalline sponge X-ray diffraction analysis, we resolved the absolute stereochemistry of prespatane, the major sesquiterpene product of LphTPS-A, and thereby functionally define LphTPS-A as the first bourbonane-producing sesquiterpene synthase and the first biochemically characterized sesquiterpene synthase from red algae. Our study showcases a workflow integrating multiomics approaches, synthetic biology, and the crystalline sponge method, which is generally applicable for uncovering new terpene chemistry and biochemistry from source-limited living organisms.

Biomimetic Total Synthesis of Hyperjapones A-E and Hyperjaponols A and C

Hyperjapones A-E and hyperjaponols A-C are complex natural products of mixed aromatic polyketide and terpene biosynthetic origin that have recently been isolated from Hypericum japonicum. We have synthesized hyperjapones A-E using a biomimetic, oxidative hetero-Diels-Alder reaction to couple together dearomatized acylphloroglucinol and cyclic terpene natural products. Hyperjapone A is proposed to be the biosynthetic precursor of hyperjaponol C through a sequence of: 1) epoxidation; 2) acid-catalyzed epoxide ring-opening; and 3) a concerted, asynchronous alkene cyclization and 1,2-alkyl shift of a tertiary carbocation. Chemical mimicry of this proposed biosynthetic sequence allowed a concise total synthesis of hyperjaponol C to be completed in which six carbon-carbon bonds, six stereocenters, and three rings were constructed in just four steps.

Bis-Calix[4]arenes: From Ligand Design to the Directed Assembly of a Metal-Organic Trigonal Antiprism

Calix[4]arenes (C[4]s) are versatile platforms for the construction of polymetallic clusters containing paramagnetic metal ions. Synthetic modification at the C[4] methylene bridge allows for the design of bis-C[4]s that, depending on the linker employed, can be used to either dictate which clusters can be formed or direct the assembly of a new metal-organic polyhedron (MOP). The assembly resulting from the latter approach displays thermal stability and uptake of N2 or H2 gas, confirming that this is a viable route to the synthesis of new, functional supramolecular architectures.

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.