Functional Plasticity of a Viral Terpene Synthase, OILTS, that Shows Non-Specific Metal Cofactor Binding and Metal-Dependent Biosynthesis.

OILTS is a viral class I terpene synthase found from the giant virus Orpheovirus IHUMI-LCC2. It exhibits a unique structure and demonstrates high plasticity to metal cofactors, allowing it to biosynthesize different cyclic terpene frameworks. Notably, while OILTS produces only (+)-germacrene D-4-ol with the most common cofactor, Mg2+, it also biosynthesizes a different cyclic terpene, (+)-cubebol, with Mn2+, Co2+, or Ni2+, presenting a rare instance of cofactor-dependent enzyme catalysis. This is the first report of (+)-cubebol biosynthesis, to our knowledge. In addition, OILTS can uptake Zn2+ as a cofactor, which is uncommon among ordinary terpene synthases. These findings suggest that OILTS's functional plasticity may benefit the virus in diverse host environments, highlighting potential evolutionary implications.

Conformational Analysis of (+)-Germacrene D-4-ol Using the Crystalline Sponge Method to Elucidate the Origin of its Instability.

Unsaturated cyclic terpenes often exhibit instability due to the proximation of C=C bonds in the cyclic skeleton, leading to nonenzymatic degradation. In this study, the crystalline sponge (CS) method was employed for the X-ray conformational analysis of a minute amount of oily and cyclic terpene compound, (+)-germacrene D-4-ol, which was produced by a terpene synthase OILTS under in vitro conditions. The CS method revealed a reactive conformation of the cyclic terpene with proximal double bonds. Under weakly acidic in vivo conditions, OILTS gave four pseudo-natural products or artifacts. The CS method also elucidated the structures of these degraded compounds, proposing a degradation mechanism triggered by the transannular reactions.

Selective Synthesis and Functionalization of an Acyclic Methylene-Bridged-Arene Trimer in a Cage.

Arene-formaldehyde condensation is a versatile reaction for producing various oligomeric/polymeric materials. However, the precise control of oligomerization degree is still challenging because the starting materials and intermediates have similar reactivities. Here, we demonstrate the selective synthesis of a methylene-bridged arene trimer using the confined cavity of a coordination cage. The limited space of the cavity prevents unregulated polymerization. The confinement effect for the kinetic protection is also demonstrated by the subsequent site-selective iodination of the trimer product within the cage.

Chemical Site-Differentiation of Calix[4]arenes through Enforced Conformations by Confinement in a Cage.

Desymmetrization of a symmetric skeleton enables late-stage functionalization of molecules. However, reagent-controlled desymmetrization by site-selective reactions of symmetric molecules remains a difficult synthetic strategy. Here, we found that complete confinement of a symmetric molecule within a coordination cage can desymmetrize the guest conformation, making it possible to site-selectively activate or protect the otherwise equivalent reaction sites of calix[4]arene derivatives. Multistep, one-cage reactions also demonstrated the transformation of an AAAA-type calix[4]arene into a lower symmetry ABAC-type one.

Tetradehydro-Diels-Alder Reactions of Flexible Arylalkynes via Folding Inside a Molecular Cage.

The tetradehydro-Diels-Alder (TDDA) reaction is a useful transformation for the rapid assembly of polycyclic scaffolds from simple linear precursors in a single synthetic step. However, the reaction requires careful substrate design and harsh reaction conditions to overcome the inherent entropic cost for this transformation. Herein we report an efficient site-selective TDDA transformation within a self-assembled Pd6L4 cage. Despite the large size, the flexibility of the employed substrates allows for efficient encapsulation within the host cavity. The rate of thermal cyclization of the encapsulated guest was found to be greatly enhanced, and high product selectivity for an unsymmetrical substrate was observed. The efficiency of this system relies on the precise conformational control of the substrate within the confined space of the host cage.

Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome.

Giant viruses are nonstandard viruses with large particles and genomes. While previous studies have shown that their genomes contain various sequences of interest, their genes related specifically to natural product biosynthesis remain unexplored. Here we analyze the function and structure of a terpene synthase encoded by the gene of a giant virus. The enzyme is phylogenetically separated from the terpene synthases of cellular organisms; however, heterologous gene expression revealed that it still functions as a terpene synthase and produces a cyclic terpene from a farnesyl diphosphate precursor. Crystallographic analysis revealed its protein structure, which is relatively compact but retains essential motifs of the terpene synthases. We thus suggest that like cellular organisms, giant viruses produce and utilize natural products for their ecological strategies.

X-ray and Electron Diffraction Observations of Steric Zipper Interactions in Metal-Induced Peptide Cross-ß Nanostructures.

The steric zipper is a common hydrophobic packing structure of peptide side chains that forms between two adjacent ß-sheet layers in amyloid and related fibrils. Although previous studies have revealed that peptide fragments derived from native protein sequences exhibit steric zipper structures, their de novo designs have rarely been studied. Herein, steric zipper structures were artificially constructed in the crystalline state by metal-induced folding and assembly of tetrapeptide fragments Boc-3pa-X1-3pa-X2-OMe (3pa: ß-(3-pyridyl)-l-alanine; X1 and X2: hydrophobic amino acids). Crystallographic studies revealed two types of packing structures, interdigitation and hydrophobic contact, that result in a class 1 steric zipper geometry when the X1 and X2 residues contain alkyl side chains. Furthermore, a class 3 steric zipper geometry was also observed for the first time among any reported steric zippers when using tetrapeptide fragments with (X1, X2) = (Thr, Thr) and (Phe, Leu). The system could also be extended to a knob-hole-type zipper using a pentapeptide sequence.

[M8L4]8+-Type Squares Self-Assembled by Dipalladium Corners and Bridging Aromatic Dipyrazole Ligands for Iodine Capture.

Square-like metallamacrocyclic palladium(II) complexes [M8L4]8+ (1-7) were synthesized by reacting aromatic dipyrazole ligands (H2L1-H2L3 with pyromellitic arylimide-, 1,4,5,8-naphthalenetetracarboxylic arylimide-, and anthracene-based aromatic groups, respectively) with dipalladium corners ([(bpy)2Pd2(NO3)2](NO3)2, [(dmbpy)2Pd2(NO3)2](NO3)2, or [(phen)2Pd2(NO3)2](NO3)2, where bpy = 2,2'-bipyridine, dmbpy = 4,4'-dimethyl-2,2'-bipyridine, and phen = 1,10-phenanthroline) in aqueous solutions via metal-directed self-assembly. Metallamacrocycles 1-7 were fully characterized by 1H and 13C nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry, and the square structure of 7·8NO3- was further confirmed via single crystal X-ray diffraction. These square-like metallamacrocycles exhibit effective performance for iodine adsorption.

[A Case of Primary Liver Cancer and Gastric Glomus Tumor Diagnosed Preoperatively and Treated with Liver Segmentectomy and Local Gastrectomy].

A man in his 70s was concurrently suspected of having a submucosal tumor(SMT)of the stomach and a liver tumor during a medical examination. Abdominal contrast-enhanced CT scan revealed S8 hepatocellular carcinoma(HCC)and an SMT of the stomach, which was strongly enhanced from the early to the later phase. Upper gastrointestinal endoscopy revealed a 20 mm SMT in the antrum of the stomach. Endoscopic ultrasonography showed a hyperechoic tumor in the fourth layer of the gastric wall. T2-weighted MRI showed a 25 mm SMT in the antrum of the stomach with a faint high signal intensity compared with that of the gastric wall. The patient was diagnosed with HCC and gastric glomus tumor, and a liver segmentectomy and a local gastrectomy were performed. Immunohistochemistry of the SMT revealed the expression of α-SMA but no expression of desmin, c-kit, CD34, or S-100. Therefore, a diagnosis of a Glomus tumor of the stomach was made. Gastric Glomus tumors are very rare; therefore, we have reviewed some citations and would like to discuss our case.

Interconversion of Highly Entangled Polyhedra into Concave Polyhedra by Nitrate-Induced Ternary Coordination.

Entangled (M3 L2 )n polyhedral complexes represent a unique class of supramolecular architectures that are stabilized by relatively weak metal-acetylene interactions in cooperation with conventional metal-pyridyl coordination. Counter-anion exchange of these complexes with a nitrate (NO3 - ) ion triggered formal metal insertion between the metal centers, and a heteroleptic ternary coordination mode with acetylenic, pyridyl, and nitrate donors was generated on the metal centers. As a result, the main frameworks of the polyhedral complexes M18 L12 and M12 L8 were formally extended into a new series of concave polyhedra having the compositions M21 L12 and M13 L8 , respectively. This transformation also resulted in the local disconnection of the highly entangled trifurcate topology of the framework, providing clues toward the skeletal editing of extended and complex three-dimensional (3D) architectures.

Synthetic Modulation of an Unstable Dehydrosecodine-type Intermediate and Its Encapsulation into a Confined Cavity Enable Its X-ray Crystallographic Observation.

Numerous indole alkaloids such as the iboga- and aspidosperma-type are believed to be biosynthesized via a common hypothetical intermediate, dehydrosecodine. The highly reactive nature of dehydrosecodine-type compounds has hampered their isolation and structural elucidation. In this study, we achieved the first X-ray structural determination of a dehydrosecodine-type compound by integrating synthetic optimization of the reactivity and stabilizing the fragile molecule by encapsulation into a supramolecular host. Formation of a 1 : 1 complex of the dehydrosecodine-type labile guest bearing both vinyl indole and dihydropyridine units with the host was observed. This integrated approach not only provides insights into the biosynthetic conversions but also allows stabilization and storage of the reactive and otherwise short-lived intermediate within the confined hydrophobic cavity.

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.

A self-assembled coordination cage enhances the reactivity of confined amides via mechanical bond-twisting.

Self-assembled coordination cages composed of metal cations and ligands can enhance the hydrolysis of non-covalently trapped amides in mild conditions as demonstrated in recent experiments. Here, we reveal the mechanism that accelerates base-catalyzed amide hydrolysis inside the octahedral coordination cage, by means of a quantum mechanics/molecular mechanics/polarizable continuum model. The calculated activation barrier of the nucleophilic OH- addition to a planar diaryl amide drastically decreases in the cage because of mechanical bond-twisting due to host-guest π-stacking. By contrast, the OH- addition to an N-acylindole, which possesses a twisted amide bond in bulk water, is not enhanced in the cage. Even though the cage hinders OH- collisions with the confined amide, the cage can twist the dihedral angle of the planar amide so as to mimic the transition state of OH- addition.

Self-assembly of tetravalent Goldberg polyhedra from 144 small components.

Rational control of the self-assembly of large structures is one of the key challenges in chemistry, and is believed to become increasingly difficult and ultimately impossible as the number of components involved increases. So far, it has not been possible to design a self-assembled discrete molecule made up of more than 100 components. Such molecules-for example, spherical virus capsids-are prevalent in nature, which suggests that the difficulty in designing these very large self-assembled molecules is due to a lack of understanding of the underlying design principles. For example, the targeted assembly of a series of large spherical structures containing up to 30 palladium ions coordinated by up to 60 bent organic ligands was achieved by considering their topologies. Here we report the self-assembly of a spherical structure that also contains 30 palladium ions and 60 bent ligands, but belongs to a shape family that has not previously been observed experimentally. The new structure consists of a combination of 8 triangles and 24 squares, and has the symmetry of a tetravalent Goldberg polyhedron. Platonic and Archimedean solids have previously been prepared through self-assembly, as have trivalent Goldberg polyhedra, which occur naturally in the form of virus capsids and fullerenes. But tetravalent Goldberg polyhedra have not previously been reported at the molecular level, although their topologies have been predicted using graph theory. We use graph theory to predict the self-assembly of even larger tetravalent Goldberg polyhedra, which should be more stable, enabling another member of this polyhedron family to be assembled from 144 components: 48 palladium ions and 96 bent ligands.

Selective Confinement of Rare-Earth-Metal Hydrates by a Capped Metallo-Cage under Aqueous Conditions.

The properties of rare-earth-metal ions in aqueous media often depend on their various hydration modes, which allow them to exist as monomeric or oligomeric species with different coordination numbers. Capturing rare-earth-metal ions in a confined cavity can fix their hydration modes and thus enable their intrinsic properties to be distinguished. However, the isolation of ionic species from bulk aqueous media is not an easy task due to competitive interaction with bulk water. Here, we report the encapsulation of hydrated rare-earth-metal ions in a hydrophobic cavity of a synthetic cage. Cap-like counter anions located at the cage's portals play an important role in capturing the rare-earth metals at a fixed position via electrostatic interactions. Preferential encapsulation of early lanthanoid (III) ions was observed even though all the rare-earth metals have the same hydration number and geometry, as visualized by the competitive inclusion of a dye molecule. Accordingly, the early lanthanoid ion was selectively extracted from a mixture of two rare-earth-metal ions.

Electrophilic Spirocyclization of a 2-Biphenylacetylene via Conformational Fixing within a Hollow-Cage Host.

A 2-biphenylacetylene was fixed into a specific conformation within the confined cavity of a hollow cage, where it underwent a regioselective spirocyclization in the presence of an electrophile. A 5-endo-dig cyclization proceeded selectively in the cage, which stands in sharp contrast to the 6-endo-dig cyclization that normally occurs in common organic media. The folded conformation adopted by the substrate within the cage was examined by 1 H NMR spectroscopy and X-ray crystallographic analysis.

A Highly Entangled (M3L2)8 Truncated Cube from the Anion-Controlled Oligomerization of a π-Coordinated M3L2 Subunit.

The cooperation of weak acetylene π-coordination and relatively strong metal-heteroatom coordination has emerged as a promising strategy for the construction of highly complex but well-ordered nanostructures. Here, we report the formation of an (M3L2)8 truncated cube (M = AgI) via the oligomerization of an M3L2 subunit stabilized by the secondary π-coordination of an acetylene spacer. This large framework cannot be obtained directly from its components (M and L) but is instead formed by counteranion exchange (BF4- to NO3-) of the presynthesized smallest oligomer, the dimeric (M3L2)2 cage. Single-crystal X-ray diffraction analyses revealed that the cubic framework of (M3L2)8 exhibits a π-coordination-supported highly entangled structure, which is formally constructed via alternation of the cubic corners and edges with helical M3L2 subunits and double lines with two twists, respectively. This observation enabled us to understand the complicated structures of the series of (M3L2)n polyhedral cages (n = 2, 4, 6, 8) as a fundamentally new type of molecular entanglements based on trifurcate motifs, which can be obtained selectively by adjusting the self-assembly conditions.

Metal-Peptide Nonafoil Knots and Decafoil Supercoils.

Despite the frequent occurrence of knotted frameworks in protein structures, the latent potential of peptide strands to form entangled structures is rarely discussed in peptide chemistry. Here we report the construction of highly entangled molecular topologies from Ag(I) ions and tripeptide ligands. The efficient entanglement of metal-peptide strands and the wide scope for design of the amino acid side chains in these ligands enabled the construction of metal-peptide 91 torus knots and 1012 torus links. Moreover, steric control of the peptide side chain induced ring opening and twisting of the torus framework, which resulted in an infinite toroidal supercoil nanostructure.

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.