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.

Rapid Synthesis of Chiral Figure-Eight Macrocycles Using a Preorganized Natural Product-Based Scaffold.

Chiral D2 -symmetric figure-eight shaped macrocycles are promising scaffolds for amplifying the chiroptical properties of π-conjugated systems. By harnessing the inherent and adaptable conformational dynamics of a chiral C2 -symmetric bispyrrolidinoindoline (BPI) manifold, we developed an enantio-divergent modular synthetic platform to rapidly generate a diverse range of chiral macrocycles, spanning from 14- to 66-membered rings, eliminating the need for optical resolution. Notably, a 32-membered figure-eight macrocycle showed excellent circularly polarized luminescence (CPL: |glum |=1.1×10-2 ) complemented by a robust emission quantum yield (Φfl =0.74), to achieve outstanding CPL brightness (BCPL : ϵ×Φfl ×|glum |/2=480). Using quadruple Sonogashira couplings, this versatile synthetic platform enables precise adjustments of the angle, distance, and length among intersecting π-conjugated chromophores. Our synthetic strategy offers a streamlined and systematic approach to significantly enhance BCPL values for a variety of chiral D2 -symmetric figure-eight macrocycles.

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.

Imprinting Spatial Helicity Structure of Vector Vortex Beam on Spin Texture in Semiconductors.

We present the transfer of the spatially variant polarization of topologically structured light to the spatial spin texture in a semiconductor quantum well. The electron spin texture, which is a circular pattern with repeating spin-up and spin-down states whose repetition rate is determined by the topological charge, is directly excited by a vector vortex beam with a spatial helicity structure. The generated spin texture efficiently evolves into a helical spin wave pattern owing to the spin-orbit effective magnetic fields in the persistent spin helix state by controlling the spatial wave number of the excited spin mode. By tuning the repetition length and azimuthal angle, we simultaneously generate helical spin waves with opposite phases by a single beam.

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.

π-Extended Doublet Open-Shell Graphene Fragments Exhibiting One-Dimensional Chain Stacking.

The hitherto elusive benzo[c]anthanthrenyl radical derivatives composed of seven fused six-membered rings are synthesized and isolated in the crystalline form, representing a laterally π-extended doublet open-shell graphene fragment compared to the phenalenyl and olympicenyl radical structures. X-ray crystallographic analysis revealed one-dimensional chain stacking with relatively close intermolecular contacts, which is an important precondition for achieving single-component conductors. The magnetic, optical, and redox properties are investigated in the solution phase. In combination with the good stability, such open-shell molecular systems have potentials as functional electronic materials.

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.

Photo-conversion of self-assembled structures into continuous covalent structures via [2 + 2]-cycloaddition reactions.

In this study, the conversion of self-assembled structures into continuous polymeric structures by linking the self-assembled molecules using the [2 + 2]-cycloaddition reaction was investigated. Synthesized bio-inspired thymine-based bolaamphiphilic molecules were designed to force the interactions between two molecules to engage two thymines in their self-assembled structure to undergo a cycloaddition reaction. Thymine-based bolaamphiphilic molecules were designed and synthesized using different phenylene spacers based on aromatic substituents (ortho-) (meta-) (para-). The formed self-assembled structures from these molecules were characterized and compared using molecular mechanical simulations. Simulations were performed to discuss the relationship between the inter- and intramolecular cycloaddition sensitivity to different substituents. This study provides a strategy for creating higher molecular weight linear polymers by controlling the photocyclization sites within the self-assembly by spacers between thymines. An intermolecular [2 + 2] cycloaddition reaction of thymine-based bolaamphiphilic molecules proceeded within the self-assembled nano-ribbon-like structure to form the continuous covalent structure.

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.

Synthesis of a Negatively Curved Nanocarbon Molecule with an Octagonal Omphalos via Design-of-Experiments Optimizations Supplemented by Machine Learning.

A saddle-shaped nanocarbon molecule was synthesized, which revealed the existence of negative Gauss curvatures on a >3-nm molecular structure possessing 192 π-electrons. The synthesis was facilitated by a protocol developed with Design-of-Experiments optimizations and machine-learning predictions, and spectroscopy and crystallography were used to reveal the saddle-shaped structure of the molecule. Solution-phase analyses showed the presence of dimeric assembly, and crystallographic analyses revealed the stacked dimeric structures. The stacked crystal structure was scrutinized by various methods, including Gauss curvatures derived from the discrete surface theory of geometry, to reveal the important role of the molecular Gauss curvature in dimeric assembly.

Overcrowded Ethylene-Bridged Nanohoop Dimers: Regioselective Synthesis, Multiconfigurational Electronic States, and Global Hückel/Möbius Aromaticity.

The design and preparation of molecular systems with multiple geometric and electronic configurations are the cornerstones for multifunctional materials with stimuli-responsive behaviors. We describe here the regioselective and facile synthesis of two types of overcrowded ethylene-bridged nanohoop dimers, with folded and twisted geometric structures as well as closed-shell, diradical and dication electronic structures. The strained nanohoop structures have a profound effect on the overall molecular and electronic configurations, which resulted in the destabilized diradical state. X-ray crystallographic analysis revealed the folded molecular geometry for the neutral species and twisted geometry for the dication species. The unique molecular dynamics, optical properties, and dynamic redox properties were disclosed in the solution phase by spectroscopic and electrochemical methods. Furthermore, the global Hückel and Möbius aromaticity were revealed by a combination of experimental and theoretical approaches. Our studies shed light on the design of nanohoop-incorporated multiconfigurational materials with unique topologies and functions.

Cycloparaphenylene-Phenalenyl Radical and Its Dimeric Double Nanohoop*.

The first example of a neutral spin-delocalized carbon-nanoring radical was achieved by integration of the open-shell phenalenyl unit into cycloparaphenylene (CPP). Spin distribution in this hydrocarbon is localized primarily on the phenalenyl segment and partially on the CPP segment as a consequence of steric and electronic effects. The resulting geometry is reminiscent of a diamond ring, with pseudo-perpendicular arrangement of the radial and the planar π-surface. The phenylene rings attached directly to the phenalenyl unit give rise to a steric effect that governs a highly selective dimerization pathway, yielding a giant double nanohoop. Its π-framework made of 158 sp2 -carbon atoms was elucidated by single-crystal X-ray diffraction, which revealed a three-segment CPP-peropyrene-CPP structure. This nanocarbon shows a fluorescence profile characteristic of peropyrene, regardless of which segment gets excited. These results in conjunction with DFT suggest that adjusting the size of the CPP segments in this double nanohoop could deliver donor-acceptor systems.

Chemical Reduction of a Nanosized [6]Cyclo-2,7-naphthylene Macrocycle.

Chemical reduction of a naphthylene macrocycle, [6]cyclo-2,7-naphthylene ([6]CNAP, 1), with alkali metals, Li and K, revealed the accessibility of the doubly-reduced state of 1. The macrocyclic 12- anion was isolated in different coordination environments and crystallographically characterized. The single-crystal X-ray diffraction confirmed the formation of contact-ion complexes with one Li+ and two K+ ions in THF, and a "naked" dianion in the solvent-separated ion product with K+ ions in the presence of 18-crown-6 ether. The detailed structural analysis of 12- showed that the π-conjugation over the biaryl linkages between naphthylene panels were enhanced upon two-fold reduction, which was rationally explained by theoretical calculations.

Fluorescence Enhancement of Aromatic Macrocycles by Lowering Excited Singlet State Energies.

A series of cyclo-meta-phenylene congeners with a variation of interphenylene bridges was synthesized by adopting concise synthetic routes to investigate the structure-fluorescence relationships of macrocycles. With fundamental UV-vis absorption and fluorescence spectra, no unique effect of the macrocyclic structures was noted. However, the fluorescence quantum yields were dramatically affected by the macrocyclic structures and varied at a range of 5-92%. The quantum yields qualitatively depended on the number of the vinylene-bridged phenanthrenylene panels, and the theoretical investigations revealed the energetic and structural effects of the phenanthrenylene panels during nanosecond photodynamic processes. A high energy barrier along the S0/S1 internal conversion path to reach the minimum energy conical intersection was necessary to hamper a nonradiative process, and with the transition state energy level of the excited singlet state being insensitive to macrocyclic structures, a low energy level of excited singlet states (S1MIN) was required to facilitate efficient fluorescence.

Synthesis and stereoisomerism of [n]cyclo-2,9-phenanthrenylene congeners possessing alternating E/Z- and R/S-biaryl linkages.

The synthesis and cyclostereoisomerism of [n]cyclo-2,9-phenanthrenylenes ([n]CPhen2,9, n = 4, 6 and 8), possessing hybrid E/Z- and R/S-biaryl linkages, were elaborated. The dimer of a phenanthrene derivative was used as a starting material and underwent Ni-mediated Yamamoto-type coupling to afford [6]CPhen2,9 as a major cyclic product, as well as [4]CPhen2,9 and [8]CPhen2,9 as minor products. The stereoisomers of [n]CPhen2,9 were isolated and characterized, and the number of stereoisomers indicated that E/Z linkages did not provide any experimentally separable isomers, whereas the chirality in [n]CPhen2,9 originated from the intrinsic axial chirality at constrained R/S linkages. Theoretical calculations predicted that the 2,2'-linkages in [n]CPhen2,9 adopted a fixed Z- or E-configuration, which suggested a novel type of dynamics of atropisomerism in contrast to the reported rigid or flexible behavior. This study enriches our understanding of the stereochemical features of E/Z linkages in aromatic macrocycles.

Chiral intertwined spirals and magnetic transition dipole moments dictated by cylinder helicity.

The presence of anomalous chirality in a roll of graphitic carbon sheets has been recognized since the discovery of carbon nanotubes, which are becoming available in higher quantities through the isolation of chiral single-wall congeners with high purity. Exploration of the properties arising from cylinder chirality is expected to expand the scope of tubular entities in the future. By studying molecular fragments of helical carbon nanotubes, we herein reveal interesting properties that arise from this chirality. The chirality of nanoscale cylinders resulted in chirality of larger dimensions in the form of a double-helix assembly. Cylinder chirality in solution gave rise to a large dissymmetry factor of metal-free entities in circular polarized luminescence. Theoretical investigations revealed the pivotal role of cylindrical shapes in enhancing magnetic dipole transition moments to yield extreme rotatory strength. Unique effects of cylinder chirality in this study may prompt the development of tubular entities, for instance, toward chiroptical applications.

Ineffective OH Pinning of the Flipping Dynamics of a Spherical Guest within a Tight-Fitting Tube.

A supramolecular/synthetic method has been devised to affix a sterically hindered substituent onto a fullerene guest encapsulated in a tubular host. A two-wheeled complex of (C59 N)-(C59 N) with a tubular host was oxidatively bisected to afford a C59 N+ cation captured in the tube. The C59 N+ cation in the tube was then trapped by ethanol or water, which led to an oxy substituent pinned on the guest. The guest motions within the tube were modulated by the pinned substituent, and up-and-down flipping motions were halted by an ethoxy substituent. A hydroxy substituent, however, was ineffective in halting the flipping motions, despite the tight-fitting relationship between the tubular host and the spherical guest. Theoretical calculations of the dynamics revealed that the flipping motions were assisted by OH-π hydrogen bonds between the guest and the carbon-rich wall and that sliding motions of the OH group were also facilitated by deformations of the tube.

Synthesis of a Hemispherical Geodesic Phenine Framework by a Polygon Assembling Strategy.

A synthetic strategy to construct large geodesic structures of phenine (1,3,5-trisubstituted benzene) was devised. In this strategy, five pentagons were assembled on an omphalos pentagon, and bridging peripheral pentagons furnished five additional hexagons. Thirty phenine units were synthetically assembled to afford a large C220 H180 molecule with a phenine framework isoreticular to a hemispherical, bisected segment of C60 . Although a hemispherical structure of the phenine framework was suggested by solution-phase NMR spectra, crystallographic analysis revealed an oval-like deformation of the molecular shape. In-depth structural analyses, including theoretical calculations, showed that structural fluctuations observed as variations in the biaryl torsion angles allowed structural deformations and, at the same time, that the dynamic fluctuations resulted in the spectroscopic observation of a hemisphere as a time-averaged structure.

A Simple Ex Vivo Semiquantitative Fluorescent Imaging Utilizing Planar Laser Scanner: Detection of Reactive Oxygen Species Generation in Mouse Brain and Kidney.

OBJECTIVE: Oxidative stress plays an important role in the onset of many neuronal and peripheral disorders. We examined the feasibility of obtaining semiquantitative fluorescent images of reactive oxygen species (ROS) generation in mouse brain and kidney utilizing a planar laser scanner and dihydroethidium (DHE). METHODS: To investigate ROS generation in brain, sodium nitroprusside was injected into the striatum. Dihydroethidium was injected into the tail vein. After DHE injection, tissue slices were analyzed utilizing a planar laser scanner. For kidney study, cis-diamminedichloroplatinum [II] (cisplatin) was intraperitoneally administrated into mice. RESULTS: Clear and semiquantitative fluorescent images of ROS generation in the mouse brain and kidney were obtained. Furthermore, the fluorescence intensity was stable and not affected by fading. Sodium nitroprusside induced approximately 6 times the fluorescence accumulation in the brain. Cisplatin caused renal injury in all mice, and in comparison with control mice, more than 10 times fluorescence accumulation was observed in the renal medulla with tubular necrosis and vacuolization. CONCLUSIONS: We successfully obtained ex vivo semiquantitative fluorescent images of ROS generation utilizing a planar laser scanner and DHE. This simple method is useful for ROS detection in several ROS-related animal models and would be applicable to a variety of biochemical processes.