A Steric-Repulsion-Driven Clutch Stack of Triaryltriazines: Correlated Molecular Rotations and a Thermoresponsive Gearshift in the Crystalline Solid.

We report that a newly developed type of triaryltriazine rotor, which bears bulky silyl moieties on the para position of its peripheral phenylene groups, forms a columnar stacked clutch structure in the crystalline phase. The phenylene units of the crystalline rotors display two different and interconvertible correlated molecular motions. It is possible to switch between these intermolecular geared rotational motions via a thermally induced crystal-to-crystal phase transition. Variable-temperature solid-state 2H NMR measurements and X-ray diffraction studies revealed that the crystalline rotor is characterized by a vertically stacked columnar structure upon introducing a bulky Si moiety with bent geometry as the stator. The structure exhibits correlated flapping motions via a combination of 85° and ca. 95° rotations between 295 and 348 K, concurrent with a negative entropy change (ΔS‡ = -23 ± 0.3 cal mol-1 K-1). Interestingly, heating the crystal beyond 348 K induces an anisotropic expansion of the column and lowers the steric congestion between the adjacent rotators, thus altering the correlated motions from a flapping motion to a correlated 2-fold 180° rotation with a lower entropic penalty (ΔS‡ = -14 ± 0.5 cal mol-1 K-1). The obtained results of our study suggest that the intermolecular stacking of the C3-symmetric rotator driven by the steric repulsion of the bulky stator represents a promising strategy for producing various correlated molecular motions in the crystalline phase. Moreover, direct and reversible modulation of the intermolecularly correlated rotation is achieved via a thermally induced crystal-to-crystal phase transition, which operates as a gearshift function at the molecular level.

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals.

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

Vapor-Induced Assembly of a Platinum(II) Complex Loaded on Layered Double Hydroxide Nanoparticles.

Controlled self-assembly of PtII complexes is key to the development of optical and stimuli-responsive materials, but designing and precisely controlling them is still difficult owing to weak intermolecular interactions. Herein, we report the successful water-vapor-induced assembly of an anionic PtII complex [Pt(CN)2 (ppy)]- (Hppy=2-phenylpyridine) electrostatically loaded onto cationically charged layered double hydroxide (LDH) nanoparticles consisting of Mg2+ and Al3+ ions. When the PtII complexes were densely loaded onto the LDH nanoparticles, the assembly was maintained, even in dilute aqueous media. In the case of sparse loading, the PtII complexes were loaded discretely in the dry state; however, when water vapor was adsorbed, the increased mobility of the PtII complexes led to their assembly on the LDH nanoparticles. The presence of water vapor led to a drastic change in luminescence from green to orange.

Vapor-Induced Assembly of a Platinum(II) Complex Loaded on Layered Double Hydroxide Nanoparticles.

Invited for the cover of this issue is the group of Masaki Yoshida and Masako Kato at Hokkaido University/Kwansei Gakuin University. The image depicts the changes in the assembly of PtII complexes with humidity on layered double hydroxide (LDH) nanoparticles, resulting in a drastic emission color change from green to orange. Read the full text of the article at 10.1002/chem.202301993.

Direct observation of ligand migration within human hemoglobin at work.

Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and ß subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), ß15Trp(A12), and ß71Phe(E15). We also observe electron density evidence for the distal histidine [α58/ß63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in ß subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or ß subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.

Giant Crystalline Molecular Rotors that Operate in the Solid State.

Molecular motion in the solid state is typically precluded by the highly dense environment, and only molecules with a limited range of sizes show such dynamics. Here, we demonstrate the solid-state rotational motion of two giant molecules, i.e., triptycene and pentiptycene, by encapsulating a bulky N-heterocyclic carbene (NHC) Au(I) complex in the crystalline media. To date, triptycene is the largest molecule (surface area: 245 Å2 ; volume: 219 Å3 ) for which rotation has been reported in the solid state, with the largest rotational diameter among reported solid-state molecular rotors (9.5 Å). However, the pentiptycene rotator that is the subject of this study (surface area: 392 Å2 ; volume: 361 Å3 ; rotational diameter: 13.0 Å) surpasses this record. Single-crystal X-ray diffraction analyses of both the developed rotors revealed that these possess sufficient free volume around the rotator. The molecular motion in the solid state was confirmed using variable-temperature solid-state 2 H spin-echo NMR studies. The triptycene rotor exhibited three-fold rotation, while temperature-dependent changes of the rotational angle were observed for the pentiptycene rotor.

X-ray fluorescence holography of biological metal sites: Application to myoglobin.

X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.

Molecular mechanism of photoactivation of a light-regulated adenylate cyclase.

The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light- and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.

Saturated Fatty Acids Undergo Intracellular Crystallization and Activate the NLRP3 Inflammasome in Macrophages.

OBJECTIVE: Inflammation provoked by the imbalance of fatty acid composition, such as excess saturated fatty acids (SFAs), is implicated in the development of metabolic diseases. Recent investigations suggest the possible role of the NLRP3 (nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3) inflammasome, which regulates IL-1ß (interleukin 1ß) release and leads to inflammation, in this process. Therefore, we investigated the underlying mechanism by which SFAs trigger NLRP3 inflammasome activation. APPROACH AND RESULTS: The treatment with SFAs, such as palmitic acid and stearic acid, promoted IL-1ß release in murine primary macrophages while treatment with oleic acid inhibited SFA-induced IL-1ß release in a dose-dependent manner. Analyses using polarized light microscopy revealed that intracellular crystallization was provoked in SFA-treated macrophages. As well as IL-1ß release, the intracellular crystallization and lysosomal dysfunction were inhibited in the presence of oleic acid. These results suggest that SFAs activate NLRP3 inflammasome through intracellular crystallization. Indeed, SFA-derived crystals activated NLRP3 inflammasome and subsequent IL-1ß release via lysosomal dysfunction. Excess SFAs also induced crystallization and IL-1ß release in vivo. Furthermore, SFA-derived crystals provoked acute inflammation, which was impaired in IL-1ß-deficient mice. CONCLUSIONS: These findings demonstrate that excess SFAs cause intracellular crystallization and subsequent lysosomal dysfunction, leading to the activation of the NLRP3 inflammasome, and provide novel insights into the pathogenesis of metabolic diseases.

Shape Rememorization of an Organosuperelastic Crystal through Superelasticity-Ferroelasticity Interconversion.

As altering permanent shapes without loss of material function is of practical importance for material molding, especially for elastic materials, shape-rememorization ability would enhance the utility of elastic crystalline materials. Since diffusionless plastic deformability can preserve the crystallinity of materials, the interconversion of diffusionless mechanical deformability between superelasticity and ferroelasticity could enable shape rememorization of superelastic single crystals. This study demonstrates the shape rememorization of an organosuperelastic single crystal of 1,4-dicyanobenzene through time-reversible interconversion of superelasticity-ferroelasticity relaxation by holding the mechanically twinned crystal without heating. The shape-rememorization ability of the organosuperelastic crystal indicates the compatibility of superelasticity (antiferroelasticity) and ferroelasticity as well as the intrinsic workability of organic crystalline materials capable of recovering their crystal functions under mild conditions.

Protein crystallography beamline BL2S1 at the Aichi synchrotron.

The protein crystallography beamline BL2S1, constructed at one of the 5 T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7-17 keV (1.8-0.7 Å) with an asymmetric-cut curved single-crystal monochromator [Ge(111) or Ge(220)], and a platinum-coated Si mirror is used for vertical focusing and as a higher-order cutoff filter. The beamline is equipped with a single-axis goniometer, a CCD detector, and an open-flow cryogenic sample cooler. High-pressure protein crystallography with a diamond anvil cell can also be performed using this beamline.

Cooling dynamics of self-assembled monolayer coating for integrated gold nanocrystals on a glass substrate.

Picosecond time-resolved X-ray diffraction has been used to study the nanoscale thermal transportation dynamics of bare gold nanocrystals and thiol-based self-assembled monolayer (SAM)-coated integrated gold nanocrystals on a SiO2 glass substrate. A temporal lattice expansion of 0.30-0.33% was observed in the bare and SAM-coated nanocrystals on the glass substrate; the thermal energy inside the gold nanocrystals was transported to the contacted substrate through the gold-SiO2 interface. The interfacial thermal conductivity between the single-layered gold nanocrystal film and the SiO2 substrate is estimated to be 45 MW m(-2) K(-1) from the decay of the Au 111 peak shift, which was linearly dependent on the transient temperature. For the SAM-coated gold nanocrystals, the thermal dissipation was faster than that of the bare gold nanocrystal film. The thermal flow from the nanocrystals to the SAM-coated molecules promotes heat dissipation from the laser-heated SAM-coated gold nanocrystals. The thermal transportation of the laser-heated SAM-coated gold nanocrystal film was analyzed using the bidirectional thermal dissipation model.

Crystal melting by light: X-ray crystal structure analysis of an azo crystal showing photoinduced crystal-melt transition.

Trans-cis photoisomerization in an azo compound containing azobenzene chromophores and long alkyl chains leads to a photoinduced crystal-melt transition (PCMT). X-ray structure analysis of this crystal clarifies the characteristic coexistence of the structurally ordered chromophores through their π···π interactions and disordered alkyl chains around room temperature. These structural features reveal that the PCMT starts near the surface of the crystal and propagates into the depth, sacrificing the π···π interactions. A temporal change of the powder X-ray diffraction pattern under light irradiation and a two-component phase diagram allow qualitative analysis of the PCMT and the following reconstructive crystallization of the cis isomer as a function of product accumulation. This is the first structural characterization of a compound showing the PCMT, overcoming the low periodicity that makes X-ray crystal structure analysis difficult.

Application of singular value decomposition analysis to time-dependent powder diffraction data of an in-situ photodimerization reaction.

Singular value decomposition (SVD) analysis has important applications for time-dependent crystallographic data, extracting significant information. Herein, a successful application of SVD analysis of time-resolved powder diffraction data over the course of an in-situ photodimerization reaction of anthracene derivatives is introduced. SVD revealed significant results in the case of 9-methylanthracene and 1-chloroanthracene. The results support the formation of the 9-methylanthracene stable dimer phase and suggest the existence of an excimer state.

Green/red light-sensing mechanism in the chromatic acclimation photosensor.

Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.

Solvent-dependent molecular structure of ionic species directly measured by ultrafast x-ray solution scattering.

Ionic species often play important roles in chemical reactions occurring in water and other solvents, but it has been elusive to determine the solvent-dependent molecular structure with atomic resolution. The triiodide ion has a molecular structure that sensitively changes depending on the type of solvent and its symmetry can be broken by strong solute-solvent interaction. Here, by applying pump-probe x-ray solution scattering, we characterize the exact molecular structure of I(3)(-) ion in water, methanol, and acetonitrile with subangstrom accuracy. The data reveal that I(3)(-) ion has an asymmetric and bent structure in water. In contrast, the ion keeps its symmetry in acetonitrile, while the symmetry breaking occurs to a lesser extent in methanol than in water. The symmetry breaking of I(3)(-) ion is reproduced by density functional theory calculations using 34 explicit water molecules, confirming that the origin of the symmetry breaking is the hydrogen-bonding interaction between the solute and solvent molecules.

Determination of the structural features of a long-lived electron-transfer state of 9-mesityl-10-methylacridinium ion.

Extensive efforts have been devoted to developing electron donor-acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor-acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr(+)-Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The N-methyl group in Acr(+) was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO(4)) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr(+)-Mes for mimicking photosynthesis efficiently.

Transient photoinduced 'hidden' phase in a manganite.

Photoinduced phase transitions are of special interest in condensed matter physics because they can be used to change complex macroscopic material properties on the ultrafast timescale. Cooperative interactions between microscopic degrees of freedom greatly enhance the number and nature of accessible states, making it possible to switch electronic, magnetic or structural properties in new ways. Photons with high energies, of the order of electron volts, in particular are able to access electronic states that may differ greatly from states produced with stimuli close to equilibrium. In this study we report the photoinduced change in the lattice structure of a charge and orbitally ordered Nd(0.5)Sr(0.5)MnO(3) thin film using picosecond time-resolved X-ray diffraction. The photoinduced state is structurally ordered, homogeneous, metastable and has crystallographic parameters different from any thermodynamically accessible state. A femtosecond time-resolved spectroscopic study shows the formation of an electronic gap in this state. In addition, the threshold-like behaviour and high efficiency in photo-generation yield of this gapped state highlight the important role of cooperative interactions in the formation process. These combined observations point towards a 'hidden insulating phase' distinct from that found in the hitherto known phase diagram.

Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography.

A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study.

A time-resolved powder diffraction study of in-situ photodimerization kinetics of 9-methylanthracene using a CCD area detector and parametric Rietveld refinement.

The [4π + 4π] photodimerization process of the 9-substituted anthracene derivative crystalline 9-methylanthracene (9-MA) was investigated using time-resolved X-ray powder diffraction. The study was carried out in-situ using a CCD area detector. Sequential and parametric Rietveld refinement was applied for quantitative phase analysis. The results of traditional sequential Rietveld refinement showed that the evolution of the dimerization process can be described using the Johnson-Mehl-Avrami-Kolmogorov (JMAK) model. The parameters of the JMAK equation were obtained successfully by parametric Rietveld refinement and suggest that the reaction follows heterogeneous nucleation and one-dimensional growth with a decreasing nucleation rate.