A Bis-Porphyrin Cavitand Breathing-In to Constrict Bucky Balls.

Bis-porphyrin cages have long been exploited to bind fullerenes selectively for various applications. The major consideration for an effective binding here had been the cavity size. Herein, we structurally demonstrate that a bis-Ni-porphyrin cavitand having even a smaller cavity can host a larger fullerene by a breathing and ruffling mechanism. It has also been shown that both the electronic and steric influence at the meso- positions of the porphyrin in fact dictate the binding character. The smaller cavity of 2NiD exhibits preferential binding for C70 over C60; however, surprisingly, the larger cavities in 2HD and 2NiTD display stronger affinities for C60 over the larger fullerene. We show here that the structural elasticity infused both by the metalloporphyrins and the connecting bridges play a major role in directing the binding. These conclusions have adequately been supported by structural and spectroscopic investigations. Additionally, the suitability of one of the conjugates for photoinduced charge-separation has been investigated using ultrafast transient absorption measurements. 2NiD⊃C60 has a charge separation timescale of ~0.8 ps, while charge recombination occurs at a longer timescale of ~920 ps.

Supramolecular Hydrogels and Water Channels of Differing Diameters from Dipeptide Isomers.

Dipeptides stereoisomers and regioisomers composed of norleucine (Nle) and phenylalanine (Phe) self-assemble into hydrogels under physiological conditions that are suitable for cell culture. The supramolecular behavior, however, differs as the packing modes comprise amphipathic layers or water channels, whose diameter is defined by either four or six dipeptide molecules. A variety of spectroscopy, microscopy, and synchrotron-radiation-based techniques unveil fine details of intermolecular interactions that pinpoint the relationship between the chemical structure and ability to form supramolecular architectures that define soft biomaterials.

Self-assembly of heterochiral, aliphatic dipeptides with Leu.

This work describes the self-assembly behavior of heterochiral, aliphatic dipeptides, l-Leu-d-Xaa (Xaa = Ala, Val, Ile, Leu), in green solvents such as acetonitrile (MeCN) and buffered water at neutral pH. Interestingly, water plays a structuring role because at 1% v/v, it enables dipeptide self-assembly in MeCN to yield organogels, which then undergo transition towards crystals. Other organic solvents and oils were tested for gelation, and metastable gels were formed in tetrahydrofuran, although at high peptide concentration (80 mM). Single-crystal X-ray diffraction revealed the dipeptides' supramolecular packing modes in amphipathic layers, as opposed to water channels reported for the homochiral Leu-Leu, or hydrophobic columns reported for homochiral Leu-Val and Leu-Ile.

Selective Water Pore Recognition and Transport through Self-Assembled Alkyl-Ureido-Trianglamine Artificial Water Channels.

In nature, aquaporins (AQPs) are proteins known for fast water transport through the membrane of living cells. Artificial water channels (AWCs) synthetic counterparts with intrinsic water permeability have been developed with the hope of mimicking the performances and the natural functions of AQPs. Highly selective AWCs are needed, and the design of selectivity filters for water is of tremendous importance. Herein, we report the use of self-assembled trianglamine macrocycles acting as AWCs in lipid bilayer membranes that are able to transport water with steric restriction along biomimetic H-bonding-decorated pores conferring selective binding filters for water. Trianglamine [(±)Δ, (mixture of diastereoisomers) and (R,R)3Δ and (S,S)3Δ], trianglamine hydrochloride (Δ.HCl), and alkyl-ureido trianglamines (n = 4, 6, 8, and 12) [(±)ΔC4, (±)ΔC8, (±)ΔC6, and (±)ΔC12] were synthesized for the studies presented here. The single-crystal X-ray structures confirmed that trianglamines form a tubular superstructure in the solid state. The water translocation is controlled via successive selective H-bonding pores (a diameter of 3 Å) and highly permeable hydrophobic vestibules (a diameter of 5 Å). The self-assembled alkyl-ureido-trianglamines achieve a single-channel permeability of 108 water molecules/second/channel, which is within 1 order of magnitude lower than AQPs with good ability to sterically reject ions and preventing the proton transport. Trianglamines present potential for engineering membranes for water purification and separation technologies.

The Unexpected Helical Supramolecular Assembly of a Simple Achiral Acetamide Tecton Generates Selective Water Channels.

Invited for the cover of this issue is the collaborative research team coordinated by Arie van der Lee at the University of Montpellier. The image depicts chiral channels with highly mobile water molecules resulting from the robust self-organization of a simple achiral acetamide. Fully reversible release and re-uptake of water molecules takes place near ambient conditions, with efficient water transport and a good selectivity against NaCl suggesting it to be an efficient candidate for desalination processes. Read the full text of the article at 10.1002/chem.20200383.

The Unexpected Helical Supramolecular Assembly of a Simple Achiral Acetamide Tecton Generates Selective Water Channels.

Achiral 2-hydroxy-N-(diphenylmethyl)acetamide (HNDPA) crystallizes in the P61 chiral space group as a hydrate, building up permeable chiral crystalline helical water channels. The crystallization-driven chiral self-resolution process is highly robust, with the same air-stable crystalline form readily obtained under a variety of conditions. Interestingly, the HNDPA supramolecular helix inner pore is filled by a helical water wire. The whole edifice is mainly stabilized by robust hydrogen bonds involving the HNDPA amide bonds and CH… π interactions between the HNDPA phenyl groups. The crystalline structure shows breathing behavior, with completely reversible release and re-uptake of water inside the chiral channel under ambient conditions. Importantly, the HNDPA channel is able to transport water very efficiently and selectively under biomimetic conditions. With a permeability per channel of 3.3 million water molecules per second in large unilamellar vesicles (LUV) and total selectivity against NaCl, the HNDPA channel is a very promising functional nanomaterial for future applications.

Dipeptide self-assembly into water-channels and gel biomaterial.

Dipeptides are convenient building blocks for supramolecular gel biomaterials that can be produced on a large scale at low cost and do not persist in the environment. In the case of unprotected sequences, hydrophobicity is a key requirement to enable gelation, with Phe-Phe standing out for its self-assembling ability. Conversely, more hydrophilic sequences such as homochiral dipeptides Phe-Val and Val-Phe neither fibrillate nor gel aqueous buffers and their crystal structures reveal amphipathic layers. In this work, we test emerging rules for the design of self-assembling dipeptides using heterochiral Phe-Val and Val-Phe. Each dipeptide is characterized by 1H- and 13C-NMR, LC-MS, circular dichroism, infrared and Raman spectroscopies, rheology, electron microscopy, and single-crystal X-ray diffraction. In particular, D-Phe-L-Val is the first heterochiral dipeptide to self-assemble into supramolecular water-channels whose cavity is defined by four peptide molecules arranged head-to-tail. This minimalistic sequence is devoid of amyloid character as probed by thioflavin T fluorescence and it displays excellent biocompatibility in vitro. The dataset provided, through comparison with the literature, significantly advances the definition of molecular design rules for minimalistic unprotected dipeptides that self-assemble into water-channels and biocompatible gels, to assist with the future development of supramolecular biomaterials with fine control over nanomorphological features for a variety of applications.

Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.

In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga Chlamydomonas reinhardtii (CrPRK) and the land plant Arabidopsis thaliana (AtPRK). PRK is an elongated homodimer characterized by a large central ß-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both AtPRK and CrPRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.

A Family of Lanthanide Hydroxo Carboxylates with 1D Polymeric Topology and Ln4 Butterfly Core Exhibits Switchable Supramolecular Arrangement.

The unique family of coordination polymers [Ln4(OH)2(piv)10(H2O)2]∞ of 11 lanthanides (Ln = La-Er) has been prepared by a simple solution method based on controlled hydrolysis. The ribbon-like polymeric structure consisting of connected tetranuclear clusters and supported by pivalate ligands and a framework of H-bonds has been revealed by single-crystal X-ray diffraction. While the compounds demonstrate similar PXRD patterns and unit cell parameters, the joint single-crystal XRD and pair distribution function data suggest the significant local structure change along the lanthanide series. The compounds exist as two packing polymorphs (α and ß) with similar ribbon geometry, but different supramolecular arrangement of the ribbons. Dehydration of either polymorph does not disturb the tetranuclear core but leads to a translational symmetry loss along the ribbon and a transformation of the 3D-ordered crystal into a 2D-ordered mesostructure. Rehydration of the mesostructure leads to the ß polymorph (except La and Ce), allowing the deliberate switching between the polymorphs via dehydration-rehydration evidenced by means of powder X-ray diffraction, pair distribution function analysis, and density functional theory calculations. Ab initio calculations reveal significant magnetic anisotropy of Ln3+ ions with ferro- and antiferromagnetic interactions within tetranuclear [Ln4(OH)2(piv)10(H2O)2] species. Magnetic susceptibility measurements demonstrated antiferromagnetic coupling, slow magnetic relaxation for Dy, Ho, and Er complexes, and field-induced single-chain magnetism for the Dy compound.

Direct Imaging of Radiation-Sensitive Organic Polymer-Based Nanocrystals at Sub-Ångström Resolution.

Seeing the atomic configuration of single organic nanoparticles at a sub-Å spatial resolution by transmission electron microscopy has been so far prevented by the high sensitivity of soft matter to radiation damage. This difficulty is related to the need to irradiate the particle with a total dose of a few electrons/Å2, not compatible with the electron beam density necessary to search the low-contrast nanoparticle, to control its drift, finely adjust the electron-optical conditions and particle orientation, and finally acquire an effective atomic-resolution image. On the other hand, the capability to study individual pristine nanoparticles, such as proteins, active pharmaceutical ingredients, and polymers, with peculiar sensitivity to the variation in the local structure, defects, and strain, would provide advancements in many fields, including materials science, medicine, biology, and pharmacology. Here, we report the direct sub-ångström-resolution imaging at room temperature of pristine unstained crystalline polymer-based nanoparticles. This result is obtained by combining low-dose in-line electron holography and phase-contrast imaging on state-of-the-art equipment, providing an effective tool for the quantitative sub-ångström imaging of soft matter.

A nine-ring fused terrylene diimide exhibits switching between red TADF and near-IR room temperature phosphorescence.

Herein, we report the first example of a terrylene diimide derivative that switches emission between thermally activated delayed fluorescence (TADF) and room temperature phosphorescence (RTP) in the red region. By design, the molecule TDI-cDBT boasts a symmetrical, consecutively fused nine-ring motif with a kite-like structure. The rigid core formed by the annulated dibenzothiophene moiety favoured efficient intersystem crossing and yielded a narrow-band emission with a full-width half maxima (FWHM) of 0.09 eV, along with high colour purity. A small ΔE S1-T1 of 0.04 eV facilitated thermally activated delayed fluorescence, enhancing the quantum yield to 88% in the red region. Additionally, it also prefers a direct triplet emission from the aggregated state. The room temperature phosphorescence observed from the aggregates has a longer emission lifetime of 1.8 ms, which is further prolonged to 8 ms at 77 K in the NIR region. Thus, the current strategy is successful in not only reducing ΔE S1-T1 to favour TADF but also serves as a novel platform that can switch emission from TADF to RTP depending upon the concentration.

Electrospray deposition of starch-containing laccase: A green technique for low-cost and eco-friendly biosensors.

Recently a laccase-based biosensors with unprecedented reuse and storage capabilities in the detection of catechol compound has been manufactured using ambient Electrospray Deposition (ESD) technique. These biosensors showed to be reused up to 63 measurements on the same electrode just prepared at room temperature and pressure. In this new work the reasons behind such a high-performance functioning have been investigated by analysing the commercial sample of laccase with different chemical physics methods: Electrophoresis, Fourier Transform Infrared Spectroscopy, X-ray Fluorescence and Nuclear Magnetic Resonance Spectroscopy. The analyses reveal the presence of the starch in the sample and its essential role as stabilizing agent. Indeed, comparing the performance of starch/laccase-based biosensors with starch-free/laccase-based biosensors, both produced via ESD, showed that the starch-free biosensors lost about 40% of their performance after just the first wash. This suggests that the presence of starch in the laccase sample is a key factor in providing the high wash and storage resistance, which are essential for the fabrication of such devices.

Luminescent [CO2@Ag20(SAdm)10(CF3COO)10(DMA)2] nanocluster: synthetic strategy and its implication towards white light emission.

Owing to the quantized size and associated discrete energy levels, atomically precise silver nanoclusters (Ag NCs) hold great potential for designing functional luminescent materials. However, the thermally activated non-radiative transition of Ag(I)-based NCs has faded the opportunities. To acquire the structurally rigid architecture of cluster nodes for constraining such transitions, a new synthetic approach is unveiled here that utilizes a neutral template as a cluster-directing agent to assemble twenty Ag(I) atoms that ensure the maximum number of surface-protecting ligand attachment possibilities in a particular solvent medium. The solvent polarity triggers the precise structural design to circumvent the over-reliance of the templates, which results in the formation of [CO2@Ag20(SAdm)10(CF3COO)10(DMA)2] NC (where SAdm = 1-adamantanethiolate and DMA = N,N-dimethylacetamide) exhibiting an unprecedented room-temperature photoluminescence emission. The high quantum yield of the generated blue emission ensures its candidature as an ideal donor for artificial light-harvesting system design, and it is utilized with the two-step sequential energy transfer process, which finally results in the generation of ideal white light. For implementing perfect white light emission, the required chromophores in the green and red emission regions were chosen based on their effective spectral overlap with the donor components. Due to their favorable energy-level distribution, excited state energy transfers occurred from the NC to ß-carotene at the initial step, then from the conjugate of the NC and ß-carotene to another chromophore, Nile Blue, at the second step via a sequential Förster resonance energy transfer pathway.

Structural study of X-ray induced activation of carbonic anhydrase.

Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid-base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131-137], but a structure of an HCAII in complex with CO(2) or HCO(3)(-) has remained elusive. Here, we report previously undescribed structures of HCAII:CO(2) and HCAII:HCO(3)(-) complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006) Curr Opin Struct Biol 16:624-629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.

Mixed 3D-2D Perovskite Flexible Films for the Direct Detection of 5 MeV Protons.

This study reports on a novel, flexible, proton beam detector based on mixed 3D-2D perovskite films deposited by solution onto thin plastic foils. The 3D-2D mixture allows to obtain micrometer-thick and highly uniform films that constitute the detector's active layer. The devices demonstrate excellent flexibility with stable electric transport properties down to a bending radius of 3.1 mm. The detector is characterized under a 5 MeV proton beam with fluxes in the range [4.5 × 105 - 1.4 × 109 ] H+ cm-2 s-1 , exhibiting a stable response to repetitive irradiation cycles with sensitivity up to (290 ± 40) nC Gy-1 mm-3 and a limit of detection down to (72±2) µGy s-1 . The detector radiation tolerance is also assessed up to a total of 1.7 × 1012 protons impinging on the beam spot area, with a maximum variation of the detector's response of 14%.

Self-Assembly of Homo- and Hetero-Chiral Cyclodipeptides into Supramolecular Polymers towards Antimicrobial Gels.

There is an increasing interest towards the development of new antimicrobial coatings, especially in light of the emergence of antimicrobial resistance (AMR) towards common antibiotics. Cyclodipeptides (CDPs) or diketopiperazines (DKPs) are attractive candidates for their ability to self-assemble into supramolecular polymers and yield gel coatings that do not persist in the environment. In this work, we compare the antimicrobial cyclo(Leu-Phe) with its heterochiral analogs cyclo(D-Leu-L-Phe) and cyclo(L-Leu-D-Phe), as well as cyclo(L-Phe-D-Phe), for their ability to gel. The compounds were synthesized, purified by HPLC, and characterized by 1H-NMR, 13C-NMR, and ESI-MS. Single-crystal X-ray diffraction (XRD) revealed details of the intermolecular interactions within the supramolecular polymers. The DKPs were then tested for their cytocompatibility on fibroblast cells and for their antimicrobial activity on S. aureus. Overall, DKPs displayed good cytocompatibility and very mild antimicrobial activity, which requires improvement towards applications.

Temperature-Dependent Structural Phase Transition in Rubrene Single Crystals: The Missing Piece from the Charge Mobility Puzzle?

Accurate structural models for rubrene, the benchmark organic semiconductor, derived from synchrotron X-ray data in the temperature range of 100-300 K, show that its cofacially stacked tetracene backbone units remain blocked with respect to each other upon cooling to 200 K and start to slip below that temperature. The release of the blocked slippage occurs at approximately the same temperature as the hole mobility crossover. The blocking between 200 and 300 K is caused by a negative correlation between the relatively small thermal expansion along the crystallographic b-axis and the relatively large widening of the angle between herringbone-stacked tetracene units. DFT calculations reveal that this blocked slippage is accompanied by a discontinuity in the variation with temperature of the electronic couplings associated with hole transport between cofacially stacked tetracene backbones.

Synchrotron soft X-ray imaging and fluorescence microscopy reveal novel features of asbestos body morphology and composition in human lung tissues.

BACKGROUND: Occupational or environmental exposure to asbestos fibres is associated with pleural and parenchymal lung diseases. A histopathologic hallmark of exposure to asbestos is the presence in lung parenchyma of the so-called asbestos bodies. They are the final product of biomineralization processes resulting in deposition of endogenous iron and organic matter (mainly proteins) around the inhaled asbestos fibres. For shedding light on the formation mechanisms of asbestos bodies it is of fundamental importance to characterize at the same length scales not only their structural morphology and chemical composition but also to correlate them to the possible alterations in the local composition of the surrounding tissues. Here we report the first correlative morphological and chemical characterization of untreated paraffinated histological lung tissue samples with asbestos bodies by means of soft X-ray imaging and X-Ray Fluorescence (XRF) microscopy, which reveals new features in the elemental lateral distribution. RESULTS: The X-ray absorption and phase contrast images and the simultaneously monitored XRF maps of tissue samples have revealed the location, distribution and elemental composition of asbestos bodies and associated nanometric structures. The observed specific morphology and differences in the local Si, Fe, O and Mg content provide distinct fingerprints characteristic for the core asbestos fibre and the ferruginous body. The highest Si content is found in the asbestos fibre, while the shell and ferruginous bodies are characterized by strongly increased content of Mg, Fe and O compared to the adjacent tissue. The XRF and SEM-EDX analyses of the extracted asbestos bodies confirmed an enhanced Mg deposition in the organic asbestos coating. CONCLUSIONS: The present report demonstrates the potential of the advanced synchrotron-based X-ray imaging and microspectroscopy techniques for studying the response of the lung tissue to the presence of asbestos fibres. The new results obtained by simultaneous structural and chemical analysis of tissue specimen have provided clear evidence that Mg, in addition to Fe, is also involved in the formation mechanisms of asbestos bodies. This is the first important step to further thorough investigations that will shed light on the physiopathological role of Mg in tissue response to the asbestos toxicity.

Zeta-carbonic anhydrases show CS2 hydrolase activity: A new metabolic carbon acquisition pathway in diatoms?

CDCA1 is a very peculiar member of the Carbonic Anhydrase (CA) family. It has been the first enzyme to show an efficient utilization of Cd(II) ions in Nature and a unique adaptation capability to live on the surface ocean. Indeed, in this environment, which is extremely depleted in essential metal ions, CDCA1 can utilize Zn(II) or Cd(II) as catalytic metal to support the metabolic needs of fast growing diatoms. In this paper we demonstrate a further catalytic versatility of this enzyme by using a combination of X-ray crystallography, molecular dynamics simulations and enzymatic experiments. First we identified the CO2 binding site and the way in which this substrate travels from the environment to the enzyme active site. Then, starting from the observation of a structural similarity with the substrate entry route of CS2 hydrolase from Acidanius A1-3, we hypothesized and demonstrated that also CS2 is a substrate for CDCA1. This finding is new and unexpected since until now only few CS2 hydrolases have been characterized, and none of them is reported to have any CO2 hydratase action. The physiological implications of this supplementary catalytic activity still remain to be unveiled. We suggest here that it could represent another ability of diatoms expressing CDCA1 to adapt to the external environment. Indeed, the ability of this enzyme to convert CS2 could represent an alternative source of carbon acquisition for diatoms, in addition to CO2.

Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments.

Fragment screening is a powerful drug discovery approach particularly useful for enzymes difficult to inhibit selectively, such as the thiol/selenol-dependent thioredoxin reductases (TrxRs), which are essential and druggable in several infectious diseases. Several known inhibitors are reactive electrophiles targeting the selenocysteine-containing C-terminus and thus often suffering from off-target reactivity in vivo. The lack of structural information on the interaction modalities of the C-terminus-targeting inhibitors, due to the high mobility of this domain and the lack of alternative druggable sites, prevents the development of selective inhibitors for TrxRs. In this work, fragments selected from actives identified in a large screen carried out against Thioredoxin Glutathione Reductase from Schistosoma mansoni (SmTGR) were probed by X-ray crystallography. SmTGR is one of the most promising drug targets for schistosomiasis, a devastating, neglected disease. Utilizing a multicrystal method to analyze electron density maps, structural analysis, and functional studies, three binding sites were characterized in SmTGR: two sites are close to or partially superposable with the NADPH binding site, while the third one is found between two symmetry related SmTGR subunits of the crystal lattice. Surprisingly, one compound bound to this latter site stabilizes, through allosteric effects mediated by the so-called guiding bar residues, the crucial redox active C-terminus of SmTGR, making it finally visible at high resolution. These results further promote fragments as small molecule probes for investigating functional aspects of the target protein, exemplified by the allosteric effect on the C-terminus, and providing fundamental chemical information exploitable in drug discovery.