Diffusion of a disordered protein on its folded ligand

Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 k_BT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.

Specific molecular interactions orchestrate a multitude of simultaneous cellular processes. The discovery of intrinsically disordered proteins (IDPs) (1, 2) has substantially aided our understanding of such interactions. More than two decades of research revealed a plethora of functions and mechanisms (2–6) that complemented the prevalent structure-based view on protein interactions. Even the idea that IDPs always ought to fold upon binding has largely been dismantled by recent discoveries of high-affine–disordered complexes (7, 8). Classical shape complementary is indeed superfluous in the complex between prothymosin-α and histone H1, in which charge complementary is the main driving force for binding (7). However, complexes between IDPs and folded proteins can also be highly dynamic [e.g., Sic1 and Cdc4 (9), the Na⁺/H⁺ exchanger tail and ERK2 (10), nucleoporin tails, and nuclear transport receptors (11)]. Yet timescales of motions and their spatial amplitudes are often elusive, such that it is unclear how precisely the surfaces of folded proteins alter the dynamics of bound IDPs. Answering this question is a key step in understanding how specificity, affinity, and flexibility can be simultaneously realized in such complexes.To address this question, we focused on the dynamics of the cell adhesion complex between E-cadherin (E-cad) and β-catenin (β-cat), which is involved in growth pathologies and cancer (12). E-cad is a transmembrane protein that mediates cell–cell adhesions by linking actin filaments of adjacent epithelial cells (Fig. 1A). Previous NMR results showed that the cytoplasmic tail of E-cad is intrinsically disordered (13). E-cad binds β-cat, which establishes a connection to the actin-associated protein α-catenin (14–16). β-cat, on the other hand, is a multifunctional repeat protein (17–20) that mediates cadherin-based cell adhesions (21) and governs cell fate decisions during embryogenesis (22). It contains three domains: an N-terminal domain (130 amino acids [aa]), a central repeat domain (550 aa), and a C-terminal domain (100 aa). Whereas the N- and C-terminal domains of β-cat are in large parts unstructured (17), with little effect on the affinity of the E-cad/β-cat complex (23), the 12 repeats of the central domain arrange in a superhelix (24). The X-ray structure showed that the E-cad wraps around this central domain of β-cat (24) (Fig. 1B). However, not only is half of the electron density of E-cad missing, the X-ray unit cell also comprises two structures with different resolved parts of E-cad (Fig. 1B). In fact, only 45% of all resolved E-cad residues are found in both structures (Fig. 1C). Although this ambiguity together with the large portion of missing residues (25) suggests that E-cad is highly dynamic in the complex with β-cat, the timescales and amplitudes of these dynamics are unknown.Open in a separate windowFig. 1.Complex between the cytoplasmic tail of E-cad and β-cat. (A) Schematics of cell–cell junctions mediated by E-cad and β-cat. (B) The two X-ray structures of the complex between the tail of E-cad (red) and the central repeat domain of β-cat (white) resolve different parts of E-cad (Protein Data Bank: 1i7x), indicating the flexibility of E-cad in the complex. (Bottom) Cartoon representation of the resolved E-cad parts. (C) Scheme showing the resolved parts of E-cad (red).Here, we integrated single-molecule Förster resonance energy transfer (smFRET) experiments with molecular simulations to directly measure the dynamics of E-cad on β-cat with high spatial and temporal resolution. In our bottom-up strategy, we first probed intramolecular interactions within E-cad using smFRET to parameterize a coarse-grained (CG) model. In a second step, we monitored E-cad on β-cat, integrated this information into the CG model, and obtained a dynamic picture of the complex. We found that all segments of E-cad diffuse on the surface of β-cat at submillisecond timescales and obtained a residue-resolved understanding of these motions: A small number of persistent interactions provide specificity, whereas many weak multivalent contacts boost affinity, which confirms the idea that regulatory enzymes access their recognition motifs on E-cad and β-cat without requiring the complex to dissociate (24).     

Recent Advances in Archaeological Science Techniques Special Feature: A Neandertal dietary conundrum: Insights provided by tooth enamel Zn isotopes from Gabasa,Spain

The characterization of Neandertals’ diets has mostly relied on nitrogen isotope analyses of bone and tooth collagen. However, few nitrogen isotope data have been recovered from bones or teeth from Iberia due to poor collagen preservation at Paleolithic sites in the region. Zinc isotopes have been shown to be a reliable method for reconstructing trophic levels in the absence of organic matter preservation. Here, we present the results of zinc (Zn), strontium (Sr), carbon (C), and oxygen (O) isotope and trace element ratio analysis measured in dental enamel on a Pleistocene food web in Gabasa, Spain, to characterize the diet and ecology of a Middle Paleolithic Neandertal individual. Based on the extremely low δ⁶⁶Zn value observed in the Neandertal’s tooth enamel, our results support the interpretation of Neandertals as carnivores as already suggested by δ¹⁵N isotope values of specimens from other regions. Further work could help identify if such isotopic peculiarities (lowest δ⁶⁶Zn and highest δ¹⁵N of the food web) are due to a metabolic and/or dietary specificity of the Neandertals.

Over the last 30 years, analyses of nitrogen isotopes in collagen (δ¹⁵N_collagen) have provided direct evidence for Neandertal diets across Europe and Asia. These studies all indicate a carnivorous (1–12), or at least a meat-heavy, diet for European Neandertals. However, one peculiarity of Neandertal δ¹⁵N_collagen remains the subject of an ongoing debate. From the one Siberian and eight western European sites, where both Neandertal and associated fauna have been analyzed, nitrogen isotope ratios in Neandertal collagen are systematically higher than that of other carnivores (3, 6–8, 10, 11, 13, 14). An explanation for such elevated values could be the consumption of herbivores, such as mammoths, which themselves exhibit elevated δ¹⁵N values due to the consumption of plants growing on arid soils (1, 2, 7). While mammoth remains are usually scarce at Neandertal fossil localities, they were nonetheless occasionally consumed, as suggested by remains with cut marks and other human butchery signatures (15). The absence of mammoth remains at Middle Paleolithic sites could be a result of 1) Neandertals chose to leave large bone elements at the kill site and transport other edible carcass products, mainly meat, back to the habitation site (15), or 2) mammoths were not frequently consumed, and the δ¹⁵N peculiarity consequently reflects the consumption of other resources enriched in ¹⁵N.Alongside this δ¹⁵N peculiarity, one major obstacle to our knowledge of Neandertals’ subsistence patterns is that the preservation of organic matter limits the application of collagen-bound nitrogen isotope analysis to fossil specimens. Collagen degrades over time at a varying speed depending on climatic and environmental conditions (16). The oldest hominin specimen in which bone protein is preserved is that of Scladina (Belgium), which dates to 90,000 cal BP (calibrated years before the present) (17), but most studied specimens are younger than 50,000 cal BP (1–3, 6–8, 10–13, 18). Furthermore, these specimens are only from sites in northwestern and central Europe and Siberia, where climatic conditions favored collagen preservation. As a result, the variability of Neandertals’ diet over time and between regions may not accurately be reflected by the currently available isotope data. In Iberia, where the latest surviving Neandertals have been discovered (19, 20), collagen was successfully extracted for only one site (21). Therefore, our knowledge of Iberian Neandertal diets mostly relies on zooarcheological and dental calculus data, which show some inconsistencies (21–25). For instance, similar to other western European sites, zooarcheological studies emphasize the consumption of terrestrial mammals and birds (21). In contrast, analysis of dental calculus for microremains and ancient DNA metagenomic analysis (26–28) highlight the frequent consumption of plants and mushrooms. Indeed, Weyrich et al. (26) even suggest that Neandertals at El Sidrón (Fig. 1) rarely consumed meat but often ate mushrooms, which would also result in elevated δ¹⁵N values (29). The consumption of marine foods is also attested for coastal Neandertals, but its frequency cannot be truly assessed in the absence of isotope studies (21, 23–25, 30). Finally, cannibalism has been documented at two Iberian sites (El Sidrón and Zafarraya) (22, 31) (Fig. 1), though such practices appear limited and most likely occurred only during periods of nutritional stress (32). Therefore, it is challenging to confirm the homogeneity of Neandertals’ diets across time and space, calling into question a direct link between their subsistence strategy and disappearance.Open in a separate windowFig. 1.(A) Location of the Gabasa site as well as other Neandertal sites mentioned in the text. (B) Detailed map of the Gabasa region. San Estaban de Litera and Benabarre are nearby modern cities.This study aims to investigate if the Zn isotope proxy could help elucidate the dietary behaviors of Neandertals and the source of their δ¹⁵N peculiarity, specifically by studying a Late Pleistocene Iberian food web where the presence of mammoth has not been documented (33). The development of Zn isotope analysis (⁶⁶Zn/⁶⁴Zn, expressed as δ⁶⁶Zn) has proven that trophic level information can be retrieved from mammalian tooth enamel (δ⁶⁶Zn_enamel) (34, 35), including fossil samples from Pleistocene food webs where organic matter is typically not preserved (36, 37). Previous studies have demonstrated that δ⁶⁶Zn_enamel decreases by ca. 0.30 to 0.60 ‰ with each step in archeological and modern food webs (34–38) and that δ⁶⁶Zn values associated with breastfeeding are higher than postweaning-associated values (39). While the main source of variation of δ⁶⁶Zn_enamel values is diet, local geology can also likely influence the isotope ratio of a given animal (36, 39). To date, three modern assemblages from Koobi Fora (Kenya), Kruger Park, and the western Cape (South Africa) (40), a few animals from a historical site (Rennes, France) (41), and three Late Pleistocene sites (Tam Hay Marklot, Nam Lot, and Tam Pa Ling, Laos) (36, 37) are the only terrestrial food webs for which Zn isotope data in teeth and/or bones have been published (SI Appendix, Fig. S14). In the modern Koobi Fora savannah food web, δ⁶⁶Zn_enamel differences have been observed between browsers and grazers (35), but this pattern was not seen in any of the three Pleistocene Asian forest food webs (36, 37). Among modern and historical human populations, historically documented diets relying on plants are associated with higher δ⁶⁶Zn values than those that include a substantial quantity of animal products (41–44). Zinc isotopes of ancient hominins have been analyzed only in one Pleistocene Homo sapiens individual (37) from Southeast Asia, but not yet in any Neandertal specimen.This current study contributes significantly to our understanding of Iberian Neandertal diets by providing information on their trophic ecology for a region where traditional nitrogen isotope analyses are unfeasible due to the poor preservation of organic matter. We use the Zn isotopic tool as well as other mobility, ecological, and dietary proxies applied on tooth enamel from hominin and animal remains from the cave site Cueva de los Moros 1 (Gabasa, Pyrenees, Spain; Fig. 1). The site, excavated in the 1980s, is very well documented [for stratigraphic context, see Montes and Utrilla (45) and SI Appendix, Section S1]. All remains come from layers e, f, and g of a single stratigraphic layer directly above layer h dated to 143 ± 43 ka. Numerous carnivore remains were recovered along with Neandertal remains (layers e and f), allowing for comparison of the different meat-eating taxa. Coexisting herbivores from three different types of environmental contexts are homogeneously represented in layers e, f, and g: mountains (Iberian ibex [Capra pyrenaica], chamois [Rupicapra rupicapra]), forest (cervids including red deer [Cervus elaphus]), and open environments (horses [Equus ferus], European wild asses [Equus hydruntinus]).     

Enabling multiple intercavity polariton coherences by adding quantum confinement to cavity molecular polaritons

In this study, the “particle in a box” idea, which was broadly developed in semiconductor quantum dot research, was extended into mid-infrared (IR) cavity modes by applying lateral confinement in an optical cavity. The discrete cavity modes hybridized with molecular vibrational modes, resulting in a quartet of polariton states that can support multiple coherence states in the IR regime. We applied tailored pump pulse sequences to selectively prepare these coherences and verified the multi-coherence existence. The simulation based on Lindblad equation showed that because the quartet of polariton states resided in the same cavity, they were specifically robust toward decoherence caused by fluctuations in space. The multiple robust coherences paved the way for entangled states and coherent interactions between cavity polaritons, which would be critical for advancing polariton-based quantum information technology.

Molecular vibrational polaritons (1–18) are half-matter, half-light quasiparticles that possess unique abilities to change chemical reactions (3, 10, 12, 15, 17, 19–22), modify energy transfer pathways (7, 14, 23, 24), and have the potential to be an alternative platform for quantum simulation (9, 25–32). When the collective dipole coupling between cavity photon modes and molecular vibrational modes is so strong that the two modes exchange energy at a rate faster than the lifetimes of either mode, the upper and lower polaritons (UP and LP) are formed and the systems reach the so-called vibrational strong coupling (VSC) regime (31–33). Up to now, the majority of molecular vibrational polaritons are formed in Fabry-Perot (FP) cavity, which has one corresponding cavity photon mode for each specific in-plane momentum. These modes at different in-plane momentum form a continuous parabolic dispersion curve. As such, an FP cavity can support only one pair of UP and LP at a specific in-plane momentum, and thereby, have one coherence (30) (i.e., off-diagonal density matrix elements), namely |UP〉〈LP| (or its complex conjugate, Fig. 1A). Thus, UP and LP can be treated as one polariton qubit system at ambient conditions (28, 29, 34).Open in a separate windowFig. 1.Challenges of creating multiple coherences in cavity polaritons. (A) In an FP cavity composed by two flat mirrors, one pair of UP and LP is supported and thereby can only form one coherence |UP〉〈LP| and its conjugate. (B) In the dual cavity, two cavity modes are supported due to the longitudinal cavity thickness difference along the lateral dimension. This cavity can support two pairs of UP and LP and enrich the varieties of coherences. However, coherences such as |UP_B〉〈LP_A| cannot survive the fluctuations between cavities. (C) In this work, we demonstrated the confined cavity by implementing the “particle in a box” concept. In this way, two cavity modes and two pairs of polariton modes are supported in the same spatial location, enabling the creation of coherences among any pairs of polaritons. To clearly show the confinement in the illustration, the vertical dimension was exaggerated. (D) A close view of the confined-cavity pattern obtained by optical profilometer. The lateral dimension of the cavity (the short side of the trench) is 25 μm. The depth of the trench is 1 μm. (E) The linear transmission spectra obtained by focusing IR beams center at the trenched area on the sample. Two peaks at 1,971 cm^–1 and 1,995 cm^–1 are from the confined cavity, whereas the peak at 2,099 cm^–1 is from the unconfined region. The dashed line is the simulation result.The molecular vibrational polariton-based qubits is a potential platform for quantum simulation with several advantages, such as operating at ambient temperature, ease of tunability of cavities, intrinsic systems for quantum light molecular spectroscopy, and the customizable “designer” vibrational chromophores (35–37). Although similar efforts have been made on exciton polaritons, the single qubit property of the FP cavity has limited the scalability of molecular vibrational polaritons for advancing quantum simulation (34). One way to overcome the limitations is to form multi-qubit systems, also called qudits, using multi-cavity polariton systems. Early work from our group extended the FP cavity into two pairs of polaritons in spatially neighboring cavities (9, 26), which we termed as dual-cavity system herein (Fig. 1B). However, the high-frequency coherences composed of polaritons from different cavity modes (referred as intercavity coherences) cannot survive due to decoherence, because polaritons reside in different spatial locations. To address this limitation, a novel cavity structure is needed to multiplex polariton coherences for simulating complex quantum phenomena.In this work, we overcome the FP cavity limitations and create two cavity modes with distinct energies by applying an orthogonal confinement in FP cavity system. This confinement effect is similar to “particle in a box,” which is widely applied in semiconductor materials (38–45), including quantum dots and wells. Simply put, when the dimensions of a system are close to the wavelength of the particles, only certain wave functions can survive the boundary condition of the spatial confinement, leading to distinct quantum states and tunable energy gaps. However, compared to the confinement effect in semiconductor materials, this phenomenon has not been heavily explored in the IR regime. Here, we implemented confinement to IR cavities to create two photonic modes at a specific in-plane momentum, and we showed that the confined cavity had a discrete dispersion relation with respect to in-plane momentum. We further demonstrated that under VSC conditions, a quadruplet of polaritons (polaritonic qudits) was created which formed coherences between any pairs of polaritons (Fig. 1C). Thus, introducing confinement in a single cavity created a foundation for generating qudits with complex coherence states or even entanglements in the future (46–48). This advance could create a potential platform for quantum light spectroscopy and other quantum science and technology (49, 50). Therefore, this was a valuable step for molecular polaritonic quantum information technology.     

A synthetic porphyrin as an effective dual antidote against carbon monoxide and cyanide poisoning

Simultaneous poisoning by carbon monoxide (CO) and hydrogen cyanide is the major cause of mortality in fire gas accidents. Here, we report on the invention of an injectable antidote against CO and cyanide (CN^–) mixed poisoning. The solution contains four compounds: iron(III)porphyrin (Fe^IIITPPS, F), two methyl-β-cyclodextrin (CD) dimers linked by pyridine (Py3CD, P) and imidazole (Im3CD, I), and a reducing agent (Na₂S₂O₄, S). When these compounds are dissolved in saline, the solution contains two synthetic heme models including a complex of F with P (hemoCD-P) and another one of F with I (hemoCD-I), both in their iron(II) state. hemoCD-P is stable in its iron(II) state and captures CO more strongly than native hemoproteins, while hemoCD-I is readily autoxidized to its iron(III) state to scavenge CN^– once injected into blood circulation. The mixed solution (hemoCD-Twins) exhibited remarkable protective effects against acute CO and CN^– mixed poisoning in mice (~85% survival vs. 0% controls). In a model using rats, exposure to CO and CN^– resulted in a significant decrease in heart rate and blood pressure, which were restored by hemoCD-Twins in association with decreased CO and CN^– levels in blood. Pharmacokinetic data revealed a fast urinary excretion of hemoCD-Twins with an elimination half-life of 47 min. Finally, to simulate a fire accident and translate our findings to a real-life scenario, we confirmed that combustion gas from acrylic cloth caused severe toxicity to mice and that injection of hemoCD-Twins significantly improved the survival rate, leading to a rapid recovery from the physical incapacitation.

Fire accidents frequently occur around the world and the consequent inhalation of combustion gases represents the leading cause of death under these circumstances (1–10). Typically, combustion gases consist, among others, of carbon dioxide, water (H₂O), carbon monoxide (CO), hydrogen cyanide (HCN), hydrochloric acid, nitrogen oxide, and sulfur oxide. Their amounts depend on the materials of combustion (3–10) and, among them, CO and HCN are the most dangerous due to their severe toxic effects in humans (3–4, 5–15). CO is generated during incomplete combustion of carbon materials while HCN derives from carbon- and nitrogen-containing materials. Thus, CO and HCN gases are simultaneously released when synthetic materials such as plastics, acrylic cloths, and urethanes are burned in buildings. Once inhaled, CO strongly binds to ferrous iron(II) heme proteins such as hemoglobin (Hb) in erythrocytes and myoglobin in muscles (16–19), thus compromising oxygen (O₂) transport/storage in the blood circulation and tissues. On the contrary, HCN binds as cyanide ion (CN^–) to ferric iron(III) heme, preferentially targeting cytochrome c oxidase (CcO) in mitochondria and interrupting O₂-dependent energy production (11, 20–22). Likewise, the toxic effects of CO on mitochondrial respiration are ascribed to its ability to bind to cytochrome c oxidase (23–25). Therefore, both CO and HCN can inhibit aerobic respiration mediated by several heme proteins leading to anoxia-induced lethal toxicity. As the molecular mechanisms of CO and HCN toxicity are closely related, additional or synergistic deleterious effects can be expected when these two gases are produced and inhaled at the same time (26–31). Therapeutic strategies to treat either CO or HCN poisoning have been developed independently (11, 13, 22, 32–37). However, to our knowledge, there is no medical intervention at present to neutralize simultaneously CO and HCN with an effective treatment in vivo.In the present study, we have developed an injectable antidote for CO and HCN mixed poisoning. This agent contains supramolecular compounds, termed hemoCDs, composed of a water-soluble iron(II/III)porphyrin and two cyclodextrin (CD) dimers. Based on our previous research on the synthesis and characterization of heme protein model structures (38–40), the gas-binding ability and the redox status of the iron center of the porphyrin can be regulated by the linker structure of the CD dimers englobing the porphyrin. The porphyrin complexed with a CD dimer having a pyridine linker (hemoCD-P, Fig. 1 A, Left) is stable in the iron(II) state in vivo and shows much higher CO-binding affinity compared to the affinities reported for native heme proteins (41–45). On the contrary, the porphyrin complexed with a CD dimer having an imidazole linker (hemoCD-I, Fig. 1 A, Right) is stable in the iron(III) state and shows a higher binding affinity to CN^– than native ferric met-hemoglobin (met-Hb) (46, 47). These two complexes do not bind to plasma proteins in the circulation when injected separately and are quickly excreted in urines without any chemical decomposition. Therefore, these compounds have the ability to capture either CO or CN^– to their iron(II/III) centers in vivo and expel these toxic ligands from the organism (41–47). Here, we have developed hemoCD-Twins that contains both hemoCD-P and hemoCD-I in saline for simultaneous removal of CO and HCN in vivo. This paper describes the primary pharmacological properties of hemoCD-Twins and its detoxification effects in animals intoxicated with CO and CN^–. To simulate a real-life fire accident, the burning of acrylic cloth with consequent release of combustion gases was also used as an experimental approach for antidotal tests. We found that hemoCD-Twins exhibits the following features: 1) The synthetic compounds are storable at room temperature over a year thanks to their chemical stability; 2) the solution can be quickly prepared without the need of special handlings; 3) a single administration of hemoCD-Twins shows immediate dual antidotal effect against CO and CN^–; and 4) the injected solution is quickly eliminated from the body without significant side effects. We are envisioning a scenario whereby a person who is accidentally exposed to fire gases containing CO and HCN can be promptly treated at the site by infusion with hemoCD-Twins.Open in a separate windowFig. 1.hemoCD-Twins as an antidote system against CO and CN^– mixed poisoning. (A) Biomimetic heme protein model compounds hemoCD-P and hemoCD-I that are used as CO and CN^– scavengers in vivo. (B) Chemical structures of the four components P, I, F, and S contained in hemoCD-Twins. (C) Preparation of hemoCD-Twins. Three powder compounds, F, P, and I, were dissolved in PBS in a 2:1:1 molar ratio, where the solution contains hemoCD-P and hemoCD-I in ferric iron(III) states. The solution is stable and storable at room temperature. The reducing agent S is added just before use. (D) Schematic illustration for the simultaneous removal of CO and CN^– by a single injection of hemoCD-Twins in vivo. CO and CN^– are removed from living organisms and excreted in the urine with hemoCD-P and hemoCD-I in ferrous iron(II) and ferric iron(III) complexes, respectively.     

Conjugated polymers based on metalla-aromatic building blocks

Conjugated polymers usually require strategies to expand the range of wavelengths absorbed and increase solubility. Developing effective strategies to enhance both properties remains challenging. Herein, we report syntheses of conjugated polymers based on a family of metalla-aromatic building blocks via a polymerization method involving consecutive carbyne shuttling processes. The involvement of metal d orbitals in aromatic systems efficiently reduces band gaps and enriches the electron transition pathways of the chromogenic repeat unit. These enable metalla-aromatic conjugated polymers to exhibit broad and strong ultraviolet–visible (UV–Vis) absorption bands. Bulky ligands on the metal suppress π–π stacking of polymer chains and thus increase solubility. These conjugated polymers show robust stability toward light, heat, water, and air. Kinetic studies using NMR experiments and UV–Vis spectroscopy, coupled with the isolation of well-defined model oligomers, revealed the polymerization mechanism.

Conjugated polymers are macromolecules usually featuring a backbone chain with alternating double and single bonds (1–3). These characteristics allow the overlapping p-orbitals to form a system with highly delocalized π-electrons, thereby giving rise to intriguing chemical and physical properties (4–6). They have exhibited many applications in organic light-emitting diodes, organic thin film transistors, organic photovoltaic cells, chemical sensors, bioimaging and therapies, photocatalysis, and other technologies (7–10). To facilitate the use of solar energy, tremendous efforts have been devoted in recent decades to developing previously unidentified conjugated polymers exhibiting broad and strong absorption bands (11–13). The common strategies for increasing absorption involve extending π-conjugation by incorporating conjugated cyclic moieties, especially fused rings; modulating the strength of intramolecular charge transfer between donor and acceptor units (D–A effect); increasing the coplanarity of π conjugation through weak intramolecular interactions (e.g., hydrogen bonds); and introducing heteroatoms or heavy atoms into the repeat units of conjugated polymers (11–16). Additionally, appropriate solubility is a prerequisite for processing and using polymers and is usually achieved with the aid of long alkyl or alkoxy side chains (12, 17).Aromatic rings are among the most important building blocks for conjugated polymers. In addition to aromatic hydrocarbons, a variety of aromatic heterocycles composed of main-group elements have been used as fundamental components. These heteroatom-containing conjugated polymers show unique optical and electronic properties (4–10). However, while metalla-aromatic systems bearing a transition metal have been known since 1979 due to the pioneering work by Thorn and Hoffmann (18), none of them have been used as building blocks for conjugated polymers. The HOMO–LUMO gaps (E_g) of metalla-aromatics are generally narrower (Fig. 1) than those of their organic counterparts (19–22). We reasoned that this feature should broaden the absorption window if polymers stemming from metalla-aromatics are achievable.Open in a separate windowFig. 1.Comparison of traditional organic skeletons with metalla-aromatic building blocks (the computed energies are in eV). (A) HOMO–LUMO gaps of classic aromatic skeletons. (B) Carbolong frameworks as potential building blocks for novel conjugated polymers with broad absorption bands and improved solubility.In recent years, we have reported a series of readily accessible metal-bridged bicyclic/polycyclic aromatics, namely carbolong complexes, which are stable in air and moisture (23–25). The addition of osmium carbynes (in carbolong complexes) and alkynes gave rise to an intriguing family of d_π–p_π conjugated systems, which function as excellent electron transport layer materials in organic solar cells (26, 27). These observations raised the following question: Can this efficient addition reaction be used to access metalla-aromatic conjugated polymers? It is noteworthy that incorporation of metalla-aromatic units into conjugated polymers is hitherto unknown. In this contribution, we disclose a polymerization reaction involving M≡C analogs of C≡C bonds, which involves a unique carbyne shuttling strategy (Fig. 2A). This led to examples of metalla-aromatic conjugated polymers (polycarbolongs) featuring metal carbyne units in the main chain. On the other hand, the development of polymerization reactions plays a crucial role in involving certain building blocks in conjugated polymers (28–32). These efficient, specific, and feasible polymerizations could open an avenue for the synthesis of conjugated polymers.Open in a separate windowFig. 2.Design of polymers and synthesis of monomers. (A) Schematic illustration of the polymerization strategy. (B) Preparation of carbolong monomers. Insert: X-ray molecular structure for the cations of complex 3. Ellipsoids are shown at the 50% probability level; phenyl groups in PPh₃ are omitted for clarity.     

Electrochemical borylation of carboxylic acids

A simple electrochemically mediated method for the conversion of alkyl carboxylic acids to their borylated congeners is presented. This protocol features an undivided cell setup with inexpensive carbon-based electrodes and exhibits a broad substrate scope and scalability in both flow and batch reactors. The use of this method in challenging contexts is exemplified with a modular formal synthesis of jawsamycin, a natural product harboring five cyclopropane rings.

Boronic acids are among the most malleable functional groups in organic chemistry as they can be converted into almost any other functionality (1–3). Aside from these versatile interconversions, their use in the pharmaceutical industry is gaining traction, resulting in approved drugs such as Velcade, Ninlaro, and Vabomere (4). It has been shown that boronic acids can be rapidly installed from simple alkyl halides (5–19) or alkyl carboxylic acids through the intermediacy of redox-active esters (RAEs) (Fig. 1A) (20–24). Our laboratory has shown that both Ni (20) and Cu (21) can facilitate this reaction. Conversely, Aggarwal and coworkers (22) and Li and coworkers (23) demonstrated photochemical variations of the same transformation. While these state-of-the-art approaches provide complementary access to alkyl boronic acids, each one poses certain challenges. For example, the requirement of excess boron source and pyrophoric MeLi under Ni catalysis is not ideal. Although more cost-effective and operationally simple, Cu-catalyzed borylation conditions can be challenging on scale due to the heterogeneity resulting from the large excess of LiOH•H₂O required. In addition to its limited scope, Li and coworkers’ protocol requires 4 equivalence of B₂pin₂ and an expensive Ir photocatalyst. The simplicity of Aggarwal and coworkers’ approach is appealing in this regard and represents an important precedent for the current study.Open in a separate windowFig. 1.(A) Prior approaches to access alkyl boronic esters from activated acids. (B) Inspiration for initiating SET events electrochemically to achieve borylation. (C) Summary of this work.At the heart of each method described above, the underlying mechanism relies on a single electron transfer (SET) event to promote decarboxylation and form an alkyl radical species. In parallel, the related borylation of aryl halides via a highly reactive aryl radical can also be promoted by SET. While numerous methods have demonstrated that light can trigger this mechanism (Fig. 1B) (16, 25–31), simple electrochemical cathodic reduction can elicit the same outcome (32–35). It was postulated that similar electrochemically driven reactivity could be translated to alkyl RAEs. The development of such a transformation would be highly enabling, as synthetic organic electrochemistry allows the direct addition or removal of electrons to a reaction, representing an incredibly efficient way to forge new bonds (36–40). This disclosure reports a mild, scalable, and operationally simple electrochemical decarboxylative borylation (Fig. 1C) not reliant on transition metals or stoichiometric reductants. In addition to mechanistic studies of this interesting transformation, applications to a variety of alkyl RAEs, comparison to known decarboxylative borylation methods, and a formal synthesis of the polycyclopropane natural product jawsamycin [(–)-FR-900848] are presented.     

Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals

Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.

As an analogy to atomic crystals, colloidal crystals are highly ordered structures formed by colloidal particles with sizes ranging from 100 nm to several micrometers (1–6). In addition to engineering applications such as photonics, sensing, and catalysis (4, 5, 7, 8), colloidal crystals have also been used as model systems to study some fundamental processes in statistical mechanics and mechanical behavior of crystalline solids (9–14). Depending on the nature of interparticle interactions, many equilibrium and nonequilibrium colloidal self-assembly processes have been explored and developed (1, 4). Among them, the evaporation-induced colloidal self-assembly presents a number of advantages, such as large-size fabrication, versatility, and cost and time efficiency (3–5, 15–18). In a typical synthesis where a substrate is immersed vertically or at an angle into a colloidal suspension, the colloidal particles are driven to the meniscus by the evaporation-induced fluid flow and subsequently self-assemble to form a colloidal crystal with the face-centered cubic (fcc) lattice structure and the close-packed {111} plane parallel to the substrate (2, 3, 19–23) (see Fig. 1A for a schematic diagram of the synthetic setup).Open in a separate windowFig. 1.Evaporation-induced coassembly of colloidal crystals. (A) Schematic diagram of the evaporation-induced colloidal coassembly process. “G”, “M”, and “N” refer to “growth,” “meniscus,” and “normal” directions, respectively. The reaction solution contains silica matrix precursor (tetraethyl orthosilicate, TEOS) in addition to colloids. (B) Schematic diagram of the crystallographic system and orientations used in this work. (C and D) Optical image (Top Left) and scanning electron micrograph (SEM) (Bottom Left) of a typical large-area colloidal crystal film before (C) and after (D) calcination. (Right) SEM images of select areas (yellow rectangles) at different magnifications. Corresponding fast-Fourier transform (see Inset in Middle in C) shows the single-crystalline nature of the assembled structure. (E) The 3D reconstruction of the colloidal crystal (left) based on FIB tomography data and (right) after particle detection. (F) Top-view SEM image of the colloidal crystal with crystallographic orientations indicated.While previous research has focused on utilizing the assembled colloidal structures for different applications (4, 5, 7, 8), considerably less effort is directed to understand the self-assembly mechanism itself in this process (17, 24). In particular, despite using the term “colloidal crystals” to highlight the microstructures’ long-range order, an analogy to atomic crystals, little is known regarding the crystallographic evolution of colloidal crystals in relation to the self-assembly process (3, 22, 25). The underlying mechanisms for the puzzling—yet commonly observed—phenomenon of the preferred growth along the close-packed <110> direction in evaporation-induced colloidal crystals are currently not understood (3, 25–29). The <110> growth direction has been observed in a number of processes with a variety of particle chemistries, evaporation rates, and matrix materials (3, 25–28, 30), hinting at a universal underlying mechanism. This behavior is particularly intriguing as the colloidal particles are expected to close-pack parallel to the meniscus, which should lead to the growth along the <112> direction and perpendicular to the <110> direction (16, 26, 31)^*.Preferred growth along specific crystallographic orientations, also known as texture development, is commonly observed in crystalline atomic solids in synthetic systems, biominerals, and geological crystals. While current knowledge recognizes mechanisms such as the oriented nucleation that defines the future crystallographic orientation of the growing crystals and competitive growth in atomic crystals (32–34), the underlying principles for texture development in colloidal crystals remain elusive. Previous hypotheses based on orientation-dependent growth speed and solvent flow resistance are inadequate to provide a universal explanation for different evaporation-induced colloidal self-assembly processes (3, 25–29). A better understanding of the crystallographically preferred growth in colloidal self-assembly processes may shed new light on the crystal growth in atomic, ionic, and molecular systems (35–37). Moreover, mechanistic understanding of the self-assembly processes will allow more precise control of the lattice types, crystallography, and defects to improve the performance and functionality of colloidal assembly structures (38–40).     

Chlorination of arenes via the degradation of toxic chlorophenols

Aryl chlorides are among the most versatile synthetic precursors, and yet inexpensive and benign chlorination techniques to produce them are underdeveloped. We propose a process to generate aryl chlorides by chloro-group transfer from chlorophenol pollutants to arenes during their mineralization, catalyzed by Cu(NO₃)₂/NaNO₃ under aerobic conditions. A wide range of arene substrates have been chlorinated using this process. Mechanistic studies show that the Cu catalyst acts in cooperation with NO_x species generated from the decomposition of NaNO₃ to regulate the formation of chlorine radicals that mediate the chlorination of arenes together with the mineralization of chlorophenol. The selective formation of aryl chlorides with the concomitant degradation of toxic chlorophenol pollutants represents a new approach in environmental pollutant detoxication. A reduction in the use of traditional chlorination reagents provides another (indirect) benefit of this procedure.

Chlorophenols are widely encountered moieties present in herbicides, drugs, and pesticides (1). Owing to the high dissociation energies of carbon‒chloride bonds, chlorophenols biodegrade very slowly, and their prolonged exposure leads to severe ecological and environmental problems (Fig. 1A) (2–4). Several well-established technologies have been developed for the treating of chlorophenols, including catalytic oxidation (5–11), biodegradation (12–15), solvent extraction (16, 17), and adsorption (18–20) Among these methods, adsorption is the most versatile and widely used method due to its high removal efficiency and simple operation, but the resulting products are of no value, and consequently, these processes are not viable.Open in a separate windowFig. 1.Background and reaction design. (A) Examples of chlorophenol pollutants. (B) Examples of aryl chlorides. (C) The chlorination process reported herein was based on chloro-group transfer from chlorophenol pollutants.With the extensive application of substitution reactions (21, 22), transfunctionalizations (23, 24), and cross-coupling reactions (25, 26), aryl chlorides are regarded as one of the most important building blocks widely used in the manufacture of polymers, pharmaceuticals, and other types of chemicals and materials (Fig. 1B) (27–31). Chlorination of arenes is usually carried out with toxic and corrosive reagents (32–34). Less toxic and more selective chlorination reagents tend to be expensive [e.g., chloroamides (35, 36)] and are not atom economic (37–39). Consequently, from the perspective of sustainability, the ability to transfer a chloro group from unwanted chlorophenols to other substrates would be advantageous.Catalytic isofunctional reactions, including transfer hydrogenation and alkene metathesis, have been widely exploited in organic synthesis. We hypothesized that chlorination of arenes also could be achieved by chloro-group transfer, and since stockpiles of chlorophenols tend to be destroyed by mineralization and chlorophenol pollutants may be concentrated by adsorption (18–20), they could be valorized as chlorination reagents via transfer of the chloro group to arene substrates during their mineralization, thereby adding value to the destruction process (Fig. 1C). Although chlorophenol pollutants are not benign, their application as chlorination reagents, with their concomitant destruction to harmless compounds, may be considered as not only meeting the criteria of green chemistry but also potentially surpassing it. Herein, we describe a robust strategy to realize chloro-group transfer from chlorophenol pollutants to arenes and afford a wide range of value-added aryl chlorides.     

Growth and thermal maturation of the Toba magma reservoir

The Toba volcanic system in Indonesia has produced two of the largest eruptions (>2,000 km³ dense-rock equivalent [DRE] each) on Earth since the Quaternary. U–Pb crystallization ages of zircon span a period of ∼600 ky before each eruptive event, and in the run-up to each eruption, the mean and variance of the zircons’ U content decrease. To quantify the process of accumulation of eruptible magma underneath the Toba caldera, we integrated these observations with thermal and geochemical modeling. We show that caldera-forming eruptions at Toba are the result of progressive thermal maturation of the upper crustal magma reservoir, which grows and chemically homogenizes, by sustained magma influx at average volumetric rates between 0.008 and 0.01 km³/y over the past 2.2 My. Protracted thermal pulses related to magma-recharge events prime the system for eruption without necessarily requiring an increased magma-recharge rate before the two supereruptions. If the rate of magma input was maintained since the last supereruption of Toba at 75 ka, eruptible magma is currently accumulating at a minimum rate of ∼4.2 km³ per millennium, and the current estimate of the total volume of potentially eruptible magma available today is a minimum of ∼315 km³. Our approach to evaluate magma flux and the rate of eruptible magma accumulation is applicable to other volcanic systems capable of producing supereruptions and thereby could help in assessing the potential of active volcanic systems to feed supereruptions.

Supereruptions are events that eject ≥450-km³ dense-rock equivalent (DRE) of magma with a volcanic explosivity index of ≥8 (1, 2). They are commonly fed by giant silicic magma reservoirs in the upper continental crust (less than or equal to ∼15 km in depth; refs. 3–5). While it is clear that these reservoirs are assembled by protracted input of magma into the crust, it is debated whether a sudden increase of the rate of magma input is required to initiate large eruptions (6–9). High-precision zircon dating has confirmed the prolonged lifetime (10⁵ to 10⁶ y) of large magma reservoirs, but the total duration of zircon crystallization varies for different systems (8, 10–12). The varying “incubation” times could reflect differences in the rate of magma input into the reservoir, thermal maturity, and/or extrusive–intrusive ratio (e.g., ref. 7). Due to the rarity of these events, it is difficult to statistically determine the recurrence rate of supereruptions (13, 14). Thus, identifying the processes leading to these events is vital to quantify the potential hazard associated with supereruptions at a local and global scale.The Toba volcanic system has produced two supereruptions within the past 1 My (15), which provides a natural laboratory for investigating the processes that repeatedly lead to large volcanic events. Toba is located on the continental margin of the Sunda arc on Sumatra Island, Indonesia (Fig. 1A). The onset of explosive volcanism was marked by the 1.20 ± 0.16 Ma Haranggaol Dacite Tuff (HDT; ref. 16), followed by the 0.84 ± 0.03 Ma Oldest Toba Tuff (OTT; ref. 17), the 0.501 ± 0.005 Ma Middle Toba Tuff (MTT; ref. 18), and the 75.0 ± 0.9 ka Youngest Toba Tuff (YTT; ref. 19). Intense structural uplift of the Samosir Island until at least ∼2700 B.P. indicates post-YTT magmatic unrest underneath the Toba caldera (e.g., ref. 20). The OTT and YTT are supereruptions that released at least 2,300 km³ and 2,800 km³ of magma, respectively (21, 22), and generated calderas that are partly occupied by Lake Toba today. The HDT and MTT are relatively small in volume (tens of cubic kilometers DRE; ref. 15) and sourced from a similar vent location in the northern part of the large caldera (Fig. 1A). Based on a present-day low-velocity zone beneath Toba, the magma reservoir footprint is estimated to be a minimum of 70 × 30 km (23). Comparatively, using the caldera floor as a proxy for the magma reservoir footprint, it was ∼55 × 20 km for the OTT and 100 × 30 km for the YTT (15).Open in a separate windowFig. 1.Topographic map of the Toba caldera, along with age-distribution spectrum and U content of zircons from the four eruptions of Toba. (A) Approximate source-caldera areas of the HDT, OTT, MTT, and YTT are outlined (15). Stars represent the sampling locations. (Inset) The location of the Toba caldera in northern Sumatra, Indonesia. (B) Zircon age distributions for the HDT, OTT, MTT, and YTT. The colored arrows pointing to the x axis indicate zircons with older ages in respective eruptions. We present the density of the natural ages with a bandwidth equal to 1σ analytical error. Eruption ages (Ma) and number of zircon (N) analyzed in each eruption are also specified. (C) Variation of U content of zircons as a function of age for each eruption. Gray dotted lines represent the mean trend of zircon U contents of the OTT and YTT eruptions with age.     

Macrophages eat cancer cells using their own calreticulin as a guide: Roles of TLR and Btk

Macrophage-mediated programmed cell removal (PrCR) is an important mechanism of eliminating diseased and damaged cells before programmed cell death. The induction of PrCR by eat-me signals on tumor cells is countered by don’t-eat-me signals such as CD47, which binds macrophage signal-regulatory protein α to inhibit phagocytosis. Blockade of CD47 on tumor cells leads to phagocytosis by macrophages. Here we demonstrate that the activation of Toll-like receptor (TLR) signaling pathways in macrophages synergizes with blocking CD47 on tumor cells to enhance PrCR. Bruton’s tyrosine kinase (Btk) mediates TLR signaling in macrophages. Calreticulin, previously shown to be an eat-me signal on cancer cells, is activated in macrophages for secretion and cell-surface exposure by TLR and Btk to target cancer cells for phagocytosis, even if the cancer cells themselves do not express calreticulin.Programmed cell removal (PrCR) is a process of macrophage-mediated immunosurveillance by which target cells are recognized and phagocytosed (1). PrCR previously was known to be a key step concurrent with programmed cell death for the clearance of apoptotic cells, but when apoptosis is blocked, PrCR of neutrophils that are living (because of the enforced expression of bcl2) occurs precisely at the same time that PrCR removes dying wild-type neutrophils (2). Recently a role for PrCR in eliminating living tumor cells has been revealed (1). Several studies have indicated a crucial function of CD47 as an antiphagocytic don''t-eat-me signal dominating over PrCR (3–10). During cancer development, tumor cells up-regulate CD47, which protects them from PrCR (1, 3, 4, 6). Blockade of the interaction between CD47 on target cells and its receptor, signal-regulatory protein α (SIRPα), on macrophages elicits efficient PrCR of cancer cells but not of most normal cells in vitro and in vivo (Fig. 1A) (1, 3). When CD47 is blocked, cancer cells, but not normal cells, are phagocytosed because prophagocytic eat-me signals such as calreticulin (CRT) are commonly expressed on many leukemias, lymphomas, and solid tumors (Fig. 1A) (11). CRT normally is an endoplasmic reticulum (ER) protein possessing ER retention KDEL sequences but can be released to the cell surface in many instances of cell damage by cytotoxic drugs or inflammation and is recognized by macrophage LRP1/CD91 during phagocytosis of apoptotic cells (12, 13). Bruton’s tyrosine kinase (Btk) is a member of the Tec nonreceptor protein tyrosine kinase family, which plays a crucial role in the regulation of the innate immune response (14, 15). A defect of Btk leads to immunodeficiencies including X-linked hypo- or agammaglobulinemia (16–18), presumably caused by the blockade of B-cell development and perhaps related to inefficient clearance of defective B-lineage cells as well (19). Thus far, however, little is known about the molecular mechanisms by which macrophages recognize and phagocytose living cancer cells. We show here that macrophages express CRT and that Toll-like receptor (TLR) signaling through Btk results in its trafficking to the cell surface, where it can be used to mediate PrCR of appropriate tumor cells.Open in a separate windowFig. 1.Activation of TLR signaling leads to enhanced PrCR of living cancer cells. (A, Left) Schematic showing PrCR of living tumor cells by macrophages. Blockade of CD47 leads to an imbalance of eat-me over don’t-eat-me pathways, which elicits phagocytosis of tumor cells, either Fc-dependent (elicited by Fc–FcR interaction) or Fc-independent (labeled in red, representing cancer-specific eat-me signals other than Fc). (Right) A phagocytosis assay showing blockade of CD47-induced phagocytosis, with SW620 cells [control IgG-treated, anti-CD47 antibody (B6H12)–treated, or CD47^KO] as target cells and BMDMs from RAG2^−/−, γc^−/− mice. Fc receptor blocker (FcRB) reversed phagocytosis of B6H12-treated cells to the same level as inf CD47^KO cells. **P < 0.01, t test; ns, not significant. (B) A phagocytosis assay showing a screen of TLR agonists, with SW620 cells [PBS-treated, anti-CD47 antibody (Hu5F9-G4)–treated, or CD47^KO] as target cells and BMDMs from BALB/c mice. TLR agonists used in the screen were Pam3CSK4 (Pam, TLR1/2), heat-killed Listeria monocytogenes (HKLM, TLR2), poly (I:C) HMW [poly (I:C), TLR3)], lipopolysaccharide (LPS, TLR4), flagellin from Salmonella typhimurium (FLA-ST, TLR5), Pam2CGDPKHPKSF (FSL-1, TLR6/2), imiquimod (Imi, TLR7), and class B CpG oligonucleotide (ODN 1826, TLR9). Dashed lines indicate twofold phagocytosis of each condition [PBS-treated, anti-CD47 antibody (Hu5F9-G4)-treated, or CD47^KO] in the control macrophage group. Error bars represent SD.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Chirality-matched catalyst-controlled macrocyclization reactions

Macrocycles, formally defined as compounds that contain a ring with 12 or more atoms, continue to attract great interest due to their important applications in physical, pharmacological, and environmental sciences. In syntheses of macrocyclic compounds, promoting intramolecular over intermolecular reactions in the ring-closing step is often a key challenge. Furthermore, syntheses of macrocycles with stereogenic elements confer an additional challenge, while access to such macrocycles are of great interest. Herein, we report the remarkable effect peptide-based catalysts can have in promoting efficient macrocyclization reactions. We show that the chirality of the catalyst is essential for promoting favorable, matched transition-state relationships that favor macrocyclization of substrates with preexisting stereogenic elements; curiously, the chirality of the catalyst is essential for successful reactions, even though no new static (i.e., not “dynamic”) stereogenic elements are created. Control experiments involving either achiral variants of the catalyst or the enantiomeric form of the catalyst fail to deliver the macrocycles in significant quantity in head-to-head comparisons. The generality of the phenomenon, demonstrated here with a number of substrates, stimulates analogies to enzymatic catalysts that produce naturally occurring macrocycles, presumably through related, catalyst-defined peripheral interactions with their acyclic substrates.

Macrocyclic compounds are known to perform a myriad of functions in the physical and biological sciences. From cyclodextrins that mediate analyte separations (1) to porphyrin cofactors that sit in enzyme active sites (2, 3) and to potent biologically active, macrocyclic natural products (4) and synthetic variants (5–7), these structures underpin a wide variety of molecular functions (Fig. 1A). In drug development, such compounds are highly coveted, as their conformationally restricted structures can lead to higher affinity for the desired target and often confer additional metabolic stability (8–13). Accordingly, there exists an entire synthetic chemistry enterprise focused on efficient formation and functionalization of macrocycles (14–18).Open in a separate windowFig. 1.(A) Examples of macrocyclic compounds with important applications. HCV, hepatitis C virus. (B) Use of chiral ligands in metal-catalyzed or mediated stereoselective macrocyclization reactions. (C) Remote desymmetrization using guanidinylated ligands via Ullmann coupling. (D) This work: use of copper/peptidyl complexes for macrocyclization and the exploration of matched and mismatched effect.In syntheses of macrocyclic compounds, the ring-closing step is often considered the most challenging step, as competing di- and oligomerization pathways must be overcome to favor the intramolecular reaction (14). High-dilution conditions are commonly employed to favor macrocyclization of linear precursors (19). Substrate preorganization can also play a key role in overcoming otherwise high entropic barriers associated with multiple conformational states that are not suited for ring formation. Such preorganization is most often achieved in synthetic chemistry through substrate design (14, 20–22). Catalyst or reagent controls that impose conformational benefits that favor ring formation are less well known. Yet, critical precedents include templating through metal-substrate complexation (23, 24), catalysis by foldamers (25) or enzymes (26–29), or, in rare instances, by small molecules (discussed below). Characterization of biosynthetic macrocyclization also points to related mechanistic issues and attributes for efficient macrocyclizations (30–34). Coupling macrocyclization reactions to the creation of stereogenic elements is also rare (35). Metal-mediated reactions have been applied toward stereoselective macrocyclizations wherein chiral ligands transmit stereochemical information to the products (Fig. 1B). For example, atroposelective ring closure via Heck coupling has been applied in the asymmetric total synthesis of isoplagiochin D by Speicher and coworkers (36–40). Similarly, atroposelective syntheses of (+)-galeon and other diarylether heptanoid natural products were achieved via Ullman coupling using N-methyl proline by Salih and Beaudry (41). Finally, Reddy and Corey reported the enantioselective syntheses of cyclic terpenes by In-catalyzed allylation utilizing a chiral prolinol-based ligand (42). While these examples collectively illustrate the utility of chiral ligands in stereoselective macrocyclizations, such examples remain limited.We envisioned a different role for chiral catalysts when addressing intrinsically disfavored macrocyclization reactions. When unfavorable macrocyclization reactions are confronted, we hypothesized that a catalyst–substrate interaction might provide transient conformational restriction that could promote macrocyclization. To address this question, we chose to explore whether or not a chiral catalyst-controlled macrocyclization might be possible with peptidyl copper complexes. In the context of the medicinally ubiquitous diarylmethane scaffold, we had previously demonstrated the capacity for remote asymmetric induction in a series of bimolecular desymmetrizations using bifunctional, tetramethylguanidinylated peptide ligands. For example, we showed that peptidyl copper complexes were able to differentiate between the two aryl bromides during C–C, C–O, and C–N cross-coupling reactions (Fig. 1C) (43–45). Moreover, in these intermolecular desymmetrizations, a correlation between enantioselectivity and conversion was observed, revealing the catalyst’s ability to perform not only enantiotopic group discrimination but also kinetic resolution on the monocoupled product as the reaction proceeds (44). This latter observation stimulated our speculation that if an internal nucleophile were present to undergo intramolecular cross-coupling to form a macrocycle, stereochemically sensitive interactions (so-called matched and mismatched effects) (46) could be observed (Fig. 1D). Ideally, we anticipated that transition state–stabilizing interactions might even prove decisive in matched cases, and the absence of catalyst–substrate stabilizing interactions might account for the absence of macrocyclization for these otherwise intrinsically unfavorable reactions. Herein, we disclose the explicit observation of these effects in chiral catalyst-controlled macrocyclization reactions.     

Volcanically driven lacustrine ecosystem changes during the Carnian Pluvial Episode (Late Triassic)

The Late Triassic Carnian Pluvial Episode (CPE) saw a dramatic increase in global humidity and temperature that has been linked to the large-scale volcanism of the Wrangellia large igneous province. The climatic changes coincide with a major biological turnover on land that included the ascent of the dinosaurs and the origin of modern conifers. However, linking the disparate cause and effects of the CPE has yet to be achieved because of the lack of a detailed terrestrial record of these events. Here, we present a multidisciplinary record of volcanism and environmental change from an expanded Carnian lake succession of the Jiyuan Basin, North China. New U–Pb zircon dating, high-resolution chemostratigraphy, and palynological and sedimentological data reveal that terrestrial conditions in the region were in remarkable lockstep with the large-scale volcanism. Using the sedimentary mercury record as a proxy for eruptions reveals four discrete episodes during the CPE interval (ca. 234.0 to 232.4 Ma). Each eruptive phase correlated with large, negative C isotope excursions and major climatic changes to more humid conditions (marked by increased importance of hygrophytic plants), lake expansion, and eutrophication. Our results show that large igneous province eruptions can occur in multiple, discrete pulses, rather than showing a simple acme-and-decline history, and demonstrate their powerful ability to alter the global C cycle, cause climate change, and drive macroevolution, at least in the Triassic.

The Carnian Pluvial Episode (CPE; ca. 234 to ∼232 Ma; Late Triassic) was an interval of significant changes in global climate and biotas (1, 2). It was characterized by warming (3, 4) and enhancement of the hydrological cycle (5–7), linked to repeated C isotope fluctuations (8–11) and accompanied by increased rainfall (1), intensified continental weathering (9, 12), shutdown of carbonate platforms (13), widespread marine anoxia (4), and substantial biological turnover (1, 2, 10). Available stratigraphic data indicate that the Carnian climatic changes broadly coincide with, and could have been driven by, the emplacement of the Wrangellia large igneous province (LIP) (2, 4, 7, 8, 10, 14, 15) (Fig. 1A). It is postulated that the voluminous emission of volcanic CO₂, with consequent global warming and enhancement of a mega-monsoonal climate, was responsible for the CPE (9, 16), although the link is imprecise (2, 17) because the interval of Wrangellian eruptions have not yet been traced in the sedimentary records encompassing the CPE.Open in a separate windowFig. 1.Location and geological context for the study area. (A) Paleogeographic reconstruction for the Carnian (∼237 to 227 Ma) Stage (Late Triassic), showing locations of the study area and volcanic centers (revised after ref. 4, with volcanic data from refs. 4, 7, 49, and 50). (B) Tectono-paleogeographic map of the NCP during the Late Triassic (modified from ref. 21), showing the location of the study area. (C) Stratigraphic framework of the Upper Chunshuyao Formation (CSY) to the Lower Yangshuzhuang (YSZ) Formation from the Jiyuan Basin (modified from ref. 20). Abbreviations: LIP, Large Igneous Province; QDOB, Qingling-Dabie Orogenic Belt; S-NCP, southern NCP; SCP, South China Plate; Fm., Formation; m & s, coal, mudstone, and silty mudstone; s., sandstone; c, conglomerate; Dep. env., Depositional environment; and C.-P., Coniopteris-Phoenicopsis.The CPE was originally identified because of changes in terrestrial sedimentation, but most subsequent studies have been on marine strata (2, 4, 7–10). By contrast, much less is known about the effects of this climatic episode on terrestrial environments (2), although there were major extinctions and radiations among animals (including dinosaurs, crocodiles, turtles, and the first mammals and insects) and modern conifer families (2). Some of the new organisms may have flourished because of the spread of humid environments, such as the turtles and metoposaurids (18, 19).In this study, we have investigated terrestrial sediments from the Zuanjing-1 (ZJ-1) borehole in the Jiyuan Basin of the southern North China Plate (NCP) and use zircon U–Pb ages from two tuffaceous claystone horizons, fossil plant biostratigraphy, and organic C isotope (δ¹³C_org) and Hg chemostratigraphy to identify the CPE and volcanic activity.     

Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism

Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides were engineered to vary the electronic properties of a key tyrosine (M210) close to an essential electron transfer component via its replacement with site-specific, genetically encoded noncanonical amino acid tyrosine analogs. High fidelity of noncanonical amino acid incorporation was verified with mass spectrometry and X-ray crystallography and demonstrated that RC variants exhibit no significant structural alterations relative to wild type (WT). Ultrafast transient absorption spectroscopy indicates the excited primary electron donor, P*, decays via a ∼4-ps and a ∼20-ps population to produce the charge-separated state P⁺H_A⁻ in all variants. Global analysis indicates that in the ∼4-ps population, P⁺H_A⁻ forms through a two-step process, P*→ P⁺B_A⁻→ P⁺H_A⁻, while in the ∼20-ps population, it forms via a one-step P* → P⁺H_A⁻ superexchange mechanism. The percentage of the P* population that decays via the superexchange route varies from ∼25 to ∼45% among variants, while in WT, this percentage is ∼15%. Increases in the P* population that decays via superexchange correlate with increases in the free energy of the P⁺B_A⁻ intermediate caused by a given M210 tyrosine analog. This was experimentally estimated through resonance Stark spectroscopy, redox titrations, and near-infrared absorption measurements. As the most energetically perturbative variant, 3-nitrotyrosine at M210 creates an ∼110-meV increase in the free energy of P⁺B_A⁻ along with a dramatic diminution of the 1,030-nm transient absorption band indicative of P⁺B_A^– formation. Collectively, this work indicates the tyrosine at M210 tunes the mechanism of primary electron transfer in the RC.

Photosynthetic reaction centers (RCs) are the integral membrane protein assemblies responsible for nearly all the solar energy conversion maintaining our biosphere. In this study, we focus on the initial electron transfer (ET) steps in bacterial RCs from Rhodobacter sphaeroides, a three-subunit (H, L, and M) ∼100-kDa integral membrane protein complex. RCs in R. sphaeroides possess two branches of chromophores, the A and B (or L and M) branches (Fig. 1A), and each possesses nearly identical chromophore composition, orientation, and distances. The protein secondary structure is pseudo-C2 symmetric, and the symmetry-related amino acids that differ are often structurally similar (Fig. 1A) (1). Despite this high structural symmetry, ET proceeds rapidly down only the A branch of chromophores with near-unity quantum yield (2, 3). Additionally, RC ET is remarkably robust, as few structurally verified single mutations that maintain RC chromophore composition and positioning significantly impact ET kinetics or yield (1, 4–11).Open in a separate windowFig. 1.RC chromophore arrangement and energetics. (A) Chromophore arrangement in WT RCs (PDB ID: 2J8C; accessory carotenoid, chromophore phytyl tails, and quinone isoprenoid tails are removed here for clarity). Tyr at M210, the target in this work, and its symmetry-related residue Phe at L181 are shown in purple. The blue arrow indicates unidirectionality of ET down the A branch. (B) Schematic free-energy diagram of different charge-separated states in WT RCs, where P* is 1.40 eV above ground state and P⁺H_A^– is 0.25 eV below P*. The dashed magenta line and double-headed arrow next to P⁺B_A^– indicates the expected major effect of ncAA incorporation at M210 on the free energy of this state.To understand RC ET asymmetry or unidirectionality and factors underlying its robust nature, a thorough understanding of the mechanism of ET is required. In the model largely accepted in the current literature (1, 12–14), ET is initiated by excitation of the excitonically coupled bacteriochlorophyll pair P. The lowest singlet excited state P* transfers an electron to the bacteriochlorophyll B_A with a time constant of ∼3 ps to form P⁺B_A^–. B_A^– subsequently transfers an electron to the bacteriopheophytin H_A with a time constant of 1 ps, thus forming P⁺H_A^– in a two-step primary ET process, P* → P⁺B_A^– → P⁺H_A^– (1, 12, 13). An alternative model for ET has been proposed in which P* transfers an electron to H_A directly through a superexchange mechanism, as defined by Parson et al. (1). Here, the B_A chromophore mediates the electronic coupling between P* and H_A, and experimental evidence for superexchange ET must be inferred spectroscopically from the absence of P⁺B_A^– formation during transient absorption (TA) measurements and generally slower ET. In wild-type (WT) RCs, evidence favors two-step ET at room temperature (1, 12, 13, 15, 16). It has been previously proposed that minor degrees of superexchange occur in WT RCs, likely arising from or enhanced by the inherent distribution in the energies of P*, P⁺B_A^–, and P⁺H_A^– caused by protein populations with slight variations in amino acid nuclear coordinates around chromophores (5, 17–19), but this has been difficult to study experimentally (1, 12).The ET mechanisms in RCs likely have their origins in the different energies of the various charge-separated states for the two branches relative to P* and each other (Fig. 1B) (20–22), but it is difficult to determine these energetics either experimentally or theoretically (1, 23). Contributions of individual symmetry-breaking amino acid have been thoroughly studied (1, 15, 24–28), and while the importance of certain amino acids has been ascertained, the roles of local protein–chromophore interactions are not always fully understood (8, 24, 25). One highly examined residue has been the tyrosine at site M210 (RC residue numbers are preceded by the protein subunit designation: H, L, or M) because it is a clear deviation in symmetry between A and B branches (Fig. 1A), it is close to B_A, and it is the only one of 27 tyrosines that lacks a hydrogen bond acceptor. Theoretical studies indicate that the magnitude and orientation of the hydroxyl dipole of tyrosine M210 may play an important role in energetically stabilizing P⁺B_A^– (29, 30). Indeed, previous efforts to change the orientation of this tyrosine’s hydroxyl dipole significantly slowed ET (31). It is difficult, however, to subtly vary the electrostatic nature of this tyrosine using canonical mutagenesis without entirely removing the phenolic hydroxyl.To perturb the effects of the tyrosine at M210 in WT protein, we used amber stop codon suppression (32–34) to site-specifically replace it with five noncanonical amino acids (ncAAs), each a tyrosine with a single electron-donating or electron-withdrawing meta-substituent (at the 3 position). We will refer to RC protein variants by acronyms for the amino acid incorporated at M210: 3-methyltyrosine (MeY), 3-nitrotyrosine (NO₂Y), 3-chlorotyrosine (ClY), 3-bromotyrosine (BrY), and 3-iodotyrosine (IY) (Fig. 2 and SI Appendix, Fig. S1 and Table S1). In this way, we engineered a series of RC variants with more systematic electrostatic ET perturbation at this important tyrosine while minimally affecting other RC features.Open in a separate windowFig. 2.RC variants made and structurally characterized in this study, in which truncated P_A and B_A chromophores are depicted for each variant (in teal and magenta, respectively) and electron density maps from solved X-ray structures are shown (2F_o-F_c contoured at 1 σ) for tyrosine analogs at M210. Halogen variants required two different tyrosine ring conformers to model halogen substituent orientations with the contribution of each indicated, one with the halogen oriented toward P (only P_A depicted above) and the other with halogen toward B_A. The resolution for each crystal structure is denoted in black next to the P_A of each RC variant (PDB IDs for NO₂Y, MeY, ClY, BrY, and IY RCs are 7MH9, 7MH8, 7MH3, 7MH4, and 7MH5, respectively; SI Appendix, Table S2).     

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

RAS driven cancers are common (1), difficult to treat (2), and a major cause of death worldwide (3). KRAS, the isoform most frequently associated with disease, is mutated in nearly all pancreatic cancers and often in lung and colorectal cancers (4, 5). Only recently, with the development of covalent inhibitors of the G12C mutant (6), has direct targeting of RAS been successful, and more broadly applicable inhibitors are needed.The RAS subfamily comprises peripheral membrane proteins with a conserved globular GTP-binding domain (G-domain) (7) that is tethered to the cell membrane by a prenylated ∼20-residue C-terminal domain called the hypervariable region (HVR) (8, 9). RAS proteins function as molecular switches whose active conformations, stabilized by GTP binding, interact with several protein effectors to control cell growth, proliferation, differentiation, and migration (10). Constitutive activation of oncogenic RAS perturbs several cellular signaling cascades, including the MAPK pathway, which RAS accesses via activation of RAF kinase at the plasma membrane (PM).There is substantial interest in assessing the ability of RAS molecules to dimerize (11–13) or colocalize (14–17) at the membrane, because RAS-dependent RAF activation requires dimerization of RAF (18–20). Although wild-type KRAS4b, a common splice variant of KRAS (hereafter referred to as RAS), does not dimerize on two-component supported lipid bilayers (21), it preferentially colocalizes with anionic lipids in the liquid-disordered domains of giant unilamellar vesicles (22) and clusters on the scale of tens of nanometers in extracted PM sheets (14, 23, 24).Preferential interaction of RAS with anionic lipids is mediated by 11 positively charged lysines in its HVR (25, 26). However, charge complementarity is insufficient to fully describe RAS nanoclustering, which is exquisitely sensitive to lipid composition (27–29). Even less is known about the influence of RAS–lipid coupling on RAS self-assembly and effector activation. While several feasible dimer interfaces have been reported (11–13, 15, 30–37), how RAS forms dimers, if at all, remains a major area of interest.The fundamental challenge of investigating RAS activation events is that many of the proposed mechanisms involve time and lengths scales currently not accessible. For example, functional events in RAS dynamics that may preferentially depend on local depletion or enrichment of specific lipids are extremely difficult to observe directly, either in computational or biological experiments. Experimentally, we use single-particle tracking (SPT) to follow HaloTag-conjugated RAS via total internal reflection fluorescence microscopy in live HeLa cells. While the broad heterogeneity in lateral diffusion observed by SPT (Fig. 1A) is indicative of multiple RAS subpopulations that have distinct patterns of interaction with lipids and other cellular components, it provides little insight on local lipid environments and their effect on RAS behavior. Similarly, we can use detailed molecular dynamics (MD) simulations to probe specific lipid environments, but systems large enough to support substantial fluctuations in lipid and protein concentrations cannot be practically simulated long enough to observe relevant fluctuations. Instead, we present a multiscale infrastructure that directly couples a macroscale continuum simulation capable of observing RAS clustering and long-range lipid rearrangement, with a massive ensemble of microscale MD simulations that provides detailed insights into local dynamics. Both scales are connected through a machine learning (ML) informed dynamic sampling process (38), which enables mapping of findings from the MD simulations onto the continuum simulation, resulting in microscale insights that are observable over macrospatial and temporal scales.Open in a separate windowFig. 1.Experimental input and computational approach. (A) Diffusion mapping of single molecules of KRAS4b tethered to or within 100 nm of the PM in a 16 × 16-μm² region of a live HeLa cell accumulated over 10 s. (B) Crystal structures of wild-type KRAS in active (green and blue; GppNHp-bound) and inactive (gray; GppCH2p-bound configurations). (C) Average macro model lipid composition. (D–F) The Multiscale Machine-learned Modeling Infrastructure (MuMMI). (D) Representative snapshots of each of the different lipid distributions in the inner leaflet of a 0.3 × 0.3-μm² region of the full 1 × 1-μm² macro simulation; color saturation indicates local lipid density. (E) Schematic illustrating latent space encoding of lipid composition in 30 × 30-nm² membrane patches. From the candidate patches (blue and green), those that are most dissimilar (green) to existing (white) CG simulations are selected and used to spawn new CG simulations. (F) Representative CG simulation systems (water not shown). (G) Improvement of macro model parameter inputs from feedback iteration. (H) Distribution of CG simulation duration and (Inset) number of RAS per patch.More specifically, to enable simulations of active wild-type RAS, we solve its crystal structure bound to the GTP analog GppNHp at a resolution of 2.5 Å (Fig. 1B and SI Appendix, S1.2.2). We choose to focus the effort on wild-type GTP-loaded KRAS4b because GTP hydrolysis will not occur on the time scale of the simulations, and because available structures of wild-type or oncogenic KRAS4b bound to the RAS binding domain (RBD) of RAF1 are similar. This present work will serve as the foundation for understanding activation of RAF by GTP-loaded RAS. We mimic the composition of a biologically relevant PM (39) by employing an asymmetric eight-lipid mixture (40), here called the average RAS lipid composition (ARC) and is composed of cholesterol, phosphatidylcholines (PC), phosphatidylethanolamines (PE), phosphatidylserine (PS), phosphatidylinositol bisphosphate (PIP2), and sphingomyelin (SM), with varying acyl chain length and saturation (Fig. 1C and SI Appendix, S1.2.1).     

From the Cover: INAUGURAL ARTICLE by a Recently Elected Academy Member:Nickel phlorin intermediate formed by proton-coupled electron transfer in hydrogen evolution mechanism

The development of more effective energy conversion processes is critical for global energy sustainability. The design of molecular electrocatalysts for the hydrogen evolution reaction is an important component of these efforts. Proton-coupled electron transfer (PCET) reactions, in which electron transfer is coupled to proton transfer, play an important role in these processes and can be enhanced by incorporating proton relays into the molecular electrocatalysts. Herein nickel porphyrin electrocatalysts with and without an internal proton relay are investigated to elucidate the hydrogen evolution mechanisms and thereby enable the design of more effective catalysts. Density functional theory calculations indicate that electrochemical reduction leads to dearomatization of the porphyrin conjugated system, thereby favoring protonation at the meso carbon of the porphyrin ring to produce a phlorin intermediate. A key step in the proposed mechanisms is a thermodynamically favorable PCET reaction composed of intramolecular electron transfer from the nickel to the porphyrin and proton transfer from a carboxylic acid hanging group or an external acid to the meso carbon of the porphyrin. The C–H bond of the active phlorin acts similarly to the more traditional metal-hydride by reacting with acid to produce H₂. Support for the theoretically predicted mechanism is provided by the agreement between simulated and experimental cyclic voltammograms in weak and strong acid and by the detection of a phlorin intermediate through spectroelectrochemical measurements. These results suggest that phlorin species have the potential to perform unique chemistry that could prove useful in designing more effective electrocatalysts.Direct solar-to-fuel processes are important components of global energy sustainability efforts (1, 2). Such processes include the hydrogen evolution reaction (HER), oxidation of water to oxygen, and reduction of CO₂ to hydrocarbons (3, 4). Proton-coupled electron transfer (PCET), which is generally defined in terms of coupling between electron transfer (ET) and proton transfer (PT) reactions, is essential to all of these processes. PCET can be classified as occurring via either a sequential or a concerted mechanism (5, 6). The mechanism is determined to be sequential rather than concerted if a stable intermediate associated with initial ET or PT can be identified. This distinction is not rigorous, however, because the identification of a stable intermediate may depend on the experimental approach or the level of theory, as well as the lifetime of the intermediate. Regardless of the specific mechanism, the coupling of ET and PT plays a significant role in a wide range of energy conversion processes (7–11). Moreover, the coupling of ET and PT can be enhanced by incorporating proton relays into molecular catalysts, exploiting the proximal positioning of the proton donor and acceptor (12–16). Recognition and characterization of successful PCET motifs within molecular electrocatalysts provides insight into the design of efficient catalytic processes (17–19).Cobalt and nickel metalloporphyrins, depicted in Fig. 1, have been investigated as HER electrocatalysts (20, 21). Experimental (22) and theoretical (23) examination of the key PCET step within the HER mechanism of the cobalt “hangman” complex (the cobalt analog of [1-H] in Fig. 1) revealed a sequential ET–PT mechanism, with an experimentally measured PT rate constant k_PT = 8.5 × 10⁶ s⁻¹ (22). In the proposed mechanism, the formally Co(I) is reduced to a Co(“0.5”) complex in which the unpaired electron is shared between the metal and the ligands, breaking the aromaticity of the porphyrin ring. Subsequent PT from the carboxylic acid proton of the hangman moiety to the porphyrin meso carbon, forming a cobalt phlorin intermediate, was hypothesized on the basis of a theoretical study (23). In particular, the calculations indicated that this PT to the porphyrin is structurally and thermodynamically favored over PT to the metal center, and the calculated PT rate constant k_PT = 1.4 × 10⁶ s⁻¹ is consistent with the experimental value. Upon protonation of the hangman carboxylate by benzoic acid and additional electrochemical reduction, H₂ is thermodynamically favored to self-eliminate from the complex (23). With strong acid, H₂ is evolved through the more traditional protonation of the metal to generate a metal-hydride, which is more thermodynamically favorable than phlorin formation. For the nickel hangman complex ([1-H] in Fig. 1), previous computational results suggested that the PT step involves a proton acceptor other than the nickel center (21), as was the case for the cobalt analog (23), but the specific mechanism was not determined.Open in a separate windowFig. 1.Structures of nickel porphyrins [1-H] and [3]. Select carbon atoms of the porphyrin ring are labeled according to position, including meso carbons 5, 10, 15, and 20. Complex [2] is the analog of [1-H], where a bromine atom replaces the carboxylic acid substituent.In this paper, we use computational and experimental methods to elucidate the full catalytic cycle for the electrochemical HER catalyzed by the nickel metalloporphyrins [1-H] and [3]. On the basis of density functional theory (DFT) calculations, referenced to values from experimental cyclic voltammetry to enhance the quantitative accuracy, we propose mechanisms for the HER in the presence of weak or strong acid. Our calculations indicate that [1-H] and [3] evolve H₂ through key phlorin intermediates, in which the meso carbon of the porphyrin is protonated, and that no nickel-hydride complexes are formed. Spectroelectrochemical experiments provide evidence of the phlorin intermediate formed via protonation of the dianionic species [3]^2–. Moreover, simulated cyclic voltammograms (CVs) based on the proposed mechanism, in conjunction with the calculated reduction potentials, pK_a’s, and free energy barriers, provide further support of this mechanism through agreement with experimental CVs.     

Two-dimensional fractal nanocrystals templating for substantial performance enhancement of polyamide nanofiltration membrane

In this study, we report the emergence of two-dimensional (2D) branching fractal structures (BFS) in the nanoconfinement between the active and the support layer of a thin-film-composite polyamide (TFC-PA) nanofiltration membrane. These BFS are crystal dendrites of NaCl formed when salts are either added to the piperazine solution during the interfacial polymerization process or introduced to the nascently formed TFC-PA membrane before drying. The NaCl dosing concentration and the curing temperature have an impact on the size of the BFS but not on the fractal dimension (∼1.76). The BFS can be removed from the TFC-PA membranes by simply dissolving the crystal dendrites in deionized water, and the resulting TFC-PA membranes have substantially higher water fluxes (three- to fourfold) without compromised solute rejection. The flux enhancement is believed to be attributable to the distributed reduction in physical binding between the PA active layer and the support layer, caused by the exertion of crystallization pressure when the BFS formed. This reduced physical binding leads to an increase in the effective area for water transport, which, in turn, results in higher water flux. The BFS-templating method, which includes the interesting characteristics of 2D crystal dendrites, represents a facile, low-cost, and highly practical method of enhancing the performance of the TFC-PA nanofiltration membrane without having to alter the existing infrastructure of membrane fabrication.

Thin-film composite polyamide (TFC-PA) membranes are widely used in reverse osmosis and nanofiltration (NF), which have extensive and continuously growing applications in water treatment, desalination, and wastewater reuse (1–4). Typical TFC-PA membranes are fabricated using interfacial polymerization (IP), which involves a polymerizing reaction between amine and acid chloride precursors at the water–oil interface (5–9). In a typical IP for producing TFC-PA NF membranes, a polyether sulfone (PES) ultrafiltration membrane is first impregnated with an aqueous solution of piperazine (PIP) and then placed into contact with a hexane solution of trimesoyl chloride (TMC). The PIP monomers diffuse across the water–hexane interface and react with the TMC to form a cross-linked dense PA film that serves as the active layer for water–salt separation (3, 8, 10). This PA film is tightly bound to the underlying PES support layer, and the way they bind to each has a strong impact on the water flux of the resulting TFC-PA membrane (11–15).Enhancing the water flux of an NF membrane without compromising its solute rejection can potentially lead to substantial savings in treatment cost and has sizable practical impacts due to the broad application of TFC-PA membranes. While extensive research (9, 10, 16–25) has been performed with the goal of performance enhancement, many promising approaches (10, 16–25) reported in the literature require significant modifications of the existing infrastructure or method of manufacturing TFC-PA membranes and thus are prohibitively complex or too expensive to implement. A desirable approach for enhancing TFC-PA membrane performance should be simple, low cost, effective, and readily integrated into the existing method of TFC-PA membrane fabrication.Herein, we report an elegant and highly practical method using two-dimensional (2D) fractal crystal dendrites to dramatically increase the water permeance of the TFC-PA NF membrane while maintaining its solute rejection performance. By adding NaCl to the aqueous PIP solution during the IP process, we observed that NaCl crystal dendrites emerged in the confinement between the PA layer and the PES support when the TFC-PA membrane was cured by heat (Fig. 1 A–C). These spectacular branching fractal structures (BFS) are considered to be 2D because they are less thick when compared with the overall size of the BFS sprawling along the plane parallel to the membrane surface. Dissolving the PES support using dimethylformamide revealed a large number of crystals adhering to the bottom of the PA film (SI Appendix, Figs. S1 and S2), confirming the position of the BFS to be between the PA active layer and the PES support. Elemental analysis using energy-dispersive X-ray spectroscopy (Fig. 1 D and E) and crystal structure analysis using X-ray diffraction (SI Appendix, Fig. S3) confirmed that these 2D BFS were indeed NaCl crystals.Open in a separate windowFig. 1.Formation process and surface morphology of BFS-templated TFC-PA membrane. (A) Schematic illustration of the process for preparing a BFS-templated TFC-PA membrane via interfacial polymerization. (B) Surface morphology of the BFS-templated TFC-PA membrane. (C) Close-up surface morphology of the BFS-templated TFC-PA membrane. (D and E) Elemental mapping images of Na (D) and Cl (E) on the surface of a BFS-templated TFC-PA membrane. (NaCl concentration in PIP solution: 8 g·L⁻¹; curing temperature: 60 °C).