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.     

Electrophilic aromatic substitution reactions of compounds with Craig-Möbius aromaticity

Electrophilic aromatic substitution (EAS) reactions are widely regarded as characteristic reactions of aromatic species, but no comparable reaction has been reported for molecules with Craig-Möbius aromaticity. Here, we demonstrate successful EAS reactions of Craig-Möbius aromatics, osmapentalenes, and fused osmapentalenes. The highly reactive nature of osmapentalene makes it susceptible to electrophilic attack by halogens, thus osmapentalene, osmafuran-fused osmapentalene, and osmabenzene-fused osmapentalene can undergo typical EAS reactions. In addition, the selective formation of a series of halogen substituted metalla-aromatics via EAS reactions has revealed an unprecedented approach to otherwise elusive compounds such as the unsaturated cyclic chlorirenium ions. Density functional theory calculations were conducted to study the electronic effect on the regioselectivity of the EAS reactions.

Aromaticity, a core concept in chemistry, was initially introduced to account for the bonding, stability, reactivity, and other properties of many unsaturated organic compounds. There have been many elaborations and extensions of the concept of aromaticity (1, 2). The concepts of Hückel aromaticity and Möbius aromaticity are widely accepted (Fig. 1A). A π-aromatic molecule of the Hückel type is planar and has 4n + 2 conjugated π-electrons (n = 0 or an integer), whereas a Möbius aromatic molecule has one twist of the π-system, similar to that in a Möbius strip, and 4n π-electrons (3, 4). Since the discovery of naphthalene in 1821, aromatic chemistry has developed into a rich field and with a variety of subdisciplines over the course of its 200-y history, and the concept of aromaticity has been extended to other nontraditional structures with “cyclic delocalization of mobile electrons” (5). For example, benzene-like metallacycles—predicted by Hoffmann et al. as metallabenzenes—in which a metal replaces a C–H group in the benzene ring (6), have garnered extensive research interest from both experimentalists and theoreticians (7–12). As paradigms of the metalla-aromatic family, most complexes involving metallabenzene exhibit thermodynamic stability, kinetic persistence, and chemical reactivity associated with the classical aromaticity concept (13–15). Typically, like benzene, metallabenzene can undergo characteristic reactions of aromatics such as electrophilic aromatic substitution (EAS) reactions (16–18) (Fig. 1B, I) and nucleophilic aromatic substitution reactions (19–21).Open in a separate windowFig. 1.Schematic representations of aromaticity classification (A) and EAS reactions (B) of benzene, metallabenzene, and polycyclic metallacycles with Craig-Möbius aromaticity.The incorporation of transition metals has also led to an increase in the variety of the aromatic families (22–25). We have reported that stable and highly unusual bicyclic systems, metallapentalenes (osmapentalenes), benefit from Craig-Möbius aromaticity (26–30). In contrast to other reported Möbius aromatic compounds with twisted topologies, which are known as Heilbronner-Möbius aromatics (31–34), the involvement of transition metal d orbitals in π-conjugation switches the Hückel anti-aromaticity of pentalene into the planar Craig-Möbius aromaticity of metallapentalene (35–38) (Fig. 1A, III). Both the twisted topology and the planar Craig-Möbius aromaticity are well established and have been accepted as reasonable extensions of aromaticity (39–43). There has been no experimental evidence, however, as to whether these Möbius aromatic molecules can undergo classical aromatic substitution reactions, such as EAS reactions, instead of addition reactions. Given the key role of EAS in aromatic chemistry to obtain various derivatives, we sought to extend the understanding of the reactivity paradigm in the metalla-aromatic family.Our recent synthetic efforts associated with the metallapentalene system prompted us to investigate whether typical EAS reactions could proceed in these Craig-Möbius aromatics. If so, how could substitution be achieved in the same way that it is with traditional Hückel aromatics such as benzenes? In this paper, we present EAS reactions, mainly the halogenation of osmapentalene, osmafuran-fused osmapentalene, and osmabenzene-fused osmapentalene, which follow the classic EAS mechanistic scheme (Fig. 1B). With the aid of density functional theory (DFT) calculations, we characterized the effects on EAS reactivity and regioselectivity.     

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.     

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.     

Self-assembly of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with predictable size and number of bilayers

A constitutional isomeric library synthesized by a modular approach has been used to discover six amphiphilic Janus dendrimer primary structures, which self-assemble into uniform onion-like vesicles with predictable dimensions and number of internal bilayers. These vesicles, denoted onion-like dendrimersomes, are assembled by simple injection of a solution of Janus dendrimer in a water-miscible solvent into water or buffer. These dendrimersomes provide mimics of double-bilayer and multibilayer biological membranes with dimensions and number of bilayers predicted by the Janus compound concentration in water. The simple injection method of preparation is accessible without any special equipment, generating uniform vesicles, and thus provides a promising tool for fundamental studies as well as technological applications in nanomedicine and other fields.Most living organisms contain single-bilayer membranes composed of lipids, glycolipids, cholesterol, transmembrane proteins, and glycoproteins (1). Gram-negative bacteria (2, 3) and the cell nucleus (4), however, exhibit a strikingly special envelope that consists of a concentric double-bilayer membrane. More complex membranes are also encountered in cells and their various organelles, such as multivesicular structures of eukaryotic cells (5) and endosomes (6), and multibilayer structures of endoplasmic reticulum (7, 8), myelin (9, 10), and multilamellar bodies (11, 12). This diversity of biological membranes inspired corresponding biological mimics. Liposomes (Fig. 1) self-assembled from phospholipids are the first mimics of single-bilayer biological membranes (13–16), but they are polydisperse, unstable, and permeable (14). Stealth liposomes coassembled from phospholipids, cholesterol, and phospholipids conjugated with poly(ethylene glycol) exhibit improved stability, permeability, and mechanical properties (17–20). Polymersomes (21–24) assembled from amphiphilic block copolymers exhibit better mechanical properties and permeability, but are not always biocompatible and are polydisperse. Dendrimersomes (25–28) self-assembled from amphiphilic Janus dendrimers and minidendrimers (26–28) have also been elaborated to mimic single-bilayer biological membranes. Amphiphilic Janus dendrimers take advantage of multivalency both in their hydrophobic and hydrophilic parts (23, 29–32). Dendrimersomes are assembled by simple injection (33) of a solution of an amphiphilic Janus dendrimer (26) in a water-soluble solvent into water or buffer and produce uniform (34), impermeable, and stable vesicles with excellent mechanical properties. In addition, their size and properties can be predicted by their primary structure (27). Amphiphilic Janus glycodendrimers self-assemble into glycodendrimersomes that mimic the glycan ligands of biological membranes (35). They have been demonstrated to be bioactive toward biomedically relevant bacterial, plant, and human lectins, and could have numerous applications in nanomedicine (20).Open in a separate windowFig. 1.Strategies for the preparation of single-bilayer vesicles and multibilayer onion-like vesicles.More complex and functional cell mimics such as multivesicular vesicles (36, 37) and multibilayer onion-like vesicles (38–40) have also been discovered. Multivesicular vesicles compartmentalize a larger vesicle (37) whereas multibilayer onion-like vesicles consist of concentric alternating bilayers (40). Currently multibilayer vesicles are obtained by very complex and time-consuming methods that do not control their size (39) and size distribution (40) in a precise way. Here we report the discovery of “single–single” (28) amphiphilic Janus dendrimer primary structures that self-assemble into uniform multibilayer onion-like dendrimersomes (Fig. 1) with predictable size and number of bilayers by simple injection of their solution into water or buffer.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo

Abscisic acid (ABA) is a key plant hormone that mediates both plant biotic and abiotic stress responses and many other developmental processes. ABA receptor antagonists are useful for dissecting and manipulating ABA’s physiological roles in vivo. We set out to design antagonists that block receptor–PP2C interactions by modifying the agonist opabactin (OP), a synthetically accessible, high-affinity scaffold. Click chemistry was used to create an ∼4,000-member library of C4-diversified opabactin derivatives that were screened for receptor antagonism in vitro. This revealed a peptidotriazole motif shared among hits, which we optimized to yield antabactin (ANT), a pan-receptor antagonist. An X-ray crystal structure of an ANT–PYL10 complex (1.86 Å) reveals that ANT’s peptidotriazole headgroup is positioned to sterically block receptor–PP2C interactions in the 4′ tunnel and stabilizes a noncanonical closed-gate receptor conformer that partially opens to accommodate ANT binding. To facilitate binding-affinity studies using fluorescence polarization, we synthesized TAMRA–ANT. Equilibrium dissociation constants for TAMRA–ANT binding to Arabidopsis receptors range from ∼400 to 1,700 pM. ANT displays improved activity in vivo and disrupts ABA-mediated processes in multiple species. ANT is able to accelerate seed germination in Arabidopsis, tomato, and barley, suggesting that it could be useful as a germination stimulant in species where endogenous ABA signaling limits seed germination. Thus, click-based diversification of a synthetic agonist scaffold allowed us to rapidly develop a high-affinity probe of ABA–receptor function for dissecting and manipulating ABA signaling.

The phytohormone abscisic acid (ABA) controls numerous physiological processes in plants ranging from seed development, germination, and dormancy to responses for countering biotic and abiotic stresses (1). ABA binds to the PYR/PYL/RCAR (Pyrabactin Resistance 1/PYR1-like/Regulatory Component of ABA Receptor) soluble receptor proteins (2, 3) and triggers a conformational change in a flexible “gate” loop flanking the ligand-binding pocket such that the ABA–receptor complex can then bind to and inhibit clade A type II C protein phosphatases (PP2Cs), which normally dephosphorylate and inactivate SNF1-related protein kinase 2 (SnRK2). This, in turn, leads to SnRK2 activation, phosphorylation of downstream targets, and multiple cellular outputs (4, 5).Chemical modulators of ABA perception have been sought as both research tools for dissecting ABA’s role in plant physiology and for their potential agricultural utility (6, 7). Dozens of ABA receptor agonists, which reduce transpiration and water use by inducing guard cell closure, have been developed and are being explored as chemical tools for mitigating the effects of drought on crop yields (7–23), most of them either being analogs of ABA or sulfonamides similar to quinabactin (24). ABA receptor antagonists could conceivably be useful in cases where water is not limiting, for example, to increase transpiration and gas exchange under elevated CO₂ in glasshouse agriculture, as germination stimulators, and for studying the ABA dependence of physiological processes, among other applications (25–31). Thus, both ABA receptor agonists and antagonists have potential uses as research tools and for plant biotechnology.In principle, there are at least two mechanisms for blocking ABA receptor activation: by preventing gate closure, which is necessary for PP2C binding, or by sterically disrupting the activated, closed-gate receptor conformer from binding to PP2Cs. Prior efforts to design antagonists have focused on the latter strategy and include multiple ABA-derived ligands such as AS6 (25), PanMe (26), 3′-alkyl ABA (30–32), 3′-(phenyl alkynyl) ABA (33), or ligands derived from tetralone ABA (34) with varying degrees of conformational restriction (27, 28, 35). With the exception of PanMe, these antagonists have linkers attached to the 3′ carbon of ABA or 11′ carbon of tetralone ABA, which is positioned to disrupt receptor–PP2C interactions by protruding through the 3′ tunnel. PanMe was created by modifying ABA’s C4′ (Fig. 1) with a toluylpropynyl ether substituent designed to occupy the 4′ tunnel, a site of close receptor–PP2C contact (26). Structural studies showed that this 4′ moiety adopts two conformations, one that resides in the 4′ tunnel and another that occupies the adjacent 3′ tunnel (26). Collectively, these elegant studies have demonstrated that antagonists of receptor–PP2C interactions can be designed by modifying agonists at sites situated proximal to the 3′ or 4′ tunnels. Despite these advances, current antagonists have limitations. For example, PanMe, which has low nanomolar affinity for the subfamily II receptor PYL5, is limited by relatively low activity on subfamily I and III ABA receptors, and as we show here, the ABA antagonist AA1 (36) (Fig. 1) lacks detectable antagonist activity in vitro and is, therefore, unlikely to be a true ABA receptor antagonist. Together, these data suggest that higher-affinity pan-antagonists and/or molecules with increased bioavailability will be necessary to more efficiently block endogenous ABA signaling. We set out to address these limitations by modifying the scaffold of the synthetic ABA agonist opabactin (OP), which has an approximately sevenfold increase in both affinity and bioactivity relative to ABA (21). We describe an OP derivative called antabactin (ANT) and show that it is a high-affinity binder and antagonist of ABA receptors that disrupts ABA-mediated signaling in vivo.Open in a separate windowFig. 1.Structures of ABA, PanMe, and AA1.     

Volatile-consuming reactions fracture rocks and self-accelerate fluid flow in the lithosphere

Hydration and carbonation reactions within the Earth cause an increase in solid volume by up to several tens of vol%, which can induce stress and rock fracture. Observations of naturally hydrated and carbonated peridotite suggest that permeability and fluid flow are enhanced by reaction-induced fracturing. However, permeability enhancement during solid-volume–increasing reactions has not been achieved in the laboratory, and the mechanisms of reaction-accelerated fluid flow remain largely unknown. Here, we present experimental evidence of significant permeability enhancement by volume-increasing reactions under confining pressure. The hydromechanical behavior of hydration of sintered periclase [MgO + H₂O → Mg(OH)₂] depends mainly on the initial pore-fluid connectivity. Permeability increased by three orders of magnitude for low-connectivity samples, whereas it decreased by two orders of magnitude for high-connectivity samples. Permeability enhancement was caused by hierarchical fracturing of the reacting materials, whereas a decrease was associated with homogeneous pore clogging by the reaction products. These behaviors suggest that the fluid flow rate, relative to reaction rate, is the main control on hydromechanical evolution during volume-increasing reactions. We suggest that an extremely high reaction rate and low pore-fluid connectivity lead to local stress perturbations and are essential for reaction-induced fracturing and accelerated fluid flow during hydration/carbonation.

Hydration and carbonation reactions in the crust and mantle transport H₂O and CO₂ from Earth’s surface to the interior and control volatile budgets within the Earth (1–6). These reactions are characterized by solid-volume increase, by up to several tens of vol%, which induces stress that may lead to fracturing (7–10). The driving force of such stress generation is the thermodynamic free energy released when metastable anhydrous/noncarbonate minerals react with fluids (7). The stress generated by the reaction has the potential to cause rock fracture and fragmentation (7, 11–13), thereby increasing the reactive surface area and fluid flow and further accelerating the reactions (7, 8, 14). Such chemical breaking of rocks, or reaction-induced fracturing, appears to be important in driving hydration and carbonation reactions to completion (8, 15, 16) in an otherwise self-limiting process where reaction products can clog pores and suppress fluid flow, thereby hindering the reaction (15, 17).Observations of naturally serpentinized and fractured ultramafic rocks indicate a volume increase of 20 to 60% during hydration reactions (13, 18–20), providing evidence of an accelerated supply of fluids during hydration (Fig. 1 A and B). Natural carbonation of ultramafic rocks is also associated with extensive fracture networks, and reaction-induced fracturing is considered a key process in mineral carbonation (Fig. 1C) (7, 8, 21). Numerical simulations indicate a positive feedback between volume-increasing reaction, fracturing, and fluid flow (10, 22–32). Laboratory experiments partially reproduce fracturing during peridotite carbonation, serpentinization, and periclase hydration (29, 33–36); however, hydrothermal flow-through experiments of peridotite serpentinization and carbonation show a decrease in permeability and deceleration of fluid flow and reaction rate (37–42). Observations of the natural carbonation of serpentinized peridotite indicate the decrease in permeability and reduced fluid flow and reaction rate are a consequence of pore clogging related to carbonation (43). Until now, no experimental studies have shown a clear increase in permeability during expansive fluid–rock reactions under confining pressure. As such, despite their geological and environmental importance, the evolution of expansive fluid–rock reactions remains difficult to predict, owing to the complex hydraulic–chemical–mechanical feedbacks underlying these reactions (15, 16, 44). The processes controlling the self-acceleration or deceleration of these reactions remain largely unknown.Open in a separate windowFig. 1.Reaction-induced fractures related to natural hydration/carbonation. (A) Polygonal block of serpentinite cut by planar lizardite veins, extracted from a serpentinite body, San Andreas Lake, California. (B) Photomicrograph of mesh structure in partly serpentinized peridotite, Redwood City serpentinite, California [crossed-polarized light (61)]. (C) Quartz veins in silica–carbonate rocks (i.e., listvenite, a carbonated ultramafic rock) that occur along the boundaries of serpentinite bodies, San Jose, California. ol, olivine; serp, serpentine (lizardite ± antigorite mixture); br, brucite.Here, we use the hydration of periclase to brucite [MgO + H₂O → Mg(OH)₂] as an analog for solid-volume–increasing reactions in the Earth. This reaction produces an extreme solid-volume increase of 119%, with a high reaction rate at 100 to 600 °C (45). Previous experimental studies on periclase hydration have revealed that extensive fracturing occurs under certain conditions (29, 33, 35), yet the links between fracturing experiments (periclase hydration), nonfracturing experiments (peridotite hydration/carbonation), and natural observations are unknown. On the basis of in situ observations of fluid flow during the reactions, we clearly show that fluid flow and associated permeability are strongly enhanced by solid-volume–increasing reactions under confining pressure (i.e., at simulated depth). Based on the experimental results and nondimensional parameterization, we propose that the ratio of the initial fluid flow rate to the reaction rate has a primary control on the self-acceleration and deceleration of fluid flow and reactions during hydration and carbonation within the Earth.     

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.     

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).     

Opacity and conductivity measurements in noble gases at conditions of planetary and stellar interiors

The noble gases are elements of broad importance across science and technology and are primary constituents of planetary and stellar atmospheres, where they segregate into droplets or layers that affect the thermal, chemical, and structural evolution of their host body. We have measured the optical properties of noble gases at relevant high pressures and temperatures in the laser-heated diamond anvil cell, observing insulator-to-conductor transformations in dense helium, neon, argon, and xenon at 4,000–15,000 K and pressures of 15–52 GPa. The thermal activation and frequency dependence of conduction reveal an optical character dominated by electrons of low mobility, as in an amorphous semiconductor or poor metal, rather than free electrons as is often assumed for such wide band gap insulators at high temperatures. White dwarf stars having helium outer atmospheres cool slower and may have different color than if atmospheric opacity were controlled by free electrons. Helium rain in Jupiter and Saturn becomes conducting at conditions well correlated with its increased solubility in metallic hydrogen, whereas a deep layer of insulating neon may inhibit core erosion in Saturn.Noble gases play important roles in the evolution and dynamics of planets and stars, especially where they appear in a condensed, purified state. In gas giant planets, helium and neon can precipitate as rain in metallic hydrogen envelopes, leading to planetary warming and specifically the anomalously slow cooling of Saturn (1–8). In white dwarf stars cooling can be especially fast due to the predicted low opacity of dense helium atmospheres, affecting the calibration of these objects as cosmological timekeepers (9–12). In these systems, the transformation of dense noble gases (particularly He) from optically transparent insulators to opaque electrical conductors is of special importance (2, 9, 11, 12).Dense noble gases are expected to show systematic similarities in their properties at extreme conditions (13–17); however, a general understanding of their insulator–conductor transformation remains to be established. Xe is observed to metallize near room temperature under pressures similar to those at Earth’s core–mantle boundary (18, 19). Ar and He are observed to conduct only at combined high pressure and temperature (12, 13, 17). Ne is predicted to have the highest metallization pressure of all known materials—10³ times that of Xe and 10 times that of He (14, 18, 20, 21)—and has never been documented outside of its insulating state. Experimental probes of extreme densities and temperatures in noble gases have previously relied on dynamic compression by shock waves (12, 13, 17, 22–24). However, in such adiabatic experiments, light and compressible noble gases heat up significantly and can ultimately reach density maxima (12, 13, 17, 21, 24, 25), so that conditions created often lie far from those deep within planets (7, 8) and stars (9).Here we report experiments in the laser-heated diamond anvil cell (15, 16, 26–29) on high-density and high-temperature states of the noble gases Xe, Ar, Ne, and He (Fig. 1). Rapid heating and cooling of compressed samples using pulsed laser heating (26, 27) is coupled with time domain spectroscopy of thermal emission (26) to determine sample temperature and transient absorption to establish corresponding sample optical properties (Figs. S1 and S2). A sequence of heat cycles to increasing temperature documents optical changes in these initially transparent insulators.Open in a separate windowFig. 1.Creating and probing extreme states of noble gases. (A) Configuration of laser heating and transient absorption probing of the diamond anvil cell, with probe beams transmitted through the cell into the detection system. (B) Microscopic view of the diamond cell cavity, which contains a noble gas sample and a metal foil (Ir) which converts laser radiation to heat and has small hole at the heated region through which probe beams are transmitted to test optical character of samples. (C) Finite element model (26) (Fig. S3) of the temperature distribution in heated Ar at 51 GPa (Fig. 2), with solid–melt (16) and insulator–conductor (α = 0.1 μm⁻¹) boundaries in the sample marked dashed and dotted, respectively. (D) Schematic of time domain probing during transient heating. Temperature is determined from thermal emission (red) and absorption from transmitted probe beams: a continuous laser (cw; green) and pulsed supercontinuum broadband (bb; blue).     

Coevolution can reverse predator–prey cycles

A hallmark of Lotka–Volterra models, and other ecological models of predator–prey interactions, is that in predator–prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator–prey coevolution can also drive population cycles where the opposite of canonical Lotka–Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage–cholera, mink–muskrat, and gyrfalcon–rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator–prey coevolution and reveal unique ways in which predator–prey coevolution can shape, and possibly reverse, community dynamics.Population cycles, e.g., predator–prey cycles, and their ecological drivers have been of interest for the last 90 y (1–4). Classical models of predator–prey systems, developed first by Lotka (5) and Volterra (6), share a common prediction: Prey oscillations precede predator oscillations by up to a quarter of the cycle period (7). When plotted in the predator–prey phase plane, these cycles have a counterclockwise orientation (4). These cycles are driven by density-dependent interactions between the populations. When predators are scarce, prey increase in abundance. As their food source increases, predators increase in abundance. When the predators reach sufficiently high densities, the prey population is driven down to low numbers. With a scarcity of food, the predator population crashes and the cycle repeats.While many cycles, like the classic lynx–hare cycles (Fig. 1A) (3), exhibit the above characteristics, predator–prey cycles with different characteristics have also been observed. For example, antiphase cycles where predator oscillations lag behind prey oscillations by half of the cycle period (Fig. 1B) (8) and cryptic cycles where the predator population oscillates while the prey population remains effectively constant (Fig. 1C) (9) have been observed in experimental systems. This diversity of cycle types motivates the question, “Why do cycle characteristics differ across systems?”Open in a separate windowFig. 1.Examples of different kinds of predator–prey cycles. (A) Counterclockwise lynx–hare cycles (3). (B) Antiphase rotifer–algal cycles (8). (C) Cryptic phage-bacteria cycles (9). In all time series, red and blue correspond to predator and prey, respectively. See SI Text, section C for data sources.In Lotka–Volterra and other ecological models, predator and prey life history traits are assumed to be fixed. However, empirical studies across taxa have shown that prey (9–16) and predators (17–20) can evolve over ecological time scales. That is, changes in allele frequencies (and associated phenotypes) can occur at the same rate as changes in population densities or spatial distributions and alter the ecological processes driving the changes in population densities or distributions; this phenomenon has been termed “eco-evolutionary dynamics” (21, 22). Furthermore, predator–prey coevolution is important for driving community composition and dynamics (16, 19, 20, 23–26). This body of work suggests that the interaction between ecological and evolution processes has the potential to alter the ecological dynamics of communities.Experimental (8, 9, 13, 14) and theoretical studies (13, 27, 28) have shown that prey or predator evolution alone can alter the characteristics of predator–prey cycles and drive antiphase (Fig. 1B) and cryptic (Fig. 1C) cycles. Additional theoretical work has shown that predator–prey coevolution can also drive antiphase and cryptic cycles (29). Thus, evolution in one or both species is one mechanism through which antiphase or cryptic predator–prey cycles can arise. However, it is unclear if coevolution can drive additional kinds of cycles with characteristics different from those in Fig. 1.The main contribution of this study is to show that predator–prey coevolution can drive unique cycles where peaks in predator abundance precede peaks in prey abundance, the opposite of what is predicted by classical ecological models. We refer to these reversed cycles as “clockwise cycles.” The theoretical and empirical finding of clockwise cycles represents an example of how evolution over ecological time scales can alter community-level dynamics.     

Arenium ions are not obligatory intermediates in electrophilic aromatic substitution

Our computational and experimental investigation of the reaction of anisole with Cl₂ in nonpolar CCl₄ solution challenges two fundamental tenets of the traditional S_EAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition–elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the S_EAr nor the AE mechanisms involve the formation of a σ-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (S_EAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition–elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling.Interest in the chemistry of electrophilic aromatic substitution reactions continues because of their widespread application for the production of a great variety of chemicals and materials (1–4). Electrophilic substitution, considered to be the most characteristic reaction of aromatic systems, is typically described in textbooks, monographs, and reviews by the two-stage S_EAr mechanism depicted in Fig. 1 (5–11). Arenium ion (σ-complex) intermediates are often ascribed to Wheland (9) inaccurately, since Pfeiffer and Wizinger (10) laid out the principles of such species for bromination in 1928. Following Brown and Pearsall (11), they are widely believed to have σ-complex structures. Arenium ions (σ-complexes) (9–11) are widely accepted to be obligatory intermediates and are used to rationalize ortho/para vs. meta position orientation preferences (6–11).Open in a separate windowFig. 1.Typical depiction of the arenium ion mechanism for S_EAr reactions.We now reinforce our challenges (12, 13) of this conventional “reaction mechanism paradigm” (14) by a combined computational and experimental study of the facile chlorination of anisole (methoxybenzene) with Cl₂ in CCl₄ solution (15, 16). We find that Fig. 1 is not the favored pathway. Instead, addition reactions of Cl₂ to anisole have the lowest activation energies (Fig. 2). Ready HCl elimination from the initially formed adducts leads to ortho- and para-chloroanisole as the predominate products. This addition–elimination (AE) mechanism (the historical antecedent to Fig. 1) (17–26) predicts the same positional orientation as the usually assumed direct substitution (“S_EAr”) alternative. Instead of this classic S_EAr mechanism (Fig. 1), we find that direct concerted substitution, not involving an arenium ion, σ-complex (“Wheland”) (9–11) intermediate, competes energetically with the AE route. Like some earlier computational studies on aromatic substitution (12, 13, 27, 28) (Rzepa H, www.ch.imperial.ac.uk/rzepa/blog/?p=2423, accessed March 10, 2013), our study finds no such intermediates in the direct substitution of anisole by Cl₂. A concerted mechanism without an arenium ion intermediate was computed at some levels for the related arene nitrosation, but reaction medium and counter ion effects were not considered. Gwaltney et al. (28) reported a single concerted transition state after reoptimizing all saddle points at CCSD(T)/6-31G(d,p) and modeling bulk solvation by the Onsager approximation, and Rzepa (www.ch.imperial.ac.uk/rzepa/blog/?p=2423, accessed March 10, 2013) also found a concerted transition state including a trifluoroacetate counterion. Instead, one-step reactions via single transition states take place (Fig. 2). Our experimental investigations of the chlorination of anisole in CCl₄ solution revealed tetrachloro by-products, which must have arisen by further reaction of intermediate dichloro-adducts. Both our UV-visible (UV-VIS) spectroscopic investigation and our theoretical modeling of this reaction clearly verified the autocatalytic effect of the HCl by-product, in harmony with Andrews and Keefer’s (29, 30) early experimental kinetic studies of the chlorination of arenes, which found that HCl reduces the activation barriers significantly.Open in a separate windowFig. 2.The HCl-catalyzed concerted and addition–elimination pathways of para-chlorination of anisole in nonpolar media.We also applied reliable theoretical methods to model a typical experimental example of the highly investigated S_EAr electrophilic aromatic halogenations, the electrophilic chlorination of anisole by molecular chlorine in simulated CCl₄ solution (15, 16). Although the elucidation of the classic S_EAr mechanism [Fig. 1, involving the initial formation of a π-complex, followed by a transition state leading to a σ-complex (arenium) intermediate in the rate-controlling stage, and, finally, proton loss from the ipso-position leading to the reaction product] is considered to be a triumph of physical organic chemistry (1, 31–37), an alternative addition–elimination pathway leading to substitution products has been discussed since the 19th century (19–26, 38, 39). Nevertheless, it is commonly believed that the classic multistep S_EAr mechanism involving the formation of a σ-complex intermediate in the rate-controlling stage is the only mechanistic route to aromatic substitution products. Our present and previous (12, 13) results challenge the generality of such traditional interpretations. Although the initial stages of the alternative AE route seem unattractive because aromaticity is lost, many arenes are known experimentally to give addition products in considerable amounts (19–26, 38, 39). Thus, de la Mare (21, 25, 38, 39) demonstrated the formation of halogen adduct intermediates. Polybenzenoid hydrocarbons (PBHs) react with halogens to give isolable addition products, which then give substitution products easily by hydrogen halide elimination (23). Our computational investigations of arene bromination with molecular bromine (12) and sulfonation with SO₃ (13) provided clear evidence that the mechanisms of the inherent substitution reactions (i.e., uncatalyzed, gas phase, or weakly solvated) are concerted and do not involve the conventional σ-complex (or any other) intermediates. Moreover, the energetics of the bromination processes document the significance of competition between AE and direct substitution mechanisms leading to the same substitution products. Thus, the computed barrier in a simulated nonpolar (CCl₄) medium is 4 kcal/mol lower for Br₂ addition to benzene (followed by HBr elimination) than that for the direct substitution pathway to bromobenzene (12).Previous theoretical studies of electrophilic aromatic halogenation processes have been based on the classic S_EAr mechanism, involving arenium ion intermediates (Fig. 1). Osamura et al.’s (40) Hartree-Fock computations of the AlCl₃-catalyzed electrophilic aromatic chlorination mechanism found an initial π-complex, a transition state preceding the intermediate σ-complex, and a second transition state leading to final products. Aluminum chloride was important as a Lewis acid catalyst throughout the process. AlCl₃ coordination polarizes Cl₂ and thereby assists its reaction with the arene. Rasokha and Kochi (41) considered the interaction of Br₂ with benzene and toluene in detail in their survey of theoretical and experimental data on the prereactive charge-transfer complexes in electrophilic aromatic substitutions. They argued that the structures and properties of the prereactive complexes provide important mechanistic insights for the S_EAr reactions. Wei et al.’s (42) theoretical study of the iodination of anisole by iodine monochloride at the B3LYP/6-311G* and MP2//B3LYP/6-311G* levels (B3LYP, Becke''s three parameter hybrid functional, using the Lee-Yang-Parr correlation functional; MP2, second order Møller-Plesset perturbation theory computations) found that the highest energy transition state precedes the formation of an intermediate, which they interpreted to be a σ-complex. Instead, the structure of this complex represents a protonated iodobenzene. Volkov et al.’s MP2/LANL2DZ(d)+ study (43) of the chlorination of benzene established that dimers of group 13 metal halides catalyzed the processes more effectively. Optimized geometries of π- and σ-complexes as well as transition structures were reported. Theoretical investigations by Ben-Daniel et al. (44) and by Filimonov et al. (45) of the chlorination of benzene with Cl₂ (and other related processes) reported structural details of transition states purported to lead to the chlorobenzene product. Our reinvestigations revealed errors in major suppositions of both these studies. Our IRC computations show clearly that the transition states in question lead to 1,2 Cl₂–benzene addition products (rather than to chlorobenzene). Zhang and Lund (46) investigated the neat chlorination of toluene by Cl₂ experimentally and theoretically at B3LYP/cc-pVTZ(-f) [cc-pVTZ(-f), correlation consistent polarized triple-zeta without f-functions basis set]. Although we verified their reported geometry of the concerted transition state (figure 6 in ref. 46), our stability check revealed that its wavefunction is unstable. This casts doubt on their conclusions because of the homolysis vs. heterolysis issues. In contrast, all wavefunctions in our paper were checked and all are stable. Most prior theoretical studies of S_EAr halogenations did not consider the connections between transition states, intermediates, and products explicitly, as we have done.Experimental findings not always have been in accord with the prevailing mechanistic assumption for aromatic halogenation: that arenium ion formation is the rate-limiting step. Thus, Olah et al. (47), Kochi and coworkers (48), and Fukuzumi and Kochi (49) have emphasized that substrate and positional selectivity are inconsistent (e.g., low toluene/benzene reactivity ratios but high toluene ortho–para vs. meta regiospecificity) for some electrophiles under certain conditions. This disparity indicates the existence of at least one other mechanistic pathway. It has been suggested that π-complexes may control product formation. Olah et al.’s (47) kinetics of the ferric chloride-catalyzed bromination of benzene and alkyl benzenes provided strong evidence for low substrate selectivity in the rate-determining step, which precedes the formation of a σ-complex intermediate (Fig. 1). High positional selectivity is governed by the transition state associated with the second step of the reaction.However, our earlier study (50) examined the possible participation of π-complexes in the key mechanistic steps of S_EAr bromination reactions in detail but found no link between the energy of formation of these complexes and the overall reactivity. Although there is no doubt that π-complexes form easily (via essentially barrierless processes) in most S_EAr reactions after mixing the electrophile and the aromatic substrate, it is unlikely that these low-energy “bystander” structures influence rates of S_EAr reactions significantly. Thus, the lack of accord between substrate and positional selectivity, established by Olah et al. (47), Kochi and coworkers (48), and Fukuzumi and Kochi (49) may be due to other mechanistic differences. De la Mare and Bolton (21) and de la Mare (51) have stressed the plurality of aromatic substitution mechanisms, depending on the substrate and the conditions.Reactive substrates are known to undergo uncatalyzed aromatic substitution in nonpolar solvents at room temperature. Thus, our computational investigations modeled Watson’s careful experiments on the chlorination of anisole in CCl₄ at 25 °C (15, 16). His low conversion (25%) conditions for chlorophenol permitted more accurate determination of the initial product ratios (and avoided further Cl₂ additions to 4-chloroanisole, which ultimately gave 1,3,4,5,6-pentachloro-4-methoxycyclohexene). After introduction of gaseous Cl₂ into a CCl₄ solution of anisole for 1 h, the products were 4-chloroanisole (76%), 2-chloroanisole (13.6%), 2,6-dichloro anisole (2.1%), 2,4-dichloroanisole (3.0%), and 2,4,6-trichloroanisole (0.4%).Analogous chlorinations of phenol, 2-methylphenol, and 2-chlorophenol in CCl₄ also have been carried out with high conversion rates at the reflux temperature (79 °C) (16). Chlorination of phenol with Cl₂ in CCl₄ has been reported by other groups (52, 53).     

Cultural implications of late Holocene climate change in the Cuenca Oriental,Mexico

There is currently no consensus on the importance of climate change in Mesoamerican prehistory. Some invoke drought as a causal factor in major cultural transitions, including the abandonment of many sites at 900 CE, while others conclude that cultural factors were more important. This lack of agreement reflects the fact that the history of climate change in many regions of Mesoamerica is poorly understood. We present paleolimnological evidence suggesting that climate change was important in the abandonment of Cantona between 900 CE and 1050 CE. At its peak, Cantona was one of the largest cities in pre-Columbian Mesoamerica, with a population of 90,000 inhabitants. The site is located in the Cuenca Oriental, a semiarid basin east of Mexico City. We developed a subcentennial reconstruction of regional climate from a nearby maar lake, Aljojuca. The modern climatology of the region suggests that sediments record changes in summer monsoonal precipitation. Elemental geochemistry (X-ray fluorescence) and δ¹⁸O from authigenic calcite indicate a centennial-scale arid interval between 500 CE and 1150 CE, overlaid on a long-term drying trend. Comparison of this record to Cantona’s chronology suggests that both the city’s peak population and its abandonment occurred during this arid period. The human response to climate change most likely resulted from the interplay of environmental and political factors. During earlier periods of Cantona’s history, increasing aridity and political unrest may have actually increased the city’s importance. However, by 1050 CE, this extended arid period, possibly combined with regional political change, contributed to the city’s abandonment.A key uncertainty in the history of pre-Columbian Mesoamerica is the precise relationship between climatic change and major cultural transitions. While some scholars argue for a direct causal link between aridity and the abandonment of many sites (1–4), others argue that anthropogenic landscape transformations were more important in facilitating cultural change (5, 6). A focal point of this debate is the dramatic cultural change that occurred during the Terminal Classic, from ∼850 CE through 1000 CE. Much of this debate has focused on the Maya lowlands (3, 7), although researchers have also explored linkages between climate and cultural change in Terminal Classic highland Mexico (1, 2, 4). However, these comparisons have been hindered by a lack of high-resolution paleoclimate records: While paleoclimate records from across Mesoamerica suggest arid conditions at some point during this interval (1–3, 6–8), patterns of climatic change may have been regionally heterogeneous.The Cuenca Oriental, or Oriental Basin, offers an important setting in which to assess hypotheses about past human−environment relationships. Located east of the Basin of Mexico, in the eastern Trans-Mexican Volcanic Belt (TMVB), the region is marginal for maize agriculture today. Paleoclimate records from this area therefore have broad implications for our understanding of the importance of past climate change in altering the “northern frontier of Mesoamerica,” defined as the northern limit of maize agriculture (9). Moreover, this area was controlled by powerful pre-Columbian city-states in the Classic and Post-Classic periods, and served as an important site of contact between highland Mexico and the cultures of the Atlantic Gulf Coast (10).The site of Cantona, in the northern Cuenca Oriental, is particularly intriguing because of its size and mysterious abandonment. The city drew its economic importance from the exploitation of obsidian at the site of Oyameles-Zaragoza, and was a key supplier of obsidian to settlements along the Gulf of Mexico (11, 12). The site covered over 12 km² and housed an estimated population of 90,000 at its peak, but was abandoned between 900 CE and 1050 CE (Fig. 1). Several authors have speculated that drought was responsible for this abandonment (11), but before the present study, no detailed paleoclimate records have been available for the Cuenca Oriental. The present climate is strongly seasonal, with rainfall primarily occurring from May through October (Fig. S1). This summertime increase in convective activity is driven by the seasonal heating of the land surface, and is linked to the broader circulation regime known as the North American, or Mexican, Monsoon (13). High-resolution paleoclimatic records can help us understand the long-term variability of this monsoonal system.Open in a separate windowFig. 1.Locations of Cantona (red square) and other major sites in central highland Mexico (black circles), along with location of Aljojuca maar. Topography from 1,500 m above sea level (masl) to 4,500 masl, contoured by 500 m. Gray line shows outline of the Cuenca Oriental. (Inset) Map shows Google Earth satellite imagery of region around Cantona, with outline of the city shown in gray. Labels designate the southern, central, and northern architectural clusters within the city. Modified from ref. 11.Here we report on a subcentennially resolved paleoclimate record from a maar lake, Aljojuca, in the eastern Cuenca Oriental, 30 km south of Cantona (Fig. 1). We discuss the implications of the record for our understanding of late Holocene climate variability in Mesoamerica. We also explore the cultural implications of these paleoclimate changes for Cantona and other important pre-Columbian sites in highland Mexico (Fig. 1).     

Number neurons in the nidopallium of young domestic chicks

Numerical cognition is ubiquitous in the animal kingdom. Domestic chicks are a widely used developmental model for studying numerical cognition. Soon after hatching, chicks can perform sophisticated numerical tasks. Nevertheless, the neural basis of their numerical abilities has remained unknown. Here, we describe number neurons in the caudal nidopallium (functionally equivalent to the mammalian prefrontal cortex) of young domestic chicks. Number neurons that we found in young chicks showed remarkable similarities to those in the prefrontal cortex and caudal nidopallium of adult animals. Thus, our results suggest that numerosity perception based on number neurons might be an inborn feature of the vertebrate brain.

Be it a number of conspecifics in a group (1), a number of food items (2), or a number of motifs in a song (3), correct estimation of quantities is of vital importance for animals. Several behavioral studies have confirmed that numerical competence is not a prerogative of human beings but is a widespread phenomenon in the animal kingdom (reviewed by refs. 4 and 5). Mammals (6–8), birds (3, 9, 10), reptilians (11), amphibians (12), fishes (13), and invertebrates (14), although evolutionarily distant, all can spontaneously assess quantities using an approximate number system (15).For the approximate number system, which is based on Weber’s law (16), the perception of cardinal numbers resembles the perception of continuous physical stimuli, and the just noticeable difference is proportionate to the quantity being estimated. As a consequence, discrimination of quantities is imprecise and depends on the numerical distance between stimuli. In other words, it is easier to tell apart 5 and 10 than 9 and 10. Moreover, discrimination of quantities becomes increasingly difficult with the numerical size. For a given numerical distance (e.g., one), it is easier to discriminate between numbers with low magnitudes (1 vs. 2) than with high magnitudes (9 vs. 10).Recent research has uncovered that the approximate number system relies on the activity of a specific neuronal population. Neurons that respond to abstract numerosity irrespective of objects’ physical appearance (shape, color, size) have been found in the forebrain of human and nonhuman primates (17, 18) and in crows (19). In mammals, numerical responses were recorded in the parietal and the prefrontal cortices (PFCs) (17). In birds, similar neurons have been described in the caudolateral nidopallium (NCL) (19). The NCL is believed to be an analog of the PFC in the avian brain (20) and is involved in a variety of cognitive processes, including memory formation (21, 22), abstract rule learning (23), and action planning (24).Both monkeys and crows are among the most evolutionarily advanced species of their phylogenetic groups. They independently developed sophisticated intellectual capacities (25), and both possess enlarged forebrains (26). The neural representations of numerosities described in these species also share remarkable similarities (19, 27–29). In both species, the number neurons show the strongest response to a preferred numerosity, which gradually decreases along with the numerical distance (numerical distance effect, but see ref. 30). Their tuning curves are skewed toward larger numerosities and become progressively broader (less selective) with increasing numerosities (numerical size effect). However, it is unclear whether the presence of similar number neurons in these two species emerges as a consequence of their elaborate cognitive skills and enlarged forebrains. To understand the evolution of the number sense, we need to explore its neural correlates in distant bird species with more ancestral traits.Moreover, until now, number neurons have been described only in adult animals (e.g., refs. 19, 27–29, and 31). At the same time, behavioral data from human infants (32) and young domestic chicks (10, 33) indicate that some core numerical abilities might be an inborn or spontaneously emerging (34, 35) property of the vertebrate brain. Testing the presence of number neurons in young and untrained organisms is crucial to verify this hypothesis.In our study, we aimed to describe the neural correlates of the number sense in domestic chicks (Gallus gallus), which belong to a sister group of modern Neoaves (36). The domestic chick is a well-established developmental model for studying numerical cognition. Soon after hatching, these birds are already capable of discriminating quantities (33, 37) and even performing basic arithmetic operations (10). It has also been shown that young chicks represent numbers across the mental number line (38), a cognitive ability that had been previously attributed only to humans.We hypothesized that neural processing of numerical information in young untrained chicks might be similar to that in crows, despite them having evolved independently over the last ∼70 million years (36). In a domestic chicken, the NCL is morphologically different from that of corvids (39), but it is unclear whether this reflects any functional difference. Therefore, we decided to search for neural responses to numerical stimuli in the NCL of domestic chicks. For this purpose, we habituated young chicks to a computer monitor, where numerical stimuli were presented (Fig. 1A). We explored neural responses to numerosities from one to five. To control for nonnumerical parameters, we presented three different categories of stimuli: “radius-fixed,” “area-fixed,” and “perimeter-fixed” (Fig. 1B).Open in a separate windowFig. 1.Experimental design. (A) Schematic drawing of the experimental setup. Young chicks were placed in a small wooden box in front of the screen, where numerical stimuli appeared. They were trained to pay attention to the stimuli without any further discrimination between different numerosities. (B) Examples of different types of numerosity stimuli that we presented in every neural recording: “radius-fixed,” “area-fixed,” and “perimeter-fixed.”     

Ultrahigh electrical conductivity in solution-sheared polymeric transparent films

With consumer electronics transitioning toward flexible products, there is a growing need for high-performance, mechanically robust, and inexpensive transparent conductors (TCs) for optoelectronic device integration. Herein, we report the scalable fabrication of highly conductive poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) thin films via solution shearing. Specific control over deposition conditions allows for tunable phase separation and preferential PEDOT backbone alignment, resulting in record-high electrical conductivities of 4,600 ± 100 S/cm while maintaining high optical transparency. High-performance solution-sheared TC PEDOT:PSS films were used as patterned electrodes in capacitive touch sensors and organic photovoltaics to demonstrate practical viability in optoelectronic applications.Conductive films of high optical transparency are required in a myriad of applications, including electromagnetic shielding, antistatic layers, lighting displays, touch sensors, and as electrodes for photovoltaics (1, 2). As flexible, lightweight displays for televisions and portable consumer electronics become closer to reality, emerging transparent conductors (TCs) need to be mechanically robust (3). An ideal TC, therefore, should have a sheet resistance <100 Ω/□, transmissivity greater than 0.90, and be inherently flexible, all while remaining inexpensive to process on a mass scale (4).Indium tin oxide (ITO) is the most widely used TC material due to the combination of low sheet resistance and high transparency when grown on a variety of substrates. Although common to use, ITO is an expensive material due to the requirement for vacuum deposition and a number of postprocessing steps (5). For example, in organic photovoltaic (OPV) modules ITO was estimated to represent 24% of the module cost (6). However, alternative transparent conductor materials, such as poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) are estimated to comprise only ∼1% of an OPV module cost. Additionally, ITO is not compatible with flexible applications, because small applied strains of as little as 4.5% lead to an order of magnitude increase in the resistance (7).In recent years there have been a number of emerging TC materials studied in the literature ranging from metal nanowires (Au, Ag, Cu) (8–11), conducting carbon allotropes (graphene, carbon nanotubes) (12–15), conducting polymers (16, 17), and other hybrid approaches (18). Recent attempts using metal nanotroughs by Wu et al. have resulted in superior optoelectronic properties with a sheet resistance of 2 Ω/□ at 90% transmission (19). The use of metal mesoscale grids further enhanced the properties of metal nanowires electrodes to a sheet resistance of 0.36 Ω/□ at 92% transmission (20). Although metal nanowires combine low resistance and high transparency, they have inferior flexibility and stretchability compared with polymer-based TCs (3).PEDOT:PSS consists of insoluble PEDOT that is charge stabilized by PSS (Fig. 1A), which affords good solubility in aqueous formulations. Within these solutions, PEDOT:PSS forms micelles where hydrophilic PSS is in contact with water and hydrophobic PEDOT is located in the micelle core (21). Upon spin-coating from solution, the micelles are deposited as a film and can have conductivities on the order of ∼1 S/cm (22). Subsequent annealing, treatment with cosolvents, and postprocessing steps can increase the conductivity of films to over 3,000 S/cm (23, 24). High-performing spin-cast PEDOT:PSS TCs have reached a sheet resistance of 46 Ω/□ at 90% transmission (25, 26). Furthermore, it is compatible with flexible electronics as films can withstand over 90% applied strain without electrical breakdown (7).Open in a separate windowFig. 1.Schematic of solution shearing process. (A) Chemical structure of PEDOT:PSS. (B) Schematic of the solution shearing design and (C) patterning PEDOT:PSS via selective patterning of solvent wetting and dewetting regions.There is a wide variety of solution processing techniques used to deposit uniform, low-roughness films (27). Spin-casting is a popular laboratory-scale deposition technique due to its simplicity and ability to deposit high-quality films with a variety of materials. However, it is a batch process that is difficult to implement on a continuous mass production scale. Furthermore, it is difficult to use elevated substrate temperatures during spin-coating, a parameter that may play a role in the final film characteristics. Contrarily, scalable fabrication through solution shearing allows for tunable deposition conditions which enable enhanced kinetic control resulting in large impacts on the electrical performance of organic electronics (28–30).In this work we use solution shearing to fabricate high-performance TC PEDOT:PSS films (Fig. 1B). Tunable control of PEDOT backbone orientation, local ordering, and phase separation is demonstrated via precise control of the deposition parameters. Record-high PEDOT:PSS conductivities of 4,600 ± 100 S/cm are obtained and reach a sheet resistance of 17 ± 1 Ω/□ at 97.2 ± 0.4% transmission. A patterning method (Fig. 1C) is also developed which enables the use of high-conductivity transparent conductive films in capacitive pressure sensors and OPV devices.     

Inside-out regulation of E-cadherin conformation and adhesion

Cadherin cell–cell adhesion proteins play key roles in tissue morphogenesis and wound healing. Cadherin ectodomains bind in two conformations, X-dimers and strand-swap dimers, with different adhesive properties. However, the mechanisms by which cells regulate ectodomain conformation are unknown. Cadherin intracellular regions associate with several actin-binding proteins including vinculin, which are believed to tune cell–cell adhesion by remodeling the actin cytoskeleton. Here, we show at the single-molecule level, that vinculin association with the cadherin cytoplasmic region allosterically converts weak X-dimers into strong strand-swap dimers and that this process is mediated by myosin II–dependent changes in cytoskeletal tension. We also show that in epithelial cells, ∼70% of apical cadherins exist as strand-swap dimers while the remaining form X-dimers, providing two cadherin pools with different adhesive properties. Our results demonstrate the inside-out regulation of cadherin conformation and establish a mechanistic role for vinculin in this process.

E-cadherins (Ecads) are essential, calcium-dependent cell–cell adhesion proteins that play key roles in the formation of epithelial tissue and in the maintenance of tissue integrity. Ecad adhesion is highly plastic and carefully regulated to orchestrate complex movement of epithelial cells, and dysregulation of adhesion is a hallmark of numerous cancers (1). However, little is known about how cells dynamically regulate the biophysical properties of individual Ecads.The extracellular region of Ecads from opposing cells bind in two distinct trans orientations: strand-swap dimers and X-dimers (Fig. 1 A and B). Strand-swap dimers are the stronger cadherin adhesive conformation and are formed by the exchange of conserved tryptophan (Trp) residues between the outermost domains of opposing Ecads (2–4). In contrast, X-dimers, which are formed by extensive surface interactions between opposing Ecads, are a weaker adhesive structure and serve as an intermediate during the formation and rupture of strand-swap dimers (5–7). Using cell-free, single-molecule experiments we previously showed that X-dimers and strand-swap dimers can be distinguished based on their distinctly different response to mechanical force. When a strand-swap dimer is pulled, its lifetime decreases with increasing force, resulting in the formation of a slip bond (8, 9) (Fig. 1B). In contrast, an X-dimer responds to pulling force by forming a catch bond, where bond lifetime initially increases up to a threshold force and then subsequently decreases (8, 10) (Fig. 1B). It has also been shown that wild-type Ecad ectodomains in solution can interconvert between X-dimer and strand-swap dimer conformations (9, 11). However, the biophysical mechanisms by which Ecad conformations (and adhesion) are regulated on the cell surface are unknown.Open in a separate windowFig. 1.Overview of experiment. (A) The extracellular region of Ecad from opposing cells mediates adhesion. The cytoplasmic region of Ecad associates either directly or indirectly with p120 catenin, β-catenin, α-catenin, vinculin, and F-actin. (B) Strand-swap dimers form slip bonds (blue) and X-dimers form catch bonds (red). Ecads interconvert between these two dimer conformations. Structures were generated from the crystal structure of mouse Ecad (PDB ID code 3Q2V); the X-dimer was formed by alignment to an X-dimer crystal structure (PDB ID code 3LNH). (C) Graphics showing the cell lines used in experiments and Western blot analysis of corresponding cell lysates.The cytoplasmic region of Ecad associates with the catenin family of proteins, namely, p120-catenin, β-catenin, and α-catenin. The Ecad–catenin complex, in turn, links to filamentous actin (F-actin) either by the direct binding of α-catenin and F-actin or by the indirect association of α-catenin and F-actin via vinculin (12) (Fig. 1A). Adhesive forces transmitted across intercellular junctions by Ecad induce conformational changes in α-catenin (13, 14), strengthen F-actin binding (15), and recruit vinculin to the sites of force application (16, 17). However, vinculin and α-catenin do not merely serve as passive cytoskeletal linkers; they also dynamically modulate cytoskeletal rearrangement and recruit myosin to cell–cell junctions (13, 18–20). Studies show that α-catenin and vinculin play important roles in strengthening and stabilizing Ecad adhesion: bead-twisting experiments show force-induced stiffening of Ecad-based junctions and cell doublet stretching experiments demonstrate reinforcement of cell–cell adhesion in vinculin- and α-catenin–dependent manners (18, 19, 21).Currently, actin anchorage and cytoskeletal remodeling are assumed to be the exclusive mechanisms by which α-catenin and vinculin strengthen Ecad adhesion (22–24). Here, we directly map the allosteric effects of cytoplasmic proteins on Ecad ectodomain conformation and demonstrate, at the single-molecule level, that vinculin association with the Ecad cytoplasmic region switches X-dimers to strand-swap dimers. We show that cytoskeletal tension, due to vinculin-mediated recruitment of myosin II, regulates Ecad ectodomain structure and adhesion. Finally, we demonstrate that only ∼50% of Ecads are linked to the underlying cytoskeleton and that while about 70% of Ecads form strand-swap dimers the remaining form X-dimers, which provides cells with two Ecad pools with different adhesive properties.     

A 5,000-year vegetation and fire history for tierra firme forests in the Medio Putumayo-Algodón watersheds,northeastern Peru

This paper addresses an important debate in Amazonian studies; namely, the scale, intensity, and nature of human modification of the forests in prehistory. Phytolith and charcoal analysis of terrestrial soils underneath mature tierra firme (nonflooded, nonriverine) forests in the remote Medio Putumayo-Algodón watersheds, northeastern Peru, provide a vegetation and fire history spanning at least the past 5,000 y. A tree inventory carried out in the region enables calibration of ancient phytolith records with standing vegetation and estimates of palm species densities on the landscape through time. Phytolith records show no evidence for forest clearing or agriculture with major annual seed and root crops. Frequencies of important economic palms such as Oenocarpus, Euterpe, Bactris, and Astrocaryum spp., some of which contain hyperdominant species in the modern flora, do not increase through prehistoric time. This indicates pre-Columbian occupations, if documented in the region with future research, did not significantly increase the abundance of those species through management or cultivation. Phytoliths from other arboreal and woody species similarly reflect a stable forest structure and diversity throughout the records. Charcoal ¹⁴C dates evidence local forest burning between ca. 2,800 and 1,400 y ago. Our data support previous research indicating that considerable areas of some Amazonian tierra firme forests were not significantly impacted by human activities during the prehistoric era. Rather, it appears that over the last 5,000 y, indigenous populations in this region coexisted with, and helped maintain, large expanses of relatively unmodified forest, as they continue to do today.

More than 50 y ago, prominent scholars argued that due to severe environmental constraints (e.g., poor natural resources), prehistoric cultures in the Amazon Basin were mainly small and mobile with little cultural complexity, and exerted low environmental impacts (1, 2). Contentious debates ensued and have been ongoing ever since. Empirical data accumulated during the past 10 to 20 y have made it clear that during the late Holocene beginning about 3,000 y ago dense, permanent settlements with considerable cultural complexity had developed along major watercourses and some of their tributaries, in seasonal savannas/areas of poor drainage, and in seasonally dry forest. These populations exerted significant, sometimes profound, regional-scale impacts on landscapes, including with raised agricultural fields, fish weirs, mound settlements, roads, geometric earthworks called geoglyphs, and the presence of highly modified anthropic soils, called terra pretas or “Amazonian Dark Earths” (Fig. 1) (e.g., refs. 3–15).Open in a separate windowFig. 1.Location of study region (MP-A) and other Amazonian sites discussed in the text. River names are in blue. The black numbers represent major pre-Columbian archaeological sites with extensive human alterations (1, Marajó Island; 2, Santarém; 3, Upper Xingu; 4, Central Amazon Project; 5, Bolivian sites) (3, 5–10, 14, 15). ADE, terra preta locations (e.g., refs. 19 and 20); triangles are geoglyph sites (6, 8). The white circles are terrestrial soil locations previously studied by Piperno and McMichael (29, 31–33, 54) (Ac, Acre; Am, Amacayacu; Ay, Lake Ayauchi; B, Barcelos; GP, lakes Gentry-Parker; Iq, Iquitos to Nauta; LA, Los Amigos; PVM, Porto Velho to Manaus; T, Tefe).An important, current debate that frames this paper centers not on whether some regions of the pre-Columbian Amazon supported large and complex human societies, but rather on the spatial scales, degrees, and types of cultural impacts across this continental-size landscape. Some investigators drawing largely on available archaeological data and studies of modern floristic composition of selected forests, argue that heavily modified “domesticated” landscapes were widespread across Amazonia at the end of prehistory, and these impacts significantly structure the vegetation today, even promoting higher diversity than before (e.g., refs. 14–21). It is believed that widespread forms of agroforestry with planted, orchard-like formations or other forest management strategies involving the care and possible enrichment of several dozens of economically important native species have resulted in long-term legacies left on forest composition (e.g., refs. 14–22). Some (20) propose that human influences played strong roles in the enrichment of “hyperdominant” trees, which are disproportionately common elements in the modern flora (sensu ref. 23). Some even argue that prehistoric fires and forest clearance were so spatially extensive that post-Columbian reforestation upon the tragic consequences of European contact was a principal contributor to decreasing atmospheric CO₂ levels and the onset of the “Little Ice Age” (24, 25).However, modern floristic studies are often located in the vicinity of known archaeological sites and/or near watercourses (26). Many edible trees in these studies are early successional and would not be expected to remain as significant forest elements for hundreds of years after abandonment. Historic-period impacts well-known in some regions to have been profound have been paid little attention and may be mistaken for prehistoric legacies (26–28). Moreover, existing phytolith and charcoal data from terrestrial soils underneath standing tierra firme forest in some areas of the central and western Amazon with no known archaeological occupations nearby exhibit little to no evidence for long-term human occupation, anthropic soils, agriculture, forest clearing or other significant vegetation change, or recurrent/extensive fires during the past several thousand years (Fig. 1) (29–33). Even such analyses of terrestrial soils of lake watersheds in western Amazonia known to have been occupied and farmed in prehistory revealed no spatially extensive deforestation of the watersheds, as significant human impacts most often occurred in areas closest to the lakes (Fig. 1) (34). Furthermore, vast areas have yet to be studied by archaeologists and paleoecologists, particularly the tierra firme forests that account for 95% of the land area of Amazonia.To further inform these issues, we report here a vegetation and fire history spanning 5,000 y derived from phytolith and charcoal studies of terrestrial soils underneath mature tierra firme forest in northeastern Peru. Phytoliths, the silica bodies produced by many Neotropical plants, are well preserved in terrestrial soils unlike pollen, and are deposited locally. They can be used to identify different tropical vegetational formations, such as old-growth forest, early successional vegetation typical of human disturbances including forest clearings, a number of annual seed and root crops, and trees thought to have been cultivated or managed in prehistory (e.g., refs. 29–33 and 35).     

Transition pathways connecting crystals and quasicrystals

Due to structural incommensurability, the emergence of a quasicrystal from a crystalline phase represents a challenge to computational physics. Here, the nucleation of quasicrystals is investigated by using an efficient computational method applied to a Landau free-energy functional. Specifically, transition pathways connecting different local minima of the Lifshitz–Petrich model are obtained by using the high-index saddle dynamics. Saddle points on these paths are identified as the critical nuclei of the 6-fold crystals and 12-fold quasicrystals. The results reveal that phase transitions between the crystalline and quasicrystalline phases could follow two possible pathways, corresponding to a one-stage phase transition and a two-stage phase transition involving a metastable lamellar quasicrystalline state, respectively.

Since the discovery of quasicrystals characterized by quasiperiodic positional order with nonclassical rotational symmetries (1), tremendous progresses have been made on the understanding of these fascinating materials (2, 3). Various quasicrystals have been reported (1, 4–7). Besides examples from metallic alloys, quasicrystalline order has been observed in different systems, including Faraday waves and soft matter (8–16). Although the structures of quasicrystals are now well understood (17), the nucleation of quasicrystals, which involves the transition from periodic crystalline structures to quasiperiodic structures, still represents a long-standing unsolved problem.In general, nucleation of a stable state from a metastable state could be examined by using three approaches, i.e., classical nucleation theory, atomistic theory, and density-functional theory (18, 19). Within the framework of the density-functional theory, the free-energy landscape of the system is described by a free-energy functional determined by the density of molecular species. Stable and metastable phases of the system correspond to local minima of the free-energy landscape, whereas the minimum energy paths (MEPs) on the free-energy landscape represent the most probable transition pathways between different phases. Transition states (i.e., index-1 saddle points) on the pathways could be identified as critical nuclei, representing critical states along the transition pathways. This theoretical framework has been applied successfully to various problems undergoing phase transitions (Fig. 1)—for instance, the (rapid) cooling of liquids, the melting of a solid, or the nucleation of crystalline structures (20–25). However, the study of the phase transition between periodic structures and quasiperiodic structures remains a challenge due to incompatible lattice mismatch. Thus, a fundamental question in material sciences is: How does a quasicrystalline structure emerge from a crystalline structure?Open in a separate windowFig. 1.Schematic diagram of nucleation and phase transitions between disordered liquid, periodic crystals, and quasicrystals.In this article, we examine the transition pathways connecting quasicrystals and crystals within the framework of density-functional theory. Specifically, we apply an efficient numerical method based on the high-index saddle dynamics (HiSD) to a Landau free-energy functional, i.e., the Lifshitz–Petrich (LP) model (26), with local minima corresponding to two-dimensional (2D) crystalline and quasicrystalline phases. MEPs connecting various local minima of the model are obtained, and critical nuclei of the 6-fold crystalline and 12-fold quasicrystalline states are identified. In particular, two MEPs connecting two ordered phases are obtained, revealing that the phase transitions between the crystalline and quasicrystalline phases could follow two possible pathways, corresponding to either a one-stage phase transition or a two-stage phase transition involving a metastable intermediate quasicrystalline state, respectively.