Pathways for abiotic organic synthesis at submarine hydrothermal fields

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H₂-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH₄ and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H₂ generation during active serpentinization. Rather, our results indicate that CH₄ found in vent fluids is formed in H₂-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO₂ reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond.Seawater-derived hydrothermal fluids venting at oceanic spreading centers are a net source for dissolved carbon to the deep sea, with vent fluid carbon contents directly tied to the sustenance of the subseafloor biosphere (1). Highly reducing fluids rich in dissolved H₂, such as those discharging from serpentinizing hydrothermal systems, are of particular interest because of the potential for abiotic reduction of dissolved inorganic carbon (ΣCO2=CO2+HCO3−+CO32−) to organic compounds (2–6) and their potential role as precursor compounds for prebiotic chemistry associated with the origin of life (7). Although there is increasing evidence that supports an abiotic origin for CH₄ and other low-molecular weight organic compounds in ultramafic-hosted hydrothermal systems (8–10), the physical conditions, reaction pathways, and timescales that control abiotic organic synthesis at oceanic spreading centers remain elusive. Working models for the formation of abiotic CH₄ and other hydrocarbons observed in vent fluids involve reduction of ΣCO₂ and/or CO through Fischer–Tropsch-type processes during active circulation of seawater-derived hydrothermal fluids that are highly enriched in dissolved H₂ because of serpentinization of host rocks; however, this mechanism has not been conclusively shown in natural systems. Others have suggested that leaching of CH₄ and low-molecular weight hydrocarbons from magmatic fluid inclusions hosted in plutonic rocks may contribute at some level to the inventory of organic compounds observed in axial hot-spring fluids (1, 11, 12). The relative influence of these processes has important implications for the total flux and real-time concentrations of aqueous organic compounds delivered to the oceans by ridge-crest hydrothermal activity. Here, we use multiple lines of evidence to preclude abiotic reduction of ΣCO₂ to CH₄ during active fluid circulation but show that it is reduced to the metastable intermediate species formate instead.     

Hydrothermal synthesis of long-chain hydrocarbons up to C24 with NaHCO3-assisted stabilizing cobalt

Abiotic CO₂ reduction on transition metal minerals has been proposed to account for the synthesis of organic compounds in alkaline hydrothermal systems, but this reaction lacks experimental support, as only short-chain hydrocarbons (<C₅) have been synthesized in artificial simulation. This presents a question: What particular hydrothermal conditions favor long-chain hydrocarbon synthesis? Here, we demonstrate the hydrothermal bicarbonate reduction at ∼300 °C and 30 MPa into long-chain hydrocarbons using iron (Fe) and cobalt (Co) metals as catalysts. We found the Co⁰ promoter responsible for synthesizing long-chain hydrocarbons to be extraordinarily stable when coupled with Fe−OH formation. Under these hydrothermal conditions, the traditional water-induced deactivation of Co is inhibited by bicarbonate-assisted CoO_x reduction, leading to honeycomb-native Co nanosheets generated in situ as a new motif. The Fe−OH formation, confirmed by operando infrared spectroscopy, enhances CO adsorption on Co, thereby favoring further reduction to long-chain hydrocarbons (up to C₂₄). These results not only advance theories for an abiogenic origin for some petroleum accumulations and the hydrothermal hypothesis of the emergence of life but also introduce an approach for synthesizing long-chain hydrocarbons by nonnoble metal catalysts for artificial CO₂ utilization.

Apart from the well-known microbial and thermogenic origin of hydrocarbons, the scenario of their abiogenic origin has emerged as an assumption and has been demonstrated on a few occasions (1, 2). Abiotic hydrocarbons production from inorganic carbon is considered to be driven by serpentinization in H₂-rich alkaline hydrothermal fluids, and, recently, the hydrocarbons generated are proposed to be transported through deep faults to shallower regions in the Earth’s crust and contribute to some petroleum reserves (3). In addition, the current scenarios suggest that the abiotic synthesis of hydrocarbons in natural hydrothermal systems is also a potential source of prebiotic organic compounds for life’s emergence (4). However, the mechanisms by which long-chain hydrocarbons are synthesized remains unclear and controversial because such reactions presently lack experimental support despite numerous artificial simulations of hydrocarbon formation, although short-chain hydrocarbons (<C₅) have been synthesized (5).In general, the abiotic formation of hydrocarbons is assumed to proceed through the Fischer–Tropsch synthesis (FTS) pathway catalyzed by natural minerals (6, 7). The predominant, oxidized forms of dissolved carbon under high pressure, CO_2(aq) or HCO₃⁻ (>70%), react with dissolved hydrogen H_2(aq) to produce hydrocarbons. The process can be described as follows:CO2(aq)+[3+(1/n)]H2(aq) → (1/n)CnH2n+2+2H2O,[1]HCO3−+[3+(1/n)]H2(aq) → (1/n)CnH2n+2+2H2O+OH−.[2]Fe(II) in the rock-forming minerals reduces H₂O to H₂, while the Fe(II) is converted to Fe(III) (8). In addition to Fe(II), as the H₂ electron donor, clues from biological mechanism and the chemical literature suggest that the native metals can act as the prebiotic source of electrons to fix CO₂ (9–13). The native Fe or the nickel–iron (awaruite, Ni₃Fe) and cobalt–iron (wairauite, CoFe; CoFe₂) alloys have been found in the Earth’s serpentinized ultramafic rocks, where the occurrence of the cobalt–iron alloy is associated with iron minerals, such as chromite and awaruite (14–18). Thus, the native Fe, abundant natural Fe species, or its minerals combined with other transition metals are considered as promising reductants and/or catalysts to reduce CO₂ in hydrothermal systems were thermodynamic conditions to be far enough from equilibrium. To prove the hydrocarbon formation under geochemical conditions, many efforts have been made, and only short-carbon chains (≤C₅) can be produced from CO₂/HCO₃⁻/CO₃⁻, for example, with Fe–Cr oxide (chromite) (7) or awaruite (Ni₃Fe) in alkaline conditions (200 to ∼400 °C, 40 to 50 MPa) (1) or with Fe-bearing dolomite (ankerite) at a higher temperature and pressure (600 to ∼1,200 °C and 1 to ∼6 GPa) (19). However, the long-chain hydrocarbons (>C₅) have not been formed, and it remains an open question as to how hydrothermal conditions might favor direct, long-chain hydrocarbon synthesis from CO₂/HCO₃⁻/CO₃⁻. Indeed, the lack of direct experimental evidence and mechanisms for long-chain hydrocarbon formation from CO₂/HCO₃⁻ in artificial alkaline hydrothermal systems has led to serious doubts regarding the supposed abiogenic origin of hydrocarbons, as well as the hypothesized evolutionary transition from geochemical to biochemical processes. Identifying hydrothermal settings that activate H₂–CO₂ redox reactions with a transition metal catalyst for long-chain hydrocarbon synthesis is an important step toward understanding prebiotic chemistry on the early Earth.Additionally, the utilization of CO₂ as a feedstock for chemical fuel synthesis has received considerable research interest to reduce the carbon footprint and achieve a carbon-neutral cycle (20–22). Our previous efforts of hydrothermal CO₂ reduction with metals have shown that CO₂/HCO₃⁻ can be easily converted into C₁ products such as formate and methane (23, 24); however, it remains challenging to synthesize products beyond C₃, especially of long-chain hydrocarbons. In the traditional FTS performed with dry CO₂ gas and H₂, Co does exhibit catalytic activity for synthesizing long-chain hydrocarbons, yet it must be born in mind that Co is extremely unstable because of its easy oxidation when exposed to wet vapor (25–27). Moreover, the CoO_x formed is difficult to reduce, as the ambient water acts as an oxidant, thus deactivating the Co catalyst (28). Thus, this chemical engineering field has been left to the noble metal catalysts (29–31) or organic solvents (32), seriously limiting their applications. Recently, we found that a minor portion of the Co remained in the metallic phase during the hydrothermal reduction of CO₂ to acetate (33). Although the mechanism by which the portion of the Co phase remains under hydrothermal conditions is unknown, the phenomenon brought to mind the unique role of hydrothermal systems to stabilize the valence state of Co, thus making possible the synthesis of long-chain hydrocarbons.Here, we report the hydrothermal synthesis of long-chain hydrocarbons with the use of metal Fe (as a reductant) and Co as a catalyst by designing a dynamic redox equilibrium system for maintaining Co stability. We demonstrate that CoO_x can be reduced via CoCO₃ in the presence of bicarbonate under hydrothermal conditions that inhibit Co deactivation in water, as honeycomb nanosheets are generated in situ as new motif. The unique stability and honeycomb nanosheets of Co coupled with the synergistic effect of Fe−OH and Co metal result in long-chain hydrocarbon formation (up to 24 carbons) from HCO₃⁻ reduction at ∼300 °C and ∼30 MPa. Such hydrothermal synthesis in a manner comparable to geochemical expectations of serpentinization of ultramafic rocks comprising the oceanic crust is of significance not only to the abiogenic origin of petroleum, the emergence of life, but also to the demonstration of how such hydrocarbons can be generated in the absence of noble metals of significance to the chemical industry.     

The missing enzymatic link in syntrophic methane formation from fatty acids

The microbial production of methane from organic matter is an essential process in the global carbon cycle and an important source of renewable energy. It involves the syntrophic interaction between methanogenic archaea and bacteria that convert primary fermentation products such as fatty acids to the methanogenic substrates acetate, H₂, CO₂, or formate. While the concept of syntrophic methane formation was developed half a century ago, the highly endergonic reduction of CO₂ to methane by electrons derived from β-oxidation of saturated fatty acids has remained hypothetical. Here, we studied a previously noncharacterized membrane-bound oxidoreductase (EMO) from Syntrophus aciditrophicus containing two heme b cofactors and 8-methylmenaquinone as key redox components of the redox loop–driven reduction of CO₂ by acyl–coenzyme A (CoA). Using solubilized EMO and proteoliposomes, we reconstituted the entire electron transfer chain from acyl-CoA to CO₂ and identified the transfer from a high- to a low-potential heme b with perfectly adjusted midpoint potentials as key steps in syntrophic fatty acid oxidation. The results close our gap of knowledge in the conversion of biomass into methane and identify EMOs as key players of β-oxidation in (methyl)menaquinone-containing organisms.

The microbial conversion of natural polymers into methane plays an important role in the global carbon cycle and accounts for more than one-half of all methane produced on Earth per year (1, 2). Methane is formed in anoxic environments, including marine and freshwater sediments, but also in biogas reactors of wastewater treatment plants and other engineered systems. A complex syntrophic association between fermenting bacteria and methanogenic archaea is involved in the degradation of biomass to CH₄ and CO₂. Primary fermenting bacteria hydrolyze complex polymers into monomers and degrade them mainly into short chain fatty acids (scFA) and alcohols. Secondary fermenting bacteria then oxidize these products to the methanogenic substrates acetate, H₂, CO₂, and formate that are finally converted into methane by hydrogenotrophic or acetotrophic archaea (Fig. 1A) (3). The reduction of CO₂ to CH₄ depends on interspecies electron transfer from secondary fermenting bacteria to methanogenic archaea usually via the diffusible low-potential carriers formate and/or H₂ (3–5) or, as recently proposed, directly via nanowires (6).Open in a separate windowFig. 1.Syntrophic degradation of organic matter to methane. (A) Major metabolic processes involving primary fermenters, secondary fermenters, and methanogenic archaea (for simpler presentation, acetogenic conversion of monomers is not depicted here). (B) Model for syntrophic β-oxidation of butyrate to two acetates coupled to the reduction of protons or CO₂. The enzyme mediating electron transfer from reduced ETF to FDH has not been studied before and was assigned to noncharacterized DUF224 based on omics-based predictions.The oxidation of scFA to acetate coupled to the reduction of H⁺ or CO₂ is endergonic under standard conditions (+48 kJ/mol butyrate) but becomes clearly exergonic at an H₂ partial pressure below 10 Pa (3, 7). On the other side, the H₂ threshold partial pressure of hydrogenotrophic methanogenesis is around 8 Pa corresponding to E′(2H⁺/H₂) ∼ −290 mV or around 10 µM formate, resulting in similar values for the CO₂/formate redox couple (2). The syntrophic oxidation of the scFA model compound butyrate to acetate is accomplished by gram-positive Firmicutes (model organism Syntrophomonas wolfei) or gram-negative Deltaproteobacteria (model organism Syntrophus aciditrophicus) (3, 4, 7). It proceeds via two unequal β-oxidation steps (SI Appendix, Fig. 1) (8, 9): 1) Butyryl-CoA is oxidized to crotonyl-CoA by an acyl-CoA dehydrogenase (DH) (E°′ ∼ −10 mV) (10) with an electron-transferring flavoprotein (ETF) serving as electron acceptor, and 2) the 3-hydroxybutyryl-CoA formed by crotonase is subsequently oxidized to acetoacetyl-CoA by 3-hydroxybutyryl-CoA DH (ΔE°′ = −250 mV) (11) using NAD⁺ as acceptor. The reduction of H⁺ or CO₂ by the NADH formed is feasible under syntrophic conditions, whereas butyryl-CoA oxidation coupled to H⁺ or CO₂ reduction has to overcome a gap of ΔE ∼ −280 mV, giving ΔG°′ ∼ +54 kJ ⋅ mol^–1 (3–5). Considering that only one ATP is gained via substrate-level phosphorylation, the energy metabolism of syntrophic butyrate oxidation has remained enigmatic.Omics-based studies have led to the proposal of models for energy coupling processes during syntrophic scFA oxidation (12–16). The redox loop model is based on the identification of a putative membrane-bound gene product (DUF224) (14–16). It proposes that electrons are transferred from acyl-CoA via ETF, DUF224, and menaquinone (MK) to a membrane-bound formate dehydrogenase (FDH) or hydrogenase driven by the translocation of protons to the cytoplasm, resulting in two energetically unequal half reactions:Acyl-CoA + MK →Enoyl-CoA + MKH2 ΔG°’ = +12.5 kJ mol–1CO2+ MKH2→Formate + H++ MKΔG’ = +41.5 kJ mol–1.In agreement, a protonophore inhibited formation of H₂ from butyrate in whole-cell suspension of S. wolfei (17), and MK was reported in S. wolfei and S. aciditrophicus (12, 17). In an alternative model, an electron-confurcating ETF couples endergonic reduction of NAD⁺ by ETF_red to the exergonic reduction of NAD⁺ by reduced ferredoxin (Fd_red^–) (18). The NADH formed then may serve as an electron donor for a cytoplasmic FDH. Biochemical evidence for either of the two models is lacking.Here, we study the missing membrane components that link fatty acid oxidation to CO₂ reduction during syntrophic methane production. We provide biochemical evidence that a membrane-bound diheme oxidoreductase and a modified methylmenaquinone with perfectly adjusted redox potentials are the key players of this process. We further propose that related enzymes play a previously overlooked role in the lipid catabolism of the majority of microorganisms.     

Sulfur radical species form gold deposits on Earth

Current models of the formation and distribution of gold deposits on Earth are based on the long-standing paradigm that hydrogen sulfide and chloride are the ligands responsible for gold mobilization and precipitation by fluids across the lithosphere. Here we challenge this view by demonstrating, using in situ X-ray absorption spectroscopy and solubility measurements, coupled with molecular dynamics and thermodynamic simulations, that sulfur radical species, such as the trisulfur ion S3−, form very stable and soluble complexes with Au⁺ in aqueous solution at elevated temperatures (>250 °C) and pressures (>100 bar). These species enable extraction, transport, and focused precipitation of gold by sulfur-rich fluids 10–100 times more efficiently than sulfide and chloride only. As a result, S3− exerts an important control on the source, concentration, and distribution of gold in its major economic deposits from magmatic, hydrothermal, and metamorphic settings. The growth and decay of S3− during the fluid generation and evolution is one of the key factors that determine the fate of gold in the lithosphere.The formation of gold deposits on Earth requires aqueous fluids that extract gold from minerals and magmas and transport and precipitate the metal as economic concentrations in ores that are three to six orders of magnitude larger than the Au mean content (∼0.001 ppm) of common crustal and mantle rocks (1–9). However, natural data on gold contents in fluids are very scarce due to difficulties of direct access to deep geothermal fluid samples, rarity of representative fluid inclusions trapped in minerals, and analytical limitations for this chemically most inert metal (1, 4, 9, 10). The paucity of direct data makes it difficult to quantify the capacity of the fluids to transport gold and the factors controlling the sources, formation, and distribution of the economic resources of gold and associated metals across the lithosphere. Thus, knowledge of gold speciation and solubility in the fluid phase is required.Terrestrial hydrothermal fluids systematically contain sulfur and chloride—compounds that have long been known to favor gold dissolution in aqueous solution (e.g., refs. 11 and 12). Following this common knowledge, the interpretation of gold transfers across the lithosphere has been based on the fundamental assumption that only hydrogen sulfide (HS⁻) and chloride (Cl⁻) can form stable complexes with aurous gold, Au⁺, which is the main gold oxidation state in hydrothermal fluids (1–6, 11–15). Among these species, aurous bis(hydrogen sulfide), Au(HS)2−, and dichloride, AuCl2−, have long been regarded as the major carriers of gold in hydrothermal fluids, depending on temperature (T), pressure (P), acidity (pH), redox potential (f_O2), and salt and sulfur concentrations (1, 5, 6, 13, 15). In addition, other minor hydroxide, chloride, and sulfide species (AuOH, AuCl, AuHS) have also been tentatively suggested in some studies to account for the low Au solubility (typically part-per-billion level, ppb) measured in dilute S- and Cl-poor experimental solutions (e.g., refs. 6 and 15). Most available data suggest that the sulfide complexes attain significant concentrations (>1 ppm Au) only in H₂S-rich neutral-to-alkaline (pH > 6–7) solutions at low-to-moderate temperatures (<250–300 °C), whereas the chloride complexes contribute to Au solubility only in highly acidic (pH < 3) chloride-rich (typically >10 wt% NaCl equivalent) and strongly oxidizing [above the oxygen fugacity of the hematite–magnetite (HM) buffer] solutions above 300 °C.In between these two contrasting hydrothermal solution compositions lies a vast domain of geological fluids, which are commonly generated by magma degassing at depth (2, 3, 9) or prograde metamorphism of sedimentary rocks at high temperatures (7, 8, 10). These fluids are characterized by variable salt content, slightly acidic to neutral pH, and the presence of both oxidized (sulfate and sulfur dioxide) and reduced (H₂S) sulfur forms in a wide temperature range (∼300–700 °C). Predicted concentrations of the gold sulfide and chloride species in such fluids are generally rather low (<0.1–1.0 ppm) to account for a number of enigmatic features of gold geochemistry such as the existence of large deposits without relation to magmatic plutons in metamorphic and sedimentary rocks (e.g., Carlin-type and orogenic) implying deep, likely mantle-derived, Au-rich sources, the observation of highly anomalous Au grades (up to thousands of parts per million) in hydrothermal veins, and huge variations (more than three orders of magnitude) of the ratio of Au to other metals (e.g., Cu, Ag, Mo) in ores (1–4, 6–10, 16). These fluids, which have created the major part of economic gold resources on Earth (1–4), may carry much higher Au concentrations, of tens to hundreds of parts per million, as reported from rare fluid inclusion analyses (4, 6, 9, 10) and a few laboratory experiments of Au solubility (17–20). How gold is transported by such fluids remains, however, controversial, and a variety of other species with H₂S, Cl, As, and alkali metal ligands (3, 14, 17–20) or Au nanoparticles (4, 6, 12) were suggested. Thus, a consistent picture of Au speciation and transport in deep and hot crustal fluids is lacking, hampering our understanding of geochemical fluxes of gold across the lithosphere and the formation of gold economic resources.In particular, all existing Au speciation models ignore sulfur radical species such as the trisulfur ion S3−, which is ubiquitous in chemical and engineering products (21) and was recently shown to be stable in the aqueous fluid phase over a wide temperature (T from 200 °C to ∼700 °C) and pressure (P from saturated vapor pressure to ∼30 kbar) range (22–24). The omission of S3− in current models of hydrothermal fluids is due to its very rapid breakdown to sulfate and sulfide in aqueous solution upon cooling, which prohibits the detection of S3− in experimental and natural fluid (and melt) samples brought to ambient conditions. It is thus only recently that the abundance and thermodynamic stability of this important sulfur species could be systematically characterized at high T−P using in situ Raman spectroscopy (22–24). These studies showed that significant amounts of trisulfur ion (>10–100 ppm) may be reached in fluids typical of magmatic and metamorphic environments, which are characterized by elevated dissolved S concentrations (>1,000 ppm), slightly acidic to neutral pH (between ∼3 and 7), and redox conditions enabling coexistence of sulfate (or sulfur dioxide) and hydrogen sulfide.To quantify the effect of S3− on Au behavior in hydrothermal fluids, here we combined in situ X-ray absorption spectroscopy (XAS) and hydrothermal reactor measurements with first-principles molecular dynamics (FPMD) and thermodynamic modeling of Au local atomic structure and solubility in aqueous solutions saturated with gold metal and containing hydrogen sulfide, sulfate and S3− (SI Appendix). These solutions are representative of fluids that formed major types of gold deposits in the crust: 200–500 °C, 300–1,000 bar, 0.1–3.0 wt% S, 3 < pH < 8, and oxygen fugacity f_O2 between the nickel−nickel oxide (NNO) and HM buffer (1–4).     

Structures and topological defects in pressure-driven lyotropic chromonic liquid crystals

Lyotropic chromonic liquid crystals are water-based materials composed of self-assembled cylindrical aggregates. Their behavior under flow is poorly understood, and quantitatively resolving the optical retardance of the flowing liquid crystal has so far been limited by the imaging speed of current polarization-resolved imaging techniques. Here, we employ a single-shot quantitative polarization imaging method, termed polarized shearing interference microscopy, to quantify the spatial distribution and the dynamics of the structures emerging in nematic disodium cromoglycate solutions in a microfluidic channel. We show that pure-twist disclination loops nucleate in the bulk flow over a range of shear rates. These loops are elongated in the flow direction and exhibit a constant aspect ratio that is governed by the nonnegligible splay-bend anisotropy at the loop boundary. The size of the loops is set by the balance between nucleation forces and annihilation forces acting on the disclination. The fluctuations of the pure-twist disclination loops reflect the tumbling character of nematic disodium cromoglycate. Our study, including experiment, simulation, and scaling analysis, provides a comprehensive understanding of the structure and dynamics of pressure-driven lyotropic chromonic liquid crystals and might open new routes for using these materials to control assembly and flow of biological systems or particles in microfluidic devices.

Lyotropic chromonic liquid crystals (LCLCs) are aqueous dispersions of organic disk-like molecules that self-assemble into cylindrical aggregates, which form nematic or columnar liquid crystal phases under appropriate conditions of concentration and temperature (1–6). These materials have gained increasing attention in both fundamental and applied research over the past decade, due to their distinct structural properties and biocompatibility (4, 7–14). Used as a replacement for isotropic fluids in microfluidic devices, nematic LCLCs have been employed to control the behavior of bacteria and colloids (13, 15–20).Nematic liquid crystals form topological defects under flow, which gives rise to complex dynamical structures that have been extensively studied in thermotropic liquid crystals (TLCs) and liquid crystal polymers (LCPs) (21–29). In contrast to lyotropic liquid crystals that are dispersed in a solvent and whose phase can be tuned by either concentration or temperature, TLCs do not need a solvent to possess a liquid-crystalline state and their phase depends only on temperature (30). Most TLCs are shear-aligned nematics, in which the director evolves toward an equilibrium out-of-plane polar angle. Defects nucleate beyond a critical Ericksen number due to the irreconcilable alignment of the directors from surface anchoring and shear alignment in the bulk flow (24, 31–33). With an increase in shear rate, the defect type can transition from π-walls (domain walls that separate regions whose director orientation differs by an angle of π) to ordered disclinations and to a disordered chaotic regime (34). Recent efforts have aimed to tune and control the defect structures by understanding the relation between the selection of topological defect types and the flow field in flowing TLCs. Strategies to do so include tuning the geometry of microfluidic channels, inducing defect nucleation through the introduction of isotropic phases or designing inhomogeneities in the surface anchoring (35–39). LCPs are typically tumbling nematics for which α2α3 < 0, where α2 and α3 are the Leslie viscosities. This leads to a nonzero viscous torque for any orientation of the director, which allows the director to rotate in the shear plane (22, 29, 30, 40). The tumbling character of LCPs facilitates the nucleation of singular topological defects (22, 40). Moreover, the molecular rotational relaxation times of LCPs are longer than those of TLCs, and they can exceed the timescales imposed by the shear rate. As a result, the rheological behavior of LCPs is governed not only by spatial gradients of the director field from the Frank elasticity, but also by changes in the molecular order parameter (25, 41–43). With increasing shear rate, topological defects in LCPs have been shown to transition from disclinations to rolling cells and to worm-like patterns (25, 26, 43).Topological defects occurring in the flow of nematic LCLCs have so far received much more limited attention (44, 45). At rest, LCLCs exhibit unique properties distinct from those of TLCs and LCPs (1, 2, 4–6, 44). In particular, LCLCs have significant elastic anisotropy compared to TLCs; the twist Frank elastic constant, K2, is much smaller than the splay and bend Frank elastic constants, K1 and K3. The resulting relative ease with which twist deformations can occur can lead to a spontaneous symmetry breaking and the emergence of chiral structures in static LCLCs under spatial confinement, despite the achiral nature of the molecules (4, 46–51). When driven out of equilibrium by an imposed flow, the average director field of LCLCs has been reported to align predominantly along the shear direction under strong shear but to reorient to an alignment perpendicular to the shear direction below a critical shear rate (52–54). A recent study has revealed a variety of complex textures that emerge in simple shear flow in the nematic LCLC disodium cromoglycate (DSCG) (44). The tumbling nature of this liquid crystal leads to enhanced sensitivity to shear rate. At shear rates γ˙<1 s−1, the director realigns perpendicular to the flow direction adapting a so-called log-rolling state characteristic of tumbling nematics. For 1 s−1<γ˙<10 s−1, polydomain textures form due to the nucleation of pure-twist disclination loops, for which the rotation vector is parallel to the loop normal, and mixed wedge-twist disclination loops, for which the rotation vector is perpendicular to the loop normal (44, 55). Above γ˙>10 s−1, the disclination loops gradually transform into periodic stripes in which the director aligns predominantly along the flow direction (44).Here, we report on the structure and dynamics of topological defects occurring in the pressure-driven flow of nematic DSCG. A quantitative evaluation of such dynamics has so far remained challenging, in particular for fast flow velocities, due to the slow image acquisition rate of current quantitative polarization-resolved imaging techniques. Quantitative polarization imaging traditionally relies on three commonly used techniques: fluorescence confocal polarization microscopy, polarizing optical microscopy, and LC-Polscope imaging. Fluorescence confocal polarization microscopy can provide accurate maps of birefringence and orientation angle, but the fluorescent labeling may perturb the flow properties (56). Polarizing optical microscopy requires a mechanical rotation of the polarizers and multiple measurements, which severely limits the imaging speed. LC-Polscope, an extension of conventional polarization optical microscopy, utilizes liquid crystal universal compensators to replace the compensator used in conventional polarization microscopes (57). This leads to an enhanced imaging speed and better compensation for polarization artifacts of the optical system. The need for multiple measurements to quantify retardance, however, still limits the acquisition rate of LC-Polscopes.We overcome these challenges by using a single-shot quantitative polarization microscopy technique, termed polarized shearing interference microscopy (PSIM). PSIM combines circular polarization light excitation with off-axis shearing interferometry detection. Using a custom polarization retrieval algorithm, we achieve single-shot mapping of the retardance, which allows us to reach imaging speeds that are limited only by the camera frame rate while preserving a large field-of-view and micrometer spatial resolution. We provide a brief discussion of the optical design of PSIM in Materials and Methods; further details of the measurement accuracy and imaging performance of PSIM are reported in ref. 58.Using a combination of experiments, numerical simulations and scaling analysis, we show that in the pressure-driven flow of nematic DSCG solutions in a microfluidic channel, pure-twist disclination loops emerge for a certain range of shear rates. These loops are elongated in the flow with a fixed aspect ratio. We demonstrate that the disclination loops nucleate at the boundary between regions where the director aligns predominantly along the flow direction close to the channel walls and regions where the director aligns predominantly perpendicular to the flow direction in the center of the channel. The large elastic stresses of the director gradient at the boundary are then released by the formation of disclination loops. We show that both the characteristic size and the fluctuations of the pure-twist disclination loops can be tuned by controlling the flow rate.     

Fragile charge order in the nonsuperconducting ground state of the underdoped high-temperature superconductors

The normal state in the hole underdoped copper oxide superconductors has proven to be a source of mystery for decades. The measurement of a small Fermi surface by quantum oscillations on suppression of superconductivity by high applied magnetic fields, together with complementary spectroscopic measurements in the hole underdoped copper oxide superconductors, point to a nodal electron pocket from charge order in YBa₂Cu₃O6+δ. Here, we report quantum oscillation measurements in the closely related stoichiometric material YBa₂Cu₄O₈, which reveals similar Fermi surface properties to YBa₂Cu₃O6+δ, despite the nonobservation of charge order signatures in the same spectroscopic techniques, such as X-ray diffraction, that revealed signatures of charge order in YBa₂Cu₃O6+δ. Fermi surface reconstruction in YBa₂Cu₄O₈ is suggested to occur from magnetic field enhancement of charge order that is rendered fragile in zero magnetic fields because of its potential unconventional nature and/or its occurrence as a subsidiary to more robust underlying electronic correlations.The normal state of the underdoped copper oxide superconductors has proven to be even more perplexing than the d-wave superconducting state in these materials. At high temperatures in zero magnetic fields, the normal state of the underdoped cuprates comprises an unconventional Fermi surface of truncated “Fermi arcs” in momentum space, which is referred to as the pseudogap state (1). At low temperatures in high magnetic fields, quantum oscillations reveal the nonsuperconducting ground state in various families of underdoped hole-doped copper oxide superconductors to comprise small Fermi surface pockets (2–15). These small Fermi pockets in YBa₂Cu₃O6+δ have been identified as nodal electron pockets (2, 3, 11, 16, 17) originating from Fermi surface reconstruction associated with charge order measured by X-ray diffraction (18–20), ultrasound (21), nuclear magnetic resonance (22), and optical reflectometry (23). However, various aspects of the underlying charge order and the associated Fermi surface reconstruction remain obscure. A central question pertains to the origin of this charge order, curious features of which include a short correlation length in zero magnetic field that grows with increasing magnetic field and decreasing temperature (20). It is crucial to understand the nature of this ground-state order that is related to the high-temperature pseudogap state and delicately balanced with the superconducting ground state. Here, we shed light on the nature of this state by performing extended magnetic field, temperature, and tilt angle-resolved quantum oscillation experiments in the stoichiometric copper oxide superconductor YBa₂Cu₄O₈ (24). This material with double CuO chains has fixed oxygen stoichiometry, making it a model system to study. YBa₂Cu₄O₈ avoids disorder associated with the fractional oxygen stoichiometry in the YBa₂Cu₃O6+δ chains, which has been shown by microwave conductivity to be the dominant source of weak-limit (Born) scattering (25).Intriguingly, we find magnetic field- and angle-dependent signatures of quantum oscillations in YBa₂Cu₄O₈ (13, 14) that are very similar to those in YBa₂Cu₃O6+δ, indicating a similar nodal Fermi surface that arises from Fermi surface reconstruction by charge order with orthogonal wave vectors (16). However, the same X-ray diffraction measurements that show a Bragg peak characteristic of charge order in YBa₂Cu₃O6+δ for a range of hole dopings from 0.084≤p≤0.164 (19, 20, 26) have, thus far, not revealed a Bragg peak in the case of YBa₂Cu₄O₈ (19). We suggest that charge order enhanced by applied magnetic fields reconstructs the Fermi surface in YBa₂Cu₄O₈, whereas charge order is revealed even in zero magnetic fields in YBa₂Cu₃O6+δ because of pinning by increased disorder from oxygen vacancies.     

Vanishing nematic order beyond the pseudogap phase in overdoped cuprate superconductors

During the last decade, translational and rotational symmetry-breaking phases—density wave order and electronic nematicity—have been established as generic and distinct features of many correlated electron systems, including pnictide and cuprate superconductors. However, in cuprates, the relationship between these electronic symmetry-breaking phases and the enigmatic pseudogap phase remains unclear. Here, we employ resonant X-ray scattering in a cuprate high-temperature superconductor La1.6−xNd0.4SrxCuO4 (Nd-LSCO) to navigate the cuprate phase diagram, probing the relationship between electronic nematicity of the Cu 3d orbitals, charge order, and the pseudogap phase as a function of doping. We find evidence for a considerable decrease in electronic nematicity beyond the pseudogap phase, either by raising the temperature through the pseudogap onset temperature T* or increasing doping through the pseudogap critical point, p*. These results establish a clear link between electronic nematicity, the pseudogap, and its associated quantum criticality in overdoped cuprates. Our findings anticipate that electronic nematicity may play a larger role in understanding the cuprate phase diagram than previously recognized, possibly having a crucial role in the phenomenology of the pseudogap phase.

There is a growing realization that the essential physics of the cuprate high-temperature superconductors, and perhaps other strongly correlated materials, involves a rich interplay between different electronic symmetry-breaking phases (1–3) like superconductivity, spin or charge density wave (SDW or CDW) order (4–7), antiferromagnetism, electronic nematicity (8–14), and possibly other orders such as pair density wave order (15) or orbital current order (16).One or more of these orders may also be linked with the existence of a zero-temperature quantum critical point (QCP) in the superconducting state of the cuprates, similar to heavy-fermion, organic, pnictide, and iron-based superconductors (17–19). The significance of the QCP in describing the properties of the cuprates, as a generic organizing principle where quantum fluctuations in the vicinity of the QCP impact a wide swath of the cuprate phase diagram, remains an open question. Evidence for such a QCP and its influence include a linear in temperature resistivity extending to low temperature, strong mass enhancement via quantum oscillation studies (20), and an enhancement in the specific heat (21) in the field induced normal state, with some of the more-direct evidence for a QCP in the cuprates coming from measurements in the material La1.6−xNd0.4SrxCuO4 (Nd-LSCO). Moreover, the QCP also appears to be the endpoint of the pseudogap phase (21) that is marked, among other features, by transition of the electronic structure from small Fermi surface that is folded or truncated by the antiferromagnetic zone boundary in the pseudogap phase to a large Fermi surface at higher doping (22, 23) that is consistent with band structure calculations (24). However, in the cuprates, neither the QCP nor the change in the electronic structure have been definitively associated with a particular symmetry-breaking phase.In this article, we interrogate the possibility that the cuprates exhibit a connection between electronic nematic order, the pseudogap, and its associated QCP. In the pnictide superconductors, which are similar in many respects to the cuprates, electronic nematic order is more clearly established experimentally, and there have been reports of nematic fluctuations (25), non-Fermi liquid transport (26), and a change in the topology of the Fermi surface associated with a nematic QCP (27). Electronic nematicity refers to a breaking of rotational symmetry of the electronic structure in a manner that is not a straightforward result of crystalline symmetry, such that an additional electronic nematic order parameter beyond the structure would be required to describe the resulting phase. The manifestation of nematic order may therefore depend on the details of the crystal structure of the materials, such as whether the structure is tetragonal or orthorhombic. However, such a state can be difficult to identify in materials that have orthorhombic structures, which would naturally couple to any electronic nematic order and vice versa. Despite these challenges, experimental evidence for electronic nematic order that is distinct from the crystal structure include reports of electronic nematicity from bulk transport (8–10) and magnetometry measurements (11) in YBa2Cu3Oy (YBCO), scanning tunneling microscopy (STM) (13, 14, 28) in Bi2Sr2CaCu2O8+δ (Bi2212), inelastic neutron scattering (12) in YBCO, and resonant X-ray scattering (29) in (La,Nd,Ba,Sr,Eu)₂CuO₄. Moreover, STM studies in Bi2212 have reported intraunit cell nematicity disappearing around the pseudogap endpoint (30), which also seems to be a region of enhanced electronic nematic fluctuations (31, 32). In YBCO, there have also been reports of association between nematicity and the pseudogap onset temperature (9, 11).Here, we use resonant X-ray scattering to measure electronic nematic order in the cuprate Nd-LSCO as a function of doping and temperature to explore the relationship of electronic nematicity with the pseudogap phase. While evidence that a quantum critical point governs a wide swath of the phase diagram in hole-doped cuprates and is generic to many material systems remains unclear, investigation of Nd-LSCO provides the opportunity to probe the evolution of electronic nematicity over a wide range of doping in the same material system where some of the most compelling signatures of quantum criticality and electronic structure evolution have been observed. These include a divergence in the heat capacity (21), a change in the electronic structure from angle-dependent magnetoresistance (ADMR) measurements (24) in the vicinity of the QCP at x = 0.23, and the onset of the pseudogap (23). Our main result is that we observe a vanishing of the electronic nematic order in Nd-LSCO as hole doping is either increased above x = 0.23, which has been identified as the QCP doping for this system (21), or when temperature is increased above the pseudogap onset temperature T* (23). These observations indicate that electronic nematicity in Nd-LSCO is intimately linked to the pseudogap phase.     

Layering transitions and metastable structures of cholesteric liquid crystals in cylindrical confinement

Our study of cholesteric lyotropic chromonic liquid crystals in cylindrical confinement reveals the topological aspects of cholesteric liquid crystals. The double-twist configurations we observe exhibit discontinuous layering transitions, domain formation, metastability, and chiral point defects as the concentration of chiral dopant is varied. We demonstrate that these distinct layer states can be distinguished by chiral topological invariants. We show that changes in the layer structure give rise to a chiral soliton similar to a toron, comprising a metastable pair of chiral point defects. Through the applicability of the invariants we describe to general systems, our work has broad relevance to the study of chiral materials.

Chiral liquid crystals (LCs) are ubiquitous, useful, and rich systems (1–4). From the first discovery of the liquid crystalline phase to the variety of chiral structures formed by biomolecules (5–9), the twisted structure, breaking both mirror and continuous spatial symmetries, is omnipresent. The unique structure also makes the chiral nematic (cholesteric) LC, an essential material for applications utilizing the tunable, responsive, and periodic modulation of anisotropic properties.The cholesteric is also a popular model system to study the geometry and topology of partially ordered matter. The twisted ground state of the cholesteric is often incompatible with confinement and external fields, exhibiting a large variety of frustrated and metastable director configurations accompanying topological defects. Besides the classic example of cholesterics in a Grandjean−Cano wedge (10, 11), examples include cholesteric droplets (12–16), colloids (17–19), shells (20–22), tori (23, 24), cylinders (25–29), microfabricated structures (30, 31), and films between parallel plates with external fields (32–40). These structures are typically understood using a combination of nematic (achiral) topology (41, 42) and energetic arguments, for example, the highly successful Landau−de Gennes approach (43). However, traditional extensions of the nematic topological approach to cholesterics are known to be conceptually incomplete and difficult to apply in regimes where the system size is comparable to the cholesteric pitch (41, 44).An alternative perspective, chiral topology, can give a deeper understanding of these structures (45–47). In this approach, the key role is played by the twist density, given in terms of the director field n by n⋅∇×n. This choice is not arbitrary; the Frank free energy prefers n⋅∇×n≈−q0=2π/p0 with a helical pitch p0, and, from a geometric perspective, n⋅∇×n≠0 defines a contact structure (48). This allows a number of new integer-valued invariants of chiral textures to be defined (45). A configuration with a single sign of twist is chiral, and two configurations which cannot be connected by a path of chiral configurations are chirally distinct, and hence separated by a chiral energy barrier. Within each chiral class of configuration, additional topological invariants may be defined using methods of contact topology (45–48), such as layer numbers. Changing these chiral topological invariants requires passing through a nonchiral configuration. Cholesterics serve as model systems for the exploration of chirality in ordered media, and the phenomena we describe here—metastability in chiral systems controlled by chiral topological invariants—has applicability to chiral order generally. This, in particular, includes chiral ferromagnets, where, for example, our results on chiral topological invariants apply to highly twisted nontopological Skyrmions (49, 50) (“Skyrmionium”).Our experimental model to explore the chiral topological invariants is the cholesteric phase of lyotropic chromonic LCs (LCLCs). The majority of experimental systems hitherto studied are based on thermotropic LCs with typical elastic and surface-anchoring properties. The aqueous LCLCs exhibiting unusual elastic properties, that is, very small twist modulus K2 and large saddle-splay modulus K24 (51–56), often leading to chiral symmetry breaking of confined achiral LCLCs (53, 54, 56–61), may enable us to access uncharted configurations and defects of topological interests. For instance, in the layer configuration by cholesteric LCLCs doped with chiral molecules, their small K2 provides energetic flexibility to the thickness of the cholesteric layer, that is, the repeating structure where the director n twists by π. The large K24 affords curvature-induced surface interactions in combination with a weak anchoring strength of the lyotropic LCs (62–64).We present a systematic investigation of the director configuration of cholesteric LCLCs confined in cylinders with degenerate planar anchoring, depending on the chiral dopant concentration. We show that the structure of cholesteric configurations is controlled by higher-order chiral topological invariants. We focus on two intriguing phenomena observed in cylindrically confined cholesterics. First, the cylindrical symmetry renders multiple local minima to the energy landscape and induces discontinuous increase of twist angles, that is, a layering transition, upon the dopant concentration increase. Additionally, the director configurations of local minima coexist as metastable domains with point-like defects between them. We demonstrate that a chiral layer number invariant distinguishes these configurations, protects the distinct layer configurations (45), and explains the existence of the topological defect where the invariant changes.     

Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin

Subseafloor mixing of reduced hydrothermal fluids with seawater is believed to provide the energy and substrates needed to support deep chemolithoautotrophic life in the hydrated oceanic mantle (i.e., serpentinite). However, geosphere-biosphere interactions in serpentinite-hosted subseafloor mixing zones remain poorly constrained. Here we examine fossil microbial communities and fluid mixing processes in the subseafloor of a Cretaceous Lost City-type hydrothermal system at the magma-poor passive Iberia Margin (Ocean Drilling Program Leg 149, Hole 897D). Brucite−calcite mineral assemblages precipitated from mixed fluids ca. 65 m below the Cretaceous paleo-seafloor at temperatures of 31.7 ± 4.3 °C within steep chemical gradients between weathered, carbonate-rich serpentinite breccia and serpentinite. Mixing of oxidized seawater and strongly reducing hydrothermal fluid at moderate temperatures created conditions capable of supporting microbial activity. Dense microbial colonies are fossilized in brucite−calcite veins that are strongly enriched in organic carbon (up to 0.5 wt.% of the total carbon) but depleted in ¹³C (δ¹³C_TOC = −19.4‰). We detected a combination of bacterial diether lipid biomarkers, archaeol, and archaeal tetraethers analogous to those found in carbonate chimneys at the active Lost City hydrothermal field. The exposure of mantle rocks to seawater during the breakup of Pangaea fueled chemolithoautotrophic microbial communities at the Iberia Margin, possibly before the onset of seafloor spreading. Lost City-type serpentinization systems have been discovered at midocean ridges, in forearc settings of subduction zones, and at continental margins. It appears that, wherever they occur, they can support microbial life, even in deep subseafloor environments.Serpentinized mantle rocks constitute a major component of oceanic plates, subduction zones, and passive margins. Serpentinization systems have existed throughout most of Earth’s history, and it has been suggested that mixing of serpentinization fluids with Archean seawater produced conditions conducive to abiotic synthesis and the emergence of life on Earth (1). The Lost City hydrothermal field, located ∼15 km off the Mid-Atlantic Ridge axis at 30°N (2–4), represents the archetype of low-temperature seafloor serpentinization systems at slow-spreading midocean ridges and serves as an excellent present-day analog to fossil serpentinite-hosted hydrothermal systems in such environments. Lost City vents warm (≤ 91 °C), high-pH (9–11) fluids enriched in dissolved calcium, H₂, CH₄, formate, and other short-chain hydrocarbons (2, 5, 6). In contrast to high-temperature black smoker-type chimneys consisting of Cu−Fe sulfides, the Lost City chimneys are composed of brucite and calcium carbonate (aragonite, calcite), which form when serpentinization fluids (SF) mix with seawater (SW) (7),Ca2++OH-+HCO3-=CaCO3+H2OSF SF SWMg2++2OH-=Mg(OH)2.SW SFNascent Lost City chimneys are dominated by aragonite and brucite, whereas older structures are dominated by calcite. During aging, brucite undersaturated in seawater dissolves and aragonite recrystallizes to calcite (7).Actively venting chimneys host a microbial community with a relatively high proportion of methanogenic archaea (the Lost City Methanosarcinales), methanotrophic bacteria, and sulfur-oxidizing bacteria, whereas typical sulfate-reducing bacteria are rare (8–10). Geochemical evidence for significant microbial sulfate reduction in basement lithologies and distinct microbial communities in Lost City vent fluids and chimneys suggest that subsurface communities may be different from those in chimney walls (8, 9, 11). The lack of modern seawater bicarbonate and low CO₂/³He in Lost City fluids clearly indicate bicarbonate removal before venting, but it remains unclear if bicarbonate removal occurred by “dark” microbial carbon fixation in a serpentinization-fueled deep biosphere, by carbonate precipitation, or both (12).Other active and fossil seafloor hydrothermal systems similar to Lost City exist in a range of seafloor environments, including the Mid-Atlantic Ridge (13), New Caledonia (14), and the Mariana forearc (15, 16). Bathymodiolus mussels are, in some places, associated with these systems, suggesting that active serpentinization is supporting not only microbial chemosynthetic ecosystems but also macrofaunal communities (16). However, biological processes in the subseafloor of these Lost City-type systems are poorly understood.     

From the Cover: Folding pathway of a multidomain protein depends on its topology of domain connectivity

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant.Topology of protein conformation, or the spatial arrangement of structural units and the chain connectivity among them, is a key determinant of the folding mechanisms of proteins (1–5). However, predicting a folding pathway is a subtle problem when a protein comprises multiple regions of cooperative structure formation (i.e., foldons or domains). Given that a protein has n such cooperative regions and each region tends to show a two-state–like structural transition between ordered and disordered states, the protein as a whole can have 2ⁿ conformation states and multiple folding routes passing through them are allowed. The statistical weights of these folding routes should be determined both by the interactions among structural regions and the strength of cooperativity within individual regions (6). When multiple competitive routes coexist, the observed folding pathway of an ensemble of molecules should be a superposition of these routes, and the dominant folding pathway should be flexibly changed by changing the solution conditions or by mutations. The multiplicity and flexibility of pathways are important, even for small single-domain proteins like ribosomal protein S6 (7, 8), and are evident for proteins that have repeating structures (9–13). For proteins comprising multiple domains (14), the multiplicity of possible folding pathways is significant. The relative importance among 2ⁿ conformation states in the folding process in proteins with n independently foldable domains should be determined by length, structure (13), the topological connectivity of linkers between domains (3), and the interactions at the interface between domains (3, 15, 16). Fig. 1A shows an example protein for the case n = 2.Open in a separate windowFig. 1.Examples of two-domain proteins with different topological complexities. (A) Human γD-crystallin (PDB ID: 1HK0), which has two independently foldable domains connected by a single linker. (B) DHFR (PDB ID: 1rx1), which is topologically more complex, comprising two domains, DLD (blue) and ABD (pink). DLD is a discontinuous domain comprising the N- and C-terminal parts of the chain, and ABD and DLD are connected by two linkers. The positions of linkers are designated by red arrows.The above mechanism for determining folding intermediates and pathways of multidomain proteins is not applicable when domains have mutually correlated folding tendencies. In particular, the correlation between domains may be significant in a topologically complex protein, which has a domain comprising multiple discontinuous parts of a chain. For example, consider one domain, a discontinuous domain, consisting of residues 1 ≤ i ≤ N₁ and N₂ ≤ i ≤ N, and another domain, a continuous domain, consisting of residues N₁ < i < N₂. Because there is a tendency that the continuous parts of the chain form “islands” of ordered structures (17, 18) and that these continuous parts of a sequence can be the nuclei for folding, the discontinuous domain may not be an independent folding unit, but may depend on the continuous domain. In this paper, we theoretically analyze the problem of how a folding pathway is selected in multidomain proteins that have a discontinuous domain by using Escherichia coli dihydrofolate reductase (DHFR) as an example and compare it with its circular permutant that consists only of continuous domains.As shown in Fig. 1B, DHFR is a 159-residue α/β protein consisting of two domains: a discontinuous loop domain (DLD) (residues 1–37 and 107–159) and an adenosine-binding domain (ABD) (residues 38–106). Because DLD does not include a single contiguous region of the chain, but rather includes separate N- and C-terminal parts, the structural ordering of DLD can be correlated with the structural ordering of ABD. As a model protein, DHFR has been intensively investigated (19–29), which has resulted in a picture that DHFR folds along the following pathway:U→τ7I6→τ6I5→τ5IHF→τ1,…,τ4{N}.[1]Here I₆ is an intermediate exhibiting heterogeneous compactness with DLD being only partially compacted but ABD attaining a native-like compactness (19). I₆ appeared in τ₇ < 35?μs after folding was initiated from the unfolded state (U). During τ₆ ～ 550?μs, further structural development was observed both in ABD and in DLD (19), which led to I₅ in which the secondary structures were reasonably formed (20–22) and two subsets of hydrogen-bonding networks were formed in ABD and DLD (23). During τ₅ ～ 200 ms, structures of ABD and DLD were further organized, which led to the hyperfluorescent intermediate state, I_HF, consisting of four substates, I₁, …, I₄, which matured through four parallel pathways on timescales of τ₁, …, τ₄ = 1 ? 100 s to reach the four native conformers, collectively denoted by {N} in Eq. 1 (24–27). It is plausible that the slow process (several hundred seconds) during the τ₁ ? τ₄ phases is due to intense “internal friction” (30–32) in the glassy dynamics of conformation (33), including formation/disruption of nonnative contacts, the effects of proline isomerization, and the cis–trans isomerization of Gly95 and Gly96. Apart from this complexity during the last phase, the folding scheme in Eq. 1 can be regarded as a hierarchical assembly of structures that begins from the ordering of each domain at the early phase of τ₇ and proceeds to the formation of the whole protein during the later phase of τ₅ (19). Therefore, the questions are the mechanisms for how such a sequential pathway is realized in DHFR and how the topological complexity of DHFR affects the pathway selection.     

Magnetoelastic standing waves induced in UO2 by microsecond magnetic field pulses

Magnetoelastic dilatometry of the piezomagnetic antiferromagnet UO₂ was performed via the fiber Bragg grating method in magnetic fields up to 150 T generated by a single-turn coil setup. We show that in microsecond timescales, pulsed-magnetic fields excite mechanical resonances at temperatures ranging from 10 to 300 K, in the paramagnetic as well as within the robust antiferromagnetic state of the material. These resonances, which are barely attenuated within the 100-µs observation window, are attributed to the strong magnetoelastic coupling in UO₂ combined with the high crystalline quality of the single crystal samples. They compare well with mechanical resonances obtained by a resonant ultrasound technique and superimpose on the known nonmonotonic magnetostriction background. A clear phase shift of π in the lattice oscillations is observed in the antiferromagnetic state when the magnetic field overcomes the piezomagnetic switch field Hc=−18 T. We present a theoretical argument that explains this unexpected behavior as a result of the reversal of the antiferromagnetic order parameter at Hc.

The antiferromagnetic (AFM) insulator uranium dioxide UO₂ has been the subject of extensive research during the last decades predominantly due to its widespread use as nuclear fuel in commercial power reactors (1). Besides efforts to understand the unusually poor thermal conductivity of UO₂, which impacts its performance as nuclear fuel (2), a recent magnetostriction study in pulsed magnetic fields up to 92 T uncovered linear magnetostriction in UO₂ (3), a hallmark of piezomagnetism.Piezomagnetism is characterized by the induction of a magnetic polarization by application of mechanical strain, which, in the case of UO₂, is enabled by broken time-reversal symmetry in the 3-k AFM structure that emerges below TN=30.8 K (4–7) and is accompanied by a Jahn–Teller distortion of the oxygen cage (8–11). This also leads to a complex hysteretic magnetoelastic memory behavior where magnetic domain switching occurs at fields around ±18 T at T=2.5 K. Interestingly, the very large applied magnetic fields proved unable to suppress the AFM state that sets in at TN (3). These earlier results provide direct evidence for the unusually high energy scale of spin-lattice interactions and call for further studies in higher magnetic fields.Here we present axial magnetostriction data obtained in a UO₂ single crystal in magnetic fields to 150 T. These ultrahigh fields were produced by single-turn coil pulsed resistive magnets (12, 13) and applied along the [111] crystallographic axis at various temperatures between 10 K and room temperature. At all temperatures, we observe a dominant negative magnetostriction proportional to H² accompanied by unexpectedly strong oscillations that establish a mechanical resonance in the sample virtually instantly upon delivery of the 102 T/μs pulsed magnetic field rate of change. The oscillations are long-lasting due to very low losses and match mechanical resonances obtained with a resonant ultrasound spectroscopy (RUS) technique (14). Mechanical resonances were suggested to explain anomalies in magnetostriction measurements during single-turn pulses (15, 16); however, their potential to elucidate magnetic dynamics was not explored so far. When the sample is cooled below room temperature, the frequencies soften, consistent with observations in studies of the UO₂ elastic constant c₄₄ as a function of temperature (17, 18).In the AFM state, i.e., T<30.8 K, the characteristic magnetic field sign switch in our single-turn coil magnet (a feature of destructive magnets) results in applied field values in excess of the UO₂ AFM domain switch field of Hc≈−18 T. This field sign switch exposes yet another unexpected result, namely, a π (180°) phase shift in the magnetoelastic oscillations. We use a driven harmonic oscillator and an analytical model to shed light on the origin of the observed phase shift.     

Natural Fe-bearing aluminous bridgmanite in the Katol L6 chondrite

Bridgmanite, the most abundant mineral of the Earth’s lower mantle, has been reported in only a few shocked chondritic meteorites; however, the compositions of these instances differ from that expected in the terrestrial bridgmanite. Here, we report the first natural occurrence of Fe-bearing aluminous bridgmanite in shock-induced melt veins within the Katol L6 chondrite with a composition that closely matches those synthesized in high-pressure and temperature experiments over the last three decades. The Katol bridgmanite coexists with majorite and metal-sulfide intergrowths. We found that the natural Fe-bearing aluminous bridgmanite in the Katol L6 chondrite has a significantly higher Fe³⁺/ΣFe ratio (0.69 ± 0.08) than coexisting majorite (0.37 ± 0.10), which agrees with experimental studies. The Katol bridgmanite is arguably the closest natural analog for the bridgmanite composition expected to be present in the Earth’s lower mantle. Textural observations and comparison with laboratory experiments suggest that the Katol bridgmanite formed at pressures of ∼23 to 25 gigapascals directly from the chondritic melt generated by the shock event. Thus, the Katol L6 sample may also serve as a unique analog for crystallization of bridgmanite during the final stages of magma ocean crystallization during Earth’s formation.

Bridgmanite is a dominant phase in the Earth’s lower mantle (1, 2) where it constitutes about 75 wt% of peridotitic composition (3) and is stable from 660- to 2,700-km depth. The crystal structure of natural bridgmanite with the unit formula (Mg_0.75Fe_0.20Na_0.03Ca_0.02Mn_0.01)SiO₃ has been reported for the first time in the shock-melt veins of the Tenham L6 chondrite (4). The fine-grained polycrystalline bridgmanite in the Tenham L6 chondrite is formed by solid-state phase transformation from orthoenstatite and contains almost no Al₂O₃ (close to 0.2 wt%) (4, 5). More recently, Bindi et al. (6) reported the discovery of a Fe-rich analog of bridgmanite (hiroseite) in the Suizhou L6 chondrite with a composition (Fe²⁺_0.44Mg_0.37Fe³⁺_0.10Al_0.04Ca_0.03Na_0.02)(Si_0.89Al_0.11)O₃ containing 6.5 wt% Al₂O₃. Although these findings in natural materials may resemble the mineralogy of the Earth’s lower mantle, their chemical compositions differ significantly from those produced experimentally (7, 8). High-pressure experimental studies provide evidence that bridgmanite takes up most of the Al₂O₃ (9) of the mantle and contains up to 5 wt% of Al₂O₃ in a peridotitic bulk composition (10–12). The few natural occurrences of bridgmanite-like inclusions in superdeep diamonds contain variable amounts of Al₂O₃ ranging from less than 2 to 13 wt% (13–15). However, these inclusions represent the residue of back-transformation reactions occurred during the ascent of kimberlite magma from the deep mantle to the surface. The variation of Al content in bridgmanite has been explained in light of two substitution mechanisms for the incorporation of Al³⁺ into bridgmanite (16).The first coupled substitution is represented as follows:Al3+VI+Al3+VIII ⇆ Si4+VI+Mg2+VIII ,[1]where aluminum enters both cation sites and corresponds to the exchange vector [Al^(VI)Al^(VIII)][Si^(VI)Mg^(VIII)]_-1. Italic numbers in parentheses indicate the coordination number of the respective cation.The second mechanism is described as follows:2Al3+VI+V0O.. ⇆ 2Si4+VI+O2−,[2]where aluminum replaces silicon and oxygen vacancies provide charge balance (V⁰ indicates vacancy) corresponding to the exchange vector [Al₂^(VI)V⁰][ Si₂^(VI)O]_-1. Reaction 1 is the energetically most favorable coupled substitution mechanism (e.g., 17).Furthermore, the observed linear dependence between Al and Fe³⁺ in synthetic bridgmanite has been explained by a coupled substitution (7, 8, 18) corresponding to the exchange vector [Mg^(VIII)Si^(VI)][Fe^3+(VIII)Al^(VI)]_-1:Mg2+VIII+Si4+VI⇆ Fe3+VIII+Al3+VI.[3]High-pressure experiments supported by natural observations suggest that bridgmanite shows Fe³⁺/ΣFe ratios higher than 0.6 at lower-mantle P-T conditions and low oxygen fugacity (fo₂), which is significantly higher than what exhibited by upper mantle silicate minerals at low fo₂ (19, 20). Here, we report the first natural occurrence of Fe-bearing aluminous bridgmanite and discuss its formation mechanisms through the analyses of coexisting majorite and metal–sulfide intergrowths in the Katol L6 chondrite. We propose that Fe-bearing aluminous bridgmanite from Katol was crystallized at pressures of 23 to 25 GPa from the chondritic melt generated by the shock event. We also measured Fe³⁺/ΣFe of natural bridgmanite and majorite formed by shock metamorphism. Our results reveal that Fe-bearing aluminous bridgmanite has a higher Fe³⁺/ΣFe than coexisting majorite and confirm the experimental observations of high Fe³⁺ content in bridgmanite at lower-mantle conditions.     

Rational prioritization strategy allows the design of macrolide derivatives that overcome antibiotic resistance

Antibiotic resistance is a major threat to global health; this problem can be addressed by the development of new antibacterial agents to keep pace with the evolutionary adaptation of pathogens. Computational approaches are essential tools to this end since their application enables fast and early strategical decisions in the drug development process. We present a rational design approach, in which acylide antibiotics were screened based on computational predictions of solubility, membrane permeability, and binding affinity toward the ribosome. To assess our design strategy, we tested all candidates for in vitro inhibitory activity and then evaluated them in vivo with several antibiotic-resistant strains to determine minimal inhibitory concentrations. The predicted best candidate is synthetically more accessible, exhibits higher solubility and binding affinity to the ribosome, and is up to 56 times more active against resistant pathogens than telithromycin. Notably, the best compounds designed by us show activity, especially when combined with the membrane-weakening drug colistin, against Acinetobacter baumanii, Pseudomonas aeruginosa, and Escherichia coli, which are the three most critical targets from the priority list of pathogens of the World Health Organization.

The resistance of bacterial pathogens against antibiotics is a global problem that requires the constant development of new antibacterial agents (1, 2). The design of new derivatives, based on the modification of existing antibiotics or natural products, relies on extensive structural optimization (3). This process can be time consuming and costly given the possible synthetic routes and the need to consider key factors such as binding affinity, pharmacokinetics, and toxicity. Efficient computational strategies are thus essential to address this problem.Macrolides are an important class of antibiotics that act against the bacterial ribosome. The first described natural macrolide, erythromycin, is the precursor of semisynthetic modern antibiotics such as azithromycin, clarithromycin, telithromycin, and solithromycin. The design of new macrolide antibiotics commonly relies on semisynthesis and, more recently, on total synthesis (4–11). The synthetic routes comprise 6 linear steps in the case of clarithromycin and 10 or more linear steps for telithromycin or for fully synthetic macrolides. Macrolides bind a conserved position in the bacterial ribosome and only show a small number of polar contacts with ribosomal RNA (12, 13). Crystal structures of bound clarithromycin (14) revealed that the cladinose moiety does not directly interact with the ribosome. Thus, modifications of this side chain can be used to address resistance mechanisms (15–17). As an additional benefit, the cladinose moiety can be replaced by a more synthesizable aryl acetic acid derivative to form acylides (5, 6).Here, we outline a rational design strategy and apply it to find candidates with improved antibacterial activity based on a prioritization scheme that draws inspiration from branch-and-bound optimization algorithms (18). Candidates are eliminated or prioritized based on theoretical lower and upper bounds for chemical properties that are essential for activity. The protocol provides design decisions as fast and early as possible, aiming for a computational prioritization within a matter of days to guide the synthesis and testing efforts.Six conditions must be met by a candidate to proceed through the different stages of the prioritization scheme. The molecule must be synthetically accessible (stage I), soluble in aqueous solution (stage IIa), and exhibit sufficient membrane permeability (stage IIb) as well as high binding affinity toward the target (stages IIIa to IIId). Moreover, candidates should avoid resistance mechanisms (stage IV) and must be nontoxic (stage V). The design process is simplified when the optimization starts from an approved drug since therapeutic agents generally fulfill most of these conditions. Thus, the focus lies on eliminating modifications that lead to a loss of essential properties and on favoring candidates for which these properties are improved or at least conserved. From one stage to the next, fewer molecules are evaluated but with increasing rigor. The rational design starts with a strategy for synthesis, followed by prioritization through a series of computational techniques. The prioritized molecules are then tested both in vitro and in vivo. The toxicity of the most active candidates is evaluated in the final stage.In this work, we validate our design strategy with the study of 19 acylide replacements of the cladinose moiety of clarithromycin using four linear synthesis steps (Fig. 1). This is two steps shorter than that for telithromycin. The numbering of the library starts with the original clarithromycin molecule (1; CTY). Its derivatives include substituents with different polarities and electron densities, aliphatic analogs, or inflexible spacers between the macrolide core and the aryl substituent. The set was designed to evaluate the effects of nitro substituents (5, 6), an extended π system, an electron-donating substituent, and a cyclohexyl derivative (as a nonaromatic comparison), as well as halogenated and methylated derivatives. Both the spatial and electronic constraints on the scaffold are explored.Open in a separate windowFig. 1.Synthesis of the acylide library. CTY denotes clarithromycin. (i) 6.1 eq. ArCH2CO2H, 6.0 eq. 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide· HCl, 1.1 eq. 4-dimethylaminopyridine (DMAP), dichloromethane (DCM), room temperature or 3.3 eq. ArCH2CO2H, 3.3 eq. trimethylacetyl chloride, 3.3 eq. Et3N, 1 eq. DMAP, DCM, −15° C → RT. (ii) MeOH, RT, 48 h. (iii) 2 eq. NiCl2·6H2O, 4 eq. NaBH4, MeOH, 0° C. Computed structures are highlighted in red. *Previously described compounds.     

How amide hydrogens exchange in native proteins

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.Before the tightly packed and densely H-bonded structure of globular proteins had been established, Hvidt and Linderstrøm-Lang (1) showed that all backbone amide hydrogens of insulin exchange with water hydrogens, implying that all parts of the polypeptide backbone are, at least transiently, exposed to solvent. In the following 60 y, hydrogen exchange (HX), usually monitored by NMR spectroscopy (2) or mass spectrometry (3), has been widely used to study protein folding and stability (4–10), structure (11, 12), flexibility and dynamics (13–15), and solvent accessibility and binding (16, 17), often with single-residue resolution. However, because the exchange mechanism is unclear, HX data from proteins can, at best, be interpreted qualitatively (18–25).Under most conditions, amide HX is catalyzed by hydroxide ions (26, 27) at a rate that is influenced by inductive and steric effects from adjacent side chains (28). For unstructured peptides, HX is a slow process simply because the hydroxide concentration is low. For example, at 25° C and pH 4, HX occurs on a time scale of minutes. Under similar conditions, amides buried in globular proteins exchange on a wide range of time scales, extending up to centuries. HX can only occur if the amide is exposed to solvent, so conformational fluctuations must be an integral part of the HX mechanism (18).Under sufficiently destabilizing conditions HX occurs from the denatured-state ensemble, but under native conditions few amides exchange by such global unfolding (9, 29–31). For example, in bovine pancreatic trypsin inhibitor (BPTI), 8 amides in the core β-sheet exchange by global unfolding under native conditions (7, 32), whereas the remaining 45 amides require less extensive conformational fluctuations. Much of the debate in the protein HX field over the past half-century has concerned the nature of these subglobal fluctuations and their frequency, duration, amplitude, and cooperativity (18–25).According to the standard HX model (18), each amide can exist in a closed (C) state, where exchange cannot occur, or in an open (O) state, where exchange proceeds at a rate k_int. The kinetic scheme for H exchange into D₂O then reads as(N−H)C⇌kclkop(N−H)O→kint(N−D)Oand the measured steady-state HX rate is k_HX = k_op?k_int/(k_op + k_cl + k_int). To make this phenomenological model practically useful, two auxiliary assumptions are needed to disentangle the conformational and intrinsic parts of the process: (i) The conformational fluctuations (k_op and k_cl) are independent of pH, and (ii) HX from the O state proceeds at the same rate as in model peptides with the same neighboring side chains, so that kint=kHX0.Two HX regimes are distinguished with reference to the pH dependence of k_HX (18). If k_HX is constant in some pH range, it follows that k_int ? k_op + k_cl so that k_HX = k_op. In this so-called EX1 limit, the HX experiment measures the opening rate, or the mean residence time (MRT), of the C state, τ_C = 1/k_op. For BPTI, such pH invariance has only been observed for the eight core amides, and then only in a narrow pH interval (32).More commonly, HX experiments are performed in the EX2 limit, where k_int ? k_op + k_cl. Then k_HX = k_int/(κ + 1), where κ ≡ k_cl/k_op = τ_C/τ_O is the protection factor (PF). At equilibrium, the fractional populations, f_C and f_O, and the rates are linked by detailed balance, k_op?f_C = k_cl?f_O, so the PF may also be expressed as κ = f_C/f_O. Clearly, 1/(κ + 1) is the probability of finding the amide in the O state, 1/κ is the C  ?  O equilibrium constant, and β?ΔG = ln?κ is the free energy difference between the O and C states in units of k_B?T ≡ 1/β. The PF can thus be deduced from the HX rates measured (under EX2 conditions) for the amide in the protein and in a model peptide as κ=kHX0/kHX−1.The vast majority of the available protein HX data pertains to the EX2 regime and thus provides no information about the time scales, τ_C and τ_O, of the conformational fluctuations, except for the EX2 bound: 1/τC+1/τO≫kint≈kHX0. In the typical case where kHX≪kHX0, so that τ_C ? τ_O, we therefore only know that τO≪1/kHX0, which is in the millisecond range at pH 9 (EX2 HX data are usually measured at lower pH, where 1/kHX0 is even longer). Our analysis indicates that τ_O is seven orders of magnitude shorter than this upper bound estimate.The HX experiment is unique in probing sparsely populated conformational states with single-residue resolution. However, the physical significance of the PF is obscured by our ignorance about the structure and dynamics of the O state. Several attempts have been made to correlate experimental PFs with physical attributes of the amides, such as solvent contact (33–37), burial depth (38), intramolecular H-bonds (35, 38–40), packing density (38, 41), or electric field (42). Where significant correlations have been found, they suggest that the chosen attribute can serve as a proxy for the propensity for C → O fluctuations. However, whether based on crystal structures or molecular dynamics (MD) trajectories, these studies examined the time-averaged protein structure, which is dominated by the C state and therefore provides little or no information about the nature of the C → O fluctuations.In principle, the O state can be identified from molecular simulations, but this requires extensive conformational sampling because most C → O transitions are exceedingly rare. To date, this approach has been tried only with coarse-grained and/or empirical protein models without explicit solvent (43–45), or for HX from the denatured-state ensemble (46). The recent availability of ultralong MD simulations with realistic force fields opens up new opportunities in the search for the elusive O state. We have thus analyzed the millisecond MD trajectory of fully solvated native BPTI performed by Shaw et al. (47). Fortunately, BPTI is also among the proteins that have been most thoroughly studied by HX experiments.     

Catalytic role of formaldehyde in particulate matter formation

Formaldehyde (HCHO), the simplest and most abundant carbonyl in the atmosphere, contributes to particulate matter (PM) formation via two in-cloud processing pathways. First, in a catalytic pathway, HCHO reacts with hydrogen peroxide (H₂O₂) to form hydroxymethyl hydroperoxide (HMHP), which rapidly oxidizes dissolved sulfur dioxide (SO_2,aq) to sulfate, regenerating HCHO. Second, HCHO reacts with dissolved SO_2,aq to form hydroxymethanesulfonate (HMS), which upon oxidation with the hydroxyl radical (OH) forms sulfate and also reforms HCHO. Chemical transport model simulations using rate coefficients from laboratory studies of the reaction rate of HMHP with SO_2,aq show that the HMHP pathways reduce the SO₂ lifetime by up to a factor of 2 and contribute up to ∼18% of global sulfate. This contribution rises to >50% in isoprene-dominated regions such as the Amazon. Combined with recent results on HMS, this work demonstrates that the one-carbon molecules HMHP and HCHO contribute significantly to global PM, with HCHO playing a crucial catalytic role.

Particulate matter (PM) formation has a significant impact on cloud properties, climate, and human health (1). Higher toxicity has been attributed to small-size particles (particles with aerodynamic diameter smaller than 2.5 μm) due to their ability to enter the respiratory and cardiovascular system, causing adverse health effects in highly polluted environments (2–7). A substantial fraction of PM corresponds to sulfate, which is primarily formed from atmospheric oxidation of SO₂ emitted anthropogenically by coal combustion and smelters (8). Important SO₂ oxidation pathways include reaction with the hydroxyl radical (OH) in the gas phase and reaction with hydrogen peroxide (H₂O₂), ozone, multifunctional organic hydroperoxides (RXOOH), and NO₂ in cloud droplets (9–13). Simple organic hydroperoxides, such as methylhydroperoxide and peroxyacetic acid, are unlikely to contribute due to their low Henry’s law constants, on the order of 10² to 10³ M ⋅ atm⁻¹ and lower rate constants for oxidation of SO₂, up to 10² M⁻¹ ⋅ s⁻¹ compared to multifunctional organic hydroperoxides (RXOOH), such as isoprene hydroxyl hydroperoxides (ISOPOOH), which have two orders of magnitude higher Henry’s law constants and at least an order of magnitude higher oxidation rate constants (9, 12). The contribution of transition metal chemistry and reactions on the surface of aerosols are more uncertain but could also play an important role (14). Formation of sulfate by SO₂ oxidation competes with removal of SO₂ by deposition (15). A complete understanding of the contribution of all pathways is important to quantify the SO₂ lifetime (τSO₂) against oxidation and the implied formation rate of sulfate, especially as recent studies showed that models underestimate sulfate in SO₂ source regions (16–23). Competition between gas-phase and condensed-phase pathways has a crucial role in new particle formation (9). Understanding sulfur oxidation pathways is especially important under changing atmospheric conditions (e.g., in areas where observed decreases in anthropogenic NO_x emissions are observed, such as in the southeast United States [SE-US]).In-cloud oxidation of SO_2,aq to sulfate is considered the main source of global PM sulfur, with H₂O₂ presumed to be the most important oxidant (9–11, 24). Atmospheric models overestimate the global sulfur dioxide concentration by ∼50%, but some also underestimate the sulfate concentration by ∼20% globally and >20% on regional scales (16–23). Kim et al. (23) reported that GEOS-Chem underestimates sulfate by 34% in the SE-US. Similarly, Pai et al. (21) showed that GEOS-Chem underestimates sulfate significantly in low-NO_x isoprene-rich regions such as the Amazon and the SE-US. Simulations using large-scale sulfate aerosol models or a global chemical tracer model have shown overestimation of SO_2(g) and underestimation of sulfate in the Northern Hemisphere during winter (16, 17). Studies with Lagrangian atmospheric models across Europe and North America also underestimate sulfate in winter but overestimate sulfate during summer (19, 20). Modeling additional SO₂ oxidation pathways in these regions could decrease τSO₂ and increase regional sulfate production and burden.Another important compound that could contribute to PM formation is formaldehyde. Formaldehyde (HCHO) is the most abundant and simplest carbonyl in the atmosphere, formed primarily via photochemical oxidation of volatile organic compounds, such as isoprene, its main biogenic precursor (25). Having a high Henry’s law constant (∼5.5⋅103 M⋅atm−1) (26), HCHO can partition into cloud and fog water. The term HCHO, as used in this work, refers to both free HCHO and its hydrated form, which is the dominant form in clouds and fog droplets. In cloud droplets, HCHO reacts with SO_2,aq to form hydroxymethanesulfonate (HMS; HOCH2SO3−) (27–30). HMS is stable at pH <6 and resistant to oxidation by hydrogen peroxide (H₂O₂) and ozone (O₃) but can be oxidized by OH to form sulfate and reform HCHO in the aqueous phase (31–34). HMS has recently received attention primarily from the perspective of the PM sulfur budget (30, 35), whereas contribution to the organic carbon budget has not been explicitly discussed. HCHO also reacts with aqueous H₂O₂ to form hydroxymethyl hydroperoxide (HMHP) (36). HMHP is also formed in the gas phase via reaction of the CH₂OO Criegee intermediate with water (36). HMHP has a higher Henry’s law constant (∼2⋅106 M⋅atm−1) (37) than H₂O₂, and as an RXOOH, it has the potential to be an efficient oxidant for SO_2,aq, as recently shown for ISOPOOH (12).In this work, we evaluate the contribution of two species with only one carbon atom, HCHO and HMHP, to PM formation. Laboratory results are integrated into the GEOS-Chem model in order to investigate the importance of HCHO and HMHP to global and regional PM. We calculate the contribution of a pathway, the oxidation of SO_2,aq by HMHP, to PM formation. We discuss the role HCHO plays, especially in the competition between 1) formation of HMS via direct reaction of HCHO with SO_2,aq and 2) formation of sulfate via reaction of HCHO with H₂O₂ to form HMHP, which subsequently oxidizes SO_2,aq to sulfate and reforms HCHO.     

Nature of dynamic gradients,glass formation,and collective effects in ultrathin freestanding films

Molecular, polymeric, colloidal, and other classes of liquids can exhibit very large, spatially heterogeneous alterations of their dynamics and glass transition temperature when confined to nanoscale domains. Considerable progress has been made in understanding the related problem of near-interface relaxation and diffusion in thick films. However, the origin of “nanoconfinement effects” on the glassy dynamics of thin films, where gradients from different interfaces interact and genuine collective finite size effects may emerge, remains a longstanding open question. Here, we combine molecular dynamics simulations, probing 5 decades of relaxation, and the Elastically Cooperative Nonlinear Langevin Equation (ECNLE) theory, addressing 14 decades in timescale, to establish a microscopic and mechanistic understanding of the key features of altered dynamics in freestanding films spanning the full range from ultrathin to thick films. Simulations and theory are in qualitative and near-quantitative agreement without use of any adjustable parameters. For films of intermediate thickness, the dynamical behavior is well predicted to leading order using a simple linear superposition of thick-film exponential barrier gradients, including a remarkable suppression and flattening of various dynamical gradients in thin films. However, in sufficiently thin films the superposition approximation breaks down due to the emergence of genuine finite size confinement effects. ECNLE theory extended to treat thin films captures the phenomenology found in simulation, without invocation of any critical-like phenomena, on the basis of interface-nucleated gradients of local caging constraints, combined with interfacial and finite size-induced alterations of the collective elastic component of the structural relaxation process.

Spatially heterogeneous dynamics in glass-forming liquids confined to nanoscale domains (1–7) play a major role in determining the properties of molecular, polymeric, colloidal, and other glass-forming materials (8), including thin films of polymers (9, 10) and small molecules (11–15), small-molecule liquids in porous media (2, 4, 16, 17), semicrystalline polymers (18, 19), polymer nanocomposites (20–22), ionomers (23–25), self-assembled block and layered (26–33) copolymers, and vapor-deposited ultrastable molecular glasses (34–36). Intense interest in this problem over the last 30 y has also been motivated by the expectation that its understanding could reveal key insights concerning the mechanism of the bulk glass transition.Considerable progress has been made for near-interface altered dynamics in thick films, as recently critically reviewed (1). Large amplitude gradients of the structural relaxation time, τ(z,T), converge to the bulk value, τ_bulk(T), in an intriguing double-exponential manner with distance, z, from a solid or vapor interface (13, 37–42). This implies that the corresponding effective activation barrier, F_total(z,T,H) (where H is film thickness), varies exponentially with z, as does the glass transition temperature, T_g (37). Thus the fractional reduction in activation barrier, ε(z,H), obeys the equation ε(z,H)≡1−Ftotal(z,T,H)/Ftotal,bulk(T)=ε0⁡exp(−z/ξF), where F_total,bulk(T) is the bulk temperature-dependent barrier and ξ_F a length scale of modest magnitude. Although the gradient of reduction in absolute activation barriers becomes stronger with cooling, the amplitude of the fractional reduction of the barrier gradient, quantified by ε₀, and the range ξ_F of this gradient, exhibit a weak or absent temperature dependence at the lowest temperatures accessed by simulations (typically with the strength of temperature dependence of ξ_F decreasing rather than increasing on cooling), which extend to relaxation timescales of order 10⁵ ps. This finding raises questions regarding the relevance of critical-phenomena–like ideas for nanoconfinement effects (1). Partially due to this temperature invariance, coarse-grained and all-atom simulations (1, 37, 42, 43) have found a striking empirical fractional power law decoupling relation between τ(z,T) and τ_bulk(T):τ(T,z)τbulk(T)∝(τbulk(T))−ε(z).[1]Recent theoretical analysis suggests (44) that this behavior is consistent with a number of experimental data sets as well (45, 46). Eq. 1 also corresponds to a remarkable factorization of the temperature and spatial location dependences of the barrier:Ftotal(z,T)=[1−ε(z)]Ftotal,bulk(T).[2]This finding indicates that the activation barrier for near-interface relaxation can be factored into two contributions: a z-dependent, but T-independent, “decoupling exponent,” ε(z), and a temperature-dependent, but position-insensitive, bulk activation barrier, F_total,bulk(T). Eq. 2 further emphasizes that ε(z) is equivalent to an effective fractional barrier reduction factor (for a vapor interface), 1−Ftotal(z,T,H)/Ftotal,bulk(T), that can be extracted from relaxation data.In contrast, the origin of “nanoconfinement effects” in thin films, and how much of the rich thick-film physics survives when dynamic gradients from two interfaces overlap, is not well understood. The distinct theoretical efforts for aspects of the thick-film phenomenology (44, 47–50) mostly assume an additive summation of one-interface effects in thin films, thereby ignoring possibly crucial cooperative and whole film finite size confinement effects. If the latter involve phase-transition–like physics as per recent speculations (14, 51), one can ask the following: do new length scales emerge that might be truncated by finite film size? Alternatively, does ultrathin film phenomenology arise from a combination of two-interface superposition of the thick-film gradient physics and noncritical cooperative effects, perhaps in a property-, temperature-, and/or thickness-dependent manner?Here, we answer these questions and establish a mechanistic understanding of thin-film dynamics for the simplest and most universal case: a symmetric freestanding film with two vapor interfaces. We focus on small molecules (modeled theoretically as spheres) and low to medium molecular weight unentangled polymers, which empirically exhibit quite similar alterations in dynamics under “nanoconfinement.” We do not address anomalous phenomena [e.g., much longer gradient ranges (29), sporadic observation of two distinct glass transition temperatures (52, 53)] that are sometimes reported in experiments with very high molecular weight polymers and which may be associated with poorly understood chain connectivity effects that are distinct from general glass formation physics (54–56).We employ a combination of molecular dynamics simulations with a zero-parameter extension to thin films of the Elastically Cooperative Nonlinear Langevin Equation (ECNLE) theory (57, 58). This theory has previously been shown to predict well both bulk activated relaxation over up to 14 decades (44–46) and the full single-gradient phenomenology in thick films (1). Here, we extend this theory to treat films of finite thickness, accounting for coupled interface and geometric confinement effects. We compare predictions of ECNLE theory to our previously reported (37, 43) and new simulations, which focus on translational dynamics of films comprised of a standard Kremer–Grest-like bead-spring polymer model (see SI Appendix). These simulations cover a wide range of film thicknesses (H, from 4 to over 90 segment diameters σ) and extend to low temperatures where the bulk alpha time is ∼0.1 μs (10⁵ Lennard Jones time units τ_LJ).The generalized ECNLE theory is found to be in agreement with simulation for all levels of nanoconfinement. We emphasize that this theory does not a priori assume any of the empirically established behaviors discovered using simulation (e.g., fractional power law decoupling, double-exponential barrier gradient, gradient flattening) but rather predicts these phenomena based upon interfacial modifications of the two coupled contributions to the underlying activation barrier– local caging constraints and a long-ranged collective elastic field. It is notable that this strong agreement is found despite the fact the dynamical ideas are approximate, and a simple hard sphere fluid model is employed in contrast to the bead-spring polymers employed in simulation. The basic unit of length in simulation (bead size σ) and theory (hard sphere diameter d) are expected to be proportional to within a prefactor of order unity, which we neglect in making comparisons.As an empirical matter, we find from simulation that many features of thin-film behavior can be described to leading order by a linear superposition of the thick-film gradients in activation barrier, that is:ε(z,H)=1−Ftotal(z,T,H)/Ftotal,bulk(T)≈ε0[exp(−z/ξF)+exp(−(H−z)/ξF)],[3]where the intrinsic decay length ξ_F is unaltered from its thick-film value and where ε₀ is a constant that, in the hypothesis of literal gradient additivity, is invariant to temperature and film thickness. We employ this functional form [originally suggested by Binder and coworkers (59)], which is based on a simple superposition of the two single-interface gradients, as a null hypothesis throughout this study: this form is what one expects if no new finite-size physics enters the thin-film problem relative to the thick film.However, we find that the superposition approximation progressively breaks down, and eventually entirely fails, in ultrathin films as a consequence of the emergence of a finite size confinement effect. The ECNLE theory predicts that this failure is not tied to a phase-transition–like mechanism but rather is a consequence of two key coupled physical effects: 1) transfer of surface-induced reduction of local caging constraints into the film, and 2) interfacial truncation and nonadditive modifications of the collective elastic contribution to the activation barrier.     

Dynamic rupture initiation and propagation in a fluid-injection laboratory setup with diagnostics across multiple temporal scales

Fluids are known to trigger a broad range of slip events, from slow, creeping transients to dynamic earthquake ruptures. Yet, the detailed mechanics underlying these processes and the conditions leading to different rupture behaviors are not well understood. Here, we use a laboratory earthquake setup, capable of injecting pressurized fluids, to compare the rupture behavior for different rates of fluid injection, slow (megapascals per hour) versus fast (megapascals per second). We find that for the fast injection rates, dynamic ruptures are triggered at lower pressure levels and over spatial scales much smaller than the quasistatic theoretical estimates of nucleation sizes, suggesting that such fast injection rates constitute dynamic loading. In contrast, the relatively slow injection rates result in gradual nucleation processes, with the fluid spreading along the interface and causing stress changes consistent with gradually accelerating slow slip. The resulting dynamic ruptures propagating over wetted interfaces exhibit dynamic stress drops almost twice as large as those over the dry interfaces. These results suggest the need to take into account the rate of the pore-pressure increase when considering nucleation processes and motivate further investigation on how friction properties depend on the presence of fluids.

The close connection between fluids and faulting has been revealed by a large number of observations, both in tectonic settings and during human activities, such as wastewater disposal associated with oil and gas extraction, geothermal energy production, and CO₂ sequestration (1–11). On and around tectonic faults, fluids also naturally exist and are added at depths due to rock-dehydration reactions (12–15) Fluid-induced slip behavior can range from earthquakes to slow, creeping motion. It has long been thought that creeping and seismogenic fault zones have little to no spatial overlap. Nonetheless, growing evidence suggests that the same fault areas can exhibit both slow and dynamic slip (16–19). The existence of large-scale slow slip in potentially seismogenic areas has been revealed by the presence of transient slow-slip events in subduction zones (16, 18) and proposed by studies investigating the physics of foreshocks (20–22).Numerical and laboratory modeling has shown that such complex fault behavior can result from the interaction of fluid-related effects with the rate-and-state frictional properties (9, 14, 19, 23, 24); other proposed rheological explanations for complexities in fault stability include combinations of brittle and viscous rheology (25) and friction-to-flow transitions (26). The interaction of frictional sliding and fluids results in a number of coupled and competing mechanisms. The fault shear resistance τres is typically described by a friction model that linearly relates it to the effective normal stress σ^n via a friction coefficient f:τres=f σ^n=f (σn−p),[1]where σn is the normal stress acting across the fault and p is the pore pressure. Clearly, increasing pore pressure p would reduce the fault frictional resistance, promoting the insurgence of slip. However, such slip need not be fast enough to radiate seismic waves, as would be characteristic of an earthquake, but can be slow and aseismic. In fact, the critical spatial scale h* for the slipping zone to reach in order to initiate an unstable, dynamic event is inversely proportional to the effective normal stress (27, 28) and hence increases with increasing pore pressure, promoting stable slip. This stabilizing effect of increasing fluid pressure holds for both linear slip-weakening and rate-and-state friction; it occurs because lower effective normal stress results in lower fault weakening during slip for the same friction properties. For example, the general form for two-dimensional (2D) theoretical estimates of this so-called nucleation size, h*, on rate-and-state faults with steady-state, velocity-weakening friction is given by:h*=(μ*DRS)/[F(a,b)(σn−p)],[2]where μ*=μ/(1−ν) for modes I and II, and μ*=μ for mode III (29); DRS is the characteristic slip distance; and F(a, b) is a function of the rate-and-state friction parameters a and b. The function F(a, b) depends on the specific assumptions made to obtain the estimate: FRR(a,b)=4(b−a)/π (ref. 27, equation 40) for a linearized stability analysis of steady sliding, or FRA(a,b)=[π(b−a)2]/2b, with a/b>1/2 for quasistatic crack-like expansion of the nucleation zone (ref. 30, equation 42).Hence, an increase in pore pressure induces a reduction in the effective normal stress, which both promotes slip due to lower frictional resistance and increases the critical length scale h*, potentially resulting in slow, stable fault slip instead of fast, dynamic rupture. Indeed, recent field and laboratory observations suggest that fluid injection triggers slow slip first (4, 9, 11, 31). Numerical modeling based on these effects, either by themselves or with an additional stabilizing effect of shear-layer dilatancy and the associated drop in fluid pressure, have been successful in capturing a number of properties of slow-slip events observed on natural faults and in field fluid-injection experiments (14, 24, 32–34). However, understanding the dependence of the fault response on the specifics of pore-pressure increase remains elusive. Several studies suggest that the nucleation size can depend on the loading rate (35–38), which would imply that the nucleation size should also depend on the rate of friction strength change and hence on the rate of change of the pore fluid pressure. The dependence of the nucleation size on evolving pore fluid pressure has also been theoretically investigated (39). However, the commonly used estimates of the nucleation size (Eq. 2) have been developed for faults under spatially and temporally uniform effective stress, which is clearly not the case for fluid-injection scenarios. In addition, the friction properties themselves may change in the presence of fluids (40–42). The interaction between shear and fluid effects can be further affected by fault-gauge dilation/compaction (40, 43–45) and thermal pressurization of pore fluids (42, 46–48).Recent laboratory investigations have been quite instrumental in uncovering the fundamentals of the fluid-faulting interactions (31, 45, 49–57). Several studies have indicated that fluid-pressurization rate, rather than injection volume, controls slip, slip rate, and stress drop (31, 49, 57). Rapid fluid injection may produce pressure heterogeneities, influencing the onset of slip. The degree of heterogeneity depends on the balance between the hydraulic diffusion rate and the fluid-injection rate, with higher injection rates promoting the transition from drained to locally undrained conditions (31). Fluid pressurization can also interact with friction properties and produce dynamic slip along rate-strengthening faults (50, 51).In this study, we investigate the relation between the rate of pressure increase on the fault and spontaneous rupture nucleation due to fluid injection by laboratory experiments in a setup that builds on and significantly develops the previous generations of laboratory earthquake setup of Rosakis and coworkers (58, 59). The previous versions of the setup have been used to study key features of dynamic ruptures, including sub-Rayleigh to supershear transition (60); rupture directionality and limiting speeds due to bimaterial effects (61); pulse-like versus crack-like behavior (62); opening of thrust faults (63); and friction evolution (64). A recent innovation in the diagnostics, featuring ultrahigh-speed photography in conjunction with digital image correlation (DIC) (65), has enabled the quantification of the full-field behavior of dynamic ruptures (66–68), as well as the characterization of the local evolution of dynamic friction (64, 69). In these prior studies, earthquake ruptures were triggered by the local pressure release due to an electrical discharge. This nucleation procedure produced only dynamic ruptures, due to the nearly instantaneous normal stress reduction.To study fault slip triggered by fluid injection, we have developed a laboratory setup featuring a hydraulic circuit capable of injecting pressurized fluid onto the fault plane of a specimen and a set of experimental diagnostics that enables us to detect both slow and fast fault slip and stress changes. The range of fluid-pressure time histories produced by this setup results in both quasistatic and dynamic rupture nucleation; the diagnostics allows us to capture the nucleation processes, as well as the resulting dynamic rupture propagation. In particular, here, we explore two injection techniques: procedure 1, a gradual, and procedure 2, a sharp fluid-pressure ramp-up. An array of strain gauges, placed on the specimen’s surface along the fault, can capture the strain (translated into stress) time histories over a wide range of temporal scales, spanning from microseconds to tens of minutes. Once dynamic ruptures nucleate, an ultrahigh-speed camera records images of the propagating ruptures, which are turned into maps of full-field displacements, velocities, and stresses by a tailored DIC) analysis. One advantage of using a specimen made of an analog material, such as poly(methyl meth-acrylate) (PMMA) used in this study, is its transparency, which allows us to look at the interface through the bulk and observe fluid diffusion over the interface. Another important advantage of using PMMA is that its much lower shear modulus results in much smaller nucleation sizes h* than those for rocks, allowing the experiments to produce both slow and fast slip in samples of manageable sizes.We start by describing the laboratory setup and the diagnostics monitoring the pressure evolution and the slip behavior. We then present and discuss the different slip responses measured as a result of slow versus fast fluid injection and interpret our measurements by using the rate-and-state friction framework and a pressure-diffusion model.     

Mechanism of H+ dissociation–induced O–O bond formation via intramolecular coupling of vicinal hydroxo ligands on low-valent Ru(III) centers

The understanding of O–O bond formation is of great importance for revealing the mechanism of water oxidation in photosynthesis and for developing efficient catalysts for water oxidation in artificial photosynthesis. The chemical oxidation of the Ru^II₂(OH)(OH₂) core with the vicinal OH and OH₂ ligands was spectroscopically and theoretically investigated to provide a mechanistic insight into the O–O bond formation in the core. We demonstrate O–O bond formation at the low-valent Ru^III₂(OH) core with the vicinal OH ligands to form the Ru^II₂(μ-OOH) core with a μ-OOH bridge. The O–O bond formation is induced by deprotonation of one of the OH ligands of Ru^III₂(OH)₂ via intramolecular coupling of the OH and deprotonated O⁻ ligands, conjugated with two-electron transfer from two Ru^III centers to their ligands. The intersystem crossing between singlet and triple states of Ru^II₂(μ-OOH) is easily switched by exchange of H⁺ between the μ-OOH bridge and the auxiliary backbone ligand.

Water oxidation to produce O₂ (Eq. 1) is an important biological reaction in photosynthesis. The geometric structure of the active site with a manganese-oxo core (Mn₄CaO₅) for water oxidation, so called oxygen-evolving complex (OEC), has been characterized by recently advanced X-ray crystallographic analysis (1–5). The elucidation of the water oxidation mechanism at OEC on the basis of their geometric structure is a high-interest topic in photosynthesis studies. On the other hand, water oxidation is also a crucial process to use water as an electron source for the solar fuel production in artificial photosynthesis technology that is participated as a future solar energy conversion system (6–8). There has been a great deal of interest in developing active catalysts to promote water oxidation to establish efficient artificial photosynthesis systems (9–13). The elucidation of the water oxidation mechanism provides a key clue of the guideline for developing active catalysts for water oxidation.2H2O→O2+ 4H++ 4e−.[1]In a water oxidation process to produce O₂ (Eq. 1), formation of an O–O bond from two molecules of water is necessary with removal of either consecutive or concerted four electrons and four protons from the water (14–16). Commonly, the O–O bond formation is assisted by catalysts (OEC in photosynthesis) with one or two molecules of water bound on them to decrease thermodynamic energy for formation of the intermediate species. Two main classes of the mechanism for the O–O bond formation on metal centers of the catalysts have been reported: water nucleophilic attack (WNA) on metal-oxo centers (Mⁿ = O) (17–22) and interaction of two Mⁿ = O centers (I2M) (23–29). In the WNA mechanism (17–20), a water molecule nucleophilically attacks onto the Mⁿ = O center to generate a Mⁿ⁻²-OOH hydroperoxide intermediate. Therefore, the high-valent Mⁿ = O center (e.g., Ru^{IV or V}) with electrophilic properties is required. In the I2M mechanism (23–27), the coupling of either two Mⁿ⁻¹-O· oxyl radicals (formally Mⁿ = O) or coupling of one Mⁿ⁻¹-O· oxyl radical with another unit (e.g., Mⁿ = O) of nonradical character affords a Mⁿ⁻¹-OO-Mⁿ⁻¹ peroxide intermediate. For this mechanism, the high-valent Mnⁿ = O centers are not necessarily attained, in contrast to the required high-valent Mⁿ = O center in the WNA mechanism. However, O–O bond formation via coupling of relatively low-valent Mⁿ = O units (e.g., Ru^III) has not been demonstrated so far.proximal,proximal-[Ru₂(tpy)₂(pyan)(OH)(OH₂)]³⁺ (Ru^II₂(OH) (OH₂)) (tpy = 2,2′;6′,2″-terpyridine and pyan = 5-phenyl-2,8-di(2-pyridyl)-1,9,10-anthyridine) with the vicinal OH and OH₂ ligands in the Ru^II₂ core was reported to work efficiently for electrocatalytic water oxidation in a homogenous solution (26). The O–O bond formation via intramolecular coupling between the Ru^V = O units, derived from the Ru^II₂ core with the vicinal OH and OH₂ ligands, was suggested for O₂ production. Recently, we reported that O₂ is produced via the intramolecular coupling between the Ru^IV = O and Ru^IV-OH units for the proximal,proximal-[Ru₂(cptpy)₂(pyan)(OH)(OH₂)]⁺ (Hcptpy = 4′-(4-carboxyphenyl)-2,2′;6′,2″-terpyridine) derivative with 4-carboxyphenyl linkers adsorbed on the TiO₂ surface (27). However, the direct spectroscopic evidence has not yet been provided for the O–O bond formation via intramolecular coupling between the Ru^{IV or V} = O units. Herein, we spectroscopically and theoretically investigate chemical oxidation of Ru^II₂(OH)(OH₂) by a Na₂S₂O₈ oxidant in an aqueous solution to provide a mechanistic insight into the O–O bond formation in the unique Ru₂ core. We demonstrate that the O–O bond formation via intramolecular coupling of vicinal OH ligands on Ru^III-OH units is induced by dissociation of one proton of two OH ligands in the core. This is an observation of the O–O bond formation at the low-valent Ru^III centers. The mechanism of the O–O bond formation is revealed to propose the important role of the central N atom (N_c) of the anthyridine moiety on the pyan backbone ligand as a neighboring proton acceptor site for concerted intramolecular electron/proton transfers.