Development and validation of a general-purpose ReaxFF reactive force field for earth material modeling.

ReaxFF reactive force field bridges the gap between nonreactive molecular simulations and quantum mechanical calculations and has been widely applied during the past two decades. However, its application to earth materials, especially those under high T-P conditions relevant to Earth's interior, is still limited due to the lack of available parameters. Here, we present the development and validation of a ReaxFF force field containing several of the most common elements in Earth's crust, i.e., Si/Al/O/H/Na/K. The force field was trained against a large data set obtained from density functional theory (DFT) calculations, including charges, bond/angle distortion curves, equation of states, ion migration energy profiles, and condensation reaction energies. Different coordination environments were considered in the training set. The fitting results showed that the current force field can well reproduce the DFT data (the Pearson correlation coefficient, Rp, is 0.95). We validated the force field on mineral-water interfaces, hydrous melts/supercritical geofluids, and bulk crystals. It was found that the current force field performed excellently in predicting the structural, thermodynamic, and transport properties of various systems (Rp = 0.95). Moreover, possible applications and future development have been discussed. The results obtained in this study suggest that the current force field holds good promise to model a wide range of processes and thus open opportunities to advance the application of ReaxFF in earth material modeling.

Research on the decomposition mechanisms of lithium silicate ores with different crystal structures by autotrophic and heterotrophic bacteria.

Ores serve as energy and nutrient sources for microorganisms. Through complex biochemical processes, microorganisms disrupt the surface structure of ores and release metal elements. However, there is limited research on the mechanisms by which bacteria with different nutritional modes act during the leaching process of different crystal structure ores. This study evaluated the leaching efficiency of two types of bacteria with different nutritional modes, heterotrophic bacterium Bacillus mucilaginosus (BM) and autotrophic bacterium Acidithiobacillus ferrooxidans (AF), on different crystal structure lithium silicate ores (chain spodumene, layered lepidolite and ring elbaite). The aim was to understand the behavioral differences and decomposition mechanisms of bacteria with different nutritional modes in the process of breaking down distorted crystal lattices of ores. The results revealed that heterotrophic bacterium BM primarily relied on passive processes such as bacterial adsorption, organic acid corrosion, and the complexation of small organic acids and large molecular polymers with metal ions. Autotrophic bacterium AF, in addition to exhibiting stronger passive processes such as organic acid corrosion and complexation, also utilized an active transfer process on the cell surface to oxidize Fe2+ in the ores for energy maintenance and intensified the destruction of ore lattices. As a result, strain AF exhibited a greater leaching effect on the ores compared to strain BM. Regarding the three crystal structure ores, their different stacking modes and proportions of elements led to significant differences in structural stability, with the leaching effect being highest for layered structure, followed by chain structure, and then ring structure. These findings indicate that bacteria with different nutritional modes exhibit distinct physiological behaviors related to their nutritional and energy requirements, ultimately resulting in different sequences and mechanisms of metal ion release from ores after lattice damage.

Davemaoite as the mantle mineral with the highest melting temperature.

Knowledge of high-pressure melting curves of silicate minerals is critical for modeling the thermal-chemical evolution of rocky planets. However, the melting temperature of davemaoite, the third most abundant mineral in Earth's lower mantle, is still controversial. Here, we investigate the melting curves of two minerals, MgSiO3 bridgmanite and CaSiO3 davemaoite, under their stability field in the mantle by performing first-principles molecular dynamics simulations based on the density functional theory. The melting curve of bridgmanite is in excellent agreement with previous studies, confirming a general consensus on its melting temperature. However, we predict a much higher melting curve of davemaoite than almost all previous estimates. Melting temperature of davemaoite at the pressure of core-mantle boundary (~136 gigapascals) is about 7700(150) K, which is approximately 2000 K higher than that of bridgmanite. The ultrarefractory nature of davemaoite is critical to reconsider many models in the deep planetary interior, for instance, solidification of early magma ocean and geodynamical behavior of mantle rocks.

Molecular Insights into the Salinity Effects on Movability of Oil-Brine in Shale Nanopore-Throat Systems.

Low-salinity flooding has been well recognized as a promising strategy to increase shale oil recovery, but the underlying mechanism remains unclarified, especially for complex nanopore networks filled with oil-brine fluids. In this study, the pressure-driven flow of an oil-brine fluid with varying salinities in shale nanopore-throat channels was first investigated based on molecular dynamics simulations. The critical pressure driving oil to intrude into a nanothroat filled with brine of varying salinities was determined. Simulation results indicate that the salinity of brine exhibits great effects on the movability of oil, and low salinity favors the increase of oil movability. Further analysis of the interactions between fluid and pore walls as well as the displacement pressures reveals dual effects of brine salinity on oil transportation in a nanopore-throat. On the one hand, hydrated cations anchoring onto throat walls enlarge the effective flow width in the throat before the hydration complexes reach the maximum. On the other hand, the interfacial tension between oil and brine increases with the brine salinity, which increases the capillary resistance and leads to a higher displacement pressure. These findings highlight the effects of brine salinity on oil movability in a nanopore-throat, which will promote the understanding of oil accumulation and dissipation in petroleum systems, as well as help to develop enhanced oil recovery.

Lithium extraction from typical lithium silicate ores by two bacteria with different metabolic characteristics: Experiments, mechanism and significance.

Microorganisms obtain inorganic nutrients or energy from specific minerals to selectively weather minerals, but few studies on the differences in metabolic components of different functional bacteria lead to different weathering effects. This study evaluated the leaching effects of two bacteria with distinct metabolic characteristics on lithium silicate minerals with different structures. We aimed to understand the microscopic mechanism of crystal destruction of lithium silicate minerals with different structures under the action of microorganisms. The results showed that the metabolites produced by an acid producing silicate strain Raoultella sp. Z107 (strain Z107) had a high content of organic acids, among which lactic acid was up to about 11 g/L. Bacillus mucilaginosus 21,699 (strain BM) secreted capsular polysaccharide with a high content of 14.84 mg/L. The metabolic activities of the two strains were significantly different. Through the analysis of the leaching residue, it was found that the lithium silicate minerals were acid etched, interlayer domains expanded, crystallinity decreased, and metal bonds were broken under the action of bacteria. The dissolution of lithium silicate minerals by bacteria is a combination of bacterial adsorption, organic acid corrosion, and complexation of small molecular organic acids and macromolecular polymers with metal ions. The acid erosion and complexation effects of organic acids are greater than the single complexation of capsular polysaccharides, and the layered lepidolite is more likely to be decomposed by the weathering of bacterial metabolites than the chain structure spodumene. These results indicate that the diversity of metabolic activity of bacteria from different sources and the sequence and decomposition mechanism of metal ions released from minerals after lattice destruction are also different. Microorganisms decompose minerals for energy and nutrients, and eventually become the main players in the transformation of elements in biogeology.

Vertical distribution of dissimilatory iron reducing communities in the sediments of Taihu Lake.

The reduction of Fe(III) coupled with the oxidation of organic matter, primarily stimulated by dissimilatory iron-reducing bacteria (DIRB) under anoxic conditions, is a critical biogeochemical process in lacustrine sediments. Many single strains have been recovered and investigated, however, the changes in the diversity of culturable DIRB communities with sedimentary depth have not been fully revealed. In this study, 41 DIRB strains affiliated to ten genera of phylum Firmicutes, Actinobacteria, and Proteobacteria were isolated from the sediments of Taihu Lake at three depths (0-2 cm, 9-12 cm, and 40-42 cm), referring to distinct nutrient conditions. Fermentative metabolisms were identified in nine genera (except genus Stenotrophomonas). The DIRB community diversity and the microbial iron reduction (MIR) patterns vary in vertical profiles. The community abundance varied with the TOC contents in vertical profiles. The DIRB communities, containing 17 strains of 8 genera, were most diverse in the surface sediments (0-2 cm), where organic matter was most abundant among the three depths. 11 DIRB strains of five genera were identified in the 9-12 cm sediments with the lowest content of organic matter, while 13 strains of seven genera were identified in deep sediments (40-42 cm). Among the isolated strains, phylum Firmicutes dominated the DIRB communities at three depths, while its relative abundance increased with depth. Fe2+ ion was recognized as the dominant microbial ferrihydrite-reducing product of DIRB from 0 to 12 cm sediments. Instead, lepidocrocite and magnetite were the main MIR products of DIRB retrieved from 40 to 42 cm. The results indicate that the MIR driven by fermentative DIRB is crucial in lacustrine sediments and that the distribution of nutrients and iron (minerals) likely influences the diversity of DIRB communities in the lacustrine sediments.

Structure, Stability, and Acidity of the Uranyl Arsenate Dimer in Aqueous Solution.

The migration of uranium (U) in the surficial environment has received considerable attention. Due to their high natural abundance and low solubility, autunite-group minerals play a key role in controlling the mobility of U. However, the formation mechanism for these minerals has yet to be understood. In this work, we took the uranyl arsenate dimer ([UO2(HAsO4)(H2AsO4)(H2O)]22-) as a model molecule and carried out a series of first-principles molecular dynamics (FPMD) simulations to explore the early stage of the formation of trögerite (UO2HAsO4·4H2O), a representative autunite-group mineral. By using the potential-of-mean-force (PMF) method and vertical energy gap method, the dissociation free energies and the acidity constants (pKa's) of the dimer were calculated. Our results show that the U in the dimer holds a 4-coordinate structure, which is consistent with the coordination environment observed in trögerite mineralogy, in contrast to the 5-coordinate U in the monomer. Furthermore, the dimerization is thermodynamically favorable in solution. The FPMD results also suggest that tetramerization and even polyreactions would occur at pH > 2, as observed experimentally. Additionally, it is found that trögerite and the dimer have very similar local structural parameters. These findings imply that the dimer could serve as an important link between the U-As complexes in solution and the autunite-type sheet of trögerite. Given the nearly identical physicochemical properties of arsenate and phosphate, our findings suggest that uranyl phosphate minerals with the autunite-type sheet may form in a similar manner. This study therefore fills a critical gap in atomic-scale knowledge of the formation of autunite-group minerals and provides a theoretical basis for regulating uranium mobilization in P/As-bearing tailing water.

Acidity and metal complexation of edge surface of birnessite-type MnO2: Insight from first principles simulations.

Birnessite-type MnO2 plays key roles in scavenging trace elements in numerous natural environments and has also been regarded as a promising energy storage material. The interfacial properties of birnessite are highly pH-dependent due to the presence of various amphoteric groups on its edges, and, therefore, the acidity constants (pKa) of these groups are vital to the understanding of its electrochemical and environmental performances. However, an accurate acidity dataset for birnessite is absent yet. In this study, we employed first-principles molecular dynamics simulations and the vertical energy gap method to calculate the pKas of groups on the birnessite (010) edge. The interfacial hydration structure was characterized with a focus on the hydrogen bonding network. The obtained pKas suggest that MnOH2 is active while Mn2OH remains inert in a common pH range. Based on these results, the incorporation of transition metals on the edge surface was investigated by taking Ni2+ and Zn2+ as the model cations. The energy changes associated with the incorporation process of Ni2+ from the outer-sphere state indicate that incorporation on the edge surface is more feasible than that on the basal surface presumed in previous studies. Overall, the results obtained provide an atomic-scale insight into the acid-base chemistry of birnessite and form a physical basis for understanding the interfacial processes of birnessite.

Ecological networks of dissolved organic matter and microorganisms under global change.

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.

Superionic Silica-Water and Silica-Hydrogen Compounds in the Deep Interiors of Uranus and Neptune.

Silica, water, and hydrogen are known to be the major components of celestial bodies, and have significant influence on the formation and evolution of giant planets, such as Uranus and Neptune. Thus, it is of fundamental importance to investigate their states and possible reactions under the planetary conditions. Here, using advanced crystal structure searches and first-principles calculations in the Si-O-H system, we find that a silica-water compound (SiO_{2})_{2}(H_{2}O) and a silica-hydrogen compound SiO_{2}H_{2} can exist under high pressures above 450 and 650 GPa, respectively. Further simulations reveal that, at high pressure and high temperature conditions corresponding to the interiors of Uranus and Neptune, these compounds exhibit superionic behavior, in which protons diffuse freely like liquid while the silicon and oxygen framework is fixed as solid. Therefore, these superionic silica-water and silica-hydrogen compounds could be regarded as important components of the deep mantle or core of giants, which also provides an alternative origin for their anomalous magnetic fields. These unexpected physical and chemical properties of the most common natural materials at high pressure offer key clues to understand some abstruse issues including demixing and erosion of the core in giant planets, and shed light on building reliable models for solar giants and exoplanets.

Surface Acidity and As(V) Complexation of Iron Oxyhydroxides: Insights from First-Principles Molecular Dynamics Simulations.

Iron hydroxides are ubiquitous in soils and aquifers and have been adopted as adsorbents for As(V) removal. However, the complexation mechanisms of As(V) have not been well understood due to the lack of information on the reactive sites and acidities of iron hydroxides. In this work, we first calculated the acidity constants (pKas) of surface groups on lepidocrocite (010), (001), and (100) surfaces by using the first-principles molecular dynamics (FPMD)-based vertical energy gap method. Then, the desorption free energies of As(V) on goethite (110) and lepidocrocite (001) surfaces were calculated by using constrained FPMD simulations. The point of zero charges and reactive sites of individual surfaces were obtained based on the calculated pKas. The structures, thermodynamics, and pH dependence for As(V) complexation were derived by integrating the pKas and desorption free energies. The pKa data sets obtained are fundamental parameters that control the charging and adsorption behavior of iron oxyhydroxides and will be very useful in investigating the adsorption processes on these minerals. The pH-dependent complexation mechanisms of As(V) derived in this study would be helpful for the development of effective adsorbent materials and the prediction of the long-term behavior of As(V) in natural environments.

Enhanced Fluoride Uptake by Layered Double Hydroxides under Alkaline Conditions: Solid-State NMR Evidence of the Role of Surface >MgOH Sites.

Layered double hydroxides (LDHs) are potential low-cost filter materials for use in fluoride removal from drinking water, but molecular-scale defluoridation mechanisms are lacking. In this research, we employed 19F solid-state NMR spectroscopy to identify fluoride sorption products on 2:1 MgAl LDH and to reveal the relationship between fluoride sorption and the LDH structure. A set of six 19F NMR peaks centered at -140, -148, -156, -163, -176, and -183 ppm was resolved. Combining quantum chemical calculations based on density function theory (DFT) and 19F{27Al} transfer of populations in double resonance (TRAPDOR) analysis, we could assign the peaks at -140, -148, -156, and -163 ppm to Al-F (F coordinated to surface Al) and those at -176 and -183 ppm to Mg-F (F coordinated to surface Mg only). Interestingly, the spectroscopic data reveal that the formation of Al-F is the predominant mode of F- sorption at low pH, whereas the formation of Mg-F is predominant at high pH (or a higher Mg/Al ratio). This finding supports the fact that the F- uptake of 2:1 MgAl LDH was nearly six times that of activated alumina at pH 9. Overall, we explicitly revealed the different roles of the surface >MgOH and >AlOH sites of LDHs in defluoridation, which explained why the use of classic activated alumina for defluoridation is limited at high pH. The findings from this research may also provide new insights into material screening for potential filters for F- removal under alkaline conditions.

Mixed Coordination Silica at Megabar Pressure.

Silica (SiO_{2}), as a raw material of silicon, glass, ceramics, abrasive, and refractory substances, etc., is of significant importance in industrial applications and fundamental research such as electronics and planetary science. Here, using a crystal structure searching method and first-principles calculations, we predicted that a ground state crystalline phase of silica with R3[over ¯] symmetry is stable at around 645-890 GPa, which contains six-, eight-, and nine-coordinated silicon atoms and results in an average coordination number of eight. This mixed-coordination silica fills in the density, electronic band gap, and coordination number gaps between the previously known sixfold pyrite-type and ninefold Fe_{2}P-type phases, and may appear in the core or mantle of super-Earth exoplanets, or even the solar giant planets such as the Neptune. In addition, we also found that some silicon superoxides, Cmcm SiO_{3} and Ccce SiO_{6}, are stable in this pressure range and may appear in an oxygen-rich environment. Our finding enriches the high-pressure phase diagram of silicon oxides and improves understanding of the interior structure of giant planets in our solar system.

Facet-Dependent Photodegradation of Methylene Blue by Hematite Nanoplates in Visible Light.

The expression of specific crystal facets in different nanostructures is known to play a vital role in determining the sensitivity toward the photodegradation of organics, which can generally be ascribed to differences in surface structure and energy. Herein, we report the synthesis of hematite nanoplates with controlled relative exposure of basal (001) and edge (012) facets, enabling us to establish direct correlation between the surface structure and the photocatalytic degradation efficiency of methylene blue (MB) in the presence of hydrogen peroxide. MB adsorption experiments showed that the capacity on (001) is about three times larger than on (012). Density functional theory calculations suggest the adsorption energy on the (001) surface is 6.28 kcal/mol lower than that on the (012) surface. However, the MB photodegradation rate on the (001) surface is around 14.5 times faster than on the (012) surface. We attribute this to a higher availability of the photoelectron accepting surface Fe3+ sites on the (001) facet. This facilitates more efficient iron valence cycling and the heterogeneous photo-Fenton reaction yielding MB-oxidizing hydroxyl radicals at the surface. Our findings help establish a rational basis for the design and optimization of hematite nanostructures as photocatalysts for environmental remediation.

Stoichiometry-Controlled Chirality Induced by Co-assembly of Tetraphenylethylene Derivative, γ-CD, and Water-Soluble Pillar[5]arene.

A stoichiometry-controlled chirality induction was successfully achieved through coassemblies of amphiphilic tetraphenylethylene derivative TPEA, γ-cyclodextrin (γ-CD), and water-soluble pillar[5]arene WP5 in aqueous solution. Stoichiometric variation of WP5 was found to be an effective strategy to induce topological transition between the pseudo[4]rotaxane and the vesicular form. Interestingly, the formation of pseudo[4]rotaxane triggered dual chirality induction from chiral γ-CD to TPEA (negative ICD1), and then, to dynamically racemic WP5 (positive ICD2), whereas both ICD1 and ICD2 were silent in the vesicular form.

Selection of Planar Chiral Conformations between Pillar[5,6]arenes Induced by Amino Acid Derivatives in Aqueous Media.

Chiral α-amino acids play critical roles in the metabolic process in nearly all life forms. So far, chiral recognition of α-amino acids has mainly focused on the determination of l/d enantiomers. Herein, selection of planar chiral conformations between water-soluble pillar[5]arene WP5 and pillar[6]arene WP6 was observed due to α-side chain or ethyl ester moieties of l-α-amino acid ethyl ester hydrochlorides binding with WP5 and WP6, respectively. Therefore, α-side chain and ethyl ester moieties of l-α-amino acid ethyl ester hydrochlorides were recognized by observing the induced CD signal and its inversion. This is a rare example of being able to detect the chiral region around α-carbon of a chiral α-amino acid molecule.

Molecular dynamics simulation of CO2-switchable surfactant regulated reversible emulsification/demulsification processes of a dodecane-saline system.

CO2-Switchable surfactants are of great potential in a wide range of industrial applications related to their ability to stabilize and destabilize emulsions upon command. Molecular dynamics simulations have been performed to reveal the fundamental mechanism of the reversible emulsification/demulsification processes of a dodecane-saline system by a CO2-switchable surfactant that switches between active (i.e., N'-dodecyl-N,N-dimethylacetamidinium (DMAAH+)) and inactive (i.e., N'-dodecyl-N,N-dimethylacetamidine (DMAA)) forms. The density profiles indicate that DMAAH+ could increase the oil-water interfacial thickness to a greater extent compared to DMAA. DMAAH+ could sharply reduce the interfacial tension of the dodecane-saline system, while DMAA only exhibits a limited decrease, which is in accordance with the experimental observation that DMAAH+/DMAA can reversibly emulsify/demulsify alkane-water systems. Our simulations showed that both the number and lifetime of hydrogen bonds (HBs) between DMAA and water are almost equal to those between DMAAH+ and water. In DMAA, the N atom connecting with the alkyl tail acted as a HB acceptor, while the N atom attached by a proton in DMAAH+ acted as a HB donor. Furthermore, the HBs between DMAAH+ and HCO3- at the interfaces are relatively limited. Hence, it is deduced that the HBs are insufficient to achieve the CO2-switchability of DMAA/DMAAH+. The Lennard Jones and coulombic potentials between DMAA/DMAAH+ and other species show that the coulombic potentials between DMAAH+ and water or anions (i.e., Cl- and HCO3-) sharply decrease with the increase of DMAAH+ and are much lower than those in models with DMAA. The enhanced coulombic interactions between DMAAH+ and anions lead to a remarkable reduction in interfacial tension and the emulsification of the alkane-saline system. Therefore, coulombic interactions are of crucial importance to the reversible emulsification/demulsification processes regulated by CO2-switchable surfactants, namely DMAAH+/DMAA.

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments.

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

Closest-Packing Water Monolayer Stably Intercalated in Phyllosilicate Minerals under High Pressure.

The directional hydrogen-bond (HB) network and nondirectional van der Waals (vdW) interactions make up the specificity of water. Directional HBs could construct an ice-like monolayer in hydrophobic confinement even in the ambient regime. Here, we report a water monolayer dominated by vdW interactions confined in a phyllosilicate interlayer under high pressure. Surprisingly, it was in a thermodynamically stable state coupled with bulk water at the same pressure (P) and temperature (T), as revealed by the thermodynamic integration approach on the basis of molecular dynamics (MD) simulations. Both classical and ab initio MD simulations showed water O atoms were stably trapped and exhibited an ordered hexagonal closest-packing arrangement, but OH bonds of water reoriented frequently and exhibited a specific two-stage reorientation relaxation. Strikingly, hydration in the interlayer under high pressure had no relevance with surface hydrophilicity rationalized by the HB forming ability, which, however, determines wetting in the ambient regime. Intercalated water molecules were trapped by vdW interactions, which shaped the closest-packing arrangement and made hydration energetically available. The high pressure-volume term largely drives hydration, as it compensates the entropy penalty which is restricted by a relatively lower temperature. This vdW water monolayer should be ubiquitous in the high pressure but low-temperature regime.