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.

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.

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.

Felsic volcanism as a factor driving the end-Permian mass extinction.

The Siberian Traps large igneous province (STLIP) is commonly invoked as the primary driver of global environmental changes that triggered the end-Permian mass extinction (EPME). Here, we explore the contributions of coeval felsic volcanism to end-Permian environmental changes. We report evidence of extreme Cu enrichment in the EPME interval in South China. The enrichment is associated with an increase in the light Cu isotope, melt inclusions rich in copper and sulfides, and Hg concentration spikes. The Cu and Hg elemental and isotopic signatures can be linked to S-rich vapor produced by felsic volcanism. We use these previously unknown geochemical data to estimate volcanic SO2 injections and argue that this volcanism would have produced several degrees of rapid cooling before or coincident with the more protracted global warming. Large-scale eruptions near the South China block synchronous with the EPME strengthen the case that the STLIP may not have been the sole trigger.

Understanding the Heterogeneous Nucleation of Heavy Metal Phyllosilicates on Clay Edges with First-Principles Molecular Dynamics.

The nucleation and precipitation of heavy metal phyllosilicates can occur in the course of sorption onto clay edges, which will provide a long-term stabilization of heavy metal pollutants. However, a quantitative understanding of their reaction mechanisms is still lacking. Taking Ni2+ as the model cation, we characterized the atomic scale structures and thermodynamics of the early stage of nucleation by carrying out systematic first-principles molecular dynamics (FPMD) simulations, and the microscopic nucleation mechanisms were revealed. Two possible nucleation pathways were examined: a stepwise pathway (denoted as Path1) and a synchronous pathway (denoted as Path2). In Path1, Ni(OH)2 forms first and then transforms to Ni phyllosilicate via silicification; in Path2, Ni phyllosilicate forms on clay edges directly. The computed free energies of complexation and condensation reactions indicate that Path2 is much more thermodynamically favorable than Path1, meaning that, given that the solution contains dissolved Si initially, heavy metal phyllosilicates will nucleate on clay edges through Path2. By comparing these free energies with their counterpart values of the reaction in bulk solution, the effect of the surface has been uncovered. These findings provide valuable insights for an improved understanding of the stabilization and transformation of heavy metal elements in nature. The derived results form a quantitative basis for future studies on the heterogenous nucleation and precipitation of heavy metal cations.

Uranyl Arsenate Complexes in Aqueous Solution: Insights from First-Principles Molecular Dynamics Simulations.

In this study, the structures and acidity constants (p Ka's) of uranyl arsenate complexes in solutions have been revealed by using the first principle molecular dynamics technique. The results show that uranyl and arsenate form stable complexes with the U/As ratios of 1:1 and 1:2, and the bidentate complexation between U and As is highly favored. Speciation-pH distributions are derived based on free energy and p Ka calculations, which indicate that for the 1:1 species, UO2(H2AsO4)(H2O)3+ is the major species at pH < 7, while UO2(HAsO4)(H2O)30 and UO2(AsO4)(H2O)3- dominate in acid-to-alkaline and extreme alkaline pH ranges. For the 1:2 species, UO2(H2AsO4)2(H2O)0 is dominant under acid-to-neutral pH conditions, while UO2(HAsO4)(H2AsO4)(H2O)-, UO2(HAsO4)(HAsO4)(H2O)2-, and UO2(AsO4)(HAsO4)(H2O)3- become the major forms in the pH range of 7.2-10.7, 10.7-12.1, and >12.1, respectively.

Complexation of carboxylate on smectite surfaces.

We report a first principles molecular dynamics (FPMD) study of carboxylate complexation on clay surfaces. By taking acetate as a model carboxylate, we investigate its inner-sphere complexes adsorbed on clay edges (including (010) and (110) surfaces) and in interlayer space. Simulations show that acetate forms stable monodentate complexes on edge surfaces and a bidentate complex with Ca2+ in the interlayer region. The free energy calculations indicate that the complexation on edge surfaces is slightly more stable than in interlayer space. By integrating pKas and desorption free energies of Al coordinated water calculated previously (X. Liu, X. Lu, E. J. Meijer, R. Wang and H. Zhou, Geochim. Cosmochim. Acta, 2012, 81, 56-68; X. Liu, J. Cheng, M. Sprik, X. Lu and R. Wang, Geochim. Cosmochim. Acta, 2014, 140, 410-417), the pH dependence of acetate complexation has been revealed. It shows that acetate forms inner-sphere complexes on (110) in a very limited mildly acidic pH range while it can complex on (010) in the whole common pH range. The results presented in this study form a physical basis for understanding the geochemical processes involving clay-organics interactions.

Structures and Acidity Constants of Silver-Sulfide Complexes in Hydrothermal Fluids: A First-Principles Molecular Dynamics Study.

In order to quantify the speciation and structures of silver-sulfide complexes in aqueous solutions, we have carried out systematic first-principles molecular dynamics (FPMD) simulations at three temperatures (25, 200, and 300 °C). It is found that monosulfide (i.e., Ag(HS)) and disulfide species (i.e., Ag(HS)2-) are the major silver-sulfide species over a wide T-P range, while Ag(HS)32- can hold stably only at ambient temperatures, and Ag(HS)43- does not exist even at the ambient conditions. Ag(H2S)+ has a tetrahedral structure up to 300 °C (i.e., Ag(H2S)(H2O)3+). Ag(H2S)2+ remains 4-coordinated to 200 °C (i.e., Ag(H2S)2(H2O)2+), but it transforms to 3-coordinated at 300 °C (i.e., Ag(H2S)2(H2O)+). All of the other mono- and disulfide species (Ag(HS)(H2O)0, Ag(HS)(OH)-, Ag(HS)(H2S)0, Ag(HS)2-, and AgS(HS)2-) have 2-fold linear structures. For their solvation structures, the H2S ligands donate weak H-bonds to water O; the HS- ligands accept weak H-bonds from water H; the dangling S2- form strong H-bonds with H of water molecules, and the OH- ligands can form strong H-bonds as donors and weak H-bonds as acceptors. We further calculated the acidity constants (i.e., pKas) of Ag(H2S)+ and Ag(H2S)2+ complexes using FPMD based vertical energy gap method. Based on the calculated pKas, the mono- and disulfide species distributions versus pH have been derived. We found that for monosulfide species, Ag(HS)(H2O)0, is the major species in near neutral pH, while Ag(H2S)(H2O)3+ and Ag(HS)(OH)- exist in the acid and alkaline pH range at T ≤ 200 °C, respectively. At 300 °C, both Ag(HS)(OH)- and Ag(HS)(H2O)0 are dominant in the neutral pH range, and Ag(H2S)(H2O)2+ only exists in acidic solutions. For disulfide species, Ag(HS)2- is dominative in near neutral pH condition at the three temperatures; Ag(HS)(H2S)0 stays in mild acidic pH range only at 25 °C; AgS(HS)2- and Ag(H2S)2(H2O)2+ (Ag(H2S)2(H2O)+ at 300 °C) are trivial at the three conditions. The results of structures and acidity constants provide quantitative and microscopic basis for understanding the behavior of silver complexes in hydrothermal fluids.

Acidity constants and redox potentials of uranyl ions in hydrothermal solutions.

We report a first principles molecular dynamics (FPMD) study of the structures, acidity constants (pKa) and redox potentials (E0) of uranyl (UO22+) from ambient conditions to 573 K. It is found that UO22+ keeps five coordination up to 573 K whereas UO2+ transforms from 5 to 4-coordinate as temperature increases to 573 K. The FPMD-based vertical energy gap method is used to derive pKas and E0s. The method is validated by comparing with available experimental data (for E0 under the ambient conditions and for pKas from ambient conditions to 367 K), with an uncertainty of 1-2 pKa units and 0.2 V for pKa and E0. The encouraging results demonstrate that the method may be used to predict the pH-Eh diagrams of f-block elements under the conditions of hydrothermal solutions. The results show that the acidity constants of uranyl decrease with temperature and are lower than 3.0 when the temperature is above 473 K, indicating that hydrolytic forms are dominant for U(vi) in the near neutral pH range. The reduction potential increases with temperature, indicating that the reduced state is more significant at higher temperatures.

Young asteroidal fluid activity revealed by absolute age from apatite in carbonaceous chondrite.

Chondritic meteorites, consisting of the materials that have formed in the early solar system (ESS), have been affected by late thermal events and fluid activity to various degrees. Determining the timing of fluid activity in ESS is of fundamental importance for understanding the nature, formation, evolution and significance of fluid activity in ESS. Previous investigations have determined the relative ages of fluid activity with short-lived isotope systematics. Here we report an absolute 207Pb/206Pb isochron age (4,450±50 Ma) of apatite from Dar al Gani (DaG) 978, a type ∼3.5, ungrouped carbonaceous chondrite. The petrographic, mineralogical and geochemical features suggest that the apatite in DaG 978 should have formed during metamorphism in the presence of a fluid. Therefore, the apatite age represents an absolute age for fluid activity in an asteroidal setting. An impact event could have provided the heat to activate this young fluid activity in ESS.

Redox potentials of aryl derivatives from hybrid functional based first principles molecular dynamics.

We report the redox potentials of a set of organic aryl molecules, including quinones, juglone, tyrosine and tryptophan, calculated using a first principles molecular dynamics (FPMD) based method. The hybrid functional HSE06 reproduces the redox potentials spanning from -0.25 V to 1.15 V within an error of 0.2 V, whereas the errors with the BLYP functional are much larger (up to 0.7 V). It is found that the BLYP functional predicts consistently lower electron affinities/ionization potentials than HSE06 both in gas phase and in an aqueous solution. In water, the ionization potentials are significantly underestimated by BLYP due to the exaggeration of the mixing between the solute states and the valence band states of liquid water. Hybrid HSE06 markedly improves both the solute levels and water band positions, leading to accurate redox potentials. This study suggests that the current FPMD based method at the level of hybrid functionals is able to accurately compute the redox potentials of a wide spectrum of organic molecules.

High-pressure minerals in eucrite suggest a small source crater on Vesta.

High-pressure minerals in meteorites are important records of shock events that have affected the surfaces of planets and asteroids. A widespread distribution of impact craters has been observed on the Vestan surface. However, very few high-pressure minerals have been discovered in Howardite-Eucrite-Diogenite (HED) meteorites. Here we present the first evidence of tissintite, vacancy-rich clinopyroxene, and super-silicic garnet in the eucrite Northwest Africa (NWA) 8003. Combined with coesite and stishovite, the presence of these high-pressure minerals and their chemical compositions reveal that solidification of melt veins in NWA 8003 began at a pressure of >~10 GPa and ceased when the pressure dropped to <~8.5 GPa. The shock temperature in the melt veins exceeded 1900 °C. Simulation results show that shock events that create impact craters of ~3 km in diameter (subject to a factor of 2 uncertainty) are associated with sufficiently high pressures to account for the occurrence of the high-pressure minerals observed in NWA 8003. This indicates that HED meteorites containing similar high-pressure minerals should be observed more frequently than previously thought.

Surface acidity of quartz: understanding the crystallographic control.

We report a first principles molecular dynamics (FPMD) study of surface acid chemistry of the two growth surfaces of quartz, (101̄0) (including Alpha and Beta terminations) and (101̄1) facets. The interfacial hydration structures are characterized in detail and the intrinsic pKas of surface silanols are evaluated using the FPMD based vertical energy gap method. The calculated acidity constants reveal that every surface termination shows a bimodal acid-base behavior. It is found that all doubly-protonated forms (i.e. SiOH2) on the three terminations have pKas lower than -2.5, implying that the silanols hardly get protonated in a common pH range. The pKas of surface silanols can be divided into 3 groups. The most acidic silanol is the donor SiOH on the (101̄0)-beta surface (pKa = 4.8), the medium includes the germinal silanol on (101̄0)-alpha and the outer silanol on (101̄1) (pKa = 8.5-9.3) and the least acidic are inner silanols on the (101̄1)-facet, acceptor SiOH on (101̄0)-beta, and the secondly-deprotonated OH (i.e. Si(O-)(OH)) on (101̄0)-alpha (pKa > 11.0). With the pKa values, we discuss the implication for understanding metal cations complexing on quartz surfaces.

Understanding hydration of Zn2+ in hydrothermal fluids with ab initio molecular dynamics.

With ab initio molecular dynamics simulations, the free-energy profiles of hydrated Zn(2+) are calculated for both gaseous and aqueous systems from ambient to supercritical conditions, and from the derived free-energy information, the speciation of hydrated Zn(2+) has been revealed. It is shown that the 4, 5 and 6 fold complexes coexist in both phases at ambient condition. As T-P increases a clear trend is found for both phases: the 6 fold states gradually become unstable and cannot exist stably any more over 620 K, but in contrast, the 4 and 5 fold states can hold up to 1000 K with similar probabilities. It is found that the stability of the 4 and 5 fold states has an entropic origin. This study constitutes a relatively complete speciation picture for aqua-zinc complexes over a broad T-P range.

In silico calculation of acidity constants of carbonic acid conformers.

In order to explore the aqueous acid chemistry of carbonic acid, we employ a constrained ab initio molecular dynamics (AIMD) technique to study acid dissociations of its three conformers including CC (cis-cis), CT (cis-trans), and TT (trans-trans). The simulations of reagent states reveal similar hydration characteristics for them: the hydroxyls donate H-bonds to solvating waters but no obvious H-bonding exists between hydroxyl oxygen atoms and waters. It is found that the CC conformer dissociates spontaneously to bicarbonate within picoseconds whereas the other two can stay for relatively long simulation times. This suggests that CC has the strongest acidity among the three conformers and it is not stable in water. The simulations indicate that the symmetrical hydroxyls of TT conformer have a pKa value of 3.11 and the two asymmetrical hydroxyls of CT show different pKa values: 2.60 and 3.75, respectively. Overall, these results confirm the recent experimental measurement: about 4.0 for deuterated carbonic acid. By analyzing the dissociation processes, it is revealed that the differences of the acid constants stem from the initial steps of hydroxyls stretches. This simulation study provides a quantitative and microscopic basis for better understanding the reactivity of aqueous carbonate species.

Hydration mechanisms of Cu(2+): tetra-, penta- or hexa-coordinated?

To shed light on the hydration mechanisms of Cu(2+), we carried out simulations in both gas and aqueous phases by using the ab initio molecular dynamics technique equipped with the method of constraint. The simulations provide relatively complete free-energy information, from which the coexisting coordination pictures are clearly revealed. In both phases, the 5-fold complex is the most thermodynamically favorable state whereas the classically-accepted 6-fold occurs as a very weak stable state. In the gas phase, the 4-fold complex is a more reachable state than the 6-fold, but it cannot hold stably in the aqueous phase. The extracted thermodynamic values illustrate that in the gas phase the entropy term dominates the evolution processes to the 5-fold whereas in the aqueous case the energy term is dominant.

[Vertical distribution of physicochemical characteristics and the microbial diversity in different spatial sediments samples in Lake Taihu].

The physicochemical characteristics, nutritions and the microbial community diversity of sediment core samples of three different space locations in the Lake Taihu were studied by fumigation-digestion and PCR-DGGE analysis respectively. The results indicated that below the surface of sediments Eh declined rapidly with increase of sediment depth and it was under anaerobic condition except the top layer of sediment. pH value changed silightly in the profile of sediments, which ranged from 7.2 to 7.8. TN and TP concentrations in sediments of Lake Taihu were high,and the maximum concentrations reached 2.436 mg/g and 0.731 mg/g, respectively. Their vertical profiles showed that TN and TP concentrations in surface sediments were much higher than in deeper layers and decreased with the increase of the depth of sediment layers. OM concentrations declined rapidly at the top 15 cm of sediment layers. There were prominent difference spatially in microbial diversity and the comparability and dynamics of community structure between different sediment samples of different space locations and different depth. The little significant correlation at alpha < or = 0.05 level was observed between the Eh, pH, percentage organic matter, TN concentration and TP concentration and microbial community structure diversity index except of TN concentration and percentage organic matter.

A new integrated method for characterizing surface energy heterogeneity from a single adsorption isotherm.

To characterize surface energy heterogeneity of fine particles, this paper presents an integrated strategy from a single adsorption isotherm. By coupling the well-known integral equation method and derivative isotherm summation (DIS) procedure based on a patchwise model, the newly proposed strategy could calculate adsorption energy distributions (AEDs) for different surface patches. Correspondingly, the surface heterogeneity of materials can be described by weighted summation of patch AEDs, that is, the total AED. The validity of this new method is confirmed by both tests of rutile nanoparticles and multiwalled carbon nanotubes (MWNTs). The total AED obtained by the new method agrees well with the result from solving the integral equation directly, and it shows that AED peaks can be assigned to specific energy patches of real surface exactly. Furthermore, a detailed comparison showed that some artificial oscillation in the results can be identified with the new strategy, and the patches with low area and high surface energy could be characterized as well. In conclusion, this strategy constructs a correspondence between derived AEDs and different patches of real surface, so it will be more effective to understand surface heterogeneity by using the adsorption probe method.