First-principles surface characterization and water adsorption of Fe3P schreibersite

The meteoritic mineral schreibersite, e.g., Fe3P, is a proposed abiotic source of phosphorus for phosphate ion (PO4-) production, needed for nucleobases, phospholipids, and other life building materials. Schreibersite could have acted as both a source of elemental phosphorus and as a catalyst, and the hostile conditions on early Earth could have accelerated its degradation in different environments. Here, we present results from quantum calculations of bulk schreibersite and of its low Miller index surfaces. We also investigate water surface adsorption and identify possible dissociation pathways on the most stable facet. Our calculations provide useful chemical insights into schreibersite interactions in aqueous environments, paving the way for further detailed investigation on more reactive surfaces. Our results help provide a ``bottom-up'' understanding for phosphorylated organic synthesis on the primitive planet and its role in producing life building molecules.

Environmental Remediation of Metribuzin Herbicide by Mesoporous Carbon—Rich from Wheat Straw

Contemporary farming practices and rapid industrialization over the last few decades, have raised significant soil and water pollution with extreme toxic effects to humans and ecosystems. The widespread and inefficient use of pesticides, which surpass the soil’s self purification capability, has accelerated soil pollution. In this study, wheat straw biochar was obtained using the traditional pyrolysis technique and its characterization; in addition, the adsorption efficiency of metribuzin was investigated. Biochars’ physical and chemical characteristics were qualified using scanning electron microscopy and Fourier transform infrared spectroscopy. A batch sorption test and liquid chromatography coupled with mass spectrometry were also used to assess the biochar efficiency. SEM and FTIR confirmed the highly reactive surfaces of biochar, establishing efficient biomass conversion in low-oxygen conditions. The adsorption process showed best fit with pseudo second-order kinetic and Langmuir models, suggesting a chemisorption procedure and monolayer-type removal. Regarding its environmental and agricultural application, wheat straw biochar can be advanced as a recommendation solution for further research, which is fundamental for soil rehabilitation and the immobilization of contaminations.

On the constitutive equations for coupled chemical reaction and deformation of porous rocks

<p>Deformation, chemical reactions, and fluid flow in the geological materials are coupled processes. While some reactions are thought to be a consequence of fluid assisted dissolution on the stressed mineral surfaces and precipitation on the free surface, other reactions are caused by mineral replacement wherein a less stable mineral phase is replaced by a more stable phase, involving a change in solid volume and build-up of stresses on grain contacts, also known as a force of crystallization. Most of the existing models of chemical reactions coupled with fluid transport either assume dissolution-precipitation process or mineral growth in rocks. However, dissolution-precipitation models used together with fluid flow modelling predict a very limited extent of reaction hampered by pore clogging and blocking of reactive surfaces, which will stop reaction progress due to the limited supply of fluid to reactive surfaces. Yet, field observations report that natural rocks can undergo 100% hydration/carbonation. Mineral growth models, on the other hand, preserve solid volume but do not consider its feedback on porosity evolution. In addition, they predict the unrealistically high force of crystallization on the order of several GPa that must be developed in minerals during the reaction. Here, using a combination of effective media theory and irreversible thermodynamics approaches, we propose a new model for reaction-driven mineral expansion, which preserves porosity and limits unrealistically high build-up of the force of crystallization by allowing inelastic failure processes at the pore scale. To fully account for the coupling between reaction, deformation, and fluid flow we derive macroscopic poroviscoelastic stress-strain constitute laws, that account for chemical alteration and viscoleastic deformation of porous rocks. These constitutive equations are then used to simulate the reactive transport in porous rocks.</p>

A molecular dynamic study of Soil Organic Matter stabilization mechanisms

<p>It is well known that some fractions of soil organic matter (SOM) can resist to physical and (bio)chemical degradation which can be attributed to factors ranging from molecular properties to the preference for digesting other molecular species by microorganisms. Some mechanisms, by which organic matter is protected, are often referred to as: physical stabilization through microaggregation, chemical stabilization by formation of SOM-mineral aggregates, and biochemical stabilization through the formation of recalcitrant SOM.</p><p>Protection mechanisms are responsible for the accumulation process of organic carbon, reducing the exposure of organic matter and making it less vulnerable to microbial, enzymatic or chemical attacks. In these mechanisms, water molecular bridges and metal cation bridges play a key role. Cation bridges serve as aggregation sites on humic substances, forming dense matter, in comparison to systems where bridges are missing. This effect is enhanced in systems with cations at higher oxidation states.</p><p>By using the modeler tool developed in our group (Vienna Soil–Organic–Matter Modeler, VSOMM2) (Escalona et al., 2021), we generated aggregate models of humic substances at atomistic scale reflecting the diversity in composition, size and conformations of the constituting molecules. Further, we built models of organo-clay aggregates using kaolinite and montmorillonite as typical soil minerals. This allowed a systematic study to understand the effect of the surrounding environment at microscopic scale, not fully accessible experimentally.</p><p>Molecular simulations of the adsorption process of SOM aggregates on the reactive surfaces of led to two observations: 1) the humic substances aggregates were able to interact with the reactive surfaces mainly via hydrogen bonds forming stable organic matter-clay complexes and 2) the aggregates subsequently lost rigidity and stability after metal cations removing, consequently leading to a gradual loss of humic substance molecules, evidencing the role of metal cations in the protection mechanism of soil organic matter aggregates and possibly explaining its recalcitrance (Galicia-Andrés et al., 2021).</p><p>References</p><ul><li>Escalona, Y., Petrov, D., & Oostenbrink, C. (2021). Vienna soil organic matter modeler 2 (VSOMM2). Journal of Molecular Graphics and Modelling, 103, 107817. https://doi.org/10.1016/j.jmgm.2020.107817</li> <li>Galicia-Andrés, E., Grančič, P., Gerzabek, M. H., Oostenbrink, C., & Tunega, D. (2021). Modeling of interactions in natural and synthetic organoclays. In I. C. Sainz Diaz (Ed.), Computational modeling in clay mineralogy.</li> </ul>

Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics

Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO2-) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO2-), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO2- and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO2- reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO2- reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO2- isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO2- reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO2- loss in the mineral-only experiments exhibited only a small N isotope effect (<+1 ‰). The NO2--O isotope effect was very low in both set-ups (18εNO2 <1 ‰), which was most likely due to substantial O isotope exchange with ambient water. Moreover, under low-turnover conditions (i.e. in the mineral-only experiments as well as initially in experiments with DB), the observed NO2- isotope systematics suggest, transiently, a small inverse isotope effect (i.e. decreasing NO2- δ15N and δ18O with decreasing concentrations), which was possibly related to transitory surface complexation mechanisms. Site preference (SP) of the 15N isotopes in the linear N2O molecule for both set-ups ranged between 0 ‰ and 14 ‰, which was notably lower than the values previously reported for chemodenitrification. Our results imply that chemodenitrification is dependent on the available reactive surfaces and that the NO2- (rather than the N2O) isotope signatures may be useful for distinguishing between chemodenitrification catalysed by minerals, chemodenitrification catalysed by dead microbial biomass, and possibly true enzymatic NDFeO.

Crossing hydrological and geochemical modeling to understand the spatiotemporal variability of water chemistry in a headwater catchment (Strengbach, France)

Understanding the variability of the chemical composition of surface waters is a major issue for the scientific community. To date, the study of concentration–discharge relations has been intensively used to assess the spatiotemporal variability of the water chemistry at watershed scales. However, the lack of independent estimations of the water transit times within catchments limits the ability to model and predict the water chemistry with only geochemical approaches. In this study, a dimensionally reduced hydrological model coupling surface flow with subsurface flow (i.e., the Normally Integrated Hydrological Model, NIHM) has been used to constrain the distribution of the flow lines in a headwater catchment (Strengbach watershed, France). Then, hydrogeochemical simulations with the code KIRMAT (i.e., KInectic Reaction and MAss Transport) are performed to calculate the evolution of the water chemistry along the flow lines. Concentrations of dissolved silica (H4SiO4) and in basic cations (Na+, K+, Mg2+, and Ca2+) in the spring and piezometer waters are correctly reproduced with a simple integration along the flow lines. The seasonal variability of hydraulic conductivities along the slopes is a key process to understand the dynamics of flow lines and the changes of water transit times in the watershed. The covariation between flow velocities and active lengths of flow lines under changing hydrological conditions reduces the variability of water transit times and explains why transit times span much narrower variation ranges than the water discharges in the Strengbach catchment. These findings demonstrate that the general chemostatic behavior of the water chemistry is a direct consequence of the strong hydrological control of the water transit times within the catchment. Our results also show that a better knowledge of the relations between concentration and mean transit time (C–MTT relations) is an interesting new step to understand the diversity of C–Q shapes for chemical elements. The good match between the measured and modeled concentrations while respecting the water–rock interaction times provided by the hydrological simulations also shows that it is possible to capture the chemical composition of waters using simply determined reactive surfaces and experimental kinetic constants. The results of our simulations also strengthen the idea that the low surfaces calculated from the geometrical shapes of primary minerals are a good estimate of the reactive surfaces within the environment.

Grafting, self-organization and reactivity of double-decker rare-earth phthalocyanine

Unveiling the interplay of semiconducting organic molecules with their environment, such as inorganic materials or atmospheric gas, is the first step to designing hybrid devices with tailored optical, electronic or magnetic properties. The present article focuses on a double-decker lutetium phthalocyanine known as an intrinsic semiconducting molecule, holding a Lu ion in its center, sandwiched between two phthalocyanine rings. Carrying out experimental investigations by means of electron spectroscopies, X-ray diffraction and scanning probe microscopies together with advanced ab initio computations, allows us to unveil how this molecule interacts with weakly or highly reactive surfaces. Our studies reveal that a molecule–surface interaction is evidenced when molecules are deposited on bare silicon or on gold surfaces together with a charge transferred from the substrate to the molecule, affecting to a higher extent the lower ring of the molecule. A new packing of the molecules on gold surfaces is proposed: an eclipse configuration in which molecules are flat and parallel to the surface, even for thick films of several hundreds of nanometers. Surprisingly, a robust tolerance of the double-decker phthalocyanine toward oxygen molecules is demonstrated, leading to weak chemisorption of oxygen below 100 K.