Effect of temperature on the degradation of glyphosate by Mn-oxide: Products and pathways of degradation.

Glyphosate is the most commonly used herbicide in the United States. In the environment, glyphosate residues can either degrade into more toxic and persistent byproducts such as aminomethylphosphonic acid (AMPA) or environmentally benign species such as sarcosine or glycine. In this research, the birnessite-catalyzed degradation of glyphosate was studied under environmentally relevant temperatures (10-40 °C) using high-performance liquid chromatography, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and theoretical calculations. Our results show a temperature-dependent degradation pathway preference for AMPA and glycine production. The AMPA and glycine pathways are competitive at short reaction times, but the glycine pathway became increasingly preferred as reaction time and temperature increased. The measured free energy barriers are comparable for both the glycine and AMPA pathways (93.5 kJ mol-1 for glycine and 97.1 kJ mol-1 for AMPA); however, the entropic energy penalty for the AMPA pathway is significantly greater than the glycine pathway (-TΔS‡ = 26.2 and 42.8 kJ mol-1 for glycine and AMPA, respectively). These findings provide possible routes for biasing glyphosate degradation towards safer products, thus to decrease the overall environmental toxicity.

The role of iron in the formation of Ediacaran 'death masks'.

The Ediacara biota are an enigmatic group of Neoproterozoic soft-bodied fossils that mark the first major radiation of complex eukaryotic and macroscopic life. These fossils are thought to have been preserved via pyritic "death masks" mediated by seafloor microbial mats, though little about the chemical constraints of this preservational pathway is known, in particular surrounding the role of bioavailable iron in death mask formation and preservational fidelity. In this study, we perform decay experiments on both diploblastic and triploblastic animals under a range of simulated sedimentary iron concentrations, in order to characterize the role of iron in the preservation of Ediacaran organisms. After 28 days of decay, we demonstrate the first convincing "death masks" produced under experimental laboratory conditions composed of iron sulfide and probable oxide veneers. Moreover, our results demonstrate that the abundance of iron in experiments is not the sole control on death mask formation, but also tissue histology and the availability of nucleation sites. This illustrates that Ediacaran preservation via microbial death masks need not be a "perfect storm" of paleoenvironmental porewater and sediment chemistry, but instead can occur under a range of conditions.

Position-specific isotope effects during alkaline hydrolysis of 2,4-dinitroanisole resolved by compound-specific isotope analysis, 13C NMR, and density-functional theory.

Compound-specific isotope analysis (CSIA), position-specific isotope analysis (PSIA), and computational modeling (e.g., quantum mechanical models; reactive-transport models) are increasingly being used to monitor and predict biotic and abiotic transformations of organic contaminants in the field. However, identifying the isotope effect(s) associated with a specific transformation remains challenging in many cases. Here, we describe and interpret the position-specific isotope effects of C and N associated with a SN2Ar reaction mechanism by a combination of CSIA and PSIA using quantitative 13C nuclear magnetic resonance spectrometry, and density-functional theory, using 2,4-dinitroanisole (DNAN) as a model compound. The position-specific 13C enrichment factor of O-C1 bond at the methoxy group attachment site (εC1) was found to be approximately -41‰, a diagnostic value for transformation of DNAN to its reaction products 2,4-dinitrophenol and methanol. Theoretical kinetic isotope effects calculated for DNAN isotopologues agreed well with the position-specific isotope effects measured by CSIA and PSIA. This combination of measurements and theoretical predictions demonstrates a useful tool for evaluating degradation efficiencies and/or mechanisms of organic contaminants and may promote new and improved applications of isotope analysis in laboratory and field investigations.

Alkaline hydrolysis pathway of 2,4-dinitroanisole verified by 18O tracer experiment.

The environmental fate of insensitive munitions compounds, such as 2,4-dinitroanisole (DNAN), has drawn increasing attention because of their growing use in military activities. One of the main attenuation mechanisms of DNAN degradation in aqueous environments is alkaline hydrolysis. We investigated the pathway for alkaline hydrolysis of DNAN at pH 12 by a combined approach of experiment and theory. An experiment using 18O-labeled water was performed to verify the reaction pathway. Calculated free energies for two putative reaction pathways by density-functional theory optimized at the SMD(Pauling)/M06-2X/6-311++G(2d,2p) level including explicit solvation of DNAN by 10 H2O molecules and one OH- ion gave a prediction in agreement with the experimental result. The verified reaction pathway for alkaline hydrolysis of DNAN is a SN2Ar nucleophilic aromatic substitution with a methoxy leaving group (OCH3) at the C1 site.

Degradation of Glyphosate by Mn-Oxide May Bypass Sarcosine and Form Glycine Directly after C-N Bond Cleavage.

Glyphosate is the active ingredient of the common herbicide Roundup. The increasing presence of glyphosate and its byproducts has raised concerns about its potential impact on the environment and human health. In this research, we investigated abiotic pathways of glyphosate degradation as catalyzed by birnessite under aerobic and neutral pH conditions to determine whether certain pathways have the potential to generate less harmful intermediate products. Nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography (HPLC) were utilized to identify and quantify reaction products, and density functional theory (DFT) calculations were used to investigate the bond critical point (BCP) properties of the C-N bond in glyphosate and Mn(IV)-complexed glyphosate. We found that sarcosine, the commonly recognized precursor to glycine, was not present at detectable levels in any of our experiments despite the fact that its half-life (∼13.6 h) was greater than our sampling intervals. Abiotic degradation of glyphosate largely followed the glycine pathway rather than the AMPA (aminomethylphosphonic acid) pathway. Preferential cleavage of the phosphonate adjacent C-N bond to form glycine directly was also supported by our BCP analysis, which revealed that this C-N bond was disproportionately affected by the interaction of glyphosate with Mn(IV). Overall, these results provide useful insights into the potential pathways through which glyphosate may degrade via relatively benign intermediates.

Mechanisms of Bond Cleavage during Manganese Oxide and UV Degradation of Glyphosate: Results from Phosphate Oxygen Isotopes and Molecular Simulations.

Degradation of glyphosate in the presence of manganese oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). The preference of C-P or C-N bond cleavage was found to vary with changing glyphosate/manganese oxide ratios, indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation, and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in manganese oxide- and UV light-mediated degradation. The DFT results reveal that the C-P bond could be cleaved by water, OH- or •OH, with the energy barrier opposing bond dissociation being lowest in the presence of the radical species, and that C-N bond cleavage is favored by the formation of both nitrogen- and carbon-centered radicals. Overall, these results highlight the factors controlling the dominance of C-P or C-N bond cleavage that determines the composition of intermediate/final products and ultimately the degradation pathway.

Proteins from the past.

Some fragments of ancient protein are less prone to degradation because they bind strongly to the surfaces of minerals.

CRYSTAL GROWTH. Crystallization by particle attachment in synthetic, biogenic, and geologic environments.

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments.

A unifying model for Neoproterozoic-Palaeozoic exceptional fossil preservation through pyritization and carbonaceous compression.

Soft-tissue fossils capture exquisite biological detail and provide our clearest views onto the rise of animals across the Ediacaran-Cambrian transition. The processes contributing to fossilization of soft tissues, however, have long been a subject of debate. The Ediacaran Gaojiashan biota displays soft-tissue preservational styles ranging from pervasive pyritization to carbonaceous compression, and thus provides an excellent opportunity to dissect the relationships between these taphonomic pathways. Here geochemical analyses of the Gaojiashan fossil Conotubus hemiannulatus show that pyrite precipitation was fuelled by the degradation of labile tissues through bacterial sulfate reduction (BSR). Pyritization initiated with nucleation on recalcitrant tube walls, proceeded centripetally, decelerated with exhaustion of labile tissues and possibly continued beneath the BSR zone. We propose that pyritization and kerogenization are regulated principally by placement and duration of the decaying organism in different microbial zones of the sediment column, which hinge on post-burial sedimentation rate and/or microbial zone thickness.

Replica exchange methods in biomineral simulations.

Replica exchange methods are widely used for the purposes of accelerating the conformational sampling of small organic molecules and biopolymers and, to a lesser extent, to explore structural transformations in small Lennard-Jones clusters. Though the general ability of such approaches to enhance the sampling efficiency of both inorganic and organic systems makes replica exchange methods ideal candidates for simulations of biominerals and biomineralization, inherent limitations have largely restricted their applicability to small system sizes and/or short timescales, and their potential in this area has not yet been thoroughly explored. This chapter provides an introduction to the standard replica exchange molecular dynamics method and presents more advanced algorithmic variants, which are designed to improve the efficiency of the replica exchange procedure in large solvent-dominated systems.

Microscopic evidence for liquid-liquid separation in supersaturated CaCO3 solutions.

Recent experimental observations of the onset of calcium carbonate (CaCO3) mineralization suggest the emergence of a population of clusters that are stable rather than unstable as predicted by classical nucleation theory. This study uses molecular dynamics simulations to probe the structure, dynamics, and energetics of hydrated CaCO3 clusters and lattice gas simulations to explore the behavior of cluster populations before nucleation. Our results predict formation of a dense liquid phase through liquid-liquid separation within the concentration range in which clusters are observed. Coalescence and solidification of nanoscale droplets results in formation of a solid phase, the structure of which is consistent with amorphous CaCO3. The presence of a liquid-liquid binodal enables a diverse set of experimental observations to be reconciled within the context of established phase-separation mechanisms.

Molecular dynamics of ion hydration in the presence of small carboxylated molecules and implications for calcification.

The aspartate-rich macromolecules found at nucleation sites of calcifying organisms are widely implicated in regulating biomineral formation. Anecdotal evidence suggests that their ability to influence the onset of nucleation and composition of calcified structures may arise from effects on ion hydration. This study investigates the interactions of acidic amino acids and dipeptides with hydrated cations using molecular dynamics. By monitoring the hydration states of Mg2+, Ca2+, and Sr2+ during their approach to negatively charged molecules, we show that carboxylate moieties of Asp promote dehydration of Ca2+ and Sr2+. A contact ion pair (CIP) is not required to disrupt cation hydration, and we demonstrate that reductions and rearrangements of first shell water can begin at ion-Asp separation distances as large as approximately 4.9 A for Ca2+ and approximately 5.1 A for Sr2+. CIP formation between Ca2+ and Sr2+ and carboxylate groups decreases the total first shell coordination number from an average of 8.0 and 8.4 in bulk water to 7.5 and 8.0, respectively. The energy barrier to physically replacing waters about Ca2+ with carboxylate oxygen atoms is small (approximately 2 kcal/mol) as compared to a somewhat larger barrier for Sr2+ (approximately 4 kcal/mol). This may be explained by differences in the strength of Coulombic interactions between the cations and the Asp, resulting in different paths of approach toward Asp for Ca2+ and Sr2+. In contrast, the primary solvation shell of Mg2+ remains largely unchanged during interactions with Asp until the abrupt physical replacement of water by carboxylate oxygen atoms, which comes at a high energetic cost. These insights support the claim that carboxylated biomolecules increase the growth rate of calcite by lowering the energy barrier to Ca2+ dehydration. The findings also suggest a physical basis for the idea that ion-specific behaviors of Ca2+ and Mg2+ in cellular systems arise from a critical balance between water binding in the ion hydration shells versus their interactions with ligands present in intracellular environments.

Influence of ion-associated water on the hydrolysis of Si-O bonded interactions.

Previous studies show the demineralization of biogenic, amorphous, and crystalline forms of silica is enhanced in the presence of alkali and alkaline earth cations. The origins of this effect are difficult to explain in light of work suggesting predominantly weak outer-sphere type interactions between these ions and silica. Here we investigate the ability of M(II) aqua ions to promote the hydrolysis of Si-O bonded interactions relative to ion-free water using electronic structure methods. Reaction pathways for Si-O hydrolysis are calculated with the B3LYP and PBE1PBE density functionals at the 6-31G(d) and 6-311+G(d,p) levels in the presence of water, and both inner- and outer-sphere adsorption complexes of Mg(2+)(6H(2)O) and Ca(2+)(6H(2)O). All reaction trajectories involving hydrated ions are characterized by one or more surmountable barriers associated with the rearrangement of ion-associated water molecules, and a single formidable barrier corresponding to hydrolysis of the Si-O bonded interaction. The hydrolysis step for outer-sphere adsorption is slightly less favorable than the water-induced reaction. In contrast, the barrier opposing Si-O hydrolysis in the presence of inner-sphere species is generally reduced relative to the water-induced pathway, indicating that the formation of inner-sphere complexes may be prerequisite to the detachment of Si species from highly coordinated surface sites. The results suggest a two-part physical model for ion-promoted Si-O hydrolysis that is consistent with experimental rate measurements. First, a bond path is formed between the cation and a bridging oxygen site on the silica surface that weakens the surrounding Si-O interactions, making them more susceptible to attack by water. Second, Si-O hydrolysis occurs adjacent to these inner-sphere species in proportion to the frequency of ion-associated solvent reorganization events. Both processes are dependent upon the particular ion hydration environment, which suggests measured cation-specific demineralization rates arise from differential barriers opposing reorganization of ion-associated solvent molecules at the silica-water interface.

Carboxylated molecules regulate magnesium content of amorphous calcium carbonates during calcification.

With the realization that many calcified skeletons form by processes involving a precursor phase of amorphous calcium carbonate (ACC), a new paradigm for mineralization is emerging. There is evidence the Mg content in biogenic ACC is regulated by carboxylated (acidic) proteins and other macromolecules, but the physical basis for such a process is unknown. We test the hypothesis that ACC compositions express a systematic relationship to the chemistry of carboxyl-rich biomolecules. A series of inorganic control experiments were conducted to establish the dependence of Mg/Ca ratios in ACC on solution composition. We then determined the influence of a suite of simple carboxylated organic acids on Mg content. Molecules with a strong affinity for binding Ca compared with Mg promote the formation of Mg-enriched ACC that is compositionally equivalent to high-magnesium calcites and dolomite. Measurements show Mg/Ca ratios are controlled by a predictable dependence upon the binding properties of the organic molecules. The trend appears rooted in the conformation and electrostatic potential topology of each molecule, but dynamic factors also may be involved. The dependence suggests a physical basis for reports that specific sequences of calcifying proteins are critical to modulating mineralization. Insights from this study may provide a plausible explanation for why some biogenic carbonates and carbonaceous cements often contain higher Mg signatures than those that are possible by classical crystal growth processes. The findings reiterate the controls of microenvironment on mineralization and suggest an origin of compositional offsets, or vital effects, long recognized by the paleoclimate community.

Kinetics of silica nucleation on carboxyl- and amine-terminated surfaces: insights for biomineralization.

An in situ, atomic force microscopy- (AFM-)-based experimental approach is developed to directly measure the kinetics of silica nucleation on model biosubstrates under chemical conditions that mimic natural biosilica deposition environments. Relative contributions of thermodynamic and kinetic drivers to surface nucleation are quantified by use of amine-, carboxyl-, and hybrid NH(3)(+)/COO(-)-terminated surfaces as surrogates for charged and ionizable groups on silica-mineralizing organic matrices. The data show that amine-terminated surfaces do not promote silica nucleation, whereas carboxyl and hybrid NH(3)(+)/COO(-) substrates are active for silica deposition. The rate of silica nucleation is approximately 18x faster on the hybrid substrates than on carboxylated surfaces, but the free energy barriers to cluster formation are similar on both surface types. These findings suggest that surface nucleation rates are more sensitive to kinetic drivers than previously believed and that cooperative interactions between oppositely charged surface species play important roles in directing the onset of silica nucleation. Further experiments to test the importance of these cooperative interactions with patterned NH(3)(+)/COO(-) substrates, and aminated surfaces with solution-borne anionic species, confirm that silica nucleation is most rapid when oppositely charged species are proximal. By documenting the synergy that occurs between surface groups during silica formation, these findings demonstrate a new type of emergent behavior underlying the ability of self-assembled molecular templates to direct mineral formation.

Kinetics of amorphous silica dissolution and the paradox of the silica polymorphs.

The mechanisms by which amorphous silica dissolves have proven elusive because noncrystalline materials lack the structural order that allows them to be studied by the classical terrace, ledge, kink-based models applied to crystals. This would seem to imply amorphous phases have surfaces that are disordered at an atomic scale so that the transfer of SiO(4) tetrahedra to solution always leaves the surface free energy of the solid unchanged. As a consequence, dissolution rates of amorphous phases should simply scale linearly with increasing driving force (undersaturation) through the higher probability of detaching silica tetrahedra. By examining rate measurements for two amorphous SiO(2) glasses we find, instead, a paradox. In electrolyte solutions, these silicas show the same exponential dependence on driving force as their crystalline counterpart, quartz. We analyze this enigma by considering that amorphous silicas present two predominant types of surface-coordinated silica tetrahedra to solution. Electrolytes overcome the energy barrier to nucleated detachment of higher coordinated species to create a periphery of reactive, lesser coordinated groups that increase surface energy. The result is a plausible mechanism-based model that is formally identical with the classical polynuclear theory developed for crystal growth. The model also accounts for reported demineralization rates of natural biogenic and synthetic colloidal silicas. In principle, these insights should be applicable to materials with a wide variety of compositions and structural order when the reacting units are defined by the energies of their constituent species.