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1. Potassium and Calcium K ‐Edge XANES in Chemical Compounds and Minerals: Implications for Geological Phase Identification

   https://doi.org/10.1111/ggr.12351  

   Li, Wenshuai ; Liu, Xiao‐Ming ; Hu, Yongfeng ( August 2020 , Geostandards and Geoanalytical Research)

   Potassium (K) and calcium (Ca)K‐edge X‐ray adsorption near‐edge (XANES) spectroscopy were performed on thirty‐three chemical compounds and geological materials, including chemical reagents, organometallic compounds, silicates, carbonates and igneous rock reference materials. The results confirm that the fine structure of theK‐edges for specimens is unique and distinguishable. The results suggest that compositional and local atomic variations strongly regulate spectral characteristics. Acquired XANES spectra with the library of distinctive spectral features of model references approve the fingerprint identification of different phases of K and Ca involved in geological materials. Moreover, this reveals that typical compositional changes in geological samples could strongly affect spectral features. As an example, we quantitatively determined the silicate species of K and Ca in two igneous rock reference materials by linear combination fitting. The dominant hosts and molecular environments of K and Ca can be interpreted based on pre‐edge/post‐edge peak position, intensity, shifts and resonance features, thus improving the understanding of the (bio)geochemical cycling, partitioning and isotopic fractionation of K and Ca. The outcomes serve as a complementary database for a vast number of scientific contexts, including aspects of geological and environment sciences.

    

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2. Distal scaffold flexibility accelerates ligand substitution kinetics in manganese( i ) tricarbonyls: flexible thianthrene versus rigid anthracene scaffolds

   https://doi.org/10.1039/D2DT04048D  

   Labrecque, Jordan ; Cho, Yae-In ; McIntosh, Daniel K. ; Agboola, Faridat ; Rose, Michael J. ( March 2023 , Dalton Transactions)

   This work investigates the effect of molecular flexibility on fundamental ligand substitution kinetics in a pair of manganese( i ) carbonyls supported by scaffold-based ligands. In previous work, we reported that the planar and rigid, anthracene-based scaffold with two pyridine ‘arms’ ( Anth-py 2 , 2) serves as a bidentate, cis donor set, akin to a strained bipyridine (bpy). In the present work, we have installed a more flexible and dynamic scaffold in the form of thianthrene ( Thianth-py 2 , 1), wherein the scaffold in the free ligand exhibits a ∼130° dihedral angle in the solid state. Thianth-py 2 also exhibits greater flexibility (molecular motion) in solution compared with Anth-py 2 , as evidenced by longer 1 H NMR T 1 times Thianthy-py 2 ( T 1 = 2.97 s) versus Anth-py 2 ( T 1 = 1.91 s). Despite the exchange of rigid Anth-py2 for flexible Thianth-py2 in the complexes [( Anth-py 2 )Mn(CO) 3 Br] (4) and [( Thianth-py 2 )Mn(CO) 3 Br] (3), respectively, nearly identical electronic structures and electron densities were observed at the Mn center: the IR of 3 exhibits features at 2026, 1938 and 1900 cm −1 , nearly identical to the features of the anthracene-based congener (4) at 2027, 1936 and 1888 cm −1 . Most importantly, we assessed the effect of ligand-scaffold flexibility on reactivity and measured the rates of an elementary ligand substitution reaction. For ease of IR study, the corresponding halide-abstracted, nitrile-bound (PhCN) cations [( Thianth-py 2 )Mn(CO) 3 (PhCN)](BF 4 ) (6) and [( Anth-py 2 )Mn(CO) 3 (PhCN)](BF 4 ) (8) were generated in situ , and the PhCN → Br – back-reaction was monitored. The more flexible 3 (thianth-based) exhibited ∼3–4× faster ligand substitution kinetics ( k 25 C = 22 × 10 −2 min −1 , k 0 C = 43 × 10 −3 min −1 ) than the rigid analogue 4 (anth-based: ( k 25 C = 6.0 × 10 −2 min −1 , k 0 C = 9.0 × 10 −3 min −1 ) on all counts. Constrained angle DFT calculations revealed that despite large changes in the thianthrene scaffold dihedral angle, the bond metrics of 3 about the metal center remain unchanged; i.e. the ‘flapping’ motion is strictly a second coordination sphere effect. These results suggest that the local environment of molecular flexibility plays a key role in determining reactivity at the metal center, which has essential implications for understanding the reactivity of organometallic catalysts and metalloenzyme active sites. We propose that this molecular flexibility component of reactivity can be considered a thematic ‘third coordination sphere’ that dictates metal structure and function. 

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3. On the distribution of Verwey transition temperatures in natural magnetites

   https://doi.org/10.1093/gji/ggaa516  

   Jackson, Mike J ; Moskowitz, Bruce ( November 2020 , Geophysical Journal International)

   null (Ed.)

   SUMMARY The Verwey transition in magnetite is a crystallographic phase transition occurring in the temperature range 80–125 K and depends on stoichiometry and cation substitution, which may in turn serve as an indicator of the conditions under which magnetite was formed or altered in nature. We have analysed the distribution of Verwey transition temperatures (TV) in a large set of samples (N = 1110) from a wide variety of rocks, sediments, and other natural and synthetic materials containing magnetite, mined from the database of the Institute for Rock Magnetism and from published studies. The analysis is restricted to measurements of remanence while warming through the transition from which TV was determined by the derivative method. Our analysis showed that the TV distribution exhibited a generally bimodal distribution of Verwey transition temperatures, both for the entire data set and for almost all of the lithological subsets. There is a sharp peak for values in the range 118–120 K, and a broad, relatively flat or polymodal distribution from about 98 to 118 K. The upper end of the distribution was sharp, with only a few values exceeding 124 K, and the tail on the lower end extended down to about 80 K. Virtually all of the sample types exhibited polymodal distributions, almost always with one peak near 120 K, and with one or more additional peaks at lower temperatures. Biogenic magnetites produced by magnetotactic bacteria had the lowest modal value of TV (100 K). Loesses (103.5 K) and igneous extrusives (102.5 K) also had low modal transition temperatures and distributions with dominant low-TV peaks. Lithological groups with the highest modal transition temperatures were modern soils (119.5 K), silicate minerals with exsolved magnetite (119 K) and sedimentary rocks (119 K). Numerical experiments confirmed that the derivative method for the determination of TV was reasonably robust and that the observed distributions cannot be explained as an artefact related to the determination of TV from individual thermomagnetic runs but rather is a general characteristic of natural magnetites. The results provide context for studies that interpret TV in particular samples in terms of natural processes or conditions during formation or alteration of magnetite. 

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4. An ab-initio study on the thermodynamics of disulfide, sulfide, and bisulfide incorporation into apatite and the development of a more comprehensive temperature, pressure, pH, and composition-dependent model for ionic substitution in minerals

   https://doi.org/10.2138/am-2022-8250  

   Kim, YoungJae ; Konecke, Brian ; Simon, Adam ; Fiege, Adrian ; Becker, Udo ( November 2022 , American Mineralogist)

   The mineral apatite, Ca10(PO4)6(F,OH,Cl)2, incorporates sulfur (S) during crystallization from S-bearing hydrothermal fluids and silicate melts. Our previous studies of natural and experimental apatite demonstrate that the oxidation state of S in apatite varies systematically as a function of oxygen fugacity (fO2). The S oxidation states –1 and –2 were quantitatively identified in apatite crystallized from reduced, S-bearing hydrothermal fluids and silicate melts by using sulfur K-edge X-ray absorption near-edge structure spectroscopy (S-XANES) where S 6+/ΣS in apatite increases from ~0 at FMQ-1 to ~1 at FMQ+2, where FMQ refers to the fayalite-magnetite-quartz fO2 buffer. In this study, we employ quantum-mechanical calculations to investigate the atomistic structure and energetics of S(-I) and S(-II) incorporated into apatite and elucidate incorporation mechanisms.

   One S(-I) species (disulfide, S22−) and two S(-II) species (bisulfide, HS−, and sulfide, S2−) are investigated as possible forms of reduced S species in apatite. In configuration models for the simulation, these reduced S species are positioned along the c-axis channel, originally occupied by the column anions F, Cl, and OH in the end-member apatites. In the lowest-energy configurations of S-incorporated apatite, disulfide prefers to be positioned halfway between the mirror planes at z = 1/4 and 3/4. In contrast, the energy-optimized bisulfide is located slightly away from the mirror planes by ~0.04 fractional units in the c direction. The energetic stability of these reduced S species as a function of position along the c-axis can be explained by the geometric and electrostatic constraints of the Ca and O planes that constitute the c-axis channel.

   The thermodynamics of incorporation of disulfide and bisulfide into apatite is evaluated by using solid-state reaction equations where the apatite host and a solid S-bearing source phase (pyrite and Na2S2(s) for disulfide; troilite and Na2S(s) for sulfide) are the reactants, and the S-incorporated apatite and an anion sink phase are the products. The Gibbs free energy (ΔG) is lower for incorporation with Na-bearing phases than with Fe-bearing phases, which is attributed to the higher energetic stability of the iron sulfide minerals as a source phase for S than the sodium sulfide phases. The thermodynamics of incorporation of reduced S is also evaluated by using reaction equations involving dissolved disulfide and sulfide species [HnS(aq)(2−n) and HnS(aq)(2−n); n = 0, 1, and 2] as a source phase. The ΔG of S-incorporation increases for fluorapatite and chlorapatite, and decreases for hydroxylapatite, as these species are protonated (i.e., as n changes from 0 to 2). These thermodynamic results demonstrate that the presence of reduced S in apatite is primarily controlled by the chemistry of magmatic and hydrothermal systems where apatite forms (e.g., an abundance of Fe; solution pH). Ultimately, our methodology developed for evaluating the thermodynamics of S incorporation in apatite as a function of temperature, pH, and composition is highly applicable to predicting the trace and volatile element incorporation in minerals in a variety of geological systems. In addition to solid-solid and solid-liquid equilibria treated here at different temperatures and pH, the methodology can be easily extended to different pressure conditions by just performing the quantum-mechanical calculations at elevated pressures.

    

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5. An ab-initio study on the thermodynamics of disulfide, sulfide, and bisulfide incorporation into apatite and the development of a more comprehensive temperature, pressure, pH, and composition-dependent model for ionic substitution in minerals

   Young Jae Kim, Brian Konecke ( September 2022 , The American mineralogist)

   The mineral apatite, Ca10(PO4)6(F,OH,Cl)2, incorporates sulfur (S) during crystallization from S-bearing hydrothermal fluids and silicate melts. Our previous studies of natural and experimental apatite demonstrate that the oxidation state of S in apatite varies systematically as a function of oxygen fugacity (fO2). The S oxidation states –1 and –2 were quantitatively identified in apatite crystallized from reduced, S-bearing hydrothermal fluids and silicate melts by using sulfur K-edge X‑ray absorption near-edge structure spectroscopy (S-XANES) where S6+/ΣS in apatite increases from ~0 at FMQ-1 to ~1 at FMQ+2, where FMQ refers to the fayalite-magnetite-quartz fO2 buffer. In this study, we employ quantum-mechanical calculations to investigate the atomistic structure and energetics of S(-I) and S(-II) incorporated into apatite and elucidate incorporation mechanisms. One S(-I) species (disulfide, S22−) and two S(-II) species (bisulfide, HS−, and sulfide, S2−) are investigated as possible forms of reduced S species in apatite. In configuration models for the simulation, these reduced S species are positioned along the c-axis channel, originally occupied by the column anions F, Cl, and OH in the end-member apatites. In the lowest-energy configurations of S-incorporated apatite, disulfide prefers to be positioned halfway between the mirror planes at z = 1/4 and 3/4. In contrast, the energy-optimized bisulfide is located slightly away from the mirror planes by ~0.04 fractional units in the c direction. The energetic stability of these reduced S species as a function of position along the c-axis can be explained by the geometric and electrostatic constraints of the Ca and O planes that constitute the c-axis channel. The thermodynamics of incorporation of disulfide and bisulfide into apatite are evaluated by using solid-state reaction equations where the apatite host and a solid S-bearing source phase (pyrite and Na2S2(s) for disulfide; troilite and Na2S(s) for sulfide) are the reactants, and the S-incorporated apatite and an anion sink phase are the products. The Gibbs free energy (ΔG) is lower for incorporation with Na-bearing phases than with Fe-bearing phases, which is attributed to the higher energetic stability of the iron sulfide minerals as a source phase for S than the sodium sulfide phases. The thermodynamics of incorporation of reduced S are also evaluated by using reaction equations involving dissolved disulfide and sulfide species [HnS2(aq)(2–n) and HnS(aq)(2–n); n = 0, 1, and 2] as a source phase. The ΔG of S-incorporation increases for fluorapatite and chlorapatite and decreases for hydroxylapatite as these species are protonated (i.e., as n changes from 0 to 2). These thermodynamic results demonstrate that the presence of reduced S in apatite is primarily controlled by the chemistry of magmatic and hydrothermal systems where apatite forms (e.g., an abundance of Fe; solution pH). Ultimately, our methodology developed for evaluating the thermodynamics of S incorporation in apatite as a function of temperature, pH, and composition is highly applicable to predicting the trace and volatile element incorporation in minerals in a variety of geological systems. In addition to solid-solid and solid-liquid equilibria treated here at different temperatures and pH, the methodology can be easily extended also to different pressure conditions by just performing the quantum-mechanical calculations at elevated pressures. 

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