The widespread Balıkesir bentonite deposits within the Miocene volcano-sedimentary units in western Anatolia have economic potential; they are important raw materials for the paper and bleaching industries in Turkey. No detailed geological, mineralogical, geochemical, or genesis characterizations of these bentonite deposits have been carried out to date. The present study was undertaken to close this gap. The mineralogical characteristics of the bentonites and their parent rocks were examined using polarized-light microscopy, X-ray powder diffractometry (XRD), scanning- and transmission-electron microscopies (SEM–EDX and TEM), and chemical (ICP–AES and –MS) methods. In the bentonite deposits, smectite is associated with smaller amounts of illite, chlorite, quartz, feldspar, dolomite, calcite, opal-CT, and amphibole. The smectite was identified by sharp basal reflections at 14.42–14.93 Å. Plagioclase and sanidine crystals in volcanic units are altered and sericitized. Biotite and hornblende are partly to completely Fe-(oxyhydr)oxidized and chloritized. Smectite flakes occur on altered feldspar and mica grains and devitrified volcanic glass fragments in association with or without calcite ± dolomite crystals. Increasing Al+Fe+Mg/Si ratios with increasing degree of alteration reveal that hydration of volcanogenic grains (feldspar, mica, hornblende, glass shard) favored precipitation of smectite with montmorillonite composition, with an average structural formula: (Ca0.31Na0.05K0.08)(Al2.72Fe0.17Mg1.27Ti0.011Mn0.01)(Si7.94Al0.06)O20(OH)4. The concentration of Al2O3 and MgO and increase of LREE/HREE ratio, and a distinct, negative Eu anomaly show that smectite was probably formed as a result of the decomposition of volcanic feldspar, mica, amphibole, and volcanic glass. Association of carbonate rocks within the smectite-rich material and the absence of chlorite and detrital materials such as rock fragments in the bentonites suggest that the bentonite deposits formed authigenetically as ‘primary bentonites’ from volcanoclastic materials deposited in a calm lacustrine–palustrine environment during an early diagenetic process.

Diffraction effects from interstratified phyllosilicates have been studied extensively, and several computer programs such as NEWMOD© are available to facilitate interpretation of X-ray diffraction (XRD) profiles. However, accurate quantification of samples containing multiple interstratified phyllosilicate minerals is difficult due to the generally subjective nature of interpretations. More recent automated fitting interpretations require extensive computational effort, involving numerous calculations of profiles with different fitting-parameter values. Computational cost in time per calculation is the key factor influencing the overall efficiency of automated profile fitting. In general, the matrix methodology developed by Kakinoki and Komura is more efficient than the NEWMOD© architecture. A new matrix methodology was developed that reduces the number of matrix operations such as multiplication and addition, and these modifications improve calculation efficiency by up to a factor of three, with even greater improvement for small crystallite sizes (< 20 layers). A new computer program, ClayStrat, based on the modified matrix methodology, was developed to calculate one-dimensional XRD profiles from interstratified phyllosilicates along the Z direction.

The growing use of nano titanium dioxide (TiO2) in consumer and agricultural products has accelerated its introduction into terrestrial environments, where its impact has not been documented extensively. TiO2 toxicity arises primarily from its ability to photochemically generate reactive oxygen species (ROS), including hydrogen peroxide (H2O2). While common ligands in soil porewaters can either hinder or enhance the degradation of organic contaminants by TiO2, their effects on ROS production by TiO2 have not been understood clearly. The objective of this study was to assess the effect of phosphate (P) and nitrate on UV-irradiated anatase, nano-TiO2. Accordingly, H2O2-generation kinetics experiments were conducted in UV-irradiated TiO2 under environmentally relevant concentrations of the ligands (0, 50, 100, and 250 μM) and pH values (4.00 ± 0.02 and 8.00 ± 0.02) from 0–100 min. Under all conditions, H2O2 grew logarithmically and reached between 5.38 and 22.98 μM after 100 min. At pH 4.00 ± 0.02, H2O2 production was suppressed by P but not by nitrate. Conversely, at pH 8.00 ± 0.02, nitrate did not affect H2O2 concentration while P increased it. Non-specific, minimal adsorption of nitrate prevented interference with the photoreactivity of TiO2. Due to the pH-dependent behavior of suspended TiO2 and H2O2 degradation rates, specific adsorption of P on TiO2 impeded its ability to produce H2O2 photochemically at pH 4.00 ± 0.02 but amplified it at pH 8.00 ± 0.02.

This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems. The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis. Due to the data structure used, atoms and molecules can be operated upon based on different chemical names or attributes, such as atom- or molecule-ID, name, residue name, charge, positions, etc. Furthermore, the Bond Valence Method and a neighbor-distance analysis can be performed to assign many chemical properties of inorganic molecules. Apart from reading and writing common coordinate files (.pdb, .xyz, .gro, .cif) and trajectories (.dcd, .trr, .xtc; binary formats are parsed via third-party packages), the atom library can also be used to generate topology files with bonding and angle information taking the periodic boundary conditions into account, and supports basic Gromacs, NAMD, LAMMPS, and RASPA2 topology file formats. Focusing on clay-mineral systems, the library supports CLAYFF (Cygan, 2004) but can also generate topology files for the INTERFACE forcefield (Heinz, 2005, 2013) for Gromacs and NAMD.

Vermiculite is a mineral with many potential uses in various industrial areas, such as in insulation, horticulture, and environmental applications. The regolith of the Sokli carbonatite intrusion in northern Finland consists of weathered micas which reportedly contain vermiculite. The aim of the present study was to characterize the weathered mica in order to determine if the weathered regolith contains vermiculite. If so, the value of the apatite-rich Sokli intrusion may increase, because the vermiculite could be classified as an ore in Sokli. For the characterization, mica fractions were investigated using electron probe microanalysis (EPMA), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). The EPMA results show that the potassium (K2O) content of the mica investigated varies between 6.20 and 0.31 wt.%. The XRD results provided evidence that the interlayer distances in the mica vary between 10.1 and 14.7 Å. The TGA shows that the dehydration of the samples varies between 6 and 12 wt.% for temperatures up to 170°C. Dehydroxylation takes place in three steps, as is characteristic for vermiculite. The results from this study revealed that mica in the weathered parts of the Sokli carbonatite is mostly vermiculite, and that the vermiculite was formed by the weathering of phlogopite. These results can be used to determine whether vermiculite is a possible future commodity at the Sokli carbonatite complex.

Although multiple types of adsorption sites have long been observed in montmorillonite, a consistent explanation about the chemical structure of these adsorption sites has not yet been established. Identifying the cation interlayer adsorption sites based on the octahedral cation distribution on montmorillonite was investigated in this study by using a Density Functional Theory (DFT) simulation. A clay structural model (H[Al6MgFe]Si16O40(OH)8) with a similar composition to Wyoming SWy-1 montmorillonite was built, where two octahedral Al were respectively substituted by Fe and Mg, and H+ was the charge compensating cation. This model had twenty-one different possible configurations as a function of the distribution of octahedral Al, Fe, and Mg cations. The DFT simulations of 15 of these different configurations showed no preference for the formation of any configuration with a specific octahedral Fe-Mg distance. However, the H+ adsorption energy was separated into three distinct groups based on the number of octahedral jumps from Fe to Mg atoms. The H+ adsorption energy significantly decreased with increasing number of octahedral jumps from Fe to Mg. Assuming an even probability of occurrence of 21 octahedral structures in montmorillonite, the percentages of these three groups are 43, 43, and 14%, respectively, which are very close to the three major sites on montmorillonite from published cation adsorption data. These DFT simulations offer an entirely new explanation for the location and chemical structure of the three major adsorption sites on montmorillonite, namely, all three sites are in the interlayer, and their adsorption strengths are a function of the number of octahedral jumps from Fe to Mg atoms.

Six-membered ring heterocyclic compounds are widely present in the Earth's surface environments as biological organic molecules composed of soil organic matter including plant and microbial residues, while little is known about their effect on the dissolution of silicate minerals including amorphous silica. To evaluate the effect of these biological molecules on amorphous silica dissolution, dissolution experiments were carried out by the flow-through method using 0.1 g of amorphous silica and 0.1 mM NaCl electrolyte solutions containing 0.0, 0.1, 1.0, or 10.0 mM of the heterocyclic compounds, piperidine (pK = 11.12), pyridine (pK = 5.25), or pyridazine (pK = 2.33), at a pH of 6, 5, or 4. Additionally, adsorption experiments of the compounds on the amorphous silica surface were performed to confirm the adsorption affinity for the amorphous silica surface. The results demonstrated that these heterocyclic compounds enhance the dissolution rate of amorphous silica in the following order: piperidine > pyridine > pyridazine. When 10.0 mM solutions were used, the heterocyclic compounds enhanced greatly the dissolution rate up to enhancement factors of 6.0 to ~14.8, 5.0 to ~14.0, and 1.0 to ~2.6 through an interaction of piperidine, pyridine, and pyridazine, respectively, in the pH range of approximately 6 to ~ 4. The adsorption experiments indicated that the heterocyclic compounds exhibited significant adsorption affinity for the amorphous silica surface as follows: piperidine > pyridine > pyridazine, which was consistent with the order of their effects on the dissolution enhancement. The geochemical calculation revealed that this order of enhancement was in good agreement with the concentrations of cationic species of heterocyclic compounds at corresponding pH conditions. Consequently, the enhancement of amorphous silica dissolution is likely to be influenced by the electrostatic complexation of the cationic species of the heterocyclic compounds with the negative >SiO– sites on the amorphous silica surface.