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.

Clays have traditionally been linked to health care, being used for centuries in the fight against infections and diseases. Similarly, biohybrids produced by combinations of clays and biological species through ‘bottom-up’ approaches have been evaluated over the past decade for biomedical and pharmaceutical uses. These biohybrids show interesting features such as biocompatibility and biodegradability which make them suitable for healthcare applications. The aim of the present communication was to review recent research contributions describing progress and the role of biohybrid materials based on clays in biomedicine and pharmacy disciplines. Emphasis will be on the authors’ own experience of this topic, particularly on aspects related to controlled drug-delivery systems, adjuvants of vaccines, and vectors for non-viral gene transfection. Bionanocomposites offer several advantages for use in the design of new and efficient pharmacological formulations for cutaneous and oral administration. In these systems, the drug is typically entrapped in the clay and protected by a biopolymer matrix, and both components contribute to a gradual release of the drug. Clay-based hybrids have also shown their efficacy in vaccines as they can act as nanocarriers of viral particles, due to the biomimetic interface created on the clay surface after adsorption of suitable biomolecules such as phospholipids, while the clay acts as an adjuvant to increase the efficacy of the vaccine. Finally, a new application of clays as non-viral vectors for controlled gene delivery is attracting increasing interest in the treatment of diverse diseases; clays such as sepiolite have demonstrated their ability to act as nanocarriers of nucleic acids and facilitate their transfection in mammalian cells.

The double hydroxide of Li+ and Al3+ is an anionic clay comprising positively charged metal hydroxide layers and intercalated anions. While the structure of the iono-covalently bonded metal hydroxide layer is well known, relatively less knowledge is available regarding the manner in which the anions and water molecules are packed in the interlayer region. The sulfate ion is of special interest as it can potentially intercalate in a multiplicity of orientations and grow an extended hydration sphere. The sulfate-intercalated double hydroxide was synthesized by the imbibition of Li2SO4 into both the gibbsite and bayerite forms of Al(OH)3 to obtain layered double hydroxides with the nominal formula Li2Al4(OH)12SO4·nH2O (n = 4–8). The as-prepared compounds were poorly ordered and did not yield any structural information. Temperature-induced partial dehydration yielded ordered phases of different structures in the two systems. Simulation of the powder patterns of different model structures, followed by structure refinement in both direct and reciprocal spaces, showed that the gibbsite-derived phase yielded a two-layer polytype of hexagonal symmetry (space group P63/m). The local symmetry of the sulfate ion was close to D2d with one of the C2 axes of the SO42− being nearly parallel to the c axis of the crystal. The bayerite-derived phase yielded a one-layer polytype of monoclinic symmetry (space group C2/m). The sulfate ion was oriented with its C3 axes tilted away from the stacking direction. Cooling and rehydration (relative humidity ~70%) resulted in a reversible expansion of the basal spacing due to the ingress of water molecules from the ambient humidity into the interlayer region. Hydration in both cases resulted in turbostratic disorder. The disorder in the bayerite-derived phase was a result of random intergrowth of motifs with rhombohedral and monoclinic symmetries.

When present at elevated levels in drinking water, arsenic is toxic, and magnesian clays are gaining recognition as a source of elevated arsenic in groundwater. In the crust and upper mantle of Earth, arsenic incorporation into clay minerals is influenced by geochemical conditions associated with hydrothermal fluids and metamorphic processes (e.g. serpentinization), meaning that As is a useful tracer of fluid-flow in the deep Earth. To improve understanding of arsenic speciation in groundwater, sediments, soils, and hydrothermal-metamorphic systems, the present study examined arsenic incorporation into magnesian clays by synthesis of serpentine minerals (200oC, 10 d) with varied concentrations of Si, Al, As5+, and As3+. The synthesis experiments produced two distinct crystal types, tubular and platy serpentines, each with 10–15% randomly interstratified talc layers. X-ray absorption spectroscopy indicated that As5+ and As3+ occurred in the tetrahedral sheet. Single-crystal analysis revealed that tubular crystals contained up to 1 wt.% arsenic [Mg2.8(Si1.8As0.2)O5(OH)4] (mean 0.2 wt.% As). The mean composition of platy, high-Al crystals is (Mg1.8Al0.7)(Si2.0)O5(OH)4, and that of platy, medium-Al crystals with As3+ is (Mg2.07Al0.52) (Si1.97As3+0.03)O5(OH)4. Charge, geometry, and radius of tetrahedral AsO43– oxyanions are similar to tetrahedral SiO44–, and this facilitates fixation of As5+ into the tetrahedral sheet of clay minerals. The geometry and size of the larger As3+ in tetrahedral sites (as a pyramidal AsO33– oxyanion) may limit incorporation relative to As5+. Arsenic-bearing Mg clays crystallize in alkaline environments where AsO43– or AsO33– are the dominant As species and where high pH accompanies crystallization of serpentine, talc, chlorite, or Mg-smectite. The presence of tetrahedral As in these clays raises the possibility of tetrahedral As in other Mg clays (e.g. sepiolite or kerolite) as well.

Salt solutions have complex effects on the swelling characteristics of compacted bentonite; these effects are caused by the inhibitory action of salinity and the ion-exchange reaction between the solution and bentonite. In order to characterize the swelling properties of compacted bentonite in a salt solution, swelling deformation tests were carried out for Gao-Miao-Zi (GMZ) bentonite specimens in NaCl and CaCl2 solutions. Swelling characteristics decreased with increasing salt concentration. Swelling strains in NaCl solution were larger than those in CaCl2 solution, even though the ionic concentration of 1.0 mol/L (M) NaCl solution is larger than that of 0.5 M CaCl2. According to the exchangeable cations tests, cation exchange was different for specimens immersed in different salt solutions. The swelling fractal model was used to predict the swelling strains of compacted bentonite in a concentrated salt solution. In this model, the effective stress incorporating osmotic suction was applied to take the effect of salinity into consideration, and the swelling coefficient, K, was employed to describe the swelling properties affected by the variation in exchangeable cations. In the model, fractal dimension was measured by nitrogen adsorption, and the salt solution had little effect on fractal dimension. K was estimated by the diffuse double layer (DDL) model for osmotic swelling in distilled water. Comparison of fractal model estimations with experimental data demonstrated that the new model performed well in predicting swelling characteristics affected by a salt solution.

In the soils of western Jilin Province in northeastern China, some significant gaps have been observed between the fraction of the soil existing as clay-size particles (<0.002 mm) and the amount attributable to crystalline clay minerals, and that the relative proportions of crystalline clay minerals to the total clay-size fraction (CP) apparently varies with latitude. The purpose of the present study was to identify the reason for this discrepancy and to explain the dependence on latitude. The grain sizes and mineral compositions of the whole soils from western Jilin Province, China, were analyzed by laser particle-size analysis (LPSA) and X-ray diffraction (XRD), and the <0.002 mm particle-size fraction was analyzed by XRD and X-ray fluorescence (XRF). The results confirmed that the percentage gaps between the clay fraction and clay minerals increased with increasing latitude. The theoretical illite percentage calculated from K2O content was compared with the illite percentage measured by XRD, and the results suggested that the measured illite accounted for only a small proportion of the theoretical illite. Structures of some special minerals below the identification threshold of XRD was suggested to be the reason for the percent gaps. The grain size and mineral crystallization both changed with latitude: the soil particle size and the CP decreased. In addition, clay minerals were more sensitive to climate than particle sizes were, and the CP of clay minerals in the soils within 0~180 cm depth all decreased with increasing latitude; however, the grain size showed patterns with latitude only in relatively shallow soil layers. The present study provides a reference and error analysis for the testing of clay minerals in alpine regions, and more suitable methods may be considered for development of clay-mineral testing in future studies.

Adsorption of uranyl (UO22+) ions to mineral surfaces is a potentially effective method for removing this hazardous metal from water, but other toxic trace metal ions (Xn+: Rb+, Sr2+, Cr3+, Mn2+, Ni2+, Zn2+, Cd2+) in uraniferous wastewaters compete with UO22+ for adsorption sites and thus may diminish the capacity of adsorbents to sequester UO22+. A better understanding of competitive adsorption among these metal ions and the development of better adsorbents are, therefore, of critical importance. The purpose of the present study was to synthesize and characterize magnetic adsorbents, consisting of MFe2O4 (M = Mn, Fe, Zn, Co, or Ni) nanoparticles synthesized on montmorillonite (Mnt) edge sites, and to investigate their use as adsorbents for UO22+, including competitive adsorption with trace metal ions. Selective adsorption was studied using Langmuir, Freundlich, and Dubinin-Radushkevich isotherms, and the results showed that Xn+ ions were adsorbed primarily on MFe2O4-montmorillonite surfaces, and the UO22+ ions were adsorbed on the interfaces between montmorillonite edge surfaces and MFe2O4 nanoparticles. Using the Freundlich model, the interface adsorption capacity of UO22+ reached 25.1 mg·g–1 in mixed solution. Further, the UO22+ and Cr3+ ions had a redox reaction on the interfaces with synergistic adsorption. Herein, the adsorption capacity of Cr3+ was 60.2 mg·g–1 using the Freundlich isotherm. The results demonstrated that the MFe2O4-montmorillonite with highly selective adsorption of UO22+ ions is applicable to UO22+ treatment in the presence of toxic trace metal ions.

Graphical abstract

Clays have played an important role in medicine since the dawn of mankind and are still applied widely as active ingredients and/or excipients in pharmaceutical formulations. Due to their outstanding properties of large retention capacity, swelling and rheological properties, and relative low cost, they have been used widely as advanced carriers for the efficient delivery of drugs by modifying their release (rate and/or time), increasing the stability of the drug, improving the dissolution profile of a drug, or enhancing their intestinal permeability. In addition, recent studies have shed new light on the potential of clay minerals in the nanomedicine field due to their biocompatibility, beneficial effects of clay nanoparticles on cellular adhesion, proliferation, and differentiation. Use as active ingredients and excipients are exerted via the oral and topical administration pathways. Skin drug delivery represents an attractive alternative to the oral route, providing local and/or systemic drug delivery. Due to their complex structures, however, most drugs penetrate the human skin only with difficulty. Enormous efforts have been invested, therefore, in developing advanced drug delivery systems able to overcome the skin barrier. Most strategies require the use of singular materials with new properties. In particular, and on the basis of their inherent properties, clay minerals are ideal candidates for the development of intelligent skin drug delivery systems. In this article, the properties of clay materials and their use in the skin-addressed pharmaceutical field are reviewed. A brief introduction of skin physiology and biopharmaceutical features of penetration by a drug through the skin layers is also included and is designed to shed light on the optimum properties of ideal nanosystems for advanced skin drug delivery. Special attention is devoted to the pharmacological functions of clays and their biomedical applications in pelotherapy, wound healing, regenerative medicine, antimicrobial, and dermocosmetics.

Large kaolin deposits developed by weathering on Precambrian granitic rocks have been discovered in the Caluquembe area, Huíla province, Angola. To determine accuracy of analysis and to evaluate the kaolinite grade, a full-profile Rietveld refinement by X-ray Powder Diffraction (XRPD) and Thermal Gravimetric Analysis (TGA) was used. Caluquembe kaolin is composed mainly of kaolinite (44–93 wt.%), quartz (0–23 wt.%), and feldspar (4–14 wt.%). The Aparicio-Galán-Ferrell index (AGFI), calculated by XRPD profile refinement, indicates low- and medium-defect kaolinite. Kaolinite particles show a platy habit and they stack together forming ‘booklets’ or radial aggregates; they also occur as small anhedral particles in a finer-grained mass. Muscovite-kaolinite intergrowths have also been found. Whole-rock chemical analysis included major, trace, and Rare Earth Elements (REE). Chondrite-normalized REE patterns show the same tendency for all samples, with a significant enrichment in Light Rare Earth Elements (LREE). Mineralogical and compositional features of the Caluquembe kaolin indicate that it is a suitable material for the manufacture of structural products, such as bricks, paving stones, and roofing tiles. In addition, the significant REE contents of the Caluquembe kaolin can be considered as a potential future target of mining exploration.

Although fluorescence detection is a sensitive method in the field of pollutant analysis, its application is restricted due to the fluorescence shown by organic material being quenched after aggregation and to low photo-thermal stability. To address these issues, a novel mineral/dye composite material was prepared by intercalating a fluorescence molecule, Rhodamine (R6G), into the interlayer space of montmorillonite (Mnt). This composite material greatly enhanced the light stability and efficiency of R6G. After enhancement, the fluorescence lifetime of R6G-Mnt was eight times longer than originally and the luminous intensity was 20 times greater. Chromium at the mmol/L (mM) level can be detected by the naked eye when its enhanced fluorescent property is fabricated into a solid test paper, even though a fluorescence spectrophotometer should be used for detection at the 0.01 μmol/L level in the sensing range 0.01 μmol/L to 100 mmol/L. These results can provide new avenues as well as a theoretical and experimental foundation for the development of novel supramolecular luminescent material.

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.

Tumor theranostics (a portmanteau of therapeutics and diagnostics) is now achieved in various ways with complex nanoparticle systems. Layered double hydroxide (LDH) nanoparticles are effective at drug/gene delivery and as imaging agents in potential tumor theranostics. This mini-review paper summarizes recent progress in developing LDH nanoparticles as a pH-sensitive magnetic resonance imaging (MRI) contrast agent, as a positron emission tomography (PET) imaging agent, and as a co-delivery platform for two therapeutic agents for tumor diagnosis and therapy. These results have indicated clearly the potential application of LDH nanoparticles for simultaneous diagnosis and treatment of cancers.

The increased detection of pharmaceuticals in finished drinking water has become a growing cause of concern in recent years. The removal of atenolol, ranitidine, and carbamazepine by sepiolite, following functionalization of its surface by organosilane grafting, constituted the subject of this investigation. Silylated surfaces include octyl, γ-aminopropyl, 3-chloropropyl, and triphenyl moieties. The sorption of atenolol and ranitidine was higher on sepiolite functionalized with 3-chloropropyl, while carbamazepine showed a higher sorption on sepiolite with triphenyl groups. Filtration experiments of both ranitidine and carbamazepine on octyl- and triphenyl-sepiolite, respectively, showed a higher retention of ranitidine in comparison to carbamazepine, in spite of the fact that the number of sorption sites was lower due to its higher binding rate.

A review of the models proffered to advance the notion of the metastability of illite shows that these models are not supported by the various data groups that have become available. Given that clay minerals are products of water–rock interactions, low-temperature hydrothermal experiments provide singular insights into their relative stabilities; such experiments with natural materials of contrasting pedigree (illites, sericites, muscovites, and chlorites) show that clay-mineral behaviors in low-temperature hydrothermal solutions are amenable to equilibrium thermodynamic conventions. The data from hydrothermal experiments coupled with data from geothermal fields indicate that muscovite is not a stable phase in the P-T-X range in which authigenic illite occurs; given that experimental data and field occurrence suggest that muscovite and illite have different P-T stability regimes, the continued use of muscovite as a proxy for illite in thermodynamic models is of questionable utility. Furthermore, morphometric studies of clays undergoing illitization show that crystal-size distributions exhibit log-normal patterns. Because log-normal distributions derive from maximum entropy effects, these crystal-size distributions may reflect the effects of entropy production during crystallization rather than kinetically driven Ostwald ripening of illitic phases; the small crystal size of clay minerals may derive from constraints imposed by the physicochemical conditions of their environments of formation. Presumably, irreversible thermodynamics provides the framework for a quantitative understanding of the evolution of complex clay minerals in space and time.

Hydrophobicity, high viscosity, and dispersion are important properties for organo-montmorillonites, and all organo-montmorillonite configurations have yet to be fully characterized with respect to this property. High-viscosity montmorillonite (Mnt) is useful in gels and as an adsorber. The current study focused on modifying Mnt using organic cations and anions of various chain lengths in batch experiments with various concentrations and ratios. The viscosity of organic Mnt reached up to 395 mP.s. Molecular dynamics simulations and X-ray diffraction (XRD) were used to identify the conditions and arrangement of organic cations and anions in the Mnt interlayer area. The intercalation mechanism of organic cations and anions was also determined, providing a theoretical basis for the preparation of high-viscosity Mnt.

Waste brownfield-site soils contaminated with heavy metals such as Zn and Cr are of critical environmental concern because of the rapid urbanization and industrialization that is occurring in China. Thermal treatment can fix heavy metals in specific mineral structures, which might be a promising technology for remediation and reutilization of the metal-contaminated soils. The objective of the present study was to elucidate the stabilization mechanisms of Zn and Cr through thermal treatment of mixtures of ZnO + Cr2O3 to form ZnCr2O4 and to confirm that Zn and Cr were incorporated simultaneously into the spinel structure. The incorporation efficiency for Zn was quantified, with the value ranging from 70.6 to 100% over the temperature range 700–1300°C. Leaching results further confirmed that ZnCr2O4 spinel was a superior product for Zn and Cr immobilization. Then, by artificially sintering Zn- and Cr-enriched soils, both Zn and Cr were immobilized effectively (with three orders of magnitude reduction in Zn leachability) in the ZnCr2O4 spinel as the predominant product phase. In addition, multiple heavy metals such as Zn, Cu, and Cr in the actual brownfield-site soils were well immobilized after sintering, which confirmed the potential for practical application of the thermal treatment technology utilized in this study.

Geophagy is the intentional consumption of earth. Although widely documented among vulnerable populations, including children and pregnant women, the causes and consequences of geophagy remain poorly understood. Relevant literature was, therefore, reviewed to describe geophagy across species, geographies, life stages, and disease states. After a brief consideration of hypothesized etiologies, the potential harmful and beneficial consequences of geophagy are described, considering current evidence for each. Data available to date suggest that the greatest potential risks of geophagy include toxicity or heavy metal poisoning, and diseases resulting from consumed clays binding nutrients and beneficial pharmaceuticals in the gut. Evidence also suggests that geophagy may be beneficial by protecting against harmful pathogens and toxins through two distinct physiological pathways. Future research should explore causal relationships between geophagy and iron deficiency, as well as investigate the biological and psychosocial conditions that govern geophagy.

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.

To identify the mechanisms for and to estimate the photochemical reaction efficiency of molecules in solid-state host materials is difficult. The objective of the present research was to measure the photogeneration efficiency of the methylviologen cation radical (MV+•) hosted in a semi-transparent hybrid film composed of MV2+ and saponite, a 2:1 clay mineral. MV+• is the one-electron reduced species of MV2+. MV+• was generated by UV irradiation of these films. The fluorescence intensity of MV2+ and the photogeneration efficiency of MV+• depended on the loading level of MV2+. When the loading level of MV2+ was high (75% of the cation exchange capacity (abbreviated as % CEC) of saponite), its fluorescence was reduced considerably because of the self-fluorescence quenching reaction, and the photogeneration efficiency of MV+• was relatively high (quantum yield φ = 3.5×10–2) compared to that of films with low adsorption density (10% CEC, φ = 1.1×10–2). Furthermore, when the loading level of MV2+ was very low (0.13% CEC), a self-fluorescence quenching reaction was not observed and MV+• was not generated. From these observations, one of the principal mechanisms of the self-quenching reaction and MV+• formation in saponite is the electron transfer reaction between excited MV2+ and adjacent MV2+ molecules in the ground state.