Quartz (trigonal, low-temperature α-quartz) is the most important polymorph of the silica (SiO₂) group and one of the purest minerals in the Earth crust. The mineralogy and mineral chemistry of quartz are determined mainly by its defect structure. Certain point defects, dislocations and micro-inclusions can be incorporated into quartz during crystallisation under various thermodynamic conditions and by secondary processes such as alteration, irradiation, diagenesis or metamorphism. The resulting real structure is a fingerprint of the specific physicochemical environment of quartz formation and also determines the quality and applications of SiO₂raw materials. Point defects in quartz can be related to imperfections associated with silicon or oxygen vacancies (intrinsic defects), to different types of displaced atoms, and/or to the incorporation of foreign ions in lattice sites and interstitial positions (extrinsic defects). Due to mismatch in charges and ionic radii only a limited number of ions can substitute for Si⁴⁺in the crystal lattice or can be incorporated in interstitial positions. Therefore, most impurity elements in quartz are present at concentrations below 1 ppm. The structural incorporation in a regular Si⁴⁺lattice site has been proven for Al³⁺, Ga³⁺, Fe³⁺, B³⁺, Ge⁴⁺, Ti⁴⁺, P⁵⁺and H⁺, of which Al³⁺is by far the most common and typically the most abundant. Unambiguous detection and characterisation of defect structures in quartz are a technical challenge and can only be successfully realised by a combination of advanced analytical methods such as electron paramagnetic resonance (EPR) spectroscopy, cathodoluminescence (CL) microscopy and spectroscopy as well as spatially resolved trace-element analysis such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and secondary-ion mass spectrometry (SIMS). The present paper presents a review of the state-of-the-art knowledge concerning the mineralogy and mineral-chemistry of quartz and illustrates important geological implications of the properties of quartz.

Agate—a spectacular form of SiO₂ and a famous gemstone—is commonly characterized as banded chalcedony. In detail, chalcedony layers in agates can be intergrown or intercalated with macrocrystalline quartz, quartzine, opal-A, opal-CT, cristobalite and/or moganite. In addition, agates often contain considerable amounts of mineral inclusions and water as both interstitial molecular H₂O and silanol groups. Most agate occurrences worldwide are related to SiO₂-rich (rhyolites, rhyodacites) and SiO₂-poor (andesites, basalts) volcanic rocks, but can also be formed as hydrothermal vein varieties or as silica accumulation during diagenesis in sedimentary rocks. It is assumed that the supply of silica for agate formation is often associated with late- or post-volcanic alteration of the volcanic host rocks. Evidence can be found in association with typical secondary minerals such as clay minerals, zeolites or iron oxides/hydroxides, frequent pseudomorphs (e.g., after carbonates or sulfates) as well as the chemical composition of the agates. For instance, elements of the volcanic rock matrix (Al, Ca, Fe, Na, K) are enriched, but extraordinary high contents of Ge (>90 ppm), B (>40 ppm) and U (>20 ppm) have also been detected. Calculations based on fluid inclusion and oxygen isotope studies point to a range between 20 and 230 °C for agate formation temperatures. The accumulation and condensation of silicic acid result in the formation of silica sols and proposed amorphous silica as precursors for the development of the typical agate micro-structure. The process of crystallisation often starts with spherulitic growth of chalcedony continuing into chalcedony fibers. High concentrations of lattice defects (oxygen and silicon vacancies, silanol groups) detected by cathodoluminescence (CL) and electron paramagnetic resonance (EPR) spectroscopy indicate a rapid crystallisation via an amorphous silica precursor under non-equilibrium conditions. It is assumed that the formation of the typical agate microstructure is governed by processes of self-organization. The resulting differences in crystallite size, porosity, kind of silica phase and incorporated color pigments finally cause the characteristic agate banding and colors.

Quartz samples of different origin from 10 localities in the Southern Ural region, Russia have been investigated to characterize their trace element compositions and defect structures. The analytical combination of cathodoluminescence (CL) microscopy and spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and trace-element analysis by inductively coupled plasma mass spectrometry (ICP-MS) revealed that almost all investigated quartz samples showed very low concentrations of trace elements (cumulative concentrations of <50 ppm with <30 ppm Al and <10 ppm Ti) and low abundances of paramagnetic defects, defining them economically as “high-purity” quartz (HPQ) suitable for high-tech applications. EPR and CL data confirmed the low abundances of substitutional Ti and Fe, and showed Al to be the only significant trace element structurally bound in the investigated quartz samples. CL microscopy revealed a heterogeneous distribution of luminescence centres (i.e., luminescence active trace elements such as Al) as well as features of deformation and recrystallization. It is suggested that healing of defects due to deformation-related recrystallization and reorganization processes of the quartz lattice during retrograde metamorphism resulted in low concentrations of CL activator and other trace elements or vacancies, and thus are the main driving processes for the formation of HPQ deposits in the investigated area.

Discovery of moganite in a lunar meteorite indicates the possibility of H ₂ O ice accumulated in the Moon’s regolith.

The occurrence and formation of silicified wood from five late Paleozoic basins in Central Europe was investigated. Fossil wood from diverse geological settings was studied using field observations, taphonomic determinations as well as mineralogical analyses (polarizing microscopy, cathodoluminescence (CL) microscopy and spectroscopy). The results indicate that silicification is either a monophase or multiphase process under varying physico-chemical conditions. In particular, CL studies revealed complex processes of silica accumulation and crystallization. The CL characteristics of quartz phases in silicified wood can mostly be related to blue (390 and 440 nm), yellow (580 nm), and red (650 nm) emission bands, which may appear in different combinations and varying intensity ratios. Yellow CL is typical for initial silicification, reflecting quick precipitation under oxygen-deficient conditions caused by initial decay of the organic material. Blue CL is predominantly of secondary origin, resulting from replacement of precursor phases by a secondary hydrothermal quartz generation or subsequent silicification of wood. The red CL can be related to a lattice defect (non-bridging oxygen hole center—NBOHC).