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.

The absence of mixing between Y³⁺ and Cu²⁺ results in a more idealized Kagomé lattice in YCu₃(OH)₆Cl₃ compared to hebertsmithite and kapellasite.

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.