Supramolecular chemistry

From Wikipedia, the free encyclopedia

• 

  Self-Assembly of a Circular Double Helicate^[1]
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  Host-guest complex within another host (cucurbit[10]uril)^[2]
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  mechanically interlocked molecules (rotaxane)^[3]
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  An example of a host-guest chemistry^[4]
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  host-guest complex with a p-xylylenediammonium bound within a cucurbituril^[5]
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  Intramolecular self-assembly of a foldamer.^[6]
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  3D interpenetrated network in the crystal structure of silsesquioxane.^[7]

Supramolecular chemistry is the domain of chemistry beyond that of molecules that focuses on the chemical systems made up of a discrete number of assembled molecular subunits or components. The forces responsible for the spatial organization may vary from weak (intermolecular forces, electrostatic or hydrogen bonding) to strong (covalent bonding), provided that the degree of electronic coupling between the molecular component remains small with respect to relevant energy parameters of the component. While traditional chemistry focuses on the covalent bond, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules.. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions and electrostatic effects. Important concepts that have been demonstrated by supramolecular chemistry include molecular self-assembly, folding, molecular recognition, host-guest chemistry, mechanically-interlocked molecular architectures, and dynamic covalent chemistry. The study of non-covalent interactions is crucial to understanding many biological processes from cell structure to vision that rely on these forces for structure and function. Biological systems are often the inspiration for supramolecular research.

Supermolecules are to molecules and the intermolecular bond what molecules are to atoms and the covalent bond.

History

The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals in 1873. However, Nobel laureate Hermann Emil Fischer developed supramolecular chemistry's philosophical roots. In 1894,^[13] Fischer suggested that enzyme-substrate interactions take the form of a "lock and key", the fundamental principles of molecular recognition and host-guest chemistry. In the early twentieth century noncovalent bonds were understood in gradually more detail, with the hydrogen bond being described by Latimer and Rodebush in 1920.

The use of these principles led to an increasing understanding of protein structure and other biological processes. For instance, the important breakthrough that allowed the elucidation of the double helical structure of DNA occurred when it was realized that there are two separate strands of nucleotides connected through hydrogen bonds. The use of noncovalent bonds is essential to replication because they allow the strands to be separated and used to template new double stranded DNA. Concomitantly, chemists began to recognize and study synthetic structures based on noncovalent interactions, such as micelles and microemulsions.

Eventually, chemists were able to take these concepts and apply them to synthetic systems. The breakthrough came in the 1960s with the synthesis of the crown ethers by Charles J. Pedersen. Following this work, other researchers such as Donald J. Cram, Jean-Marie Lehn and Fritz Vögtle became active in synthesizing shape- and ion-selective receptors, and throughout the 1980s research in the area gathered a rapid pace with concepts such as mechanically interlocked molecular architectures emerging.

The importance of supramolecular chemistry was established by the 1987 Nobel Prize for Chemistry which was awarded to Donald J. Cram, Jean-Marie Lehn, and Charles J. Pedersen in recognition of their work in this area.^[14] The development of selective "host-guest" complexes in particular, in which a host molecule recognizes and selectively binds a certain guest, was cited as an important contribution.

In the 1990s, supramolecular chemistry became even more sophisticated, with researchers such as James Fraser Stoddart developing molecular machinery and highly complex self-assembled structures, and Itamar Willner developing sensors and methods of electronic and biological interfacing. During this period, electrochemical and photochemical motifs became integrated into supramolecular systems in order to increase functionality, research into synthetic self-replicating system began, and work on molecular information processing devices began. The emerging science of nanotechnology also had a strong influence on the subject, with building blocks such as fullerenes, nanoparticles, and dendrimers becoming involved in synthetic systems.

Control

Thermodynamics

Supramolecular chemistry deals with subtle interactions, and consequently control over the processes involved can require great precision. In particular, noncovalent bonds have low energies and often no activation energy for formation. As demonstrated by the Arrhenius equation, this means that, unlike in covalent bond-forming chemistry, the rate of bond formation is not increased at higher temperatures. In fact, chemical equilibrium equations show that the low bond energy results in a shift towards the breaking of supramolecular complexes at higher temperatures.

However, low temperatures can also be problematic to supramolecular processes. Supramolecular chemistry can require molecules to distort into thermodynamically disfavored conformations (e.g. during the "slipping" synthesis of rotaxanes), and may include some covalent chemistry that goes along with the supramolecular. In addition, the dynamic nature of supramolecular chemistry is utilized in many systems (e.g. molecular mechanics), and cooling the system would slow these processes.

Thus, thermodynamics is an important tool to design, control, and study supramolecular chemistry. Perhaps the most striking example is that of warm-blooded biological systems, which entirely cease to operate outside a very narrow temperature range.

Environment

The molecular environment around a supramolecular system is also of prime importance to its operation and stability. Many solvents have strong hydrogen bonding, electrostatic, and charge-transfer capabilities, and are therefore able to become involved in complex equilibria with the system, even breaking complexes completely. For this reason, the choice of solvent can be critical.

Concepts

Molecular self-assembly

Molecular self-assembly is the construction of systems without guidance or management from an outside source (other than to provide a suitable environment). The molecules are directed to assemble through noncovalent interactions. Self-assembly may be subdivided into intermolecular self-assembly (to form a supramolecular assembly), and intramolecular self-assembly (or folding as demonstrated by foldamers and polypeptides). Molecular self-assembly also allows the construction of larger structures such as micelles, membranes, vesicles, liquid crystals, and is important to crystal engineering.^[15]

Molecular recognition and complexation

Molecular recognition is the specific binding of a guest molecule to a complementary host molecule to form a host-guest complex. Often, the definition of which species is the "host" and which is the "guest" is arbitrary. The molecules are able to identify each other using noncovalent interactions. Key applications of this field are the construction of molecular sensors and catalysis.

Template-directed synthesis

Molecular recognition and self-assembly may be used with reactive species in order to pre-organize a system for a chemical reaction (to form one or more covalent bonds). It may be considered a special case of supramolecular catalysis. Noncovalent bonds between the reactants and a "template" hold the reactive sites of the reactants close together, facilitating the desired chemistry. This technique is particularly useful for situations where the desired reaction conformation is thermodynamically or kinetically unlikely, such as in the preparation of large macrocycles. This pre-organization also serves purposes such as minimizing side reactions, lowering the activation energy of the reaction, and producing desired stereochemistry. After the reaction has taken place, the template may remain in place, be forcibly removed, or may be "automatically" decomplexed on account of the different recognition properties of the reaction product. The template may be as simple as a single metal ion or may be extremely complex.

Mechanically interlocked molecular architectures

Mechanically interlocked molecular architectures consist of molecules that are linked only as a consequence of their topology. Some noncovalent interactions may exist between the different components (often those that were utilized in the construction of the system), but covalent bonds do not. Supramolecular chemistry, and template-directed synthesis in particular, is key to the efficient synthesis of the compounds. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, molecular Borromean rings^[20] and ravels.^[21]

Dynamic covalent chemistry

In dynamic covalent chemistry covalent bonds are broken and formed in a reversible reaction under thermodynamic control. While covalent bonds are key to the process, the system is directed by noncovalent forces to form the lowest energy structures.^[22]

Biomimetics

Many synthetic supramolecular systems are designed to copy functions of biological systems. These biomimetic architectures can be used to learn about both the biological model and the synthetic implementation. Examples include photoelectrochemical systems, catalytic systems, protein design and self-replication.^[23]

Imprinting

Molecular imprinting describes a process by which a host is constructed from small molecules using a suitable molecular species as a template. After construction, the template is removed leaving only the host. The template for host construction may be subtly different from the guest that the finished host binds to. In its simplest form, imprinting utilizes only steric interactions, but more complex systems also incorporate hydrogen bonding and other interactions to improve binding strength and specificity.^[24]

Molecular machinery

Molecular machines are molecules or molecular assemblies that can perform functions such as linear or rotational movement, switching, and entrapment. These devices exist at the boundary between supramolecular chemistry and nanotechnology, and prototypes have been demonstrated using supramolecular concepts.^[25] Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa shared the 2016 Nobel Prize in Chemistry for the 'design and synthesis of molecular machines'.^[26]

Building blocks

Supramolecular systems are rarely designed from first principles. Rather, chemists have a range of well-studied structural and functional building blocks that they are able to use to build up larger functional architectures. Many of these exist as whole families of similar units, from which the analog with the exact desired properties can be chosen.

Synthetic recognition motifs

• The pi-pi charge-transfer interactions of bipyridinium with dioxyarenes or diaminoarenes have been used extensively for the construction of mechanically interlocked systems and in crystal engineering.
• The use of crown ether binding with metal or ammonium cations is ubiquitous in supramolecular chemistry.
• The formation of carboxylic acid dimers and other simple hydrogen bonding interactions.
• The complexation of bipyridines or tripyridines with ruthenium, silver or other metal ions is of great utility in the construction of complex architectures of many individual molecules.
• The complexation of porphyrins or phthalocyanines around metal ions gives access to catalytic, photochemical and electrochemical properties as well as complexation. These units are used a great deal by nature.

Macrocycles

Macrocycles are very useful in supramolecular chemistry, as they provide whole cavities that can completely surround guest molecules and may be chemically modified to fine-tune their properties.

• Cyclodextrins, calixarenes, cucurbiturils and crown ethers are readily synthesized in large quantities, and are therefore convenient for use in supramolecular systems.
• More complex cyclophanes, and cryptands can be synthesised to provide more tailored recognition properties.
• Supramolecular metallocycles are macrocyclic aggregates with metal ions in the ring, often formed from angular and linear modules. Common metallocycle shapes in these types of applications include triangles, squares, and pentagons, each bearing functional groups that connect the pieces via "self-assembly."^[27]
• Metallacrowns are metallomacrocycles generated via a similar self-assembly approach from fused chelate-rings.

Structural units

Many supramolecular systems require their components to have suitable spacing and conformations relative to each other, and therefore easily employed structural units are required.

• Commonly used spacers and connecting groups include polyether chains, biphenyls and triphenyls, and simple alkyl chains. The chemistry for creating and connecting these units is very well understood.
• nanoparticles, nanorods, fullerenes and dendrimers offer nanometer-sized structure and encapsulation units.
• Surfaces can be used as scaffolds for the construction of complex systems and also for interfacing electrochemical systems with electrodes. Regular surfaces can be used for the construction of self-assembled monolayers and multilayers.
• The understanding of intermolecular interactions in solids has undergone a major renaissance via inputs from different experimental and computational methods in the last decade. This includes high-pressure studies in solids and in situ crystallization of compounds which are liquids at room temperature alongwith the utilization of electron density analysis, crystal structure prediction and DFT calculations in solid state to enable a quantitative understanding of the nature, energetics and topological properties associated with such interactions in crystals. ^[28]

Photo-/electro-chemically active units

• Porphyrins, and phthalocyanines have highly tunable photochemical and electrochemical activity as well as the potential for forming complexes.
• Photochromic and photoisomerizable groups have the ability to change their shapes and properties (including binding properties) upon exposure to light.
• TTF and quinones have more than one stable oxidation state, and therefore can be switched with redox chemistry or electrochemistry. Other units such as benzidine derivatives, viologens groups and fullerenes, have also been utilized in supramolecular electrochemical devices.

Biologically-derived units

• The extremely strong complexation between avidin and biotin is instrumental in blood clotting, and has been used as the recognition motif to construct synthetic systems.
• The binding of enzymes with their cofactors has been used as a route to produce modified enzymes, electrically contacted enzymes, and even photoswitchable enzymes.
• DNA has been used both as a structural and as a functional unit in synthetic supramolecular systems.

Applications

Materials technology

Supramolecular chemistry has found many applications,^[29], in particular molecular self-assembly processes have been applied to the development of new materials. Large structures can be readily accessed using bottom-up synthesis as they are composed of small molecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology are based on supramolecular chemistry.^[30] Many smart materials ^[31] are based on molecular recognition.^[32]

Catalysis

A major application of supramolecular chemistry is the design and understanding of catalysts and catalysis. Noncovalent interactions are extremely important in catalysis, binding reactants into conformations suitable for reaction and lowering the transition state energy of reaction. Template-directed synthesis is a special case of supramolecular catalysis. Encapsulation systems such as micelles, dendrimers, and cavitands^[33] are also used in catalysis to create microenvironments suitable for reactions (or steps in reactions) to progress that is not possible to use on a macroscopic scale.

Medicine

Design based on supramolecular chemistry has led to numerous applications in the creation of functional biomaterials and therapeutics.^[34] Supramolecular biomaterials afford a number of modular and generalizable platforms with tunable mechanical, chemical and biological properties. These include systems based on supramolecular assembly of peptides, host-guest macrocycles, high-affinity hydrogen bonding, and metal-ligand interactions.

A supramolecular approach has been used extensively to create artificial ion channels for the transport of sodium and potassium ions into and out of cells.^[35]

Supramolecular chemistry is also important to the development of new pharmaceutical therapies by understanding the interactions at a drug binding site. The area of drug delivery has also made critical advances as a result of supramolecular chemistry providing encapsulation and targeted release mechanisms.^[36] In addition, supramolecular systems have been designed to disrupt protein-protein interactions that are important to cellular function.^[37]

Data storage and processing

Supramolecular chemistry has been used to demonstrate computation functions on a molecular scale. In many cases, photonic or chemical signals have been used in these components, but electrical interfacing of these units has also been shown by supramolecular signal transduction devices. Data storage has been accomplished by the use of molecular switches with photochromic and photoisomerizable units, by electrochromic and redox-switchable units, and even by molecular motion. Synthetic molecular logic gates have been demonstrated on a conceptual level. Even full-scale computations have been achieved by semi-synthetic DNA computers.

Future robots need no motors HKU Engineering invents world’s first nickel-hydroxide actuating material that can be triggered by both light and electricity

31 May 2018

For the journal paper, please click: http://robotics.sciencemag.org/content/3/18/eaat4051.full

Original link:  https://www.hku.hk/press/press-releases/detail/17948.html

Professor Alfonso Ngan and Dr Kwan Kin-wa introduce the
new actuating material powered by light.

To develop micro- and biomimetic-robots, artificial muscles and medical devices, actuating materials that can reversibly change their volume under various stimuli are researched in the past thirty years to replace traditional bulky and heavy actuators including motors and pneumatic actuators.

A mechanical engineering team led by Professor Alfonso Ngan Hing-wan, Chair Professor in Materials Science and Engineering, and Kingboard Professor in Materials Engineering, Faculty of Engineering, the University of Hong Kong (HKU) published an article in Science Robotics on 30 May 2018 (EST) that introduces a novel actuating material – nickel hydroxide-oxyhydroxide – that can be powered by visible (Vis) light, electricity, and other stimuli. The material actuation can be instantaneously triggered by Vis light to produce a fast deformation and exert a force equivalent to 3000 times of its own weight. The material cost of a typical actuator is as low as HKD 4 per cm² and can be easily fabricated within three hours.

Among various stimuli, light-induced actuating materials are highly desirable because they enable wireless operation of robots. However, very few light driven materials are available in the past, and their material and production costs are high, which hinder their development in actual applications such as artificial muscles for robotics and human assist device, and minimally invasive surgical and diagnostic tools.

Developing actuating materials was identified as the top of the 10 challenges in “The grand challenges of Science Robotics”¹. Research in actuating materials can radically change the concept of robots which are now mainly motor-driven. Therefore, materials that can be actuated by wireless stimuli including a change in temperature, humidity, magnetic fields and light is one of the main research focus in recent years.  In particular, a material that can be actuated by Vis light and produces strong, quick and stable actuation has never been achieved. The novel actuating material system – nickel hydroxide-oxyhydroxide that can be actuated by Vis light at relatively low intensity to produce high stress and speed comparable to mammalian skeletal muscles has been developed in this research initiated by engineers in HKU.

In addition to its Vis light actuation properties, this novel material system can also be actuated by electricity, enabling it to be integrated into the present well-developed robotics technology. It is also responsive to heat and humidity changes so that they might potentially be applied in autonomous machines that harness the tiny energy change in the environment. Because the major component is nickel, the material cost is low. The fabrication only involves electrodeposition which is a simple process, and the time required for the fabrication is around three hours, therefore the material can be easily scaled up and manufactured in industry.

The newly invented nickel hydroxide-oxyhydroxide responses to light almost instantaneously and produces a force corresponding to about 3000 times of its own weight (Figure 1).

¹ Yang, Guang-Zhong, et al. "The grand challenges of Science Robotics." Science Robotics 3.14 (2018): eaar7650.

Figure 1  Actuating force of a 0.3-mg nickel hydroxide-oxyhydroxide actuator of under periodic light can reach about 1000-mg.

When integrated into a well-designed structure, a “mini arm” made by two hinges of actuating materials can easily lift an object 50 times of its weight (Figure 2). Similarly, by utilizing a light blocker, a mini walking-bot in which only the “front leg” bent and straighten alternatively and therefore moves under illumination was made so that it can walk towards the light source (Figure 3). These demonstrate that future applications in micro-robotics including rescue robots are possible.

Figure 2 A mini arm with two actuating hinges lifting a weight 50 time heavier than itself under light.

Figure 3  A mini walking-bot with the “front leg” straightened under light, while the light blocker blocks the light illumination on the “back leg” and therefore it remains curled. Therefore, the walking-bot walks towards the light source.

The evidences above revealed that this nickel hydroxide-oxyhydroxide actuating material can have different applications in the future, including rescue robots or other mini-robots. The intrinsic actuating properties of the materials obtained from our research show that by scaling up the fabrication, artificial muscles comparable to that of mammalian skeletal muscles can be achieved, and applying it in robotics, human assist device and medical devices are possible.

From a scientific point of view, this nickel hydroxide-oxyhydroxide actuating material is the world’s first material system that can be actuated directly by Vis light and electricity without any additional fabrication procedures. This also opens up a new research field on light-induced actuating behaviour for this material type (hydroxide-oxyhydroxides) because it has never been reported before.

The research team members are all from the Department of Mechanical Engineering at HKU Faculty of Engineering, led by Professor Alfonso Ngan’s group in collaboration with Dr Li Wen-di. ’s group on light actuation experiment and Dr Feng Shien-ping’s group on electrodeposition experiment. The research has been published in the prestigious journal Science Robotics on 30 May 2018 with a title of “Light-stimulated actuators based on nickel hydroxide-oxyhydroxide”. The first author of this paper is Dr Kwan Kin-wa who is currently a post-doctoral fellow in Prof. Ngan’s group. The corresponding author is Prof. Ngan. The complete author list is as below: K-W. Kwan, S-J. Li, N-Y. Hau, W-D. Li, S-P. Feng, A.H.W. Ngan. This research is funded by the Research Grants Council, Hong Kong.

For the powerpoint slides about this research, please click here, and for video clips, please click here.  (Please credit “The University of Hong Kong” if adopt the images in the powerpoint and videos.)

Media enquiry:
Faculty of Engineering:
Dr Kwan Kin-wa (Email: kkwkwan@connect.hku.hk)
Professor Alfonso Ngan (Tel: 39177900; Email: hwngan@hku.hk)
Ms Rhea Leung (Tel: 3917-8519/ 9022-7446; Email: rhea.leung@hku.hk)
Communication and Public Affairs Office:
Ms Trinni Choy (Tel: 2859 2606/ Email: pychoy@hku.hk)
Ms Rashida Suffiad (Tel: 2857 8555/ email: rsuffiad@hku.hk)

Mineralogy

From Wikipedia, the free encyclopedia

 

Mineralogy is a mixture of chemistry, materials science, physics and geology.

Mineralogy is a subject of geology specializing in the scientific study of chemistry, crystal structure, and physical (including optical) properties of minerals and mineralized artifacts. Specific studies within mineralogy include the processes of mineral origin and formation, classification of minerals, their geographical distribution, as well as their utilization.

History

Page from Treatise on mineralogy by Friedrich Mohs (1825)

 

The Moon Mineralogy Mapper, a spectrometer that mapped the lunar surface^[3]

 

Early writing on mineralogy, especially on gemstones, comes from ancient Babylonia, the ancient Greco-Roman world, ancient and medieval China, and Sanskrit texts from ancient India and the ancient Islamic World.^[4] Books on the subject included the Naturalis Historia of Pliny the Elder, which not only described many different minerals but also explained many of their properties, and Kitab al Jawahir (Book of Precious Stones) by Persian scientist Al Biruni. The German Renaissance specialist Georgius Agricola wrote works such as De re metallica (On Metals, 1556) and De Natura Fossilium (On the Nature of Rocks, 1546) which began the scientific approach to the subject. Systematic scientific studies of minerals and rocks developed in post-Renaissance Europe.^[4] The modern study of mineralogy was founded on the principles of crystallography (the origins of geometric crystallography, itself, can be traced back to the mineralogy practiced in the eighteenth and nineteenth centuries) and to the microscopic study of rock sections with the invention of the microscope in the 17th century.^[4]

Nicholas Steno first observed the law of constancy of interfacial angles (also known as the first law of crystallography) in quartz crystals in 1669.^[5]:4 This was later generalized and established experimentally by Jean-Baptiste L. Romé de l'Islee in 1783.^[6] René Just Haüy, the "father of modern crystallography", showed that crystals are periodic and established that the orientations of crystal faces can be expressed in terms of rational numbers, as later encoded in the Miller indices.^[5]:4 In 1814, Jöns Jacob Berzelius introduced a classification of minerals based on their chemistry rather than their crystal structure.^[7] William Nicol developed the Nicol prism, which polarizes light, in 1827–1828 while studying fossilized wood; Henry Clifton Sorby showed that thin sections of minerals could be identified by their optical properties using a polarizing microscope.^[5]:4[7]:15 James D. Dana published his first edition of A System of Mineralogy in 1837, and in a later edition introduced a chemical classification that is still the standard.^[5]:4[7]:15 X-ray diffraction was demonstrated by Max von Laue in 1912, and developed into a tool for analyzing the crystal structure of minerals by the father/son team of William Henry Bragg and William Lawrence Bragg.^[5]:4

More recently, driven by advances in experimental technique (such as neutron diffraction) and available computational power, the latter of which has enabled extremely accurate atomic-scale simulations of the behaviour of crystals, the science has branched out to consider more general problems in the fields of inorganic chemistry and solid-state physics. It, however, retains a focus on the crystal structures commonly encountered in rock-forming minerals (such as the perovskites, clay minerals and framework silicates). In particular, the field has made great advances in the understanding of the relationship between the atomic-scale structure of minerals and their function; in nature, prominent examples would be accurate measurement and prediction of the elastic properties of minerals, which has led to new insight into seismological behaviour of rocks and depth-related discontinuities in seismograms of the Earth's mantle. To this end, in their focus on the connection between atomic-scale phenomena and macroscopic properties, the mineral sciences (as they are now commonly known) display perhaps more of an overlap with materials science than any other discipline.

Physical properties

Calcite is a carbonate mineral (CaCO₃) with a rhombohedral crystal structure.

 

Aragonite is an orthorhombic polymorph of calcite.

An initial step in identifying a mineral is to examine its physical properties, many of which can be measured on a hand sample. These can be classified into density (often given as specific gravity); measures of mechanical cohesion (hardness, tenacity, cleavage, fracture, parting); macroscopic visual properties (luster, color, streak, luminescence, diaphaneity); magnetic and electric properties; radioactivity and solubility in hydrogen chloride (HCl).^{[5]:97–113[8]:39–53}

Hardness is determined by comparison with other minerals. In the Mohs scale, a standard set of minerals are numbered in order of increasing hardness from 1 (talc) to 10 (diamond). A harder mineral will scratch a softer, so an unknown mineral can be placed in this scale by which minerals it scratches and which scratch it. A few minerals such as calcite and kyanite have a hardness that depends significantly on direction.^{[9]:254–255} Hardness can also be measured on an absolute scale using a sclerometer; compared to the absolute scale, the Mohs scale is nonlinear.^[8]:52

Tenacity refers to the way a mineral behaves when it is broken, crushed, bent or torn. A mineral can be brittle, malleable, sectile, ductile, flexible or elastic. An important influence on tenacity is the type of chemical bond (e.g., ionic or metallic).^{[9]:255–256} Of the other measures of mechanical cohesion, cleavage is the tendency to break along certain crystallographic planes. It is described by the quality (e.g., perfect or fair) and the orientation of the plane in crystallographic nomenclature. Parting is the tendency to break along planes of weakness due to pressure, twinning or exsolution. Where these two kinds of break do not occur, fracture is a less orderly form that may be conchoidal (having smooth curves resembling the interior of a shell), fibrous, splintery, hackly (jagged with sharp edges), or uneven.^{[9]:253–254}

If the mineral is well crystallized, it will also have a distinctive crystal habit (for example, hexagonal, columnar, botryoidal) that reflects the crystal structure or internal arrangement of atoms.^[8]:40–41 It is also affected by crystal defects and twinning. Many crystals are polymorphic, having more than one possible crystal structure depending on factors such as pressure and temperature.^{[5]:66–68[8]:126}

Crystal structure

The perovskite crystal structure. The most abundant mineral in the Earth, bridgmanite, has this structure.^[10] Its chemical formula is (Mg,Fe)SiO₃; the red spheres are oxygen, the blue spheres silicon and the green spheres magnesium or iron.

The crystal structure is the arrangement of atoms in a crystal. It is represented by a lattice of points which repeats a basic pattern, called a unit cell, in three dimensions. The lattice can be characterized by its symmetries and by the dimensions of the unit cell. These dimensions are represented by three Miller indices.^[11]:91–92 The lattice remains unchanged by certain symmetry operations about any given point in the lattice: reflection, rotation, inversion, and rotary inversion, a combination of rotation and reflection. Together, they make up a mathematical object called a crystallographic point group or crystal class. There are 32 possible crystal classes. In addition, there are operations that displace all the points: translation, screw axis, and glide plane. In combination with the point symmetries, they form 230 possible space groups.^{[11]:125–126}

Most geology departments have X-ray powder diffraction equipment to analyze the crystal structures of minerals.^[8]:54–55 X-rays have wavelengths that are the same order of magnitude as the distances between atoms. Diffraction, the constructive and destructive interference between waves scattered at different atoms, leads to distinctive patterns of high and low intensity that depend on the geometry of the crystal. In a sample that is ground to a powder, the X-rays sample a random distribution of all crystal orientations.^[12] Powder diffraction can distinguish between minerals that may appear the same in a hand sample, for example quartz and its polymorphs tridymite and cristobalite.^[8]:54

Isomorphous minerals of different compositions have similar powder diffraction patterns, the main difference being in spacing and intensity of lines. For example, the NaCl (halite) crystal structure is space group Fm3m; this structure is shared by sylvite (KCl), periclase (MgO), bunsenite (NiO), galena (PbS), alabandite (MnS), chlorargyrite (AgCl), and osbornite (TiN).^{[9]:150–151}

Chemical elements

Portable Micro-X-ray fluorescence machine

A few minerals are chemical elements, including sulfur, copper, silver, and gold, but the vast majority are compounds. The classical method for identifying composition is wet chemical analysis, which involves dissolving a mineral in an acid such as hydrochloric acid (HCl). The elements in solution are then identified using colorimetry, volumetric analysis or gravimetric analysis.^{[9]:224–225}

Since 1960, most chemistry analysis is done using instruments. One of these, atomic absorption spectroscopy, is similar to wet chemistry in that the sample must still be dissolved, but it is much faster and cheaper. The solution is vaporized and its absorption spectrum is measured in the visible and ultraviolet range.^{[9]:225–226} Other techniques are X-ray fluorescence, electron microprobe analysis and optical emission spectrography.^{[9]:227–232}

Optical

Photomicrograph of olivine adcumulate, Archaean Komatiite, Agnew, Western Australia.

In addition to macroscopic properties such as color or lustre, minerals have properties that require a polarizing microscope to observe.

Transmitted light

When light passes from air or a vacuum into a transparent crystal, some of it is reflected at the surface and some refracted. The latter is a bending of the light path that occurs because the speed of light changes as it goes into the crystal; Snell's law relates the bending angle to the Refractive index, the ratio of speed in a vacuum to speed in the crystal. Crystals whose point symmetry group falls in the cubic system are isotropic: the index does not depend on direction. All other crystals are anisotropic: light passing through them is broken up into two plane polarized rays that travel at different speeds and refract at different angles.^{[9]:289–291}

A polarizing microscope is similar to an ordinary microscope, but it has two plane-polarized filters, a (polarizer) below the sample and an analyzer above it, polarized perpendicular to each other. Light passes successively through the polarizer, the sample and the analyzer. If there is no sample, the analyzer blocks all the light from the polarizer. However, an anisotropic sample will generally change the polarization so some of the light can pass through. Thin sections and powders can be used as samples.^{[9]:293–294}

When an isotropic crystal is viewed, it appears dark because it does not change the polarization of the light. However, when it is immersed in a calibrated liquid with a lower index of refraction and the microscope is thrown out of focus, a bright line called a Becke line appears around the perimeter of the crystal. By observing the presence or absence of such lines in liquids with different indices, the index of the crystal can be estimated, usually to within ± 0.003.^{[9]:294–295}

Systematic

Hanksite, Na₂₂K(SO₄)₉(CO₃)₂Cl, one of the few minerals that is considered a carbonate and a sulfate

Systematic mineralogy is the identification and classification of minerals by their properties. Historically, mineralogy was heavily concerned with taxonomy of the rock-forming minerals. In 1959, the International Mineralogical Association formed the Commission of New Minerals and Mineral Names to rationalize the nomenclature and regulate the introduction of new names. In July 2006, it was merged with the Commission on Classification of Minerals to form the Commission on New Minerals, Nomenclature, and Classification.^[13] There are over 6,000 named and unnamed minerals, and about 100 are discovered each year.^[14] The Manual of Mineralogy places minerals in the following classes: native elements, sulfides, sulfosalts, oxides and hydroxides, halides, carbonates, nitrates and borates, sulfates, chromates, molybdates and tungstates, phosphates, arsenates and vanadates, and silicates.^[9]

Formation environments

The environments of mineral formation and growth are highly varied, ranging from slow crystallization at the high temperatures and pressures of igneous melts deep within the Earth's crust to the low temperature precipitation from a saline brine at the Earth's surface.

Various possible methods of formation include:^[15]

• sublimation from volcanic gases
• deposition from aqueous solutions and hydrothermal brines
• crystallization from an igneous magma or lava
• recrystallization due to metamorphic processes and metasomatism
• crystallization during diagenesis of sediments
• formation by oxidation and weathering of rocks exposed to the atmosphere or within the soil environment.

Biomineralogy

Biomineralogy is a cross-over field between mineralogy, paleontology and biology. It is the study of how plants and animals stabilize minerals under biological control, and the sequencing of mineral replacement of those minerals after deposition.^[16] It uses techniques from chemical mineralogy, especially isotopic studies, to determine such things as growth forms in living plants and animals^[17][18] as well as things like the original mineral content of fossils.^[19]

A new approach to mineralogy called "mineral evolution" explores the co-evolution of the geosphere and biosphere, including the role of minerals in the origin of life and processes as mineral-catalyzed organic synthesis and the selective adsorption of organic molecules on mineral surfaces.^[20][21]

Uses

A color chart of some raw forms of commercially valuable metals.^[22]

Minerals are essential to various needs within human society, such as minerals used as ores for essential components of metal products used in various commodities and machinery, essential components to building materials such as limestone, marble, granite, gravel, glass, plaster, cement, etc.^[15] Minerals are also used in fertilizers to enrich the growth of agricultural crops.

Collecting

Mineral collecting is also a recreational study and collection hobby, with clubs and societies representing the field.^[23][24] Museums, such as the Smithsonian National Museum of Natural History Hall of Geology, Gems, and Minerals, the Natural History Museum of Los Angeles County, the Natural History Museum, London, and the private Mim Mineral Museum in Beirut, Lebanon,^[25][26] have popular collections of mineral specimens on permanent display.