Crystallography

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A crystalline solid: atomic resolution image of strontium titanate. Brighter atoms are strontium and darker ones are titanium. Stohrem.jpg
A crystalline solid: atomic resolution image of strontium titanate. Brighter atoms are strontium and darker ones are titanium.

Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids (see crystal structure). The word "crystallography" is derived from the Greek words crystallon "cold drop, frozen drop", with its meaning extending to all solids with some degree of transparency, and graphein "to write". In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography. [1] X-ray crystallography is used to determine the structure of large biomolecules such as proteins. Before the development of X-ray diffraction crystallography (see below), the study of crystals was based on physical measurements of their geometry. This involved measuring the angles of crystal faces relative to each other and to theoretical reference axes (crystallographic axes), and establishing the symmetry of the crystal in question. This physical measurement is carried out using a goniometer. The position in 3D space of each crystal face is plotted on a stereographic net such as a Wulff net or Lambert net. The pole to each face is plotted on the net. Each point is labelled with its Miller index. The final plot allows the symmetry of the crystal to be established.

Crystal structure Ordered arrangement of atoms, ions, or molecules in a crystalline material

In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric patterns that repeat along the principal directions of three-dimensional space in matter.

Greek language Language spoken in Greece, Cyprus and Southern Albania

Greek is an independent branch of the Indo-European family of languages, native to Greece, Cyprus and other parts of the Eastern Mediterranean and the Black Sea. It has the longest documented history of any living Indo-European language, spanning more than 3000 years of written records. Its writing system has been the Greek alphabet for the major part of its history; other systems, such as Linear B and the Cypriot syllabary, were used previously. The alphabet arose from the Phoenician script and was in turn the basis of the Latin, Cyrillic, Armenian, Coptic, Gothic, and many other writing systems.

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The United Nations (UN) is an intergovernmental organization tasked with maintaining international peace and security, developing friendly relations among nations, achieving international co-operation, and being a centre for harmonizing the actions of nations. It was established after World War II, with the aim of preventing future wars, and succeeded the ineffective League of Nations. Its headquarters, which are subject to extraterritoriality, are in Manhattan, New York City, and it has other main offices in Geneva, Nairobi, Vienna and The Hague. The organization is financed by assessed and voluntary contributions from its member states. Its objectives include maintaining international peace and security, protecting human rights, delivering humanitarian aid, promoting sustainable development, and upholding international law. The UN is the largest, most familiar, most internationally represented and most powerful intergovernmental organization in the world. At its founding, the UN had 51 member states; there are now 193.

Contents

Crystallographic methods now depend on analysis of the diffraction patterns of a sample targeted by a beam of some type. X-rays are most commonly used; other beams used include electrons or neutrons. This is facilitated by the wave properties of the particles. Crystallographers often explicitly state the type of beam used, as in the terms X-ray crystallography, neutron diffraction and electron diffraction . These three types of radiation interact with the specimen in different ways.

Diffraction refers to various phenomena that occur when a wave encounters an obstacle or a slit

Diffraction refers to various phenomena that occur when a wave encounters an obstacle or a slit. It is defined as the bending of waves around the corners of an obstacle or through an aperture into the region of geometrical shadow of the obstacle/aperture. The diffracting object or aperture effectively becomes a secondary source of the propagating wave. Italian scientist Francesco Maria Grimaldi coined the word "diffraction" and was the first to record accurate observations of the phenomenon in 1660.

X-ray Röntgen radiation

X-rays make up X-radiation, a form of high-energy electromagnetic radiation. Most X-rays have a wavelength ranging from 0.01 to 10 nanometers, corresponding to frequencies in the range 30 petahertz to 30 exahertz (3×1016 Hz to 3×1019 Hz) and energies in the range 100 eV to 100 keV. X-ray wavelengths are shorter than those of UV rays and typically longer than those of gamma rays. In many languages, X-radiation is referred to as Röntgen radiation, after the German scientist Wilhelm Röntgen, who discovered it on November 8, 1895. He named it X-radiation to signify an unknown type of radiation. Spelling of X-ray(s) in the English language includes the variants x-ray(s), xray(s), and X ray(s).

Electron subatomic particle with negative electric charge

The electron is a subatomic particle, symbol
e
or
β
, whose electric charge is negative one elementary charge. Electrons belong to the first generation of the lepton particle family, and are generally thought to be elementary particles because they have no known components or substructure. The electron has a mass that is approximately 1/1836 that of the proton. Quantum mechanical properties of the electron include an intrinsic angular momentum (spin) of a half-integer value, expressed in units of the reduced Planck constant, ħ. Being fermions, no two electrons can occupy the same quantum state, in accordance with the Pauli exclusion principle. Like all elementary particles, electrons exhibit properties of both particles and waves: they can collide with other particles and can be diffracted like light. The wave properties of electrons are easier to observe with experiments than those of other particles like neutrons and protons because electrons have a lower mass and hence a longer de Broglie wavelength for a given energy.

In physics, a charged particle is a particle with an electric charge. It may be an ion, such as a molecule or atom with a surplus or deficit of electrons relative to protons. It can also be an electron or a proton, or another elementary particle, which are all believed to have the same charge. Another charged particle may be an atomic nucleus devoid of electrons, such as an alpha particle.

Charge density Electric charge per volume, length or area

In electromagnetism, charge density is the amount of electric charge per unit length, surface area, or volume. Volume charge density is the quantity of charge per unit volume, measured in the SI system in coulombs per cubic meter (C•m−3), at any point in a volume. Surface charge density (σ) is the quantity of charge per unit area, measured in coulombs per square meter (C•m−2), at any point on a surface charge distribution on a two dimensional surface. Linear charge density (λ) is the quantity of charge per unit length, measured in coulombs per meter (C•m−1), at any point on a line charge distribution. Charge density can be either positive or negative, since electric charge can be either positive or negative.

Magnetic moment extensive physical property

The magnetic moment is the magnetic strength and orientation of a magnet or other object that produces a magnetic field. Examples of objects that have magnetic moments include: loops of electric current, permanent magnets, elementary particles, various molecules, and many astronomical objects.

Because of these different forms of interaction, the three types of radiation are suitable for different crystallographic studies.

Theory

An image of a small object is made using a lens to focus the beam, similar to a lens in a microscope. However, the wavelength of visible light (about 4000 to 7000 ångström) is three orders of magnitude longer than the length of typical atomic bonds and atoms themselves (about 1 to 2 Å). Therefore, obtaining information about the spatial arrangement of atoms requires the use of radiation with shorter wavelengths, such as X-ray or neutron beams. Employing shorter wavelengths implied abandoning microscopy and true imaging, however, because there exists no material from which a lens capable of focusing this type of radiation can be created.[ citation needed ] Scientists have had some success focusing X-rays with microscopic Fresnel zone plates made from gold, and by critical-angle reflection inside long tapered capillaries. [2] Diffracted X-ray or neutron beams cannot be focused to produce images, so the sample structure must be reconstructed from the diffraction pattern. Sharp features in the diffraction pattern arise from periodic, repeating structure in the sample, which are often very strong due to coherent reflection of many photons from many regularly spaced instances of similar structure, while non-periodic components of the structure result in diffuse (and usually weak) diffraction features - areas with a higher density and repetition of atom order tend to reflect more light toward one point in space when compared to those areas with fewer atoms and less repetition.

An order of magnitude is an approximate measure of the number of digits that a number has in the commonly-used base-ten number system. It is equal to the whole number floor of logarithm (base 10). For example, the order of magnitude of 1500 is 3, because 1500 = 1.5 × 103.

Chemical bond lasting attraction between atoms that enables the formation of chemical compounds

A chemical bond is a lasting attraction between atoms, ions or molecules that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between oppositely charged ions as in ionic bonds or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force and hydrogen bonding.

Atom smallest unit of a chemical element

An atom is the smallest constituent unit of ordinary matter that constitutes a chemical element. Every solid, liquid, gas, and plasma is composed of neutral or ionized atoms. Atoms are extremely small; typical sizes are around 100 picometers. They are so small that accurately predicting their behavior using classical physics – as if they were billiard balls, for example – is not possible. This is due to quantum effects. Current atomic models now use quantum principles to better explain and predict this behavior.

Because of their highly ordered and repetitive structure, crystals give diffraction patterns of sharp Bragg reflection spots, and are ideal for analyzing the structure of solids.

Notation

A bracket is a tall punctuation mark commonly used in matched pairs within text, to set apart or interject other text. The members of the matched pair may be described as opening and closing brackets. Less formally, in a left-to-right context, they may be described as left and right, and in a right-to-left context, as right and left.

Crystal system Classification of crystalline materials by their three dimensional structural geometry

In crystallography, the terms crystal system, crystal family, and lattice system each refer to one of several classes of space groups, lattices, point groups, or crystals. Informally, two crystals are in the same crystal system if they have similar symmetries, although there are many exceptions to this.

Normal (geometry) in geometry, an object that is perpendicular to a given object

In geometry, a normal is an object such as a line or vector that is perpendicular to a given object. For example, in two dimensions, the normal line to a curve at a given point is the line perpendicular to the tangent line to the curve at the point.

Techniques

Some materials that have been analyzed crystallographically, such as proteins, do not occur naturally as crystals. Typically, such molecules are placed in solution and allowed to slowly crystallize through vapor diffusion. A drop of solution containing the molecule, buffer, and precipitants is sealed in a container with a reservoir containing a hygroscopic solution. Water in the drop diffuses to the reservoir, slowly increasing the concentration and allowing a crystal to form. If the concentration were to rise more quickly, the molecule would simply precipitate out of solution, resulting in disorderly granules rather than an orderly and hence usable crystal.

Once a crystal is obtained, data can be collected using a beam of radiation. Although many universities that engage in crystallographic research have their own X-ray producing equipment, synchrotrons are often used as X-ray sources, because of the purer and more complete patterns such sources can generate. Synchrotron sources also have a much higher intensity of X-ray beams, so data collection takes a fraction of the time normally necessary at weaker sources. Complementary neutron crystallography techniques are used to identify the positions of hydrogen atoms, since X-rays only interact very weakly with light elements such as hydrogen.

Producing an image from a diffraction pattern requires sophisticated mathematics and often an iterative process of modelling and refinement. In this process, the mathematically predicted diffraction patterns of an hypothesized or "model" structure are compared to the actual pattern generated by the crystalline sample. Ideally, researchers make several initial guesses, which through refinement all converge on the same answer. Models are refined until their predicted patterns match to as great a degree as can be achieved without radical revision of the model. This is a painstaking process, made much easier today by computers.

The mathematical methods for the analysis of diffraction data only apply to patterns, which in turn result only when waves diffract from orderly arrays. Hence crystallography applies for the most part only to crystals, or to molecules which can be coaxed to crystallize for the sake of measurement. In spite of this, a certain amount of molecular information can be deduced from patterns that are generated by fibers and powders, which while not as perfect as a solid crystal, may exhibit a degree of order. This level of order can be sufficient to deduce the structure of simple molecules, or to determine the coarse features of more complicated molecules. For example, the double-helical structure of DNA was deduced from an X-ray diffraction pattern that had been generated by a fibrous sample.

Materials science

Crystallography is used by materials scientists to characterize different materials. In single crystals, the effects of the crystalline arrangement of atoms is often easy to see macroscopically, because the natural shapes of crystals reflect the atomic structure. In addition, physical properties are often controlled by crystalline defects. The understanding of crystal structures is an important prerequisite for understanding crystallographic defects. Mostly, materials do not occur as a single crystal, but in poly-crystalline form (i.e., as an aggregate of small crystals with different orientations). Because of this, the powder diffraction method, which takes diffraction patterns of polycrystalline samples with a large number of crystals, plays an important role in structural determination.

Other physical properties are also linked to crystallography. For example, the minerals in clay form small, flat, platelike structures. Clay can be easily deformed because the platelike particles can slip along each other in the plane of the plates, yet remain strongly connected in the direction perpendicular to the plates. Such mechanisms can be studied by crystallographic texture measurements.

In another example, iron transforms from a body-centered cubic (bcc) structure to a face-centered cubic (fcc) structure called austenite when it is heated. The fcc structure is a close-packed structure unlike the bcc structure; thus the volume of the iron decreases when this transformation occurs.

Crystallography is useful in phase identification. When manufacturing or using a material, it is generally desirable to know what compounds and what phases are present in the material, as their composition, structure and proportions will influence the material's properties. Each phase has a characteristic arrangement of atoms. X-ray or neutron diffraction can be used to identify which patterns are present in the material, and thus which compounds are present. Crystallography covers the enumeration of the symmetry patterns which can be formed by atoms in a crystal and for this reason is related to group theory and geometry.

Biology

X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, particularly protein and nucleic acids such as DNA and RNA. In fact, the double-helical structure of DNA was deduced from crystallographic data. The first crystal structure of a macromolecule was solved in 1958, a three-dimensional model of the myoglobin molecule obtained by X-ray analysis. [3] The Protein Data Bank (PDB) is a freely accessible repository for the structures of proteins and other biological macromolecules. Computer programs such as RasMol, Pymol or VMD can be used to visualize biological molecular structures. Neutron crystallography is often used to help refine structures obtained by X-ray methods or to solve a specific bond; the methods are often viewed as complementary, as X-rays are sensitive to electron positions and scatter most strongly off heavy atoms, while neutrons are sensitive to nucleus positions and scatter strongly even off many light isotopes, including hydrogen and deuterium. Electron crystallography has been used to determine some protein structures, most notably membrane proteins and viral capsids.

Reference literature

The International Tables for Crystallography [4] is an eight-book series that outlines the standard notations for formatting, describing and testing crystals. The series contains books that covers analysis methods and the mathematical procedures for determining organic structure though x-ray crystallography, electron diffraction, and neutron diffraction. The International tables are focused on procedures, techniques and descriptions and do not list the physical properties of individual crystals themselves. Each book is about 1000 pages and the titles of the books are:

Vol A - Space Group Symmetry,
Vol A1 - Symmetry Relations Between Space Groups,
Vol B - Reciprocal Space,
Vol C - Mathematical, Physical, and Chemical Tables,
Vol D - Physical Properties of Crystals,
Vol E - Subperiodic Groups,
Vol F - Crystallography of Biological Macromolecues, and
Vol G - Definition and Exchange of Crystallographic Data.

Scientists of note

See also

Related Research Articles

X-ray crystallography Technique used in studying crystal structure

X-ray crystallography (XRC) is a technique used to determine the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their crystallographic disorder, and various other information.

Electron diffraction refers to the wave nature of electrons. However, from a technical or practical point of view, it may be regarded as a technique used to study matter by firing electrons at a sample and observing the resulting interference pattern. This phenomenon is commonly known as wave–particle duality, which states that a particle of matter can be described as a wave. For this reason, an electron can be regarded as a wave much like sound or water waves. This technique is similar to X-ray and neutron diffraction.

Neutron diffraction

Neutron diffraction or elastic neutron scattering is the application of neutron scattering to the determination of the atomic and/or magnetic structure of a material. A sample to be examined is placed in a beam of thermal or cold neutrons to obtain a diffraction pattern that provides information of the structure of the material. The technique is similar to X-ray diffraction but due to their different scattering properties, neutrons and X-rays provide complementary information: X-Rays are suited for superficial analysis, strong x-rays from synchrotron radiation are suited for shallow depths or thin specimens, while neutrons having high penetration depth are suited for bulk samples.

Synchrotron light source particle accelerator designed to produce intense x-ray beams

A synchrotron light source is a source of electromagnetic radiation (EM) usually produced by a storage ring, for scientific and technical purposes. First observed in synchrotrons, synchrotron light is now produced by storage rings and other specialized particle accelerators, typically accelerating electrons. Once the high-energy electron beam has been generated, it is directed into auxiliary components such as bending magnets and insertion devices in storage rings and free electron lasers. These supply the strong magnetic fields perpendicular to the beam which are needed to convert high energy electrons into photons.

In physics, Bragg's law, or Wulff–Bragg's condition, a special case of Laue diffraction, gives the angles for coherent and incoherent scattering from a crystal lattice. When X-rays are incident on an atom, they make the electronic cloud move, as does any electromagnetic wave. The movement of these charges re-radiates waves with the same frequency, blurred slightly due to a variety of effects; this phenomenon is known as Rayleigh scattering. The scattered waves can themselves be scattered but this secondary scattering is assumed to be negligible.

Diamond Light Source UKs national synchrotron science facility located in Oxfordshire

Diamond Light Source is the UK's national synchrotron light source science facility located at the Harwell Science and Innovation Campus in Oxfordshire. Its purpose is to produce intense beams of light whose special characteristics are useful in many areas of scientific research. In particular it can be used to investigate the structure and properties of a wide range of materials from proteins, and engineering components to conservation of archeological artifacts.

Biological small-angle scattering

Biological small-angle scattering is a small-angle scattering method for structure analysis of biological materials. Small-angle scattering is used to study the structure of a variety of objects such as solutions of biological macromolecules, nanocomposites, alloys, and synthetic polymers. Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are the two complementary techniques known jointly as small-angle scattering (SAS). SAS is an analogous method to X-ray and neutron diffraction, wide angle X-ray scattering, as well as to static light scattering. In contrast to other X-ray and neutron scattering methods, SAS yields information on the sizes and shapes of both crystalline and non-crystalline particles. When used to study biological materials, which are very often in aqueous solution, the scattering pattern is orientation averaged.

In physics, the phase problem is the problem of loss of information concerning the phase that can occur when making a physical measurement. The name comes from the field of X-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data. The phase problem is also met in the fields of imaging and signal processing. Various approaches have been developed over the years that attempt to solve it.

Electron backscatter diffraction

Electron backscatter diffraction (EBSD) is a scanning electron microscope–based microstructural-crystallographic characterization technique commonly used in the study of crystalline or polycrystalline materials. The technique can provide information about the structure, crystal orientation, phase, or strain in the material. Traditionally these types of studies have been carried out using X-ray diffraction (XRD), neutron diffraction and/or electron diffraction in a Transmission electron microscope.

Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM).

A diffractometer is a measuring instrument for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles interacts with it.

Powder diffraction Experimental methods in X-Ray diffraction

Powder diffraction is a scientific technique using X-ray, neutron, or electron diffraction on powder or microcrystalline samples for structural characterization of materials. An instrument dedicated to performing such powder measurements is called a powder diffractometer.

Selected area diffraction crystallographic experimental technique that can be performed inside a transmission electron microscope

Selected area (electron) diffraction, is a crystallographic experimental technique that can be performed inside a transmission electron microscope (TEM).

In condensed matter physics and crystallography, the static structure factor is a mathematical description of how a material scatters incident radiation. The structure factor is a critical tool in the interpretation of scattering patterns obtained in X-ray, electron and neutron diffraction experiments.

Fiber diffraction

Fiber diffraction is a subarea of scattering, an area in which molecular structure is determined from scattering data. In fiber diffraction the scattering pattern does not change, as the sample is rotated about a unique axis. Such uniaxial symmetry is frequent with filaments or fibers consisting of biological or man-made macromolecules. In crystallography fiber symmetry is an aggravation regarding the determination of crystal structure, because reflexions are smeared and may overlap in the fiber diffraction pattern. Materials science considers fiber symmetry a simplification, because almost the complete obtainable structure information is in a single two-dimensional (2D) diffraction pattern exposed on photographic film or on a 2D detector. 2 instead of 3 co-ordinate directions suffice to describe fiber diffraction.

Magnetic structure ordered arrangement of magnetic spins in a material

The term magnetic structure of a material pertains to the ordered arrangement of magnetic spins, typically within an ordered crystallographic lattice. Its study is a branch of solid-state physics.

A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal.

In solid state physics, a superstructure is some additional structure that is superimposed on a given crystalline structure. A typical and important example is ferromagnetic ordering.

Zone axis

Zone axis, a term sometimes used to refer to "high-symmetry" orientations in a crystal, most generally refers to any direction referenced to the direct lattice of a crystal in three dimensions. It is therefore indexed with direct lattice indices, instead of with Miller indices.

References

  1. UN announcement "International Year of Crystallography". iycr2014.org. 12 July 2012
  2. Snigirev, A. (2007). "Two-step hard X-ray focusing combining Fresnel zone plate and single-bounce ellipsoidal capillary". Journal of Synchrotron Radiation. 14 (Pt 4): 326–330. doi:10.1107/S0909049507025174. PMID   17587657.
  3. Kendrew, J. C.; Bodo, G.; Dintzis, H. M.; Parrish, R. G.; Wyckoff, H.; Phillips, D. C. (1958). "A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis". Nature. 181 (4610): 662–6. Bibcode:1958Natur.181..662K. doi:10.1038/181662a0. PMID   13517261.
  4. Prince, E. (2006). International Tables for Crystallography Vol. C: Mathematical, Physical and Chemical Tables. Wiley. ISBN   978-1-4020-4969-9.