X-ray crystallography

An x-ray crystallograph in motion

X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause 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 disorder, and various other information.

Since many materials can form crystals—such as salts, metals, minerals, semiconductors, as well as various inorganic, organic, and biological molecules—X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and alloys. The method also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystallography is still the chief method for characterizing the atomic structure of new materials and in discerning materials that appear similar by other experiments. X-ray crystal structures can also account for unusual electronic or elastic properties of a material, shed light on chemical interactions and processes, or serve as the basis for designing pharmaceuticals against diseases.

In a single-crystal X-ray diffraction measurement, a crystal is mounted on a goniometer. The goniometer is used to position the crystal at selected orientations. The crystal is illuminated with a finely focused monochromatic beam of X-rays, producing a diffraction pattern of regularly spaced spots known as reflections. The two-dimensional images taken at different orientations are converted into a three-dimensional model of the density of electrons within the crystal using the mathematical method of Fourier transforms, combined with chemical data known for the sample. Poor resolution (fuzziness) or even errors may result if the crystals are too small, or not uniform enough in their internal makeup.

X-ray crystallography is related to several other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or neutrons, which are likewise interpreted by Fourier transformation. If single crystals of sufficient size cannot be obtained, various other X-ray methods can be applied to obtain less detailed information; such methods include fiber diffraction, powder diffraction and (if the sample is not crystallized) small-angle X-ray scattering (SAXS). If the material under investigation is only available in the form of nanocrystalline powders or suffers from poor crystallinity, the methods of electron crystallography can be applied for determining the atomic structure.

For all above mentioned X-ray diffraction methods, the scattering is elastic; the scattered X-rays have the same wavelength as the incoming X-ray. By contrast, inelastic X-ray scattering methods are useful in studying excitations of the sample, rather than the distribution of its atoms.[ citation needed]

History

Early scientific history of crystals and X-rays

Drawing of square (Figure A, above) and hexagonal (Figure B, below) packing from Kepler's work, Strena seu de Nive Sexangula.

Crystals, though long admired for their regularity and symmetry, were not investigated scientifically until the 17th century. Johannes Kepler hypothesized in his work Strena seu de Nive Sexangula (A New Year's Gift of Hexagonal Snow) (1611) that the hexagonal symmetry of snowflake crystals was due to a regular packing of spherical water particles. [1]

As shown by X-ray crystallography, the hexagonal symmetry of snowflakes results from the tetrahedral arrangement of hydrogen bonds about each water molecule. The water molecules are arranged similarly to the silicon atoms in the tridymite polymorph of SiO2. The resulting crystal structure has hexagonal symmetry when viewed along a principal axis.

The Danish scientist Nicolas Steno (1669) pioneered experimental investigations of crystal symmetry. Steno showed that the angles between the faces are the same in every exemplar of a particular type of crystal, [2] and René Just Haüy (1784) discovered that every face of a crystal can be described by simple stacking patterns of blocks of the same shape and size. Hence, William Hallowes Miller in 1839 was able to give each face a unique label of three small integers, the Miller indices which remain in use today for identifying crystal faces. Haüy's study led to the correct idea that crystals are a regular three-dimensional array (a Bravais lattice) of atoms and molecules; a single unit cell is repeated indefinitely along three principal directions that are not necessarily perpendicular. In the 19th century, a complete catalog of the possible symmetries of a crystal was worked out by Johan Hessel, [3] Auguste Bravais, [4] Evgraf Fedorov, [5] Arthur Schönflies [6] and (belatedly) William Barlow (1894). From the available data and physical reasoning, Barlow proposed several crystal structures in the 1880s that were validated later by X-ray crystallography; [7] however, the available data were too scarce in the 1880s to accept his models as conclusive.

X-ray crystallography shows the arrangement of water molecules in ice, revealing the hydrogen bonds (1) that hold the solid together. Few other methods can determine the structure of matter with such precision (resolution).

Wilhelm Röntgen discovered X-rays in 1895, just as the studies of crystal symmetry were being concluded. Physicists were initially uncertain of the nature of X-rays, but soon suspected (correctly) that they were waves of electromagnetic radiation, in other words, another form of light. At that time, the wave model of light—specifically, the Maxwell theory of electromagnetic radiation—was well accepted among scientists, and experiments by Charles Glover Barkla showed that X-rays exhibited phenomena associated with electromagnetic waves, including transverse polarization and spectral lines akin to those observed in the visible wavelengths. Single-slit experiments in the laboratory of Arnold Sommerfeld suggested that X-rays had a wavelength of about 1 angstrom. However, X-rays are composed of photons, and thus are not only waves of electromagnetic radiation but also exhibit particle-like properties. Albert Einstein introduced the photon concept in 1905, [8] but it was not broadly accepted until 1922, [9] [10] when Arthur Compton confirmed it by the scattering of X-rays from electrons. [11] Therefore, these particle-like properties of X-rays, such as their ionization of gases, caused William Henry Bragg to argue in 1907 that X-rays were not electromagnetic radiation. [12] [13] [14] [15] Nevertheless, Bragg's view was not broadly accepted and the observation of X-ray diffraction by Max von Laue in 1912 [16] confirmed for most scientists that X-rays were a form of electromagnetic radiation.

X-ray diffraction

The incoming beam (coming from upper left) causes each scatterer to re-radiate a small portion of its intensity as a spherical wave. If scatterers are arranged symmetrically with a separation d, these spherical waves will be in sync (add constructively) only in directions where their path-length difference 2d sin θ equals an integer multiple of the wavelength λ. In that case, part of the incoming beam is deflected by an angle 2θ, producing a reflection spot in the diffraction pattern.

Crystals are regular arrays of atoms, and X-rays can be considered waves of electromagnetic radiation. Atoms scatter X-ray waves, primarily through the atoms' electrons. Just as an ocean wave striking a lighthouse produces secondary circular waves emanating from the lighthouse, so an X-ray striking an electron produces secondary spherical waves emanating from the electron. This phenomenon is known as elastic scattering, and the electron (or lighthouse) is known as the scatterer. A regular array of scatterers produces a regular array of spherical waves. Although these waves cancel one another out in most directions through destructive interference, they add constructively in a few specific directions, determined by Bragg's law:

Here d is the spacing between diffracting planes, is the incident angle, n is any integer, and λ is the wavelength of the beam. These specific directions appear as spots on the diffraction pattern called reflections. Thus, X-ray diffraction results from an electromagnetic wave (the X-ray) impinging on a regular array of scatterers (the repeating arrangement of atoms within the crystal).

X-rays are used to produce the diffraction pattern because their wavelength λ is typically the same order of magnitude (1–100 angstroms) as the spacing d between planes in the crystal. In principle, any wave impinging on a regular array of scatterers produces diffraction, as predicted first by Francesco Maria Grimaldi in 1665. To produce significant diffraction, the spacing between the scatterers and the wavelength of the impinging wave should be similar in size. For illustration, the diffraction of sunlight through a bird's feather was first reported by James Gregory in the later 17th century. The first artificial diffraction gratings for visible light were constructed by David Rittenhouse in 1787, and Joseph von Fraunhofer in 1821. However, visible light has too long a wavelength (typically, 5500 angstroms) to observe diffraction from crystals. Prior to the first X-ray diffraction experiments, the spacings between lattice planes in a crystal were not known with certainty.

The idea that crystals could be used as a diffraction grating for X-rays arose in 1912 in a conversation between Paul Peter Ewald and Max von Laue in the English Garden in Munich. Ewald had proposed a resonator model of crystals for his thesis, but this model could not be validated using visible light, since the wavelength was much larger than the spacing between the resonators. Von Laue realized that electromagnetic radiation of a shorter wavelength was needed to observe such small spacings, and suggested that X-rays might have a wavelength comparable to the unit-cell spacing in crystals. Von Laue worked with two technicians, Walter Friedrich and his assistant Paul Knipping, to shine a beam of X-rays through a copper sulfate crystal and record its diffraction on a photographic plate. After being developed, the plate showed a large number of well-defined spots arranged in a pattern of intersecting circles around the spot produced by the central beam. [16] [17] Von Laue developed a law that connects the scattering angles and the size and orientation of the unit-cell spacings in the crystal, for which he was awarded the Nobel Prize in Physics in 1914. [18]

Scattering

As described in the mathematical derivation below, the X-ray scattering is determined by the density of electrons within the crystal. Since the energy of an X-ray is much greater than that of a valence electron, the scattering may be modeled as Thomson scattering, the interaction of an electromagnetic ray with a free electron. This model is generally adopted to describe the polarization of the scattered radiation.

The intensity of Thomson scattering for one particle with mass m and charge q is: [19][ clarification needed]

Hence the atomic nuclei, which are much heavier than an electron, contribute negligibly to the scattered X-rays.

Development from 1912 to 1920

Although diamonds (top left) and graphite (top right) are identical in chemical composition—being both pure carbon—X-ray crystallography revealed the arrangement of their atoms (bottom) accounts for their different properties. In diamond, the carbon atoms are arranged tetrahedrally and held together by single covalent bonds, making it strong in all directions. By contrast, graphite is composed of stacked sheets. Within the sheet, the bonding is covalent and has hexagonal symmetry, but there are no covalent bonds between the sheets, making graphite easy to cleave into flakes.

After Von Laue's pioneering research, the field developed rapidly, most notably by physicists William Lawrence Bragg and his father William Henry Bragg. In 1912–1913, the younger Bragg developed Bragg's law, which connects the observed scattering with reflections from evenly spaced planes within the crystal. [20] [21] [22] The Braggs, father and son, shared the 1915 Nobel Prize in Physics for their work in crystallography. The earliest structures were generally simple and marked by one-dimensional symmetry. However, as computational and experimental methods improved over the next decades, it became feasible to deduce reliable atomic positions for more complicated two- and three-dimensional arrangements of atoms in the unit-cell.

The potential of X-ray crystallography for determining the structure of molecules and minerals—then only known vaguely from chemical and hydrodynamic experiments—was realized immediately. The earliest structures were simple inorganic crystals and minerals, but even these revealed fundamental laws of physics and chemistry. The first atomic-resolution structure to be "solved" (i.e., determined) in 1914 was that of table salt. [23] [24] [25] The distribution of electrons in the table-salt structure showed that crystals are not necessarily composed of covalently bonded molecules, and proved the existence of ionic compounds. [26] The structure of diamond was solved in the same year, [27] [28] proving the tetrahedral arrangement of its chemical bonds and showing that the length of C–C single bond was 1.52 angstroms. Other early structures included copper, [29] calcium fluoride (CaF2, also known as fluorite), calcite (CaCO3) and pyrite (FeS2) [30] in 1914; spinel (MgAl2O4) in 1915; [31] [32] the rutile and anatase forms of titanium dioxide (TiO2) in 1916; [33] pyrochroite Mn(OH)2 and, by extension, brucite Mg(OH)2 in 1919;. [34] [35] Also in 1919 sodium nitrate (NaNO3) and caesium dichloroiodide (CsICl2) were determined by Ralph Walter Graystone Wyckoff, and the wurtzite (hexagonal ZnS) structure became known in 1920. [36]

The structure of graphite was solved in 1916 [37] by the related method of powder diffraction, [38] which was developed by Peter Debye and Paul Scherrer and, independently, by Albert Hull in 1917. [39] The structure of graphite was determined from single-crystal diffraction in 1924 by two groups independently. [40] [41] Hull also used the powder method to determine the structures of various metals, such as iron [42] and magnesium. [43]

Cultural and aesthetic importance

In what has been called his scientific autobiography, The Development of X-ray Analysis, Sir William Lawrence Bragg mentioned that he believed the field of crystallography was particularly welcoming to women because the techno-aesthetics of the molecular structures resembled textiles and household objects. Bragg was known to compare crystal formation to "curtains, wallpapers, mosaics, and roses". [44]

In 1951, the Festival Pattern Group at the Festival of Britain hosted a collaborative group of textile manufacturers and experienced crystallographers to design lace and prints based on the X-ray crystallography of insulin, china clay, and hemoglobin. One of the leading scientists of the project was Dr. Helen Megaw (1907–2002), the Assistant Director of Research at the Cavendish Laboratory in Cambridge at the time. Megaw is credited as one of the central figures who took inspiration from crystal diagrams and saw their potential in design. [45] In 2008, the Wellcome Collection in London curated an exhibition on the Festival Pattern Group called "From Atom to Patterns". [45]

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