Tag Archives: structure determination



Schematic of ordering in 1, 2, and 3 dimensions.  Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge.  1-D ordering is a row of 5 associated subunits.  2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits on top of the 20 subunits in the 2-D array.   (http:dr-monsrs.net)
Schematic of ordering in 1, 2, and 3 dimensions. Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge. 1-D ordering is a row of 5 associated subunits. 2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits above the 20 subunits in 2-D array.  (http://dr-monsrs.net)

2014 is the 100th year since the discovery that a beam of x-rays directed onto a single crystal comes out as multiple beams forming discrete spots.  That monumental finding has been called one the most important scientific research discoveries of all time.  Everyone in the entire public now is invited to celebrate this special 2014, designated by the United Nations as the International Year of Crystallography (IYCr2014)!  Below, I give the briefest possible non-mathematical introduction to the basic essentials of crystals and crystallography, along with some recommended internet websites where much further information is available.

What are crystals? 

We all encounter crystals every day, but most know little about them.  Crystals consist of matter whose smallest subunits (i.e., molecules or macromolecules) are very highly ordered in all 3 dimensions (3-D), as depicted in the opening figure above.  Some typical examples of the numerous crystals we commonly see are table salt (sodium chloride), diamonds in rings and jewelry (carbon), ice (water), and small granules of sugar (glucose).  If you have a magnifier, take a look now at what is in your salt shaker and you will observe many tiny crystals!

The 3-D ordering of the components making up crystals is so perfect that each and every subunit has exactly the same orientation and positioning as do all its neighbors.  This means that the atoms making up each subunit also have identical positioning to those in other subunits.  When a beam of x-rays is directed onto a single crystal in a suitable manner, each atom in the highly ordered complex scatters the incoming radiation identically into discrete spots.  The array of different spots produced from one crystal is the sum of the rays scattered by all its component atoms; because the innumerable atoms are so highly ordered, the many scattered rays join to form discrete spots.

What is diffraction? 

Diffraction is a fundamental property of atoms whereby incoming x-rays, electrons, or neutrons are scattered at characteristic angles and intensities.  The numerous scattered rays form an ordered array of diffraction spots and rings known as a diffraction pattern.  A single crystal produces one set of periodic diffraction spots, 2 crystals produce 2 sets of spots (at different rotations), and multiple crystals in polycrystalline materials will produce diffraction rings (i.e., many sets of the same spots at numerous different rotations).  The periodic order in diffraction patterns directly corresponds to the ordered position of the different atoms inside crystals; this means that diffraction patterns show atomic structure of the material making up each crystal.  The diffraction pattern is totally distinctive for each crystalline material, since the locations (atomic spacings) and brightness (kinds and numbers of atoms) of spots or rings are unique for each kind of crystalline matter.

What is crystallography? 

Crystallography is a research methodology for studying crystals.  Diffraction patterns are used in crystallography to tell us about the arrangement of the component atoms inside many different materials.  Since the beginning of x-ray crystallography one century ago, many thousands of materials have been crystallized and examined by crystallography; these include catalysts, enzymes, metals, minerals and biominerals, newly synthesized chemical compounds, proteins, salts, viruses, etc.   Because the atoms inside crystals are so highly ordered in an identical manner, diffraction patterns can be recorded, measured, and then processed by computation to determine structure down to the level of individual atoms.  This atomic structure determination of crystalline matter is the magic of crystallography!

Crystallography is a global activity for both science and industry, and almost all countries have scientists working as crystallographers.  X-ray diffraction is the most frequently used approach for crystallography, and now is quite automated through the use of computers to carry out the extensive numerical calculations needed to define an unknown structure to a high level of resolution.  Crystallography can be performed with laboratory x-ray sources or with very powerful and very fast x-rays produced by synchrotrons.   The hugely expensive synchrotron facilities are rather few in number, but have well-organized programs permitting their use by many visiting scientists.  Diffraction of electrons or neutrons also provides valuable special knowledge about structure at the atomic level.  When all is said and done, crystallography simply is a special way of looking at structure.

Not all materials are crystalline

Not all substances are naturally crystalline or can be induced to form crystals.  If the atoms in some substance are not ordered at all (i.e., they are randomly distributed), then this material is said to be in the amorphous state.  Examples of amorphous materials we see frequently include liquid water, many plastics, and air.  Inducing the formation of very highly ordered crystals is an essential requirement for structure determination by x-ray crystallography, since amorphous materials do not produce any diffraction spots or rings.

How does crystallography matter to you and me? 

Why do research scientists spend so much time and effort to use the magic of crystallography for determining the atomic structure of many kinds of physical, chemical, and biological materials?  The answer is that this knowledge about structure always provides information about functional capabilities and mechanisms for activities.  As one example, consider what can be derived from new knowledge about the high resolution structure of a virus; this will often increase  understanding about its biogenesis, mechanism for infecting host cells, immunoreactivity, and differences from other viruses.  Knowledge about functional capabilities  always is immensely valuable for both science and industry; for example: functioning of some inorganic catalyst or enzyme (e.g., mechanisms for activity and activation), interactions with other ions and molecules (e.g., changed functioning upon binding), formation of functional complexes (e.g., complex multi-protein assemblies), arrangement to form some more complex object (e.g., associations of 2-D polymers), changes producing specific toxic effects, prerequisites for binding to various ligands. sequential steps in genesis, characteristics of new materials (e.g., nano-materials made in university or industrial labs), etc.

Where can more information be found about crystals, crystallography, and IYCr2014? 

In the year-long world-wide celebration of crystallography and crystallographers during IYCr2014, many very fascinating programs for non-scientists now are being featured on the internet.  A large directory of instructive videos about crystals and crystallography for IYCr2014 is available at:  http://iycr2014.org/learn/watch .  Dr.M gives a rating of ‘outstanding’ to “Diving into the Heart of the Molecules of Life”, which shows how modern protein crystallography is done (http://www.youtube.com/watch?v=GfOyZch6llo ); regardless of which branch of science you prefer, Dr.M encourages everyone to see this video.

The International Union of Crystallography, which coordinates the international congresses on crystallography, has a special area on its website explaining the current celebration of IYCr2014 (see  http://www.iycr2014.org/about/video , and,  http://www.iycr2014.org/about  ).  Other large areas provide a listing of many internet resources and web tutorials dealing with crystals and crystallography; these include educational materials for students and teachers, and, recipes and instructions for growing your own crystals ( http://www.iycr2014.org/learn/educational-materials ).  The American Crystallographic Association has annual meetings that always include a special presentation aimed to instruct ordinary people about crystals and crystallography ( http://www.amercrystalassn.org/ ); this and many other national or regional crystallography societies also feature special IYCr2014 programs on their websites.

Visitors to Dr.M’s website are urged to take a look at any of these internet resources.  You don’t have to be a scientist to love crystals!  The IYCr2014 is for everyone, and that includes you!



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