jMol series: Easier? unknown #2

Evaluating data from tools which extend our senses to the nano-scale is going to be increasingly important in a wide range of technical fields in the days ahead. These fields include product support of all sorts, clinical medicine, and crime scene investigation as well as the traditional but growing application areas of materials and biological science, metallurgy, catalyst design/application, geology, and the laboratory study of extraterrestrial materials.

When someone tells a good microscopist (or a good crime scene investigator) what might be present in a specimen, they will try to determine what is actually going on for themselves. With aberration-corrected electron microscopes of the future, one will be able to see nano-particle lattices almost as clearly as that seen in the model below. But even with such views of the specimen, combined with tools that allow quantitative measurement of angles and distances and atom-type in 3D (these are available here, and in development for real microscopes), the job of lattice determination is far from trivial!

In this exercise, you are encouraged to imagine, rotate, zoom, measure, analyze, and perhaps even do image capture and Fourier transforms, but in the end should address this question: How would you quantitatively describe the crystal lattice illustrated below? For example, what is the particle diameter and aspect ratio? (Hint: Double-clicking on two atoms in sequence will draw a scale-bar between them.) Is the lattice cubic, hexagonal, or something else? How about a set of approximate lattice parameters that describe its periodicity? What is its likely space group, and its "conventional" unit cell? Caution: The structure of this particular nano-particle may, or may not, have ever been previously imagined.

Hit reload to view the tilt sequence again, or simply use the mouse to orient the specimen at will.

A curious detective could go further as well. For example, what is your favorite direction for viewing this particle? What atoms is the nanocrystal made up of? What's its stoichiometry? Approximately what is its density in grams per cubic centimeter (or in other words, will it float)? What kind of nearest neighbor environments do the carbon atoms experience? Is there any sign of faceting, or surface reconstruction? Any bulk defects, like dislocations or precipitates? Is this stuff a likely absorber of light in the visible or infrared? Will a single crystal of it be harder, or softer, than diamond?

Ok, so how does one figure all this stuff out from 3D sub-Angstrom resolution data on a single nano-crystal? Let's go through some of the questions: