[Sorry for the blog-like nature of this message. I'm not ready to blog yet
-- maybe Henry Rzepa can take this on :) ]
I have just come back from the IUCr World Congress meeting in Montreal
conference: http://www.iucr2014.org
presentation: http://stolaf.edu/depts/chemistry/bh/iucr2014
and the SMARTER 4 conference in Durham UK
conference: http://www.ccpnc.ac.uk/smarter4
presentation: http://stolaf.edu/depts/chemistry/bh/durham2014
[Note that That is not meant to be self-explanatory, but the pictures are
pretty!]
Now back to normal life after 15 months of sabbatical during which the main
foci ended up being
(a) database integration with Jmol and
(b) crystallography,
I thought I would give a bit of update on (b). I won't cover everything
here. Just get a discussion going.
XRD and XRPD
Jmol is thriving like never before. It has been embraced in all areas of
chemistry, in materials science, in computational physics, and in
crystallography (both single-crystal [XRD] and powder diffraction [XRPD]).
We are really having a very broad impact on science!
XRPD, in particular, has made many advances recently, and is now providing
full structure models, just like XRD. Estimates I heard were in the range
of roughly 100 new XRPD structures per year, and growing.
Jmol is the preferred viewer in this area because it can handle all aspects
of CIF file structure definition.
3D EDT
If you do not know about the emergent field of Precession 3D Electron
Diffraction Tomography <http://www.edt3d.com/> [3D EDT], you might want to
do some Googling. See, for example,
http://www.microscopy-analysis.com/magazine/issues/structure-determination-nanocrystals-precession-3d-electron-diffraction-tomography
Expect one or more Nobel prizes in this area. It is set to totally
revolutionize crystallography.
The basic idea is that it is now possible to take a nanocrystal, place it
in the vacuum of a *standard *scanning electron microsope, and record the
diffraction of electrons from it at various beam angles. The phrase "anyone
can do it" is not far off. The results can be integrated to get unit cell
measurements in minutes and atomic resolution crystal structures after
further analysis. Software is still under development, but it is likely
that Jmol will be a significant part of that.
[3+n]D
Jmol is one of just a few software packages that can be used to
visualize *incommensurately
modulated* crystal structures, which can be understood using higher
dimensional space groups (4D, 5D, thus [3+n]D where n=1 or n=2). see
http://infoscience.epfl.ch/record/183336/files/aperiodic_structures_infoscience.pdf
These are crystal structures that have unit cells, but each one is slightly
different. It's really not so difficult to understand why that might be. A
classic case is a "misfit layer" compound. See, for example, <
http://www.mdpi.com/1996-1944/3/4/2606>.
These crystalline compounds have two or more semi-independent unit cells.
Each unit cell is "incommensurate" with the other -- one or more of its
dimensions is not a multiple or rational fraction of the other -- so they
never line up, and since they are in the same physical crystal, the
presence of one "modulates" the structure of the other.
There aren't a lot of these structures around, but their numbers are
growing as crystallographers become more familiar with the new techniques
and software tools that are being developed that can be used for structure
solving and visualization.
The images you can create of these systems using Jmol are stunning and
informative. I'm pretty sure there is absolutely nothing else like Jmol out
there that can do this sort of thing. Expect Jmol integration into
"standard" processing programs used in this area (such as Jana2006) soon.
I had better stop there for now....
Bob
-
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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