Wow!! Thank you for the update and the glimpse into a busy present and a
promising future.
(‘The world of Jmol’, nice title for an ongoing story)
Jaim
On Sep 4, 2014, at 2:53 PM, Robert Hanson
<[email protected]<mailto:[email protected]>> wrote:
[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<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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