Dear spinlanders,
I thought I would share with this erudite group the results of the past 6
months of work here at St. Olaf.
As you may know, we have a fully robotic Bruker 400 that allows our organic
students and researchers full 24/7 access to the instrument, both for
experiment submission and analysis. The system has a BACS 120 autosampler,
and has customized hooks into the Bruker TCL code to handle sample
submission and to manage the IconNMR queue. It has been running essentially
flawlessly since 2003, and I think the number of spectra taken since then
here at St. Olaf is on the order of 28,000 spectra (about 3000 per year at
last count). I don't know if that sounds like a lot, but for us, it is.
Heck, we used to do this by hand!
Earlier this summer I asked about the calculation of coupling constants.
The overall synopsis of that is that modern software makes this relatively
painless, with most people printing tables or peak-annotated spectra in Hz
and then taking differences to 0.00 precision and rounding to 0.0. If you
use data that are in ppm, be sure to use 0.0000 precision, not the common
default of 0.000, or you will find your coupling constants oddly
common-factored -- 2.4, 2.8.3.2, 3.6, 4.0, etc. for a 400; 3.5, 4.2, 4.9,
5.6, etc. for a 700. I was amused to go to Organic Letters and within
minutes find just such a report!
Several people replied with lessons about how to "really" get coupling
constant information, beyond the sort of typical organic-lab needs. These
include, for example, apodization and zero filling to round out the data
points. I did a quick check of software that I have, and I noticed that
pretty much what they do is just pick the highest data point to define the
peak center. I decided not to do that. Instead, I decided to go with
parabolic interpolation, which sure seems to do the trick. I'd be
interested in what people think of that. Is this common practice? Does it
compare well with apodization and zero-filling? I'd be interested to know.
Anyway, now we have a way to compare results in case you are interested...
This past summer, we have been working here at St. Olaf to upgrade the
analysis side of OleNMR, integrating into it JSpecView. Our work is now
ready for inspection and comment.
The actual portal is at
http://chemapps.stolaf.edu/nmr
but you would need a St. Olaf password to get in. A working demo version of
the final analysis part, which uses the latest developments in JSpecView,
can be found at
http://chemapps.stolaf.edu/nmr/viewspec2
Several screen shots can be found at
http://chemapps.stolaf.edu/nmr/help
A few sample PDFs are at
http://chemapps.stolaf.edu/nmr/doc
To see where we are headed with this, see
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf .
Features of the system currently include:
-- direct creation of PDF files and/or PDF data (for transmission to the
server)
-- direct printing
-- shift reference adjustment
-- saving of integration and shift changes
-- super easy normalization of integrals
-- full-precision on-spectrum peak listings in ppm with peak differences in
Hz
-- point-and-click coupling constant calculation
-- parabolic interpolation (or not) of peak centers (provides precision
similar to that achieved with zero-filling?)
-- quick emailing of JDX data and PDF results to yourself or one or more
collaborators
-- easy link to original data for use in other software systems
-- saving/sending of notes
-- linked 1D/2D spectra for very fast on-line correlation of multiple
spectra
-- automatic combining of 1D/2D Bruker data based on curdat2 information
-- automatic switching to non-Java (OlenNMR original, limited) version for
iPads and iPhones.
-- help page
Really, this is just for St. Olaf students and faculty, but I thought I
would share it with you. Perhaps it will give some of you an idea of what
is now possible with JSpecView and the sort of fun our students at St. Olaf
are having.
Happy spinning,
Bob Hanson
ps -- One item not on that list is simple 1D phasing. If anyone wants to
give me a few tips on how to do that, I'd love to add that. We deliver
real+imaginary data to the browser.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
Received on Fri Jul 27 2012 - 14:44:29 MST