The issue of shift prediction in different solvent environments could be
very useful. In monitoring reactions by H NMR we have observed significant
reproducible shifts over the course of a reaction, presumably because of a
change in the composition of the solution.
On 9/15/07, Christoph Steinbeck <[EMAIL PROTECTED]> wrote:
>
> Peter,
>
> thanks very much for the interesting posting.
>
> Warren Here from Wavefunction has been calculating Spektra for all
> NMRShiftDB structures using Spartan on Hartree-Fock level. We have a CD
> with all of them (Stefan, is that right) but we never got all the
> information on the format, I think.
>
> I myself have been calculating about 2000 Gaussian spectra for
> NMRShiftDB on a 16-node cluster which came for exactly this purpose with
> my NMRShiftDB grant.
>
> BTW, there has been an interesting article on the topic:
>
> Structure Validation of Natural Products by Quantum-Mechanical GIAO
> Calculations of 13C NMR Chemical Shifts
> Giampaolo Barone, et al.
> Chemistry - A European Journal
> Volume 8, Issue 14 , Pages 3233 - 3239
>
> I would suggest an extended protocol, which slows down things a bit but
> make a better research project: We should start with the generation of a
> number of lowest energy conformers (probably not for molecules like
> alpha-Pinene, http://en.wikipedia.org/wiki/Alpha-Pinene), but for more
> floppy compounds, do a Gaussian calculation for each of them and try
> averaging shifts.
> The protocol will be a bit more fragile, though, I guess.
> Another issue will be if there is an option for simulating polar
> solvents and their effects on the shifts?!
>
> There seems to be a general agreement that you get best results with
> calculating both the geometry optimization as well as the GIAO shifts on
> B3LYP/6-31G(d) level, but I trust whatever Henry suggests :-)
> With my own Gaussian calculations, I got excellent results for rigid and
> unpolar compounds, just as Barone suggested in his paper.
>
> Please let me know if I can help.
>
> Cheers,
>
> Chris
>
>
> peter murray-rust wrote:
> > Is the NMRShiftDB list active?
> >
> > Here's what we want to do anyway...
> >
> > It is now possible to compute the 13C chemical shifts of organic
> > compounds to an exciting degree of accuracy. Henry and I were talking
> > about this yesterday and if the compound is fairly rigid the results
> > are believable enough to assign most peaks and to correct errors.
> >
> > We want to apply this method to as many spectra in NMRShiftDB as we
> > can. It will be limited by time, flexibility and lots of scientific
> > effects that we haven't thought of and which will be discovered by the
> process.
> >
> > The MW limit is ca 500 (several days) though we'd prefer smaller ones
> > to start with in which case they might take half a day each. Nick Day
> > has already setup an effective workflow for crystals from crystalEye
> > and runs these on much the same timescale - we have processed many
> > thousand jobs on the Condor system. We now have Gaussian which -
> > according to Henry - should be easy to configure.
> >
> > Nick is finishing the experimental part of his thesis and this would
> > form an interesting final piece.
> >
> > So what we have to do is (and it must be automatic)
> > * extract spectra and connection table from NMRShiftDB
> > * generate 3D coordinates
> > * generate Gaussian input according to Henry's protocols.
> > * run the jobs on Condor (or elsewhere)
> > * collect the output
> > * parse into CML
> > * expose the results on our web site (this is where the Open Science
> comes in).
> > * annotate the results (humans and machine)
> > * display the results (primarily agreement between observed and
> > calculated values, but also much else).
> >
> > The immediate difficulties we can see are:
> > * not knowing the stereochemistry. *** WHAT IS THE POSITION IN
> > NMRSHIFTDB? We can filter out anything that has more than one
> > potential stereocentre.
> > * assumptions about completeness of data in NMRShiftDB
> > * syntactic problems (almost certain to occur in any large data set)
> > * generating initial 3d coordinates. There are several simple
> approaches:
> > - look up the moiety in crystaleye
> > - join moieties in crystaleye
> > - use CDK - I think Christoph had something here?
> > - use the 2D coordinates for "flat" molecules
> > *** NEW APPROACHES - MUST BE BLUEOBELISK
> > * optimising the coordinates. Probably a cheap level of theory (PM3)
> > would work.
> > * parsing the Gaussian output (though JUMBOMarker has already been
> > tuned for some Gaussian jobs). It may also be that the archive is enough
> > * scale. After a few hundred jobs SOME effect of scale will hit us.
> > We don't know what but every project of this sort has these scale
> problems
> > * wikifying the results. Ideally we like to expose the results in a
> > very similar way to crystaleye with 2D and 3D coordinates and with an
> > observed/calc graph. Then we have to protect against spam.
> > Suggestions would be welcome
> >
> > At present I'd like to know of any immediate problems that we haven't
> > thought of. If not I suspect Nick will simply download all the data.
> >
> > Compute resources are probably not the problem at present. But later
> > we may ask for volunteers.
> >
> > If this is a success there is a much wider vision. You don't need me
> > to spell it out, and it's probably a good idea to keep things low key.
> >
> > P.
> >
> >
> >
> > Peter Murray-Rust
> > Unilever Centre for Molecular Sciences Informatics
> > University of Cambridge,
> > Lensfield Road, Cambridge CB2 1EW, UK
> > +44-1223-763069
> >
> >
> >
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>
> --
> PD Dr. Christoph Steinbeck
> Lecturer in Chemoinformatics
> Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
> Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
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