From FID to Structure in 30 Minutes? Investigating the CASE Limiting Step

December 8, 2009

by Ryan Sasaki, NMR Product Manager, ACD/Labs

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In yesterday’s post I pointed you to an article that has become the most accessed article of all time in the Journal of Cheminformatics, co-authored by representatives of ACD/Labs.

This article is a very comprehensive outline of the different approaches, developments, and successes of the development of CASE (Computer-Assisted Structure Elucidation) systems . I hope you agree that this technology has come a very, very, very long way, to the point that there are many spectroscopists around the world using ACD/Structure Elucidator routinely to identify unknowns in thier labs whether they be natural products, impurities, degradants, metabolites, etc.

Anna Codina from Pfizer is an example of just one of those users. She has been a long-time user of Structure Elucidator, and one of the very best in the world. She, along with her group, has really stretched the limits and applications of the software and has also been instrumental in the ongoing improvement of this software over the years.

At SMASH 2009, Anna shared some of her most recent experiences with the software in a presentation entitled, “From FID to Structure in 30 minutes?” This presentation can be accessed here.

For this presentation, she wanted to see whether it was possible to do a full elucidation starting from the raw data, all the way to the solution in less than 30 minutes. She was able to achieve this with several of her in-house Pfizer compounds, and then, for the purposes of this presentation reproduced these findings with compounds she could share in a pubic forum.

In this presentation she goes through 3 such examples.

The most interesting piece for me was her discussion regarding the CASE limiting step in slides 9 and 10.

In an ideal world, we would be talking about completely automated structure elucidation. Of course, we are not quite there yet, but it is still a dream, as Elyashberg et. al refer to it in the J. Chem. Inf. article.

In the meantime, the process generally involves some manually handling of the data. For this process the general principle applies, “Garbage IN- Garbage OUT”

So the quality of data as well as the peak picking of said data is crucial.

The peak picking of multiple spectra is what Anna was referring to as the CASE-limiting step. We have made tremendous strides over the years to simplify this process as much as possible (Check out the demonstration movie here). But the traditional argument seems to still apply for some:

Why would I spend so much time peak picking all my 2D spectra?

By the time I finish picking and grooming the data, I have already solved the structure, so what’s the point?

I will try to address these questions in a different post, but in the meantime, what’s Anna’s answer?

NMR Workbook, and specifically the NMRSync technology that we developed and released late last year. Note, that NMR Workbook is included with ACD/Structure Elucidator.

Anna proclaims that thanks to NMR Workbook, there is no longer a CASE-limiting step. With syncrhonized peak picking which carries through peak picking applied in one spectrum, to all others associated with the sample, the time spent to prepare the data is drastically reduced and is more consistent with the natural workflow.

For those unfamiliar with NMR Workbook and the NMRSync functionality, I introduced it on the blog about a year ago:

http://acdlabs.typepad.com/my_weblog/2008/12/if-all-of-these-spectra-are-from-the-same-compound-why-am-i-handling-them-all-separately.html

If you want to skip right to the demonstration go here:

http://www.acdlabs.com/products/spec_lab/exp_spectra/nmrworkbook/movie/NMRWorkbookFlash.htm

This product has turned out to be immensely popular and has evolved a long way in just one short year. Admittedly, it’s probably been the biggest reason I have not been blogging as much over the past year, I have been touring the world showcasing this product, as well as our other solutions.

I hope over the next little while I can dive a bit more into the details of the product.

Stay Tuned.

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