An article co-authored by several ACD/Labs scientists, the Russian Academy of Scientists, and ChemZoo, Inc. has been generating a lot of interest over the past year.

In fact, this article entitled, "Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream" is the most accessed article of all time, on the Journal of Cheminformatics website.

The news gets better. This article is FREE for your reading pleasure! As per the policy of the Journal:

"The Journal of Cheminformatics offers scientists the opportunity to publish their research rapidly in an open access medium that is freely available online to researchers worldwide. All manuscripts submitted to the journal are subject to rigorous peer review. Published material may include electronic supplementary material, such as animations (e.g. graphical chemical structures) or data (e.g. spectra) that can be downloaded for a reader's use.

The Journal of Cheminformatics aims to work closely with operators of open data repositories such as PubChem. Requests for collaboration are welcome; please contact the Editorial Office."

This motivation for this article was to mark the 40 year anniversary of published developments regarding CASE (computer assisted structure elucidation systems).

It a very interesting read that draws from many meaningful publications on CASE over the last 40 years and tracks history to outline some of the approaches that have been considered, implemented, and successful.

Some of the more significant developments such as fuzzy generation, used to deal with the ambiguity of 2D NMR experiments, as well as the determination of relative stereochemistry of large and rigid molecules with many stereocenters are discussed in this article.

I could spend more time talking about this article, but as I've already mentioned, it's FREE and can be accessed here:

Enjoy and feel free to leave any comments for the authors, and I will be sure to get them. 

This is a continuation of a series of posts that began here.

Here's a short and sweet one.

In my last post, I talked about how having immediate access to the processed data is something that most chemists like. From there, for a lot of chemists the workflow is very simple. Let's just get the integrals looking nice.  Note: They don't generally look nice from automated processing off the instrument unless multiplets are really well resolved and separated.

So for some chemists, re-cutting their integrals and then printing off the spectrum, just might be the peak of their use of an NMR software package.

But what if this very simple process that generally takes no more than 2 minutes could also provide the chemist with much more valuable information about their spectrum beyond integrals?

I'll address that on my next post. 

This is a continuation of a series of posts that began here.

I learned an interesting lesson a few years ago when I was presenting our software on-site to a group of chemists. I began the demonstration by opening up an FID. The response from most of the room was a mix of confusion as well as horror! What is that squigly line you have up on the screen?

It was then I learned that most chemists don't need fancy processing, nor go through the manual steps of FT, baseline correction, phasing, etc. Provided that the sample was prepared and acquired well, the chemist generally doesn't need to do anything fancy to make their ¹H NMR spectrum look reasonable.

This is why in many open access environments that I have visited, chemists are not required to process their data at all. No need to FT their data, nor baseline correct it, nor phase it.

This can be accomplished in a couple of different ways.

You can supply the chemists with processed data from the instrument. In Bruker-speak that's the 1r file. In Varian-speak, it's a phasefile. This is really useful for a chemist because it saves them the additional mouse-clicks for processing data every single time. The only drawback of this approach is that the integrals are usually not all that nice. So a standard workflow for this, is deleting the integrals and re-cutting them a small price to pay, in my opinion.  And of course there are always going to be some cases where the phasing is off, or the spectrum will need some additional baseline correction.

Some other ways, for example, in our software, is to use macros to automatically process the data with one button click. Essentially, you need only create a macro with all the steps set to your liking. Once complete, you can use this macro on all your data. Simply import the FID and click the button. Of course you can also import processed Bruker or Varian files and work with them straightaway in the software. Finally, one of the things we added in the software back in version 10 was Shortcut Mode. With this mode, when you import or drop an FID into the software, it will auto-execute a set of pre-defined processing steps. For example FT, phasing, baseline correction, weighting functions, etc.

All in all, there are a variety of ways to greatly simplify the software interaction for a chemist. I recommend if you are a chemist, or the NMR person responsible for setting up the instrument, that you investigate the possibility of getting direct access to processed data. From there, it's just a matter of cutting integrals, and you're away!

One of the really nice things that has been available in our software for many years has been the ability to characterize multiplet patterns and coupling constants and to quickly generate a multiplet report like this one:

1H NMR (400 MHz, DMSO-d6)  ppm 0.96 (t, J=7.30 Hz, 3 H) 1.27 (t, J=7.18 Hz, 6 H) 1.41 - 1.54 (m, 2 H) 1.71 - 1.83 (m, 2 H) 3.20 (q, J=7.05 Hz, 4 H) 3.26 - 3.31 (m, 2 H) 3.73 (q, J=6.29 Hz, 2 H) 4.45 (t, J=6.55 Hz, 2 H) 7.20 (s, 1 H) 7.47 (ddd, J=8.31, 7.05, 1.26 Hz, 1 H) 7.70 (ddd, J=8.37, 6.99, 1.51 Hz, 1 H) 7.81 (dd, J=8.31, 0.76 Hz, 1 H) 8.09 (dd, J=8.31, 1.01 Hz, 1 H) 9.12 (t, J=5.67 Hz, 1 H) 10.63 (br. s., 1 H)

Now while the generation of this report in this format is as simply as one button click, characterizing the multiplets can be more labor intensive.

In our software you can characterize a multiplet in one of two ways, automatically, or manually. In the automatic mode, with one button click, you can generate multiplet patterns and coupling constants for all of the multiplets in your spectrum. In the manual way, you can generate the peak picking, integrals, multiplet pattern, and coupling constants, by simply left-clicking and dragging over a multiplet of interest. I prefer the latter method (although a close second is to generate them all automatically and then simply go back and check each individual multiplet for errors).

During the development process of Version 12 of our software, based on customer feedback primarily, we took a look at our multiplet analysis routine, specifically at how a user must interact with the software in the case that the algorithm incorrectly characterized a multiplet (due to missed peaks, severe overlap, significant roofing or tenting, etc.)

Let’s consider an example.  I have a multiplet that the software has incorrectly characterized as a doublet of triplets. Instead I want to make this two overlapping triplets. How would you do it pre- Version 12?:

Now in Version 12:

My hope is that, the method to create 2 triplets is MUCH clearer in Version 12.
To come to the decision of how the New Multiplet Analysis Tool should look, we polled a group of people from different backgrounds: Current users, non-users, expert users of our software, novices, spectroscopists, chemists, students, etc.

We provided an example like this one with 5 different prototypes of the J-Coupler dialog box to see which one was the most clear. The new one we implemented in version 12 was obviously first place by a landslide compared to the others. The implementation from version 11 finished dead last in usability testing.

Here’s hoping that you agree!

If you are interested in future usability testing with our software, please drop me a line.