Ryan's Blog on NMR Software

How do Medicinal and Synthetic Chemists use NMR Software?- Part 6

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

In the previous post of this series, I discussed how chemists can extract multiplet reports in journal format on the fly using the same procedure to re-cut integrals in the spectrum. Well in addition to having this nice reporting tool, the software can make valuable use out of this multiplicity information.

The software has the ability to assist the chemist with the interpretation of their spectrum. It does this by using the NMR prediction algorithms embedded in the software. With the use of these algorithms structure interpretation and verification can be employed.

Essentially when a chemical structure is attached to a spectrum, the software will predict a spectrum in the background and automatically compare the predicted spectrum to the experimental spectrum. To do this automatic evaluation, the software will compare three properties between the spectra:

1) Chemical Shift
2) Integration
3) Multiplicity information

As a result, by re-cutting your integrals in the software (and hence defining multiplet patterns and coupling constants) the software will use this information to help a chemist interpret their spectrum. Specifically, it will use this information to provide the chemist with immediate feedback as to what atoms in the chemical structure a multiplet is consistent with. See the movie below:

How do Medicinal and Synthetic Chemists use NMR Software?- Part 5

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

In my last post, I promised to address how, by simply spending 2 minutes re-cutting their integrals, a chemist can extract much more valuable information from their spectra.

The #1 thing in our NMR software that blows chemists away is the production of the following:

¹H NMR (DMSO-d6) Shift d: 7.90 - 7.95 (m, 2H), 7.79 (s, 1H), 7.45 (d, J = 8.6 Hz, 1H), 7.33 (dd, J = 8.6, 1.8 Hz, 1H), 4.30 (q, J = 7.1 Hz, 2H), 4.21 (q, J = 7.1 Hz, 2H), 2.53 (s, 1H), 1.25 (t, J = 7.0 Hz, 3H), 1.24 (t, J = 7.1 Hz, 3H)

To elucidate and format this information for experimental sections in patents, reports, and publications, this is a very time consuming process by hand.

Can software make it easier?

This capability has been available in our software for a long time. However, in older versions of our software, while it was much easier than doing it by hand, it was a little time-consuming and not obvious how to do this. For example you would have to first pick your peaks in peak picking mode, then you would have to integrate those peaks in integration mode, and finally you would enter Multiplet Mode and create those multiplets. 

As I've already mentioned, Chemists like to re-cut their integrals to make them look nice and normalized. Well now, when chemists do this procedure they are also peak picking and defining multiplet patterns and extracting coupling constant on the fly. Below is an 11 second video clip showing this capability in action. 

Prior to the implementation of this feature, using our software to create these reports was something that was done around patent-writing time. If a patent was being written and experimental sections were needed, the chemist would go back to find their old spectra, and create these reports then.

Now that this process is so quick, easy, and intuitive, I've talked to many chemists around the world who are creating multiplet reports for virtually every spectrum they acquire. They can then paste their multiplet information in a report or ELN, and it will save them time in the patent writing process down the road. And that's not the only benefit chemists can potentially get from extracting this information each time they acquire a spectrum. I'll talk about another, next time.

I wish all the Moms out there a Happy Mother's Day!

How do Medicinal and Synthetic Chemists use NMR Software?- Part 4

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. 

How do Medicinal and Synthetic Chemists use NMR Software?- Part 3

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!