Ryan's Blog on NMR Software

False Negatives and False Positives are Waiting...

Great post from Derek Lowe from In the Pipeline the other day talking about the dangers of not quality checking those fine-looking starting compounds for your project. Chemistry happens and yes, mistakes do too.

In fact, it appears that Derek has been on a kick as of late referring to personal QC.

I Can Has Ugly Molecules?

Oops.

I thought this would once again be a good opportunity to provide you with a link to a poster Sergey Golotvin presented at ENC 2008 entitled, "Validating the Quality of Large Collections of NMR Spectra Automatically".

Long story short, 15,000 1H NMR Spectra from the Aldrich collection were evaluated in complete automation and the software was able to confirm 88% of the collection as having chemical structures that were consistent with the respective spectra. In addition, 4% were flagged by the software as being inconsistent. A closer, manual look at those 5% revealed that there were indeed some truly wrong structures (or incorrect tautomers) in the collection.

This was evaluating the 1H NMR data only. Using additional 2D experiments, such as HSQC, will likely improve these results.

Just an example of a check an organization can build into their process for additional QC of their registration database for example.

Is it perfect? Absolutely not. There are perhaps a few more false positives in there that the software didn't catch, and of course the software provided some false negatives as well, annoying because presumable someone has to look over them manually only to realize that they were indeed the right structure all along. But at least this doesn't involve manually pining over 15,000 spectra!

We continue to run these datasets, and actually have a consortium consisting of several NMR experts in the industry we call ASCI (Automated Structure Confirmation Initiative) where we are testing and validating this technology in the real pharmaceutical world. Identifying the common areas where false negatives and false positives occur and trying to address them with algorithms.

Will we ever solve all the problems, especially in the world of novel chemistry? Of course not, and for that matter there are some existing problems that appear to be too hard to solve.

But that being said, what is the acceptable limit of false positives and false negatives for automated verification by software for the verification of  registered compounds in a library?

Interested in hearing your thoughts.

Looking for a Great Weekend Read?

In fact, to borrow a phrase from a colleague, this might be the defacto article on Computer Assisted Structure Elucidation (CASE) for the next decade!

This article written by Mikhail Elyashberg, Antony Williams, and Gary Martin spans across two issues of the review journal, Progress in Nuclear Magnetic Resonance Spectroscopy. 

This article entitled, entitled, "Computer-Assisted Structure Verification and Elucidation Tools in NMR-based Structure Elucidation" is available online and you can review a preview of the content at:

http://dx.doi.org/10.1016/j.pnmrs.2007.04.003

This is a very important and comprehensive review of modern expert CASE systems over many years. It includes specific examples of complex natural product structures that have been automatically elucidated using such systems.

I thank the authors of this publication for their contributions in this area, and the efforts they have now put forth to communicate this story to the scientific community.

Please obtain a copy for yourself, I can promise that it is a very informational and intriguing read for those of you who do NMR regularly.

Automated Structure Verification by 1H NMR Only

I've blogged several times about the progress and applications of automated structure verification with the help of ACD/Labs software.

There are really two main approaches right now:

1. Combined verification which includes automatically verifying the correspondence between a proposed chemical structure and the 1D ¹H and 2D HSQC spectra. I've blogged about the publications and applications of this method previously.
2. ¹H only verification. Of course the first approach is preferable from an accuracy standpoint as the additional information gained from the HSQC spectrum increases the selectivity and specificity of the results.

However, I always get questions on how well we perform on ¹H NMR only because in some organizations and environments it is simply not feasible to always run an HSQC in tandem with a routine ¹H NMR analysis.

As mentioned in previous posts, we've already conducted a validation study on this approach and it was published in a 2006 article in MRC. We've continued to investigate and validate this approach and we recently presented our latest results using 1D ¹H NMR data only at ENC 2008.

The poster highlighted a study on the automatic evaluation of over 15,000 Aldrich compounds and spectra from Aldrich NMR Spectra Database.

The results of this study revealed that the software was able to confirm 88%of all spectra as consistent and flagged less than 5% as inconsistent.

One of the more interesting discoveries in this study was that it revealed some truly wrong structures in the Aldrich NMR database.

More information on these as well as shortcomings in prediction, processing, and analysis are provided in the poster that can be downloaded:

http://www.acdlabs.com/download/publ/2008/enc08_aldrich.pdf

Do You Run 15N, 19F, and 31P Experiments?

As I am closely approaching my one year anniversary of this blog (how time flies!), Arvin's post entitled, "How Do I Know if my Unknown Contains a Fluorine Atom",  reminded me an X-nuclei related post from almost a year ago.

In that post I highlighted a best practice document written by Gary Martin for acquiring ¹⁵N-¹H heteronuclear shift correlation data where he highlights an interesting application for ¹⁵N NMR prediction.

If you think that only benefits of a ¹⁵N NMR Predictor is for structure verification or validation, Gary is providing you with some additional tips and suggestions.

Check out his document here.

I want to personally thank Gary for his incredible contributions to the NMR community as well as for his guidance, collaboration, and contributions to the ongoing development and growth of ACD/Labs software.

Avoiding the Love/Hate Relationship in Software

I had a conversation with Geoff, one of my ACD/Labs colleagues just yesterday.

He provided me with a great quote from a person he was talking to about software and usability.

He said:

"User-Friendly...hrmph...what that means to me is: love it for the first week, hate it forever!"

I think that's a great quote.

I think usability is incredibly important and should take high priority in the development of a software package.

However, while it is important we can't forget the term USE in "Ease of Use"

I find a lot of software packages out there that are very pretty, very intuitive, and very easy to use. They make a great first impression. You can use it for few days and fall in love. However, often times what happens is that after a week you decide you want to do more sophisticated things with the software but you can't. All of a sudden that love, turns to frustration, and sometimes ends up in hate.

I think this is one of the more difficult aspects of software development. I think most Product Managers and developers want their products to be easy to use. But you can't go overboard and oversimplify.

We went through the simplification process with the development of ACD/1D NMR Assistant. In the very early stages, we thought it might be a good idea to create a 1D NMR Processor Lite for chemists. We knew that 1D NMR Assistant would have the same NMR processing component as ACD/1D NMR Processor. But we also came to the conclusion that the interface and workflow in a duplicated form would not be appropriate for a new market, after all ACD/1D NMR Processor was developed for years with the NMR Spectroscopist in mind as they were the ones using it, providing feedback, and NFRs (New Feature Requests).

So while ACD/1D NMR Processor contains many features we don't anticipate most chemists will make use of (a quantitation tool, macro capabilities, group macro capabilities, intelligent bucketing, multiple baseline and phase correction algorithms, arithmetic, peak fitting, etc.) we decided to leave EVERYTHING in there. Perhaps 1 in 50 will become frustrated when their software can't execute a particular function for them, we're hoping we've avoided this issue by including all the features available in 1D NMR Processor within the Assistant package.

Using NMR for Quantitative Analysis

Do you currently use NMR for quantitative analysis?

At the University of Ottawa NMR Facility Blog, Glenn Facey provides some acquisition tips for ¹H NMR spectra.

If you perform quantitative analysis on your spectra, how do you do it? Do you do it manually by hand, or do you use some software to help?

I am not sure how many of you are aware of Quanalyst, a quantitation tool available in ACD/1D and 2D NMR Processor that can measure different spectral attributes and automatically measure the result.

For example, some common applications of the tool are to:

• Calculate the ratio of components in a sample mixture. ( I think this application is especially useful for those in the chemical industry)

• Reaction Monitoring

• Finding and quantifying a multiplet for a specific atom

• Quantifying coupling constant changes in a specific multiplet across a series of spectrum

Here are a couple of application notes available that describe a few of the different applications of Quanalyst:

Reaction Monitoring with Quanalyst (PDF)

Optimizing the Process of Quantifying: From Manual to High-Throughput (PDF)

I will also provide you with a link to an old movie on Quanalyst from an older version of ACD/1D NMR Processor that I still think will give you an idea of how Quanlyst works. Note, if you can't view the movie, you can download it here.

Perhaps it's time for a new version of this movie!...I'll try to get to that and share it with you.

In the meantime, if you are currently doing quantitative analysis, I invite you to share your thoughts, insights, workflows, etc. in the comments section.

Download a Trial of ACD/1D NMR Assistant!-Expired

This offer is now expired.

Let's See your Printed Spectra Do This!- Part 2.

Back to the chemists with their ELN who continue to resort to their paper spectra.

Is it just an old habit?

No. I think it is something else. In fact I think there are two major (and completely understandable) reasons why some chemist continue to resist the complete transition to the electronic world:

1. One of our users who I really enjoy speaking with when I get a chance once told me, "The only way you are going to get chemist to fully adopt these tools is when they can access and interact with the spectra JUST as fast as they can do it on paper." I think it's a great point. For some chemists having to sit in front of a new piece (or old piece) of software to try and get your data out can be a daunting task. But I think significant strides have been made in this regard. With the transition to open access, NMR Spectroscopists have done a nice job (in conjunction with software vendors) to automate processing and create software macros to provide chemists with access to fully processed spectra. In addition, I think that the usability of NMR software for manual processing (See Shortcut Mode for example) has greatly improved over the years, but there is of course still work to do.
2. I think the other reason is that perhaps the benefits associated with electronic handling of NMR data have historically been not convincing enough or educated clearly enough to the user. For example, I have beaten the multiplet report topic to death on here, but I am continually amazed by the number of chemists who have had our software for a long time that aren't aware of this feature.

But perhaps easy access to data from your desk and formatted multiplet reports is not enough for a chemist to let go of the paper and embrace the electronic world. In fact, I am convinced it isn't. After all, an NMR spectrum is a means to an end. Sure, the delivery of the results in a readable form in a convenient place is essential and it has increased producitivity in open access environments, but the bottom line is that there is a reason the chemist ran an NMR experiment. In most cases that reason is to determine if their compound's proposed structure is consistent with their spectrum. Historically, NMR processing software has not provided any assistance in regards to data interpretation. 

I am hoping that ACD/1D NMR Assistant addresses this challenge and finally convinces the chemist to let go of their paper spectra for good and fully embrace the electronic world. To see how 1D NMR Assistant helps chemists interpret and assign their ¹H NMR spectra check out my previous vlog postings (with video) here and here.

Are You Attached to the Paper Printouts of Your Spectra?-Part 1

This is the topic I will be presenting on at our annual ENC Symposium on March 9, 2008. If you happen to be attending this conference in Asilomar, check out the agenda and register here.

I mentioned this before, but I follow the Depth-First Blog authored by Rich Apodaca rather closely and I highly recommend it.

I mention it again because Rich had a very interesting post a few weeks back inspired by a discussion about Electronic Lab Notebooks (ELNs) that took place on Derek Lowe's In the Pipeline Blog (which is another blog I follow frequently and highly recommend!)

Fascinating posts and discussion for sure!

Rich notes:

The wasteful process of entombing valuable scientific data often begins with the paper lab notebook, so the subject of ELNs should be of great interest to anyone involved in creating, using, or reprocessing chemical information.

Why do paper notebooks continue to persist in chemistry?

The issue is complex, but in my view stems from the lack of a truly usable and affordable tool. Although the term "tool" may suggest software, it actually involves a much more complex beast consisting of hardware, software, an ergonomic hardware/software user interface, and a computer network. In chemistry, the problem is compounded by the centrality of chemical structures and the inability of most generic ELN products to capture or use them. Given these constraints, and the costs associated with creating and marketing general-purpose products designed to work within them, it's not surprising that many organizations decide to roll their own ELN. And it's even less surprising that many others decide sticking with paper is a better option - at least for now.

I think this is a good argument, and I want to add to it with the question, "Why does paper spectra continue to persist in chemistry?"

Personally, I am amazed by the number of times I have encountered groups who are already using ELNs, but are still routinely using paper spectra. Sure when the time comes to attach their PDFs (Rich has shared his feelings on this format as well, but that's an entirely different discussion!) to their notebook records, they will extract the electronic file, but until that point many chemists will walk back to the instrument room, pick up their data printout, study it, and then toss it in the recycling bin or toss it on their bench!

For example, I was recently visiting with some chemists in the pharmaceutical industry who were providing me with feedback on our products and discussing their workflow. They mentioned that while they religiously use the desktop NMR processing software for viewing, processing, analysis, interpretation, and reporting to their ELN right on their laptops, in their lab...many chemists from their group still make the walk to the instrument room for their piece of paper instead.

Paperless environment?

Old habits, I guess.

Why use a piece of paper when you can access the data electronically? Meaning you can zoom in and zoom out on regions of the spectra to take a closer look? I guess in most cases, you don't really need to do that but in many labs where the data can be accessed electronically on a laptop in your lab, why make the walk back to the instrument room for that piece of paper?

What are your thoughts? Are you still attached to the paper printout? If so, why?

I'll share my opinion in part 2 of this topic tomorrow.

New Blog by Arvin Moser

Those of you who are current users may recognize the name Arvin Moser as he has spent many years as both a Technical Support Specialist and Application Scientist at ACD/Labs.

Arvin has decided to start a blog and share his knowledge and experience about structure elucidation. I think this blog promises to be a very interesting one as Arvin has a wealth of experience in both manual and computer assisted structure elucidation (CASE).

From Arvin's About Page:

My goal is to focus on the science of data interpretation and structure elucidation. I would like to pass on my experiences including what I have learnt from the experts. By sharing these experiences with the scientific community, I think an emerging elucidator can be better equipped with handling anything that comes their way.

Visit Arvin's Blog here.