Ryan's Blog on NMR Software

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.

Love/Hate Continued...

To follow my post from yesterday, Rich made a very interesting comment that I was hoping to address in today's post.

He suggests that perhaps a NMR Lite would be a good approach. I gave reason as to why we didn't take that approach and strip away existing features from 1D NMR Processor when developing the processing component in ACD/1D NMR Assistant yesterday.

But Rich makes a very good point in his comments:

For everyone else, it's all too easy to not even look at a piece of software who's fundamental purpose is obscured by layer upon layer of expert features. They just tune out and the only ones who end up using the software and giving feedback are the power users - which unfortunately reinforces the misconception.

For me, the key is to make sure that all these features don't get in the way of the primary reason someone is using the software. I don't have a problem with a wealth of features as long as it does not interfere with the main workflow.

Cathy Sierra is a blogger that I dearly miss for her daily insight on how to "create passionate users". Here's one of her takes. Specifically I like:

One of the themes I heard over and over at ETech and SXSW (Jason Fried, Craig Newmark, and others) was the developer mantra of "get out of the way." In other words, build the thing so that it stays the hell out of the way and lets the user get on with what they really want to do.

 

So as an adaptation of Rich's comment. Make the 20% REALLY clear, and hide the other 80% but still offer it.

I'm not sure it's the perfect solution, but I think it's a different approach.

For example, here's the first thing a user will see when they open a raw data file in 1D NMR Processor:

On the other hand, here is ACD/1D NMR Assistant:

Of course you don't want to create an environment where a user is drilling through menus looking for useful features, but we do provide users with the ability to hide or show toolbar buttons and action buttons on the interface so they can choose the interface most appropriate to them which can be altered as they get more comfortable with the software.

What do you think Rich?

Anyone else have an opinion they want to share in the comments section?

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.

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.

Dereplication? Version 11- Searching PubChem using ACD/Structure Elucidator

This resource will likely only be useful to readers who are currently using ACD/Structure Elucidator, however, I do have two questions for my general audience and I would greatly appreciate your comments.

First things first, a technical note has been created to explain how to install and search the PubChem Database. It can be downloaded here:

http://www.acdlabs.com/download/technotes/110/nmr/pubchem.pdf

You'll notice in the introductory paragraph of this technical note it uses the term "dereplication" to describe the process of searching a spectral database with the NMR data of an "unknown" prior to elucidation.

Can this process REALLY be called Dereplication?

How do you define the term, "dereplication"?

The first hit from Google (not necessarily the most accurate) provides the following definition:

De`rep`li`ca´tion

the process of testing samples of mixtures which are active in a screening process, so as to recognize and eliminate from consideration those active substances already studied; - a stage subsequent to the preliminary screening in the process of discovery of new pharmacologically active substances in mixtures of natural products; - also called countersceening.

I think this is a reasonable definition based on my understanding of the process.

A few years back, I did quite a bit of research talking to some natural products scientists to try and uncover this idea. I got various different views on the topic and the definition of this term and it's applications. A common response that I got was something like:

"If it is an unknown compound, and I am able to use spectral databases to identify known compounds prior to elucidation, I'd call that dereplication"

And there were this valued added comment:

"If I am able to identify known compounds using a NMR search method, and avoid even two repeat elucidations per year, that's incredibly valuable"

Probably the best, and most comprehensive responses I got were:

"Usually dereplication is done as early as possible in the process. If you have already isolated the compound to NMR purity most of the costs have already been incurred. Typically LC-MS and/or LC-UV on an early crude subsample is the most cost effective. However some pharma use LC-NMR, and using this technique is where NMR database searching can reap rewards."

"Dereplication is done on only a small crude sub-sample of the organism/extract long before large-scale isolation by chromatography is performed. Dereplication only makes sense at an early enough stage in natural product discovery to prevent the high cost isolation chemistry from being undertaken. Hence, only early stage dereplication makes business sense. It would be better to classify dereplication based on the hyphenated techniques. Your late-stage dereplication is really known structure matching/identification - a worthwhile and necessarry pursuit as dereplication is NEVER perfect."

"Searching databases by NMR prior to an elucidation represents dereplication in only some laboratory instances. This workflow would work very well in those laboratories that employ employ LC-NMR as a tool for the separation of natural product extracts. A fraction's NMR spectrum can automatically be searched in a database to identify isolates that contain known compounds. However, this type of analysis is not done in all research labs. Therefore, without this type of analysis, the major costs of natural products research are generally incurred prior to NMR analysis. NMR is introduced as an elucidation tool after separation and purification. A combination of LC-MS and LC-UV, for example, can be used effectively for dereplication purposes as MS can provide an accurate mass and structural information and UV can provide insight on existing chromophores and a compound's structure."

It appears that hyphenated techniques are likely the key to dereplication.

Some good work has be done here using LC-UV-MS, for example:

Merck in NJ:

http://www.massspec.com/downloads/ASMS2006_Poster_Zink_TuP313.pdf

http://www.cosmoscience.org/pdfs/Session%20IV_Presentation%20I_Zink.pdf

Microbial Screening Technologies developed an in-house, metabolite recognition software called COMET that compiles and analyses co-metabolite patterns in natural product mixtures:

http://www.microbialscreening.com/

Dereplication using LC-NMR:

http://www3.interscience.wiley.com/cgi-bin/abstract/76509553/ABSTRACT
http://www3.interscience.wiley.com/cgi-bin/abstract/110574737/ABSTRACT

The late, great John Faulkner once said in a Philosophical Basis for Structure Elucidation:

"The problem with using NMR for dereplication is that no reliable method of searching NMR spectral libraries  has yet been devised, although there have some attempts to construct and search ¹³C NMR libraries. It is possible that computers will, in the future will be able to recognize and compare the patterns that are found in NMR spectra but that seems a long way off."

I think that computers can do this now. But what to call it?

Can an NMR DB search be termed dereplication?

Should it be positioned around and to only those people who use LC-NMR?

What do we call the discovery of known compounds by NMR prior to structure elucidation?

Provide your own thoughts on this.

What's New in Version 11- Improved Multiplet Analysis

In case you didn't know, version 11 of ACD/Labs software was released in November of 2007.

While there are several updates to the software over the course of a year, a major new version of each of our NMR products is released on an annual basis.

Over the next couple of weeks on this blog, I will try to mix in some new features and improvements that have been implemented in version 11.

First up, I'll talk a bit about improvements in the automated multiplet analysis algorithm in ACD/1D NMR Assistant, ACD/1D and 2D NMR Processor, ACD/1D and 2D NMR Manager, and ACD/1D and 2D NMR Expert.

For those unfamiliar with this process, automated multiplet analysis refer to the use of a software algorithm that automatically characterizes coupling patterns and extracts coupling constants from multiplets in an NMR spectrum.

The most popular application of this feature is that it provides an incredibly fast way of generating a formatted multiplet report for patents and publications:

¹H NMR (400 MHz, DMSO-d₆) d ppm 2.34 (dd, J=15.97, 8.06 Hz, 1 H) 2.64 (dd, J=16.05, 5.35 Hz, 1 H) 3.81 (tt, J=7.71, 5.33 Hz, 1 H) 4.47 (d, J=7.47 Hz, 1 H) 4.87 (d, J=5.13 Hz, 1 H) 5.68 (d, J=2.20 Hz, 1 H) 5.88 (d, J=2.34 Hz, 1 H) 6.58 (dd, J=8.13, 1.98 Hz, 1 H) 6.68 (d, J=8.06 Hz, 1 H) 6.71 (d, J=1.91 Hz, 1 H) 8.

So how well does this automated algorithm perform in Version 11?

Significant development efforts were put into improving the automated routine for Version 11 and I will present the results of a direct comparison to version 10 of the software.

For this study, two different data sets each consisting of the ¹H NMR spectra of 30 samples were studied (~250 multiplets in total).

Test Set 1- A set of 30 spectra (~250 multiplets) with reasonably good signal to noise:

We ran the automated multiplet analysis routine on all 30 spectra and got the following results in Version 10:

In version 10, 53% of the multiplet patterns in the spectra for the 30 samples were correctly defined, 32% were undefined, leaving 15% that were incorrectly defined. Multiplets that are termed as undefined are simply given a "m" designation for multiplets. In standard practices and manual analysis the "m" designation is often assigned by users to multiplets with unresolved peaks, often due to strong coupling.

Version 11 Results:

As you can see, while the number of correctly defined multiplets increased by 5%, the most notable observation is the reduction of incorrectly defined multiplets from 15% to 1%.

Test Set 2- A set of 30 spectra (~250 multiplets) with lower signal to noise:

 

Version 10 Results:

Version 11 Results:

As you can see in the second study, we did sacrifice some correctly defined multiplets (6%), but we were able to reduce the number of incorrectly defined multiplets significantly from 14% to 3%.

So how does this improved accuracy impact the end user?

First of all, this will result in significant time savings with more accurate automated multiplet analysis and report creation for spectroscopists' and chemists' patents, publications, etc.

But perhaps of more scientific relevance, is that improved automated multiplet analysis heavily impacts both the performance of automated structure verification in ACD/1D and 2D NMR Expert, as well as the structure verification algorithm included in ACD/1D NMR Assistant.

How much impact are we talking about here?

Stay tuned, it will be the topic of my next post.

If you are currently using Version 11, try it out, and share your results in the comments section.

ACD/1D NMR Assistant Part 3-Structure Verification

The movie in this post will highlight the new structure verification feature available in ACD/1D NMR Assistant.

In the last posting, I highlighted the multiplet assignment preview (MAP) that provides users with input during the assignment process.

The purpose of this posting is to highlight another feature that is very unique in the NMR software world. ACD/1D NMR Assistant includes a structure verification algorithm that can help users quickly verify the consistency between a proposed chemical structure and a ¹H NMR spectrum.

As you will see in the movie, in addition to providing a simple verification result, the software will automatically assign experimental multiplets (based on their chemical shifts, multiplet properties, and integration values) to protons in the chemical structure. Finally, if any inconsistencies exists they are clearly labeled on the structure and a detailed explanation is provided to focus the user on the specific area on the spectrum where the inconsistency exists.

If you can't get the above video to work, or if you want a bigger version, click here to watch the demonstration of the structure verification feature in ACD/1D NMR Assistant.

Once again, this demonstration is for illustration purposes. 

ACD/1D NMR Assistant Part 2- Assigning NMR Data

The movie below (if you receive this by email you will have to come to the blog) highlights the unique Multiplet Assignment Preview available in ACD/1D NMR Assistant.

This feature helps users evaluate potential assignments by considering the chemical shifts, multiplet properties, and integration values of experimental multiplets in the spectrum.

Just another reason to embrace NMR software. A piece of paper can't do this:

If you can't get the above video to work, or if you want a bigger version , click here to watch the demonstration.

The above example is just for illustration purposes. The best way to evaluate the software on your own data is to go to the ACD/Labs website and request a free trial.

Stay Tuned....next up, the structure verification algorithm in ACD/1D NMR Assistant!

Spectrum-to-Structure Integration - What is it?

One of the unique features that ACD/Labs software has embraced over the years is something called spectrum-to-structure integration.

It's the idea of not only attaching a chemical structure to a piece of analytical data but to also assign that data to pieces of the chemical structure.

This topic gives me a good opportunity to show you one of the new additions in version 11 of ACD/1D NMR Processor (and ACD/1D NMR Assistant) and to perhaps emphasize my point.

I have blogged about the ability to create a multiplet report before, but now in version 11, enhancements have been added. It is now possible to select from a list of pre-formatted templates for multiplet reports based on official journal and patent formats:

Furthermore, you can also create a report of a different format defined by you, the user:

To get back on topic let's look at a formatted multiplet report for the Journal of Natural Products:

¹H NMR (400MHz, DMSO-d₆) d = 10.40 (1H, br. s., H-13), 8.49 (1H, t, J = 5.5 Hz, H-10), 7.63 (2H, d, J_{5, 3,6, 2} = 8.7 Hz, H-5, 3), 6.54 (2H, d, J_{6, 2,5, 3} = 8.7 Hz, H-6, 2), 5.69 (2H, s, H-7), 3.58 (2H, q, J = 6.0 Hz, H-11), 3.04 - 3.25 (6H, m, H-16<''>, 14<''>, 12, 16<'>, 14<'>), 1.22 (6H, t, J = 7.2 Hz, H-17, 15)

The thing I really like about the Journal of Natural Products report is that it includes the assignments in their multiplet report (see assigned atom labels in bold).

This is a nifty time-saving feature, but more on my point regarding spectrum-to-structure integration, notice that the software assigns an experimental multiplet. Not a peak in a multiplet nor a region of the spectrum.

Within ACD/1D NMR Processor or ACD/1D NMR Assistant, users can assign experimental multiplets, meaning that when assigning an atom to the spectrum it is associating the multiplet and all of it's properties (including chemical shift, coupling constants, integration values, etc.)

This of course becomes incredibly important when considering software for automated structure verification. ACD/Labs' solution is not just based on chemical shift prediction, but also on observed and predicted multiplet characteristics, and integration information.

It is these characteristics that are important in the implementation of the algorithms used in tools such as ACD/1D NMR Assistant, ACD/1D NMR Expert, and ACD/2D NMR Expert.

When evaluating different NMR software packages, keep an eye out for true spectrum-to-structure integration.

ACD/1D NMR Assistant Part 1-Processing

So here is my first attempt at showing you some of the features available in ACD/1D NMR Assistant.

The first video will highlight how easy it is to process an NMR spectrum in 1D NMR Assistant.

Make sure to check back early next week and I will post another video showing how the software can help you assign your data.

Enjoy!

If you can't get the above video to work, or if you want a bigger version , click here to watch the demonstration.

A note to people who receive this post via email or RSS feed. If you would like to watch the video, you may need to come to the blog to check it out if you can't see it in your reader: