The ACD/1D NMR Assistant Blog

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Philosophy Phriday- Is there Value Beyond Processing?

Clearly we think so.

The truth of the matter is, there are many different NMR processing softwares out there. You are probably most familiar with the vendor software but I am sure you have investigated others as well.

My colleagues and I have talked an awful lot about ease of use on this blog, and while it is VERY important it is only part of the equation.

The foundation behind the development of ACD/1D NMR Assistant is really all about one basic idea:

The acquisition and processing of an NMR spectrum is a means to an end.

In other words, there is a reason why you run an NMR experiment.

For a synthetic chemist, most of the time (but certainly not all of the time) you run an NMR spectrum to confirm the success of your reaction.

Considering this scenario, should NMR post-acquisition software be limited to simply NMR processing?

ACD/Labs has long been in the business of NMR prediction. More recently (over the past 4-5 years) we have been heavily focused on NMR verification based on NMR prediction.We have made great strides in this arena, and what you see in ACD/1D NMR Assistant is only one direction. We've also been heavily focused on Combined Verification using both ¹H and HSQC data (Article from MRC here).

So, if the algorithms are sophisticated, and the performance is acceptable, is this the next major step and expectation for NMR software? 

From my days as a chemist in the lab, I was not mandated to thoroughly assign all the peaks in my spectrum to ensure that my reaction successfully reached completion. As a result, I wasn't as diligent as perhaps the resident NMR Spectroscopist who had to provide a proof of structure and in doing so, assign the data for many types of spectra. Were their chemists in my group and lab who were as diligent as NMR Spectroscopists? Absolutely, I think you'll find a few in every lab. Kudos to them!

Generally, I knew what I was looking for. A new peak here, a lost peak here. All is good.

Was this a poor practice? Perhaps. But the majority of the time, things worked out OK for me.

This type of scenario represents the value that I believe 1D NMR Assistant provides.

It applies a robust and thorough investigation of your spectrum-structure correspondence every single time. And it does it quickly and easily with one click of the Verify button.   

So while you are busy focusing primarily on one or two specific peaks in the spectrum, ACD/1D NMR Assistant does the rest of the work for you. If it finds something weird anywhere in the spectrum, it's going to tell you about it. Maybe it points out an impurity you already knew about. Or maybe it picks up a bit of residual solvent left over from your purification. But I am willing to bet every once in awhile it's going to catch something real. Something you overlooked. And on other occasions, maybe the results provided will save you a few visits to the NMR Spectroscopist or from running an additional experiment only to find out that your intuition and interpretation was right all along.

P.S. If you are of the belief that all chemists should be thorough and diligent with every NMR spectrum they interpret and thus physically assign all of the peaks in their spectrum to atoms in a structure and maintain this knowledge gained somewhere (That's an entirely different topic that perhaps I will leave one of my other colleagues to address), than I think ACD/1D NMR Assistant remains a great tool to accomplish this.

In my days in the lab, this simply wasn't feasible. I didn't have access to the tools that are available today. ACD/1D NMR Assistant offers interpretation assistance by suggesting the most probable assignments with it's MAP (Multiplet Assignment Preview) functionality. In addition, when you click Verify, it automatically assigns your spectra. Is it right for every single multiplet for every spectra every time? Of course not. But it's a great starting point and will save you a lot of time if your goal is to completely assign your data. For example maybe it got 10 of 12 assignments right. That 10 less assignments you have to do manually.

Finally, if the mandate is put down on you that you need to assign all your spectra, than the expectation should also be clear that you will be running a lot more 2D NMR experiments on a routine basis since it will be quite difficult to unambiguously assign all your data in a manner that will hold up using ¹H NMR exclusively.

Working with Specrta in a Series

The following clip will illustrate how to build a series of ¹H NMR data, modify the offset and integrate the ¹H NMR spectra at the same start and end points.

Philosophy Phriday - On Focus

Mass spectrometry isn't that hard.  You can become a decent mass spectrometrist with a little focus.  Everyone learned this stuff in school.  You learned rules about ionization, fragmentation, resolution, calibration, . . . you're off to the races.  You've just got to keep it all in focus when you're running experiments and interpreting data.

Chromatography isn't that hard.  You can become a decent chromatographer if you just focus on it.  Everyone learned this stuff in school.  You learned about solvents, buffers, stationary phases, resolution, detection, . . . you can do some great separations.  You've just got to keep it all in focus when you're running experiments and interpreting data.

Your company bureaucracy isn't that hard.  You can learn to work through the bureaucracy if you just focus on it.  Everyone learned this stuff in school.  You learned all the forms, the meetings, the players, the gatekeepers, the slouches, . . . you can get your projects to happen.  You've just got to keep it all in focus when you're running experiments and interpreting data.

NMR isn't that hard . . . You get the picture.

It's all complex.  We all learned it all, and learned how to do it properly.  (OK, some of us didn't.)  But we have the things we focus on and specialize in and do well at, and the things that don't get a lot of attention.  Some of us have incredible breadth, and the abilty to train our full attention on anything immediately.  But we're not being serious if we claim that all people are fully successful at all things all of the time.  That's where tools come in.  A computer can remember a lot more than any one of us, and can apply knowledge objectively - or, perhaps, only with the bias of the development team.

That's why we have ACD/1D NMR Assistant.  It's never going to replace the need for understanding of NMR or the need for real spectroscopists.  But it's a fantastic tool to help the bench chemist who is really focusing on what is happening in the hood.  It's a tool that seemlessly integrates chemical structure with previously understood spectroscopic knowledge.  It helps keep the chemist's attention only on anomalies of difficult assignments, not the details of software operation or chemical shift lists.

It's about focus.

Philosophy Phriday- NMR Data and ELNs

Electronic Lab Notebooks-it seems like every chemist I talk to these days is either working inside one, is piloting one, or their company is thinking about evaluating one. I believe this is for good reason. The ELN vendors put a great deal of effort into ensuring a quality product (i.e., good workflows, links to chemical inventory, some even link to assay results).

So my job these days for ACD/Labs is (among other things…many different hats :)) helping to manage all of our partner relationships. So I can’t help but commandeer Ryan’s blog for a day, and ping you readers that are using (or plan to use in the short future) ELN implementations in your daily life; specifically, I’m keen to know what type of integration you’d like to see between your ELN and analytical data. Since it’s an NMR Assistant themed blog, let’s focus on NMR data. In my mind there is a pretty wide range of ways to link analytical results with ELN records. Here’s how I see it (tell me if I’m wrong, of course):

1) Writing “NMR data consistent with reaction product” in a text field in the ELN. I suppose you could also add a filename of resultant NMR data

2) PDF report. Whether it’s straight from the spectrometer, or processed by your favorite offline processing software (:)), a pdf of the summary report provides a visual representation of the spectrum, plus chemical shift, integration, multiplicity, and perhaps even assignments. Of course the level of detail contained in the report can vary, but you get my point…a static representation of the data, and resultant analysis

3) Link to Processing Software. I know of several places that have established a link to remote processing/visualization software, and have the enhanced capability to –in addition to the reporting capabilities outlined above-replot/reprocess/reanalyze on the fly.

4) Embedding Spectral Processing within the notebook. There are a few folks that have done this too…a one-stop-shop to get you as chemists through your day. There’s several technologies that would afford this (ActiveX, Web Services, etc.), but it’s a bit of work to do it.

So all things being equal, what’s ideal for you as chemists? For me, having the direct processing capabilities within the ELN would be perfect, so long that my IT staff would support it.

That said, I’m for sure not a chemist-the last time I performed a standard organic reaction, there was a IR Probe hooked up to the RBF. I managed to break (er, dissolve) two of our 10K Chalcogenide Probes, but that’s another story (sorry Doug, Cathy J). Anyhow, I’d be keen to hear if you’d like a tighter integration between your present (or future) ELN and tools like NMR Assistant.

You’re also welcome to share any lab mishaps :)

Easy PDF Reporting of NMR Data

This movie will show you how to easily create structure-searchable ChemSketch or PDF reports in ACD/1D NMR Assistant:

Philosophy Phriday- NMR Prediction or Verification?

If you haven't already realized it at this point, ACD/1D NMR Assistant is not an NMR prediction software.

In other words, you can't simply draw a chemical structure and predict a simulated spectrum in the traditional way.

One of the things that led us down the path to a structure verification workflow (as opposed to NMR prediction) in the development of ACD/1D NMR Assistant was market research that suggested that NMR prediction was something that chemists in general did not want on a routine basis as it didn't really suit their workflow.

The feedback we got was mostly from chemists who didn't want to see a predicted spectrum and that looking at one piece of experimental data was more than enough. Furthermore, many of the Directors and Spectroscopists didn't love the idea of supplying their synthetic chemists with simulated spectra.

I have one story of an NMR Spectroscopist who thought he would do a favor for his chemists by rolling in a predicted spectrum to their standard processing macro. Unfortunately, the chemists didn't like that. They felt that it confused them and made them think too much and really slowed them down.

Stories like this led us down the structure verification path for development which we thought was the right direction in the first place. Here was the initial product plan:

All kidding aside, that essentially was what we were thinking. A simple NMR processing package was not enough, yet a bundle of processing and prediction probably was too much and didn't quite hit the mark.

We felt that processing wasn't enough because in reality an NMR spectrum is a means to an end. There's a reason a chemist is acquiring and then processing the data. From a chemist's standpoint it is because they want to use NMR to confirm that they "made what they were trying to make" We felt that with our experience developing NMR prediction software, and our more recent development efforts towards structure verification algorithms, that we could do a lot more for chemists than simply processing their data and providing them with a formatted multiplet report.

On the other side of the coin, we felt that simply bundling our NMR Processor with our NMR Predictor was not the right solution either for reasons stated in the beginning of this post.

In the end, we felt that the structure verification routine was simply more consistent with the chemist's workflow and was useful because it provided a very quick and diagnostic overview of the entire spectrum correspondence with a proposed chemical structure.

I remember from my days in the lab, I would do a reaction and then run an NMR spectrum. I would then proceed to focus my attention primarily on a specific region in the spectrum. I expect a peak to appear here, and another to disappear there. If that happened, I'd move onto the next step. It's not really a spectroscopists way of doing things...but I wasn't a spectroscopist, I was a chemist.

ACD/1D NMR Assistant does all the other work for the chemists. You can focus on those "regions of interest", but 1D NMR Assistant quickly takes a brute force approach, predicts the properties in the background and attempts to match the protons on the structure with the appropriate multiplet properties in the experimental spectrum. If it finds any discrepancies, it will let you know whether it is in your "region of interest" or not.

I certainly would have loved to have a tool like this for back in my days in the lab. Probably would have saved me from back-tracking on a synthesis a time or two.

So there's our justification for taking the structure verification route in the development of ACD/1D NMR Assistant.

Learn more about this software, and download a 30 day trial, here.

Want Your Cake and Eat it Too?

We anticipated that some people would want the predicted spectrum in the software. In fact, we've already had some groups evaluate ACD/1D NMR Assistant and decide that in addition to that, they want their chemists to have the option to see a predicted spectrum as well.

Therefore if you purchase ACD/1D NMR Assistant and ACD/HNMR Predictor you have the ability to do both. You can use the HNMR Predictor by itself or you can even predict the spectrum in the same interface and compare your experimental spectrum directly with the predicted spectrum:

So just to clear things up.

If you want an NMR processing package that can perform structure verification and also provide a predicted spectrum view (image above), you want ACD/1D NMR Assistant and ACD/HNMR Predictor together.

If all you want is a program that can simply predict a simulated NMR spectrum from a chemical structure, learn more about ACD/HNMR Predictor here:

http://www.acdlabs.com/products/spec_lab/predict_nmr/hnmr/

Make sense?

Housekeeping Tip #3

You may have discovered a feature in the software that you like, but find you need to dig through the menus to get it.

It's possible that we have a toolbar button for it but we just aren't showing it in the default view.

If you right click on the tool bar section (next to the other toolbar button, you will be provided with a list of toolbar buttons that you can chose to see or hide. If there is a particular button you want to place on your interface, just make sure it is checked in the drop down menu. Alternatively you can also remove buttons that you don't find useful to make your interface cleaner.

The same thing can be done in the level lower on the Action Bar. Right click on this area and you can create quicker access to various modes in the software like Peak Picking, Phase Correction, Baseline Correction, Annotation, etc.

Housekeeping Tip #2

I spoke about activating your zoom button with a right click in Housekeeping Tip #1.

In the same Common Preferences dialog box (accessed from the options menu) I always like to activate the Autodisplay Zoom Area. This automatically opens a Zoom Window in the interface for easy manipulation. I find this especially useful when performing peak picking, integration, and multiplet analysis when I like to get a close look at each multiplet I am analyzing.

Here's how it works:

To set up  the Autodisplay Zoom Area once again go to the Options menu and select Common Preferences...

From the Common Preferences dialog box select the Windows tab and choose the Autodisplay Zoom Area radio button (click Image to Enlarge).

Philosophy Phriday- How Do you Archive?

Do you store or archive your NMR spectra? Does your organization have an ELN?

How do you store this data?

If you use PDF, is this what your PDFs look like?

Would you prefer they look like this?

Stay tuned to the blog next week and I'll show you how to easily create PDF reports in ACD/1D NMR Assistant.

In the meantime, if you interested in archiving or reporting NMR spectra, I think you should download the application note below for some weekend reading. Especially if you have an electronic lab notebook (ELN):

Archiving NMR Data in an Electronic Lab Notebook World

Don't Be Shy- Tell us What You Think

If you haven't already done so, please go here to fill out a short survey and provide us with feedback on the first version of ACD/1D NMR Assistant.

If you'd rather share your opinions on a more public forum, feel free to leave some comments on the blog for all to see.

Philosophy Phriday-On Being Busy Enough Already

It turns out that I had the wrong introduction to NMR software.

I found myself working at a startup biotech in Carlsbad.  The place had a phenomenal work ethic -- a lot of folks there still do -- and my boss had just quit to pursue a career as a venture capitalist.  That left me -very inexperienced - as 'the NMR expert.'  It was not unusual for me to spend my lunch hour in the NMR lab.  I would sit in there, munching away on a sandwich, feet propped up on my desk, with the NMR system manual open.  I would try stuff.  Solve problems that were too hard during the busy parts of the day.  Write macros to simplify different tasks.  It was really OK for me to spend hours learning how to solve operational problems and make configuration changes.  I had the time - with plenty of 70-hour work weeks.

After a few years, I really was an 'NMR expert' of a sort.  I was no spin jockey, but I was a pretty proficient magnet driver.  I could reliably keep my 10-year old system productive, swap probes like a genie, and put any set of experiments in place in a flash.  I kept my bench chemists very happy.

Then things changed:  I got married and we bought a house.  I needed to be home by 7, and 6 was better!  No longer did I have time to work out the fastest, best ways to make complex tasks simple.  I needed to make things happen now!  I lost patience with the unclear manuals and crazy procedures and repetitive tasks.  I figured out how all of my bench chemists had been feeling all along.  It wasn't that they weren't capable of figuring this kind of stuff out, it was just that they had enough else on their minds.  I began to appreciate tools that really made my life simpler and more productive, by helping me complete more difficult tasks quickly, with a minimum learning curve.

ACD/Labs has been about making chemistry applications simpler and more productive for a long time.  But the standards for simpler keep advancing.  When the founders started things 14 years ago, using a GUI for NMR processing and prediction was a big improvement over the prevailing command line-intensive processing.  But this isn't just the day of the GUI any more, it's the iPod era.  Chemists have more to do, and less time to learn how to do it.  Folks want an application that is "easy to learn" to the point of intuitively obvious.   

ACD/1D NMR Assistant is a big step toward that goal.  It's a solution with lots of powerful capabilities, but getting going with it won't take real time away from everything else that has to happen in the lab.  And if a chemist needs more powerful capabilities, ACD/1D NMR Assistant integrates with a whole host of them.  It's great software for chemists who are "busy enough already."

Derek Lowe's In the Pipeline

I am going to make the broad assumption that since ACD/1D NMR Assistant was developed for synthetic chemists that at this point plenty of the readers coming to this blog are synthetic chemists. Perhaps some in the pharmaceutical industry, chemical, and some graduate and undergraduate students who may want to work in industry soon.

I thought I'd take the time to point to a blog I personally enjoy very much:

Derek Lowe's In the Pipeline Blog.

The link above points to an interesting piece of advice from Derek on how chemists looking to work in pharma need to branch out and understand the broader science of drug discovery.

It's some very interesting advice and has led to a very interesting conversation in the comments section of his blog entry.

I think it's an interesting piece of advice regardless of what field you are in. Pharma, chemical, academic, software, etc.

Check it out if you have a few moments.

Why Are Some of My Peaks Shaded?-Automated Dark Regions

This has got to be my vote for algorithm of the year. Sergey Golotvin, the Project leader behind 1D NMR Assistant, has come up with a way for the software to automatically identify solvent and water peaks in your 1D proton spectrum. The best part is how well it distinguishes these peaks from actual peaks that can be in the same area.

First let me explain dark regions. Dark regions are what we use to identify what regions of the spectrum the software (and user) should ignore. We use these dark regions to cover solvent peaks, water, TMS and other known impurities like acetone for example. There are two reasons you would want to do this. The first is to make the normalization of the integrals easier. If only relevant peak area is left outside of dark regions in your proton spectrum, then we simply divide it up according to the number of protons present in the molecule and all the integrals are correct. Second, by dark regioning extraneous peaks, we don’t accidentally assign them to the structure through manual or automatic assignment.

Creating dark regions is simple. Creating them in the right location automatically is difficult. This is where Sergey’s genius comes in. First the algorithm takes some guidance from the spectrum parameters. If a solvent is indicated in the parameter file associated with the FID, then we use this information to go look for that peak. The software also knows that when you use methanol or DMSO, it should also look for a water peak as well. And TMS is easy. It just looks for a peak at 0 ppm!

So why is this so great? Because it’s AUTOMATED!! No input required. Just open your spectrum and the dark regions are created for you. Brilliant. (Check our Ryan’s previous post for a video of this process in action.)

Try it yourself, you won’t be disappointed. The routine currently works for DMSO, water, methanol and TMS, with more to come.

Here are a few screen captures of the result of the automated routine.  Click on the image for a larger view. In this example, you can see that the routine does not need the solvent or water peaks to be significantly sized.  The routine will actively dark region any solvent or water peak that contributes more than 4% to the total spectrum area.  (4% is a threshold we have arbitrarily chosen.  Anything less than that normally does not interfere with the integral normalization or assignment.)

You can see that it is incredibly good at avoiding covering extra peak area that could be from a real peak.  In this second example, a real peak is half buried under the DMSO.  The automatic routine keeps as much of the real peak as possible and dark regions only the DMSO peak here.

 

This last example shows how it also works seamlessly on Methanol.

It also uses structure information when possible. For example, when your structure has an O-CH₃, it is less aggressive around the water impurity so it doesn’t accidentally dark region a real peak!

Housekeeping Tip #1

As I play around with the evaluation version of ACD/1D NMR Assistant, I've come across a few tips that I think may make your interaction with the software more pleasant.

For example, in all of my movies I activate the zoom feature with a simple right-click of the mouse button. I just realized that this is not the default in your installations. Instead you get a drop down menu.

(Unbeknownst to me, there's an even easier way to do it. Check out Brent's suggestion in the comments).

If you'd like to activate this feature for easier zoom go to the Options menu and select Common Preferences...

From the Common Preferences dialog box select the Mouse tab and choose the Zoom radio button to activate on the zoom feature on a right click.

(click Image to enlarge)

Once activated you can activate the zoom feature quickly by right clicking on your mouse. Once you see the magnifying glass replace your cursor, simply left-click and drag over your region of interest.

To Zoom out, click this toolbar button

1D NMR Assistant-The Administrator's Perspective

We all wear many hats...I for one have worn a sales hat for the last six years.  When Ryan asked me to contribute to this blog, I thought long and hard about what hat to wear in writing about 1D NMR Assistant.  So rather than try and wear my sales hat when writing this, I thought it would be most appropriate to put on a hat that I haven't worn in a long time, that of the open access administrator. 

So I had to think back on my time in the Analytical Lab at Pfizer La Jolla.  My most immediate recollection was the challenge our group had in demonstrating our value in Drug Discovery.  We didn't generate compounds; we didn't generate assay results (at least of a biological nature); we didn't  help in the CMC process development (that was managed by our Development Analytical brethren).  In a nutshell, we were problem solvers and service providers.  We took a tool set of analytical methodologies to address chemistry centric challenges to keep projects going.

If a project team has an active compound in screening that doesn't show activity upon re-synthesis, we'd figure out what that original compound was.  Need LogD, Aqueous Solubility, pKa?  Send it our way...

Then Open Access came along...this was about 1998 for our lab.  I took the role of Open Access Admin for Discovery in 2001.  Thinking back, I look at what the challenges of my customers were back then.  I've heard many times that Medicinal Chemists aren't skilled in the ability to assign NMR spectra, for example.  I would assert that there may be some that aren't but the majority of my old colleagues were very skilled in this art.  The challenge presented wasn't the ability to assign, but rather the conveyance used to report the assigned spectrum. 

So  looking back, in addition to all of the Services our group provided, Discovery Analytical provided the ability to make the Chemists lives easier.  Think about IT/Informatics...same model (I hope...but that's another blog entry!).

So now we get to remote processing tools for analytical data.  I think that there are three critical capabilities for any processing tools for chemists:

1) Relate structure to spectrum.  The whole point of running the experiment is to confirm that the structure is what the chemists draws.  If it isn't, no SAR... you can argue that IP position is also relevant, but the structural fidelity comes first.

2) Convey this relationship in a report.  I recall having to write at the end of every structure confirmation experiment, "structure is consistent (or not), with proposed structure"  As scientists, do we not want to ensure that a person reviewing your notebook entry could understand our rationale for making this statement?  This leads me to my last capability requirement.

3) This report has to be pasted, linked, etc., to the Notebook page.  I for one don't miss the days of literally pasting my spectra into my lab notebook (and initialing across the edge of the pasted spectrum, for the GMP enthusiasts :)).  As we collectively transition to the electronic notebook, this process is a heck of a lot easier with PDF renditions of our results.

From what I've seen with NMR Assistant, it sure looks like it would be a tool I'd think about employing if I were still an open access admin. 

I'm sure that Ryan, Brent, Arvin, et al. will tell you about the more technical stuff, but I thought it would be nice to think about how this helps solidify our (speaking as if I still have the NMR admin hat on :)) value in the minds of Drug Discovery manager types. 

Looking forward to hearing your comments... 

 

Consistent or Inconsistent?

One of the things we struggled with when designing the output of the verification routine for 1D NMR Assistant, was what information to provide to the user. For this product, we were hearing from our chemist testers that simple was what they wanted. Sounds easy enough. In reality, delivering simple is not so simple for one reason…verification is not perfect.

If we were able to provide perfect verification results, then simple would be easy. All we would have to do is tell the user whether the structure is correct or not. In reality, verification is not perfect for two reasons. The first is that 1D proton spectra don’t have enough information in them for the software to unambiguously say that this structure matches, but no other structure does. This means that we can’t really call the structure “correct”, but we can call it “consistent”. Second, the software evaluation is not perfect. Unexpected problems in processing, or structures that are sufficiently novel, cause problems with the prediction as well. What we need to do then, is to keep the output simple, but give the user enough information so that they can check over the results of the software and decide for themselves whether they agree or disagree with the automated evaluation.

What we came up with was three scenarios for the 1D NMR Assistant user. Consistent, Minor Inconsistencies and Major Inconsistencies. Let’s take a look at what each category is actually telling us.

Consistent – The Structure is consistent with the spectrum.

This is the one the chemist always wants to see. The balance is to give it to them as often as possible, but never when the structure is inconsistent. Since the software is not perfect, this means that it can’t be 100% of the time. The amount a chemist will get the “consistent” message will depend heavily on the quality of the spectra and the novelty of the structures. I would expect users to get this evaluation somewhere between 50 and 75% of the time.

For an example of a consistent result see the video from this previous post.

Minor Inconsistencies – All assignments have been created between the structure and spectrum, but there are some small problems that should be reviewed by the user.

In this case, the user is needed to weigh in on a decision the software has made. In some cases, the predicted chemical shift may not be as accurate as we would like, or an unexpected coupling pattern may be present. In these cases, the user is informed that minor inconsistencies exist and they are then presented with what the minor inconsistencies are. Along with the list of inconsistencies, the user is given the ability to ignore them. This means the user is comfortable with the inconsistency and is deciding that they should not contribute to a poor match between the spectrum and structure. If the user dismisses enough of the inconsistencies, then the evaluation will change to “Consistent (by User)”. This category acknowledges that the match is now good, but only with user input.

For an example of a minor inconsistency result see the video from this previous post.

Major Inconsistencies – Not all assignments between the spectrum and structure have been created and some manual intervention is needed in processing or assignment.

Here, the software was not able to assign all of the protons on the structure. In this case, the user is again presented with the list of inconsistencies, but no ability to dismiss them. Since some assignments are missing, the user must intervene and create an assignment manually, or create or change some property of a multiplet. If the user corrects the situation on the spectrum, and tries verification again, they will likely receive some minor inconsistencies that can then be dismissed so the “Consistent (by User)” designation is now possible.

For an example of a major inconsistency result see the video from this previous post.

What we have really tried hard to do is not tell the user that their structure is wrong. Really, we don’t know that. All the software can see, is that there is an inconsistency between the spectrum and structure. With a little help from the user, the inconsistency can be resolved, and everyone wins.

Confirming Structures- Part 3

One of the truly unique applications of ACD/1D NMR Assistant is that it is a software package that will provide the user with insight on the consistency between a proposed chemical structure and an experimental NMR spectrum.

After you have attached a proposed chemical structure and completed the processing and analysis of your spectrum, you can make use of the structure verification algorithm in the software.

See the video below for a "how to" and explanation of the results. This is part 3 of 3 videos (Part 1 is here, part 2 is here) to be highlighted regarding the structure verification algorithm in the software.

In this video we are working with a scenario in which the software recognizes a major inconsistency between the proposed structure and the experimental spectrum:

Confirming Structures- Part 2

One of the truly unique applications of ACD/1D NMR Assistant is that it is a software package that will provide the user with insight on the consistency between a proposed chemical structure and an experimental NMR spectrum.

After you have attached a proposed chemical structure and completed the processing and analysis of your spectrum, you can make use of the structure verification algorithm in the software.

See the video below for a "how to" and explanation of the results. This is part 2 of 3 videos (Part 1 is here) to be highlighted regarding the structure verification algorithm in the software.

In this video we are working with a scenario in which the software recognizes a minor inconsistency between the proposed structure and the experimental spectrum:

Confirming Structures-Part 1

One of the truly unique applications of ACD/1D NMR Assistant is that it is a software package that will provide the user with insight on the consistency between a proposed chemical structure and a proposed NMR spectrum.

After you have attached a proposed chemical structure and completed the processing and analysis of your spectrum, you can make use of the structure verification algorithm in the software.

See the video below for a "how to" and explanation of the results. This is part 1 of 3 videos to be highlighted regarding the structure verification algorithm in the software. In this video we are working with a scenario in which the proposed chemical structure is correct:

The Formatted Multiplet Report

Do you have to create the following reports for patents, publications, etc.?:

¹H NMR (DMSO-d6) Shift: 9.19 (s, 1H), 8.95 (s, 1H), 8.85 (d, J = 19.6 Hz, 2H), 6.72 (d, J = 1.5 Hz, 1H), 6.66 - 6.71 (m, 1H), 6.59 (dd, J = 8.1, 1.6 Hz, 1H), 5.89 (d, J = 2.1 Hz, 1H), 5.69 (d, J = 2.1 Hz, 1H), 4.88 (d, J = 5.3 Hz, 1H), 4.48 (d, J = 7.6 Hz, 1H), 3.75 - 3.86 (m, 1H), 2.65 (dd, J = 16.1, 5.3 Hz, 1H), 2.35 (dd, J = 16.0, 8.1 Hz, 1H)

In previous posts we have shown you how to create and edit multiplets in the software.

Once this is done, creating a formatted report is a piece of cake. Check out the video below:

Ease of Use

Ease of use is an interesting thing. Much easier to ask for than to deliver. Not that I am complaining. It is just that ease of use is not universal. However, there are some commonalities in user experiences that we can use to make software easier to use.

First, you need to draw on common experiences. We already know that everyone who is using our software will be working in a Microsoft environment. Like it or not, Windows and MS Office are used by many people, and these people learn to expect your software to respond in a consistent way to their input. So, following Microsoft standards as much as possible, helps improve ease of use.

Second, ease of use is much easier to achieve if you have a defined workflow in mind. This is where 1D NMR Assistant has a real leg up on 1D NMR Processor, (it’s predecessor). 1D NMR Processor was built to handle ANY workflow. This is great for a diverse set of users, in that any of them can extract some value out of the tool. But it is hard to be everything to everyone. By defining a strict workflow, you can reduce the complexity of the interface by only giving the user a limited set of options. The user will then find this defined workflow easier to accomplish and the software is now easier to use.

What this means is that 1D NMR Assistant is easier to use because we have made a specific workflow the focus of the product. This software application is designed to help a user confirm that their proposed chemical structure is correct. To do this, a user only needs to import a 1D NMR spectrum, prepare the multiplets for reporting automatically or manually and then help the user assign their chemical structure to these signals through a guided manual assignment or a completely automatic assignment if they wish. The product is easy to use because the user is not inundated with functionality that is not relevant to their workflow.

Fortunately for those users who demand more, we have kept all of the functionality of 1D NMR Processor in 1D NMR Assistant. We have just tucked it away. Buttons that were formerly on the interface have been hidden. So, you can get to these operations, (like peak fitting), through the menus, or you can add the buttons back to the interface if you wish.

So, go ahead and redefine your workflow if you wish. Once you are savvy enough with the software, it is perfectly appropriate for you to do this. However, for new users the software is easy to use out of the box because it easily does what they want to do.

Editing a multiplet

The following clip illustrates how to edit a multiplet, i.e. add extra peak picking information, and allow J-coupler to calculate the coupling constants and coupling pattern for a dd multiplet.

Referencing, Peak Picking, Integration, and Multiplet Analysis

Watch the movie below to see how easy it is to reference your spectrum and peak pick, integrate, and characterize the multiplets in your spectrum.

How to Attach a Chemical Structure to a Spectrum

Here are three ways to attach a chemical structure to an NMR spectrum in the software:

How to Import Files in ACD/1D NMR Assistant

The following short movie will show you how to import files into ACD/1D NMR Assistant along with a couple of basic spectrum manipulations (zoom and enlarge regions).

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