Ryan's Blog on NMR Software

New Article on NMR Software!

And no...this one is not about Indirect Covariance :)

I am very pleased to inform you that a new article on Automated Structure Verification based on the combined verification algorithms in ACD/Labs NMR software is now available for early view online at:

http://dx.doi.org/10.1002%2Fmrc.2034

This is a follow up to an article that was written last year that evaluated how well the software could automatically confirm the identity of chemical structures using ¹H NMR data. That article is also available here:

http://www3.interscience.wiley.com/cgi-bin/abstract/112422887/ABSTRACT

The most recent article is really neat stuff. In a nutshell it outlines our software's latest performance on automatically  identifying correct and incorrect chemical structures based on their ¹H and 2D HSQC NMR data. The key here is not that it simply uses both spectra to determine an answer, but that it combines the algorithms to intelligently make a decision based on the peaks and correlations present in both spectra. While it shouldn't necessarily come as a surprise that including an HSQC for automatic determination of this dataset improves the results, it is very impressive to see how reliable the software is at identifying correct AND incorrect structures using multiple, real-life datasets.

Unfortunately this work is now the property of John Wiley and Sons, Ltd. so I cannot share copies of the publication on my blog. If you want to learn more about combined verification before purchasing the article, we have presented a couple of posters on this topic over the last year.

From SMASH 2006:

Automated Evaluation of a Chemical Structure with only 1D ¹H and 2D ¹H-¹³C HSQC

From ENC 2007:

Validating Automated Structure Confirmation in a Blind Study

Would you like to freely share your spectra?

I've blogged and pointed a little bit to the ChemSpider service over the last few months. It's a service that my former colleague, Tony Williams along with others is working on, so I think it has great potential.

It looks as if they have taken another step in the right direction by allowing users to add spectra of different analytical types to the database records.

Instructions on how to do this can be downloaded at:

http://www.chemspider.com/docs/Uploading_Spectra_onto_ChemSpider.pdf

Currently, you can only upload spectra in JCAMP format (.jdx or .dx extension) as JSpecView viewing component is integrated in ChemSpider.

NMR software users of ACD/1D NMR Processor or Manager can easily export their data files into the JCamp format. Simply choose Export... from the File menu and select JCAMP (*.jdx,*.dx) from the Save as type: drop-down menu (click to enlarge images):

Of course you can also import JCAMP files into the Processor or Manager.

Go ahead and share your spectra with the chemistry community!

What Do All Your Products Do?!

It's a fair question. We have a lot of different NMR software products that do many different things. In total, ACD/Labs actually has over 100 different products as in addition to NMR software we also develop chemical drawing, naming, and databasing, MS, Chrom, UV-IR, PhysChem and more.

Sometimes this sheer amount of choice and complexity can confuse someone or cause anxiety. I'll try and point you to all of ACD/Labs' NMR Software packages with a quick and easy blurb on what each does and doesn't do.

ACD/1D NMR Processor:

What it does: This is our standard 1D NMR processing package. With it you can import all the major vendor formats and process and analyze all 1D NMR spectra. This product comes with the multiplet analysis tool that I have talked alot about on here in the past. One of it's unique features is the ability to attach chemical structures and electronically assign multiplets in the spectra to the atoms in the chemical structure.

What it doesn't do: It does not allow you to import 2D NMR data. You also cannot database your spectra, or predict any NMR spectra with this tool (see below for these products).

ACD/2D NMR Processor:

What it does:  You can import, process, and analyze all your 1D and 2D NMR data. It includes all the functionality and features available in ACD/1D NMR Processor. In addition much like 1D NMR Processor you can attach chemical structures and easily electronically assign  correlations to atoms in the structure. Because it also includes 1D NMR Processor, users can transfer assignments from 1D spectra to 2D spectra and vice versa.

What it doesn't do: You also cannot database your spectra, or predict any NMR spectra with this tool (see below for these products).

ACD/1D NMR Manager:

What it does: First and foremost this is a databasing tool. However, it includes all of the functionality available in ACD/1D NMR Processor. In addition to that it allows you to build your own database of 1D NMR data that can be searched in a variety of ways. The ability to electronically assign data to chemical structures is valuable here as it allows you to store completely assigned NMR spectra.

What it doesn't do: You cannot predict any NMR spectra with this tool (see below for these products).

ACD/2D NMR Manager:

What it does: This is a databasing tool for both 1D and 2D NMR data. It includes all of the functionality available in ACD/1D and 2D NMR Processor. It allows you to build your own database of 1D and 2D NMR data that can be searched in a variety of ways. All types of 1D and 2D NMR data can be stored in one database record. The ability to electronically assign data to chemical structures is valuable here as it allows you to store completely assigned NMR spectra.

What it doesn't do: You cannot predict any NMR spectra with this tool (see below for these products).

ACD/HNMR Predictor:

What it does:  It predicts 1H NMR spectra, chemical shifts, and coupling constants. In addition you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. The primary purpose of this database is to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) but this database can also be searched in a variety of ways (structure, substructure, chemical shift, etc.)

What it doesn't do: It only predicts 1H NMR spectra, chemical shifts, and coupling constants. Therefore it does not predict any other nuclei (see below for these products). It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/CNMR Predictor:

What it does:  It is the 13C equivalent of HNMR Predictor. It predicts 13C NMR spectra, chemical shifts, and coupling constants. In addition you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. The primary purpose of this database is to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) but this database can also be searched in a variety of ways (structure, substructure, chemical shift, etc.)

What it doesn't do: It only predicts 13C NMR spectra, chemical shifts, and coupling constants. Therefore it does not predict any other nuclei (see other predictors). It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/2D NMR Predictor:

What it does:  It predicts 2D NMR spectra, chemical shifts, and coupling constants. In addition you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. This product also includes ACD/HNMR, CNMR Predictor, and ACD/2D NMR Processor. As a result, you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) that can also be searched in a variety of ways (structure, substructure, chemical shift, etc.) In addition, you can import, process, and analyze all of your 1D and 2D NMR data because this product includes 2D NMR Processor. This is an excellent product for an NMR Spectroscopist. 

What it doesn't do: It only predicts 1H-1H homonuclear 2D NMR spectra and 1H-13C heteronuclear NMR spectra, chemical shifts, and coupling constants. If you want to predict other heteronuclear NMR spectra such as 1H-15N, you will also need the ACD/NNMR Predictor. You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/NNMR Predictor:

What it does:  It is the 15N equivalent of HNMR Predictor. It predicts 15N NMR chemical shifts, and coupling constants. Much like the other predictors, you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. The primary purpose of this database is to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) but this database can also be searched in a variety of ways (structure, substructure, chemical shift, etc.)

What it doesn't do: It only predicts 15N NMR spectra, chemical shifts, and coupling constants. Therefore it does not predict any other nuclei (see other predictors). Note that unlike the HNMR and CNMR Predictor, ACD/NNMR Predictor does not generate a predicted spectrum it only provides a table of predicted chemical shifts and coupling constants.It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/FNMR Predictor:

What it does:  It is the 19F equivalent of HNMR Predictor. It predicts 19F NMR chemical shifts, and coupling constants. Much like the other predictors, you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. The primary purpose of this database is to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) but this database can also be searched in a variety of ways (structure, substructure, chemical shift, etc.)

What it doesn't do: It only predicts 19F NMR spectra, chemical shifts, and coupling constants. Therefore it does not predict any other nuclei (see other predictors). Note that unlike the HNMR and CNMR Predictor, ACD/FNMR Predictor does not generate a predicted spectrum it only provides a table of predicted chemical shifts and coupling constants.It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/PNMR Predictor:

What it does:  It is the 31P equivalent of HNMR Predictor. It predicts 31P NMR chemical shifts, and coupling constants. Much like the other predictors, you can build your own database of chemical structures, chemical shifts, coupling constants, user data, etc. The primary purpose of this database is to improve the accuracy of the NMR predictions (data imported in your database can be used to train the NMR prediction algorithm) but this database can also be searched in a variety of ways (structure, substructure, chemical shift, etc.)

What it doesn't do: It only predicts 31P NMR spectra, chemical shifts, and coupling constants. Therefore it does not predict any other nuclei (see other predictors). Note that unlike the HNMR and CNMR Predictor, ACD/PNMR Predictor does not generate a predicted spectrum it only provides a table of predicted chemical shifts and coupling constants.It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot database NMR spectra with this program only structures and tables of chemical shifts and coupling constant data.

ACD/HNMR DB:

What it does: This product provides users with access to the NMR data we have compiled over the years for use in the ACD/HNMR Predictor. The database contains over 193,000 chemical structures and 1,578,000 chemical shifts that can be searched extensively. The database sizes are increased annually with every new version of the software.

What it doesn't do: It does not predict 1H NMR spectra. It only contains the NMR data available in the HNMR Predictor. It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot build your own database of NMR data with this product. 

ACD/CNMR DB:

What it does: This product provides users with access to the NMR data we have compiled over the years for use in the ACD/CNMR Predictor. The database contains over 186,000 chemical structures and 2,351,000 chemical shifts that can be searched extensively. The database sizes are increased annually with every new version of the software.

What it doesn't do: It does not predict 13C NMR spectra. It only contains the NMR data available in the CNMR Predictor. It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot build your own database of NMR data with this product.

ACD/NNMR DB:

What it does: This product provides users with access to the NMR data we have compiled over the years for use in the ACD/NNMR Predictor. The database contains over 8,800 chemical structures and 20,700 chemical shifts that can be searched extensively. The database sizes are increased annually with every new version of the software.

What it doesn't do: It does not predict 15N NMR spectra. It only contains the NMR data available in the NNMR Predictor. It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot build your own database of NMR data with this product.

ACD/FNMR DB:

What it does: This product provides users with access to the NMR data we have compiled over the years for use in the ACD/FNMR Predictor. The database contains over 15,400 chemical structures and 32,790 chemical shifts that can be searched extensively. The database sizes are increased annually with every new version of the software.

What it doesn't do: It does not predict 19F NMR spectra. It only contains the NMR data available in the FNMR Predictor. It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot build your own database of NMR data with this product.

ACD/PNMR DB:

What it does: This product provides users with access to the NMR data we have compiled over the years for use in the ACD/PNMR Predictor. The database contains over 26,170 chemical structures and 32,470 chemical shifts that can be searched extensively. The database sizes are increased annually with every new version of the software.

What it doesn't do: It does not predict 31P NMR spectra. It only contains the NMR data available in the PNMR Predictor. It also does not do any NMR processing or analysis (see ACD/1D and 2D NMR Processor above). You cannot build your own database of NMR data with this product.

ACD/1D NMR Expert:

What it does: It is a processing and databasing software that is more suited for high-throughput work. In addition it offers the ability to perform high-throughput quantiation and verification on large batches of spectra. This product comes with ACD/1D NMR Processor, ACD/1D NMR Manager, HNMR Predictor and ACD/CNMR Predictor and thus includes all the functionality and features available in these products.

What it doesn't do: It does not process or database batches of 2D NMR data and thus does not provide the quantitation and verification workflows for 2D NMR data.

ACD/2D NMR Expert:

What it does: This product provides users with the ability to perform combined verification. For a more information on the performance of combined verification, download the the two posters from the link below:

http://www.nmrsoftware.com/download/publ/2006/enc06_combverif.pdf

http://www.acdlabs.com/download/publ/2007/enc2007_gsk.pdf

It is a 1D and 2D NMR processing and databasing software that is more suited for high-throughput work. In addition it offers the ability to perform high-throughput quantiation and verification on large batches of spectra. This product comes with ACD/1D NMR Processor, ACD/2D Processor, ACD/1D NMR Manager, ACD/2D NMR Manager,  ACD/HNMR Predictor, and ACD/CNMR Predictor and thus includes all the functionality and features available in these products.

What it doesn't do: Because it includes most of the NMR products I have already described there isn't much it can't do with respect to the other products in this product line. It does not provide the ability to do Computer Assisted Structure Elucidation (CASE) which is the next topic.

ACD/Structure Elucidator:

What it does: It's a software tool that makes Computer Assisted Structure Elucidation a reality. It has been the topic of many peer-reviewed articles over the years. This tool uses 1D and 2D NMR, MS, Chromatography, and UV-IR data to automatically propose the chemical structure identity of unknown compounds. It includes ACD/1D NMR Processor, ACD/1D NMR Manager, ACD/2D NMR Processor, ACD/2D NMR Manager, ACD/ChromManager, ACD/MS Manager, ACD/UV-IR Manager, ACD/HNMR Predictor, ACD/CNMR Predictor, and ACD/2D NMR Predictor. Because it includes all of these software products it can process and database 1D and 2D NMR, MS, Chrom, and UV-IR data. In addition it can be used to predict 1H and 13C NMR spectra.

What it doesn't do: It cannot perform the high-throughput verification and quantitation that is available in 1D and 2D NMR Expert.

Finally, ACD/1D NMR Manager has a couple of additional database add-ons. In order to have access to these databases, users must have a copy of ACD/1D NMR Manager:

ACD/Polymer Database: It is a pre-built database for ACD/1D NMR Manager users that contains the assigned 1D NMR spectra for over 430 polymer compounds. Because it is a 1D NMR Manager add-on, it uses all of the NMR Manager searching capabilities.

Chenomx Metabolite Database for ACD/Labs:  It's another pre-built database for 1D NMR Manager users who wish to access the Chenomx library containing 800 MHz ¹H NMR spectra of 265 of the most common metabolites found in urine and blood.

Aldrich NMR Library for ACD/Labs: One more pre-built database for 1D NMR Manager users that provides access to the 1H and 13C NMR spectra of over 15,000 Aldrich compounds.

That's it! Whew!....I hope that is useful for someone out there.

In addition to all of these products, many of them integrate with each other to bring very useful workflows for specific end-users. I'll save that topic for another entry. 

P.S. All of the products mentioned above also include ACD/ChemSketch a chemical drawing package.

The Top 10 Best Kept Secrets in ACD/Labs NMR Software

To follow up with my post on the "Curse of Knowedge" I thought I would make an attempt to share some more things that we dangerously "assume" you know about, but in fact, you might not.

Here, in my opinion, are 5 of the best kept secrets in our NMR software. Features, products, and applications that you may not know about that you absolutely should.

5. The Chenomx Metabolite Database for ACD/Labs. Back in late 2005 we partnered with Chenomx to provide users of our NMR Manager product to access and search the Chenomx library containing 800 MHz ¹H NMR spectra of 265 of the most common metabolites found in urine and blood. This add-on provides a niche application to those metabolomics users out there who have adopted ACD/Labs processing tools. By the way, check out the Chenomx Blog.

4. The ACD/HNMR, CNMR, PNMR, NNMR, and FNMR DBs. Most people are aware of our our prediction software for all of these nuclei. What some people don't know is that the databases of chemical structures and assigned experimental values that we have compiled and quality checked over the years for NMR prediction are also available separately. With these tools a user can search chemical shifts, structures, substructures, etc. The database records include information such as chemical structures, chemical shifts, coupling constants, experimental parameters, and conditions, original references and more. With these tools you have a huge amount of experimental NMR data at your fingertips.

3. The Calculation Protocol. I am amazed by how many times I show users this for the first time. Following a prediction, users can view which chemical structure's experimental values were taken under consideration to generate a predicted chemical shift. Many users find this feature useful in helping them judge whether or not a predicted value can be trusted:

To access this protocol simply right-click on the atom that you wish to see more information about. More information can be found in this document:
http://www.acdlabs.com/download/technotes/100/nmr/chnmr_predictor.pdf

2. Multiplet Report . I've mentioned this a few times before on here but it bears repeating. You can use J-Coupler to either automatically or manually characterize multiplets in ACD/1D NMR Processor. While the time savings of automatically measuring coupling constants was termed as "useful" (you can put away those rulers now), this wasn't the "killer" application.

Surprisingly it was the simple creation of a multiplet report in journal format. One like this:
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) 8.82 (s, 1 H) 8.87 (s, 1 H) 8.94 (s, 1 H) 9.18 (s, 1 H)

Apparently this is one of the most tedious things a chemist has to perform when writing a patent or publication. Typing, formatting, editing, etc. The fact that they can do it with one mouse click, is apparently, "invaluable."

Recently one of our application scientists went on-site at a pharma company that has ACD/1D NMR Processor for all of their chemists. When he showed them this feature he got a heavy round of applause!

Once you have characterized your multiplets, simply click on the "Report" button in the J-Coupler box to create the formatted report. It can then be easily copy and pasted into another application.

Download or view the movie on how to use J-Coupler and create a formatted report.

1. Structure and Substructure Searchable Reports. My hope is that most of you know that all of ACD/Labs software products also come with a copy of ACD/ChemSketch. Of course as a stand-alone product, it's a really nice chemical structure drawing package. However, when combined with ACD/1D or 2D NMR Processor or Manager, it becomes a very nice reporting tool. Perhaps the best part is that once you create these reports you can easily retrieve these documents from your hard drive by searching by structures, substructures, or similar structures. In ACD/ChemSketch, go to the Tools menu and select, "Search for Structure..." From here you can select the directory you want to search and hit "Search"

Then by double-clicking on your result, you will launch the report:

Feel free to add your own comments on this entry.

 

The Curse of Knowledge

I recently read a great book by brothers, Chip and Dan Heath called Made to Stick.

It's basically a book about how to make ideas stick. It's a terrific read and I would highly recommend it to anyone who teaches chemistry, NMR, or anything for that matter. There are some great insights in the book.

In the book they talk a lot about the Curse of Knowledge. From the book:

"Lots of us have expertise in particular areas. Becoming an expert in something means that we become more and more fascinated by nuance and complexity. That's when the Curse of Knowledge kicks in and we start to forget what it's like not to know what we know. At that point, making something simple can seem like "dumbing down." As an expert, we don't want to be accused of propagating sound bites or pandering to the lowest common denominator. Simplifying, we fear can devolve into oversimplifying."

In the business of software development, we run into this all the time. Fact is, we are experts in our own software. Many of us have been working for the company for a while and using the software every day. We know the ins and outs and all the hidden features in the software. Workflows within the software come to us without even having to think about which button to click and which option to select. For this reason, we sometimes get trapped in software development and assume some tasks are incredibly clear and easy when they are in fact not. Let me give you an example.

One of the most common question I am asked about NMR Processor for example, is, "How do I attach a structure?"

My first thought is that this is dead easy. But is it? Or am I a victim of the curse of knowledge? I think it's the former. Let's start from the beginning. Let's say I have a processed spectrum in the processor window and I am ready to add a structure. The screenshot below is an example of what I see (click to enlarge):

So if I am looking at this screen from my own perspective, it's pretty obvious what I do next. But if I try and look at this from a first-time user's perspective, well, it's pretty hard to figure out what to do next.

Unfortunately,the word "structure" is nowhere to be found on the screen. For those of you who know how to do this, you can stop reading now, I hope that I have emphasized one of the biggest challenges we face in software development. For those of you who don't know how to add a structure, I will take the time to explain it in the remainder of this entry.

1) From the Processor window, switch to ChemSketch by clicking on the "ChemSketch" button on the bottom left-hand corner of the screen.

2) Once in ChemSketch, open a file by selecting the "File" menu and clicking on "Open" (Ensure you identify your Files of type using the drop down menu). Alternatively, you can copy and paste a chemical structure from a different drawing program into ACD/ChemSketch.

3) Once the structure is added, simply click on the "Processor" button on the bottom of the screen. The "Select Action" box will appear and you will need to choose the "Attach structure to the current spectrum" option and click OK. You're done.

Of course it isn't just software managers and developers that are victims of the Curse of Knowledge, it's anyone who has expertise in a particular area, who then tries to teach or communicate that knowledge to someone else. So if you are an NMR spectroscopist who is responsible for training chemists how to use the instrument, or if you are a professor at a university trying to teach NMR to undergrads, or if you are a researcher preparing to present your research at a conference...beware the Curse of Knowledge.

To learn more about the Curse of Knowledge and how to make ideas stick, visit Chip and Dan's blog at:

http://www.madetostick.com/blog/

Antony J. Williams

Over at the ChemSpider Blog, Antony Williams has gone public with his decision to leave ACD/Labs in pursuit of something new. This marks a very sad event for our company as over the years Tony has contributed immensely to the development and growth of this company in so many different ways. While I have worked closely with Tony over the last 4 years, I cannot begin to comment on all the things he has achieved within this company as it would require me to talk to several different people of ACD/Labs past and present, and would result in a very, very long blog positing.

As it relates to the NMR software product line, some of you are likely aware that Tony was formerly the Product Manager for NMR at ACD/Labs before moving on to various other positions within the company. Brent Lefebvre has since taken over and in my opinion has done a terrific job of managing the product line as we continue to improve on our current offerings and bring exciting new software products to the market. Trust me when I say that Tony has left the NMR product line in very good hands.

While Tony left that position behind, he still remained over the years heavily involved in the research and development and business aspects of the product line. He served as a great resource for market insight as well as technical expertise in the field of NMR. He also was very eager to pick up the phone and keep in touch with many of our NMR software users.

Overall I think the best characteristic Tony brought to this company was his passion. For any one of my readers who have met Tony, I think you will agree that his passion for science is something that comes through from the very beginning. That passion bled through into his various roles in this company and is a big reason why ACD/Labs is the successful company that it is today. We have an incredible team at ACD/Labs but despite that, I truly do not believe we would be where we are today if not for Tony.

This being said, I think Tony (along with many other key players) have built a strong foundation for this company. While his exit certainly marks a sad event for this company, he has instilled much of his qualities, ethics, knowledge, and passion in many different people throughout our company. I am confident that the people that remain at ACD/Labs will continue to improve our software offerings and business practices. There will be challenges ahead but I am confident that we have the right people in the right places to continue to move forward and innovate.

Tony is a tremendous colleague and a very good friend. His openness and personable nature came through from the first conversation I had with him when I interviewed for ACD/Labs. I will certainly miss him and he will no doubt be missed by all in the company.

Tony, I wish you the best of luck in your future endeavors, and hope you truly enjoy the next few months of downtime with your family and friends.