Structure Elucidation

May 20, 2008

SMASH 2008-Session on Computer Aided Structure Structure Identification

Speaking of the CASE review article in Progress in NMR, I thought I would take the opportunity to mention the upcoming session on Computer Aided Structure Identification that will take place at the SMASH 2008 Conference in Santa Fe New Mexico in September.

One of the presenters in the session will be none other than Mikhail E. Elyashberg who has made tremendous contributions to this area. In his presentation he plans to lay out the 40 year history of CASE and I am sure it will be a terrific presentation.

Stataward

8 years ago Mikhail was one member of a team of 4 who received the State Award of the Russian Federation for their pioneering work into the automated analysis of complex compounds. It is great to see Mikhail continue to work, publish, and present on this topic.

Rich Beger from the National Center for Toxicological Research and Richard Newmark will also be presenting in this session.

Not to mention that Gary Martin (another Co-author of the CASE article in Progress in NMR) is slated to speak in the New Experimental NMR Techniques session.

So there's a number of reasons for you to get away from the lab for a few days in September and attend SMASH 2008.

May 15, 2008

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.


February 18, 2008

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.

February 01, 2008

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.

January 22, 2008

More on Indirect Covariance

Gary Martin has added a comment to an earlier post I wrote on Indirect Covariance and was kind enough to post an updated publication list on this topic. I have simply copy and pasted his comments in this post to provide more exposure to his list:

Ryan, it has been a while since you updated the publication list on indirect covariance methods, so I thought it appropriate to do that with a post:

F. Zhang and R. Bruschweiler, J. Am. Chem. Soc., 126, 13180 (2004).

K. A. Blinov, N. I. Larin, M. P. Kvasha, A. Moser, A. J. Williams, and G. E. Martin, Magn. Reson. Chem., 43, 999 (2005).

K. A. Blinov, N. I. Larin, A. J. Williams, M. Zell, and G. E. Martin, Magn. Reson. Chem., 44, 107 (2006).

K. A. Blinov, N. I. Larin, A. J. Williams, K. A. Mills, and G. E. Martin, J. Heterocyclic Chem., 43, 163 (2006).

K. A. Blinov, A. J. Williams, B. D. Hilton, P. A. Irish, and G. E. Martin, Magn. Reson. Chem., 45 544 (2007).

W. Schoefberger, V. Smrečki, D. Vikić-Topić, and N. Müller, Magn. Reson. Chem., 45, 583 (2007).

G.E. Martin, P. A. Irish, B. D. Hilton, K. A. Blinov, and A. J. Williams, Magn. Reson. Chem., 45, 624 (2007).

G.E. Martin, B.D. Hilton, P.A. Irish, K.A. Blinov, and A.J. Williams, J. Heterocyclic Chem., 44, 1219 (2007).

G.E. Martin, B.D. Hilton, P.A. Irish, K.A. Blinov, and A.J. Williams, J. Nat. Prod., 70, 1393 (2007).

G.E. Martin, P. A. Irish, B. D. Hilton, K. A. Blinov, and A. J. Williams, Magn. Reson. Chem., 45, 883 (2007).

B. Hu, J.-P. Amourex, and J. Trebose, Solid State Nuclear Magnetic Resonance, 31, 163 (2007).

G.E. Martin, B.D. Hilton, P.A. Irish, K.A. Blinov, and A.J. Williams, J. Nat. Prod., 70, 1966 (2007).

D. A. Snyder, Y. Xu, D. Yang, and R. Bruschweiler, J. Am. Chem. Soc., 129, 14126 (2007).

G.E. Martin, B. D. Hilton, K. A. Blinov, and A. J. Williams, Magn. Reson. Chem., 46, 138 (2008).

G.E. Martin, B.D. Hilton, K. A. Blinov, and A. J. Williams, J. Heterocyclic Chem., 45, in press (2008).

This is the list I currently have. Note that this list does not contain additional papers that pertain to homonuclear covariance processing methods. I don't have that list of publications handy that I can cut and paste into this post.

Thanks Gary!

October 19, 2007

Meet Quindolinocryptotackiene

Tony over at ChemSpider takes us on a trip down memory lane to one of the most successful stories surrounding Computer Assisted Structure Elucidation (CASE).

It is also the best example of achieving symbiosis between a spectroscopist (in this case Gary Martin) and software (ACD/Structure Elucidator) I have ever seen.

He is referring to "Solving a structure computationally after 10 years of human effort" that was presented by Gary and Tony at the ASP Meeting in 2003 (It's a long presentation but skip to slide 44 to get to the meat of the presentation).

There is also a publication on this story

Tony's purpose for resurrecting this story is as follows:

Now, we THINK we have it elucidated correctly. However, we would like to confirm it. Synthesis of the molecule in question, further NMR data generation and a crystal structure would help finish this work fully. This is a call to organic chemists to participate in a hobby project. Anybody want to help? We guarantee a publication etc. The structure is shown below. Contact me at antonyDOTwilliamsATChemspiderDOTcom. Thanks!

Hopefully someone is willing to step up to the plate.

I'd also like to take this opportunity to, once again, point out that CASE is not simply about piling a bunch of data in a piece of software and getting the answer out the other end. Sure this is possible, but it usually benefits when an experienced spectroscopist works with it and shares their knowledge of the existing chemistry. I think Gary's story is a perfect example of that.

That being said, in Gary's case, along with comments I have received from Dr. Shaun Tennant (another elucidator user) in the past, the software is an unbiased approach that will propose some things that the spectroscopist simply might not think about. Knowledge can sometimes be your enemy.

September 27, 2007

2DNMR.com

Remaining on the topic of Computer-Assisted Structure Elucidation (CASE), one of our most experienced users, Shaun Tennant, has devoted a website to Structure Elucidator where he shares some of his experiences with the software and provides a guide for users including his own tips and tricks to get started.

A must read for any elucidator users out there or anyone interested in how the software works.

Check out his site at www.2DNMR.com

September 25, 2007

Truths and Myths of ACD/Structure Elucidator

I have returned from SMASH after an enjoyable week in Chamonix. What a truly beautiful place. It was great to be in that atmosphere with many nice people from all over the world. I also must applaud the organizing committee for doing another wonderful job of coordination. I already find myself looking forward to next year's SMASH conference.

The week kicked off with our Annual SMASH seminar. Several excellent talks and I would specifically like to thank our guest speaks Jack Newton from Chenomx, Patrick Wheeler for Pfizer, and George Crull from BMS. Most of the presentations are available on the ACD/Labs website, and the rest will be added shortly.

On that topic, I want to specifically point you to a presentation given by my colleague Brent Lefebvre entitled, "Uncovering the Truths and Dispelling the Myths Behind ACD/Structure Elucidator"

There is a lot of great content in here. The two most important pieces in this presentation in my opinion were:

1) Price/Usage- One thing I think people may not be aware of is that ACD/Structure Elucidator is not just one black box product that only serves one function. In fact, it is made up of a bunch of ACD/Labs software products including ACD/1D and 2D NMR Processor and Manager, HNMR Predictor, CNMR Predictor, 2D NMR Predictor, UV-IR, Chrom, and MS Processor and Manager. In other words, the software can be used for much more that just structure elucidation. In fact it can be used every day to view, process, and database different analytical data types, and predict NMR spectra.

2) The Learning Curve- In my opinion, by far the biggest adjustment a Spectroscopist has to make in order to use Structure Elucidator is to adopt ACD/2D NMR Processor as a processing tool. The data work up and in particular the peak picking process is perhaps the most crucial step for Computer-Assisted Structure Elucidation (CASE). I am certainly not implying that 2D NMR Processor is difficult to use, in fact it is quite the opposite. The issue is that it generally requires a spectroscopist to switch over from their favorite vendor software package. This involves them getting used to a new interface, new shortcuts, and new navigation sometimes after years of use. There is certainly an adjustment period, but the rewards are great. Once a user gets used to 2D NMR Processor, they then have the option to take advantage of databasing and structure elucidation tools.

Check out the rest of the presentation to learn more.

P.S. If you would like to see if Structure Elucidator can handle one of your most difficult  problems, submit your data to the challenge here

August 21, 2007

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.

July 11, 2007

Another Article! Also, the Hexacyclinol Debate

OK, if you don't know it by now Antony J. Williams, M.E. Elyashberg, and Gary E. Martin are publication writing machines.

On the Chemspider Blog, Tony points us to their latest publication (reportedly 2 years in the making) that is in press entitled,  "Computer-assisted Structure Verification and Elucidation Tools In NMR-Based Structure Elucidation (Reference: JPNMRS1239)" to be published in Progress in Nuclear Magnetic Resonance Spectroscopy.

In the very same post, Tony discusses the hexacyclinol controversy. If you haven't heard about this, you can catch up via the following resources (including some great blogs!):

TotallySynthetic.com
In the Pipeline

Chemical and Engineering News Article
C&E News Weblog
The Chem Blog
The Curious Wavefunction

Now that you are caught up, the news from ACD/Labs is that they we have worked with John Porco's group (the group that actually synthesized the alternative structure). The work involves using ACD/Structure Elucidator to generate the correct assignments for the molecule.

Surprise, surprise Tony is promising a publication outlining this work. Head over to the Chemspider Blog to read the abstract for this publication presently being submitted as well as a schematic of the final 1H NMR assignments.

Keep those publications coming guys!