I’ve been involved in a number of conversations recently around how monoisotopic masses can be used and the chance of “elucidating a structure” from a molecular formula. There are some shockingly naive views of this possibility. With the availability of accurate mass determinations by mass spectrometry, and the possibility to extract a molecular formula from the data, there are some who believe it is possible to “elucidate structures” using a monoisotopic mass. Let’s clear this naivety up…

Recently I gave a presentation at a local university regarding informatics. During the presentation I asked the students how many structures could be generated “withint the rules of basic organic chemistry” for some very short elemental formulae. General rules means no inappropriate valences but no limitations on the nature of the rings (except none base don 2-carbons ) etc. EVERYONE underestimated by many factors.

While working on a structure elucidation software program the issue of how many structures could be generated from some fairly nominal formulae became very clear. Below are some example formulae, the “correct” structure associated with the data under analysis and the number of chemical structures that can be generated from this formula. Notice those numbers….numbers like: 138,136,211,624 structures from a formula of C15H22O2 !

Therefore,_the story that monoisotopic mass, that can give a single molecular formula, can give you an unambiguous chemical structure needs to stop. Now, that said, since we have close to 20 million structures online at present the question “What is the distribution of molecular formulae across ChemSpider?” was an interesting question. So, we ran a query to determine the highest frequency of formulae. The formula C18H20N2O3 occurred 5110 times in the database, 4804 times when looking at single components only. Some representative structures are shown:

I imported the data into Excel (Office 2003) with a 65000 row limit. While there are single molecular formula compounds in the list at the end of the file (viewed in wordpad) at the 65000′th row the frequency was still 45 entries in the database. It’s a long tail..

Now, many people are using mI masses to examine metabonomics data so it may be more appropriate to do the analysis on a more restricted dataset. For example, databases of interest to metabonomics people include KEGG and HMDB. Isolating the search to such databases shows that while there is a much shorter list of unique formulae (8590) a similar distribution persists . The most common formula is C6H12O6 with 71 hits. Searching this in the database shows a number of linear and cyclic carbohydrates, some with stereo, some without as shown below. if you are confused about “linear versus cyclic” see this Wikipedia article.

Monoisotopic mass isn’t going to provide the stereo information anyways and all you will get is a lot of similar structures…but of course there are MANY carbohydrates with that formula. I’ve the listed a group of some of the top formulae here and leave it to you to investigate!

Formula Number

C12H22O11 = 55 hits

C6H8O7 = 52 hits

C5H10O5 = 46 hits

C20H3205 = 46 hits

C8H803 = 40 hits

C20H32O3 = 39 hits

C20H32O4 = 38 hits

C2H4O2 = 38 hits

C24H40O4 = 37 hits

CH4O3S = 36 hits

Bottom line…even removing stereo issues and isolating to a small number of databases it is still an issue to declare that a structure is elucidated just from a mass and some form of prior knowledge or additional information such as elution order or time is necessary.

Now, this observation may not be surprising to many people. The response may be that tandem Mass Spectrometry would give an ambiguous structure. This is also not true unfortunately and in general even tandem MS (MS^n) cannot give a conclusive structure. Certainly, if stereochemistry is involved (as with many carbohydrate molecules) you are still stuck. While library look-ups using monoisotopic mass ARE valuable, and tandem MS adds more criteria for structure identification, neither are unambiguous.

I was approached today with a question regarding the contents of the ChemSpider database. I have commented previously about the fact that there are quality issues based on some of the depositions but that these are being cleaned up fairly quickly because of the efforts of our curation processes, both robotic and manual. The question was regarding the fact that there were two structures on ChemSpider with the registry number 34090-76-1. This is not uncommon. There are occasions when a registry number is appropriate for a particular salt form while the associated structure is the neutral compound. So, the registry number will be on the database for both the neutral compound and the salt. However, this situation was different…it was down to the position of the double bond. The person was out to confirm the position of that double bond. It was not easy for me to confirm.

What was MORE confusing was what the person had already extracted information from an STN Registry Search. That search provided the following information:

CAS Name: 1,3-Isobenzofurandione, tetrahydro-5-methyl- (CA INDEX NAME)
Other listed names:
Cyclohexene-1,2-dicarboxylic anhydride, 4-methyl- (8CI)
4-Methyltetrahydrophthalic acid anhydride
5-Methyltetrahydroisobenzofuran-1,3-dione

And the following structure:

Compare this structure with the other two off of ChemSpider shown below in the array of three.

Every_single name from STN is listed as a “tetrahydro” compounds so, there needs to be a double bond in the molecule by default. If there isn’t then the compound is a “hexahydro” compound.

Obviously one of the alternative names for the compound was derived from phthalic acid anhydride and this suggests that the “missing double bond” should be at the ring junction as shown.

Included in the STN record is the tag “IDS” tag in the “CI” or “chemical Indexing” field. The term IDS stands for “Incompletely Defined Substance”. So, this is an example of a registry number being allocated to a compound that, in this case, is known to have an additional double bond but it is not shown on the chemical structure displayed in the STN search results but ICS declares it as being “incompletely defined”. Some might say that the fact that ChemSpider has two structures associated with the registration number but each with the double bond in a different position is appropriate. But likely those specific compounds have their OWN registry numbers. So, what should we do?

1) Remove the registry number 34090-76-1 associated with both structures?
2) Leave as is?
3) Add a new term ICS for such records and submit the new incompletely defined substance as a new form of structure?
4) Add NEW registry numbers associated with the individual structures (which someone will need to source since I don’t have them)
5) Something else?

I welcome any or all input. Based on input I will simply login to ChemSpider, make the edit and the information is changed (for addition or removal of identifiers). By working together like this there is an iterative improvement in the quality of structure-name pairs for the benefit of chemists, just as shown with the recent Wikipedia examination of Taxol.

Attention synthetic organic chemists. Most scientists have skeletons in the closet. Problems they cannot solve and observations they cannot explain. A couple of years ago I was involved in a project to slve the structure of a compound. It had remained unresolved by manual interrogation of the NMR data for over a decade. The application of a computer-assisted structure elucidation system helped resolve the structure. It is described in detail in this publication.

Quindolinocryptotackieine: the elucidation of a novel indoloquinoline alkaloid structure through the use of computer-assisted structure elucidation and 2D NMR

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!