Dalke Scientific Software: More science. Less time. Products
[ previous | newer ]     /home/writings/diary/archive/2003/10/14/molecular_formula

Molecular Formula - History of Chemical Nomenclature

This has been a hard set of essays to write because I actually know very little of the real history of chemical nomenclature and because it's a complicated topic. I know how things work now, for computers, but not how we got here. John Bradshaw's talk at MUG '01 (which I missed) and other MUGs, and Eugene Garfield's PhD thesis An Algorithm for Translating Chemical Names to Molecular Formulas were very helpful, as was an email exchange with Dave Weininger. I hope to chat with Dave some more, to help fill in the missing parts. Perhaps I'll even interview him. :)

Where do chemical names come from? If you ever read very old books which mention chemistry you might have come across names like "spirit of salt" (hydrochloric acid) or, since the early chemists were German, names like äpfelsäuer (malic acid). Cool sounding names, but not used any more. That tradition evolved out of the alchemy tradition where you described things on the basis of where they came from (along with a lot of obsfucation because you didn't want anyone else to know your secrets). "Spirit of salt" was made by mixing sulphuric acid ("spirit of vitriol", where "vitriol" is the glassy metal sulphate) and salt. Malic acid is what makes the apple taste sour, and is the source of the taste of many a hard candy. Here's another fun one; formic acid was so named because the carboxylic acid was originally distilled from ants (Latin: formicae).

I was looking for a good on-line reference to a story which used old chemistry terms. I couldn't find one, but I did recall that Jules Verne's Mysterious Island had some nice chemistry in it. Chapter 17 describes making nitroglycerin ("dynamite was not yet known at the time when the settlers worked on Lincoln Island") with phrases like:

Cyrus Harding could have manufactured this substance by treating the carbonate of potash, which would be easily extracted from the cinders of the vegetables, by azotic acid
The novel was writen in 1875, which when you compared it to the next section gives some indication in the advances of chemistry during sixty years.

Modern chemical nomenclature started with Berzeluis, one of the so-called fathers of chemistry, back in the early 1800s. He said that chemicals should be named by what they are, not by where they came from. (After all, you can find malic acid elsewhere, like in cherries.) He created the system of 1-letter and 2-letter atomic symbols taught today in secondary school, with the letters taken from the Latin words for the element (hence "Pb" for plumbum; lead).

He proposed that compounds be described by chemical formulas based on their elemental composition. His paper on the topic, published in 1813, is a short and enjoyable read. The purpose of a molecular formula is

to facilitate the expression of chemical proportions, and to enable us to indicate, without long periphrases, the relative number of volumes of the different constituents contained in each compound body. By determining the weight of the elementary volumes, these figures will enable us to express the numeric result of an analysis as simply, and in a manner as easily remembered, as the algebraic formulas in mechanical philosophy.
A formula was not meant as a way to replace the old symbols developed by "fellow-laborers in the antiphlogistic revolution" which were used to mark the sides of the jars in the lab. (Am I also a laborer in the antiphlogistic revolution? It sounds exciting!)

Analytic chemistry gives "the relative number of volumes of the different constituents contained in each compound body." That is, the number of each element in the molecule. Sort this list of elements alphabetically and you've got a description of the molecule which is invariant; it won't change no matter the source of the sample nor the person doing the analysis.

Chemists like carbon so they actually use a slightly more complicated set of rules called the Hill order.

Thus, ethanol and dimethyl ether are both written C2H6O.

Another name for a rule is a canon. The Hill order creates a canonical molecular formula for a compound.


Andrew Dalke is an independent consultant focusing on software development for computational chemistry and biology. Need contract programming, help, or training? Contact me



Copyright © 2001-2013 Andrew Dalke Scientific AB