Let’s turn our attention now to other kind of acids. You know what I’m talking about: carboxylic acids. Here’s the simplest one (a):
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If we compare the structure (a) with that of our old friend, carbonic acid (b), we’ll notice that the only difference between them amounts to one oxygen atom.
The descriptors ‘α’ and ‘β’ are also used in carbohydrate nomenclature to specify configuration of cyclic monosaccharides [1, P-102.3.4.2.1]. You may remember that aldehydo-glucose, the open-chain form of glucose, has four chiral centres. Consider the structures (a) and (b):
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Upon cyclisation of either enantiomer, an extra chiral centre is created at the position 1. This centre is referred to as anomeric centre [2, 2-Carb-6.1] and two resulting stereoisomers are anomers. For example, cyclisation of aldehydo-D-glucose (a) brings about two major forms of D-glucose, (c) and (d):
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Here’s a molecule everybody must have heard about: testosterone (a).
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Have a look at the structures (a) and (b). They are the stereoisomers of laballenic acid, with (a) is naturally occurring in plants of the Lamiaceae family. What kind of stereoisomers are they?
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-laballenic_acid.png) |
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If there was just one double bond in the middle of the molecule, we’ll be dealing with cis/trans isomerism. But we have two cumulative double bonds, which makes our molecules chiral, even though there are no chiral atoms. Why?
What’s the difference between the structures (a) and (b)?
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Have a look at the structures (a) and (b).
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I’m sure you came across names such as ‘ethyl alcohol’ or ‘vinyl chloride’. Do they remind you of binary-type names so common in inorganic chemistry? This is because they also consist of two words. There is an important difference though. The inorganic binary-type names always comprise positive/negative pairs, as in ‘sodium chloride’. The names like ‘ethyl alcohol’ consist of “specific” part followed by “generic” part*. Thus ethyl alcohol is an alcohol. All alcohols have a generic formula R–OH; in our alcohol, R = ethyl group.
These names are easily interpretable in terms of linear formulae. So ethyl alcohol (substitutive name ethanol) has a formula C2H5–OH and vinyl chloride (substitutive name chloroethene) is H2C=CH–Cl.
The prefix ‘cyclo’ is used in chemical names to indicate a ring structure. In additive nomenclature, this prefix is usually italicised and followed by a hyphen, as we have seen for polynuclear entities such as cyclo-tri-μ-oxido-tris(dioxidotungsten). On the other hand, in substitutive nomenclature ‘cyclo’ is not italicised, there is no hyphen, and no other prefixes could be inserted between ‘cyclo’ and the root, as in cyclopropane.
Somewhat confusingly, this prefix is also employed in skeletal modification nomenclature when an additional ring is created [1]. In the names generated thus, ‘cyclo’ has to be preceded by the locants of the skeletal atoms that form a new bond.
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Both skeletal replacement and ‘nor’-type subtractive naming methods can be considered subtypes of skeletal modification nomenclature. And there are more.
Consider homocysteine (a):
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A variant of subtractive nomenclature employs the prefix ‘nor’. Probably the most famous example is the neurotransmitter noradrenaline aka norepinephrine (a):
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These names are derived from the trivial names of (b), adrenaline or epinephrine. In this particular example, the meaning of ‘nor’ is the same as ‘demethyl’.
Humans were consuming, growing and trading (in this order) the psychoactive plants and derived substances since time immemorial. Most governments tried (and failed) to control and restrict them. Without these plants, not only pharmacology as we know it would not exist, but the whole human history would be completely different. Surely Guía de las plantas psicoactivas by Dr. Josep Lluís Berdonces i Serra [1], published by Ediciones Invisibles (I am not joking) is not the first and not the last book dealing with this topic. Why would we need another one? That’s exactly the question Jonathan Ott, the author of classic Pharmacotheon [2], asks (and answers) in the preface, which also mentions such classics as Plants of the Gods [3] and The Encyclopedia of Psychoactive Plants [4]. As for me, I just saw this beautifully illustrated book on display in the library and felt compelled to borrow it. It is written in a lively, easy-to-read Spanish. For such a relatively slim volume (333 pages including appendices and index), it’s surprisingly informative. I learned that...
It also contains a short chapter on psychoactive fungi and another one on pharmacology of principal active compounds, including (o joy!) their structural formulae. Perhaps inevitably, there are some omissions (which I hope will be addressed in the subsequent editions). For example, Guía dedicates enough space to coffee and kola, but where is tea? To fix that oversight, we’ve published our own short guide to psychoactive plants illustrated by Tamara Kulikova.
In Dr Ott’s view, this book “viene a expandir nuestros horizontes” (came to expand our horizons) — without the necessary consumption of its protagonists. With a cup of tea, maybe.
I was intrigued by the article in New Scientist which starts with the question, “Do you speak chemistry?” [1]. So much that I asked my friend to send me the original paper [2] authored by the Bartosz Grzybowski group of Northwestern University in Evanston, Illinois. It is a curious reading.
Don’t get me wrong. I have nothing against the analogies. I love the analogies. If the linguistic analogy works for chemistry, it’s fine by me. As long as everybody understands that it is just an analogy.
The authors try to “demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments”. How do they do that? They start by looking at the maximum common substrings (MCS) found in 100 sentences randomly chosen from English Wikipedia.
Perhaps not surprisingly, the most common fragment of the sentences is “e”, followed by “a” and “o”.That is surprising to me though, considering that only “a” is a word in English. I wouldn’t be surprised if it happened to be Spanish Wikipedia. Are the authors talking about letter frequency per chance? But the “top three” letters in English (from most to least common) are known to be E, T, A while in Spanish they are E, A, O. Anyway, they show that the distribution of the fragments, whatever they are, follows the power law. Then they show that the distribution of the common molecular fragments, derived from the corpus of organic molecules, also follows the power law. Big deal: so do the earthquake magnitudes, populations of cities and stock market crashes [3]. Cadeddu et al. do not seem to be bothered with that at all:
We have just shown that there exists a set of molecular fragments with which organic molecules can be described akin to a language.So far so bad; whether you are a linguist, a computational chemist or an organic chemist, both methodology and conclusions of this paper are bound to make you cringe. So, my immediate reaction was to dismiss it altogether. Ogres are not like cakes. Organic molecules are not like a language. End of story.
But could it be that I am missing something? On the one hand, the language of chemistry — whether we are talking trivial names, systematic names, or graphical diagrams — is very much like any other language: a system of communication. On the other hand, the molecules themselves are not. Unless they are the information macromolecules. The message encoded in a single DNA molecule can be very much abstracted from its chemical structure. Without any doubt, genetic code is a communication system, therefore it is a language, although not man-made.
It’s interesting that the authors view organic molecules as “sentences” rather than “words”; the latter would be the nomenclaturist’s approach. I guess it depends on your taste, or language preferences. Most systematic chemical names look alien in English but would fit rather nicely in German or Finnish. I personally view any chemical name as a noun phrase describing a corresponding molecular entity; a molecular entity itself is not a noun phrase. However, in natural languages, there rarely is a confusion regarding the boundaries of a word:
a word is the smallest element that may be uttered in isolation with semantic or pragmatic content (with literal or practical meaning).On the contrary, Grzybowski’s “words” are the molecular fragments which do not exist in isolation. It is also worth noting that in the world of biopolymers, say nucleic acids, each monomer (as complex as any of Grzybowski’s “sentences”), is often represented as a letter, while an entire bacterial genome (still a single DNA molecule) could be considered a War and Peace (or Crime and Punishment).
Cadeddu et al. further claim that linguistic approach identifies the symmetry/repeat units in molecules such as α-cyclodextrin and porphyrin:
We emphasize that this is not a small feat given we have not even considered any (x, y, z) coordinates of the atoms making up these molecules and performed no linear-algebra analyses to find symmetries which, incidentally, can be a computationally intensive procedure involving manipulation of matrices.I find this modest remark regarding the size of the “feat” within the body of a scientific article in a respectable journal really cute. Are the authors even aware that there are chemical similarity/substructure search engines? You don’t need atomic coordinates to identify the fragments with the same connectivity.
Which brings me to the final point. What is the “chemical linguistics” anyway? If the “words” of chemistry, as postulated in [2], are nothing else but molecular fragments, or substructures, then the chemoinformaticians were doing the substructure search of chemical databases for donkey’s years without knowing that it is called chemical linguistics. I am aware of completely different use of this term in a sense “mining of natural language texts for chemical information” [4, 5]. This latter use is well-established and I think applying the name “chemical linguistics” to unrelated area will only confuse everybody.
That’s right: the smell of pine trees from boreal forests could mitigate the global warming — provided that the global warming doesn’t kill the forests first [1]. The volatile organic compounds (VOCs), responsible for the smell of pine, react with atmospheric oxygen to form aerosols. These aerosols scatter solar radiation and also act as cloud condensation nuclei, thereby affecting the Earth’s radiation balance. An international group including researchers from Finland, Germany, Denmark and USA has discovered a direct pathway leading from several biogenic VOCs, such as monoterpenes, to the formation of extremely low-volatility vapours (ELVOCs) [2].
These vapours form at significant mass yield in the gas phase and condense irreversibly onto aerosol surfaces to produce secondary organic aerosol, helping to explain the discrepancy between the observed atmospheric burden of secondary organic aerosol and that reported by many model studies. We further demonstrate how these low-volatility vapours can enhance, or even dominate, the formation and growth of aerosol particles over forested regions, providing a missing link between biogenic VOCs and their conversion to aerosol particles.
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| Structures of the main VOCs studied by Ehn et al. [2] |
The air was sampled in Hyytiälä, Finland and the chamber experiments were conducted at the Jülich Research Centre in Germany.
I really enjoyed the latest issue of Chemistry International. Did you know that pterin is called “pterin” because it was first isolated from butterfly wings, and folic acid is “folic” because it was first found in leafy vegetables (from Latin folium)? I just learned that from Edward Taylor’s illuminating article on Alimta [1].
Next, two papers on kilogram in the “New SI”. Currently, kilogram is defined as a unit of mass equal to mass of the international prototype kilogram (IPK), which is a cylinder made of 90% platinum—10% iridium alloy kept at the International Bureau of Weights and Measures in France. The problem is, IPK is losing mass! But even if it did not, it is still not good that one of SI base units is linked to an artifact rather than to something more fundamental. The chemist in me prefers the definition of kilo based on carbon-12 mass [2] to the one based on Planck constant [3].
Finally, essay by Jan Trofast on discovery of selenium [4]. I didn’t know that Swedes discovered so many elements!
The crystal structure of the P450 monooxygenase from Actinoplanes teichomyceticus (CYP165D3) involved in biosynthesis of antibiotic teicoplanin has been solved [1].
Following the call to the community from Antony Williams, I indulged in some chemical drawing. I did redraw structure 1 from this paper from scratch to get (a). This is very much like structure of digitonin in ChEBI (b), except for methyl group at C-20 which goes up in (a).
 (a) |  (b) |
Muhr et al. wrote:
With our investigations, it was possible for the first time to confirm beyond all doubt the structure suggested by Tschesche and Wulff for digitonin by means of modern NMR techniques, and to assign all proton and carbon resonances.
Now I was not able to get to the full text of Tschesche and Wulff, but at least their abstract contains the German name “3[β-D-Glucopyranosyl(I)(1→3Galakt.II)-β-D-galaktopyranosyl(II)(1→2Gluc.III)-β-D-xylopyranosyl(1→3Gluc.III)-β-D-glucopyranosyl(III) (1→4Galakt.IV)-β-D-galaktopyranosyl(IV)(1→3-Digitog.)]5α,20βF,25α Spirostantriol(2α,3β,15β)”, which kind of confirms 20β configuration. (The default configuration of spirostan is 20α.)
I guess this still does not answer what the “correct” structure of digitonin is. All we can say that Muhr et al. reported the structure (a).
We’ve got this wonderful, profusely illustrated book bought for the office, called Molecules That Changed the World, by K. C. Nicolaou and T. Montagnon. I’d say some of the molecules mentioned there (like LSD) change not so much the world per se but our perception of the world. Still, I’d recommend every chemistry or chemistry-related department/lab to have this book.
On p. 42, it quotes Sir Robert Robinson’s wise words on the value of basic research (from his Nobel Lecture):
The synthesis of brazilin would have no industrial value; its biological importance is problematical, but it is worth while to attempt it for the sufficient reason that we have no idea how to accomplish the task. There is a close analogy between organic chemistry in its relation to biochemistry and pure mathematics in its relation to physics. In both disciplines it is in the course of attack of the most difficult problems, without consideration of eventual applications, that new fundamental knowledge is most certainly garnered.
Continuing with hard rock theme: the December 2008 ChEBI Entity of the Month was a natural fluorochrome epicocconone, also known as “Deep Purple” and “Lightning Fast”. I think that will increase our traffic a bit as more and more Deep Purple fans discover wonders of ChEBI.
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