STRUCTURAL FORMULAE - INFO

 STRUCTURAL FORMULAE (By Chemical Name)

 STRUCTURAL FORMULAE (By Page Name)

 <-- By Chemical Name

 <-- By Page Name

The 'By Chemical Name' heading lists all those by Chemical Name, whereas the 'By Page Name' may list a whole host of chemical structural formulae under just the one Page Name. Thus 'By Page Name' allows the user to see all the chemical formulae without missing any and without seeing the same page twice, or more.

Chemical structural formulae of natural compounds found in plants.

Of course, many thousands of different chemicals are produced in every plant, some poisonous, some useful in medicine, others useful in industry, but many of only use to the plant itself (although it is quite possible that some are of no use whatsoever to the plant and are just relics of past natural selection, hybridization, random mutation or infections by virii, etc.).

This category highlights only those compounds of extra special interest.

The plant may produce substances toxic to those that try to eat it as a defence against being eaten, within the seeds especially. Or it may produce substances that are fungicides as protection from being invaded by fungi.

Contrarily, it may produce sweet substances designed especially to be eaten, especially within berries, in order that its undigested seeds are dispersed in droppings. Or it may produce compounds in the flowers that are pleasantly odorous (perhaps insect pheromones) or that taste sweet (nectar) in order to attract insects who will inadvertently pollinate other flowers of the same type as itself. On the other hand, some flowers go out of their way to produce chemicals that smell nauseously of decaying matter, or of droppings, specifically to attract those that eat carrion or dung. Presumably the motive is incidental pollination; the transfer of pollen from one flower of the same species to another.

Most flowers are coloured in striking colours by anthocyanins, designed to attract attention by sight rather than smell. Some flowers have striking patterns visible by only those insects that can detect reflected ultraviolet light, or that can see optically polarised light (such as some flying insects).

Many plants produce coloured compounds (mostly reds) to protect the leaves from the excesses of strong sunlight, and may turn red in response under such circumstances. Herb Robert is one such plant which exhibits this response, but there are many others.

Before the leaves drop off in the autumn it is essential that the plant tries to recover and sequestrate as as much as possible of the precious nitrogenous compounds, especially for those plants that cannot fixate nitrogen (almost all Families except the Pea Family). In the autumn chlorophyll decomposes into a plethora of compounds, many orange, yellow or red coloured anthocyanins or xanthophylls, turning the leaves first limey-green, then yellow through orange to reds and eventually to brown. The anthocyanins and xanthophylls are there to protect the nitrogen sequestration process.

It is obvious that plants are capable of synthesizing a great many exotic chemicals that are otherwise extremely difficult to synthesize in the laboratory, so it is little wonder that, even in these days, plants are still grown for the intricate and varied chemicals that they can manufacture with ease.


NOMENCLATURE OF PLANT CHEMICALS

Many, but not all, plant manufactured chemicals are named after the Latinish name of the plant within which it was first discovered. This does not necessarily mean that that particular plant produces the highest concentration of that particular chemical (rather than some other plant).

Examples include:

  • Taxol from Taxus brevifolia (Pacific Yew).
  • Tanacetin from Tanacetum Vulgare (Tansy)
  • Solanine from the Solanaceae Family (Nightshade Family)
  • Ptaquiloside from Pteridium Aquilinum (Bracken)
  • Humulene from Humulus Lupulus (Hop)
  • Lupulone from Humulus Lupulus (Hop)
  • Euparin from Eupatorium Cannabinum (Hemp Agrimony)
  • Damascenine from Nigella Damascena (Love-in-a-Mist)

Whole books have been written on the chemical nomenclature of organic compounds. Several links follow:
 IUPAC nomenclature of Organic Chemistry

And for those really into chemical nomenclature, let them read from the horses mouth (but be warned, this is not for the feint-hearted or the light-hearted ponderer):
 IUPAC Nomenclature

Good luck!


SYNONYMS

It is quite obvious that a great many compounds have an excess of synonyms assigned to the very same chemical. This may have happened because in the dim and distant past biologists must have named the compound as soon as they found it within a plant without properly ascertaining its chemical formulae or structure. Thus the same compound ends up with numerous names, each associated with a differing plant. For instance, Senecionine, a poisonous pyrrolizidine alkaloid [found in Common Ragwort (Senecio jacobaea)] is also called 'Aureine' and 'Squalidine' [from Oxford Ragwort (Senecio squalidus)]. This profusion of names must have caused endless confusion, and still does to this day. The legacy lingers on. It wasn't until better methods of chemical analysis of very small samples in the 20th Century got underway before the chemists could be certain of the chemical structural formulae of samples from plants. The early analysis was probably also confounded by the samples containing more than just one substance.


STRUCTURAL CONFORMATION

Structural Formulae are notorious for being shown in a plethora of differing ways. Not only is the orientation of the molecule shown in variously differing rotational alignments and reversals, but the shape of even the simplest ring is often shown differently.

It is possible to show a three-membered ring in only one way: an equilateral triangle. As the number of atoms in the ring increases, so too does the number of conformational ways in which these rings can be drawn.

A five-membered ring can be shown as a regular pentagon, or with two parallel sides.

A six-membered ring is almost invariably shown as a regular hexagon, but can also be depicted in a 'chair' (as in sugars) or 'boat' configurations.

The difficulty arises more with macro-cyclic molecules. These are variously shown as regular polygons, rectangles, heaxagonal arrays with the mid-spokes missing or any number of other convoluted shapes. All to represent the same molecule. This all makes recognition and appreciation of similarities between differing chemicals very much more difficult.

There is arguably only one correct way to show the molecules, and that is as a 3D molecular model, but even these may be subject to conformational changes (rotating side branches, stereo-isomers, and other bi-stable (or multi-stable) conformational changes, some dependant upon pH or presence of water or other chemical surroundings). But 3D models are not the easiest of representations to comprehend, especially without 3D glasses.

The author is endeavouring to standardise his drawings in ways that help comprehension and show similarity to other chemicals, but this is not always possible. The reader may have to flex the molecules shown in order to see the relationships between them and others.


All chemical Structural Diagrams are drawn using Stephen Browns' !2Dchemist application, which runs only under RISC OS.



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