The Emergence of Organic Chemistry

Congeneric arrays – sets of chemical species with linear structure and reactivity behaviour traits – can react with each other to produce new arrays which are NOT congeneric.

A Bit of Personal History...

"In January 2000, I was in my office playing with the congeneric array interactions discussed over the previous few pages. I was using my all time favourite graphics package – Macromedia Freehand – to cut-n-paste, when I built the following array interaction:

[methyl anion to fluoride ion] x [alkyl substituted carbenium ions]

"I started to write how this was yet another congeneric planar with regularly changing properties of bond length (true), % ionic bond character (true) and reaction chemistry behaviour... when I suddenly realised that this was not the case at all. The species were simply NOT congeneric. Instead, some of the most common and distinct functional groups of organic chemistry emerged: alkanes, amines, alkanols and alkyl fluorides. These are chemicals known to every chemistry student, and as a set they are not congeneric.

"I spent several minutes staring at the screen in amazement. I had travelled from the main group elemental hydrides and the five hydrogen probe experiments to congeneric array interactions, where I had found a volume consisting of 80 congeneric species. Extending this array interaction logic, the 'complexity' and richness of organic chemistry had simply appeared!"

Mark Leach

The products of the carbenium ion/period 2 anion interaction are alkanes, amines, alkanols and alkyl fluorides and the formation of these chemically distinct species marks the place in reaction chemistry space where organic chemistry breaks away from main group chemistry and assumes its own distinct identity.

The reason why this particular planar bifurcates - forks - is twofold:

Firstly, the alkanes are not isoelectronic with respect to the corresponding amines and alkanols because the alkanes do not possess a functional group with a lone pair of electrons.

The two relevant series of congeneric Lewis bases run:


Notice that there is a "frame shift" between the two series, C to F and N: to Ne:. The effect is that while carbanions are congeneric with nitranions (also called amide ions), alkanes are not congeneric with amines. This is an inevitable property of congeneric array interaction logic.

Secondly, we know the chemistry of alkanes, amines, etc., by their common chemistry: aqueous solubility, chemical reactivity, etc. The crucial point is that many reaction pathways that become available over the pH range from: concentrated acid (<0) through water (7) to strong alkali solutions (>14), and this experience dominates our understanding of the materials produced by congeneric array interactions.

  • Alkanes are insoluble in acid, neutral water and alkali. Alkanes are chemically inert with respect to these environments.

  • Amines are very soluble in aqueous mineral acids where they form the corresponding ammonium salt. Amines are much less soluble in neutral water or alkaline solutions. Indeed, amines are commonly separated from other organic functions by extracting with aqueous acid, changing the pH to alkaline (basic), and extracting into a non-polar solvent.

  • Alkanols (of lower molecular weight) are fully miscible with water which they hydrogen bond.

  • Alkyl fluorides are chemically inert, they are not soluble in aqueous acid or alkali.

Very interestingly, if instead of using aqueous Brønsted acids and bases we move to aprotic solvent systems the distinction between the functional groups is much less clear. (Recall that in water, the strongest acid that can exist is [H3O]+ and the strongest base is HO.

  • Under George Olah "super [Brønsted] acid" conditions, H+/[SbF6] in liquid SO2, alkanes, amines, alkanols and alkyl fluorides are all protonated and dissolve.

Carbon, Emergent Behaviour and The Game of Life

There is an additional reason for the emergence of organic chemistry as a distinct entity.

We saw, here, that ligand exchange congeneric array interactions lead to the formation of linear and cyclic alkanes. The same logic extends to the methyl, ethyl, isopropyl and tertiary butyl series of carbenium ions used above.

There are general types of array interaction behaviour. They may be:

Null (no chemistry), for example: Lewis acid + Lewis acid

Interaction: Lewis acid + Lewis base

Recursive Interaction: This occurs where the product of an interaction is able to undergo one or more subsequent interactions.

For example, the anionic Lewis base hydroxide ion, HO, can be protonated to the conjugate Brønsted acid water, H2O. But water is also a Lewis base which can be protonated to the oxonium ion, [H3O]+.

Thus, the protonation of hydroxide ion has two interaction steps.

If we start with the oxide ion, O2–, there are three recursive steps:

oxide   →   hydroxide   →   water  →   oxonium ion.

The addition of methylene, –CH2–, functions to methane to give ethane, propane, butane, pentane is infinitely recursive.

Chemistry is a generative science, in that successive interaction steps from the periodic table lead to reaction chemistry, and this is the approach of the chemogenesis argument.

Language is also a generative system:

letters → words → phrases → sentences → paragraphs → books → libraries → Internet

One of the central findings of complex systems science – also known as complexity theory – is that emergent behaviour can develop in simple generative systems called cellular automata. One of the best known and studied examples The Game of Life invented by the British mathematician John Conway in the late nineteen sixties. A fully interactive Game of Life web site can be found here.

The Game of Life consists of a two dimensional array of squares on a computer screen. The game is played over a series of steps or generations with two simple rules:

  • If a square is off, it turns on if exactly three of its neighbours are on.
  • If a square is on, it stays on if exactly two or three neighbours are on, otherwise it turns off.

Cellular automata like of The Game of Life often develop in bewilderingly involved ways, but patterns can be seen. Games of Life have three common types of ending:

  • On screen object may grow for a few generations until it becomes static and unchanging or becomes a "blinker".
  • An object may grow for a few generations and then shrink, self-destruct and vanish.
  • Or an on screen object may eject a "glider", a Game of Life term, which moves away from the place where it formed until it collides with the edge of the playing area.

Now, there are close analogies between The Game of Life and reaction chemistry in that larger chemical structures are always built using generative chemical steps which employ the interaction rules of reaction chemistry space (reaction mechanisms).

There are differences:

• Chemistry has more species
• The interaction rules are more involved
• The playing area is not bound

But, just like The Game of Life, the reaction chemistry system has a propensity to complexity. And there are structures in reaction chemistry space which are analogous with The Game of Life endgames.

  • Many chemical interactions are null, as seen with the many the hydrogen probe experiments with white squares, here.
  • Many objects, like the congeneric volume are generational dead ends.
  • The most dramatic similarity to a Game of Life endgame is seen with ligand replacement alkane homologous series: methane, ethene, propane, butane, pentane, hexane, etc.

This system is a glider which emerges from main group chemistry and spreads out defining organic chemistry space as goes...

Isomers and Emergent Complexity

Consider again growing alkane chains: methane, ethane, propane, etc... and look at the associated isomers. There are some beautiful examples of emergent behaviour within this system:

We will add a hydroxy, –OH, functional group for clarity:

The is one structural isomer of the C1 alcohol, there is one structural isomer of the C2 alcohol, there are two structural isomers of the C3 alcohol, there are four structural isomers of the C4 alcohol and there are eight structural isomers of the C5 alcohol...

But, what about the alcohols in blue in the diagram above? What is special about these species?

These molecules have a chiral centre, and each can exist as a pair of d/l or R/S of optical isomers.

Thus, the is one isomer (structural and optical) of the C1 alcohol, there is one isomer of the C2 alcohol, there are two isomers of the C3 alcohol, there are five isomers of the C4 alcohol and there are eleven isomers of the C5 alcohol...

Systems which exhibit emergent behaviour are inherently complex, and experience shows that it is not possible to make predictions about how such systems will evolve.

The subject of complexity and emergent behaviour in chemistry is discussed here.

Congeneric Array Database
The Five Reaction Chemistries

© Mark R. Leach 1999-

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