Emergence of Organic Chemistry
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...
2000, I was in my office playing with the congeneric array
interactions discussed over the previous few pages. I was using
my favourite graphics package (Macromedia Freehand, here)
to cut-n-paste, when I built the following array interaction:
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!"
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:
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.
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.
are insoluble in acid, neutral water and alkali. Alkanes are chemically
inert with respect to these environments.
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.
(of lower molecular weight) are fully miscible with water which they
- Alkyl fluorides
are chemically inert, they are not soluble in aqueous acid or alkali.
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
- 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:
(no chemistry), for example: Lewis acid + Lewis acid
Lewis acid + Lewis base
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
Thus, the protonation
of hydroxide ion has two interaction steps.
If we start with
the oxide ion, O2, there are three recursive steps:
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
Language is also a generative
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
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
- 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
There are differences:
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,
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
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
is special about these species?
have a chiral centre, and each can exist as a pair of d/l or R/S of
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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