The Mechanism Matrix
analysis identifies five types of electronic mechanism, here,
and 10 types of unit & compound mechanistic step involving molecular
fragments, here. It follows that
it should be possible to arrange these into a 5 x 10 mechanism matrix.
However and very unfortunately the resulting interaction schema
is not as useful as hoped, although it is interesting to investigate why
this is the case.
Students of chemistry often
get confused with the terms:
- Electrophilic addition
- Nucleophilic substitutionRadical elimination
- and their various
It is important to recognise
that the terms substitution, addition and elimination
can be seen with the structural changes that occur to the molecule:
- Substitution, one
moiety replaces another
- Addition, a double
bond becomes single bond
- Elimination, double
but that the terms electrophilic,
nucleophilic and radical require a knowledge of the electronic
mechanism that is occurring.
To aid understanding, the substitution,
addition and elimination changes to molecular structure
can be arranged against the electrophilic, nucleophilic
and radical electronic mechanisms in a mechanism matrix so that
any combination of substitution, addition & elimination
AND electrophilic, nucleophilic & radical is
The chemogenesis analysis identifies
five distinct types of electron accountancy and five associated
reaction chemistries, here:
Analysis of atom-to-atom
mapping can be understood in terms of unit and compound mechanistic
Multistep name reaction
The five reaction chemistries
can be arranged against the atom-to-atom mappings to give a matrix of
Alas and Alack, Where
Is The Perfect Data?
Unfortunately, the mechanism
matrix does not generate perfect data far from it
and it is most instructive to examine some of the reasons why:
- Not all of the five
reaction chemistries have associated atom-to-atom mappings with the result
that there are many blank or null cells. For example:
excitation, emission and transfer (equivalent to complexation, fragmentation
and STAD) are possible. A photoexcited species may undergo homolytic
bond fission, but this is better classified as radical fragmentation,
not as a photochemical process.
Diradicals do not
abstract or displace other diradicals.
not (obviously) occur by redox mechanisms.
- There is significant
duplication in the matrix.
into a CBr bond to give the Grignard reagent, RMgBr,
can be considered as an insertion, an oxidative process (Mg° > Mg2+), a 1,1-addition or as a special case of complexation.
can be hidden by providing different examples for each instance, for
example, use Grignard reagent formation for insertion and the Heck reaction
for oxidative 1,1-addition.
- There is simply too
much data, too many examples and too many exceptions.
A schema should collect specific information into the general themes, provide a meta-view and simplify the system. The reader may reasonably feel that the mechanism matrix
fails to achieve this.
- Name reactions are often
multistep processes that mix-and-match between the five reaction chemistries.
- After Lewis acid/base
complexation and heterolytic bond fission, "ionic" mechanisms
bifurcate into electrophilic and nucleophilic subtypes, for example: both
electrophilic and nucleophilic aromatic substitutions, SEAr
and SNAr, are known.
- The mechanism matrix
does not explicitly accommodate pericyclic reactivity.
decision was made early in the development chemogenesis argument
when Diels-Alder cycloaddition, here,
was deemed to be a Lewis acid/base complexation between a π-LUMO
Lewis acid and a π-HOMO
Lewis base to give a type 20 complex, see here.
to consider cycloaddition within Lewis acid/base chemistry
is at odds with the view that cycloaddition is a pericyclic reaction
process, and that pericyclic reactivity is a distinct, sixth type
of reaction chemistry.
This is certainly
the view taken by Ian Fleming in Pericyclic Reactions,
here, where three
distinct types of reaction chemistry are identified: radical,
pericyclic and ionic... [for 'ionic', read Lewis acid/base].
comes into its own when it is realised addition, elimination and
rearrangement processes are always better understood in terms of
FMO analysis. There
is no conflict between the chemogenesis and the Fleming views, in
fact an understanding of both positions leads to a better understanding
of the system as a whole.
reactions can be considered to be both a Lewis acid/base complexation
and a pericyclic process, in the same way that a hydride ion can
be considered to be both a nucleophilic Lewis base and a reducing
- Many reactions
particularly some of the most common main group chemical reactions
do not proceed by "obvious" mechanisms at all. Consider the
combustion reaction of hydrogen with oxygen to give water:
+ O2 >
What is the mechanism of this reaction? The reaction is clearly a "redox process" because the hydrogen is oxidised and the oxygen is reduced, and the overall reactivity can be predicted using standard reduction potential data. But how exactly does the combustion reaction occur... remembering that each discrete step must be a STAD process?
mechanism of the 2H2 + O2
reaction (shown below) has at least 11 discrete steps involving: radicals
(H, HO and HOO), diradicals (O2 and O), the neutral species H2 and
HOOH (hydrogen peroxide is an intermediate species in the combustion
of hydrogen and oxygen!) and the species, m and m*, which
carry away the kinetic energy of gas phase complexation (coupling),
as discussed here:
The combustion of methane,
CH4, with oxygen has several dozen steps.
Consider the thermal elimination
of hydrogen chloride, HCl, from 1,2-dichloroethane (ethylene dichloride,
EDC) to give chloroethene (vinyl chloride monomer, VCM):
The mechanism of the solution
phase, [Brønsted] base catalysed elimination reaction is clear.
In a concerted manner, the [Brønsted] base abstracts a beta-hydrogen,
forms, and a chloride ion (nucleofugal, Lewis base leaving group) is
ejected. For the reaction to proceed, the molecule must adopt an anti
(diaxial) conformation so that there is a 180° dihedral angle between
the H and the Cl, a requirement can be rationalised using FMO theory.
However, the industrial
process is carried out by pyrolysing EDC at high temperature, in
the gas phase and under pressure (reaction 1, below). The reaction
proceeds by a number of discrete radical reaction steps.
- First a chlorine
radical is formed by thermal fission of a CCl bond (2)
and this is the initiation step.
- The chlorine radical propagates via a two step chain elimination
- There are numerous possible side reactions, some of which are
given below (4):
Overall, the industrial process
has been optimised to give a 99% conversion of EDC to VCM + HCl. While
this sounds like an excellent percentage conversion and it is
a large VCM plant may produce 5,000 tons of VCM per day, and
that means 50 tons per day of by-product (largely waste) is formed.
One of the biggest process problems, but not eluded to on the diagram
above, is the build up of coke (carbon).
Likewise, the Haber ammonia
+ N2 >
is, overall, a redox process.
But the "gas phase" reaction has a solid phase catalyst consisting
of small crystallites of Fe with small amounts of K and Al2O3.
The reaction and associated
mechanism takes place at the heterogeneous gas-solid interface where mechanisms
are both very involved and very difficult to study. (There is an excellent
heterogeneous catalysis web book by Per
In fact, most "real
world reactions" such as the combustion of hydrogen and oxygen,
the Haber ammonia synthesis or VCM production: very, very, very involved!
Indeed, the mechanism
matrix marks the end of the chemogenesis story. The
mechanism matrix marks the places in reaction chemistry space where
the traditional organic, inorganic and industrial methodologies assume
their distinct identities and explode with information and data.
The amount of reaction
chemistry information published in the primary literature (journals),
in patents and held in industrial databases is quite simply staggering.
The RDMS To The Rescue
Reaction chemistry space
in toto is not well modelled with linear books, even hyper-linked
web books like the chemogenesis web book.
It is much more efficient to
use a relational database management system (RDMS) to arrange [database]
tables of chemical species, chemical reaction and reactions mechanism
into a coherent whole.
The Chemical Thesaurus
reaction chemistry database another free offering from
Mark R. Leach and meta-synthesis was
ported to the web in January 2006:
|Unit & Compound Mechanistic Steps
© Mark R. Leach 1999-
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