The Chemogenesis Analysis: Overview
Abstract... What It's All About... In a Nutshell... Executive Summary... Chemogenesis in 500 Seconds...
Chemogenesis explores the nature of chemical structure and reactivity in logical steps, each described
over one or two pages of this web book. This page gives an overview of the
Main Group Element Hydrides
The story starts with the main
group elements, as their hydrides.
This set includes many common
chemicals with well known and understood properties and behaviours: hydrogen,
methane, water, hydrogen bromide, argon, etc.
The Five hydrogen Probe Experiments
Five hydrogen probe experiments
are performed upon the set of main group elemental hydrides:
- Add a proton:
- Remove a proton:
- Add a hydride:
- Remove a hydride
- Remove a hydrogen
- Due to periodicity, species
naturally collect into congeneric (of the same family) arrays.
- Observed array dimensions are: [1
x 1] [1 x 4]
[1 x 5] & [4 x 4]
- The species resulting from
the five hydrogen probe experiments present as:
Concentrating on the Lewis
acid and Lewis base arrays:
- It is well known that Lewis
acids interact with Lewis bases
to give Lewis acid/base complexes.
- So it should come as no
surprise that congeneric arrays of Lewis acids
interact with congeneric arrays of Lewis bases
to give congeneric arrays of Lewis acid/base complexes.
- The usual rules of array
algebra hold, so that
a [5 x 1] array of Lewis acids vs. a [4 x 1] array of Lewis bases
gives a [5 x 4] array of Lewis acid/base complexes:
- Congeneric interaction logic
can even give rise volumes of chemical species, where the chemistry
varies in a regular (linear) way over the array:
Several pages chemogenesis
web book are spent exploring how linear structural and reactivity traits
can be found with respect to atomic ionic radii, bond length, electronegativity,
% ionic bond character and pKa.
At this point we introduce
some simple frontier molecular orbital (FMO) theory: Theory, diatomics, polyatomics & π-systems.
FMO theory identifies that
reactive chemical species interact with each other via a rather limited
set of frontier molecular orbitals, the FMOs:
or Highest Occupied Molecular Orbital
or Lowest Unoccupied Molecular Orbital
or Singly Occupied Molecular Orbital
Collecting It All Together...
Using data from the hydrogen probe experiments, taking information about the MO structure of diatomic and polyatomic species, considering pericyclic interactions, slicing and dicing data in spreadsheets and The Chemical Thesaurus reaction chemistry database, etc., it is found that there are five general types of reactive species and associated electronic chemical reactivity behaviour:
- Lewis acids,
Lewis bases and Lewis acid/base complexes
- Electron pair acceptor Lewis
acids react via their LUMO
- Electron pair donating Lewis
bases react via their HOMO
acid/base complexes have a bonding MO resulting from a HOMO/LUMO
couple via SOMO/SOMO interactions to give a bonding MO
- Triplet diradicals
have two SOMOs
- Singlet diradicals
have a HOMO plus a LUMO
[and otherwise] activated species
- Highly excited
- Oxidising and
reducing (redox) species
Types of Lewis acid and Lewis base
The next step is to take the
arrays of Lewis acid and Lewis
base species generated by the five hydrogen probe experiments and
sort them by frontier molecular orbital type, topology (3D geometrical
shape + phase information) and reactivity behaviour.
At this point we slide
into the analysis three additional types Lewis acid and Lewis base:
electron rich π-system
Lewis acids, electron poor π-system
Lewis bases and heavy metal Lewis acids.
It transpires that there are
Four general types of Lewis base and Six
general types of Lewis acid:
Lewis bases: hydride ion, H, and hydrogen, H2
Anion Lewis bases: tetrafluoroborate ion, [BF4]
Lewis bases: hydroxide ion, HO, water, H2O:,
methylcarbanion, H3C, etc.
Lewis bases electron rich π-systems:
ethene, benzene, etc.
Proton Lewis acid: the proton, H+
Lewis acids: Group 1 and 2 cations: Li+, Mg2+,
Ion Lewis acids: ammonium ion, [NH4]+,
oxonium ion, [OH3]+, etc.
Lewis acids: boron trifluoride, BF3, the
carbenium ion, H3C+
Lewis acids: electron poor π-systems,
enones, tetracyanoethylene, etc.
Metal Lewis acids: cations and bulk metals of the transition metals,
post-transition metals, lanthanides and actinides
are always found within a Lewis acid or Lewis base type, and the never
crossing types. That said, there can be debate about assigning
a particular array to a particular Lewis acid, base or complex type.
The Lewis Acid/Base Interaction Matrix
Each of the four types of Lewis
base and six types of Lewis acid exhibits
distinct electronic structure and characteristic reaction chemistry behaviour.
It follows that the four
types of Lewis base interact with the six
types of Lewis acid to produce a matrix
of Lewis acid/base complexes.
and every cell of the Lewis acid/base interaction matrix encapsulates
and exhibits distinct electronic structure and characteristic reaction
For example, an s-LUMO
Lewis acid such as the sodium ion, Na+, interacts with a Lobe-HOMO
Lewis base such as the hydroxide ion, HO, to give
sodium hydroxide, a Type 7 complex.
The point is that most of
the basic, proton abstracting reagents and many of the neutral inorganic
salts used in the chemistry laboratory are Type
7 Lewis acid/base complexes, including:
potassium hydroxide, KOH
sodium carbonate, Na2CO3
sodium hydrogen carbonate, NaHCO3
lithium fluoride, LiF
calcium hydroxide, Ca(OH)2
sodium sulfide, Na2S
sodium cyanide, NaCN
magnesium oxide, MgO
barium sulfate, BaSO4
Like the periodic table, the
Lewis acid/base interaction matrix is a schema and an extraordinary object
with many properties. For
example, the vast majority of the reaction chemistry taught
to school and university students can be mapped to the Lewis acid/base
interaction matrix with the effect that the chemistry has context, rather
than existing as isolated facts.
Roald Hoffmann, who won the Nobel prize for his work
FMO theory, wrote in a personal communication:
combination of frontier orbital (of course I like that) and chemical
ways. I like it."
The Mechanism Matrix
The chemogenesis story continues
with an analysis of reaction mechanisms. First, the various types of simple
atom-to-atom mapping are considered:
- Pericyclic processes
These are arranged against
the five types of electronic mechanism introduced above, Lewis acid/base,
radical, redox, diradical & photo:
The mechanism matrix helps
put the various types of mechanism into context as it formally separates
the electronic aspects of mechanism from the atom-to-atom mappings.
substitution. The analysis separates the notion of nucleophilic
from the notion of substitution.
However, due to the complexity
of reaction chemistry the full mechanism matrix is actually not that useful
as it is better to map the species and reaction information to a relational
system (RDMS) such as The Chemical
Thesaurus reaction chemistry database.
There follows a discussion
about chemistry and complexity, where the term complexity is used
in a technical sense.
the idea of the system is reviewed, areas where linear behaviour might be expected (dilute solutions, homologous series, scale-up,etc.) are studied before moving on to regions of chemistry space where complexity
emerges, such as reaction mechanism space, diffusion controlled processes and organic synthesis.
Chemogenesis: The Map of Ideas
There are various routes through
the chemogenesis analysis, as the map below shows:
The arrows show
the logical steps through the Chemogenesis argument. For
example, the Five Reaction Chemistries are arrived at in at least three
ways: by analysing the results of the hydrogen probe experiments, by
analysis of linear π-system
structure and by a study of species/species interactions:
To Sum Up
Without chemogenesis, it is necessary to learn about chemical reactions and chemical reactivity by the accumulation and assimilation of facts.
chemogenesis, sense is made of a morass of chemical reaction information
and the structure of reaction chemistry space logically emerges
from physics, complexity and all.
|Classification of Matter
Main Group Elements & Hydrides
© Mark R. Leach 1999-
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