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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 chemogenesis approach.


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: H+
  • Remove a proton: H+
  • Add a hydride: H
  • Remove a hydride ion: H
  • Remove a hydrogen radical: H


  • 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:
    Lewis acids
    Lewis bases

Array Interactions

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.

FMO Theory

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:

  • HOMO or Highest Occupied Molecular Orbital
  • LUMO or Lowest Unoccupied Molecular Orbital
  • SOMO 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
    • Lewis acid/base complexes have a bonding MO resulting from a HOMO/LUMO interaction

  • Radicals
    • Radicals have SOMOs
    • Radicals couple via SOMO/SOMO interactions to give a bonding MO

  • Diradicals
    • Triplet diradicals have two SOMOs
    • Singlet diradicals have a HOMO plus a LUMO

  • Photochemically [and otherwise] activated species
    • Highly excited SOMO states

  • Oxidising and reducing (redox) species
    • Pairs of single electrons can transfer from a HOMO to a LUMO to give a LUMO + HOMO

      Zn + Cu2+ Zn2+ + Cu       (There are other redox behaviours as well.)

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:

  • s-HOMO Lewis bases: hydride ion, H, and hydrogen, H2
  • Complex Anion Lewis bases: tetrafluoroborate ion, [BF4]
  • Lobe-HOMO Lewis bases: hydroxide ion, HO, water, H2O:, methylcarbanion, H3C, etc.
  • π-System Lewis bases electron rich π-systems: ethene, benzene, etc.
  • The Proton Lewis acid: the proton, H+
  • s-LUMO Lewis acids: Group 1 and 2 cations: Li+, Mg2+, etc.
  • Onium Ion Lewis acids: ammonium ion, [NH4]+, oxonium ion, [OH3]+, etc.
  • Lobe-LUMO Lewis acids: boron trifluoride, BF3, the carbenium ion, H3C+
  • π-LUMO Lewis acids: electron poor π-systems, enones, tetracyanoethylene, etc.
  • Heavy Metal Lewis acids: cations and bulk metals of the transition metals, post-transition metals, lanthanides and actinides

Congeneric arrays 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.

Crucially, each and every cell of the Lewis acid/base interaction matrix encapsulates and exhibits distinct electronic structure and characteristic reaction chemistry behaviour:

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:

methyl lithium, H3CLi
potassium hydroxide, KOH
sodium carbonate, Na2CO3
sodium hydrogen carbonate, NaHCO3
sodamide, NaNH2
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.

Prof. Roald Hoffmann, who won the Nobel prize for his work FMO theory, wrote in a personal communication:

"A great 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:

  • Complexation
  • Fragmentation
  • Substitution
  • Insertion
  • Pericyclic processes
  • Metathesis
  • Addition
  • Elimination
  • Rearrangement
  • Multistep

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.

Consider nucleophilic 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.

First, 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.

With 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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This free, open access web book is an ongoing project and your input is appreciated.