Introduction & Overview

Chemogenesis tells the story of how chemical structure & reactivity emerge from the periodic table of the elements. This introductory page gives an overview of the new analysis, and introduces some graphical metaphors that help to describe the reaction chemistry landscape.

A Tree Metaphor

In the Chemogenesis web book we consider the science of chemistry to be something like a tree:

The roots of this metaphorical tree are those strands of science, often physics, upon which chemistry is built:

  • Nucleosynthesis of the chemical elements inside stars

  • One-at-a-time discovery of the chemical elements

  • Classical theory

  • Quantum mechanics

  • Nuclear structure

  • Electronic atomic structure

  • Spectroscopy

The Periodic Table of The Elements forms the base of the trunk of the reaction chemistry tree.

This is apt because the science of chemistry – the study of matter and its changes – in a very real sense grows out of the periodic table using the chemical elements as building blocks.

Our planet and all its associated biology is made from periodic table stuff.

Inorganic and organic chemistry develop from the upper trunk of the chemistry tree. From these grow the leaves, buds and growing tips where chemical science research is actively carried out. Data is published in the primary literature (academic journals) or is held in commercial databases.

  • Analytical science
  • Biochemistry
  • Medicinal chemistry
  • Molecular biology
  • Geochemistry
  • Industrial chemistry
  • Materials science
  • etc., etc., etc...

Physical chemistry is not missing; it is omnipresent. Physics provides the intellectual tools to understand: chemical structure & bonding, kinetics, thermodynamics & spectroscopy.

The chemogenesis web book re-examines the trunk of the chemistry tree.

New analysis is used to explore the rich science that exists between the periodic table and organic & inorganic reaction chemistry science.

  • Chemogenesis tells the story of how chemical structure, reaction mechanisms and chemical reactivity emerge from the periodic table of the elements and develop into the rich and complex science we experience.

  • Chemogenesis exists in main group chemistry space.

  • Chemogenesis is general chemistry.

The Chemogenesis Narrative

University level chemistry textbooks are usually structured in three, rather similar, ways:

  • General Chemistry textbooks are written for the large American market of 1st year university students who are majoring in science or engineering. From Pauling's 1947 General Text text to the contemporary versions by Atkins and Zumdahl, these textbooks are numerous and they are generally excellent. They progress through the subject: atoms, shape, stoichiometry, periodicity, equilibrium, kinetics & thermochemisty. This is followed by reaction chemistry topics: main group chemistry, organic chemistry, transition metal chemistry, biochemistry and nuclear chemistry, illustrated with pertinent examples of chemical reactions.

  • Organic Chemistry texts tend to progress through their subject by functional group by functional group: alkanes, alkenes, alkynes, carboxylic acids, enols & enolates, aromatics, heteroaromatics, small biological molecules, sugars, peptides, proteins, DNA...

  • Inorganic Chemistry textbooks tend to be structured in terms of the Periodic Table: Hydrogen, Group 1 alkali metals, Group 2 alkaline earth metals, Group 17 halogens, transition metals, lanthanides & actinides, etc... followed by important topics like nucleosynthesis, semiconductors...

This Chemogenesis web book is very different. To begin with, there is no distinction between organic chemistry and inorganic chemistry.

The crucial chemogenesis analysis sits directly after the: atoms, moles, stoichiometry, periodicity, equilibrium, kinetics & thermochemisty parts of the General Chemistry textbooks.

There are six sections to the chemogenesis web book:

    1. Roots-of-chemical-science ideas: nucleosynthesis, isotopes, atomic structure and the periodic table.

    2. Chemical structure, bonding & material type are discussed with respect to substances that possess only one type of chemical bond: metallic, ionic, network covalent or molecular materials. Topics like electronegativity, binary compounds and material type are covered.

    3. Next the core chemogenesis analysis is unfolded. The narrative moves through: the main group elemental hydrides, the five hydrogen probe experiments, congeneric arrays, the five reaction chemistries, the Lewis acid/base interaction matrix and the mechanism matrix.

      There is a overview, or executive summary page: Chemogenesis in 500 Seconds.

    4. Then, there is a review of chemical theory: Lewis theory, the Gibbs functions, a discussion about the structure of diatomic & polyatomic molecules, π-systems & pericyclic reactivity.

    5. This is followed by a discussion about complexity, emergence, linear & non-linear chemical systems.

    6. Finally some extras: the author's afterword, an introduction to The Chemical Thesaurus reaction chemistry database, a collection of the literature references that lie behind this project, links to the Chemistry Tutorials & Drills web site, etc.:

The Tip of The Cone of Increasing Complexity

Chemistry-as-a-tree can be mapped to a cone of increasing complexity in reaction chemistry space which, through generative steps, emanates from the periodic table of the elements:

  • As reaction chemistry space is explored, knowledge expands and increasingly involved and complex systems are understood.

  • Chemogenesis is concerned with chemistry close to the cone's vertex or beginning. The analysis explores the very simplest chemical interactions & reactions.

Synthlets, Databases & Videos

Synthlets & Databases are small software applications – apps – written in PHP, JavaScript and/or MySQL that use theories, models & techniques to predict the existence and properties of small molecules and serve chemistry data. They include:

Binary Compound Synthlet Name & Stoichiometry
Binary Material Synthlet Structure, bonding & material type
Thermochemisty Synthlet Gibbs free energy ΔG & Keq

Redox Chemistry Synthlet

Redox reaction feasibility & Cell E°
Addition Synthlet Addition across a double bond
Periodic Table Formulation Database Periodic table formulations
Functional Group Database Alkanes, alkenes, alkynes, etc
Lewis Acid/Base Matrix Database Lewis acids, bases & complexes
Congeneric Array Database Dots, series, planars, volumes

Videos are short (5 – 10 min) presentations that deal with aspects, such as the Lewis Acid/Base Interaction Matrix, Structure & Bonding, Triangles and Tetrahedra of Bonding, etc. The videos are posted to YouTube and then embedded in the relevant pages. The Chemogenesis videos are listed together here.

Who Is This Web Book For?

The Chemogenesis Web Book is for academic chemists, teachers of chemistry and students of the subject.

The material has been written & drawn so that – in large part – it can be understood by first year university chemistry majors, bright and interested school students and the scientifically literate who want to know more about chemistry.

The material is intended to be accessible to professional scientists who require a knowledge of chemical reactions and chemical reactivity but who were dazed and confused by the subject at university: physicists, engineers, geologists, biochemists, biologists, medical students, etc.

The chemogenesis analysis does not just provide examples of chemical reactions, instead it attempts to show how, and in what way, reaction chemistry is complex and difficult.

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.


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."

How Long Will It Take To Read ?

As the author, I would argue that there is nothing particularly challenging about the logic of the chemogenesis analysis. While not trivial, it is simple compared with spectroscopy, thermodynamics, structural elucidation or organic synthesis. However:

The chemogenesis argument has NOT been published elsewhere. The overall logic and analysis will be new to ALL readers, even though most the reaction chemistry examples – which range across organic and inorganic chemistry – should be familiar to professional chemists.

An academic chemist should be able to surf through the central chemogenesis argument in an hour or so. There is a condensed academic paper version of the central analysis here.

A student majoring in chemistry should be able to read and assimilate the chemogenesis argument and the background pages in a day.

Chemogenesis Main Index

© Mark R. Leach 1999-

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