Introduction & Overview
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:
of the chemical elements inside stars
discovery of the chemical elements
- Classical theory
- Quantum mechanics
- Nuclear structure
The Periodic Table of
The Elements forms the base of the trunk of the reaction chemistry
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
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
- Medicinal chemistry
- Molecular biology
- 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.
are six sections to the chemogenesis web book:
- Roots-of-chemical-science ideas: nucleosynthesis, isotopes, atomic structure and the periodic table.
- 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.
- 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.
- 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.
- This is followed by a discussion about complexity,
emergence, linear & non-linear chemical systems.
- 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
|Binary Compound Synthlet
||Name & Stoichiometry
|Binary Material Synthlet
||Structure, bonding & material type
||Gibbs free energy ΔG & Keq
Redox Chemistry Synthlet
|Redox reaction feasibility & Cell E°
||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
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.
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.
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.
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.
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."
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:
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-
Bugs, Errors, Typos...
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please contact Mark R. Leach, the author, using email@example.com
This free, open
access web book is an ongoing project and your input is appreciated.