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 Theory: classical & quantum Nuclear structure Electronic atomic structure etc...

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, thermodynamics & spectroscopy.

The Chemogenesis Narrative

Textbooks about chemistry are usually structured in rather similar ways.

• Organic chemistry texts tend to progress through their subject by functional group by functional group: alkanes, alkenes, alkynes, carboxylic acids, enols & enolates, small biological molecules, large bio molecules...
  
• 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...

The Chemogenesis web book is very different, for a start there is no distinction between organic chemistry and inorganic chemistry. There are six sections:

1. First the essential roots-of-chemical-science ideas are discussed: 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. Part 2 involves electronegativity, binary compounds and the thermochemistry of binary compounds.
   
   
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. Next, there is a review of structural theory, 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 there are 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, stuff like that...

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

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

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.

QED

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.

© Mark R. Leach 1999-2009

Queries, Suggestions, Bugs, Errors, Typos...

If you have any:

Queries
Comments
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please contact Mark R. Leach, the author, using mrl@meta-synthesis.com

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