The Chemistry Tree

The science of chemistry is 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. Indeed, our planet and all its associated biology is made from periodic table stuff.
  
  
• The great areas of reaction chemistry science, inorganic and organic chemistry, develop from the upper trunk of the chemistry tree. From these develop the branches of:
  
• 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, thermodynamics & spectroscopy.
  
  
• The leaves, buds and growing tips of the chemistry tree is where chemical science research is actively carried out. Data from this fundamental research is published in the primary literature or is held in commercial databases.

The Chemogenesis Narrative

Organic chemistry texts traditionally move through their subject by functional group by functional group: Alkanes, Alkenes, Alkynes, Carboxylic acids, Enols & Enolates...

Inorganic chemistry textbooks tend to be structured in terms of the Periodic Table: Hydrogen, Group 1 Alkali Metals, Group 2 Alkali Earths, Group 17 Halogens, Transition Metals...

The chemogenesis web book is different. There are five sections:

1. First some essential roots-of-chemical-science ideas are discussed: nucleosynthesis, the periodic table, electronegativity, binary materials & thermochemistry.
   
   
2. Next the core chemogenesis analysis is unfolded, the story of how chemical structure and reactivity emerge from the periodic table of the elements. The story 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, here: Chemogenesis in 500 Seconds.
   
   
3. This is followed by a discussion about complexity, emergence, linear & non-linear chemical systems.
   
   
4. Next, there is a review of structural theory, diatomic & polyatomic molecules, p-systems & pericyclic chemistry.
   
   
5. Finally some extras: an afterword, an introduction to The Chemical Thesaurus reaction chemistry database and a collection of the literature references that lie behind the project.

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:

• 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 simplest chemical interactions and reactions.

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 and 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.

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 1999-2008

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

If you have any:

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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.