This 2018 2nd Edition of the Chemogenesis Web Book is in the process of being ported & and updated from the 2005 1st Edition.

The Chemogenesis Analysis 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 the tree graphical metaphor to describe the reaction chemistry landscape.

Unlike chemistry textbooks printed on paper, this webbook contains dynamic Synthlet and Database pages that explore and make predictions about aspects of chemical structure & reactivity and have embedded reaction chemistry YouTube Videos.

Chemical Education | CHEMISTRY IN CRISIS

The number of students studying chemistry at school and university is falling and there are many reasons why this could be, including:

  • Some of the new and emerging bioscience and drug discovery technologies are chemistry in all but name: DNA structure & function, the polymerase chain reaction, molecular biology, proteomics, etc., yet professionals in these areas are considered to be biologists rather than chemists.

  • Chemistry does not have a very green image in this environmentally conscious age.

  • Analytical science is changing from titrations with burettes, pipettes and conical flasks into an instrumental and IT based science.

  • Students realise [are advised] that to be a professional chemist – or a professional physicist, biologist, statistician, etc., – it is essential to have a PhD, a qualification that requires many years of dedicated study for moderate financial reward.

I suggest that, in addition, there is a chemical education problem which is causing students to reject the subject. I do not mean that chemists are bad teachers. On the contrary, chemistry is difficult and it is essential to be a good teacher to convey the complexity and richness of the subject. I hold that there is a structural difficulty to the subject concerning chemical reactions & chemical reactivity:

  • Students of chemistry encounter many and various chemical reactions during their studies, but they are not given an organising system – or schema – onto which this reaction chemistry information can be mapped.

  • Chemistry textbooks get larger with each edition but they fail to clarify the underlying mechanisms and processes of chemical reactivity.

  • The division of academic chemistry into organic and inorganic sub-disciplines is anachronistic and confusing.

I am concerned about how this affects professional scientists who are not chemists but who require a knowledge of chemistry. A PhD chemist will have had many years of exposure to chemical science and will have gained a deep understanding of the subject. However, academic chemistry is a priesthood and the path-to-knowledge is not readily accessible to non-chemists. While this could be said about any profession, chemistry is uniquely inaccessible amongst the major sciences:

How many popular science books are there on: mathematics, complexity theory, cosmology, quantum physics, DNA, plate tectonics, evolution, computers... and how many are there about chemical reactivity?

How many chemical reactivity articles are there in New Scientist, Discovery or Scientific American?

At present, chemical reaction pedagogy – how we teach the subject – involves exposing students to chemical interactions and reactions until they understand. I asked the members of an excellent chemistry education discussion list: "what is the simplest reaction mechanism or process you teach your students?" The most common answer was "second order nucleophilic substitution, Sn2", exactly the example I had expected and certainly the one I was first introduced to at university.

So, we introduce our students to really quite involved reactions and reaction mechanisms and we explain how these example reactions proceed. It is hoped that with experience our students "will understand". Well, yes they will... once they have been immersed long enough... to receive their PhDs. This approach – in my humble opinion – leaves physicists, biologists, geologists, material scientists, medics, chemical engineers... largely in the dark about what it is that constitutes chemical reactivity.

Ralph Pearson's Hard Soft Acid Base (HSAB) principle – very unfortunately – compounded the problem. In the 1960s there was huge optimism about understanding chemical reaction science due the development of new ideas, theories & methodologies:

  • FMO theory

  • Woodward-Hoffmann explanation of pericyclic reactivity

  • Klopman-Hudson theory

  • Pearson's HSAB principle

  • The growing utility of quantum chemistry techniques

  • Parameterisation of VSEPR theory into molecular mechanics software

These advances led to a "problem solved" attitude, and textbooks enthusiastically included the new material, particularly Pearson's HSAB principle which so naturally followed on from Lewis theory, valence bond (VB) theory and the valence shell electron pair repulsion (VSEPR) technique. Nearly all advanced inorganic and organic textbooks of the '70s and 80's had sections on hard and soft [Lewis] acids and bases... but now the topic is hardly mentioned at all.

As shown here, Pearson's HSAB principle is limited by the fact that no physical parameter correlates with hardness across Pearson's chosen sets of species. As a consequence, the HSAB analysis is ambiguous and limited. Indeed, the failure of the over-simple and over-hyped HSAB principle has meant that theoretical chemists have not really looked at this important area of physical science since the late nineteen sixties.

A Tree Metaphor

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

Tree_1.png

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.

tree_2a.png

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 leavesbuds 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 IS DIFFERENT

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 special topics like nucleosynthesis or 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 6 PARTS 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. 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. 

    The next page of this web book is a rapid overview, or executive summary page: Chemogenesis in 500 Seconds
     

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

  5. Complexity, emergence, linear & non-linear chemical systems.
     

  6. Finally some extras: 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.:

tree_3.png


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.

 

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

“A great combination of frontier orbital (of course I like that) and chemical ways. I like it.”

— Prof. Roald Hoffmann, who won the Nobel prize for his work FMO theory, wrote in a personal communication on receiving his copy of the Lewis Acid/Base Reaction Chemistry book

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 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 rapid run-thru on the next page of this web book, and an 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.


Thanks

Thanks go to the authors of web sites linked to from these pages, to members of the International Society for the Philosophy of Chemistry (ISPC), to the members of the ChemEd internet discussion list who have answered my many questions and synthesized such interesting postings and to the many chemists who have contributed to Wikipedia.

This web book is being continually updated. At present, this second edition of the web book is being ported from the meta-synthesis main site to SquareSpace: WORK IN PROGRESS (writing April 2018).

Please send comments, link suggestions, factual errors, browser problems, bug & broken link reports, etc., to the author:

Dr Mark R. Leach  mark@meta-synthesis.com  ©meta-synthesis 1999-2018