Chemogenesis Web Book
"I've never seen such a comprehensive and lucid explanation of the emergent nature of chemistry in all it's forms before... Great chemistry stuff in here!"
"While the treatment of the subject of chemistry on this site has nothing to do with any [current] academic syllabus, the Chemogenesis site is nevertheless a useful tool that can help students understand reaction chemistry and its causes (and effects) in a more complete or holistic manner."
"A well planned, well laid out site, which deals with chemical
reactions and chemical reactivity. I found it fascinating."
PSER, Nov 2004
Chemical Thesaurus Reaction Chemistry Database
"The Chemical Thesaurus is a reaction chemistry information
system that extends traditional references by providing hyperlinks between
related information. This program goes a long way toward meeting its
ambitious goal of creating a nonlinear reference for reaction information.
With its built-in connections, organizing themes, and multiple ways
to sort and view data, The Chemical Thesaurus is much greater than the
sum of the data in its database. The program does an excellent job of
removing the artificial barriers between different subdisciplinary areas
of chemistry by presenting a unified vision of inorganic and organic
K.R. Cousins, JACS, 123, 35, pp 8645-6 (2001)
Chemistry Tutorials & Drills
"Good tutorial about chemistry."
"Excellent, just what I was looking for."
"Love chemistry so this is fantastic!"
Lewis Acid/Base Reaction Chemistry Package (book + poster + CD-ROM)
"Intriguing, stimulating and of much interest and at £30 it is an absolute bargain."
The Alchemist on ChemWeb
not know of any other textbook or other work in which the many different
combination possibilities of Lewis acids and Lewis bases are treated
so thoroughly and systematically as they are here."
a broad holistic approach is used to present a very large accumulation
of reductionist data and information. Details become only details, and
yet precision is maintained throughout."
Chemistry & Industry
Leach's writing is crisp, and, although dense with facts and information,
this book is simple enough for secondary school students."
Chemistry & Industry
post graduates, teachers and professional chemists will all find much
in this package to interest them."
The Alchemist on ChemWeb
all leads me to recommend the work to anyone teaching in this area..."
Chemistry in Britain
Lewis Acid/Base YouTube Video
"As someone who does/did well in organic chemistry (up to stereoselectivity), it makes me sad to say that? I never really understood the fundamentals of it. As a result, everytime I did an Organic course, it felt new to me, because I would have to 'remember' how things work.
You make this very simple, concise and you answer why things this works. Understanding the basics will make it very easy to come up with answers as oppose to remembering them."
"Explaining chem like a BOSS! Thank you so much!"
Reviews In Full
A well planned,
well laid out site, which deals with chemical reactions and chemical
reactivity. Meta-synthesis is a publishing house, which aims to produce
material that deals with the 'over' or 'meta' view of science. To this
end, they have published a free web book entitled: "Chemogenesis" by
Mark R Leach.
Their approach to
patterns in reaction chemistry aims to separate the wood from the trees;
to separate the large scale structure of reaction chemistry from the
details of individual chemical species, their interactions and reactions.
The site has a good
introduction page that introduces how chemical structure and reactivity
'emerge from the periodic table of the elements and develop into the
rich science we experience'. The site then goes on to look at the main
group elemental hydrides and five hydrogen probe experiments, which
feed into a page that defines congeneric series and planars. Further
pages look at how to quantify congeneric behaviour and the emergence
of organic chemistry. The web-book then goes on to look at five reaction
chemistries, unit and compound mechanisms, STAD, mechanism matrix and
so on with more pages than could be effectively described in this review.
There is also an excellent chemical thesaurus page and further reading
The site is continuing
to evolve however, in that there are several pages under construction,
for example a section on Linear behaviour and Chaos in Chemistry and
Although the site
content is not suitable for the majority of my access or first year
students, there are occasionally diagrams that explain things so well
I could easily use them on the Higher Chemistry course. For example
the Segre chart is particularly good, as are the periodic tables. Any
advanced students that would like to investigate reaction chemistry
further should have no problems navigating this site with minimal lecturer
support. The vast majority of chemistry lecturers and teachers should
also find something of interest here.
According to the
site, "Chemogenesis" was designed for academic chemists, teachers of
chemistry and students. The material was designed to be understood by
a 'first year university chemistry major, a bright and interested school
student, or a scientifically literate lay person'. However, I feel that
students and lay people would get more from this web-book if the language
used was simpler and perhaps if the diagrams were explained further
in the text. If this were altered I feel this web book would be accessible
to a wider range of users, although I acknowledge that this 'dumbing
down' may put off the academic chemists. Another minor criticism would
be that the intro page is very bland and most students would probably
be put off by the page titles. A 'map of ideas' would probably pull
lay people into the text more quickly, although then I suppose it would
be less of a book and more of a website.
Overall I found
it to be a fascinating site though. It is possible to navigate around
it quickly enough and all the pictures downloaded with minimal effort.
Physical Sciences Educational Reviews, vol 5, issue 2, pp2, Nov. 2004
Lewis Acid/Base Reaction Chemistry package
As a graduate student,
I was somewhat confused. My thesis was designated as being in the area
of inorganic chemistry. However, when pressed to be more precise, I
could never decide whether what I was doing was better described as
coordination or organometallic chemistry. I was synthesising palladium
and platinum compounds of sterically demanding tertiary phosphines,
and then allowing, or forcing, these bound ligands to undergo cyclometallation,
thereby forming direct metal-carbon bonds. That confusion of mine has
been alleviated, finally, after about 15 years.
I always had a sneaky
suspicion that I was entangling myself in mounds of split hair. Is the
distinction between coordination and organometallic chemistry important?
On an even broader canvas, should we be so over-concerned with distinguishing
inorganic from organic chemistry? In the foreword to this book, it is
stated: 'The division of reaction chemistry into organic and inorganic
is anachronistic and confusing.' Thus, a broad holistic approach
is used to present a very large accumulation of reductionist data and
information. Details become only details, and yet precision is maintained
throughout. For example, the hydroxide ion is always represented
with the negative charge on the oxygen atom, -OH or HO-, and never on
the background concepts, Leach presents his material schematicallywith
a visual organising system that maps chemical species and their behaviours.
He begins with the premise that Lewis acids, bases and acid/base complexes
are ubiquitous, occurring throughout inorganic, organic and organometallic
chemistry. He has mapped all this onto a generalised interaction matrix,
reproduced on a wall chart, for which this book essentially becomes
a guide, or instruction manual. Lewis acids and bases are classified
by their frontier molecular orbital topology and are placed in a grid,
such that 24 different types of bonding interaction can be immediately
recognised. For example, ionic bond formation is seen as one type of
Lewis acid-base interaction. Complexation due to hydrogen bonding, van
der Waals attractions, anion bridge bonding and/or molecular shape recognition
do not fit within the body of the matrix, but they are included at the
foot of the grid.
writing is crisp, and, although dense with facts and information, this
book is simple enough for secondary school students. All terms are
defined along the way, and are further delineated in an excellent glossary
of terms and symbols. The book is quite comprehensive and fully referenced,
with suggestions for further reading; and thus should be as useful to
graduate students. The package (book and chart) also includes a CDROM
containing [tutorials and chemical thesaurus] software.
Finally, this is
only the first volume of a projected five-volume series called 'Patterns
in reaction chemistry'. The next four will address redox chemistry,
photochemistry, and radical and diradical chemistry. I am already freeing
up some more wall space.
John Malito is at
the department of chemistry, Cork Institute of Chemistry, Rossa Avenue,
Bishopstown, Cork, Ireland.
John Malito is
at the department of chemistry, Cook Institute of Chemistry, Ireland.
and Industry 21/8/2000
Reaction Chemistry is the first package in a series entitled Patterns
in Reaction Chemistry. It consists of a slim paperback book, a large
A1 summary colour poster, a CD-ROM containing a series of tutorials,
and a reaction chemistry database. This is an ambitious project aimed
at providing a uniform approach to the study of organic, inorganic and
physical chemistry. Without doubt the complexity of the chemistry summarised
on the poster on Lewis Acid/Base Reaction Chemistry is awesome and the
author is wise to acknowledge this and assure the reader that the classifications
and ideas will be covered step by step in the CD-ROM tutorials. Thus
you are asked to take an hour or so at the start to work through the
The software, which
is cross platform requiring 16MB memory, auto ran from the CD-ROM without
any problems using NT and Windows 95. Selection of the Tutorials pad
on the opening screen takes you to a menu offering 10 tutorials each
consisting of a series of gradually progressing slides. These include
an Introduction and Overview of the poster; two revision tutorials
one introduces Reaction Chemistry and the other revises electronic theory;
five tutorials cover redox, photochemistry, Lewis acids and bases, radicals
and diradicals; a brief explanation of the paradigm nature of these
five reaction classes; and a 'clickable' matrix of the 24 types of Lewis
acid-base and related interactions each leading to appropriate explanatory
text. Selection of the Database tab takes you to a menu allowing access
to a short overview of the database, a periodic table with elemental
properties, and an extensive list of different chemical species and
The tutorial which
introduces the poster consists of 76 slides. It begins with definitions
of the five reaction types before focusing on Lewis acid base complexation.
The four types of Lewis base and six types of Lewis acid are defined
and the ways in which these can combine to form 24 types of acid-base
complex are demonstrated one by one. The division of the matrix into
organic, organometallic, inorganic, main group and H-redox areas, called
signposting, is demonstrated before finishing with explanations of hydrogen
bonding, anion bridge bonding, VDW attraction and guest/host recognition.
The 98 slide revision
tutorial entitled "What is Reaction Chemistry" gives examples of chemical
species (both real and genera), components of chemical reactions, reaction
types/mechanisms, physical theory (classical, wave and quantum), analytical
methodology and the literature.
There is a very
good revision tutorial on electronic theory. It consists of 136 slides
and explains Lewis octet theory, valency and balancing equations, electronegativity
(including calculations of dipoles and ionic character), atomic structure,
filling of shells and frontier MO's.
There is a tutorial
on each of the five main reaction classes. The first, which concerns
the basic process of redox reactions for both organic and inorganic
reactions, is covered quite well on 55 slides. Photochemistry is likewise
covered using 67 slides. As expected there is extra emphasis (114 slides)
on Lewis acid/base complexation. The tutorial on radicals introduces
homolysis, the singlet and triplet structures of radicals, and some
examples of reactions including the chlorination of methane. In the
last tutorial on diradicals, 39 slides are used to demonstrate some
carbene chemistry with a mention of nitrenes and oxygen.
of paradigms across the five classes is pointed out briefly giving the
basic and reducing properties of the hydride ion as an example.
matrix on Lewis acid/base complexes gives the user access to explanatory
text on each of the 24 combinations. The text is basically the same
as that in the text book but reworded to some extent for this purpose.
The database is
divided into three main parts a list of 2000 chemical species,
a list of 1500 reactions and the periodic table. The species database
can be sorted into 21 fields including name, formula, reagents, reactivity
types e.g. acids, bases, redox properties etc. The reactions database
can be sorted into 19 fields e.g. reactants or products, bond formation
possibilities, functional group modifications, mechanisms, HASAB properties
etc. as well as into examples of biosynthesis. There is also a complexation
field which gives several examples for each of the 28 Lewis acid/base
complex types. The elements in the periodic table can also be sorted
into 10 fields. These include mass number, name, m.p., b.p., radii.
A complete list of isotopic abundancies is available. There is a short
overview of the database which includes a chemical thesaurus and a glossary
The 96 page text
book begins with acid-base theory including the Hard Soft Acid Base
Principle moving on to symbiosis, congeneric series and planars. Most
of the text deals with definitions and explanations of the various Lewis
Acid-Base interactions etc. The text concludes with sections on multi-step
reaction mechanisms, ambidentate reactivity using HOMO LUMO explanations,
a glossary of terms, bibliography and further reading.
The poster is very
well produced. It has good diagrams and is packed with information of
the five classes of interaction, the 24 types of acid/base interactions
and other types of complexation. It is a useful student's wall chart.
There is a lot of small print which would make is less suitable for
class room teaching.
lecturers, whose approach to chemistry is physical and mechanistic,
will find this package intriguing, stimulating and of much interest
and at £30 it is an absolute bargain. Many parts of it could be
pulled out to enhance current course materials. However, using it as
a central theme for a teaching scheme will require much thought, planning
and reorganisation of the teaching programme including how to interface
it with the rest of the chemistry syllabus. Many students would find
the approach quite daunting if faced with the objective to understand
the full pattern of possible interactions too early and too quickly.
Certainly students with find immediate use for the database information
on chemical species and organic reactions and for much of the text as
alternative explanations for key concepts. Ultimately, for graduates
and chemists to be familiar with an overarching explanation of all types
of chemical reaction must be very beneficial and undergraduates,
post graduates, teachers and professional chemists will all find much
in this package to interest them.
Reviewed by Prof.
John C. Tebby who teaches chemistry in the Division of Natural Sciences
at Staffordshire University.
© The Alchemist
on Chemweb.com, 5th May 2000
is in crisis" screams the blurb on the back page. "Thirty
pounds for 96 pages and a CD?!" screams the reviewer. But appearances
can be deceptive and once the shock has died down you realise that there's
more to this work than initially meets the eye. Its stated aim is
to map Lewis acid-base bonding diversity and behavioural variety by
means of an interaction matrix acting as a visual organising system
or schema. If that all sounds a bit off-putting, rest assured that once
you get the hang of what the author is aiming at, it mostly works very
A worthwhile and
generally readable introduction leads into the grandly titled 'Lewis
acid-base interaction matrix', which is in fact simply a correlation
table of the interaction between six classes of Lewis acid - including
onium ions, pi LUMO acids and heavy metal acids - with four types of
Lewis base. This leads to 24 varieties of acid-base interaction, each
of which then receives a page or two of detailed notes. The same format
is used for each case - including general chemistry and a list of congeneric
series - allowing comparisons to be made effectively. The final part
of the book consists of a quick look at a number of associated topics.
Its brief means
that a book such as this lives or dies by the quality of its layout
and artwork and here this is almost universally excellent (being only
rarely let down by the compact - and occasionally somewhat florid -
nature of the text). The accompanying CD includes a large searchable
database of reagents and reactions pertinent to the work together with
a very useful reference Periodic Table and tutorials (though alas the
latter appear to be only presentational in form with no capacity for
This all leads
me to recommend the work to anyone teaching in this area, for the
students on the other hand the price is likely to be a definite turn-off.
Chemistry will continue to be in crisis until innovative and informative
works such as this come at an affordable price.
Reviewed by Paul
Kelly, Department of Chemistry, Loughborough University of Technology.
in Britain, May 2000
teaching pack consists of a paperback text, a CD-ROM, and a poster.
It begins with a roll of thunder: "Chemistry is in a crisis. Textbooks
become thicker every year, but they fail to address the central problem
of what chemical reactivity really means. The division of reaction chemistry
into organic chemistry and inorganic chemistry is anachronistic and
misleading. There is no general or coherent scheme that is suitable
for describing the behavior of chemical species. Patterns in Reaction
Chemistry recognizes this problem and offers solutions." The solutions
referred to, which are arrived at by a "meta-analysis", are to be published
as an ongoing series, of which this is the first volume. If, instead
of having to work slowly and laboriously through thousands of pages
(organic and inorganic), one relies on a little book in one's hand,
a poster on the wall, and a CD in the disc drive, will that be sufficient?
That is too good to be true; however, the author's attempted solution
deserves to be discussed and its merits recognized.
Although the expression
"meta-analysis" is not defined or explained, the reader soon discovers
what it means: it is the long familiar heuristic approach in chemistry,
which is used repeatedly in classical textbooks and by many university
teachers. It means collecting together many different chemical phenomena
and properties and summarizing the observations in concepts of general
validity, though sometimes these are no more than rules of thumb. Some
examples of such concepts are those of Lewis acids and Lewis bases,
redox reactions, the HSAB principle, HOMO/LUMO interactions, the Aufbau
Prinzip (which, incidentally, is repeatedly written wrongly in the CD-ROM),
and many more. Of course, such ordering schemes make the classification
into organic and inorganic reactions unnecessary, but in all cases we
are concerned again and again with the one underlying theme of chemistry:
the formation and breaking of bonds. So, is the book just a slightly
different way of packaging and presenting the eternal truths of chemistry?
I do not know of any other textbook or other work in which the many
different combination possibilities of Lewis acids and Lewis bases are
treated so thoroughly and systematically as they are here. The author
considers altogether 24 reaction "types", which result from the combinations
of four types of Lewis bases and six types of Lewis acidsthese
range from the simple reaction of a hydride ion with a proton, to the
combination of Fe2+, a heavy metal Lewis acid, with the cyclopentadienyl
anion, a Õ-HOMO Lewis base, to give ferrocene. This way of viewing things
is very useful for the student, emphasizing common features as opposed
to those that distinguish different chemical transformations. Nevertheless,
I doubt whether beginners will benefit greatly from studying this learning
program. Every experienced teacher knows that nothing causes more difficulty
for the beginner than recognizing and applying general principles. The
beginner who is in the process of learning the vocabulary of a new language
clings to the new words acquired, but cannot yet speak fluently. The
book Lewis Acid/Base Reaction Chemistry is a compendium of the key phrases
of chemistry. One can learn the statements by rote, but one is then
still a long way from a deeper understanding. Therefore the book may
be of real value for students in the later stages of their degree course,
who already have a reasonably broad factual knowledge, and may help
them to an appreciation of more far-reaching relationships. The condensed
information in the textual part can only be digested in small morsels
if it is to stick in the mind, and the author appears to have realized
thiswhat other explanation can there be for the relatively large
mass of chemical facts (mainly without discussion) that are provided
on the CDROM, partly in the form of data banks of reactions and compounds.
This is followed in the poster by a final compressed form of the knowledge;
it is more suitable for recapitulation and revising for examinations,
rather than for conveying a deeper understanding.
knowledge in a highly concentrated form such as this takes no account
of an experience that is familiar to both students and teachers: namely
that learning is a slow process and takes time. This fact is better
recognized in a book than in the inevitably faster method of study using
electronic media. For example, whereas one can mouse-click through the
76 diagrams of Tutorial 1 on the CD-ROM in quite a short time, during
the (slow) process of reading the same information in a book one would
learn and understand more. Notwithstanding that, for revision (examination
preparation) this form of presentation has some clear advantages over
the printed text.
On the whole
this is an imaginative addition to the textbook literature, and we can
look forward with keen anticipation to the volumes that will follow.
Institut fur Organische Chemie, Technische Universitat Braunschweig
Chemie International Edition
39, No. 16
The Chemical Thesaurus
The question I
am wrestling with in reviewing this software is: what is it for? Its
title, "Chemical Thesaurus 2" suggests a systemised treasury of chemical
information, a title it lives up to. But who is it aimed at and for
The press release
suggests that the target audience includes chemistry undergraduates,
postgraduates and HE teachers and implies that it aims to supersede
reaction textbooks. In my view it succeeds in part in fulfilling these
2 is a database of reaction chemistry including 2600 reactions, along
with other data. It is a self-contained product, powered by FileMakerPro,
and ran at a satisfactory speed on my iBook direct from the CDROM with
no crashes. The CDROM is accompanied by negligible documentation, but
following the Overview's advice to "just click around" I was soon able
to get a good feel for the package.
The user interface
feels like a web page with 12 buttons on the main index screen. The
biggest and most significant buttons allow one to browse or search the
chemical species and reactions contained in the database. The search
options operate by the selection of various prescribed options (e.g.
by element or class of reaction) without the user inputting text or
structures, this system works well but was occasionally rather slow.
The data one retrieves
is generally presented graphically with some supporting text but without
references to the literature. Reaction mechanisms are discussed, using
curly arrows or molecular orbitals in some cases. So, for example, a
species search for boron gives 48 boron containing species which may
be re-ordered by various criteria, a further click on triethylborane
takes one to a screen describing the reagent as "real, long lived, electronically
neutral", with a curly arrow scheme displaying its action as a Lewis
acid, some physical data and a link to the reactions featuring it in
the database (one in this case, its synthesis from borane and ethene).
Similarly a reaction search of the pericyclic reaction category provides
links to 7 classes of reaction and selecting the Claisen rearrangement
provides two examples and a brief mechanistic description. The species
and reactions may also be browsed with the former ordered by name and
with the option to order the latter by substrate, reagent, or products
(as warned re-ordering is slow).
The smaller buttons
on the main index screen allow one to navigate around the database using
other criteria: through an attractive "Lewis acid/base interaction matrix"
that depicts the HOMO - LUMO interactions; or using a periodic table,
which also provides information and data on the elements. The other
smaller buttons provide congeneric series, a glossary of terms, and
a user definable aromatic substitution reaction predictor (though limited
and without rationales).
The data entry and
editing facility was not active on the review copy I received. Overall
I enjoyed clicking around this database and found it easy to use. But
I am still vexed by the question of what it is for. It certainly is
not where I would search for a reaction I wished to perform as no literature
references are provided and there are better and much more comprehensive
on-line databases to which I would turn, thus I consider its research
applications to be limited. It seems to me to be comparable with an
introductory undergraduate textbook, though with less actual text. The
abilities to browse, search and interconnect in a non-linear manner
are the great strengths of Chemical Thesaurus 2, as is its portability;
these facilities may prove to be useful to HE teachers and students.
To chemistry students (undergraduate and postgraduate) I would recommend
Chemical Thesaurus 2 only as a (useful, user-friendly, affordable and
possibly unique) supplement to one of the standard textbooks. HE teachers
are also likely to enjoy browsing around this database and may find
its approach to ordering material useful and challenging.
University of Wales, Bangor. Physical Science Educational Reviews, Nov.