About Mechanisms in Inorganic Chemistry
(Chemistry in the School of Natural and Environmental Sciences, University of Newcastle upon
Tyne, England)
History
These web pages were originally the results of two undergraduate web
programming projects, by Mr. J.N.R. Butler in 2003 on
dissociative substitution mechanisms in octahedral transition metal
complexes, and by Mr. J. Marshall in 2004 on associative
substitution mechanisms in square planar complexes.
In each case the aim was
to produce animated molecular models showing reactions in progress, to
illustrate topics in Inorganic Mechanisms undergraduate courses.
The models could be used with a projector as lecture aids, or in
subsequent private study by the students taking those courses.
Prof. R.A. Henderson devised the scopes of the projects, with a view
to using the models in his teaching, and advised the project students on
chemical content. Dr. B.W. Tattershall devised the required computer
programs to present the models, and taught and supervised the model-making
and website parts of the projects.
The Idea
The key feature of these pages is that they each can show two
mouse-rotatable images, side by side, of ball-and-stick models.
The models consist of a number of animation frames to show
the progress of the reaction, with the left hand model going from
a starting point to the reaction intermediate, and the right hand
model going from the intermediate to the finishing point.
When the first animation is complete, the second continues from
that point automatically. A clickable reaction scheme is
used to switch the models on or off, so allowing a particular
route to be chosen in the more complex schemes.
The Method
In the original projects, the Chime/Rasmol browser plugin was
used to show the models. It could read model files
consisting of concatenations of sets of .xyz atomic coordinates,
with one set for each animation frame. User control was
by the clickable schemes and HTML form buttons to change
the mode from Animate to First Frame Only or vice-versa, and all
such choices were interpreted by a server-side .php script to
redeliver the appropriate modified page.
Update to use Jmol/JSmol instead of Chime
Following the disappearance of the Chime plugin,
Dr. B.W. Tattershall in 2018 undertook the conversion
of the pages to use the Jmol/JSmol applet instead. This
could read the original .xyz animation files and use Chime/Rasmol
script files to create the same appearance of the models.
A bonus was that Jmol buttons could be used client side to
pause or play, etc., the two models individually, allowing more
convenient user interaction for exploring the reaction path.
The original HTML form / .php script mechanism for model
and mode selection was retained as well, though all such user interactions
result in reloading of the Jmol models and the animations,
if switched on, restarting at the beginning. Reloading JSmol
applets is a lot slower than just downloading the relatively
small .xyz files required by the client-side Chime plugin,
but is still quite tolerable for the originally intended uses.
An advantage is that the user needs only a standard browser such
as Chrome or Firefox to use the JSmol option. IE11 is
also adequate for these models.
The scripts developed for these pages could be adapted quite
easily to show other reaction mechanisms as two consecutive
animations, provided the molecular models required for the
animation frames may calculated
Why Use Rotatable Animated Models?
For some teaching purposes, molecular models are necessary.
Pre-prepared
rotatable computer models are preferable to physical model-kit
models in that there is no barrier of effort or cost to the student,
and misleading mistakes in model building are avoided.
They are particularly useful for students to explore symmetry,
as in the case of
Ring Flipping of Cyclohexane
or where a structural rearrangement
is difficult to draw convincingly or to show by manipulating a
physical model. An example of that is the
Racemisation Reaction of P3Se4I
For substitution reactions in transition metal complexes, however,
the need is not so obvious. A well-taught student should be
able to draw these structures and changes clearly and without
undue effort on paper, to show the salient points of the mechanisms.
The benefit of the present web pages is quite different: it
is to show the subject as attractive and interesting to students
who are accustomed to professionally produced computer graphics in
many areas of everyday life.
We make no claim that our models represent accurate reaction
paths. However, they convey the desired ideas about the
reactions to students, and we believe they are interesting
What Models are Used?
We need to ask 'To what extent do we wish to represent reality?',
and for this purpose we need to inquire what reality is in this
context. Clearly, a two-dimensional image on a computer screen,
of model-kit plastic balls and sticks, is a long way from what is
being represented at the molecular level. We could have
shown abstract models of starting point, transition state, and
final state, as might be drawn in a textbook, and generated
animation frames between these points. A much more
comprehensive web site about substitution mechanisms has
appeared, since our original one, at the
University of Valencia
and appears to take this approach in producing an attractive and
instructive product.
Alternatively, it
would be possible to calculate a minimum energy reaction path
along the reaction coordinate, using ab initio methods for
a real example. That was what was done, albeit at a quite
low level, and with some interpolations, for
Ring Flipping of Cyclohexane. However, for transition
metal complexes of interest, this would be a major computational
chemistry effort, well beyond the scope of an undergraduate project
at the time. Even if this was done, one could still ask
how real it was, even if calculated at a high level of theory.
In reality, there would be a spread of molecules to higher
energies than on the minimum energy path.
For the present pages, we chose to use as animation frames, the
points in Gaussian geometry optimisations, going towards the
geometries of stable molecules from starting points in which we
pulled away a substituent to a suitable distance. For
dissociation steps, which would not go spontaneously in the gas
phase, the sequence of frames for the reverse, association, step,
was used in the reverse order.
For the sake of computational speed, the calculations were done
at the pm3 semi-empirical level. While realistic ligands
could be modelled, use of pm3 in Gaussian 98 meant that the only
transition metal available was zinc, so this was used even though
zinc might not display the chemistry found for other metals which
give less labile complexes. The identity of the metal in the
models is not obvious to the user unless they look for it.
Square Planar Complexes
The substitution in square planar complexes presented the particular
difficulty that we wished to model a trigonal bipyramidal geometry, in
which halide ligands stayed in equatorial positions. The minimum
energy configuration for zinc, as for a main groups element, is with halides
in the apical positions. To deal with this, we modelled a diethylenetriamine
complex, in which the chelate tridentate ligand would preferentially occupy
both apical positions, leaving the remaining equatorial positions for the
halides. We then converted the reaction animations, frame by frame,
to have ammonia ligands rather than the original triamine, using a Z matrix
editor. We found the program Molden
extremely useful for this purpose, as well as, throughout the projects,
for building initial structures and extracting coordinates for each optimisation
step.