Exercise on modelling, using Arguslab
This exercise is intended primarily to be used in a three-hour drylab session,
with active teaching by demonstrators. After that, it should be very
useful for private study as a revision aid. Arguslab is available
directly on Campus cluster PCs. It may be run by Start, Programs,
Departmental
Software, Chemistry, ArgusLab3, ArgusLab
Arguslab offers quite good on-screen molecule-building facilities, with
a moderate library of useful molecules. The viewer is mouse-controlled
quite similarly to Rasmol/Chime. Arguslab can do geometry optimisations
using the UFF force field. This covers all elements of the Periodic
Table because it is not restricted to known atom types in its parameterisation,
though it does use some common ones. The resulting energies are distinctly
different from those obtained using some of the more conventional force
fields, and wherever possible one needs to reoptimise at a higher level.
For this, Arguslab offers geometry optimisation using the MNDO, AM1 or
PM3 semiempirical levels, as well as single point calculations using these,
though the range of elements covered is much less. There are also
single point semiempirical calculations using Extended Huckel (for a bigger
element coverage) or ZINDO (for excited states for UV/visible absorption
prediction). Version 3.1 of Arguslab has good facilities for calculating
electron density or orbital surfaces at the semiempirical levels, and displaying
them. It can also map another property, e.g. electrostatic potential,
onto a surface, similarly to the display facilities of Chime (see Notes:
An electronic model of methyl thiirane). This will be the subject
of a further document: Drylab: Calculating
Surfaces using Arguslab
File storage
Arguslab writes its own format of molecule file, .xml, but it can also
write .xyz files for input to other programs, e.g. molden. It creates
(and leaves behind) a lot of temporary files, which need to be managed.
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Arguslab has been set up to write to and read from your own H: drive file
space. I recommend that you never work directly in the home directory
of this (i.e. directly in My Documents), but rather create a folder called
Work beneath this, and then beneath that folders for your various types
of work. One of these could be Argus, for the files created and read
by Arguslab. By keeping its files separate from your other computer
acitivities, you will be able more easily to delete, using Windows Explorer,
superfluous ones it leaves behind. Once you have pointed Arguslab
to h:\work\argus (or whatever you set up), on its first read or write,
it will remember where to look at least for the duration of that signon.
Starting and Stopping in Arguslab
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To start work, you should either press the 'New' button (top left)
to get a new molecule screen, or you should press the 'Open' button
to read in a molecule which you have saved previously in the your Argus
directory.
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In Arguslab, you need to save your molecule with whatever name you want
before
doing a geometry optimisation as well as afterwards. This
is so that all the ancillary files will have the right names. If
you forget to change the file name before modifying a molecule, files will
be saved automatically with the name you used previously, possibly destroying
data which you wanted to keep.
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It is best not to maximise the molecule window, because then its title
bar will display the name by which you are currently saving the files.
Just drag its bottom right corner so that it fills most of the Arguslab
worktop.
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To stop using Arguslab, click File Exit. You will find that if you
have molecule windows open, this will just close one of these. You
need to do it repeatedly to close all the windows (if you have several
open) and then stop the program.
Conformations of cyclohexane and methylcyclohexane
Chair cyclohexane
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Press 'New' button (top left) to get a new molecule screen
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Read chair cyclohexane from the fragment library by pressing the
'Add fragment' button (pencil pointing to benzene ring), Fragment Library,
..., then when you have found the right file, right click in the window
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Click the select button (diagonal yellow arrow) then click anywhere on
the black background to get rid of the manipulator frame
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Save in your Argus directory as cc6cuff
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BWT advice: keep names to 8 characters or less, so they will be compatible
with any programs. cc6 is the petroleum industry shorthand for cyclohexane:
any ideas, which help you to make up file names self-evident to you, are
useful. The middle c stands for chair conformation.
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Include the method which will produce the files in the file name:
here the uff ending says that you are about to do a UFF geometry optimisation.
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On the Calculation menu, set up to do a UFF geometry optimisation.
OK the dialogue box, then do the calculation by pressing the calculate
button (Bunsen burner?)
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Save (this will overwrite your previous .xml file with the optimised version)
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Read the output using the list output button (looks like a sheet with writing
on it) and note down the energy onto paper (a small positive number of
Hartree units to high precision: you need all the digits!) from the
end of the output file. This is the UFF energy of chair cyclohexane.
[If you were doing this in real research, you might have a Notepad window
open (available from the PC desktop) and copy and paste the numbers with
suitable annotations, so as to avoid the possibility of copying errors,
which are only too easy with these tedious long numbers. You could
then save from Notepad to a text file afterwards.] Close the output
viewing window
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Save as cc6cpm3 ready to do a PM3 optimisation
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Set up Calculation, Optimise geometry, to do PM3. OK
Bunsen
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You will see this goes more slowly than the force field method, but is
still very fast for this size of molecule
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Save
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List the output as before: you can see that Arguslab tells you a
lot about the molecule before optimisation, but nothing about it
afterwards. It appears that you are intended to run a single point
calculation after the geometry optimisation to obtain the properties, including
the final energy.
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Set this up by Calculation, Energy: notice that you have to click
PM3 again: it does not remember from last time. Bunsen
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Now you can list the new (single point) output, and note down the energy
in Hartrees (negative: this is electronic energy) from the last page
of the output
Twist boat cyclohexane
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Open your model cc6cuff
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Save as cc6tbuff
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Remove hydrogens with the Delete Hydrogens button (H with an eraser)
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View as sticks (View, Display settings, Cylinder Normal)
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Turn the molecule so that you are looking at the ring approximately edge-ways
on, so that you can see it as a chair, with the head atom on the left and
the foot atom on the right, and so that you can see all the atoms separately
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The button with an arrow with a red ring around its shaft switches left
drag to rotate the molecule around the z axis
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The intersecting elipses button switches back to x or y rotate
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In select mode, click on the atom at the foot of the chair. It should
highlight yellow. Then press the delete button on the keyboard, to
remove that carbon. (In this program, for this molecule, it is easiest
to remove it altogether, rather than breaking just one ring bond and trying
to rotate singly attached carbon to the right position for boat.)
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Change to Add atoms mode (button to right of select mode button)
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Click on the 4-coordinate C button
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Make sure the Automatic bond button (red bond joining blue atoms) is not
lit
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If Automatic bond mode is not on, you will not accidently join atoms together
by clicking on them
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You can intentionally make a bond between two atoms by holding down the
Shift key while clicking the two atoms in succession
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With the left mouse button, select one of the currently terminal carbon
atoms
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Place the mouse cursor as carefully as possible where you judge the missing
carbon of the boat conformation should be, hold down the shift key, and
right click to put a carbon there
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Hold down shift, and click on the other terminal carbon atom, so
as to close the ring
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Change to Select mode
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Press the add hydrogens button (H)
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Save
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To do a UFF geometry optimisation you could press the pincers button (for
pulling things roughly into shape?) but you might as well use Calculation
Optimize geometry to set it up, so that you can change the maximum number
of steps from 100 to 200 before you start. Otherwise you may find
the optimisation routine stops before it finds the minimum (in which case
you can press Bunsen to continue with another bout)
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Save
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View the result by rotating the molecule
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You should not have landed back in the chair form. If you have, you
did not get your built geometry close enough to that of the required conformer,
and you need to do this experiment again
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You will not have found a boat conformer (C2v symmetry) because
this is not stable for this molecule: it is a saddle point between
two twist-boat enantiomers
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You should have found one of these twist-boat conformers. As they
are of equal energy by symmetry, it does not matter for present purposes
which one you have found.
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Find the UFF energy as for the chair conformer, then do a PM3 geometry
optimisation (file name cc6tbpm3), as before, and find the PM3 energy of
the result.
Energy comparison of the cyclohexane conformers
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Remembering that one gives positive energies and the other negative, you
should have found that the UFF and PM3 methods have given the same order
of stabilities for the two conformers. Which is the more stable?
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By careful use of hand calculator, find the energy of the less stable conformer
relative to the energy of the more stable, for each method, converting
the energies to kJ mol-1. To convert from Hartrees to J mol-1, multiply
by 2625515. If you have spare storage in your calculator, this is
a useful number to store for present purposes
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Convert each of the two energy differences to an equilibrium constant,
using the Boltzman distribution:
K = exp (-DE / RT )
Remember that DE has to be in J mol-1,
not kJ mol-1. Use T = 294 K. R is the gas constant,
8.3145 J K-1 mol-1 (another good constant to store!)
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According to Goodman, the experimental energy difference is 23 kJ mol-1,
which on the present basis (ignoring entropy), would convert to K
= [more stable]/[less stable] = 12198
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What is your assessment of the UFF and PM3 methods for finding energies
for this molecule?
Symmetry of twist-boat cyclohexane
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To know where you are in modelling methylcyclohexane conformers,
you need to find the symmetry elements in twist-boat cyclohexane.
The molecule has D2 symmetry, which means that it has
(only) three mutually perpendicular C2 axes: one
threading the centre of the ring, one through two opposite carbons, and
one through the middles of two opposite bonds
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Display sticks, and rotate the model so that you look down each of these
axes in turn, and convince yourself that they are indeed C2
axes. Leave the model so that you are looking down the axis which
passes through the bonds
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Because there are no improper axes (including planes or centres of inversion)
in D2, the molecule is chiral, i.e. this is one enantiomer
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Turn the model carefully about the x axis (i.e. downward left drag) until
you are looking down the axis which threads the ring.
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The top two carbons on your screen should now come towards you from back
left to front right, or vice-versa. If you turn the ring through
180° in either direction, you always get back to the same sense.
The other enantiomer has the bond going the other way
The five conformers of methylcyclohexane
In this part of the exercise, you use the models of the two conformers
of cyclohexane, which you have saved, to create models of the five
conformers of methylcyclohexane. For each, do a preliminary UFF optimisation,
then a PM3 geometry optimisation, then a PM3 single point calculation to
get relative energies. Write these down, and calculate energies relative
to that of the most stable of the five conformers.
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Be very careful to use Save as.. to save each model with a different name,
before
you start to construct it from the cyclohexane model, otherwise
you are very likely to overwrite the cyclohexane model by accident,
which will be a nuisance because you will need to use it again for constructing
the next conformer of methylcyclohexane
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Start with twist boat cyclohexane, while its symmetry is fresh in
your mind
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Look down the axis which passes through carbon atoms
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The two H atoms on the near carbon are related by the symmetry axis, so
replacing either by CH3 will give the same conformer
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The two H atoms on the distant carbon are related to the first two by the
C2 axis which passes through bonds, so replacing any of these
four
H's will give the same conformer
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Possible filename: mecc6tbonuff (difficult to keep this short!
the 'on' means attached to C on a C2 axis)
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Look down the axis which passes through the bonds
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On each C nearest to the axis, there are two kinds of H: one approximately
parallel to the axis, and one approximately perpendicular to it.
These will give two different conformers of methylcyclohexane
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Possible filenames: mecc6tbparuff and mecc6tbperpuff
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To substitute the methyl group, in select mode, right click on the H to
be replaced. On the drop-down menu which results, left click on Change
atom. Select C sp3
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Add hydrogens to the new carbon, using the Add H button
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Save, then do UFF optimisation. Make sure the job has converged,
rather than reaching the number of cycles limit. Save and go on to
the PM3 optimisation, etc.
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When you have done the three twist boat conformers, go on to the chair
conformer of cyclohexane
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This has D3d symmetry, so it has a S6 axis threading
the ring
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Look down this S6 axis, i.e. so that you see the ring as a regular
hexagon
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On every carbon there is a hydrogen pointing outwards, i.e. not directly
towards you
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These H's are called 'equatorial' and are related by the S6
axis, so they are all equivalent
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Possible filename for the methyl derivative: mecc6cequuff
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In the same view, there are three H atoms pointing directly towards you,
parallel to the S6 axis
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There are another three, related to these by the S6 axis, pointing
directly away from you, so you should not be able to see them
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These six H's are called 'axial'
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Possible filename for the methyl derivative: mecc6caxuff
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When you have all five conformers, see which has the lowest energy
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Calculate the PM3 energy of each of the others relative to it, in kJ mol-1
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According to Goodman, the MM2 relative energies are:
0, 7.44, 24.61, 26.68, and 30.02 kJ mol-1
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How do the differences between these compare with yours? It is not
completely clear from his pictures, which is which. When you have
the book to hand, try comparing it with your notes from these exercises
Answers
It is intended to post numerical answers for this drylab on the course
website, late in the course.