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 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.
 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
 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 userfiles directory.

 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.
 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.
 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


 Press 'New' button (top left) to get a new molecule screen
 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
 Click the select button (diagonal yellow arrow) then click anywhere on the black
 background to get rid of the manipulator frame
Save in userfiles as cc6cuff o 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.
Include the method which will produce the files in the file name: here the o uff ending says that you are about to do a UFF geometry optimisation.
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?)
 Save (this will overwrite your previous .xml file with the optimised version)
 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
Save as cc6cpm3 ready to do a PM3 optimisation
Set up Calculation, Optimise geometry, to do PM3. OK Bunsen o You will see this goes more slowly than the force field method, but is still very fast for this size of molecule
Save

 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.
 Set this up by Calculation, Energy: notice that you have to click PM3 again: it
 does not remember from last time. Bunsen
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
 Open your model cc6cuff
 Save as cc6tbuff


Remove hydrogens with the Delete Hydrogens button (H with an eraser)
 View as sticks (View, Display settings, Cylinder Normal)
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 o The button with an arrow with a red ring around its shaft switches left drag to rotate the molecule around the z axis
 o The intersecting elipses button switches back to x or y rotate
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.)


Change to Add atoms mode (button to right of select mode button)
 Click on the 4-coordinate C button
Make sure the Automatic bond button (red bond joining blue atoms) is not lit o If Automatic bond mode is not on, you will not accidently join atoms together by clicking on them o You can intentionally make a bond between two atoms by holding down the
Shift key while clicking the two atoms in succession
 With the left mouse button, select one of the currently terminal carbon atoms
 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
 Hold down shift, and click on the other terminal carbon atom, so as to close the ring
 Change to Select mode


Press the add hydrogens button (H)
 Save
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)
 Save
View the result by rotating the molecule o 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
 o o you need to do this experiment again
You will not have found a boat conformer (C
2v
symmetry) because this is not stable for this molecule: it is a saddle point between two twist-boat enantiomers
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.
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
 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?
 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
Convert each of the two energy differences to an equilibrium constant, using the
Boltzman distribution:
K = exp (-

E / RT )
Remember that

E 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!)
 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 o What is your assessment of the UFF and PM3 methods for finding energies for this molecule?
Symmetry of twist-boat cyclohexane
 To know where you are in modelling methyl cyclo hexane conformers, you need to find the symmetry elements in twist-boat cyclohexane . The molecule has D
2 symmetry, which means that it has (only) three mutually perpendicular C
2
axes:


 one threading the centre of the ring, one through two opposite carbons, and one through the middles of two opposite bonds
Display sticks, and rotate the model so that you look down each of these axes in turn, and convince yourself that they are indeed C
2
axes. Leave the model so that you are looking down the axis which passes through the bonds
Because there are no improper axes (including planes or centres of inversion) in D
2
, the molecule is chiral, i.e. this is one enantiomer o Turn the model carefully about the x axis (i.e. downward left drag) until you o are looking down the axis which threads the ring.
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.
 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
 Start with twist boat cyclohexane , while its symmetry is fresh in your mind
Look down the axis which passes through carbon atoms o The two H atoms on the near carbon are related by the symmetry axis, so o replacing either by CH3 will give the same conformer
The two H atoms on the distant carbon are related to the first two by the C
2
 o axis which passes through bonds, so replacing any of these four H's will give the same conformer
Possible filename: mecc6tbonuff (difficult to keep this short! the 'on' means attached to C on a C
2
axis)
Look down the axis which passes through the bonds o 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 o Possible filenames: mecc6tbparuff and mecc6tbperpuff
 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 sp
3
 Add hydrogens to the new carbon, using the Add H button
 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.



 When you have done the three twist boat conformers, go on to the chair conformer of cyclohexane
This has D
Look down this S o
3d
symmetry, so it has a S
6
6
axis threading the ring
axis, i.e. so that you see the ring as a regular hexagon
On every carbon there is a hydrogen pointing outwards, i.e. not directly o towards you
These H's are called 'equatorial' and are related by the S
6
axis, so they are all equivalent o o o o o
Possible filename for the methyl derivative: mecc6cequuff
In the same view, there are three H atoms pointing directly towards you, parallel to the S
6
axis
There are another three, related to these by the S
6
axis, pointing directly away from you, so you should not be able to see them
These six H's are called 'axial'
Possible filename for the methyl derivative: mecc6caxuff
 When you have all five conformers, see which has the lowest energy o Calculate the PM3 energy of each of the others relative to it, in kJ mol-1 o According to Goodman, the MM2 relative energies are:
0, 7.44, 24.61, 26.68, and 30.02 kJ mol-1 o 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.