c





 

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 ,  ,



, 
, , 

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





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.

áp 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.




áp To start work, you should 
 press the 'New' button (top left) to get a new molecule
screen,  you should press the 'Open' button to read in a molecule which you have saved
previously in the your Argus directory.
áp In Arguslab, you need to save your molecule with whatever name you want  doing
a geometry optimisation  


 . 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.
áp 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.

áp 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.

  



 








áp Press 'New' button (top left) to get a new molecule screen

áp Read chair  
  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
áp Click the select button (diagonal yellow arrow) then click anywhere on the black
background to get rid of the manipulator frame
áp Save in your Argus directory as cc6cuff
?p BWT advice: keep names to 8 characters or less, so they will be compatible with
any programs. cc6 is the petroleum industry shorthand for  
 : any
ideas, which help you to make up file names self-evident to you, are useful. The
middle c stands for chair conformation.
?p 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.
áp 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?)
áp Save (this will overwrite your previous .xml file with the optimised version)
áp 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
áp Save as cc6cpm3 ready to do a PM3 optimisation
áp Set up Calculation, Optimise geometry, to do PM3. OK Bunsen
?p You will see this goes more slowly than the force field method, but is still very
fast for this size of molecule
áp Save
áp List the output as before: you can see that Arguslab tells you a lot about the molecule
 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.
áp Set this up by Calculation, Energy: notice that you have to click PM3 again: it does not
remember from last time. Bunsen
áp 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

O 


áp Open your model cc6cuff

áp Save as cc6tbuff
áp Remove hydrogens with the Delete Hydrogens button (H with an eraser)
áp View as sticks (View, Display settings, Cylinder Normal)
áp 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
?p The button with an arrow with a red ring around its shaft switches left drag to
rotate the molecule around the z axis
?p The intersecting elipses button switches back to x or y rotate
áp 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.)
áp Change to Add atoms mode (button to right of select mode button)
áp Click on the 4-coordinate C button
áp Make sure the Automatic bond button (red bond joining blue atoms) is 
lit
?p If Automatic bond mode is not on, you will not accidently join atoms together by
clicking on them
?p You can intentionally make a bond between two atoms by holding down the Shift
key while clicking the two atoms in succession
áp With the left mouse button, select one of the currently terminal carbon atoms
áp 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
áp Hold down shift, and click on the other terminal carbon atom, so as to close the ring
áp Change to Select mode
áp Press the add hydrogens button (H)
áp Save
áp 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)
áp Save
áp View the result by rotating the molecule
 ?p 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
?p 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
?p 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.
áp 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.

c
 
 



áp 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?
áp 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
áp Convert each of the two energy differences to an equilibrium constant, using the
Boltzman distribution:

 = exp (-_c/ ° )
Remember that _chas to be in J mol-1, not kJ mol-1. Use = 294 K. ° is the gas
constant, 8.3145 J K-1 mol-1 (another good constant to store!)

áp According to Goodman, the experimental energy difference is 23 kJ mol-1, which on the

present basis (ignoring entropy), would convert to  = [more stable]/[less stable] = 12198
?p What is your assessment of the UFF and PM3 methods for finding energies for
this molecule?


 


áp To know where you are in modelling methyl 

hexane conformers, you need to find
the symmetry elements in twist-boat  
 . The molecule has 2 symmetry,
which means that it has (only) three mutually perpendicular 2 axes: one threading the
centre of the ring, one through two opposite carbons, and one through the middles of two
opposite bonds
áp Display sticks, and rotate the model so that you look down each of these axes in turn, and
convince yourself that they are indeed 2 axes. Leave the model so that you are looking
down the axis which passes through the bonds
áp Because there are no improper axes (including planes or centres of inversion) in 2, the
molecule is chiral, i.e. this is one enantiomer
 ?p Turn the model carefully about the x axis (i.e. downward left drag) until you are
looking down the axis which threads the ring.
?p The top two carbons on your screen should now come towards you from back left
to front right, or — —. 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

O







In this part of the exercise, you use the models of the two conformers of  
 , 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.

áp Be very careful to use Save as.. to save each model with a different name,  you
start to construct it from the  
  model, otherwise you are very likely to
overwrite the  
  model by accident, which will be a nuisance because you will
need to use it again for constructing the next conformer of methylcyclohexane
áp Start with twist boat  
 , while its symmetry is fresh in your mind
áp Look down the axis which passes through carbon atoms
?p The two H atoms on the near carbon are related by the symmetry axis, so
replacing either by CH3 will give the same conformer
?p 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  H's will give the same
conformer
?p Possible filename: mecc6tbonuff (difficult to keep this short! the 'on' means
attached to C  a C2 axis)
áp Look down the axis which passes through the bonds
?p 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
?p Possible filenames: mecc6tbparuff and mecc6tbperpuff
áp 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
áp Add hydrogens to the new carbon, using the Add H button
áp 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.
áp When you have done the three twist boat conformers, go on to the chair conformer of
 
 
áp This has D3d symmetry, so it has a S6 axis threading the ring
áp Look down this S6 axis, i.e. so that you see the ring as a regular hexagon
?p On every carbon there is a hydrogen pointing outwards, i.e. not directly towards
you
?p These H's are called 'equatorial' and are related by the S6 axis, so they are all
equivalent
 ?p Possible filename for the methyl derivative: mecc6cequuff
?p In the same view, there are three H atoms pointing directly towards you, parallel
to the S6 axis
?p 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
?p These six H's are called 'axial'
?p Possible filename for the methyl derivative: mecc6caxuff

áp When you have all five conformers, see which has the lowest energy
?p Calculate the PM3 energy of each of the others relative to it, in kJ mol-1
?p According to Goodman, the MM2 relative energies are:

0, 7.44, 24.61, 26.68, and 30.02 kJ mol-1

?p 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




This exercise is intended primarily to be used in a three-hour drylab session, with active teaching
by demonstrators. Students are expected to have already learnt basic modelling operations using
Arguslab, in the first drylab session, Drylab: Modelling using Arguslab, and instructions given
there will not be repeated here. As with the first exercise, the present one should be very useful
for private study as a revision aid, and will particularly help students to understand the parts of
the modelling lecture course dealing with surfaces. Arguslab is available directly on Campus
cluster PCs. It may be run by ,  , 


, 
,
.

In this exercise, you will create a model of methyl vinyl ketone ! and
display some of its molecular orbitals as surfaces. You will map its
electrostatic potential onto one of these, and come to some conclusions
about the reactivity of the molecule.

"

 





áp Start Arguslab
áp Press the New button (top left) to get a new molecule screen
?p The window is automatically set to Add Atoms mode (button with pencil pointing
to a blue ball) and Automatic bond on (button with red bond joining two blue
atoms)
 áp Set Automatic bond off, so that you will only make bonds when you shift click a
selection
áp Starting with 4-coordinate C for the methyl group, right click to add this towards the left
of the window
áp Click the 3-coordinate C button, then, at a suitable distance from the methyl carbon, shift
right click to add and join the carbonyl carbon
áp Shift right click to add the alpha vinyl carbon, and again to complete the vinyl group
áp Change to 1-coordinate O, left click the carbonyl carbon to select it, then shift right click
to add the oxygen

You should have an appropriately shaped skeleton.

áp Click the Select button to exit from Add atoms mode

áp Add hydrogens with the H button. You should get the right number
áp Save the molecule as mevnket
áp Use the pincers button to do a UFF geometry optimisation. If it stops after 100 iterations
without converging, do it again until it does converge
áp Save again

þ




Here you will measure the three bond angles at the carbonyl carbon, and set monitors on these,
so that you can follow them when you improve the geometry.

áp So that you can aim with the mouse more easily, switch the display to ball and stick,
using View Display settings... Ball cylinder Normal
áp To measure angles (here as in other modelling programs) you need to select the three
atoms forming the angle, in the order end, middle, end. In this case the middle atom is
always the carbonyl carbon
áp In Arguslab, you do multiple selections by left clicking the first atom, then holding down
the Control key while left clicking the other (two) atoms in turn
?p Do this for the first of the three angles. The correct skeletal atom balls only
should turn yellow. If everything turns yellow, you have hit a bug: simply left
click the first atom again to start again
áp The bond angle symbol nearly to the right of the top tool bar should now be ungreyed.
Click it to put a green angle monitor on the screen
áp Repeat for the other two angles
áp You may need to rotate the molecule a little, or at least set the display back to View
Display settings... Cylinder Normal, in order to read the numbers for the angles
áp Write down the three bond angles, noting which is which
?p What do you learn about (a) the equality of the angles; (b) the sum of the angles?
(The sum should be exactly 360º for planarity)

°
 




þ



áp Save as mevnketpm3
 áp Calculation Optimise Geometry PM3 OK
áp Click the Bunsen button
?p As the optimisation proceeds, you will see the angle monitor values change
áp When the optimisation has succeeded, Save again
áp Write down the new values of the bond angles
?p Why do you think they have changed in this way? (Remember VSEPR, but
consider also steric effects)












In this step you will calculate the values of some wavefunctions, and of the electrostatic
potential, at each of a cubic grid of points covering the space occupied by the molecule. For
each function you select, Arguslab will store the resulting three-dimensional array of values as a
separate file, which will be named automatically

áp Switch off the angle monitors using Monitor Remove All Monitors
áp Set up a single point Calculation Energy
?p Select PM3 and click the Surface Properties button
?p Click Electrostatic Potential
?p In the Click Orbitals to Plot box, click MOs 13, 14 (HOMO), 15 (LUMO), and 16
?p Do not change the grid spacing suggested by Arguslab
áp OK OK out of the dialog
áp Click the Bunsen button
?p You will see (in the text window) Arguslab calculating two-dimensional slices of
the cubic grid for each MO and for the ESP, but nothing yet appears in the picture





 


A 
 is a line in
-dimensional space which connects points having a particular value,
e.g. of a wavefunction. Contour plots of wavefunctions in a plane through a molecule are used in
elementary teaching of MO theory of symmetric molecules. They may be useful for bigger
molecules if a plane can be found which passes through a region of interest, e.g. it contains one
or two bonds. Generally, however, it is not possible, and hardly ever easy, to select a plane
which contains all the features of interest of a delocalised MO. We need to view the whole
molecule, in three-dimensional space.

The three-dimensional counterpart of a contour is a  which passes through all points in

-dimensional space, which have a particular value of some property. In the previous
section, you calculated some MOs and the ESP of the molecule at all points of a three-
dimensional grid. For an orbital which you want to display, Arguslab now just needs to select all
the entries in its stored array which have your selected value of a contour level. Just as it can
draw on the screen a perspective view of a plastic ball to represent an atom, so it can draw a view
of a surface connecting these selected coordinates. As you rotate the model on the screen to see
different atoms, so the surface will also rotate, so that you can see different features of it.

áp On the main menu bar, click Properties Surfaces

 áp On the left of the resulting dialog box, you have a tree of Grid Files (which you stored in
the last section)
áp Click the + against RHF MOs
áp You should see four cube symbols representing the cubic grids you have calculated.
áp Left drag the cube for MO 16 into the empty Grid box of the central work area of the
dialog box, where you will be able to set up the contour value and kind of display you
want
áp The next typein box below the name of the grid file contains a name for the surface. It is
initially set to 'Simple Surface'. You can change this to 'MO above LUMO' to remind
you of what you will be looking at

In real research, selecting the contour value usually needs to be done by trial and error, to
explore what information different values will yield. In a two-dimensional contour plot, several
different contour values are often plotted at once, since any number of non-intersecting lines in
the chosen plane can be seen at the same time. In three dimensions, it is usually practicable to
see only one surface at a time, or in the case of orbitals with nodes, one positive and one negative
surface joining points with plus or minus a particular numerical value respectively. This is
because surfaces for orbitals (or ESP) are closed surfaces, so that you cannot see one inside the
other.

áp The larger the contour value, the smaller the spatial extent of the surface, since higher
values of the wavefunction are occur nearer to the nuclei.
áp A higher value tends to emphasise the difference in size between different lobes
?p If you choose too high a value, you will not see the smaller lobes at all
?p If you choose too low a value, useful detail will be lost
áp Set the Contour Value to 0.07
áp So that you can see the model of the molecular geometry through the surface, set Render
Mode to mesh
?p Do this by clicking the Render Mode dropdown arrow, then type m, then click the
word mesh which appears
?p Do not try to alter the word in the box by typing directly, otherwise you may hit a
bug
áp Press Create
áp A new Simple Surface icon will appear in the tree of Currently Defined Surfaces on the
right side of the dialog box
áp To switch the display of the surface on, select the icon for it (an object with a torch
shining on it) and click the Toggle Display button
?p The icon in the Currently Defined Surfaces tree will light up, to show which
one(s) you want switched on
áp OK out of the dialog box
áp If you are still in ball and stick view, change to sticks with View Display settings...
Cylinder Normal
áp Positive and negative surfaces (i.e. wavefunction values of +0.07 and -0.07) are coloured
blue and red respectively
áp Turn the molecule to look in the plane of the conjugated system, so that your viewpoint is
in the O nodal plane
 ?p How many antibonding nodes are visible?
?p Can you name this orbital type (e.g. 
Õ
O or OÕ)
?p Why are the lobes on oxygen smaller than those on carbon?

Now you can look at the other three MOs you have calculated, in the same way, as follows

áp Go back to Properties Surfaces

?p The dialog box will reopen in the state in which you last saw it
áp Select the lit up surface icon, and click the Toggle Display button to turn it off (before in
due course you turn another one on)
áp Repeat the above procedure for creating surfaces, for MOs 15 (LUMO), 14 (HOMO) and
13 (MO below HOMO), in that order.
?p In each case, set the Contour Value to 0.07
?p On viewing each, answer the following questions:
áp MO 15 (LUMO):
?p Why is this orbital more stable than MO 16?
?p How many antibonding nodes are visible?
?p Observe that this MO is both bonding and antibonding at the same time
p Which atomic contacts is it bonding across, and which is it antibonding
across, and what are the types of these bonds, e.g. , O or 
?
?p Which carbon atom carries the biggest lobes?
p This will be important later, when we consider reactivity
áp MO 14 (HOMO):
?p As this MO contains electrons in the ground state of the molecule, it will have a
real bonding or antibonding effect
?p Make a list of which atomic contacts this MO is bonding across and which it is
antibonding across, and the types of these bonds or antibonding effects ( or O
?p Remember the rule from elementary MO teaching that stable molecules usually
have MOs filled with electrons up to and including the non-bonding valence
orbitals
p Would you expect this molecule to have any non-bonding valence
electrons (i.e. 'lone pairs')? If so, where should they be?
p Can you reinterpret this MO as being mainly a lone pair orbital?
p What does this tell you about the reality of lone pairs, in ordinary MO
theory like this?
p NBO analysis is able to reassign the calculated electron density to nearly
full lone pair or bonding orbitals, and nearly empty antibonding orbitals,
but MOs as they are usually calculated are delocalised and are either
exactly full (singly or usually doubly occupied) or exactly empty in a
particular state
áp MO 13 (MO below HOMO):
?p What combination of localised orbitals best corresponds to this MO?

c


Electrostatic potential is the repulsive or attractive energy felt by a unit positive charge as a result
of the combined effect of nuclei and electrons in the molecule. It is of interest when considering
the attack of charged or dipolar nucleophiles or electrophiles on the molecule. In an earlier
section you have already calculated the ESP at every point of the cubic grid covering the
molecule. It does not depend on a knowledge of individual orbitals, but on the distribution of the
whole electron density and of the nuclei. In the absence of electronic method data, it can be
calculated approximately from electronegativities.

áp From Properties Surfaces, generate a simple surface for the Electrostatic Potential
gridfile, using the same settings as for the MOs which you studied
áp This surface is not very helpful: it shows that the space around the oxygen feels a
negative potential, and that around the rest of the molecule feels a positive potential,
which you could have guessed from elementary ideas of electronegativity
?p Changing the contour level, which you can do within the Properties Surfaces
dialog box by dragging the surface icon back onto the work area in the middle,
altering the level, then pressing Update, does not allow more interesting variations
in the ESP to be identified
áp To attract a negatively charged or strongly dipolar nucleophile, there needs to be a high
positive potential where there is also a dense lobe of the LUMO
?p A method has to be used which can show the values of the LUMO wavefunction
and the ESP at the same time at the same point
?p A popular method, which we shall use here, is to show the LUMO as a translucent
surface, but colour it according to the value of the ESP at each point, using a
range of colours rather than just two for positive and negative
p If we were not interested in a covalently bonded transition state, and hence
did not want to know about the LUMO, we could instead map the ESP
onto a surface of total electron density, or, if electronic data were not
available at all (e.g. for a very large molecule), onto a Van der Waals radii
surface
áp Raise the Properties Surfaces dialog box, and toggle off the display of the ESP surface
áp Click the Mapped tab on the top of the central work area of the dialog box
?p This is similar to the simple surface work area, but has two boxes to fill in instead
of one
áp Into the Main (Grid 1) box, drag the LUMO (MO 15) Grid File cube icon
áp Into the Mapped (Grid 2) box, drag the ESP Grid File cube
áp Call the surface 'ESP onto LUMO'
áp Set the Contour Value to 0.07 as before
áp For most useful colouring (found by trial and error so as to maximise differences between
sites of attack) set
?p Max Map Value to 0.17
?p Min Map Value to -0.02
?p Num. of Colors to 200
áp Set Render Mode to transparent, so that you have a more continuous surface than a mesh
to display the colour on
áp Click Create
 áp A surface icon should appear in the Currently Defined Surfaces tree, under Mapped
Surface
áp Toggle Display of it on, and OK out
áp Look into the plane of the O node as before
?p You should see that only the lobes on the carbonyl carbon are violet, the highest
ESP on the scale (>+0.15), on the outside where they could be attacked
?p The terminal vinyl carbon, which has the biggest lobes, is tinged with cyan,
representing about +0.07
?p Only a very small portion of the LUMO, at this contour level, feels a negative
potential
áp Write down a conclusion about the likely sites of attack of
?p a soft nucleophile, depending on good overlap in a covalent transition state
?p a hard, dipolar nucleophile, in which the need for overlap is balanced against
good electrostatic attraction