Calculating Surfaces using Arguslab
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 Start, Programs,
Departmental Software, Chemistry, ArgusLab3.
In this exercise, you will create a model of methyl vinyl ketone 1 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.
Building the model geometry
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Start Arguslab
Press the New button (top left) to get a new molecule screen
o 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)
Set Automatic bond off, so that you will only make bonds when you shift click a
selection
Starting with 4-coordinate C for the methyl group, right click to add this towards the
left of the window
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
Shift right click to add the alpha vinyl carbon, and again to complete the vinyl group
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.
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Click the Select button to exit from Add atoms mode
Add hydrogens with the H button. You should get the right number
Save the molecule as mevnket
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
Save again
Monitor some bond angles
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.
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So that you can aim with the mouse more easily, switch the display to ball and stick,
using View Display settings... Ball cylinder Normal
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
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
o 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
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
Repeat for the other two angles
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
Write down the three bond angles, noting which is which
o 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)
Reoptimise the geometry at the PM3 level
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Save as mevnketpm3
Calculation Optimise Geometry PM3 OK
Click the Bunsen button
o As the optimisation proceeds, you will see the angle monitor values change
When the optimisation has succeeded, Save again
Write down the new values of the bond angles
o Why do you think they have changed in this way? (Remember VSEPR, but
consider also steric effects)
Calculate some grid files for the properties you wish to display as surfaces
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
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Switch off the angle monitors using Monitor Remove All Monitors
Set up a single point Calculation Energy
o Select PM3 and click the Surface Properties button
o Click Electrostatic Potential
o In the Click Orbitals to Plot box, click MOs 13, 14 (HOMO), 15 (LUMO),
and 16
o Do not change the grid spacing suggested by Arguslab
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OK OK out of the dialog
Click the Bunsen button
o 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
Calculate and display surfaces for molecular orbitals
A contour is a line in two-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 surface which passes through all points
in three-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.
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On the main menu bar, click Properties Surfaces
On the left of the resulting dialog box, you have a tree of Grid Files (which you
stored in the last section)
Click the + against RHF MOs
You should see four cube symbols representing the cubic grids you have calculated.
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
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 nonintersecting 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.
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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.
A higher value tends to emphasise the difference in size between different lobes
o If you choose too high a value, you will not see the smaller lobes at all
o If you choose too low a value, useful detail will be lost
Set the Contour Value to 0.07
So that you can see the model of the molecular geometry through the surface, set
Render Mode to mesh
o Do this by clicking the Render Mode dropdown arrow, then type m, then
click the word mesh which appears
o Do not try to alter the word in the box by typing directly, otherwise you may
hit a bug
Press Create
A new Simple Surface icon will appear in the tree of Currently Defined Surfaces on
the right side of the dialog box
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
o The icon in the Currently Defined Surfaces tree will light up, to show which
one(s) you want switched on
OK out of the dialog box
If you are still in ball and stick view, change to sticks with View Display settings...
Cylinder Normal
Positive and negative surfaces (i.e. wavefunction values of +0.07 and -0.07) are
coloured blue and red respectively
Turn the molecule to look in the plane of the conjugated system, so that your
viewpoint is in the  nodal plane
o How many antibonding nodes are visible?
o Can you name this orbital type (e.g. * or *)
o 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
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Go back to Properties Surfaces
o The dialog box will reopen in the state in which you last saw it
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)
Repeat the above procedure for creating surfaces, for MOs 15 (LUMO), 14
(HOMO) and 13 (MO below HOMO), in that order.
o In each case, set the Contour Value to 0.07
o On viewing each, answer the following questions:
MO 15 (LUMO):
o Why is this orbital more stable than MO 16?
o How many antibonding nodes are visible?
o Observe that this MO is both bonding and antibonding at the same time
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Which atomic contacts is it bonding across, and which is it
antibonding across, and what are the types of these bonds, e.g. , 
or ?
o Which carbon atom carries the biggest lobes?
 This will be important later, when we consider reactivity
MO 14 (HOMO):
o As this MO contains electrons in the ground state of the molecule, it will
have a real bonding or antibonding effect
o 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 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
 Would you expect this molecule to have any non-bonding valence
electrons (i.e. 'lone pairs')? If so, where should they be?
 Can you reinterpret this MO as being mainly a lone pair orbital?
 What does this tell you about the reality of lone pairs, in ordinary
MO theory like this?
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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
MO 13 (MO below HOMO):
o What combination of localised orbitals best corresponds to this MO?
Electrostatic Potential
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.
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From Properties Surfaces, generate a simple surface for the Electrostatic Potential
gridfile, using the same settings as for the MOs which you studied
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
o 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
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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
o 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
o 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
 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
Raise the Properties Surfaces dialog box, and toggle off the display of the ESP
surface
Click the Mapped tab on the top of the central work area of the dialog box
o This is similar to the simple surface work area, but has two boxes to fill in
instead of one
Into the Main (Grid 1) box, drag the LUMO (MO 15) Grid File cube icon
Into the Mapped (Grid 2) box, drag the ESP Grid File cube
Call the surface 'ESP onto LUMO'
Set the Contour Value to 0.07 as before
For most useful colouring (found by trial and error so as to maximise differences
between sites of attack) set
o Max Map Value to 0.17
o Min Map Value to -0.02
o Num. of Colors to 200
Set Render Mode to transparent, so that you have a more continuous surface than a
mesh to display the colour on
Click Create
A surface icon should appear in the Currently Defined Surfaces tree, under Mapped
Surface
Toggle Display of it on, and OK out
Look into the plane of the  node as before
o 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
o The terminal vinyl carbon, which has the biggest lobes, is tinged with cyan,
representing about +0.07
o Only a very small portion of the LUMO, at this contour level, feels a
negative potential
Write down a conclusion about the likely sites of attack of
o a soft nucleophile, depending on good overlap in a covalent transition state
o a hard, dipolar nucleophile, in which the need for overlap is balanced against
good electrostatic attraction