Workshop 1: Introduction to WebMO
WebMO is a web-based interface that lets you run computational chemistry software.
1. Accessing WebMO
Log in to the WebMO account using the following details:
URL:
Username:
Password:
Logging Out
When you’ve finished, click “Logout” on the “WebMO Job Manager” page.
Logging in logs you into the “WebMO Job Manager” page, which shows a list of currently running and
recently completed jobs. For example:
2. Building Structures Using WebMO
Put your mouse over the “New Job” Tab at the top left and click on “Create New Job”. This will bring
up the “Build Molecule” page.
As an example, build the water molecule, H2O.
 Choose “Build” mode for adding atoms and bonds from the top menu tab, or from the left hand
side button, .
 In “Build” mode, there will be a line at the bottom of the window saying “Build Mode - (click to
add atom, click and drag = add atom & bond, letter = change atom)”, as illustrated above. Common
“Build” actions are available on the left toolbar.
 You can choose an atom from the top menu tab, or use the keyboard to type the atom symbol, eg
“h” for hydrogen, “o” for oxygen etc, or use the periodic table button, .
 Clicking places an atom in the window, clicking and dragging inserts a bond.
 For H2O, take an O atom from the “Build” tab, or type “o” on the keyboard or get O from the
periodic table. Click somewhere in the main window to insert a red oxygen atom. Now press “h”
on the keyboard (or any of the other options) to change to hydrogen, click on the oxygen atom and
drag out to make an OH bond:
Similarly, click and drag to make the second OH bond
 If you make a mistake, use “control-z” or “Edit - Undo”. If you can’t undo enough, or if you’ve
made a real mess, you can always start fresh, using control-n or “File - New”.
 Once you have a geometry, use “Clean-Up – Comprehensive” or the “Clean-Up” button,
, on
the left hand menu. This adds hydrogen atoms (if required) and idealises the geometry (although it
can be a bit quirky). So, In fact, you could just have placed a single oxygen atom and pressed the
clean-up button to make water.
 Now you have water click on the spanner icon,
, forward arrow, and this will use molecular
mechanics to optimise the geometry to some (unspecified) force field.
3. Having made water gain experience using the WebMO editor to build a variety of molecules
(this experience will be invaluable in the remaining WebMO exercises).
Use the WebMO editor to build the molecules:
 cyclohexane C6H12
 bromoethene, CH2CHBr
 acetic acid, CH3COOH
 benzene, C6H6
 the water dimer (H2O)2
Cyclohexane should be fairly straightforward. Build the carbon ring and use the
hydrogen atoms. Then use the molecular mechanics button,
did it optimise to?
button to add the
, to optimise the structure. Which form
Use the rotate button,
, to rotate your molecule, the
button to translate it and the
button to
zoom. You can manually adjust bond lengths, angles and dihedrals by using the adjust button,
, to
select the relevant atoms and then the button underneath, adjust bond lengths,
, or adjust dihedrals,
, adjust bond angles,
, which appears depending on the number of atoms you have selected.
Rotate, translate, and zoom the molecule as necessary to yield a insightful orientation. Once you have a
nice image use ALT+Print Screen on a PC to capture the screen and paste it into any image editing
program (Paint etc), edit it and copy the image into this document on the next page.
Now make bromoethene, CH2CHBr. Here start with one C atom and right click to select “sp2”
hybridization, click and drag to add the second C atom, and click and drag from the first C to the
second to add the double bond. Now add a Br (use the periodic table since “B” selects Boron) and the
remaining H atoms, optimize, rotate, zoom and copy the image onto the next page. You should now be
able to make acetic acid and benzene.
Now have a go making the water dimer (H2O)2. Use molecular mechanics, , to “optimise” this structure
and copy it onto the next page.
Do you think the inbuilt molecular mechanics force field includes a hydrogen bonding term?
insert pictures of your molecules here:
Workshops 2 and 3: Running Calculations Semi-Empirical, HF, DFT
and MP2 calculations
1. Doing a geometry optimisation
 To compare with the tables in the notes, let’s start with the water molecule. Begin anew and build
H2O.
 Click on “Choose engine” on the left hand side of the window, or click the forward arrow,
Select the “Gaussian” computational engine to perform an “ab initio and semi-empirical”
electronic structure calculation using the Gaussian program.
 Now click the forward arrow:
page:
.
. This will get to the default “Configure Gaussian Job Options”
You should put your name or initials into the “Job Name” box to identify your jobs and to be able to
access them later.
Initially let’s run a HF/6-31G(d) calculation. We need to optimise the water structure to a minimum
energy and calculate the vibrational frequencies of H2O (to check we have a minimum and to look at
the vibrations) To do this:
 Pull down the “Calculation” tab to get to “Optimize + Vib Freq”.
 Pull down the “Theory” tab to get the chosen method: “Hartree-Fock” (well actually it’s the default
but you know what I mean).
 Pull down the “Basis Set” tab to give your chosen basis set. The 3-21G and 6-31G(d) basis sets are
on the tab, to get the 6-311+G(d), pull down to “other” and type “6-311+G(d)” into the box that
appears. Here let’s just use 6-31G(d)
 The Charge on the water molecule should be left at zero and the Multiplicity at “Singlet”.
For example, the HF/6-31G(d) optimization and frequency calculation will look like:
If you like you can click the “Preview” tab and the “Generate” button to show the actual input file that
will be used. You can then identify the purpose of each part of the input file and edit it if you like.
 Click the forward arrow,
, or the “Submit Job” text to submit the job. The screen will now
return to the “WebMO Job Manager” window which will update when the job is complete. For
example:
2. Analysing the Output
To view the results click on the blue job name (Here job H2O). This brings up the “View Job” window.
For example, for the job above we get:
You can open a new browser tab containing the actual raw output of the calculation by clicking on
“Raw Output”. If you like you can scroll through the output to see the quantities WebMO pulls out.
You can also export the geometry of the molecule to a new file (with various formats) using the
“Export Molecule” button. For example, the “Gaussian Cartesian” format gives you the Cartesian
coordinates in Å.
You need to describe the geometries of the optimised structures. To do this, click on the cursor box,
, on the left hand menu.
Clicking on one atom and shift clicking on another gives the distance (in Å) between the two atoms, for
example the distance between the two H atoms in H2O is 1.508 Å, as written on the bottom of the
“Molecule Viewer” window.
Clicking on one atom and shift clicking on another two gives a bond angle (°) and shift clicking on
three additional atoms gives a dihedral angle (°), the angle of the 4th atom out of the plane defined by
the first three atoms.
Scrolling down the “View Job” page gives you a summary of the various quantities that have been
calculated. For example, for the HF/6-31+G(d) calculation for the water molecule we have:
The geometry optimisation took 6
steps to converge to a minimum
energy, the final HF energy being
-76.0107465156 Hartree (which
doesn’t actually mean anything!)
The dipole moment of the optimized
H2O geometry is 2.1989 Debye
The optimized water geometry has
C2v symmetry (ie it is planar).
We actually want to record the final
RHF energy,
-76.0107465156 Hartree
:
The vibrational frequencies are all
positive numbers so we have a
minimum rather than a transition
state (ie what we want)
The Harmonic ZPE for the
optimized geometry is 0.022977
Hartree
By clicking on the Magnifying Glass icon, , next to “IR Spectrum” in the “Vibrational Modes” box,
you can generate the predicted IR spectrum of H2O. For example,
The vibrational intensities are
calculated from the transition
moment integral using the various
harmonic wavefunctions.
You can animate the various vibrations by clicking the filmstrip icon, , next to the given vibrational
frequency and you can look at individual molecular orbitals by clicking the button.
You can print the molecule or the spectrum to a file using the print icon,
entire window using Alt+Print Screen.
, or you can capture the
When you run a calculation it is important to check that all of the vibrational frequencies are real
numbers. The automated optimisation algorithm can sometimes converge to transition states, and this
becomes a more significant problem as the size of the system increases. As a transition state one of the
vibrational frequencies is negative (ie the potential goes downhill in one direction) which is indicated
by a negative sign. If you have an imaginary frequency, animate it to identify what kind of motion it
represents, and then start a “New Job Using This Geometry” from the transition state geometry but
“Adjust” it along the direction given by the imaginary frequency.
You can run a second (or subsequent) job starting from the current optimized geometry by clicking on
the “New Job Using This Geometry” button in the “Molecule Viewer” window at the top of the “View
Job” page. This will automatically select your previous computational engine (and your previous
method, options). Change these as you need to. This is particularly useful when you do your analysis
of the different methods and basis sets for the monomer and/or dimer. For a given molecule, start with
the simplest (fastest) level of theory and use this optimised geometry in the next calculations as you
work your way toward the best (and slowest) level of theory.
For example, for your water molecule you can run a “Molecular Orbital” calculation, an “NMR”
calculation… by changing the key words in the “Job Options” screen.
Take your optimised water geometry and use it to run a HF/6-31G “Molecular Orbital” calculation.
When the job has finished the molecular orbital energies will be listed on the “View Results” page. To
view the orbitals click on the “View” button next to the molecular orbital you want to look at and the
orbital automatically opens in the MOViewer application. The selected molecular orbital isosurface is
displayed around the molecule. Occupied orbitals are displayed in red/blue by default, and unoccupied
orbitals are displayed in yellow/green. Several orbitals can be displayed in separate windows for
comparison.
Do the H2O orbitals look like you expect them to?
Copy the HOMO and LUMO orbitals below and describe the nature of the HOMO-LUMO
transition:
The “Molecular Orbitals” calculation also lets you generate an electron density isosurface and an
electrostatic potential surface. The electron density surface is a representation of the size of the
molecule whereas the electrostatic potential surface gives an indication of areas of localised positive
(red regions) and negative charge (blue regions). View the electron density and electrostatic surfaces for
water. Copy the H2O electrostatic potential below and describe the charge distribution in water.
Exercises:
1. Water
Calculate the properties of water using a semi-empirical method, PM3, the Hartree-Fock method, the
B3LYP Density Functional Method and the MP2 electron correlation method for a range of basis sets,
that is, complete the following table:
Energy
Dipole
Moment 
re
<HOH
(EH)
(Debye)
(Å)
(º)
1.85
0.9572
104.5
1
2
3
(cm–1)
PM3
HF
3-21G
6-31G(d)
6-311+G(d,p)
B3LYP
3-21G
6-31G(d)
6-311+G(d,p)
MP2
3-21G
6-31G(d)
6-311+G(d,p)
Experiment
3832
1649
3943
Comment on your results and critically assess them.
A better variational basis should give a lower (more negative) energy. Is that what you see?
The experimental dipole moment of a water molecule in gas phase is 1.85 Debye. How does this agree?
Does higher level quantum chemistry improve the dipole moment?
How do your vibrational frequencies compare?
There are other ways to determine fractional charges than simple Mulliken population analysis (as is
done by default). Essentially these methods involve a fit of the charge distribution to obtain agreement
for the electrostatic field in some region. For your “best” calculation preview and generate the actual
input file and try one or a couple of these by adding the POP=keyword to the command line (the line
starting #N) as POP=NBO for a natural orbital analysis, POP=MK for Mertz-Kollman or
POP=CHELP. This should not change energy and structure but just the fractional charges on the
oxygens and the hydrogens. If you use these fractional charges, do they improve the dipole moment?
2. Vinyl alcohol conformers.
Build vinyl alcohol-0°, vinyl alcohol-180°, and acetaldehyde. When building these molecules, adjust
dihedral angles to result in planar, staggered conformations. Perform a Geometry Optimization,
Hartree-Fock 3-21G calculation adding the line “%Mem=16MB” as the first line of the input file to
reduce memory usage and speed up the calculation.
Vinyl alcohol transition state: Build an approximate transition state for the isomerization of vinyl
alcohol-0° and vinyl alcohol-180° as follows. View a geometry optimized vinyl alcohol job that
successfully ran, and choose New Job Using This Geometry. Adjust the H-O-C=C dihedral angle to
90°. Perform a “Transition State Optimization”, Hartree-Fock 3-21G calculation.
Make a table with columns for conformation, energy (Hartree), relative energy (kJ/mol). The relative
energy should be calculated relative to the global minimum. Note that 1 Hartree = 2625.5 kJ/mol.
Include both stable conformations and the transition state in the table.
3. Thermochemistry of CH3CHO  CO + CH4 in the gas phase.
Build and perform Optimize+Vib Freq Hartree-Fock, 6-31G(d) calculations on acetaldehyde, carbon
monoxide, and methane. To speed up your calculation, start your acetaldeyhde calculation from the
same geometry as a previous lower level optimization.
Make a table with columns for molecule, Cv, S, E298, H298, and G298.
Visit the NIST webbook (http://webbook.nist.gov/chemistry) and make a table with columns for
molecule, Cp, S, and fH (kcal/mol – I know it’s American…).
Comment on the agreement between Gaussian and NIST by comparing Cp, S, and rxnH in a table.
Recall: Cp = Cv + R for an ideal gas. 1 Hartree = 627.5095 kcal/mol.
4. Silane elimination reaction transition state.
In this exercise, the transition state for the reaction SiH4  SiH2 + H2 will be found. Here we will
“interpolate” a “QST2” guess for the transition state. We will also use the semi-empirical PM3 method
for increased speed, but at the cost of less accuracy. Start by building SiH4 and set up a PM3
optimization as a template for this calculation. Before submitting your job, preview and generate the
input file and edit the displayed text into the following (being very careful to include the blank lines):
#N PM3/3-21G Opt=QST2
Silane QST2: SiH2 + H2
01
Si
H 1
H 1
H 1
H 1
B1
B2 2
B3 2
B4 2
A1
A2 3
A3 3
D1
D2
A3 96.849005
A2 84.283836
A1 110.00006
D2 -99.87710
D1 -81.78112
B4 1.9999999
B3 1.9999997
B2 1.4799991
B1 1.4799999
Silane QST2: SiH4
01
Si
H 1
H 1
H 1
H 1
B1
B2 2
B3 2
B4 2
A1
A2 3
A3 3
D1
D2
A3 109.37081
A2 109.30689
A1 110.00006
D2 120.13988
D1 -120.0214
B4 1.4800000
B3 1.4800000
B2 1.4799991
B1 1.4799999
Submit the job and view the result.
Insert a picture of the transition state for this reaction below:
Which H atoms are forming hydrogen. What is their bond length. How does their bond angle with Si
compare to the other SiH2 bond angle?
Describe how the transition state search algorithm for this exercise differs from the exercise 2. When
would you use each algorithm?
Workshop4: Solvation and/or Excited States
Solvation
1. Let’s revisit the dipole moment of water. Set up a B3LYP/6-31+G(d,p) Geometry Optimization job
for water. Look at the preview file and edit the command line to include a polarizable background
(PCM) by clicking on the “Advanced Options” tab on the “Configure Gaussian Job” page and selecting
“water” as a solvent. Then go to preview and generate the input file used. You could edit the command
line (the one starting #N) in the input file directly by adding SCRF=(PCM,Solvent=Water). We also
want to add POP=MK to the command line to perform a charge calculation.
What happens with the water dipole moment? From classical simulation we would expect a higher
dipole moment about 2.25 Debye compared to 1.85 Debye in the gas phase.
2. Switch from water to H2S by changing the letter O to S in the input file. Run with geometry
optimization first in vacuum and then with SCRF=(PCM, Solvent=dichloromethane). When you add
PCM you should chose a standard solvent with a similar dielectric constant as H2S (ie somewhere
between 8 and 9 could be reasonable choices, dichloromethane is 8.93). Comments? Does the geometry
change compared to that of the water molecule? What are the bond lengths and the bond angle for H2S
compared to H2O. The experimental gas phase dipole moment is 0.97 Debye, while one seems to need
about 2.17 Debye in the liquid phase to be able to fit the experimental properties.
3. Run a methanol B3LYP/6-31+G(d,p) Geometry Optimization job in vacuum with POP=MK and/or
POP=NBO. The charge distribution on the three CH3 hydrogens may not become completely
symmetric. You may rotate around the O-C bond and see if you can fix this. Compare the fractional
charges to those of a GROMACS/GROMOS united atom model (the CH3 group is here treated as one
united atom) with the charges (H:+0.398 , O:-0.574 and CH3:+0.176 ) and with an all atom model
Pereira et.al., J. Phys. Chem. A, 105, 1909 -1925, (2001) which gives H:+0.4214, O:-0.5943, C:0.1820,3*(H:0.1183)
Check the stability of your the results if you include PCM with solvent=methanol and POP=MK and/or
POP=NBO and compare them to the figures above; the dielectric constant of methanol is around 30.
4. The smallest amino acid glycine, NH2CH2COOH, has a zwitterionic isomer, in which the carboxylic
acid proton is transferred to the amino group. Build “neutral” glycine and perform a Geometry
Optimization calculation. Using the resulting geometry, perform a Molecular Energy calculation at the
same level of theory but using the Advanced Options to select water as the solvent. Repeat the gas
phase Geometry Optimization and aqueous Molecular Energy calculations for the zwitterionic
structure.
Select the four jobs in Job Manager and click the Spreadsheet button to obtain an immediate
comparison among the four calculations. Solvation energy is the energy change upon solvation, i.e.,
Esolvation = Esolution − Egas. Make a table with columns for molecule, gas phase energy, solution energy,
and solvation energy.
Which isomer is more stable in the gas phase? Which isomer is more stable in water? Comment on the
reason for the difference in solvation energies between the two isomers.
Excited States
The default excited state method in WebMO is CI singles (which is not all that good), nevertheless…
1. UV-Vis Spectra of Conjugated Aldehydes
Build and perform a standard (ground state) “Geometry Optimization” calculations for the following
molecules, for example, at HF/6-31G. Using the resulting geometry, then perform “UV-Vis Spectra”
calculations for each molecule.
 2-propenal (Abs Max 209 nm)
 2-butenal (Abs Max 221 nm)
 2,4-pentadienal (Abs Max 251 nm)
The first calculated excited state (A″) corresponds to a forbidden n→π* transition and is therefore
extremely weak. The second excited state (A′) corresponds to an allowed π→π* transition and is
strongly absorbing. Compare the computed absorption maximum to the experimentally observed
maximum in a table with columns for molecule, computed maximum, experimental maximum, and
difference. Comment on any trends that are observed.
2. Excited State Optimization and Vibrational Frequencies of Formaldehyde
Build ground state (S0) formaldehyde, H2CO, and perform a Hartree-Fock 6-31G(d) Geometry
Optimization calculation. Using the resulting geometry, perform a Vibrational Frequencies calculation
at the same level of theory.
The first excited singlet state (S1) of formaldehyde is pyramidal. To build S1 formaldehyde move the O
atom out of the molecular plane by adjusting the O-H-H-C dihedral angle to 20 degrees. Perform a
Hartree-Fock 6-31G(d) Geometry Optimization calculation, but use the “Advanced Options” dialog
box and check the “Excited State” option. Using the resulting geometry, perform a Vibrational
Frequencies calculation at the same level of theory and with “Excited State” option checked.
Complete the following table, using the scaling factor of 0.8929 for Hartree-Fock 6-31G(d) frequency
calculations.
Mode
Description
S0
S1
S1
Scaled Frequency Scaled Frequency Literature
(cm-1)
(cm-1)
Frequency (cm-1)
ν1
CH stretch
2846
ν2
CO stretch
1183
ν3
CH2 bend
1293
ν4
Out-of-plane bend
-
ν5
Antisym CH stretch
2968
ν6
CH2 rock
904
Which vibrational modes undergo the largest change upon electronic excitation? Offer an explanation
for your result, noting that S1 is pyramidal and that the S0→S1 electronic transition is an n→π*
transition.