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 button to add the hydrogen atoms. Then use the molecular mechanics button, , to optimise the structure. Which form did it optimise to?
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, , adjust bond angles, , or adjust dihedrals, , 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: . This will get to the default “Configure Gaussian Job Options” page:
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:
:
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,
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, , or you can capture the entire window using Alt+Print Screen.
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 m / re / <HOH / w1 / w2 / w3(EH) / (Debye) / (Å) / (º) / (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 / 1.85 / 0.9572 / 104.5 / 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.