Computational Chemistry Lab


Modern chemists employ calculations side by side with wet chemistry. Calculations provide insight that is unobtainable experimentally. Computational chemistry allows us to determine and visualise the structure and bonding of complexes. While bonding in organic systems is (for the most part) straight forward this is not the case for inorganic compounds and complexes!

Computational studies can differentiate between the energy of stable conformers, but more important is the location of transition states and activated complexes that may be difficult or impossible to characterise experimentally. Thermodynamic information is obtained from the energy of stable states, and from barrier heights (energy of a transition state) we can also obtain kinetic data.

An increasing number of properties can be usefully evaluated, for example IR and Raman spectra, NMR spectra, dipole moments. Analysis of the electron density gives us information on the bonding and local interactions between atoms.

Instructions Important

The first part of the lab (day 1) is remembering how to carry out calculations, this should be familiar from last year and from calculations you have been asked to carry out as part of the Molecular Orbitals in Inorganic Chemistry course, it does contain a small amount of new material. This section is worth 30% of the marks.

The second part of the lab (day 2 and day 3) is a choice between several mini-projects where the instructions are more minimal and you are expected to apply the material and processes you have learned here and from the year1 lab, the mini-project is worth 70% of the marks.

Guidelines for the time involved have been provided, if you find yourself deviating from this significantly it is very important that you contact a demonstrator or Dr. Hunt or Dr Doidge, early rather than late!

You are welcome to work on the lab out of lab hours, and/or outside of the computer room. However, you need to manage your time, don't spend too much time on the lab, if something is not working stop and get help. It is not possible (for a non-expert) to complete the lab all on the last day, so don't try this! It is better to work in small blocks so you can get help when things go wrong. Support is available ONLY during lab hours.

REALLY important The computational lab is a bit different from the other labs: if a calculation is not working don't just keep repeating it, this is a waste of time! We expect you to ASK FOR HELP. If you cannot see, or don't understand why your job has failed there is no point in repeating it. Learning happens through trying something, making mistakes and fixing it, this is not a failure, it is a learning process.

Getting help for your lab You can find demonstrators in the 1st floor computer room, Rm 135 during lab hours. Even if you are working away from the computer room you need to come to the demonstrators in Rm 135 for help. This is because all problems are better solved when they are explained face-to-face. Students contacting staff or demonstrators outside of lab hours (or the lab) will simply be redirected to the appropriate lab and times.

Lab hours:
Demonstrators 2-5 Tue, Thur, Fri
Senior staff usually 2.30 Tue, Thur and Fri

REALLY important

  • During this lab you will receive feedback as part of the process, this will be via the demonstrators when they answer your questions.
  • You can ask the demonstrators to provide rapid-feedback on your wiki Thursday or early on Friday, this is recommended, and has the aim of advising you of any missing or miss-understood components which you will then have a chance to correct
  • You will be assessed via a wiki and through files included in your wiki, you will hand-in your wiki link via blackboard. The lab will be graded out of 20
  • You must complete the lab in the week assigned, we will check the start and end time-stamp of your wiki
  • If you are ill and/or have a personal problem or cannot attend a lab session for any reason contact Dr Doidge as soon as you know of the issue and BEFORE Friday (unless, of course, the emergency is on Friday). A 24hr extension may be offered, any further extension will require a medical certificate or information from the senior tutor. No extensions will be offered on the Friday.

More resources to help

  • Your friends: ask them to see if they have solved your problem already
  • brainstorm a solution together, but each do your own wiki and work
  • the Gaussian online manual
  • Course content for MOs in Inorganic Chemistry
  • "Exploring Chemistry with Electronic Structure Methods", by JB Foresman and A. Frisch.

Collaboration is good! While each person is doing their own project, you could each try a different conformer and then compare conformers between two or three people. Or you help each other when brainstorming a solution together. In both cases make sure you acknowledge each of your collaborators in your wiki, state clearly who did what and link back to their wiki.

Why do a wiki? Learning to create a wiki is a transferable skill, it is a skill you can take away with you. A wiki allows us to see rotatable models of your complexes and for you to report your results. You are welcome to work on the wiki at home.

use the links in the pannel to the left to navigate through the lab