Computational Chemistry Lab
Why do computational chemistry? Computational chemistry gives us insight into 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 allow us to investigate and study the "invisible" aspects of a chemical reaction, the transitions states and intermediates that cannot be observed by experimental means. We use computational studies to establish the real mechanism for a chemical reaction. A mechanism is proposed using arrow hopping or MO theory and then computational chemistry is used to establish the energy and structures of the proposed species. The highest energy transition state gives us the rate determining step, and the lowest energy product gives us the thermodynamic end state of the reaction. Very often the proposed mechanism needs to be "adjusted" in light of the computational study.
Computational studies can also 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. We obtain energies and structures for these species. 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 and dipole moments. Analysis of the electron density gives us information on the bonding and local interactions between atoms.
- an article in Chemistry World (23rd October 2019) discusses the importance of computational chemistry in the development of enzyme catalysis: The elements of life: catalysing pharmaceutical innovation
- Novel bonding modes are still being discovered and debated! Sigma-hole or halogen-halogen bonding is one such example, see this article in Chemistry World (3rd January 2018): When it comes to halogen bonds, electrostatics are not the σ-hole story
- the nobel prize in chemisty 2013 was for "for the development of multiscale models for complex chemical systems", that is, for building methods and codes in computational chemistry.
REALLY important In the first part of the lab you are learning new things and it is easy to make a mistake, but not so easy to spot it. The computational lab is a bit different from other labs: we expect you to ASK FOR HELP, don't just keep repeating calculations. 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, in this lab, this is not a failure, it is a valid learning process.
- During this part of the lab you will receive feedback as part of the process, this will be via the demonstrators when they answer your questions.
- You will be assessed via a wiki and through submitted job files. The lab will be graded out of 100
- 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 contact Prof. Hunt BEFORE the lab is due, Prof Hunt *may* offer a 24hr extension. Items of work submitted after the due date will incur a penalty mark unless there are special circumstances. In general, work submitted late will incur a 5% penalty per day, up to a limit due to the need for a timely return of the marked lab. If you are running into any personal or time management problems, it is always best to contact Prof. Hunt.
- You can ask the demonstrator to provide rapid-feedback on your wiki for Part 1 of the lab, this is recommended to ensure you know what is expected from you. Part 2 of the lab is your independent work and carries the most marks.
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, however support is only provided in the lab by the demonstrator.
use the links in the pannel to the left to navigate through the lab