Mod:dont panic

So you've done your calculations as instructed, and got your optimised structures with a whole lot of properties to boot. What else is expected of you? What does analysis exactly mean, anyway? Don't panic! Here you'll find most of what you need to know to survive Module 1 and beyond.

Analysis

"How much analysis is expected from us?", I hear you ask. The answer is: AS MUCH AS 60% OF YOUR MARK! Getting the lowest in energy conformers is quite a challenge which will test your chemical knowledge and patience to the limit, but it wouldn't do you much good if you can't extract chemical information from the exercise. There are several types of information which can be discussed from the calculated structures of compounds or transition states in organic chemistry. The most common ones are listed below:

Energies
Bond angles and dihedral angles
Molecular orbitals
Bond strength, bond lengths and vibrational frequencies

Energies

Energies show how stable your structure is and when it comes to energy, the lower the better. Watch out when you compare energies of different structures, unless the number and types of atoms involved are the same, the comparison isn't valid. Under equilibrium, species of different energies will follow the same relationship as that between Gibbs free energy and equilibrium constant.

Comparing absolute energies between different computational methods is impossible, as they are calculated as the sum of different factors. However, the difference in energy between isomeric transition states calculated by different methods has often been compared with experimentally measured selectivity to judge the accuracy of computational methods.

Bond angles and dihedral angles

These values are very useful in intepreting the breakdown components of energy from Molecular Mechanics calculation. They're still useful in quantum mechanics, although there won't be any tangible result you can directly relate them to. A strained structure is a strained structure regardless of how you calculate it.

Bond strength, bond lengths and vibrational frequencies

A bond is defined and displayed differently by Molecular Mechanics and quantum mechanics techniques. Be mindful as what you see in the visualisation doesn't necessarily be what your calculation results mean. The strength of a bond, and to some extent its multiplicity, is best judged by examining the bond length and its vibrational frequencies.

Molecular orbitals

MOs are only accessible via quantum mechanics. In organic chemistry, we're mostly concerned with the frontier orbitals. Examining their position, shape and symmetry often gives clues about the nature of the MOs (bonding vs antibonding, σ-π interaction, etc.), and more importantly the reactivity and selectivity of the molecule in reactions.

Data presentation

So you aren't as good at writing wikis as the geeks who live in a garage, who shower once a month and are on a permanent supplement course of caffeine. Neither are we!

There is no doctor-ordered style for your report and marks won't be given for visual effects or creative designs of your wiki pages. Instead, we want clear, concise communication from you so that we can fully appreciate your work. One golden rule must be remembered: IF WE CAN'T SEE IT (CLEARLY), WE CAN'T MARK IT. The same goes for your analysis. If your visual aid helps the readers understand your points, by all means include it.

Another issue, which is most relevant with the mini projects, is the context of your work. Tell us why and how. More importantly, tell us EXACTLY WHAT QUESTION ARE YOU TRYING TO ANSWER WITH YOUR CALCULATION, other than for getting marks, of course.

Occasionally, we'll contact you during the marking for your original files if we find some of your results interesting, or if we feel there wasn't enough information in your wiki page. Remember to keep your files, and name them in a way that the future you won't struggle to comprehend.

Methods of calculation

Molecular Mechanics

An excellent description of molecular mechanics has already been included at this page. Here we'll simply summarise that it's basically balls and sophisticated springs. It's fast, cheap to compute but has to rely on carefully developed force field information (the anharmonic oscillator parameters). Thus, molecular mechanics can only handle structures it has been taught to handle and those unfortunately don't include organometallic compounds.

Of particular note, bonds are treated as springs and have to be specified in the starting structure. As a results, molecular mechanics performs poorly when it comes to electronic interactions, or bond forming-breaking processes. In these cases, molecular mechanics is often employed to clean up the structure, before a more appropriate method is applied.

Semi-empirical methods

To cut computational cost in quantum mechanics, approximations were made to simplify the Schrödinger equation. Semi-empricial molecular orbitals methods were born. They're still fast, albeit at the cost of accuracy, compared to ab initio methods. Semi-quantitative description of electronic distribution, molecular structure, MOs and energies can be quickly derived using these methods. They're also capable of calculations for organometallic compounds.

Being quantum mechanic techniques, they can model electronic effect, orbital interactions or hydrogen bondings, bond formation/breaking, and transition states (all the things Molecular Mechanics can't do!).

Ab initio calculations

These fully-fledged quantum mechanic techniques are the current last words, if not the only words, in computational chemistry. They can also handle every chemical structure you can come up with, given an infinite amount of time. The price is that you'll need a supercomputer with 'brain the size of a planet', and the geeks, who write wikis for breakfast, to run it. Users are protected by a web-based or a console-based submission system. Submitted jobs will join queue and occasionally get trapped in an endless loop when you will have to contact the aforementioned IT experts to intervene.

One can optimise structure (can be quite time consumming, depending on how many electrons you have in your structure), calculate energy (enthalpy, entropy) in gas and liquid phases. Recent advances allow fairly accurate prediction of NMR chemical shifts, CD spetrum and optical rotation, as well as IR vibrational frequencies. Bewarned: optical rotation and IR vibrational frequencies calculations are time consumming and shouldn't be carried out unless there's good justification (the submission deadline on Friday is infinitesimally close compared to infinity!).

Starting structure

Just as in life, your starting point affects your destination in molecular modelling. A poor starting structure will give you a poorly optimised end-product. Your software doesn't come with an AI (yet!) and so your chemical intuition will have to suffice. Crystal structures, if found, are good places to start as they are at least real minima in solid phase. Most of your calculations, however, will be in gas phase or in solvents.

Thermodynamics vs kinetics

Reactions under equilibrium are under thermodynamic control and the more stable product will be formed predominantly, hence the term 'thermodynamic product'. When the reaction is irreversible (very slow reverse reaction), the distribution of products, i.e. the selectivity, is dictated by the relative energies of the corresponding transition states, which also means the relative rates of different pathways (Arrhenius equation), and not that of the products. The major product in this case is called 'kinetic product'.

The arbitrary end-point to a reaction also gives rise to a grey area in which the reaction mixture is approaching but has not yet reached equilibrium the “control” is effectively a mixture. One can use this knowledge to manipulate the outcome of the reaction. All reactions are initially under kinetic control, when no product means no reverse reaction.

'Thermodynamic product' and 'kinetic product' refers to the energy of different species (products and transition states), and therefore, are not mutually exclusive. It is NOT possible to define the kinetic product with knowledge of the thermodynamic product and vice versa. In many reactions, both of these are the same.

Other things

If you have questions about anything not covered on this page, talk to us. In fact, talk to us in any case. Mini project, especially, shouldn't even be attempted before some interaction with us. Computational chemistry can get extremely complicated very quickly and a chat with us would prevent you from realising you've bitten up more than you can chew the night before submission. This of course in theory can't happen because you've been following our advice to start your mini project as early as Monday of the second week.