Modelling methods

• The method is the way in which an energy is obtained to correspond to a particular geometry
• Older modelling programs may support only one method, but modern ones usually give the user a choice
• The other parts of the program, e.g. setting up molecules, the energy minimisation routine for geometry optimisation, and display facilities and geometry measurement, can be the same irrespectively of the method used
• There are two broad divisions of methods:
• molecular mechanics force field methods
• treat the molecule as a system of mechanical springs
• completely ignore the electrons
• electronic methods
• calculate the distribution and energy of the electrons using MO theory
• combine this with nucleus-nucleus repulsion energy
• The electronic methods subdivide into:
• semi-empirical methods
• consider only the valence shell electrons, with some big simplifications
• use empirically pre-set parameters for each element to produce results comparable with experiment
• ab initio methods
• consider all the electrons without using parameters from experimental data
• Computing time required by program:

Force fields < semi-empirical << ab initio
• Usually, quality of results:

Ab initio > semi-empirical > force fields
• Often, people do geometry optimisation (which requires repeated calculations of energy) using a faster method, then do a 'single point calculation' using a slower, better method on the geometry they have found
• Single point calculations can be used to model properties such as:
• total energy
• electron distribution
• orbital energies
• To get electronic properties, e.g. uv/vis spectrum or NMR shieldings, you must at least finish up with one of the electronic methods

• For medium-sized organic molecules, people normally use force-field methods to get a starting geometry for each conformer of interest, and do conformational searching
• It is then possible to do single-point semi-empirical calculations on each conformer
• It may be reasonable to reoptimise the geometry of each conformer at a semi-empirical level

• On the UCS's most powerful general service unix computer aidan, one conformer of methylcyclohexane took 14 seconds to reoptimise at the semi-empirical pm3 level
• The same molecule on the same computer took 5.5 minutes to reoptimise at a modest but useful ab initio level
• The amount of effort by the user is the same for each method:  you just leave the computer to calculate for longer, for the slower methods.  However, there are limits to the length of job you are allowed to run on shared service computers, as well as the practicality of getting your research done in time
• If you are going to do any of this practically in real research, you should read Hehre's  'Practical Strategies for Electronic Structure Calculations', which tells you how far you need to go to get models which are good enough for particular purposes

• The three main classes of methods are dealt with in separate notes:
•  Force field methods
•  Semi-empirical methods
•  Ab initio methods