What Is a Molecular Model?

What is a molecular model?

Plastic model with interchangable balls

Advantages

• Can pick it up and hold it
• Can rotate groups about bonds
• Can look for symmetry

Disadvantages

• Restricted to fixed classifications of sizes and bond lengths and bond angles - cannot represent important small variations, especially in angles
• Bonds tend to rotate to unintended positions, when we pick it up to look at it - for big molecules, it is practically impossible to pick it up without distorting it
• Can only guess at steric repulsions, p bonding hindrance to rotation, etc.

Beevers-type custom-built model

Advantages

• Accurately represents the geometry of a known structure, e.g. from crystallography
• May be able to pick it up and hold it, with care, but easily damaged

Disadvantages

• It may not represent a molecule in solution, whose geometry will be different
• It can only represent one conformer, when we want to consider several
• For a large model, may not be able to see in to the active site
• Cannot easily measure distances, angles, etc. from it:  for these need tables of data as well

Computer model of molecule

Advantages

• Has none of the above disadvantages
• Contains lots of other information, to be dealt with in this course, beyond what could be contained in a single physical model
• Can easily be published, put on a web site, emailed to coworkers, etc.

Disadvantages

• You cannot pick it up and hold it
• If you want to generate one yourself, you need access to suitable software (and hardware), and know how to use it
• You need to know how to use visualisation software, e.g. Chime, to see pictures
• Since all models contain approximations, you need to know how to evaluate them