What is a molecular model?
Plastic model with interchangable balls
Advantages
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Can pick it up and hold it
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Can rotate groups about bonds
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Can look for symmetry
Disadvantages
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Restricted to fixed classifications of sizes and bond lengths and bond
angles - cannot represent important small variations, especially in angles
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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
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Can only guess at steric repulsions, p bonding
hindrance to rotation, etc.
Beevers-type custom-built model
Advantages
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Accurately represents the geometry of a known structure, e.g. from crystallography
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May be able to pick it up and hold it, with care, but easily damaged
Disadvantages
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It may not represent a molecule in solution, whose geometry will be different
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It can only represent one conformer, when we want to consider several
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For a large model, may not be able to see in to the active site
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Cannot easily measure distances, angles, etc. from it: for these
need tables of data as well
Computer model of molecule
Advantages
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Has none of the above disadvantages
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Contains lots of other information, to be dealt with in this course, beyond
what could be contained in a single physical model
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Can easily be published, put on a web site, emailed to coworkers, etc.
Disadvantages
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You cannot pick it up and hold it
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If you want to generate one yourself, you need access to suitable software
(and hardware), and know how to use it
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You need to know how to use visualisation software, e.g. Chime, to see
pictures
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Since all models contain approximations, you need to know how to evaluate
them