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Medicine by Design
Describe and explain how proton nuclear magnetic resonance (nmr) can be used to determine molecular
structure (including splitting up to quartets)

NMR is used to determine the presence of different nuclei in a compound; there are only
certain atoms this method can detect:
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1H
13C
19F
31P

These nuclei can behave like small magnets, so when subjected to a magnetic field they can
develop a spin property which allows them to either align with or against the direction of
the field:

Aligning against the magnetic field is a higher energy
than aligning with the field – so more atoms will be
aligned with the field than against it
...


The amount of energy required to do this depends on the strength of the external and local
magnetic fields
...

The local magnetic fields will oppose the much larger external magnetic field, so the
overall field experienced by the nuclei will be slightly less than that of the external field
...


There are three areas of chemical shift, meaning there are three different proton
environments
...

At high resolution (such as this) the peaks present different splitting patterns
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This is known as coupling
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In the diagram,
the right carbon atom (with green hydrogens) has 4 peaks on the spectrum
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This is known as a quartet
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Explain how a combination of M
...
R, and N
...
R can be used to determine the structure of organic
molecules

Mass spectroscopy can be used to determine structure of molecules by ionising a sample,
passing it through a magnetic field and measuring the time taken to reach a detector:



The peak with the highest m/z is the molecular ion peak – this gives us the Mr of the
compound
Other large peaks are often fragments of the original molecule – using the Mr of
these fragments gives us a clue as to the different groups in a compound

Infra-red spectroscopy involves passing a range of infra-red frequencies through a sample
and measuring which frequencies have been absorbed by the chemical bonds:


Certain absorption peaks within a range will give the type of elements which
normally absorbs this frequency – the type of bonds present

NMR passes radio waves through a sample in a magnetic field, and measures the
transmission of waves as protons fall back down to ground state:

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

The number of different chemical shifts gives us the number of different proton
environments
The amount of chemical shift gives the type of proton environment
The area under the peak gives the number of protons in each environment
The splitting pattern of each peak gives the number of protons on adjacent carbon
atoms

Describe and explain the structure of a pharmacologically active molecule

The pharmacophore is the natural part of a molecule which binds to the active site of an
enzyme to produce the desired pharmacological activity – in the form of a biological
response
...
The molecule must be the correct shape and size as the site, and able to form
several bonds with the site to produce a biological response; known as molecular
recognition
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This means the shape, size, 3D structure, bond formation and orientation of the
molecule should be taken into account
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Competitive inhibitors have a similar structure to
the substrate, so can bind to the active site but do not react
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Describe and explain the role of chemists

A target molecule is the desired compound which has a biological effect
...
g
...

Chemists will begin the process by looking at the functional groups on the target molecule,
then working backwards in a series of steps to find suitable starting materials – this is
retrosynthesis
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This
work is theoretical, as synthons rarely exist in a stable state
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There are many different routes which can be taken to produce the target molecule
...
g
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These isomers can be removed using fractional
crystallisation or chromatography
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