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A cleavage is a chemical process by which a cleaving agent will act directly on the polymer chain making it fall into at least two separated pieces (the
oligomers). As a result of the cleavage reaction, groups originating in the cleaving molecule remain attached to the polymer at the precise cleavage location;
A fragmentation is a chemical process by which the polymer structure
is disrupted into separated pieces (the fragments) mainly because of energydependent electron doublet rearrangements leading to bond breakage.
Polymer Cleavage
We said above that, upon cleavage of a polymer, the cleaving molecule reacts
with it, and by doing so directly or indirectly “dissolves” an inter-monomer bond.
A polymer cleavage always occurs in such a way as to generate a set of true
polymers (smaller in size than the parent polymer, evidently, which is why they
are called oligomers). Indeed, let us take the example shown in Figure 3.7, where
a tripeptide (a very little protein, containing a methionyl residue at position 2)
is submitted either to a water-mediated cleavage (hydrolysis, upper panel) or to
a cyanogen bromide-mediated cleavage (lower panel). The two cases presented
in this figure are similar in some respects and different in others:
Q
In the first case the molecule that is responsible for the cleavage is water,
while in the second case it is cyanogen bromide;
Q
In both cases the bond that is cleaved is the inter-monomer bond (in
protein chemistry this is a peptidic bond);
Q
In both cases the Oligomer 2 has the same structure;
Q
The structures of the Oligomer 1 species differ when produced using water
or cyanogen bromide as the cleaving molecule.
The difference between hydrolysis and cyanogen bromide cleavage is in the generation of the Oligomer 1 species: the cyanogen bromide cleavage has a side
effect of generating a homoserine as the right end monomer of Oligomer 1,
while hydrolysis generates a genuine methionine monomer. This is because water reverses in a very symmetrical manner what polymerization did (hydrolysis
is the converse of condensation), while cyanogen bromide did some chemical
modification onto the generated Oligomer 1 species.
Nonetheless, the reader might have noted that—interestingly—all the four
oligomers do effectively have their left cap (a proton) and their right cap (the
hydroxyl). This means that in both water- and cyanogen bromide-mediated
cleavages, all the generated oligomers are indeed true polymers in the sense
that: 1) they are a chain of monomers (modified or not) and 2) they are correctly
capped (i.e. they are polymers in their finished state). This is important because
it is the basis on which we shall make the difference between a cleavage process
and a fragmentation process. Thus, the massXpert definition of an oligomer
might be: an oligomer is a polymer (of at least one monomer) in its finished
state that was generated upon cleavage of a longer polymer.
When the polymer cleavage reaction precisely reverses the reaction that was
performed for the same polymer’s synthesis, there is no special difficulty. But