Following excitation, most nucleotide fragmentation processes involve extensive molecular rearrangement. All fragment channels observed following UV
excitation are also observed upon the activation of gas-phase nucleotides and
oligonucleotides using a number of other activation methods including CID, infrared multiphoton dissociation (IRMPD), post-source decay (PSD) and blackbody
infrared radiative dissociation (BIRD) [36–40]. Many of these methods involve
thermal excitation of the parent ions, suggesting that direct bond cleavage from an
electronically excited state does not occur, and the molecule instead fragments due
to a large amount of vibrational energy.
Work in both the condensed phase and in vacuo indicates that nucleobases and
nucleotides may undergo fast internal conversion through conical intersections via
ring-puckering motion leading to pyramidalisation of the base geometry to reach a
vibrationally excited ground electronic state [1, 6, 17, 18, 41]. This is in agreement
with the interpretation that nucleotides undergo fragmentation on the electronic
ground-state surface. The electronic energy that is converted into vibrational energy
in the molecule (up to 5.8 eV in the experiments by Marcum et al. [26–28]) can then
be used to induce unimolecular fragmentation. Only the deprotonated base anion,
B
À , could in principle result from direct heterolytic bond cleavage on a repulsive
curve in an excited electronic state. While this is generally viewed as an unlikely
possibility, there are no experimental data suited to completely exclude this process, even though the majority of B
À ions produced are probably generated by
“thermal” decay from vibrationally hot ions in the electronic ground state [29].
In general, the molecular level details of the fragmentation mechanisms are not
well understood. Ho and Kebarle [42] used CID under single-collision conditions to
dissociate mononucleotide parent ions and determined threshold enthalpies for the
various fragment channels, comparing them with threshold enthalpies from semiempirical calculations and transition-state theory. Based on these data, they proposed fragmentation mechanisms for the major fragment channels. They suggested
that H 2 PO 4
À fragment formation occurs as the phosphate group abstracts a proton
from the 4
0 carbon of the sugar in an E2-type elimination (see Scheme 10.1). The
proposed mechanism for PO 3
À generation is transfer of a proton from a phosphate
OH group to the phosphoric acid ester oxygen with concomitant PO bond cleavage
(see Scheme 10.2). These mechanisms are now generally accepted and are in accord
with many processes assumed to be active in nucleotide backbone cleavage [43].
Scheme 10.1 H 2 PO 4
À fragment formation [27]
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J.M. Weber et al.
excitation are also observed upon the activation of gas-phase nucleotides and
oligonucleotides using a number of other activation methods including CID, infrared multiphoton dissociation (IRMPD), post-source decay (PSD) and blackbody
infrared radiative dissociation (BIRD) [36–40]. Many of these methods involve
thermal excitation of the parent ions, suggesting that direct bond cleavage from an
electronically excited state does not occur, and the molecule instead fragments due
to a large amount of vibrational energy.
Work in both the condensed phase and in vacuo indicates that nucleobases and
nucleotides may undergo fast internal conversion through conical intersections via
ring-puckering motion leading to pyramidalisation of the base geometry to reach a
vibrationally excited ground electronic state [1, 6, 17, 18, 41]. This is in agreement
with the interpretation that nucleotides undergo fragmentation on the electronic
ground-state surface. The electronic energy that is converted into vibrational energy
in the molecule (up to 5.8 eV in the experiments by Marcum et al. [26–28]) can then
be used to induce unimolecular fragmentation. Only the deprotonated base anion,
B
À , could in principle result from direct heterolytic bond cleavage on a repulsive
curve in an excited electronic state. While this is generally viewed as an unlikely
possibility, there are no experimental data suited to completely exclude this process, even though the majority of B
À ions produced are probably generated by
“thermal” decay from vibrationally hot ions in the electronic ground state [29].
In general, the molecular level details of the fragmentation mechanisms are not
well understood. Ho and Kebarle [42] used CID under single-collision conditions to
dissociate mononucleotide parent ions and determined threshold enthalpies for the
various fragment channels, comparing them with threshold enthalpies from semiempirical calculations and transition-state theory. Based on these data, they proposed fragmentation mechanisms for the major fragment channels. They suggested
that H 2 PO 4
À fragment formation occurs as the phosphate group abstracts a proton
from the 4
0 carbon of the sugar in an E2-type elimination (see Scheme 10.1). The
proposed mechanism for PO 3
À generation is transfer of a proton from a phosphate
OH group to the phosphoric acid ester oxygen with concomitant PO bond cleavage
(see Scheme 10.2). These mechanisms are now generally accepted and are in accord
with many processes assumed to be active in nucleotide backbone cleavage [43].
Scheme 10.1 H 2 PO 4
À fragment formation [27]
186
J.M. Weber et al.