The processes underlying the formation of fragments based on glycosidic bond
cleavage are not as clear. Based on work by Rodgers et al. [44], Ho and Kebarle
[42] proposed a mechanism involving proton transfer from the 2
0 carbon of the
sugar to the phosphate group (see Scheme 10.3) concomitant with the loss of the
base in an E2-type elimination process. The B
À ion formed in this way forms a
weakly-bound encounter complex with the phosphate-sugar fragment. This complex can subsequently dissociate forming B
À fragment ions, or a second proton
transfer step may occur prior to dissociation of the complex, resulting in BH
fragments and [M–H–BH]
À fragment ions where the negative charge is on the
phosphate-sugar fragment.
All non-cyclic mononucleotides exhibit very low abundances of B
À fragments
[26–28], while B
À is the dominant fragment for cyclic mononucleotides [27, 28]
(see Fig. 10.1). The reason for this behaviour is probably a small survival chance for
the B
À anions in the presence of sufficiently acidic protons, as proton transfer to B
À
will result in the formation of [M–H–BH]
À fragment ions and neutral BH. This is
consistent with the complete absence of C
À ions from UV photodissociation of
[dCMP-H]
À parent ions [26] as the proton affinity of C
À is ca. 0.4 eV higher than
those of the other bases, which are within 0.1 eV of each other [26, 45, 46].
In cyclic nucleotides, the phosphate group has two phosphate ester bridges to the
furanose ring (see Fig. 10.2). These two connections hinder formation of
phosphate-based products as well as the conformational rearrangement necessary
for the E2-mechanism that leads to glycosidic bond cleavage. As mentioned above,
Scheme 10.2 PO 3
À fragment formation [27]
Scheme 10.3 Glycosidic CN bond cleavage with formation of a reactive encounter complex [27]
10 UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation. . .
187
cleavage are not as clear. Based on work by Rodgers et al. [44], Ho and Kebarle
[42] proposed a mechanism involving proton transfer from the 2
0 carbon of the
sugar to the phosphate group (see Scheme 10.3) concomitant with the loss of the
base in an E2-type elimination process. The B
À ion formed in this way forms a
weakly-bound encounter complex with the phosphate-sugar fragment. This complex can subsequently dissociate forming B
À fragment ions, or a second proton
transfer step may occur prior to dissociation of the complex, resulting in BH
fragments and [M–H–BH]
À fragment ions where the negative charge is on the
phosphate-sugar fragment.
All non-cyclic mononucleotides exhibit very low abundances of B
À fragments
[26–28], while B
À is the dominant fragment for cyclic mononucleotides [27, 28]
(see Fig. 10.1). The reason for this behaviour is probably a small survival chance for
the B
À anions in the presence of sufficiently acidic protons, as proton transfer to B
À
will result in the formation of [M–H–BH]
À fragment ions and neutral BH. This is
consistent with the complete absence of C
À ions from UV photodissociation of
[dCMP-H]
À parent ions [26] as the proton affinity of C
À is ca. 0.4 eV higher than
those of the other bases, which are within 0.1 eV of each other [26, 45, 46].
In cyclic nucleotides, the phosphate group has two phosphate ester bridges to the
furanose ring (see Fig. 10.2). These two connections hinder formation of
phosphate-based products as well as the conformational rearrangement necessary
for the E2-mechanism that leads to glycosidic bond cleavage. As mentioned above,
Scheme 10.2 PO 3
À fragment formation [27]
Scheme 10.3 Glycosidic CN bond cleavage with formation of a reactive encounter complex [27]
10 UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation. . .
187