The goal of this work is to determine the proton affinities of (deoxy)nucle
oside 5'- and 3'-monophosphates (mononucleotides) using the kinetic method
with fast atom bombardment mass spectrometry. The proton affinities of the
(deoxy)nucleoside 5'- and 3'-monophosphates yielded the following trend: (d
eoxy)adenosine monophosphates > (deoxy)guanosine monophosphates > (deoxy)cy
tidine monophosphates >> deoxythymidine/uridine monophosphates. Ln all case
s the proton affinity decreases or remains the same with the addition of th
e phosphate group from those values reported for nucleosides. The proton af
finity is dependent on the location of the phosphate backbone (5'- vs. S'-p
hosphates): the 3'-monophosphates have lower proton affinities than the 5'-
monophosphates except for the thymidine/uridine monophosphates where the tr
end is reversed, Molecular modeling was utilized to determine if multiple p
rotonation sites and intramolecular hydrogen bond formation would influence
the proton affinity measurements. Semiempirical calculations of the proton
affinities at various locations on each mononucleotide were performed and
compared to the experimental results. The possible influence of intramolecu
lar hydrogen bonding between the nucleobases and the phosphate group on the
measured and calculated proton affinities is discussed. (J Am Soc Mass Spe
ctrom 2000, 11, 24-32) (C) 2000 American Society for Mass Spectrometry.