The vibrational spectrum of a hemiprotonated pair of the nucleobase cytosine has been recorded in the 300−1810 cm−1 domain using action spectroscopy on electrosprayed positive ions with a free-electron laser. The singly charged, gaseous cation has the same structure as that reported from crystallography, inferred from a strong absorption seen at 1761 cm−1, identified as the carbonyl stretch of the protonated ring mixed with in-plane bending of the bridging H+ based on a 29 cm−1 shift to lower frequency when all five of the exchangeable hydrogens are replaced by deuterium. IRMPD expels the neutral from the proton-bound dimer, leaving behind a protonated monomer. Whereas the bridging H+ in the dimer ion lies between the nitrogens of the two rings, IRMPD of the protonated monomer ion resulting from the dimer shows its H+ preferably situated on the carbonyl oxygen, indicating that the proton moves from one basic atom to another when the dimer ion dissociates.

Expansion of (CCG)n·(CGG)n trinucleotide repeats leads to hypermethylation of cytosine residues and results in Fragile X syndrome, the most common cause of inherited intellectual disability in humans. The (CCG)n·(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical protonated nucleobase pairs of cytosine (C(+)·C). Previously, we investigated the effects of 5-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present work, we extend our investigations to include protonated homo- and heteronucleobase pairs of cytosine, 1-methylcytosine, 5-methylcytosine, and 1,5-dimethylcytosine. The 1-methyl substituent prevents most tautomerization processes of cytosine and serves as a mimic for the sugar moiety of DNA nucleotides. In contrast to permethylation of cytosine at the 5-position, 1-methylation is found to exert very little influence on the BPE. All modifications to both nucleobases lead to a small increase in the BPEs, with 5-methylation producing a larger enhancement than either 1-methyl or 1,5-dimethylation. In contrast, modifications to a single nucleobase are found to produce a small decrease in the BPEs, again with 5-methylation producing a larger effect than 1-methylation. However, the BPEs of all of the protonated nucleobase pairs examined here significantly exceed those of canonical G·C and neutral C·C base pairs, and thus should still provide the driving force stabilizing DNA i-motif conformations even in the presence of such modifications. The proton affinities of the methylated cytosines are also obtained from the TCID experiments by competitive analyses of the primary dissociation pathways that occur in parallel for the protonated heteronucleobase pairs.

Vibrational spectra of the conjugate acid of Me(2)NCH(2)CH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethylputrescine) have been examined in the gaseous and crystalline phases using Infrared Multiple Photon Dissociation (IRMPD) spectroscopy, Inelastic Neutron Scattering (INS), and high pressure Raman spectroscopy. A band observed near 530 cm(-1) is assigned to the asymmetric stretch of the bridging proton between the two nitrogens, based on deuterium substitution and pressure dependence. The NN distance measured by X-ray crystallography gives a good match to DFT calculations, and the experimental band position agrees with the value predicted from theory using a 2-dimensional potential energy surface. The reduced dimensionality potential energy surface, which treats the ion as though it possesses a linear NHN geometry, shows low barriers to proton transit from one nitrogen to the other, with zero point levels close to the barrier tops. In contrast, two other related systems containing strong hydrogen bonds do not exhibit the same spectroscopic signature of a low barrier hydrogen bond (LBHB). On the one hand, the IRMPD spectra of the conjugate acid ions of the amino acid N,N,N',N'-tetramethylornithine (in which the two nitrogens have different basicities) show fewer bands and no comparable isotopic shifts in the low frequency domain. On the other hand, the IRMPD spectrum of the shorter homologue Me(2)NCH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethyl-1,3-propanediamine), for which the NHN bond angle deviates substantially from linearity, displays more than one band in the 1100-1400 cm(-1) domain, which vanish as a consequence of deuteration.

Hemiprotonated dimers of cytosine derivatives, implicated in the formation of the i-motif of DNA, have been created in solution and the gas phase. The mechanism of dimerization has been analyzed by mass spectrometry and multidimensional NMR spectroscopy.

Vibrational spectra of two gaseous cations having NH···O intramolecular ionic hydrogen bonds and of nine protonated di- and polyamines having NH···N internal proton bridges, recorded using IR Multiple Photon Dissociation (IRMPD) of mass-selected ions, are reported. The band positions of hydroxyl stretching frequencies do not shift when a protonated amine becomes hydrogen bonded to oxygen. In three protonated diamines, lower frequency bands (550-650 cm(-1)) disappear upon isotopic substitution, as well as several bands in the 1100-1350 cm(-1) region. By treating the internal proton bridge as a linear triatomic, theory assigns the lowest frequency bands to N-H···N asymmetric stretches. A 2-dimensional model, based on quantization on a surface fit to points calculated using a double hybrid functional B2-P3LYP/cc-pVTZ//B3LYP/6-31G**, predicts their positions accurately. In at least one case, the conjugate acid of 1,5-cis-bis(dimethylamino)cyclooctane, a N-H···N bend shows up in the domain predicted by DFT normal mode calculations, but in most other cases the observed bands have frequencies 20-25% lower than expected for bending vibrations. Protonated Me(2)NCH(2)CMe(2)CH(2)CH(2)CH(2)NMe(2) shows three well-resolved bands at 620, 1200, and 1320 cm(-1), of which the lowest can be assigned to the asymmetric stretch. Other ions observed include doubly protonated 1,2,4,5-(Me(2)NCH(2))(4)-benzene and 1,2,4-(Me(2)NCH(2))(3)-benzene-5-CH(2)OH. Apart from the aforementioned rigid ion derived from the alicyclic diamine, the other ions enjoy greater conformational mobility, and coupling to low-frequency C-C bond torsions may account for the shift of vibrations with N-H···N character to lower frequencies. Low-barrier hydrogen bonding (LBHB) accounts for the fact that N-H···N asymmetric stretching vibrations of near linear proton bridges occur at frequencies below 650 cm(-1).