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IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H]+ and [Cyd+H]+, have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H]+ and [Cyd+H]+ is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H]+ is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H]+. O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ~25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers. [ABSTRACT FROM AUTHOR]

Despite its success as an anticancer drug, cisplatin suffers from resistance and produces side effects. To overcome these limitations, amino-acid-linked cisplatin analogues have been investigated. Lysine-linked cisplatin, Lysplatin, (Lys)PtCl 2 , exhibited outstanding reactivity toward DNA and RNA that differs from that of cisplatin. To gain insight into its differing reactivity, the structure of Lysplatin is examined here using infrared multiple photon dissociation (IRMPD) action spectroscopy. To probe the influence of the local chemical environment on structure, the deprotonated and sodium-cationized Lysplatin complexes are examined. Electronic structure calculations are performed to explore possible modes of binding of Lys to Pt, their relative stabilities, and to predict their infrared spectra. Comparisons of the measured IRMPD and predicted IR spectra elucidate the structures contributing to the experimental spectra. Coexistence of two modes of binding of Lys to Pt is found where Lys binds via the backbone and side-chain amino nitrogen atoms, NN s , or to the backbone amino and carboxylate oxygen atoms, NO - . Glycine-linked cisplatin and arginine-linked cisplatin complexes have previously been found to bind only via the NO - binding mode. Present results suggest that the NN s binding conformers may be key to the outstanding reactivity of Lysplatin toward DNA and RNA.

Infrared multiple photon dissociation action spectra of the protonated forms of the cytidyl nucleosides, 2'-deoxycytidine, [dCyd+H](+), and cytidine, [Cyd+H](+), are acquired over the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level to determine the stable low-energy tautomeric conformations of these species generated upon electrospray ionization (ESI) and to generate the linear IR absorption spectra of these protonated nucleosides. Comparison between the experimental and theoretical spectra allows the tautomeric conformations of [dCyd+H](+) and [Cyd+H](+) populated by ESI to be determined. B3LYP predicts N3 as the preferred protonation site for both [dCyd+H](+) and [Cyd+H](+), whereas MP2 suggests that protonation at O2 is more favorable. The 2'-hydroxyl substituent does not significantly alter the structures of the B3LYP N3 and MP2 O2 protonated ground tautomeric conformations of [dCyd+H](+) vs [Cyd+H](+). [dCyd+H](+) and [Cyd+H](+) exhibit very similar spectral signatures in both regions. Nonetheless, the 2'-hydroxyl does affect the relative intensities of the IRMPD bands of [dCyd+H](+) vs [Cyd+H](+). The spectral features observed in the hydrogen-stretching region complement those of the fingerprint region and allow the N3 and O2 protonated tautomeric conformations to be readily distinguished. Comparison between the measured and computed spectra indicates that both N3 and O2 protonated tautomeric conformations coexist in the experiments, and the populations are dominated by the most stable N3 and O2 protonated tautomeric conformations. Least-squares fitting of the IRMPD spectra to the IR spectra for these most stable conformers suggests relative populations of ∼55% N3 vs 45% O2 protonated conformers of [dCyd+H](+), whereas ∼47% N3 vs 53% O2 protonated conformers of [Cyd+H](+). This change in the preferred site of protonation indicates that the 2'-hydroxyl substituent plays an important role in controlling the reactivity of the cytidyl nucleosides.

The dissociation of protonated methyl-d3 thiourea-4-butyric acid methyl amide (1), a model of thiourea-based protein cross-linking compounds, is examined both experimentally and computationally. Using a guided ion beam tandem mass spectrometer (GIBMS), the threshold collision-induced dissociation (TCID) of [1 + H](+) with Xe is examined as a function of collision energy. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for four primary and four secondary dissociation pathways, after accounting for competition between channels, sequential dissociations, unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Computations are used to explore the pathways for the various processes and elucidation of their rate-limiting transition states. These results indicate that dissociation is initiated by migration of the excess proton from sulfur to one of three nitrogen atoms in 1, similar to the "mobile proton" model of peptide fragmentation. The computational energies for the rate-limiting transition states are generally in good agreement with the experimentally derived threshold energies, with MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) results being particularly favorable. This good comparison validates the mechanisms explored theoretically and allows identification of the structures of the various product ions and neutrals.

The gas-phase conformations of protonated 2'-deoxyadenosine, [dAdo+H](+), and its RNA analogue protonated adenosine, [Ado+H](+), generated upon electrospray ionization are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques and supported by complementary theoretical electronic structure calculations. IRMPD action spectra are measured over the IR fingerprint region using the FELIX free-electron laser and the hydrogen-stretching region using an optical parametric oscillator/amplifier laser system. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of [dAdo+H](+) and [Ado+H](+) computed at the B3LYP/6-311+G(d,p) level of theory to determine the preferred site of protonation and to identify the structures populated in the experiments. N3 is found to be the most favorable site of protonation for both [dAdo+H](+) and [Ado+H](+), whereas conformers protonated at the N1 and N7 positions are much less stable by >25 kJ/mol. The 2'-hydroxyl substituent of Ado does not lead to a significant change in the structure of the ground-state conformer of [Ado+H](+) as compared to that of [dAdo+H](+), except that it provides additional stabilization via the formation of an O2'H···O3' hydrogen bond. Therefore, [dAdo+H](+) and [Ado+H](+) exhibit highly parallel IRMPD spectral features in both the fingerprint and hydrogen-stretching regions. However, the additional 2'-hydroxyl substituent markedly affects the IRMPD yield of the measured IR bands. The spectral signatures in the hydrogen-stretching region provide complementary information to that of the fingerprint region and enable facile differentiation of the conformers that arise from different protonation sites. In spite of the relative gas-phase stabilities of the N3 and N1 protonated conformers, present results suggest that both are accessed in the experiments and contribute to the measured IRMPD spectrum, indicating that the relative stabilities in solution also influence the populations generated by electrospray ionization.

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.

The gas-phase structures of protonated 2'-deoxyguanosine, [dGuo+H](+), and its RNA analogue protonated guanosine, [Guo+H](+), are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra are measured over the range extending from ∼550 to 1900 cm(-1) using the FELIX free electron laser and from ∼2800 to 3800 cm(-1) using an optical parametric oscillator/amplifier (OPO/OPA) laser system. The measured IRMPD spectra of [dGuo+H](+) and [Guo+H](+) are compared to each other and to B3LYP/6-311+G(d,p) linear IR spectra predicted for the stable low-energy conformations computed for these species to determine the most favorable site of protonation, identify the structures accessed in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and the IRMPD spectral features. Theoretical energetics and the measured IRMPD spectra find that N7 protonation is preferred for both [dGuo+H](+) and [Guo+H](+), whereas O6 and N3 protonated conformers are found to be much less stable. The 2'-hydroxyl substituent does not exert a significant influence on the structures and relative stabilities of the stable low-energy conformations of [dGuo+H](+) versus [Guo+H](+) but does provide additional opportunities for hydrogen bonding such that more low-energy structures are found for [Guo+H](+). [dGuo+H](+) and [Guo+H](+) share very parallel IRMPD spectral features in the FELIX and OPO regions, whereas the effect of the 2'-hydroxyl substituent is primarily seen in the relative intensities of the measured IR bands. The measured OPO/OPA spectral signatures, primarily reflecting the IR features associated with the O-H and N-H stretches, provide complementary information to that of the FELIX region and enable the conformers that arise from different protonation sites to be more readily distinguished. Insight gained from this and parallel studies of other DNA and RNA nucleosides and nucleotides should help better elucidate the effects of the local environment on the overall structures of DNA and RNA.

Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu < Asn < Gln.

The gas-phase structures of proton-bound dimers of cytosine and modified cytosines and their d6-analogues generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The modified cytosines examined include the 5-methyl-, 5-fluoro-, and 5-bromo-substituted species. IRMPD action spectra of seven proton-bound dimers exhibit both similar and distinctive spectral features over the range of ∼2600-3700 cm(-1). The IRMPD spectra of all of these proton-bound dimers are relatively simple, but exhibit obvious shifts in the positions of several bands that correlate with the properties of the substituent. The measured IRMPD spectra are compared to linear IR spectra calculated for the stable low-energy tautomeric conformations, determined at the B3LYP/6-31G* level of theory, to identify the conformations accessed in the experiments. Comparison of the measured IRMPD and calculated IR spectra indicates that only a single conformation, the ground-state structure, is accessed for all proton-bound homodimers, whereas the ground-state and a small population of the first-excited tautomeric conformations are accessed for all proton-bound heterodimers. In all cases, three hydrogen-bonding interactions in which the nucleobases are aligned in an antiparallel fashion analogous to that of the DNA i-motif are responsible for stabilizing the base pairing. Thus, base modifications such as 5-methyl- and 5-halo-substitution of cytosine should not alter the structure of the DNA i-motif.

The interactions of rubidium and cesium cations with four amino acids (AA) including methionine (Met), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) are examined in detail. Experimentally, the bond dissociation energies (BDEs) are determined using threshold collision-induced dissociation of the Rb(+)(AA) and Cs(+)(AA) complexes with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. 0 K BDEs of 121.0 ± 7.0 (102.8 ± 6.6), 123.8 ± 7.2 (112.9 ± 5.5), 125.8 ± 7.4 (115.6 ± 6.9), and 138.1 ± 7.5 (125.0 ± 6.8) kJ/mol are determined for complexes of Rb(+) (Cs(+)) with Met, Phe, Tyr, and Trp, respectively. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory with geometries and zero point energies calculated at the B3LYP level using def2-TZVPPD basis sets. Results obtained using all three levels show good agreement with experiment, with B3LYP values being systematically low and MP2(full) and M06 values being systematically high. At 0 and 298 K, theory predicts the ground-state conformers for M(+)(Met) either have tridentate binding of the metal cation to the carbonyl, amino, and sulfur groups (MP2 and M06) or to both oxygens of a zwitterionic conformation (B3LYP). At 298 K, binding to the carboxylic acid group and the sulfur also becomes competitive. For the aromatic amino acids at 0 K, most levels of theory favor tridentate binding of the metal ions to the backbone carbonyl and amino groups along with the π-cloud of the ring, whereas for Rb(+)(Trp) and Cs(+)(AA), B3LYP theory favors binding to only the carbonyl and ring groups. At 298 K, B3LYP favors the latter binding mode for all three Rb(+)(aromatic AA) complexes. Comparison of these results to those for the smaller alkali cations provides insight into the trends in binding affinities and structures associated with metal cation variations.