Base-Pairing Energies of Proton-Bound Heterodimers of Cytosine and Modified Cytosines: Implications for the Stability of DNA <i>i</i>‑Motif Conformations

The DNA <i>i</i>-motif conformation was discovered in (CCG)•(CGG)<i>_n</i> trinucleotide repeats, which are associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA <i>i</i>-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C⁺•C). The stronger base-pairing interactions in C⁺•C proton-bound dimers as compared to Watson–Crick G•C base pairs are the major forces responsible for stabilization of <i>i</i>-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the <i>i</i>-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE and therefore would tend to destabilize DNA <i>i</i>-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson–Crick G•C and neutral C•C base pairs, suggesting that C⁺•C mismatches are still energetically favored such that <i>i</i>-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G­(2d,2p) basis sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems

Re-Evaluation of the Proton Affinity of 18-Crown‑6 Using Competitive Threshold Collision-Induced Dissociation Techniques

The proton affinity (PA) of 18-crown-6 (18C6) is determined using competitive threshold collision-induced dissociation (TCID) techniques. The PA of 18C6 is derived from four thermochemical cycles involving the relative thresholds for production of the protonated bases, H⁺(B), and protonated crown, H⁺(18C6), from the collision-induced dissociation (CID) of four proton bound heterodimers, (B)­H⁺(18C6). The bases examined include glycine (Gly), alanine (Ala), imidazole (Imid), and 4-methylimidazole (4MeImid). In all cases, CID pathways for the loss of intact B and 18C6 are observed in competition. Loss of intact 18C6 is observed as the lowest-energy CID pathway for the (Imid)­H⁺(18C6) and (4MeImid)­H⁺(18C6) complexes. In contrast, loss of intact Gly and Ala is observed as the lowest-energy CID pathway for the (Gly)­H⁺(18C6) and (Ala)­H⁺(18C6) complexes, respectively. Excellent agreement between the measured and calculated (B)­H⁺–18C6 and (18C6)­H⁺–B bond dissociation energies (BDEs) is found with M06 theory, whereas B3LYP theory systematically underestimates these BDEs. On the basis of the relative TCID thresholds for the primary and competitive CID pathways, as well as the literature PAs of the bases, the PA of 18C6 is evaluated. The PA determined here for 18C6 exhibits excellent agreement with M06 and B3LYP theories, and very good agreement with the value reported by Meot-Ner determined using high pressure mass spectrometry (HPMS) techniques, suggesting that the PA of 18C6 reported in the NIST Webbook based on HPMS measurements by Kebarle and co-workers is overestimated

Structural and Energetic Effects in the Molecular Recognition of Protonated Peptidomimetic Bases by 18-Crown-6

Absolute 18-crown-6 (18C6) affinities of nine protonated peptidomimetic bases are determined using guided ion beam tandem mass spectrometry techniques. The bases (B) included in this work are mimics for the n-terminal amino group and the side chains of the basic amino acids, i.e., the favorable sites for binding of 18C6 to peptides and proteins. Isopropylamine is chosen as a mimic for the n-terminal amino group, imidazole and 4-methylimidazole are chosen as mimics for the side chain of histidine (His), 1-methylguanidine is chosen as a mimic for the side chain of arginine (Arg), and several primary amines including methylamine, ethylamine, n-propylamine, n-butylamine, and 1,5-diamino pentane as mimics for the side chain of lysine (Lys). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the peptidomimetic bases, as well as the proton bound complexes comprised of these species, (B)­H⁺(18C6). The measured 18C6 binding affinities of the Lys side chain mimics are larger than the measured binding affinities of the mimics for Arg and His. These results suggest that the Lys side chains should be the preferred binding sites for 18C6 complexation to peptides and proteins. Present results also suggest that competition between Arg or His and Lys for 18C6 is not significant. The mimic for the n-terminal amino group exhibits a measured binding affinity for 18C6 that is similar to or greater than that of the Lys side chain mimics. However, theory suggests that binding to n-terminal amino group mimic is weaker than that to all of the Lys mimics. These results suggest that the n-terminal amino group may compete with the Lys side chains for 18C6 complexation

Structural and Energetic Effects in the Molecular Recognition of Amino Acids by 18-Crown-6

Absolute 18-crown-6 (18C6) affinities of five amino acids (AAs) are determined using guided ion beam tandem mass spectrometry techniques. The AAs examined in this work include glycine (Gly), alanine (Ala), lysine (Lys), histidine (His), and arginine (Arg). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AAs as well as the proton bound complexes comprised of these species, (AA)­H⁺(18C6). The proton affinities (PAs) of Gly and Ala are lower than the PA of 18C6, whereas the PAs of Lys, His, and Arg exceed that of 18C6. Therefore, the collision-induced dissociation (CID) behavior of the (AA)­H⁺(18C6) complexes differs markedly across these systems. CID of the complexes to Gly and Ala produces H⁺(18C6) as the dominant and lowest energy pathway. At elevated energies, H⁺(AA) was produced in competition with H⁺(18C6) as a result of the relatively favorable entropy change in the formation of H⁺(AA). In contrast, CID of the complexes to the protonated basic AAs results in the formation of H⁺(AA) as the only direct CID product. H⁺(18C6) was not observed, even at elevated energies, as a result of unfavorable enthalpy and entropy change associated with its formation. Excellent agreement between the measured and calculated (AA)­H⁺–18C6 bond dissociation energies (BDEs) is found with M06 theory for all complexes except (His)­H⁺(18C6), where theory overestimates the strength of binding. In contrast, B3LYP theory significantly underestimates the (AA)­H⁺–18C6 BDEs in all cases. Among the basic AAs, Lys exhibits the highest binding affinity for 18C6, suggesting that the side chains of Lys residues are the preferred binding site for 18C6 complexation in peptides and proteins. Gly and Ala exhibit greater 18C6 binding affinities than Lys, suggesting that the N-terminal amino group provides another favorable binding site for 18C6. Trends in the 18C6 binding affinities among the five AAs examined here exhibit an inverse correlation with the polarizability and proton affinity of the AA. Therefore, the ability of the N-terminal amino group to compete for 18C6 complexation is best for Gly and should become increasing less favorable as the size of the side chain substituent increases

O2 Protonation Controls Threshold Behavior for N‑Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides

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

Energy-Resolved Collision-Induced Dissociation Studies of 1,10-Phenanthroline Complexes of the Late First-Row Divalent Transition Metal Cations: Determination of the Third Sequential Binding Energies

The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M²⁺(Phen)₃ complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion–neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M²⁺(Phen)_<i>x</i> complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co⁺, Ni⁺, Cu⁺, and Zn⁺, previously investigated

Silver Cation Affinities of Monomeric Building Blocks of Polyethers and Polyphenols Determined by Guided Ion Beam Tandem Mass Spectrometry

Energy-resolved collision-induced dissociation (CID) of seven silver cation–ligand complexes, Ag⁺(L), with Xe is studied using guided ion beam tandem mass spectrometry techniques. The ligands, L, investigated are monomeric building blocks of polyethers and polyphenols including phenol, 2-hydroxyphenol, 3-hydroxyphenol, 4-hydroxyphenol, 2-hydroxymethyl phenol, 3-hydroxymethyl phenol, and 4-hydroxymethyl phenol. In all cases, Ag⁺ is observed as the primary CID product, corresponding to endothermic loss of the intact neutral ligand. The kinetic-energy-dependent cross sections for CID of these Ag⁺(L) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K Ag⁺–L bond dissociation energies (BDEs). Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the neutral ligands and their complexes to Ag⁺ using either the Stuttgart RSC 1997 valence basis set and effective core potential (SRSC ECP) or DZVP-DFT to describe Ag⁺. Theoretical BDEs are determined at the B3LYP/6-311+G­(2d,2p) level of theory again using the SRSC ECP or DZVP-DFT for Ag⁺. For all systems, the most stable binding conformations found involve cation−π interactions when the SRSC ECP is used to describe Ag⁺. When DZVP-DFT is employed, the most stable binding geometries remain cation−π complexes except for the complex to 2HP, where the ground-state conformer involves bidentate binding of Ag⁺ to the hydroxyl oxygen atoms of both substituents. The agreement between the measured and calculated BDEs is excellent with a MAD of 2.9 ± 1.7 kJ/mol when the SRSC ECP is used to describe Ag⁺ and less satisfactory for DZVP-DFT, which underestimates the strength of binding in these systems by ∼14% or 26.0 ± 6.7 kJ/mol

Alkali Metal Cation Interactions with 15-Crown‑5 in the Gas Phase: Revisited

Quantitative interactions of the alkali metal cations with the cyclic 15-crown-5 polyether ligand (15C5) are studied. In this work, Rb⁺(15C5) and Cs⁺(15C5) complexes are formed using electrospray ionization and studied using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. The energy-dependent cross sections thus obtained are interpreted to yield bond dissociation energies (BDEs) using an analysis that includes consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion–neutral collisions. 0 K BDEs of 175.0 ± 9.7 and 159.4 ± 9.6 kJ/mol, respectively, are determined and exceed those previously measured [J. Am. Chem. Soc. 1999, 121, 417−423] by 68 and 57 kJ/mol, respectively, consistent with the hypothesis proposed there that excited conformers had been studied. Because the analysis techniques have advanced since this early study, we also reanalyze the published data for the Na⁺(15C5) and K⁺(15C5) systems to ensure a self-consistent interpretation of all four systems. Revised BDEs for these systems are 296.1 ± 15.5 and 215.6 ± 10.6 kJ/mol, respectively, which are within experimental uncertainty of the previously reported values. In addition, quantum chemical calculations are conducted at the B3LYP/def2-TZVPPD level of theory with theoretical BDEs in reasonable agreement with experiment. Computations are also used to explore features of the potential energy surfaces for isomerization of the M⁺(15C5) complexes

Metal Cation Dependence of Interactions with Amino Acids: Bond Energies of Rb⁺ and Cs⁺ to Met, Phe, Tyr, and Trp

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

Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated RNA Mononucleotides: Gas-Phase Conformations and Energetics

The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5′-monophosphate (A5′p), guanosine-5′-monophosphate (G5′p), cytidine-5′-monophosphate (C5′p), and uridine-5′-monophosphate (U5′p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570–1900 cm^–1, that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G­(d,p) level of theory finds that the most stable conformations of the deprotonated forms of A5′p, C5′p, and U5′p are accessed in the experiments, and these conformers adopt the C3′ <i>endo</i> conformation of the ribose moiety and the <i>anti</i> conformation of the nucleobase. In the case of deprotonated G5′p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the <i>syn</i> rather than <i>anti</i> conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2′-hydroxyl group on their structure, stability, and fragmentation behavior