Threshold Collision-induced Dissociation Techniques Research Articles

Influence of 2'-Modifications (O-Methylation, Fluorination, and Stereochemical Inversion) on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures.

Naturally occurring and chemically engineered modifications are among the most powerful strategies explored for fine-tuning the conformational characteristics and intrinsic stability of nucleic acids topologies. Modifications at the 2'-position of the ribose or 2'-deoxyribose moieties differentiate nucleic acid structures and have a significant impact on their electronic properties and base-pairing interactions. 2'-O-Methylation, a common post-transcriptional modification of tRNA, is directly involved in modulating specific anticodon-codon base-pairing interactions. 2'-Fluorinated and arabino nucleosides possess novel and beneficial medicinal properties and find use as therapeutics for treating viral diseases and cancer. However, the potential to deploy 2'-modified cytidine chemistries for tuning i-motif stability is largely unknown. To address this knowledge gap, the effects of 2'-modifications including O-methylation, fluorination, and stereochemical inversion on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, the core stabilizing interactions of i-motif structures, are examined using complementary threshold collision-induced dissociation techniques and computational methods. The 2'-modified cytidine nucleoside analogues investigated here include 2'-O-methylcytidine, 2'-fluoro-2'-deoxycytidine, arabinofuranosylcytosine, 2'-fluoro-arabinofuranosylcytosine, and 2',2'-difluoro-2'-deoxycytidine. All five 2'-modifications examined here are found to enhance the base-pairing interactions relative to the canonical DNA and RNA cytidine nucleosides with the greatest enhancements arising from 2'-O-methylation and 2',2'-difluorination, suggesting that these modifications should well be tolerated in the narrow grooves of i-motif conformations.

Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications.

DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.

Influence of 5-Methylation and the 2'- and 3'-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures.

Repetitive nucleic acid sequences, which occur in abundance throughout the mammalian genome, are of enormous research interest due to their potential to adopt fascinating and unusual molecular structures such as the i-motif. In remarkable contrast to the DNA double helix, i-motif conformations are stabilized by protonated cytosine base pairs, (Cyt)H+(Cyt), that are centrally located in the core of the i-motif and intercalated vertically in an antiparallel fashion. An in-depth understanding of how modifications influence the stability of i-motif conformations is a prerequisite to understanding their biological functions and the development of effective means of tuning their stability for specific medical and technological applications. Here, the influence of the 2'- and 3'-hydroxy substituents of the sugar moieties and 5-methylation of the cytosine nucleobases on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, (xCyd)H+(xCyd), are examined by complementary threshold collision-induced dissociation techniques and computational methods. The xCyd nucleosides examined include the canonical DNA and RNA cytidine nucleosides, 2'-deoxycytidine (dCyd) and cytidine (Cyd), as well as several modified cytidine nucleoside analogues, 2',3'-dideoxycytidine (ddCyd), 5-methyl-2'-deoxycytidine (m5dCyd), and 5-methylcytidine (m5Cyd). Comparisons among these model base pairs indicate that the 2'- and 3'-hydroxy substituents of the sugar moieties have very little influence on the strength of the base-pairing interactions, whereas 5-methylation of the cytosine nucleobases is found to enhance the strength of the base-pairing interactions. The increase in stability resulting from 5-methylation is only modest but is more than twice as large for the DNA than RNA protonated cytidine base pair. Overall, present results suggest that canonical DNA i-motif conformations should be more stable than analogous RNA i-motif conformations and that 5-methylation of cytosine residues, a significant epigenetic marker, provides greater stabilization to DNA than RNA i-motif conformations.

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations.

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m(5)dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m(5)dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m(5)dCyd)H(+)(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

Alkali metal cation binding affinities of cytosine in the gas phase: revisited.

Binding of metal cations to the nucleobases can influence base pairing, base stacking and nucleobase tautomerism. Gas-phase condensation of dc discharge generated alkali metal cations and thermally vaporized cytosine (DC/FT) has been found to produce kinetically trapped excited tautomeric conformations of the M(+)(cytosine) complexes, which influences the threshold collision-induced dissociation (TCID) behavior. In order to elucidate the effects of the size of alkali metal cation on the strength of binding to the canonical form of cytosine, the binding affinities of Na(+) and K(+) to cytosine are re-examined here, and studies are extended to include Rb(+) and Cs(+) again using TCID techniques. The M(+)(cytosine) complexes are generated in an electrospray ionization source, which has been shown to produce ground-state tautomeric conformations of M(+)(cytosine). The energy-dependent cross sections are interpreted to yield bond dissociation energies (BDEs) using an analysis that includes consideration of unimolecular decay rates, the kinetic and internal energy distributions of the reactants, and multiple M(+)(cytosine)-Xe collisions. Revised BDEs for the Na(+)(cytosine) and K(+)(cytosine) complexes exceed those previously measured by 31.9 and 25.5 kJ mol(-1), respectively, consistent with the hypothesis proposed by Yang and Rodgers that excited tautomeric conformations are accessed when the complexes are generated by DC/FT ionization. Experimentally measured BDEs are compared to theoretical values calculated at the B3LYP and MP2(full) levels of theory using the 6-311+G(2d,2p)_HW* and def2-TZVPPD basis sets. The B3LYP/def2-TZVPPD level of theory is found to provide the best agreement with the measured BDEs, suggesting that this level of theory can be employed to provide reliable energetics for similar metal-ligand 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.

Modeling Metal Cation-Phosphate Interactions in Nucleic Acids: Activated Dissociation of Mg+, Al+, Cu+, and Zn+ Complexes of Triethyl Phosphate

Threshold collision-induced dissociation techniques are employed to determine the activation energies (AEs) and bond dissociation energies (BDEs) of metal cation-triethyl phosphate complexes, M(+)(TEP), where M(+) = Mg(+), Al(+), Cu(+), and Zn(+). Activated dissociation resulting in loss of ethene, C(2)H(4), corresponds to the primary and lowest energy pathway for all four systems examined. Sequential loss of additional C(2)H(4) molecules and loss of the intact TEP ligand is also observed at elevated energies. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TEP and the M(+)(TEP) complexes, transition states, intermediates, and products of the activated dissociation of these complexes. Theoretical AEs and BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between the calculated and measured AEs for elimination of C(2)H(4) is excellent for all four systems. In contrast, less satisfactory agreement between theory and experiment is found for the M(+)-TEP BDEs and may indicate limitations in the competitive model used to analyze these high energy dissociation pathways. The influence of the valence orbital occupation of the metal cation on the binding and activation propensities for elimination of ethene from TEP is examined. The binding of metal cations to TEP is compared to that of the nucleobases to assess the binding preferences of metal cations to nucleic acids.

Inductive effects on cation–π interactions: Structures and bond dissociation energies of alkali metal cation–halobenzene complexes

The influence of halogenation on cation–π interactions is investigated both experimentally and theoretically. Bond dissociation energies (BDEs) of alkali metal cation–halobenzene complexes, M +(C 6H 5X), are determined using threshold collision-induced dissociation techniques in a guided ion beam tandem mass spectrometer, where M + = Na + and K +, and X = Cl, Br, and I. The primary dissociation pathway for all systems is endothermic loss of the neutral halobenzene from the cation–π complex. In addition, minor production of the ligand exchange product, M +Xe, is also observed. At elevated energies elimination of NaX is also observed for the Na +(C 6H 5Br) and Na +(C 6H 5I) systems. Ab initio calculations at the B3LYP/6-31+G* level of theory are used to determine the structures of the neutral π-ligands and cation–π complexes. Theoretical BDEs are determined from single point calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31+G* optimized geometries. Good agreement between the theoretical and experimental BDEs is found in all cases. The trends in the BDEs of the M +(C 6H 5X) complexes are explained in terms of the varying magnitude of the electrostatic interactions in these complexes elucidated from a binding parameter model. Comparisons are also made to BDEs previously determined for the analogous M +(C 6H 6) and M +(C 6H 5F) complexes to examine the inductive effects of the halogen substituent on the strength of the cation–π interaction.

Modeling Metal Cation−Phosphate Interactions in Nucleic Acids in the Gas Phase via Alkali Metal Cation−Triethyl Phosphate Complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations, Na+, K+, Rb+, and Cs+, to triethyl phosphate (TEP). The primary and lowest energy dissociation pathway in all cases is the endothermic loss of the neutral TEP ligand. Theoretical electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory are used to determine the structures, molecular parameters, and theoretical estimates for the BDEs of these complexes. For the complexes to Rb+ and Cs+, theoretical calculations were performed using hybrid basis sets in which the effective core potentials and valence basis sets of Hay and Wadt were used to describe the alkali metal cation, while the standard basis sets were used for all other atoms. The agreement between theory and experiment is excellent for the complexes to Na+ and K+ and is somewhat less satisfactory for the complexes to the heavier alkali metal cations, Rb+ and Cs+, where effective core potentials were used to describe the cation. The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate.

A Simple Model for Metal Cation-Phosphate Interactions in Nucleic Acids in the Gas Phase: Alkali Metal Cations and Trimethyl Phosphate

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations to trimethyl phosphate, TMP. Endothermic loss of the intact TMP ligand is the only dissociation pathway observed for all complexes. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TMP and the M+(TMP) complexes. Theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between theory and experiment is reasonably good for all complexes except Li+(TMP). The absolute M+-(TMP) BDEs are found to decrease monotonically as the size of the alkali metal cation increases. No activated dissociation was observed for alkali metal cation binding to TMP. The binding of alkali metal cations to TMP is compared with that to acetone and methanol.

Cation-π interactions with a π-excessive nitrogen heterocycle: Structures and absolute binding energies of alkali metal cation–pyrrole complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Na +, K +, Rb +, Cs +, and the bis-complex of Li +, with pyrrole, C 4H 5N. The primary and lowest energy dissociation pathway in all cases is the endothermic loss of an intact pyrrole ligand. Sequential loss of a second pyrrole ligand is observed at elevated energies for the bis-complexes. Theoretical calculations at the MP2(full)/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the MP2(full)/6-31G* optimized geometries. The agreement between theory and experiment is good for all complexes. The nature of the binding and the trends in the BDEs of these alkali metal cation–pyrrole complexes are compared to the analogous benzene and indole complexes using electrostatic potential maps and natural bond orbital analyses to examine the influence of the size of the aromatic system and the nitrogen heteroatom on the cation-π interaction. The binding of alkali metal cations to pyrrole is also compared to other metal cations and organic cations.

Influence of the d orbital occupation on the nature and strength of copper cation–π interactions: threshold collision-induced dissociation and theoretical studies

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies of a wide variety of copper cation-pi complexes, Cu(+)(pi-ligand), where pi-ligand = benzene, flurobenzene, chlorobenzene, bromobenzene, iodobenzene, phenol, toluene, anisole, pyrrole, N-methylpyrrole, indole, naphthalene, aniline, N-methylaniline, and N,N-dimethylaniline. The primary and lowest energy dissociation pathway corresponds to the endothermic loss of the intact neutral pi-ligand for all complexes except those to N-methylpyrrole, indole, aniline, N-methylaniline, and N,N-dimethylaniline. In the latter complexes, the primary dissociation pathway corresponds to loss of the intact ligand accompanied by charge transfer, thereby producing a neutral copper atom and ionized pi-ligand. Fragmentation of the pi-ligands is also observed at elevated energies in several cases. Theoretical calculations at the B3LYP/6-311G(d,p) level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Multiple low-energy conformers are found for all of the copper cation-pi complexes. Theoretical bond dissociation energies are determined from single point energy calculations at the B3LYP/6-311+G(3df,2p) level of theory using the B3LYP/6-311G(d,p) optimized geometries. The agreement between theory and experiment is very good for most complexes. The nature and strength of the binding in these copper cation-pi complexes are studied and compared with the corresponding cation-pi complexes to Na(+). Natural bond orbital analyses are carried out to examine the influence of the d orbital occupation on copper cation-pi interactions.

Cation−π Interactions with a Model for the Side Chain of Tryptophan: Structures and Absolute Binding Energies of Alkali Metal Cation−Indole Complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

Influence of Thioketo Substitution on the Properties of Uracil and Its Noncovalent Interactions with Alkali Metal Ions: Threshold Collision-Induced Dissociation and Theoretical Studies

Experimental and theoretical studies are carried out to determine the influence of thioketo substitution on the properties of uracil and its noncovalent interactions with alkali metal ions. Bond dissociation energies of alkali metal ion-thiouracil complexes, M(+)(SU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M(+) = Li(+), Na(+), and K(+) and SU = 2-thiouracil, 4-thiouracil, 2,4-dithiouracil, 5-methyl-2-thiouracil, and 6-methyl-2-thiouracil. Ab initio electronic structure calculations are performed to determine the structures and theoretical bond dissociation energies of these complexes and provide molecular constants necessary for thermodynamic analysis of the experimental data. Theoretical calculations are also performed to examine the influence of thioketo substitution on the acidities, proton affinities, and A::SU Watson-Crick base pairing energies. In general, thioketo substitution leads to an increase in both the proton affinity and the acidity of uracil. 2-Thio substitution generally results in an increase in the alkali metal ion binding affinities but has almost no affect on the stability of the A::SU base pair. In contrast, 4-thio substitution results in a decrease in the alkali metal ion binding affinities and a significant decrease in the stability of the A::SU base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of both single-stranded and double-stranded nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

Influence of Halogenation on the Properties of Uracil and Its Noncovalent Interactions with Alkali Metal Ions. Threshold Collision-Induced Dissociation and Theoretical Studies

The influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Bond dissociation energies of alkali metal ion-halouracil complexes, M+(XU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and XU = 5-fluorouracil, 5-chlorouracil, 6-chlorouracil, 5-bromouracil, and 5-iodouracil. The structures and theoretical bond dissociation energies of these complexes are determined from ab initio calculations. Theoretical calculations are also performed to examine the influence of halogenation on the acidities, proton affinities, and Watson-Crick base pairing energies. Halogenation of uracil is found to produce a decrease in the proton affinity, an increase in the alkali metal ion binding affinities, an increase in the acidity, and stabilization of the A::U base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.