Threshold Collision-induced Dissociation Research Articles

Hydration energies of calcium hydroxide cation, CaOH+(H2O)x (x = 1–6), studied using guided ion beam tandem mass spectrometry

Hydration energies of CaOH+(H2O)x, x = 1–6, were obtained using threshold collision-induced dissociation (TCID) with xenon (Xe) as conducted with a guided ion beam tandem mass spectrometer (GIBMS). The primary reaction pathway observed for all complexes is the loss of one water ligand, followed by the loss of additional water molecules at higher collision energies for x > 1. The kinetic-energy-dependent cross sections for dissociation of CaOH+(H2O)x complexes were modeled to obtain 0 K binding energies after accounting for lifetime effects, energy distributions, and pressure effects. Except for x = 5, experimental threshold energies measured through TCID agree well with theoretical hydration energies determined using B3LYP/6-311+G(d,p) structure geometries followed by single point energies calculated at B3LYP, B3P86, M06, and MP2(full) levels of theory with a 6-311+G(2d,2p) basis set. B3LYP-GD3BJ and ωB97XD calculations were also used, with the former yielding results having the best agreement with the threshold energies extracted from the analysis of the TCID cross sections.

Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation.

In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.

Gas-phase Ni(II) affinities of alternative metal binding peptides from competitive threshold collision-induced dissociation

The Ni(II) affinity of the polyhistidine tag is used in the purification of recombinant proteins by immobilized metal affinity chromatography. Here we measured the relative gas-phase Ni(II) affinities of four alternative metal binding (amb) peptides and the 7xHis tag using the competitive threshold collision-induced dissociation (TCID) technique. The general primary structure of the four amb peptides was acetyl-Aa1-Aa2-Gly3-Pro4-Aa5-Gly6-Cys7, designed to test whether the His1-Cys2 or Asp1-His2 would exhibit the higher Ni(II) affinity and whether the Tyr5 with its ability of forming long-range π-nickel interaction and hydrogen bonding would contribute to the Ni(II) affinity. The Cys7 is retained in all the amb sequences because previous research has shown that both the thiolate side group and carboxylate terminus simultaneously coordinate the metal ion. The Ni(II) affinity was measured using the dissociation of the [amb + Ni(II) + NTA]− complex, where NTA = nitrilotriacetic acid, which is a commonly used ligand for Ni(II) inside the IMAC column. The dissociation of [amb + Ni(II) + NTA]− produced two main product channels; [amb + Ni(II)]− + NTA and [NTA + Ni(II)]− + amb, whose competition was modeled by TCID to extract the relative gas-phase Ni(II) affinities. Extensive molecular modeling using PM6 located the low-energy structures whose molecular parameters were used in the TCID analyses if their collision cross sections agreed with those measured by traveling-wave ion mobility mass spectrometry and they were compatible with a concerted reaction. We compare the final results by conducting the TCID analyses using alternative PM6 parameters and by making the ternary complexes in acidic and basic solutions.

Robustness of Threshold Collision-Induced Dissociation Simulations for Bond Dissociation Energies.

The threshold collision-induced dissociation (T-CID) method is the workhorse for gas-phase bond dissociation energy (BDE) measurements. However, T-CID does not measure BDEs directly; instead, BDEs are obtained by fitting simulated data to the experimental data. We previously observed several large discrepancies between the computed and experimental BDEs. To analyze the reliability of the experimental values, we previously reported a study of the dissociation rate models in the simulation. Here, we report a study of the collision simulation part, specifically in the L-CID (ligand CID) program. We show that the BDE values are robust even to intentionally introduced mistakes in the simulations, varying in most cases by less than 3 kcal mol-1. The most significant exception is the collisional energy transfer (CET) simulation, which led to deviations larger than 10 kcal mol-1. However, we found that the BDEs obtained with explicitly simulated CET distributions deviated by only 3 kcal mol-1 from those simulated with the original model. Collectively, our results suggest that the T-CID-derived BDE values are robust and are likely to be accurate.

Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B12 Derivatives?

Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.

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.

Extending the competitive threshold collision-induced dissociation of Zn(II) ternary complexes using traveling-wave ion mobility-mass spectrometry

The competitive threshold collision-induced dissociation (TCID) of the ternary complex [amb5+Zn(II)+NTA]− → [amb5+Zn(II)]− + NTA or → [NTA+Zn(II)]− + amb5, where amb5 = His-Cys-Gly-Pro-Gly-Gly-Cys or Asp-His-Gly-Pro-Gly-Gly-Cys and NTA = nitrilotriacetic acid, were studied using traveling-wave ion mobility-mass spectrometry (TWIMMS). The analyses included calculating the reaction cross sections as a function of center-of-mass collision energy at three pressures of the argon collision gas, which covers the pressure range available in the TWIMMS instrument. The ternary complex contained one of the amb5 peptides, whose His, Cys and/or Asp substituent groups could compete with the NTA carboxylate sites for binding Zn(II). A new molecular modeling procedure was developed, initially using PM6 geometry-optimizations and thermochemical analyses to locate low-energy conformers of the ternary complex and its products that also had collision cross sections (ΩHe), measured using the ion size scaled Lennard-Jones (L-J) method, that were close to the TWIMMS measured ΩHe. A selection of these conformers were further geometry-optimized at the DFTB/3OB_D4 level of theory and using these as starting structures, molecular dynamics (MD) simulations were conducted to sample the ensemble of structures L-J ΩHe at 300 K. From these analyses, a selection of reactant and product conformers whose L-J ΩHe best matched the TWIMMS ΩHe were used in the TCID fitting of the center-of-mass energy-dependent, reaction cross sections extrapolated to zero pressure. The TCID fitting determined the threshold energies of the two product channels which in the absence of an activation barrier in excess of the energy of the products equates to the 0 K dissociation enthalpies (ΔH0). The difference in ΔH0 for the two competing reactions allowed for a relative gas-phase Zn(II) affinity scale to be constructed for the amb5 peptides studied here and from our previous published amb5 research.

Periodic trends in the hydration energies and critical sizes of alkaline earth and transition metal dication water complexes.

This review encompasses guided ion beam tandem mass spectrometry studies of hydrated metal dication complexes. Metals include the Group 2 alkaline earths (Mg, Ca, Sr, and Ba), late first-row transition metals (Mn, Fe, Co, Ni, Cu, and Zn), along with Cd. In all cases, threshold collision-induced dissociation experiments are used to quantitatively determine the sequential hydration energies for M2+ (H2 O)x complexes ranging in size from one to 11 water molecules. Periodic trends in these bond dissociation energies are examined and discussed. Values are compared to other experimental results when available. In addition to dissociation by simple water ligand loss, complexes at a select size (which differs from metal to metal) are also observed to undergo charge separation to yield a hydrated metal hydroxide cation and a hydrated proton. This leads to the concept of a critical size, xcrit , and the periodic trends in this value are also discussed.

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.

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes using Ion Mobility-Mass Spectrometry.

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold collision-induced dissociation (TCID) to measure the thermochemistry of the dissociation of negatively-charged [amb+M(II)+NTA]- ternary complexes into two product channels: [amb+M(II)] + NTA or [NTA+M(II)]-+ amb, where M = Zn or Ni and NTA is nitrilotriacetic acid. The complexes contain one of the alternative metal binding (amb) heptapeptides with the primary structures acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 or acetyl-Asp1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, where the amino acids' Aa1,2,6,7 positions are the potential metal-binding sites. Geometry-optimized stationary states of the ternary complexes and their products were selected from quantum chemistry calculations (presently the PM6 semi-empirical Hamiltonian) by comparing their electronic energies and their collision cross-sections (CCS) to those measured by ES-IM-MS. From the PM6 frequency calculations, the molecular parameters of the ternary complex and its products model the energy-dependent intensities of the two product channels using a competitive TCID method to determine the threshold energies of the reactions that relate to the 0 K enthalpies of dissociation (ΔH0). Statistical mechanics thermal and entropy corrections using the PM6 rotational and vibrational frequencies provide the 298 K enthalpies of dissociation (ΔH298). These methods describe an EI-IM-MS routine that can determine thermochemistry and equilibrium constants for a range of ternary metal ion complexes.

Potassium Binding Interactions with Aliphatic Amino Acids: Thermodynamic and Entropic Effects Analyzed via a Guided Ion Beam and Computational Study.

Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference. Notably, all levels of theory indicate that the lowest-lying isomers at 298 K have K+ binding to the carbonyl oxygen in either a monodentate ([CO]) or bidentate ([CO,OH]) fashion, isomers that are linked in a double-well potential. This complicates the analysis of the data, although does not greatly influence the final results. Analysis of the resulting cross sections includes accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates. The resulting experimental bond dissociation energies generally increase as the polarizability of the amino acid increases, results that agree well with quantum chemical calculations done at the B3LYP, B3P86, and MP2(full) levels of theory, with B3LYP-GD3BJ predicting systematically larger values.

Thermodynamics and Reaction Mechanisms for Decomposition of a Simple Protonated Tripeptide, H+GGA: From H+GGG to H+GAG to H+GGA.

We present a thorough characterization of fragmentations observed in threshold collision-induced dissociation (TCID) experiments of protonated glycylglycylalanine (H+GGA) with Xe using a guided ion beam tandem mass spectrometer. Kinetic energy dependent cross sections for nine ionic products were obtained and analyzed to provide 0 K barriers for the five primary products, [b2]+, [y1 + 2H]+, [b3]+, [y2 + 2H]+, and [a1]+; and four secondary products, [a2]+, [a3]+, high-energy [y1 + 2H]+, and CH3CHNH2+, after accounting for multiple ion-molecule collisions, the internal energy of reactant ions, unimolecular decay rates, competition between channels, and sequential dissociations. Relaxed potential energy surface scans performed at the B3LYP-GD3BJ/6-311+G(d,p) level of theory are used to identify transition states (TSs) and intermediates of the five primary and three secondary products (with the mechanism of the other secondary product previously established). Geometry optimizations and single point energy calculations of reactants, products, intermediates, and TSs were performed at several levels of theory. These theoretical energies are compared with experimental threshold energies and found to give reasonable agreement, with B3LYP-GD3BJ and M06-2X levels of theory performing slightly better than MP2 and better than B3LYP. The results obtained here are compared with previous results for decomposition of H+GGG and H+GAG to probe the effect of changing the amino acid sequence. Methylation in H+GGA has a significant effect on the competition between the primary sequence products, [b2]+ and [y1 + 2H]+, suppressing the [b2]+ cross section by raising its threshold energy, while enhancing that of [y1 + 2H]+ by lowering its threshold energy.

Thermochemical and conformational studies of Ni(II) and Zn(II) ternary complexes of alternative metal binding peptides with nitrilotriacetic acid

Energy-resolved threshold collision-induced dissociation (TCID) of negatively-charged [amb5-H+M(II)+NTA-2H]− ternary complexes were studied for how they competitively dissociated into the products [amb5-3H+M(II)]− + NTA or [NTA-3H+M(II)]− + amb5, where M = Zn or Ni and NTA is nitrilotriacetic acid. The complexes contained one of the alternative metal binding-5 (amb5) heptapeptides with primary structures acetyl-Aa1-Aa2-Gly3-Pro4-Tyr5-Aa6-Aa7, where the amino acids Aa1,2,6,7 included the potential metal binding sites of Asp, His, and/or Cys. The study included heptahistidine which represents the His affinity tag commonly used in immobilized metal affinity chromatography (IMAC) separation of recombinant proteins. Molecular modeling using PM6 located low energy, geometry-optimized conformers of the ternary complexes and their products which had collision cross sections that agreed with those measured by ion mobility. Using the molecular parameters, including vibrational and rotational frequencies, of the reactant and products from the molecular modeling, the energy-dependent intensities of the two product channels were modeled using a competitive TCID method to determine their threshold energies which equated to the two product channels 0 K dissociation enthalpies (ΔH0). Statistical mechanics thermal corrections provided the 298 K enthalpies (ΔH298) and Gibbs free energies (ΔG298) for the association reactions [amb5-3H+M(II)]− + NTA ↔ [amb5-H+M(II)+NTA-2H]− and [NTA-3H+M(II)]− + amb5 ↔ [amb5-H+M(II)+NTA-2H]−. These results were compared to determine which amb5 were effective as alternative tags for IMAC purification of recombinant proteins and is a routine that can be generally applied to compare the thermochemistry of metal ion ternary complexes.

Sodium Binding Interactions with Aliphatic Amino Acids: A Guided Ion Beam and Computational Study.

Metal binding affinities play a vital role in medicinal, biological, and industrial applications. In particular, metal cation-amino acid (AA) interactions contribute to protein stability such that analyzing analogous prototypical interactions is important. Here, we present a full description of the interactions of sodium cations (Na+) and six aliphatic amino acids (AA), where AA = glycine (Gly), alanine (Ala), homoalanine (hAla), valine (Val), leucine (Leu), and isoleucine (Ile). Experimentally, these interactions are evaluated using threshold collision-induced dissociation carried out in a guided ion beam tandem mass spectrometer, allowing for the determination of the kinetic-energy-dependent behavior of Na+-AA dissociation. Analysis of these dissociation cross sections, after accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates, allows the determination of absolute Na+-AA bond dissociation energies (BDEs) in kJ/mol of Gly (164.0), Ala (166.9), hAla (167.9), Val (172.7), Leu (173.7), and Ile (174.6). These are favorably compared to quantum chemical calculations conducted at the B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels of theory. Our combination of structural and energetic analyses provides information regarding the specific factors responsible for Na+ interactions with amino acids. Specifically, we find that the BDEs increase linearly with increasing polarizability of the amino acid.

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.

Guided Ion Beam Studies of the Thorium Monocarbonyl Cation Bond Dissociation Energy and Theoretical Unveiling of Different Isomers of [Th,O,C]+ and Their Rearrangement Mechanism.

Threshold collision-induced dissociation (TCID) of the thorium monocarbonyl cation, ThCO+, with xenon is performed using a guided ion beam tandem mass spectrometer. The only product observed is Th+ resulting from loss of the CO ligand. Analysis of the kinetic energy-dependent cross sections for this CID reaction yields the first experimental determination of the bond dissociation energy (BDE) of Th+-CO at 0 K as 0.94 ± 0.06 eV. Calculated BDEs at the CCSD(T) level of theory with cc-pVXZ (X = T and Q) basis sets and a complete basis set (CBS) extrapolation are in good agreement with the experimental result. The Feller-Peterson-Dixon composite coupled-cluster methodology was also applied on both ThCO+ and ThCO, with contributions up to CCSDT(Q) and a four-component treatment of spin-orbit coupling effects. The final 0 K Th+-CO BDE of 0.94 ± 0.04 eV is in excellent agreement with the current experimental result. The ionization energy of ThCO, as well as the atomization energies and heats of formation for both ThCO and ThCO+, is reported at this same level of theory. Complete potential energy profiles of both quartet and doublet spin are also constructed to elucidate the mechanism for the formation and interconversion of different isomers of [Th,O,C]+. Chemical bonding patterns in low-lying states of ThCO+ and potential energy curves for ThCO+ dissociation are also investigated.

Thermochemical studies of hydrated manganese dications, Mn2+(H2O)x (x = 4–9), using guided ion beam tandem mass spectrometry

The experimental hydration energies of Mn2+(H2O)x complexes, where x = 4–9, are determined by threshold collision-induced dissociation (TCID) with Xe using a guided ion beam tandem mass spectrometer, coupled with an electrospray ionization (ESI) source. The ESI source naturally produces intense beams of the x = 7–9 complexes, but smaller complexes, x = 4–6, can be formed using an in-source fragmentation technique. For all systems, the dominant fragmentation processes observed are sequential loss of water ligands, but at x = 4 and 5, charge separation (CS) reactions are observed where formation of singularly charged species becomes competitive. Kinetic energy-dependent cross sections are obtained and analyzed to yield 0 K bond dissociation energies (BDEs) for the losses of one and two water ligands, which are then converted to 298 K binding enthalpies and Gibbs energies. Barrier heights for three different CS reactions are also determined. These thermodynamic results are compared with values obtained theoretically, with reasonable agreement being achieved. Theoretical geometry and single-point energy calculations are performed at B3LYP, B3P86, M06, and MP2(full) levels of theory.

Relative Energetics of the Gas Phase Protomers of p-Aminobenzoic Acid and the Effect of Protonation Site on Fragmentation.

Guided ion beam tandem mass spectrometry (GIBMS) is used to investigate the energy-dependent threshold collision-induced dissociation (TCID) of the two protonated isomers (protomers) of p-aminobenzoic acid (p-ABA). The O-protomer of p-ABA (protonated at the carbonyl oxygen) was generated via electrospray ionization (ESI) from a methanol/water solution, whereas the N-protomer (protonated at the amine) was produced via ESI from an acetonitrile/water solution. The two protomers are clearly distinguishable from differences in the onsets of the fragmentation channels and in the abundance and identity of the products observed. Additional GIBMS experiments were performed on protonated benzoic acid (BA) and aniline, which serve as simple models for fragmentation driven by protonation at the carbonyl or amine group of p-ABA and provide insights into the dissociation channels of the two p-ABA protomers. Theoretical calculations were carried out to determine the dissociation mechanisms and for comparison with the experimental thermochemistry, which is obtained from modeling the kinetic energy dependent TCID cross sections after accounting for multiple collisions, kinetic shifts, competition between channels, and sequential dissociations. Calculations together with the energy-resolved experiments show that a product ion (C5H5+, m/z 65) common to both p-ABA protomers is produced from sequential dissociations via two different mechanisms. Furthermore, we demonstrate here that the relative stabilities of the two p-ABA protomers can be determined directly from experiment via shared product channels for which there are no barriers exceeding their asymptotic energies. Our results indicate that the two p-ABA protomers are nearly isoenergetic in the gas phase with a relative energy of 0.01 ± 0.26 eV favoring the O-protomer over the N-protomer. This result is in good agreement with calculations at the MP2 and CCSD(T) levels of theory.

Influence of a Hydroxyl Group on the Deamidation and Dehydration Reactions of Protonated Asparagine-Serine Investigated by Combined Spectroscopic, Guided Ion Beam, and Theoretical Approaches.

Deamidation of asparaginyl (Asn) peptides is a spontaneous post-translational modification that plays a significant role in degenerative diseases and other biological processes under physiological conditions. In the gas phase, deamidation of protonated peptides is a major fragmentation channel upon activation by collision-induced dissociation. Here, we present a full description of the deamidation process from protonated asparagine-serine, [AsnSer+H]+, via infrared (IR) action spectroscopy and threshold collision-induced dissociation (TCID) experiments in combination with theoretical calculations. The IR results demonstrate that deamidation proceeds via bifurcating reaction pathways leading to furanone- and succinimide-type product ion structures, with a population analysis indicating the latter product dominates. Theory demonstrates that nucleophilic attack of the peptidyl amide oxygen onto the Asn side chain leads to furanone formation, whereas nucleophilic attack by the peptidyl amide nitrogen onto the Asn side-chain carbonyl carbon leads to the formation of the succinimide product structure. TCID experiments find that furanone formation has a threshold energy of 145 ± 12 kJ/mol and succinimide formation occurs with a threshold energy of 131 ± 12 kJ/mol, consistent with theoretical energies and with the spectroscopic results indicating that succinimide dominates. The results provide information regarding the inductive and steric effects of the Ser side chain on the deamidation process. The other major channel observed in the TCID experiments of [AsnSer+H]+ is dehydration, where a threshold energy of 104 ± 10 kJ/mol is determined. A complete IR and theoretical analysis of this pathway is also provided. As for deamidation, a bifurcating pathway is found with both dominant oxazoline and minor diketopiperazine products identified. Here, the Ser side chain is directly involved in both pathways.

1-Alkyl-3-methylimidazolium cation binding preferences in hexafluorophosphate ionic liquid clusters determined using competitive TCID measurements and theoretical calculations.

Ionic liquids (ILs) exhibit unique properties that have led to their development and widespread use for a variety of applications. Development efforts have generally focused on achieving desired macroscopic properties via tuning of the IL through variation of the cations and anions. Both the macroscopic and microscopic properties of an IL influence its tunability and thus feasibility of use for selected applications. Works geared toward a microscopic understanding of the nature and strength of the intrinsic cation-anion interactions of ILs have been limited to date. Specifically, the intrinsic strength of the cation-anion interactions in ILs is largely unknown. In previous work, we employed threshold collision-induced dissociation (TCID) approaches supported and enhanced by electronic structure calculations to determine the bond dissociation energies (BDEs) and characterize the nature of the cation-anion interactions in a series of four 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations with the hexafluorophosphate anion, [2Cnmim:PF6]+. To examine the effects of the 1-alkyl chain on the structure and energetics of binding, the cation was varied over the series: 1-ethyl-3-methylimidazolium, [C2mim]+, 1-butyl-3-methylimidazolium, [C4mim]+, 1-hexyl-3-methylimidazolium, [C6mim]+, and 1-octyl-3-methylimidazolium, [C8mim]+. The variation in the strength of binding among these [2Cnmim:PF6]+ clusters was found to be similar in magnitude to the average experimental uncertainty in the measurements. To definitively establish an absolute order of binding among these [2Cnmim:PF6]+ clusters, we extend this work again using TCID and electronic structure theory approaches to include competitive binding studies of three mixed 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations and the hexafluorophosphate anion, [Cn-2mim:PF6:Cnmim]+ for n = 4, 6, and 8. The absolute BDEs of these mixed [Cn-2mim:PF6:Cnmim]+ clusters as well as the absolute difference in the strength of the intrinsic binding interactions as a function of the cation are determined with significantly improved precision. By combining the thermochemical results of the previous independent and present competitive measurements, the BDEs of the [2Cnmim:PF6]+ clusters are both more accurately and more precisely determined. Comparisons are made to results for the analogous [2Cnmim:BF4]+ and [Cn-2mim:BF4:Cnmim]+ clusters previously examined to elucidate the effects of the [PF6]- and [BF4]- anions on the binding.