Fundamental Thermochemical Properties of Amino Acids: Gas-Phase and Aqueous Acidities and Gas-Phase Heats of Formation

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers

High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol^-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.

Predicting the Mechanism and Products of CO2 Capture by Amines in the Presence of H2O

An extensive correlated molecular orbital theory study of the reactions of CO₂ with a range of substituted amines and H₂O in the gas phase and aqueous solution was performed at the G3(MP2) level with a self-consistent reaction field approach. The G3(MP2) calculations were benchmarked at the CCSD(T)/CBS level for NH₃ reactions. A catalytic NH₃ reduces the energy barrier more than a catalytic H₂O for the formation of H₂NCOOH and H₂CO₃. In aqueous solution, the barriers to form both H₂NCOOH and H₂CO₃ are reduced, with HCO₃^- formation possible with one amine present and H₂NCOO^- formation possible only with two amines. Further reactions of H₂NCOOH to form HNCO and urea via the Bazarov reaction have high barriers and are unlikely in both the gas phase and aqueous solution. Reaction coordinates for CH₃NH₂, CH₃CH₂NH₂, (CH₃)₂NH, CH₃CH₂CH₂NH₂, (CH₃)₃N, and DMAP were also calculated. The barrier for proton transfer correlates with amine basicity for alkylammonium carbamate (ΔG^‡_aq < 15 kcal/mol) and alkylammonium bicarbonate (ΔG^‡_aq < 30 kcal/mol) formation. In aqueous solution, carbamic acids, carbamates, and bicarbonates can all form in small amounts with ammonium carbamates dominating for primary and secondary alkylamines. These results have implications for CO₂ capture by amines in both the gas phase and aqueous solution as well as in the solid state, if enough water is present.

Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids

Free energies of hydration are of fundamental interest for modeling and understanding conformational and phase equilibria of macromolecular solutes in aqueous phases. Of particular relevance to systems such as intrinsically disordered proteins are the free energies of hydration and hydration structures of model compounds that mimic charged side chains of Arg, Lys, Asp, and Glu. Here, we deploy a Thermodynamic Cycle-based Proton Dissociation (TCPD) approach in conjunction with data from direct measurements to obtain estimates for the free energies of hydration for model compounds that mimic the side chains of Arg+, Lys+, Asp-, and Glu-. Irrespective of the choice made for the hydration free energy of the proton, the TCPD approach reveals clear trends regarding the free energies of hydration for Arg+, Lys+, Asp-, and Glu-. These trends include asymmetries between the hydration free energies of acidic (Asp- and Glu-) and basic (Arg+ and Lys+) residues. Further, the TCPD analysis, which relies on a combination of experimental data, shows that the free energy of hydration of Arg+ is less favorable than that of Lys+. We sought a physical explanation for the TCPD-derived trends in free energies of hydration. To this end, we performed temperature-dependent calculations of free energies of hydration and analyzed hydration structures from simulations that use the polarizable Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field and water model. At 298 K, the AMOEBA model generates estimates of free energies of hydration that are consistent with TCPD values with a free energy of hydration for the proton of ca. -259 kcal/mol. Analysis of temperature-dependent simulations leads to a structural explanation for the observed differences in free energies of hydration of ionizable residues and reveals that the heat capacity of hydration is positive for Arg+ and Lys+ and negative for Asp- and Glu-.

Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine

Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N₄₄₄₄]⁺) or tetrabutylphosphonium ([P₄₄₄₄]⁺) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N₄₄₄₄][Ad]·2H₂O, and thymine, [P₄₄₄₄][Thy]·2H₂O, as well as the double salt cocrystal, [P₄₄₄₄]₂[Ad][Thy]·3H₂O·2HThy. The cocrystal includes the anionic [Ad^-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.

Mechanistic Study of Enhanced Protonation by Chromium(III) in Electrospray Ionization: A Superacid Bound to a Peptide

Addition of trivalent chromium, Cr(III), to solutions undergoing electrospray ionization (ESI) enhances protonation and leads to formation of [M + 2H]²⁺ for peptides that normally produce [M + H]⁺. This effect is explored using electronic structure calculations at the density functional theory (DFT) level to predict the energetics of various species that are potentially important to the mechanism. Gas- and solution-phase reaction free energies for glycine and its anion reacting with [Cr(III)(H₂O)₆]³⁺ and for dehydration of these species have been predicted, where glycine is used as a simple model for a peptide. For comparison, calculations were also performed with Fe(III), Al(III), Sc(III), Y(III), and La(III). Removal of water from these complexes, as would occur during the ESI desolvation process, results in species that are highly acidic. The calculated pK_a of Cr(III) with a single solvation shell is -10.8, making [Cr(III)(H₂O)₆]³⁺ a superacid that is more acidic than sulfuric acid (pK_a = -8.8). Binding to glycine requires removal of two aqua ligands, which gives [Cr(III)(H₂O)₄]³⁺ that has an extremely acidic pK_a of -28.8. Removal of additional water further enhances acidity, reaching a pK_a of -84.7 for [Cr(III)(H₂O)]³⁺. A mechanism for enhanced protonation is proposed that incorporates computational and experiment results, as well as information on the known chemistry of Cr(III), which is substitutionally inert. The initial step involves binding of [Cr(III)(H₂O)₄]³⁺ to the deprotonated C-terminus of a peptide. As the drying process during ESI strips water from the complex, the resulting superacid transfers protons to the bound peptide, eventually leading to formation of [M + 2H]²⁺.

Weak Acid-Base Interactions of Histidine and Cysteine Affect the Charge States, Tertiary Structure, and Zn(II)-Binding of Heptapeptides

Zinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g., acetyl-His₁-Cys₂-Gly₃-Pro₄-Tyr₅-His₆-Cys₇, have discovered they exhibit pH-dependent Zn(II) chelation and have redox activities with Cu(I/II), forming a variety of metal complexes. To further understand how these 2His-2Cys oligopeptides bind these metal ions, we have undertaken a series of ion mobility-mass spectrometry and B3LYP/LanL2DZ computational studies of structurally related heptapeptides. Starting with the sequence above, we have modified the potential His, Cys, or C-terminus binding sites and report how these changes in primary structure affect the oligopeptides positive and negative charge states, conformational structure, collision-induced breakdown energies, and how effectively Zn(II) binds to these sequences. The results show evidence that the weak acid-base properties of Cys-His are intrinsically linked and can result in an intramolecular salt-bridged network that affects the oligopeptide properties.

Positive and negative ions of the amino acid histidine formed in low-energy electron collisions

Histidine is an aromatic amino acid crucial for the biological functioning of proteins and enzymes. When biological matter is exposed to ionising radiation, highly energetic particles interact with the surrounding tissue which leads to efficient formation of low-energy electrons. In the present study, the interaction of low-energy electrons with gas-phase histidine is studied at a molecular level in order to extend the knowledge of electron-induced reactions with amino acids. We report both on the formation of positive ions formed by electron ionisation and negative ions induced by electron attachment. The experimental data were complemented by quantum chemical calculations. Specifically, the free energies for possible fragmentation reactions were derived for the τ and the π tautomer of histidine to get insight into the structures of the formed ions and the corresponding neutrals. We report the experimental ionisation energy of (8.48 ± 0.03) eV for histidine which is in good agreement with the calculated vertical ionisation energy. In the case of negative ions, the dehydrogenated parent anion is the anion with the highest mass observed upon dissociative electron attachment. The comparison of experimental and computational results was also performed in view of a possible thermal decomposition of histidine during the experiments, since the sample was sublimated in the experiment by resistive heating of an oven. Overall, the present study demonstrates the effects of electrons as secondary particles in the chemical degradation of histidine. The reactions induced by those electrons differ when comparing positive and negative ion formation. While for negative ions, simple bond cleav ages prevail, the observed fragment cations exhibit partly restructuring of the molecule during the dissociation process.

An ab initio Study of the Structure and Energetics of Hydrogen Bonding in Ionic Liquids

Unlike typical hydrogen-bonded networks such as water, hydrogen bonded ionic liquids display some unusual characteristics due to the complex interplay of electrostatics, polarization, and dispersion forces in the bulk. Protic ionic liquids in particular contain close-to traditional linear hydrogen bonds that define their physicochemical properties. This work investigates whether hydrogen bonded ionic liquids (HBILs) can be differentiated from aprotic ionic liquids with no linear hydrogen bonds using state-of-the-art ab initio calculations. This is achieved through geometry optimizations of a series of single ion pairs of HBILs in the gas phase and an implicit solvent. Using benchmark CCSD(T)/CBS calculations, the electrostatic and dispersion components of the interaction energy of these systems are compared with those of aprotic ionic liquids. The inclusion of the implicit solvent significantly influenced geometries of single ion pairs, with the gas phase shortening the hydrogen bond to reduce electrostatic interactions. HBILs were found to have stronger interactions by at least 10EtMeNH0 kJ mol⁻¹ over aprotic ILs, clearly highlighting the electrostatic nature of hydrogen bonding. Geometric and energetic parameters were found to complement each other in determining the extent of hydrogen bonding present in these ionic liquids.

The influence of polyatomic primary ion chemistry on matrix effects in secondary ion mass spectrometry analysis

RATIONALE

The application of mass spectrometry imaging techniques to determine two- (2D) and three- (3D) dimensional chemical distribution ideally provides uniform, high sensitivity to multiple components and reliable quantification. These criteria are typically not met due to variations in sensitivity due to the chemistry of the analyte and surrounding surface chemistry. Here we explore the influence of projectile beam chemistry and sample chemistry in time-of-flight secondary ion mass spectrometry (TOF-SIMS). To the authors' knowledge this is the first time the combined effects of projectile chemistry and sample environment on the quantitative determination of mixed samples have been systematically studied.

METHODS

Secondary ion yields of lipid and amino acid mixtures were measured under 20 keV C₆₀ , Ar_n , and (H₂ O)_n cluster ion bombardment (n = 2000 or 4000) using TOF-SIMS. Ion suppression/enhancement effects were studied in dry sample films and in trehalose and water ice matrices.

RESULTS

The extent of the matrix effects and the secondary ion yield were found to depend on the chemistry of the primary ion beam and (for C₆₀ , Ar_n ) on the nature of the sample matrix. Under (H₂ O)_n bombardment the sample matrix had negligible effect on the analysis.

CONCLUSIONS

Compared with C₆₀ and Ar_n , water-containing cluster projectiles enhanced the sensitivity of TOF-SIMS determination of the chosen analytes and reduced the effect of signal suppression/enhancement in multicomponent samples and in different sample matrices. One possible explanation for this is that the (H₂ O)₄₀₀₀ projectile initiates on impact a nanoscale matrix environment that is very similar to that in frozen-hydrated samples in terms of the resulting ionisation effects. The competition between analytes for protons and the effect of the sample matrix are reduced with water-containing cluster projectiles. These chemically reactive projectile beams have improved characteristics for quantitative chemical imaging by TOF-SIMS compared with their non-reactive counterparts.

Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy

The binding motifs in the halide adducts with tyrosine ([Tyr + X]^-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm^-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm^-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]^- and [nitroTyr + X]^-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol^-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]^-, where the anion is placed above the face of the aromatic ring.

High-energy collision-induced dissociation of histidine ions [His + H]+ and [His - H]- and histidine dimer [His2 + H]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018;32:113-120. [PMID: 29108138 DOI: 10.1002/rcm.8027]

RATIONALE

Histidine (His) is an essential amino acid, whose side group consists of an aromatic imidazole moiety that can bind a proton or metal cation and act as a donor in intermolecular interactions in many biological processes. While the dissociation of His monomer ions is well known, information on the kinetic energy released in the dissociation is missing.

METHODS

Using a new home-built electrospray ionization (ESI) source adapted to a double-focusing mass spectrometer of BE geometry, we investigated the fragmentation reactions of protonated and deprotonated His, [His + H]⁺ and [His - H]^- , and the protonated His dimer [His₂  + H]⁺ , accelerated to 6 keV in a high-energy collision with helium gas. We evaluated the kinetic energy release (KER) for the observed dissociation channels.

RESULTS

ESI of His solution in positive mode led to the formation of His clusters [His_n + H]⁺ , n = 1-6, with notably enhanced stability of the tetramer. [His + H]⁺ dissociates predominantly by loss of (H₂ O + CO) with a KER of 278 meV, while the dominant dissociation channel of [His - H]^- involves loss of NH₃ with a high KER of 769 meV. Dissociation of [His₂ + H]⁺ is dominated by loss of the monomer but smaller losses are also observed.

CONCLUSIONS

The KER for HCOOH loss from both [His + H]⁺ and [His - H]^- is similar at 278 and 249 meV, respectively, which suggests that the collision-induced dissociation takes place via a similar mechanism. The loss of COOH and C₂ H₅ NO₂ from the dimer suggests that the dimer of His binds through a shared proton between the imidazole moieties.

Impact of Hydrogen Bonding on the Susceptibility of Peptides to Oxidation

The tendency of peptides to be oxidized is intimately connected with their function and even their ability to exist in an oxidative environment. Here we report high-level theoretical studies that show that hydrogen bonding can alter the susceptibility of peptides to oxidation, with complexation to a hydrogen-bond acceptor facilitating oxidation, and vice versa, impacting the feasibility of a diverse range of biological processes. It can even provide an energetically viable mechanistic alternative to direct hydrogen-atom abstraction. We find that hydrogen bonding to representative reactive groups leads to a broad (≈400 kJ mol^-1 ) spectrum of ionization energies in the case of model amide, thiol and phenol systems. While some of the oxidative processes at the extreme ends of the spectrum are energetically prohibitive, subtle environmental and solvent effects could potentially mitigate the situation, leading to a balance between hydrogen bonding and oxidative susceptibility.

Mechanistic study of competitive releases of H2O, NH3 and CO2 from deprotonated aspartic and glutamic acids: Role of conformation

The aims of this study were to highlight the impact of minor structural differences (e.g. an aminoacid side chain enlargement by one methylene group), on ion dissociation under collision-induced dissociation conditions, and to determine the underlying chemical mechanisms. Therefore, we compared fragmentations of deprotonated aspartic and glutamic acids generated in negative electrospray ionization. Energy-resolved mass spectrometry breakdown curves were recorded and MS³ experiments performed on an Orbitrap Fusion for high-resolution and high-mass accuracy measurements. Activated fragmentations were performed using both the resonant and non-resonant excitation modes (i.e., CID and HCD, respectively) in order to get complementary information on the competitive and consecutive dissociative pathways. These experiments showed a specific loss of ammonia from the activated aspartate but not from the activated glutamate. We mainly focused on this specific observed loss from aspartate. Two different mechanisms based on intramolecular reactions (similar to those occurring in organic chemistry) were proposed, such as intramolecular elimination (i.e. Ei-like) and nucleophilic substitution (i.e. SNi-like) reactions, respectively, yielding anions as fumarate and α lactone from a particular conformation with the lowest steric hindrance (i.e. with antiperiplanar carboxyl groups). The detected deaminated aspartate anion can then release CO₂ as observed in the MS³ experimental spectra. However, quantum calculations did not indicate the formation of such a deaminated aspartate product ion without loss of carbon dioxide. Actually, calculations displayed the double neutral (NH₃+CO₂) loss as a concomitant pathway (from a particular conformation) with relative high activation energy instead of a consecutive process. This disagreement is apparent since the concomitant pathway may be changed into consecutive dissociations according to the collision energy i.e., at higher collision energy and at lower excitation conditions, respectively. The latter takes place by stabilization of the deaminated aspartate solvated with two residual molecules of water (present in the collision cell). This desolvated anion formed is an α lactone substituted by a methylene carboxylate group. The vibrational excitation acquired by [(D-H)-NH₃]^-during its isolation is enough to allow its prompt decarboxylation with a barrier lower than 8.4kJ/mol. In addition, study of glutamic acid-like diastereomers constituted by a cyclopropane, hindering any side chain rotation, confirms the impact of the three-dimensional geometry on fragmentation pathways. A significant specific loss of water is only observed for one of these diastereomers. Other experiments, such as stable isotope labeling, need to be performed to elucidate all the observed losses from activated aspartate and glutamate anions. These first mechanistic interpretations enhance understanding of this dissociative pathway and underline the necessity of studying fragmentation of a large number of various compounds to implement properly new algorithms for de novo elucidation of unknown metabolites.

Enthalpic and Entropic Contributions to Hydrophobicity

Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called "unhappy water" molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino acids/oligopeptides, nucleosides, saccharides and their derivatives in the ideal gas state. The results of this study will be combined with the corresponding hydration/solvation results in subsequent parts of this work in order to derive the desired thermochemical quantities in aqueous solutions. The above metabolites exist in a vast conformational/isomerization space including rotational conformers, tautomers or anomers exhibiting often multiple or cooperative intramolecular hydrogen bonding. We examine the challenges posed by these features for the reliable estimation of thermochemical quantities. We discuss conformer search, conformer distribution and averaging processes. We further consider neutral metabolites as well as protonated and deprotonated metabolites. In addition to the traditional presentation of gas-phase acidities, basicities and proton affinities, we also examine heats and free energies of ionic species. We obtain simple linear relations between the thermochemical quantities of ions and the formation quantities of their neutral counterparts. Furthermore, we compare our calculations with reliable experimental measurements and predictive calculations from the literature, when available. Finally, we discuss the next steps and perspectives for this work.

Ga(+) Basicity and Affinity Scales Based on High-Level Ab Initio Calculations

The structure, relative stability and bonding of complexes formed by the interaction between Ga(+) and a large set of compounds, including hydrocarbons, aromatic systems, and oxygen-, nitrogen-, fluorine and sulfur-containing Lewis bases have been investigated through the use of the high-level composite ab initio Gaussian-4 theory. This allowed us to establish rather accurate Ga(+) cation affinity (GaCA) and Ga(+) cation basicity (GaCB) scales. The bonding analysis of the complexes under scrutiny shows that, even though one of the main ingredients of the Ga(+) -base interaction is electrostatic, it exhibits a non-negligible covalent character triggered by the presence of the low-lying empty 4p orbital of Ga(+) , which favors a charge donation from occupied orbitals of the base to the metal ion. This partial covalent character, also observed in AlCA scales, is behind the dissimilarities observed when GaCA are compared with Li(+) cation affinities, where these covalent contributions are practically nonexistent. Quite unexpectedly, there are some dissimilarities between several Ga(+) -complexes and the corresponding Al(+) -analogues, mainly affecting the relative stability of π-complexes involving aromatic compounds.

Gas-phase fragmentation of deprotonated tryptophan and its clusters [Trpn -H]- induced by different activation methods

RATIONALE

Non-covalent amino acid clusters are the subject of intense research in diverse areas including peptide bond formation studies or the determination of proton affinities or methylating abilities of amino acids. However, most of the research has focused on positive ions and little is known about anionic clusters.

METHODS

Fragmentation reactions of deprotonated tryptophan (Trp), [Trp-H](-) and Trp singly deprotonated non-covalently bound clusters [Trp(n) -H](-), n = 2, 3, 4, were investigated using low-energy collision-induced dissociation (CID) with He atoms, high-energy CID with Na atoms, and electron-induced dissociation (EID) with 20-35 eV electrons. Fragmentation of the monomeric Trp anion, where all labile hydrogens were exchanged for deuterium [d(4) -Trp-D](-), was investigated using low-energy CID and EID, in order to shed light on the dissociation mechanisms.

RESULTS

The main fragmentation channel for Trp cluster anions, [Trp(n) -H](-), n >1, is the loss of the neutral monomer. The fragmentation of the deprotonated Trp monomer induced by electrons resembles the fragmentation induced by high-energy collisions through electronic excitation of the parent. However, the excitation must precede in a different way, shown through only monomer loss from larger clusters, n >1, in case of EID, but intracluster chemistry in the case of high-energy CID.

CONCLUSIONS

The anion of the indole ring C(8)H(6) N(-) has been identified in the product ion spectra of [Trp(n) -H](-) using all activation methods, thus providing a diagnostic marker ion. No evidence was found for formation of peptide bonds as a route to prebiotic peptides in the fragmentation reactions of these singly deprotonated Trp cluster ions.

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Studying the chemistry of cationized triacylglycerols using electrospray ionization mass spectrometry and density functional theory computations

Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na(+)). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na(+), Li(+), K(+), Ag(+), NH4(+)). While most cations bind to oxygen, Ag(+) binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M](+) was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS(3)). These lactones can account for all the major product ions in the MS(3) spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

Gas-phase enthalpies of formation and enthalpies of sublimation of amino acids based on isodesmic reaction calculations

Accurate gas-phase enthalpies of formation (ΔfH298°) of 20 common α-amino acids, seven uncommon amino acids, and three small peptides were calculated by combining G4 theory calculations with an isodesmic reaction approach. The internal consistency over a set of ΔfH298°(g) values was achieved by sequential adjustment of their values through the isodesmic reactions. Four amino acids, alanine, β-alanine, sarcosine, and glycine, with reliable internally self-consistent experimental data, were chosen as the key reference compounds. These amino acids together with about 100 compounds with reliable experimental data (their accuracy was supported by G4 calculations) were used to estimate the enthalpies of formation of remaining amino acids. All of the amino acids with the previously established enthalpies of formation were later used as the reference species in the isodesmic reactions for the other amino acids. A systematic comparison was made of 14 experimentally determined enthalpies of formation with the results of calculations. The experimental enthalpies of formation for 10 amino acids were reproduced with good accuracy, but the experimental and calculated values for 4 compounds differed by 11–21 kJ/mol. For these species, the theoretical ΔfH298°(g) values were suggested as more reliable than the experimental values. On the basis of theoretical results, the recommended values for the gas-phase enthalpies of formation were also provided for amino acids for which the experimental ΔfH298°(g) were not available. The enthalpies of sublimation were evaluated for all compounds by taking into account the literature data on the solid-phase enthalpies of formation and the ΔfH298°(g) values recommended in our work. A special attention was paid to the accurate prediction of enthalpies of formation of amino acids from the atomization reactions. The problems associated with conformational flexibility of these compounds and harmonic treatment of low frequency torsional modes were discussed. The surprisingly good agreement between the ΔfH298°(g) values calculated from the atomization and isodesmic reactions is largely the result of a fortuitous mutual compensation of various corrections used in the atomization reaction procedure.

A comparison of the effects of amide and acid groups at the C-terminus on the collision-induced dissociation of deprotonated peptides

The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic c(m-2)(-) product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of c(m-3)(-); however, this is not generally as pronounced as c(m-2)(-) production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH(2)) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of c(m-2)(-) and a 6-membered ring diketopiperazine neutral requires >31.6 kcal/mol, which is 26.1 kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications.