Chrys Wesdemiotis

Amide bond dissociation in protonated peptides. Structures of the N-terminal ionic and neutral fragments

Abstract Three-stage tandem mass spectrometry (MS3) and neutral fragment reionization (NfR) are utilized to investigate the structures of the N-terminal ionic (bi) and neutral backbone fragments, respectively, produced from break-up of the amide bond in protonated peptides that have been collisionally activated. The b-type ion from [M+H]+ of C6H5CO-GF, which is produced by loss of the C-terminal phenylalanine, has the structure of protonated 2-phenyl-5-oxazolone. Conversely, the neutral fragment accompanying the y-type ion (protonated phenylalanine) is 2-phenyl-5-oxazolone. The b2 ions arising from [M+H]+ of underivatized tripeptides are also found to be protonated oxazolones. On the other hand, the neutral fragments released from the N-terminus of the tripeptides upon formation of y1 are shown to be diketopiperazines and not oxazolones. The combined MS3 and NfR data help propose dissociation mechanisms that account for the observed structures of ionic and neutral backbone fragments.

Dissociation of the peptide bond in protonated peptides.

The dissociation of the amide (peptide) bond in protonated peptides, [M + H](+), is discussed in terms of the structures and energetics of the resulting N-terminal b(n) and C-terminal y(n) sequence ions. The combined data provide strong evidence that dissociation proceeds with no reverse barriers through interconverting proton-bound complexes between the segments emerging upon cleavage of the protonated peptide bond. These complexes contain the C-terminal part as a smaller linear peptide (amino acid if one residue) and the N-terminal part either as an oxazolone or a cyclic peptide (cyclic amide if one residue). Owing to the higher thermodynamic stability but substantially lower gas-phase basicity of cyclic peptides vs isomeric oxazolones, the N-terminus is cleaved as a protonated oxazolone when ionic (b(n) series) but as a cyclic peptide when neutral (accompanying the C-terminal y(n) series). It is demonstrated that free energy correlations can be used to derive thermochemical data about sequence ions. In this context, the dependence of the logarithm of the abundance ratio log[y(1)/b(2)], from protonated GGX (G, glycine; X, varying amino acid) on the gas-phase basicity of X is used to obtain a first experimental estimate of the gas-phase basicity of the simplest b-type oxazolone, viz. 2-aminomethyl-5-oxazolone (b(2) ion with two glycyl residues).

Fragmentation pathways of polymer ions

Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers.

Cation-π effects in the complexation of Na+ and K+ with Phe, Tyr, and Trp in the gas phase

Na+ and K+ gas-phase affinities of the three aromatic amino acids Phe, Tyr, and Trp were measured by the kinetic method. Na+ binds these amino acids much more strongly than K+, and for both metal ions the binding strength was found to follow the order Phe ≤ Tyr < Trp. Quantum chemical calculations by density functional theory (DFT) gave the same qualitative ordering, but suggested a somewhat larger Phe/Trp increment. These results are in acceptable agreement with predictions based on the binding of Na+ and K+ to the side chain model molecules benzene, phenol, and indole, and are also in reasonable agreement with the predictions from purely electrostatic calculations of the side-chain binding effects. The binding energies were compared with those to the aliphatic amino acids glycine and alanine. Binding to the aromatic amino acids was found to be stronger both experimentally and computationally, but the DFT calculations indicate substantially larger increments relative to alanine than shown by the experiments. Possible reasons for this difference are discussed. The metal ion binding energies show the same trends as the proton affinities.

Stoichiometric Self-Assembly of Shape-Persistent 2D Complexes: A Facile Route to a Symmetric Supramacromolecular Spoked Wheel

An approach to multicomponent coordination-driven self-assembly of the first terpyridine-based, shape-persistent, giant two-dimensional D(6h) supramacromolecular spoked wheel is reported. Mixing core T6, rim T3, and Zn(II) or Cd(II) ions in a stoichiometric ratio (1:6:12) permitted the selective generation of a highly symmetric spoked wheel in 94% isolated yield via geometric and thermodynamic control. The products were characterized by a combination of traveling-wave ion mobility mass spectrometry and NMR techniques together with TEM imaging, which agreed with computational simulations.

Dissociation characteristics of [M + X]+ ions (X = H, Li, Na, K) from linear and cyclic polyglycols

The unimolecular reactions of protonated and metalated polyglycols with kiloelectronvolt translational energies have been studied by collisionally activated dissociation and neutralization-reionization mass spectrometry. The former method provides information on the ionic dissociation products, whereas the latter allows for the identification of the complementary neutral losses. Protonated linear polyglycols mainly undergo charge-initiated decompositions that lead to eliminations of smaller oligomers, On the other hand, protonated crown ethers (“cyclic” polyglycols) favor charge-induced reactions that proceed by cleavages of two ethylene oxide units in the form of 1,4-dioxane. Replacement of one O by NH in the crown ether dramatically changes its unimolecular chemistry; now, charge-remote 1,4-eliminations from ring-opened isomers are preferred. Charge-remote reactions are also the major decomposition channels of all metalated precursors studied. The linear polyglycols decompose primarily by 1,4-H2 eliminations and to a lesser extent by homolytic cleavages near chain ends. The reverse is true for metalated crown ethers, which preferentially produce distonic radical cations by the loss of saturated radicals; these reactions are proposed to involve prior rearrangement to open-chain isomers. The nature of the metal ion (Li+, Na+, or K+) does not greatly affect the unimolecular chemistry of the cationized polyglycol. In general, metalated precursors form many abundant fragment ions over the entire mass range; hence, collisional activation of such ions at high kinetic energy should be particularly useful for structure elucidations.

Strain-Promoted Crosslinking of PEG-based Hydrogels via Copper-Free Cycloaddition

The synthesis of a 4-dibenzocyclooctynol (DIBO) functionalized polyethylene glycol (PEG) and fabrication of hydrogels via strain-promoted, metal-free, azide-alkyne cycloaddition is reported. The resulting hydrogel materials provide a versatile alternative in which to encapsulate cells that are sensitive to photochemical or chemical crosslinking mechanisms.

Giant Molecular Shape Amphiphiles Based on Polystyrene–Hydrophilic [60]Fullerene Conjugates: Click Synthesis, Solution Self-Assembly, and Phase Behavior

This paper reports a comprehensive study on the synthesis and self-assembly of two model series of molecular shape amphiphiles, namely, hydrophilic [60]fullerene (AC(60)) tethered with one or two polystyrene (PS) chain(s) at one junction point (PS(n)-AC(60) and 2PS(n)-AC(60)). The synthesis highlighted the regiospecific multiaddition reaction for C(60) surface functionalization and the Huisgen 1,3-dipolar cycloaddition between alkyne functionalized C(60) and azide functionalized polymer to give rise to shape amphiphiles with precisely defined surface chemistry and molecular topology. When 1,4-dioxane/DMF mixture was used as the common solvent and water as the selective solvent, these shape amphiphiles exhibited versatile self-assembled micellar morphologies which can be tuned by changing various parameters, such as molecular topology, polymer tail length, and initial molecular concentration, as revealed by transmission electron microscopy and light scattering experiments. In the low molecular concentration range of equal or less than 0.25 (wt) %, micellar morphology of the series of PS(n)-AC(60) studied was always spheres, while the series of 2PS(n)-AC(60) formed vesicles. Particularly, PS(44)-AC(60) and 2PS(23)-AC(60) are synthesized as a topological isomer pair of these shape amphiphiles. PS(44)-AC(60) formed spherical micelles while 2PS(23)-AC(60) generated bilayer vesicles under identical conditions. The difference in the self-assembly of PS(n)-AC(60) and 2PS(n)-AC(60) was understood by the molecular shape aspect ratio. The stretching ratio of PS tails decreased with increasing PS tail length in the spherical micelles of PS(n)-AC(60), indicating a micellar behavior that changes from small molecular surfactant-like to amphiphilic block copolymer-like. For the series of PS(n)-AC(60) in the high molecular concentration range [>0.25 (wt) %], their micellar morphological formation of spheres, cylinders, and vesicles was critically dependent upon both the initial molecular concentration and the PS tail length. On the other hand, the series of 2PS(n)-AC(60) remained in the state of bilayer vesicles in the same concentration range. Combining both of the experimental results obtained in the low and high molecular concentrations, a systematic morphological phase diagram was constructed for the series of PS(n)-AC(60) with different PS tail lengths. The versatile and concentration-sensitive phase behaviors of these molecular shape amphiphiles are unique and have not been systematically explored in the traditional surfactants and block copolymers systems.

Proton affinities of the N- and C-terminal segments arising upon the dissociation of the amide bond in protonated peptides

Dissociation of the amide bonds in a protonated peptide leads to N-terminal sequence fragments with cyclic structures and C-terminal sequence fragments with linear structures. The ionic fragments containing the N-terminus (bn) have been shown to be protonated oxazolones, whereas those containing the C-terminus (yn) are protonated linear peptides. The coproduced neutral fragments are cyclic peptides from the N-terminus and linear peptides from the C-terminus. A likely determinant of these structural choices is the proton affinity (PA) of the described peptide segments. This study determines the PA values of such segments (Pep), i.e., cyclic and linear dipeptides and a relevant oxazolone, based on the dissociations of proton-bound dimers [Pep + Bi]H+ in which Bi is a reference base of known PA value (Cooks kinetic method). The dissociations are assessed at different internal energies to thereby obtain both proton affinities as well as entropies of protonation. For species with comparable amino acid composition, the proton affinity (and gas phase basicity) follows the order cyclic peptide ≪ oxazolone ≈ linear peptide. This ranking is consistent with dissociation of the protonated peptide via interconverting proton-bound complexes involving N-terminal oxazolone (O) or cyclopeptide (C) segments and C-terminal linear peptide segments (L), viz. O ⋯ H+ ⋯ L ⇄ C ⋯ H+ ⋯ L. N-terminal sequence ions (bn) are formed with oxazolone structures which can efficiently compete for the proton with the linear segments. On the other hand, N-terminal neutral fragments detach as cyclic peptides, with H+ now being retained by the more basic linear segment from the C-terminus to yield yn.

Stoichiometric Self-Assembly of Isomeric, Shape-Persistent, Supramacromolecular Bowtie and Butterfly Structures

Two novel macromolecular constitutional isomers have been self-assembled from previously unreported terpyridine ligands in a three-component system. The terpyridine ligands were synthesized in high yields via a key Suzuki coupling. Restrictions of the possible outcomes for self-assembly ultimately provided optimum conditions for isolation of either a molecular bowtie or its isomeric butterfly motif. These isomers have been characterized by ESI-MS, TWIM-MS, (1)H NMR, and (13)C NMR. Notably, these structural isomers have remarkably different drift times in ion mobility separation, corresponding to different sizes and shapes at high charge states.