To Be or Not To Be a Molecular Ion: The Role of the Solvent in Photoionization of Arginine.

Application of photoionization mass spectroscopy, a technique capable of assessing protonation states in complex molecules in the gas phase, is challenging for arginine due to its fragility. We report photoionization efficiencies in the valence region of aqueous aerosol particles produced from arginine solutions under various pH and vaporization conditions. By using ab initio calculations, we investigate the stability of different conformers. Our results show that neutral arginine fragments upon ionization in the gas phase but solvation stabilizes the molecular ion, resulting in different photoionization dynamics. We also report the valence-band photoelectron spectra of the aerosol solutions obtained at different pH values

Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine

A systematic conformational mapping combined with literature data leads to 85 stable neutral cysteine conformers. The implementation of the same mapping process for the protonated counterparts reveals 21 N-(amino-), 64 O-(carbonyl-), and 37 S-(thiol-)protonated cysteine conformers. Their relative energies and harmonic vibrational frequencies are given at the MP2/aug-cc-pVDZ level of theory. Further benchmark ab initio computations are performed for the 10 lowest-lying neutral and protonated amino acid conformers (for each type) such as CCSD(T)-F12a/cc-pVDZ-F12 geometry optimizations (and frequency computations for cysteine) as well as auxiliary correction computations of the basis set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation effects, second-order Douglass-Kroll relativistic effects, and zero-point energy contributions. Boltzmann-averaged 0 (298.15) K proton affinity and [298.15 K gas-phase basicity] values of cysteine are predicted to be 214.96 (216.39) [208.21], 201.83 (203.55) [194.16], and 193.31 (194.74) [186.40] kcal/mol for N-, O-, and S-protonation, respectively, also considering the previously described auxiliary corrections

The gas-phase H/D exchange mechanism of protonated amino acids

A mass spectrometry and Density Functional Theory study of gas-phase H/D exchange in protonated Ala, Cys, Ile, Leu, Met and Val is reported. Site-specific rate constants were determined and results identify the α − amino group as the protonation site. Lack of exchange on the Cys thiol group is explained by the absence of strong intramolecular hydrogen bonding within the reaction complex. In aliphatic amino acids the presence of a methyl group at the β − C atom was found to lower the site-specific H/D exchange rate for amino hydrogens. Study of the exchange mechanism showed that isotopic exchange occurs in two independent reactions: in one only the carboxylic hydrogen is exchanged and in the other both carboxylic and amino group hydrogens exchange. The proposed reaction mechanisms, calculated structures of various species and a number of structural findings are consistent with experimental data

UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides

International audienceA detailed understanding of radiative and nonradiative processes in peptides containing an aromatic chromophore requires the knowledge of the nature and energy level of low-lying excited states that could be coupled to the bright 1 * excited state. Isolated aromatic amino acids and short peptides provide benchmark cases to study, at the molecular level, the photoinduced processes that govern their excited state dynamics. Recent advances in gas phase laser spectroscopy of conformer-selected peptides have paved the way to a better, yet not fully complete, understanding of the influence of intramolecular interactions on the properties of aromatic chromophores. This review aims at providing an overview of the photophysics and photochemistry at play in neutral and charged aromatic chromophore containing peptides, with a particular emphasis on the charge (electron, proton) and energy transfer processes. A significant impact is exerted by the experimental progress in energy-and time-resolved spectroscopy of protonated species, which leads to a growing demand for theoretical supports to accurately describe their excited state properties

Computational chemistry investigation of gas-phase structures, infrared spectroscopy, and dissociation pathways of isomeric molecules

While chemical isomers typically have distinct properties, differentiating between them is often an analytical challenge, especially for mass spectrometric methods. Infrared multiple photon dissociation (IRMPD) spectroscopy and ion mobility spectrometry (IMS) can be useful in analysis of such isomeric compounds; however, experimental results alone do not directly provide in-depth structural information. In this thesis, computational chemistry is first used to explain experimental results and understand the conformational preference of the gas phase ions formed from the lithiation of cis-3, cis-4 and trans-4 hydroxyproline isomers and then used in a predictive manner to evaluate IRMPD spectroscopy and IMS as potential paths forward for the characterization of isomeric dye species. Finally, theoretical methods are used to begin to understand the dissociation pathways of lithiated hydroxyproline isomers in the gas phase, which is ongoing

Determination of Thermodynamic Properties of Non-Protein Amino Acids and Characterization of Multimers of Carbamazepine

This study has two seemingly unrelated parts that come together remarkably in displaying the comprehensive interplay between chemical structure and properties as well as the variety of analytical applications of mass spectrometry. The first part of this study describes the determination of thermodynamic properties of several non-protein amino acids using the extended kinetic method. This is a continuation of work started in the Poutsma lab in Spring of 2017. The non-protein amino acids (NPA) studied here hold notable relevance in their unique ability to be mis-incorporated into peptide chains, as shown by the Hartman group at Virginia Commonwealth University.[1] By understanding the effects of methylation on the NPA’s inherent thermochemical properties, such as proton affinity and ∆acidH , we acquire insight into how these species may alter the behavior of the peptide chains in which they are incorporated. We found the experimental ∆acidH of α-methylserine, L-penicillamine, and 3-methylthreonine to be 1379 ± 23, 1380 ± 18, and 1378 ± 23 kJ/mol respectively. Within bounds of reasonable uncertainty, these values agree with computational predictions done at the B3LYP/6-311++G**//B3LYP/6-31+G* level of theory. The second part of this study examines the gas-phase tetramer of carbamazepine (CBZ), an active pharmaceutical ingredient in anticonvulsants.[2] Highly polymorphic, CBZ is well-suited for studying the fundamentals of the self-assembly process in organic crystals, and more information on base-level assembly is required for effective predictive models of organic crystallization.[2] Because typically only one polymorph of a drug is approved by the Food and Drug Administration as a pharmaceutical active ingredient, polymorphism is an important phenomena in the pharmaceutical industry. In this study, we used High-Field Asymmetric Ion Mobility Spectrometry and traditional mass spectrometry to characterize the tetramer of CBZ and evaluate its relative stability. We confirmed that an intensity anomaly existed in both the protonated and sodiated forms in which the tetramer is larger than the trimer or the pentamer; the tetramer is a magic number cluster. This agrees with STM data taken of CBZ monolayers by our colleagues at Notre Dame

Mobile Protons Limit the Stability of Salt Bridges in the Gas Phase: Implications for the Structures of Electrosprayed Protein Ions.

Electrosprayed protein ions can retain native-like conformations. The intramolecular contacts that stabilize these compact gas-phase structures remain poorly understood. Recent work has uncovered abundant salt bridges in electrosprayed proteins. Salt bridges are zwitterionic BH+/A- contacts. The low dielectric constant in the vacuum strengthens electrostatic interactions, suggesting that salt bridges could be a key contributor to the retention of compact protein structures. A problem with this assertion is that H+ are mobile, such that H+ transfer can convert salt bridges into neutral B0/HA0 contacts. This possible salt bridge annihilation puts into question the role of zwitterionic motifs in the gas phase, and it calls for a detailed analysis of BH+/A- versus B0/HA0 interactions. Here, we investigate this issue using molecular dynamics (MD) simulations and electrospray experiments. MD data for short model peptides revealed that salt bridges with static H+ have dissociation energies around 700 kJ mol-1. The corresponding B0/HA0 contacts are 1 order of magnitude weaker. When considering the effects of mobile H+, BH+/A- bond energies were found to be between these two extremes, confirming that H+ migration can significantly weaken salt bridges. Next, we examined the protein ubiquitin under collision-induced unfolding (CIU) conditions. CIU simulations were conducted using three different MD models: (i) Positive-only runs with static H+ did not allow for salt bridge formation and produced highly expanded CIU structures. (ii) Zwitterionic runs with static H+ resulted in abundant salt bridges, culminating in much more compact CIU structures. (iii) Mobile H+ simulations allowed for the dynamic formation/annihilation of salt bridges, generating CIU structures intermediate between scenarios (i) and (ii). Our results uncover that mobile H+ limit the stabilizing effects of salt bridges in the gas phase. Failure to consider the effects of mobile H+ in MD simulations will result in unrealistic outcomes under CIU conditions

H/D Exchange Kinetics: Experimental Evidence for Formation of Different b Fragment Ion Conformers/Isomers During the Gas-Phase Peptide Sequencing

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b5+ and b4+ fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H]+) and its b5+ and b4+ fragment ions (with ND3) were observed. Isolated 12Call isotopomers of both b5+ and b4+ fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b5+ and b4+ fragment ions exist as combination of slow-exchanging (“s”) and fast-exchanging (“f”) species. The calculated rate constant for the first labile hydrogen exchange of [M + H]+ (k[M + H]+ = 3.80 ± 0.7 × 10–10 cm3 mol–1 s–1) was ∼30 and ∼5 times greater than those for the “s” and “f” species of b5+, respectively. Data from H/D exchange of isolated “s” species at longer ND3 reaction times confirmed the existence of different conformers or isomers for b5+ fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that “s” and “f” species of b5+ and b4+ fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed

Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase : dynamics in nucleotides, amino acids and beyond

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach