On the photostability of peptides after selective photoexcitation of the backbone: prompt versus slow dissociation

Anharmonically Coupled Vibrational Scaffolds for Energy Dissipation in a Terpyridine-Aldehyde Ligand

The role of intramolecular vibrational energy redistribution is critical when considering the thermal properties of coordination complexes. The interactions and redistribution of vibrational energy can be uncovered through the use of two-dimensional infrared (2D IR) spectroscopy by observing the cross-peaks between different vibrational signatures. In this study, the energetic landscape consisting of the vibrations of [6,2':6',2″-terpyridine]-2-carbaldehyde (terpyCHO) is studied directly in the region between 1400 and 1740 cm-1. Information on the anharmonic coupling between different groups of vibrations estimates the delocalization in the detected normal modes. The delocalization of the aldehyde stretch is directly comparable to that calculated from density functional theory (DFT) calculations and local mode analysis via the LModeA program, a freeware that can characterize the normal modes in terms of a nonredundant set of local modes. Tracking of the relative cross-peak intensities as a function of the waiting time reveals a complex network of energy exchange pathways responsible for energy dissipation and vibrational dephasing. These dynamics reveal the aldehyde to be an efficient inlet and outlet of vibrational energy flow and the C-H bends as energetic dumps with the pyridine ring stretches acting as bridging modes between them. Finally, signatures of vibrational coherences are observed in the diagonal peak dynamics of the 2D IR data, further revealing a network of couplings to lower energy modes that mediate this energy exchange. These findings provide new insights into the energetic landscape of organic molecules potentially useful as ligands in single molecule magnets.

Investigation on the vibrational relaxation and ultrafast electronic dynamics of S1 state in 2,4-difluoroanisole

Intramolecular vibrational energy redistribution (IVR) has a profound impact on dynamic processes. We have studied two types of IVR processes, restricted and dissipative, and ultrafast dynamics of the S1 state of 2,4-difluoroanisole using time-resolved photoelectron spectroscopy and time-of-flight mass spectroscopy. The restricted IVR occurs in the intermediate regime of 219 cm-1 vibrational level, and the dissipative IVR occurs in the statistical regime of 1200 cm-1. The lifetimes of IVR processes are measured to be 90 and 11 ps, respectively, depending on the internal energies of the S1 state and differ by a factor of eight. Similar subsequent dynamics were observed at two vibrational levels in the S1 state. The population undergoes IVR following the initial excitation and subsequently leaks into a triplet state, accompanied by intersystem crossing within ∼400 ps followed by a slower nonradiative relaxation of the triplet state on the nanosecond time scale. Furthermore, the values of 3s and 3px Rydberg states of 2,4-difluoroanisole were experimentally determined to be 5.02 and 6.28 eV.

Ultraviolet Photodissociation of Protonated Peptides and Proteins Can Proceed with H/D Scrambling

Ultraviolet photodissociation (UVPD) has recently been introduced as an ion activation method for the determination of single-residue deuterium levels in H/D exchange tandem mass spectrometry experiments. In this regard, it is crucial to know which fragment ion types can be utilized for this purpose. UVPD yields rich product ion spectra where all possible backbone fragment ion types (a/x, b/y, and c/z) are typically observed. Here we provide a detailed investigation of the level of H/D scrambling for all fragment ion types upon UVPD of the peptide scrambling probe P1 (HHHHHHIIKIIK) using an Orbitrap tribrid mass spectrometer equipped with a solid-state 213 nm UV laser. The most abundant UVPD-generated fragment ions (i.e., b/y ions) exhibit extensive H/D scrambling. Similarly, a/x and c/z ions have also undergone H/D scrambling due to UV-induced heating of the precursor ion population. Therefore, dominant b/y ions upon UVPD of protonated peptides are a strong indicator for the occurrence of extensive H/D scrambling of the precursor ion population. In contrast to peptide P1, UV-irradiation of ubiquitin did not induce H/D scrambling in the nonfragmented precursor ion population. However, the UVPD-generated b₂ and a₄ ions from ubiquitin exhibit extensive H/D scrambling. To minimize H/D scrambling, short UV-irradiation time and high gas pressures are recommended.

Effects of symmetry, methyl groups and serendipity on intramolecular vibrational energy dispersal

Intramolecular vibrational dispersal of vibrational energy is more efficient in the symmetrically-substituted p-xylene molecule than in p-fluorotoluene, p-chlorofluorobenzene or p-difluorobenzene.

Energy flow in peptides after UV photoexcitation of backbone linkages

We report on the dissociation channels after UV photoexcitation of peptide cations tagged with 18-crown-6 ether (CE). The model peptides chosen for study were singly protonated (Ala)_n-Pro (n = 1, 2, 3) and Pro-Pro (Ala = alanine, Pro = proline) that all contain at least one tertiary amide group with high absorption cross section at 210 nm (5.90 eV). Statistical dissociation was identified from the loss of CE, a process occuring remotely from the initial site of excitation, and therefore requiring flow of energy to the ammonium group where the CE is bound. However, homolytic breakage of the peptide backbone at the site of excitation is competitive, resulting in so-called a radical cations. Density functional theory calculations of dissociation energies were done on the simplest system [Ala-Pro + H⁺](CE) and found to be 1.87 eV for CE loss and 3.29 eV for the formation of a⁺(CE) and x. These numbers were used to calculate statistical branching ratios for the dissociation processes based on detailed balance. After the absorption of two 210 nm photons (according to power-dependence measurements), the branching ratio between the two channels is calculated to be less than 10^-4, far below the observed ratio of 0.65. Hence both statistical and non-statistical dissociation contribute to dissociation of these photoexcited peptides.

Direct observation of vibrational energy dispersal via methyl torsions

Explicit evidence for the role of methyl rotor levels in promoting energy dispersal is reported. A set of coupled zero-order vibration/vibration-torsion (vibtor) levels in the S₁ state of para-fluorotoluene (pFT) are investigated. Two-dimensional laser-induced fluorescence (2D-LIF) and two-dimensional zero-kinetic-energy (2D-ZEKE) spectra are reported, and the assignment of the main features in both sets of spectra reveals that the methyl torsion is instrumental in providing a route for coupling between vibrational levels of different symmetry classes. We find that there is very localized, and selective, dissipation of energy via doorway states, and that, in addition to an increase in the density of states, a critical role of the methyl group is a relaxation of symmetry constraints compared to direct vibrational coupling.

The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics

Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. Graphical abstract ᅟ.

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Peptide cation-radical fragment ions of the z-type, [^●AXAR⁺], [^●AXAK⁺], and [^●XAR⁺], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS³-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [y_n]⁺ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second (B) excited electronic states in the peptide ion R-CH^●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH⁺-C^●(O^-)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic C_α and amide nitrogen positions. Graphical Abstract ᅟ.

Vibrational and vibrational-torsional interactions in the 0-600 cm-1 region of the S1← S0 spectrum of p-xylene investigated with resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy

We assign the 0-600 cm^-1 region of the S₁← S₀ transition in p-xylene (p-dimethylbenzene) using resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy. In the 0-350 cm^-1 range as well as the intense origin band, there are a number of torsional and vibration-torsion (vibtor) features. The latter are discussed in more detail in Paper I [A. M. Gardner et al., J. Chem. Phys. 146, 124308 (2017)]. Here we focus on the origin and the 300-600 cm^-1 region, where vibrational bands and some vibtor activity are observed. From the origin ZEKE spectrum, we derive the ionization energy of p-xylene as 68200 ± 5 cm^-1. The assignment of the REMPI spectrum is based on the activity observed in the ZEKE spectra coupled with knowledge of the vibrational wavenumbers obtained from quantum chemical calculations. We assign several isolated vibrations and a complex Fermi resonance that is found to comprise contributions from both vibrations and vibtor levels, and we examine this via a two-dimensional ZEKE spectrum. A number of the vibrational features in the REMPI and ZEKE spectra of p-xylene that have been reported previously are reassigned and now largely consist of totally symmetric contributions. We briefly discuss the appearance of non-Franck-Condon allowed transitions. Finally, we find remarkably similar spectral activity to that in the related disubstituted benzenes, para-difluorobenzene, and para-fluorotoluene.

Molecular symmetry group analysis of the low-wavenumber torsions and vibration-torsions in the S1 state and ground state cation of p-xylene: An investigation using resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy

For the first time, a molecular symmetry group (MSG) analysis has been undertaken in the investigation of the electronic spectroscopy of p-xylene (p-dimethylbenzene). Torsional and vibration-torsional (vibtor) levels in the S₁ state and ground state of the cation of p-xylene are investigated using resonance-enhanced multiphoton ionization (REMPI) and zero-kinetic-energy (ZEKE) spectroscopy. In the present work, we concentrate on the 0-350 cm^-1 region, where there are a number of torsional and vibtor bands and we discuss the assignment of this region. In Paper II [W. D. Tuttle et al., J. Chem. Phys. 146, 124309 (2017)], we examine the 350-600 cm^-1 region where vibtor levels are observed as part of a Fermi resonance. The similarity of much of the observed spectral activity to that in the related substituted benzenes, toluene and para-fluorotoluene, is striking, despite the different symmetries. The discussion necessitates a consideration of the MSG of p-xylene, which has been designated G₇₂, but we shall also designate [{3,3}]D_2h and we include the symmetry operations, character table, and direct product table for this. We also discuss the symmetries of the internal rotor (torsional) levels and the selection rules for the particular electronic transition of p-xylene investigated here.

Torsion and vibration-torsion levels of the S1 and ground cation electronic states of para-fluorotoluene

We investigate the low-energy transitions (0-570 cm^-1) of the S₁ state of para-fluorotoluene (pFT) using a combination of resonance-enhanced multiphoton ionization and zero-kinetic-energy (ZEKE) spectroscopy and quantum chemical calculations. By using various S₁ states as intermediate levels, we obtain ZEKE spectra. The differing activity observed allows detailed assignments to be made of both the cation and S₁ low-energy levels. The assignments are in line with the recently published work on toluene from the Lawrance group [J. R. Gascooke et al., J. Chem. Phys. 143, 044313 (2015)], which considered vibration-torsion coupling in depth for the S₁ state of toluene. In addition, we investigate whether two bands that occur in the range 390-420 cm^-1 are the result of a Fermi resonance; we present evidence for weak coupling between various vibrations and torsions that contribute to this region. This work has led to the identification of a number of misassignments in the literature, and these are corrected.

UV Action Spectroscopy of Gas-Phase Peptide Radicals

UV photodissociation (UVPD) action spectroscopy is reported to provide a sensitive tool for the detection of radical sites in gas-phase peptide ions. UVPD action spectra of peptide cation radicals of the z-type generated by electron-transfer dissociation point to the presence of multiple structures formed as a result of spontaneous isomerizations by hydrogen atom migration. N-terminal Cα radicals are identified as the dominant components, but the content of isomers differing in the radical defect position in the backbone or side chain depends on the nature of the aromatic residue with phenylalanine being more prone to isomerization than tryptophan. These results illustrate that spontaneous hydrogen atom migrations can occur in peptide cation-radicals upon electron-transfer dissociation.

Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas-phase peptide cation-radicals

We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas-phase peptide cation-radicals produced by electron transfer dissociation. z-Type fragment ions (●) Gly-Gly-Lys(+), coordinated to 18-crown-6-ether (CE), are generated, selected by mass and photodissociated in the 200-400 nm region. The UVPD action spectra indicate the presence of valence-bond isomers differing in the position of the Cα radical defect, (α-Gly)-Gly-Lys(+) (CE), Gly-(α-Gly)-Lys(+) (CE) and Gly-Gly-(α-Lys(+))(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time-dependent density functional theory (TD-DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion-electron reactions. Specifically, z-type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation.

Combining Near-UV Photodissociation with Electron Transfer. Reduction of the Diazirine Ring in a Photomethionine-Labeled Peptide Ion

Electron transfer dissociation of peptide ions with the diazirine-containing residue photomethionine (M*) results in side-chain dissociations by loss of C3H7N2 radicals in addition to standard backbone cleavages. The side-chain dissociations are particularly prominent upon activation of long-lived, charge-reduced, cation radicals (GM*GGR + 2H)(+•). Investigation of these cation radicals by near-UV photodissociation and collisional activation revealed different fragmentation products and mechanisms resulting from these ion activation modes. The dissociations observed for photomethionine were dramatically different from those previously reported for the lower homologue photoleucine; here, a difference by a single methylene group in the side chain had a large effect on the chemistries of the cation radicals upon ETD and further activation. ETD intermediates and products were probed by tandem 355-nm UV photodissociation-collision induced dissociation and found to contain chromophores that resulted from electron attachment to the diazirine ring. The nature of the newly formed chromophores and ion energetics and kinetics were investigated by electron structure calculations combining ab initio and density functional theory methods and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The dramatic difference between the dissociations of L* and M* containing peptide cation radicals is explained by electronic effects that play a role in stabilizing critical reaction intermediates and steer the dissociations into kinetically favored reaction channels. In addition, a new alternating UVPD-ETD-UVPD MS(4) experiment is introduced and utilized for ion structure elucidation.

Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction

Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase.