Comprehensive characterization of the photodissociation pathways of protonated tryptophan

Conformer-selective Photodynamics of TrpH+ -H2 O

The photodynamics of protonated tryptophan and its mono hydrated complex TrpH⁺ -H₂ O has been revisited. A combination of steady-state IR and UV cryogenic ion spectroscopies with picosecond pump-probe photodissociation experiments sheds new lights on the deactivation processes of TrpH⁺ and conformer-selected TrpH⁺ -H₂ O complex, supported by quantum chemistry calculations at the DFT and coupled-cluster levels for the ground and excited states, respectively. TrpH⁺ excited at the band origin exhibits a transient of less than 100 ps, assigned to the lifetime of the excited state proton transfer (ESPT) structure. The two experimentally observed conformers of TrpH⁺ -H₂ O have been assigned. A striking result arises from the conformer-selective photodynamics of TrpH⁺ -H₂ O, in which a single water molecule inserted in between the ammonium and the indole ring hinders the barrierless ESPT reaction responsible for the ultra-fast deactivation process observed in the other conformer and in bare TrpH⁺ .

Tandem-trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation

RATIONALE

Tandem-ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem-ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes.

METHODS

Here, we describe the coupling of the separation capabilities of tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis.

RESULTS

We establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2-3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical-based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here ("UVnoD2"), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility-separating fragment ions produced from UVPD.

CONCLUSIONS

The data demonstrate that UVPD carried out at elevated pressures of 2-3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post-UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics.

Influence of the N atom position on the excited state photodynamics of protonated azaindole

We present a study of the photofragmentation of three protonated azaindole molecules - 7-azaindole, 6-azaindole, and 5-azaindole - consisting of fused pyrrole-pyridine bicyclic aromatic systems, in which the pyridinic (protonated) nitrogen heteroatom is located at the 7, 6, and 5 positions, respectively. Photofragmentation electronic spectra of the isolated aforementioned azaindolinium cations reveal that their photodynamics extends over timescales covering nine orders of magnitude and provide evidence about the resultant fragmentation pathways. Moreover, we show how the position of the heteroatom in the aromatic skeleton influences the excited state energetics, fragmentation pathways, and fragmentation timescales. Computed ab initio adiabatic transition energies are used to assist the assignation of the spectra, while geometry optimisation in the excited electronic states as well as ab initio calculations along the potential surfaces demonstrate the role of ππ*/πσ* coupling and/or large geometry changes in the dynamics of these species. Evidence supporting the formation of Dewar valence isomers as intermediates involved in sub-picosecond relaxation processes is discussed.

Direct Measurement of the Visible to UV Photodissociation Processes for the PhotoCORM TryptoCORM

PhotoCORMs are light-triggered compounds that release CO for medical applications. Here, we apply laser spectroscopy in the gas phase to TryptoCORM, a known photoCORM that has been shown to destroy Escherichia coli upon visible-light activation. Our experiments allow us to map TryptoCORM's photochemistry across a wide wavelength range by using novel laser-interfaced mass spectrometry (LIMS). LIMS provides the intrinsic absorption spectrum of the photoCORM along with the production spectra of all of its ionic photoproducts for the first time. Importantly, the photoproduct spectra directly reveal the optimum wavelengths for maximizing CO ejection, and the extent to which CO ejection is compromised at redder wavelengths. A series of comparative studies were performed on TryptoCORM-CH3 CN which exists in dynamic equilibrium with TryptoCORM in solution. Our measurements allow us to conclude that the presence of the labile CH3 CN facilitates CO release over a wider wavelength range. This work demonstrates the potential of LIMS as a new methodology for assessing active agent release (e.g. CO, NO, H2 S) from light-activated prodrugs.

Wavelength-Dependent Ultraviolet Photodissociation of Protonated Tryptamine

Ultraviolet photodissociation (UVPD) experiments of protonated tryptamine ([Tryp+H]⁺) have been implemented by a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer combined with a wavelength-tunable optical parametric oscillator (OPO) laser. UVPD mass spectra under different laser wavelengths have been obtained, in which the dependence of the yield of fragment ions on the laser wavelength was observed. The UVPD spectrum of [Tryp+H]⁺ has been obtained in the range of 210-310 nm. Besides the previously reported two competitive channels of H loss and NH₃ loss, two important channels of losing CH₂NH and CH₂NH₂ units were observed and further studied by UV-UV tandem mass spectrometry and theoretical calculations. Interestingly, results show that the pair of competitive channels of CH₂NH loss and CH₂NH₂ loss are both from the McLafferty-type rearrangement caused by ππ* electronic excited states. After the excitation, the two different dissociation pathways produce two different ion-neutral complexes, respectively. The wavelength-dependent dissociation and the existing competitive channels shown in this study reflect the diversity of UVPD processes of such organic molecules.

Nature and Hierarchy of Hydrogen-Bonding Interactions in Binary Complexes of Azoles with Water and Hydrogen Peroxide

In the present study, the hydrogen-bonded complexes of azole with water and hydrogen peroxide are systematically investigated by second-order Møller-Plesset perturbation theory and density functional theory with dispersion function calculations. This study suggests that the ability of pyrrolic nitrogen (NH) atom to function as hydrogen-bond donor increases with the introduction of nitrogen atoms in the ring, whereas the ability of pyridinic nitrogen (N) atom to act as hydrogen-bond acceptor reduces with successive aza substitution in the ring. With introduction of nitrogen atoms in the ring, the vibrational frequency, stabilization energy, and electron density in the σ antibonding orbitals of the X-H (X = N, C of azole) bond of the complexes all increase or decrease systematically. Decomposition analysis of total stabilization energy showed that the electrostatic energy term is a dominant attractive contribution in comparison to induction and dispersion terms in all of the complexes under study.

Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry

Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

Tautomerism and electronic spectroscopy of protonated 1- and 2-aminonaphthalene

Protonation sites can be controlled by the electrospray source as written in the figure.

Classical Dynamics Simulations of Dissociation of Protonated Tryptophan in the Gas Phase

Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule. Unlike aliphatic amino acids, protonated tryptophan dissociates via NH₃ elimination rather than the usual iminium ion formation by combined removal of H₂O and CO molecules. Also, a major fragmentation pathway in the present work involves C_α-C_β bond fission. Results of the chemical dynamics simulations reported here are in overall agreement with experiments, and detailed atomic level mechanisms are presented.

Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study

The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.

Photofragmentation mechanisms in protonated chiral cinchona alkaloids

Photo-fragmentation of protonated alkaloids results in C₈–C₉ cleavage accompanied or not by hydrogen migration, with a stereochemistry-dependent branching ratio.

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.

Ion-Induced Dipole Interactions and Fragmentation Times: Cα-Cβ Chromophore Bond Dissociation Channel

The fragmentation times corresponding to the loss of the chromophore (Cα-Cβ bond dissociation channel) after photoexcitation at 263 nm have been investigated for several small peptides containing tryptophan or tyrosine. For tryptophan-containing peptides, the aromatic chromophore is lost as an ionic fragment (m/z 130), and the fragmentation time increases with the mass of the neutral fragment. In contrast, for tyrosine-containing peptides the aromatic chromophore is always lost as a neutral fragment (mass = 107 amu) and the fragmentation time is found to be fast (<20 ns). These different behaviors are explained by the role of the postfragmentation interaction in the complex formed after the Cα-Cβ bond cleavage.

Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase

Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.

UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture

Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.

On the near UV photophysics of a phenylalanine residue: conformation-dependent ππ* state deactivation revealed by laser spectroscopy of isolated neutral dipeptides

The primary step of the near UV photophysics is investigated in pump–probe R2PI ns experiments carried out on specific conformers of model peptide chains.

UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate [5'-dAMP-H]-

The UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate ([5'-dAMP-H](-)) has been studied using a unique technique based on the coincident detection of the ion and the neutral fragments. The observed fragment ions are m/z 79 (PO(3)(-)), 97 (H(2)PO(4)(-)), 134 ([A-H](-)), 177 ([dAMP-H-A-H(2)O](-)), and 195 ([dAMP-H-A](-)), where "A" refers to a neutral adenine molecule. The relative abundances are comparable to that found in previous studies on [5'-dAMP-H](-) employing different excitation processes, i.e., collisions and UV photons. The fragmentation times of the major channels have been measured, and are all found to be on the microsecond time scale. The fragmentation mechanisms for all channels have been characterized using velocity correlation plots of the ion and neutral fragment(s). The findings show that none of the dissociation channels of [5'-dAMP-H](-) is UV specific and all proceed via statistical fragmentation on the ground state after internal conversion, a result similar to fragmentations induced by collisions.

Photodissociation dynamics of thiophenol-d1: the nature of excited electronic states along the S-D bond dissociation coordinate

The S-D bond dissociation dynamics of thiophenol-d1 (C6H5SD) pumped at 266, 243, and 224 nm are examined using the velocity map ion imaging technique. At both 266 and 243 nm, distinct peaks associated with X and A states of the phenylthiyl radical (C6H5S*) are observed in the D+ image at high and low kinetic energy regions, respectively. The partitioning of the available energy into the vibrational energy of the phenylthiyl radical is found to be enhanced much more strongly at 266 nm compared to that at 243 nm. This indicates that the pipi* electronic excitation at 266 nm is accompanied by significant vibrational excitation. Given the relatively large anisotropy parameter of -0.6, the S-D dissociation at 266 nm is prompt and should involve the efficient coupling to the upper-lying n(pi)sigma* repulsive potential energy surface. The optical excitation of thiophenol at 224 nm is tentatively assigned to the pisigma* transition, which leads to the fast dissociation on the repulsive potential energy surface along the S-D coordinate. The nature of the electronic transitions associated with UV absorption bands is investigated with high-level ab initio calculations. Excitations to different electronic states of thiophenol result in unique branching ratios and vibrational excitations for the fragment of the phenylthiyl radical in the two lowest electronic states.

Computational study on the photophysics of protonated benzene

The reaction paths in the lowest excited electronic states relevant for the photophysics of protonated benzene, C(6)H(7)(+), have been explored by ab initio techniques of electronic structure theory. For this purpose, the first four excited singlet electronic states of C(6)H(7)(+) have been calculated at the CC2/cc-pVTZ level of theory. The CC2 approach has been validated by CASPT2 and TD-DFT calculations. The calculated UV absorption spectrum is in good agreement with the experimental spectrum. It has been found that the out-of-plane and the in-plane ring deformation leads in the excited states in an essential barrierless manner to a low-lying conical intersection between the lowest excited states and with the ground state, providing a mechanism for efficient radiationless deactivation, which is expected to quench luminescence of the isolated molecular ion.