Does IVR Take Place Prior to Peptide Ion Dissociation?

Site-Selective Dissociation upon Sulfur L-Edge X-ray Absorption in a Gas-Phase Protonated Peptide

Site-selective dissociation induced by core photoexcitation of biomolecules is of key importance for the understanding of radiation damage processes and dynamics and for its promising use as "chemical scissors" in various applications. However, identifying products of site-selective dissociation in large molecules is challenging at the carbon, nitrogen, and oxygen edges because of the high recurrence of these atoms and related chemical groups. In this paper, we present the observation of site-selective dissociation at the sulfur L-edge in the gas-phase peptide methionine enkephalin, which contains only a single sulfur atom. Near-edge X-ray absorption mass spectrometry has revealed that the resonant S 2p → σ*_C-S excitation of the sulfur contained in the methionine side chain leads to site-selective dissociation, which is not the case after core ionization above the sulfur L-edge. The prospects of such results for the study of charge dynamics in biomolecular systems are discussed.

Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis

Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.

A model for ultra-fast charge transport in membrane proteins

Isolated proteins have recently been observed to transport charge and reactivity over very long distances with extraordinary rates and near perfect efficiencies in spite of their site. This is not the case if the peptide is in water, where the efficiency of charge hopping to the next site is reduced to approximately 2%. Here, water is not an ideal solvent for charge transport. The issue at hand is how to explain such enormous charge transfer quenching in water compared to another typical medium, namely lipid. We performed molecular dynamics simulations to computationally substantiate the novel long-distance charge transfer yield of the polypeptides in lipids. This is characterized by the charge transfer persistent-distance decay constant and not by the rate, which is seldom, if ever, measured and hence not directly addressed here. This model can encompass an extremely wide range of yields over very long distances in peptides in various media. The calculations here demonstrate the good charge transport efficiency in lipids in contrast to the poor efficiency in water. The protein charge transport also exhibits a very strong anisotropic effect in lipids. The peptide secondary structure effect of charge transfer in membranes is analyzed in contrast to that in water. These results suggest that this model can be useful for the prediction of charge transfer efficiency in various environments of interest and indicate that the charge transfer is highly efficient in membrane proteins.

Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides

In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types (a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.

Stability of high-mass molecular libraries: the role of the oligoporphyrin core

Molecular beam techniques are a key to many experiments in physical chemistry and quantum optics. In particular, advanced matter-wave experiments with high-mass molecules profit from the availability of slow, neutral and mass-selected molecular beams that are sufficiently stable to remain intact during laser heating and photoionization mass spectrometry. We present experiments on the photostability with molecular libraries of tailored oligoporphyrins with masses up to 25,000 Da. We compare two fluoroalkylsulfanyl-functionalized libraries based on two different molecular cores that offer the same number of anchor points for functionalization but differ in their geometry and electronic properties. A pentaporphyrin core stabilizes a library of chemically well-defined molecules with more than 1600 atoms. They can be neutrally desorbed with velocities as low as 20 m/s and efficiently analyzed in photoionization mass spectrometry.

Internal energy distribution in electrospray ionization: towards the evaluation of a thermal-like distribution from the multiple-collision model

RATIONALE

The internal energy deposition in ions that cross the desolvation region of an electrospray ionization (ESI) source affects the mass spectra that are obtained using in-source collision-induced dissociation (CID) or in tandem mass spectrometry (MS/MS) mode. It is thus important to evaluate the internal energy distributions of the ions in different parts of an ESI mass spectrometer.

METHODS

The desolvation region is considered as a collision zone and a partially elastic multiple-collision model is used to account for the accumulation of internal energy in the ions. The ion survival yields (SY(Theo) of the theoretical mass spectra calculated by MassKinetics software are fitted with the experimental ion survival yields (SY(Exp)) of the substituted benzylpyridinium cations that have been obtained with an ESI source interfaced with a quadrupole mass spectrometer. The theoretical parameters used for fitting the calculation data with the experimental results are the center-of-mass collision energy (Ecom ) of the colliding ions and a term related to the pressure of the desolvation area of the ESI interface.

RESULTS

In the proposed model, an average number of 'effective' collisions of close to 30 in the desolvation area is employed. The voltages applied to the orifice of this interface are correlated to a theoretical initial kinetic energy (E(init,Kin)) in the laboratory frame of the ions. In the present case, these theoretical initial kinetic energies range from 5.5 to 9 eV. The internal energy distributions evaluated from this model resemble the thermal distributions of ions having 'characteristic temperatures' between 1020 and 1550 K, and the results of calculations show that the mean internal energy of the ions increases linearly with the orifice voltage.

CONCLUSIONS

The model used in this study can account for the energy build-up of the ions in an ESI interface and allows the change in the internal energy distribution of the electrosprayed ions in different regions of a mass spectrometer to be evaluated.

Photodissociation pathways and lifetimes of protonated peptides and their dimers

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.

Length effects in VUV photofragmentation of protonated peptides

We have studied photoionization of protonated synthetic peptides YG(n)F (n = 0, 1, 3, 5, 10). Photon energies ranging from 8 to 30 eV were used. For YG(n)F peptides up to n = 5 small fragment ions related to the sidechains of the aromatic terminal amino acids Y and F dominate the fragmentation patterns. The associated yields scale with total photoabsorption cross section, demonstrating efficient hole migration towards the terminal amino acids upon photoionization of the peptide backbone. For n = 10 the side-chain loss channel is quenched and a series of large dications appear.

Effects of charge location on the absorptions and lifetimes of protonated tyrosine peptides in vacuo

Nearby charges affect the electronic energy levels of chromophores, with the extent of the effect being determined by the magnitude of the charge and degree of charge-chromophore separation. The molecular configuration dictates the charge-chromophore distance. Hence, in this study, we aim to assess how the location of the charge influences the absorption of a set of model protonated and diprotonated peptide ions, and whether spectral differences are large enough to be identified. The studied ions were the dipeptide YK, the tripeptide KYK (Y = tyrosine; K = lysine) and their complexes with 18-crown-6-ether (CE). The CE targets the ammonium group by forming internal ionic hydrogen bonds and limits the folding of the peptide. In the tripeptide, the distance between the chromophore and the backbone ammonium is enlarged relative to that in the dipeptide. Experiments were performed in an electrostatic ion storage ring using a tunable laser system, and action spectra based on lifetime measurements were obtained in the range from 210 to 310 nm. The spectra are all quite similar though there seems to be some changes in the absorption band between 210 and 250 nm, while in the lower energy band all ions had a maximum absorption at ~275 nm. Lifetimes after photoexcitation were found to shorten upon protonation and lengthen upon CE complexation, in accordance with the increased number of degrees of freedom and an increase in activation energies for dissociation as the mobile proton model is no longer operative.

Visible and ultraviolet spectroscopy of gas phase protein ions

Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.

Rapid, quantitative, and site specific synthesis of biomolecular radicals from a simple photocaged precursor

Novel p-iodobenzoate-based labelling reagents are shown to be effective photocaged precursors for synthesizing biomolecular radicals site-selectively in the gaseous and condensed phases. In vacuo, a single pulse of UV photons (266 nm) is sufficient to quantitatively photolyse the C-I bond. In aqueous solutions, the photolysis half-life is estimated to be 2.5 minutes when irradiating with a 15 W compact fluorescent lamp (254 nm).

Theoretical calculations for mass resolution of a quadrupole ion trap reflectron time-of-flight mass spectrometer

We have developed a theoretical method of predicting the mass resolution for a quadrupole ion trap reflectron time-of-flight (QIT-reTOF) mass spectrometer as a function of the spatial and velocity distributions of ions, voltages applied to the electrodes, and dimensions of the instrument. The flight times of ions were calculated using theoretical equations derived with an assumption of uniform electric fields inside the QIT and with the analytical description of the potential including the monopole, dipole, and quadrupole components. The mass resolution was then estimated from the flight-time spread of the ions with finite spatial and velocity distributions inside the QIT. The feasibility of the theoretical method was confirmed by the reasonable agreement of the theoretical resolution with the experimental one measured by varying the extraction voltage of the QIT or the deceleration voltage of the reflectron. We found that the theoretical resolution estimated with the assumption of the uniform electric fields inside the QIT reproduced the experimental one better than that with the analytical description of the potential. The possible applications of this theoretical method include the optimization of the experimental parameters of a given QIT-reTOF mass spectrometer and the design of new instruments with higher mass resolution.

Probing Ultrafast Purely Electronic Charge Migration in Small Peptides

A pump–probe experiment that can examine a pure charge migration on a time scale short compared to the onset of nuclear motion is discussed. The mass spectrometric studies of Schlag et al. suggest that short peptide terminated by an aromatic amino acid are particularly suitable test compounds. The pump pulse needs to ionize the molecule on a time scale short compared to the period of the electronic motion, typically sub-fs. However, ionization occurs preferentially when the electrical field of the light is maximal so that the duration of the pulse envelope can be somewhat longer. Detection by photoelectron spectrometry of the peptide cation, to produce a dication, is shown to be able to probe the electronic rearrangement.

Radical cations of amino acids and peptides: structures and stabilities

Amino acid and peptide radical cations, M*+, are formed by oxidative dissociations of [Cu(auxiliary ligand)(M)]*2+ and [Metal(III)(salen)(M)]+ complexes. The most easily formed radicals contain either an aromatic or basic amino acid residue. Aromatic amino acids have low ionization energies, are easily oxidized and delocalize the charge and spin over the ring systems; basic amino acids facilitate formation of alpha-radicals that have captodative structures in which the charge and spin are formally separated, although feeding back some of the charge onto the amide or carboxyl group adjacent to the radical center through hydrogen bonding enriches the electron-withdrawing properties and is highly stabilizing. DFT calculations located five isomers of His*+ with an alpha-radical with a captodative structure at the global minimum in a deep potential well. An IRMPD spectrum confirmed that this isomer is the experimentally observed "long-lived" isomer. When both charge and spin are on the peptide backbone, as in [GGG]*+, captodative structures have the lowest energies; the barriers to interconversion between the three isomeric alpha-radicals of [GGG]*+ are high as the charge impedes migration of a hydrogen atom. Dissociation of [GGG]*+ is charge-driven. In peptide radical cations containing a basic amino acid residue the charge is sequestered on the side chain and the radical center, either on the backbone or on another side chain, initiates the fragmentation.

Gas-phase fragmentation of long-lived cysteine radical cations formed via NO loss from protonated S-nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys(*+)), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: *COOH CH(2)S >> *CH(2)SH approximately = H(2)S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys(*+) with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH(2)S, *COOH, *CH(2)SH, and H(2)S.

Ultraviolet photofragmentation of biomolecular ions

Mass spectrometric identification of all types of molecules relies on the observation and interpretation of ion fragmentation patterns. Peptides, proteins, carbohydrates, and nucleic acids that are often found as components of complex biological samples represent particularly important challenges. The most common strategies for fragmenting biomolecular ions include low- and high-energy collisional activation, post-source decay, and electron capture or transfer dissociation. Each of these methods has its own idiosyncrasies and advantages but encounters problems with some types of samples. Novel fragmentation methods that can offer improvements are always desirable. One approach that has been under study for years but is not yet incorporated into a commercial instrument is ultraviolet photofragmentation. This review discusses experimental results on various biological molecules that have been generated by several research groups using different light wavelengths and mass analyzers. Work involving short-wavelength vacuum ultraviolet light is particularly emphasized. The characteristics of photofragmentation are examined and its advantages summarized.

Development of an ion trap/multi-turn time-of-flight mass spectrometer with potential- lift

An ion trap/multi-turn time-of-flight (ToF) mass spectrometer with potential-lift has been developed. This system consists of an external ion source, a lens system, an ion trap, a potential-lift, a multi-turn ToF mass spectrometer and a detector. The ion trap consists of hyperbolic electrode cross-sections (Paul trap) and is used as an ion storage device. The potential-lift, which is part of the flight tube, was attached between the ion trap and the multi-turn ToF mass spectrometer. The potential-lift is known to be useful for increasing the kinetic energy of the ions. In order to check the ability of the potential-lift, mass distributions of [(CsI)(n) Cs]+ clusters (n = 1-9) were measured. The relative intensity ratios of the [(CsI)(n)Cs]+ clusters were consistent with the results obtained using other apparatus. To check the properties of the new apparatus, Xe+ isotopes were analyzed using either a linear or multi-turn ToF mass spectrometer. In the linear mode, the mass resolution was 500. In the multi-turn mode, the resolution depended on the number of cycles of the multi-turn ToF mass spectrometer; the mass resolution was 4400 (FWHM) after nine cycles. This new apparatus with a high resolution will be useful for measurements of ion-molecule reactions and photodissociations.

Dissociation lifetime studies of doubly deprotonated angiotensin peptides

The doubly deprotonated [Asn,Val5] angiopeptide, in the gas phase, was irradiated with 266 nm photons. The time of flight (TOF) of the products formed following photoabsorption, namely, the monoanion and neutral fragments, was recorded with submicrosecond time resolution. Monte Carlo simulations of the TOF of the neutral fragments indicate that the dissociation occurs faster than 100 ns. A similar experiment performed on the Val5 angiopeptide also yielded a dissociation time shorter than 100 ns. We suggest dissociation mechanisms that account for the different number of photons required for the release of CO2.

Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: a statistical interpretation

Time-evolution of product ion signals in ultraviolet photodissociation (UV-PD) of singly protonated peptides with an arginine at the N-terminus was investigated by using a tandem time-of-flight mass spectrometer equipped with a cell floated at high voltage. Observation of different time-evolution patterns for different product ion types--an apparently nonstatistical behavior--could be explained within the statistical framework by invoking consecutive formation of some product ions and broad internal energy distributions for precursor ions. a(n) + 1 and b(n) ions were taken as the primary product ions from this type of peptide ions. Spectral characteristics in post-source decay, UV-PD, and collisionally activated dissociation at low and high kinetic energies could be explained via rough statistical calculation of rate constants. Specifically, the striking characteristics in high-energy CAD and UV-PD--dominance of a(n) and d(n) formed via a(n) + 1--were not due to the peculiarity of the excitation processes themselves, but due to quenching of the b(n) channels caused by the presence of arginine.

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS(3) fragmentation of radicals produced by photodetachment at lambda = 260 nm (DNA excitation) and by photodetachment at lambda > 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Förster resonance energy transfer (FRET).

Distal charge transport in peptides

Biological systems often transport charges and reactive processes over substantial distances. Traditional models of chemical kinetics generally do not describe such extreme distal processes. In this Review, an atomistic model for a distal transport of information, which was specifically developed for peptides, is considered. Chemical reactivity is taken as the result of distal effects based on two-step bifunctional kinetics involving unique, very rapid motional properties of peptides in the subpicosecond regime. The bifunctional model suggests highly efficient transport of charge and reactivity in an isolated peptide over a substantial distance; conversely, a very low efficiency in a water environment was found. The model suggests ultrafast transport of charge and reactivity over substantial molecular distances in a peptide environment. Many such domains can be active in a protein.

Efficient and reliable calculation of Rice-Ramsperger-Kassel-Marcus unimolecular reaction rate constants for biopolymers: modification of Beyer-Swinehart algorithm for degenerate vibrations

The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.

Electron capture in spin-trap capped peptides. An experimental example of ergodic dissociation in peptide cation-radicals

Electron capture dissociation was studied with tetradecapeptides and pentadecapeptides that were capped at N-termini with a 2-(4'-carboxypyrid-2'-yl)-4-carboxamide group (pepy), e.g., pepy-AEQLLQEEQLLQEL-NH(2), pepy-AQEFGEQGQKALKQL-NH(2), and pepy-AQEGSEQAQKFFKQL-NH(2). Doubly and triply protonated peptide cations underwent efficient electron capture in the ion-cyclotron resonance cell to yield charge-reduced species. However, the electron capture was not accompanied by backbone dissociations. When the peptide ions were preheated by absorption of infrared photons close to the dissociation threshold, subsequent electron capture triggered ion dissociations near the remote C-terminus forming mainly (b(11-14) + 1)(+)* fragment ions that were analogous to those produced by infrared multiphoton dissociation alone. Ab initio calculations indicated that the N-1 and N-1' positions in the pepy moiety had topical gas-phase basicities (GB = 923 kJ mol(-1)) that were greater than those of backbone amide groups. Hence, pepy was a likely protonation site in the doubly and triply charged ions. Electron capture in the protonated pepy moiety produced the ground electronic state of the charge-reduced cation-radical with a topical recombination energy, RE = 5.43-5.46 eV, which was greater than that of protonated peptide residues. The hydrogen atom in the charge-reduced pepy moiety was bound by >160 kJ mol(-1), which exceeded the hydrogen atom affinity of the backbone amide groups (21-41 kJ mol(-1)). Thus, the pepy moiety functioned as a stable electron and hydrogen atom trap that did not trigger radical-type dissociations in the peptide backbone that are typical of ECD. Instead, the internal energy gained by electron capture was redistributed over the peptide moiety, and when combined with additional IR excitation, induced proton-driven ion dissociations which occurred at sites that were remote from the site of electron capture. This example of a spin-remote fragmentation provided the first clear-cut experimental example of an ergodic dissociation upon ECD.

A systematic and efficient method to estimate the vibrational frequencies of linear peptide and protein ions with any amino acid sequence for the calculation of Rice-Ramsperger-Kassel-Marcus rate constant

A systematic method to automatically estimate the vibrational frequency sets of linear peptide and protein ions with any amino acid sequence, which is needed in Rice-Ramsperger-Kassel-Marcus (RRKM) calculations for dissociation of these ions, has been developed. The method starts from the frequencies of free amino acids calculated quantum chemically at the DFT/B3LYP/6-31G** level. Some of these were systematically eliminated to get fictitious sets of frequencies for each amino acid at the C-terminus, N-terminus, and inside the chain. By collecting these sets as needed for a specified amino acid sequence and adding vibrations appearing upon peptide bond formation and protonation, a complete set of vibrational frequencies was obtained. Other conditions for RRKM calculations have also been systematically specified. RRKM calculations performed under various conditions have shown that the present method can be useful for an order of magnitude estimation of a statistical rate constant even at low internal energy region. The fact that arbitrariness involved in constructing an entire frequency set simply through spectral correlation can be avoided, and that any protein ion can be handled systematically and rapidly once its sequence and the number of protons attached are specified, are the main advantages of the present method.

An electronic time scale in chemistry

Ultrafast, subfemtosecond charge migration in small peptides is discussed on the basis of computational studies and compared with the selective bond dissociation after ionization as observed by Schlag and Weinkauf. The reported relaxation could be probed in real time if the removal of an electron could be achieved on the attosecond time scale. Then the mean field seen by an electron would be changing rapidly enough to initiate the migration. Tyrosine-terminated tetrapeptides have a particularly fast charge migration where in <1 fs the charge arrives at the other end. A femtosecond pulse can be used to observe the somewhat slower relaxation induced by correlation between electrons of different spins. A slower relaxation also is indicated when removing a deeper-lying valence electron. When a chromophoric amino acid is at one end of the peptide, the charge can migrate all along the peptide backbone up to the N end, but site-selective ionization is probably easier to detect for tryptophan than for tyrosine.

Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction

To explore the mechanism of electron capture dissociation (ECD) of linear peptides, a set of 16-mer peptides were synthesized with deuterium labeled on the alpha-carbon position of four glycines. The ECD spectra of these peptides showed that such peptides exhibit a preference for the radical to migrate to the alpha-carbon position on glycine via hydrogen (or deuterium) abstraction before the final cleavage and generation of the detected product ions. The data show c-type fragment ions, ions corresponding to the radical cation of the c-type fragments, c*, and they also show c*-1 peaks in the deuterated peptides only. The presence of the c*-1 peaks is best explained by radical-mediated scrambling of the deuterium atoms in the long-lived, metastable, radical intermediate complex formed by initial electron capture, followed by dissociation of the complex. These data suggest the presence of at least two mechanisms, one slow, one fast. The abundance of H* and -CO losses from the precursor ion changed upon deuterium labeling indicating the presence of a kinetic isotope effect, which suggests that the values reported here represent an underestimation of radical migration and H/D scrambling in the observed fragments.

Dissociation Kinetics of Peptide Ions

The dissociation of peptide ions has been found to have ultrafast components that in many ways are uniquely different from typical unimolecular kinetics. As such, some peptide reactions provide new channels, which do not conform to statistical models of reaction kinetics. When the dissociation rates are in the 100 fs range, they are in a time scale where statistical methods do not yet apply, although molecules that have not yet dissociated will later in time undergo statistical redistribution of their excess energy, which, however, may not lead to noticeable reactivity within the experimental time frames for large peptides and hence are simply dissipative. This work is meant to reconcile the long time statistical results of Lifshitz et al. (2003) with the work of Schlag et al. (1995/6) that suggests an alternate parallel and much faster time scale for dissociation. It is argued that the two sets of results and interpretations augment one another and in fact open up a most interesting new field of peptide kinetics in addition to the unimolecular behavior, which becomes de facto arrested by the shear size of the molecule being unable to find a transition state on any reasonable time scale.

IR-Spectroscopic Characterization of Acetophenone Complexes with Fe+, Co+, and Ni+ Using Free-Electron-Laser IRMPD

The gas-phase complexes M(+)(acet)(2), where M is Fe, Co, or Ni and acet is acetophenone, were studied spectroscopically by infrared multiple-photon dissociation (IRMPD) supported by density functional (DFT) computations. The FELIX free electron laser was used to give tunable radiation from approximately 500 to 2200 cm(-1). The spectra were interpreted to determine the metal-ion binding sites on the ligands (oxygen (O) or ring (R)) and to see if rearrangement of the ligand(s) to toluene plus CO occurred. For Ni(+), O binding was found to predominate (similar to the previously studied Cr(+) case), with less than approximately 10% of R-bound ligands in the population. For Co(+), a roughly equal mixture of R-bound and O-bound ligands was present; based on the computed thermochemistry, the OR complex was considered likely to predominate. Fe(+) complexes appeared largely O-bound, but with clear evidence for some R-binding. The exceptionally large extent of R binding for Co(+) highlights the special affinity of this metal ion for aromatic ring ligands. In contrast, the predominant O binding for Ni(+) emphasizes the especially high metal-ion affinity of the O site of acetophenone compared with other ligands such as anisole where R binding of Ni(+) predominates. The spectra did not indicate significant intracomplex rearrangement of ligands to toluene plus CO, and in particular for the Co(+) case the absence of a metal-bound C triple bond O stretching peak near 2100 cm(-1) strongly ruled out such a rearrangement.

Statistical vs. non-statistical deactivation pathways in the UV photo-fragmentation of protonated tryptophan-leucine dipeptide

The excited state dynamics of protonated tryptophan-leucine ions WLH+, generated in an electrospray source, is investigated by photo-induced fragmentation in the gas phase, using femtosecond laser pulses. Two main features arise from the experiment. Firstly, the initially excited pipi* state decays very quickly with 2 time constants of 1 and 10 ps. Secondly, the transient signals recorded on different fragments are not the same which indicates two competing primary fragmentation processes. One involves a direct dissociation from the excited state that gives evidence for a non-statistical deactivation path. The other is attributed to a statistical decay following internal conversion to the ground electronic surface.

Pathways of peptide ion fragmentation induced by vacuum ultraviolet light

One Hundred Fifty-Seven nm photodissociation of singly protonated peptides generates unusual distributions of fragment ions. When the charge is localized at the C-terminus of the peptide, spectra are dominated by x-, v-, and w-type fragments. When it is sequestered at the N-terminus, a- and d-type ions are overwhelmingly abundant. Evidence is presented suggesting that the fragmentation occurs via photolytic radical cleavage of the peptide backbone at the bond between the alpha- and carbonyl-carbons followed by radical elimination to form the observed daughter ions.

Specific photodissociation of peptides with multi-stage mass spectrometry

We report collision-induced dissociation (CID) and laser-induced dissociation (LID) performed at different wavelengths between 220 and 280 nm of the peptides leucine-enkephalin (protonated) and gramicidin A (sodiated). Hydrogen-atom losses and side-chain cleavages were observed in LID experiments. These losses depend on the laser wavelength and lead to the formation of radical ions. The fragmentations of these radicals, which are not observed in CID experiments, were investigated in multi-stage mass spectrometry experiments.

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation-radicals and dications corresponding to hydrogen atom adducts to N-terminus-protonated N(alpha)-glycylphenylalanine amide (Gly-Phe-NH(2)) are studied by combined density functional theory and Møller-Plesset perturbational computations (B3-MP2) as models for electron-capture dissociation of peptide bonds and elimination of side-chain groups in gas-phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation-radicals, and hydrogen-bonded ion-radicals, and ylid-cation-radical complexes. The hydrogen-bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N-C(alpha) bonds in aminoketyl cation-radicals are 18-47 kJ mol(-1) exothermic and require low activation energies to produce ion-radical complexes as stable intermediates. Loss of the side-chain benzyl group is calculated to be 44 kJ mol(-1) endothermic and requires 68 kJ mol(-1) activation energy. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular rate constants predict fast preferential N-C(alpha) bond cleavage resulting in isomerization to ion-molecule complexes, while dissociation of the C(alpha)bond;CH(2)C(6)H(5) bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation-radicals that have thermal (298 K) energies and thus behave ergodically.