Protonated and Sodiated Cyclophosphamide Fragmentation Pathways Evaluation by Infrared Multiple Photon Dissociation Spectroscopy

Cyclophosphamide (CP or CTX) is a widely used antineoplastic agent, and the evaluation of its efficacy and its impacts on the environment are dependent on tandem mass spectrometry (MSⁿ) techniques. Because there is no dedicated experimental study to characterize the actual molecular nature of the CP fragments upon collision-induced dissociation, this work evaluated the chemical structure of the fragments of protonated and sodiated CP and CP protonation sites by infrared multiple photon dissociation spectroscopy supported by density functional theory calculations. This study allowed us to propose a new fragment structure and confirm the nature of multiple fragments, including those relevant for transitions used for CP quantitative and qualitative analyses. Our results also show that there is no spectroscopic evidence that can rule out the existence of aziridinium fragments, making it clear that further studies on the nature of iminium/aziridinium fragments in the gas phase are necessary.

A novel method for photon unfolding spectroscopy of protein ions in the gas phase

In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]¹³⁺ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]¹⁵⁺, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.

The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O( N^1.13-1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y ) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.

Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations

Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-C_α bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c₃- and c₄-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm^-1 serves as an important diagnostic feature.

Deamidation of Protonated Asparagine-Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study

Peptide deamidation of asparaginyl residues is a spontaneous post-translational modification that is believed to play a role in aging and several diseases. It is also a well-known small-molecule loss channel in the MS/MS spectra of protonated peptides. Here we investigate the deamidation reaction, as well as other decomposition pathways, of the protonated dipeptide asparagine-valine ([AsnVal + H]+) upon low-energy activation in a mass spectrometer. Using a combination of infrared ion spectroscopy, guided ion beam tandem mass spectrometry, and theoretical calculations, we have been able to identify product ion structures and determine the energetics and mechanisms for decomposition. Deamidation proceeds via ammonia loss from the asparagine side chain, initiated by a nucleophilic attack of the peptide bond oxygen on the γ-carbon of the Asn side chain. This leads to the formation of a furanone ring containing product ion characterized by a threshold energy of 129 ± 5 kJ/mol (15 kJ/mol higher in energy than dehydration of [AsnVal + H]+, the lowest energy dissociation channel available to the system). Competing formation of a succinimide ring containing product, as has been observed for protonated asparagine-glycine ([AsnGly + H]+) and asparagine-alanine ([AsnAla + H]+), was not observed here. Quantum-chemical modeling of the reaction pathways confirms these subtle differences in dissociation behavior. Measured reaction thresholds are in agreement with predicted theoretical reaction energies computed at several levels of theory.

Charge-state Resolved Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of Ubiquitin Ions in the Gas Phase

In this study, we obtained for the first time the direct infrared multiple photon dissociation (IRMPD) spectra of ubiquitin ions in the range 2700-3750 cm-1. Ubiquitin ions with different charge states showed absorption in the two regions of 2940-3000 cm-1 and 3280-3400 cm-1. The increase of the charge state of ubiquitin ions broadened the absorption peak on the high-frequency side in the second region, indicating some hydrogen bonds were weakened due to Coulomb interaction. It is also found that the relative intensity of the absorption peak in the first region compared to the absorption peak in the second region increased with increasing charge state, making the IRMPD spectra charge-state resolved. Although it is usually reasonable to suggest the origin of the absorption in the range 2940-3000 cm-1 as the C-H bond stretching modes, the results show significantly reduced absorption after the deuteration of all labile hydrogen atoms. A possible explanation for this is that the coupling coefficients between the C-H vibrational mode and other selective modes decreased greatly after the deuteration, reducing the rate of energy redistribution and probability of consecutive IR absorption.

Gas-Phase Protein Salt Bridge Stabilities from Collisional Activation and Electron Transfer Dissociation

The gas phase structures of several proteins have been studied by electron transfer dissociation (ETD) with and without prior collisional heating after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Without prior collisional heating, we find that ETD fragmentation is mostly limited to regions of the protein that are not spanned by the salt bridges known to form in solution. When protein ions are collisionally heated before ETD, new product ions are observed, and in almost all cases, these new ions arise from protein regions that are spanned by the salt bridges. Together these results confirm the existence of salt bridges in protein ions and demonstrate that a sufficient amount energy is required to disrupt these salt bridges in the gas phase. More interestingly, we also show that different salt bridges require different collisional activation voltages to be disrupted, suggesting that they have variable stabilities in the gas phase. These stabilities appear to be influenced by the gas-phase basicities of the involved residues and the presence of nearby charged residues. We also find that higher collisional activation voltages are needed to enable the formation of new product from sites spanned by multiple salt bridges.

Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N-methylacetamide molecules in the mid-IR spectral range of 1000-1800  cm^{-1}, utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N-methylacetamide are measured in the full amide I-III range.

Retention of Native Protein Structures in the Absence of Solvent: A Coupled Ion Mobility and Spectroscopic Study

Can the structures of small to medium‐sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion‐mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β‐lactoglobulin, which are prototypical examples of helical and β‐sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved.

Mid-infrared spectroscopy for protein analysis: potential and challenges

Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.

Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate

Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.

Structure and conformation of protonated D-(+)-biotin in the unsolvated state

A combined computational and infrared multiphoton dissociation (IRMPD) spectroscopic investigation shows that protonated d-(+)-biotin, formed in the gas phase by ESI-MS, acquires a folded structure with proton bonding between the ureido and valeryl carbonyls, and that only a single conformer of such a structure predominates. A uniform frequency vs distance correlation function is proposed for the O(+)-H···O and N-H···O bonds involved in the folded conformers of O2'-protonated d-(+)-biotin in the gas phase which, therefore, depends exclusively on the corresponding geometric parameters.

Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.

Kinetic control in the CID-induced elimination of H3PO4 from phosphorylated serine probed using IRMPD spectroscopy

InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy was used to assay the structural features of the fragment ions resulting from the elimination of H3PO4 in the Collision-Induced Dissociation (CID) of protonated serine. The results are interpreted with the aid of density functional theory calculations. Experiment and theory point to an aziridine-ring structure, implying participation of the vicinal amino group in the formation of this species. This finding constitutes a benchmark for investigating the same process in the CID of phosphorylated peptides.

Discrimination of 4-hydroxyproline diastereomers by vibrational spectroscopy of the gaseous protonated species

Hydroxylation of proline is a prominent oxidative post-translational modification (oxPTM) in animals, characterized by site specificity and stereochemical control. The presence of this irreversible modification and the ensuing generation of a chiral center have been assayed in (2S,4R)-4-hydroxyproline and (2S,4S)-4-hydroxyproline forming the protonated species by electrospray ionization and sampling them by infrared multiple photon dissociation (IRMPD) spectroscopy. IRMPD spectra, recorded both in the 950-1950 cm(-1) (using the CLIO free electron laser) and in the 3200-3700 cm(-1) [using a tabletop parametric oscillator/amplifier (OPO/OPA) laser] regions, have been interpreted by comparison with the absorbance spectra of the lowest energy structures calculated at MP2/6-311+G** level of theory. Remarkable spectral differences have emerged in the fingerprint region, pointing to the unambiguous discrimination between S,R and S,S diastereomers. The main differences arise from the position of the carbonyl stretching mode, a signature of nonzwitterionic structures, moving from 1750 cm(-1) for the S,R form to 1770 cm(-1) for the S,S diastereomer. Furthermore, a well-defined band associated with the NH(2) wagging mode at 1333 cm(-1) is a distinct mark of the S,S isomer. Each gaseous protonated epimer comprises a population of at least three conformers, stabilized by intramolecular hydrogen bonds linking the two hydrogens of protonated secondary amine group with the 4-hydroxy substituent and with an oxygen atom of the carboxylic group, respectively. Interestingly, a tendency to adopt either C(4)-exo (up) or C(4)-endo (down) pyrrolidine puckering upon proline 4(R)- or 4(S)-hydroxylation, respectively, is observed here. The same bias is found in neutral hydroxyprolines and in collagen model peptides. In the protonated species under examination, this bias originates chirality-induced vibrational features revealed by IRMPD spectroscopy.

Chirality effects on the IRMPD spectra of basket resorcinarene/nucleoside complexes

The IRMPD spectra of the ESI-formed proton-bound complexes of the R,R,R,R- and S,S,S,S-enantiomers of a bis(diamido)-bridged basket resorcin[4]arene (R and S) with cytosine (1), cytidine (2), and cytarabine (3) were measured in the region 2800-3600 cm(-1). Comparison of the IRMPD spectra with the corresponding ONIOM (B3LYP/6-31(d):UFF)-calculated absorption frequencies allowed the assessment of the vibrational modes that are responsible for the observed spectroscopic features. All of the complexes investigated, apart from [R⋅H⋅3](+), showed similar IRMPD spectra, which points to similar structural and conformational landscapes. Their IRMPD spectra agree with the formation of several isomeric structures in the ESI source, wherein the N(3)-protonated guest establishes noncovalent interactions with the host amidocarbonyl groups that are either oriented inside the host cavity or outside it between one of the bridged side-chains and the upper aromatic nucleus. The IRMPD spectrum of the [R⋅H⋅3](+) complex was clearly different from the others. This difference is attributed to the effect of intramolecular hydrogen-bonding interactions between the C(2')-OH group and the aglycone oxygen atom of the nucleosidic guest upon repulsive interactions between the same oxygen atom and the aromatic rings of the host.

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.

Chirality-induced conformational preferences in peptide-metal ion binding revealed by IR spectroscopy

Chirality reversal of a residue in a peptide can change its mode of binding to a metal ion, as shown here experimentally by gas-phase IR spectroscopy of peptide-metal ion complexes. The binding conformations of Li(+), Na(+), and H(+) with the LL and DL stereoisomers of PhePhe were compared through IR ion spectroscopy using the FELIX free-electron laser. For the DL isomer, both Li(+) and Na(+) exclusively coordinate to the amide O atom, the carboxyl O atom, and one of the aromatic rings (the OOR conformation), while for the LL isomer, a mixture of the OOR and NOR conformations was found. The stereochemically induced change in conformation is shown to reflect the strength of an NH···π interaction remote from the metal ion site. Protonated PhePhe shows no stereochemically induced variation in binding geometry.