IR Multiple Photon Dissociation Spectroscopy Research Articles

IRMPD spectroscopy and quantum-chemical simulations of the reaction products of cisplatin with the dipeptide CysGly

The inorganic antineoplastic drug cisplatin was made to react in solution with the dipeptide cysteinylglycine (CysGly), chosen as a functional model of glutathione, and the reaction products were analyzed using electrospray ionization mass spectrometry (ESI-MS). Selected complexes, i.e., the primary substitution product cis-[PtCl(NH3)2(CysGly)]+ and the chelate cis-[PtCl(NH3)(CysGly)]+, were submitted to IR multiple photon dissociation (IRMPD) spectroscopy obtaining their vibrational features. The experimental IR ion spectra were compared with the calculated IR absorptions of different plausible isomeric families, finding CysGly to bind preferentially platinum(II) via its deprotonated thiolic group in the monovalent complex, cis-[PtCl(NH3)2(CysGly)]+, and to evolve in the S,N-bound chelate structure cis-[PtCl(NH3)(CysGly)]+ through the SH and NH2 functionality of the cysteine residue. Moreover, our findings indicate that the platination reaction does not affect the CysGly peptide bond, which remains in its trans configuration.These results provide additional insights into the reactivity of Pt(II)-complexes with glutathione which is involved in cellular cisplatin resistance.

Protonated Forms of Naringenin and Naringenin Chalcone: Proteiform Bioactive Species Elucidated by IRMPD Spectroscopy, IMS, CID-MS, and Computational Approaches.

Naringenin (Nar) and its structural isomer, naringenin chalcone (ChNar), are two natural phytophenols with beneficial health effects belonging to the flavonoids family. A direct discrimination and structural characterization of the protonated forms of Nar and ChNar, delivered into the gas phase by electrospray ionization (ESI), was performed by mass spectrometry-based methods. In this study, we exploit a combination of electrospray ionization coupled to (high-resolution) mass spectrometry (HR-MS), collision-induced dissociation (CID) measurements, IR multiple-photon dissociation (IRMPD) action spectroscopy, density functional theory (DFT) calculations, and ion mobility-mass spectrometry (IMS). While IMS and variable collision-energy CID experiments hardly differentiate the two isomers, IRMPD spectroscopy appears to be an efficient method to distinguish naringenin from its related chalcone. In particular, the spectral range between 1400 and 1700 cm-1 is highly specific in discriminating between the two protonated isomers. Selected vibrational signatures in the IRMPD spectra have allowed us to identify the nature of the metabolite present in methanolic extracts of commercial tomatoes and grapefruits. Furthermore, comparisons between experimental IRMPD and calculated IR spectra have clarified the geometries adopted by the two protonated isomers, allowing a conformational analysis of the probed species.

Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound?

Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and the hydroxyl radical (•OH) have specific functions in biological processes, while their uncontrolled production and reactivity are known to be determining factors in pathophysiology. Methionine (Met) residues act as endogenous antioxidants, when they are oxidized into methionine sulfoxide (MetSO), thus depleting ROS and protecting the protein. We employed tandem mass spectrometry combined with IR multiple photon dissociation spectroscopy to study the oxidation induced by OH radicals produced by γ radiolysis on model cyclic dipeptides c(LMetLMet), c(LMetDMet), and c(GlyMet). Our aim was to characterize the geometries of the oxidized peptides in the gas phase and to understand the relationship between the structure of the 2-center 3-electron (2c-3e) free radical formed in the first step of the oxidation process and the final compound. Density functional theory calculations were performed to characterize the lowest energy structures of the final product of oxidation and to interpret the IR spectra. Collision-induced dissociation tandem mass spectrometry (CID-MS2) experiments of oxidized c(LMetLMet)H+ and c(LMetDMet)H+ led to the loss of one or two oxidized sulfenic acid molecules, indicating that the addition of one or two oxygen atoms occurs on the sulfur atom of both methionine side chains and no sulfone formation was observed. The CID-MS2 fragmentation mass spectrum of oxidized c(GlyMet)H+ showed only the loss of one oxidized sulfenic acid molecule. Thus, the final products of oxidation are the same regardless of the structure of the precursor sulfur-centered free radical.

Reactivity of Indolylmethylacetates with N, O, and S Soft Nucleophiles: Evidence of 2‐Alkylideneindolenines and 3‐Alkylideneindoleninium Generation by ESI‐MS and IRMPD Spectroscopy

AbstractThe synthesis of (aminomethyl), (tosylmethyl), and (aryloxymethyl) indoles starting from indolylmethylacetates and N, O, and S soft nucleophiles has been developed. ESI‐MS and IR multiple‐photon dissociation (IRMPD) spectroscopy analyses confirm the reaction proceeds through a conjugate addition of the nucleophile to 2‐alkylideneindolenines and 3‐alkylideneindoleninium.

Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes.

Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]−, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.

IR multiple photon dissociation spectroscopy of MO2 + (M = V, Nb, Ta).

A laser vaporization cluster source is coupled to the Fourier-transform ion cyclotron resonance mass spectrometer beamline of the free-electron laser for intracavity experiments. Gas phase metal ions and their oxides (VO2 +, NbO2 +, and TaO2 +) are formed and spectroscopically characterized using IR multiple-photon dissociation spectroscopy via loss of atomic oxygen and overcoming fragmentation energies of 3 eV-6 eV. The signal is observed for all MO2 + fundamental modes: the symmetric and anti-symmetric ν1 and ν3 stretch modes in the 900 cm-1-1000 cm-1 range and the ν2 bending mode in the 300 cm-1-450 cm-1 range. A remarkable substructure is observed for the bending vibration, which is at least partly due to the rovibrational substructure.

Can an Elusive Platinum(III) Oxidation State be Exposed in an Isolated Complex?

AbstractPlatinum(IV) complexes are extensively studied for their activity against cancer cells as potential substitutes for the widely used platinum(II) drugs. PtIV complexes are kinetically inert and need to be reduced to PtII species to play their pharmacological action, thus acting as prodrugs. The mechanism of the reduction step inside the cell is however still largely unknown. Gas‐phase activation of deprotonated platinum(IV) prodrugs was found to generate products in which platinum has a formal +3 oxidation state. IR multiple photon dissociation spectroscopy is thus used to obtain structural information helping to define the nature of both the platinum atom and the ligands. In particular, comparison of calculations at DFT, MP2 and CCSD levels with experimental results demonstrates that the localization of the radical is about equally shared between the dxz orbital of platinum and the pz of nitrogen on the amino group, the latter acting as a non‐innocent ligand.

Can an Elusive Platinum(III) Oxidation State be Exposed in an Isolated Complex?

Platinum(IV) complexes are extensively studied for their activity against cancer cells as potential substitutes for the widely used platinum(II) drugs. PtIV complexes are kinetically inert and need to be reduced to PtII species to play their pharmacological action, thus acting as prodrugs. The mechanism of the reduction step inside the cell is however still largely unknown. Gas-phase activation of deprotonated platinum(IV) prodrugs was found to generate products in which platinum has a formal +3 oxidation state. IR multiple photon dissociation spectroscopy is thus used to obtain structural information helping to define the nature of both the platinum atom and the ligands. In particular, comparison of calculations at DFT, MP2 and CCSD levels with experimental results demonstrates that the localization of the radical is about equally shared between the dxz orbital of platinum and the pz of nitrogen on the amino group, the latter acting as a non-innocent ligand.

IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions

Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH+ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH+ and m-OH-BZH+ only cis conformers are present in the ion population analyzed. For o-OH-BZH+ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH+ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH+ , m-OH-BZH+ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.

Off-line coupling of capillary isotachophoresis separation to IRMPD spectroscopy for glycosaminoglycans analysis: Application to the chondroitin sulfate disaccharides model solutes

Glycans analysis is challenging due to their immense structural diversity. Isotachophoresis was investigated as separation method for the purification of isobaric sulfated disaccharides prior to their characterization by Mass Spectrometry (MS) and tunable IR multiple photon dissociation (IRMPD). This proof of feasibility study was applied to the separation and characterization of chondroitin sulfate (CS) disaccharides. ITP separation conditions were optimized. Separation starts using a 2.5 mM chloride ions and 10 mM glycine at pH 3.2 solution as leading electrolyte and a terminating electrolyte composed of formic acid 2.5 mM and glycine 10 mM at pH 3.5. The CS disaccharides sample were prepared in the terminating electrolyte. The length of injection was also investigated in order to create longer plateau-like bands of pure solutes. This strategy was helpful for collecting fraction at such microseparation scale. Indeed, capillary ITP affords the injection of few tens of nanoliter of sample. Fractionation of the CS disaccharides mixture in isolated ITP bands and collection of solutes were successfully done using a HPC coated fused silica capillary of 1m-length and 75 µm of internal diameter. Collected fractions in a final of volume 10 µL were analyzed by CZE, tandem MS and IRMPD spectroscopy. The purity of each fraction is higher than 90% and is well-adapted to IRMPD characterization.

One-Electron Oxidation of Methionine-Containing Dipeptides of Reverse Sequence: Sulfur versus Sulfoxide Characterized by IRMPD Spectroscopy and Static and Dynamics DFT Simulations.

Gas-phase structural modifications induced by the oxidation of methionine of the two peptides of reverse sequence, methionine-valine (Met-Val) and valine-methionine (Val-Met), have been studied by mass-selected IR multiple photon dissociation (IRMPD) spectroscopy in the 800-2000 cm-1 fingerprint range at the Centre Laser Infrarouge d'Orsay free-electron laser facility. The oxidation has been achieved by •OH radicals generated by γ radiolysis. IRMPD spectra were interpreted by static and harmonic DFT calculations and Born-Oppenheimer molecular dynamics simulations, which are employed to take into account all anharmonic and finite-temperature effects. The diagnostic signature of the sulfoxide group in the final products of Met-Val and Val-Met oxidations, which is missing in the spectra of native peptides, has been recorded. Evidence has also been gathered that a mixture of R and S isomers of close energies is formed. An interconversion between different isomers has been unveiled in the case of the oxidized Met-Val dipeptide.

Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy.

The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH3 )2 (histidine)]+ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.

Cisplatin Binding to Biological Ligands Revealed at the Encounter Complex Level by IR Action Spectroscopy.

Cisplatin [cis-diamminedichloroplatinum(II)] was the first platinum-based antineoplastic agent and is still a cornerstone for the treatment of various solid tumors. Reactive events responsible for cisplatin activity are unveiled here at the molecular level. Simple ligands (L) representing ubiquitous functional groups in the biological environment likely to be encountered by administered cisplatin have been allowed to react with cis-[PtCl(NH3)2 (H2O)](+), the primary intermediate from cisplatin hydrolysis. The substitution reactions have been examined by a combined experimental and computational approach and the structural features of the substitution product, cis-[PtCl(NH3)2(L)](+), have been probed by IR multiple-photon dissociation (IRMPD) spectroscopy. Furthermore, IRMPD spectroscopy has been exploited to elucidate the structure of [PtCl(NH3)2(L)(H2O)](+) clusters, also obtained by electrospray ionization (ESI) from the aqueous solution and representing the major focus of this investigation. These ions conform to the encounter complex of cis-[PtCl(NH3)2 (H2O)](+) with the incoming ligand and represent the first direct evidence of a prototypical Eigen-Wilkins encounter complex in solution, lying on the reaction coordinate for ligand substitution and extracted by ESI for mass spectrometric analysis. Activated [PtCl(NH3)2(L)(H2O)](+) ions dissociate by the loss of either H2O or L, the former process implying a ligand substitution event. IRMPD spectroscopy has thus revealed both structural details and reaction dynamics at the level of the isolated encounter complex.

Oxidation of methionine-containing peptides by [rad]OH radicals: Is sulfoxide the only product? Study by mass spectrometry and IRMPD spectroscopy

Although the first steps of the oxidation of methionine containing peptides by OH radicals have been very well documented, not much is known about the final products. They have been characterized and unraveled by mass spectrometry and IR Multiple Photon Dissociation (IRMPD) spectroscopy carried out with model dipeptides and methionine enkephalin, often involving the transformation of residues other than methionine. Several products were found, in addition to methionine sulfoxide, which is omnipresent. Thus IRMPD proved to be very useful in oxidative proteomics.

Cyanide–Arene Meisenheimer Complex Generated in Electrospray Ionization Mass Spectrometry Using Acetonitrile as a Solvent

The C - C bond formation activated under negative electrospray ionization of an acetonitrile solution of 1,3,5-trinitrobenzene is reported. The solvent function is to provide a source of cyanide ion, a highly problematic reagent, which is found to attack the electron-deficient aromatic ring to form a covalently bound anionic complex (Meisenheimer complex). The structure of the complex is elucidated by means of collision induced dissociation mass spectrometry and IR multiple photon dissociation spectroscopy in the 'fingerprint' region.

Halide adducts of 1,3,5-trinitrobenzene: Vibrational signatures and role of anion–π interactions

The fluoride and chloride complexes with 1,3,5-trinitrobenzene (TNB–F− and TNB–Cl−) are obtained as gaseous species by electrospray ionization and are assayed by IR multiple photon dissociation spectroscopy along with quantum chemical calculations. The stable structure is quite different for the two complexes. A strongly covalent σ-complex (Meisenheimer complex) holding fluorine on a tetrahedral carbon at a formerly unsubstituted ring position is the stable form of TNB–F− while a σ-complex with fluorine bound to a nitro-substituted carbon is 78kJ/mol higher in energy. The TNB–Cl− complex presents an off-center binding of chlorine placed above a CH group of a scantily perturbed TNB unit. This structure conforms to a weak σ-binding motif. The observed vibrational features support two diverse binding motifs and previous findings about TNB–I− and TNB–Br− show the transition to occur between the fluoride and chloride adducts while both I− and Br− complexes are consistent with a weak σ-binding motif. Implication of these results is expected in the design of halide ion transporters.

ChemInform Abstract: High Magnetic Moments in Manganese‐Doped Silicon Clusters.

AbstractManganese‐doped silicon clusters SinMn+ (n = 6—10, 12—14, 16) are characterized by IR multiple photon dissociation spectroscopy and DFT calculations.

S-nitrosation of cysteine as evidenced by IRMPD spectroscopy

S-nitrosation of cysteine plays an important role in storage and transport of NO, a key signaling molecule in vivo. An approach to detect this modification in the bare, charged amino acid is presented, based on IR multiple photon dissociation (IRMPD) spectroscopy. Protonated and deprotonated S-nitrosocysteine ions, [SNOCys+H]+ and [SNOCys−H]−, have been obtained by electrospray ionization and assayed for IR activity in either the 1000–1900cm−1 or the 3000–3600cm−1 wavenumber range. The so-obtained IRMPD spectra display characteristic features ascribed to the presence of the S-nitrosation motif, which are missing in the corresponding IRMPD spectra of the native cysteine ions, [Cys+H]+ and [Cys−H]−. In particular, the NO stretching mode is unambiguously identified by the red shift observed for the 15N-labelled species. The interpretation of the IRMPD spectra is supported by density functional theory calculations of the optimized geometries, relative energies and IR spectra of [SNOCys+H]+ and [SNOCys−H]−. Both sampled ions comprise a thermally averaged population of conformers contributing to the experimental IRMPD spectra. This notion is supported by the agreement between the calculated IR absorption spectra of the several conformers, and the recorded IRMPD spectrum. The gathered evidence points to a characteristic NO stretching mode that emerges as a pronounced feature at 1460–1490cm−1 in the IRMPD spectrum of [SNOCys−H]−, namely in a region where [Cys−H]− displays no IRMPD activity. Conversely, the NO stretching vibration of [SNOCys+H]+ is enclosed in a wide absorption including the CO stretching mode at 1780cm−1. The [SNOCys−H]− negative ions are thus a promising benchmark in a search for S-nitrosation features using IRMPD spectroscopy.

Gas-phase structures of neutral silicon clusters

Vibrational spectra of neutral silicon clusters Si(n), in the size range of n = 6-10 and for n = 15, have been measured in the gas phase by two fundamentally different IR spectroscopic methods. Silicon clusters composed of 8, 9, and 15 atoms have been studied by IR multiple photon dissociation spectroscopy of a cluster-xenon complex, while clusters containing 6, 7, 9, and 10 atoms have been studied by a tunable IR-UV two-color ionization scheme. Comparison of both methods is possible for the Si(9) cluster. By using density functional theory, an identification of the experimentally observed neutral cluster structures is possible, and the effect of charge on the structure of neutrals and cations, which have been previously studied via IR multiple photon dissociation, can be investigated. Whereas the structures of small clusters are based on bipyramidal motifs, a trigonal prism as central unit is found in larger clusters. Bond weakening due to the loss of an electron leads to a major structural change between neutral and cationic Si(8).

Tyrosine nitration as evidenced by IRMPD spectroscopy

Protonated 3-nitrotyrosine ([nitroTyr + H] +) has been investigated by collision induced dissociation at variable energy and by IR multiple photon dissociation (IRMPD) spectroscopy in conjunction with quantum chemical calculations. Ultimately, this investigation is aimed at providing a diagnostic signature of protein tyrosine nitration, a post translational modification implied in pathological states. IRMPD spectroscopy of [nitroTyr + H] + ions has been examined in two different spectral regions, namely in the 1000–2000 cm −1 range, using the free electron laser beamline at the CLIO facility, and in the 3200–3700 cm −1 range, using a tabletop laser source. [nitroTyr + H] + ions have been assayed in parallel with intact [Tyr + H] + ions revealing characteristic bands at 1329 and 1540 cm −1. Mode assignments allowed by density functional theory calculations of the IR spectra of the most stable conformers indicate that these features are associated to vibrations of the nitro group and are endowed with enhanced activity. In the NH/OH stretching region, the remarkable difference between the IRMPD spectra is the strong absorption at 3641 cm −1 of the ring OH stretching of [Tyr + H] + which is absent in the nitrated ion due to a strong hydrogen bond engaging the ring OH and the ortho nitro group. These results suggest that IRMPD spectroscopy and tandem mass spectrometry may afford a selective method for the analysis and characterization of 3-nitrotyrosine, to be possibly extended to 3-nitrotyrosine-containing peptides.