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Liquid chromatography-mass spectrometry (LC-MS) is, due to its high sensitivity and selectivity, currently the method of choice in (bio)analytical studies involving the (comprehensive) profiling of metabolites in body fluids. However, as closely related isomers are often hard to distinguish on the basis of LC-MS(MS) and identification is often dependent on the availability of reference standards, the identification of the chemical structures of detected mass spectral features remains the primary limitation. Infrared ion spectroscopy (IRIS) aids identification of MS-detected ions by providing an infrared (IR) spectrum containing structural information for a detected MS-feature. Moreover, IR spectra can be routinely and reliably predicted for many types of molecular structures using quantum-chemical calculations, potentially avoiding the need for reference standards. In this work, we demonstrate a workflow for reference-free metabolite identification that combines experiments based on high-pressure liquid chromatography (HPLC), MS and IRIS with quantum-chemical calculations that efficiently generate IR spectra and give the potential to enable reference-standard free metabolite identification. Additionally, a scoring procedure is employed which shows the potential for automated structure assignment of unknowns. Via a simple, illustrative example where we identify lysine in the plasma of a hyperlysinemia patient, we show that this approach allows the efficient assignment of a database-derived molecular structure to an unknown.

Gas-phase conformations of the sodium-cationized forms of the 2′-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]+ and [pCyd+Na]+, are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na]+ and [pCyd+Na]+ involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.

L-Thymidine (L-dThd) is the enantiomer of D-thymidine (dThd), a naturally-occurring pyrimidine nucleoside found within DNA nucleic acids. L-dThd, also known as Telbivudine, does not occur naturally, but in the last decade has found successful application as an antiviral medication for hepatitis B virus infection. In this work, the gas-phase conformers of the protonated and sodium cationized forms of L-dThd, [L-dThd+H]+ and [L-dThd + Na]+, are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy complemented by electronic structure calculations performed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. Comparisons between the experimental IRMPD spectra and theoretical linear IR spectra elucidate the stable low-energy conformations adopted by these L-dThd complexes generated by electrospray ionization. Minor 2,4-dihydroxy tautomers (T) and O2 protonated conformers contribute to the experimental [L-dThd+H]+ population, whereas conformers involving tridentate binding of Na+ to the O2, O4′, and O5′ atoms primarily contribute to the experimental [L-dThd + Na]+ population. Theory predicts a tautomer as the protonated ground conformer of [L-dThd+H]+ with thymine in an anti orientation and a tridentate (O2O4′O5′) sodium cationized ground conformer with a syn thymine orientation, consistent with theoretical predictions for [dThd+H]+ and [dThd + Na]+, respectively. Both protonated and sodium cationized L-dThd and dThd illustrate highly parallel IRMPD spectral features as expected. Survival yield analyses of data from energy-resolved collision-induced dissociation experiments elucidate the relative stabilities of [L-dThd+H]+ and [L-dThd + Na]+ as compared to the corresponding enantiomeric systems. Identical results are exhibited in the survival yield analyses as anticipated for enantiomeric complexes to simple cations. This work employs the same robust methodology that has provided structural characterization and energetic insight for similar systems preceding it to validate the parallel theoretical and experimental behaviors expected for enantiomers.

Infrared multiple photon dissociation action spectroscopy was performed on the AlaOrn b(2)(+) and AlaAlaOrn b(3)(+) fragment ions from ornithine-containing tetrapeptides. Infrared spectra were obtained in the fingerprint region (1000 – 2000 cm(−1)) using the infrared free electron lasers at the Centre Laser Infrarouge d’Orsay (CLIO) facility in Orsay, France and the Free Electron Lasers for Infrared eXperiments (FELIX) facility in Nijmegen, the Netherlands. A novel terminal ornithine lactam AO(+) b2(+) structure was synthesized for experimental comparison and spectroscopy confirms that the b2(+) fragment ion from AOAA forms a lactam structure. Comparison of experimental spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory shows that AO(+) b(2)(+) forms a terminal lactam protonated either on the lactam carbonyl oxygen or the N-terminal nitrogen atom. Several low-lying conformers of these isomers are likely populated following IRMPD dissociation. Similarly, a comparison of the experimental IRMPD spectrum with calculated spectra shows that AAO(+) b(3)(+)-ions also adopt a lactam structure, again with multiple different protonation sites, during fragmentation. This study provides spectroscopic confirmation for the lactam cyclization proposed for the “ornithine effect” and represents an alternative b(n)(+) structure to the oxazolone and diketopiperazine/macrocycle structures most often formed.

Electrospray ionization was used to generate species such as [ZnNO3(CH3OH)2]+ from Zn(NO3)2•XH2O dissolved in a mixture of CH3OH and H2O. Collision-induced dissociation of [ZnNO3(CH3OH)2]+ causes elimination of CH3OH to form [ZnNO3(CH3OH)]+. Subsequent collision-induced dissociation of [ZnNO3(CH3OH)]+ causes elimination of 47 mass units (u), consistent with ejection of HNO2. The neutral loss shifts to 48 u for collision-induced dissociation of [ZnNO3(CD3OH)]+, demonstrating the ejection of HNO2 involves intra-complex transfer of H from the methyl group methanol ligand. Subsequent collision-induced dissociation causes the elimination of 30 u (32 u for the complex with CD3OH), suggesting the elimination of formaldehyde (CH2 = O). The product ion is [ZnOH]+. Collision-induced dissociation of a precursor complex created using CH3-18OH shows the isotope label is retained in CH2 = O. Density functional theory calculations suggested that the “rearranged” product, ZnOH with bound HNO2 and formaldehyde is significantly lower in energy than ZnNO3 with bound methanol. We therefore used infrared multiple-photon photodissociation spectroscopy to determine the structures of both [ZnNO3(CH3OH)2]+ and [ZnNO3(CH3OH)]+. The infrared spectra clearly show that both ions contain intact nitrate and methanol ligands, which suggests that rearrangement occurs during collision-induced dissociation of [ZnNO3(CH3OH)]+. Based on the density functional theory calculations, we propose that transfer of H, from the methyl group of the CH3OH ligand to nitrate, occurs in concert with the formation of a Zn–C bond. After dissociation to release HNO2, the product rearranges with the insertion of the remaining O atom into the Zn–C bond. Subsequent C–O bond cleavage, with H transfer, produces an ion–molecule complex composed of [ZnOH]+ and O = CH2.

Uranium trioxide, UO

Untargeted LC-MS based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing “grand challenge” in the utilization of this approach is metabolite identification – confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids, and are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly rendered novel insights in the pathophysiology of PDE-ALDH7A1.

Pyridoxine-dependent epilepsy (PDE-ALDH7A1), also known as antiquitin deficiency, is an inborn error of lysine metabolism that presents with refractory epilepsy in newborns. Bi-allelic ALDH7A1 variants lead to deficiency of α-aminoadipic semialdehyde dehydrogenase, resulting in accumulation of piperideine-6-carboxylate (P6C), and secondary deficiency of the important co-factor pyridoxal-5’-phosphate (PLP, active vitamin B6) through its complexation with P6C. Vitamin B6 supplementation resolves epilepsy in patients, but despite this treatment, intellectual disability may occur. Early diagnosis and treatment, preferably based on newborn screening, potentially optimize long-term clinical outcome. However, the currently known diagnostic PDE-ALDH7A1 biomarkers are incompatible with newborn screening procedures. Using a combination of the innovative analytical methods untargeted metabolomics and infrared ion spectroscopy, we have been able to discover novel biomarkers for PDE-ALDH7A1: 2S,6S-and 2S,6R-oxopropylpiperidine-2-carboxylic acid (2-OPP) and 6-oxopiperidine-2-carboxylic acid (6-oxoPIP). We demonstrate the applicability of 2-OPP as a PDE-ALDH7A1 biomarker in newborn screening. Additionally, we show that 2-OPP accumulates in brain tissue of patients and Aldh7a1 knock-out mice, and induces epilepsy-like behavior in a zebrafish model system. We speculate that 2-OPP may contribute to ongoing neurotoxicity, also in treated PDE-ALDH7A1 patients. As 2-OPP formation appears to increase upon ketosis, we emphasize the importance of avoiding catabolism in PDE-ALDH7A1 patients.

The capability of an ion trap mass spectrometer to store ions for an arbitrary amount of time allows the use of a single infrared (IR) laser to perform two-color double resonance IR–IR spectroscopic experiments on mass-to-charge (m/z) selected ions. In this single-laser IR2MS3 scheme, one IR laser frequency is used to remove a selected set of isomers from the total trapped ion population and the second IR laser frequency, from the same laser, is used to record the IR spectrum of the remaining precursor ions. This yields isomer-specific vibrational spectra of the m/z-selected ions, which can reveal the structure and identity of the initially co-isolated isomeric species. The use of a single laser greatly reduces the experimental complexity of two-color IR2MS3 and enhances its application in fields employing analytical MS. In this work, we demonstrate the methodology by acquiring single-laser IR2MS3 spectra in a forensic context, identifying two previously unidentified isomeric novel psychoactive substances (NPS) from a sample that was confiscated by the Amsterdam Police.

The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone. Prototypic native crown ethers (12-crown-4, 15-crown-5 and 18-crown-6) and aza-crown ethers (cyclen, 1-aza-18-crown-6 and hexacyclen) are investigated. For each system, Infrared action spectroscopy experiments and ab initio Molecular Dynamics computations are employed to elucidate the structural effects associated with proton diffusion and its entanglement with the conformational and vibrational dynamics of the protonated host.

The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser and an optical parametric oscillator laser system. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP-GD3BJ/6-311+G(d,p) level of theory. These comparisons show that protonated UDMH binds the proton at the methylated nitrogen atom (α) with two low-lying α conformers probably being populated. For (UDMH)2H+, the proton is shared between the methylated nitrogen atoms with several low-lying α conformers likely to be populated. Higher-lying conformers of (UDMH)2H+ in which the proton is shared between α and β (unmethylated) nitrogen atoms cannot be ruled out on the basis of the IRPMD spectrum. For (N2H4)2H+, there are four low-lying conformers that all reproduce the IRMPD spectrum reasonably well. As hydrazine and UDMH see usage as fuels for rocket engines, such spectra are potentially useful as a means of remotely monitoring rocket launches, especially in cases of unsuccessful launches where environmental hazards need to be assessed.

The identification of disease biomarkers plays a crucial role in developing diagnostic strategies for inborn errors of metabolism and understanding their pathophysiology. A primary metabolite that accumulates in the inborn error phenylketonuria is phenylalanine, however its levels do not always directly correlate with clinical outcomes. Here we combine infrared ion spectroscopy and NMR spectroscopy to identify the Phe-glucose Amadori rearrangement product as a biomarker for phenylketonuria. Additionally, we find analogous amino acid-glucose metabolites formed in the body fluids of patients accumulating methionine, lysine, proline and citrulline. Amadori rearrangement products are well-known intermediates in the formation of advanced glycation end-products and have been associated with the pathophysiology of diabetes mellitus and ageing, but are now shown to also form under conditions of aminoacidemia. They represent a general class of metabolites for inborn errors of amino acid metabolism that show potential as biomarkers and may provide further insight in disease pathophysiology., Rianne van Outersterp et al. combine mass spectrometry, NMR, and infrared ion spectroscopy to identify amino acid-hexose conjugates in the blood plasma from patients with metabolic disorders such as phenylketonuria (PKU). These conjugates, or Amadori rearrangement products, are generally not detectable in blood samples from unaffected individuals, and may therefore represent disease biomarkers.

Metallated gas-phase structures consisting of an intact and deprotonated histidine (His) ligand, M(His-H)(His)+, where M = Ca and Ni, were examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, ab initio quantum-chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using the 6-311+G(d,p) basis set. Single-point energies were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. For Ca(His-H)(His)+, the dominant structure has the metal center coordinating with the π nitrogen of the imidazole ring (Nπ) and both oxygen atoms of the carboxylate group of the deprotonated His ligand while coordinating with the backbone amine (Nα), Nπ, and the carbonyl oxygen of the carboxylic acid of the intact His ligand. The Ni(His-H)(His)+ species coordinates the metal ion through Nα, Nπ, and the carbonyl oxygen for both the deprotonated and intact His ligands, but also shows evidence for a minor secondary structure where the deprotonated His coordinates the metal at Nα, Nπ, and the deprotonated carbonyl oxygen and the intact His ligand is zwitterionic, coordinating the metal with both carboxylate oxygens. Different levels of theory predict different ground structures, highlighting the need for utilizing multiple levels of theory to help identify the gas-phase structure actually observed experimentally.

Uranium trioxide, UO3, has a T-shaped structure with bent uranyl, UO22+, coordinated by an equatorial oxo, O2-. The structure of cation UO3+ is similar but with an equatorial oxyl, O center dot-. Neutral and cationic uranium trioxide coordinated by nitrates were characterized by collision induced dissociation (CID), infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory. CID of uranyl nitrate, [UO2 (NO3)3]- (complex A1), eliminates NO2 to produce nitrate-coordinated UO3+, [UO2 (O. )(NO3)2]-(B1), which ejects NO3 to yield UO3 in [UO2 (O)(NO3)]- (C1). Finally, C1 associates with H2O to afford uranyl hydroxide in [UO2(OH)2 (NO3)]- (D1). IRMPD of B1, C1, and D1 confirms uranyl equatorially coordinated by nitrate(s) along with the following ligands: (B1) radical oxyl O.-; (C1) oxo O2-; and (D1) two hydroxyls, OH- . As the nitrates are bidentate, the equatorial coordination is six in A1, five in B1, four in D1, and three in C1. Ligand congestion in low-coordinate C1 suggests orbital-directed bonding. Hydrolysis of the equatorial oxo in C1 epitomizes the inverse trans influence in UO3, which is uranyl with inert axial oxos and a reactive equatorial oxo. The uranyl v3 IR frequencies indicate the following donor ordering: O2- [best donor] >> O.- > OH-> NO3-.

Cisplatin, (NH3)2PtCl2, has been known as a successful metal-based anticancer drug for more than half a century. Its analogue, Argplatin, arginine-linked cisplatin, (Arg)PtCl2, is being investigated because it exhibits reactivity towards DNA and RNA that differs from that of cisplatin. In order to understand the basis for its altered reactivity, the deprotonated and sodium cationized forms of Argplatin, [(Arg-H)PtCl2]− and [(Arg)PtCl2 + Na]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy in the IR fingerprint and hydrogen-stretching regions. Complementary electronic structure calculations are performed using density functional theory approaches to characterize the stable structures of these complexes and to predict their infrared spectra. Comparison of the theoretical IR spectra predicted for various stable conformations of these Argplatin complexes to their measured IRMPD spectra enables determination of the binding mode(s) of Arg to the Pt metal center to be identified. Arginine is found to bind to Pt in a bidentate fashion to the backbone amino nitrogen and carboxylate oxygen atoms in both the [(Arg-H)PtCl2]− and [(Arg)PtCl2 + Na]+ complexes, the NO− binding mode. The neutral side chain of Arg also interacts with the Pt center to achieve additional stabilization in the [(Arg-H)PtCl2]− complex. In contrast, Na+ binds to both chlorido ligands in the [(Arg)PtCl2 + Na]+ complex and the protonated side chain of Arg is stabilized via hydrogen-bonding interactions with the carboxylate moiety. These findings are consistent with condensed-phase results, indicating that the NO− binding mode of arginine to Pt is preserved in the electrospray ionization process even under variable pH and ionic strength.

We present the gas-phase infrared spectra of the phenyl cation, phenylium, in its perprotio C$_6$H$_5^+$ and perdeutero C$_6$D$_5^+$ forms, in the 260-1925 cm$^{-1}$ (5.2-38 $\mu$m) spectral range, and investigate the observed photofragmentation. The spectral and fragmentation data were obtained using Infrared Multiple Photon Dissociation (IRMPD) spectroscopy within a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) located inside the cavity of the free electron laser FELICE (Free Electron Laser for Intra-Cavity Experiments). The $^1$A$_1$ singlet nature of the phenylium ion is ascertained by comparison of the observed IR spectrum with DFT calculations, using both harmonic and anharmonic frequency calculations. To investigate the observed loss of predominantly [2C,nH] (n=2-4) fragments, we explored the potential energy surface (PES) to unravel possible isomerization and fragmentation reaction pathways. The lowest energy pathways toward fragmentation include direct H elimination, and a combination of facile ring-opening mechanisms ($\leq2.4$ eV), followed by elimination of H or CCH$_2$. Energetically, all H-loss channels found are more easily accessible than CCH$_2$-loss. Calculations of the vibrational density of states for the various intermediates show that at high internal energies, ring opening is the thermodynamically the most advantageous, eliminating direct H-loss as a competing process. The observed loss of primarily [2C,2H] can be explained through entropy calculations that show favored loss of [2C,2H] at higher internal energies., Comment: 10 pages, 6 figures and 1 table. Accepted for publication on PCCP on 04 Feb 2021; supplementary Material available on PCCP website

Sulfa drugs are an important class of pharmaceuticals in the treatment of bacterial infections. The amido/imido tautomerism of these molecules in their neutral form has been widely discussed in the literature. Here, we study the protonation preferences of sulfa drugs upon electrospray ionization (ESI) using IR action spectroscopy of the ionized gas-phase molecules in a mass spectrometer. Our set of molecules includes sulfanilamide (SA), the progenitor of the family of sulfa drugs, and the actual, sulfonamide nitrogen substituted, sulfa drugs sulfamethoxazole (SMX), sulfisoxazole (SIX), sulfamethizole (SMZ), sulfathiazole (STZ), sulfapyridine (SP) and sulfaguanidine (SG). IR multiple photon dissociation (IRMPD) spectra were recorded for the protonated sulfa drugs using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) and an optical parametric oscillator/amplifier (OPO/OPA) as well as the FELIX free electron laser (FEL) as IR sources. The OPO provides tunable IR radiation in the NH stretch region (3100–3700 cm$$^{-1}$$ - 1 ), while the FEL covers the fingerprint region (520–1750 cm$$^{-1}$$ - 1 ). Comparison of experimental IR spectra with spectra predicted using density functional theory allowed us to determine the gas-phase protonation site. For SA, the sulfonamide NH$$_2$$ 2 group was identified as the protonation site, which contrasts the situation in solution, where the anilinic NH$$_2$$ 2 group is protonated. For the derivative sulfa drugs, the favored protonation site is the nitrogen atom included in the heterocycle, except for SG, where protonation occurs at the sulfonamide nitrogen atom. The theoretical investigations show that the identified protonation isomers correspond to the lowest-energy gas-phase structures.

Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG•+) and its sequence ions [a3 + H]•+ and [b2 - H]•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a3 + H]•+ and [b2 - H]•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a3 + H]•+ and [b2 - H]•+ ions.

With the detection of C60, C70, and in the interstellar medium, fullerenes are currently the largest molecules identified in space. The relatively high proton affinities of C60 and C70 support the hypothesis that protonated fullerenes may also be abundant in the interstellar matter. Here, we present the first experimental vibrational spectrum of C70H+, recorded in the gas phase. The attachment of a proton to C70 causes a drastic symmetry lowering, which results in a rich vibrational spectrum. As compared to C60, where all C-atoms are equivalent due to the icosahedral symmetry, C70 belongs to the D5h point group and has five nonequivalent C-atoms, which are available as protonation sites. Combined analysis of the experimental spectrum and spectra computed at the density functional theory level enables us to evaluate the protonation isomers being formed. We compare the IR spectra of C60H+ and C70H+ to IR emission spectra from planetary nebulae, which suggests that a mixture of these fullerene analogs could contribute to their IR emission.

The digital revolution sets a milestone in the progressive miniaturization of working devices and in the underlying advent of molecular machines. Foldamers involving mechanically entangled components with modular secondary structures are among the most promising designs for molecular switch‐based applications. Characterizing the nature and dynamics of their intramolecular network following the application of a stimulus is the key to their performance. Here, we use non‐dissociative electron transfer as a reductive stimulus in the gas phase and probe the consecutive co‐conformational transitions of a donor‐acceptor oligorotaxane foldamer using electrospray mass spectrometry interfaced with ion mobility and infrared ion spectroscopy. A comparison of collision cross section distributions for analogous closed‐shell and radical molecular ions sheds light on their respective formation energetics, while variations in their respective infrared absorption bands evidence changes in intramolecular organization as the foldamer becomes more compact. These differences are compatible with the advent of radical‐pairing interactions., Gas‐phase non‐dissociative electron transfer is used for charge reduction of a donor‐acceptor oligorotaxane foldamer (green). The consecutive co‐conformational transition is monitored using ion mobility spectrometry and infrared ion spectroscopy. Comparing the collision cross section distributions (blue) and infrared spectra (red) recorded for analogous closed‐shell and radical systems highlights differences that can be attributed to radical‐pairing interactions.

Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor-acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα-Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (-NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of -NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm-1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.

A key decay pathway by which organic sunscreen molecules dissipate harmful UV energy involves excited-state hydrogen atom transfer between proximal enol and keto functional groups. Structural modifications of this molecular architecture have the potential to block ultrafast decay processes, and hence promote direct excited-state molecular dissociation, profoundly affecting the efficiency of an organic sunscreen. Herein, we investigate the binding of alkali metal cations to a prototype organic sunscreen molecule, oxybenzone, using IR characterization. Mass-selective IR action spectroscopy was conducted at the free electron laser for infrared experiments, FELIX (600-1800 cm-1), on complexes of Na+, K+ and Rb+ bound to oxybenzone. The IR spectra reveal that K+ and Rb+ adopt binding positions away from the key OH intermolecular hydrogen bond, while the smaller Na+ cation binds directly between the keto and enol oxygens, thus breaking the intramolecular hydrogen bond. UV laser photodissociation spectroscopy was also performed on the series of complexes, with the Na+ complex displaying a distinctive electronic spectrum compared to those of K+ and Rb+, in line with the IR spectroscopy results. TD-DFT calculations reveal that the origin of the changes in the electronic spectra can be linked to rupture of the intramolecular bond in the sodium cationized complex. The implications of our results for the performance of sunscreens in mixtures and environments with high concentrations of metal cations are discussed.

In this study, dissociative one-electron transfer dissociation of [CuII (dien)Y(G/A)W]•2+ [dien = diethylenetriamine; Y(G/A)W = tyrosyl (glycyl/alanyl)tryptophan] was used to generate the tripeptide radical cations [Y(G/A)W]•+ ; subsequent loss of the Tyr side chain formed [Gα• (G/A)W]+ . The π-centered species [YGWπ• ]+ generated the α-centered species [Gα• GW]+ through Cα -Cβ bond cleavage, as revealed using infrared multiple photon dissociation (IRMPD) measurements and density functional theory (DFT) calculations. Comparisons of experimental and theoretical IR spectra confirmed that both the charge and spin densities of [Y(G/A)Wπ• ]+ were delocalized initially at the tryptophan indolyl ring; subsequent formation of the final [Gα• (G/A)W]+ structure gave the highest spin density at the α-carbon atom of the N-terminal glycine residue, with a proton solvated by the first amide oxygen atom. The IRMPD mass spectra and action spectra of the [Gα• (G/A)W]+ species were all distinctly different from those of their isomeric [G(G/A)Wπ• ]+ species. The mechanism of formation of the captodative [Gα• (G/A)W]+ species-with the charge site separated from the radical site-from [Y(G/A)Wπ• ]+ has been elucidated. DFT calculations suggested that the Cα -Cβ bond cleavage of the tyrosine residue in the radical cationic [Y(G/A)Wπ• ]+ precursor involves (a) through-space electron transfer between the indolyl and phenolic groups; (b) formation of proton-bound dimers through Cα -Cβ cleavage of the tyrosine residue; and (c) a concerted proton rearrangement from the phenolic OH group to the carboxyl group and formation of the α-carbon-centered product [Gα• (G/A)W]+ through hydrogen bond cleavage. The barriers for the electron transfer (a), the Cα -Cβ cleavage (b), and the protonation rearrangement (c) were 12.8, 26.5, and 10.3 kcal mol-1 , respectively.

In this study, dissociative one-electron transfer dissociation of [Cu

We report herein the first detailed study of the mechanism of redox reactions occurring during the gas-phase dissociative electron transfer of prototypical ternary [CuII(dien)M]˙2+ complexes (M, peptide). The two final products are (i) the oxidized non-zwitterionic π-centered [M]˙+ species with both the charge and spin densities delocalized over the indole ring of the tryptophan residue and with a C-terminal COOH group intact, and (ii) the complementary ion [CuI(dien)]+. Infrared multiple photon dissociation (IRMPD) action spectroscopy and low-energy collision-induced dissociation (CID) experiments, in conjunction with density functional theory (DFT) calculations, revealed the structural details of the mass-isolated precursor and product cations. Our experimental and theoretical results indicate that the doubly positively charged precursor [CuII(dien)M]˙2+ features electrostatic coordination through the anionic carboxylate end of the zwitterionic M moiety. An additional interaction exists between the indole ring of the tryptophan residue and one of the primary amino groups of the dien ligand; the DFT calculations provided the structures of the precursor ion, intermediates, and products, and enabled us to keep track of the locations of the charge and unpaired electron. The dissociative one-electron transfer reaction is initiated by a gradual transition of the M tripeptide from the zwitterionic form in [CuII(dien)M]˙2+ to the non-zwitterionic M intermediate, through a cascade of conformational changes and proton transfers. In the next step, the highest energy intermediate is formed; here, the copper center is 5-coordinate with coordination from both the carboxylic acid group and the indole ring. A subsequent switch back to 4-coordination to an intermediate IM1, where attachment to GGW occurs through the indole ring only, creates the structure that ultimately undergoes dissociation.

Methionine (Met) cationized with Zn2+, forming Zn (Met-H)+(ACN) where ACN = acetonitrile, Zn (Met-H)+, and ZnCl+(Met), as well as Cd2+, forming CdCl+(Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.

The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys−H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys−H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO−,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.

With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.

The side group of the amino acid arginine is typically in its guanidinium protonated form under physiological conditions, and participates in a broad range of ligand binding and charge transfer processes of proteins. The recognition of phosphate moieties by guanidinium plays a particularly key role in the interactions of proteins with ATP and nucleic acids. Moreover, it has been recently identified as the driving force for the inhibition of kinase phosphorilation activity by guanidinium derivatives devised as potential anticancer agents. We report on a fundamental investigation of the interactions and coordination arrangements formed by guanidinium with phosphoric, phosphate and pyrophosphate groups. Action vibrational spectroscopy and $ab$ $initio$ quantum chemical computations are employed to characterize the conformations of benchmark positively-charged complexes isolated in an ion trap. The multidentate structure of guanidinium and of the phosphate groups gives rise to a rich conformational landscape with a particular relevance of tweezer-like configurations, where phosphate is effectively trapped by two guanidinium cations. The pyrophosphate complex incorporates a Na+ cation, which serves to compare the interactions associated with the localized versus diffuse charge distributions of the alkali cation and guanidinium, respectively, within a common supramolecular framework.

Infrared multiple photon dissociation (IRMPD) spectroscopy shows the [GPGG + H – H2O]+ ion to have an imidazolone structure. Collision-induced dissociation of this [b4]+ ion results in the loss of HN CH2 from the first residue; the IRMPD spectrum of this MS3 product ion is very similar to that of the [b4]+ ion itself, strongly indicating that the [b4 – HN CH2]+ ion also has an imidazolone structure. Losses of CO and glycine are the dominant dissociation pathways for the [b4 – HN CH2]+ ion. The latter loss requires tautomerism of the keto-form of the imidazolone ring to become the lower-energy enol-form, prior to dissociation. Isotopic labelling showed that loss of CO occurs from the ring of the keto-form. Density functional theory calculations were performed at both the B3LYP/6–311++G (d,p) and M06–2X/6–311++G (d,p) levels and the results are in good agreement.

The combination of a 4 K 22-pole ion trap instrument, FELion, with the widely tunable free electron lasers at the FELIX Laboratory is described in detail. It allows for wide-range infrared vibrational spectroscopy of molecular ions. In this study, the apparatus is used for infrared vibrational predissociation (IR-PD) measurements of the simple alcohol cations of methanol and ethanol as well as their protonated forms. Spectra are taken by tagging the cold molecular ions with He atoms. The infrared spectrum of protonated methanol is recorded for the first time, and the wavelength coverage for all other species is substantially extended. The bands of all spectra are analysed by comparison to ab initio calculation results at different levels of theory. Vibrational bands of different isomers and conformers (rotamers) are discussed and identified in the experimental spectra. Besides the measurement of IR-PD spectra, the method of infrared multiple photon dissociation IR-MPD is applied for some cases. Spectral narrowing due to the cold environment is observed and rotational band contours are simulated. This will help in identifying more complex species using the IR-MPD method in future measurements. Overall the IR-PD spectra reveal more bands than are observed for the IR-MPD spectra. In particular, many new bands are observed in the fingerprint region. Depletion saturation of the finite number of trapped ions is observed for the IR-PD spectra of the ethanol cation and the presence of only one isomeric species is concluded. This special feature of ion trapping spectroscopy may be used in future studies for addressing specific isomers or cleaning the ion cloud from specific isomers or conformers. In addition, the results of this study can be used as a basis to obtain high-resolution infrared vibrational and THz rotational spectra of alcohol ions in order to detect them in space.

The molecular structures of six open-shell z3-ions resulting from electron transfer dissociation mass spectrometry (ETD MS) were investigated using infrared ion spectroscopy in the 800–1850 and 3200–3700 cm−1 spectral ranges in combination with density functional theory and molecular mechanics/molecular dynamics calculations. We assess in particular the question of whether the radical remains at the Cα-site of the backbone cleavage, or whether it migrates by H-atom transfer to another, energetically more favorable position. Calculations performed herein as well as by others show that radical migration to an amino acid side chain or to an α-carbon along the peptide backbone can lead to structures that are more stable, by up to 33 kJ mol−1 for the systems investigated here, by virtue of resonance stabilization of the radical in these alternative positions. Nonetheless, for four out of the six z3-ions considered here, our results quite clearly indicate that radical migration does not occur, suggesting that the radical is kinetically trapped at the site of ETD cleavage. For the two remaining systems, a structural assignment is less secure and we suggest that a mixture of migrated and unmigrated structures may be formed.

The molecular family of nucleotide triphosphates (NTPs), with adenosine 5′-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5′-triphosphate, cytosine 5′-triphosphate and guanosine 5′-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.

Synthesis and spectra of isocytosino-8-trifluoromethylquinolone (1), as well as the gas phase InfraRed Multiple Photon Dissociation (IRMPD) spectra in the fingerprint region of the corresponding deprotonated anion (3), its d3 analogue, the monodeprotonated homodimer (2), and its d7 analogue are reported here. The anions represent nucleobase analogues having the hydrogen bonding pattern ADAAD (where A stands for acceptor and D stands for donor), in which the site of negative charge is unambiguous (as opposed to guanine, which has more than one acidic nitrogen). The match between experimental vibrational spectra and calculation is good, except for the out-of-plane HNH bends of the undeuterated and deuterated monomer anions between 400 and 600 cm−1. The anionic homodimers form in a parallel orientation.

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with metal cations. In order to determine the effects of sodium cationization on the structures of 2′-deoxycytidine and cytidine, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides, [dCyd+Na]+ and [Cyd+Na]+, are measured using the FELIX free electron laser and an OPO/OPA laser system. Energy-resolved collision-induced dissociation (ER-CID) experiments for the protonated and sodium cationized forms of the cytosine nucleosides are performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (QIT MS) to evaluate the relative propensities of protons and sodium cations for activating the glycosidic bonds of the cytosine nucleosides. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of [dCyd + Na]+ and [Cyd + Na]+. For both cytosine nucleosides, theory suggests that tridentate binding of Na+ to the O2, O4′ and O5′ atoms of the cytosine nucleobase and sugar moiety is the most stable binding mode. However, comparison of the measured IRMPD action spectrum and computed linear IR spectra suggests that anti oriented bidentate conformers of [Cyd + Na]+ are predominantly populated in the experiments. The 2′-hydroxyl substituent of Cyd stabilizes the anti oriented bidentate conformers of [Cyd + Na]+, and enables formation of a 2′OH⋯3′OH hydrogen-bonding interaction. The 2′-hydroxyl substituent is found to stabilize the glycosidic bond of Cyd vs. that of dCyd for both the protonated and sodium cationized cytosine nucleosides. Compared to protonation, sodium cationization activates the N-glycosidic bond less effectively.

The role of specific amino acid side-chains in the fragmentation chemistry of gaseous protonated peptides resulting from collisional activation remains incompletely understood. For small peptides containing asparagine and glutamine, a dominant fragmentation channel induced by collisional activations is, in addition to deamidation, the loss of neutral water. Identifying the product ion structures from H2O-loss from four protonated dipeptides containing Asn or Gln using infrared ion spectroscopy, mechanistic details of the dissociation reactions are revealed. Several sequential dissociation reactions have also been investigated and provide additional insights into the fragmentation chemistry. While water loss can in principle occur from the C-terminus, the side chain or the amide bond carbonyl oxygen, in most cases the C-terminus was found to detach H2O, leading to a b2-sequence ion with an oxazolone structure for AlaGln, and bifurcating mechanisms leading to both oxazolone and diketopiperazine species for AlaAsn and AsnAla. In contrast, GlnAla expels water from the amide side chain leading to an imino-substituted prolinyl structure.

Complexes of divalent metal ions (Cu2+ and Ni2+) with histidine tripeptide complexes (HAA, AHA and AAH) are interesting gas-phase models for some of the most widely observed patterns of metal ion binding to peptides and proteins. Gas-phase structures were characterized using infrared multiple photon dissociation (IRMPD) spectroscopy in ion-trapping mass spectrometers, along with density functional theory (DFT) computations. Ground states are square-planar with two deprotonated amide nitrogens bound to the metal ion via a double iminol rearrangement (IM binding mode), but contrary to expectations based on solution behavior, the histidine imidazole group is not bound to the metal, but instead is hydrogen bonded remote from the metal ion. The alternative “charge-solvated” (CS) binding mode (amide carbonyl oxygens binding the metal ion) lies higher in energy, but in many cases was observed to be present as conformationally unrelaxed ions with an abundance (relative to the IM conformation) that was dependent on instrument configuration and source and trap conditions. Taking advantage of the ability to form and trap both IM and CS conformations for a few of the complexes, the infrared spectroscopy of both conformations was explored in the fingerprint (1000–1800 cm−1) and hydrogen-stretching (3200–3800 cm−1) regions. For the fingerprint region, agreement is very good between the observed IRMPD spectra and the spectra predicted by DFT calculations at the B3LYP/6–311 + +g(d,p) level. Agreement in the H-stretching region is not perfect, but the characteristic IM and CS spectral patterns are evident.

The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.

Brønsted acids and protic solvents mediate acyl transfer, known as the Mumm rearrangement, from imidates to the corresponding acylamides. This represents a key step in several reactions, for example, the Ugi four-component reaction (U-4CR) and Passerini three-component reaction (P-3CR). Herein, an unprecedented break of the non-reversibility of the Mumm rearrangement is reported. A combination of electrospray tandem mass spectrometry (ESI-MS/MS), infrared multiphoton dissociation (IRMPD) ion spectroscopy and theoretical calculations demonstrates the occurrence of the retro-Mumm rearrangement of protonated isopeptides in the gas phase. In the gas phase, the extra proton acquired during ESI promotes the backward isomerisation reaction in a catalytic fashion.

Oligopeptides containing 2,3-diaminopropionic acid (Dap) serve as a unique model to study conformational effects on the ionizability of a side-chain group. In this study, conformations of acetylated isomeric dipeptide ions containing alanine (Ala) and Dap, AlaDapH+ and DapAlaH+, are studied by infrared multiple photon dissociation (IRMPD) spectroscopy and computation. The IRMPD spectra are characterized in detail by comparing them with theoretical IR spectra of a set of low-energy conformations calculated at the ωB97X-D/6-311+G(d) level of theory. The averaged IR spectra according to the Boltzmann distribution of the set of conformations have a good match to the IRMPD spectra. The characteristic amide I band of AlaDapH+ appears to be downshifted compared to that of DapAlaH+. The relative positions of the amide band suggest a stronger hydrogen-bonding interaction between the charged side-chain amino group and the amide carbonyl groups in AlaDapH+ than in DapAlaH+. The stronger hydrogen bonding in the forme...

The following gas-phase uranyl/12-crown-4 (12C4) complexes were synthesized by electrospray ionization: [UO2(12C4)2]2+ and [UO2(12C4)2(OH)]+. Collision-induced dissociation (CID) of the dication resulted in [UO2(12C4-H)]+ (12C4-H is a 12C4 that has lost one H), which spontaneously adds water to yield [UO2(12C4-H)(H2O)]+. The latter has the same composition as complex [UO2(12C4)(OH)]+ produced by CID of [UO2(12C4)2(OH)]+ but exhibits different reactivity with water. The postulated structures as isomeric [UO2(12C4-H)(H2O)]+ and [UO2(12C4)(OH)]+ were confirmed by comparison of infrared multiphoton dissociation (IRMPD) spectra with computed spectra. The structure of [UO2(12C4-H)]+ corresponds to cleavage of a C–O bond in the 12C4 ring, with formation of a discrete U–Oeq bond and equatorial coordination by three intact ether moieties. Comparison of IRMPD and computed IR spectra furthermore enabled assignment of the structures of the other complexes. Theoretical studies of the chemical bonding features of the complexes provide an understanding of their stabilities and reactivities. The results reveal bonding and structures of the uranyl/12C4 complexes and demonstrate the synthesis and identification of two different isomers of gas-phase uranyl coordination complexes.

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N–Cα 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.

We present a detailed investigation of the dynamics of impurity-trapped excitons in CaF 2 :Yb 2+ using transient photoluminescence enhancement induced via a two-frequency, sequential excitation process employing a UV optical parametric amplifier (OPA) synchronized to an infrared free electron laser (FEL). The temporal behaviour is well approximated by a multi-level rate equation model as relaxation between excited states of the exciton as well as a small contribution from local lattice heating by the FEL which becomes evident due to the 40 cm −1 splitting of the exciton excited states giving rise to the transient photoluminescence enhancement itself.

Contains fulltext : 182103.pdf (Publisher’s version ) (Open Access) Evidence is presented for cyclization to yield 2-bora-1,3-diazacycloalkanium cations in the gas phase. While the neutral compounds in solution and solid phase are known to possess an acyclic structure (as revealed by X-ray diffraction), the gaseous cations (from which borohydride BH4(-) ion has been expelled) have a cyclic structure, as revealed by InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy and collisionally activated decomposition (CAD). The IRMPD decomposition of the monocyclic ions proceeds principally via H2 expulsion, although CAD experiments show additional pathways. Pyrolyses of solid monomeric salts and small oligomers produce higher polymers that are consistent with H2 expulsion as the major pathway. Deuterium labeling experiments show that scrambling occurs prior to IRMPD or CAD decomposition in the gas phase.

Ni(II) ions can be caged by surrounding peptide ligands in two basic binding patterns: the “iminol” (IM) binding pattern, where chelation occurs by deprotonated amide nitrogens, or the charge-solvated (CS) binding pattern, where chelation occurs by amide carbonyl oxygens. Gas-phase observation may clarify the factors affecting this choice in solution and in peptide and protein matrices. Infrared spectroscopic determination of gas-phase structures shows here how microsolvation by just one water molecule switches the balance of this choice from IM to CS for the Ni2+Gly3 complex, in contrast with the always-CS structure of the Ni2+Gly4 complex. Quantum-chemical calculations indicate that CS complexation is even more favored in the aqueous limit. Considering gas-phase conditions as comparable to low-pH solutions can reconcile this prediction with the common observation of IM-type binding in solutions at higher pH. This is likely the first gas-phase observation of solvation-induced IM-to-CS transition in oligopeptide complexes with doubly charged transition-metal ions.

In the complex formed between the calcium cation (Ca2+) and a deprotonated HisHis dipeptide, the complex adopts a charge solvation (CS) structure. Ca2+, a weak binding main group metal cation, interacts with the oxygens of the peptide carbonyl moiety and the deprotonated C-terminus. In contrast, the much stronger binding Ni2+ cation deprotonates the peptide nitrogen and induces an iminolate (Im) ligand structure in the [Ni(HisHis-H)]+ complex ion. The combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum chemistry evidence these two representative binding motifs. The iminolate coordination pattern identified and characterized in the [Ni(HisHis-H)]+ complex serves as a model case for nickel complexes of poly-histidyl-domains and is thereby also of interest to better understand the fundamentals of immobilized metal ion affinity chromatography as well as of Ni co-factor chemistry in enzymology.

Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor–acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα–Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (–NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of –NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm−1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.