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Glycosylation is a common modification across living organisms and plays a central role in understanding biological systems and disease. Our ability to probe the gylcome has grown exponentially in the past several decades. However, further improvements to the analytical toolbox available to researchers would allow for increased capabilities to probe structure and function of biological systems and to improve disease treatment. This article applies the developing technique of two-dimensional Fourier transform ion cyclotron resonance mass spectrometry to a glycoproteomic workflow for the standard glycoproteins coral tree lectin (CTL) and bovine ribonuclease B (BRB) to demonstrate its feasibility as a tool for glycoproteomic workflows. 2D infrared multiphoton dissociation and electron capture dissociation spectra of CTL reveal comparable structural information to their 1D counterparts, confirming the site of glycosylation and monosaccharide composition of the glycan. Spectra collected in 2D of BRB reveal correlation lines of fragment ion scans and vertical precursor ion scans for data collected using infrared multiphoton dissociation and diagonal cleavage lines for data collected by electron capture dissociation. The use of similar techniques for glycoproteomic analysis may prove valuable in instances where chromatographic separation is undesirable or quadrupole isolation is insufficient. [ABSTRACT FROM AUTHOR]

The process of Infrared Multiphoton Dissociation (IRMPD) was studied in a mixture of vinyl bromide/chlorodifluoromethane (VBr, C2H3Br/CF2HCl) using single and double infrared pulsed transverse excitations atmospheric CO2 laser beams. The dissociation of VBr was investigated using FTIR, and the product composition was analysed, and various dissociation routes were proposed. The study found that the VBr molecules were more heavily dissociated when exposed to the CF2HCl environment than without it. By using a time-resolved LIF, the kinetics reactions with CF2HCl were explored under pseudo-first-order conditions, and the quenching rate constant for the interaction between CF2HCl and C 2 d 3 Π g was published using the classical Stern–Volmer model. The impact of pulsed laser heating on the generation of C 2 a 3 Π u radicals was also observed. The decrease in the intensity of the C 2 (a 3 Π u) LIF signal was due to faster recombination of the C 2 a 3 Π u radicals, together with a decrease in V - V ′ energy transfer and the pressure oscillations produced by the effect of pulsed laser heating in the irradiated volume and the experimental conditions. [ABSTRACT FROM AUTHOR]

We investigate the structural correlation of noncovalent crown ether/H+/L‐tryptophan (CR/TrpH+) host–guest complexes in the solution phase with those in the gas phase generated through electrospray ionization/mass spectrometry (ESI/MS) techniques. We perform quantum chemical calculations to determine their structures, relative Gibbs free energies, and infrared spectra. We compare the calculated infrared (IR) spectra with the IR multiphoton dissociation (IRMPD) spectra observed for the 18‐Crown‐6/TrpH+ complex by Polfer and co‐workers [J. Phys. Chem. A 2013, 117, 1181–1188] for assigning the IR bands. We observe that the carboxyl group remains "naked," lacking hydrogen bonding with the CR unit in the gas phase, and that this most stable conformer originates from the corresponding lowest Gibbs free energy structure in solution. Based on these findings, we propose that gas phase host–guest complexes directly correlate with those in solution, reinforcing the possibility of obtaining invaluable information about host–guest–solvent interactions in solution from the structure of the host–guest pair in the gas phase. [ABSTRACT FROM AUTHOR]

The fragmentation mechanism of D‐glucose was investigated in detail by two different fragmentation techniques, namely, collision‐induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) using all six 13C‐labeled isotopomers and 2H‐labeled isotopomers. For both CID and IRMPD energy‐resolved measurements were carried out. Individual fragmentation pathways were studied at MS2 and MS3 levels. Additionally, we have developed an HPLC‐tandem MS method to separate the anomers of D‐glucose using a HILIC column and investigated their fragmentation patterns individually. We propose a complete fragmentation landscape of D‐glucose, demonstrating that a rather simple multifunctional molecule displays extreme complexity in gas phase dissociation, following multiple parallel fragmentation routes yielding a total of 23 distinct fragment ions. The results allowed a detailed formulation of the complex fragmentation mechanism of D‐glucose. The results have immediate consequences for the full structure analysis of complex carbohydrates. [ABSTRACT FROM AUTHOR]

In uranyl coordination complexes, UO2(L)n2+, uranium in the formally dipositive [O=U=O]2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν3. This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of the enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν3 red-shift. Here, ν3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν3 frequency From computed ν3 frequencies for bare UO2 cations and neutrals, it is inferred that the effective charge of uranyl in UO2(L)n2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination.

In uranyl coordination complexes, UO2(L)n2+, uranium in the formally dipositive [O=U=O]2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν3. This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of the enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν3 red-shift. Here, ν3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν3 frequency From computed ν3 frequencies for bare UO2 cations and neutrals, it is inferred that the effective charge of uranyl in UO2(L)n2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination.

The 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. [ABSTRACT FROM AUTHOR]

Metal clusters supported on carbonaceous substrates are of interest in catalysis, hydrogen storage, and other fields. In this paper, the structures and the infrared spectra of C 60 Rh n + (n = 1–6) fullerene-metal complexes are studied by a combination of mass-selective infrared spectroscopy and theoretical calculations. It is found that clustering of Rh on the surface of the fullerene is preferred over surface wetting. For Rh 4 + and Rh 6 +, the structures of the adsorbed clusters are different from those of the free clusters. There is electron transfer from the metal cluster to the fullerene in neutral C 60 Rh n , and in cationic C 60 Rh n + the electron deficit is shared by the metal cluster and the fullerene. Adsorption of Rh n clusters leads to degeneracy lifting of the most intense C 60 features in the infrared spectra that were measured in the 300–850 cm−1 range. Agreement is obtained, in general, between the experimental infrared spectra of D 2 -tagged C 60 Rh n + and the calculated spectra for untagged C 60 Rh n +, except in the 600–750 cm−1 region, where features mainly arise from the presence of D 2 -messenger molecules adsorbed on the Rh n clusters. [Display omitted] • A combined experimental and theoretical study on the interaction of Rh clusters with C 60 is performed. • Far-IR multiple photon dissociation spectroscopy of C 60 Rh n + tagged with D 2 reveals the vibrational spectra. • In parallel, vibrational spectra are calculated using Density Functional Theory. • The comparison delivers novel information on the structure of C 60 Rh n complexes. • Clustering of Rh on the surface of the fullerene is preferred over surface wetting. [ABSTRACT FROM AUTHOR]

[Display omitted] • Chelating amino acids improve the inertness of Zeise's salt derivatives against S-donors. • Isomerism at the platinum center leads to different reactivities towards biological nucleophiles. • A penta-coordinate species was observed when the O- trans complex reacted with DMSO. • The results highlight complex 4 as promising lead compound, exhibiting enhanced aqueous stability, reduced reactivity with S-donors, and increased in vitro cytotoxic activity compared to complex 5. The interactions of sulfur-containing peptides and proteins with platinum-based anticancer agents are of significant interest in the field of bioinorganic chemistry. We previously modified the lead compound potassium {trichlorido[ η 2-(but -3- en -1- yl)-2- acetoxybenzoate ]platinate(II)} (Pt-butene-ASA) by exchanging two chlorido ligands for an amino acid chelating ligand to improve its stability in aqueous solutions. In the current study, we demonstrate how this amino acid ligand strengthens the inertness of this class of complexes against sulfur-containing compounds. We incubated four complexes, each bearing an amino acid chelating ligand, with various sulfur-containing compounds of biological interest, such as DMSO, methionine, glutathione, and substance P. The reactions were monitored using NMR spectroscopy and mass spectrometry, allowing the identification by combination with IR ion spectroscopy of exotic pentacoordinate platinum(II) complexes as reaction intermediates. The results indicated that the reactivity of complexes 1 – 4 ((ethene, N -trans)(l -alaninato-N,O)chlorido(η2-ethene)platinate(II), (ethene,O-trans)(β-alaninato-N,O)chlorido(η2-ethene)platinate(II), (l -histidinato-N,N)chlorido(η2-ethene)platinate(II), and (olefin, N -trans)(l -alaninato-N,O)chlorido(η2-(but-3-en-1-yl)-2-acetoxy benzoate)platinate(II), respectively) is determined by the inner coordination sphere, and the addition of an amino acid ligand significantly reduces the rate of nucleophilic substitutions by sulfur-containing nucleophiles. In particular, the N,ethylene- trans isomers reacted only to a low extent with the free thiol in glutathione, while the O,ethylene- trans isomer was completely consumed within 2 h. Complex 4 , the new lead compound, showed low reactivity towards S-nucleophiles in general, which confirms the concept of using amino acids as biocompatible bidentate ligands to adjust the reactivity and stability of this kind of metallodrugs. [ABSTRACT FROM AUTHOR]

This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass‐selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas‐phase action ion spectroscopy can make a large impact. [ABSTRACT FROM AUTHOR]

Polysaccharides are important biomacromolecules with numerous beneficial functions and a wide range of industrial applications. Functions and properties of polysaccharides are closely related to their structural features. Infrared (IR) spectroscopy is a well-established technique which has been widely applied in polysaccharide structural analysis. In this paper, the principle of IR and interpretation of polysaccharide IR spectrum are briefly introduced. Classical applications of IR spectroscopy in polysaccharide structural elucidation are reviewed from qualitative and quantitative aspects. Some advanced IR techniques including integrating with mass spectrometry (MS), microscopy and computational chemistry are introduced and their applications are emphasized. These emerging techniques can considerably expand application scope of IR, thus exert a more important effect on carbohydrate characterization. Overall, this review seeks to provide a comprehensive insight to applications of IR spectroscopy in polysaccharide structural analysis and highlights the importance of advanced IR-integrating techniques.

Ethylenediaminetetraacetic acid (EDTA) is an aminopolycarboxylic acid and complexation agent that is able to bind a large variety of metals. The formation of highly stable metal‐EDTA complexes is generally very quick. This has led to the use of EDTA in a variety of applications, including food, medical, and household applications. In the current study, we have investigated the fragmentation behavior of EDTA and various metal complexes under collision‐induced dissociation (CID), infrared‐multiphoton dissociation (IRMPD), and higher‐energy collisional dissociation (HCD) activation conditions. Both, positive and negative mode electrospray ionization (ESI) were applied. The metals used to complex with EDTA ranged from alkaline earth metals, such as sodium and cesium, via calcium, nickel, zinc, aluminum, copper, iron, and indium to yttrium and several lanthanides. Furthermore, the protonated and deprotonated species of EDTA, as well as disodium and trisodium species, have been subjected to fragmentation. The results show that characteristic fragmentations were obtained for EDTA and the metal complexes under the investigated conditions. The use of an ion cyclotron resonance (ICR) and an Orbitrap mass spectrometer, as high resolution‐accurate mass instruments, allowed the assignment of elemental compositions undoubtedly for the vast majority of fragments. Certain trends were observed that trend correlated with the size of the metal and the location within the periodic table. [ABSTRACT FROM AUTHOR]

Three complementary experimental approaches for elucidating human milk oligosaccharide (HMOs) isomers by Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR) are described: tandem-MS disruption by double resonance to distinguish different fragmentation pathways, examination of fragment intensity ratios arising from differential alkali metal ion affinities and monitoring competitive fragmentation rates. The interpretation of the fragmentation pattern from a mechanistic and thermochemical point of view permits the assignment of not only pure isomers but, in some cases, mixtures of them. Methodologically the procedures are simple, reliable and rapid making unnecessary both the use of previous separation techniques and tedious chemical modifications of the HMOs. In principle, the rationale can be expanded to resolve other isomeric mixtures of biological nature.

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. [ABSTRACT FROM AUTHOR]

Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.

Ion pair complexes of triethylammonium, [(CH2CH3)3NH]+, and (X = F, Cl) are studied with a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy and density functional theory calculations. IRMPD spectra show that the charge-carrying proton is oriented towards a trigonal face of the halogenated closo-dodecaborate in both derivatives. Resonant IR absorption via or [(CH2CH3)3NH]+ bands in the 800–1600 cm−1 region drives dissociation via the lowest energy proton-transfer fragmentation channel and the charge transfer (i.e. redox) threshold, which is second lowest in energy. By tuning the power of the interrogating laser or the wavenumber (to select specific vibrational transitions), one can control the degree of fragmentation via the two lowest energy dissociation thresholds. [ABSTRACT FROM AUTHOR]

Metabolomics strongly relies on liquid chromatography hyphenated to tandem mass spectrometry (LC-MS/MS) for the separation and identification of metabolites. Retention times and fragmentation mass spectra are used as identification parameters. A complementary approach is proposed here based on alternative approaches for both the separation and identification, and is illustrated in the case of isomeric forms of aminobutyric acids (C 4 H 9 NO 2). Differential mobility spectrometry (DMS), a very efficient method for the separation of isomers of small molecules, is coupled with high resolution tandem mass spectrometry Fourier transform ion cyclotron resonance (FT-ICR). Identification of the DMS peaks associated with the various isomers is based on isomer-specific infrared multiple photon dissociation (IRMPD) in the mid-infrared range. Two operation modes of the DMS-MS/MS(IRMPD) are used. Structural identification of the various isomers is first achieved based on the comparison of IRMPD spectra of DMS- and mass-selected ions with IR absorption spectra of candidate structures derived from quantum chemical calculations. For this purpose, the DMS device is used in selective mode. Alternatively, when the DMS is using in scanning mode, identification can also be achieved based on specific depletion of DMS peaks at selected IR wavelength. These two operation modes for identification of isomers are illustrated in conjunction with the use of modifier-assisted DMS separation. Image 1 • First coupling of DMS and IRMPD spectroscopy with high resolution FT-ICR mass spectrometry. • Two DMS-MS/MS(IRMPD) workflows are illustrated for the structural assignment of DMS peaks associated with three isomers. • Peak assignment and structural identification is performed through IRMPD spectroscopy of DMS- and mass-selected ions. • Peak assignment and structural characterization can also be based on selected DMS peak depletion at selected IR wavelengths. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation (IRMPD) spectroscopy shows the [GPGG + H – H 2 O]+ ion to have an imidazolone structure. Collision-induced dissociation of this [b 4 ]+ ion results in the loss of HN CH 2 from the first residue; the IRMPD spectrum of this MS3 product ion is very similar to that of the [b 4 ]+ ion itself, strongly indicating that the [b 4 – HN CH 2 ]+ ion also has an imidazolone structure. Losses of CO and glycine are the dominant dissociation pathways for the [b 4 – HN CH 2 ]+ 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. Image 1 • The [b 4 ]+ ion from [GPGG + H]+ has an imidazolone structure. • Keto-enol tautomerization is required for the loss of glycine from the [GPGG + H – H 2 O – NHCH 2 ]+ ion. • Loss of CO from the product ions occurs at the proline residue. [ABSTRACT FROM AUTHOR]

Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogues, those based on 2′,3′-dideoxyribose sugars are quite common, particularly in anti-HIV applications. The gas-phase structures of several protonated 2′,3′-dideoxyribose nucleosides are examined in this work and compared with those of the analogous protonated DNA, RNA, and arabinose nucleosides to elucidate the influence of the 2′- and combined 2′,3′-hydroxyl groups on intrinsic structure. Infrared multiple photon dissociation (IRMPD) action spectra are collected for the protonated 2′,3′-dideoxy forms of adenosine, guanosine, cytidine, thymidine and uridine, [ddAdo+H]+, [ddGuo+H]+, [ddCyd+H]+, [ddThd+H]+, and [ddUrd+H]+, in the IR fingerprint and hydrogen-stretching regions. Molecular mechanics conformational searching followed by electronic structure calculations generates low-energy conformers of the protonated 2′,3′-dideoxynucleosides and corresponding predicted linear IR spectra to facilitate interpretation of the measured IRMPD action spectra. These experimental IRMPD spectra and theoretical calculations indicate that the absence of the 2′- and 3′-hydroxyls largely preserves the protonation preferences of the canonical forms. The spectra and calculated structures indicate a slight preference for C3′-endo sugar puckering. The presence of the 3′- and further 2′-hydroxyl increases the available intramolecular hydrogen-bonding opportunities and shifts the sugar puckering modes for all nucleosides but the guanosine analogues to a slight preference for C2′-endo over C3′-endo. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • [RHg(NB)]+ ions arising from the interaction of Nucleobases with alkylmercury ions lead to the formation of [(NB)R]+ ions. • For large alkyl chains (reactions with n -BuHg+) the protonated nucleobase, NBH+ is also produced. • The nature and conformation of the products was established by combining MS/MS, IRMPD spectroscopy and DFT calculations. • The PESs associated to the formation of the main products were explored. Abstract The gas-phase interactions of uracil and thymine with alkylmercury cations, in particular [CH 3 Hg]+, n -BuHg+ and t -BuHg+, were studied through the use of electrospray ionization coupled to tandem mass spectrometry. We observed that the interaction of akylmercury compounds with the nucleobases (NB) gives rise to a single type of complex of general formula [RHg(NB)]+, except for t -butyl-mercury (no interaction). The subsequent MS/MS experiments show that the [RHg]+ ions (R = Me, n -Bu) exhibit a peculiar reactivity characterized by the transfer of the alkyl group to the nucleobases. Indeed, the main fragmentation process observed leads to the loss of neutral Hg, producing [(NB)R]+ ions. Only when the length of the alkyl chain increases, as in the case of reactions with [ n -BuHg]+, a new fragmentation path is opened, yielding the protonated nucleobase, [(NB)H]+, with the concomitant elimination of 2 C 4 H 4 + Hg. A thorough analysis of the mechanisms behind both dominant processes was carried out through the use of Infrared Multiple Photon Dissociation (IRMPD) in the fingerprint region, combined with an analysis of the corresponding potential energy surfaces by using high-level density functional theory (DFT) calculations. [ABSTRACT FROM AUTHOR]

We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1-Y1 and C1-Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]−, C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol−1) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm−1. For the B1 anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm−1 (deprotonated carbon 2-ketone structures), and at ~ 1541 cm−1 (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B1 anions.ᅟ [ABSTRACT FROM AUTHOR]

Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′-endo and C3′-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine.ᅟ [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • We present a new laboratory IRMPD spectrometer for the OH/NH stretching region. • The performance of the new setup is demonstrated on ionic asparagine monomers. • High-level quantum chemical calculations provide a robust backdrop for our study. • We corroborate earlier conclusions on the studied systems in a new spectral range. Abstract We report high level ab initio and infrared multiphoton dissociation (IRMPD) studies of protonated and sodiated asparagine, a chiral molecule, in the NH and OH stretching region using a newly completed laboratory IRMPD spectrometer. These two systems were previously investigated in the low frequency region of 520–1820 cm−1 at the FELIX facility (Heaton et al., 2009). The new laboratory IRMPD instrument features ion production by nano-electrospray ionization (ESI), using either a standard atmospheric implementation or a novel subambient pressure ionization with nano-electrospray design, a quadrupole mass filter, a 3D quadrupole ion trap for storage and irradiation of the selected ions and a reflectron time-of-flight mass spectrometer in an orthogonal configuration. In addition, the new instrument contains a second ion guide/ion trap arm for further coupling with a helium nanodroplet isolation spectrometer. A desktop, continuous wave, IR OPO laser system is used to excite the ions from ca. 3200 to 4000 cm−1. Furthermore, high level theoretical calculations and comparison of the experimental and theoretical IR spectra are used to establish the relative energy ordering of the conformers of protonated and sodiated asparagine. The new instrument will be put to use to study non-covalent interactions between chiral molecules across different cluster sizes and compositions. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000–4000 cm −1 ) were obtained at the Centre Laser Infrarouge d’Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH + , CavLi + , and CavNa + ; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK + is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs + is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000–2000 cm −1 ) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa + and ArgK + . This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (∼993 kJ/mol) forms only canonical structures with Na + , K + , and Cs + . A major difference between the zwitterionic forms of ArgM + and CavM + is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations. [ABSTRACT FROM AUTHOR]

We report distinctive spectroscopic fingerprints of the monosaccharide standards GalNAc4S and GalNAc6S by coupling mass spectrometry and ion spectroscopy in the 3-μm range. The disaccharide standards CSA and CSC are used to demonstrate the applicability of a novel approach for the analysis of sulfate position in GalNAc-containing glycosaminoglycans. This approach was then used for the analysis of a sample containing CSA and CSC disaccharides. Finally, we discuss the generalization of the coupling of mass spectrometry with ion spectroscopy for the structural analysis of glycosaminoglycans on a tetrasaccharide from dermatan sulfate source.ᅟ [ABSTRACT FROM AUTHOR]

In uranyl coordination complexes, UO 2 (L) n 2+ , uranium in the formally dipositive [O=U=O] 2+ moiety is coordinated by n neutral organic electron donor ligands, L. The extent of ligand electron donation, which results in partial reduction of uranyl and weakening of the U=O bonds, is revealed by the magnitude of the red-shift of the uranyl asymmetric stretch frequency, ν 3 . This phenomenon appears in gas-phase complexes in which uranyl is coordinated by electron donor ligands: the ν 3 red-shift increases as the number of ligands and their proton affinity (PA) increases. Because PA is a measure of the enthalpy change associated with a proton-ligand interaction, which is much stronger and of a different nature than metal ion-ligand bonding, it is not necessarily expected that ligand PAs should reliably predict uranyl-ligand bonding and the resulting ν 3 red-shift. Here, ν 3 was measured for uranyl coordinated by ligands with a relatively broad range of PAs, revealing a surprisingly good correlation between PA and ν 3 frequency From computed ν 3 frequencies for bare UO 2 cations and neutrals, it is inferred that the effective charge of uranyl in UO 2 (L) n 2+ complexes can be reduced to near zero upon ligation by sufficiently strong charge-donor ligands. The basis for the correlation between ν 3 and ligand PAs, as well as limitations and deviations from it, are considered. It is demonstrated that the correlation evidently extends to a ligand that exhibits polydentate metal ion coordination. [ABSTRACT FROM AUTHOR]

Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics.ᅟ [ABSTRACT FROM AUTHOR]

1,4,7,10‐Tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) derivatives are applied in quantitative proteomics owing to their ability to react with different functional groups, to harbor lanthanoides and hence their compatibility with molecular and elemental mass spectrometry. The new DOTA derivatives, namely Ln‐MeCAT‐Click and Ln‐DOTA‐Dimedone, allow efficient thiol labeling and targeting sulfenation as an important post‐translational modification, respectively. Quantitative applications require the investigation of fragmentation behavior of these reagents. Therefore, the fragmentation behavior of Ln‐MeCAT‐Click and Ln‐DOTA‐Dimedone was studied using collision‐induced dissociation (CID), infrared multiphoton dissociation (IRMPD) and higher‐energy collision dissociation (HCD) using different energy levels, and the efficiency of reporter ion production was estimated. The efficiency of characteristic fragment formation was in the order IRMPD > HCD (normal energy level) > CID. On the other hand, the application of HCD at high energy levels (HCD@HE; NCE > 250%) resulted in a significant increase in reporter ion production (33–54%). This new strategy was successfully applied to generate label‐specific reporter ions for DOTA amino labeling at the N‐termini and in a quantitative fashion for the estimation of amino:thiol ratio in peptides. Copyright © 2017 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Electrospray ionization of 2,6-naphthalenedicarboxylic acid readily affords its doubly deprotonated dicarboxylate dianion ( 1 2− ). This species clusters with background water and added alcohols in an ion trap at ∼10 −3 Torr. Sequential solvation is observed to afford mono and dicoordinated ions. Surprisingly, the latter cluster ( 1 2− • 2TFE ) is protonated by 2,2,2-trifluoroethanol (TFE) whereas 1 2− and 1 2− • TFE are not even though Δ H ° acid (TFE) = 361.7 ± 2.5 kcal mol −1 (as given in the NIST website at http://webbook.nist.gov ) and the B3LYP/6-31+G(d,p) proton affinities are 384.7 ( 1 2− ), 377.6 ( 1 2− • TFE ), and 362.7 ( 1 2− • 2TFE ) kcal mol −1 . That is, only the weakest base in this series, and the dianion with an equal number of solvent molecules and charged sites, undergoes proton transfer. In a FTMS instrument at lower pressures (∼10 −8 Torr) inefficient proton abstraction is observed with the monosolvated dianion. This difference, and the observed reactivities of 1 2− , 1 2− • TFE and 1 2− • 2TFE are rationalized with the aid of computed potential energy surfaces. The chemical structures of these cluster ions were also probed via collision-induced dissociations, infrared photodissociation from 2700 to 3200 cm −1 , and extensive calculations. All of the TFE species are found to be solvated dianions, but incipient proton transfer to afford electrostatically defying anion-anion clusters is noted in two cases. In proton transfer reactions, formation of the conjugate acid as a solvated ion lowers the energy of the system and reduces the Coulomb repulsion barrier facilitating the overall process. [ABSTRACT FROM AUTHOR]

We have investigated the fragmentation behavior of a number of DOTA-metal complexes under collision-induced dissociation, infrared-multiphoton dissociation and higher-energy collisional dissociation activation conditions. Both, positive and negative ion mode electrospray ionization was applied. The results show that characteristic fragmentations were obtained for the metalcomplexes under the investigated conditions. All elemental compositions of fragment ions have been unambiguously identified by high resolution-accurate mass measurements. Certain trends, for instance eliminations of carbon dioxide, alkyl and amine residues, were observed that coincidewith the size of themetal and its locationwithin the periodic table. Additionally, lanthanide, aluminium and indium species with even oxidation state or containing a radical have been detected. To further investigate the observed water capture during activation, deuterium labeling experiments have also been carried out. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H + ·Gly) and pentafluorophenylalanine/glycine (F 5 -Phe·H + ·Gly) have been acquired in the 975–1975 cm −1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F 5 -Phe·H + ·Gly is assigned predominantly to isomers exhibiting a N H + ⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F 5 -Phe. In contrast, the spectrum Phe·H + ·Gly is found to consist of a mixture of isomers exhibiting the N H + ⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a N H + ⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H + ·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions. [ABSTRACT FROM AUTHOR]

Methionine is an essential amino acid, unfortunately prone to oxidation. The mechanism of its oxidation by • OH radicals has been studied for more than 40 years and still remains misunderstood. We have reinvestigated the oxidation of this residue in model peptides, aiming at i) improving the identification of free radicals by the use of more modern quantum chemistry methods; ii) reinvestigating the one-electron reduction potentials as a function of the position in the sequence; iii) identifying the final compounds, which were still unknown; iv) reinvestigating the intramolecular electron transfer (IET) involving this residue. [ABSTRACT FROM AUTHOR]

Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-C backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization. [ABSTRACT FROM AUTHOR]

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

As our understanding of clusters has improved, we have found that rather than being models for surface and condensed phase phenomena, clusters often display chemical and physical properties that are quite distinct from those of their atomic constituents or associated bulk materials. Indeed, identifying and utilising the unique properties of dimensionally confined species is a major theme in nanotechnology. Consequently, numerous experimental and computational methods have been employed to investigate the structures and properties of cluster systems. In this article, the techniques of infrared multiple photon dissociation and differential mobility spectrometry are discussed using the examples of [Ag·B12F12]−and tetraalkylammonium/solvent ionic clusters, respectively. [ABSTRACT FROM AUTHOR]

In this work we have studied the collision induced dissociation (CID) of C-terminally amidated, protonated di- and tri-glycine by means of chemical dynamics simulations from on-the-fly electronic structure calculations using a semi-empirical Hamiltonian. The simulations represent a collision event between the peptide and an Ar-atom addressing the reactivity at “short” time-scales, i.e. up to 5 ps. Simulations were performed for different protonation sites, greatly influencing the reactivity in agreement with what is known from the “mobile proton” model of peptide dissociation. Results are then combined with ESI-MS/MS experiments to determine the fragmentation patterns. Additionally, we used IRMPD spectra to elucidate the structure of these peptides before collisional activation and the structures of some of the CID products. Results are also compared with threshold CID experiments reported in the literature for the non-amidated peptides. Chemical dynamics simulations can provide details on the fragmentation pathways observed. We also show that it is possible to identify the protonation state(s) that are populated in the different steps involved in the fragmentation process. Finally, the chemical dynamics approach is shown to be complementary to the more typical theoretical study of the potential energy surface that becomes more problematic (and sometimes impossible) for systems of increasing complexity. [ABSTRACT FROM AUTHOR]

The structure and the dynamics of the isomerization of a n ions, which are observed upon low-energy collision induced dissociation of protonated peptides in tandem mass spectrometry (MS/MS), are investigated using a combination of gas phase infrared spectroscopy and theory. IR spectra in the fingerprint region are discussed, but a particular emphasis is given to the NH stretching region which turns out to be highly structurally diagnostic. Overall, theory and infrared spectroscopy provide compelling evidence that a n ions undergo cyclisation and/or rearrangement reactions. In the cases of the a 2 and a 3 ions of oligoglycine, the analysis of the NH stretching region is fully consistent with our previous conclusions based on the IR fingerprint spectra. In the case of the a 4 ions of oligoglycine, a band observed near 3550 cm −1 provides a clear-cut signature of the permuted imine–amide structure, thus allowing for a better structural assignment. The dynamics of the rearrangement chemistry of the imine–amide structure is discussed in details, and a critical discussion on the influence of the experimental CID conditions is proposed in the case of the YG a 2 ion. [ABSTRACT FROM AUTHOR]

Infrared multiple-photon dissociation (IRMPD) spectroscopy has been used to examine the gas-phase conformations of a series of short protonated polyproline ions (Pro 3 –Pro 6 ), their CID/IRMPD fragmentation pathways, and the associated fragment identities. Consistent with previous findings, and in combination with density functional theory (DFT) and MM/MD methods, a series of conformers for the protonated parent ions having their first peptide bond in the cis conformation has been identified. This conformation maximizes the solvation of the protonated N-terminus and stabilizes these compact globular-type conformations. This is in contrast to the PPI and PPII polyproline-type helices reported for larger polyproline peptides in solution. As well, this conformation leads to a unique fragmentation pattern upon collisional or multiple-photon activation. We report observation of the uncommon, but thermodynamically favored, diketopiperazine-type b 2 + fragment ion. Formation of b 2 + ions along the diketopiperazine pathway is in line with a cis configuration of the first amide linkage in the protonated parent ion. Additionally, the parent ion conformations, fragmentation pathways, and proton affinities of the resulting fragments have been related to the observed proline-effect in CID mass spectra. [ABSTRACT FROM AUTHOR]

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]