Spectra Of Molecular Ions Research Articles

An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification.

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.

Molecular Ion Spectra in Glow Discharge Mass Spectrometry of Toxic and Physiologically Active Elements in Hydroxyapatite

Molecular Ion Spectra in Glow Discharge Mass Spectrometry of Toxic and Physiologically Active Elements in Hydroxyapatite

Spectroelectrochemical study of the reduction of 2-methyl-9H-thioxanthene-9-one and its S,S-dioxide and electronic absorption spectra of their molecular ions.

2-Methyl-9H-thioxanthene-9-one (1) and its S,S-dioxide (2) are the precursors of pendant groups that determine the reduction potentials of electro-active polyimides, which exhibit electrochromic behavior and are used in organic electronics. Electrochemical reduction of 1 and 2 leads to the formation of the corresponding persistent radical anions and dianion (for S,S-dioxide). Using 3D spectroelectrochemistry, all anions have been shown to exhibit strong absorption in the UV-VIS-NIR wavelength region. Electronic absorption spectra of 1 and 2 and their negative ions were interpreted using time-dependent DFT. According to the calculations, the most intense electronic transitions of the dianions 12- and 22- in the visible region exhibit hypsochromic shift compared to the intense transitions of the corresponding radical anions and have much higher oscillator strengths, which was confirmed experimentally for 2. An empirical kinetic model was proposed based on the analysis of the total charge passed through the cell during electrolysis and on the established mechanism of electrochemical reduction. This model perfectly described the UV-VIS-NIR optical density time dependences observed on 3D spectroelectrochemical surfaces for both compounds 1 and 2. This made it possible to explain the differences in the electrochromic behaviour of ambibolar electro-active polyimides with pendant groups based on 1, 2.

GC-MS with photoionization of cold molecules in supersonic molecular beams-Approaching the softest ionization method.

A new type of photoionization ion source was developed for the ionization of cold molecules in supersonic molecular beams (named Cold PI). The system was based on a GC-MS with supersonic molecular beams and its fly-through EI of cold molecules ion source (Cold EI) plus quadrupole mass analyzer. A continuously operated deuterium VUV photoionization lamp was added and placed above and between the supersonic nozzle and skimmer whereas the Cold EI ion source served only as a portion of the ion transfer ion optics. The supersonic nozzle and skimmer were voltage biased and the VUV light crossed the supersonic expansion about 10 mm from the nozzle. We obtained over three orders of magnitude enhancement in the relative abundance of the molecular ion of squalane in Cold PI versus in photoionization of this compound as a thermal compound. Accordingly, we also proved that standard photoionization is not as soft ionization method as previously perceived for large compounds. We found that Cold PI is as soft as and possibly softer than field ionization; thus, it could be the softest known ionization method. The ionization yield was about 200-300 times weaker than with Cold EI yet our limit of detection was about 200 femtogram in SIM mode for cholesterol and pyrene which is reasonable. Practically, all hydrocarbons gave only molecular ions with rather uniform response whereas alcohols gave some molecular ions plus major fragment ions particularly with a loss of water (similarly to field ionization). We tested Cold PI in the GC-MS analysis of diesel fuels and analyzed the time averaged data for group type information. We also found that we can analyze the diesel fuels by fast under 20-s flow injection analysis in which the generated averaged mass spectrum of molecular ions only could serve for the characterization of fuels.

Infrared spectroscopy of a small ion solvated by helium: OH stretching region of HeN-HOCO.

Messenger spectroscopy is a well-established method for recording infrared (IR) spectra of molecular ions. It relies upon the tagging of weakly bound atoms or molecules, known as the "messenger," to the ion of interest. The ideal tag species is helium since it has the weakest possible interaction with any molecular ion and is consequently the least likely to alter the structure and function. However, the attachment of a helium tag is challenging because of the exceptionally cold conditions that are inherently required. In this work, electron ionization of doped liquid helium nanodroplets has been used to create cations tagged with a variable number (N) of helium atoms. Mass-selective ion detection has made it possible to record IR spectra as a function of N, thus revealing the effect on the structure and charge distribution within the ionic core as solvation becomes more extensive. We illustrate this capability for protonated carbon dioxide tagged with up to 14 helium atoms, HeN-HOCO+. The first atom preferentially binds to the proton and results in a substantial redshift of 44 cm-1 for the OH stretching vibration, while the stepwise attachment of additional atoms up to N = 7 causes small and progressive blueshifts, which are attributed to the gradual formation of a ring of helium around the carbon atom. The methodology described herein offers a new route to obtain IR spectra of He-tagged ions and provides an insight into ion-solvent interactions at the molecular level.

A Novel Method to Measure Electronic Spectra of Cold Molecular Ions

A universal method has been developed for measuring spectra of molecular ions in a 22-pole radio frequency trap at 5 K. It is based on laser induced inhibition of complex growth (LIICG). The first successful measurements have been demonstrated on the A2Πu ← X2Σg+ electronic transition with some thousand N2+ ions, helium densities of 1015 cm–3, and storage times of 1 s. The reduction of the number of N2+–He complexes is the result of an interplay between excitation, radiative and collisional cooling, ternary association, and collision induced dissociation, which is explained by a kinetic model.

Assigning Predissociation Infrared Spectra of Microsolvated Hydronium Cations H3O+⋅(H2)n (n=0, 1, 2, 3) by Ab Initio Molecular Dynamics

Messenger predissociation spectroscopy is an important experimental method to obtain vibrational spectra of molecular ions or complexes such as protonated water clusters H(+)⋅(H(2)O)(n) in the gas phase. However, the molecular properties and thus the linear infrared spectra may be modified upon microsolvation with typical messengers such as H(2) molecules or noble gas atoms. Employing ab initio molecular dynamics for the H(2)-microsolvated hydronium ion, we investigate these effects explicitly as a function of an increasing number of messengers up to filling the first microsolvation shell, that is, for H(3)O(+)⋅(H(2))(n) (n=0, 1, 2, 3). We find that microsolvation with H(2) lowers the inversion barrier of the hydronium core, which governs the inversion tunnel splitting due to umbrella motion, and thus accelerates the inversion dynamics. By comparison to experiment a comprehensive band assignment for the O-H stretching region is given, and thereby the observed blueshift of stretching bands with increasing n is explained. Furthermore, detailed analyses reveal intricate intra- and intermolecular anharmonic mode couplings induced by the messengers, which yield a rich vibrational dynamics in these, at first glance, simple systems. Finally, the virtues but also the shortcomings of the ab initio molecular dynamics approach to vibrational spectroscopy are discussed.

Data Processing Algorithms for Analysis of High Resolution MSMS Spectra of Peptides with Complex Patterns of Posttranslational Modifications

The emergence of efficient fragmentation methods such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) provides the opportunity for detailed structural characterization of heavily covalently modified large peptides and small proteins such as intact histones. Even with effective gas phase ion isolation so that a single molecular precursor ion is selected, the MSMS spectrum of a heavily modified peptide may reveal the presence of a mixture of peptides with the same amino acid sequence and the same total number of posttranslational modification (PTM) moieties (same PTM composition) but with different PTM configurations or site-specific occupancy isoforms. Currently available data analysis methods depend on a deisotoping procedure, which becomes less effective when spectra (fragmentation patterns) contain many overlapping isotopic distributions. Peptide database search engines can only identify the most abundant PTM configuration (PTM arrangement on different residues) in such mixtures. To identify all the PTM configurations present in these mixtures and to estimate their relative abundances, we extended our fragment assignment by visual assistance program to search for ions representing all possible configurations, subjected to the total PTM composition constraint. This resulted in the identification of PTM configurations supported by unique fragment ions, and their relative abundances were estimated by use of a non-negative least squares procedure.

Ion Spectroscopy: Where Did It Come From; Where Is It Now; and Where Is It Going?

The ASMS conference on ion spectroscopy brought together at Asilomar on October 16-20, 2009 a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation "action spectroscopic" mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, high-resolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions.

Separation of small molecular peptides with the same amino acid composition but different sequences by high performance liquid chromatography-electrospray ionization-mass spectrometry

Peptidomics has emerged as a new discipline in recent years. Mass spectrometry (MS) is the most universal and efficient tool for structure identification of proteins and peptides. However, there is a limitation for the identification of peptides with the same amino acid composition but different sequences because these peptides have identical mass spectra of molecular ions. This paper presents a high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) method for the separation of small molecular peptides with the same amino acid composition but different sequences. Two tripeptides of Gly-Ser-Phe and Gly-Phe-Ser were used as a model sample. The separation behavior has been investigated and the separation conditions have been optimized. Under the optimum conditions, good repeatability was achieved. The developed method could provide a helpful reference for the separation of other peptides with the same amino acid composition but different sequences in the study of proteomics and peptidomics.

Separation of small molecular peptides with same amino acid composition but different sequences by capillary electrophoresis

The development of new analytical techniques for identifying endogenous peptides in a cell, organ, or organism (the peptidome) is an important work in the fields of peptidomics and proteomics. MS is currently employed as a powerful analytical technique in peptidomics. However, it has a limitation in the identification of peptides with the same amino acid composition but different sequences, as these peptides have the same molecular weights, and generate the same MS spectrum of molecular ions, when MS is used as the detection technique. Therefore, the development of peptide separation techniques like CE and LC coupled with MS is desirable. In this paper, a methodology for the separation of peptides with the same amino acid composition, but different sequences, by CE has been developed using two tripeptides, Gly-Ser-Phe and Gly-Phe-Ser, as a model sample. Excellent separation selectivity was achieved using the separation mode of MEKC. Separation behavior under different conditions and mechanism is discussed.

High-Resolution Rotational Spectroscopy in a Cold Ion Trap:H2D+andD2H+

The lowest-lying 1(01) <-- 0(00) transition of para-H(2)D(+) and 1(11) <-- 0(00) of ortho-D(2)H(+) has been detected by the enhancement of the D/H isotope exchange reaction in collisions with p-H2 upon rotational excitation. These are the first pure rotational spectra of molecular ions by action spectroscopy. For this purpose, a cryogenic multipole ion trap has been combined with narrow-band tunable radiation sources operating in the 1.25 to 1.53 THz range. The low temperature of the ions allows us to determine the astronomically important transitions with a relative precision of Delta nu/nu=10(-8). While the 1 476 605.708(15) MHz line center frequency for the o-D(2)H(+) transition agrees very well with previous unpublished work, the 1 370 084.880(20) MHz line center frequency for the p-H(2)D(+) transition deviates by 61 MHz. Potential future applications of this new approach to rotational spectroscopy are discussed.

Broadening of energy spectra of molecular ion fragments produced by surface small angle scattering

Relative half-widths of energy spectra of molecular hydrogen ions and their fragments scattered by a tungsten surface have been experimentally studied for various primary molecules and their isotopic analogues in the energy range of 100–4000 eV per nucleon. The spectra of fragments turned out to be broader than the spectra of the same particles that are not fragmentation products. The broadening is interpreted within the “explosion” model, i.e., dissociation of a molecular ion due to the change in the shape of the interaction potential of the fragments. The model of “explosive” dissociation of molecules agrees with the data obtained assuming an effective repulsion energy of 1.1 ± 0.1 eV for all molecules.

Combined Computational Metabolite Prediction and Automated Structure-Based Analysis of Mass Spectrometric Data

ABSTRACTAs high-throughput technologies have developed in the pharmaceutical industry, the demand for identification of possible metabolites using predominantly liquid chromatographic/mass spectrometry-mass spectrometry/mass spectrometry (LC/MS-MS/MS) for a large number of molecules in drug discovery has also increased. In parallel, computational technologies have also been developed to generate predictions for metabolites alongside methods to predict MS spectra and score the quality of the match with experimental spectra. The goal of the current study was to generate metabolite predictions from molecular structure with a software product, MetaDrug. In vitro microsomal incubations were used to ultimately produce MS data that could be used to verify the predictions with Apex, which is a new software tool that can predict the molecular ion spectrum and a fragmentation spectrum, automating the detailed examination of both MS and MS/MS spectra. For the test molecule imipramine used to illustrate the combined in vitro/in silico process proposed, MetaDrug predicts 16 metabolites. Following rat microsomal incubations with imipramine and analysis of the MSn data using the Apex software, strong evidence was found for imipramine and five metabolites and weaker evidence for five additional metabolites. This study suggests a new approach to streamline MS data analysis using a combination of predictive computational approaches with software capable of comparing the predicted metabolite output with empirical data when looking at drug metabolites.

Mid-infrared continuous wave cavity ring down spectroscopy of molecular ions using an optical parametric oscillator

A sensitive infrared detection scheme is presented in which continuous wave cavity ring down spectroscopy is used to record rovibrational spectra of molecular ions in direct absorption through supersonically expanding planar plasma. A cw optical parametric oscillator is used as a light source and combines a broad spectral coverage (2100–3600 cm −1) and narrow bandwidth (7 kHz) with a high output power (∼1 W) and excellent TEM 00 mode characteristics. The performance of the technique is demonstrated by recording a rotationally cold spectrum of formyl cation, HCO +, in the CH stretching region. For optimal conditions, absolute ion densities in the plasma expansion amount to 2 × 10 10 HCO +-ions/cm 3 in the detection zone.

Analysis of organoselenium compounds in human urine using active carbon and chemically modified silica sol-gel surface-assisted laser desorption/ionization high-resolution time-of-flight mass spectrometry.

Laser desorption/ionization time-of-flight mass spectra of three thermally labile low molecular weight organoselenium compounds (selenomethionine, selenoethionine, trimethylselenonium iodide) in human urine matrix have been obtained by using surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). Four active layers, active carbon, silica sol-gel, and silica sol-gel impregnated with crown ether and with active carbon, were deposited on three different support substrates: (i) microscope slide coverslips; (ii) Al foil; and (iii) Cu tapes. Primarily protonated molecular ions and alkali metal adducts were observed in the mass spectra. A mixed-silica sol-gel and active carbon substrate active layer gave the best signal response for all compounds. Sol-gel substrates offered very clean backgrounds compared to the pure active carbon layers; however, the mass spectral signal intensities acquired were substantially lower for the sol-gel surfaces than those of the pure active carbon under the same conditions. Cu tape and Al foil support materials gave strong mass spectra of molecular ions and alkali metal molecular ion adducts, with lower Na and K adducts found with the Cu tape than with Al foil. Glass coverslips gave no response under all experimental conditions examined. Aerosol deposition was used to prepare SALDI substrates to avoid the localized "sweet spot" phenomenon encountered in conventional SALDI substrate preparation. Various nebulizers were examined and found to be effective in producing SALDI films with controlled and reproducible thicknesses. We were able to obtain exact mass identification of all three selenium species by high-resolution TOF-MS. To the best of our knowledge, this is the first time low molecular weight organoselenium compounds have been identified by SALDI-high-resolution TOF-MS.

Ortho Effects in the Dissociation of Ionized N-Chlorophenyl- and N-Bromophenyl-2-Aminobenzamidines: Intramolecular Aromatic Substitution with Cyclization to Protonated 2-(2-Aminophenyl)-1H-Benzimidazoles

Electron ionization (70 eV) mass spectra, double-stage (MS2) 10 eV collision-induced dissociation (CID) product-ion mass spectra of molecular ions and triple-stage (MS3) sequential product-ion mass spectra of major fragment ions are reported for the parent N-phenyl and the isomeric ortho-, meta- and para- N-chlorophenyl- and N-bromophenyl-2-aminobenzamidines. Dissociation is greatly influenced by an ortho effect that favors the loss of ortho H atoms and particularly the loss of the ortho halogen substituents. Dissociation occurs via a two-step intramolecular aromatic substitution reaction and a distonic-ion intermediate inhibits scrambling of ring hydrogens thus favoring the loss of the ortho substituents. The ortho isomers form an abundant and diagnostic [M – X]+ fragment ion (X = Cl, Br) and are easily distinguished. Protonated 2-(1 H-benzimidazol-2-yl)-phenylammonium ions are likely formed; they dissociate mainly by NH3 loss upon CID and react readily with pyridine by proton transfer.

The Importance of VUV-Radiation in the Anode Region of High-Current Plasma Generators with Diverging Anode Channel

It is demonstrated that a region of a stable laminar mode of arc burning with diffuse flow of current to the anode exists in high-current (I ≥ 250 A, I/d ≥ 40 A/mm) plasma generators with a self-adjusting arc length and diverging anode channel. The most important mechanism providing for the volume ionization of the “plasma-anode wall” transition layer is the photoionization of the cold surface layer of gas by dense VUV-radiation transferred to the periphery from the arc core where the fully ionized plasma has a temperature above 20 000 K. The presence of high-intensity resonance radiation of singly charged nitrogen ions and its absorption at the periphery of the energy release region of the nitrogen arc enable one to explain the experimentally observed nonthermal pattern of distribution of intensity in the radiation spectrum of molecular ion of nitrogen.

Wavelength Dependence of Photooxidation vs Photofragmentation of Chromocene

Photooxidation and metal−ligand photolysis reactions of bis(cyclopentadienyl)chromium, chromocene, in the range 24 390−15 630 cm-1 are studied in the gas phase by using time-of-flight mass spectroscopic detection. Photooxidation of the intact chromocene molecule unexpectedly dominates in the range 23 530−24 000 cm-1. The relative importance of photooxidation compared to photofragmentation is strongly wavelength dependent. A prominent species at all wavelengths is the chromium ion, but in a wavelength region corresponding to the lowest energy ligand to metal charge transfer excited electronic state absorption, the strongest peak is from the chromocene ion. The excitation spectra are reported for three selected species: chromocene ion, mono(cyclopentadienyl)chromium ion, and the chromium ion. The spectrum obtained by monitoring the metal ion contains sharp peaks that are assigned to neutral chromium atom resonances. Sharp losses of intensities in the molecular ion spectra are observed at these wavelengths. The wavelength dependencies of the photoreactions are interpreted and explained in terms of the identity of the initially populated excited electronic state and the ionization energy of the molecule. When the initially populated excited electronic state is the ligand to metal charge transfer state, the first photon causes minimal bond weakening and the second photon excites the intact chromocene above the ionization energy, resulting in efficient ionization of the parent molecule. When the initially populated state is a lower energy ligand field excited electronic state, bond weakening occurs and absorption of a second photon results in significant photodissociation producing intense fragment peaks dominated by the metal ion peak.

Concentration modulation spectroscopy with a pulsed slit supersonic discharge expansion source

Frequency modulated discharges are combined with pulsed slit supersonic expansions to provide an intense, long path source of jet-cooled radicals/molecular ions for direct absorption laser spectroscopy. The high modulation frequency (100 kHz) permits lock-in detection of the modulated absorbance signals at sensitivities down to 7.3×10 −7 absorbance/Hz 1/2 (within 40% of the shot noise limit) and provides excellent discrimination for radical or molecular ion spectra in the presence of much higher precusor concentrations. The sensitivity of these methods is demonstrated with direct absorption spectral data on sample jet-cooled molecular ions (H + 3) and hydrocarbon radicals (CH 3CH 2).