Studying the Intrinsic Reactivity of Chromanes by Gas-Phase Infrared Spectroscopy

Tandem mass spectrometry is routinely used for the structural analysis of organic molecules, but many fragmentation reactions are not well understood. Because several potential structures can correspond to a measured mass, the assignment of product ions is ambiguous using mass spectrometry alone. Here, we combine mass spectrometry with high-resolution gas-phase infrared spectroscopy and computational chemistry tools to identify product ion structures and derive collision-induced fragmentation mechanisms of the chromane derivatives Trolox and Methyltrolox. We find that protonated Trolox and Methyltrolox fragment identically via dehydration and decarbonylation, while deprotonated ions display substantially diverging reactivities. For deprotonated Methyltrolox, we observe unusual radical fragmentation reactions and suggest a [1,2]-Wittig rearrangement involving aryl migration in the gas phase. Overall, the combined experimental and theoretical approach presented here revealed complex proton dynamics and intramolecular rearrangement reactions, which expand our understanding on structure-reactivity relationships of isolated molecules in different protonation states.

Ab initio molecular dynamics calculations on electron ionization induced fragmentations of C4F7N and C5F10O for understanding their decompositions under discharge conditions

C₄F₇N and C₅F₁₀O are the most promising SF₆ alternatives as eco-friendly insulating gaseous mediums in electrical engineering. It is necessary to clarify their electrical stability and decomposition mechanisms. In this work, we first introduced our experimental results for decomposition products of C₄F₇N/CO₂ and C₅F₁₀O/synthetic air mixtures under partial discharge and spark discharge conditions. Then, we performed ab initio molecular dynamics (AIMD) simulations on the typical decomposition products. The simulations were performed under standard electron impact mass spectrometry (EI-MS); thus, the statistical results of the mass spectra were compared with those of the experimentally obtained standard mass spectra from the NIST database. The AIMD simulation method in simulating the electron-induced ionization process was verified and found to be reliable. Finally, the calculations were also performed for C₄F₇N and C₅F₁₀O with incident electron energies of 20 eV and 70 eV, respectively. The dominant pathway for both gases is the formation of CF₃⁺ with the fracture of the C-C bond. The AIMD simulation is able to predict the decomposition channels after electron-impact ionization without any preconceived knowledge of fragmentation pathways, which provides a novel insight into understanding the decomposition mechanisms of C₄F₇N and C₅F₁₀O under different discharge conditions with different energies.

Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules

Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.

Ab Initio Molecular Dynamics of Temporary Anions Using Complex Absorbing Potentials

Dissociative electron attachment, that is, the cleavage of chemical bonds induced by low-energy electrons, is difficult to model with standard quantum-chemical methods because the involved anions are not bound but subject to autodetachment. We present here a new computational development for simulating the dynamics of temporary anions on complex-valued potential energy surfaces. The imaginary part of these surfaces describes electron loss, whereas the gradient of the real part represents the force on the nuclei. In our method, the forces are computed analytically based on Hartree-Fock theory with a complex absorbing potential. Ab initio molecular dynamics simulations for the temporary anions of dinitrogen, ethylene, chloroethane, and the five mono- to tetrachlorinated ethylenes show qualitative agreement with experiments and offer mechanistic insights into dissociative electron attachments. The results also demonstrate how our method evenhandedly deals with molecules that may undergo dissociation upon electron attachment and those which only undergo autodetachment.

From QCEIMS to QCxMS: A Tool to Routinely Calculate CID Mass Spectra Using Molecular Dynamics

Mass spectrometry (MS) is a powerful tool in chemical research and substance identification. For the computational modeling of electron ionization MS, we have developed the quantum-chemical electron ionization mass spectra (QCEIMS) program. Here, we present an extension of QCEIMS to calculate collision-induced dissociation (CID) spectra. The more general applicability is accounted for by the new name QCxMS, where "x" refers to EI or CID. To this end, fragmentation and rearrangement reactions are computed "on-the-fly" in Born-Oppenheimer molecular dynamics (MD) simulations with the semiempirical GFN2-xTB Hamiltonian, which provides an efficient quantum mechanical description of all elements up to Z = 86 (Rn). Through the explicit modeling of multicollision processes between precursor ions and neutral gas atoms as well as temperature-induced decomposition reactions, QCxMS provides detailed insight into the collision kinetics and fragmentation pathways. In combination with the CREST program to determine the preferential protonation sites, QCxMS becomes the first standalone MD-based program that can predict mass spectra based solely on molecular structures as input. We demonstrate this for six organic molecules with masses ranging from 159 to 296 Da, for which QCxMS yields CID spectra in reasonable agreement with experiments.

A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics

Metabolomics, the comprehensive study of the metabolome, and lipidomics-the large-scale study of pathways and networks of cellular lipids-are major driving forces in enabling personalized medicine. Complicated and error-prone data analysis still remains a bottleneck, however, especially for identifying novel metabolites. Comparing experimental mass spectra to curated databases containing reference spectra has been the gold standard for identification of compounds, but constructing such databases is a costly and time-demanding task. Many software applications try to circumvent this process by utilizing cutting-edge advances in computational methods-including quantum chemistry and machine learning-and simulate mass spectra by performing theoretical, so called in silico fragmentations of compounds. Other solutions concentrate directly on experimental spectra and try to identify structural properties by investigating reoccurring patterns and the relationships between them. The considerable progress made in the field allows recent approaches to provide valuable clues to expedite annotation of experimental mass spectra. This review sheds light on individual strengths and weaknesses of these tools, and attempts to evaluate them-especially in view of lipidomics, when considering complex mixtures found in biological samples as well as mass spectrometer inter-instrument variability.

Low-energy electron scattering by cyanamide: anion spectra and dissociation pathways

The low-energy anion spectra of cyanamide and its rare tautomer carbodiimide were surveyed with elastic electron scattering calculations. Our assignments differ qualitatively and quantitatively from a previous theoretical report. We support that both tautomers present two π* and two shape resonances, while cyanamide should also display a dipole bound state and a shape resonance. Available dissociative electron attachment measurements have shown several structures for dehydrogenation below 4 eV, but no sharp peaks related to vibrational Feshbach resonances. The absence of these resonances is explained by the lack of a potential barrier for tunneling of the hydrogen atom, despite the coupling between dipole bound and states. We found that the π* resonances initiate the dynamics that lead to hydrogen loss at 1.5, 2.5 and 3 eV. The later two structures arise from the anion states of cyanamide, while carbodiimide should account for the lower-lying one. The rarity of the second tautomer would be offset by its larger dissociative electron attachment cross section, enough to leave a distinct signature in the measured ion yield spectra. Low-energy electrons should thus decompose carbodiimide much more efficiently than cyanamide.

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules

We introduce a fully stand-alone version of the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) program [S. Grimme, Angew. Chem. Int. Ed., 2013, 52, 6306] allowing efficient simulations for molecules composed of elements with atomic numbers up to Z = 86. The recently developed extended tight-binding semi-empirical method GFN-xTB has been combined with QCEIMS, thereby eliminating dependencies on third-party electronic structure software. Furthermore, for reasonable calculations of ionization potentials, as required by the method, a second tight-binding variant, IPEA-xTB, is introduced here. This novel combination of methods allows the automatic, fast and reasonably accurate computation of electron ionization mass spectra for structurally different molecules across the periodic table. In order to validate and inspect the transferability of the method, we perform large-scale simulations for some representative organic, organometallic, and main-group inorganic systems. Theoretical spectra for 23 molecules are compared directly to experimental data taken from standard databases. For the first time, realistic quantum chemistry based EI-MS for organometallic systems like ferrocene or copper(ii)acetylacetonate are presented. Compared to previously used semiempirical methods, GFN-xTB is faster, more robust, and yields overall higher quality spectra. The partially analysed theoretical reaction and fragmentation mechanisms are chemically reasonable and reveal in unprecedented detail the extreme complexity of high energy gas phase ion chemistry including complicated rearrangement reactions prior to dissociation.