l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]-: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO₃H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO₃]^- was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO₃]^• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO₃]^- (S₁) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H⋯⋯N between the -COOH and -NH₂ groups, and two N-H⋯⋯O HBs between -NH₂ and -SO₃, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S₂) with the formation of an O-H⋯⋯N-H⋯⋯O-S chain-type binding motif competes with S₁ in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm^-1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure-reactivity correlation of Cys-SSO₃H in biologic settings.

Inter- and Intramolecular Proton Transfer in an Isolated (Cytosine-Guanine)H+ Pair: Direct Evidence from IRMPD Spectroscopy

The collision-induced dissociation of the protonated cytosine-guanine pair was studied using tandem mass spectrometry (MS³) coupled to infrared multiple photon dissociation spectroscopy with the free electron laser at Orsay (CLIO) to determine the structure of the CH⁺ and GH⁺ ionic fragments. The results were rationalized with the help of electronic structure calculations at the density functional theory level with the B3LYP/6-311++G(3df,2p) method. Several tautomers of each fragment were identified for the first time, some of which were previously predicted by other authors. In addition, two unexpected and minor tautomers were also found: cytosine keto-imino [CKI(1,2,3,4)H⁺] and guanine keto-amino [GKA(1,3,7)H⁺]. These results highlight the importance of the DNA base tautomerization assisted by inter- and intramolecular proton or hydrogen transfer within the protonated pairs.

New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH₃ (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.

Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories

In this paper, we report how graph theory can be used to analyze an ensemble of independent molecular trajectories, which can react during the simulation time-length, and obtain structural and kinetic information. This method is totally general and here is applied to the prototypical case of gas phase fragmentation of protonated cyclo-di-glycine. This methodology allows us to analyze the whole set of trajectories in an automatic computer-based way without the need of visual inspection but by getting all the needed information. In particular, we not only determine the appearance of different products and intermediates but also characterize the corresponding kinetics. The use of colored graph and canonical labeling allows for the correct characterization of the chemical species involved. In the present case, the simulations consist of an ensemble of unimolecular fragmentation trajectories at constant energy such that from the rate constants at different energies, the threshold energy can also be obtained for both global and specific pathways. This approach allows for the characterization of ion-molecule complexes, likely through a roaming mechanism, by properly taking into account the elusive nature of such species. Finally, it is possible to directly obtain the theoretical mass spectrum of the fragmenting species if the reacting system is an ion as in the specific example.

AutoMeKin2021: An open-source program for automated reaction discovery

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics

High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

Tabun (ethyl N,N-dimethylphosphoramidocyanidate), or GA, is a chemical warfare nerve agent produced during the World War II. The synthesis of its analogs is rather simple; thus, it is a significant threat. Furthermore, experiments with tabun and other nerve agents are greatly limited by the involved life risks and the severe restrictions imposed by the Chemical Weapons Convention. For these reasons, accurate theoretical assignment of fragmentation pathways can be especially important. In this work, we employ the Quantum Chemistry Electron Ionization Mass Spectra method, which combines molecular dynamics, quantum chemistry methods, and stochastic approaches, to accurately investigate the electron ionization/mass spectrometry (EI/MS) fragmentation spectrum and pathways of the tabun molecule. We found that different rearrangement reactions occur including a McLafferty involving the nitrile group. An essential and characteristic pathway for identification of tabun and analogs, a two-step fragmentation producing the m/z 70 ion, was confirmed. The present results will be also useful to predict EI/MS spectrum and fragmentation pathways of other members of the tabun family, namely, the O-alkyl/cycloalkyl N,N-dialkyl (methyl, ethyl, isopropyl, or propyl) phosphoramidocyanidates.

Modeling the Effects of O-Sulfonation on the CID of Serine

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of O-sulfonation on the collision-induced dissociation for serine. Toward this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m/z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m/z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The m/z 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also observed that the RM1 semiempirical method was not able to obtain all of the major peaks seen in experimens for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

Insights into Cisplatin Binding to Uracil and Thiouracils from IRMPD Spectroscopy and Tandem Mass Spectrometry

The monofunctional primary complexes cis-[PtCl(NH₃)₂(L)]⁺, formed by the reaction of cisplatin, a major chemotherapeutic agent, with four nucleobases L, i.e., uracil (U), 2-thiouracil (2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU), have been studied by a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy in both the fingerprint (900-1900 cm^-1) and the N-H/O-H stretching (3000-3800 cm^-1) ranges, energy-resolved collision-induced dissociation (CID) mass spectrometry, and density functional calculations at the B3LYP/LACVP/6-311G** level. On the basis of the comparison across the experimental features and the linear IR spectra of conceivable structures, the cisplatin residue is found to promote a monodentate interaction preferentially with the O4(S4) atoms of the canonical forms of U, 4SU, and 24dSU and to the S2 atom of 2SU, yielding the most stable structures. Additional absorptions reveal the presence of minor, alternative tautomers in the sampled ion populations of 2SU and 24dSU, underlying the ability of cisplatin to increase the prospect of (therapeutically beneficial) nucleic acid strand disorder. Implication of these evidence may provide insights into drug mechanism and design.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

Fragmentation Spectra Prediction and DNA Adducts Structural Determination

In this work, chemical dynamics simulations were optimized and used to predict fragmentation mass spectra for DNA adduct structural determination. O⁶-methylguanine (O⁶-Me-G) was used as a simple model adduct to calculate theoretical spectra for comparison with measured high-resolution fragmentation data. An automatic protocol was established to consider the different tautomers accessible at a given energy and obtain final theoretical spectra by insertion of an initial tautomer. In the work reported here, the most stable tautomer was chosen as the initial structure, but in general, any structure could be considered. Allowing for the formation of the various possible tautomers during simulation calculations was found to be important to getting a more complete fragmentation spectrum. The calculated theoretical results reproduce the experimental peaks such that it was possible to determine reaction pathways and product structures. The calculated tautomerization network was crucial to correctly identifying all the observed ion peaks, showing that a mobile proton model holds not only for peptide fragmentation but also for nucleobases. Finally, first principles results were compared to simple machine learning fragmentation models.