Quasiclassical dynamics simulation of the collision-induced dissociation of Cr(CO)6+ with Xe

Dynamically Hidden Reaction Paths in the Reaction of CF3+ + CO

Reaction paths on a potential energy surface are widely used in quantum chemical studies of chemical reactions. The recently developed global reaction route mapping (GRRM) strategy automatically constructs a reaction route map, which provides a complete picture of the reaction. Here, we thoroughly investigate the correspondence between the reaction route map and the actual chemical reaction dynamics for the CF₃⁺ + CO reaction studied by guided ion beam tandem mass spectrometry (GIBMS). In our experiments, FCO⁺, CF₂⁺, and CF⁺ product ions were observed, whereas if the collision partner is N₂, only CF₂⁺ is observed. Interestingly, for reaction with CO, GRRM-predicted reaction paths leading to the CF⁺ + F₂CO product channel are found at a barrier height of about 2.5 eV, whereas the experimentally obtained threshold for CF⁺ formation was 7.48 ± 0.15 eV. In other words, the ion was not obviously observed in the GIBMS experiment, unless a much higher collision energy than the requisite energy threshold was provided. On-the-fly molecular dynamics simulations revealed a mechanism that hides these reaction paths, in which a non-statistical energy distribution at the first collisionally reached transition state prevents the reaction from proceeding along some reaction paths. Our results highlight the existence of dynamically hidden reaction paths that may be inaccessible in experiments at specific energies and hence the importance of reaction dynamics in controlling the destinations of chemical reactions.

Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations

Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in order to provide a detailed description of recent experimental measurements [Braud et al., J. Chem. Phys., 2019, 150, 014303], collision simulations between low-energy protonated uracil water clusters (H₂O)_1-7,11,12UH⁺ and an Ar atom were performed using a quantum mechanics/molecular mechanics formalism based on the self-consistent-charge density-functional based tight-binding method. The theoretical proportion of formed neutral vs. protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the present simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. We demonstrate that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and of their relative abundances demonstrate that, up to 7 water molecules, a direct dissociation mechanism occurs after collision whereas for 11 and 12 water molecules a statistical mechanism is more likely to participate. Although scarce in the literature, the present simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular species.

Simulation of the electron ionization mass spectra of the Novichok nerve agent

Novichok is one of the most feared and controversial nerve agents, which existence was confirmed only after the Salisbury attack in 2018. A new attack on August 2020, in Russia, was confirmed. After the 2018 attack, the agent was included in the list of the most dangerous chemicals of the Chemical Weapons Convention (CWC). However, information related to its electron ionization mass spectrometry (EI/MS), essential for unambiguous identification, is scarce. Therefore, investigations about Novichok EI/MS are urgent. In this work, we employed Born-Oppenheimer molecular dynamics through the Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) method to simulate and rationalize the EI/MS spectra and fragmentation pathways of 32 Novichok molecules recently incorporated into the CWC. The comparison of additional simulations with the measured EI spectrum of another Novichok analog is very favorable. A general scheme of the fragmentation pathways derived from simulation results was presented. The present results will be useful for elucidation and prediction of the EI spectra and fragmentation pathways of the dangerous Novichok nerve agent.

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.

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.

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.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide

Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).

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.

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales

In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol⁻¹ (300 kcal mol⁻¹ in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH⁻ group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH⁻ as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.

On the gas phase fragmentation of protonated uracil: a statistical perspective

The major fragmentation pathways of protonated uracil calculated in this work using statistical methods agree with mass spectrometry experiments.

Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments

In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide-M(2+) (M = Ca, Sr)

A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.

Dissociation of the anthracene radical cation: a comparative look at iPEPICO and collision-induced dissociation mass spectrometry results

The dissociation of the anthracene radical cation has been studied using two different methods: imaging photoelectron photoion coincidence spectrometry (iPEPCO) and atmospheric pressure chemical ionization-collision induced dissociation mass spectrometry (APCI-CID). Four reactions were investigated: (R1) C14H10(+•) → C14H9(+) + H, (R2) C14H9(+) → C14H8(+•) + H, (R3) C14H10(+•) → C12H8(+•) + C2H2 and (R4) C14H10(+•) → C10H8(+•) + C4H2. An attempt was made to assign structures to each fragment ion, and although there is still room for debate whether for the C12H8(+•) fragment ion is a cyclobuta[b]naphthalene or a biphenylene cation, our modeling results and calculations appear to suggest the more likely structure is cyclobuta[b]naphthalene. The results from the iPEPICO fitting of the dissociation of ionized anthracene are E0 = 4.28 ± 0.30 eV (R1), 2.71 ± 0.20 eV (R2), and 4.20 ± 0.30 eV (average of reaction R3) whereas the Δ(‡)S values (in J K(-1) mol(-1)) are 12 ± 15 (R1), 0 ± 15 (R2), and either 7 ± 10 (using cyclobuta[b]naphthalene ion fragment in reaction R3) or 22 ± 10 (using the biphenylene ion fragment in reaction R3). Modeling of the APCI-CID breakdown diagrams required an estimate of the postcollision internal energy distribution, which was arbitrarily assumed to correspond to a Boltzmann distribution in this study. One goal of this work was to determine if this assumption yields satisfactory energetics in agreement with the more constrained and theoretically vetted iPEPICO results. In the end, it did, with the APCI-CID results being similar.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.

Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer

Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes.

The mechanisms of collisional activation of ions in mass spectrometry

This article is a review of the mechanisms responsible for collisional activation of ions in mass spectrometers. Part I gives a general introduction to the processes occurring when a projectile ion and neutral target collide. The theoretical background to the physical phenomena of curve-crossing excitation (for electronic and vibrational excitation), impulsive collisions (for direct translational to vibrational energy transfer), and the formation of long-lived collision intermediates is presented. Part II highlights the experimental and computational investigations that have been made into collisional activation for four experimental conditions: high (>100 eV) and intermediate (1-100 eV) center-of-mass collision energies, slow heating collisions (multiple low-energy collisions) and collisions with surfaces. The emphasis in this section is on the derived post-collision internal energy distributions that have been found to be typical for projectile ions undergoing collisions in these regimes.

Ab initio and analytic intermolecular potentials for Ar–CH3OH

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar-CH(3)OH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH(3)OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar-C, Ar-O, Ar-H(C), and Ar-H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol(-1), and adding an additional r(-n) term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar-CH(3)OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol(-1) with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol(-1) smaller than this value. The well depths of the other two minima are within 0.16 kcal mol(-1) of the global minimum. The analytic Ar-CH(3)OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol(-1) of the ab initio values. Combining this Ar-CH(3)OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.