thermochemical-studies-ni-ii-zn-ii-ternary-complexes-using-ion

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold ...

Sorbonne Université

Dissociation chemistry of the diproline anion [Pro-H] is studied using chemical dynamics simulations coupled with quantum-chemical calculations and RRKM analysis. Pro is chosen due to its reduced size and the small number of sites where deprotonation can take place. The mechanisms leading to the two dominant collision-induced dissociation (CID) product ions are elucidated. Trajectories from a variety of isomers of [Pro-H] were followed in order to sample a larger range of possible reactivity. While different mechanisms yielding y product ions are proposed, there is only one mechanism yielding the b ion. This mechanism leads to formation of a b fragment with a diketopiperazine structure. The sole formation of a diketopiperazine b sequence ion is experimentally confirmed by infrared ion spectroscopy of the fragment anion. Furthermore, collisional and internal energy activation simulations are used in parallel to identify the different dynamical aspects of the observed reactivity.

Unimolecular Fragmentation of Deprotonated Diproline [Pro-H] Studied by Chemical Dynamics Simulations and IRMPD Spectroscopy.

In a recent direct dynamics simulations of the collision induced dissociation (CID) of the doubly protonated tripeptide threonine-isoleucine-lysine and threonine-leucine-lysine ions, TIK(H+)2 and TLK(H+)2, a shattering fragmentation mechanism was found, in which the ion fragmented upon impact with N2 (Z. Homayoon et al., Phys. Chem. Chem. Phys., 2018, 20, 3614). In using models to interpret experiments of biological ion CID, it is important to know the collision energy threshold for the shattering mechanism. In the work presented here, direct dynamics simulations were performed to study shattering fragmentation versus the collision energy (Erel) for N2 + TIK(H+)2. From the probability of shattering fragmentation and the minimum energy transfer for fragmentation versus Erel, a threshold of ∼55 kcal mol-1 was identified for N2 + TIK(H+)2 shattering fragmentation. This threshold is substantially higher than the lowest activation energy of 14.7 kcal mol-1, found from direct dynamics simulations, for the thermal dissociation of TIK(H+)2.

Threshold for shattering fragmentation in collision-induced dissociation of the doubly protonated tripeptide TIK(H).

Low-energy collision-induced dissociation (CID) of deprotonated l-cysteine S-sulfate, [cysS-SO], delivered in the gas phase by electrospray ionization, has been found to provide a means to form deprotonated l-cysteine sulfenic acid, which is a fleeting intermediate in biological media. The reaction mechanism underlying this process is the focus of the present contribution. At the same time, other novel species are formed, which were not observed in previous experiments. To understand fragmentation pathways of [cysS-SO], reactive chemical dynamics simulations coupled with a novel algorithm for automatic determination of intermediates and transition states were performed. This approach has allowed the identification of the mechanisms involved and explained the experimental fragmentation pathways. Chemical dynamics simulations have shown that a roaming-like mechanism can be at the origin of l-cysteine sulfenic acid.

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

In the present work, we have investigated the possibility of using the quantum thermal bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is used in introducing nuclear quantum effects with a computational time, which is basically the same as in Newtonian simulations. At this end, we have considered the model fragmentation of CH for which an analytical function is present in the literature. Moreover, based on the same model, a microcanonical algorithm, which monitors the zero-point energy of products and eventually modifies trajectories, was recently proposed. We have thus compared classical and quantum rate constants with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study, with molecular simulations, unimolecular fragmentation of much complex systems. The role of a QTB thermostat in rotational degrees of freedom is also analyzed and discussed.

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulation.

In this work, chemical dynamics simulations were optimized and used to predict fragmentation mass spectra for DNA adduct structural determination. O-methylguanine (O-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.

Fragmentation Spectra Prediction and DNA Adducts Structural Determination.

A novel approach has been developed to synthesize complex organic molecules (COMs) relevant to prebiotic chemistry, using infrared (IR) radiation to trigger the reaction. An original laboratory reactor working at low gas density and using IR irradiation was developed. In this way, glycine, the simplest brick of life, has been synthesized by assisting ion-molecule reaction with IR laser light. The ion-molecule complex constituted by acetic acid and hydroxylamine was formed in a mass spectrometer reactor and then irradiated with IR photons. As photoproducts, we obtained both glycine structures and some of its isomers. Anharmonic vibrational frequency calculations and fragmentation dynamics simulations allow for a better interpretation of the experimental data. This novel approach can be now extended to study other new synthetic pathways responsible for the formation of further COMs also with potential prebiotic relevance.

Infrared-Assisted Synthesis of Prebiotic Glycine.

High pressure effects on the Diels-Alder reaction in condensed phase are investigated by means of theoretical methods, employing advanced multiscale modeling approaches based on physically grounded models. The simulations reveal how the increase of pressure from 1 to 10 000 atm (10 katm) does not affect the stability of the reaction products, modifying the kinetics of the process by lowering considerably the transition state energy. The reaction profile at high pressure remarkably differs from that at 1 atm, showing a submerged TS and a pre-TS structure lower in energy. The different solvation between endo and exo pre-TS is revealed as the driving force pushing the reaction toward a much higher preference for the endo product at high pressure.

Solvation effects drive the selectivity in Diels-Alder reaction under hyperbaric conditions.

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding in reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal mol-1 which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal mol-1 identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile.

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

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.

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

Atomic nitrogen is formed in the high-temperature shock layer of hypersonic vehicles and contributes to the ablation of their thermal protection systems (TPSs). To gain atomic-level understanding of the ablation of carbon-based TPS, collisions of hyperthermal atomic nitrogen on representative carbon surfaces have recently be investigated using molecular beams. In this work, we report direct dynamics simulations of atomic-nitrogen [N(S)] collisions with pristine, defected, and oxidized graphene. Apart from non-reactive scattering of nitrogen atoms, various forms of nitridation of graphene were observed in our simulations. Furthermore, a number of gaseous molecules, including the experimentally observed CN molecule, have been found to desorb as a result of N-atom bombardment. These results provide a foundation for understanding the molecular beam experiment and for modeling the ablation of carbon-based TPSs and for future improvement of their properties.

Exploring reactivity and product formation in N(S) collisions with pristine and defected graphene with direct dynamics simulations.

Thermometer ions are widely used to calibrate the internal energy of the ions produced by electrospray ionization in mass spectrometry. Typically, benzylpyridinium ions with different substituents are used. More recently, benzhydrylpyridinium ions were proposed for their lower bond dissociation energies. Direct dynamics simulations using M06-2X/6-31G(d), DFTB, and PM6-D3 are performed to characterize the activation energies of two representative systems: -methylbenzylpyridinium ion (-Me-BnPy) and methyl,methylbenzhydrylpyridinium ion (Me,Me-BhPy). Simulation results are used to calculate rate constants for the two systems. These rate constants and their uncertainties are used to find the Arrhenius activation energies and RRK fitted threshold energies which give reasonable agreement with calculated bond dissociation energies at the same level of theory. There is only one fragmentation mechanism observed for both systems, which involves C-N bond dissociation via a loose transition state, to generate either benzylium or benzhydrylium ion and a neutral pyridine molecule. For -Me-BnPy using DFTB and PM6-D3 the formation of tropylium ion, from rearrangement of benzylium ion, was observed but only at higher excitation energies and for longer simulation times. These observations suggest that there is no competition between reaction pathways that could affect the reliability of internal energy calibrations. Finally, we suggest using DFTB with a modified-Arrhenius model in future studies.

Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations.

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.

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

Article	Year
Unimolecular Fragmentation of Deprotonated Diproline [Pro-H] Studied by Chemical Dynamics Simulations and IRMPD Spectroscopy. The journal of physical chemistry. A\| PubMed ID: 29451797	2018
Threshold for shattering fragmentation in collision-induced dissociation of the doubly protonated tripeptide TIK(H). Physical chemistry chemical physics : PCCP\| PubMed ID: 30039132	2018
l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. The journal of physical chemistry. A\| PubMed ID: 30945861	2019
On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulation. The journal of physical chemistry. A\| PubMed ID: 31509415	2019
Fragmentation Spectra Prediction and DNA Adducts Structural Determination. Journal of the American Society for Mass Spectrometry\| PubMed ID: 31696434	2019
Infrared-Assisted Synthesis of Prebiotic Glycine. Chemphyschem : a European journal of chemical physics and physical chemistry\| PubMed ID: 31990427	2020
Solvation effects drive the selectivity in Diels-Alder reaction under hyperbaric conditions. Chemical communications (Cambridge, England)\| PubMed ID: 32432613	2020
Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide. Physical chemistry chemical physics : PCCP\| PubMed ID: 32596702	2020
Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces. Journal of the American Society for Mass Spectrometry\| PubMed ID: 32881516	2020
Exploring reactivity and product formation in N(S) collisions with pristine and defected graphene with direct dynamics simulations. The Journal of chemical physics\| PubMed ID: 33187414	2020
Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations. Journal of the American Society for Mass Spectrometry\| PubMed ID: 33210535	2021
Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories. The Journal of chemical physics\| PubMed ID: 34598552	2021

Riccardo Spezia

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