Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H+)2and TLK(H+)2fragmentation dynamics, and with thermal simulations

Homayoon, Zahra; Macaluso, Veronica; Somer, Ana Martín; Muniz, Maria Carolina; Borges, Itamar; Hase, William L.; Spezia, Riccardo

doi:10.1039/c7cp06818b

Cited by 25 publications

(30 citation statements)

References 65 publications

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“…In order to confirm the above scenario, simulations and/or evaporation rates calculation would have to be conducted to describe the fragmentation channels in details. Such molecular dynamics simulations have already been performed by Spezia and coworkers to understand the collisional induced dissociation of various organic molecules [9,10,43,44]. Although in the present case the initial position of the excess proton appears as a key parameter to explain the evaporation of neutral uracil, such simulations could be additionally conducted to provide a clearer picture on the various evaporation pathways.…”

Section: Discussionmentioning

confidence: 93%

Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study

Braud

Zamith

Cuny

et al. 2019

The Journal of Chemical Physics

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A collision-induced dissociation study of hydrated protonated uracil (H 2 O) n=1-15 UH + clusters is reported. The mass-selected clusters collide with water molecules and rare gases at a controlled center of mass collision energy. From these measurements, absolute fragmentation cross sections and branching ratios are extracted as a function of the uracil hydration. For small clusters, up to n = 4, we observe that only neutral water molecules are evaporated upon collisions, whereas for larger clusters neutral uracil is also evaporated: this transition in the nature of the evaporation products is interpreted considering the lowest-energy isomers of each species that are obtained from a combination of density-functional based tight-binding (DFTB) and MP2 calculations. The simulations show that in (H 2 O) 1-4 UH + the proton is located on the uracil molecule or on a water molecule strongly bound to uracil whereas, in larger clusters, the proton is bound to water molecules far from uracil. This correlation between the structure of the low-energy isomers and the experimental fragmentation channel suggests that dissociation may occur in a very short time after collisions, so that energy has not enough time to be redistributed among all degrees of freedom and the ground-state geometry of the parent cluster partly determines the nature of the favored fragmentation channels. Of course, thermal dissociations originating from long lived, thus thermalized, collision complexes cannot be ruled out but they are not expected to play the major role since experimental results can be satisfactorily accounted for by assuming that the fragmentation processes are mainly impulsive.

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Section: Discussionmentioning

confidence: 93%

Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study

Braud

Zamith

Cuny

et al. 2019

The Journal of Chemical Physics

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“…However, when employing static theoretical methods, some essential aspects of the fragmentation dynamics are ignored. Chemical dynamics simulations properly address these aspects, 14–16 even for molecules as large as peptides 17, 18 . This powerful and relatively novel approach named “theoretical MS” was pioneered by Hase and coworkers for modeling mass spectrometric behavior 19–21 .…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

2020

Self Cite

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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. K E Y W O R D Schemical defense, chemical warfare nerve agents, ethyl N,Ndimethylphosphoramidocyanidate, fragmentation pathways, GA, mass spectrometry, molecular dynamics, tabun

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“…The prediction of mass spectra remains much of a challenge for the community of computational chemists. The common computational approaches employed for such endeavor include statistical rate theory calculations, MD simulations and electronic structure calculations [102][103][104][105][106][107][108][109][110][111][112][113][114][115][116]. Our automated method is very useful in this regard and can easily be coupled with MD simulations of collisions to generate theoretically-based mass spectra as described below.…”

Section: Mass Spectrometrymentioning

confidence: 99%

A Trajectory-Based Method to Explore Reaction Mechanisms

Vázquez¹,

Otero²,

Martı́nez-Núñez³

2018

Preprint

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The method tsscds, 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. The source code can be downloaded from: http://forge.cesga.es/wiki/g/tsscds/HomePage

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Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H⁺)₂and TLK(H⁺)₂fragmentation dynamics, and with thermal simulations

Cited by 25 publications

References 65 publications

Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study

Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

A Trajectory-Based Method to Explore Reaction Mechanisms

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