Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Bauer, Christoph; Grimme, Stefan

doi:10.1021/jp5096618

Cited by 44 publications

(55 citation statements)

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“…The pair of ions that can originate from a single cleavage of the original molecular ion (in the case of tabun, m/z 162) is known as complementary fragments. Because they occur in the same trajectory, the sum of the statistical charges of complementary fragments is always equal to one 41 . Naturally, the mechanism of generation of both fragments is identical.…”

Section: Resultsmentioning

confidence: 99%

“…The result is a value between 0 and 1, representing respectively that the spectra have nothing in common or that they overlap exactly 39 . The composite matching score algorithm includes additionally to the dot product algorithm the comparison between neighboring peaks; hence, it computes a spectral topology (i.e., the distribution of the peaks in the EI/MS) 39, 41 …”

Section: Methodsmentioning

confidence: 99%

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Molecular dynamics simulation of the electron ionization mass spectrum of tabun

2020

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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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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

2020

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“…Concurrent with our own work presented here, Grimme reported a QC‐based approach to predict EI mass spectra in an attempt to fill the gap in the theoretical prediction of mass spectra . This method is named Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) and is based on Born–Oppenheimer Ab Initio Molecular Dynamics .…”

Section: Introductionmentioning

confidence: 97%

Quantum chemical mass spectrometry:ab initioprediction of electron ionization mass spectra and identification of new fragmentation pathways

et al. 2016

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The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6-311 + G* level of theory. This prediction is performed 'ab initio', i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.

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“…The purpose of this article is to investigate the performance of, QCEIMS, which, although having been applied to many molecules, has not yet been tested by the conventional MSp matching algorithms used to identify compounds from the MSp; an essential task if it is to be used for de novo compound identification. For this purpose, we make use of the standard programs and databases from the National Institute of Standards (NIST).…”

Section: Introductionmentioning

confidence: 99%

Quantum chemical electron impact mass spectrum prediction for de novo structure elucidation: Assessment against experimental reference data and comparison to competitive fragmentation modeling

Spackman

Bohman

Karton

et al. 2017

Int J of Quantum Chemistry

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We investigate the success of the quantum chemical electron impact mass spectrum (QCEIMS) method in predicting the electron impact mass spectra of a diverse test set of 61 small molecules selected to be representative of common fragmentations and reactions in electron impact mass spectra. Comparison with experimental spectra is performed using the standard matching algorithms, and the relative ranking position of the actual molecule matching the spectra within the NIST-11 library is examined. We find that the correct spectrum is ranked in the top two matches from structural isomers in more than 50% of the cases. QCEIMS, thus, reproduces the distribution of peaks sufficiently well to identify the compounds, with the RMSD and mean absolute difference between appropriately normalized predicted and experimental spectra being at most 9% and 3% respectively, even though the most intense peaks are often qualitatively poorly reproduced. We also compare the QCEIMS method to competitive fragmentation modeling for electron ionization, a training-based mass spectrum prediction method, and remarkably we find the QCEIMS performs equivalently or better. We conclude that QCEIMS will be very useful for those who wish to identify new compounds which are not well represented in the mass spectral databases.machine learning, mass spectrometry, quantum chemistry, simulation 1 | I N TR ODU C TI ON Mass spectrometry (MS) is of major importance for identifying the presence of small quantities of a compound in a mixture, particularly because it is several orders of magnitude more sensitive than equivalent structure determination methods. [1] Indeed, MS is often the only feasible identification method [2][3][4] in contexts like the identification of semiochemicals, [5][6][7] where abundances of critical compounds may be in the ng range.Electron-impact mass spectrometry (EIMS) coupled to some chromatographic separation techniques is, at present, likely to be the predominant form of MS practiced for small molecules. The typical protocol for identifying unknown compounds using EIMS involves matching against a known mass spectrum (MSp), using spectral libraries in conjunction with software to identify matches. [8][9][10][11][12][13] For example, the National Institute of Standards and Technology (NIST) mass spectral library (version 11) contains electron impact (EI) spectra of more than 2310 5 compounds, and may be readily searched using the NIST MS Search program. However large, such a library may only contain a tiny fraction of the total number of small molecular species found in the universe, which for molecules less than 500 Daltons in weight is estimated to be in excess of 10 60 . [14] Simply put, the huge number of possible structural isomers for each molecular formula renders it practically impossible for a library to be exhaustive. If the identification of a compound whose spectra has yet to be characterized (i.e., its spectra is not in a library) is desired, much of the value provided by MS matching/ library methods is lost (although ...

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Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Cited by 44 publications

References 44 publications

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

Quantum chemical mass spectrometry:ab initioprediction of electron ionization mass spectra and identification of new fragmentation pathways

Quantum chemical electron impact mass spectrum prediction for de novo structure elucidation: Assessment against experimental reference data and comparison to competitive fragmentation modeling

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