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A Molecular Fragment Database Generated through Simulated Sequential Single-Bond-Breaking.

Jesse Fraser1,2, Arun S Moorthy1,2

  • 1Applied Modelling and Quantitative Methods Graduate Program, Trent University, Peterborough, ON K9L 0G2, Canada.

Journal of the American Society for Mass Spectrometry
|September 17, 2025
PubMed
Summary
This summary is machine-generated.

We developed the Simulated Sequential Single-Bond-Breaking (3S2B) algorithm to generate molecular fragments. This creates a database for predicting structures, evaluating mass spectra, and identifying unknown compounds.

Keywords:
algorithmdrug identificationmass spectral interpretationnumerical simulation

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Area of Science:

  • Computational Chemistry
  • Cheminformatics
  • Mass Spectrometry

Background:

  • Accurate molecular structure elucidation is crucial in chemistry.
  • Mass spectrometry is a powerful tool for molecular analysis.
  • Generating and utilizing molecular fragment databases can aid structure determination.

Purpose of the Study:

  • To introduce the Simulated Sequential Single-Bond-Breaking (3S2B) algorithm.
  • To create a searchable molecular fragment database.
  • To demonstrate the utility of this database in mass spectrometry applications.

Main Methods:

  • The 3S2B algorithm simulates sequential single-bond cleavages to generate molecular fragments.
  • A database of these fragments was constructed from a list of chemical structures.
  • The database was applied to predict structures from mass values, evaluate spectra, and identify unknowns.

Main Results:

  • A straightforward algorithm for generating molecular fragments was successfully implemented.
  • A searchable database of molecular fragments was created.
  • The database demonstrated utility in predicting molecular structures, assessing mass spectra quality, and identifying unknown compounds.

Conclusions:

  • The 3S2B algorithm provides a novel method for generating molecular fragments.
  • The resulting molecular fragment database is a valuable resource for mass spectrometry-based compound identification and structure elucidation.
  • The developed algorithm and database offer potential for advancing chemical analysis.