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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

4.8K
The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
4.8K
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

2.0K
The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example, the...
2.0K
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

2.1K
The molecular ions of linear alkanes prefer to fragment at the carbon-carbon bond away from the end of the chain since the cleavage of an inner bond creates a stable carbocation and a stable radical. Consequently, the mass signals of linear alkanes feature intense peaks in the middle of the mass-to-charge ratio plot with weaker peaks on either end. The fragmentation of each carbon-carbon bond with the release of a methyl group in each splitting leads to prominent peaks in the mass spectra...
2.1K
Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

4.1K
Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. ⍺-cleavage and dehydration. During ⍺-cleavage, the bond at the ⍺-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular...
4.1K
Mass Spectrometry: Aldehyde and Ketone Fragmentation01:09

Mass Spectrometry: Aldehyde and Ketone Fragmentation

4.3K
In mass spectrometry, the fragmentation of aliphatic aldehydes and ketones generally occurs through three key mechanisms: α-cleavage, inductive cleavage, and the McLafferty rearrangement.
4.3K
Mass Spectrometry: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

1.4K
This lesson delves into the mass spectrometry of branched alkane fragmentation. Branched alkanes possess secondary or tertiary carbon atoms, which generate relatively stable carbocations if the cleavage occurs at the branching point. The high stability of carbocations drives the instant fragmentation of branched alkanes. Accordingly, the branched alkane's molecular ion peak is very weak or invisible in the mass spectra, especially in comparison to a linear alkane.
1.4K

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Updated: Nov 21, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

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Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution

Simon Müller1

  • 1Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073, Hamburg, Germany. simon.mueller@tuhh.de.

Journal of Cheminformatics
|January 12, 2021
PubMed
Summary
This summary is machine-generated.

Automated molecular fragmentation enables faster development of predictive thermodynamic models. New algorithms successfully fragment diverse molecules for group contribution methods like UNIFAC.

Keywords:
CheminformaticsGroup contribution methodIncrementationMolecule fragmentationProperty predictionRDKitUNIFAC

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Area of Science:

  • Chemical Engineering
  • Computational Chemistry

Background:

  • Predictive thermodynamic models are crucial for industrial process development.
  • Group contribution methods rely on molecular fragmentation, often a manual bottleneck.

Purpose of the Study:

  • To develop automated strategies for molecular fragmentation.
  • To create algorithms for efficient and comprehensive group contribution analysis.

Main Methods:

  • Implementation of two novel fragmentation algorithms: one finding a single solution, the other finding all possible solutions.
  • Testing algorithms on a large database of over 20,000 molecules for the UNIFAC model.

Main Results:

  • Both algorithms successfully automated the fragmentation of all tested molecules.
  • The methods demonstrated capability in fragmenting complex structures previously considered impossible.

Conclusions:

  • Automated molecular fragmentation significantly accelerates the development of group contribution methods.
  • These algorithms enhance the scalability and applicability of predictive thermodynamic modeling.