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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

6.6K
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...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
3.0K
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

2.8K
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...
2.8K
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

2.7K
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...
2.7K
Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

4.8K
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...
4.8K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.9K
Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
3.9K

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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules.

Hai-Anh Le1, Hwee-Jia Tan1, John F Ouyang1

  • 1Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543.

Journal of Chemical Theory and Computation
|November 25, 2015
PubMed
Summary
This summary is machine-generated.

A novel combined fragmentation method simplifies molecular analysis by creating small, conformation-independent fragments. This robust and accurate approach enhances energy-based fragmentation for diverse molecular studies.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biochemistry

Background:

  • Energy-based fragmentation is crucial for molecular analysis.
  • Existing methods have limitations in simplicity, robustness, or fragment characteristics.
  • Previous work provides a foundation for improved fragmentation techniques.

Purpose of the Study:

  • To introduce a new, simplified energy-based fragmentation method.
  • To combine advantageous features of existing fragmentation approaches.
  • To develop a robust and accurate method for molecular fragmentation.

Main Methods:

  • Assigning bonded atoms into groups within the target molecule.
  • Forming fragment molecules from bonded pairs of these groups.
  • Calculating interaction energy by summing initial fragmentation energy and group interactions.

Main Results:

  • The combined fragmentation method is simple to implement and robust.
  • Generated fragments are small and independent of molecular conformation and size.
  • The method demonstrates accuracy in tests on biologically relevant molecules.

Conclusions:

  • The combined fragmentation method offers a significant advancement in molecular fragmentation.
  • Its simplicity, robustness, and accuracy make it suitable for various applications.
  • The method is effective in both vacuum and continuum solvent environments.