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Related Concept Videos

Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

5.2K
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...
5.2K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

3.0K
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

2.6K
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,...
2.6K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.7K
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...
3.7K
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

2.5K
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...
2.5K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

2.1K
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
2.1K

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Updated: Apr 27, 2026

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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The combined fragmentation and systematic molecular fragmentation methods.

Michael A Collins1, Milan W Cvitkovic, Ryan P A Bettens

  • 1Research School of Chemistry, Australian National University , Canberra ACT 0200, Australia.

Accounts of Chemical Research
|June 28, 2014
PubMed
Summary
This summary is machine-generated.

Computational chemistry can now estimate molecular energies using fragmentation methods like combined fragmentation method (CFM) and systematic molecular fragmentation (SMF). These techniques accurately predict reactivity and properties for large organic and biological molecules, saving time and cost.

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
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Last Updated: Apr 27, 2026

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

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Area of Science:

  • Computational Chemistry
  • Quantum Chemistry
  • Organic Chemistry

Background:

  • Molecular reactivity is traditionally linked to functional groups, but sophisticated quantum calculations often obscure this relationship.
  • Accurate estimation of molecular electronic energy is crucial for understanding chemical reactivity.
  • Calculating energies for large molecules using traditional ab initio methods is computationally intensive and time-consuming.

Purpose of the Study:

  • To introduce and explain two fragmentation methods: combined fragmentation method (CFM) and systematic molecular fragmentation (SMF).
  • To demonstrate the application of these methods for estimating energies and properties of molecules and nonconducting crystals.
  • To highlight the practical advantages of fragmentation methods in computational chemistry.

Main Methods:

  • Decomposing molecules into small fragments of adjacent functional groups.
  • Estimating electronic energy as a sum of fragment energies.
  • Applying systematic molecular fragmentation (SMF) to periodic crystal structures for energy and property calculations.

Main Results:

  • Fragmentation methods (CFM and SMF) enable accurate estimation of molecular electronic energy to chemical accuracy.
  • These methods significantly reduce computational time and cost, making calculations for large molecules feasible.
  • The approaches accurately estimate derivatives of molecular and crystal energies, enabling property predictions like NMR and vibrational spectra.

Conclusions:

  • Fragmentation methods represent a significant practical advancement in computational chemistry.
  • CFM and SMF allow for accurate and efficient energy calculations of large organic and biological molecules.
  • These methods facilitate the study of molecular reactivity and properties, previously limited by computational constraints.