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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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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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Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

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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...
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Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

4.7K
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...
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Mass Spectrometry: Amine Fragmentation00:55

Mass Spectrometry: Amine Fragmentation

2.6K
Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single...
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Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

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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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Comprehensive Comparison of Molecular Fragmentation Schemes for Proteins.

Katharina Rüther1, Ken Bunge1, Lasse M Hilmer1

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Molecular fragmentation methods enable quantum chemical calculations for large systems like proteins. The pair-pair approximation to the generalized many-body expansion (pp-GMBE) showed the best accuracy, while molecular fractionation with hydrogen caps (MFHC) offered a good balance of cost and accuracy.

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Area of Science:

  • Computational chemistry
  • Quantum chemistry
  • Biomolecular modeling

Background:

  • Conventional quantum chemical (QC) methods face computational limitations with increasing system size, hindering the study of large molecules like proteins.
  • Molecular fragmentation methods offer a viable solution to overcome these scaling issues in QC calculations.
  • A common formalism has been developed for benchmarking various molecular fragmentation schemes.

Purpose of the Study:

  • To numerically compare the performance of different molecular fragmentation methods for large systems.
  • To evaluate methods including molecular fractionation with hydrogen caps (MFHC), pair-pair approximation to the generalized many-body expansion (pp-GMBE), molecules-in-molecules (MIM), and kernel energy method (KEM).
  • To assess single- and multilevel schemes with electrostatic embedding for fragment calculations.

Main Methods:

  • Implementation of a common formalism for molecular fragmentation.
  • Application of MFHC, pp-GMBE, MIM, and KEM to a set of protein systems.
  • Inclusion of single- and multilevel schemes with electrostatic embedding.
  • Evaluation of energy calculations and computational demand for each method.

Main Results:

  • The pair-pair approximation to the generalized many-body expansion (pp-GMBE) demonstrated the highest agreement with supermolecular QC reference calculations.
  • Molecular fractionation with hydrogen caps (MFHC), with added pair couplings, provided a favorable cost-accuracy ratio.
  • A direct numerical comparison of different fragmentation schemes was achieved.

Conclusions:

  • pp-GMBE is a highly accurate molecular fragmentation method for large biomolecules.
  • MFHC offers a practical alternative with good performance and computational efficiency.
  • The developed framework facilitates consistent benchmarking of molecular fragmentation techniques.