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Mass Spectrometry: Cycloalkene Fragmentation00:54

Mass Spectrometry: Cycloalkene Fragmentation

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The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels–Alder reaction.
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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.
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Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

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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.
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Mass Spectrometry: Aldehyde and Ketone Fragmentation01:09

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In mass spectrometry, the fragmentation of aliphatic aldehydes and ketones generally occurs through three key mechanisms: α-cleavage, inductive cleavage, and the McLafferty rearrangement.
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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Mass Spectrometry: Alkene Fragmentation00:59

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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...
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FragmentRetro: A Quadratic Retrosynthetic Method Based on Fragmentation Algorithms.

Yu Shee1, Anthony M Smaldone1, Anton Morgunov1

  • 1Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States.

Journal of Chemical Theory and Computation
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Summary

FragmentRetro significantly improves computer-aided synthesis planning by using fragmentation algorithms to achieve quadratic complexity, outperforming traditional tree-search methods. This novel approach enhances efficiency in retrosynthesis for complex molecule discovery.

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Area of Science:

  • Computational Chemistry
  • Organic Synthesis
  • Cheminformatics

Background:

  • Retrosynthesis is essential for computer-aided synthesis planning (CASP).
  • Existing tree-search methods in CASP face challenges with exponential computational complexity.
  • Efficient retrosynthetic analysis is critical for accelerating drug discovery and chemical synthesis.

Purpose of the Study:

  • To introduce FragmentRetro, a novel method for retrosynthesis.
  • To address the computational complexity limitations of current CASP methods.
  • To develop a scalable and efficient approach for identifying retrosynthetic solutions.

Main Methods:

  • FragmentRetro utilizes fragmentation algorithms (BRICS, r-BRICS) combined with stock-aware exploration.
  • Employs pattern fingerprint screening to reduce substructure matching complexity.
  • Achieves quadratic time complexity, O(h^2), compared to exponential complexity of tree search.

Main Results:

  • FragmentRetro demonstrates high solved rates and competitive runtime on benchmark datasets (PaRoutes, USPTO-190, natural products).
  • The method successfully solves cases where tree search methods fail.
  • Fingerprint screening significantly enhances the efficiency of substructure matching.

Conclusions:

  • FragmentRetro offers a computationally advantageous method for retrosynthesis, achieving quadratic complexity.
  • The approach provides strategic starting candidates for synthesis planning.
  • FragmentRetro serves as a foundational component for scalable and automated synthesis planning systems.