Empirical approach for predicting mass spectra

Thread starter Spathi
Start date Jun 22, 2024

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The discussion centers on predicting mass spectra for new molecules through semi-empirical Born-Oppenheimer Molecular Dynamics (BOMD) computations and the potential benefits of incorporating empirical knowledge. A proposed program aims to allow users to input a molecule's structure and a specific peak position in the mass spectrum to identify possible fragment ions responsible for that peak. The conversation highlights the challenge of excluding rearrangement ions, which frequently appear in mass spectra. Notable rearrangements mentioned include the McLafferty rearrangement and double bond migrations, prompting inquiries about other common rearrangements. The proposed algorithm would analyze bond pairs, remove them, and explore the resulting fragment structures. The utility of this approach for chemists working with mass spectrometry is questioned, suggesting it could enhance the understanding of fragmentation patterns.

Jun 22, 2024

Spathi

Gold Member

TL;DR: I know about the McLafferty rearrangement and the migration of the double bond; maybe there are some other such well-known rearrangements?

One of ways of predicting a mass spectrum of a new molecule is to run a semi-empirical BOMD computation where the molecule is ionized, gets a big energy and starts dissociating. However, I suppose that in many cases a better approach is using some empirical knowledge about the molecule.
I plan to implement a program where you can specify the structure of your molecule, then type the position of a peak in your mass spectrum, and the program will enumerate all possible fragment ions which can produce this peak. One approach is to exclude all rearrangement ions. However, I suppose that the rearrangement ions occur in the mass spectrums quite oftenly. What are the most typical types of rearrangements in the mass spectrum? I know about the McLafferty rearrangement and the migration of the double bond; maybe there are some other such well-known rearrangements?
I am thinking of implementing the following algorithm for checking possible ions. Consider you have this molecule:

The program will enumerate all pairs of bonds, remove these bonds and see possible structures obtained via the re-unition of the fragments. For example, when it removes the C1-C11 and C4-C21 bonds, these recombination fragments will be possible:

Would such approach be useful for chemists dealing with mass spectrometry?

Last edited: Jun 22, 2024

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