Empirical approach for predicting mass spectra

Thread starter Spathi
Start date Jun 22, 2024

Click For Summary

SUMMARY

The discussion focuses on predicting mass spectra of new molecules using a semi-empirical Born-Oppenheimer Molecular Dynamics (BOMD) computation. The proposed program allows users to input a molecule's structure and a peak position in the mass spectrum, subsequently enumerating possible fragment ions that could produce that peak. The conversation highlights the significance of empirical knowledge in mass spectrometry, particularly regarding common rearrangements like the McLafferty rearrangement. The algorithm aims to systematically explore bond removals and fragment recombinations to enhance the understanding of mass spectral data.

PREREQUISITES

Understanding of mass spectrometry principles
Familiarity with semi-empirical BOMD computations
Knowledge of molecular structure representation
Basic concepts of ion fragmentation and rearrangement mechanisms

NEXT STEPS

Research common rearrangements in mass spectrometry, focusing on the McLafferty rearrangement
Explore algorithms for molecular fragmentation and recombination
Learn about software tools for simulating mass spectra
Investigate empirical approaches to mass spectrum prediction

USEFUL FOR

Chemists, computational chemists, and researchers in mass spectrometry who are interested in molecular fragmentation and spectrum prediction techniques.

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: