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Mass Spectrometry: Molecular Fragmentation Overview

Mass Spectrometry: Molecular Fragmentation Overview

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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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

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GAMA: A Robust and Automated Fragment-Based Quantum Chemistry Method for Biomolecular Systems.

Sujan Kundu¹, Arjun Saha¹

¹Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States.

The Journal of Physical Chemistry Letters

|March 18, 2026

Summary

This summary is machine-generated.

The new grid-adapted many-body analysis (GAMA2) framework accurately treats covalently bonded biomolecules. This computational chemistry method overcomes limitations in fragment-based approaches for complex molecular systems.

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Area of Science:

Computational Chemistry
Quantum Chemistry
Biomolecular Modeling

Background:

Fragment-based methods struggle with covalently bonded biomolecules due to disrupted electron correlation.
Existing methods often fail to accurately and efficiently treat both covalent and noncovalent systems.

Purpose of the Study:

To extend the grid-adapted many-body analysis (GAMA) framework to handle covalently bonded biomolecules.
To develop GAMA2, an automated protocol for accurate quantum chemical treatment of biomolecular systems.

Main Methods:

GAMA2 utilizes a grid-based fragmentation scheme with overlapping fragments.
It employs a many-body expansion truncated at the two-body order.
A multilayer low-level correction is integrated into the framework.

Main Results:

GAMA2 accurately reproduces supersystem MP2/6-311G(d,p) energies for diverse peptides with low absolute errors (0.01-5 kcal/mol).
Performance significantly improves over Hartree-Fock (HF) when using accurate DFT-based methods.
Demonstrates substantial computational speedup compared to full MP2 calculations.

Conclusions:

GAMA2 overcomes limitations in fragment-based quantum chemical treatments of biomolecules.
It offers a scalable, efficient, and systematically improvable method for correlated quantum chemical calculations.
This framework provides a novel approach for studying complex biomolecular systems.