Introduction to QCxMS2

What is QCxMS2 ?

QCxMS2 is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using automated reaction network discovery. The program is designed to simulate the fragmentation of molecules. It is the successor of the QCxMS program, in which fragmentation reactions are simulated via Born-Oppenheimer Molecular Dynamics (MD). The different MS methods of the program are described in short below. A full list of QCxMS2 related publications is provided elsewhere.

The QCxMS2 program is available and free-of-charge at the QCxMS2 GitHub page

MS methods available

Electron Ionization

The program was originally developed to calculate Electron Ionization (EI) mass spectra, in which a (typically 70 eV) electron beam is focused on a molecule in order to create an open-shell radical ion (uneven number of valence electrons). This process not only ionizes the molecule, but simultaneously increases the internal energy of the species, which in turn leads to bond breaking, fragmentation, rearrangement, etc of the ion. A more detailed description can be found in the original publication.

Dissociative Electron Attachment

In contrast to the positive ions created by the EI process, the Dissociative Electron Attachment (DEA) ionizes the molecule under study by adding an electron. This creates a negatively charged ion (open-shell ion).

Note

The DEA mode is not yet tested for QCxMS2 but works technically. It should therefore be used with caution. The negative ions have to be described by using DFT and diffuse basis functions which increases the computational costs significantely.

Collision Induced Dissociation

Ionization of molecules can be done by (de)protonation, e.g., by the popular electrospray ionization (ESI) method. This ionization process produces closed-shell ions (even number of valence electrons) and is softer than the EI or DEA methods. It is often implemented by (de-)protonation of the molecule under study, leading to positivly or negativly charged molecular ions. The following Collision Induced Dissociation (CID) leads to a spectrum normally under lower energy conditions than in the other MS methods.

A more detailed description can be found in the respective publication.

Note

It is recommended to start with an upper estimate of the average energy, e.g. -esiatom 0.5 eV for an initial QCxMS2 calculation, and then simulate afterwards in the same directory with the -esim mode different energies (e.g. 0.2-0.5 eV) to find suitable settings for your respective molecule and experimental setup.