Introduction to QCxMS


What is QCxMS ?

QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x (x=EI, CID) to account for the greater general applicability of the program. The different MS methods of the program are described in short below. A full list of QCxMS and QCEIMS related publications is provided elsewhere.

The QCxMS program is available and free-of-charge at the QCxMS 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), which has to be described by diffuse basis functions. This increases the computational cost because DFT has to be used to compute the PES. Details on this MS method are described in this publication.

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. Activation of the ion has to be conducted in a second step, i.e., by acceleration and subsequent collisions with neutral collision gas atoms. The following Collision Induced Dissociation (CID) leads to a spectrum normally under lower energy conditions than in the other MS methods. The simulation conditions and specific details are extensively covered in this paper.