The default settings provided in QCxMS are a good starting point for the calculations. The default setting is performing an EI calculation.
To change the behavior of the program, keywords have to be put into a qcxms.in file. The file can be created manually, or is created automatically by first running the program, using the default settings. If other run modes are required (e.g. CID or DEA), example inputs are given below. The keywords provided are points of orientation and there are more settings that can be used to tune the calculations which are described in detail in section Running QCxMS.
The default values are not always giving the best results, but are set to cover the majority of systems. Molecules have different characteristics that can significantely influence the outcome. Changing the input settings can improve upon the final result, e.g. decreasing the molecular ion peak abundance or producing more low m/z fragments.
EI - positive Ion Electron Ionization¶
ei xtb2 ntraj *<integer>* tmax *<real>*
The EI run mode is automatically used with the [default] settings described by the keywords, leading to a run using
xtb2, so actually there is no keyword required in the qcxms.in file.
To provide some guidance, the setting showed above can be used and the <integer> and <real> placeholders switched to
DEA - negative Ion Electron Ionization¶
ei <functional> <basis> charge -1 upper 15 lower 0
For EA calculations, the ma-def2-SVP/ma-def2-TZVP basis sets are recommended.
Production runs are recommended to be conducted at DFT level, however, these are computationally very expensive and GFN-xTB can be
used for a quantitative overview.
The most cost-effordable DFT settings are <functional> =
PBE | <basis> =
Less IEE energy is required for DEA fragmentation, so it is recommended to reduce the IEE distribution limits
by using the
lower keywords (the old keywords
scan are obsolete).
CID - positive Ion Collision Induced Dissociation¶
cid xtb2 charge 1 elab 40 lchamb 0.25
The general activation method is automatically used, but can also be expicitely switched on using the
For the forced activation run-type, use
The number of collisions are set by using
collno <integer> to set number of collisions (including fragment-gas
For setting ONLY ion–gas collisions, use
The thermal activation method is switched on with
temprun and scales the internal energy to a value given by the
This is the fastest method, but requires a good initial guess for the internal energy value.
For more details, see section Running QCxMS.