.
Modeling kinetic isotope effect
(KIE), effective temperature (Teff) and kinetic energy release (KER)
of selected protonated alkylamine dimers
Welcome!
We would like to give you a short introduction
to the modeling of the dissociation of protonated alkylamine dimers.
Various properties of the selected systems, such as kinetic
isotope effect, effective temperature and kinetic energy release can be
calculated using the following known parameters:
·
experimental setup (instrumental setup, lengths, source
temperature, acceleration voltages)
·
reaction enthalpy, vibrational frequencies for reactants and
products, preexponential factor for defining the transitional state
These
parameters can be found in the first window of each MassKintetics project file.
The
details of these calculations, the summarized results for all the tested system
and the conclusions can be found in the following article:
L. Drahos, J. Sztáray and K. Vékey Int.
J. Mass Spectrom., 225 233–248 (2003)
Also one can find excellent references for the kinetic method
that was used to get the interested data from the ion ratios and also for the
KER.
The theoretical background of the MassKinetics program can be
found in the following article:
L.
Drahos and K. Vékey J. Mass Spectrom., 36, 237-263 (2001)
The types of calculations presented here:
1.
Modeling KIE and Teff
2.
Modeling KER with calculating internal energy partitioning
and calculating the kinetics energy release distributions for the product ions
3.
Modeling energy distributions: calculating the
internal energy distributions of the fragmenting parent ions and of the product
ions at different places.
The required data for each of these
calculations as well as the parameters, which have been used in the modeling
can be found in the first page of the MassKinetics project file.
Two types of experiments were
modeled: using the high-pressure ion source (VG), and using the low-pressure
ion source (JEOL). One can find the MassKinetics project files for both
systems.
Also there were 11 protonated
alkylamine systems, which were modeled and presented in the referred article.
We would like to present here two systems of those: the smallest one and the
biggest one that is the protonated methyl-amin-methyld3-amin and the protonated
dietil-amin-dietil-d2-amin system. As for the example of the distributions
calculations we only dealt with the first, smallest system, so that is
presented here too.
1. Modeling KIE and Teff
The kinetic isotope effect and the effective temperature can
be calculated of the interested system without calculating the internal energy
partitioning between the corresponding products. This means that only the
molecular ion and the two possible fragment ions are considered in the
modeling.
MassKinetics
project file for the protonated methyl-amin-methyld3-amin system using high-pressure
ion source:
Click here to download this
MassKinetics project file.
and using low-pressure ion source:
Click here to
download this MassKinetics project file.
MassKinetics
project file for the protonated diethyl-amin-diethyld2-amin system using
high-pressure ion source:
Click here to
download this MassKinetics project file.
and using low-pressure ion source:
Click here to
download this MassKinetics project file.
2.
Modeling KER with calculating internal energy partitioning
Calculating the kinetic energy release (KER) it is required
to calculate the internal energy partitioning over the products. It can be
selected in the Molecular System/General window in the MassKinetics
project file. Because calculating the internal energy partitioning involves the
neutral products also, one has to make a few changes comparing to the upper
project files. The Reaction Scheme should include the two possible
neutral products and these have to be considered in the Reactions window
too. Also the frequency model of the fragment ions has to be loaded in the Molecular
System/Molecules window and neutral products have to be loaded in the Molecular
System/Reactions window. The rest of the project file is very similar to
the upper ones.
MassKinetics
project file for the protonated methyl-amin-methyld3-amin system using high-pressure
ion source:
Click here to
download this MassKinetics project file.
and using low-pressure ion source:
Click here to
download this MassKinetics project file.
MassKinetics
project file for the protonated diethyl-amin-diethyld2-amin system using
high-pressure ion source:
Click here to
download this MassKinetics project file.
and using low-pressure ion source:
Click here to
download this MassKinetics project file.
And of course one can calculate the KER distribution for the
fragment ions. In order to do that you have to go to the Results/Reaction (M®X) window and select the 2D curve for
KER distribution. Here is an example for M®A dissociation.
Click here to
download this MassKinetics project file.
3.
Modeling energy distributions
Throughout
this section the low pressure ion source (JEOL instrument) setup will be used.
a,
Thermal energy distributions of the molecular ion
First let’s calculate the thermal internal energy
distributions for the molecular ions at selected temperature.
The temperature can be given at the Molecular System/Molecules
window by setting the internal energy of the molecular ion. The 2D curve has to
be selected at Result/Reactant/Molecular Ion. The presented project file
calculates the IED at 450K (internal energy of the molecular ion).
Click here to
download this MassKinetics project file.
b,
Internal energy distributions of the fragmenting ions at various place of the
mass spectrometer
In the referred article it is shown, that the molecular ions
can dissociate through two channels:
either the deuterated or the non-deuterated product ion can be formed.
It is interesting to check the difference in the internal
energy distributions of the two possible product ions.
MassKinetics project file for the protonated methyld3-amin
product ion using low-pressure ion source:
Click here to
download this MassKinetics project file.
MassKinetics
project file for the protonated methyl-amin product ion using low-pressure
ion source:
Click here to download
this MassKinetics project file.
Since there is only a minor difference in the distributions
of the two product ions, we decided to deal only with one of the two product
ions during the modeling of the energy distributions of the ions.
To set
the place where the energy distributions should be calculated it has to be
defined when the 2D curves are being selected. Here are three examples:
1.
Ions reaching the field free flight (FFR): this is right before the third
region
Click here to
download this MassKinetics project file.
2.
Ions leaving the field free flight (FFR): this is right after the third region
Click here to
download this MassKinetics project file.
3. Ions fragmenting in the field free region: in order to get
this distribution the difference between the first two distributions has to be
taken, that is the ions leaving the FFR and the ions reaching the FFR. So you
really don’t need a project file for doing this. J
Hope you enjoy it!
If you have any question or comment regarding the calculations or anything else, please don’t hesitate to ask us: szj@unc.edu or masskinetics@ttk.mta.hu