Supporting Information For
The Effective Temperature of Ions Stored in a Linear Quadrupole Ion
Trap Mass Spectrometer
William A. Donald,1,2,* George N. Khairallah,1 and Richard A. J. O’Hair1
1
School of Chemistry, Bio21 Institute of Molecular Science and Biotechnology, & Australian Research Council
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Melbourne, Victoria, 3010,
Australia
2
Present address: School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052,
Australia
*
Address correspondence to this address: w.donald@unsw.edu.au
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Supporting Experimental Details
Electrospray Ionization Conditions. Using electrospray ionization (ESI), N,Ndimethylglycine (D) containing clusters, [(D + Ag − H)n−1 + Ag]+, were formed from 50:50:1
water:methanol:acetic acid solutions containing ~1 mM D and ~0.3 mM AgNO3,
thiophenolate (PhS–) was formed from an aqueous solution containing 100 uM thioanisole
and 100 uM tetrabutyl ammonium hydroxide, and acetate (Ac–) was formed from a 50:50:1
water:methanol:acetic acid solution. For ESI, a positive or negative potential of 4-5 kV to the
ESI capillary relative to the heated capillary entrance to the mass spectrometer (200-300ºC).
Solutions were introduced into the ESI capillary at a flow rate of 3-5 µL/min. For CID, ions
of interest were isolated using an isolation window of 1.1 m/z that was centered on the m/z
ion of the most abundant peak of the isotopic envelope.
Ion-molecule Reactions. The linear quadrupole ion trap has been modified to perform
ion-molecule reactions [1]. For reactions with neutral reagents, the neutral is injected at a
constant flow rate (10-100 uL/min; heated to ~50ºC) into the He supply line upstream of the
He entrance to the ion trap mass spectrometer. The majority of the gaseous mixture exits to
atmosphere through a flow meter (2-5 L/min) and a small portion of the mixture is introduced
into the mass spectrometer using a restriction capillary that bypasses the standard pressure
regulator. The helium pressure in the ion trap is controlled manually by matching the pressure
in the vacuum chamber surrounding the ion trap to that under normal operating conditions
(corresponding to 2 mTorr in the ion trap). Although the uncertainty in the partial pressure of
the neutral is relatively high (± 25%), this uncertainty corresponds to relatively minor
uncertainty in the <Teff> values. The vast majority of the propagated uncertainty in the <Teff>
values results from the uncertainty in the measured thermometer reaction enthalpies and
entropy values.
2
The measured <Teff> values are highly reproducible. For example, the <Teff> values
obtained from the thiophenolate/TFE reaction equilibrium data that were measured 7 months
apart are essentially the same (an average of 331.7 K for both data sets and a respective
standard deviation of 0.5 K and 0.9 K). For all reactions investigated, the average number of
detected precursor and product ions does not change significantly with reaction time. These
results indicate that the precursor and product ions are detected with similar efficiencies and
that any mass discrimination effects are minor and should not affect the effective temperature
values obtained in these experiments.
As suggested by a reviewer, the number of ions that are trapped in a given experiment
may potentially influence the effective temperature of trapped ions. Thus, the effect of the
number of trapped ions on the effective temperatures that are obtained using the
thiophenolate/TFE reaction was investigated. The initial abundance of thiophenolate can be
readily controlled by varying the ESI source conditions. Because ions should be thermalized
within ms of being trapped, varying the source conditions should not affect the effective
temperature values that are obtained using the thermometer reaction method. In Figure S3,
the ratio between the measured abundance of PhS–(TFE) and PhS– are plotted as a function of
time for (1) experiments in which many ions are trapped (circles; an average of 2.6 x 106
precursor and product ions are detected) and (2) those in which relatively low numbers of
ions are trapped (squares; an average of 8.5 x 103 precursor and product ions are detected);
Figure S3. That is, in the former set of experiments, an average of 300 times more precursor
and product ions were trapped and detected than in the latter set of experiments.
With increasing reaction time, the relative abundance of the ion-molecule association
product, i.e., [PhS–(TFE)]/[PhS–], increases from <1% at 30 ms to ca. 13% for reaction times
of 5 s and longer for both experiments in which either a high or low number of precursor and
product ions are trapped (Figure S3). These data indicate that equilibrium is established
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between the reactant and product ions for reaction times that are longer than about 4 s under
these conditions. In addition, the [PhS–(TFE)]/[PhS–] values do not depend significantly on
the number of precursor and product ions that are detected in each experiment for a given
reaction time. For example, the average absolute difference between the [PhS–(TFE)]/[PhS–]
values that are obtained from the experiments in which relatively large and small numbers of
precursor and product ions are trapped is less than 0.5%. The average effective temperature
values that are obtained from the set of experiments in which relatively large and small
numbers of ions are trapped and detected are essentially identical (an average of 331.7 K for
both sets of experiments with respective standard deviations of 0.9 and 0.5 K). Given the
factor of ca. 300 difference in the number of ions that are detected in each set of experiments,
these results suggest that the effective temperature values obtained using the thermometer
reaction method do not depend significantly on the number of trapped ions under these
conditions.
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Table S1. Average effective temperature values measured for five thermometer reactions for
ion trap qz values from 0.1 to 0.8.
qz Ag5+/Et Ag3+Et Ag3+Et/Et Ag7+Et Ag7+Et/Et
0.10 295.1
352.8
298.5
311.0
297.6
0.25 295.2
352.8
299.9
310.1
299.8
0.45 295.7
352.8
298.3
N/Aa
N/Aa
0.60 296.7
353.0
300.0
N/Aa
N/Aa
0.80 301.2
355.7
301.6
312.6
302.6
a
Not available (N/A)
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Figure S1. ln[(MzLn/MzLn–1)x(760/PL)] values obtained from ion-molecule equilibrium
measurements (open triangles; left axis) and corresponding average effective temperature values
(<Teff>; closed triangles; right axis) vs. reaction time (t) for addition of one and two C2H4 molecules to
Ag7+ (+1C2H4 and +2 C2H4). The dashed line corresponds to room temperature (295 K) and error bars
are shown.
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Figure S2. Average effective temperature of reactants and products of ion-molecule
equilibrium reactions, <Teff>, obtained from equilibrium measurements in a linear quadrupole
ion trap as a function of (A) the negative of the enthalpy, (B) negative entropy, (C) negative
Gibbs free energy of forming the ion-molecule complex from the separated reactants, (D) the
number of vibrational degrees of freedom in the ion-molecule collision complex, (E) the
ligand binding enthalpy per vibrational mode, and (F) the derivative of natural logarithm of
the equilibrium constant with respect to temperature (T = 295 K) for each ion-molecule
thermometer reaction.
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Figure S3. Relative abundance of the ion-molecule reaction complex that is formed between
thiophenolate and trifluoroethanol ([PhS–(TFE)]/[PhS–]) as a function of reaction time for an
average number of 2.6 x 106 (squares) and 8.5 x 103 (circles) precursor and product ions that
are trapped and detected.
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References
1. Donald, W.A., McKenzie, C.J., O'Hair, R.A.J.; C-H bond activation of methanol and
ethanol by a high-spin FeIV-oxo biomimetic complex. Angew. Chem. Int. Ed. 50, 8379-8383
(2011); Donald, W.A., O'Hair, R.A.J.; Shapeshifting: Ligation by 1,4-cyclohexadiene induces
a structural change in Ag5+. Dalton Trans. 41, 3185-3193 (2012); Waters, T., O'Hair, R.A.J.,
Wedd, A.G.; Catalytic gas phase oxidation of methanol to formaldehyde. J. Am. Chem. Soc.
125, 3384-3396 (2003)
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