There are two important datasets built into the
{eprscope} 📦. The first one is the nuclear isotope table
summarizing the essential properties of the nuclei in order to analyze
the EPR spectra with HF (hyperfine) structure. While, the second one
shows the solvent properties important for variable temperature (VT),
double-resonance (ENDOR) and EPR spectroelectrochemical experiments.
This dataset was taken from the open source EasySpin
package, reformatted and column of Larmor-frequencies in MHz at 0.35 mT were added for better orientation in
double-resonance ENDOR spectra, see the details in
?isotopes_ds documentation as well as R
file in `data-raw` folder. The data frame is not only used to
analyze the ENDOR spectra however, it is also essential for the
simulations of EPR spectra and their fitting onto the experimental ones.
See the documentation of the eval_sim_EPR_iso(),
eval_sim_EPR_isoFit() as well as
eval_nu_ENDOR().
# interactive data frame by `{DT}` package with option to select columns
# and to save table as `.csv`, `.pdf` or `.xlsx` format
DT::datatable(isotopes_ds,
extensions = "Buttons",
options = list(
dom = "Bfrtip",
buttons = c("colvis","csv","pdf","excel")
),
caption = "Dataset with the following variables/columns: Proton number, isotope,
stability (either stable, STB or radio-active, RA), isotope name,
nuclear spin quantum number, nuclear g-value, natural abundance in %,
nuclear quadrupolar moment in Barns and the ENDOR/Larmor frequency
in MHz at 0.35 T. The negative sign of Larmor frequency values
points to clockwise precession direction according to convention."
) %>%
DT::formatRound("nu_ENDOR_MHz_035T",digits = 3) # rounding must be also performed by the `DT` pkg.When performing the EPR experiments, especially X-band
continuous wave (CW) spectroscopy in solution, solvent plays an
important role. Namely, prior to measurement one has to decide which
type of cell will be applied depending on solvent polarity. For polar
solvents, such as acetonitrile or dimethyl sulfoxide, either capillary
(with i.d. ≤ 1 mm )
or special quartz
flat cell ( with a flat-part thickness ≈ (0.3 − 0.6) mm) must be used. While for
non-polar or solvents with lower polarity, e.g. toluene, chloroform or
tetrahydrofuran, a sample can be analyzed within any kind of cell
including common
EPR quartz-tubes with i.d. ≈ (2 − 4) mm.
Additionally, the solvent properties like melting/boiling point as well
as viscosity are essential for the variable temperature (VT) experiments
and particularly for the CW ENDOR as well as for spectroelectrochemical
ones. Table details can be found in ?solvents_ds
documentation and in R
file in `data-raw` folder. Solvent properties can be also obtained
by the specialized readEPR_solvent_props() function.
# similar interactive table like before
DT::datatable(solvents_ds,
extensions = "Buttons",
options = list(
dom = "Bfrtip",
buttons = c("colvis","csv","pdf","excel"),
columnDefs = list(list(visible=FALSE, targets=c(7))) # hide solubility/miscibility column
),
caption = "Dataset with the following variables/columns: solvent name,
molecular formula, relative molecular weight, boiling point in °C,
melting point in °C, density in g/mL, solubility
in g/(100 g of water)-not shown, visibility can be switched
by the 'column visibility', relative electric permittivity,
flash point in °C and dynamic viscosity in cp."
)These involve the ASCII text
data (with the extensions like .txt , .asc ,
.csv ), coming from the EPR spectrometer and correspond
either to an EPR spectrum data frame1 or the accompanying ASCII text files with
the (instrumental) parameters (with .par or
.DSC / .dsc extensions) used to record the
corresponding spectra. While the files containing parameters are
generated automatically during the spectral data saving, the tabular
ones, related to an EPR spectrum, must be generated by the instrument
operator (usually by File ➝ Export ASCII
workflow). Some of these files are compressed (as .zip) in
order to save storage space within the package. Additionally, the
{eprscope} 📦 contains .mat (Matlab)
file from the EasySpin simulation as well as output from DFT
quantum chemical computation or related structural data either with
.inp.log.zip or .sdf extensions, respectively.
All these file types are summarized within the following table.
| File and Short Description | Examples in Functions/Tests |
|---|---|
ASCII text table file corresponding to EPR spectrum of an aminoxyl/nitroxyl radical derivative measured in deionized H2O and recorded by the Xenon acquisition software. |
|
ASCII text file including parameters to record the
EPR spectrum of an aminoxyl/nitroxyl radical derivative corresponding to
the above-listed |
|
Matlab/EasySpin output file containing all
experimental parameters, EPR spectrum table form (B vs
Intensity) as well as simulation and fitting parameters to
reproduce the experimental spectrum saved in the above-listed
|
readMAT_params_file() |
Structured data file (based MOL-file format) containing structure of the N,N,N’,N’-Tetramethyl-p-phenylenediamine (TMPD) radical cation. Structure (optimized geometry) was calculated by Density Functional Theory (DFT). |
draw_molecule_by_rcdk() |
Compressed output file from Gaussian quantum
chemical package software. Standard Gaussian output
from DFT calculations of EPR parameters (g and a/A)
corresponding to TMPD.+ . See also
|
|
ASCII text table file corresponding to EPR spectrum of electrochemically generated TMPD.+ by the potentiostatic electrolysis of 1 mM TMPD solution in 0.3 M TBAPF6/DMSO at 0.308 V vs Ag-quasiref. electrode. Spectral data were recorded by the WinEpr acquisition software. |
|
ASCII text file including parameters to record the
EPR spectrum of electrochemically generated TMPD.+
corresponding to the above-listed
|
|
ASCII text table file corresponding to CW EPR ENDOR spectrum of phenalenyl (perinaphthenyl) radical, commonly used as a standard for the CW ENDOR experiments. Spectrum recorded by the Xenon acquisition software. |
|
ASCII text file including parameters to record the
CW ENDOR spectrum of phenalenyl radical corresponding to the
above-listed |
readEPR_param_slct() |
ASCII text table file including double integrals (Area)
vs. time and additional parameters like g-value, linewidth,
lineshape of each CW EPR spectrum of a triarylamine radical cation,
recorded right after its electrochemical oxidative generation and
disconnecting the potentiostat. File was created by the Xenon
acquisition software, where the integration of the simulated and fitted
EPR spectra, of the experimental ones, was performed. Potentiostatic
electrolysis (at 0.49 V vs Fc/Fc+) and EPR measurements were
carried out in 0.2 M TBAPF6/CH3CN triarylamine
solution. The individual spectral data are stored in
|
|
This file is identical with
|
|
Compressed ASCII text table file containing 100 EPR CW
spectral data recorded as time series upon checking the
stability of a triarylamine radical cation. Details of the EPR
spectroelectrochemical experiment are listed in description of the
|
|
ASCII text file including parameters to record the EPR
spectral time series described in details of
|
|
Compressed ASCII text table file (in |
readEPR_Exp_Specs() |
ASCII text file including parameters to record the CW EPR
spectrum of an acridine derivative radical described in
|
|
ASCII text file table consisting of potential, time, current columns/variables which was generated by the Ivium potentiostat electrochemical acquisition software after recording the cyclic voltammetry (in anodic direction) of a triarylamine derivative in 0.2 M TBAPF6/CH3CN. |
|
Usually the following variables/columns are included in the ASCII tables of the corresponding EPR spectra: “index”, “Field [G]”/“X [G]”/“RF [MHz]” and “Intensity []”/“Intensity”↩︎