Package Datasets • eprscope

Built-In Datasets

There are two important datasets built into the eprscope 📦. The first one is the nuclear isotope table, summarizing the essential properties of 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.

Nuclear Isotope Data Frame

This dataset was taken from the open source EasySpin package, reformatted and column of Larmor-frequencies in $\mathrm{MHz}$ at $0.35\,\mathrm{mT}$ 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.

Solvent Properties

When performing EPR experiments, especially the 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 $i.d. \leq 1\,\mathrm{mm}$ ) or special quartz flat cell ( with a flat-part thickness $\approx (0.3-0.6)\,\mathrm{mm}$ ) must be used. While for non-polar solvents or those 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 $i.d. \approx (2-4)\,\mathrm{mm}$ . 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 the ?solvents_ds documentation and in the 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."
)

Datasets for Examples and Tests

These involve the ASCII text data (with the extensions like .txt , .asc , .csv ), coming from EPR spectrometers and correspond either to an EPR spectrum data frame¹ or accompanying ASCII text files with the (instrumental) parameters (having the .par or .DSC / .dsc extensions) used to record the corresponding spectra. While the files containing parameters are generated automatically during the 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

File and Short Description	Examples in Functions/Tests
`Aminoxyl_radical_a.txt` 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.	`eval_DeltaXpp_Spec()` `eval_sim_EPR_isoFit()` `plot_EPR_Specs()` `plot_theme_In_ticks()` `plot_theme_NoY_ticks()` `readEPR_Exp_Specs()` `test-eval_sim_EPR_iso` `test-eval_sim_EPR_isoFit`
`Aminoxyl_radical_a.DSC` ASCII text file including parameters to record the EPR spectrum of an aminoxyl/nitroxyl radical derivative corresponding to the above-listed `Aminoxyl_radical_a.txt` The file was automatically generated by the Xenon acquisition software upon measurement data saving.	`readEPR_params_slct_quant()` `test-eval_sim_EPR_iso` `test-eval_sim_EPR_isoFit`
`Aminoxyl_radical_a.mat` 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 `Aminoxyl_radical_a.txt`	`readMAT_params_file()`
`TMPD.sdf` Structured data file (MOL-file-based 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()`
`TMPDAradCatEPRa.inp.log.zip` *Compressed output file from Gaussian* quantum chemical package** software (v. G16). Standard Gaussian output from DFT calculations of EPR parameters (g and a/A) corresponding to TMPD^.+ . See also `vignette("functionality")` .	`eval_gFactor_QCHcomp()` `rearrange_aAiso_QCHorgau()`
`TMPDA_specelchem_accu_b.asc` ASCII text table file corresponding to EPR spectrum of electrochemically generated TMPD^.+ by the potentiostatic electrolysis of $1\,\mathrm{mM}$ TMPD solution in $0.3\,\mathrm{M}$ TBAPF₆/DMSO at $0.308\,\mathrm{V}$ vs Ag-quasiref. electrode. Spectral data were recorded by the WinEpr acquisition software.	`eval_extremeX_Spec()` `eval_gFactor_Spec()` `eval_peakPick_Spec()` `plot_EPR_Specs2D_interact()` `plot_theme_Out_ticks()` `plot_EPR_Specs_integ()` `readEPR_Exp_Specs()` `present_EPR_Sim_Spec()`
`TMPDA_specelchem_accu_b.par` ASCII text file including parameters to record the EPR spectrum of electrochemically generated TMPD^.+ corresponding to the above-listed `TMPD_specelchem_accu_b.asc` . The file was automatically created by the WinEpr acquisition software upon data saving.	`readEPR_param_slct()` `readEPR_params_slct_sim()` `readEPR_params_tabs()` `present_EPR_Sim_Spec()`

`PNT_ENDOR_a.txt` 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.	`eval_DeltaXpp_Spec()` `plot_EPR_Specs()` `plot_EPR_Specs2D_interact()` `plot_layout2D_interact()` `readEPR_Exp_Specs()`
`PNT_ENDOR_a.DSC` ASCII text file including parameters to record the CW ENDOR spectrum of phenalenyl radical corresponding to the above-listed `PNT_ENDOR_a.txt` . This file was automatically generated by the Xenon acquisition software upon data saving.	`readEPR_param_slct()`
`Triarylamine_radCat_decay_a.txt` 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, were 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 `Triarylamine_radCat_decay_series.zip` .	`eval_kinR_EPR_modelFit()` `eval_kinR_EPR_ODE_model()` `plot_labels_xyz()` `plot_theme_NoY_ticks()` `readEPR_Exp_Specs()`
`Triarylamine_radCat_decay_a.DSC` This file is identical with `Triarylamine_radCat_decay_series.DSC` .	`eval_kinR_EPR_modelFit()` `readEPR_param_slct()`
`Triarylamine_radCat_decay_series.zip` 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 `Triarylamine_radCat_decay_a.txt` file.	`plot_EPR_Specs()` `plot_EPR_Specs3D_interact()` `eval_integ_EPR_Spec()` `readEPR_Exp_Specs_kin()` `smooth_EPR_Spec_by_npreg()`
`Triarylamine_radCat_decay_series.DSC` ASCII text file including parameters to record the EPR spectral time series described in details of `Triarylamine_radCat_decay_a.txt` as well as `Triarylamine_radCat_decay_series.zip` . The file was automatically generated by the Xenon acquisition software upon data saving.	`plot_EPR_Specs()` `plot_EPR_Specs3D_interact()` `eval_integ_EPR_Spec()` `smooth_EPR_Spec_by_npreg()` `readEPR_Exp_Specs_kin()` `readEPR_params_slct_kin()`
`AcridineDeriv_Irrad_365nm.csv.zip` Compressed ASCII text table file (in `.csv` format) corresponding to CW EPR spectrum of an acridine derivative radical irradiated by 365 nm LED to form the corresponding acridinium (+) redox state. Spectrum recorded on Magnettech ESR5000 [11-0422].	`readEPR_Exp_Specs()`
`AcridineDeriv_Irrad_365nm.dsc` ASCII text file including parameters to record the CW EPR spectrum of an acridine derivative radical described in `AcridineDeriv_Irrad_365nm.csv.zip` . The file was automatically generated by the Magnettech/Bruker acquisition software upon data saving.	`readEPR_params_slct_sim()` `readEPR_params_tabs()`
`Triarylamine_ECh_CV_ivium.txt` 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.	`plot_ECh_VoC_amperogram()` `eval_ECh_QNe_chronoamp()`

Aminoxyl_radical_a.txt

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.

eval_DeltaXpp_Spec()

eval_sim_EPR_isoFit()

plot_EPR_Specs()

plot_theme_In_ticks()

plot_theme_NoY_ticks()

readEPR_Exp_Specs()

test-eval_sim_EPR_iso

test-eval_sim_EPR_isoFit

Aminoxyl_radical_a.DSC

ASCII text file including parameters to record the EPR spectrum of an aminoxyl/nitroxyl radical derivative corresponding to the above-listed Aminoxyl_radical_a.txt The file was automatically generated by the Xenon acquisition software upon measurement data saving.

readEPR_params_slct_quant()

test-eval_sim_EPR_iso

test-eval_sim_EPR_isoFit

Aminoxyl_radical_a.mat

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 Aminoxyl_radical_a.txt

readMAT_params_file()

TMPD.sdf

Structured data file (MOL-file-based 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()

TMPDAradCatEPRa.inp.log.zip

Compressed output file from Gaussian quantum chemical package software (v. G16). Standard Gaussian output from DFT calculations of EPR parameters (g and a/A) corresponding to TMPD^.+ . See also vignette("functionality") .

eval_gFactor_QCHcomp()

rearrange_aAiso_QCHorgau()

TMPDA_specelchem_accu_b.asc

ASCII text table file corresponding to EPR spectrum of electrochemically generated TMPD^.+ by the potentiostatic electrolysis of $1\,\mathrm{mM}$ TMPD solution in $0.3\,\mathrm{M}$ TBAPF₆/DMSO at $0.308\,\mathrm{V}$ vs Ag-quasiref. electrode. Spectral data were recorded by the WinEpr acquisition software.

eval_extremeX_Spec()

eval_gFactor_Spec()

eval_peakPick_Spec()

plot_EPR_Specs2D_interact()

plot_theme_Out_ticks()

plot_EPR_Specs_integ()

readEPR_Exp_Specs()

present_EPR_Sim_Spec()

TMPDA_specelchem_accu_b.par

ASCII text file including parameters to record the EPR spectrum of electrochemically generated TMPD^.+ corresponding to the above-listed TMPD_specelchem_accu_b.asc . The file was automatically created by the WinEpr acquisition software upon data saving.

readEPR_param_slct()

readEPR_params_slct_sim()

readEPR_params_tabs()

present_EPR_Sim_Spec()

PNT_ENDOR_a.txt

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.

eval_DeltaXpp_Spec()

plot_EPR_Specs()

plot_EPR_Specs2D_interact()

plot_layout2D_interact()

readEPR_Exp_Specs()

PNT_ENDOR_a.DSC

ASCII text file including parameters to record the CW ENDOR spectrum of phenalenyl radical corresponding to the above-listed PNT_ENDOR_a.txt . This file was automatically generated by the Xenon acquisition software upon data saving.

readEPR_param_slct()

Triarylamine_radCat_decay_a.txt

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, were 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 Triarylamine_radCat_decay_series.zip .

eval_kinR_EPR_modelFit()

eval_kinR_EPR_ODE_model()

plot_labels_xyz()

plot_theme_NoY_ticks()

readEPR_Exp_Specs()

Triarylamine_radCat_decay_a.DSC

This file is identical with Triarylamine_radCat_decay_series.DSC .

eval_kinR_EPR_modelFit()

readEPR_param_slct()

Triarylamine_radCat_decay_series.zip

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 Triarylamine_radCat_decay_a.txt file.

plot_EPR_Specs()

plot_EPR_Specs3D_interact()

eval_integ_EPR_Spec()

readEPR_Exp_Specs_kin()

smooth_EPR_Spec_by_npreg()

Triarylamine_radCat_decay_series.DSC

ASCII text file including parameters to record the EPR spectral time series described in details of Triarylamine_radCat_decay_a.txt as well as Triarylamine_radCat_decay_series.zip . The file was automatically generated by the Xenon acquisition software upon data saving.

plot_EPR_Specs()

plot_EPR_Specs3D_interact()

eval_integ_EPR_Spec()

smooth_EPR_Spec_by_npreg()

readEPR_Exp_Specs_kin()

readEPR_params_slct_kin()

AcridineDeriv_Irrad_365nm.csv.zip

Compressed ASCII text table file (in .csv format) corresponding to CW EPR spectrum of an acridine derivative radical irradiated by 365 nm LED to form the corresponding acridinium (+) redox state. Spectrum recorded on Magnettech ESR5000 [11-0422].

readEPR_Exp_Specs()

AcridineDeriv_Irrad_365nm.dsc

ASCII text file including parameters to record the CW EPR spectrum of an acridine derivative radical described in AcridineDeriv_Irrad_365nm.csv.zip . The file was automatically generated by the Magnettech/Bruker acquisition software upon data saving.

readEPR_params_slct_sim()

readEPR_params_tabs()

Triarylamine_ECh_CV_ivium.txt

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.

plot_ECh_VoC_amperogram()

eval_ECh_QNe_chronoamp()