add Figs. S5 and S6

analyses/Makefile

@@ -9,3 +9,5 @@ all:
 	python plot_CIP.py -o ../FigureS2.pdf
 	python plot_pairs.py -o ../FigureS3.pdf
 	python plot_pot_hammet.py -o ../FigureS4.pdf
+	python plot_cplx_r.py -o ../FigureS5.pdf
+	python plot_cplx_Gx1.py -o ../FigureS6.pdf

analyses/plot_cplx_Gx1.py

@@ -0,0 +1,74 @@
+import pandas
+import matplotlib.pyplot as plt
+import numpy
+import sys
+import argparse
+
+from matplotlib.ticker import AutoMinorLocator, MultipleLocator
+from nitroxides.commons import AU_TO_ANG, AU_TO_KJMOL, G_NME4, G_BF4, RADII_BF4, RADII_NME4, C_NITROXIDE, dG_DH_cplx_Kx1
+
+T = 298.15
+R = 8.3145e-3 # kJ mol⁻¹
+
+def plot_Kx1(ax, data: pandas.DataFrame, family: str, solvent: str, epsilon_r: float, color: str):
+    subdata_k01 = data[(data['family'] == family) & (data['solvent'] == solvent) & (data['has_anion'] == True)] # K_01 → N+ + A-
+    subdata_k21 = data[(data['family'] == family) & (data['solvent'] == solvent) & (data['has_cation'] == True)] # K_21 → N- + C+
+
+    dG_DH_k01_0 = dG_DH_cplx_Kx1(subdata_k01['z'] + 1, subdata_k01['z'], -1, subdata_k01['r_A'] / AU_TO_ANG, subdata_k01['r_AX'] / AU_TO_ANG, RADII_BF4[solvent] / AU_TO_ANG, epsilon_r, c_elt=0.1)
+    dG_DH_k21_0 = dG_DH_cplx_Kx1(subdata_k21['z'] - 1, subdata_k21['z'], 1, subdata_k21['r_A'] / AU_TO_ANG, subdata_k21['r_AX'] / AU_TO_ANG, RADII_NME4[solvent] / AU_TO_ANG, epsilon_r, c_elt=0.1)
+
+    dG_DH_k01 = dG_DH_cplx_Kx1(subdata_k01['z'] + 1, subdata_k01['z'], -1, subdata_k01['r_A'] / AU_TO_ANG, subdata_k01['r_AX'] / AU_TO_ANG, RADII_BF4[solvent] / AU_TO_ANG, epsilon_r)
+    dG_DH_k21 = dG_DH_cplx_Kx1(subdata_k21['z'] - 1, subdata_k21['z'], 1, subdata_k21['r_A'] / AU_TO_ANG, subdata_k21['r_AX'] / AU_TO_ANG, RADII_NME4[solvent] / AU_TO_ANG, epsilon_r)
+
+    dG_k01_0 = (subdata_k01['G_cplx'] - G_BF4[solvent] + dG_DH_k01_0) * AU_TO_KJMOL
+    dG_k21_0 = (subdata_k21['G_cplx'] - G_NME4[solvent] + dG_DH_k21_0) * AU_TO_KJMOL
+
+    dG_k01 = (subdata_k01['G_cplx'] - G_BF4[solvent] + dG_DH_k01) * AU_TO_KJMOL
+    dG_k21 = (subdata_k21['G_cplx'] - G_NME4[solvent] + dG_DH_k21) * AU_TO_KJMOL
+
+    ax.plot([int(x.replace('mol_', '')) for x in subdata_k01['name']], dG_k01, 'o', color=color, label=family.replace('Family.', ''))
+    ax.plot([int(x.replace('mol_', '')) for x in subdata_k21['name']], dG_k21, 's', color=color)
+    ax.plot([int(x.replace('mol_', '')) for x in subdata_k01['name']], dG_k01_0, 'o', markerfacecolor='none', markeredgecolor=color)
+    ax.plot([int(x.replace('mol_', '')) for x in subdata_k21['name']], dG_k21_0, 's', markerfacecolor='none', markeredgecolor=color)
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input', default='../data/Data_cplx_Kx1.csv')
+parser.add_argument('-o', '--output', default='Data_cplx_Gx1.pdf')
+
+args = parser.parse_args()
+
+data = pandas.read_csv(args.input)
+
+figure = plt.figure(figsize=(10, 8))
+ax1, ax2 = figure.subplots(2, 1, sharey=True, sharex=True)
+
+plot_Kx1(ax1, data, 'Family.AMO', 'water', 80.,'tab:pink')
+plot_Kx1(ax1, data, 'Family.P6O', 'water', 80.,'tab:blue')
+plot_Kx1(ax1, data, 'Family.P5O', 'water', 80., 'black')
+plot_Kx1(ax1, data, 'Family.IIO', 'water', 80., 'tab:green')
+plot_Kx1(ax1, data, 'Family.APO', 'water', 80., 'tab:red')
+
+ax1.legend(ncols=5)
+ax1.set_xlim(0.5,61.5)
+ax1.text(38, 0.5, "Water", fontsize=18)
+ax1.xaxis.set_minor_locator(MultipleLocator(2))
+ax1.grid(which='both', axis='x')
+ax1.plot([0, 62], [0, 0], '-', color='grey')
+
+plot_Kx1(ax2, data, 'Family.P6O', 'acetonitrile', 35.,'tab:blue')
+plot_Kx1(ax2, data, 'Family.P5O', 'acetonitrile', 35., 'black')
+plot_Kx1(ax2, data, 'Family.IIO', 'acetonitrile', 35., 'tab:green')
+plot_Kx1(ax2, data, 'Family.APO', 'acetonitrile', 35., 'tab:red')
+
+ax2.set_xlabel('Molecule id') 
+ax2.set_xlim(0.5,61.5)
+ax2.text(38, 0.5, "Acetonitrile", fontsize=18)
+ax2.xaxis.set_minor_locator(MultipleLocator(2))
+ax2.grid(which='both', axis='x')
+ax2.plot([0, 62], [0, 0], '-', color='grey')
+
+[ax.set_ylabel('$\\Delta G^\\star_{pair}$ (kJ mol$^{-1}$)') for ax in [ax1, ax2]]
+
+plt.tight_layout()
+figure.savefig(args.output)

analyses/plot_cplx_Kx1.py

@@ -47,7 +47,7 @@ def helpline_K01(ax, data: pandas.DataFrame, solvent: str, epsilon_r: float, col
 data = pandas.read_csv(args.input)
 
 figure = plt.figure(figsize=(10, 8))
-ax1, ax2 = figure.subplots(2, 1, sharey=True)
+ax1, ax2 = figure.subplots(2, 1, sharey=True, sharex=True)
 
 helpline_K01(ax1, data, 'water', 80, 'black')
 

analyses/plot_cplx_Kx2.py

@@ -48,7 +48,7 @@ def helpline_K02(ax, data: pandas.DataFrame, solvent: str, epsilon_r: float, col
 data = pandas.read_csv(args.input)
 
 figure = plt.figure(figsize=(10, 8))
-ax1, ax2 = figure.subplots(2, 1, sharey=True)
+ax1, ax2 = figure.subplots(2, 1, sharey=True, sharex=True)
 
 helpline_K02(ax1, data, 'water', 80, 'black')
 

nitroxides.tex

@@ -388,7 +388,7 @@ \subsection{Impact of the electrolytes}
 \begin{figure}[!h]
 \centering
 \includegraphics[width=\linewidth]{Figure11}
-\caption{Value of the complexation equilibrium constants $K_{01}$ (round markers, $\bullet$) and $K_{21}$ (square markers, $\blacksquare$) for the 3 oxidation state of nitroxides, as computed at the $\omega$B97X-D/6-311+G(d) level in water (top) and acetonitrile (bottom) using SMD and $[X]=\SI{1}{\mole\per\liter}$.  The dashed line is there to help visualization. }
+\caption{Value of the complexation equilibrium constants $K_{01}$ (round markers, $\bullet$) and $K_{21}$ (square markers, $\blacksquare$), as computed at the $\omega$B97X-D/6-311+G(d) level in water (top) and acetonitrile (bottom) using SMD and $[X]=\SI{1}{\mole\per\liter}$.  The dashed line is there to help visualization. }
 \label{fig:Kx1}
 \end{figure}
 

nitroxides_SI.tex

@@ -41,5 +41,17 @@
 	\includegraphics [width=\linewidth]{FigureS4}
 	\caption{Correlation between absolute oxidation (left) and reduction (right) and the Hammet constant of their substituent for compounds of the P5O (black markers) and P6O (blue markers) families.}
 \end{figure}
+
+\begin{figure}[!h]
+\centering
+\includegraphics [width=\linewidth]{FigureS5}
+\caption{Difference between the oxygen of the nitroxide redox center ($>$\ce{N=O}) and the center of the counteranion (\ce{A-}, $d_{OX}$) or countercation (\ce{C+}, $d_{red}$) as measured on the geometries optimized at the $\omega$B97X-D/6-311+G(d) level in water (top) and acetonitrile (bottom) using SMD.}
+\end{figure}
+
+\begin{figure}[!h]
+\centering
+\includegraphics [width=\linewidth]{FigureS6}
+\caption{Value of the complexation free Gibs energy change for $K_{01}$ (round markers, $\bullet$) and $K_{21}$ (square markers, $\blacksquare$), as computed at the $\omega$B97X-D/6-311+G(d) level in water (top) and acetonitrile (bottom) using SMD at two concentration: $[X]=\SI{1}{\mole\per\liter}$ (filled markers) and  $[X]=\SI{0.1}{\mole\per\liter}$ (empty markers). }
+\end{figure}
 
 \end{document}