fix SI

README.md

@@ -1,6 +1,6 @@
-# A publication on nitroxides
+# Solvent effects on the prediction of redox potentials: application to nitroxides
 
-A publication about nitroxides (aminoxyls) and their redox potential in solution, by Dr. [P. Beaujean](https://pierrebeaujean.net).
+A publication about nitroxides (aminoxyls) and their redox potential in solution (including electrolytes and ion-pairs), by Dr. [P. Beaujean](https://pierrebeaujean.net).
 
 This repository contains the [structures](./structures), the [curated data](./data), the [analysis scripts](./analyses), [the source for other images](./im), and the text.
 

TODO.md

@@ -35,5 +35,5 @@ For v3.0 (to be submitted):
 - [x] Description of the SI? → Nope
 - [x] Mat → Matsui
 - [x] Data availability
-- [ ] Update SI (!!)
+- [x] Update SI (!!)
 - [ ] Address last comments

nitroxides_SI.tex

@@ -19,22 +19,24 @@
 \renewcommand{\thetable}{S\arabic{table}}
 \renewcommand{\thefigure}{S\arabic{figure}}
 
+\paragraph{Note to reviewers.} While the computational results dataset is under embargo until the publication, you may access it using the following link: \url{https://zenodo.org/records/12751130?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjZlNjM0ZmU0LTMzZmMtNDFlYy05ODYxLTRmZGFjNjI3Y2Y3MyIsImRhdGEiOnt9LCJyYW5kb20iOiJhNjMxNjEyNmMxNzNmZDkzYjJiZjg2ZWYyOGFkYzIzNCJ9.ft-YmetAcpD_q9-_3u28iLC-LylgS3-SGZBtgBm-1xJitmQTLnJxukzsvUzAmeWAjv8NviHWw-smqh2ztkNr8g}. 
+
 \begin{figure}[!h]
 	\centering
 	\includegraphics [width=\linewidth]{FigureS1}
-	\caption{Evolution of (left) the Born solvation energy, $\Delta G^\star_{Born}$ [computed with Eq.~(4)] as a function of the dielectric constant of the solvent for different radii of  the spherical cavities ($a$) and of (right) the Debye-Huckel correction, $\Delta G^\star_{DH}$  [computed with Eq.~(5)] as a function of the concentration in electrolyte, $[X]$ (right) in water and acetonitrile.}
+	\caption{Evolution of (left) the Born solvation energy, $\Delta G^\star_{Born}$ [computed with Eq.~(7)] as a function of the dielectric constant of the solvent for different radii of  the spherical cavities ($a$) and of (right) the Debye-Hückel correction, $\Delta G^\star_{DH}$  [computed with Eq.~(5)] as a function of the concentration in electrolyte, $[X]$, in water and acetonitrile.}
 \end{figure}
 
 \begin{figure}[!h]
 \centering
 \includegraphics [width=.5\linewidth]{FigureS2}
-\caption{Impact of the concentration of electrolyte on the formal oxidation potential [computed with Eq.~(9)] , $E^f_{abs}(\ce{N+}|\ce{N^.})$, considering a fictitious case where $E^0_{abs} = \SI{0}{\volt}$.}
+\caption{Impact of the concentration of electrolyte on the formal oxidation potential [computed with Eq.~(10)] , $E^f_{abs}(\ce{N+}|\ce{N^.})$, considering a fictitious case where $E^0_{abs} = \SI{0}{\volt}$.}
 \end{figure}
 
 \begin{figure}[!h]
 \centering
 \includegraphics [width=.7\linewidth]{FigureS3}
-\caption{Evolution of the cologarithm of the equilibrium constant, $pK_{pair}$ [computed from Eq.~(12)] between two ions as a function of $\chi$, the ratio between the radii of the two ions and for 3 values of dipole cavity shape factor ($s_2$). The ion charges are set to $\pm 1$, and two possible scaling factor for  the close contact distance is used ($s_1$, left and right). }
+\caption{Evolution of the cologarithm of the equilibrium constant, $pK_{pair}$ [computed from Eq.~(12)] between two ions as a function of $\chi$, the ratio between the radii of the two ions and for 3 values of dipole cavity shape factor ($s_2$). The ion charges are set to $\pm 1$, and two possible scaling factors for  the close contact distance are used ($s_1$, left and right). }
 \end{figure}
 
 
@@ -271,7 +273,7 @@
 
 
 \clearpage
-\begin{longtblr}[caption={Distances ($d$, in \si{\angstrom}) between $>$\ce{N+=O} and \ce{A-} (left, measured as the distance between the nitrogen and the boron of \ce{A-}) and between \ce{N-O-} and \ce{C+} (right, measured as the distance between the oxygen and the nitrogen of \ce{C+}) toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}) in two different cases: in front of the methyls ($f$, near the redox center) and behind the methyls ($b$, near the substituent), as computed at the $\omega$B97X-D/6-311+G(d) level in water (SMD), with $[\ce{X}]=\SI{0}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]X[c]X[c]cX[c]X[c]X[c]X[c]}, width = \linewidth,rowhead=2}
+\begin{longtblr}[caption={Distances ($d$, in \si{\angstrom}) between $>$\ce{N+=O} and \ce{A-} (left, measured as the distance between the nitrogen and the boron of \ce{A-}) and between \ce{N-O-} and \ce{C+} (right, measured as the distance between the oxygen and the nitrogen of \ce{C+}) together with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}) in two different cases: in front of the methyls ($f$, near the redox center) and behind the methyls ($b$, near the substituent), as computed at the $\omega$B97X-D/6-311+G(d) level in water (SMD), with $[\ce{X}]=\SI{0}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]X[c]X[c]cX[c]X[c]X[c]X[c]}, width = \linewidth,rowhead=2}
 \hline
 &  \SetCell[c=4]{c} \ce{N+A-} & & & & &  \SetCell[c=4]{c} \ce{N^-C+} &  & & \\ 
 \cline{2-5} \cline{7-10}
@@ -341,7 +343,7 @@
 \end{longtblr}
 
 \clearpage
-\begin{longtblr}[caption={Distances ($d$, in \si{\angstrom}) between $>$\ce{N+=O} and \ce{A-} (left, measured as the distance between the nitrogen and the boron of \ce{A-}) and between \ce{N-O-} and \ce{C+} (right, measured as the distance between the oxygen and the nitrogen of \ce{C+}) toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}) in two different cases: in front of the methyls ($f$, near the redox center) and behind the methyls ($b$, near the substituent), as computed at the $\omega$B97X-D/6-311+G(d) level in acetonitrile (SMD), with $[\ce{X}]=\SI{0}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]X[c]X[c]cX[c]X[c]X[c]X[c]}, width = \linewidth,rowhead=2}
+\begin{longtblr}[caption={Distances ($d$, in \si{\angstrom}) between $>$\ce{N+=O} and \ce{A-} (left, measured as the distance between the nitrogen and the boron of \ce{A-}) and between \ce{N-O-} and \ce{C+} (right, measured as the distance between the oxygen and the nitrogen of \ce{C+}) together with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}) in two different cases: in front of the methyls ($f$, near the redox center) and behind the methyls ($b$, near the substituent), as computed at the $\omega$B97X-D/6-311+G(d) level in acetonitrile (SMD), with $[\ce{X}]=\SI{0}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]X[c]X[c]cX[c]X[c]X[c]X[c]}, width = \linewidth,rowhead=2}
 \hline
 &  \SetCell[c=4]{c} \ce{N+A-} & & & & &  \SetCell[c=4]{c} \ce{N^-C+} &  & & \\ 
 \cline{2-5} \cline{7-10}
@@ -372,9 +374,9 @@
 
 \clearpage
 
-\begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in water (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
+\begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, together with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in water (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
 	\hline
-	&  \SetCell[c=2]{c} \ce{N+ + A- <=> N+A-} & & & \SetCell[c=2]{c} \ce{N^. + C+ <=> N^.C^+} & & & \SetCell[c=2]{c} \ce{N- + C+ <=> N-C+}  & \\ 
+	&  \SetCell[c=2]{c} \ce{N+ + A- <=> N+A-} & & & \SetCell[c=2]{c} \ce{N^. + C+ <=> N^.C^+} & & & \SetCell[c=2]{c} \ce{N- + C+ <=> N^-C+}  & \\ 
 	\cline{2-3} \cline{5-6} \cline{8-9}
 	& $a_{\ce{N+A-}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^.C+}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^-C+}}$ & $\Delta{G}_{cplx}^\star$\\
 	\hline
@@ -443,9 +445,9 @@
 \end{longtblr}
 
 \clearpage
-\begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in acetonitrile (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
+\begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, together with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in acetonitrile (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
 	\hline
-	&  \SetCell[c=2]{c} \ce{N+ + A- <=> N+A-} & & & \SetCell[c=2]{c} \ce{N^. + C+ <=> N^.C^+} & & & \SetCell[c=2]{c} \ce{N- + C+ <=> N-C+}  & \\ 
+	&  \SetCell[c=2]{c} \ce{N+ + A- <=> N+A-} & & & \SetCell[c=2]{c} \ce{N^. + C+ <=> N^.C^+} & & & \SetCell[c=2]{c} \ce{N- + C+ <=> N^-C+}  & \\ 
 	\cline{2-3} \cline{5-6} \cline{8-9}
 	& $a_{\ce{N+A-}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^.C+}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^-C+}}$ & $\Delta{G}_{cplx}^\star$\\
 	\hline
@@ -481,7 +483,7 @@
 \clearpage
 \begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in water (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
 	\hline
-	&  \SetCell[c=2]{c} \ce{N+ + A- + C+ <=> N+AC} & & & \SetCell[c=2]{c} \ce{N^. + A- + C+ <=> N^.AC} & & & \SetCell[c=2]{c} \ce{N- + A- + C+ <=> N-AC}  & \\ 
+	&  \SetCell[c=2]{c} \ce{N+ + A- + C+ <=> N+AC} & & & \SetCell[c=2]{c} \ce{N^. + A- + C+ <=> N^.AC} & & & \SetCell[c=2]{c} \ce{N- + A- + C+ <=> N^-AC}  & \\ 
 	\cline{2-3} \cline{5-6} \cline{8-9}
 	& $a_{\ce{N+AC}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^.AC}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^-AC}}$ & $\Delta{G}_{cplx}^\star$\\
 	\hline
@@ -552,7 +554,7 @@
 \clearpage
 \begin{longtblr}[caption={Radii ($a$, in \si{\angstrom}) of the ion-pair for the 3 oxidation states of the nitroxides, toghether with their corresponding Gibbs free energy of complexation ($\Delta G^\star_{cplx}$, in \si{\kilo\joule\per\mole}), as computed at the $\omega$B97X-D/6-311+G(d) level in acetonitrile (SMD), with $[\ce{X}]=\SI{1}{\mole\per\liter}$.}]{colspec={>{\bfseries}lX[c]X[c]cX[c]X[c]cX[c]X[c]}, width =\linewidth,rowhead=2}
 	\hline
-	&  \SetCell[c=2]{c} \ce{N+ + A- + C+ <=> N+AC} & & & \SetCell[c=2]{c} \ce{N^. + A- + C+ <=> N^.AC} & & & \SetCell[c=2]{c} \ce{N- + A- + C+ <=> N-AC}  & \\ 
+	&  \SetCell[c=2]{c} \ce{N+ + A- + C+ <=> N+AC} & & & \SetCell[c=2]{c} \ce{N^. + A- + C+ <=> N^.AC} & & & \SetCell[c=2]{c} \ce{N- + A- + C+ <=> N^-AC}  & \\ 
 	\cline{2-3} \cline{5-6} \cline{8-9}
 	& $a_{\ce{N+AC}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^.AC}}$ & $\Delta{G}_{cplx}^\star$ &  & $a_{\ce{N^-AC}}$ & $\Delta{G}_{cplx}^\star$\\
 	\hline
@@ -580,7 +582,7 @@
 \end{longtblr}
 
 \clearpage
-\begin{longtblr}[caption={Litterature experimental $E^0_{rel}(\ce{N+}|\ce{N^.})$ (in \si{\milli\volt} vs SHE), measured in water and acetonitrile. When two values reported, the first one is used in the regressions and discussions.},
+\begin{longtblr}[caption={Litterature experimental $E^0_{rel}(\ce{N+}|\ce{N^.})$ (in \si{\milli\volt} vs SHE), measured in water and acetonitrile. When two values are reported, the first one is used in the regressions and discussions.},
 		note{a} = {From Ref.~\citenum{goldsteinStructureActivityRelationship2006}.},
 		note{b} = {From Ref.~\citenum{morrisChemicalElectrochemicalReduction1991}, converted from SCE to SHE with +\SI{244}{\milli\volt} \cite{pavlishchukConversionConstantsRedox2000}.},
 		note{c}={From Ref.~\citenum{blincoExperimentalTheoreticalStudies2008}.},
@@ -610,7 +612,7 @@
 \begin{figure}[!h]
 	\centering
 	\includegraphics[width=.75\linewidth]{FigureS7}
-	\caption{Comparison between experimental ($E^0_{rel} $ vs SHE, from Table \ref{tab:exp}) and calculated relative oxidation potential ($E^f_{rel}$ vs SHE) in water (top) and acetonitrile (bottom)  as computed at the $\omega$B97X-D/6-311+G(d) level  using SMD, and no correction due to DH or pair formation.  The dashed line is a linear regression.}
+	\caption{Comparison between experimental ($E^0_{rel} $ vs SHE, from Table \ref{tab:exp}) and calculated relative oxidation potential ($E^f_{rel}$ vs SHE) in water (top) and acetonitrile (bottom)  as computed at the $\omega$B97X-D/6-311+G(d) level  using SMD, but \textbf{without} correction due to DH or ion-pair formation.  The dashed line is a linear regression.}
 	\label{fig:expvstheo}
 \end{figure}