add structures

TODO.md

@@ -1,13 +1,17 @@
 # TODOs
 
+For v1.0: 
+
 - [x] **12**!!
 - [x] 62 → 61
 - [x] Use $E^f$ in Fig. 15 (and check discussion, especially **4**)
-- [x] Fig. 16: $E_{SHE}$ → $E^0_{abs}$
+- [x] Fig. 16: $E_{SHE}$ → $E^0_{abs}(SHE)$
 - [x] Conclude & abstract & keywords
 - [x] Aknowledgements
 - [x] Clean up the bibliography, check for duplicates
 
+For v2.0:
+
 - [x] prepare a TOC
 - [x] Research highlight
 - [x] mark (and address) missing values in Tables
@@ -22,10 +26,14 @@
 - [x] Extra explanation solv. (diff of $\varepsilon$ is not enough)
 - [x] All tables in the SI should be updated (!)
 
+For v3.0 (to be submitted):
+
 - [x] Fig. or Figure? → Fig. ;-)
 - [x] PACS code, MSC code? → not relevant, also PACS is discontinued
 - [ ] tries to move labels as much as possible in graphs
-- [ ] pack the geometries
+- [x] pack the geometries
 - [x] Description of the SI? → Nope
 - [x] Mat → Matsui
-- [ ] Data availability
+- [x] Data availability
+- [ ] Update SI (!!)
+- [ ] Address last comments

nitroxides.tex

@@ -595,11 +595,13 @@ \section*{Acknowledgements}
 	\item on Lucia, the Tier-1 supercomputer of the Walloon Region, infrastructure funded by the Walloon Region (grant agreement No. 1910247).
 \end{inparaenum} 
 
-\section{Data availability}
+\section*{Data availability}
 
-xxx.
-
+Computational results (checkpoint files) are available at \url{https://dx.doi.org/10.5281/zenodo.12751130}.
+Curated data and analyses scripts are available at \url{https://github.com/pierre-24/publi-nitroxides/}.
+Further data will be available from the corresponding author upon reasonable request.
 
+
 \bibliographystyle{elsarticle-num-names} 
 \bibliography{biblio}
 

structures/README.md

@@ -0,0 +1,11 @@
+This dataset contains the optimized structures of the nitroxides, as XYZ files.
+
+They are organized as `{solvent}/{complexation_state}/mol_{n}/mol_{n}_{state}.xyz`, where:
+
+- `{solvent}`: the implicit solvent used in optimization (`water`, `acetonitrile`),
+- `{complexation_state}`: the complexation state of the nitroxide (`singles`, `pairs`, `ACs`),
+- `{n}`: the index of the nitroxide, as defined in Fig. 7,
+- `{state}`: redox state of the nitroxide (`ox`, `rad`, `red`).
+
+The title of the XYZ file is the final SCF energy, as computed at the wB97X-D/6-311+G* level in Gaussian 16C01.
+

structures/acetonitrile/BF4.xyz

@@ -0,0 +1,8 @@
+5
+
+B   0.00011086 -0.00005071 -0.00002861
+F  -0.23014579  0.30913561  1.35712644
+F   1.32861215 -0.44646865 -0.16192416
+F  -0.89051703 -1.01523274 -0.40858174
+F  -0.20801091  1.15259395 -0.78660464
+

structures/acetonitrile/NMe4.xyz

@@ -0,0 +1,20 @@
+17
+
+N   0.00000000  0.00000000  0.00000000
+C   0.86117157  0.86117157  0.86117157
+C  -0.86117157 -0.86117157  0.86117157
+C  -0.86117157  0.86117157 -0.86117157
+C   0.86117157 -0.86117157 -0.86117157
+H  -0.22105758 -1.48392743  1.48392743
+H   0.22105758  1.48392743  1.48392743
+H   1.48392743  0.22105758  1.48392743
+H   1.48392743  1.48392743  0.22105758
+H   1.48392743 -0.22105758 -1.48392743
+H   1.48392743 -1.48392743 -0.22105758
+H   0.22105758 -1.48392743 -1.48392743
+H  -1.48392743  1.48392743 -0.22105758
+H  -0.22105758  1.48392743 -1.48392743
+H  -1.48392743  0.22105758 -1.48392743
+H  -1.48392743 -0.22105758  1.48392743
+H  -1.48392743 -1.48392743  0.22105758
+

structures/acetonitrile/nitroxide_ACs/mol_02/mol_02_anion.xyz

@@ -0,0 +1,54 @@
+51
+Total Energy                               R     -1.122686780611405E+03
+C  -0.78089888  2.14130415 -0.69882346
+C  -1.82482898  2.00417742 -1.81218105
+C  -1.05164092  3.50307796 -0.03418415
+N  -0.98210065  0.99917002  0.25223261
+O  -1.02584165 -0.19411536 -0.50023502
+C   0.09349349  0.85863730  1.28918714
+C   0.00198764  1.95061360  2.37038924
+C  -0.13458268 -0.47138141  2.01523917
+C   1.49684334  0.84527125  0.65430806
+C   1.73635634  2.03301856 -0.27555832
+C   0.62788776  2.11821868 -1.32389166
+H  -2.83938803  2.00859704 -1.39543277
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+H  -1.74392872  2.84696967 -2.50762538
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+H  -1.24117226  4.25421299 -0.80779908
+H  -0.22639031  3.87931613  0.56767855
+H  -1.04021523  2.13049088  2.65285253
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+H   0.69359740  1.24065772 -1.97588500
+H   0.76318886  3.00354586 -1.95804031
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+C  -3.96695579 -0.41852472  0.70325545
+C  -2.83347303 -2.53304598  0.34696133
+C  -5.25078844 -2.38085649  0.01992592
+C  -3.71366767 -1.29666236 -1.54206382
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+H  -4.13348829 -0.69228684  1.74519071
+H  -3.00037002  0.07496192  0.57566788
+H  -4.78142485  0.21614094  0.35349684
+H  -4.52302937 -0.64714976 -1.87517426
+H  -2.74860612 -0.78027095 -1.56439615
+H  -3.69761875 -2.20841712 -2.13885689
+H  -5.40299135 -2.63573634  1.06798055
+H  -6.05214377 -1.72951981 -0.32667457
+H  -5.21913201 -3.28693122 -0.58384780
+H  -3.00008005 -2.78630023  1.39386059
+H  -2.82299433 -3.43917231 -0.25860924
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+F   4.88881185 -0.17890300  0.38224816
+F   3.63442396 -2.10607958  0.55056582
+

structures/acetonitrile/nitroxide_ACs/mol_02/mol_02_cation_rev.xyz

@@ -0,0 +1,54 @@
+51
+Total Energy                               R     -1.122421144489823E+03
+C   1.53460247 -1.05606248 -0.96132888
+C   0.10675328 -1.57699570 -0.99832062
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+H  -1.97794792 -0.86411542  0.97095877
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+H  -5.57191826 -0.50214742  1.41003212
+B  -0.91264696  2.61666889 -0.29730836
+F  -1.19693505  1.73715414 -1.36323967
+F  -1.64336742  2.23162132  0.84328146
+F   0.46938852  2.57430334 -0.01057681
+F  -1.27337975  3.92944668 -0.66652845
+

structures/acetonitrile/nitroxide_ACs/mol_02/mol_02_rad.xyz

@@ -0,0 +1,54 @@
+51
+Total Energy                               R     -1.122602485115017E+03
+C   0.02269621  1.54435982 -0.71518117
+C   0.12334854  1.26861302 -2.21546991
+C  -1.20036171  2.43057800 -0.44367034
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+C   1.54882543  0.72971631  1.71412758
+C   1.50038282  2.18274753  1.26836625
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+F   4.30930946 -1.67456380  0.70604429
+F   3.26023910 -0.99512243 -1.23010993
+

structures/acetonitrile/nitroxide_ACs/mol_03/mol_03_anion.xyz

@@ -0,0 +1,57 @@
+54
+Total Energy                               R     -1.311267534741841E+03
+C   1.68254659  1.66272933 -0.94620783
+C   0.84565774  2.02321624 -2.17871725
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+F  -2.04848243 -2.56824461  1.21982975
+F  -2.67234907 -2.32469298 -0.98860079
+

structures/acetonitrile/nitroxide_ACs/mol_03/mol_03_cation.xyz

@@ -0,0 +1,57 @@
+54
+Total Energy                               R     -1.310996492480821E+03
+C   0.28822507 -0.58083404 -0.58406942
+C   0.96486359  0.55366897 -1.33953086
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+C  -2.24684673 -1.09480866  0.95238486
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+F  -2.71196646  3.88614136 -0.71476655
+F  -3.64200763  2.48743739  0.86248753
+F  -1.50552749  2.10166199  0.09411408
+