Supporting information readme for "Beyond strain release: Delocalization-enabled organic reactivity"
ChemRxiv 2021: https://doi.org/10.26434/chemrxiv-2021-n0xm9-v2
This readme contains information on the supporting data that accompanies the manuscript described above. The file structure is depicted, followed by a description of the contents of each directory, subdirectory and file.
CartesianCoordinates > CCl3_addition > 111P
> BC210P
> BCB
> CH3_addition > 111P
> 211P
> 221P
> 222P
> 311P
> BC210P
> BC220H
> BC310H
> BCB
> cyclobutane
> cyclopropane
> ethane
> Cycloaddition > cyclodecyne
> cycloheptyne
> cyclononyne
> cyclooctyne
> dibenzocyclooctyne
> distal_monobenzocyclooctyne
> F2-cyclooctyne
> hex-3-yne
> monobenzocyclooctyne
> NS-cyclooctyne
> NH2_addition > 111P
> 211P
> 221P
> 222P
> 311P
> BC210P
> BC220H
> BC310H
> BCB
> cyclobutane
> cyclopropane
> ethane
> Strain_database
pdfs > Plot1.pdf
Plot2.pdf
Plot3.pdf
Plot4.pdf
Plot5.pdf
Plot6.pdf
Plot7.pdf
Plot8.pdf
Plot9.pdf
Plot10.pdf
Plot11.pdf
Plot12.pdf
Plot13.pdf
Plot14.pdf
Plot15.pdf
Plot16.pdf
Plot17.pdf
Plot18.pdf
Plot19.pdf
Plot20.pdf
Plot21.pdf
amide_data.csv
cycloaddition_data.csv
Hoz_data.csv
hydrocarbons_data.csv
SRE.csv
SRE.xlsx
energies.xlsx
mlr_models.py
Supporting_Information.pdf
"Supporting_Information.pdf" contains a detailed description of the methodologies employed in this work, as well as supplementary figures, tables, and references.
"SRE.csv" is a database containing strain release energies (kcal/mol) of unique bonds of 35 molecules (81 total data points). The columns contain the following information:
Column:
- 0 - Name of strained molecule
- 1 - Name of unstrained product molecule
- 2 - SMILES string representation of balanced reaction to obtain strain release energy, where dots (".") are used to separate individual molecules, and a double chevron (">>") indicates the reaction arrow
- 3 - Bond type designation, when there are multiple unique bond types in a given molecule
- 4 - Strain release energy (SRE, kcal/mol)
- 5 - Delocalisation value for the breaking bond (2–Nocc, e)
N.B. Strain release energy is defined as the change in enthalpy (∆H in kcal/mol) at the DLPNO-CCSD(T)/def2-QZVPP//B2PLYP-D3BJ/def2-TZVP level, and 2–Nocc values (in e) at are obtained from the B2PLYP/def2-TZVP relaxed density.
"mlr_models.py" is a script to plot all figures. Multiple linear regression is carried out using the Scikit-learn Python package, and plotting is done using Matplotlib. "mlr_models.py" can either be run interactively, or to generate all plots, run:
for i in {1..21}; do echo $i | python mlr_models.py -v; done
Plots are generated inside the “pdfs” directory. Each plot contains the following:
- Plot 1: y = ∆H‡, x0 = ∆H0, x1 = 2-Nocc (CH3• addition)
- Plot 2: y = ∆H‡, x0 = ∆H0, x1 = D/D_0 (CH3• addition)
- Plot 3: y = ∆H‡, x0 = ∆H0, x1 = n3 (CH3• addition)
- Plot 4: y = ∆H‡, x0 = ∆H0 (CH3• addition); ∆Hr vs ∆H‡
- Plot 5: y = ∆H‡, x0 = ∆H0 (CH3• addition); ∆H‡ calc vs pred
- Plot 6: y = ∆H‡, x0 = ∆H0, x1 = 2-Nocc, x2 = (∆H0)^2 (CH3• addition)
- Plot 7: y = ∆H‡, x0 = ∆H0, x1 = D/D_0, x2 = (∆H0)^2 (CH3• addition)
- Plot 8: y = ∆H‡, x0 = (∆r‡)^2 (CH3• addition)
- Plot 9: y = (∆r‡)^2, x0 = ∆H0 (CH3• addition)
- Plot 10: y = ∆r‡, x0 = ∆H0, x1 = 2-Nocc (CH3• addition)
- Plot 11: y = ∆r‡, x0 = ∆H0, x1 = D/D_0 (CH3• addition)
- Plot 12: y = ∆H‡, x0 = ∆H0, x1 = n3 (NH2- addition)
- Plot 13: y = Marcus Ea error, x0 = n3 (heterosubstitution)
- Plot 14: y = ∆H‡, x0 = ∆H0, x1 = (∆H0)^2 (CH3• addition)
- Plot 15: y = ∆H‡, x0 = ∆H0, x1 = 2-Nocc (NH2- addition)
- Plot 16: y = ∆H‡, x0 = ∆H0 (cycloaddition); ∆H‡ calc vs pred
- Plot 17: y = ∆H‡, x0 = ∆H0, x1 = mean 2-Nocc (cycloaddition)
- Plot 18: y = ∆H‡, x0 = ∆H0, x1 = E_HOMO (CH3• addition)
- Plot 19: y = ∆H‡, x0 = ∆H0, x1 = E_LUMO (CH3• addition)
- Plot 20: y = ∆H‡, x0 = ∆H0, x1 = ∆E_HOMO-LUMO (CH3• addition)
- Plot 21: y = ∆H‡, x0 = ∆H0, x1 = D/D_0 (NH2- addition)
The directory CartesianCoordinates contains all xyz files generated in this study, split into subdirectories (CCl3_addition, CH3_addition, Cycloaddition, NH2_addition, Strain_database). The numbering of molecules in “Strain_database” follows that defined in “smiles.csv” contained within the same subdirectory. Geometries were optimised at the levels of theory described in the corresponding tabs in “energies.xlsx”, the Supporting Information, and below in this readme.
The format of "hydrocarbons_data.csv" is as follows:
Column:
- 0 - Molecule identifier
- 1 - TS enthalpy / kcal/mol
- 2 - reaction enthalpy / kcal/mol
- 3 - 1–ELF (B2PLYP/def2-TZVP)
- 4 - 2–N_{occ} (B2PLYP/def2-TZVP, relaxed density)
- 5 - Number of three membered rings appended to breaking bond
- 6 - SM breaking C-C / Angstrom
- 7 - TS breaking C-C / Angstrom
- 8 - HOMO energy associated with breaking bond / Ha
- 9 - LUMO energy associated with breaking bond / Ha
Row:
- 1 - ethane, A
- 2 - cyclopropane, B
- 3 - cyclobutane, C
- 4 - bicyclo[1.1.0]butane, BCB, D
- 5 - bicyclo[2.1.0]pentane, BC210P, E
- 6 - bicyclo[3.1.0]hexane, BC310H, F
- 7 - bicyclo[2.2.0]hexane, BC220H, G
- 8 - [1.1.1]propellane, 111P, H
- 9 - [2.1.1]propellane, 211P, I
- 10 - [3.1.1]propellane, 311P, J
- 11 - [2.2.1]propellane, 221P, K
- 12 - [2.2.2]propellane, 222P, L
The format of "amide_data.csv" is as follows:
Column:
- 0 - Molecule identifier
- 1 - TS enthalpy / kcal/mol
- 2 - reaction enthalpy / kcal/mol
- 3 - Number of three membered rings appended to breaking bond
- 4 - 2-Nocc (B2PLYP/def2-TZVP, relaxed density)
Row:
- 1 - ethane, A
- 2 - cyclopropane, B
- 3 - cyclobutane, C
- 4 - bicyclo[1.1.0]butane, BCB, D
- 5 - bicyclo[2.1.0]pentane, BC210P, E
- 6 - bicyclo[3.1.0]hexane, BC310H, F
- 7 - bicyclo[2.2.0]hexane, BC220H, G
- 8 - [1.1.1]propellane, 111P, H
- 9 - [2.1.1]propellane, 211P, I
- 10 - [3.1.1]propellane, 311P, J
- 11 - [2.2.1]propellane, 221P, K
- 12 - [2.2.2]propellane, 222P, L
The format of "Hoz_data.csv" is as follows:
Column:
- 0 - Reaction type (anionic or radical)
- 1 - Reactant
- 2 - Substrate
- 3 - Reaction energy / kcal/mol
- 4 - TS energy (activation energy) / kcal/mol
- 5 - Marcus intrinsic activation barrier / kcal/mol
- 6 - Marcus predicted activation barrier / kcal/mol
- 7 - Difference between calculated and predicted (Marcus) activation energies / kcal/mol
- 8 - 2–N_{occ} (B2PLYP/def2-TZVP, relaxed density)
- 9 - Number of three membered rings appended to breaking bond
- 10 - Leaving group heteroatom type
The format of "cycloaddition_data.csv" is as follows:
Column:
- 0 - Alkyne reactant (syn / anti denotes stereochemistry of the product)
- 1 - TS enthalpy (kcal/mol)
- 2 - Reaction enthalpy (kcal/mol)
- 3 - Mean 2–N_{occ} value (from the two 2–N_{occ} values obtained for the two alkyne pi bonds)
The format of "energies.xlsx" is as follows:
Tab 1
TS and reaction energies for the addition of CH3 radical to H12 hydrocarbons. Raw energies in Ha, energy differences in kcal/mol.
Optimisation: B2PLYP D3BJ def2-TZVP Grid5 FinalGrid6 GridX6 def2/J def2/TZVP/C RIJCOSX TightOpt NumFreq
Single point: DLPNO-CCSD(T) AutoAux def2-QZVPP TightSCF PAL4 Grid6 FinalGrid6 GridX6 TightPNO RIJCOSX
Tab 2
TS and reaction energies for the addition of NH2– to H12 hydrocarbons. Raw energies in Ha, energy differences in kcal/mol.
Optimisation: B2PLYP D3BJ def2-TZVP Grid5 FinalGrid6 GridX6 def2/J def2/TZVP/C RIJCOSX TightOpt NumFreq SMD(THF) NB: ma-def2-TZVP basis set added to nucleophilic N
Single point: DLPNO-CCSD(T) AutoAux ma-def2-QZVPP TightSCF PAL4 Grid6 FinalGrid6 GridX6 TightPNO SMD(THF)
Tab 3
VdW complex, TS and reaction energies for the addition of CCl3 radical to [1.1.1]propellane, bicyclo[1.1.0]butane and bicyclo[2.1.0]pentane. Raw energies in Ha, energy differences in kcal/mol.
Optimisation: B2PLYP D3BJ def2-TZVP Grid5 FinalGrid6 GridX6 def2/J def2/TZVP/C RIJCOSX TightOpt NumFreq
Single point: DLPNO-CCSD(T) AutoAux def2-QZVPP TightSCF PAL4 Grid6 FinalGrid6 GridX6 TightPNO RIJCOSX
Tab 4
Data extracted from 10.1021/jo001412t and 10.1039/b314869f in kcal/mol
Tab 5
2–N_{occ} and n3 values for molecules studied in this paper
Tab 6
Balanced hydrogen transfer reactions for the dataset in Figure 5c. Raw energies in Ha, energy differences in kcal/mol.
Optimisation: B2PLYP D3BJ def2-TZVP Grid6 FinalGrid6 GridX6 def2/J def2/TZVP/C RIJCOSX TightOpt NumFreq
Single point: DLPNO-CCSD(T) AutoAux def2-QZVPP TightSCF PAL4 Grid6 FinalGrid6 GridX6 TightPNO RIJCOSX
Tab 7
Cycloaddtion TSs and minima for the addition of methyl azide to a selection of alkynes. Raw energies in Ha, energy differences in kcal/mol. Mean 2–N_{occ} values obtained from the two 2–N_{occ} values corresponding to each of the pi bonds of the alkyne.
Optimisation: B2PLYP D3BJ def2-TZVP Grid6 FinalGrid6 GridX6 def2/J def2/TZVP/C RIJCOSX TightOpt NumFreq