Conformational analysis of compound 7 and intramolecular 1,3-dipolar cycloaddition

see http://limor3.nioch.nsc.ru/moloko/2018/Horoshunova_w.pdf, Scheme 6
There is huge discrepancy between experiment (barrier ~28 kcal/mol) and theory (barrier 14-15 kcal/mol)




Conformational search: crest (GFN2-xTB)
Geometry optimization: DFT/PBE/L1 (Priroda)

On figure(s) below click on the level title to download xyz file ==>
Click on energy level to view 3D structure in browser (run JSmol) ==>

-12.20 -12.20 -11.19 -11.19 -11.08 -11.08 -10.45 -10.45 -10.28 -10.28 -10.21 -10.21 -9.72 -9.72 -9.37 -9.37 -8.98 -8.98 -8.90 -8.90 -8.83 -8.83 -8.65 -8.65 -8.33 -8.33 -7.40 -7.40 -7.28 -7.28 -7.05 -7.05 -7.00 -7.00 -6.95 -6.95 -6.36 -6.36 -5.35 -5.35 -4.33 -4.33 0.00 0.00 0.13 0.13 0.13 0.13 0.21 0.21 0.21 0.21 0.26 0.26 0.27 0.27 0.28 0.28 0.28 0.28 0.32 0.32 0.33 0.33 0.36 0.36 0.37 0.37 0.39 0.39 0.40 0.40 0.43 0.43 0.44 0.44 0.45 0.45 0.54 0.54 0.57 0.57 0.58 0.58 0.60 0.60 0.65 0.65 0.71 0.71 0.79 0.79 0.81 0.81 0.84 0.84 0.84 0.84 0.90 0.90 0.94 0.94 1.00 1.00 1.03 1.03 1.17 1.17 1.25 1.25 1.25 1.25 1.33 1.33 1.38 1.38 1.40 1.40 1.42 1.42 1.45 1.45 1.50 1.50 1.61 1.61 1.78 1.78 1.80 1.80 1.88 1.88 2.08 2.08 2.26 2.26 2.32 2.32 2.44 2.44 2.45 2.45 2.58 2.58 2.65 2.65 2.80 2.80 2.81 2.81 2.83 2.83 2.85 2.85 2.87 2.87 2.94 2.94 3.06 3.06 3.26 3.26 3.45 3.45 3.53 3.53 3.78 3.78 3.85 3.85 3.99 3.99 4.40 4.40 4.46 4.46 4.72 4.72 13.53 13.53 14.42 14.42 16.23 16.23 16.89 16.89 16.93 16.93 18.08 18.08 18.22 18.22 18.50 18.50 18.54 18.54 21.68 21.68 21.76 21.76 22.32 22.32 22.53 22.53 23.31 23.31

13.12.2018

Conformational analysis of nitrone 6

Conformational search: crest (GFN2-xTB)
Geometry optimization: M06-2X/def2-TZVP/CPCM(toluene) (ORCA)


On figure(s) below click on the level title to download xyz file ==>
Click on energy level to view 3D structure in browser (run JSmol) ==>

0.00 0.00 0.08 0.08 0.15 0.15 0.20 0.20 0.22 0.22 0.24 0.24 0.28 0.28 0.33 0.33 0.43 0.43 0.43 0.43 0.47 0.47 0.48 0.48 0.52 0.52 0.52 0.52 0.58 0.58 0.68 0.68 0.70 0.70 0.77 0.77 0.80 0.80 0.82 0.82 0.84 0.84 0.86 0.86 0.89 0.89 0.92 0.92 0.93 0.93 0.97 0.97 0.98 0.98 0.99 0.99 1.03 1.03 1.05 1.05 1.09 1.09 1.10 1.10 1.13 1.13 1.15 1.15 1.18 1.18 1.19 1.19 1.22 1.22 1.23 1.23 1.30 1.30 1.30 1.30 1.34 1.34 1.47 1.47 1.52 1.52 1.59 1.59 1.60 1.60 2.12 2.12 2.37 2.37 2.37 2.37 3.73 3.73 3.79 3.79 3.88 3.88 3.89 3.89 3.90 3.90 3.90 3.90 4.06 4.06 4.11 4.11 4.18 4.18 4.23 4.23 4.28 4.28 4.30 4.30 4.30 4.30 4.48 4.48 4.72 4.72 4.86 4.86 5.08 5.08 5.17 5.17 5.22 5.22 5.51 5.51

Transition states of intramolecular 1,3-dipolar cycloaddition

Conformational search: GOAT/GFN2-xTB (ORCA)
Geometry optimization: M06-2X/def2-TZVP/CPCM(toluene) (ORCA)
Zero level of energy is conformer 01 of nitrone 6

On figure(s) below click on the level title to download xyz file ==>
Click on energy level to view 3D structure in browser (run JSmol) ==>

23.73 23.73 24.36 24.36 26.74 26.74 26.87 26.87 27.60 27.60 27.60 27.60 27.88 27.88 28.99 28.99 29.20 29.20 29.21 29.21 31.44 31.44 31.50 31.50 32.07 32.07 32.39 32.39 33.44 33.44 33.72 33.72 56.77 56.77 64.77 64.77 67.98 67.98

Conformational analysis of the products

Conformational search: GOAT/GFN2-xTB (ORCA)
Geometry optimization: M06-2X/def2-TZVP/CPCM(toluene) (ORCA)
Zero level of energy is conformer 01 of nitrone 6

On figure(s) below click on the level title to download xyz file ==>
Click on energy level to view 3D structure in browser (run JSmol) ==>

-15.30 -15.30 -13.40 -13.40 -13.14 -13.14 -12.88 -12.88 -12.35 -12.35 -12.21 -12.21 -12.13 -12.13 -11.98 -11.98 -11.53 -11.53 -11.36 -11.36 -10.56 -10.56 -10.49 -10.49 -9.68 -9.68 -9.67 -9.67 -8.83 -8.83 -8.72 -8.72 -8.55 -8.55 -8.42 -8.42 -8.35 -8.35 -7.85 -7.85 -7.77 -7.77 -7.18 -7.18 -7.13 -7.13 -6.49 -6.49 -3.95 -3.95 -3.75 -3.75 -3.37 -3.37 0.60 0.60 4.69 4.69 5.96 5.96

26.10.2025