Establishment of atropisomerism in 3-indolyl furanoids: a synthetic, experimental and theoretical perspective

Introduction of axial chirality in bioactive 3-indolyl furanoids has been achieved by systematic alteration of functional groups around the stereogenic axis, keeping in mind that atropisomerically pure analogues may possess different binding affinities and selectivities towards a target protein. The kinetics of racemization of axially chiral 3-indolyl furanoids have been studied through chiral HPLC analysis, electronic circular dichroism (ECD) spectroscopy, and computational modeling. The results identify the configurational parameters for optically pure 3-indolyl furanoids to exist as stable and isolable atropisomeric form.


Section E: Determination of kinetic and thermodynamical parameters of 3db, 3dg, 3dh, and 3di from HPLC analysis
Decrease of enantiomeric excess (ee) of (S)-3db as a function of time (min for 353 K and 333 K, days for 300 K) were plotted at different temperatures ( fig. S59, fig. S69 and fig.   S77). The decay constants (t 1 ), rate constants (k rac ), and enantiomerisation rate constant (k enant ) were determined from the exponential decay curves for each of the temperatures by using the following equations Eqn.1 and 2 respectively.

Section F: Temperature dependent CD spectral analysis of 3db [a] CD spectra of (S)-3db at 353 K with the course of time
To perform the Electronic Circular Dichroism (ECD) analysis, 1.03 mM solution of (S)-3db was prepared by dissolving 1.0 mg of (S)-3db in 1.0 mL EtOH. 400 µL of the above solution was taken in a screw cap quartz cuvette (screw cap is necessary to stop the change of concentration of sample due to solvent evaporation) and placed inside the CD spectrophotometer equipped with thermoelectric temperature controller. Sample was placed inside the preheated CD spectrophotometer at 353 K. CD spectra were recorded with respect to variable time regime up to 30 min at fixed temperature of 353 K. The spectral data was obtained is represented below. Figure S107: CD spectra of (S)-3db at 353 K in different time scale [b] CD spectra of (S)-3db at 333 K with the course of time

S66
The above indicated CD spectral analysis was also applied to record at 333 K. Sample was placed inside the preheated CD spectrophotometer at 333 K. CD spectra were recorded with respect to variable time regime up to 10 h at fixed temperature of 333 K. The spectral data was obtained is represented below.  Figure S108: CD spectra of (S)-3db at 333 K in different time scale     The activation enthalpy (ΔH ≠ ) and activation entropy (ΔS ≠ ) of the isomerization of atropisomer 3db were further determined employing the Eyring equation:

Eqn. 3:
The values for ∆H ≠ and ∆S ≠ were determined from kinetic data obtained from a vs.   Table   S4.

S72
Suitable single crystal with approximate dimensions of 0.12 × 0.10 × 0.05 mm 3 was used for X-ray diffraction analyses by mounting on the tip of a glass fiber in air. Data were collected on a Bruker kappa apex 2 with Mo Kα (λ=0.71073 Å) at 296.15 K. The structure was solved by direct method using program SHELXL-97 and subsequent Fast Fourier Transform technique. Crystallographic data and experimental details for 3dg are summarized in Table   S5. Olex2 , the structure was solved with the ShelXT structure solution program using Intrinsic Phasing and refined with the ShelXL refinement package using Least Squares minimization.
Crystallographic data and experimental details for 3di are summarized in Table S7.

Comparative study of isomerization energy barrier of 2-methyl indole substitution (3bb) with 2-phenyl indole substitution (3db) through DFT modelling
The predicted isomerization energy barrier of Molecule 3bb, which has a methyl group at the 2-indole position, is 22.9 kcal/mol (24.4 kcal/mol G ‡ ). This is 2.6 kcal/mol lower than the barrier of 3db, which has a phenyl at the same position (1.6 kcal/mol lower in G ‡ ). That the methyl substituted species presents a lower barrier might seem counterintuitive, as a methyl is sterically bulkier than a phenyl (when measured normal to the plane of the aromatic ring). However, the furan bond angles at the 2 and 4 positions orient the phenyl groups towards the indole. The predicted transition states show the phenyl groups acting as rigid leaver arms, which must pass the indole to allow axial inversion. In the more favourable of the two 3bb transition states, the 4-furan phenyl slides over the 2-indole methyl group causing the angle between the 4-furan carbon, 1-phenyl carbon, and 4-phenyl carbon to bend out of plane to 175.7° ( Figure S112). By comparison, in the corresponding 3db transition state, nonplanarity of the matching atoms increases to 170.5° ( Figure S112 right).

Additional analysis regarding the barrier of rotation of 3dg
Molecule 3dg interconverts relatively rapidly compared to similar species. However, its overall barrier height is predicted to be in the same range as the more stable molecules (predicted G ‡ of 27.6 kcal/mol vs. 26.0 for 3db G ‡ ). A notable observation from 3dg modelling is that the 2-methoxy phenyl substitution leads to a second local minimum pose which is ~4 kcal/mol above the predicted global minimum ( Figure S113, bottom). In the higher energy structure, the methoxy oxygen sits proximal to the furan ring oxygen. The higher energy structure is predicted to be metastable-a potential energy surface for rotation around the furan-dimethoxyphenyl bond shows a barrier in the range of 2 kcal/mol ( Figure  S113, top).

Tables of selected atom coordinates and absolute energies:
Optimized coordinates of 3db min in vacuo (Ground State):