Single point DFT, QM/MM MD simulation, and trajectory data extraction

The structures of TEMPOL-amino acid complexes were optimized in water phase at the M06-2X/6–311G** level using Gaussian16⁶⁷. All the molecular orbitals were described by cubegen module of Gaussian program. The solvation effect was introduced via polarizable continuum model (PCM). We performed an exhaustive configurational search for the TEMPOL-amino acid complexes at each binding site, and kept the lowest-energy configuration. The vibrational frequencies were calculated to confirm the local minima with all positive frequencies. The Gibbs free energies (including the solvation energy) of the TEMPOL-amino acid complexes are given in Supplementary Table ⁵.

The quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulation of indole-TEMPO complex was performed with the explicit CCl₄ solvent environment. The initial TEMPO-indole complex was constructed starting from the TEMPO-CHCl₃ complex²⁰ by replacing CHCl₃ with indole. Subsequently, the TEMPO-indole complex was optimized in a carbon tetrachloride solvent environment at the M06-2X/6–311 G** level⁶⁸ using the Gaussian16 program^67,68. Polarizable Continuum Model (PCM) was applied to mimic the solvent environment.

Next, the TEMPO-indole complex was placed at the center of a rectangular box containing 498 carbon tetrachloride molecules. Force field parameters for carbon tetrachloride and the TEMPO-indole complex were taken from the Generalized Amber force field (GAFF)⁶⁹ with the HF/6–31G* RESP charges. Minimization using the Amber force field was first performed to relax the system with a weak constraint. Then the system was brought to room temperature (300 K) in 100 ps with a weak constraint. After that, 100 ps classical MD simulation of the weakly restrained TEMPO-indole complex was carried out to further relax the system with the periodic boundary condition at 300 K and 1 atm. The integration time step was set to 1.0 fs.

Finally, 10 ps QM/MM MD simulation was performed after the pre-equilibrium simulation.

Currently, this simulation is set as a long-run task on the computational platform and a glimpse into the 20 ps result can be found in Supplementary Figs. ^5t and  ^6t. The TEMPO-indole complex was partitioned into the QM region and the rest of the system was treated by MM. The QM region was calculated by M06–2X/6–311G**⁶⁸. The electronic coupling between the QM and MM regions was treated by including the MM charges in the QM Hamiltonian. A 15 Å cutoff was utilized to treat QM/MM electrostatic interactions. The integration time step for QM/MM MD simulation was also set to 1.0 fs. The atomic spin densities of the TEMPO-indole complex were obtained from the QM/MM calculations. The Amber18 program⁷⁰ was utilized to perform the MD simulations, and the Sander module with an interface to the Gaussian16 program was employed to carry out QM/MM MD simulations. The 10 ps trajectory calculation took 1 × 10⁴ h CPU (Intel Xeon E5–2650 2.30 GHz) time on our cluster. The time evolutions of the spin density and molecular geometry (H-bond length, H-bond angle, TEMPO-CCl₄ distance, methyl rotation angle) were extracted from the QM/MM MD trajectory using in-house scripts. The 3D profiles of SOMO of selected conformations/frames were generated using GaussView. The QM/MM simulation was conducted on 20-core Intel Xeon E5–2650 2.30 GHz processors at the Supercomputer Center of East China Normal University (ECNU).