SimDyn: A software package for spin dynamics simulations of ENDOR spectra

Electron nuclear double resonance (ENDOR) spectroscopy is a method to detect the interactions between electron and nuclear spins to obtain structural information on molecular systems. Usually, this information is derived by extracting magnetic parameters from experimental spectra using spectral simulations. Thus, the derived information is limited to the representation of the experiment by the simulation. Advances in experimental setup constantly increase the resolution of spectra, and more sophisticated and detailed simulations are required, especially when the effect of pulse sequences can no longer be approximated by simple line shape functions. A suitable method to quantify these effects are spin dynamics simulations. Here, we describe the spin dynamics simulation package SimDyn, which is optimised to efficiently simulate ENDOR spectra of S = 1/2 paramagnetic systems, particularly Mims ENDOR for nitroxide-based ¹⁹F-ENDOR distance measurements. Besides the effects of orientation selection, the software is able to treat small terms in the spin Hamiltonian that are usually neglected in EPR and ENDOR but can still be directly observed, such as nuclear chemical shielding and nuclear-nuclear dipolar couplings. Moreover, relaxation effects are phenomenologically implemented as decay rates of density matrix elements in the Liouville space. Applications are presented for the analysis of ¹⁹F-ENDOR spectra, demonstrating how spin dynamics simulations can be used to gain insight on the experiment and subtle features of the detected spectra.