A novel approach to the simulation of nitroxide spin label EPR spectra from a single truncated dynamical trajectory

EPR spectroscopy and molecular dynamics modelling: a combined approach to study liquid crystals

“…This timescale, however, is much shorter compared to the sampling time of T >3 μs required to the propagation of the density matrix in EPR spectral simulations. Oganesyan has shown [27,28] that, in fact, the propagation of the density matrix along the entire sampling time T is not strictly necessary, and an accurate simulation can be achieved from a truncated MD trajectory until the point when the autocorrelation function of the re-orientational motion of a spin probe has completely relaxed. The evolution of the spin density matrix for the remaining working length can then be predicted from the truncated trajectory [27,28].…”

“…Oganesyan has shown [27,28] that, in fact, the propagation of the density matrix along the entire sampling time T is not strictly necessary, and an accurate simulation can be achieved from a truncated MD trajectory until the point when the autocorrelation function of the re-orientational motion of a spin probe has completely relaxed. The evolution of the spin density matrix for the remaining working length can then be predicted from the truncated trajectory [27,28]. The reported simulation method employs the following: (i) the propagation of the spin density matrix in the Liouville space for this initial time interval (T,10τ, where τ is the effective correlation time for the re-orientational motion of the spin probe) is carried out numerically according to Equations (5-6); (ii) after the autocorrelation function of the spin probe motions has completely relaxed, the rest of the magnetisation trajectory (t>T) for the sampling time is calculated using well-defined parameters (see for details [12,27,28]).…”

“…The evolution of the spin density matrix for the remaining working length can then be predicted from the truncated trajectory [27,28]. The reported simulation method employs the following: (i) the propagation of the spin density matrix in the Liouville space for this initial time interval (T,10τ, where τ is the effective correlation time for the re-orientational motion of the spin probe) is carried out numerically according to Equations (5-6); (ii) after the autocorrelation function of the spin probe motions has completely relaxed, the rest of the magnetisation trajectory (t>T) for the sampling time is calculated using well-defined parameters (see for details [12,27,28]). For example, when the calculation of transverse magnetisation based on Equation (10) is justifiable, calculation of only two parameters for each of the three hyperfine coupling lines, namely…”

“…First, this substantially reduces the amount of computational time for the simulation of EPR spectra. Second, the method relies on the EPR simulation from relatively short DT trajectories over timescales that are within the reach of current MD computational methods [27,28]. This approach has paved the way for the first-time prediction of motional EPR spectra directly and completely from MD trajectories of actual molecular structures.…”

“…It has been successfully applied to proteins [29,30], DNA [31], lipid bilayers [32] and also LCs [33][34][35]. A computer code developed by the author [27,28], which includes both options, namely the propagation of the trajectories along the entire sampling time and the use of truncated trajectories combined with autocorrelation function method, has been employed for the simulation of EPR spectra of LC systems reported in this review.…”