Electron Paramagnetic Resonance Spectra Simulation Directly from Molecular Dynamics Trajectories of a Liquid Crystal with a Doped Paramagnetic Spin Probe

We report simulation of EPR spectra directly and entirely from trajectories generated from molecular dynamics simulations. Results are reported for a model $3\beta$-DOXYL-$5\alpha$-cholestane spin probe in a coarse-grained solvent representing a 5CB nematic host. The results are in excellent agreement with the experimental spectra. The calculated order parameters associated with the paramagnetic probe show strong correlation with the order parameter of 5CB mesogens and are in agreement with those reported in the literature. Simulation of EPR spectra entirely from molecular dynamics of real structures provides direct correlation between molecular motions and the features observed in the spectra, allowing unambiguous interpretation of the spectra. This method opens the possibility for “computer engineering” of spin-labeled materials with the desired properties, such as spin-labeled proteins, prior to experiment.

Figure 1

Molecular structures of 5CB mesogen (a) and cholesteric nitroxide spin probe (b). The orientation of $x$, $y$, and $z$ axes of the magnetic frame together with the long rotational diffusion axis of spin probe ${\mathbf{D}}_{\mathrm{SP}}$ are indicated.

Figure 2

$X$-band EPR spectra predicted from MD calculations carried out at four different regimes (solid lines): ($a$) nematic phase ($T=25°\mathrm{C}$), ($b$) and ($c$) $N\mathrm{\text{−}}I$ phase transition ($T=35.3°\mathrm{C}$) as approached from $N$ and $I$ starting configurations, respectively, and ($d$) isotropic phase ($T=39°\mathrm{C}$). Distributions of magnetic $z$ axis on a unit sphere (points accumulated during the 20 ns runs) are shown for each spectrum. Available experimental EPR spectra are shown by dotted lines. EPR spectrum corresponding to isotropic phase ($d$) is taken from the literature [9]. In the simulations $T_2^m=0.18\mu \mathrm{s}$ and $0.25\mu \mathrm{s}$ for ($a$),($b$) and ($c$),($d$), respectively.

Figure 3

Autocorrelation function for the $\theta$ angle between magnetic $z$ axis of the nitroxide probe and the director in the nematic phase of 5CB [$D_{00}^2=(3{cos}^2\theta -1)/2$]. MD trajectory used in the simulation of EPR spectrum ($a$) in Fig. 2 is shown in the subplot.