•Rn and MTSL (R1) protein spin labels by EPR and fully atomistic MD simulations.•Comparative study between the motions of Rn and R1 attached to Myoglobin.•Evidence for intrinsic low rotameric mobility of Rn spin label.•Uncovering the potential for using Rn as a sensitive reporter of protein dynamics.EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.

Correction for ‘EPR detection and characterisation of a paramagnetic Mo(III) dihydride intermediate involved in electrocatalytic hydrogen evolution’ by Christopher Prior, et al., Dalton Trans., 2016, 45, 2399–2403.

EPR spectroscopy and theoretical data show that the slow heterogeneous electron-transfer kinetics associated with the reduction of an 18-electron Mo(IV) acetato dihydride are a consequence of an η2–η1 rearrangement of the carboxylate ligand which gives a unique paramagnetic 17-electron Mo(III) dihydride.

We report successful simulation of motional EPR spectra of the liquid crystal 8CB doped with a cholestane nitroxide spin probe from fully atomistic molecular dynamics (MD) simulations. The spectra are calculated directly and completely from MD trajectories using our novel MD-EPR methodology. Predicted changes in molecular order, dynamics and EPR spectra across the N–I phase transitions show excellent agreement with experimental results. A nanosecond exchange dynamics between disordered and partially ordered meta-stable states is revealed at the N–I transition point and is confirmed by EPR measurements. This study demonstrates that a unique combination of state-of-the-art molecular modelling at the atomistic level and EPR spectroscopy, with introduced paramagnetic probes, allows accurate estimation of the local order and motional parameters of the mesogens. In particular, it is shown that an accurate estimation of the rotation correlation times for different molecular axes in liquid crystals can be achieved and correlated directly with the motions of the spin probe. We also demonstrate the successful simulation of a low temperature smectic-A liquid crystal phase in 8CB. Here, the simulations correctly predict the experimental layer spacing in 8CB and show directly the presence of a strong local preference for anti-parallel arrangements of molecules. The latter leads to a layer-spacing of D ≈ 1.4 molecular lengths.

A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.

A nitroxide spin label (SL) has been used to probe the electron spin relaxation times and the magnetic states of the oxygen-binding heme–copper dinuclear site in Escherichia coli cytochrome bo3, a quinol oxidase (QO), in different oxidation states. The spin lattice relaxation times, T1, of the SL are enhanced by the paramagnetic metal sites in QO and hence show a strong dependence on the oxidation state of the latter. A new, general form of equations and a computer simulation program have been developed for the calculation of relaxation enhancement by an arbitrary fast relaxing spin system of S ≥ 1/2. This has allowed us to obtain an accurate estimate of the transverse relaxation time, T2, of the dinuclear coupled pair Fe(III)–CuB(II) in the oxidized form of QO that is too short to measure directly. In the case of the F′ state, the relaxation properties of the heme–copper center have been shown to be consistent with a ferryl [Fe(IV)=O] heme and CuB(II) coupled by approximately 1.5–3 cm−1 to a radical. The magnitude suggests that the coupling arises from a radical form of the covalently linked tyrosine–histidine ligand to Cu(II) with unpaired spin density primarily on the tyrosine component. This work demonstrates that nitroxide SLs are potentially valuable tools to probe both the relaxation and the magnetic properties of multinuclear high-spin paramagnetic active sites in proteins that are otherwise not accessible from direct EPR measurements.

In the search for enhanced control over the process of resonance energy transfer in multichromophore molecular systems, all-optical mechanisms offer many significant advantages over other systems. One recently conceived scheme, based on the optical switching of energy transfer, is achieved by coupling a normally forbidden decay transition with pulses of off-resonant laser light. Earlier work has suggested that such systems could offer levels of efficiency that might approach those associated with the usual Förster mechanism. In this Letter, the ab initio results of specific calculations on stacked and coplanar polycyclic chromophores are reported. The results show that by judicious choice of electronic state and laser wavelength, much higher levels of efficiency are achievable. A possible scheme for the implementation of such a system is discussed with regard to its potential use in energy harvesting and optical switching applications.Keywords (keywords): ab initio calculations; computational chemistry; energy transfer; nonlinear optics; quantum theory;

A simple effective method for calculation of EPR spectra from a single truncated dynamical trajectory of spin probe orientations is reported. It is shown that an accurate simulation can be achieved from the small initial fraction of a dynamical trajectory until the point when the autocorrelation function of re-orientational motion of spin label has relaxed. This substantially reduces the amount of time for spectra simulation compared to previous approaches, which require multiple full length trajectories (normally of several microseconds) to achieve the desired resolution of EPR spectra. Our method is applicable to trajectories generated from both Brownian dynamics and molecular dynamics (MD) calculations. Simulations of EPR spectra from Brownian dynamical trajectories under a variety of motional conditions including bi-modal dynamics with different hopping rates between the modes are compared to those performed by conventional method. Since the relatively short timescales of spin label motions are realistically accessible by modern MD computational methods, our approach, for the first time, opens the prospect of the simulation of EPR spectra entirely from MD trajectories of real proteins structures.

X- and W-band EPR spectra, at room and low temperatures, are reported for nitroxide spin labels attached to cysteine residues selectively introduced into two proteins, the DNase domain of colicin-E9 and its immunity protein, Im9. The dynamics of each site of attachment on the individual proteins and in the tight DNase-Im9 complex have been analysed by computer simulations of the spectra using a model of Brownian dynamics trajectories for the spin label and protein. Ordering potentials have been introduced to describe mobility of labels restricted by the protein domain. Label mobility varies with position from completely immobilised, to motionally restricted and to freely rotating. Bi-modal dynamics of the spin label have been observed for several sites. We show that W-band spectra are particularly useful for detection of anisotropy of spin label motion. On complex formation significant changes are observed in the dynamics of labels at the binding interface region. This work reveals multi-frequency EPR as a sensitive and valuable tool for detecting conformational changes in protein structure and dynamics especially in protein–protein complexes.

EPR spectroscopy and theoretical data show that the slow heterogeneous electron-transfer kinetics associated with the reduction of an 18-electron Mo(IV) acetato dihydride are a consequence of an η2–η1 rearrangement of the carboxylate ligand which gives a unique paramagnetic 17-electron Mo(III) dihydride.

A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.

Correction for ‘EPR detection and characterisation of a paramagnetic Mo(III) dihydride intermediate involved in electrocatalytic hydrogen evolution’ by Christopher Prior, et al., Dalton Trans., 2016, 45, 2399–2403.