Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach.

Förster Resonance Energy Transfer (FRET) experiments probe molecular distances via distance dependent energy transfer from an excited donor dye to an acceptor dye. Single molecule experiments not only probe average distances, but also distance distributions or even fluctuations, and thus provide a powerful tool to study biomolecular structure and dynamics. However, the measured energy transfer efficiency depends not only on the distance between the dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages are usually made, limiting the accuracy of the distance distributions extracted from FRET experiments. Here, we demonstrate that by combining single molecule FRET experiments with the mutual dye orientation statistics obtained from Molecular Dynamics (MD) simulations, improved estimates of distances and distributions are obtained. From the simulated time-dependent mutual orientations, FRET efficiencies are calculated and the full statistics of individual photon absorption, energy transfer, and photon emission events is obtained from subsequent Monte Carlo (MC) simulations of the FRET kinetics. All recorded emission events are collected to bursts from which efficiency distributions are calculated in close resemblance to the actual FRET experiment, taking shot noise fully into account. Using polyproline chains with attached Alexa 488 and Alexa 594 dyes as a test system, we demonstrate the feasibility of this approach by direct comparison to experimental data. We identified cis-isomers and different static local environments as sources of the experimentally observed heterogeneity. Reconstructions of distance distributions from experimental data at different levels of theory demonstrate how the respective underlying assumptions and approximations affect the obtained accuracy. Our results show that dye fluctuations obtained from MD simulations, combined with MC single photon kinetics, provide a versatile tool to improve the accuracy of distance distributions that can be extracted from measured single molecule FRET efficiencies.

Validity of the classical monte carlo method to model the magnetic properties of a large transition-metal cluster: Mn19.

The susceptibility of the large transition-metal cluster [Mn19O12(MOE)14(MOEH)10].MOEH (MOE = OC2H2O-CH3) has been fitted through classical Monte Carlo simulation, and an estimation of the exchange coupling constants has been done. With these results, it has been possible to perform a full-matrix diagonalization of the cluster core, which was used to provide information on the nature of the low-lying levels.

Rationalisation of weak ferromagnetism in manganese(III) chains: the relation between structure and ordering phenomena.

The synthesis, structure and magnetic properties of the one-dimensional chain compounds [Mn(cyclam)(SO4)]ClO4.H2O (1) and [Mn(cyclam)(HCOO)](CF3SO3)(ClO4) (2) are reported. Cyclam is the cyclic tetradentate ligand 1,4,7,11-tetraazacyclotetradecane. Both chain compounds exhibit antiferromagnetic interactions within the chains. A magnetic ordering phase transition at 5.5 K in (1) is investigated by magnetisation measurements along the three principal crystallographic axes of a single crystal and the results show unambiguously that the ferromagnetic ordering is only taking place along one crystallographic axis. The spin structure of the magnetic ordered phase and the magnitude of the ferromagnetic moment are correlated with the crystal structure and symmetry of the compound.