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The avian compass and many other of nature's magnetoreceptive traits are widely ascribed to the protein cryptochrome. There, magnetosensitivity is thought to emerge as the spin dynamics of radicals in the applied magnetic field enters in competition with their recombination. The first and dominant model makes use of a radical pair. However, recent studies have suggested that magnetosensitivity could be markedly enhanced for a radical triad, the primary radical pair of which undergoes a spin-selective recombination reaction with a third radical. Here, we test the practicality of this supposition for the reoxidation reaction of the reduced FAD cofactor in cryptochrome, which has been implicated with light-independent magnetoreception but appears irreconcilable with the classical radical pair mechanism (RPM). Based on the available realistic cryptochrome structures, we predict the magnetosensitivity of radical triad systems comprising the flavin semiquinone, the superoxide, and a tyrosine or ascorbyl scavenger radical. We consider many hyperfine-coupled nuclear spins, the relative orientation and placement of the radicals, their coupling by the electron–electron dipolar interaction, and spin relaxation in the superoxide radical in the limit of instantaneous decoherence, which have not been comprehensively considered before. We demonstrate that these systems can provide superior magnetosensitivity under realistic conditions, with implications for dark-state cryptochrome magnetoreception and other biological magneto- and isotope-sensitive radical recombination reactions. [ABSTRACT FROM AUTHOR]

The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations. [ABSTRACT FROM AUTHOR]

A computational approach combining molecular dynamic simulations and density functional theory (DFT) calculations is implemented to evaluate the second-order nonlinear optical (NLO) responses of photoresponsive self-assembled monolayers (SAMs) based on indolino–oxazolidine molecular switches. These numerical simulations provide a complete atomistic picture of the morphology of the SAMs, revealing a high degree of positional disorder and an almost isotropic orientation of the chromophores. Subsequent DFT calculations, carried out to evaluate the average first hyperpolarizability of indolino–oxazolidine switches within the SAM, predict that the structural disorder does not significantly reduce the NLO contrast compared to that of the isolated molecules. Chromophores in the SAM can assume a limited number of specific conformations, due to the high rotational barrier that characterize the conjugated bonds along the indolino/oxazolidine-dyene-thiophene sequence. A notable exception is the rotation about the thiophene–thioalkyl bond, which is not only almost free, but also strongly correlated with the magnitude of the first hyperpolarizability. Controlling this rotation by chemical design could thus be a viable strategy to optimize the SAMs NLO response and the performance of photoresponsive devices based on indolino/oxazolidine switches. [ABSTRACT FROM AUTHOR]