Time-resolved electron paramagnetic resonance of radical pair intermediates in cryptochromes

Applications of some EPR methods to the investigation of the radical species produced by the reactions of hydroxyl radicals with PEFC-related fluorinated organic acids

Fundamental information on the reactions of ˙OH radicals with perfluoroalkyl sulfonic acids and carboxylic acids is important for understanding the degradation of polymer electrolyte fuel cells (PEFCs). In the present research, the intermediate radicals produced by these reactions were detected and analyzed by means of three methods of electron paramagnetic resonance (EPR) spectroscopy. The conventional CW-EPR technique was applied to both frozen and flowing aqueous solution systems for detecting the reaction intermediates, while the time-resolved (TR) EPR technique was applied to the flowing solution system for analyzing spin dynamics parameters. The reactants tested were CF₃SO₃H, CHF₂CF₂SO₃H, CH₃SO₃H, CF₃COOH, CHF₂COOH, etc., and the ˙OH radical was generated from H₂O₂ by the irradiation of a UV laser. The radicals detected were ˙SO₃^-, ˙CO₂^-, ˙CF₃, ˙CF₂CF₂SO₃H, ˙CF₂COOH, etc. Based on the measurements of TR-EPR spectra, the dependences of the signal intensity on the time and magnetic field were analyzed, and then the longitudinal relaxation time (T₁) and the lifetime of these radical species were evaluated. The three EPR methods for detecting the intermediate radicals were compared to show the limitations of these techniques. Based on the detected radicals, the degradation mechanism reported for perfluoro acids was discussed.

Two competing acceptors: Electronic structure of PNDITBT probed by time-resolved electron paramagnetic resonance spectroscopy

Balanced charge transport is particularly important for transistors. Hence, ambipolar organic semiconductors with comparable transport capabilities for both positive and negative charges are highly sought-after. Here, we report detailed insights into the electronic structure of PNDITBT, which is an alternating copolymer of naphthalene diimide (NDI), thiophene, benzothiodiazole (B), and thiophene (T) units, as gained by time-resolved electron paramagnetic resonance (TREPR) spectroscopy combined with quantum-chemical calculations. The results are compared to those obtained for PNDIT2 and PCDTBT, which are derivatives without B and NDI acceptor units, respectively. These two polymers show dominant n- and p-channel behavior in organic field-effect transistors. The TBT moiety clearly dominates the electronic structure of PNDITBT, although less so than in PCDTBT. Furthermore, the triplet exciton most probably delocalizes along the backbone, exhibits a highly homogeneous environment, and planarizes the polymer backbone. Obtaining the zero-field splitting tensors of these triplet states by means of quantum-chemical calculations reveals the triplet energy sublevel associated with the molecular axis parallel to the backbone to be preferentially populated, while the one perpendicular to the aromatic plane is not populated at all, consistent with the spin-density distribution. PNDITBT consisting of two acceptors (NDI and B) has a complex electronic structure, as evident from the two charge-transfer bands in its absorption spectrum. TREPR spectroscopy provides a detailed insight on a molecular level not available by and complementing other methods.

Impact of Side Chains of Conjugated Polymers on Electronic Structure: A Case Study

Processing from solution is a crucial aspect of organic semiconductors, as it is at the heart of the promise of easy and inexpensive manufacturing of devices. Introducing alkyl side chains is an approach often used to increase solubility and enhance miscibility in blends. The influence of these side chains on the electronic structure, although highly important for a detailed understanding of the structure-function relationship of these materials, is still barely understood. Here, we use time-resolved electron paramagnetic resonance spectroscopy with its molecular resolution to investigate the role of alkyl side chains on the polymer PCDTBT and a series of its building blocks with increasing length. Comparing our results to the non-hexylated compounds allows us to distinguish four different factors determining exciton delocalization. Detailed quantum-chemical calculations (DFT) allows us to further interpret our spectroscopic data and to relate our findings to the molecular geometry. Alkylation generally leads to more localized excitons, most prominent only for the polymer. Furthermore, singlet excitons are more delocalized than the corresponding triplet excitons, despite the larger dihedral angles within the backbone found for the singlet-state geometries. Our results show TREPR spectroscopy of triplet excitons to be well suited for investigating crucial aspects of the structure-function relationship of conjugated polymers used as organic semiconductors on a molecular basis.

Structure-Function Relationship of Organic Semiconductors: Detailed Insights From Time-Resolved EPR Spectroscopy

Organic photovoltaics (OPV) is a promising technology to account for the increasing demand for energy in form of electricity. Whereas the last decades have seen tremendous progress in the field witnessed by the steady increase in efficiency of OPV devices, we still lack proper understanding of fundamental aspects of light-energy conversion, demanding for systematic investigation on a fundamental level. A detailed understanding of the electronic structure of semiconducting polymers and their building blocks is essential to develop efficient materials for organic electronics. Illuminating conjugated polymers not only leads to excited states, but sheds light on some of the most important aspects of device efficiency in organic electronics as well. The interplay between electronic structure, morphology, flexibility, and local ordering, while at the heart of structure-function relationship of organic electronic materials, is still barely understood. (Time-resolved) electron paramagnetic resonance (EPR) spectroscopy is particularly suited to address these questions, allowing one to directly detect paramagnetic states and to reveal their spin-multiplicity, besides its clearly superior spectral resolution compared to optical methods. This article aims at giving a non-specialist audience an overview of what EPR spectroscopy and particularly its time-resolved variant (TREPR) can contribute to unraveling aspects of structure-function relationship in organic semiconductors.

Magnetic sensitivity mediated by the Arabidopsis blue-light receptor cryptochrome occurs during flavin reoxidation in the dark

Arabidopsis cryptochrome mediates responses to magnetic fields that have been applied in the absence of light, consistent with flavin reoxidation as the primary detection mechanism. Cryptochromes are highly conserved blue-light-absorbing flavoproteins which have been linked to the perception of electromagnetic stimuli in numerous organisms. These include sensing the direction of the earth's magnetic field in migratory birds and the intensity of magnetic fields in insects and plants. When exposed to light, cryptochromes undergo flavin reduction/reoxidation redox cycles leading to biological activation which generate radical pairs thought to be the basis for magnetic sensitivity. However, the nature of the magnetically sensitive radical pairs and the steps at which they act during the cryptochrome redox cycle are currently a matter of debate. Here, we investigate the response of Arabidopsis cryptochrome-1 in vivo to a static magnetic field of 500 μT (10 × earth's field) using both plant growth and light-dependent phosphorylation as an assay. Cryptochrome responses to light were enhanced by the magnetic field, as indicated by increased inhibition of hypocotyl elongation and increased cryptochrome phosphorylation. However, when light and dark intervals were given intermittently, a plant response to the magnetic field was observed even when the magnetic field was given exclusively during the dark intervals between light exposures. This indicates that the magnetically sensitive reaction step in the cryptochrome photocycle must occur during flavin reoxidation, and likely involves the formation of reactive oxygen species.

Probing Exciton Delocalization in Organic Semiconductors: Insight from Time-Resolved Electron Paramagnetic Resonance and Magnetophotoselection Experiments

Delocalization of excited states of organic semiconductors is directly related to their efficiency in devices. Time-resolved electron paramagnetic resonance spectroscopy provides unique capabilities in this respect because of its high spectral resolution and capability to probe the geometry and extent of excitons. Using magnetophotoselection experiments, the mode of exciton delocalization, along the backbone or parallel to the π-π stacking direction of the conjugated polymers, can be revealed. We demonstrate the robustness of this approach by applying it to building blocks of a prototypical conjugated polymer showing a symmetry of their excited states being far from ideal for this experiment. This renders magnetophotoselection superior to other approaches because it is applicable to a wealth of other organic semiconductors. The insight gained into exciton delocalization is crucial to the structure-function relationship of organic semiconductors and directly relevant for developing highly efficient materials.

Solvent-mediated aggregate formation of PNDIT2: decreasing the available conformational subspace by introducing locally highly ordered domains

Time-resolved EPR spectroscopy proves aggregation of PNDIT2 to introduce highly ordered domains and to change the exciton delocalisation mode.

Direct S0→T Excitation of a Conjugated Polymer Repeat Unit: Unusual Spin-Forbidden Transitions Probed by Time-Resolved Electron Paramagnetic Resonance Spectroscopy

A detailed understanding of the electronic structure of semiconducting polymers and their building blocks is essential to develop efficient materials for organic electronics. (Time-resolved) electron paramagnetic resonance (EPR) is particularly suited to address these questions, allowing one to directly detect paramagnetic states and to reveal their spin-multiplicity, besides its clearly superior resolution compared to optical methods. We present here evidence for a direct S₀→T optical excitation of distinct triplet states in the repeat unit of a conjugated polymer used in organic photovoltaics. These states differ in their electronic structure from those populated via intersystem crossing from excited singlet states. This is an additional and so far unconsidered route to triplet states with potentially high impact on efficiency of organic electronic devices.

Photoactivation of cryptochromes from Drosophila melanogaster and Sylvia borin: insight into the chemical compass mechanism by computational investigation

Although behavioral studies demonstrated light-induced magnetoreception in the insect Drosophila melanogaster, gaining insight into the possibility that a radical-pair mechanism accounts for the magnetic response of the cryptochrome (DmCry1) is complicated by a number of factors. In addition, the mechanism of magnetoreception for the cryptochrome from the garden warbler bird Sylvia borin (gwCry1a), which demonstrated a long-lived radical pair by transient optical absorption measurements, has also not been rationalized. To assess potential feasibility of a radical-pair mechanism in DmCry1 and gwCry1a, formed by excitation and electron transfer between a Trp-triad and flavin adenine dinucleotide (FAD), further separated by electron transfer within the triad, we applied a combination of theoretical methods, including homology modeling and molecular dynamics (MD) for structure refinement, high-level ab initio theory, and MD simulations using a polarizable force-field for prediction of pKa and the electron transfer rate. Calculated excitation energies, followed by electron transfer in model compounds of DmCry1 that assume proton transfer in conjunction with electron transfer from Trp (W420) to FAD and the predicted pKa for the proximate residue to FAD (Cys416), support a radical-pair mechanism. Furthermore, free-energy and reorganization energies for the Trp-triad in DmCry1 demonstrate facile electron transfer, explained by the local protein environment and exposure to solvent, which in turn enables a large enough distance separation for the radical-pair partners. Results for gwCry1a demonstrated the importance of accounting for relaxed excited-state geometries in validating the first stage of a radical-pair mechanism. This work provides insight into the so-called chemical compass mechanism to explain magnetic-field sensing in DmCry1 and gwCry1a, expanding on previous work on the cyrptochrome from the plant Arabidopsis thaliana (Solov'yov et al. J. Am. Chem. Soc. 2012, 134, 18046-18052. Solov'yov et al., Sci. Rep. 2014, 4, 1-8.).

Probing a chemical compass: novel variants of low-frequency reaction yield detected magnetic resonance

We present a study of a carotenoid-porphyrin-fullerene triad previously shown to function as a chemical compass: the photogenerated carotenoid-fullerene radical pair recombines at a rate sensitive to the orientation of an applied magnetic field. To characterize the system we develop a time-resolved Low-Frequency Reaction Yield Detected Magnetic Resonance (tr-LF-RYDMR) technique; the effect of varying the relative orientation of applied static and 36 MHz oscillating magnetic fields is shown to be strongly dependent on the strength of the oscillating magnetic field. RYDMR is a diagnostic test for involvement of the radical pair mechanism in the magnetic field sensitivity of reaction rates or yields, and has previously been applied in animal behavioural experiments to verify the involvement of radical-pair-based intermediates in the magnetic compass sense of migratory birds. The spectroscopic selection rules governing RYDMR are well understood at microwave frequencies for which the so-called 'high-field approximation' is valid, but at lower frequencies different models are required. For example, the breakdown of the rotating frame approximation has recently been investigated, but less attention has so far been given to orientation effects. Here we gain physical insights into the interplay of the different magnetic interactions affecting low-frequency RYDMR experiments performed in the challenging regime in which static and oscillating applied magnetic fields as well as internal electron-nuclear hyperfine interactions are of comparable magnitude. Our observations aid the interpretation of existing RYDMR-based animal behavioural studies and will inform future applications of the technique to verify and characterize further the biological receptors involved in avian magnetoreception.

Mechanisms for control of biological electron transfer reactions

Electron transfer (ET) through and between proteins is a fundamental biological process. The rates and mechanisms of these ET reactions are controlled by the proteins in which the redox centers that donate and accept electrons reside. The protein influences the magnitudes of the ET parameters, the electronic coupling and reorganization energy that are associated with the ET reaction. The protein can regulate the rates of the ET reaction by requiring reaction steps to optimize the system for ET, leading to kinetic mechanisms of gated or coupled ET. Amino acid residues in the segment of the protein through which long range ET occurs can also modulate the ET rate by serving as staging points for hopping mechanisms of ET. Specific examples are presented to illustrate these mechanisms by which proteins control rates of ET reactions.

Photochemistry of flavoprotein light sensors

Three major classes of flavin photosensors, light oxygen voltage (LOV) domains, blue light sensor using FAD (BLUF) proteins and cryptochromes (CRYs), regulate diverse biological activities in response to blue light. Recent studies of structure, spectroscopy and chemical mechanism have provided unprecedented insight into how each family operates at the molecular level. In general, the photoexcitation of the flavin cofactor leads to changes in redox and protonation states that ultimately remodel protein conformation and molecular interactions. For LOV domains, issues remain regarding early photochemical events, but common themes in conformational propagation have emerged across a diverse family of proteins. For BLUF proteins, photoinduced electron transfer reactions critical to light conversion are defined, but the subsequent rearrangement of hydrogen bonding networks key for signaling remains highly controversial. For CRYs, the relevant photocycles are actively debated, but mechanistic and functional studies are converging. Despite these challenges, our current understanding has enabled the engineering of flavoprotein photosensors for control of signaling processes within cells.

From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World

Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far.