Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states

Proton transfer reactions are complex transitions due to the size and flexibility of the hydrogen-bonded networks along which the protons may “hop”. The combination of molecular dynamics based sampling of water positions and orientations with direct sampling of proton positions is an efficient way to capture the interplay of these degrees of freedom in a transition network. The energetically most favourable pathway in the proton transfer network computed for an aspartate-water cluster shows the pre-orientation of water molecules and aspartate side chains to be a pre-requisite for the subsequent concerted proton transfer to the product state

Nanosecond time-resolved infrared spectroscopy for the study of electron transfer in photosystem I

Microsecond time-resolved step-scan FTIR difference spectroscopy was used to study photosystem I (PSI) from Thermosynechococcus vestitus BP-1 (T. vestitus, formerly known as T. elongatus) at 77 K. In addition, photoaccumulated (P700+–P700) FTIR difference spectra were obtained at both 77 and 293 K. The FTIR difference spectra are presented here for the first time. To extend upon these FTIR studies nanosecond time-resolved infrared difference spectroscopy was also used to study PSI from T. vestitus at 296 K. Nanosecond infrared spectroscopy has never been used to study PSI samples at physiological temperatures, and here it is shown that such an approach has great value as it allows a direct probe of electron transfer down both branches in PSI. In PSI at 296 K, the infrared flash-induced absorption changes indicate electron transfer down the B- and A-branches is characterized by time constants of 33 and 364 ns, respectively, in good agreement with visible spectroscopy studies. These time constants are associated with forward electron transfer from A1– to FX on the B- and A-branches, respectively. At several infrared wavelengths flash-induced absorption changes at 296 K recover in tens to hundreds of milliseconds. The dominant decay phase is characterized by a lifetime of 128 ms. These millisecond changes are assigned to radical pair recombination reactions, with the changes being associated primarily with P700+ rereduction. This conclusion follows from the observation that the millisecond infrared spectrum is very similar to the photoaccumulated (P700+–P700) FTIR difference spectrum

Activation energies for two steps in the S_2 → S_3 transition of photosynthetic water oxidation from time-resolved single-frequency infrared spectroscopy

The mechanism of water oxidation by the Photosystem II (PSII) protein–cofactor complex is of high interest, but specifically, the crucial coupling of protonation dynamics to electron transfer (ET) and dioxygen chemistry remains insufficiently understood. We drove spinach-PSII membranes by nanosecond-laser flashes synchronously through the water-oxidation cycle and traced the PSII processes by time-resolved single-frequency infrared (IR) spectroscopy in the spectral range of symmetric carboxylate vibrations of protein side chains. After the collection of IR-transients from 100 ns to 1 s, we analyzed the proton-removal step in the S2 ⇒ S3 transition, which precedes the ET that oxidizes the Mn4CaOx-cluster. Around 1400 cm−1, pronounced changes in the IR-transients reflect this pre-ET process (∼40 µs at 20 °C) and the ET step (∼300 µs at 20 °C). For transients collected at various temperatures, unconstrained multi-exponential simulations did not provide a coherent set of time constants, but constraining the ET time constants to previously determined values solved the parameter correlation problem and resulted in an exceptionally high activation energy of 540 ± 30 meV for the pre-ET step. We assign the pre-ET step to deprotonation of a group that is re-protonated by accepting a proton from the substrate–water, which binds concurrently with the ET step. The analyzed IR-transients disfavor carboxylic-acid deprotonation in the pre-ET step. Temperature-dependent amplitudes suggest thermal equilibria that determine how strongly the proton-removal step is reflected in the IR-transients. Unexpectedly, the proton-removal step is only weakly reflected in the 1400 cm−1 transients of PSII core complexes of a thermophilic cyanobacterium (T. elongatus)

Untersuchung topologie-getriebener magnetischer Rekonnektion mithilfe von CWENO Finite-Volumen Numerik

Magnetic reconnection is a process in a plasma that changes the magnetic field topology due to finite electrical resistivity in the field’s plasma environment. A possible trigger for the onset of reconnection is a high entanglement of the field lines which can exponentially amplify the influence of small resistive effects. This type of topology-driven reconnection is investigated by direct numerical simulations based on finite-volume numerics, in which the plasma is described by the ideal magnetohydrodynamic (MHD) equations. Numerical dissipation is utilized as a proxy of viscous and resistive non-idealities. A simple numerical configuration is used to study the relation of potential reconnection events and field line entanglement. The application of an external velocity field induces magnetic field line movement through the frozen-in condition. It is used to drive the field lines of an initially homogeneous magnetic field with constant mean value pointing in the z-direction to a high degree of entanglement. The footpoints of the field lines are fixed at the boundaries in the z-direction, such that reconnection events can be observed by changes in the footpoint mapping from one z-boundary to the other. Damping layers at these boundaries are included in order to damp any perturbations caused by Alfvén waves propagating along the field lines. The boundary conditions orthogonal to the z-direction of the box-shaped simulation volume are periodic. In this configuration the system initially relaxes into a stationary state, in which the forces acting on the plasma balance each other and the field lines settle into a twisted state. This state of force-balance is spontaneously disrupted and a fast transition from the stationary state to a chaotic state is observed, which is accompanied by a sudden increase in both kinetic and magnetic energy. The influence of the grid resolution, the forcing amplitude and the damping coefficient is investigated and discussed.The chaotic phase is further investigated and shown to be characterized by locally enhanced current densities, large separations of neighboring field lines and a change in the mapping of footpoints of particular field line bundles. The correlation of two key diagnostics is used to investigate the proposed connection between high entanglement and reconnection: the exponentiation number, which quantifies the separation of field lines and which is a measure of the degree of entanglement, and the foot point velocity, which is an indicator for potential reconnection events. It is shown that these two quantities are indeed temporally correlated, supporting the proposed theory. Furthermore, individual field lines undergo distinct reconnection events which happen on sub-Alfvénic timescales and which are correlated with high footpoint velocities. The abruptness of the events suggests that it is reconnection rather than resistive diffusion that causes the motion of the field lines

Locally Enhanced and Tunable Optical Chirality in Helical Metamaterials

We report on a numerical study of optical chirality. Intertwined gold helices illuminated with plane waves concentrate right and left circularly polarized electromagnetic field energy to sub-wavelength regions. These spots of enhanced chirality can be smoothly shifted in position and magnitude by varying illumination parameters, allowing for the control of light-matter interactions on a nanometer scale