Structure and Efficiency in Bacterial Photosynthetic Light Harvesting

Photosynthetic organisms use networks of chromophores to absorb sunlight and deliver the energy to reaction centres, where charge separation triggers a cascade of chemical steps to store the energy. We present a detailed model of the light-harvesting complexes in purple bacteria, including explicit interaction with sunlight; energy loss through radiative and non-radiative processes; and dephasing and thermalizing effects of coupling to a vibrational bath. An important feature of the model is that we capture the effect of slow vibrational modes by introducing time-dependent disorder. Our model describes the experimentally observed high efficiency of light harvesting, despite the absence of long-range quantum coherence. The one-exciton part of the quantum state fluctuates due to slow vibrational changes, but remains highly mixed at all times. This lack of long-range coherence suggests a relatively minor role for structure in determining the efficiency of bacterial light harvesting. To investigate this we built hypothetical models with randomly arranged chromophores, but still observed high efficiency when typical nearest-neighbour distances are comparable with those found in nature. This helps to explain the efficiency of energy transport in organisms whose chromophore networks differ widely in structure, while also suggesting new design criteria for efficient artificial light-harvesting devices

Proposal to use superparamagnetic nanoparticles to test the role of cryptochrome in magnetoreception

Evidence is accumulating to support the hypothesis that some animals use light‐induced radical pairs to detect the direction of the Earth’s magnetic field. Cryptochrome proteins seem to be involved in the sensory pathway but it is not yet clear if they are the magnetic sensors: they could, instead, play a non‐magnetic role as signal transducers downstream of the primary sensor. Here we propose an experiment with the potential to distinguish these functions. The principle is to use superparamagnetic nanoparticles to disable any magnetic sensing role by enhancing the electron spin relaxation of the radicals so as to destroy their spin correlation. We use spin dynamics simulations to show that magnetoferritin, a synthetic, protein‐based nanoparticle, has the required properties. If cryptochrome is the primary sensor, then it should be inactivated by a magnetoferritin particle placed 12‐16 nm away. This would prevent a bird from using its magnetic compass in behavioural tests and abolish magnetically sensitive neuronal firing in the retina. The key advantage of such an experiment is that any signal transduction role should be completely unaffected by the tiny magnetic interactions (<< kBT ) required to enhance the spin relaxation of the radical pair

Quantum dynamics of excited state proton transfer in green fluorescent protein

Data supporting the calculations in the paper. These include the input and output files for the Quantics program to run DD-vMCG and iMCG simulations of a GFP cluster model, as well as the database files with the quantum chemistry results. These files can be used together with Quantics to generate the data in the paper Bourne-Worster and Worth (JCP, 160, 065102, 2024). The input files are standard ascii files, grouped into directories for the different systems studied. The databases with the points calculated during the direct dynamics simulations are SQLite format with tables for geometries, energies, gradients etc. More details are in the paper. The Quantics program is a mostly Fortran code for running quantum dynamics simulations. It is open source and runs on linux workstations. It is freely available on request to the authors of the paper. For further details of the program see Comp. Phys. Comm., 248:107040–15, 2020.</p

Unraveling the Ultrafast Photochemical Dynamics of Nitrobenzene in Aqueous Solution

Nitroaromatic compounds are major constituents of the brown carbon aerosol particles in the troposphere that absorb near-ultraviolet (UV) and visible solar radiation and have a profound effect on the Earth’s climate. The primary sources of brown carbon include biomass burning, forest fires and residential burning of biofuels, and an important secondary source is photochemistry in aqueous cloud and fog droplets. Nitrobenzene is the smallest nitroaromatic molecule and a model for the photochemical behaviour of larger nitroaromatic compounds. Despite the obvious importance of its droplet photochemistry to the atmospheric environment, there have not been any detailed studies of the ultrafast photochemical dynamics of nitrobenzene in aqueous solution. Here, we combine femtosecond transient absorption spectroscopy, time-resolved infrared spectroscopy, and quantum chemistry calculations, to investigate the primary steps following the near-UV (λ ≥ 340 nm) photoexcitation of aqueous nitrobenzene. To understand the role of the surrounding water molecules on the photochemical dynamics of nitrobenzene, we compare the results of these investigations with analogous measurements in solutions of methanol, acetonitrile, and cyclohexane. We find that vibrational energy transfer to the aqueous environment quenches internal excitation and therefore, unlike the gas phase, we do not observe any evidence for formation of photoproducts on timescales up to 500 ns. We also find that hydrogen-bonding between nitrobenzene and surrounding water molecules slows the S1/S0 internal conversion process