Changes in metal specificity due to iron ligand substitutions in reaction centers fromRhodobacter sphaeroides

Bacterial reaction centers have a single nonheme iron that is located between two bound quinones, Q_A and Q_B, which are the primary and secondary electron acceptors during photosynthesis, respectively. InRhodobacter sphaeroides, the iron is coordinated by four nitrogen atoms, contributed by histidines at L190, L230, M219, and M266, and two oxygen atoms, contributed by Glu at M234. The roles of these ligands in determining the metal-binding specificity and electron transfer properties of the quinones were investigated by mutagenesis. Each of the four His ligands was changed to Glu, Gln, and Cys, whereas Glu was changed to His, Gln, Cys, and Asp. All mutants supported photosynthetic growth except for those with substitutions of Glu or Cys at L190 or M219. The metal specificity of isolated mutant RCs was determined by measurements using atomic absorption and 35 GHz electron paramagnetic resonance spectroscopy. The M234 mutants had a lesser iron specificity than the wild type with a mole fraction of 0.7 to 0.8 iron but retained a total metal content of 1.0. All His mutants had an even lower iron content with mole fractions of 0.04 to 0.16. The His to Cys at M266 mutant had a significantly greater amount of bound zinc that was further enhanced when the strain was grown in zinc-supplemented media. The charge recombination rates from Q _B ^?. , which ranged from 0.5 to 1 s^?1 in the mutants, were comparable to the 1 s^?1 value for the wild type. Charge recombination from Q _A ^?. showed complex kinetics, with rates of 15 to 30 s^?1 for the L190, L230, and M234 mutants and 200 s^?1 for the M266 mutants compared with 8 s^?1 for the wild type. The faster rates in the mutants most likely reflected a smaller free energy difference between Q _A ^?. and Φ _A ^? , a nearby bacteriopheophytin, with the smaller energy difference facilitating indirect recombination. All of the mutants transferred electrons to the secondary quinone, with rates (1200 to 4700 s^?1) comparable to that of the native (3700 s^?1). The data demonstrate that neither the ligands nor the bound metal play a critical role in the electron transfer processes at the acceptor side.     

Local strain and defects in silicon wafers due to nanoindentation revealed by full‐field X‐ray microdiffraction imaging

Quantitative characterization of local strain in silicon wafers is critical in view of issues such as wafer handling during manufacturing and strain engineering. In this work, full‐field X‐ray microdiffraction imaging using synchrotron radiation is employed to investigate the long‐range distribution of strain fields in silicon wafers induced by indents under different conditions in order to simulate wafer fabrication damage. The technique provides a detailed quantitative mapping of strain and defect characterization at the micrometer spatial resolution and holds some advantages over conventional methods.     

Pd Uptake and H2S Sensing by an Amphoteric Metal–Organic Framework with a Soft Core and Rigid Side Arms

Molecular components of opposite character are often incorporated within a single system, with a rigid core and flexible side arms being a common design choice. Herein, molecule L has been designed and prepared featuring the reverse design, with rigid side arms (arylalkynyl) serving to calibrate the mobility of the flexible polyether links in the core. Crystallization of this molecule with Pb^II ions led to a dynamic metal–organic framework (MOF) system that not only exhibits dramatic, reversible single‐crystal‐to‐single‐crystal transformations, but combines distinct donor and acceptor characteristics, allowing for substantial uptake of PdCl₂ and colorimetric sensing of H₂S in water.     

Simulating ion channel activation mechanisms using swarms of trajectories

Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's “swarms of trajectories” approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function. © 2019 Wiley Periodicals, Inc.     

Electrochemistry, electrogenerated chemiluminescence, and excimer formation dynamics of intramolecular π-stacked 9-naphthylanthracene derivatives and organic nanoparticles

We report the electrochemical characterization and the observation of excimer emission from a series of 9-naphthylanthracene-based dimer- and trimer-bridged high steric hindrance aromatic groups during photoluminescence (PL) measurements in the solid state and in solution electrogenerated chemiluminescence (ECL) measurements. Cyclic voltammetry of 4,4'-bis(9-(1-naphthyl)anthracen-10-yl)biphenyl (4A) and 1,3,5-tris(9-(1-naphthyl)anthracen-10-yl)benzene (4C) showed two or three reversible, closely spaced one-electron transfers on oxidation in dichloromethane. The ECL emission spectra of 4A and 4C resulting from the annihilation reaction in benzonitrile showed two bands: one at the same wavelength as the PL peak in the solution state, and a broad band at longer wavelength. With a coreactant, such as peroxydisulfate, ECL spectra showed a single peak that was less broad in shape. PL measurement in the solid state and measurement of representative time traces of PL intensity, lifetimes, and picosecond time-correlated single-photon counting confirmed excimer emission at long wavelength. A reprecipitation method was used to prepare well-dispersed organic nanoparticles (NPs) of 4A in both aqueous and acetonitrile solutions. The smallest stable size of NPs produced was ~15 ± 6 nm, as analyzed by transmission electron microscopy. These organic NPs produced stable and weak ECL emission from the annihilation reaction in both aqueous and MeCN solutions. With a coreactant, such as peroxydisulfate, the ECL signal on reduction was sufficiently strong to obtain an ECL spectrum.     

Molecular simulation and theory of a liquid crystalline disclination core

Molecular simulations of a nematic liquid crystal confined in cylinder geometry with homeotropic anchoring have been carried out. The core structure of a disclination line defect of strength +1 has been examined, and comparison made with various theoretical treatments, which are presented in a unified way. It is found that excellent fits to the cylindrically symmetrized order tensor profiles may be obtained with appropriate parameter choices; notwithstanding this, on the time scales of the simulation, the cylindrical symmetry of the core is broken and two defects of strength +1 / 2 may be resolved.     

Tensors,spinors, and functions on the unit sphere

A representation of tensors and spinors at a point of space-time as spin and conformally weighted functions on the unit sphere is derived. Methods for performing algebraic operations on tensors and spinors in this representation are discussed.Supported in part by grants Nos. GP-35773X1 and MPS74-18020 from the National Science Foundation.     

A dynamic study of earthworm feeding ecology -using stable isotopes

Changes in the specific diet of earthworms with time in relation to landuse changes and two different climates were studied by analysing (13)C and (15)N natural abundance in soils and animals. Soil samples from three depths (0-10, 10-20 and 20-30 cm) and earthworms were collected from two sites: Santiago (Northwest Spain) and North Wyke (Southwest England) both consisting of replicated long-term grasslands and recently converted to maize plots. Earthworms were hand-sorted in the field at the peak of the maize growth and after harvesting at both sites. In the Spanish plots, nine and eight earthworm species, all belonging to the three ecological categories (epigeic, anecic and endogeic), were found under maize and permanent pasture, whereas at the English site five and seven different species were, respectively, identified. At both sites (13)C isotopic values of the earthworm tissues reflected changes in diet from C(3) to C(4) with epigeic and epi/anecic worms in the maize plots showing one delta unit difference in relation to the ones found in the grassland plots. Anecic worms seemed to be less responsive to landuse changes. The higher (13)C values of the Spanish soils were also reflected in the earthworm tissues when compared with the English samples. (15)N values showed no clear relationship with the cropping treatments but were clearly related to the ecological grouping, with endogeic worms reaching the highest values whereas for the epigeic and epi/anecic species the lowest values were obtained. This finding was also previously recorded by other authors1 and suggests that, in the future, stable isotope techniques could also be a useful tool in taxonomic studies. Copyright 1999 John Wiley & Sons, Ltd.