Richard A. Lerner (1938–2021)—a structural biochemist and president of Scripps Institute

Structural Chemistry - Richard A. Lerner (1938-2021) was both a chemist and an MD. He investigated the structure of peptides and proteins, identified a sleep-inducing lipid, and is best known for...     

Los Alamos and “Los Arzamas”

Marking the seventieth anniversary of the Los Alamos Laboratory provides an opportunity for comparison with its Soviet counterpart, Arzamas-16 (nicknamed “Los Arzamas”). There were similarities and differences, but in their principal motivations and treatments of their scientists, they diverged irrevocably. This Editorial is based on an invited presentation on June 12, 2013, at the Norris E. Bradbury Science Museum, Los Alamos National Laboratory, in Los Alamos, New Mexico.     

Thermal oxidation of irradiated magnetic fluids and their component surfactants and dispersing oils

Magnetic fluid applications require stability under demanding conditions. Complete magnetic fluids and their component surfactants and dispersing oils were irradiated. Their subsequent thermal oxidation was characterized by chemiluminescence and DSC. Except for polyisobutylsuccinic anhydride, irradiation sensitized the components toward oxidation. The components were ranked by stability. Complete fluids were more stable than would be predicted from their components suggesting that they may be used for nuclear applications.

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Wiener Chaos and Nonlinear Filtering

The paper discusses two algorithms for solving the Zakai equation in the time-homogeneous diffusion filtering model with possible correlation between the state process and the observation noise. Both algorithms rely on the Cameron-Martin version of the Wiener chaos expansion, so that the approximate filter is a finite linear combination of the chaos elements generated by the observation process. The coefficients in the expansion depend only on the deterministic dynamics of the state and observation processes. For real-time applications, computing the coefficients in advance improves the performance of the algorithms in comparison with most other existing methods of nonlinear filtering. The paper summarizes the main existing results about these Wiener chaos algorithms and resolves some open questions concerning the convergence of the algorithms in the noise-correlated setting. The presentation includes the necessary background on the Wiener chaos and optimal nonlinear filtering.     

The CO Photodissociation and Recombination Dynamics of the W172Y/F282T Ligand Channel Mutant of Rhodobacter sphaeroides aa3 Cytochrome c Oxidase

In the ligand channel of the cytochrome c oxidase from Rhodobacter sphaeroides (Rs aa₃) W172 and F282 have been proposed to generate a constriction that may slow ligand access to and from the active site. To explore this issue, the tryptophan and phenylalanine residues in Rs aa₃ were mutated to the less bulky tyrosine and threonine residues, respectively, which occupy these sites in Thermus thermophilus (Tt) ba₃ cytochrome oxidase. The CO photolysis and recombination dynamics of the reduced wild‐type Rs aa₃ and the W172Y/F282T mutant were investigated using time‐resolved optical absorption spectroscopy. The spectral changes associated with the multiple processes are attributed to different conformers. The major CO recombination process (44 μs) in the W172Y/F282T mutant is ~500 times faster than the predominant CO recombination process in the wild‐type enzyme (~23 ms). Classical dynamic simulations of the wild‐type enzyme and double mutant showed significant structural changes at the active site in the mutant, including movement of the heme a₃ ring‐D propionate toward Cu_B and reduced binuclear center cavity volume. These structural changes effectively close the ligand exit pathway from the binuclear center, providing a basis for the faster CO recombination in the double mutant.     

On the performance of two-component energy-consistent pseudopotentials in atomic Fock-space coupled cluster calculations

The four-component atomic intermediate-Hamiltonian Fock-space coupled cluster (IHFSCC) code of Landau et al. [J. Chem. Phys. 115, 6862 (2001)] has been adapted to two-component calculations with relativistic pseudopotentials of the energy-consistent variety. Recently adjusted energy-consistent pseudopotentials for group 11 and 12 transition elements as well as group 13 and 14 post-d main group elements, which were fitted to atomic valence spectra from four-component multiconfiguration Dirac-Hartree-Fock calculations, are tested in IHFSCC calculations for ionization potentials, electron affinities, and excitation energies of a variety of atoms and ions. Where comparison is possible, the deviations from experimental data are in good agreement with those found in previously published IHFSCC all-electron calculations: experimental data are usually reproduced within a few hundred wavenumbers.     

Michael Polanyi—pupils and crossroads—on the 125th anniversary of his birth

Michael Polanyi (1891–1976) was a Hungarian-born British physician turned physical chemist turned philosopher. His milestone epistemological treatise Personal Knowledge followed his substantial discoveries in adsorption studies, X-ray crystallography, materials science, and the mechanism of chemical reactions. Michael Polanyi was one of the last polymaths and his teachings impacted the world views of other outstanding contributors to twentieth century science and culture.     

Transition energies of atomic lawrencium

Transition energies of the superheavy element lawrencium, including the ionization potential, excitation energies and electron affinities, are calculated by the intermediate Hamiltonian coupled cluster method. A large basis set (37s31p26d21f16g11h6i) is used, as well as an extensive P space (6s5p4d2f1g). The outer 43 electrons are correlated. Accuracy is monitored by applying the same approach to lutetium, the lighter homologue of Lr, and comparing with experimentally known energies. QED corrections are included. The main goal is to predict excitation energies, in anticipation of planned spectroscopy of Lr. The ground state of Lr is , unlike the of Lu. Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20 000–30 000 cm^-1, are 7p→8s at 20 100 cm^-1 and 7p→7d at 28 100 cm^-1. The average absolute error of 20 excitation energies of Lu is 423 cm ^-1, and the error limits for Lr are put at 700 cm^-1. The two electron affinities measured recently for Lu are reproduced within 55 cm^-1, and a third bound state of Lu^- is predicted.     

Uptake, degradation and chiral discrimination of N-acyl-D/L-homoserine lactones by barley (Hordeum vulgare) and yam bean (Pachyrhizus erosus) plants

Bacterial intraspecies and interspecies communication in the rhizosphere is mediated by diffusible signal molecules. Many Gram-negative bacteria use N-acyl-homoserine lactones (AHLs) as autoinducers in the quorum sensing response. While bacterial signalling is well described, the fate of AHLs in contact with plants is much less known. Thus, adsorption, uptake and translocation of N-hexanoyl- (C6-HSL), N-octanoyl- (C8-HSL) and N-decanoyl-homoserine lactone (C10-HSL) were studied in axenic systems with barley (Hordeum vulgare L.) and the legume yam bean (Pachyrhizus erosus (L.) Urban) as model plants using ultra-performance liquid chromatography (UPLC), Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and tritium-labelled AHLs. Decreases in AHL concentration due to abiotic adsorption or degradation were tolerable under the experimental conditions. The presence of plants enhanced AHL decline in media depending on the compounds' lipophilicity, whereby the legume caused stronger AHL decrease than barley. All tested AHLs were traceable in root extracts of both plants. While all AHLs except C10-HSL were detectable in barley shoots, only C6-HSL was found in shoots of yam bean. Furthermore, tritium-labelled AHLs were used to determine short-term uptake kinetics. Chiral separation by GC-MS revealed that both plants discriminated D-AHL stereoisomers to different extents. These results indicate substantial differences in uptake and degradation of different AHLs in the plants tested.     

Richard E. Dickerson,Present at the Flood: How structural molecular biology came about

Structural Chemistry -