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At least 1,315 records · Page 73

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization

Abstract HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA NTD -CA NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A a α9-helices compared to WT, E45A/R132T, WT PF74 , WT Nup153 , and WT CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.

60 APPLIED LIFE SCIENCES↗

Zero-field J-spectroscopy of quadrupolar nuclei

Abstract Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) allows molecular structure elucidation via measurement of electron-mediated spin-spinJ-couplings. This study examines zero-fieldJ-spectra from molecules with quadrupolar nuclei, exemplified by solutions of various isotopologues of ammonium cations. The spectra reveal differences between various isotopologues upon extracting preciseJ-coupling values from pulse-acquire measurements. A primary isotope effect,$$\triangle J=\left({\gamma }_{{}^{14}{{{{{\rm{N}}}}}}}/{\gamma }_{{}^{15}{{{{{\rm{N}}}}}}}\right){J}_{{}^{15}{{{{{\rm{N}}}}}}{{{{{\rm{H}}}}}}}-{J}_{{}^{14}{{{{{\rm{N}}}}}}{{{{{\rm{H}}}}}}}\approx -58$$ △ J = γ 14 N / γ 15 N J 15 N H − J 14 N H ≈ − 58 mHz, is deduced by analysis of the proton-nitrogenJ-coupling ratios. This study points toward further experiments with symmetric cations containing quadrupolar nuclei, promising applications in biomedicine, energy storage, and benchmarking quantum chemistry calculations.

Science & Technology - Other Topics↗

Synthesis and disassembly of an organometallic polymer comprising redox-active Co 4 S 4 clusters and Janus biscarbene linkers

Here, we show for the first time that main-chain organometallic polymers (MCOPs) can be prepared from Janus N-heterocyclic carbene (NHC) linkers and polynuclear cluster nodes. The crosslinked framework Co 4 S 4 -MCOP is synthesized via ligand displacement reactions and undergoes reversible electron transfer in the solid state. Discrete molecular cluster species can be excised from the framework by digesting the solid in solutions of excess monocarbene. Lastly, we demonstrate a synthetic route to monodisperse framework particles via coordination modulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches

We address the calculation of microcanonical reaction rates for processes involving significant nuclear quantum effects using ring-polymer molecular dynamics (RPMD), both with and without electronically non-adiabatic transitions. After illustrating the shortcomings of the naive free-particle direct-shooting method, in which the temperature of the internal ring-polymer modes is set to the translational energy scale, we investigate alternative strategies based on the expression for the microcanonical rate in terms of the inverse Laplace transform of the thermal reaction rate. It is shown that simple application of the stationary-phase approximation (SPA) dramatically improves the performance of the microcanonical rates using RPMD, particularly in the low-energy region where tunneling dominates. Using the SPA as a Bayesian prior, numerically exact RPMD microcanonical rates are then obtained using maximum entropy inversion of the thermal reaction rates for both electronically adiabatic and non-adiabatic model systems. Finally, the direct-shooting method is revisited using the SPA-determined temperature for the internal ring-polymer modes, leading to a simple, direct-simulation method with improved accuracy in the tunneling regime. This work suggests a general strategy for the extraction of microcanonical dynamical quantities from RPMD (or other approximate thermal) simulations.

Tao, Xuecheng↗

Equation of state for 304L stainless steel

Here, a new equation of state for 304L stainless steel has been constructed and entered in the Los Alamos National Laboratory SESAME database with material ID 4273. The equation of state is based on a multiphase approach. The solid and liquid phases were fitted to available experimental data for thermal expansion, heat capacity, and shock Hugoniot, as well as to data from density functional theory calculations of the cold curve and quantum molecular dynamics of the liquid regime. The electronic thermal contribution over the entire equation of state range is based on Tartarus (Green’s functions) average atom calculations. For this low-carbon stainless steel both the density functional and electronic thermal calculations are comprised of 19 wt% Cr, 10 wt% Ni, and the remainder Fe.

36 MATERIALS SCIENCE↗

Computational quantum chemistry of metal–organic frameworks

Metal–organic frameworks (MOFs) have premium exceptional properties for a variety of functions, such as gas separation and storage and catalysis. The large variety of possible inorganometallic nodes and organic linkers provide an almost unlimited number of combinations for assembling MOFs, which makes the experimental characterization and examination of all potentially useful combinations practically impossible. Furthermore, experimental studies of MOFs typically fall short in uncovering crucial details regarding their mechanisms of action or the molecular details responsible for their functional properties, such as the nature of adsorbate binding or the structures of transition states. Computational modeling has, therefore, become an efficient and important tool for strategizing the functionalization of MOFs and explicating the mechanisms of their functions. Furthermore, we review the computational methodologies used for computational studies of MOFs, especially Kohn–Sham density functional theory and combined quantum mechanical and molecular mechanical methods for calculating their structural, electronic, and magnetic properties, as well as for understanding the mechanisms of MOFs' applications to magetic devices, thermal conduction, gas adsorption, separation, storage, and sensing, thermal catalysis, photocatalysis, and electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decomposition characteristics of C4F7N-based SF6-alternative gas mixtures

C4F7N [2,3,3,3-tetrafluoro-2-(trifluoromethyl)propanenitrile]/CO2 gas mixtures are being developed as an eco-friendly electrical insulator to replace SF6, the most potent greenhouse industrial gaseous dielectric. However, recent studies have reported complicated and often conflicting decomposition pathways for C4F7N/CO2 gas mixtures, which has raised concerns. In this work, the decomposition characteristics of C4F7N/CO2 gas mixtures were studied comprehensively by both designed computations and experiments. Computations were performed starting from fundamental propositions of C4F7N/CO2 decompositions, which were further experimentally verified by pyrolysis, long-term thermal aging with/without catalytic materials (industrial-grade molecular sieves 4A), and electrical decomposition by spark discharge. The results of both computations and experiments suggest that in an ideal thermal decomposition, C4F7N is likely to decompose into C2F6 and small fluoronitriles first at high temperatures. The generation of C3F6 and C2N2 from C4F7N thermal decomposition at lower temperatures appears because of the catalytic effect of incompatible materials, for example, the industrial-grade molecular sieves 4A that we tested. The electron impact dissociation of C4F7N plays an important role in C4F7N electrical decomposition, leading to additional formation of distinctive small molecules of CF4 and C2N2 of low concentrations. It was pointed out based on a real arcing test in a load disconnector that the decomposition of C4F7N gas mixtures in real applications will be at a much moderate and manageable rate than what was obtained from the highly accelerated laboratory tests presented in this work. The signatures of decomposition products extracted in this study provide invaluable guidance for developing decomposition-based diagnosis and fixation of decomposition byproducts toward SF6-free power grids.

Physics↗

Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes

The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.

36 MATERIALS SCIENCE↗

Attosecond Time Delay Trends across the Isoelectronic Noble Gas Sequence

The analysis and measurement of Wigner time delays can provide detailed information about the electronic environment within and around atomic and molecular systems, with one the key differences being the lack of a long-range potential after a halogen ion undergoes photoionization. In this work, we use relativistic random-phase approximation to calculate the average Wigner delay from the highest occupied subshells of the atomic pairings (2p, 2s in Fluorine, Neon), (3p, 3s in Chlorine, Argon), (4p, 4s, 3d, in Bromine, Krypton), and (5p, 5s, 4d in Iodine, Xenon). The qualitative behaviors of the Wigner delays between the isoelectronic pairings were found to be similar in nature, with the only large differences occurring at photoelectron energies less than 20 eV and around Cooper minima. Interestingly, the relative shift in Wigner time delays between negatively charged halogens and noble gases decreases as atomic mass increases. All atomic pairings show large differences at low energies, with noble gas atoms showing large positive Wigner delays, while negatively charged halogen ions show negative delays. The implications for photoionization studies in halide-containing molecules is also discussed.

Grafstrom, Brock↗

Fast chemistry in ion wakes

A common aspect of the models of such processes as track formation and induced desorption of molecular ions is the requirement that the electronic excitation have a sufficiently long lifetime (of the order of picoseconds) so that energy can be transferred to atomic motion. Attention is called to several phenomena recently observed indicating that atomic motion/chemical rearrangement can occur even when the electronic excitation is shorter lived (of the order of femtoseconds). Two such processes, which are also induced by MeV ion bombardment, are track damage in heavily doped compound semiconductors and greatly enhanced adhesion of metal films to metallic and semiconducting substrates. Since neither of these effects can easily be accommodated within the existing theoretical models, it is thought possible that an even richer variety of ion-induced effects will be discovered.

Tombrello, T. A.↗

Low defect densities in molecular beam epitaxial GaAs achieved by isoelectronic In doping

A study has been made of the effects of adding small amounts of In (0.2-1.2 pct) to GaAs grown by molecular beam epitaxy. The density of four electron traps decreases in concentration by an order of magnitude, and the peak intensities of prominent emissions in the excitonic spectra are reduced with increase in In content. Based on the higher surface migration rate of In, compared to Ga, at the growth temperatures it is apparent that the traps and the excitonic transitions are related to point defects. This agrees with earlier observations by Briones and Collins (1982) and Skromme et al. (1985).

Bhattacharya, P. K.↗

Influence of gap states on the nonresonant second hyperpolarizabilities of conjugated organic polymers

The presence of conjugation and substitution defects introduces gap states in finite polyenes that are shown to influence the size and sign of the second molecular hyperpolarizability (SMH). Using a one-electron tight-binding model, the dependence of SMH on the defect-state occupancy and energy in finite polyenes is calculated. Defects can cause a significant decrease or enhancement of SMH by impeding charge delocalization or by creating partly filled bands (mimicking the one-band limit), respectively. Concomitant sign changes in SMH are predicted. Calculation results suggest strategies for designing molecules that can be either photochemically or electrochemically switched between states with considerably different SMHs.

Beratan, David N.↗

An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2

Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.

Lee, Timothy J.↗

A Remarkable Auroral Event on Jupiter Observed in the Ultraviolet with the Hubble Space Telescope

Two sets of ultraviolet images of the Jovian north aurora were obtained with the Faint Object Camera on board the Hubble Space Telescope. The first series shows an intense discrete arc in near corotation with the planet. The maximum apparent molecular hydrogen emission rate corresponds to an electron precipitation of approximately 1 watt per square meter, which is about 30,000 times larger than the solar heating by extreme ultraviolet radiation. Such a particle heating rate of the auroral upper atmosphere of Jupiter should cause a large transient temperature increase and generate strong thermospheric winds. Twenty hours after initial observations, the discrete arc had decreased in brightness by more than one order of magnitude. The time scale and magnitude of the change in the ultraviolet aurora leads us to suggest that the discrete Jovian auroral precipitation is related to large-scale variations in the current system as is the case of for Earth's discrete aurorae.

Gerard, J. C.↗