Continuous Electron Density Research Articles

Variability of Ionospheric Total Electron Content Over Morocco During the Godzilla Sand and Dust Storm of June 2020

During sand and dust storm (SDS) events, atmospheric suspension and transport of sand and dust brings a reasonable amount of electrification in the atmosphere which plays a very important role in the atmosphere-ionosphere coupling. The Godzilla SDS began on 5<sup>th</sup> June 2020 in Algeria following a decrease in pressure and spread to other areas across the Sahara between 6<sup>th</sup> and 28<sup>th</sup> June 2020. Using SDS data from Copernicus Sentinel-5P satellite mission and Vertical Total Electron Content (VTEC) data from four GNSS receiver stations: IFR1 (Ifrane Seismic), MELI (Melilla), TETN (Tetouan) and OUCA (Ouca) over Morocco, we investigate the possible ionospheric TEC variability over the four GNSS receiver stations during the Godzilla SDS event which was tracked using the Sentinel-5P Satellite mission. Solar wind parameters: Horizontal component of Interplanetary Magnetic Field (IMF-Bz), interplanetary Electric Field (IEF-Ey) and solar wind speed (V) and geomagnetic indices: Disturbance Storm Time (Dst) and Planetary K (Kp) indices were examined and showed very minimal geomagnetic influence during the period. We observed major ionospheric disturbances over the four Global Navigation Satellite System (GNSS) receiver stations on 16<sup>th</sup>, 17<sup>th</sup>, 18<sup>th</sup>, 21<sup>st</sup>, 22<sup>nd</sup>, 23<sup>rd</sup> 25<sup>th</sup> and 26<sup>th</sup> June 2020: the period with the Sentinel-5P Aerosol Index (SAI) of more than 4 as recorded by the Sentinel-5P Satellite engine. The daily VTEC values over the four GNSS receiver stations recorded continuous electron density perturbations during these days. Apart from the ionospheric TEC perturbations, significant enhancements and decreases in daily maximum VTEC values over the four GNSS receiver stations were also noted. These were attributed to the changes in the atmospheric electric fields generated by the SDS event. The VTEC plots for each day exhibited similar trends, hence exhibited the same ionospheric dynamics. VTEC depletions of depths 3 to 6 TECU over all the four GNSS receiver stations were noted on 12<sup>th</sup>, 14<sup>th</sup>, 17<sup>th</sup>, 20<sup>th</sup> and 25<sup>th</sup> June 2020. Nighttime VTEC enhancements were also noted and majorly occurred between 20:00 and 21:00 UT on 9<sup>th</sup>, 13<sup>th</sup>, 15<sup>th</sup>, 17<sup>th</sup>, 19<sup>th</sup>, 20<sup>th</sup> and 21<sup>st</sup> June 2020. This was attributed to the development of the electron avalanche processes including dust and electron absorption or losses and the active conversion to electron dissociative attachment leading to electron excitation. In conclusion, the Godzilla SDS of June 2020 led to the electron density perturbations over Morocco.

Investigation of air breakdown and plasma evolution on microstrip antenna surface using the particle-in-cell method

This paper investigates the breakdown of two microstrip antennas through experiments and particle-in-cell simulations. The breakdown thresholds of a microstrip dipole antenna and a double-layer patch microstrip antenna are investigated experimentally and found to be 15.6 and 30.8 kW, respectively. Ablation is observed on the surface of the antennas, indicating that the local electric field is particularly intense. To further understand the breakdown process, the particle-in-cell and Monte Carlo collision methods are combined to investigate the inception and development of partial discharge on the surface of the antennas. Under the criterion of continuous electron density growth, the breakdown thresholds of the dipole and double-layer patch antennas are estimated to be 19.4 and 52.9 kW in our simulations. The simulation results are in reasonable agreement with the experimental measurements. In the microstrip dipole antenna, the plasma evolution of the partial discharge is initiated near the tip, while the electric field close to the tip is distorted and a positive streamer directed toward the tip is observed. In the double-layer patch microstrip antenna, a more uniform discharge is observed at the edge of the circular patch in the simulations.

Two-dimensional recurrence relations and Takagi–Taupin equations. I. Dynamical X-ray diffraction by a perfect crystal

The dynamical diffraction of spatially restricted X-ray beams in a thick perfect crystal is studied using two-dimensional recurrence relations and the Takagi–Taupin (T-T) equations. It is shown that the two-dimensional recurrence relations are transformed into T-T equations when passing from a crystal with an array of discrete lattice planes to a model of continuous periodic electron density. The results of calculations of the X-ray diffraction field inside the crystal and the angular distribution of the scattering intensity in reciprocal space based on these two approaches are presented. It is shown that, when using the two-dimensional recurrence relations and T-T equations, the calculated contours of reciprocal-space maps and their qx sections are similar to each other, and the qz sections completely coincide.

Lactobacillus brevis CGMCC 1306 glutamate decarboxylase: Crystal structure and functional analysis

Glutamate decarboxylase (GAD), which is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme, can catalyze α-decarboxylation of l-glutamate (L-Glu) to γ-aminobutyrate (GABA). The crystal structure of GAD in complex with PLP from Lactobacillus brevis CGMCC 1306 was successfully solved by molecular-replacement, and refined at 2.2 Å resolution to an Rwork factor of 18.76% (Rfree = 23.08%). The coenzyme pyridoxal 5-phosphate (PLP) forms a Schiff base with the active-site residue Lys279 by continuous electron density map, which is critical for catalysis by PLP-dependent decarboxylase. Gel filtration showed that the active (pH 4.8) and inactive (pH 7.0) forms of GAD are all dimer. The residues (Ser126, Ser127, Cys168, Ile211, Ser276, His278 and Ser321) play important roles in anchoring PLP cofactor inside the active site and supporting its catalytic reactivity. The mutant T215A around the putative substrate pocket displayed an 1.6-fold improvement in catalytic efficiency (kcat/Km) compared to the wild-type enzyme (1.227 mM−1 S−1 versus 0.777 mM−1 S−1), which was the highest activity among all variants tested. The flexible loop (Tyr308–Glu312), which is positioned near the substrate-binding site, is involved in the catalytic reaction, and the conserved residue Tyr308 plays a vital role in decarboxylation of L-Glu.

What have we learned about the dynamics of peptide loading from structures of TAP binding protein, related (TAPBPR)?

Abstract Understanding the molecular details of peptide loading in the MHC-I pathway is crucial to approaches to manipulate recognition of peptide/MHC-I complexes in treating autoimmunity, tumors, and for vaccine design. Recent insights have been provided by two X-ray structures of TAPBPR, in complex with MHC-I molecules. Although structures determined in the two laboratories are remarkably similar (pdb ID: 5WER and 5OPI), the structural models based on X-ray data obtained at similar resolution, 3.4 and 3.3 Å respectively, reveal a discrepancy in the disposition of the TAPBPR 22–36 loop. This loop was not modeled in 5WER due to a lack of electron density, whereas it was modeled as a 3,10 helix in 5OPI and ascribed a significant function in peptide loading. In an attempt to resolve this structural discrepancy, we reanalyzed 5OPI based on the authors’ deposited structure factors. We calculated the refined average B-factor, an indication of positional uncertainty, as 247 Å2 and 153 Å2 for the 22–36 loop and the entire TAPBPR/MHC-I complex, respectively. Prompted by the unusually high B-factors we reexamined the 22–36 loop by calculating composite omit-simulated annealing maps from deposited structure factors of 5OPI as well as of 5WER. When model bias was eliminated in this way, continuous electron density was not visible in this loop region. Thus, we conclude that although the 22–36 loop of TAPBPR may play a role in peptide exchange, there presently is no reliable crystallographic evidence that this loop is a 3,10 helix and is positioned as modeled in 5OPI. Further structural studies of TAPBPR and of tapasin should help to resolve in detail the mechanism by which these molecules facilitate MHC-I stabilization and peptide exchange.

On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations

Solution techniques such as small-angle X-ray scattering (SAXS) play a central role in structural studies of intrinsically disordered proteins (IDPs); yet, due to low resolution, it is generally necessary to combine SAXS with additional experimental sources of data and to use molecular simulations. Computational methods for the calculation of theoretical SAXS intensity profiles can be separated into two groups, depending on whether the solvent is modeled implicitly as continuous electron density or considered explicitly. The former offers reduced computational cost but requires the definition of a number of free parameters to account for, for example, the excess density of the solvation layer. Overfitting can thus be an issue, particularly when the structural ensemble is unknown. Here, we investigate and show how small variations of the contrast of the hydration shell, δρ, severely affect the outcome, analysis and interpretation of computed SAXS profiles for folded and disordered proteins. For both the folded and disordered proteins studied here, using a default δρ may, in some cases, result in the calculation of non-representative SAXS profiles, leading to an overestimation of their size and a misinterpretation of their structural nature. The solvation layer of the different IDP simulations also impacts their size estimates differently, depending on the protein force field used. The same is not true for the folded protein simulations, suggesting differences in the solvation of the two classes of proteins, and indicating that different force fields optimized for IDPs may cause expansion of the polypeptide chain through different physical mechanisms.

Polyelectrolyte Capping As Straightforward Approach toward Manipulation of Diffusive Transport in MOF Films.

We present experimental results demonstrating the suitability of polyelectrolyte capping as a simple and straightforward procedure to modify hydrophilic/hydrophobic character of porous films, thus allowing additional control on transport properties. In particular, we synthesized ZIF-8 metal organic framework (MOF) films, an archetypal hydrophobic zeolitic imidazolate framework, constituted by Zn2+ ions tetrahedrally coordinated with bidentate 2-methylimidazolate organic linker, and poly(4-styrenesulfonic acid) as capping agent (PSS). MOF films were synthesized via sequential one pot (SOP) steps over conductive substrates conveniently modified with primer agents known to enhance heterogeneous nucleation, followed by dip-coating with PSS aqueous solutions. Crystallinity, morphology, and chemical composition of ZIF-8 films were confirmed with traditional methods. Continuous electron density depth profile obtained with synchrotron light X-ray reflectivity (XRR) technique, suggest that PSS capped-films do not adopt segregated configurations in which PSS remains surface-confined. This affects functional properties conferred by PSS capping, which were assessed using cyclic voltammetry with both positively and negatively charged redox probe molecules. Furthermore, taking advantage of the control attained, we successfully carried in situ synthesis of film-hosted d-block metal nanoparticles (Au and Pt-NPT@5x-ZIF-8+PSS) via direct aqueous chemical reduction of precursors (diffusion-reaction approach).

Structural dataset for the PPARγ V290M mutant.

Loss-of-function mutation V290M in the ligand-binding domain of the peroxisome proliferator activated receptor γ (PPARγ) is associated with a ligand resistance syndrome (PLRS), characterized by partial lipodystrophy and severe insulin resistance. In this data article we discuss an X-ray diffraction dataset that yielded the structure of PPARγ LBD V290M mutant refined at 2.3 Å resolution, that allowed building of 3D model of the receptor mutant with high confidence and revealed continuous well-defined electron density for the partial agonist diclofenac bound to hydrophobic pocket of the PPARγ. These structural data provide significant insights into molecular basis of PLRS caused by V290M mutation and are correlated with the receptor disability of rosiglitazone binding and increased affinity for corepressors. Furthermore, our structural evidence helps to explain clinical observations which point out to a failure to restore receptor function by the treatment with a full agonist of PPARγ, rosiglitazone.

PLATONSQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.

Monitoring MCM-41 synthesis by X-ray mesostructure analysis

The electron density maps calculated from X-ray diffraction patterns of the mesoporous silica material МСМ-41 present averaged mesostructure images which in contrast to transmission electron microscopy (TEM) images are exceptionally repeating and represent the whole sample. It was shown that the averaged mesostructure parameters such as a unit cell parameter, a pore diameter, a wall width, a pore shape estimated from the X-ray powder diffraction data in combination with the continuous electron density function approach allow monitoring continuous set of the silica framework states at different stages of the material synthesis.The mentioned technique supplemented by N2-adsorption measurements and transmission electron microscopy was applied for consideration of the МСМ-41 hydrothermal stability. Attention has been given to the variations of the synthesis conditions affecting the hydrothermal stability, in particular the maintaining the basicity of the synthesis solution as well the substitution of the synthesis solution with water or a salt solution at hydrothermal treatment. The averaged pore shape was observed to be changed from cylindrical to hexagonal-prismatic form. The observed wall thickness was in the range from 0.75 to 1.25nm. The competition of silica polycondensation and surface hydrolysis was shown to be responsible for the variety of framework geometry and hydrothermal stability. It has been established that the pore diameter increases generally due to the osmotic pressure of water. If the pores acquire the average prismatic hexagonal shape, the sample has low hydrothermal stability. Under the conditions favorable for the polycondensation the pores have averaged cylindrical shape and material demonstrates higher hydrothermal stability. Cooperative mechanism of mesostructure destruction under hydrothermal conditions was observed using TEM data and was discussed in connection with irregular polycondensation.

Fueling Performance of Supersonic Molecular Beam Injection on the J-TEXT Tokamak

A supersonic molecular beam injection (SMBI) system was developed on the J-TEXT tokamak. With SMBI fueling, a continuous electron density increase was successfully achieved when multiple-pulse injection was employed. A steeper density profile was observed during the penetration process. A high fueling efficiency, between 20% and 45%, was obtained in limiter/ohmic discharges, suggesting that SMBI is a superior fueling method. SMBI efficiency decreased with increasing background electron density. Analyses of the penetration process with a Hα array and a CCD camera suggest the ionization mainly concentrates in the SOL and plasma edge region.

Structure of Nanometer Wide Heavy-Ion Tracks in Muscovite

Radial electron densities within 63-67 μm long ion damage trails,latent ion tracks, created in {001} muscovite by irradiation with 11.1-28.7 MeV/A U and Pb ions, have been derived by small-angle X-ray scattering. Track diameters are 8.0-10.2 nm. The tracks exhibit continuous and uniform electron density decrease of ~4%. Complementary microscopy has revealed loss of atomic order in the tracks. These ion-induced effects undoubtedly accelerate preferential through track permeability of inert and corrosive agents, a property that is important for track applications.

Dimers and trimers of polycyclic aromatic hydrocarbons as models of graphene bilayers and trilayers: enhanced electron density at the edges

Structures of dimers and trimers of polycyclic aromatic hydrocarbons (PAHs) having zig-zag edges, and continuous electron density and molecular electrostatic potential (MEP) distributions in these systems were studied in gas phase. Dimers of benzene and naphthalene for which high-accuracy results are available were used to test the reliability of four different functionals of density functional theory in combination with the 6-31G(d,p) basis set. The dispersion-corrected WB97XD functional was found to be distinctly superior to the other three functionals used and was employed to study PAH dimers and trimers. Electronic structures and geometries of dimers of a four benzene ring and a nine benzene ring systems and trimers of the four benzene ring system were investigated. The dimers and trimers of PAHs were found to be of parallel-displaced type, as observed experimentally for graphene. The enhanced electron density edge effect found in the PAH monomers earlier is found to exist in the dimers and trimers also.

Structures of the PelD Cyclic Diguanylate Effector Involved in Pellicle Formation in Pseudomonas aeruginosa PAO1

The second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays a vital role in the global regulation in bacteria. Here, we describe structural and biochemical characterization of a novel c-di-GMP effector PelD that is critical to the formation of pellicles by Pseudomonas aeruginosa. We present high-resolution structures of a cytosolic fragment of PelD in apo form and its complex with c-di-GMP. The structure contains a bi-domain architecture composed of a GAF domain (commonly found in cyclic nucleotide receptors) and a GGDEF domain (found in c-di-GMP synthesizing enzymes), with the latter binding to one molecule of c-di-GMP. The GGDEF domain has a degenerate active site but a conserved allosteric site (I-site), which we show binds c-di-GMP with a K(d) of 0.5 μm. We identified a series of residues that are crucial for c-di-GMP binding, and confirmed the roles of these residues through biochemical characterization of site-specific variants. The structures of PelD represent a novel class of c-di-GMP effector and expand the knowledge of scaffolds that mediate c-di-GMP recognition.

Polycyclic aromatic hydrocarbons as finite size models of graphene and graphene nanoribbons: Enhanced electron density edge effect

Distinct edge effects on physical and chemical properties are known to exist in graphene and graphene nanoribbons (GNRs). The present study provides a clue to understand the origin of these effects in terms of electron density distribution. Continuous electron density, molecular electrostatic potential and net charges obtained using density functional theory in several polycyclic aromatic hydrocarbons (PAHs) taken as finite size models of graphene and GNRs are analyzed. Electron density is found to be enhanced at the edges in comparison to those in the other parts of several PAHs and a similar distribution is also shown by spin densities in triplet ground states. Electron density is enhanced even at the hydrogen passivated internal edges created by removing carbon atoms of an inner benzene ring. Various experimental observations relating to distinct properties of edges of graphene and GNRs can be explained on the basis of the enhanced electron density edge effect.

Enhanced Electron Density Edge Effect in Polycyclic Aromatic Hydrocarbons as Finite Size Models of Graphene and Graphene Nanoribbons

Several polycyclic aromatic hydrocarbons (PAHs) were studied as finite size models of graphene and graphene nanoribbons using density functional theory. Continuous electron density, molecular electrostatic potential (MEP) and MEP-derived net charge distributions in these systems were analyzed. It is found that the edges of all the PAHs studied are associated with appreciably enhanced electron density in comparison to their other parts. Internal edges created by removing carbon atoms of an inner benzene ring followed by attachment of hydrogens to carbon atoms with unsatisfied valencies are also found to be associated with enhanced electron density. Experimental observations reported on graphene and GNRs showing enhanced reactivity of their edges can be explained on the basis of the enhanced electron density edge effect found in the PAHs.

Structural Studies of the Molybdenum Center of Mitochondrial Amidoxime Reducing Component (mARC) by Pulsed EPR Spectroscopy and 17O-Labeling

Mitochondrial amidoxime reducing components (mARC-1 and mARC-2) represent a novel group of Mo-containing enzymes in eukaryotes. These proteins form the catalytic part of a three-component enzyme complex known to be responsible for the reductive activation of several N-hydroxylated prodrugs. No X-ray crystal structures are available for these enzymes as yet. A previous biochemical investigation [Wahl, B., et al. (2010) J. Biol. Chem., 285, 37847-37859 ] has revealed that two of the Mo coordination positions are occupied by sulfur atoms from a pyranopterindithiolate (molybdopterin, MPT) cofactor. In this work, we have used continuous wave and pulsed electron paramagnetic resonance (EPR) spectroscopy and density functional theoretical (DFT) calculations to determine the nature of remaining ligands in the Mo(V) state of the active site of mARC-2. Experiments with samples in D(2)O have identified the exchangeable equatorial ligand as a hydroxyl group. Experiments on samples in H(2)(17)O-enriched buffer have shown the presence of a slowly exchangeable axial oxo ligand. Comparison of the experimental (1)H and (17)O hyperfine interactions with those calculated using DFT has shown that the remaining nonexchangeable equatorial ligand is, most likely, protein-derived and that the possibility of an equatorial oxo ligand can be excluded.

The Structure of Neurexin 1α Reveals Features Promoting a Role as Synaptic Organizer

α-neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The α-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how α-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1α extracellular domain (n1α) to 2.65 Å. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 Å structure of n1α carrying splice insert SS#3 in LNS4 reveals that SS#3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables α-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

Temperature-Dependent Spin Crossover in Neuronal Nitric Oxide Synthase Bound with the Heme-Coordinating Thioether Inhibitors

A series of L-arginine analogue nitric oxide synthase inhibitors with a thioether tail have been shown to form an Fe-S thioether interaction as evidenced by continuous electron density between the Fe and S atoms. Even so, the Fe-S thioether interaction was found to be far less important for inhibitor binding than the hydrophobic interactions between the alkyl group in the thioether tail and surrounding protein (Martell et al. J. Am. Chem. Soc. 2010 , 132 , 798). However, among the few thioether inhibitors that showed Fe-S thioether interaction in crystal structures, variations in spin state (high-spin or low-spin) were observed dependent upon the heme iron oxidation state and temperature. Since modern synchrotron X-ray data collection is typically carried out at cryogenic temperatures, we reasoned that some of the discrepancies between cryo-crystal structures and room-temperature UV-visible spectroscopy could be the result of temperature-dependent spin-state changes. We, therefore, have characterized some of these neuronal nitric oxide synthase (nNOS)-thioether inhibitor complexes in both crystal and solution using EPR and UV-visible absorption spectrometry as a function of temperature and the heme iron redox state. We found that some thioether inhibitors switch from high to low spin at lower temperatures similar to the "spin crossover" phenomenon observed in many transition metal complexes.

Using multipole point charge distributions to provide the electrostatic potential in the variational explicit polarization (X-Pol) potential

The equations defining the variational explicit polarization (X-Pol) potential introduced in earlier work are modified in the present work so that multipole point charge distributions are used instead of Mulliken charges to polarize the monomers that comprise the system. In addition, when computing the electrostatic interaction between a monomer whose molecular orbitals are being optimized and a monomer whose electron density is being used to polarize the first monomer, the electron densities of both monomers are represented by atom-centered multipole point charge distributions. In the original formulation of the variational X-Pol potential, the continuous electron density of the monomer being optimized interacts with external Mulliken charges, but this corresponds to the monopole truncation in a multipole expansion scheme in the computation of the Fock matrix elements of the given monomer. The formulation of the variational X-Pol potential introduced in this work (which we are calling the "multipole variational X-Pol potential") represents the electron density of the monomer whose wave function is being variationally optimized in the same way that it represents the electron densities of external monomers when computing the Coulomb interactions between them.