Modification Of Electron Density Research Articles

Deep-learning map segmentation for protein X-ray crystallographic structure determination.

When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification. In this manuscript, the use of convolutional neural networks (CNNs) for segmentation of the initial experimental phasing electron-density maps is proposed. The results reported demonstrate that a CNN with U-net architecture, trained on several thousands of electron-density maps generated mainly using X-ray data from the Protein Data Bank in a supervised learning, can improve current density-modification methods.

Evidence of CME‐Magnetospheric Shock Disturbance of the D‐Region Observed in the VLF Signal

AbstractThe observation of the D‐region response to the interplanetary shock (IS) during the storm of 17 March 2015 is carried out using two very low frequency (VLF) transmitter signals (NRK and GQD) recorded at Algiers and Tunis. Data from THEMIS‐E and RBSP are used to correlate between the ground and satellite observations. The important finding is the wavy structure of the perturbations observed on the two VLF signals tens of seconds after the space detection of the shock, in concordance with the RBSP electric field measurements. The measured VLF signal amplitude and phase perturbations were: −0.65 dB, 5.81° for NRK and −0.12 dB, −126° for GQD measured at Algiers. For Tunis receiver, the perturbations were: −0.58 dB, 4.7° for NRK and 0.15 dB, −1.19° for GQD. In addition to the observations, simulations of the NRK signal perturbations were done using the long wavelength propagating capability code to determine the electron density modification that lead to the measured perturbations. The simulation results showed that the modified Wait's parameters above the NRK transmitter were: 80.391 km for h′ and 0.43 km−1 for β in the case of NRK‐Tunis path. Concerning the NRK‐Algiers path, the simulation gave 80.316 km for h′ and 0.431 km−1 for β. From these parameters values, the modified electron density was not important to explain the observed perturbations. Therefore, the IS effect could be explained by induced heating of the ionosphere due to the penetration of the electric field which leads to the changes of the ionospheric conductivity.

Asymmetric cobalt porphyrins for oxygen reduction reactions: Boosted catalytic activity by the use of triphenylamine

Asymmetric metalloporphyrins have been rarely investigated in oxygen reduction reaction (ORR), which is probably due to the remaining unclear structural effects on electrocatalytic performance and the low synthetic yields. A remarkable feature of these molecules is their inherent large dipole moments, which can benefit the charge separation and electron density modification. Here we synthesize two asymmetric molecules A-Cb-CoPor and A-TPA-CoPor by substituting one of the meso-positions with carbazole and triphenylamine (TPA) derivatives, respectively, to coat on carbon black as ORR electrocatalysts. Density functional theory calculations suggest the well separation of electron density on the cobalt porphyrins. The electrochemical performances of the composites are performed in acid with comparing to a symmetric Co porphyrin-coated catalyst CoPor1/C. A-TPA-CoPor/C attains better ORR activity and selectivity than A-Cb-CoPor/C due to the structural merits of TPA unit. However, an identical electron transfer number of 3.6 is obtained by A-TPA-CoPor/C and CoPor1/C, which is possibly a trade-off result of the use of TPA from its structural advantage and deleterious electron-donating ability. Impressively, both asymmetric porphyrin-based composites exhibit greater limiting current densities than CoPor1/C, which mainly originates from the reduced charge transfer resistance as suggested by the impedance measurements. Our work demonstrates the promise of the asymmetric molecular approach as a viable strategy for efficient ORR catalysts.

Rational design of Schottky heterojunction with modulating surface electron density for high-performance overall water splitting

The development of non-precious metal electrocatalysts to synergistically expose more active sites and optimize intrinsic activity still remains a huge challenge. Transition metal layered double hydroxide (LDH) has a great potential in electrocatalysis due to its unique sheet-like nanostructure and low cost. However, the poor electrical conductivity and sluggish water dissociation process hinder their development. Herein, the interface effect of Schottky heterostructure between cobalt-iron hydroxide and MXene and surface electron density modification with phosphorus (P) doping provide an efficient method to solve these crucial issues. The novel Schottky heterostructure catalyst (P-CoFe-LDH@MXene/NF) with self-driven charge transfer can enhance electron transport efficiency. In addition, the surface electron density optimized by P-doping will promote the ability of H+/OH- ion adsorption and redox reaction for overall water splitting. The as-prepared P-CoFe-LDH@MXene/NF requires overpotentials of only 85 mV at 10 mA cm−2 for HER and 252 mV at 200 mA cm−2 for OER in 1.0 M KOH, respectively. And under an alkaline electrolyzer, it can be driven 10 mA cm−2 at a low voltage of 1.52 V for overall water splitting with remarkable durability for 100 h. More broadly, this design concept is universal and it can be extended to design other transition metal-based catalysts.

Controllable synthesis of nitrogen-doped carbon containing Co and Co3Fe7 nanoparticles as effective catalysts for electrochemical oxygen conversion

Sufficient and well-distributed active sites and highly conductive carbon matrix are two important factors to achieve highly efficient electrocatalysts. In this study, we report an adjusted metal-organic frameworks (MOF)-based route for the preparation of nitrogen-doped Fe/Co bimetallic electrocatalysts. With suitable Fe/Co molar ratio (Fe/Co = 1/4.15), Co nanoparticles (NPs) with mild oxidation state and Co3Fe7 alloys wrapped with thin graphene layers are embedded in an integrated and continuous carbon network. The corresponding FC@NCs-4.15 catalyst exhibits excellent oxygen reduction reaction (ORR) activity (onset potential (Eonset) of 0.94 V and half-wave potential (E1/2) of 0.84 V vs RHE) in alkaline medium, close to commercial Pt/C and superior to the other two FC@NCs. The desirable ORR performance results from the uniform distribution Co3Fe7 active sites, electron density modification from Co NPs to surrounding carbon layers, hierarchical pore structure with large surface area, low carbon content, high pyridinic and graphitic N components. The FC@NCs-4.15 also displays satisfactory methanol crossover tolerance and durability.

Origins and properties of the tetrel bond.

The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.

CAB: a cyclic automatic model-building procedure.

The program Buccaneer, a well known fast and efficient automatic model-building program, is also a tool for phase refinement: indeed, input phases are used to calculate electron-density maps that are interpreted in terms of a molecular model, from which new phase estimates may be obtained. This specific property is shared by all other automatic model-building programs and allows their cyclic use, as is usually performed in other phase-refinement methods (for example electron-density modification techniques). Buccaneer has been included in a cyclic procedure, called CAB, aimed at increasing the rate of success of Buccaneer and the quality of the molecular models provided. CAB has been tested on 81 protein structures that were solved via molecular-replacement, anomalous dispersion and ab initio methods. The corresponding phases were submitted to a phase-refinement process that synergically combines current phase-refinement techniques and out-of-mainstream refinement methods [Burla et al. (2017), Acta Cryst. D73, 877-888]. The phases thus obtained were used as input for CAB. The experimental results were compared with those obtained by the sole use of Buccaneer: it is shown that CAB improves the Buccaneer results, both in completeness and in accuracy.

Evaluating the electron density model by applying an imaginary modification

A function has been proposed to evaluate the electron density model constructed by inverse Fourier transform using the observed structure amplitudes and trial phase set. The strategy of this function is applying an imaginary electron density modification to the model, and then measuring how well the calculated structure amplitudes of the modified model matches the expected structure amplitudes for the modified correct model. Since the correct model is not available in advance, a method has been developed to estimate the structure amplitudes of the modified correct model. With the estimated structure amplitudes of the modified correct model, the evaluation function can be calculated approximately. Limited tests on simulated diffraction data indicate that this evaluation function may be valid at the data resolution better than 2.5 Å.

Synergy among phase-refinement techniques in macromolecular crystallography.

Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD-MAD and ab initio techniques.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

About difference electron densities and their properties.

Difference electron densities do not play a central role in modern phase refinement approaches, essentially because of the explosive success of the EDM (electron-density modification) techniques, mainly based on observed electron-density syntheses. Difference densities however have been recently rediscovered in connection with the VLD (Vive la Difference) approach, because they are a strong support for strengthening EDM approaches and for ab initio crystal structure solution. In this paper the properties of the most documented difference electron densities, here denoted as F - Fp, mF - Fp and mF - DFp syntheses, are studied. In addition, a fourth new difference synthesis, here denoted as {\overline F_q} synthesis, is proposed. It comes from the study of the same joint probability distribution function from which the VLD approach arose. The properties of the {\overline F_q} syntheses are studied and compared with those of the other three syntheses. The results suggest that the {\overline F_q} difference may be a useful tool for making modern phase refinement procedures more efficient.

Solving proteins at non-atomic resolution by direct methods: update

Direct methods can be used to solve proteins of great structural complexity even when diffraction data are at non-atomic resolution. However, one of the main obstacles to the wider application of direct methods is that they reliably phase only a small fraction of the observed reflections, those with a sufficiently large value of the normalized structure factor amplitude. The subsequent phase expansion and refinement required for full structure solution are difficult. Here a new phase refinement procedure is described, which combines (1–2) difference Fourier synthesis with electron density modification techniques and thevive la differenceand Free Lunch algorithms. This procedure is able to solve data resistant to other direct space refinement procedures.

Modification of electron density in F layer of ionosphere by dust suspension

The effect of the suspension of high/low work function dust in the F layer ionospheric plasma has been investigated. On the basis of kinetics formulation of the F-layer dusty plasma, the local electron density is shown to reduce or enhance by inserting fine dust of appropriate physical/material properties. The formulation includes the number and energy balance of the plasma constituents along with the charging of the dust particles; a novel approach to investigate the effect of diffusion on plasma particles in the F-layer has been outlined. The consequence of the physical parameters of dust, namely, number density, material work function, photo-efficiency, and surface temperature, on the charging of dust and local plasma parameters at different ionospheric altitudes in the F layer has been worked out and presented graphically; the significance of plasma diffusion has been highlighted. The modification in local plasma density in the midday F-layer is seen to be sensitive to the dust parameters and altitude profile of the ionospheric plasma. Such modification in the local electron density is certainly of interest for radio wave propagation through the F layer.

Modification of ionospheric electron density by dust suspension

On the basis of a dynamic analysis the effectiveness of dust suspension for the reduction and enhancement of electron density in the E-layer of the ionosphere has been investigated in this paper. The analysis is based on the modelling of the E-layer as the Chapman α layer (validated earlier); the electron/ion production function, arrived at by Chapman and effective electron temperature-dependent electron–ion recombination coefficients in agreement with observations have been used. The balance of the charge on the particles and the number/energy balance of the constituents have been taken into account. The following is the physics of the change in electron density in the ionosphere by the suspension of dust. First, the dust provides a source (emission) and sink (accretion) of electrons. Second, the dust emits photoelectrons with energies much higher than those of ambient electrons, which enhances the electron temperature, leading to a reduced electron–ion recombination coefficient, and thus to a higher electron density. An interplay of these processes and the natural processes of electron production/annihilation determines the electron density and temperature in the dust suspension in the ionosphere. The numerical results, corresponding to suspension of dust of silicate (high work function) and Cs coated bronze (low work function) in the E-layer at are presented and discussed.

The reaction fragility spectrum.

We report an original method that provides a new insight into the reaction mechanism by direct observation of bond breaking and formation. Variations of the diagonal elements of the Hessian along the IRC are shown to reflect the anharmonic properties of the system that are induced by electron density modifications upon the reaction. This information is presented in the form of the reaction spectrum, demonstrating how particular atoms engage in the reorganization of bonds. The test reactions are: HCOF synthesis and HONS isomerization.

An ab initio electronic density study of the CH4–Ar, CH4–Xe, CH4–H2O and CH4–H2S complexes: insights into the nature of the intermolecular interaction

The main point of this paper concerns the theoretical characterisation of the effects induced by the intermolecular interaction on the electron density upon the formation of CH4-H2X (X=O,S) and CH4–Ng (Ng=Ar,Xe) complexes. The work has been stimulated by recent molecular scattering beams experiments, which point out differences in both strength and anisotropy of the intermolecular potential between CH4–H2X respect to reference CH4–Ng systems. Herein, attention is focused on the electronic charge polarisation and particularly charge transfer (CT) effects between involved partners, directly related to the topology of the full potential energy surface. The modification of electron density and the occurrence of CT have been evaluated via the charge displacement function worked out by high level ab initio calculations. Moreover, in the case of a specific configuration of CH4–H2O system, we define the leading interaction components, including their relative stabilising role and test our intermolecular potential model with reference to ab initio calculations. The results obtained indicate that CT clearly affects the strength and the anisotropy of CH4–H2O complex, and covers a minor and negligible role for CH4–H2S and the noble gas complexes, respectively.

Vertical coupling between troposphere and lower ionosphere by electric currents and fields at equatorial latitudes

Thunderstorms play significant role in the upward electrical coupling between the troposphere and lower ionosphere by quasi-static (QS) electric fields generated by quiet conditions (by slow variations of electric charges), as well as during lightning discharges when they can be strong enough to produce in the nighttime lower ionosphere sprites. Changes are caused in lower ionosphere by the QS electric fields before a sprite-producing lightning discharge which can play role in formation of the stronger sprite-driving transient QS electric fields due to lightning. These changes include electron heating, modifications of conductivity and electron density, etc. We demonstrate that such changes depend on the geomagnetic latitude determining the magnetic field lines inclination, and thus, the anisotropic conductivity. Our previous results show that the QS electric fields in the lower ionosphere above equatorial thunderstorms are much bigger and have larger horizontal extension than those generated at high and middle altitudes by otherwise same conditions. Now we estimate by modeling the electric currents and fields generated in lower ionosphere above equatorial thunderstorms of different horizontal dimensions during quiet periods and of their self-consistent effects to conductivity whose modifications can play role in formation of post-lightning sprite-producing electric fields. Specific electric currents configurations and distributions of related electric fields are estimated first by ambient conductivity. Then, these are evaluated self-consistently with conductivity modification. The electric currents are re-oriented above ~85km and flow in a narrow horizontal layer where they dense. Respectively, the electric fields and their effect on conductivity have much larger horizontal scale than at middle latitudes (few hundred of kilometers). Horizontally large sources, such as mesoscale convective structures, cause enhancements of electric fields and their effects. These modified features may affect production of sprites.

Refining a model electron-density map via the Phantom Derivative method.

The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques.

Electron density modification in ionospheric E layer by inserting fine dust particles

In this paper, we have developed the kinetics of E-region ionospheric plasma comprising of fine dust grains and shown that the electron density in E-layer can purposely be reduced/enhanced up to desired level by inserting fine dust particles of appropriate physical/material properties; this may certainly be promising for preferred rf-signal processing through these layers. The analytical formulation is based on average charge theory and includes the number and energy balance of the plasma constituents along with charge balance over dust particles. The effect of varying number density, work function, and photo-efficiency of dust particles on ionospheric plasma density at different altitude in E-layer has been critically examined and presented graphically.

Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination.

Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (φ1 and φ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ(DS) list as a criterion to select optimized phases φ(am) from φ1 or φ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases φ(SAD) has been developed. Based on this work, reflections with an angle θ(DS) in the range 35-145° are selected for an optimized improvement, where θ(DS) is the angle between the initial phase φ(SAD) and a preliminary density-modification (DM) phase φ(DM)(NHL). The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.