Charge Density Data Research Articles

Chloride Adsorption on Au (111) Electrodes

There are still numerous open questions with regards to adsorption phenomena and partial charge transfer at electrode interfaces. The dynamic nature electrode structure and adsorbate ordering makes an analysis solely based on thermodynamic considerations limited. Here we present recently collected data with such an analysis, using different concentrations of chloride anions in both acidic and neutral electrolytes, for well-defined Au (111) electrodes. Cyclic voltammograms and charge density data is obtained. Then the electrocapillary equation: "-dγ = σMdE + ΓCl-RTdln(cKCl)" is used to get the relative interfacial tension plot and later the electrosorption valency. In the future we will improve on this by more accurately placing the PZC of charge density measurements, using laser induced temperature jump transients and combining our interpretation with state-of-the-art molecular-dynamics using ground state machine learned potentials. Figure 1

A Nickel-doped, lanthanum gallium germanate-based phosphor as an ultra-broadband short-wavelength infrared region emitter for optical imaging

Short-wavelength infrared region light source (SWIR, λ = 1000–2000 nm) is useful for optical imaging of biological tissues for lack of auto-fluorescence, low intrinsic absorption, and low scattering. Here, we report the synthesis, characterization, and mechanistic studies of a Ni2+-doped, lanthanum gallium germanate-based phosphor, La3Ga5GeO14:Ni2+, that emits SWIR with an ultra-broad bandwidth emission of 1000–2000 nm, a full-width at half maximum (FWHM) of 340 nm, which covers near infrared-II and III regions. The analysis of crystal structure suggests that Ga3+ ions in [GaO6] octahedron lattices are replaced by Ni2+ ions, possibly due to the similar radius shared by both ions. The observed ultra-broadband SWIR luminescence with large Stokes shift is most likely originated from the influence of a strong crystal field on the extent of the cleavage of energy levels of Ni2+ ions, which is supported by the charge density data of [GaO6] octahedra in La3Ga5GeO14 derived from state density functional calculation. A SWIR pc-LED was constructed by packaging the La3Ga5GeO14:Ni2+ phosphor with a near-ultraviolet LED chip, and its potential application in optical imaging of human bodies was explored.

A representation-independent electronic charge density database for crystalline materials

In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.

First-principles prediction of outstanding mechanical and thermodynamic properties of YX2Si2 (X = Pd and Rh) superconductors

Superconductivity is a macroscopic quantum phenomenon with unprecedented applications in high-efficient power transmission, electric motors, generators, transportation, particle accelerators, and computing. Although the superconducting capabilities of YX2Si2 (X = Pd, and Rh) compounds have been experimentally realized, the physical aspects of these two superconductors are yet to be understood. Herein, employing first-principle-based Density Functional Theory (DFT) calculations, we realized the excellent mechanical strength of the YRh2Si2 compound. Firstly, the estimated X-ray diffraction, as well as unit cell parameters of both superconductors, show excellent conformity with prior experimental data. Also, mechanical parameters which are most fundamental, including bulk modulus, shear modulus, Young's modulus, Poisson's ratio, anisotropy factor, ductility, and Vickers hardness factors of both superconductors have been evaluated. Despite the brittle nature, YRh2Si2 shows excellent mechanical strength compared to that of YPd2Si2. Besides, the assessment of the density of states, Mulliken atomic populations, and charge density map reveals a complex chemical bonding in both superconductors including ionic, covalent, and metallic features. Furthermore, charge density data suggest that Si-Si, Si-Pd, and Si-Rh bonds are indeed covalent while Pd-Pd and Rh-Rh demonstrate metallic features. Afterward, different optical parameters such as dielectric functions, reflectivity, absorption coefficient, refractive index, photoconductivity, and loss function of both superconductors have been anticipated. Notably, it has been unveiled that both superconductors show excellent absorption and photoconductivity in the ultraviolet region of the electromagnetic spectrum. Additionally, sound velocity, Debye temperature, melting point, and minimum thermal conductivity of both superconductors have been estimated from DFT computation. Interestingly, most of the thermodynamic parameters of YRh2Si2 are notably higher compared to those of the YPd2Si2 compound. Remarkably, the DFT results suggest that YRh2Si2 exhibits excellent mechanical as well as thermodynamic properties compared to other reported superconductors of identical classes.

Effect of Selected Anionic and Cationic Drugs Affecting the Central Nervous System on Electrical Properties of Phosphatidylcholine Liposomes: Experiment and Theory.

Interactions between phospholipid membranes and selected drugs affecting the central nervous system (CNS) were investigated. Small, unilamellar liposomes were used as biomimetic cell membrane models. Microelectrophoretic experiments on two-component liposomes were performed using the electrophoretic light scattering technique (ELS). The effect of both positively (perphenazine, PF) and negatively (barbituric acid, BA) charged drugs on zwitterionic L-α-phosphatidylcholine (PC) membranes were analyzed. Experimental membrane surface charge density (δ) data were determined as a function of pH. Quantitative descriptions of the adsorption equilibria formed due to the binding of solution ions to analyzed two-component membranes are presented. Binding constants of the solution ions with perphenazine and barbituric acid-modified membranes were determined. The results of our research show that both charged drugs change surface charge density values of phosphatidylcholine membranes. It can be concluded that perphenazine and barbituric acid are located near the membrane surface, interacting electrostatically with phosphatidylcholine polar heads.

First coupled GENE–XGC microturbulence simulations

Covering the core and the edge region of a tokamak, respectively, the two gyrokinetic turbulence codes Gyrokinetic Electromagnetic Numerical Experiment (GENE) and X-point Gyrokinetic Code (XGC) have been successfully coupled by exchanging three-dimensional charge density data needed to solve the gyrokinetic Poisson equation over the entire spatial domain. Certain challenges for the coupling procedure arise from the fact that the two codes employ completely different numerical methods. This includes, in particular, the necessity to introduce mapping procedures for the transfer of data between the unstructured triangular mesh of XGC and the logically rectangular grid (in a combination of real and Fourier space) used by GENE. Constraints on the coupling scheme are also imposed by the use of different time integrators. First, coupled simulations are presented. We have considered collisionless ion temperature gradient turbulence, in both circular and fully shaped plasmas. Coupled simulations successfully reproduce both GENE and XGC reference results, confirming the validity of the code coupling approach toward a whole device model. Many lessons learned in the present context, in particular, the need for a coupling procedure as flexible as possible, should be valuable to our and other efforts to couple different kinds of codes in pursuit of a more comprehensive description of complex real-world systems and will drive our further developments of a whole device model for fusion plasmas.

Numerical Optimization Applying Trust Region Algorithm to Optimize Parameters Related to Charge Transport Model in LDPE

Recently, a numerical model has been developed for describing bipolar charge transport with two levels of traps (shallow and deep traps) in low density polyethylene (LDPE). This paper presents an optimization method, which is based on trust region algorithm. However, the enterprise has to be done with laying out the determination of physical parameters pertaining to bipolar charge transport model. Experimental data that have been used are net density charge measured by the pulse electro acoustic method (PEA) along with what is known as external charging current measurements. Simulated data are computed by the bipolar charge transport model, which is developed for LDPE. In essence, this paper sheds the light on the advanced algorithm that can give rise to a unique set of parameters for the model. Parameters will be reckoned using two different cost functions depending on current density and charge density data's. Conclusions on the best-to-use cost function are presented.

Accurate experimental charge-density data: tips and tricks for data collection and processing

Accurate experimental charge-density data: tips and tricks for data collection and processing

Spectroelectrochemical Characterization of 1,2-Dipalmitoyl- sn-glycero-3-cytidine Diphosphate Nucleolipid Monolayer Supported on Gold (111) Electrode.

The effect of the electrode potential on the orientation and conformation of the 1,2-dipalmitoyl- sn-glycero-3-cytidine monolayer deposited on a gold (111) electrode surface was described. The potential of zero free charge ( Epzc) for the monolayer-covered electrode was determined to be -0.2 V vs SCE. The differential capacitance and charge density data indicated that the monolayer is stable at the electrode surface when ( E - Epzc) > 0.0 V. At negative rational potentials, a progressive detachment (electrodewetting) of the monolayer occurs. The monolayer is fully detached from the electrode surface at ( E - Epzc) < -0.6 V. The conformation and orientation of the acyl chains and the orientation of the cytosine moiety were determined with the help of photon polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). The IR measurements demonstrate that the acyl chains are predominantly in the gel phase in the adsorbed state and tilted at an angle of ∼30° with respect to the electrode surface normal. The tilt angle of the acyl chains increases when the film is detached from the gold surface, indicating that the monolayer becomes more disordered. At ( E - Epzc) > 0.0 V, the plane of the cytosine moiety assumes a small angle of ∼20° with respect to the surface. At negative potentials, the tilt angle of the cytosine fragment increases and rotates. With the help of DFT calculations, these changes were explained by the repulsion of the positive pole of the cytosine permanent dipole moment by the positively charged gold surface and its attraction to the metal surface at negative electrode potentials. This work provides unique information for the future development of sensors based on the molecular recognition of nucleoside targets.

An Examination of the Electron Densities in a Series of Tripodal Cobalt Complexes Bridged by Magnesium, Calcium, Strontium, and Barium †

X-ray crystallographic and theoretical charge-density data for a series of compounds—[(Co(Ts3tren))M(Co(Ts3tren))], (M = Mg, Ca, Sr and Ba)—were examined. The crystal structures were isostructural, and the alkaline-earth-metal ions had the same six-coordinate environment oxygen donor atoms which was octahedral despite the large variation in their ionic radii. The isomorphism of these molecules was surprising, and a theoretical examination of their electronic structures, with various metal ions along the series, provided detailed insight into their stabilities. The theoretical and experimental data were consistent and agreed well. The local properties of the Co(II) ion and its donor atoms were relatively independent of the alkaline earth metals.

Structure Simulation and Host–Guest Interaction of Histidine-Intercalated Hydrotalcite–Montmorillonite Complex

The structures of histidine intercalated hydrotalcite–montmorillonite complex (His–LDHs–MMT) were studied using the DMol3 code, GGA/PW91 function, and DND basis set of the density functional theory (DFT). The geometries of His–LDHs–MMT were optimized, and their electronic properties were calculated. The results showed that the structure of the complex can be seen as that the quaternary ammonium group of histidine was adsorbed on the oxygen of MMT lamella, and its oxygen on the carboxylic acid anion was combined with the hydrogen atoms of the LDHs lamella. It was determined that the interaction mainly consisted in hydrogen bonding and electrostatic force. The average binding energies per histidine of His–LDHs and His–MMT were about −65.89 and −78.44 kcal/mol, respectively. The density of states of the complexes showed that the 2p orbitals of oxygen were dominant, and the 1s orbit of hydrogen near the Fermi level indicate the formation of hydrogen bonds in the complex. The charge density data displayed the density field of histidine carboxylic acid anion overlapped with that of hydrotalcite layer, indicating that a strong hydrogen bond interaction existed between histidine and hydrotalcite layer. The analysis of the electrostatic potential of complex indicated that the electrostatic interaction between histidine and MMT is obviously stronger than that of LDHs. The simulated XRD spectra showed the special diffraction peaks of LDHs and MMT layer in the complex.

Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH- anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.

Synthesis, spectroscopic (UV–Vis, FT-IR and NMR), single crystal XRD of 3,5-diethyl -2,6-di(thiophen-2-yl)piperidin-4-on-1-ium picrate: A comprehensive experimental and computational study

A piperidin-4-one containing picrate 3,5-diethyl -2,6-di(thiophen-2-yl)piperidin-4-on-1-ium picrate [3,5-DPPP] was synthesized. The molecular structure of 3,5-DPPP was confirmed by FT-IR, NMR, Uv-Vis, single crystal XRD analysis and DFT and HF methods with 6–31G(d,p) basis set. The XRD data confirm the transfer of protons from picric acid (O2) to piperidin-4-one ring (N1). The 3,5-DPPP compound is stabilized by the presence of intermolecular and intramolecular hydrogen bonds (N-H⋯O, C-H⋯S and C-H⋯O). Density functional theory and HF calculations have been used widely for calculating a wide variety of molecular properties such as optimized structure, FT-IR and Uv-Vis spectra, and provided reliable results which are in agreement with experimental data. The charge density data have been used to understand the properties of molecular systems. Furthermore, several quantum chemical insights have been obtained in the form of the total and partial density of states, the HOMO–LUMO energy gap and electrostatic potential map etc. In addition, the polarizability and first hyperpolarizability were calculated to show the potential applications of 3,5-DPPP in nonlinear optics.

Experimental and Theoretical Electron Density Analysis of Copper Pyrazine Nitrate Quasi-Low-Dimensional Quantum Magnets.

The accurate electron density distribution and magnetic properties of two metal-organic polymeric magnets, the quasi-one-dimensional (1D) Cu(pyz)(NO3)2 and the quasi-two-dimensional (2D) [Cu(pyz)2(NO3)]NO3·H2O, have been investigated by high-resolution single-crystal X-ray diffraction and density functional theory calculations on the whole periodic systems and on selected fragments. Topological analyses, based on quantum theory of atoms in molecules, enabled the characterization of possible magnetic exchange pathways and the establishment of relationships between the electron (charge and spin) densities and the exchange-coupling constants. In both compounds, the experimentally observed antiferromagnetic coupling can be quantitatively explained by the Cu-Cu superexchange pathway mediated by the pyrazine bridging ligands, via a σ-type interaction. From topological analyses of experimental charge-density data, we show for the first time that the pyrazine tilt angle does not play a role in determining the strength of the magnetic interaction. Taken in combination with molecular orbital analysis and spin density calculations, we find a synergistic relationship between spin delocalization and spin polarization mechanisms and that both determine the bulk magnetic behavior of these Cu(II)-pyz coordination polymers.

An empirical correction for the influence of low-energy contamination

Low-energy contamination caused by focusing multilayer optics has been known for a long time. So far, the only method to avoid this problem is attenuation by interposition of a low-density material foil into the beam. However, attenuation lowers the intensity, which might be crucial, especially for charge density data collection, and is of course not possible for already measured data. In this article, an empirical correction is proposed as an alternative or addition. The low-energy contamination mainly affects the reflections with indices 3h3k3l. In the programSADABS, a 3λ correction in analogy to the earlier 2/λ correction is now implemented. The correction factor can be determined from the model, but for most cases, a default value depending on the experimental settings is acceptable. Alternatively, the correction can be refined inSHELXL, similarly to a twin refinement. An investigation of several data sets collected with and without attenuation revealed that the empirical correction and attenuation lead to similar improvements. The empirical correction is of special interest for charge density investigations, where the loss of intensity could hinder the data collection up to very high resolution. Here, the improvements in the model, especially for the noise level of the residual density, are even more pronounced.

Modulating the fixed charge density in silicon nitride films while monitoring the surface recombination velocity by photoluminescence imaging

Several important semiconductor devices such as solar cells and photodetectors may be fabricated based on surface inversion layer junctions induced by fixed charge in a dielectric layer. Inversion layer junctions can easily be fabricated by depositing layers with a high density of fixed charge on a semiconducting substrate. Increasing the fixed charge improves such devices; for instance, the efficiency of a solar cell can be substantially increased by reducing the surface recombination velocity, which is a function of the fixed charge density. Methods for increasing the charge density are therefore of interest. In this work, the fixed charge density in silicon nitride layers deposited by plasma enhanced chemical vapor deposition is increased to very high values above 1 × 1013 cm−2 after the application of an external voltage to a gate electrode. The effect of the fixed charge density on the surface recombination velocity was experimentally observed using the combination of capacitance-voltage characterization and photoluminescence imaging, showing a significant reduction in the surface recombination velocity for increasing charge density. The surface recombination velocity vs. charge density data was analyzed using a numerical device model, which indicated the presence of a sub-surface damage region formed during deposition of the layers. Finally, we have demonstrated that the aluminum electrodes used for charge injection may be chemically removed in phosphoric acid without loss of the underlying charge. The injected charge was shown to be stable for a prolonged time period, leading us to propose charge injection in silicon nitride films by application of soaking voltage as a viable method for fabricating inversion layer devices.

More about systematic errors in charge-density studies.

In order to detect and graphically visualize the absence or presence of systematic errors in fit data, conditional probabilities are employed to analyze the statistical independence or dependence of fit residuals. This concept is completely general and applicable to all scientific fields in which model parameters are fitted to experimental data. The applications presented in this work refer to published charge-density data.

Experimental Charge Density studies of Ge(II) complexes using beamline I19

Interest in the p-block elements has recently been stimulated by the need for new reagents for materials and electronics applications, as well as the intrinsic interest in the unprecedented structures and properties observed. For germanium the development of low-valent compounds, organometallics, multiply bonded species, radicals and clusters is of significant importance. We have probed the coordination chemistry of Ge(II) with a range of neutral ligands, few examples of which were reported until recently. They exhibit many striking features including diverse structural motifs and highly variable coordination numbers (between 3 and 8) [1] suggesting the Ge centre does not to have a strong stereochemical preference and small differences in steric and electronic properties of the donor ligands have a significant role. Bonding models have been used to rationalise the observed structures with a Ge-based lone pair occupying the stabilised Ge 4s orbital. However these models are not entirely satisfactory and experimental charge density studies could provide valuable insights into the structures and chemistry of these compounds. [GeCl2(2,2'-bipyridine)], 1, and [GeCl2(1,2-bis(dimethylphosphino)benzene], 2, were selected as targets for initial experimental charge density studies and data have been collected using 3 different experimental configurations of the small molecule single-crystal diffraction beamline I19 [2] at Diamond Light Source. Using a Rigaku Saturn 724+ CCD detector on a 4-circle kappa-geometry CrystalLogic goniometer, data for 1 were collected at λ=0.6889Å without bimorph focussing mirrors in place, and for 2 data were collected at both λ=0.6889Å with bimorph mirrors and λ=0.4859Å without mirrors giving data to 0.48 and 0.38 Å resolution respectively. Details of the analysis of the topology of the electron density will be presented with the insights gained into the bonding in these unusual complexes.

Experimental charge density studies: Discard valid data and overfit?

In experimental charge density investigation it is indispensable to use the highest possible quality of data. Therefore the multiplicity should be as high as possible, but poor data should be omitted. To decide about resolution limit and discarding outlier data often limits for Rint or I/σ(I) are used. A better approach is the `paired refinement method' [1] comparing two data sets by the fit of the models derived by the same refinement protocol to both data sets. For macromolecular data sets it could be shown that a higher resolution should be used than normally derived from the above mentioned criteria. First results for charge density data seem to show the same tendency but of course on a different level. The paired refinement strategy can also be used to investigate the influence of different scaling methods. In a recent version of SADABS [2] a new error model and a 3λ correction is implemented. With the paired refinement strategy the improvement in data quality gets obvious. A further concern in charge density investigation is the question of overfitting. In macromolecular refinement this is answered by the Rfree concept [3]. Here a refinement protocol is developed by refining against a work set of reflections, e.g. 90 % of the data. The remaining reflections are untouched in the whole refinement process but an Rfree value is calculated using only this test set of reflections. An overfitting can clearly be identified by a decrease in Rwork but an increase in Rfree. This refinement protocol is then used for a final refinement against all data. It will be discussed how this method could support charge density studies.

Charge density analysis of paracetamol, acetotoluidine and methacetin

Paracetamol (p-hydroxyacetanilide, Pbca), acetotoluidine (p-methylacetanilide, P21/c) and methacetin (p-methoxyacetanilide, Pbca) contain acetamide group included in molecular fragments, which play an important role in many drugs and proteins. As all of them are derivatives of acetanilide used in medicine, and due to the presence of the amide bond, their charge density analysis is important for better understanding amide infinite peptide chains. Thus, comparing the data obtained for paracetamol with acetotoluidine and with methacetin charge density data can provide deeper insight into NH···O bonding. Another point of interest is the possibility of methyl group rotation that remains to be ambiguous in these acetanilide molecule based compounds. In the present study we have attempted to elucidate these problems using precise X-ray diffraction at 100K with subsequent charge density topological analysis. All charge density refinements were based on the Hansen and Coppens multipolar atom model. The topologies of the inter- and intramolecular interactions are carefully analyzed for compounds. The atomic charges, bond orders, and the electrostatic energy in molecules are discussed. The topological characteristics in the critical point of the NH···O bond of paracetamol, acetotoluidine and methacetin are shown in the table below. In contrast to similarity in NH···O bonds for all studied compounds, intermolecular interactions between the double bonded oxygen atom and the hydrogen of dimer's methyl group are different. In acetotoluidine and methacetin the (3, –1) critical points with the same topological characteristics were detected between these atoms. In comparison to them, paracetamol with disordered methyl group [1, 2] has no such point. That can be related to the absence of the methyl group disorder in acetotoluidine and methacetin.