Charge Density Analysis from X-Ray Diffraction

Alzheimer’s disease (AD) is the most devastating neurodegenerative disorder which alters the memory of a person. It is a common form of senile dementia characterized by memory loss, personal skills and disorientation. The current treatment for AD is fully focused to control the disease based on symptoms. Based on the tau hypothesis, GSK3β is an interesting drug target, this also alters the course of AD. The recent experimental report outlines that the indirubin derivatives inhibit GSK3β, however, the detailed binding mechanism of indrubin-GSK3β is not yet known. To understand the exact binding mechanism of indirubin derivatives in the active site of GSK3β, the molecular conformation, intermolecular interactions, charge density distribution, electrostatic properties and the stability were determined. To accomplish this, indirubin derivatives were screened via molecular docking and further molecular dynamics (MD) and QM/MM-based charge density analysis have been performed. The molecular docking was carried out to investigate the binding affinity and the intermolecular interactions of indirubin molecule in the active site of GSK3β. QM/MM based charge density (CD) analysis has been carried out to emphasize the nature of chemical bonding (topology of electron density) and the electrostatic properties of ligand in the binding pocket. We have performed the CD analysis of intermolecular interaction between indirubin-3-monoxime and the active site amino acids of GSK3β. Further, the stability of the molecule has been confirmed from the MD simulation and the binding free energy of the indirubin-3-monoxime-GSK3β complex has been determined using MM/PBSA method to validate the binding affinity of indirubin-3-monoxime.Communicated by Ramaswamy H. Sarma

Accurate powder diffraction experiment by synchrotron radiation has made progress on the charge density study by the Maximum Entropy Method (MEM). So far, our developed analytical method which is the combination of the MEM and Rietveld refinement, so called MEM/Rietveld method, has been successfully applied to the structure analysis of novel nano materials, ferroelectric materials, manganites and superconductors by synchrotron radiation powder data 1,2 . The obtained MEM charge density enabled us structure refinement as well as observation of interplays between atoms and molecules, such as, bonding nature, charge transfer and etc. The electrostatic potential based on the experimental charge density should be more informative to see the interaction between atoms and molecules. Recently, we have succeeded in developing electrostatic potential and electric field imaging based on MEM charge density analysis 3 . The visualized electrostatic potential of the typical ferroelectric material, tetragonal PbTiO3 has uncovered the feature of electronic polarization in Ti-O and Pb charge densities. In addition, the result shows very good agreement with that obtained from the ab initio calculation 4 . Very recently, we have also succeeded in visualization of charge order associated with orbital order in manganites 5 . Our new method is promising and extending potential of powder diffraction structure refinement. In the talk, the detail of the method and application to the study of the metal-insulator transition of -(BEDT-TTF)2I3 will be presented.

For Abstract see ChemInform Abstract in Full Text.

Crystal structure and charge density analysis of Ca(BH4)2

density distribution using the single crystal X-ray intensity data. The charge density of this material has been studied including and excluding the quasi-forbidden h+k +l = 4n+2 type reflections using the maximum entropy method (MEM). Both the pictorial and numerical results of the experimental electron density show mixed ionic and covalent character in InSb. The use of InSb as a thermoelectric material is supported through charge density analysis.

The compounds m‐Tolylacetic acid and 2‐amino‐4‐Picoline were used as a precursor to synthesize the molecular complex 2‐amino‐4‐methylpyridinium 2‐(3‐methylphenyl)‐acetate by means of proton transfer. High‐resolution X‐ray diffraction data were collected for the crystallized complex at 100 K. The structure was solved spherically and further an aspherical model refinement was performed using Hansen and Coppens multipole formalism. Topological properties using AIM analysis were carried out for the title compound to understand the atom–atom interactions and the strength of the bond. The structure exhibits interesting patterns of N–H…O and C–H…O hydrogen bonds. A pair of N–H…O hydrogen bonds links the anion and cation of the molecular complex generating an R22(8) ring motif. These ring motifs are linked to adjacent anions and cations through another intermolecular N–H…O hydrogen bond generating a bifurcated R22(8)ring motif. Hirshfeld surface analysis was carried out to understand the types of inter‐molecular interactions and their strengths.

A compact model is proposed to derive the charge density of the AlInSb/InSb HEMT devices by considering the variation of Fermi level, the first subband, the second subband and sheet carrier charge density with applied gate voltage. The proposed model considers the Fermi level dependence of charge density and vice versa. The analytical results generated by the proposed model are compared and they agree well with the experimental results. The developed model can be used to implement a physics based compact model for an InSb HEMT device in SPICE applications.

The article demonstrates an original, non-destructive technique that could be used to in situ monitor charge transport in organic light-emitting diodes. Impedance spectroscopy was successfully applied to determine an OLED’s charge carrier mobility and average charge density in the hole- and electron-transport layer in a range of applied voltages. The fabricated devices were composed of two commercially available materials: NPB (N,N′-di(1-naphthyl)-N,N′-diphenyl-(1,1′-biphenyl)-4,4′-diamine) and TPBi (2,2′,2″-(1,3,5-Benzinetriyl)-tris(1-phenyl-1-H-benzimidazole)) as hole- and electron-transport layers, respectively. By varying the thicknesses of the hole-transport layer (HTL) and the electron-transport layer (ETL), correlations between layer thickness and both charge carrier mobility and charge density were observed. A possibility of using the revealed dependencies to predict diode current–voltage characteristics in a wide range of applied voltage has been demonstrated. The technique based on a detailed analysis of charge carrier mobilities and densities is useful for choosing the appropriate transport layer thicknesses based on an investigation of a reference set of samples. An important feature of the work is its impact on the development of fundamental research methods that involve AC frequency response analysis by providing essential methodology on data processing.

Neutron powder diffraction study of methane hydrate by the Rietveld refinement and maximum entropy method

Contrary to the empirical Miedema and Hume-Rothery rules and a recent theoretical prediction, we report experimental evidence on the formation of Li-Cs alloys at very low pressure (>0.1 GPa). We also succeeded in synthesizing a pure nonstoichiometric and ordered crystalline phase from an approximately equimolar mixture and resolved its structure using the maximum entropy method. The new alloy has a primitive cubic cell with the Li atom situated in the center and the Cs at the corners. This structure is stable to at least 10 GPa and has an anomalously high coefficient of thermal expansion at low pressure. Analysis of the valence charge density shows that electrons are donated from Cs to the Li "p"-orbitals, resulting in a rare formal oxidation state of -1 for Li. The observation indicates the diversity in the bonding of the seeming simple group I Li element.

Adaptive estimated maximum-entropy distribution model

Charge density measurement in MgH2 by synchrotron X-ray diffraction

The maximum entropy method (MEM) has been used to determine electron density in superspace of incommensurately modulated chromium pyrophosphate from X-ray diffraction data measured by Palatinus et al. [(2006), Acta Cryst. B62, 556-566]. Chromium pyrophosphate, Cr(2)P(2)O(7), contains ordered regions (83% of the volume) and regions with disorder. Analysis of the MEM density has allowed the determination of the displacive modulation functions within ordered regions. The disordered regions can be described as the alternate occupation of two conformations of the pyrophosphate group and two positions of the chromium atom, with occupational probabilities that depend continuously on the phase of modulation t. A structure model based on the interpretation of the MEM density provides a fit to the diffraction data of the same quality as the model given by Palatinus et al. (2006). The failure to find a model that better fits the data is attributed to the intrinsic inaccuracy of approximately 0.01 A for positions derived from the MEM and to the difficulties in constructing an appropriate model for the anharmonic ADPs and their modulation functions from electron densities.

Lead‐free halide double perovskites have emerged as sustainable alternatives to toxic lead‐based materials for next‐generation photovoltaic (PV) and optoelectronic applications. In this study, a comprehensive first‐principles investigation is conducted on A 2 GeX 6 (A = K, Rb; X = Cl, Br) double perovskites to explore their structural, X‐ray diffraction, electronic, optical, mechanical, charge density, phonon, molecular dynamics (MD), thermal and energetic stability, thermodynamic, vibrational, and thermoelectric properties using density functional theory combined with SCAPS‐1D device simulations. All compounds exhibit excellent thermodynamic, mechanical, and dynamic stability, with negative formation energies and phonon spectra confirming the absence of imaginary frequencies. The bandgap values, ranging from 0.83 to 3.52 eV, can be tuned via halide and alkali substitutions, enabling both visible and UV light absorption. Optical analysis reveals strong absorption coefficients (∼10 5 cm −1 ), high dielectric constants, and favorable refractive indices, indicating efficient light‐harvesting capability. Charge density and MD analyses confirm robust Ge–X bonding and thermal resilience, maintaining structural integrity up to 1000 K. Thermodynamic and vibrational studies further validate their energetic stability, while thermoelectric evaluation suggests good potential for energy conversion. SCAPS‐1D simulations demonstrate promising device performance, achieving up to 22.3% power conversion efficiency for Rb 2 GeBr 6 with optimized absorber parameters. These findings establish A 2 GeX 6 double perovskites as nontoxic, structurally stable, and optoelectronically efficient candidates for future PV, thermoelectric, and optoelectronic devices.

Regioselectivity of reduction of nitro groups in 3, 5-dinitrosalicylic acid monohydrate explored by experimental and theoretical charge density analysis