Crystal Charge Density Research Articles

Unexpected Ag-H bond in the predictive silver hydride phase under high pressure

Silver, typically acknowledged for its inertness toward hydrogen under standard conditions, exhibits a noteworthy shift in reactivity under elevated pressures. Employing first-principles variable-composition evolutionary search calculations, our investigation unveils the presence of thermodynamically stable Ag-H compounds. A novel stoichiometry, Ag2H, characterized by P3¯m1 symmetry, emerges as the thermodynamically stable phase at 100 GPa. Notably, the trigonal-Ag2H phase at 100 GPa demonstrates both mechanical and dynamic stability, as ascertained through the computation of elastic constants and phonon dispersions, respectively. Examination of the electronic band structure and density of states manifests the metallic nature of the resulting Ag2H compound. A comprehensive analysis involving crystal orbital bond index, Bader charge, and charge density plots substantiates the ionic character of Ag2H, attributable to effective charge transfer from silver atoms to hydrogen. Furthermore, application of the Allen-Dynes modified McMillan equation indicates the absence of superconducting behavior in Ag-H systems at the elevated pressure of 100 GPa.

Investigation of Electronic Structure and Electrochemical Properties of Na2MnSiO4 as a Cathode Material for Na Ion Batteries

The polyanionic compound Na2MnSiO4 is regarded as one of the promising cathode materials for Na-ion batteries due to good specific capacity with its attractive prospect of utilization of two electrons in the redox processes. So, in this study, we have performed the thermodynamic and electronic structure analysis of Na2MnSiO4 using first principles density functional theory calculations. The intermediate ground state configurations for Na2MnSiO4of Na de-intercalation were found using the cluster expansion method and are used to obtain the 0 K voltage profile as a function of Na concentration. This material shows an average voltage of 4.2 V and the finite temperature analysis at 300 K using Monte Carlo simulations indicates that this material undergoes two phase mixing when desodiate beyond 1.5 Na/f.u. The chemical bonding interactions between the constituents are analyzed using the density of states, crystal orbital Hamilton population, charge density, charge transfer and electron localization function analyses. From these analyses we found that the interaction between Mn and O is iono-covalent and that between Si-O is mainly covalent in nature. The involvement of oxygen in the redox reaction apart from the transition metal is identified using the Bader charge analysis. Relevant Na diffusion pathways and their corresponding calculated energy barriers are compared with the partially Fe substituted Na2MnSiO4 to understand the effect of Mn-site substitution on the process of Na migration through this material.

Investigation on the interlayer coupling and bonding in layered nitride-halides ThNF and ThNCl.

Motivated by recent experimental observation [N. Z. Wang, et al., Inorg. Chem., 2019, 58, 9897], we investigated the electronic properties and chemical bonding in layered nitride-halide compounds ThNF and ThNCl using first-principles calculations to illustrate the interlayer interaction. The energy gaps and chemical valences of both compounds are in agreement with experimental data. The crystal orbital Hamiltonian population (COHP) and charge density differential analysis show that interlayer chemical bonding plays a more important role than that van der Waals interactions in ThNF and ThNCl, in contrast to isostructural ZrNCl and HfNCl. These results explain why it is difficult to intercalate ThNF and ThNCl with charged particles, as observed in experiments.

Doxycycline hydrate and doxycycline hydrochloride dihydrate – crystal structure and charge density analysis

Abstract High-resolution low-temperature X-ray diffraction experiments for doxycycline monohydrate and hydrochloride dihydrate have been performed. Translation-Libration-Screw (TLS) analysis for both crystal forms as well as the data from neutron diffraction experiment for hydrochloride combined with the Hansen-Coppens formalism resulted in precise charge density distribution models for both the zwitterionic monohydrate and a protonated hydrochloride crystal forms. Their detailed topological analysis suggested that the electron structure of doxycycline’s amide moiety undergoes significant changes during protonation due to formation of a very strong resonance-assisted hydrogen bond. A notably increased participation of amide nitrogen atom and hydrogen-accepting oxygen atom in the resonance upon doxycycline protonation was observed. A comparison of TLS- and neutron data-derived hydrogen parameters confirmed the experimental neutron data to be vital for proper description of intra- and inter-molecular interactions in this compound. Finally, calculated lattice and interaction energies quantified repulsive Dox-Dox interactions in the protonated crystal form of the antibiotic, relating with a good solubility of doxycycline hydrochloride relative to its hydrate.

Approaches to crystal structure landscape exploration.

Three approaches to the exploration of the crystal structure landscape are outlined. These are crystal structure prediction, non-ambient crystallography and charge density analysis.

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.

Nanoscale symmetry fluctuations in ferroelectric barium titanate, BaTiO3.

Crystal charge density is a ground-state electronic property. In ferroelectrics, charge is strongly influenced by lattice and vice versa, leading to a range of interesting temperature-dependent physical properties. However, experimental determination of charge in ferroelectrics is challenging because of the formation of ferroelectric domains. Demonstrated here is the scanning convergent-beam electron diffraction (SCBED) technique that can be simultaneously used for imaging ferroelectric domains and identifying crystal symmetry and its fluctuations. Results from SCBED confirm the acentric tetragonal, orthorhombic and rhombohedral symmetry for the ferroelectric phases of BaTiO3. However, the symmetry is not homogeneous; regions of a few tens of nanometres retaining almost perfect symmetry are interspersed in regions of lower symmetry. While the observed highest symmetry is consistent with the displacive model of ferroelectric phase transitions in BaTiO3, the observed nanoscale symmetry fluctuations are consistent with the predictions of the order-disorder phase-transition mechanism.

Atomic and Electronic Structures of WTe2 Probed by High Resolution Electron Microscopy and ab Initio Calculations

Transition metal dichalcogenides (TMDs) are a class of two-dimensional (2D) materials that have attracted growing interest because of their unique electronic and optical properties. Under ambient conditions, most TMDs generally exhibit 2H or 1T structures. Unlike other group VIb TMDs, bulk crystals and powders of WTe2 exist in a distorted 1T structure (Td) at room temperature and have semimetallic properties. There is so far a lack of direct atom-by-atom visualization, limiting our understanding of this distorted 2D layered material system. We present herein atomic resolution images of Td structured WTe2. The Td structure can be distinguished in the three major orientations along the [100], [010], and [001] zone axes. Subtle structural distortions are detected by atomic resolution imaging, which match well with the optimized structure relaxed by ab initio calculations. The calculations also showed that both crystal field splitting and charge density wave (CDW) interactions contribute to the stabilization ...

高電位鉄イオウタンパク質HiPIPの超高分解能結晶構造と電荷密度解析

高電位鉄イオウタンパク質HiPIPの超高分解能結晶構造と電荷密度解析

An investigation of the electron density of a Jahn-Teller-distorted Cr(II) cation: the crystal structure and charge density of hexakis(acetonitrile-κN)chromium(II) bis(tetraphenylborate) acetonitrile disolvate.

In the crystal structure of the title homoleptic Cr(II) complex, [Cr(CH3CN)6](C24H20B)2·CH3CN, the [Cr(CH3CN)6](2+) cation is a high-spin d(4) complex with strong static, rather than dynamic, Jahn-Teller distortion. The electron density of the cation was determined by single-crystal X-ray refinements using aspherical structure factors from wavefunction calculations. The detailed picture of the electronic density allowed us to assess the extent and directionality of the Jahn-Teller distortion of the Cr(II) cation away from idealized octahedral symmetry. The topological analysis of the aspherical d-electron density about the Cr(II) cation showed that there are significant valence charge concentrations along the axial Cr-N axes. Likewise, there were significant valence charge depletions about the Cr(II) cation along the equatorial Cr-N bonds. These charge concentrations are in accordance with a Jahn-Teller-distorted six-coordinate complex.

Tuning bulk and surface conduction in the proposed topological Kondo insulator SmB(6).

Bulk and surface state contributions to the electrical resistance of single-crystal samples of the topological Kondo-insulator compound SmB_{6} are investigated as a function of crystal thickness and surface charge density, the latter tuned by ionic liquid gating with electrodes patterned in a Corbino disk geometry on a single (100) surface. By separately tuning bulk and surface conduction channels, we show conclusive evidence for a model with an insulating bulk and metallic surface states, with a crossover temperature that depends solely on the relative contributions of each conduction channel. The surface conductance, on the order of 100 e^{2}/h, exhibits a field-effect mobility of 133 cm^{2}/Vs and a large carrier density of ∼2×10^{14} cm^{-2}, in good agreement with recent photoemission results. With the ability to gate modulate surface conduction by more than 25%, this approach provides promise for both fundamental and applied studies of gate-tuned devices structured on bulk crystal samples.

Host perturbation in a β-hydroquinone clathrate studied by combined X-ray/neutron charge-density analysis: implications for molecular inclusion in supramolecular entities.

X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.

Ab initio crystal structure and charge density distribution of a highly energetic 2,4-dinitrobenzoic acid molecule

The energetic parameters, such as density, bond strength, and sensitivity of explosives/ propellants decide their detonation power and safety. Experimentally, optimization of these parameters is found to be a difficult task; therefore, prior to synthesis, it makes sense to estimate these parameters by computational techniques, ab initio crystal structure prediction, and quantum chemical calculation coupled with the AIM analysis. Here, we predict the density of an energetic 2,4-dinitrobenzoic acid (DNBA) molecule from different ab initio crystal structure models and validate the results through comparisons with experimental data. The bond topological characterization reveals that the C NO2 bonds are the weakest bonds and are identified as sensitive bonds in the molecule. The bond sensitivity is estimated from Murray’s method. The impact sensitivity of this molecule is also calculated. Large negative electrostatic potential regions are found near the NO2 and carboxylic groups, which are the reactive sites of the molecule.

Interrelations between crystal architecture, charge density and energy of uracil derivatives

Interrelations between crystal architecture, charge density and energy of uracil derivatives

Convergent-beam electron diffraction

This paper reviews the convergent-beam electron diffraction (CBED) technique. Point- and space-group determination methods of ordinary crystals are described, along with an example of the determination method for Sr₃Ru₂O₇. The symmetry determination of one-dimensionally incommensurate crystals and quasicrystals is explained. The large-angle CBED technique, which is indispensable for lattice defect and lattice strain analysis, is also described. A real procedure for lattice strain analysis is provided, using an example of a multilayer Si₁-xGe(x)/Si material. A nanometer-scale crystal structure refinement method and charge density and crystal potential determination method by CBED are briefly described.

Mg-Al水滑石“记忆效应”及其对Cr(VI)阴离子吸附性能研究

Mg-Al hydrotalcite (MAH) with high crystallinity was prepared using urea method. The memory effect and the chromium(VI) adsorption property of Mg-Al Hydrotalcites were studied. The MAH, recon- structed MAH (RMAH), calcined MAH (MAO) and calcined RMAH (RMAO) were characterized by XRD, FT-IR, SEM and DSC as well as self-deconvolution analyses. The results showed that the MAH and RMAH possessed a layered structure of hydrotalcites with high crystallinity, and there was little difference in crystal structures and charge density of brucite-like sheets between MAH and RMAH. The brucite-like sheets were still held in MAO, and a little remained in RMAO with more MgAl2O4. The adsorbility of Mg-A1 LDOs(MAO and RMAO) to Cr(VI) anions was substantially higher than that of Mg-A1 LDHs(MAH and RMAH), mainly because of the structure memory effect of hydrotalcites. The adsorbility of the MAO was higher than that of the RMAO. The adsorbility decrease of the RMAO might be due to the increase of the content of spinel MgAl2O4 phase and the decline of brucite-like sheets in RMAO that resulted in the descent of the memory effect reconstruction property. This newly discovery for anionic clays is useful for the de- contamination of waste waters. The Mg-Al hydrotalcite can be considered as a potential material for sorption of anions in wastewater treatment systems.

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

Abstract Calcium borohydride Ca(BH4)2 is one of the promising new hydrogen storage materials because of its large amount of hydrogen desorption capability (9.6 mass%). The crystal structures of α-Ca(BH4)2 (space group: Fddd, lattice constants: a = 8.7782(2) A, b = 13.129(1) A, c = 7.4887(9) A) and β-Ca(BH4)2 (P42/m, a = 6.9509(5) A, c = 4.3688(3) A) were refined by synchrotron X-ray diffraction at 300 and 433 K, respectively. The unsolved structures of γ-Ca(BH4)2 (Pbca, a = 7.525(1) A, b = 13.109(2) A, c = 8.403(1) A) and Ca(BH4)2·H2O (Pnma, a = 8.200(1) A, b = 5.8366(7) A, c = 11.851(2) A) were determined. In α-, β- and γ-Ca(BH4)2 structures, six boron atoms around a calcium atom construct CaB6 octahedron. The polymorphism of Ca(BH4)2 is formed by the different connection with adjacent octahedrons sharing vertexes and edges of the CaB6 octahedron. Furthermore, the charge density distribution in α-Ca(BH4)2 was experimentally determined by maximum entropy method. It is clarified that the bonding nature in α-Ca(BH4)2 ionic crystal is constructed from Ca2+ cation and BH4− anion.

Determination of the crystal structure and charge density of (Ba 0.5Sr 0.5)(Co 0.8Fe 0.2)O 2.33 by Rietveld refinement and maximum entropy method analysis

The crystal structure and charge density of (Ba 0.5Sr 0.5)(Co 0.8Fe 0.2)O 2.33, a promising cathode material for solid oxide fuel cells with lower operating temperatures, were investigated by the Rietveld refinement method and the maximum entropy method (MEM) using neutron and synchrotron X-ray diffraction data. The crystal structure of (Ba 0.5Sr 0.5)(Co 0.8Fe 0.2)O 2.33 was refined by using the orthorhombic Pnma space group and the split atom model to cation sites. The occupancy of O1 ( 4 c ) and O2 ( 8 d ) sites are 0.59 and 0.87, respectively. From the MEM analysis, we found that (Ba 0.5Sr 0.5)(Co 0.8Fe 0.2)O 2.33 possessed both covalent and ionic bonds.

Perovskite-type hydrides – synthesis, structures and properties

Abstract The present study gives an overview of the fundamental material properties of perovskite-type hydrides. Formation ability of the perovskite-type hydrides has been reasonably explained on the basis of the geometric restrictions on the composed ions using the Goldschmidt tolerance factor. Characteristic crystal structures and charge density maps of the perovskite-type hydrides without/with transition metals, such as NaMgH3/CaNiH3, were also examined in detail to clarify the relationship between the structures (atomic and electronic) and the hydriding properties.

Crystal Structure and Charge Density Analysis of Li2NH by Synchrotron X‐Ray Diffraction.

AbstractFor Abstract see ChemInform Abstract in Full Text.