Crystal Unit Cell Research Articles

Contributions of higher-order proximal distribution functions to solvent structure around proteins.

The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.

Growth, structural, optical, z-scan, dielectric and mechanical studies of ethyl para-hydroxybenzoate crystal for optical applications

Ethyl substituted para-hydroxybenzoate known as ethyl para-hydroxybenzoate (EHB) organic single crystal is grown by solvent controlled slow evaporation system with methanol as a solvent. The grown EHB crystal unit cell geometry is investigated using a single crystal XRD system. The Plasma, Fermi and Penn energy analyses also the molecular electronic polarizabilities are evaluated by different methods such as Clausius-Mossotti, coupled dipole method and Lorentz relations. The optical absorption and transmittance spectrum are assessed by UV–visible spectrum. The different optical constants as wavelength cut-off range, optical energy gap, extinction and absorption coefficient, refractive index, the position of conduction and valance band, optical electronegativity, nonlinear absorption coefficient, etc are calculated. The dielectric nature and molecular orbital analysis are evaluated. From the z-scan analysis, third-order nonlinear optical assets are estimated.

Nanoparticles exploring the macroscopic world

Nanoparticles exploring the macroscopic world

Synthesis, identification, density functional and Hirshfeld surface studies of 2,2'-disulfanediylbis(tetrahydro-4H-cyclopenta[d][1,3,2]dioxaphosphole-2-sulfide).

The new compound 2,2'-disulfanediylbis (tetrahydro-4H-cyclo penta[d][1,3,2]dioxaphosphole 2-sulfide), the dimeric form of 2-mercaptotetrahydro-4H-cyclopenta[d] [1,3,2] dioxaphosphole 2-sulfide, has been synthesized and characterized by elemental analysis, molecular weight determination and spectral data (1 H-NMR, 13 C-NMR, 31 P-NMR, FTIR). The molecular geometry was confirmed by single X-Ray crystallography. The ground state property was examined by PBE0 and B3LYP density functionals using aug-cc-pV(Q+d)Z basis set in the gas phase and in DMSO solution. The preference of PBE0 functional was statistically established. Thermodynamic parameters and standard heat of dissociation reaction ( ) have been established. The calculated equilibrium constants at different temperatures reflect the stability of the dimer over the monomers at low temperatures and vice versa. Valency and Fukui indices calculations showed that the monomer is more reactive than the dimer. 2D-fingerprint revealed that, while the H…X; [X=H, O and S] nonbonding intermolecular interactions and reciprocals play a crucial role in strengthening of molecules packing in the crystal unit cell while the S…S ones contribute negatively on it.

INVERSE DESIGN OF PHONONIC CRYSTALS BY ARTIFICIAL NEURAL NETWORKS

Phononic crystals represent a special kind of artificial periodic composite materials. The peculiar band-gap characteristics provide potential applications in the vibration reduction, wave filtering, sound insulation and acoustic functional devices. However, how to accurately manipulate acoustic and elastic waves is a major challenge for designing phononic crystals. The conventional design method is based on matching the specific application requirements by analyzing and adjusting the geometrical and material parameters of the phononic crystal structures. This method has a low efficiency and can hardly achieve the optimal performance. An artificial neural networks inverse design method for muti-layered phononic crystals based on the Softmax logistic regression and the multi-task learing is proposed in this study. In the proposed method, the Softmax logistic regression is used to choose the material type and the multi-task learing is used to determine the material distribution for each area of the multi-layered structure, so the phononic crystal reverse design problem is transformed into the classification problem of multi-component materials for the unit cell by the proposed method. First, a large number of the samples for the topological structures are randomly generated. Second, the band-gap structures of the samples are obtained by parallel finite element calculation. After that, the relationship between the topological structures and the band-gaps are established by the neural networks. Finally, the trained neural network is ultimately employed to design a phononic crystal structure with the targeted band-gaps, that is, the targeted band gap is used as the input of the neural network, and the trained neural network will output the corresponding cell topology of the phononic crystal unit cell directly. The example shows that the proposed method can obtain one-dimensional (1D) phononic crystals with the targeted band-gaps for the specified application requirements quickly and efficiently. This method provides a new way for the inverse design of phononic crystals.

Spectra and nature of the electronic states of [1]Benzothieno[3,2-b][1]benzothiophene (BTBT): Single crystal and the aggregates.

Absorption, fluorescence, and phosphorescence spectra of single crystals of [1]benzothieno[3,2-b][1]benzothiophene (BTBT) and BTBT dispersed in frozen n-nonane, n-hexadecane, and dichloromethane matrices were studied at 5K. Observation of a new absorption band and related changes in the fluorescence to phosphorescence intensity ratio, when the concentration of BTBT in the matrix increased above 10-4M, indicated the presence of BTBT aggregates. Quantum-chemistry calculations performed for the simplest aggregate, isolated dimer, showed that its structure is similar to the "herringbone" element in the BTBT crystal unit cell and the lowest electronic excited singlet state of the dimer has the intermolecular charge-transfer character. A qualitatively different nature of this state in dimers and in crystals, when compared with the situation in BTBT monomer [locally excited (LE) state], is associated with a decrease in the intersystem crossing yield. The structured vibronic structure of phosphorescence spectra in the studied systems indicated LE character of the triplet states.

In‐doped LiCa2.98MgV3O12 rare‐earth‐free phosphor with a high photoluminescence quantum yield of 67.4%

AbstractRare earth resources applied in numerous novel materials, are increasingly scarce in worldwide. Meanwhile, great attention has been focused on the blue rare‐earth‐free fluorescent phosphors as an excitation source of near‐ultraviolet (NUV) chips, which are available in white‐light‐emitting diodes (WLEDs) that combined with yellow commercial phosphors. Many solutions have been found to improve the photoluminescence quantum yield (PLQY) of phosphor. In this study, we effectively increased PLQY by introducing indium ion to vanadate garnet phosphor forming a series of LiCa3−XMgV3O12: xIn3+ (x = 0.01, 0.02, 0.04, 0.06, 0.08, and 0.10). The resultant In‐doped vanadate garnet phosphors exhibit a relative increase in PLQY, and the optimal phosphors is LiCa2.98MgV3O12: 0.02In3+ with a PLQY as high as 67.4%. These In‐doped vanadate garnet phosphors have a broad emission at 480 under 320 nm where near UV‐light excitation. It is revealed that the distortion of V‐V and V‐O bond length in [VO4] crystal structure and unit cell volume data of phosphors have an extensive influence on PLQY. Therefore, these novel vanadate garnet phosphors can be the essential blue color choice for WLED devices application in illumination.

Quantum billiards with correlated electrons confined in triangular transition metal dichalcogenide monolayer nanostructures

Forcing systems through fast non-equilibrium phase transitions offers the opportunity to study new states of quantum matter that self-assemble in their wake. Here we study the quantum interference effects of correlated electrons confined in monolayer quantum nanostructures, created by femtosecond laser-induced quench through a first-order polytype structural transition in a layered transition-metal dichalcogenide material. Scanning tunnelling microscopy of the electrons confined within equilateral triangles, whose dimensions are a few crystal unit cells on the side, reveals that the trajectories are strongly modified from free-electron states both by electronic correlations and confinement. Comparison of experiments with theoretical predictions of strongly correlated electron behaviour reveals that the confining geometry destabilizes the Wigner/Mott crystal ground state, resulting in mixed itinerant and correlation-localized states intertwined on a length scale of 1 nm. The work opens the path toward understanding the quantum transport of electrons confined in atomic-scale monolayer structures based on correlated-electron-materials.

Influence of Calcination conditions on the Adsorption Properties of the Wasted Sea Shell to the Dibutyl phthalate

<p>The calcined clam seashell powders were applied as adsorbent to adsorb Dibutyl phthalate (DBP), from an aqueous solution. The influence of calcination conditions including temperature and time on its adsorption capability to DBP was investigated. The shell powders calcined at 500 oC had the best adsorption capability. As the calcination time extending under different temperatures, the adsorption capabilities showed the same tendency and reached peak values at the calcination time of 10mins. Calcination time extension also led to the increase of crystal unit cell Sizes of CaCO3 inside the clam seashells at the first 10mins and then decreased to the stable value, Correspondingly, the calcined shell specific surface areas decreased firstly to the minimum at 10mins and then gradually increased, as the calcination process lasting at 500oC. The maximum adsorption capability as 1.237mg/g, the lowest specific surface area as 14.2m2/g, and the largest unit cell size as 60.7nm of CaCO3 simultaneously exhibited at the calcination time of 10mins. The Freundlich isotherm model and the pseudo-second-order-kinetics model were appropriate for describing the adsorption isotherm and kinetics of DBP at 30oC, respectively. It is inferred that the interaction between calcined shell and DBP is chemical adsorption.</p>

Temperature-dependent crystal structure and structural evolution of poly(glycolide-co-lactide) induced by comonomeric defect inclusion/exclusion

Comonomeric defects can lead the semicrystalline polymers to form unique crystal structures; this offers potential way to tailor the microstructure and macroscopic property of polymers. However, the role of comonomeric defects in the crystal structure and structural evolution of copolymer is not well understood. Herein, we synthesized the poly (glycolide-co-lactide) (PGLA) copolymers with minor L-lactide (LA) units and investigated their crystallization kinetics, crystal structure, and thermally-induced structural evolution. Crystallization of PGLA is strongly influenced by copolymer composition and crystallization temperature (Tc). Crystallization rate of PGLA reduces with increasing the LA content and the PGLA cannot crystallize at high LA content (≥40%). LA units can be included in crystal lattice as defects during the crystallization of PGLA, which is kinetically-controlled and results in the enlargement of crystal unit cell. Inclusion of LA units in crystal lattice is favored at low Tc but unfavored at high Tc, causing the contraction of crystal unit cell with increasing Tc. The defect-rich crystals of PGLA formed at low Tc are metastable and transform into thermodynamically stable crystals upon heating and annealing. This study shed light on the role of comonomeric defects in the crystal structure and structural evolution of random copolymers.

Quantifying the data quality of focal series for inline electron holography

Inline electron holography, the recovery of amplitude and phase of an electron wave function having passed through a thin specimen from a focal series recorded in a transmission electron microscope is being applied in many labs worldwide. At medium range magnification (i.e. typically ≥0.8 nm where the lattice of small unit cell crystals such as silicon is not resolved), where the defocus needs to be varied over a rather large range of several hundred nm or even μm, the retrieval of low spatial frequency information is severely affected by the choice of experimental parameters as well as the way of data normalization. Methods to quantitatively analyze the reliability of phase maps obtained by inline electron holography are presented, and data recorded and processed in different ways are compared. While, even under optimized conditions, the phase reconstructed from an experimental focal series still lacks very low spatial frequency components, regularization schemes exist and are demonstrated to effectively hide artifacts associated with this lack of information.

Remote Temperature Sensor Based on Tamm Resonance

A highly-sensitive remote temperature sensor based on Tamm resonance is proposed using a one-dimensional photonic crystal. The proposed structure is prism/Ag/Toluene/SiO2 /(PSi1/PSi2)N/Si. The transfer matrix method is used to discuss the interaction between the structure and the S-polarization of the incident radiation waves. We optimized the structure by studying the effect of the incident angle, the thickness of the first and second layers of the photonic crystal unit cell, the porosity of them, and the thickness of the toluene layer. High sensitivity, high signal-to-noise ratio, and very low resolution are achieved due to the coupling between the porous silicon photonic crystal properties and Tamm resonance that makes it very distinguished compared to previous works.

Topological Rainbow Concentrator Based on Synthetic Dimension.

Synthetic dimension provides a new platform for realizing topological photonic devices. Here, we propose a method to realize a rainbow concentrator of topological photonic states based on the synthetic dimension concept. The synthetic dimension is constructed using a translational degree of freedom of the nanostructures inside the unit cell of a two-dimensional photonic crystal. The translational deformation induces a nontrivial topology in the synthetic dimension, which gives rise to robust interface states at different frequencies. The topological rainbow can trap states with different frequencies, controlled by tuning the spatial modulation of interface state group velocities. The operation frequency as well as the bandwidth of the topological rainbow can be easily tuned by controlling the band gap of the photonic crystal. The topological principle can be applied to photonic crystals of any symmetry and arbitrary material composition, as long as a complete band gap exists. This Letter provides a new and general scheme for the realization of a topological rainbow concentrator and will be useful for the development of topological photonic devices.

Changes of the TiO2 thin film electro-optical properties in the Ar and N2 glow discharge plasma due to effects of the electric field in plasma's sheath

Titanium dioxide thin films were prepared on glass substrates by spin-coating sol-gel method. The samples were exposed to the N2 and Ar glow discharge plasmas. The properties of the crystal structure and electro-optical features were measured. The average crystallite size of the thin films was decreased at 30% and 41% by the plasma of N2 and Ar, respectively. We showed the changes in the charge distribution of the crystal unit cells and the chemical bonds’ characteristics that lead to alteration of the single-oscillator parameters. Due to the N2 and Ar plasmas, the third-order nonlinear susceptibility in long-wavelength was increased about 25% and 123%, respectively. An alteration occurred in the optical band gap through TiN formation on the surface of the TiO2 thin film in the N2 plasma. This empirical study illustrated more considerable changes in TiO2/Ar thin film, due to the stronger electric field in the sheath of Ar plasma.

A SUPRAMOLECULAR STRUCTURE OF PHOSPHORYLATED N-PHENYL-1,2,4-TRIAZOLE- 3-THIONE AND ITS CRYSTAL SOLVATE

A comparative analysis of the molecular and crystal structures is performed for 5-[(diphenylphosphoryl) methyl]-4-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (1) in individual crystal (1a) and a crystal solvate with dimethylformamide (DMF) in the 1:1 ratio (1b). The crystals of both modifications have the identical geometries of the molecule of the key compound, and the crystals (despite their different crystal systems and unit cells parameters) are characterized by the formation of an identical one-dimensional supramolecular motif in them due to classical N–H...O hydrogen bonds and weaker noncovalent – C-H ... S interactions in crystal 1a and CH ... N in crystal 1b. A tetragonal packing of one-dimensional motifs oriented along the smallest unit cell parameter are observed in both cases. Solvate molecules are localized in zero-dimensional cavities in crystal 1b. Despite a denser molecular packing in crystal 1b, the solid-state phase transformation is observed for its polycrystalline sample, and the powder X-ray diffraction method shows that it partially transforms into form 1a with time. The latter form is characterized by a less dense molecular packing in the crystal.

Exploring CO2 @sI Clathrate Hydrates as CO2 Storage Agents by Computational Density Functional Approaches.

The formation of specific clathrate hydrates and their transformation at given thermodynamic conditions depends on the interactions between the guest molecule/s and the host water lattice. Understanding their structural stability is essential to control structure-property relations involved in different technological applications. Thus, the energetic aspects relative to CO2 @sI clathrate hydrate are investigated through the computation of the underlying interactions, dominated by hydrogen bonds and van der Waals forces, from first-principles electronic structure approaches. The stability of the CO2 @sI clathrate is evaluated by combining bottom-up and top-down approaches. Guest-free and CO2 guest-filled aperiodic cages, up to the gradually CO2 occupation of the entire sI periodic unit cells were considered. Saturation, cohesive and binding energies for the systems are determined by employing a variety of density functionals and their performance is assessed. The dispersion corrections on the non-covalent interactions are found to be important in the stabilization of the CO2 @sI energies, with the encapsulation of the CO2 into guest-free/empty cage/lattice being always an energetically favorable process for most of the functionals studied. The PW86PBE functional with XDM or D3(BJ) dispersion corrections predicts a lattice constant in accord to the experimental values available, and simultaneously provides a reliable description for the guest-host interactions in the periodic CO2 @sI crystal, as well as the energetics of its progressive single cage occupancy process. It has been found that the preferential orientation of the single CO2 in the large sI crystal cages has a stabilizing effect on the hydrate, concluding that the CO2 @sI structure is favored either by considering the individual building block cages or the complete sI unit cell crystal. Such benchmark and methodology cross-check studies benefit new data-driven model research by providing high-quality training information, with new insights that indicate the underlying factors governing their structure-driven stability, and triggering further investigations for controlling the stabilization of these promising long-term CO2 storage materials.

Prospects of Using Small Scale Testing to Examine Different Deformation Mechanisms in Nanoscale Single Crystals—A Case Study in Mg

The advent of miniaturised testing techniques led to excessive studies on size effects in materials. Concomitantly, these techniques also offer the capability to thoroughly examine deformation mechanisms operative in small volumes, in particular when performed in-situ in electron microscopes. This opens the feasibility of a comprehensive assessment of plasticity by spatially arranging samples specifically with respect to the crystal unit cell of interest. In the present manuscript, we will showcase this less commonly utilised aspect of small-scale testing on the case of the hexagonal metal Mg, where, besides dislocation slip on different slip planes, twinning also exists as a possible deformation mechanism. While it is close to impossible to examine individual deformation mechanisms in macroscale tests, where local multiaxial stress states in polycrystalline structures will always favour multiple mechanisms of plasticity, we demonstrate that miniaturised uniaxial experiments conducted in-situ in the scanning electron microscope are ideally suited for a detailed assessment of specific processes.

Analytical Approach to Screen Semiconducting MOFs Using Bloch Mode Analysis and Spectroscopic Measurements.

A rapid and simple analytical approach is developed to screen the semiconducting properties of metal organic frameworks (MOFs) by modeling the band structure and predicting the density of state of isoreticular MOFs (IRMOFs). One can consider the periodic arrangement of metal nodes linked by organic subunits as a 1D periodic array crystal model, which can be aligned with any unit-cell axis included in the IRMOF's primitive cubic lattice. In such a structure, each valence electron of a metal atom feels the potential field of the entire periodic array. We allocate the 1D periodic array in a crystal unit cell to three IRMOFs-n (n = 1, 8, and 10) of the Zn4O(L)3 IRMOF series and apply the model to their crystal lattices with unit-cell constants a = 25.66, 30.09, and 34.28 Å, respectively. By solving Schrödinger's equation with a Kronig-Penney periodic potential and fitting the computed energy spectra to IRMOFs' experimental spectroscopic data, we model electronic band structures and obtain densities of state. The band diagram of each IRMOF reveals the nature of its electronic structures and density of state, allowing one to identify its n- or p-type semiconducting behavior. This novel analytical approach serves as a predictive and rapid screening tool to search the MOF database to identify potential semiconducting MOFs.

The effects of strontium-doped bioactive glass and fluoride on hydroxyapatite crystallization

ObjectivesThis study investigated the effects of a new strontium-doped bioactive glass and fluoride on hydroxyapatite crystallization. MethodsWe designed an in vitro experiment with calcium phosphate (CaCl2·2H2O + K2HPO4 in buffer solution) with different concentrations of strontium-doped bioactive glass (1 mg/mL or 5 mg/mL), and different concentrations of fluoride (0 ppm, 1 ppm or 5 ppm). Tris-buffered saline served as negative control. After incubation at 37 ℃ for 48 h, the shape and organization of crystals were examined by transmission electron microscopy (TEM) and electron diffraction. Structure of the crystals was assessed by powder X-ray diffraction (P-XRD) and unit cell parameters were calculated. Characterization of the crystals were performed by Raman spectroscopy and Fourier Transform Infrared Spectroscopy (FTIR). ResultsTEM and selected-area electron diffraction revealed that the precipitates in all experimental groups were crystalline apatite. There was an interaction between strontium and fluoride with different concentrations on crystal thickness (p = 0.008). P-XRD indicated the formation of strontium-substituted-fluorohydroxyapatite and strontium-substituted-hydroxyapatite in the groups with both bioactive glass and fluoride. Expansion or contraction of crystal unit cell was influenced by the concentrations of strontium and fluoride. Raman spectra showed strong phosphate band at 960 cm−1 in all experimental groups and displayed no obvious shift. FTIR results confirmed the formation of apatite. ConclusionsThe results of this study suggest that strontium-doped bioactive glass and fluoride have synergistic effects on hydroxyapatite crystallization. Clinical SignificanceStrontium-doped bioactive glass and fluoride have synergistic effects on hydroxyapatite crystallization by producing strontium-substituted-hydroxyapatite and strontium-substituted-fluorohydroxyapatite with enhanced bioactivity and reduced solubility which could be beneficial for caries management.

Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals.

Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, alow-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.