Crystal Unit Research Articles

Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography.

A molecular dynamics (MD)-based pipeline has been designed and implemented to emulate the entire process of collecting diffraction photographs and calculating crystallographic structures of proteins from them. Using a structure of lysozyme solved in-house, a supercell comprising 125 (5 × 5 × 5) crystal unit cells containing a total of 1000 protein molecules and explicit interstitial solvent was constructed. For this system, two 300 ns MD trajectories at 298 and 250 K were recorded. A series of snapshots from these trajectories were then used to simulate a fully realistic set of diffraction photographs, which were further fed into the standard pipeline for structure determination. The resulting structures show very good agreement with the underlying MD model not only in terms of coordinates but also in terms of B factors; they are also consistent with the original experimental structure. The developed methodology should find a range of applications, such as optimizing refinement protocols to solve crystal structures and extracting dynamics information from diffraction data or diffuse scattering.

Density Functional Theory Study of Metal-Organic Frameworks for Enhancement of Photo-Anode Properties

The optoelectronic properties of dye zinc and titanium-based metal-organic framework (MOF) compounds with regard to their application as photo-anode material characterized in solar cells were investigated. Analyses of the optoelectronic properties were performed on the MOF single crystal unit cell with adsorbed dye to determine the electronic and optical properties of the relevant materials. The electronic and optical properties were predicted by density functional theory (DFT) calculations. The results show that the absorption of light occurs for the examined MoF compounds from the near UV to the (visible) blue spectral range, at optical band gap sizes from 2.8 eV up to 3.88 eV. Dye sensitization of MOF with eosin Y or crown ether gave additive UV-Vis spectra. An improvement in band gap or an improved electron injection could be archived as well. Moreover, the light absorption does not solely depend on the linkers used, but also from the metal atoms in the secondary building unit. The fluorescence of MOFs depends on the linker and especially on the linker coordination and their rotation relative to each other. The utilizations of MOFs and their derivatives as electrodes, photoactive materials, charge carriers and additives in different solar cells are highlighted.

ОПРЕДЕЛЕНИЕ ПАРАМЕТРОВ УРАВНЕНИЯ СОСТОЯНИЯ МОЛЕКУЛЯРНЫХ КРИСТАЛЛОВ НА ОСНОВЕ ДИФРАКТОМЕТРИЧЕСКИХ ИССЛЕДОВАНИЙ

The paper presents the results of determining the crystal structure of PETN, hexogen, and HMX samples by X-ray diffractometry and calculations of the unit cell parameters of molecular crystals associated with the processing of X-ray diffractometry results, and experimental relationships between the unit cell volumes of molecular crystals on temperature. The obtained experimental data on the isobaric compression and expansion of the studied molecular crystals allowed us to specify the thermal component of the equations of the state of molecular crystals and obtain an expression for the isobaric thermal expansion coefficient associated with the mathematical model of the thermal component of the equations of state of molecular crystals. The obtained analytical dependence of the isobaric coefficient of thermal expansion on the temperature of the considered samples correctly describes the limiting transition to low temperatures. We propose a method of approximation for the obtained experimental relationships between temperature and the unit cell volume of the studied substances under isobaric compression/expansion based on a mathematical model of the semi-empirical equations of state of molecular crystals. This approach allowed us to obtain analytical relationships between the crystal unit cell volume and temperature, which describes the results of X-ray diffractometry of the molecular crystal samples considered in the work with an accuracy of up to 3 %.

Geochronology, Geochemistry, and Geodynamic Implications of Permo-Triassic Back-Arc Basin Successions in the North Pamir, Central Asia

Abstract The Permo-Triassic period marks the time interval between Hercynian (Variscan) orogenic events in the Tien Shan and the North Pamir, and the Cimmerian accretion of the Gondwana-derived Central and South Pamir to the southern margin of the Paleo-Asian continent. A well-preserved Permo-Triassic volcano-sedimentary sequence from the Chinese North Pamir yields important information on the geodynamic evolution of Asia’s pre-Cimmerian southern margin. The oldest volcanic rocks from that section are dated to the late Guadalupian epoch by a rhyolite and a dacitic dike that gave zircon U-Pb ages of ~260 Ma. Permian volcanism was largely pyroclastic and mafic to intermediate. Upsection, a massive ignimbritic crystal tuff in the Chinese Qimgan valley was dated to 244.1±1.1 Ma, a similar unit in the nearby Gez valley to 245±11 Ma, and an associated rhyolite to 233.4±1.1 Ma. Deposition of the locally ~200 m thick crystal tuff unit follows an unconformity and marks the onset of intense, mainly mafic to intermediate, calc-alkaline magmatic activity. Triassic volcanic activity in the North Pamir was coeval with the major phase of Cimmerian intrusive activity in the Karakul-Mazar arc-accretionary complex to the south, caused by northward subduction of the Paleo-Tethys. It also coincided with the emplacement of basanitic and carbonatitic dikes and a thermal event in the South Tien Shan, to the north of our study area. Evidence for arc-related magmatic activity in a back-arc position provides strong arguments for back-arc extension or transtension and basin formation. This puts the Qimgan succession in line with a more than 1000 km long realm of extensional Triassic back-arc basins known from the North Pamir in the Kyrgyz Altyn Darya valley (Myntekin formation), the North Pamir of Tajikistan and Afghanistan, and the Afghan Hindukush (Doab formation) and further west from the Paropamisus and Kopet Dag (Aghdarband, NE Iran).

An experiment demonstrating the capability of a symmetrical layout type double crystal monochromator controlled using electronic cam technology

A demonstration test of a newly developed double crystal monochromator was performed on beamline BL06 in the NewSUBARU synchrotron radiation facility of Hyogo University. Due to the symmetrical layout of the 1st crystal and 2nd crystal units of the monochromator, a maximum rotation speed of the main axis of up to 5.0 degrees/sec could be achieved. The monochromator is controlled by a newly developed control board programmed with an electronic cam algorithm. The control system allows the speed of both Z1 and Z2 axes to be successively synchronized as the Bragg angle changes. The Z 1 and Z 2 axes are moved apart by equal amounts from the center of gravity of the monochromator as the Bragg angle is increased. Also, the speed at which the Z1 and Z2 axes are moved apart increases with larger Bragg angle. This newly developed monochromator can maintain a stable exit beam height just as well as previous mechanical cam type monochromators proved on the height of the exit beam measured by an encoder system and observed by fluorescent screen. Due to the symmetrical layout and newly developed control system, the monochromator is suitable for industrial use because it can handle a wide energy range and allows high-throughput experiments to be carried out.

Mechanical Properties Evaluation of Polymer-Binding C-S-H Structure from Nanoscale to Macroscale: Hydroxyl-Terminated Polydimethylsiloxane (PDMS) Modified C-S-H

Exploring and modifying the C-S-H structure at a micro-nano level is an effective solution to improve the performance of Portland cement. Compared with organics inserting C-S-H, the research on the performance of a polymer-binding C-S-H structure from nanoscale to macroscale is limited. In this work, the mechanical properties of a modified C-S-H, using hydroxyl-terminated polydimethylsiloxane (PDMS) as the binders, are evaluated. The PDMS-modified C-S-H structures are introduced into macro-defect-free cement to obtain stress-strain curves changes at a macro scale. The AFM-FM was adopted to measure the morphology and elastic modulus of C-S-H at a nano scale. The molecular dynamics (MD) simulation was performed to assess the toughness, tensile properties, and failure mechanism. The results show that the PDMS-modified C-S-H powders change the break process and enhance ductility of MDF cement. The elastic modulus of PDMS-modified C-S-H is lower than pure C-S-H. When PDMS molecules are located between the stacking crystal units, it can enhance the toughness of C-S-H aggregates. The PDMS-modified C-S-H stacking structure has better plasticity, and its tensile strains are higher than the pure C-S-H. PDMS molecules hinder the initial crack expansion, leading to the branching of the initial crack. In addition, the measurement of AFM-FM can identify and obtain the mechanical properties of basic units of C-S-H. This paper enhances the understanding of cement strength sources and modification methods.

Atomic structures of grain boundaries for Si and Ge: A simulated annealing method with artificial-neural-network interatomic potentials

To accurately predict low-energy structures for symmetric tilt grain boundaries (GBs) in Si and Ge, artificial-neural-network (ANN) interatomic potentials are constructed and are combined with a simulated annealing (SA) method based on molecular dynamics simulations. The ANN-driven SA method is demonstrated to predict GB structures that are in good agreement with previous electron microscopy observations, without prior knowledge about their atomic configurations. Their GB energies also reasonably agree with density-functional-theory (DFT) calculations. By contrast, a conventional empirical potential fails to predict those GB structures. For misorientation angles 2θ≥93.37°, the lowest-energy structures are found to contain atomic configurations that cannot be reproduced by one repeat unit of the perfect crystal along the tilt axis. Such GB structures cannot be obtained using the γ-surface method, although it is most commonly used for exploring low-energy GB structures. These results highlight the importance of using simulation cells with multiple repeat units along the tilt axis and of performing the SA method with high-accuracy interatomic potentials transferable to GBs.

An integrated process for struvite recovery and nutrient removal from ship domestic sewage

Marine pollution caused by the untreated and substandard discharge of ship domestic sewage has received widespread attention. A novel integrated process for struvite recovery and nutrient removal from ship domestic sewage (SRNR-SDS) based on seawater magnesium source was developed in this study. Removal efficiencies of the total nitrogen (TN) and total phosphorus (TP) for the activated sludge unit in SRNR-SDS process were approximately 67.61% and 41.35%, respectively, under the salinity of 7.85 g/L. The coupling-induced struvite crystallization unit significantly improved the removal efficiency of TN and TP, and the scanning electron microscopy and X-ray diffraction demonstrated that magnesium ammonium phosphate (MAP) crystals were successfully formed on the surface of zeolite. The SRNR-SDS process had an ideal performance for pollutant removal and MAP recovery under the optimal hydraulic retention time of 20 h. The effluent concentrations of COD, NH4+-N, TN and TP in SRNR-SDS process were approximately 34.73 mg/L, 4.31 mg/L, 10.07 mg/L and 0.23 mg/L, respectively, which meet the Chinese and international ship sewage discharge standards. SRNR-SDS process has obvious environmental, social and economic benefits, which could save 6.20%∼57.14% of the operation cost of ship domestic sewage treatment via MAP recovery. The results could provide theoretical and technical support for the development and application of ship sewage treatment process with the functions of pollutant removal and resource recovery.

Structure and function of the NS5 methyltransferase domain from Usutu virus

Usutu virus (USUV), is a mosquito-borne flavivirus currently spreading outside the African continent producing substantial avian mortality. In contrast, infected humans could exhibit mild neurological symptoms or remain asymptomatic. As in other flaviviruses, the capped USUV genome encodes three structural and seven non-structural (NS) proteins. Among the NS proteins, NS5 plays crucial roles in virus replication, harbouring the capping and methyltransferase (MTase) activities in its N-terminal domain and the RNA-dependent RNA polymerase (RdRP) activity at the C-terminus. In this work, we present the first structural and functional characterization of the USUV MTase domain. The first structure of the USUV MTase has been determined in complex with its natural ligands (S-adenosyl-L-methionine [SAM]) and S-adenosyl-L-homocysteine [SAH]) at 2.2 Å resolution, showing a molecular dimer in the crystal asymmetric unit. One molecule is bound to the methyl donor SAM while the second is bound to the reaction by-product SAH. Both molecules are almost identical and also show a high structural similarity to the MTase domains of other flaviviruses. The structure of the USUV MTase bound to the inhibitor sinefungin at 1.8 Å resolution is also described. Careful comparisons of the interactions in the SAM-binding cavity prompt us to hypothesize about the strength and weakness of the structure-based design of antivirals directed to the SAM/SAH binding site that could be effective to deal with this threat.

Life cycle assessment for waste acid treatment in zinc smelting

Lift cycle assessment (LCA) methodology was applied to evaluating and comparing two waste acid disposal processes in zinc smelting. The results indicate that environmental impacts of gas—liquid vulcanization technologies are human toxicity, abiotic depletion potential, and global warming risk, which are mainly caused in neutralizing— evaporating—crystallization unit and electrodialysis unit. As for traditional lime neutralization method, vulcanization unit is the main factor. In this regard, the total environmental impact of traditional lime neutralization method is much higher than that of gas—liquid vulcanization technologies. Furthermore, the sensitive analysis shows that electricity and sodium sulfide (60%) are sensitive factors in two waste acid disposal technologies. In addition, the total cost of disposing a functional unit waste acid in traditional lime neutralization process is nearly 27 times that of the gas—liquid vulcanization waste acid disposal technologies.

Correcting π-delocalisation errors in conformational energies using density-corrected DFT, with application to crystal polymorphs

We consider several molecules characterised by π-electron conjugation whose extent changes along a flexible torsional coordinate, and which represent the monomer units of polymorphic molecular crystals. Delocalisation error in density functional theory (DFT) adversely impacts conformational energies in these species, overstabilising the conformation that maximises conjugation length and leading to incorrect relative energies for the corresponding crystal polymorphs. We demonstrate that density-corrected (DC-)DFT, in which a DFT exchange-correlation functional is evaluated using a Hartree–Fock density, significantly reduces these conformational energy errors. When DC-DFT monomer energies are used as a low-cost intramolecular correction to a periodic DFT calculation of the molecular crystal, the resulting relative polymorph energies are within 1 kJ/mol of benchmark results.

Design and Robustness Evaluation of Valley Topological Elastic Wave Propagation in a Thin Plate with Phononic Structure

Based on the concept of band topology in phonon dispersion, we designed a topological phononic crystal in a thin plate for developing an efficient elastic waveguide. Despite that various topological phononic structures have been actively proposed, a quantitative design strategy of the phononic band and its robustness assessment in an elastic regime are still missing, hampering the realization of topological acoustic devices. We adopted a snowflake-like structure for the crystal unit cell and determined the optimal structure that exhibited the topological phase transition of the planar phononic crystal by changing the unit cell structure. The bandgap width could be adjusted by varying the length of the snow-side branch, and a topological phase transition occurred in the unit cell structure with threefold rotational symmetry. Elastic waveguides based on edge modes appearing at interfaces between crystals with different band topologies were designed, and their transmission efficiencies were evaluated numerically and experimentally. The results demonstrate the robustness of the elastic wave propagation in thin plates. Moreover, we experimentally estimated the backscattering length, which measures the robustness of the topologically protected propagating states against structural inhomogeneities. The results quantitatively indicated that degradation of the immunization against the backscattering occurs predominantly at the corners in the waveguides, indicating that the edge mode observed is a relatively weak topological state.

Pressure effect on lidocaine conformational equilibria in scCO2: A study by 2D NOESY

The work reports the results of an analysis of the lidocaine molecule conformational behavior in a supercritical carbon dioxide medium. Based on the nuclear Overhauser effect spectroscopy (2D NOESY) data, the authors determine the fractions of lidocaine molecule conformers in scCO2 at temperatures and pressures exceeding the critical point (308.15 K; 10–20 MPa). The paper also shows the effect of conformational inversion for this system at 308.15 K and 22 MPa. Since lidocaine polymorphic transformations can be accompanied by changes in the molecule conformation in the crystal elemental unit cell, it is quite urgent to determine the conformer fractions of this compound.

Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of new 2-oxo-1,2-dihydroquinoline-4-carboxylate derivative

• A new 2-oxo-1,2-dihydroquinoline-4-carboxylate derivative has been synthesized. • It is characterized using NMR spectroscopy and X-ray crystallography. • Intercontacts between crystal units are identified by Hirshfeld surface analysis. • Good correlations are obtained between the X-ray data with the predicted ones. Prop-2-ynyl 6‑chloro-1,2-dihydro-2-oxo-1-(prop‑2-ynyl)quinoline-4-carboxylate was synthesized by an alkylation reaction under phase transfer catalysis (PTC) conditions. This compound was characterized through 1 H- and 13 C NMR spectroscopy and single crystal X-ray diffraction techniques. The crystal belongs to the monoclinic space group C2/c. The lattice parameters obtained are: a = 22.3050(12) Å, 11.9577(6) Å, c = 13.4295(7) Å, α = 90°, β = 124.939(2)°, γ = 90° and Z = 4. In addition, Hirshfeld surface analysis (2D and 3D) was performed to understand the different intermolecular interactions in the crystal structure and to determine the percentage contributions of these interactions on the surface. Theoretical calculations were carried out using Density functional theory (DFT) to develop optimized geometry and frontier molecular orbital analysis.

Isothermal crystallization of polyhydroxyalkanoate (PHA) utilizing Raman spectroscopy to follow chain packing as well as molecular motion

Raman spectra of bioplastic poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHx at 13.8 % Hx) were recorded between −250 cm−1 and 3200 cm−1 during isothermal crystallization at 25⁰C after quenching from the melt in liquid nitrogen. At room temperature the crystallization proceeds slowly, so spectra were recorded over a 14-hour period. While there are spectral changes throughout the spectrum, the focus was on interpretable bands known to be sensitive to crystalline form. These bands included the carbonyl band that sharpens and shifts, a pair of bands on the high energy side of the carbon-hydrogen stretch, and a low frequency band that we assign to the molecular phonon in the crystal unit cell. After appropriate pre-processing of the spectra, they were further analyzed by 2D-COS (two-dimensional correlation spectroscopy) that provides determination of the order in which the polymer functional regions assemble into the crystalline state. According to this analysis one of the methyl CH’s interacts with the carbonyl bond to produce a line at 3000 cm−1. Following that, multiple changes appear in the carbonyl region, the strong CH band at 2930 cm−1 of the crystalline phase grows, then the 80 cm−1 phonon band, and the splitting of the methyl CH only appears after the phonon. From this sequence one can derive a picture of how the polymer unit locks into the crystal form. This can be of interest to commercialization of the materials because mechanical properties are intimately controlled by the crystallinity of the material. By understanding how the crystallization process proceeds, it can be engineered to be “fit for purpose” for a polymer targeted for a specific use.

Morpho-Structural Investigations and Carbon Nanoclustering Effects in Cr-Al-C Intermetallic Alloys.

Intermetallic Cr-Al-C thin films from the 211 class of MAX phases were fabricated via ion beam deposition and structural investigations were undertaken to obtain information about morpho-structural effects propelled by carbon excess in the stoichiometry of the films. In order to promote the occurrence of the Cr2AlC MAX phase, the stoichiometric thin films were subsequently annealed at two temperature values: 650 °C and 700 °C in UHV conditions for 30 min. The morpho-structural effects in both as-deposited and annealed films were monitored using scanning electron microscopy, X-ray diffraction, and Raman spectroscopy. XRD analysis showed that the as-deposited sample was almost completely crystallized in the hexagonal Cr2AlC structure, with a remaining amorphous fraction of about 17%, most probably rich in carbon. Raman analysis allowed the identification of three spectral regions, two of them encompassing the Raman optical modes belonging to the Cr2AlC 211 MAX phase, while the third one gave strong evidence of highly intense and large D- and G-bands of carbon. Structural parameters such as the crystal lattice parameters as well as the volume of the crystal unit cell were found to decrease upon annealing; this decrease is attributed to the grain growth. The average crystallite dimension was proven to increase after annealing, while the lattice micro-strain lowered to approximately 63% in the annealed thin film compared to the as-deposited one. Well-formed and intense Raman peaks attributed to D- and G-bands of carbon were also observed and, corroborated with the structural data, seemed to indicate an overall increased level of crystal ordering as well as potential carbon nanoclustering after thermal treatments with thin Cr2AlC films. This observed phenomenon concords with previously documented reports on ab initio modelling of possible Cr2AlC structures with carbon excess.

Enabling the drug combination of celecoxib through a spherical co-agglomeration strategy with controllable and stable drug content and good powder properties

Combining celecoxib with other chemopreventive drugs is a promising method of chemoprevention for cancer, especially for colorectal cancer. However, the traditional drug combination approaches are restricted with high-cost apparatus, complex and numerous unit operations. This work aims to develop an efficient spherical co-agglomeration strategy for celecoxib in combination with lovastatin, which can achieve drug combination in a single crystallization unit. The ternary solvent system was determined based on molecular simulation, and then a stable spherical agglomeration process was developed through the design of molar fraction of anti-solvent (MFA) and stirring rate to produce spherical agglomerates with high sphericity (84.2–89.9 %) and narrow size distribution. On this basis, celecoxib-benzoic acid spherical co-agglomerates were designed to form a complete spherical co-agglomeration strategy, which includes solvent system selection, spherical agglomeration and spherical co-agglomeration. Finally, celecoxib-lovastatin spherical co-agglomerates with synergistic efficacy were successfully produced by this strategy, with controllable and stable drug content (fluctuation < 2.7 %), good powder properties, and improved tabletability.

A simple green synthesis of pure and sterling silver nanoparticles via pulsed laser ablation in deionized water: characterization and comparison

Pure silver (Ag) and its alloy nanoparticles (NPs) with intense and tunable SPR bands in the visible region are widely exploited for biosensors, information storage, and solar energy systems. Pure Ag and Sterling silver (Ag92.5Cu7.5) NPs were synthesized by the laser ablation method in deionized water using a pulsed Nd:YAG laser. The prepared NPs were characterized and compared for their structural, morphological, and optical properties. The x-ray diffraction (XRD) and selected area electron diffraction (SAED) results revealed that the NPs have polycrystalline nature with five lattice directions. The diffraction peak positions for Ag92.5Cu7.5 NPs exhibited an average redshift of 0.1 ̊ compared to pure Ag NPs due to the presence of copper atoms in the composite crystal unit cell structure. The formation of spherical NPs with an average size of 9.1 nm and 8.4 nm for Ag and Ag92.5Cu7.5 NPs was confirmed using transmission electron microscopy (TEM) and high-resolution TEM (HRTEM). It was found that the concentration of synthesized Ag92.5Cu7.5 alloy NPs was considerably higher than that of pure Ag NPs. Going from pure to alloy silver NPs, the wavelength of surface plasmonic resonance (SPR) peak shifted from 400 nm to 395 nm. The UV–vis absorption spectra at different aging times revealed that pure Ag colloidal solution is relatively stable. Both colloidal solutions exhibited a similar pattern of photoluminescence (PL) emission spectra with peaks in the blue region.

Recovery of Lithium Carbonate from Dilute Li-Rich Brine via Homogenous and Heterogeneous Precipitation.

An extensive experimental campaign on Li recovery from relatively dilute LiCl solutions (i.e., Li+ ∼ 4000 ppm) is presented to identify the best operating conditions for a Li2CO3 crystallization unit. Lithium is currently mainly produced via solar evaporation, purification, and precipitation from highly concentrated Li brines located in a few world areas. The process requires large surfaces and long times (18–24 months) to concentrate Li+ up to 20,000 ppm. The present work investigates two separation routes to extract Li+ from synthetic solutions, mimicking those obtained from low-content Li+ sources through selective Li+ separation and further concentration steps: (i) addition of Na2CO3 solution and (ii) addition of NaOH solution + CO2 insufflation. A Li recovery up to 80% and purities up to 99% at 80 °C and with high-ionic strength solutions was achieved employing NaOH solution + CO2 insufflation and an ethanol washing step.

Mechanochromism and crystallization-induced emission enhancement of carbazole derivatives with different terminal groups

Two D-A carbazole derivatives (TBCA and NCA) were synthesized to investigate the influence of terminal group on the photophysical and mechanofluorochromic (MFC) properties in solution and crystal state. Results suggest that TBCA with t-butylphenyl as terminal group has a slightly smaller optical bandgap than that of NCA with naphthyl as terminal group because NCA adopts a more distorted conformation. Both compounds exhibited crystallization-induced emission enhancement (CIEE). TBCA crystals are rod-like and emitted strong blue fluorescence and the lamellar NCA crystals have a red-shifted emission in comparison with that of TBCA. The single-crystal structure analysis indicates that the two molecules adopt a more distorted conformation in their crystal. CN⋯H–CC hydrogen bonds help TBCA molecules to form a 1D chain stacking, but no strong π-stacking between TBCA molecules exists. Obvious π-π interaction is present between the carbazole units in NCA crystal, which results in a longer emission wavelength that of TBCA. Furthermore, two compounds exhibited reversible MFC behaviors. Force stimuli promoted a larger bathochromic shift for TBCA than that of NCA because a more pronounced planarization for TBCA existed after force damaged ordered stacking in crystal.