Eglė Šidlauskaitė, Andrius Merkys, Antanas Vaitkus
et al.
X-ray crystallography rarely captures chemical bonding between atoms of a structure in question. Most of the time distance-based heuristics are applied to establish the pairs of bonded atoms. One class of such heuristics depends on a set of bonding radii that estimate the idealised size of each chemical element in a bond. This publication describes an unsupervised workflow for deriving a bonding radii set from crystal structure data in the Crystallography Open Database.
Stasis Chuchurka, Milaim Kas, Andrei Benediktovitch
et al.
In this work, we extend the x-ray constrained wavefunction fitting approach, a key method in quantum crystallography for charge density reconstruction, to incorporate experimental observables beyond x-ray diffraction. Unlike traditional quantum crystallography methods, which are typically limited to molecules in their ground states, our approach integrates excited states. This advancement will enable simultaneous fitting of x-ray diffraction data alongside optical and x-ray spectroscopic data. We introduce a comprehensive theoretical framework that allows for the inclusion of any experimental observable as a constraint in wavefunction reconstruction. Furthermore, we provide detailed derivations and instructions for implementation of this method using two electronicstructure methods: a generalized Hartree-Fock method for excited states and the Coupled Cluster Equation-of-motion method.
In this paper, we introduce a comprehensive theoretical study to obtain an optimal highly sensitive fluidic sensor based on the one-dimensional phononic crystal (PnC). The mainstay of this study strongly depends on the high impedance mismatching due to the irregularity of the considered quasi-periodic structure, which in turn can provide better performance compared to the periodic PnC designs. In this regard, we performed the detection and monitoring of the different concentrations of lead nitrate (Pb(NO<sub>3</sub>)<sub>2</sub>) and identified it as being a dangerous aqueous solution. Here, a defect layer was introduced through the designed structure to be filled with the Pb(NO<sub>3</sub>)<sub>2</sub> solution. Therefore, a resonant mode was formed within the transmittance spectrum of the considered structure, which in turn shifted due to the changes in the concentration of the detected analyte. The numerical findings demonstrate the role of the different sequences such as Fibonacci, Octonacci, Thue–Morse, and double period on the performance of the designed PhC detector. Meanwhile, the findings of this study show that the double-period quasi-periodic sequence provides the best performance with a sensitivity of 502.6 Hz/ppm, a damping rate of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mn>5.9</mn><mo>×</mo><msup><mrow><mn>10</mn></mrow><mrow><mo>−</mo><mn>5</mn></mrow></msup></mrow></semantics></math></inline-formula>, a maximum quality factor of 8463.5, and a detection limit of 2.45.
Silicon nitride (Si<sub>3</sub>N<sub>4</sub>) possesses excellent mechanical properties and high thermal conductivity, which is an important feature in many applications. However, achieving the theoretically high thermal conductivity of Si<sub>3</sub>N<sub>4</sub> in practice is challenging. In this study, we adopted a first-principles calculation method to assess the effects of doping β-Si<sub>3</sub>N<sub>4</sub> and γ-Si<sub>3</sub>N<sub>4</sub> with carbon and oxygen atoms. Applying geometric structure optimization combined with calculation of the electronic phonon properties generated a stable doped structure. The results revealed that carbon and oxygen doping have little effect on the Si<sub>3</sub>N<sub>4</sub> unit cell size, but that oxygen doping increases the unit cell volume. Energy band structure and state density calculation results showed that carbon doping reduces the nitride band gap width, whereas oxygen doping results in an n-type Si<sub>3</sub>N<sub>4</sub> semiconductor. The findings from this study are significant in establishing a basis for targeted increase of the thermal conductivity of Si<sub>3</sub>N<sub>4</sub>.
Nohaila Rharmili, Omar Abdellaoui, Fouad Ouazzani Chahdi
et al.
The indoline portion of the title molecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C—H...O hydrogen bonds and C—H...π(ring), π-stacking and C=O...π(ring) interactions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (43.0%), H...C/C...H (25.0%) and H...O/O...H (22.8%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined molecular structure in the solid state.
We consider the finite alphabet phase retrieval problem: recovering a signal whose entries lie in a small alphabet of possible values from its Fourier magnitudes. This problem arises in the celebrated technology of X-ray crystallography to determine the atomic structure of biological molecules. Our main result states that for generic values of the alphabet, two signals have the same Fourier magnitudes if and only if several partitions have the same difference sets. Thus, the finite alphabet phase retrieval problem reduces to the combinatorial problem of determining a signal from those difference sets. Notably, this result holds true when one of the letters of the alphabet is zero, namely, for sparse signals with finite alphabet, which is the situation in X-ray crystallography.
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies, or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared to those of high-resolution x-ray crystal structures. Our current work investigates this result in more detail, and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and side chain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by x-ray crystallography at high-resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and x-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments.
Electromagnetic levitation (EML) was employed for studying the velocity and morphology of the solidification front as a function of undercooling of metallic materials. The limitation of the EML technique with respect to low melting alloys that emit outside the visible light spectrum was overcome by employing state-of-the-art high-speed mid-wavelength infrared cameras (MWIR cameras) with a photon detector. Due to the additional thermography contrast provided by the emission contrast of the solid and liquid phases, conductor, and semi-conductor, the pattern formation of Al-based alloys was studied in detail, revealing information on the nucleation, phase selection during solidification, and the influence of convection.
Peter V. Dubovskii, Kira M. Dubova, Gleb Bourenkov
et al.
Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from <i>Naja naja</i> cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both “water” and “membrane” conformations of the central loop (loop-2) were determined by X-ray crystallography. The “water” conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The “membrane” conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from <i>N. oxiana</i> (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step—the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their “water” NMR models. We found that the both toxins transform their “water” conformation of loop-2 into the “membrane” one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.
"Underlying the whole treatment is the assumption that the physical properties of a solid are closely related to its structure, and that the first step to understanding the physical properties is to understand the structure." Helen D. Megaw, Preface to Ferroelectricity in Crystals, Methuen & Co Ltd, London, 1957.
The use of computers and the role of women in radio astronomy and X-ray crystallography research at the Cavendish Laboratory between 1949 and 1975 have been investigated. We recorded examples of when computers were used, what they were used for and who used them from hundreds of papers published during these years. The use of the EDSAC, EDSAC 2 and TITAN computers was found to increase considerably over this time-scale and they were used for a diverse range of applications. The majority of references to computer operators and programmers referred to women, 57% for astronomy and 62% for crystallography, in contrast to a very small proportion, 4% and 13% respectively, of female authors of papers.
A large spherulite structure deteriorates the mechanical properties of crystalline polymers, and therefore various methods have been explored to increase primary nucleation density. Recently, chain-end modification has been proposed as an effective approach for regulating polymer crystal nucleation. However, the relevant nucleation mechanism still requires investigation. Therefore, in this work, 2-ureido-4[1H]-pyrimidinone (UPy) units, which can form stacks via quadruple hydrogen bonds with each other, are introduced as end groups for the preparation of interacting telechelic poly(butylene succinate) (PBS-UPy) oligomers with different molecular weights (<i>M</i><sub>n</sub>s). The crystallization, especially the nucleation behavior of PBS-UPy, is studied in detail by comparing with the corresponding pre-polymer, the hydroxyl-terminal PBS (PBS-OH). The thermal properties of PBS-UPy exhibit similar <i>M</i><sub>n</sub>-dependent tendency to those of PBS-OH, but with weaker total crystallization rate. The spherulite growth rate is significantly reduced, whereas the primary nucleation density is highly promoted, after introducing UPy groups. Further investigation reveals that the mechanism of UPy stacks’ influence on nucleation ability changes from inhibition to promotion with respect to <i>M</i><sub>n</sub>. Even under an inhibition of nucleation ability, the final nucleation density is obviously increased because of a significant decline of the growth rate. In addition, the change in the impact of UPy stacks on nucleation ability is speculated to originate from the memory expression feasibility of ordered conformation in the melt during crystallization.
Robert Bücker, Pascal Hogan-Lamarre, R. J. Dwayne Miller
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D ED), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
Tuan Thien Tran, Lukas Jablonka, Christian Lavoie
et al.
We demonstrate a novel approach for non-destructive in-situ characterization of phase transitions of ultrathin nickel silicide films using 3D medium-energy ion scattering. The technique provides simultaneously composition and real-space crystallography of silicide films during the annealing process using a single sample. We show, for 10 nm Ni films on Si, that their composition follows the normal transition sequence, such as Ni-Ni2Si-NiSi. For samples with initial Ni thickness of 3 nm, depth-resolved crystallography using a position-sensitive detector, shows that the Ni film transform from an as-deposited disordered layer to epitaxial silicide layers at a relatively low temperature of ~290 °C.
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures---in the root-mean-square deviations of the C$_α$ atomic positions, identities of core amino acids, backbone and sidechain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modelling protein cores as jammed packings of amino-acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to generate the packings. For an athermal protocol, we find that the average jammed packing fraction is identical to that observed in the cores of protein structures solved by x-ray crystallography. In contrast, highly thermalized packing-generation protocols yield jammed packing fractions that are even higher than those observed in NMR structures. These results indicate that thermalized systems can pack more densely than athermal systems, which suggests a physical basis for the structural differences between protein structures solved by NMR and x-ray crystallography.
In condensed matter theory many invaluable models rely on the possibility of subsuming fundamental particle interactions in constitutive relations for macroscopic fields in near equilibrium assemblies of particles. Should one wish to maintain relativistic covariance this substitution generates a problem that can only be addressed by expanding the dimension of the space-time base manifold (four) to that of its tangent bundle (eight). The linear vector space of the octonions over the real (or conceivably rational) field seem to offer definite advantages in doing this.
In order to make a rational design of magnesium alloys for bone repair, four kinds of Mg alloy ingots were prepared by vacuum induction furnace, namely Mg-3Zn-0.2Ca (wt.%) (ZX30), Mg-3Zn-0.8Zr (wt.%) (ZK30), Mg-3Zn-0.8Zr-0.3Sr (wt.%) (ZKJ300) and Mg-3Zn-0.8Zr-0.3Ca-0.3Ag (wt.%) (ZKXQ3000) alloys. The four ingots were extruded into bar materials through a hot-extrusion process under different temperatures with different extrusion ratios, the mechanical performances and the corrosion behaviors in the simulated body fluid (SBF) of the four alloys were investigated, and the mechanism of fracture and corrosion was characterized by scanning electron microscopy (SEM). The results showed the ultimate compressive strength (UCS) of all the alloys were found to be around 360 MPa, while ultimate tensile strengths (UTS) of ZKJ300 (334.61 ± 2.92 MPa) and ZKXQ3000 (337.56 ± 2.19 MPa) alloys were much higher than those of ZX30 (298.17 ± 0.93 MPa) and ZK30 (293.26 ± 2.71 MPa) alloys. The electrochemical noise and immersion tests in the SBF indicated that ZK30 alloy performed better in corrosion resistance.