Crystallographic Unit Research Articles

Biological control of crystallographic architecture: Hierarchy and co-alignment parameters

Mytilus edulis prismatic calcite and nacre layers exhibit a crystallographic structural hierarchy which differs substantially from the morphological hierarchy. This makes these biomaterials fundamentally different from classical crystalline materials. Morphological building units are defined by their surrounding organic matrix membranes, e.g. calcite fibers or nacre tablets. The crystallographic building units are defined by crystallographic co-orientation. Electron backscatter diffraction quantitatively shows how crystallographic co-orientation propagates across matrix membranes to form highly co-oriented low-mosaic composite-crystal grains, i.e. calcite fiber bundles with an internal mosaic spread of 0.5° full width at half maximum (FWHM) or nacre towergrains with an internal mosaic spread of 2° FWHM. These low-mosaic composite crystals form much larger composite-crystal supergrains, which exhibit a high mosaicity due to misorientations of their constituting calcite fiber bundles or nacre towergrains. For the aragonite layer these supergrains nucleate in one of three aragonite {110} twin orientations; as a consequence the nacre layer exhibits a twin-domain structure, i.e. the boundaries of adjacent supergrains exhibit a high probability for misorientations around the aragonite c-axis with an angle near 63.8°. Within the supergrains, the constituting towergrains exhibit a high probability for misorientations around the aragonite a-axis with a geometric mean misorientation angle of 10.6°. The calcite layer is composed of a single composite-crystal supergrain on at least the submillimeter length scale. Mutual misorientations of adjacent fiber bundles within the calcite supergrain are mainly around the calcite c-axis with a geometric mean misorientation angle of 9.4°. The c-axis is not parallel to the long axis of the fibers but rather to the (107) plane normal. The frequency distribution for the occurrence of misorientation angles within supergrains reflects the ability of the organism to maintain homoepitaxial crystallization over a certain length scale. This probability density is distributed log-normally which can be described by a geometric mean and a multiplicative standard deviation. Hence, those parameters are suggested to be a numerical measure for the biological control over crystallographic texture.

Crystallization control of etherethersulfone copolymers by regular insertion of an allyl functionality

Acyclic diene metathesis (ADMET) polymerisation and nucleophilic aromatic substitution polycondensation are used to synthesize alternating copolymers based on polyetherethersulfone (PEES) blocks. ADMET results in incorporation of trans-allyl groups with more than 94 to 98% selectivity. The resulting polymers have a Mw of up to 13600 g mol−1 and low dispersity (Đ = 1.1 to 1.4). Polycondensation, on the other hand, allows incorporation of either cis- or trans-allyl groups depending on the starting monomers. Molecular weights in the same range are obtained, but with much larger dispersity (up to 2.3), as expected. Characterization by differential scanning calorimetry and wide angle X-ray diffraction shows that incorporation of the cis group completely suppresses crystallization, whereas that of the trans group results in semi-crystalline polymers. Crystallinity is lost post-melting, but can be restored using appropriate solvent treatments. The crystal form changes with the length of the etherethersulfone (EES) group indicating that, when the repeat unit is small (containing a 4-ring etherethersulfone (EES) block), the allyl function is incorporated into the crystallographic repeat, whereas when the EES segment increases to eight rings, the allyl group is excluded from the crystal phase. Post-functionalization of the allyl group is demonstrated by using hydrogenation. The resulting polymer adopts a different crystal form for the 4-ring block, but the same crystal form for the 8-ring block, confirming the dependence on the block length for incorporation into the crystallographic repeat unit.

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Molecular replacement is a powerful method for determining macromolecular crystal structures. The method remains limited by the requirement for a template structure that is similar to the structure to be determined. Here we describe two approaches for carrying out molecular replacement with distant homology models, each approach bringing in new information about the structure to be determined.The first approach combines the power of Rosetta structure modeling with macromolecular structure determination. Rosetta and other tools from the structure-modeling field have optimized force fields that are focused on obtaining a physically plausible model. In contrast, crystallographic model-building tools focus on interpretation of patterns of density in an electron density map. As these sources of information are nearly orthogonal, putting them together can increase the range of cases where crystal structures of macromolecules can be determined. An easy-to-use tool has been developed in the Phenix crystallographic software system for carrying out extensive molecular replacement searches followed by model-building using both Rosetta and crystallographic tools. This mr_rosetta software is able to find solutions to challenging molecular replacement problems.The second approach takes advantage of the observation that many pairs of proteins have local structures that can be superimposed much more closely than can their complete structures. For example, a β-sheet in one protein may be locally similar to a sheet in another, but when the two structures are superimposed using all atoms, the sheets may be translated relative to each other. We have developed a method for applying local distortions to a structure (morphing it) using an electron density map to guide the distortions. This procedure allows local similarity to be maintained while global structure is changed. We show that morphing molecular replacement templates after placing them in their approximate locations in the crystallographic unit cell can greatly improve subsequent model-building.

Probing crystal structure and mesoscale assembly of cellulose microfibrils in plant cell walls, tunicate tests, and bacterial films using vibrational sum frequency generation (SFG) spectroscopy.

This study reports that the noncentrosymmetry and phase synchronization requirements of the sum frequency generation (SFG) process can be used to distinguish the three-dimensional organization of crystalline cellulose distributed in amorphous matrices. Crystalline cellulose is produced as microfibrils with a few nanometer diameters by plants, tunicates, and bacteria. Crystalline cellulose microfibrils are embedded in wall matrix polymers and assembled into hierarchical structures that are precisely designed for specific biological and mechanical functions. The cellulose microfibril assemblies inside cell walls are extremely difficult to probe. The comparison of vibrational SFG spectra of uniaxially-aligned and disordered films of cellulose Iβ nanocrystals revealed that the spectral features cannot be fully explained with the crystallographic unit structure of cellulose. The overall SFG intensity, the alkyl peak shape, and the alkyl/hydroxyl intensity ratio are sensitive to the lateral packing and net directionality of the cellulose microfibrils within the SFG coherence length scale. It was also found that the OH SFG stretch peaks could be deconvoluted to find the polymorphic crystal structures of cellulose (Iα and Iβ). These findings were used to investigate the cellulose crystal structure and mesoscale cellulose microfibril packing in intact plant cell walls, tunicate tests, and bacterial films.

Investigating the Gas Sorption Mechanism in an rht-Metal–Organic Framework through Computational Studies

Grand canonical Monte Carlo (GCMC) simulations were performed to investigate CO2 and H2 sorption in an rht-metal–organic framework (MOF) that was synthesized with a ligand having a nitrogen-rich trigonal core through trisubstituted triazine groups and amine functional groups. This MOF was synthesized by two different groups, each reporting their own distinct gas sorption measurements and crystal structure. Electronic structure calculations demonstrated that the small differences in the atomic positions between each group’s crystal structure resulted in different electrostatic parameters about the Cu2+ ions for the respective unit cells. Simulations of CO2 sorption were performed with and without many-body polarization effects and using our recently developed CO2 potentials, in addition to a well-known bulk CO2 model, in both crystallographic unit cells. Simulated CO2 sorption isotherms and calculated isosteric heats of adsorption, Qst, values were in excellent agreement with the results reported previousl...

Calculating NMR parameters in aluminophosphates: evaluation of dispersion correction schemes

Periodic density functional theory (DFT) calculations have recently emerged as a popular tool for assigning solid-state nuclear magnetic resonance (NMR) spectra. However, in order for the calculations to yield accurate results, accurate structural models are also required. In many cases the structural model (often derived from crystallographic diffraction) must be optimised (i.e., to an energy minimum) using DFT prior to the calculation of NMR parameters. However, DFT does not reproduce weak long-range "dispersion" interactions well, and optimisation using some functionals can expand the crystallographic unit cell, particularly when dispersion interactions are important in defining the structure. Recently, dispersion-corrected DFT (DFT-D) has been extended to periodic calculations, to compensate for these missing interactions. Here, we investigate whether dispersion corrections are important for aluminophosphate zeolites (AlPOs) by comparing the structures optimised by DFT and DFT-D (using the PBE functional). For as-made AlPOs (containing cationic structure-directing agents (SDAs) and framework-bound anions) dispersion interactions appear to be important, with significant changes between the DFT and DFT-D unit cells. However, for calcined AlPOs, where the SDA-anion pairs are removed, dispersion interactions appear much less important, and the DFT and DFT-D unit cells are similar. We show that, while the different optimisation strategies yield similar calculated NMR parameters (providing that the atomic positions are optimised), the DFT-D optimisations provide structures in better agreement with the experimental diffraction measurements. Therefore, it appears that DFT-D calculations can, and should, be used for the optimisation of calcined and as-made AlPOs, in order to provide the closest agreement with all experimental measurements.

A Novel Heterometallic Cluster-Based Coordinational Polymer with 2-[Bis-(2-hydroxy-ethyl)-Amino]-Ethanesulfonic Acid: Synthesis and Crystal Structure

A rare heterometallic cluster-based polymer [Cu4(Hbhea)4(μ 2-OCH3) K(CH3OH))] n ·(H2O) n (1) (H3bhea = 2-[bis-(2-hydroxy-ethyl)-amino]-ethanesulfonic acid), has been synthesized and structurally determined by single crystal X-ray diffraction, elemental analysis. Crystallographic unit of 1 consists of four Cu(II), four Hbhea ligands, one methanol molecule, one methanol anion, one K ion and one crystal lattice water and formed anion cluster [Cu4(Hbhea)4(CH3O)]− which further constructed a 3-D polymer by linking the six-coordination K ions.

Hingeless negative linear compression in the mechanochromic gold complex [(C6F5Au)2(μ-1,4-diisocyanobenzene)

The compression of a crystalline material under hydrostatic pressure always results in a reduction in volume of the solid, with the observed reduction typically occurring in all crystallographic cell parameters.1 However, there are a number of exceptional materials that have been shown to expand in a specific direction upon hydrostatic compression while maintaining a positive volume compression. The phenomenon of uni-or biaxial expansion under compression is known as negative linear compressibility (NLC).1 Rare examples of NLC have attracted attention recently owing to the potential applications in a range of materials, including body armor, artificial muscle actuators, and pressure sensors.2

Reinvestigation of Np2Se5: A Clear Divergence from Th2S5 and Th2Se5 in Chalcogen–Chalcogen and Metal–Chalcogen Interactions

Single crystals of Np2Se5 have been prepared through the reactions of Np and Se at 1223 K in an Sb2Se3 flux. The structure of Np2Se5, which has been characterized by single-crystal X-ray diffraction methods, crystallizes in the tetragonal space group P42/nmc. The crystallographic unit cell includes one unique Np and two Se positions. Se(1) atoms form one-dimensional infinite chains along the a and b axes with alternating intermediate Se-Se distances of 2.6489 (8) and 2.7999 (8) Å, whereas Se(2) is a discrete Se(2-) anion. Each Np is coordinated to 10 Se atoms and every NpSe10 polyhedron shares faces, edges, or vertices with 14 other identical metal polyhedra to form a complex three-dimensional structure. Np LIII-edge X-ray Absorption Near Edge Structure (XANES) measurements show a clear shift in edge position to higher energies for Np2Se5 compared to Np3Se5 (Np(3+)2Np(4+)Se(2-)5). Magnetic susceptibility measurements indicate that Np2Se5 undergoes a ferromagnetic-type ordering below 18(1) K. Above the transition temperature, Np2Se5 behaves as a paramagnet with an effective moment of 1.98(5) μB/Np, given by a best fit of susceptibilities to a modified Curie-Weiss law over the temperature range 50-320 K.

Incommensurate spin spiral of the geometrically-frustrated antiferromagnet CdCr2O4

CdCr2O4 is a cubic spinel with geometrically-frustrated antiferromagnetic interactions between Cr3+ ions. We investigated the structural and magnetic phase transitions in powder samples by using magnetization and neutron diffraction measurements. An antiferromagnetic phase transition was observed at TN = 8.1 K, below which the crystallographic unit cell was tetragonal (c < a = b). Its incommensurate antiferromagnetic ordering below TN resembles dimerized spin chains in the ab planes with the propagation vector k = (0, 0.088, 1). We argue that the Dzyaloshinskii-Moriya interaction and the magnetic frustration play important roles in establishing the observed magnetic ordering.

Synthesis, structure and electrochemistry behavior of a cobalt(III) compound with azide and methyl 2-pyridyl ketone semicarbazone ligands

An unprecedented cobalt(III) compound with methyl 2-pyridyl ketone semicarbazone (HL) and the auxiliary azide ligand, [Co(L)2] [Co(L)(N3)3] (1) was synthesized and further characterized crystallographically and spectroscopically. Compound 1 crystallizes in the triclinic system and space group of P-1 and its structure consists of two mononuclear crystallographic units with metal chromophore comprising two cobalt(III) centers revealing distorted octahedral geometries and formed by distinct ligands in the inner coordination spheres. Interestingly, compound 1 represents the first complex formed by two distinct mononuclear units involving this ligand. As consequence of various donor and acceptor groups in both crystallographic units, there are several strong NH⋯N and NH⋯O hydrogen bonding interactions interconnecting adjacent moieties, ultimately leading to a three-dimensional supramolecular network. Furthermore, the electrochemical behavior of the HL and compound 1 were investigated.

Neutron diffraction study on the magnetic structure of Fe2P-based Mn0.66Fe1.29P1−xSix melt-spun ribbons

We report on the magnetic and structural properties of Mn0.66Fe1.29P1−xSix melt-spun ribbons with 0.34≤x≤0.42 that are promising candidates for high-temperature magnetocaloric applications. A magnetic moment of up to 4.57μB/f.u. for x=0.34 indicates high magnetic density in the system, which is certainly advantageous for the magnetocaloric effects. Introducing site disorder at the 3g site by replacing 1/3 of Fe with Mn appears to enhance the magnetic interaction, while the strong magnetoelastic coupling is maintained. This site disorder also shows a stabilizing effect on the hexagonal crystal structure, which is maintained to a high Si content. The moment alignment within the crystallographic unit cell is also affected when the Si content is increased from x=0.34 to 0.42 in the Mn0.66Fe1.29P1−xSix compounds as the canting angle with respect to the c-direction increases.

X-ray diffraction analysis of secondary phases in zirconium alloys before and after neutron irradiation at the MARS synchrotron radiation beamline

To further advance understanding of microstructural evolution in zirconium alloys for high burnup applications in PWR, it is important to obtain precise characterizations of second-phase particles present in the bulk alloys as a function of the neutron-irradiation fluence.X-ray diffraction from a synchrotron radiation source (SOLEIL) was used to identify and follow the evolution of second-phase particles that are in very small volume fractions in two zirconium alloys: Zy-4 in stress-relieved metallurgical state before irradiation and Zr–1%Nb (M5®) in recrystallized metallurgical state before and after neutron irradiation. Despite the fact the neutron irradiated sample is not in the as-irradiated state due to a thermal treatment and creep test performed after irradiation, interesting results have been obtained on secondary phases using XRD techniques.Analyses have been performed at the MARS beamline, fully dedicated to advanced structural and chemical characterizations of radioactive matter.A first proof of the improvement brought by these new analyses performed at the MARS beamline is given with Zr(Fe, Cr)2 precipitates found in unirradiated Zy-4 alloy in stress relieved metallurgical state, highly textured and displaying significant residual stresses and numerous dislocations: lattice parameters, crystallite size and microstrains (line profile analysis using the Williamson–Hall method after correction for instrumental broadening) have been estimated with very good accuracy.Then, second phase particles of the Zr–1%Nb alloy (M5®) have been analyzed before and after irradiation. For the Zr(Fe, Nb)2 Laves phase, the diffraction line disappeared after neutron irradiation. For β-Nb phases, the evolution of diffraction peaks clearly show the convolution of two phenomena: in one hand slight decreases in Nb content for native β-Nb particles and on the other hand irradiation-enhanced precipitation of nano-sized needle-like β-Nb particles. To our knowledge, this is the first time that the crystallographic unit cell, lattice parameter and Nb content of the β-Nb irradiation-enhanced precipitates have been determined using synchrotron radiation on irradiated Zr–1%Nb (M5®) alloy.

Hydrophobic Interaction Drives Surface-Assisted Epitaxial Assembly of Amyloid-like Peptides

The molecular mechanism of epitaxial fibril formation has been investigated for GAV-9 (NH(3)(+)-VGGAVVAGV-CONH(2)), an amyloid-like peptide extracted from a consensus sequence of amyloidogenic proteins, which assembles with very different morphologies, "upright" on mica and "flat" on the highly oriented pyrolytic graphite (HOPG). Our all-atom molecular dynamics simulations reveal that the strong electrostatic interaction induces the "upright" conformation on mica, whereas the hydrophobic interaction favors the "flat" conformation on HOPG. We also show that the epitaxial pattern on mica is ensured by the lattice matching between the anisotropic binding sites of the basal substrate and the molecular dimension of GAV-9, accompanied with a long-range order of well-defined β-strands. Furthermore, the binding free energy surfaces indicate that the longitudinal assembly growth is predominantly driven by the hydrophobic interaction along the longer crystallographic unit cell direction of mica. These findings provide a molecular basis for the surface-assisted molecular assembly, which might also be useful for the design of de novo nanodevices.

On the Hydrogen Bonding Structure at the Aqueous Interface of Ammonium-Substituted Mica: A Molecular Dynamics Simulation

Molecular dynamics (MD) computer simulations were performed for an aqueous film of 3 nm thickness adsorbed at the (001) surface of ammonium-substituted muscovite mica. The results provide a detailed picture of the near-surface structure and topological characteristics of the interfacial hydrogen bonding network. The effects of deuterium=hydrogen isotopic substitution in N(H=D)4+ on the dynamics and consequently on the convergence of the structural properties have also been explored. Unlike many earlier simulations, a much larger surface area representing 72 crystallographic unit cells was used, which allowed for a more realistic representation of the substrate surface with a more disordered distribution of aluminium=silicon isomorphic substitutions in muscovite. The results clearly demonstrate that under ambient conditions both interfacial ammonium ions and the very first layer of water molecules are H-bonded only to the basal surface of muscovite, but do not form H-bonds with each other. As the distance from the surface increases, the H-bonds donated to the surface by both N(H=D)4+ and H2O are gradually replaced by the H-bonds to the neighbouring water molecules, with the ammonia ions experiencing one reorientational transition region, while the H2O molecules experiencing three such distinct consecutive transitions. The hydrated N(H=D)4+ ions adsorb almost exclusively as inner-sphere surface complexes with the preferential coordination to the basal bridging oxygen atoms surrounding the aluminium=silicon substitutions.

Atomic-layer synthesis and imaging uncover broken inversion symmetry in La2−xSrxCuO4films

Materials with broken inversion symmetry are of great interest for their exotic electronic properties but are relatively rare. We show here that even if a material is inversion-symmetric in the bulk form, in epitaxial thin films of the same compound the crystallographic unit cell can be quite asymmetric. To demonstrate this, we have used atomic layer-by-layer molecular beam epitaxy to synthesize La${}_{2\ensuremath{-}x}$Sr${}_{x}$CuO${}_{4}$ films with Sr-dopant atoms deposited above, below, or on both sides of each CuO${}_{2}$ layer. Surface x-ray diffraction experiments analyzed by the Coherent Bragg Rod Analysis (COBRA) method have been carried out in combination with energy-differential diffraction measurements to determine whether the actual Sr distribution coincided with the nominal one (that would be expected in absence of La-Sr interdiffusion). The differential approach minimizes the systematic errors, and the combination with COBRA is potentially capable to determine the concentration of atomic species on a monoatomic layer-by-layer basis. The results show that the concentration of Sr in La/Sr layers just above the CuO${}_{2}$ layers is much larger than in layers just below them, irrespective of the deposition sequence, and drastically breaking the inversion symmetry.

Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit

We performed molecular dynamics simulations for crystal structures of yeast F1-ATPase whose crystallographic unit contains two different states. One complex binds Pi in the βE subunit, and the other liberated it. In the latter structure, the position of central stalk is rotated +16° in the hydrolysis direction. Because single molecule experiments have proven that Pi release occurs at the βE subunit, and the γ subunit is rotated after ATP hydrolysis and Pi release, these structures are supposed to represent snapshots before and after Pi releases for the 40° substep, respectively.We describe how the F1-ATPase complex changes the structure after Pi release, based on the results of the MD simulations for yF1II and yF1I. Then, we propose a possible mechanism of the 40° rotation of the γ subunit.

Syntheses, structures and properties of two Cu complexes with 4-(1H-imidazol-4-ylmethyl)aminophthalic acid

Two temperature-dependent copper(II) complexes {[Cu(HL)][Cu(HL)(H2O)]} n (1) and {[Cu(HL)]·H2O} n (2) [H3L = 4-(1H-imidazol-4-ylmethyl)aminophthalic acid] have been synthesised under hydrothermal conditions. X-ray diffraction analysis reveals that complex 1 displays two crystallographic independent units, 1D chain and binuclear unit, respectively. The 1D chains and binuclear molecules are staggered arrangements along the c-axis in an (…ABAB…) fashion. When increasing the reaction temperature, complex 2 was obtained with only 1D chains structure. In addition, the magnetic property of complex 2 was studied, which indicates antiferromagnetic interactions between the neighbouring Cu(II) centres. The electrochemical and electrocatalytic properties of complex 2 have also been studied by modified glassy carbon electrode of 2.

Hydrazine-Processed Ge-Substituted CZTSe Solar Cells

The p-type Cu2ZnSn(SxSe1–x)4 (with x ≈ 0; CZTSe) thin-film solar cell absorber, made from earth-abundant elements, was substituted with Ge using a hydrazine-based mixed particle-solution approach for the film deposition. The crystallographic unit cell parameters of the absorber layer decrease with gradual incorporation of Ge. A solar cell fabricated from a 40% Ge-substituted absorber showed a 9.1% power conversion efficiency, a higher open-circuit voltage, and a wider band gap compared with the device based on the unsubstituted absorber layer. This result shows the possibility of substituting, using the hydrazine-processing approach, the metal site of CZTSe with Ge for further device optimization. One area for further improvement in the substituted absorber layer devices includes reduction of a ZnSe secondary phase, which was apparent in the higher-Ge-content films.

The crystallographic structure of Panicum Mosaic Virus (PMV).

The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.