SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Crystallographic database

163

CeB2O4F is the first cerium fluoride borate, which is exclusively built up of one-dimensional, infinite chains of condensed trigonal-planar [BO3](3-) groups. This new cerium fluoride borate was synthesized under high-pressure/high-temperature conditions of 0.9 GPa and 1450 °C in a Walker-type multianvil apparatus. The compound crystallizes in the orthorhombic space group Pbca (No. 61) with eight formula units and the lattice parameters a=821.63(5), b=1257.50(9), c=726.71(6) pm, V=750.84(9) Å(3), R 1=0.0698, and wR 2=0.0682 (all data). The structure exhibits a 9+1 coordinated cerium ion, one three-fold coordinated fluoride ion and a one-dimensional chain of [BO3](3-) groups. Furthermore, IR spectroscopy, Electron Micro Probe Analysis and temperature-dependent X-ray powder diffraction measurements were performed.

Concepts: Diffraction, Crystallography, Materials science, X-ray crystallography, Crystal system, Powder diffraction, Neutron diffraction, Crystallographic database

61

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Concepts: Protein, Protein structure, Amino acid, Crystal, Crystallography, Crystal system, Utility, Crystallographic database

42

Seven particles captured by the Stardust Interstellar Dust Collector and returned to Earth for laboratory analysis have features consistent with an origin in the contemporary interstellar dust stream. More than 50 spacecraft debris particles were also identified. The interstellar dust candidates are readily distinguished from debris impacts on the basis of elemental composition and/or impact trajectory. The seven candidate interstellar particles are diverse in elemental composition, crystal structure, and size. The presence of crystalline grains and multiple iron-bearing phases, including sulfide, in some particles indicates that individual interstellar particles diverge from any one representative model of interstellar dust inferred from astronomical observations and theory.

Concepts: Crystal, Atom, Solar System, Solid, Crystallographic database, Dust, Astronomical unit, Comet

33

After decades of vituperative debate over the classical or nonclassical structure of the 2-norbornyl cation, the long-sought x-ray crystallographic proof of the bridged, nonclassical geometry of this prototype carbonium ion in the solvated [C7H11](+)[Al2Br7](-) • CH2Br2 salt has finally been realized. This achievement required exceptional treatment. Crystals obtained by reacting norbornyl bromide with aluminum tribromide in CH2Br2 undergo a reversible order-disorder phase transition at 86 kelvin due to internal 6,1,2-hydride shifts of the 2-norbornyl cation moiety. Cooling with careful annealing gave a suitably ordered phase. Data collection at 40 kelvin and refinement revealed similar molecular structures of three independent 2-norbornyl cations in the unit cell. All three structures agree very well with quantum chemical calculations at the MP2(FC)/def2-QZVPP level of theory.

Concepts: Crystal, Crystallography, Molecule, Chemistry, Atom, Chemical bond, Solid, Crystallographic database

28

Porous coordination networks are materials that maintain their crystal structure as molecular “guests” enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Concepts: Crystal, Diffraction, Crystallography, Chemistry, Solid, X-ray crystallography, Powder diffraction, Crystallographic database

28

The origin of the narrow particle size distributions obtained in the oleic acid-based synthesis of hexagonal phase β-NaREF(4) nanocrystals (RE = Sm, Eu, Gd, Tb) has been investigated. Compared to the standard synthesis, the growth conditions were simplified by using small purified particles of either α-NaREF(4) (cubic phase) or β-NaREF(4) (hexagonal phase) as single-source precursors, thereby avoiding the complications arising from the simultaneous presence of molecular educts and intermediately formed small particles. The study shows that α-phase as well as β-phase particles grow by Ostwald-ripening but narrow particle size distributions of the β-NaREF(4) product particles are only obtained when α-phase precursor particles are employed. Since the small particles are also formed as intermediate products in the standard synthesis of β-NaSmF(4), β-NaEuF(4), β-NaGdF(4) and β-NaTbF(4) particles, their crystal phase is an important parameter to obtain a narrow size distribution in these systems.

Concepts: Crystal, Crystallography, Particle size distribution, Crystal system, Particle, Liquid crystal, Crystallographic database, Atomic packing factor

27

The enzymes LinBUT and LinBMI catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino-acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinBMI and its seven point mutants. The mutation analysis revealed that the seven amino-acid residues uniquely found in LinBMI were categorized into three groups based on the efficiency of the first-step (from β-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. The crystal structure analyses of the wild-type LinBMI and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinBMI. The dynamics simulation analyses of the wild-type LinBMI and LinBUT revealed that the entrance of the substrate access tunnel of LinBUT was more flexible than that of LinBMI, which could lead to the different efficiencies in the dehalogenation activity between these dehalogenases.

Concepts: Protein, Mutation, Enzyme, Crystal, Crystallography, Site-directed mutagenesis, Mutagenesis, Crystallographic database

27

Electron diffraction is a unique tool for analysing the crystal structures of very small crystals. In particular, precession electron diffraction has been shown to be a useful method for ab initio structure solution. In this work it is demonstrated that precession electron diffraction data can also be successfully used for structure refinement, if the dynamical theory of diffraction is used for the calculation of diffracted intensities. The method is demonstrated on data from three materials - silicon, orthopyroxene (Mg,Fe)(2)Si(2)O(6) and gallium-indium tin oxide (Ga,In)(4)Sn(2)O(10). In particular, it is shown that atomic occupancies of mixed crystallographic sites can be refined to an accuracy approaching X-ray or neutron diffraction methods. In comparison with conventional electron diffraction data, the refinement against precession diffraction data yields significantly lower figures of merit, higher accuracy of refined parameters, much broader radii of convergence, especially for the thickness and orientation of the sample, and significantly reduced correlations between the structure parameters. The full dynamical refinement is compared with refinement using kinematical and two-beam approximations, and is shown to be superior to the latter two.

Concepts: Crystal, Diffraction, X-ray, Crystallography, X-ray crystallography, Neutron diffraction, Crystallographic database, Electron diffraction

27

Only one crystal structure is currently available for tumor marker AKR1B10, complexed with NADP(+) and tolrestat, which is an aldose reductase inhibitor (ARI) of the carboxylic acid type. Here, the X-ray structure of the complex of the V301L substituted AKR1B10 holoenzyme with fidarestat, an ARI of the cyclic imide type, was obtained at 1.60 Å resolution by replacement soaking of crystals containing tolrestat. Previously, fidarestat was found to be safe in phase III trials for diabetic neuropathy and, consistent with its low in vivo side effects, was highly selective for aldose reductase (AR or AKR1B1) versus aldehyde reductase (AKR1A1). Now, inhibition studies showed that fidarestat was indeed 1300-fold more selective for AR as compared to AKR1B10, while the change of Val to Leu (found in AR) caused a 20-fold decrease in the IC(50) value with fidarestat. Structural analysis of the V301L AKR1B10-fidarestat complex displayed enzyme-inhibitor interactions similar to those of the AR-fidarestat complex. However, a close inspection of both the new crystal structure and a computer model of the wild-type AKR1B10 complex with fidarestat revealed subtle changes that could affect fidarestat binding. In the crystal structure, a significant motion of loop A was observed between AR and V301L AKR1B10, linked to a Phe-122/Phe-123 side chain displacement. This was due to the presence of the more voluminous Gln-303 side chain (Ser-302 in AR) and of a water molecule buried in a subpocket located at the base of flexible loop A. In the wild-type AKR1B10 model, a short contact was predicted between the Val-301 side chain and fidarestat, but would not be present in AR or in V301L AKR1B10. Overall, these changes could contribute to the difference in inhibitory potency of fidarestat between AR and AKR1B10.

Concepts: Amino acid, Crystal, Crystallography, Model theory, Aldose reductase, Crystallographic database, Aldo-keto reductase, Aldose reductase inhibitor

14

Stress relaxation in crystalline solids is mediated by the formation and diffusion of defects. Although it is well established how externally generated stresses relax, through the proliferation and motion of dislocations in the lattice, it remains relatively unknown how crystals cope with internal stresses. We investigate, both experimentally and in simulations, how highly localized stresses relax in 2D soft colloidal crystals. When a single particle is actively excited, by means of optical tweezing, a rich variety of highly collective stress relaxation mechanisms results. These relaxation processes manifest in the form of open strings of cooperatively moving particles through the motion of dissociated vacancy-interstitial pairs, and closed loops of mobile particles, which either result from cooperative rotations in transiently generated circular grain boundaries or through the closure of an open string by annihilation of a vacancy-interstitial pair. Surprisingly, we find that the same collective events occur in crystals that are excited by thermal fluctuations alone; a large thermal agitation inside the crystal lattice can trigger the irreversible displacements of hundreds of particles. Our results illustrate how local stresses can induce large-scale cooperative dynamics in 2D soft colloidal crystals and shed light on the stabilization mechanisms in ultrasoft crystals.

Concepts: Crystal, Crystal structure, Crystallography, Solid, Materials science, Crystallographic defect, Crystallographic database