SciCombinator

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

Concept: Powder diffraction

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

160

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Concepts: DNA, Diffraction, X-ray, Crystallography, X-ray crystallography, Powder diffraction, Neutron diffraction, Bragg's law

150

A series of new (E)-3(5)-[β-(aryl)-ethenyl]-5(3)-phenyl-1H-pyrazoles bearing fluorine atoms at different positions of the aryl group have been synthesized starting from the corresponding β-diketones. All compounds have been characterized by elemental analysis, DSC as well as NMR (¹H, (13)C, (19)F and (15)N) spectroscopy in solution and in solid state. Three structures have been solved by X-ray diffraction analysis, confirming the tautomeric forms detected by solid state NMR. The in vitro study of their inhibitory potency and selectivity on the activity of nNOS and eNOS (calcium-calmodulin dependent) as well as iNOS (calcium-calmodulin independent) isoenzymes is presented. A qualitative structure-activity analysis allowed the establishment of a correlation between the presence/ absence of different substituents with the inhibition data proving that fluorine groups enhance the biological activity. (E)-3(5)-[β-(3-Fluoro-4-hydroxyphenyl)-ethenyl]-5(3)-phenyl-1H-pyrazole (13), is the best inhibitor of iNOS, being also more selective towards the other two isoforms.

Concepts: DNA, Diffraction, X-ray, Chemical element, In vitro, X-ray crystallography, Bragg diffraction, Powder diffraction

150

A series of Fe(3+)-bearing Li7La3Zr2O12 (LLZO) garnets was synthesized using solid-state synthesis methods. The synthetic products were characterized compositionally using electron microprobe analysis and inductively coupled plasma optical emission spectroscopy (ICP-OES) and structurally using X-ray powder diffraction and (57)Fe Mössbauer spectroscopy. A maximum of about 0.25 Fe(3+) pfu could be incorporated in Li7-3x Fe x La3Zr2O12 garnet solid solutions. At Fe(3+) concentrations lower than about 0.16 pfu, both tetragonal and cubic garnets were obtained in the synthesis experiments. X-ray powder diffraction analysis showed only a garnet phase for syntheses with starting materials having intended Fe(3+) contents lower than 0.52 Fe(3+) pfu. Back-scattered electron images made with an electron microprobe also showed no phase other than garnet for these compositions. The lattice parameter, a 0, for all solid-solution garnets is similar with a value of a 0≈12.98 Å regardless of the amount of Fe(3+). (57)Fe Mössbauer spectroscopic measurements indicate the presence of poorly- or nano-crystalline FeLaO3 in syntheses with Fe(3+) contents greater than 0.16 Fe(3+) pfu. The composition of different phase pure Li7-3x Fe x La3Zr2O12 garnets, as determined by electron microprobe (Fe, La, Zr) and ICP-OES (Li) measurements, give Li6.89Fe0.03La3.05Zr2.01O12, Li6.66Fe0.06La3.06Zr2.01O12, Li6.54Fe0.12La3.01Zr1.98O12, and Li6.19Fe0.19La3.02Zr2.04O12. The (57)Fe Mössbauer spectrum of cubic Li6.54Fe0.12La3.01Zr1.98O12 garnet indicates that most Fe(3+) occurs at the special crystallographic 24d position, which is the standard tetrahedrally coordinated site in garnet. Fe(3+) in smaller amounts occurs at a general 96h site, which is only present for certain Li-oxide garnets, and in Li6.54Fe0.12La3.01Zr1.98O12 this Fe(3+) has a distorted 4-fold coordination.

Concepts: Spectroscopy, Diffraction, Crystallography, Chemical synthesis, X-ray crystallography, Powder diffraction, Neutron diffraction, Electron microprobe

147

One hundred years after the original formulation by Petrus J.W. Debije (aka Peter Debye), the Debye Scattering Equation (DSE) is still the most accurate expression to model the diffraction pattern from nanoparticle systems. A major limitation in the original form of the DSE is that it refers to a static domain, so that including thermal disorder usually requires rescaling the equation by a Debye-Waller thermal factor. The last is taken from the traditional diffraction theory developed in Reciprocal Space (RS), which is opposed to the atomistic paradigm of the DSE, usually referred to as Direct Space (DS) approach. Besides being a hybrid of DS and RS expressions, rescaling the DSE by the Debye-Waller factor is an approximation which completely misses the contribution of Temperature Diffuse Scattering (TDS). The present work proposes a solution to include thermal effects coherently with the atomistic approach of the DSE. A deeper insight into the vibrational dynamics of nanostructured materials can be obtained with few changes with respect to the standard formulation of the DSE, providing information on the correlated displacement of vibrating atoms.

Concepts: Time, Diffraction, Fundamental physics concepts, Laser, Temperature, Heat, Powder diffraction, Peter Debye

28

A Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method.

Concepts: Scientific method, Crystallography, Monte Carlo, Powder diffraction, Standard, Neutron diffraction, Bayes' theorem, Rietveld refinement

28

Much consideration has been given to the role of spin-orbit coupling (SOC) in 5d oxides, particularly on the formation of novel electronic states and manifested metal-insulator transitions (MITs). SOC plays a dominant role in 5d(5) iridates (Ir(4+)), undergoing MITs both concurrent (pyrochlores) and separated (perovskites) from the onset of magnetic order. However, the role of SOC for other 5d configurations is less clear. For example, 5d(3) (Os(5+)) systems are expected to have an orbital singlet with reduced effective SOC. The pyrochlore Cd2Os2O7 nonetheless exhibits a MIT entwined with magnetic order phenomenologically similar to pyrochlore iridates. Here, we resolve the magnetic structure in Cd2Os2O7 with neutron diffraction and then via resonant inelastic X-ray scattering determine the salient electronic and magnetic energy scales controlling the MIT. In particular, SOC plays a subtle role in creating the electronic ground state but drives the magnetic order and emergence of a multiple spin-flip magnetic excitation.

Concepts: Diffraction, X-ray, X-ray crystallography, Powder diffraction, Neutron diffraction, Excited state, Resonant inelastic X-ray scattering, Magnetic structure

28

Treatment of 3-(1-hexynyl)perylene with Co(2)(CO)(8) resulted in the formation of the dinuclear cobalt complex [Co(2)(CO)(6)(μ-η(2)-C(4)H(9)C[triple bond, length as m-dash]C-Per)] (Per = 3-perylenyl) (). The perylene derivatives 3-(2,3,5,6-tetrafluorophenyl)perylene (PerC(6)F(4)H) and 3-(2,3,5,6-tetrafluorophenyl)-9(10)hexylperylene (C(6)-PerC(6)F(4)H) were prepared and used to synthesize [AuR(CN(t)Bu)] (R = PerC(6)F(4)), [AuR(CN(C(6)H(2))-3,4,5-(OC(12)H(25))(3))] (R = PerC(6)F(4) (), R = C(6)-PerC(6)F(4) ()), trans-[PdR(PR'(3))(2)X] (R = PerC(6)F(4), R' = Ph, X = I ()); (R = C(6)-PerC(6)F(4), R' = Ph, X = I ()); (R = PerC(6)F(4), R' = Et, X = I ()); (R = C(6)-PerC(6)F(4), R' = Et, X = I ()); (R = PerC(6)F(4), R' = Ph, X = NCS ()), and trans-[Pd(PerC(6)F(4))(PEt(3))(2)X] (X = Br (); X = I ()). The molecular structure of complexes , , and has been determined by X-ray diffraction analysis. The perylenyl fragments of complexes or are essentially planar and make dihedral angles to the tetrafluorophenyl plane of 57.49° () and 77.75° (). No π-π stacking of perylenyl rings is observed in any of the three molecules, but shows association of two monomers (arranged almost antiparallel), with an AuAu distance of 3.114 Å. DFT calculations were performed on the absorption spectra of representative PerC(6)F(4)Y (Y = H, F, Au(CNMe), PtBr(PMe(3))(2) and PdBr(PMe(3))(2)). All complexes exhibit fluorescence associated with the perylene fragment with emission quantum yields, in solution at room temperature, in the range 0.20-0.90 and emission lifetimes ∼4 ns, and no significant differences in the emission maxima, due to an efficient electronic decoupling of the metal fragment from the HOMO and LUMO of the perylene chromophore. The latter is confirmed by DFT calculations.

Concepts: DNA, Protein structure, Diffraction, X-ray, Crystallography, Molecule, X-ray crystallography, Powder diffraction

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

Two novel bpy-bridged Co(II) Schiff base complexes have been synthesized by the hydro(solvo)thermal reactions of corresponding amino-acid-based Schiff bases, bpy and Co(NO(3))(2)·6H(2)O. The following formulae identify the two complexes: {[Co(napala)(bpy)(0.5)]·H(2)O}(n) () and [Co(napgly)(bpy)(0.5)](n) () [H(2)napala = N-(2-hydroxy-1-naphthylmethylidene)-d/l-alanine, H(2)napgly = N-(2-hydroxy-1-naphthylmethylidene)-glycine and bpy = 4,4'-bipyridine]. These two compounds have been characterized using single-crystal X-ray diffraction, infrared, powder X-ray diffraction, thermogravimetric analysis, optical spectra analysis, and magnetic measurement. Complex features an unprecedented threefold interpenetrated diamond network based on the fan-shaped Co(II)(4)(μ(2)-napala)(4) molecular square node and bpy linker, which represents the first example of 3D framework among the amino-acid-based Schiff base complexes with salicylaldehyde or its derivatives. In , adjacent Co(II) ions are bridged by μ(2)-napgly(2-) to form left- and right-handed [Co(II)(μ(2)-napgly)](n) helical chains. These two types of helical chains are sustained alternately by a symmetrical bpy co-ligand into a 2D grid-based layer. The solid-state fluorescence of complexes and are quenched almost completely compared with free mixed-ligands at room temperature. Moreover, magnetic studies show the dominant antiferromagnetic coupling between the Co(II) centers mediated by the syn-anti-COO(-)-bridges in both complexes.

Concepts: Electron, Diffraction, X-ray, Functional groups, Powder diffraction, Imine, Schiff base, Hugo Schiff