Crystal structures of cubic nitroprussides: M[Fe(CN)5NO]·xH2O(M=Fe, Co, Ni). Obtaining structural information from the background

2007 ◽  
Vol 22 (1) ◽  
pp. 27-34 ◽  
Author(s):  
A. Gómez ◽  
J. Rodríguez-Hernández ◽  
E. Reguera
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Model ◽  
Structural Information ◽  
Structural Disorder ◽  
Crystal Water ◽  
Metal Centers ◽  
Charge Delocalization ◽  
Positional Disorder ◽  
Local Environments

A new structural model is proposed for cubic nitroprussides and the crystal structure for the complex salts of Fe(2+), Co(2+), and Ni(2+) refined in that model. In cubic nitroprussides the building unit, [Fe(CN)5NO]2−, and the assembling metal (M=Fe2+, Co2+, Ni2+), have ¾ occupancy with three formula units per cell (Z=3). This leads to certain structural disorder and to different local environments for the outer metal. The crystallographic results are supported by the Mössbauer and infrared data. The XRD powder patterns, index in a cubic cell (Fm3m space group), show a sinuous background because of diffuse scattering from positional disorder of the metal centers. Because of this, the crystal structures were refined allowing the metal centers to move from the (0,0,0) and (0,0,1/2) positions (away from positional symmetry restrictions). The refinement under these conditions leads to excellent agreement factors (Rwp, Rp, S), good pattern background fitting, and produced a refined structural model consistent with the crystal chemistry of nitroprussides. The studied materials are obtained as hydrates. On heating, the crystal water evolves, and below 100°C an anhydrous phase is obtained, preserving the framework of the original hydrates. The loss of the crystal water leads to cell contraction that represents around 2% of cell volume reduction. On cooling down from room temperature to 77 and 12 K, a slight expansion for the -M-N≡C-Fe-C≡N-M- chain length is observed, suggesting that at low temperature and reduction in the metals charge delocalization on the CN bridges takes place. For M=Fe and Co the crystal structure was also refined for the anhydrous phase at 12, 77, and 300 K.

scholarly journals Substitutions of Zr4+/V5+ for Y3+/Mo6+ in Y2Mo3O12 for Less Hygroscopicity and Low Thermal Expansion Properties

Materials ◽  
2019 ◽  
Vol 12 (23) ◽  
pp. 3945 ◽  
Author(s):  
Qiang Ma ◽  
Lulu Chen ◽  
Heng Qi ◽  
Qi Xu ◽  
Baohe Yuan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Expansion ◽  
Crystal Structures ◽  
Room Temperature ◽  
Crystal Water ◽  
Thermal Expansion Property ◽  
Expansion Property ◽  
Low Thermal Expansion ◽  
Substitution Content ◽  
Structure And Microstructure

In this investigation, ZrxY2−xVxMo3−xO12 (0 ≤ x ≤ 1.4) is developed and the effects of the substitutions of Zr4+/V5+ for Y3+/Mo6+ in Y2Mo3O12 on the hygroscopicity and thermal expansion property are investigated. For the smaller substitution content (x ≤ 0.5), their crystal structures remain orthorhombic, while there is crystal water still in the lattice. The linear coefficients of thermal expansions (CTEs), for x = 0.1, 0.3, 0.5, and 0.7, are about −4.30 × 10−6, −0.97 × 10−6, 0.85 × 10−6, and 0.77 × 10−6 K−1, respectively, from 476 to 773 K, which means that the linear CTE could be changed linearly with the substitution content of Zr4+/V5+ for Y3+/Mo6+ in Y2Mo3O12. As long as the substitution content reaches x = 1.3/1.4, almost no hygroscopicity and low thermal expansion from room temperature are obtained and are discussed in relation to the crystal structure and microstructure.

Structure of an aluminophosphate EMM-8: a multi-technique approach

2007 ◽  
Vol 63 (1) ◽  
pp. 56-62 ◽  
Author(s):  
Guang Cao ◽  
Mobae Afeworki ◽  
Gordon J. Kennedy ◽  
Karl G. Strohmaier ◽  
Douglas L. Dorset
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Solid State Nmr ◽  
Structural Information ◽  
Local Symmetry ◽  
Unit Cell ◽  
Local Environments ◽  
Synchrotron Powder Diffraction ◽  
The Relationship

The crystal structure of an aluminophosphate, EMM-8 (ExxonMobil Material #8), was determined in its calcined, anhydrous form from synchrotron powder diffraction data using the computer program FOCUS. A linkage of double four-ring (D4R) building units forms a two-dimensional framework with 12-MR and 8-MR channels, and differs from a similar SAPO-40 (AFR) framework only by the relationship between paired D4R units. Rietveld refinement reveals a fit of the model to the observed synchrotron data by R wp = 0.1118, R(F 2) = 0.1769. Local environments of the tetrahedral phosphorus and aluminium sites were established by solid-state NMR, which detects distinct differences between as-synthesized and calcined materials. Distinct, reversible changes in the local symmetry of the P and Al atoms were observed by NMR upon calcination and subsequent hydration. These NMR data provided important constraints on the number of tetrahedral (T) atoms per unit cell and the connectivities of the T atoms. Detailed local structural information obtained by solid-state NMR thereby guided the ultimate determination of the structure of AlPO EMM-8 from the powder data. Comparisons are made to the recently published crystal structure of the fluoride-containing, as-synthesized SSZ-51, indicating that the unit-cell symmetry, axial dimensions and framework structure are preserved after calcination.

scholarly journals ChemEnv: a fast and robust coordination environment identification tool

2020 ◽  
Vol 76 (4) ◽  
pp. 683-695 ◽  
Author(s):  
David Waroquiers ◽  
Janine George ◽  
Matthew Horton ◽  
Stephan Schenk ◽  
Kristin A. Persson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Open Source ◽  
Crystal Structures ◽  
Coordination Environment ◽  
Fast Implementation ◽  
Local Environments ◽  
Large Databases ◽  
Environment Identification ◽  
Web App ◽  
Identification Tool

Coordination or local environments have been used to describe, analyze and understand crystal structures for more than a century. Here, a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner, is presented. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can also be used through a web app available on http://crystaltoolkit.org through the Materials Project.

scholarly journals Exploring the Role of Crystal Water in Potassium Manganese Hexacyanoferrate as a Cathode Material for Potassium-Ion Batteries

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 895
Author(s):  
Polina A. Morozova ◽  
Ivan A. Trussov ◽  
Dmitry P. Rupasov ◽  
Victoria A. Nikitina ◽  
Artem M. Abakumov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Chemical Composition ◽  
Electrochemical Performance ◽  
Structural Model ◽  
Electrode Materials ◽  
Iron Oxidation ◽  
Specific Capacity ◽  
Potassium Ion ◽  
Potential Range ◽  
Crystal Water

The Prussian Blue analogue K2−δMn[Fe(CN)6]1−ɣ∙nH2O is regarded as a key candidate for potassium-ion battery positive electrode materials due to its high specific capacity and redox potential, easy scalability, and low cost. However, various intrinsic defects, such as water in the crystal lattice, can drastically affect electrochemical performance. In this work, we varied the water content in K2−δMn[Fe(CN)6]1−ɣ∙nH2O by using a vacuum/air drying procedure and investigated its effect on the crystal structure, chemical composition and electrochemical properties. The crystal structure of K2−δMn[Fe(CN)6]1−ɣ∙nH2O was, for the first time, Rietveld-refined, based on neutron powder diffraction data at 10 and 300 K, suggesting a new structural model with the Pc space group in accordance with Mössbauer spectroscopy. The chemical composition was characterized by thermogravimetric analysis combined with mass spectroscopy, scanning transmission electron microscopy microanalysis and infrared spectroscopy. Nanosized cathode materials delivered electrochemical specific capacities of 130–134 mAh g−1 at 30 mA g−1 (C/5) in the 2.5–4.5 V (vs. K+/K) potential range. Diffusion coefficients determined by potentiostatic intermittent titration in a three-electrode cell reached 10−13 cm2 s−1 after full potassium extraction. It was shown that drying triggers no significant changes in crystal structure, iron oxidation state or electrochemical performance, though the water level clearly decreased from the pristine to air- and vacuum-dried samples.

Reinvestigation of crystal structure and structural disorder of Ba3MgSi2O8

2009 ◽  
Vol 24 (3) ◽  
pp. 180-184 ◽  
Author(s):  
Tomoyuki Iwata ◽  
Tatsuya Horie ◽  
Koichiro Fukuda
Keyword(s):  
Crystal Structure ◽  
Structural Model ◽  
Rietveld Method ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Structural Disorder ◽  
Entropy Method ◽  
Reliability Indices ◽  
Distribution Maps ◽  
Atom Model

Crystal structure and structural disorder of Ba3MgSi2O8 were reinvestigated by laboratory X-ray powder diffraction. The title compound was found to be trigonal with space group P3m1, Z=1, and unit-cell dimensions a=0.561 453(4) nm, c=0.727 629(4) nm, and V=0.198 641(2) nm3. The initial structural model used for structure refinement was taken from that of glaserite (K3NaS2O8) and modified by a split-atom model. In the split-atom model, one of the two types of Ba sites and that of SiO4 tetrahedra were, respectively, positionally and orientationally disordered. The new crystal structure and structural disorder were refined by the Rietveld method. The maximum-entropy-method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The final reliability indices calculated from MPF were Rwp=6.52%, S=1.36, Rp=4.84%, RB=0.97%, and RF=0.52%. Details of the disorder structure of Ba3MgSi2O8 are shown in the three-dimensional and two-dimensional electron-density distribution maps determined by MPF.

scholarly journals ChemEnv : A Fast and Robust Coordination Environment Identification Tool

2019 ◽  
Author(s):  
David Waroquiers ◽  
Janine George ◽  
Matthew Horton ◽  
Stephan Schenk ◽  
Kristin Persson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Open Source ◽  
Crystal Structures ◽  
Coordination Environment ◽  
Fast Implementation ◽  
Local Environments ◽  
Large Databases ◽  
Environment Identification ◽  
Web App ◽  
Identification Tool

Coordination or local environments have been used to describe, analyze, and understand crystal structures for more than a century. Here, we present a new tool called <i>ChemEnv</i>, which can identify coordination environments in a fast and robust manner. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the <i>pymatgen</i> package and the software can as well be used through a web app available on http://crystaltoolkit.org through the Materials Project.

Crystal structures and thermal decomposition of permanganates AE[MnO4]2·n H2O with the heavy alkaline earth elements (AE=Ca, Sr and Ba)

2017 ◽  
Vol 72 (8) ◽  
pp. 555-562 ◽  
Author(s):  
Harald Henning ◽  
Jörg M. Bauchert ◽  
Maurice Conrad ◽  
Thomas Schleid
Keyword(s):  
Crystal Structure ◽  
Thermal Decomposition ◽  
Crystal Structures ◽  
Alkaline Earth ◽  
Earth Metal ◽  
Orthorhombic Space Group ◽  
Crystal Water ◽  
Space Group ◽  
The Third ◽  
Cation Exchange Column

AbstractReexamination of the syntheses and crystal structures as well as studies of the thermal decomposition of the heavy alkaline earth metal permanganates Ca[MnO4]2·4 H2O, Sr[MnO4]2·3 H2O and Ba[MnO4]2 are the focus of this work. As an alternative to the very inelegant Muthmann method, established for the synthesis of Ba[MnO4]2 a long time ago, we employed a cation-exchange column loaded with Ba2+ cations and passed through an aqueous potassium-permanganate solution. We later used this alternative also with strontium- and calcium-loaded columns and all the compounds synthesized this way were indistinguishable from the products of the established methods. Ca[MnO4]2·4 H2O exhibiting [CaO8] polyhedra crystallizes in the orthorhombic space group Pccn with the lattice parameters a=1397.15(9), b=554.06(4) and c=1338.97(9) pm with Z=4, whereas Sr[MnO4]2·3 H2O with [SrO10] polyhedra adopts the cubic space group P213 with a=964.19(7) pm and Z=4. So the harder the AE2+ cation, the higher its demand for hydration in aqueous solution. Consequently, the crystal structure of Ba[MnO4]2 in the orthorhombic space group Fddd with a=742.36(5), b=1191.23(7) and c=1477.14(9) pm with Z=8 lacks any crystal water, but contains [BaO12] polyhedra. During the thermal decomposition of Ca[MnO4]2·4 H2O, the compound expels up to two water molecules of hydration, before the crystal structure collapses after the loss of the third H2O molecule at 157°C. The crystal structure of Sr[MnO4]2·3 H2O breaks down after the expulsion of the third water molecule as well, but this already occurs at 148°C. For both the calcium and the strontium permanganate samples, orthobixbyite-type α-Mn2O3 and the oxomanganates(III,IV) AEMn3O6 (AE=Ca and Sr) remain as final decomposition products at 800°C next to amorphous phases. On the other hand, the already anhydrous Ba[MnO4]2 thermally decomposes to hollandite-type BaMn8O16 and BaMnO3 at 800°C.

Solving crystal structures inP1: an automated procedure for finding an allowed origin in the correct space group

2000 ◽  
Vol 33 (2) ◽  
pp. 307-311 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Model ◽  
Structure Refinement ◽  
Human Intervention ◽  
Space Group ◽  
Space Groups ◽  
Structure Solution ◽  
Actual Space ◽  
Complex Crystal

Crystal structure solution inP1 may be particularly suitable for complex crystal structures crystallizing in other space groups. However, additional efforts and human intervention are often necessary to locate correctly the structural model so obtained with respect to an allowed origin of the actual space group. An automatic procedure is described which is able to perform such a task, allowing the routine passage to the correct space group and the subsequent structure refinement. Some tests are presented proving the effectiveness of the procedure.

HRTEM of antigorite: The structure as a polysomatic series

1988 ◽  
Vol 46 ◽  
pp. 566-567
Author(s):  
Gerard E. Spinnler ◽  
Max T. Otten
Keyword(s):  
Crystal Structures ◽  
Structural Information ◽  
Structure Refinement ◽  
Structural Data ◽  
Structural Disorder ◽  
Fourier Synthesis ◽  
Flat Plates ◽  
Serpentine Minerals ◽  
Transmission Electron ◽  
Approximate Composition

Antigorite is one of the serpentine minerals, a group of 1:1 layer silicates with the approximate composition of Mg3Si2O5(OH)4. These minerals display an unusual variety of crystal structures even though they are almost identical in composition; chrysotile has an elongated-tube structure, lizardite occurs as flat plates, and antigorite has corrugates layers.The details of the crystal structures of the serpentine minerals are not completely known. Threedimensional structure refinements only exist for one- and two- layer lizardite. For antigorite, the only direct structural information consists of a two-dimensional Fourier synthesis of hOI diffractions. The lack of detailed structural data on these minerals arises from the complexity of the structures as well as the paucity of sufficiently large, well-formed single crystals. In addition, structural disorder is common in these minerals, making structure refinement difficult.High resolution transmission electron microscopy (HRTEM) has been used to study antigorite in order to discriminate among various structural models of antigorite and to characterize its microstructures

scholarly journals ‘All That Glitters Is Not Gold’: High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses

2021 ◽  
Vol 22 (13) ◽  
pp. 6830
Author(s):  
Sohini Chakraborti ◽  
Kaushik Hatti ◽  
Narayanaswamy Srinivasan
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structural Information ◽  
Protein Complexes ◽  
Structural Quality ◽  
Quality Metric ◽  
Global Quality ◽  
Standard Quality ◽  
Moderate Resolution

Our understanding of the structure–function relationships of biomolecules and thereby applying it to drug discovery programs are substantially dependent on the availability of the structural information of ligand–protein complexes. However, the correct interpretation of the electron density of a small molecule bound to a crystal structure of a macromolecule is not trivial. Our analysis involving quality assessment of ~0.28 million small molecule–protein binding site pairs derived from crystal structures corresponding to ~66,000 PDB entries indicates that the majority (65%) of the pairs might need little (54%) or no (11%) attention. Out of the remaining 35% of pairs that need attention, 11% of the pairs (including structures with high/moderate resolution) pose serious concerns. Unfortunately, most users of crystal structures lack the training to evaluate the quality of a crystal structure against its experimental data and, in general, rely on the resolution as a ‘gold standard’ quality metric. Our work aims to sensitize the non-crystallographers that resolution, which is a global quality metric, need not be an accurate indicator of local structural quality. In this article, we demonstrate the use of several freely available tools that quantify local structural quality and are easy to use from a non-crystallographer’s perspective. We further propose a few solutions for consideration by the scientific community to promote quality research in structural biology and applied areas.

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