Showing papers in "Zeitschrift Fur Kristallographie in 2019"

Stress, strain and Raman shifts

Abstract: Abstract The concept of the phonon-mode Grüneisen tensor is reviewed as method to determine the elastic strains across crystals from the changes in the wavenumbers of Raman-active phonon modes relative to an unstrained crystal. The symmetry constraints on the phonon-mode Grüneisen tensor are discussed and the consequences for which combinations of strains can be determined by this method are stated. A computer program for Windows, stRAinMAN, has been written to calculate strains from changes in Raman (or other phonon) mode wavenumbers, and vice-versa. It can be downloaded for free from www.rossangel.net.

Tetrachloromethane as halogen bond donor toward metal-bound halides

Abstract: Abstract Two annulated triazapentadiene systems, viz. 1,3,5,7,9-pentaazanona-1,3,6,8-tetraenate chloride complexes of PtII, form CCl4 solvates, containing the Cl3C–Cl···Cl–Pt halogen bonds. These halogen bonds are firstly reported type of Cl3C–Cl···Cl–M contacts. In the X-ray structures of two solvates different non-covalent interactions were detected and studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method at the M06/DZP-DKH level of theory. Estimated energies of these supramolecular contacts vary from 0.6 to 2.4 kcal/mol.

A first principle evaluation of the adsorption mechanism and stability of volatile organic compounds into NaY zeolite

Abstract: © 2019 Walter de Gruyter GmbH, Berlin/Boston 2019. Removal of volatile organic compounds (VOCs) from indoor or outdoor environments is an urgent challenge for the protection of human populations. Inorganic sorbents such as zeolites are a promising solution to tackle this issue. Using dispersion corrected periodic DFT calculations, we have studied the interaction between sodium-exchanged faujasite zeolite and a large set of VOCs including aromatics, oxygenates and chlorinated compounds. The computed interaction energies range from about -25 (methane) to -130 kJ/mol (styrene). Methane is by far the less interacting specie with the NaY zeolite. All other VOCs present interaction energies higher in absolute value than 69 kJ/mol. Most of them show a similar adsorption strength, between -70 and -100 kJ/mol. While the electrostatic interactions are important in the case of oxygenates and acrylonitrile, van der Waals interactions predominate in hydrocarbons and chlorides. By monitoring the variation of molecular bond lengths of the different VOCs before and after adsorption, we have then evaluated the tendency of adsorbate to react and form by-products, since a significant stretching would evidently lead to the activation of the bond. While hydrocarbons, tetrachloroethylene and acrylonitrile seem to be not activated upon adsorption, all oxygenates and 1,1,2-trichloroethane could possibly react once adsorbed.

Photocatalytic and antibacterial activities study of prepared self-cleaning nanostructure surfaces using synthesized and coated ZnO nanoparticles with Curcumin nanodispersion

Abstract: Abstract Zinc oxide nanoparticles had been synthesized and encapsulated using Curcumin nanoemulsions, Zn(Cur)O NPs, under subcritical water conditions. The effects of temperature (120, 140 and 160 °C) and pH values of the reaction solution (4, 7 and 10) on the particle size, grain size, cristallinity, specific surface area, band gap, Urbach energy, morphology, photocatalytic activity and antibacterial properties of the prepared Zn(Cur)O NPs were evaluated using XRD, FT-IR, SEM, EDX and UV-Vis spectroscopy analysis. The obtained results indicate that the prepared spherical and rod shapes Zn(Cur)O NPs had a crystallite size distribution of 10–100 nm. Furthermore, the results reveal that most uniform Zn(Cur)O NPs with highest photocatalytic activity, quantum yield (0.161 mol·m−2 s−1), specific surface area (242 m2/g), minimum band gap (2.62 eV) and Urbach energy (0.125 meV) were formed at 160 °C and natural pH. The highest antibacterial activities against both Gram positive and negative bacteria strains, were achieved using the synthesized Zn(Cur)O at 160 °C and basic pH(10).

Effect of shock waves on structural and dielectric properties of ammonium dihydrogen phosphate crystal

Abstract: Abstract In this research article, the authors pay attention to investigate the effect of structural and dielectric properties of ammonium dihydrogen phosphate (ADP) crystal under pre and post shock loaded conditions. A shock wave of Mach number 1.9 was utilized for the present investigation which was generated by a table-top pressure driven shock tube. The crystalline nature and grain size variations were estimated by powder X-ray diffraction technique. The grain size of post shock wave loaded ADP crystal is found to be larger than that of the pre shock wave loaded ADP crystal. The dielectric properties of the pre and post shock loaded crystals were analyzed by impedance analyzer as a function of frequency (1 kHz–1 MHz) at ambient temperature. The dielectric constant is observed to be varying from 346 to 362 at the frequency of 400 kHz for pre and post shock wave loaded ADP crystals, respectively. The obtained results suggest that shock waves can be an alternate tool to tailor the physical properties of materials without creating any change in the original crystal system and surface morphology.

Supramolecular association in the triclinic (Z′=1) and monoclinic (Z′=4) polymorphs of 4-(4-acetylphenyl)piperazin-1-ium 2-amino-4-nitrobenzoate

Abstract: Crystallography reveals two polymorphs for the salt [4-(4- acetylphenyl)piperazin-1-ium][2-amino-4-nitrobenzoate], a monoclinic form (2; modelled as P21/n with Z' = 4) formed directly from the reaction mixture, and a triclinic form (1; Z' = 1) isolated from recrystallisation. Relatively minor differences are noted in the conformations of the anions and of the cations, mainly relating to the twist of, respectively, the carboxylate groups and piperazin-1-ium rings with respect to the phenyl rings they are connected to. The key feature of the packing of both forms is the formation of charge-assisted ammonium-N‒H…O(carboxylate) hydrogen bonds which lead to cyclic 12-membered {...HNH...OCO}2 synthons in the case of 1 but, supramolecular chains in 2. The three-dimensional architecture in the crystal of 1 is further stabilised by amine-N‒H…O(nitro) and amine-N‒H…O(acetyl) hydrogen bonds, leading to double-layers in the bc-plane, which are linked along the a-axis by methylene-C10‒H…O(carboxylate) and -stacking interactions. The combination of ammonium-N‒H…O(carboxylate) and amine-N‒H…O(carboxylate, acetyl) hydrogen bonds consolidate the three-dimensional packing in the crystal of 2. The greater crystal density, packing efficiency and calculated lattice energy for 1 compared with 2, suggest the former to be the thermodynamically most stable crystal. An analysis of the Hirshfeld surfaces for 1 and 2 reveal distinctive features that differentiate between the constituents of the two forms and between the ions comprising the asymmetric unit of 2.

The impact of lattice vibrations on the macroscopic breathing behavior of MIL-53(Al)

Abstract: The mechanism inducing the breathing in flexible metal-organic frameworks, such as MIL-53(Al), is still not fully understood. Herein, the influence of lattice vibrations on the breathing transition in MIL-53(Al) is investigated to gain insight in this phenomenon. Through solid-state density-functional theory calculations, the volume-dependent IR spectrum is computed together with the volume-frequency relations of all vibrational modes. Furthermore, important thermodynamic properties such as the Helmholtz free energy, the specific heat capacity, the bulk modulus, and the volumetric thermal expansion coefficient are derived via these volume-frequency relations using the quasi-harmonic approximation. The simulations expose a general volume-dependency of the vibrations with wavenumbers above 300 cm(-1 )due to their localized nature. In contrast, a diverse set of volume-frequency relations are observed for vibrations in the terahertz region (<300 cm(-1) ) containing the vibrations exhibiting collective behavior. Some terahertz vibrations display large frequency differences over the computed volume range, induced by either repulsion or strain effects, potentially triggering the phase transformation. Finally, the impact of the lattice vibrations on the thermodynamic properties is investigated. This reveals that the closed pore to large pore phase transformation in MIL-53(Al) is mainly facilitated by terahertz vibrations inducing rotations of the organic linker, while the large pore to closed pore phase transformation relies on two framework-specific soft modes.

High-throughput assessment of hypothetical zeolite materials for their synthesizeability and industrial deployability

Abstract: Zeolites are important microporous framework materials, where 200+ structures are known to exist and many millions so-called hypothetical materials can be computationally created. Here, we screen the “Deem” database of hypothetical zeolite structures to find experimentally feasible and industrially relevant materials. We use established and existing criteria and structure descriptors (lattice energy, local interatomic distances, TTT angles), and we develop new criteria which are based on 5-th neighbor distances to T-atoms, tetrahedral order parameters (or, tetrahedrality), and porosity and channel dimensionality. Our filter funnel for screening the most attractive zeolite materials that we construct consists of 9 different types of criteria and a total of 53 subcriteria. The funnel reduces the pool of candidate materials from initially >300,000 to 24 and 11, respectively, depending on the channel dimensionality constraint applied (2- and 3-dimensional vs only 3-dimensional channels). We find that it is critically important to define longer range and more stringent criteria such as the new 5-th neighbor distances to T-atoms and the tetrahedrality descriptor in order to succeed in reducing the huge pool of candidates to a manageable number. Apart from one experimentally achieved structure (SSF), all other candidates are hypothetical frameworks, thus, representing most valuable targets for synthesis and application. Detailed analysis of the screening data allowed us to also propose an exciting future direction how such screening studies as ours could be improved and how framework generating algorithms could be competitively optimized.

Crystal and molecular structures of boldenone and four boldenone steroid esters

Abstract: Abstract Androsta-1,4-dien-17β-ol-3-one, also known as boldenone, is an anabolic-androgenic steroid derived from testosterone. The crystal structures of boldenone base, boldenone acetate, boldenone propionate, boldenone cypionate and a boldenone acetate polymorph obtained by high throughput screening were investigated. Hirshfeld surfaces and fingerprint plots breakdown revealed that the molecular packing in the crystals are driven by dominant H⋯H intermolecular contacts, followed by O⋯H/H⋯O contacts and to a lesser degree C⋯H/H⋯C contacts. The steroid skeleton rings, for all the reported compounds, adopt the following conformation: planar in A, chair in B and C, whereas C(13) envelope conformations are found for the five-membered D rings. The total lattice energies were calculated as a sum of four terms (Coulombic, polarization, dispersion, repulsion).

Computational screening of structure directing agents for the synthesis of zeolites. A simplified model

Abstract: Abstract Zeolite micropores become more energetically stable by the occlusion of organic structure directing agents (templates). This energetic stabilisation, if approximated by van der Waals zeo-template interactions, can be calculated in a fast way by using modern computing techniques incorporating big data handling algorithms for massive screening. A software suite is presented which calculates an arbitrarily large 2-D matrix (template×zeolite) giving the zeo-template van der Waals interaction energy corresponding to the minimum energy conformation assuming one template molecule in a pure silica zeolite unit cell. With the goal of simplicity, the software only needs two coordinate input files of template and zeolite unit cell. Though a number of approximations have been considered, the software allows to compare, for a given template, which competing zeolite phases may become more stabilised. Applied to zeolite hypothetical databases, it may be of help to suggest templates for their synthesis.

Water in zeolite L and its MOF mimic

Abstract: Abstract Confinement of molecules in one dimensional arrays of channel-shaped cavities has led to technologically interesting materials. However, the interactions governing the supramolecular aggregates still remain obscure, even for the most common guest molecule: water. Herein, we use computational chemistry methods (#compchem) to study the water organization inside two different channel-type environments: zeolite L – a widely used matrix for inclusion of dye molecules, and ZLMOF – the closest metal-organic-framework mimic of zeolite L. In ZLMOF, the methyl groups of the ligands protrude inside the channels, creating nearly isolated nanocavities. These cavities host well-separated ring-shaped clusters of water molecules, dominated mainly by water-water hydrogen bonds. ZLMOF provides arrays of “isolated supramolecule” environments, which might be exploited for the individual confinement of small species with interesting optical or catalytic properties. In contrast, the one dimensional channels of zeolite L contain a continuous supramolecular structure, governed by the water interactions with potassium cations and by water-water hydrogen bonds. Water imparts a significant energetic stabilization to both materials, which increases with the water content in ZLMOF and follows the opposite trend in zeolite L. The water network in zeolite L contains an intriguing hypercoordinated structure, where a water molecule is surrounded by five strong hydrogen bonds. Such a structure, here described for the first time in zeolites, can be considered as a water pre-dissociation complex and might explain the experimentally detected high proton activity in zeolite L nanochannels.

Natural tilings and free space in zeolites: models, statistics, correlations, prediction

Abstract: Abstract We review two concepts in description of free space in the zeolite-like frameworks: topological (natural tiling) and geometrical-topological (Voronoi net). Advantages and disadvantages as well as similarities and differences of both concepts are discussed. We also consider the packing model of zeolite framework assemblage, which is derived from the natural tiling approach. New statistical data are given for natural tilings and Voronoi models of all known 239 zeolite frameworks. A route to modeling and prediction of new zeolite frameworks is outlined.

A new structural motif for cadmium dithiocarbamates: crystal structures and hirshfeld surface analyses of homoleptic zinc and cadmium morpholine dithiocarbamates

Abstract: The crystal and molecular structures of two homoleptic morpholine-derived dithiocarbamates of zinc, binuclear {Zn[S2CN(CH2CH2)2O)2]2}2 (1), and cadmium, one-dimensional coordination polymer {Cd[S2CN(CH2CH2) 2O)2]2}2 (2), are described. In 1, a centrosymmetric binuclear molecule is found as there are equal numbers of chelating and bidentate bridging dithiocarbamate ligands; weak transannular Zn · · · S interactions are found within the resultant eight-membered { · · · SCSZn}2 ring which has the form of a chair. The resultant 4 + 1 S5 donor set is highly distorted with the geometry tending towards a squarepyramid. By contrast, a square-planar geometry is found in centrosymmetric 2 defined by symmetrically chelating dithiocarbamate ligands. The presence of Cd · · · S secondary bonding in the crystal of 2 leads to a distorted 4 + 2 S6 octahedron and a linear coordination polymer, which is unprecedented in the structural chemistry of cadmium dithiocarbamates. The analyses of the Hirshfeld surfaces for 1 and 2 show the dominance of H · · · H, S · · · H/H · · · S and O · · · H/H · · · O contacts to the surface, i.e. contributing around 90 and 80%, respectively.

Crystal structure refinement of MnTe2, MnSe2, and MnS2: Cation-anion and anion-anion bonding distances in pyrite-type structures

Abstract: Abstract The stability of hauerite (MnS2) as compared to that of pyrite (FeS2) can be explained by the long Mn–S distance and departure from the typical pyrite-type structures. The structural differences of MnX2 compounds (X=S, Se, and Te) are the result of spin configurations that are different than those of other MX2 compounds; however, the arrangement of d-electrons and the size of the ions in MnX2 compounds do not clearly explain why Mn2+ in MnX2 does not exist as a low spin state. To investigate the structural differences of MnX2 compounds, we synthesized single-crystal MnTe2 and MnSe2 and performed single-crsytal X-ray diffraction experiments. The single-crystal X-ray diffraction experiments were conducted on MnTe2 [a=6.9513(1) Å, u-parameter=0.38554(2), space group Pa3̅, Z=4], MnSe2 [a=6.4275(2) Å, u-parameter=0.39358(2)], MnS2 [hauerite; a=6.1013(1) Å, u-parameter=0.40105(4), obtained from Osorezan, Aomori, Japan], and FeS2 [pyrite; a=5.4190(1) Å, u-parameter 0.38484(5), obtained from Kawarakoba, Nagasaki, Japan]. The X-ray intensity datasets of these compounds do not show any evidence of symmetry reduction. In MnS2, the S–S distance is 2.0915(8) Å, which is significantly shorter than that of FeS2 (2.1618(9) Å), and the mean square displacement of S (U11=0.00915(9) Å2) is smaller than that of Mn (U11=0.01137(9) Å2). The thermal vibration characteristics of MnX2 compounds are significantly different than those of FeS2. Based on structural refinement data, we discuss the low spin state of MnX2 compounds and the structural stability of pyrite-type structures.

Reliable Sn–Ag–Cu lead-free melt-spun material required for high-performance applications

Abstract: Abstract This study investigates the structural, mechanical, thermal and electrical properties of B-1 JINHU, EDSYN SAC5250, and S.S.M-1 commercial materials, which have been manufactured at China, Malaysia, and Germany, respectively. The commercial materials have been compared with the measurements of Sn–Ag–Cu (SAC) melt-spun materials that are only indicative of what can be expected for the solder application, where the solder will have quite different properties from the melt-spun materials due to the effects of melt-spinning technique. Adding Cu to the eutectic Sn–Ag melt-spun material with 0.3 wt.% significantly improves its electrical and mechanical properties to serve efficiently under high strain rate applications. The formed Cu3Sn Intermetallic compound (IMC) offers potential benefits, like high strength, good plasticity, consequently, high performance through a lack of dislocations and microvoids. The results showed that adding 0.3 wt.% of Cu has improved the creep resistance and delayed the fracture point, comparing with other additions and commercial solders. The tensile results showed some improvements in 39.3% tensile strength (25.419 MPa), 376% toughness (7737.220 J/m3), 254% electrical resistivity (1.849 × 10−7 Ω · m) and 255% thermal conductivity (39.911 w · m−1 · k−1) when compared with the tensile strength (18.24 MPa), toughness (1625.340 J/m3), electrical resistivity (6.56 × 10−7 Ω · m) and thermal conductivity (11.250 w · m−1 · k−1) of EDSYN SAC5250 material. On the other hand, the Sn93.5–Ag3.5–Cu3 melt-spun solder works well under the harsh thermal environments such as the circuits located under the automobiles’ hood and aerospace applications. Thus, it can be concluded that the melt-spinning technique can produce SAC melt-spun materials that can outperform the B-1 JINHU, EDSYN SAC5250 and S.S.M-1 materials mechanically, thermally and electrically.

The steric influence of extra-framework cations on framework flexibility: An LTA case study

Abstract: Abstract The theoretical extent of framework flexibility of Zeolite A (LTA) in response to the steric and geometric effects of different Si/Al compositions and extra-framework cation content has been explored using GASP software. Flexibility windows and compression mechanisms for siliceous LTA and aluminosilicate Na-LTA, Ca-LTA and K-LTA have been modelled. As expected, relatively small cations in the zeolite pores have little effect on the range of flexibility observed. Aluminosilicate LTA, Na-LTA and Ca-LTA frameworks exhibit identical flexibility windows and these frameworks also follow the same compression mechanisms. The introduction of larger K+ ions, however, results in greater steric hindrance. This restricts the flexibility of the framework and alters the compression mechanism to accommodate these larger cations. It is shown that the limits of the flexibility window of Zeolite A are dependent on framework aluminium content and extra-framework cation size.

HKLF5Tools: a program for processing diffraction data of non-merohedrally twinned crystals

Abstract: Abstract The HKLF5Tools program provides useful tools for structure refinement against non-merohedrally twinned datasets. The software shows statistical information on each twin component, can delete or rename twin components, merge reflection data, and add an inversion twin component to any of the existing twin components. Also, the software can convert ShelXL FCF files into HKL reflection files so that refinement against detwinned data in the final stages of the refinement becomes possible.

PolyDis: simple quantification tool for distortion of polyhedra in crystalline solids

Abstract: Abstract A new simple approach to quantitative measures of coordination polyhedra distortions from ideal symmetry is provided with PolyDis. Within the mathematical basis, it minimizes the normalized displacements of given polyhedra to the ideal shape. Applications are discussed, where PolyDis was used to analyze the temperature dependent distortion of LaAlO3, rare earth metal radius dependent distortion of RMnO3 and the increasing structural distortion of (A3N)As with varying alkaline earth metal, all being perovskites. Additionally, the more complex structures of SrCuRSe3 and CsCu3R2Se5 comprising trigonal prisms, octahedra and tetrahedra are treated with PolyDis.

Order/disorder processes and electromechanical properties of monoclinic GdCa4O(BO3)3

Abstract: Abstract Large single crystals of GdCa4O(BO3)3 (space group Cm) were grown by the Czochralski method. Dielectric, piezoelectric and elastic coefficients at room temperature as well as specific heat capacity, thermal expansion and cation disorder were studied employing a variety of methods including resonant ultrasound spectroscopy, differential scanning calorimetry, dilatometry and X-ray diffraction techniques. The electromechanical parameters (4 dielectric, 10 piezoelectric and 13 elastic stiffness coefficients) obtained on different samples are in excellent agreement indicating high internal consistency of our approach, whereas the values reported in literature differ significantly. The elastic behaviour of GdCa4O(BO3)3 resembles the one of structurally related fluorapatite, i.e. the elastic anisotropy is relatively small and the longitudinal effect of the deviations from Cauchy-relations exhibit a pronounced minimum along the direction of the dominating chains of cation polyhedra. GdCa4O(BO3)3 exhibits a maximum longitudinal piezoelectric effect of 7.67 × 10−12 CN−10, a value in the order of that of langasite-type materials. Significant changes of the calcium/gadolinium distribution on the 3 independent cation sites accompanied by characteristic anomalies of heat capacity and thermal expansion suggest processes of nonconvergent cation ordering above about 900 K in GdCa4O(BO3)3.

Structural features of uranyl acrylate complexes with s-, p-, and d-monovalent metals

Abstract: Abstract A series of uranyl acrylate complexes with s-, p-, and d- monovalent cations (Li, Na, Tl, and Ag) was synthesized and characterized by single crystal X-ray diffraction and IR spectroscopy. We demonstrated that the nature of the monovalent cation strongly affects the composition and crystal structure of an uranyl acrylate. Li[UO2(acr)3]·H2O (1, acr=CH2CHCOO−) crystallizes in the tetragonal crystal system and is built of chains which are connected through hydrogen bonding. The presence of an acrylic acid dimer in the reaction results in the monoclinic compound Na3[UO2(acr)3][UO2(acr)2.5(CH2CHCOOCH2CH2COO)0.5]2·5H2O (2), in which the acrylic dimer shares a position with both the acrylate anion and a water molecule. Tl[UO2(acr)3] (3) exists as two polymorphs and crystallizes in either P1̅ (3a) or P213 (3b) space groups. The polymorphs differ in the dimensionality, 2D for 3a and 3D for 3b, and density. Ag2[UO2(NO3)2(acr)2]·2Hacr (4) is the first example of the Ag atom coordination to the acrylate anion through the vinyl group. In 4, the Ag–C bonds enhances the connectivity of the trinuclear [Ag2UO2(acr)2(Hacr)2(NO3)2] clusters into a layered coordination polymer. A detailed structural study of the obtained compounds was performed using Voronoi-Dirichlet tessellation.

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

Abstract: Abstract Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

Phonons in deformable microporous crystalline solids

Abstract: Phonons are quantum elastic excitations of crystalline solids. Classically, they correspond to the collective vibrations of atoms in ordered periodic structures. They determine the thermodynamic properties of solids and their stability in the case of structural transformations. Here we review for the first time the existing examples of the phonon analysis of adsorption-induced transformations occurring in microporous crystalline materials. We discuss the role of phonons in determining the mechanism of the deformations. We point out that phonon-based methodology may be used as a predictive tool in characterization of flexible microporous structures; therefore, relevant numerical tools must be developed.

Influence of the alkali cation size on the Cu2+ coordination environments in (AX)[Cu(HSeO3)2] (A=Na, K, NH4, Rb, Cs; X=Cl, Br) layered copper hydrogen selenite halides

Abstract: Abstract Using solution evaporation techniques, we succeeded in preparation of new members essentially extending the layered copper hydrogen selenite family, (AX)[Cu(HSeO3)2] with A = Na, K, Rb, Cs, and NH4, and X = Cl and Br. Bromides and chlorides are isostructural in the family of described new compounds crystallizing in three different structure types. (NaX)[Cu(HSeO3)2] and (KX)[Cu(HSeO3)2] (X = Cl, Br) are monoclinic, whereas (AX)[Cu(HSeO3)2] (A = NH4, Rb, Cs; X = Cl, Br) are orthorhombic. Upon the enlargement of the A+ ionic radii inserted in the interlayer between the neighboring [Cu(HSeO3)2] slabs, the effective distance is increasing and results in essential elongation of the apical Cu-X (X = Cl, Br) distances. Three different types of CuO4Xn (n = 0–2) polyhedra are formed. The observed trend is an interesting example of the chemical tuning of the Cu2+ coordination environments.

Maximal B-factors in protein crystal structures

Abstract: Abstract Since the contribution of proteins atoms with exceptionally large B-factors, much larger than those of other atoms, to the observed structure factors is negligible, it is therefore recommended to consider with a care the parts of the models where B-factors are inflated to extremely large values. Otherwise, molecular biologists risk to over-interpret structural data, since the positions of these atoms is highly uncertain. In the present communication, maximal B-factor values, over which the atoms can be considered ‘invisible’, are estimated based on the relationships between B-factors and solvent accessible surface areas.

Open-framework sodium uranyl selenate and sodium uranyl sulfate with protonated morpholino-N-acetic acid

Abstract: Abstract The reaction of sodium N-morpholine acetate with selenic and sulfuric acid and uranyl nitrate results in the formation of two novel open-framework compounds, |Na(Hmfa)|[(UO2)2(SeO4)3(H2O)](H2O)2 (NaUSe) and [Na2(SO3OH)(Hmfa)]|(UO2)(SO4)2| (NaUS), respectively. Despite identical synthetic procedures, sulfate structure dramatically differs from selenate compound. Their common feature is an open-framework featuring two-dimensional system of channels occupied by protonated morpholino-N-acetic acid species. Coordination of Na atoms is different. In NaUSe, [(UO2)2 (SeO4)3(H2O)]2− layers are pillared by {Na2O8(H2O)2(Hmfa)2} complexes to form a microporous framework. In NaUS, UO7 and SO4 polyhedra of [(UO2)(SO4)2]2− chains share common oxygen atoms with Na-centered tetrameric complexes providing a three-dimensional integrity of the structure. Both of the compounds are characterized by IR spectroscopy.

Intermolecular hydrogen bonding H···Cl in crystal structure of palladium(II)-bis(diaminocarbene) complex

Abstract: Abstract The reaction of bis(isocyanide)palladium complex cis-[PdCl2(CNXyl)2] (Xyl=2,6-Me2C6H3) with excess of 4,5-dichlorobenzene-1,2-amine in a C2H4Cl2/MeOH mixture affords monocationic bis(diaminocarbene) complex cis-[PdClC{(NHXyl)=NHC6H2Cl2NH2}{C(NHXyl)=NHC6H2Cl2NH2}]Cl (3) in moderate yield (42%). Complex 3 exists in the solid phase in the H-bonded dimeric associate of two single charged organometallic cations and two chloride anions according to X-ray diffraction data. The Hirshfeld surface analysis for the X-ray structure of 3 reveals that the crystal packing is determined primarily by intermolecular contacts H–Cl, H–H, and H–C. The intermolecular hydrogen bonds N–H···Cl and C–H···Cl in the H-bonded dimeric associate of 3 were studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method, and estimated energies of these supramolecular contacts vary from 1.6 to 9.1 kcal/mol. Such non-covalent bonding means that complex 3 is an anionic receptor for the chloride anions.

Copper hydroselenite nitrates (A +NO3) n [Cu(HSeO3)2] (A=Rb+, Cs+ and Tl+, n=1, 2) related to Ruddlesden – Popper phases

Abstract: Abstract Three new layered copper hydrogen selenite nitrates, (ANO3)[Cu(HSeO3)2] (A = Cs, and Tl), and (RbNO3)2[Cu(HSeO3)2] have been prepared via isothermal evaporation of concentrated nitric acid solutions. The Tl and Cs compounds adopt a motif related to previously known (NH4Cl)[Cu(HSeO3)2]; the structure of the Rb compound represents a new structure type. The structures of (ANO3)[Cu(HSeO3)2] (A = Cs, Tl), (RbNO3)2[Cu(HSeO3)2], and (NH4NO3)3[Cu(HSeO3)2] form a unique homological series distantly related to Ruddlesden – Popper series of layered perovskites.

Stacking polytypes of mixed alkali gallides/indides A 1–2(Ga/In)3 (A=K, Rb, Cs): synthesis, crystal chemistry and chemical bonding

Abstract: Abstract The Ga/In phase width (y) and the distribution of the two triels within the polyanions of known binary (x = 1, 2) and new ternary ‘intermediate’ (x = 1–2) alkali trielides Ax(Ga1−yIny)3 (A = K, Rb, Cs) was investigated in a synthetic (slow cooling of the melts of the three elements), crystallographic (X-ray single crystal) and bond theoretical (FP-LAPW DFT bandstructure calculation) study. The Cs2In3-type structure (x = 2, series A, tetragonal, I 4/mmm) exhibits layers of four-connected closo octahedra [M6]4−. Ternary K compounds of this type were yielded within a large range (y = 0–0.87), whereas isotypic Rb/Cs trielides exist only at higher In contents (>52/69%). Geometric criteria determine not only the Ga/In stability ranges but also the occurrence of a commensurate superstructure at approx. 33% In (K2Ga2.17In0.83: P 42/ncm, a = 879.83(4), c = 1557.66(10) pm, R 1 = 0.0887), in which the octahedra are slightly tilted against the layers. Cesium compounds of the RbGa3-type structure (x = 1, C, tetragonal, I 4̅m2), which exhibits a 3D network of all-exo bonded closo dodecahedra [M8]2− and four-bonded M− anions, are stable throughout the whole substitutional range CsGa3–CsIn3. The maximum possible In content increases with increasing size of A+ (Cs: 100%, Rb: 30%, K: 8% In). The similarities between these two tetragonal structures are consistent with the occurrence of two new structure types of ‘intermediate’ compounds A7M15 (x = 1.4, 1B/2B), which differ in the stacking sequences of double layers of novel six-fold exo-bonded pentagonal bipyramidal closo clusters [M7]3− connected via four-bonded M− (e.g. 1B: Cs7Ga8.4In6.6, P 4̅m2, a = 656.23(3), c = 1616.0(1) pm, R 1 = 0.0742; 2B: Rb7Ga8.1In6.9, P 42/nmc, a = 665.64(2), c = 3140.9(2) pm, R 1 = 0.0720). The Rb/Cs compounds of these types are only stable in a limited Ga/In region and with a distinct Ga/In distribution within the [M7] clusters. According to the close relation between the structures A, B and C, the structure family is characterised by the occurrence of stacking faults and diffuse scattering, indicating the existence of further members of this series. The new compound Cs5Ga3.1In5.9 (x = 1.667, P 4̅m2, a = 654.62(2), c = 3281.5(2) pm, R 1 = 0.1005) is a reasonably periodically ordered stacking variant containing layers A and double layers B in parallel.

Synthesis and structural variety of first Mn and Bi selenites and selenite chlorides

Abstract: Abstract Single crystals of new Mn2[Bi2O](SeO3)4 (I), MnBi(SeO3)2Cl (II), MnIIMnIII(SeO3)2Cl (III), Mn5(SeO3)2Cl6 (IV), and Mn4(Mn5,Bi)(SeO3)8Cl5 (V) have been synthesized by chemical vapour transport and hydrothermal methods. They have been structurally characterized by single crystal X-ray diffraction analysis. The compounds II–V are the first Mn selenite chlorides, while the I, II and V compounds are the first Bi-containing Mn oxoselenites. Structural relationships of the new phases with other compounds are discussed. An overview of the mixed-ligand MnOmCln polyhedra in inorganic compounds is given.

Evaluation of N–H···O hydrogen bond interactions in two new phosphoric triamides with a P(O)[NHCH(CH3)2]2 segment by means of topological (AIM) calculations, Hirshfeld surface analysis and 3D energy framework approach

Abstract: Abstract Two new phosphoric triamides having a common part XP(O)[NHCH(CH3)2]2, with X =[2,3,6-F3–C6H2C(O)NH] (1) and [C6H11(CH3)N] (2), were prepared and characterized by spectroscopic techniques (FT-IR and 1H-, 13C-, 31P-NMR) and single crystal X-ray diffraction. The asymmetric unit of 1 is composed of one molecule, whereas for 2 it consists of six symmetry independent molecules. In all molecules, the P atoms are in a distorted tetrahedral environment of one oxygen and three nitrogen atoms. The latter have mainly sp2 character and a nearly planar environment. The crystal structures are stabilized via N–H · · · O hydrogen bond interactions, forming a linear arrangement for 1 and three independent parallel linear chains for 2, along the b and a axis, respectively. The intermolecular interactions in the molecular packing were analyzed using the Hirshfeld surface methodology, two-dimensional (2D) fingerprint plots and enrichment ratios (E). The prevalent interactions revealed by Hirshfeld surfaces are O · · · H type interactions for both structures 1 and 2, additionally C · · · O for 1 and H · · · H interactions for 2. The most favored contacts responsible for the molecular packing are C · · · F, N · · · H and O · · · H for 1 confirmed by E values greater than 1.30, whereas for 2, O · · · H and N · · · H intermolecular interactions with E values about 1.04 representing the favored contacts. Thus, the N–H · · · O hydrogen bond interactions are the dominant interactions in both compounds. For more details, a topological AIM analysis of N–H · · · O hydrogen bond interactions was performed: NCP–H · · · O=C hydrogen bond (the NCP is referred to the nitrogen atom within the C(O)NHP(O) segment) interactions in 1 are stronger than N–H · · · O=P interactions in both 1 and 2. Furthermore, a 3D topology of the molecular packing via the energy framework approach showed that the N–H · · · O hydrogen bond interactions in C(O)NHP(O)-based phosphoric triamide are predominantly electrostatic based, while they are electrostatic-dispersion based for other phosphoric triamides with a [N]P(O)[NH]2 skeleton.