Single Crystal Refinement of the Incommensurately Modulated Mn0.55Ta0.45O1.7, an Oxygen Deficient Fluorite Type Compound

A structural investigation of the incommensurately ordered compound Mn_0.55Ta_0.45O_1.7 has been carried out, using single‐crystal X‐ray diffraction data. The basic structure is related to the fluorite type with a monoclinic distortion. Electron diffraction (ED) patterns for various crystal orientations were used for determination of unit cell, incommensurate modulation vector and superspace group. The unit cell parameters and the length and direction of the incommensurate vector were refined using X‐ray powder diffraction (XRPD) data. P2/m was chosen as the three‐dimensional space group for a subcell with parameters a = 3.5005(2) Å (√2/2 · a_f), b = 3.5730(2) (√2/2 · a_f), c = 5.0015(2) Å (a_f) and β = 91.677(7)°. From the systematic absences hklm: k + m ≠ 2n, the four‐dimensional superspace group was determined to be B : P2/m(α 0 c) with determined modulation vector components α = –0.1833(1) and γ = 0.3582(2). A total of 511 unique reflections (79 basic fluorite type, 268 first‐order and 164 second‐order satellites) were used in the structure refinement, which resulted in weighted R‐values of 5.6% for the fluorite type sublattice reflections, 5.5% for the first‐order satellites and 7.4% for the second‐order satellites. The Mn and Ta atoms were found to be both positionally and occupationally modulated and the oxygen atoms to be highly disordered. The structure is the first fluorite‐related modulated structure of an oxide that has been determined from single‐crystal data. The structural relation to the previously characterised disordered cubic phase Mn_0.6Ta_0.4O_1.65 and the diffuse scattering exhibited by it are discussed in the article.     

A New Dimeric Stilbenoid with a Five‐Membered Lactone Ring from Shorea hemsleyana

From the stem bark of Shorea hemsleyana, a new dimeric stilbenoid with a five‐membered lactone ring, shorealactone ( 1 ) was isolated. The absolute configuration was determined by means of 2D NMR techniques and X‐ray crystal‐structure analysis of its 4‐bromobenzoyl derivative 1e by means of anomalous scattering of the Br‐atom.     

Reinterpretation of the monohydrate of clarithromycin from X‐ray powder diffraction data as a trihydrate

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst. (2012), E 68 , o667–o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X‐ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion‐corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.     

In1.08Gd0.92Ge2O7: a new member of the thortveitite family

Indium gadolinium digermanium heptaoxide, In_1.08Gd_0.92Ge₂­O₇, with a thortveitite‐type structure, has been prepared as a polycrystalline powder material by a high‐temperature solid‐state reaction. As in the mineral thortveitite, the crystal structure belongs to the monoclinic system, with space group C2/m (No. 12). The precise structural parameters were obtained by applying the Rietveld method of refinement to the X‐ray powder diffraction data. This layered structure presents, on one side, a honeycomb‐like arrangement of the unique octahedral site, which is occupied randomly by In and Gd atoms, and, on the other side, sheets of isolated Ge₂O₇ diortho‐groups made up of double tetrahedra sharing a common vertex and displaying C_2h point symmetry. This compound showed a remarkable photoluminescence effect when it was irradiated with the X‐ray beam during the X‐ray diffraction measurements, and with the α beam during the Rutherford back‐scattering spectrometry experiments employed to analyze the chemical stoichiometry.     

Protonation of Ferrocene: A Low‐Temperature X‐ray Diffraction Study of [Cp2FeH](PF6) Reveals an Iron‐Bound Hydrido Ligand

Ferrocene, Cp₂Fe, is quantitatively protonated in a mixture of liquid HF/PF₅ to yield [Cp₂FeH](PF₆), which was characterized by ¹H/¹³C NMR and ⁵⁷Fe Mössbauer spectroscopy as well as single‐crystal X‐ray diffraction analysis. X‐ray diffraction analysis at 100 K revealed a disordered, iron‐coordinated hydrido ligand, which was unambiguously located by aspherical atom refinement at 100 K, and by analyzing the non‐disordered crystal structure at 30 K, revealing a non‐agostic structure.     

Phenyl‐(2‐pyridyl)‐(3‐pyridyl)‐(4‐pyridyl)methane: Synthesis,Chiroptical Properties,and Theoretical Calculation of Its Absolute Configuration

The title compound, a prototypical chiral molecule based on a tetraarylmethane framework, has been synthesized in five steps from (2‐pyridyl)‐(3‐pyridyl)ketone. X‐ray crystallographic analysis revealed the tetraarylmethane framework of the molecule but did not determine the positions of the nitrogen atoms because the crystal is a racemic compound and the aryl groups are disordered in the crystal. The optical resolution of the title compound was achieved by chiral HPLC with a Chiralcel OD column. The CD spectra of the two fractions in acetonitrile exhibited opposite signs as expected for a pair of enantiomers. Their CD spectra are changed in 2 M HCl due to protonation. The calculated CD curve for the target molecule based on time‐dependent density functional theory (TDDFT) reproduces the experimental result very well, thus suggesting that the first eluted fraction is the R isomer in terms of absolute configuration.     

Synthesis of Enantiopure Sulfonimidamides and Elucidation of Their Absolute Configuration by Comparison of Measured and Calculated CD Spectra and X‐Ray Crystal Structure Determination

Straightforward syntheses of enantiopure N‐benzoyl‐ and N‐tert‐butyloxycarbonyl‐protected sulfonimidamides, which can be used as building blocks in newly designed catalysts, are presented. Key synthetic step is a dynamic resolution of a racemic sulfinic acid sodium salt. All subsequent transformations proceed stereospecifically. The absolute configurations at the sulfur atoms of both sulfonimidamides were determined by comparison of measured and calculated CD spectra. An X‐ray crystal structure determination of a sulfonimidoylguanidine derivative confirmed this result.     

Ab initio X‐ray structural characterization of an inclusion compound with a compositionally disordered chiral guest: no prior knowledge of the crystal composition

The crystal structure and absolute configuration of a molecular host/guest/impurity inclusion complex were established unequivocally in spite of our having no prior knowledge of its chemical composition. The host (4R,5R)‐4,5‐bis(hydroxydiphenylmethyl)‐2,2‐dimethyl‐1,3‐dioxolane, (I), displays expected conformational features. The crystal‐disordered chiral guest 4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one, (II), is present in the crystal 85.1 (4)% of the time. It shares a common site with 4a‐hydroperoxymethyl‐4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one, (III), present 14.9 (4)% of the time, which is the product of autoxidation of (II). This minor peroxide impurity was isolated, and the results of nuclear magnetic resonance, mass spectrometry, and X‐ray fluorescence studies are consistent with the proposed structure of (III). The complete structure was therefore determined to be (4R,5R)‐4,5‐bis(hydroxydiphenylmethyl)‐2,2‐dimethyl‐1,3‐dioxolane–4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one–4a‐hydroperoxymethyl‐4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one (1/0.85/0.15), C₃₁H₃₀O₄·0.85C₁₀H₁₄O·0.15C₁₀H₁₄O₃, (IV). There are host–host, host–guest, and host–impurity hydrogen‐bonding interactions of types S and D in the solid state. We believe that the crystals of (IV) were originally prepared to establish the chirality of the guest (II) by means of X‐ray diffraction analysis of host/guest crystals obtained in the course of chiral resolution during cocrystallization of (II) with (I). In spite of the absence of `heavy' elements, the absolute configurations of all anomeric centres in the structure are assigned as R based on resonant scattering effects.     

Crystal Structure,Magnetic Exchange Interaction,and DFT Study of 2,2′‐(1‐Oxidopyridine‐2,6‐diyl)bis[4,5‐dihydro‐4,4,5,5‐tetramethyl‐3‐oxido‐1H‐imidazol‐1‐oxyl] Hydrate

The structure of a novel oxido‐aminoxyl (=`nitronyl nitroxide') biradical, 2,2′‐(1‐oxidopyridine‐2,6‐diyl)bis[4,5‐dihydro‐4,4,5,5‐tetramethyl‐3‐oxido‐1H‐imidazol‐1‐oxyl] hydrate ( 1 ⋅H₂O) was established by X‐ray analysis in the solid state: monoclinic, space group P2₁/c, Z=4 with a=12.621(4), b=15.704(5), and c=13.001(4) Å, and β=115.202(6)°. Variable‐temperature magnetic susceptibilities show a weak antiferromagnetic interaction between the two oxido‐substituted aminoxyl moieties of 1 , indicative of a singlet ground state. AM1 Calculations located minima for the possible structure based on the X‐ray crystal structure. A hybride density‐functional‐theory calculation with the UB3LYP method from the X‐ray crystal structure establishes the same spin sign in the two aminoxyl moieties and shows that a small spin density is localized at the C‐atoms of the pyridine moiety. These theoretic results are in good agreement with the determined weak antiferromagnetic interaction of 1 .     

Aspherical‐Atom Modeling of Coordination Compounds by Single‐Crystal X‐ray Diffraction Allows the Correct Metal Atom To Be Identified

Single‐crystal X‐ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid‐state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical‐atom least‐squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld‐atom refinement (Acta Crystallogr. Sect. A­ 2008 , 64, 383–393; IUCrJ. 2014 , 1,61–79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B­ 2013 , 69, 91–104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear‐coordinate 3d metal complexes, for which the wrong element is found if standard independent‐atom model scattering factors are relied upon, are studied, and it is shown that only aspherical‐atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.     

Lithium Argyrodites with Phosphorus and Arsenic: Order and Disorder of Lithium Atoms,Crystal Chemistry,and Phase Transitions

Crystal chemical data of high‐ (HT) and low‐temperature (LT) modifications of lithium argyrodites with the compositions Li₇PCh₆ (Ch=S, Se), Li₆PCh₅X (X=Cl, Br, I), Li₆AsS₅Br, and Li₆AsCh₅I (Ch=S, Se) based on single‐crystal, powder X‐ray (113 K<T<503 K) and neutron measurements (5 K<T<293 K) are presented. In the HT modifications, the Li atoms are strongly disordered over a fraction of the available tetrahedral holes, whereas in the LT modifications they occupy ordered crystallographic positions with a pronounced site preference that is analysed on a crystal chemical basis. The Ch/X partial structures remain nearly unchanged upon the reversible phase transitions. Crystal chemical and crystallographic relations between HT and LT modifications based on the Frank–Kasper model of tetrahedral close packing are discussed. X‐ray single‐crystal data for HT‐Li₆PS₅I show the electron density of the disordered Li to be smeared out over an extended region preferably inside face‐sharing double tetrahedra. A series of temperature‐dependent powder neutron data for Li₆PS₅I gives clear evidence for an HT/LT phase transition at ≈175 K with an ordering of the Li atoms in different polyhedra with coordination numbers between three and four.     

Crystal Structure of the Dietary Supplement Ferrous Glycine Sulfate

The crystal structure of ferrous glycine sulfate (a ferroglycine sulfate complex with chemical formula FeSO₄(C₂H₅NO₂), a compound extensively used as an iron dietary supplement, was refined from synchrotron X‐ray powder diffraction data. The crystal structure of an (so‐far unreported) isostructural manganese analogue was also structurally detailed by a Rietveld refinement against the corresponding X‐ray powder diffraction pattern. All studied compounds crystallize in the monoclinic P2₁ space group, building layers of metal cations coordinated by the oxygen atoms of sulfate groups and glycine ligands. Neighboring layers are parallel packed, bonded by hydrogen bonds. The coordination polyhedra around the cations can be regarded as distorted and elongated octahedral, presumably due to severe strains present in the crystal structure of the layers.     

Confirmation of the Structures of Lutein and Zeaxanthin

A series of new esters of lutein ( 1a ) have been prepared with the aim of confirming the structure of lutein via an X‐ray crystal‐structure analysis. Although well crystallized, only one of the derivatives, the (?)‐(1R)‐menthyl carbonate ( 1i ) proved to be useful for a complete structure analysis. The same derivative of zeaxanthin ( 2a ) also allowed its crystal structure to be determined. Both analyses represent the first successful X‐ray crystal structure analyses of the most important xanthophylls. At the same time, they confirm both the constitution and absolute configuration of 1a and 2a that had been deduced earlier by classical methods.     

Absolute‐structure reports

All the 139 noncentrosymmetric crystal structures published in Acta Crystallographica Section C between January 2011 and November 2012 inclusive have been used as the basis of a detailed study of the reporting of absolute structure. These structure determinations cover a wide range of space groups, chemical composition and resonant‐scattering contribution. Defining A and D as the average and difference of the intensities of Friedel opposites, their level of fit has been examined using 2AD and selected‐D plots. It was found, regardless of the expected resonant‐scattering contribution to Friedel opposites, that the Friedel‐difference intensities are often dominated by random uncertainty and systematic error. An analysis of data collection strategy is provided. It is found that crystal‐structure determinations resulting in a Flack parameter close to 0.5 may not necessarily be from crystals twinned by inversion. Friedif_stat is shown to be a robust estimator of the resonant‐scattering contribution to Friedel opposites, very little affected by the particular space group of a structure nor by the occupation of special positions. There is considerable confusion in the text of papers presenting achiral noncentrosymmetric crystal structures. Recommendations are provided for the optimal way of treating noncentrosymmetric crystal structures for which the experimenter has no interest in determining the absolute structure.<!?tpb=25.7pt>     

Structural Aspects of the β‐Polymorph of (E)‐4‐Formylcinnamic Acid: Structure Determination Directly from Powder Diffraction Data and Elucidation of Structural Disorder from Solid‐State NMR

Among the derivatives of (E)‐cinnamic acid for which the solid‐state photochemical properties have been studied, (E)‐4‐formylcinnamic acid ( 1 ) has already received much attention. Given the inability to prepare single crystals of the β‐polymorph of 1 that are of suitable size and quality for structural characterization by single‐crystal X‐ray diffraction, the structure of this material was determined directly from powder X‐ray‐diffraction data by means of the genetic‐algorithm technique for structure solution, followed by Rietveld refinement. High‐resolution solid‐state ¹³CNMR was also applied to elucidate details of structural disorder concerning the orientation of the formyl group, and provided independent support for the disorder model established form the Rietveld refinement. The reported structure establishes that the β‐phase of 1 is not structurally anomalous among photoreactive (E)‐cinnamic acid crystals, and finally resolves a long‐standing controversy concerning the structural properties of this material.     

Synthesis,Characterization, and Crystal Structure of Na3B20, determined and refined from X‐ray and Neutron Powder Data

At 1050 ?C boron combines with sodium forming a boride of formerly unknown composition and crystal structure. The investigation of the homogeneous, monophasic, and crystalline powder was performed using X‐ray (23 ?C) and neutron (–271.5 ?C) diffraction methods. The structure solution led to an unusual arrangement of boron atoms, characterized by two different types of polyhedra, a distorted pentagonal bipyramid and a distorted octahedron. The Rietveld refinement of the crystal structure was carried out in the orthorhombic space group Cmmm (X‐ray: a = 18.6945(6) Å, b = 5.7009(2) Å, c = 4.1506(1) Å, V = 442.35(1) ų, Z = 2; R_wp = 0.087, R_p = 0.067).     

Melamium Thiocyanate Melam,a Melamium Salt with Disordered Anion Sites

Melamium salts are a group of ionic carbon nitride type compounds that has been investigated only scarcely. We herein present a novel representative of this group. A melamium thiocyanate melam (1:1) adduct was synthesized from dicyandiamide and ammonium thiocyanate in sealed glass ampoules. The structure of the adduct was determined from single‐crystal X‐ray diffraction. Melamium thiocyanate melam crystallizes in monoclinic space group P2₁/c (no. 14) with lattice parameters of a = 3.6041(11), b = 28.532(7), c = 10.937(4) Å, β = 99.051(14)°, and Z = 4. While the melamium ions form 2D extended hydrogen bridged networks, the thiocyanate ions are disordered and no distinct structural sites could be assigned to the respective atoms. Instead, continuous columns of electron density located in channels in the porous structure were identified as potential space for anion locations. The compound was further characterized by elemental analysis, FTIR spectroscopy and solid‐state MAS‐NMR spectroscopy of the nuclei ¹H, ¹³C and ¹⁵N. Rietveld refinement of powder samples was performed for phase analysis. Furthermore, DSC‐TG was used to investigate the thermal behavior of the compound.     

A hierarchical algorithm for fast debye summation with applications to small angle scattering

Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three‐dimensional space, arises in computations performed in crystallography, small/wide angle X‐ray scattering (SAXS/WAXS), and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy ? in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and show that these methods may result in inaccurate profile computations, unless an error‐bound derived in this article is used. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy. © 2012 Wiley Periodicals, Inc.     

Zintl‐Phase Sr3LiAs2H: Crystal Structure and Chemical Bonding Analysis by the Electron Localizability Approach

The compound Sr₃LiAs₂H was synthesized by reaction of elemental strontium, lithium, and arsenic, as well as LiH as hydrogen source. The crystal structure was determined by single‐crystal X‐ray diffraction: space group Pnma; Pearson symbol oP28; a = 12.0340(7), b = 4.4698(2), c = 12.5907(5) Å; V = 677.2(1) ų; R_F = 0.047 for 1021 reflections and with 36 parameters refined. The positions of the hydrogen atoms were first revealed by the electron localizability indicator and subsequently confirmed by crystal structure refinement. In the crystal structure of Sr₃LiAs₂H the metal atoms are arranged in a Gd₃NiSi₂‐type motif, whereas the hydrogen atoms are arranged in a distorted tetrahedral environment formed by strontium. The calculated band structure revealed that Sr₃LiAs₂H is a semiconductor, which is in agreement with its diamagnetic behavior. Thus, Sr₃LiAs₂H is considered as a (charge‐balanced) Zintl phase.     

The perchlorotriphenylmethyl (PTM) radical

In spite of the considerable understanding and development of perchlorotriphenylmethyl (PTM) radical derivatives, the preparation of crystals of the pure unsubstituted PTM radical, C₁₉Cl₁₅, suitable for single‐crystal X‐ray diffraction has remained a challenge since its discovery, and only two studies dealing with the crystal structure of the unsubstituted PTM radical have been published. In one study, the radical forms clathrates with aromatic solvents [Veciana, Carilla, Miravitlles & Molins (1987). J. Chem. Soc. Chem. Commun. pp. 812–814], and in the other the structure was determined ab initio from powder X‐ray diffraction data [Rius, Miravitlles, Molins, Crespo & Veciana (1990). Mol. Cryst. Liq. Cryst. 187 , 155–163]. We report here the preparation of PTM crystals for single‐crystal X‐ray diffraction and their resolution. The structure, which shows monoclinic symmetry (C2/c), revealed a nonsymmetric molecular propeller conformation (D₃ symmetry) caused by the steric strain between the ortho‐Cl atoms, which protect the central C atom (sp²‐hybridization and major spin density) and give high chemical and thermal persistence to the PTM. The supramolecular structure of PTM shows short Cl...Cl intermolecular interactions and can be described in terms of layers formed by rows of molecules positioned in a head‐to‐tail manner along the c axis.