Incommensurate Phase in Λ-cobalt (III) Sepulchrate Trinitrate Governed by Highly Competitive N-H⋠⋠⋠O and C-H⋠⋠⋠O Hydrogen Bond Networks.

Phase transitions in molecular crystals are often determined by intermolecular interactions. The cage complex of [Co(C12 H30 N8 )]3+ ⋅ 3 NO3 - is reported to undergo a disorder-order phase transition at Tc1 ≈133 K upon cooling. Temperature-dependent neutron and synchrotron diffraction experiments revealed satellite reflections in addition to main reflections in the diffraction patterns below Tc1 . The modulation wave vector varies as function of temperature and locks in at Tc3 ≈98 K. Here, we demonstrate that the crystal symmetry lowers from hexagonal to monoclinic in the incommensurately modulated phases in Tc1

Single-crystal-to-single-crystal phase transitions of commensurately modulated sodium saccharinate 1.875-hydrate.

This work reports reversible, single-crystal-to-single-crystal phase transitions of commensurately modulated sodium saccharinate 1.875-hydrate [Na(sac)(15/8)H2O]. The phases were studied in the temperature range 298 to 20 K. They exhibit complex disordered states. An unusual reentrant disorder has been discovered upon cooling through a phase transition at 120 K. The disordered region involves three sodium cations, four water molecules and one saccharinate anion. At room temperature, the structure is an eightfold superstructure that can be described by the superspace group C2/c(0σ20)s0 with q = (0, 3/4, 0). It demonstrates maximum disorder with the disordered chemical entities having slightly different but close to 0.50:0.50 disorder component ratios. Upon cooling, the crystal tends to an ordered state, smoothly reaching a unified disorder component ratio of around 0.90:0.10 for each of the entities. Between 130 and 120 K a phase transition occurs involving a sudden increase of the disorder towards the disorder component ratio 0.65:0.35. Meanwhile, the space group and general organization of the structure are retained. Between 60 and 40 K there is another phase transition leading to a twinned triclinic phase. After heating the crystal back to room temperature its structure is the same as before cooling, indicating a complete reversibility of the phase transitions.

On the puzzling case of sodium saccharinate 1.875-hydrate: structure description in (3+1)-dimensional superspace.

The structure of sodium saccharinate 1.875-hydrate is presented in three- and (3+1)-dimensional space. The present model is more accurate than previously published superstructures, due to an excellent data set collected up to a high resolution of 0.89 Å-1. The present study confirms the unusual complexity of the structure comprising a very large primitive unit cell with Z' = 16. A much smaller degree of correlated disorder of parts of the unit cell is found than is present in the previously published models. As a result of pseudo-symmetry, the structure can be described in a higher-dimensional space. The X-ray diffraction data clearly indicate a (3+1)-dimensional periodic structure with stronger main reflections and weaker superstructure reflections. Furthermore, the structure is established as being commensurate. The structure description in superspace results in a four times smaller unit cell with an additional base centring of the lattice, resulting in an eightfold substructure (Z' = 2) of the 3D superstructure. Therefore, such a superspace approach is desirable to work out this high-Z' structure. The displacement and occupational modulation of the saccharinate anions have been studied, as well as their conformational variation along the fourth dimension.

Cyanobacterial promoted enrichment of rare earth elements europium, samarium and neodymium and intracellular europium particle formation.

In the recovery of rare earth elements (REE) microbial biosorption has shown its theoretical ability as an extremely economically and environmentally friendly production method in the last few years. To evaluate the ability of two cyanobacterial strains, namely Anabaena spec. and Anabaena cylindrica to enrich dissolved trivalent REE, a simple protocol was followed. The REE tested in this study include some of the most prominent representatives, such as europium (Eu), samarium (Sm) and neodymium (Nd). Within the experiments, a fast decrease of the REE3+ concentration in solution was tracked by inductively coupled plasma mass spectrometry (ICP-MS). It revealed an almost complete (>99%) biosorption of REE3+ within the first hour after the addition of metal salts. REE3+ uptake by biomass was checked using laser-induced breakdown spectroscopy (LIBS) and showed that all three selected REE3+ species were enriched in the cyanobacterial biomass and the process is assigned to a biosorption process. Although the biomass stayed alive during the experiments, up to that, a distinction whether the REE3+ was intra- or extracellularly sorbed was not possible, since biosorption is a metabolism independent process which occurs on living as well as non-living biomass. For europium it was shown by TEM that electron dense particles, presumably europium particles with particle sizes of about 15 nm, are located inside the vegetative cyanobacterial cells. This gave clear evidence that Eu3+ was actively sorbed by living cyanobacteria. Eu3+ biosorption by cell wall precipitation due to interaction with extracellular polysaccharides (EPS) could therefore be excluded. Finally, with XRD analysis it was shown that the detected europium particles had an amorphous instead of a crystalline structure. Herein, we present a fast biosorptive enrichment of the rare earth elements europium, samarium and neodymium by Anabaena spec. and Anabaena cylindrica and for the first time the subsequent formation of intracellular europium particles by Anabaena spec.

The role of PbI2 in CH3NH3PbI3 perovskite stability, solar cell parameters and device degradation.

We report a systematic investigation on the role of excess PbI2 content in CH3NH3PbI3 perovskite film properties, solar cell parameters and device storage stability. We used the CH3NH3I vapor assisted method for the preparation of PbI2-free CH3NH3PbI3 films under a N2 atmosphere. These pristine CH3NH3PbI3 films were annealed at 165 °C for different time intervals in a N2 atmosphere to generate additional PbI2 in these films. From XRD measurements, the excess of PbI2 was quantified. Detailed characterization using scanning electron microscopy, X-ray diffraction, UV-Visible and photoluminescence for continuous aging of CH3NH3PbI3 films under ambient condition (50% humidity) is carried out for understanding the influence of different PbI2 contents on degradation of the CH3NH3PbI3 films. We find that the rate of degradation of CH3NH3PbI3 is accelerated due to the amount of PbI2 present in the film. A comparison of solar cell parameters of devices prepared using CH3NH3PbI3 samples having different PbI2 contents reveals a strong influence on the current density-voltage hysteresis as well as storage stability. We demonstrate that CH3NH3PbI3 devices do not require any residual PbI2 for a high performance. Moreover, a small amount of excess PbI2, which improves the initial performance of the devices slightly, has undesirable effects on the CH3NH3PbI3 film stability as well as on device hysteresis and stability.

Incommensurately modulated structure of morpholinium tetrafluoroborate and configurational versus chemical entropies at the incommensurate and lock-in phase transitions.

Morpholinium tetrafluoroborate, [C4H10NO]+[BF4]-, belongs to a class of ferroelectric compounds ABX4. However, [C4H10NO]+[BF4]- does not develop ferroelectric properties because the incommensurate phase below Tc,I = 153 K is centrosymmetric with superspace group Pnam(σ100)00s and σ1 = 0.42193 (12) at T = 130 K; the threefold superstructure below Tc,II = 117-118 K possesses the acentric but non-ferroelectric space group P212121. At ambient conditions, [C4H10NO]+[BF4]- comprises orientationally disordered [BF4]- anions accommodated in cavities between four morpholinium cations. A structure model for the incommensurately modulated phase, which involves modulated orientational ordering of [BF4]- together with modulated distortions and displacements of the morpholinium ions is reported. A mechanism is proposed for the phase transitions, whereby at low temperatures morpholinium cations are shaped around the tetrafluoroborate anion in order to optimize the interactions with one orientation of this anion and, thus, forcing [BF4]- into this orientation. This mechanism is essentially different from a pure order-disorder phase transition. It is supported by consideration of the transition entropy. The difference in configurational entropy between the disordered and incommensurate phases has been computed from the structure models. It is shown to be much smaller than the experimental transition entropy reported by Owczarek et al. [Chem. Phys. (2011), 381, 11-20]. These features show that the order-disorder contribution is only a minor contribution to the transition entropy and that other factors, such as conformational changes, play a larger role in the phase transitions.

The Z' = 12 superstructure of Λ-cobalt(III) sepulchrate trinitrate governed by C-H...O hydrogen bonds.

Λ-Cobalt(III) sepulchrate trinitrate crystallizes in P6322 with Z = 2 (Z' = 1/6) at room temperature. Slabs perpendicular to the hexagonal axis comprise molecules Co(sepulchrate) alternating with nitrate groups A and B. Coordinated by six sepulchrate molecules, highly disordered nitrate groups C are accommodated between the slabs. Here we report the fully ordered, low-temperature crystal structure of Co(sep)(NO3)3. It is found to be a high-Z' structure with Z' = 12 of the 12-fold 6a_{h}\times\sqrt{3}b_{h}\times c_{h} superstructure with monoclinic symmetry P21 (c unique). Correlations between structural parameters are effectively removed by refinements within the superspace approach. Superstructure formation is governed by a densification of the packing in conjunction with ordering of nitrate group C, the latter assuming different orientations for each of the Z' = 12 independent copies in the superstructure. The Co(sep) moiety exhibits small structural variations over its 12 independent copies, while orientations of nitrate groups A and B vary less than the orientations of the nitrate group C do. Molecular packing in the superstructure is found to be determined by short C-H...H-C contacts, with H...H distances of 2.2-2.3 Å, and by short C-H...O contacts, with H...O distances down to 2.2 Å. These contacts presumably represent weak C-H...O hydrogen bonds, but in any case they prevent further densification of the structure and strengthening of weak N-H...O hydrogen bonds with observed H...O distances of 2.4-2.6 Å.

Time-dependent growth of crystalline Au(0)-nanoparticles in cyanobacteria as self-reproducing bioreactors: 2. Anabaena cylindrica.

Microbial biosynthesis of metal nanoparticles as needed in catalysis has shown its theoretical ability as an extremely environmentally friendly production method in the last few years, even though the separation of the nanoparticles is challenging. Biosynthesis, summing up biosorption and bioreduction of diluted metal ions to zero valent metals, is especially ecofriendly, when the bioreactor itself is harmless and needs no further harmful reagents. The cyanobacterium Anabaena cylindrica (SAG 1403.2) is able to form crystalline Au(0)-nanoparticles from Au(3+) ions and does not release toxic anatoxin-a. X-ray powder diffraction (XRD), transmission electron microscopy (TEM) and laser-induced breakdown spectroscopy (LIBS) are applied to monitor the time-dependent development of gold nanoparticles for up to 40 hours. Some vegetative cells (VC) are filled with nanoparticles within minutes, while the extracellular polymeric substances (EPS) of vegetative cells and the heterocyst polysaccharide layer (HEP) are the regions, where the first nanoparticles are detected on most other cells. The uptake of gold starts immediately after incubation and within four hours the average size remains constant around 10 nm. Analyzing the TEM images with an image processing program reveals a wide distribution for the diameter of the nanoparticles at all times and in all regions of the cyanobacteria. Finally, the nanoparticle concentration in vegetative cells of Anabaena cylindrica is about 50% higher than in heterocysts (HC). These nanoparticles are found to be located along the thylakoid membranes.

Resonance-stabilized partial proton transfer in hydrogen bonds of incommensurate phenazine-chloranilic acid.

The co-crystal of phenazine (Phz) and chloranilic acid (H2ca) becomes ferroelectric upon cooling through the loss of inversion symmetry. Further cooling results in the development of an incommensurate ferroelectric phase, followed by a lock-in transition towards a twofold superstructure. Here we present the incommensurately modulated crystal structure of Phz-H2ca at T = 139 K with a symmetry given by the superspace group P2(1)(½ σ(2) ½)0 and σ(2) = 0.5139. The modulation mainly affects the positions of the protons within half of the intermolecular hydrogen bonds that are responsible for the spontaneous polarization in all three low-temperature phases. Evidence for proton transfer in part of the hydrogen bonds is obtained from the correlated dependence on the phase of the modulation of the lengths of bonds involved in resonance stabilization of the acidic anion, and much smaller variations of bond lengths of atoms not involved in the resonance mechanism. Incommensurability is explained as competition between proton transfer favored for single hydrogen bonds on the basis of pKa values and avoiding unfavorable Coulomb repulsion within the lattice of the resulting ionic molecules.

N-H···O and C-H···F hydrogen bonds in the incommensurately modulated crystal structure of adamantan-1-ammonium 4-fluorobenzoate.

At low temperatures the organic salt adamantan-1-ammonium 4-fluorobenzoate, C10H18N(+)·C7H4FO2(-), possesses an incommensurately modulated crystal structure. The effect of the modulation on the atomic arrangement and intermolecular interactions is studied by analysing single-crystal X-ray diffraction data within the (3 + 1)-dimensional superspace approach and superspace group P2(1)/n(α0γ)00. The modulation strongly affects the position of the atoms as well as their atomic displacement parameters. Nevertheless, the molecular cations and anions are built by rigid moieties, which vary their orientation with respect to each other as a function of the phase of the modulation t. Cations and anions are connected into slabs by dense N-H···O and C-H···F hydrogen-bonded networks, which are characterized by being rather rigid and which show only a little variation as a function of the phase of the modulation t.

More about residual values.

The usual residual values are complemented by expectation values based solely on the experimental data and the number of model parameters. These theoretical R values serve as benchmark values when all of the basic assumptions for a least-squares refinement, i.e. no systematic errors and a fully adequate model capable of describing the data, are fulfilled. The prediction of R values as presented here is applicable to any field where model parameters are fitted to data with known precision. For crystallographic applications, F(2)-based residual benchmark values are given. They depend on the first and second moments of variance, intensity and significance distributions, <σ(2)>, , . Possible applications of the theoretical R values are, for example, as a data-quality measure or the detection of systematic deviations between experimental data and model predicted data, although the theoretical R values cannot identify the origin of these systematic deviations. The change in R values due to application of a weighting scheme is quantified with the theoretical R values.

Antiviral agents derived from novel 1-adamantyl singlet nitrenes.

BACKGROUND: Amantadine constitutes an interesting, diamond crystal lattice-shaped, antivirally active amine with an inhibitory effect on influenza A viruses causing common 'flu' in humans. Unfortunately, amantadine forfeited most of its therapeutic potential because of resistance development in recent influenza A virus isolates. The antiviral efficacy of amantadine congeners can be chemically modified, resulting in re-constitution, improvement and/or extension of antiviral activities mediated by amino-adamantyls. METHODS: Newly synthesized compounds were evaluated towards HIV type-1 (HIV-1) replication in primary human lymphocytes. One N-phenacyl amantadine derivative was investigated for inhibiting the in vitro replication of respiratory viruses (influenza A viruses, influenza B virus, human parainfluenza virus type 3 and severe acute respiratory syndrome coronavirus). RESULTS: Two ketone-stabilized 1-adamantyl singlet nitrenes were discovered serendipitously. To our best knowledge these are the first persistently stable nitrenes to be reported. Their structure was proved by determining the X-ray single crystal structure of one hydrolytic elaboration product. This salt adduct revealed an incommensurately modulated crystal structure, which was solved by extensive computational refinement. We could show that ketone-stabilized 1-adamantyl singlet nitrenes are versatile synthons for the synthesis of antiviral drug candidates. An amantadine-folate conjugate was inhibitory on HIV-1 replication in primary human lymphocytes, and one N-phenacyl amantadine derivative was inhibitory towards low pathogenic avian influenza A virus (H5N1) replication in vitro. CONCLUSIONS: These results indicate that the aromatic-aliphatic ketone-stabilized 1-adamantyl singlet nitrenes, beyond being of fundamental interest in organic chemistry, represent versatile synthons for the synthesis of new amantadine-related potentially antiviral drugs.

Electron-deficient and polycenter bonds in the high-pressure γ-B28 phase of boron.

The peculiar bonding situation in γ boron is characterized on the basis of an experimental electron-density distribution which is obtained by multipole refinement against low-temperature single-crystal x-ray diffraction data. A topological analysis of the electron-density distribution reveals one-electron-two-center bonds connecting neighboring icosahedral B(12) clusters. A unique polar-covalent two-electron-three-center bond between a pair of atoms of an icosahedral cluster and one atom of the interstitial B(12) dumbbell explains the observed charge separation in this high-pressure high-temperature polymorph of boron.

Modulated anharmonic ADPs are intrinsic to aperiodic crystals: a case study on incommensurate Rb2ZnCl4.

A combination of structure refinements, analysis of the superspace MEM density and interpretation of difference-Fourier maps has been used to characterize the incommensurate modulation of rubidium tetrachlorozincate, Rb(2)ZnCl(4), at a temperature of T = 196 K, close to the lock-in transition at T(lock-in) = 192 K. The modulation is found to consist of a combination of displacement modulation functions, modulated atomic displacement parameters (ADPs) and modulated third-order anharmonic ADPs. Up to fifth-order Fourier coefficients could be refined against diffraction data containing up to fifth-order satellite reflections. The center-of-charge of the atomic basins of the MEM density and the displacive modulation functions of the structure model provide equivalent descriptions of the displacive modulation. Modulations of the ADPs and anharmonic ADPs are visible in the MEM density, but extracting quantitative information about these modulations appears to be difficult. In the structure refinements the modulation parameters of the ADPs form a dependent set, and ad hoc restrictions had to be introduced in the refinements. It is suggested that modulated harmonic ADPs and modulated third-order anharmonic ADPs form an intrinsic part, however small, of incommensurately modulated structures in general. Refinements of alternate models with and without parameters for modulated ADPs lead to significant differences between the parameters of the displacement modulation in these two types of models, thus showing the modulation of ADPs to be important for a correct description of the displacive modulation. The resulting functions do not provide evidence for an interpretation of the modulation by a soliton model.

Modulated structure of nepheline.

The incommensurately modulated structure of a natural nepheline of composition K(0.54)Na(3.24)Ca(0.03)Al(3.84)Si(4.16)O(16) has been determined in superspace. The compound crystallizes in the trigonal centered superspace group X3(00γ)0 with γ = 0.2048 (10), X = (0, 0, 0, 0), (1/3, 2/3, 0, 2/3), (2/3, 1/3, 0, 1/3), a = 17.2889 (8) and c = 8.3622 (10) Å. The structure is characterized by a framework of corner-connected (Al,Si)O(4) tetrahedra. The additional cations are incorporated in two different types of channels of the framework. All atoms in the structure are displacively modulated with amplitudes below 0.1 Å. The modulation can be well described taking into account harmonics of first order only. Atomic positions in the smaller channels of the framework are fully occupied by Na(+). Cationic positions in the larger channel are occupationally modulated, yet the variation of electron density as a function of the internal coordinate t is very small and indicates that the incorporation of different types of cations (K(+), Na(+), Ca(2+)) and vacancies is realised in a highly disordered way. Average T-O distances indicate a nearly complete Al/Si ordering in the tetrahedral framework. A large part of the O atoms are approximated by split-atom positions, which are additionally affected by occupational modulation resulting in a high degree of disorder in the modulated structure. Occupational probabilities for the split-atom positions are complementary. Occupational modulations of the cations in the larger channels and the O atoms of the tetrahedral framework are coupled and correlations between occupational and displacive modulations exist.

Orientational disorder in Lambda-cobalt(III) sepulchrate trinitrate.

The crystal structure of Lambda-(1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]eicosane)cobalt(III) trinitrate, [Co(C(12)H(30)N(8))](NO(3))(3), consists of a sepulchrate moiety that serves as a macrobicyclic nitrogen cage for the Co(3+) cation, which is six-coordinated by N atoms, and three nitrate anions. The Co-sepulchrate group lies on a threefold axis (site symmetry 32), as do two symmetry-related and ordered nitrate groups (site symmetry 3), with which it is connected via N-H...O hydrogen bonds [Co-N = 5.1452 (12) A]. The third nitrate group is disordered as a result of symmetry requirements around the origin (site symmetry 32), and is further away from the Co-sepulchrate cage [Co-N = 6.3160 (8) A]. The structure is described by applying orientational disorder over six equivalent orientations for the disordered nitrate group, which is considered as an ideal planar molecule of regular trigonal geometry with its molecular plane rotated out of the ab plane and the molecular centre of gravity slightly shifted away from the origin. This new model for disorder clearly improves a previous crystal structure determination.

Modulation functions of incommensurately modulated Cr2P2O7 studied by the maximum entropy method (MEM).

The maximum entropy method (MEM) has been used to determine electron density in superspace of incommensurately modulated chromium pyrophosphate from X-ray diffraction data measured by Palatinus et al. [(2006), Acta Cryst. B62, 556-566]. Chromium pyrophosphate, Cr(2)P(2)O(7), contains ordered regions (83% of the volume) and regions with disorder. Analysis of the MEM density has allowed the determination of the displacive modulation functions within ordered regions. The disordered regions can be described as the alternate occupation of two conformations of the pyrophosphate group and two positions of the chromium atom, with occupational probabilities that depend continuously on the phase of modulation t. A structure model based on the interpretation of the MEM density provides a fit to the diffraction data of the same quality as the model given by Palatinus et al. (2006). The failure to find a model that better fits the data is attributed to the intrinsic inaccuracy of approximately 0.01 A for positions derived from the MEM and to the difficulties in constructing an appropriate model for the anharmonic ADPs and their modulation functions from electron densities.

A non-mathematical introduction to the superspace description of modulated structures.

The X-ray analysis of (6R,7aS)-6-(tert-butyl-dimethylsilanyloxy)-1-hydroxy-2-phenyl-5,6,7,7a-tetrahydropyrrolizin-3-one, C19H27NO3Si, revealed a diffraction pattern which is typical for modulated structures: strong Bragg peaks surrounded by weaker reflections which cannot be indexed with the same three reciprocal lattice vectors that are used to describe the strong peaks. For this class of crystal structures the concept of superspace has been developed which, however, for many crystallographers still constitutes a Gordian Knot. As a possible tool to cut this knot the crystal structure of the above-mentioned tetrahydropyrrolizinone derivative is presented as an illustrative example for handling and describing the modulated structure of a typical pharmaceutical (i.e. molecular) compound. Having established a working knowledge of the concepts and terminology of the superspace approach a concise and detailed description of the complete process of peak indexing, data processing, structure solution and structure interpretation is presented for the incommensurately modulated crystal structure of the above-mentioned compound. The superspace symmetry applied is P2(1)(alpha0gamma)0; the (incommensurate) q vector components at 100 K are alpha = 0.1422 (2) and gamma = 0.3839 (8).

Superspace description of the crystal structures of Ca(n)(Nb,Ti)nO3n + 2 (n = 5 and 6).

The crystal structures of two members of the homologous series Ca(n)(Nb,Ti)(n)O(3n + 2), with n = 5 and 6, are presented within the superspace formalism. A common (3 + 1)-dimensional superspace model is used to describe the crystal structures of both compositions within a particular homologous series, where the primary modulation wavevector and the width of the atomic domains vary systematically with composition. The two crystal structures are characterized as commensurately modulated structures consisting of discontinuous atomic domains described by occupational crenel functions. The displacive modulation functions for the two compounds exhibit similarities, but they also show that the idea of a unified superspace model does not extend toward the precise atomic positions. For n = 6, the centrosymmetric (3 + 1)-dimensional superspace symmetry provides a natural explanation for the pseudo-symmetries that are present in the non-centrosymmetric (three-dimensional) superstructure of this compound. The efficiency of the superspace approach is demonstrated by structure refinements in (3 + 1)-dimensional superspace and by comparing these results with the refinements in their three-dimensional superstructures.

Description of Ba(1 + x)Ni(x)Rh(1 - x)O3 with x = 0.1170 (5) in superspace: modulated composite versus modulated-layer structure.

The structure of the compound Ba(1 + x)Ni(x)Rh(1 - x)O3 [x = 0.1170 (5)] has been analyzed at room temperature within the (3 + 1)-dimensional superspace approach using single-crystal X-ray diffraction data. Two different models are presented, the compound is refined as modulated composite as well as modulated-layer structure. In both models discontinuous atomic domains are applied to describe the structural modulations. While the first approach stresses the pseudo-one-dimensional constitution, the latter highlights the layered character of these structures.