Biomedical subjects

Sander van Smaalen

Publications and source records attributed to Sander van Smaalen.

17 recordsLinked to original sources

PubMed2005

Twinning and structure of Eu(0.6)Sr(0.4)MnO3.

The crystal structure of europium strontium manganese trioxide, Eu(0.6)Sr(0.4)MnO3, has been refined using a multiply twinned single crystal containing six twin components. The MnO6 octahedra show Jahn-Teller distortions with nearly fourfold symmetry, but the octahedral tilting scheme reduces the crystal symmetry to orthorhombic (space group Pbnm). The refinement of site occupancies and the analysis of difference Fourier maps show that the Eu3+ and Sr2+ cations occupy different crystallographic positions with eightfold and twelvefold coordination, respectively.

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PubMed2005

Monoclinic La1-xBaxMnO3 (x=0.185) at 160 K.

Single-crystal X-ray diffraction has shown that lanthanum barium manganese trioxide, La0.815Ba0.185MnO3, is monoclinic (I2/c) below a first-order phase transition at 187.1 (3) K. This result differs from the Pbnm symmetry usually assigned to colossal magnetoresistance oxides, A1-xA'xMnO3 with x approximately 0.2, which adopt a distorted perovskite-type crystal structure. The Mn atom lies on an inversion center, the disordered Li/Ba site is on a twofold axis and one of the two independent O atoms also lies on a twofold axis.

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PubMed2005

Shear strain in Nd0.5Ca0.5MnO3 at high pressures.

High-pressure x-ray powder diffraction has been measured on the half doped rare earth manganite Nd0.5Ca0.5MnO3 up to a pressure of 15 GPa. We report the presence of a quantifiable amount of shear distortion of the MnO6 octahedra in Nd0.5Ca0.5MnO3 at high pressures. The lattice strain of Nd0.5Ca0.5MnO3 is minimal at a crossover pressure of p* approximately 7 GPa, with the same lattice strain above and below this pressure achieved by shear and Jahn-Teller-type distortions, respectively. The increase in shear strain with increasing pressure provides a mechanism for the insulating behavior of manganites at high pressures that has not been considered before.

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PubMed2005

The twofold superstructure of titanium(III) oxybromide at T = 17.5 K.

The low-temperature (T = 17.5 K) structure of titanium(III) oxybromide, TiOBr, is reported as a twofold superstructure of the crystal structure at room temperature. Weak superlattice reflections were measured with synchrotron radiation X-rays and were analyzed by structure refinements employing superspace techniques. Both the low-temperature and the room-temperature structures of TiOBr are isostructural with the corresponding structures of TiOCl. The results indicate that at low temperatures TiOBr is in a spin-Peierls state, similar to that of TiOCl, but with the modulations and relevant interactions smaller than in the latter compound.

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PubMed2005

The prior-derived F constraints in the maximum-entropy method.

The method of the prior-derived F constraints (PDC) enhances the quality of reconstructions of electron densities from X-ray diffraction data by the maximum-entropy method (MEM). The method concentrates on artifacts arising due to inaccurate extrapolation of non-measured data by the MEM. While these artifacts are unavoidable, when a flat prior is used, they can be effectively suppressed, if the prior information about the structure is known in the form of a procrystal prior electron density. The missing, usually high-angle, structure factors can be effectively substituted by the structure factors derived from the procrystal prior. This approach eliminates the occurrence of spurious peaks in the difference electron densities in the vicinity of the atomic positions. The method is illustrated with a simple one-dimensional example. Its use is then demonstrated on simulated data of oxalic acid dihydrate and on experimental data of sodium nitrite.

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PubMed2005

Effect of crystal packing on the structures of polymeric metallocenes.

The pressure dependencies of the crystal structures of the polymeric metallocenes lithium cyclopentadienide (LiCp) and potassium cyclopentadienide (KCp) have been determined by synchrotron X-ray powder diffraction. The decrease of the volume of LiCp by 34% up to a pressure of p = 12.2 GPa and of KCp by 23% at p = 5.3 GPa as well as the bulk moduli of K = 7.7 GPa for LiCp and 4.9 GPa for KCp indicate a high compressibility for these compounds. The crystal structures of KCp have been determined up to p = 3.9 GPa. An increase of the bend angle is found from 45 degrees at p = 0 GPa up to 51 degrees at p = 3.9 GPa. This variation is completely explained by a model invoking attractive K+ Cp- interaction and repulsive nonbonded carbon-carbon interactions. It is proposed that the bend angle in the polymeric alkali metal metallocenes is the result of the optimization of the crystal packing.

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PubMed2004

The Peierls transition in low-dimensional electronic crystals.

An overview is presented of low-dimensional electronic crystals that undergo a phase transition towards a low-temperature charge-density-wave (CDW) state. The emphasis is on inorganic compounds that develop an one-dimensional (1D) CDW. Low-dimensional features of crystal structures are discussed in relation to 1D electronic properties. X-ray diffraction is discussed as a tool to obtain quantitative information about the normal state and its structural fluctuations, and about the CDW, both in equilibrium and in its non-linear conducting state.

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PubMed2004

Incommensurate nature of the multilayered molecular ferromagnetic metals based on bis(ethylenedithio)tetrathiafulvalene and bimetallic oxalate complexes.

The salt [ET]x[MnRh(ox)(3)].CH(2)Cl(2) (x = 2.526(1)) has been obtained and characterized. This paramagnetic metal is essentially isostructural to the ferromagnetic metal [ET]y[MnCr(ox)(3)].CH(2)Cl(2) (y approximately equal to 3) and provides a definite answer on the origin of the structural disorder present on such systems. As in the ferromagnetic analogue, this material shows high electrical conductivity at room temperature (13 S.cm(-1)) and metallic behavior.

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PubMed2004

Structure of incommensurate ammonium tetrafluoroberyllate studied by structure refinements and the maximum entropy method.

Incommensurately modulated ammonium tetrafluoroberyllate (AFB) occurs in a narrow temperature interval between the paraelectric room-temperature phase with space group Pnma (Ti = 178 K) and the ferroelectric low-temperature phase with space group Pna2(1) (Tc = 173 K). The structure is determined from accurate single-crystal X-ray diffraction data collected with synchrotron radiation at 175 K. The superspace group of the structure is Pnma(alpha00)0ss with alpha = 0.4796 (4). Both structure refinements and the maximum entropy method lead to the same structure model, which involves only single harmonic modulations. The building units of the structure are BeF4(2-) and NH4+ complex ions with approximately tetrahedral point symmetry. They are relatively rigid and the modulations consist mainly of translations of the tetrahedra and their rotations around a fixed axis. The modulation is related to changes in the network of the hydrogen bonds. The low-temperature superstructure can be described as a commensurately modulated structure with the same superspace symmetry. The first harmonic modulations of the low-temperature and incommensurate phases are related by a scale factor with a value of approximately two. In addition, the low-temperature phase exhibits a second harmonic modulation that is responsible for shifts along c and the ferroelectricity in this phase. The experimental data of the incommensurate phase do not contain any evidence for the presence of a second harmonic in the modulation functions. This suggests that the development of the second harmonic, i.e. the development of the spontaneous polarization, is responsible for the lock-in transition.

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PubMed2003

Two-dimensionally modulated structure of the rare-earth polysulfide GdS(2-x) (x = 0.18 approximately equal to 13/72).

The crystal structure of GdS(2-x) is determined by single-crystal X-ray diffraction as a 144-fold superstructure of the ZrSSi structure type. The superstructure is described as a two-dimensional, commensurately modulated structure with the superspace group P4/n(alphabeta 1/2)(00)(ss) and with alpha = 1/4 and beta = 1/3. Structure refinements within the classical approach, employing the 144-fold supercell, fail because most of the superlattice reflections have zero intensities within the experimental resolution. Within the superspace approach the absent superlattice reflections are systematically classified as higher-order satellite reflections. Accordingly, the superspace approach has been used to refine the structure model comprising the basic structure positions and the amplitudes of the modulation functions of the three crystallographically independent atoms. The quality of fit to the diffraction data and the values of the refined parameters are independent of the assumption on the true symmetry (incommensurate or a 12 x 12 x 2, I-centred superlattice with different symmetries). Arguments of structural plausibility then suggest that the true structure is a superstructure with space group I4, corresponding to sections of superspace given by (t1, t2) equal to [(4n - 1)/48, (4m - 3)/48] or [(4n - 3)/48, (4m - 1)/48] (n and m are integers). Analysis of the structure, employing both superspace techniques (t plots) and the supercell structure model all show that the superstructure corresponds to an ordering of vacancies and an orientational ordering of S2(2-) dimers within the square layers of the S2 atoms.

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PubMed2003

The maximum-entropy method in superspace.

One of the applications of the maximum-entropy method (MEM) in crystallography is the reconstruction of the electron density from phased structure factors. Here the application of the MEM to incommensurately modulated crystals and incommensurate composite crystals is considered. The MEM is computed directly in superspace, where the electron density in the (3+d)-dimensional unit cell (d > 0) is determined from the scattering data of aperiodic crystals. Periodic crystals (d = 0) are treated as a special case of the general formalism. The use of symmetry in the MEM is discussed and an efficient algorithm is proposed for handling crystal symmetry. The method has been implemented into a computer program BayMEM and applications are presented to the electron density of the periodic crystal NaV(2)O(5) and the electron density of the incommensurate composite crystal (LaS)(1.14)NbS(2). The MEM in superspace is shown to provide a model-independent estimate of the shapes of the modulation functions of incommensurate crystals. The discrete character of the electron density is found to be the major source of error, limiting the accuracy of the reconstructed modulation functions to approximately 10% of the sizes of the pixels. MaxEnt optimization using the Cambridge and Sakata-Sato algorithms are compared. The Cambridge algorithm is found to perform better than the Sakata-Sato algorithm, being faster, always reaching convergence, and leading to more reliable density maps. Nevertheless, the Sakata-Sato algorithm leads to similar density maps, even in cases where it does not reach complete convergence.

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PubMed2003

influence of the molecular structures on the high-pressure and low-temperature phase transitions of plastic crystals.

The crystal structures of tert-butyl-tris(trimethylsilyl)silane, Si[C(CH(3))(3)](1)[Si(CH(3))(3)](3) (Bu1), and di-tert-butyl-bis(trimethylsilyl)silane, Si[C(CH(3))(3)](2)[Si(CH(3))(3)](2) (Bu2), at room temperature and at 105 K have been determined by X-ray powder diffraction; the high-pressure behavior for pressures between 0 and 5 GPa is reported. The room-temperature structures have cubic Fm3m symmetry (Z = 4) with a = 13.2645 (2) A, V = 2333.87 (4) A(3) for Bu1 and a = 12.9673 (1) A, V = 2180.46 (3) A(3) for Bu2. The molecules are arranged in a cubic close packing (c.c.p.) and exhibit at least 48-fold orientational disorder. Upon cooling both compounds undergo a first-order phase transition at temperatures T(c) = 230 (5) K (Bu1) and T(c) = 250 (5) K (Bu2) into monoclinic structures with space group P2(1)/n. The structures at 105 K have a = 17.317 (1), b = 15.598 (1), c = 16.385 (1) A, gamma = 109.477 (4) degrees, V = 4172.7 (8) A(3) and Z = 8 for Bu1and a = 17.0089 (9), b = 15.3159 (8), c = 15.9325 (8) A, gamma = 110.343 (3) degrees, V = 3891.7 (5) A(3) and Z = 8 for Bu2. The severe disorder of the room-temperature phase is significantly decreased and only a two- or threefold rotational disorder of the molecules remains at 105 K. First-order phase transitions have been observed at pressures of 0.13-0.28 GPa for Bu1 and 0.20-0.24 GPa for Bu2. The high-pressure structures are isostructural to the low-temperature structures. The pressure dependencies of the unit-cell Volumes were fitted with Vinet equations of state and the bulk moduli were obtained. At still higher pressures further anomalies in the pressure dependencies of the lattice parameters were observed. These anomalies are explained as additional disorder-order phase transitions.

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PubMed2003

Perovskite-related LaTiO3.41.

Crystals of pentalanthanum pentatitanium heptadecaoxide (La(5)Ti(5)O(17) with 0.3% oxygen excess, or LaTiO(3.41)) have been synthesized by floating-zone melting, and the structure has been solved using single-crystal X-ray diffraction intensities. The monoclinic (P2(1)/c) structure consists of perovskite-like slabs of vertex-sharing TiO(6) octahedra, which are separated by additional oxygen layers. The slabs are five octahedra wide. Due to the adjustment of the TiO(6) octahedra to meet the coordination requirements of the La(3+) cations, a superstructure develops along the a axis.

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PubMed2002

The generalized F constraint in the maximum-entropy method--a study on simulated data.

One of the classical problems in the application of the maximum-entropy method (MEM) to electron-density reconstructions is the uneven distribution of the normalized residuals of the structure factors [|F(obs)(H)|-|F(calc)(H)|]/sigma(H) of the resulting electron density. This distribution does not correspond to the expected Gaussian distribution and it leads to erroneous features in the MEM reconstructions. It is shown that the classical chi(2) constraint is only one of many possible constraints, and that it is too weak to restrict the resulting distribution to the expected Gaussian shape. It is proposed that constraints should be used that are based on the higher-order central moments of the distribution of the structure-factor residuals. In this work, the influence of different constraints on the quality of the MEM reconstruction is investigated. It is proposed that the use of a combined constraint on more than one central moment simultaneously would lead to again improved results. Oxalic acid dihydrate was chosen as model structure, from which several data sets with different resolutions and different levels of noise were calculated and subsequently used in the MEM. The results clearly show that the use of different constraints leads to significantly improved results.

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PubMed2002

Intersubsystem chemical bonds in the misfit layer compounds (LaS)(1.13)TaS(2) and (LaS)(1.14)NbS(2).

The modulated structures of incommensurate composite crystals (La(0.912)S)(1.13)TaS(2) at room temperature and of (La(0.949)S)(1.14)NbS(2) at T = 115 K are refined against high-resolution X-ray data. The compounds are isostructural with superspace group F'm2m(alpha,0,0)00s. For (LaS)(1.13)TaS(2), lattice parameters of the first subsystem TaS(2) were obtained as a = 3.2922 (1), b = 5.7776 (2) and c = 23.013 (2) A. For the second subsystem LaS, the same b and c parameters were found, but a = 5.8090 (8) A. Refinements led to a final structure model with R = 0.036 for 4767 observed unique reflections (R = 0.023 for 2147 main reflections, R = 0.099 for 1554 first-order satellites and R = 0.112 for 1042 second-order satellites). The final model includes modulation parameters up to the second-order harmonics for the displacements of the atoms, for the occupational parameters and for the temperature parameters. A clear correlation is found between the relative positions of the subsystems, the displacement modulation, the occupational modulation and the modulation of the temperature parameters. The analysis shows that the variations in environments are resolved by correlated variations in the temperature factors. For (LaS)(1.14)NbS(2), lattice parameters at T = 115 K of the NbS(2) subsystem were obtained as a = 3.3065 (4), b = 5.7960 (5) and c = 22.956 (3) A. For the LaS subsystem, the same values for b and c were obtained, but a = 5.7983 (7) A. Refinements led to a final structure model with R = 0.048 for 5909 observed unique reflections (R = 0.034 for 2528 main reflections, R = 0.092 for 2171 first-order satellites and R = 0.113 for 1103 second-order satellites). The final structure model is similar to that of (LaS)(1.13)TaS(2). In particular, it is found that the values of the modulation parameters are almost equal and it is concluded that the modulations are independent of the temperature and the replacement of Ta with Nb, and thus represent a general mechanism of resolving the strain between the mutually incommensurate layers.

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PubMed2001

Synchrotron-radiation study of the two-leg spin-ladder (VO)2P2O7 at 120 K.

The crystal structure of the ambient-pressure phase of vanadyl pyrophosphate, (VO)2P2O7, has been precisely determined at 120 K from synchrotron X-ray diffraction data measured on a high-quality single crystal. The structure refinement unambiguously establishes the orthorhombic space group Pca2(1) as the true crystallographic symmetry. Moreover, it improves the accuracy of previously published atomic coordinates by one order of magnitude, and provides reliable anisotropic displacement parameters for all atoms. Along the a axis, the structure consists of infinite two-leg ladders of vanadyl cations, (VO)2+, which are separated by pyrophosphate anions, (P2O7)4-. Parallel to the c axis, the unit cell comprises two alternating crystallographically inequivalent chains of edge-sharing VO5 square pyramids bridged by PO4 double tetrahedra. No structural phase transition has been observed in the temperature range between 300 and 120 K.

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PubMed2001

Structure of compounds E(SnMe3)4 (E = Si, Ge) as seen by high-resolution X-ray powder diffraction and solid-state NMR.

The compounds tetrakis(trimethylstannyl)germane, Ge(SnMe3)4 (1), and tetrakis(trimethylstannyl)silane, Si(SnMe3)4 (2), have crystal structures with the quasispherical molecules in a closed-packed stacking. At room temperature both structures have the space group P1 (Z = 2) with a = 9.94457 (5), b = 14.52927 (8), c = 9.16021 (5) A, alpha = 90.53390 (30), beta = 111.73080 (30), gamma = 90.0049 (4) degrees, and V = 1229.414 (12) A3 for (1) and a = 9.92009 (7), b = 14.51029 (11), c = 9.13585 (7) A, alpha = 90.4769 (4), beta = 111.6724 (4), gamma = 89.9877 (6) degrees, and V = 1222.037 (16) A3 for (2). The molecules are found to be ordered as a result of steric interactions between neighboring molecules, as shown by analyzing the distances between the atoms. Upon heating, both compounds undergo a first-order phase transition at temperatures T(c) = 348 +/- 5 K, as characterized by a relative jump of the lattice parameter of approximately 16%. At 353 K, both structures have the space group P1 (Z = 4), with a = 14.2037 (2) A, and V = 2865.52 (7) A3 for (1) and a = 14.1346 (2) A, and V = 2823.90 (7) A3 for (2). Rietveld refinements were performed for the low-temperature phases measured at T = 295 K [R(wp) = 0.0844 for (1), R(wp) = 0.0940 for (2)] and for the high-temperature phases measured at T = 353 K [R(wp) = 0.0891 for (1), R(wp) = 0.0542 for (2)]. The combination of high-resolution X-ray powder diffraction measurements and variable-temperature magic-angle-spinning 13C, 29Si and 119Sn NMR experiments demonstrates low crystallographic and molecular (C1) symmetries for the low-temperature phases of (1) and (2) at temperatures T < 348 +/- 5 K and high crystallographic symmetry due to rotational disorder for the high-temperature phases at temperatures T > 348 +/- 5 K.

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