Anisotropic Displacement Parameters (anisotropic + displacement_parameter)

Distribution by Scientific Domains


Selected Abstracts


Torsional Motion in (tert -Butyl)ammonium Hemispheraplexes: Rotational Barriers and Energy of Binding

HELVETICA CHIMICA ACTA, Issue 5 2003
Emily
The ADPs (ADPs=atomic anisotropic displacement parameters) from the single-crystal X-ray studies of nine related TBA+ (TBA+=(tert -butyl)ammonium) hemispheraplexes are analyzed, and the results compared to the free energy of binding of this guest by the nine hosts. The lipophilic hosts (Fig.,1) were synthesized over a number of years, with increasing pre-organization for and specificity of binding. Structural studies for six of the complexes have been published, but the remaining three structures, including those of the strongest binders of TBA+, are disordered and have only now been completed. New area-detector data has been analyzed for the TBA+ClO complexes of 5 and of 8 at two temperatures, while the original data for 9,TBA+SCN, has been treated with a disorder model. In addition, improved models are presented for the complexes of 6 and 7. Methods for assessing the precision of the ADP analyses are discussed. Although most of the structures are imprecise, the TBA+ groups do demonstrate some of the characteristics of independent motion. The general trend in calculated libration amplitudes for the TBA+ group suggests that the guests with the greatest free energy of binding, and the shortest distances from N+ to the ligand plane, are those with the highest barriers to internal rotation. [source]


Experimental charge-density study of paracetamol , multipole refinement in the presence of a disordered methyl group

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009
Joanna M. B
A high-resolution single-crystal X-ray study of paracetamol has been performed at 85,K. Different approaches to modeling the experimental electron density (ED) were tested for the dynamically disordered portions of the molecule in order to check to what extent it is possible to obtain a proper ED distribution in the ordered part. Models were examined in which the methyl-group ED was built from pseudoatoms taken from the University at Buffalo Pseudoatom Databank or the Invariom database, with multipole parameters for the remaining atoms being obtained from free refinement. The ,, restricted multipolar model (KRMM) and free ,, refinements were compared; restriction of the ,, parameters was essential in order to obtain values of the electrostatic interaction energy consistent with the results of theoretical single-point periodic calculations. After simultaneous use of KRMM refinement and the databases to model the methyl group, the bond critical point properties and interaction electrostatic energy values were found to be closer to those obtained from theory. Additionally, some discrepancies in the ED distribution and dipole moment among transferred aspherical atom model refinements utilizing both theoretical databases and parameters from theoretical periodic calculations are shown. Including the influence of the crystal field in the periodic calculations increases the ED in the hydroxyl and amide groups, thus leading to higher values of the electrostatic interaction energy, changes in the electrostatic potential values mapped on the isodensity surface and changes in the shape of the anisotropic displacement parameters with respect to results found for both database models. [source]


Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2000

A new model for analysing the temperature evolution of anisotropic displacement parameters (ADP's) is presented. It allows for a separation of temperature-dependent from temperature-independent contributions to ADP's and provides a fairly detailed description of the temperature-dependent large-amplitude molecular motions in crystals in terms of correlated atomic displacements and associated effective vibrational frequencies. It can detect disorder in the crystal structure, systematic error in the diffraction data and the effects of non-spherical electron-density distributions on ADP's in X-ray data. The analysis requires diffraction data measured at multiple temperatures. [source]


Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2000

The temperature evolution of atomic anisotropic displacement parameters (ADP's) of perdeuterobenzene and of urea in the temperature range between 12 and 123,K is investigated in terms of the model presented in paper I. For the benzene molecule, the temperature-dependent contributions to the ADP's are well described by three molecular librations and three molecular translations. For the urea molecule, the analysis revealed a low-frequency high-amplitude normal mode (~64,cm,1), which combines out-of-plane deformations of the NH2 groups with molecular libration. The pyramidalization motion allows the hydrogen-bonding pattern to be retained quite well, whereas this pattern is heavily distorted in the higher-frequency molecular librations. The results presented for urea go a step beyond those obtainable in a conventional rigid-body or segmented-rigid-body analysis because they show how correlations of atomic displacements in molecular crystals can be determined from the temperature evolution of ADP's. For both molecules, the analysis reveals temperature-independent contributions to the ADP's accounting for the high-frequency internal vibrations. It is the first time that such contributions have been extracted directly from single-crystal diffraction data for light atoms like hydrogen and deuterium as well as for heavier atoms like carbon, nitrogen and oxygen. These contributions agree well with those calculated from independent spectroscopic information. [source]


Following an isosymmetric phase transition by changes in bond lengths and anisotropic displacement parameters: the case of meta -carboxyphenylammonium phosphite

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2009
El-Eulmi Bendeif
Crystal structure studies in the 100,345,K temperature range were performed to relate the molecular structure changes of meta -carboxyphenylammonium phosphite (m -CPAMP) to its first-order phase transition at Tc = 246,(2),K. Thermal displacement parameters and most bond distances show an abrupt jump at the transition. Such a structural change is related to collective effects leading to competition between intra- and intermolecular interactions. [source]


The structure of orange HgI2.

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2002

The metastable orange crystals of HgI comprise three different crystal structures, all of which are built from corner-linked HgI supertetrahedra. Two of them are end members with the maximum degree of order (MDO) of a polytypic layer structure; the third shows a three-dimensional linkage. This paper presents the determination from X-ray diffraction data of the tetragonal polytypic structures and their stacking disorder. Diffraction patterns show sharp Bragg reflections and rods of diffuse intensity with pronounced maxima. In a first step, the diffuse intensity was neglected and all maxima were treated as Bragg reflections. The crystal was supposed to be a conglomerate of the two MDO structures diffracting independently, and their parameters and volume ratio were refined against the single data set. The geometries and anisotropic displacement parameters of the layers in the two structures are shown to be nearly identical. Layer contacts in the two stacking modes are identical. The structures are fractal complications of the stable red form of HgI. In a second step, the stacking disorder has been quantitatively analyzed with a Markov chain model. Two probabilities describing next-nearest-layer interactions were visually adjusted to observed intensity profiles extracted from image-plate detector data. Results consistently show that the crystal comprises nearly equal volumes of MDO structures with an average domain thickness of about 5 layers or 30,Å. [source]


Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction.

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002
Comparison of thermal expansion, molecular dynamics with spectroscopic results
Crystalline 4-isopropylphenol, C9H12O, an optically non-linear material, was studied by X-ray diffraction in order to deter­mine its structure at several temperatures in the 95,300,K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra. [source]


K2ScSn(AsO4)3: an arsenate-containing langbeinite

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010
William T. A. Harrison
The title compound, dipotassium tri-,-arsenato-scandium(III)tin(IV), is the first arsenate-containing langbeinite to be characterized by single-crystal methods and crystallizes in the aristotype P213 cubic symmetry for this structure type in which the K+ ions and the octahedral scandium and tin cations lie on crystallographic threefold axes. The ScIII and SnIV ions show a slight segregation over the two octahedral sites, with Sc/Sn populations of 0.582,(5):0.418,(5) on one site and 0.418,(5):0.582,(5) on the other. Bond-valence-sum calculations indicate that the K+ ions are significantly underbonded in this structure and the O atoms show large anisotropic displacement parameters, as also seen in other langbeinites. The crystal studied was found to be a merohedral twin with a 0.690,(16):0.310,(16) domain ratio. [source]


Hexagonal high-temperature form of aluminium phosphate tridymite from X-ray powder data

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2001
Heribert A. Graetsch
Similar to silica tridymite, AlPO4 tridymite shows a sequence of displacive phase transitions resulting in a dynamically disordered hexagonal high-temperature modification. Rietveld refinement reveals that the thermal motions of the tetrahedra can be described either by strongly anisotropic displacement parameters for oxy­gen or by split O atoms. Due to the ordered distribution of aluminium and phospho­rus over alternating tetrahedra, the space group symmetry of high-temperature AlPO4 tridymite is reduced with respect to SiO2 tridymite from P63/mmc to P63mc. [source]


A single-crystal neutron diffraction study of RbTiOAsO4

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2000
Jenni Nordborg
A rubidium titanyl arsenate single-crystal has been studied by neutron diffraction (, = 1.207,Å). The polished sample used was 5 × 3 × 2,mm and was cut from a crystal made by top-seeded solution growth. The crystal showed severe extinction. It was, however, possible to obtain a structural model with well defined oxy­gen sites and reasonable anisotropic displacement parameters. [source]


Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009
Daisuke Hira
The crystal structure of native pseudoazurin (HdPAz) from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans has been determined at a resolution of 1.18,Å. After refinement with SHELX employing anisotropic displacement parameters and riding H atoms, Rwork and Rfree were 0.135 and 0.169, respectively. Visualization of the anisotropic displacement parameters as thermal ellipsoids provided insight into the atomic motion within the perturbed type 1 Cu site. The asymmetric unit includes three HdPAz molecules which are tightly packed by head-to-head cupredoxin dimer formation. The shape of the Cu-atom ellipsoid implies significant vibrational motion diagonal to the equatorial xy plane defined by the three ligands (two His and one Cys). The geometric parameters of the type 1 Cu site in the HdPAz structure differ unambiguously from those of other pseudoazurins. It is demonstrated that their structural aspects are consistent with the unique visible absorption spectrum. [source]


Monellin (MNEI) at 1.15,Å resolution

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2007
J. R. Hobbs
The X-ray crystal structure of a single-chain monellin protein (MNEI) has been determined at 1.15,Å resolution. The model was refined to convergence employing anisotropic displacement parameters and riding H atoms to produce a final model with Rwork and Rfree values of 0.132 and 0.162, respectively. The crystal contains a single MNEI protein in the asymmetric unit and unusually lacks the dimer interface observed in all previous crystal structures of monellin and its single-chain derivatives. The high resolution allowed a more detailed view of MNEI than previously possible, with 38 of the 96 residues modelled with alternative side-chain conformations, including four core residues Thr12, Cys41, Leu62 and Ile75. Four stably bound negative ions were also located, providing new insight into potential electrostatic interactions of MNEI with the largely negatively charged surface of the sweet taste receptor T1R2,T1R3. [source]