scholarly journals From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

2018 ◽  
Vol 74 (7) ◽  
pp. 621-631 ◽  
Author(s):  
Pavel V. Afonine ◽  
Paul D. Adams ◽  
Alexandre Urzhumtsev
Keyword(s):  
Rigid Body ◽  
Atomic Displacement ◽  
Atomic Group ◽  
Acta Cryst ◽  
Atomic Models ◽  
Atomic Displacement Parameters ◽  
Atomic Parameters

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63–76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate

2011 ◽  
Vol 67 (1) ◽  
pp. 53-62 ◽  
Author(s):  
Stef Smeets ◽  
Pascal Parois ◽  
Hans-Beat Bürgi ◽  
Martin Lutz
Keyword(s):  
Three Dimensional ◽  
Atomic Displacement ◽  
Thermal Motion ◽  
Temperature Phase ◽  
Acta Cryst ◽  
Bond Behaviour ◽  
Different Temperatures ◽  
Jahn Teller ◽  
Atomic Displacement Parameters ◽  
A Site

The crystal structures of the title compounds have been determined in the temperature range 140–290 K for the zinc complex, and 190–270 K for the copper complex. The two structures are isostructural in the trigonal space group P{\bar{3}1c} with the sulfate anion severely disordered on a site with 32 (D 3) symmetry. This sulfate disorder leads to a disordered three-dimensional hydrogen-bond network, with the N—H atoms acting as donors and the sulfate O atoms as acceptors. The displacement parameters of the N and C atoms in both compounds contain disorder contributions in the out-of-ligand plane direction owing to ring puckering and/or disorder in hydrogen bonding. In the Zn compound the vibrational amplitudes in the bond directions are closely similar. Their differences show no significant deviations from rigid-bond behaviour. In the Cu compound, a (presumably) dynamic Jahn–Teller effect is identified from a temperature-independent contribution to the displacement ellipsoids of the N atom along the N—Cu bond. These conclusions derive from analyses of the atomic displacement parameters with the Hirshfeld test, with rigid-body models at different temperatures, and with a normal coordinate analysis. This analysis considers the atomic displacement parameters (ADPs) from all different temperatures simultaneously and provides a detailed description of both the thermal motion and the disorder in the cation. The Jahn–Teller radii of the Cu compound derived on the basis of the ADP analysis and from the bond distances in the statically distorted low-temperature phase [Lutz (2010). Acta Cryst. C66, m330–m335] are found to be the same.

Distortion of Crystal Structures of Some CoIII Ammine Complexes. III. Distortion of Crystal Structure of [Co(NH3)5NO2]Cl2 at Hydrostatic Pressures up to 3.5 GPa

1998 ◽  
Vol 54 (6) ◽  
pp. 798-808 ◽  
Author(s):  
E. V. Boldyreva ◽  
D. Yu. Naumov ◽  
H. Ahsbahs
Keyword(s):  
Atomic Displacement ◽  
Structural Distortion ◽  
X Ray Diffraction ◽  
Full Data ◽  
Ammine Complexes ◽  
Acta Cryst ◽  
Cell Parameters ◽  
Diamond Anvil ◽  
Atomic Displacement Parameters

This contribution continues comparative studies on the anisotropy of structural distortion of some CoIII ammine complexes induced by various actions [Boldyreva, Kivikoski & Howard (1997a). Acta Cryst. B53, 394–404; Boldyreva, Kivikoski & Howard (1997b). Acta Cryst. B53, 405–414]. Changes in the cell parameters of (OC-6-22)-pentaamminenitro-N-cobalt(III) dichloride were measured by single-crystal X-ray diffraction at pressures up to 3.5 GPa in a diamond anvil cell (DAC). At several pressures (ambient, 0.24, 0.52, 1.25, 1.91 and 3.38 GPa) a full data collection was carried out, and the atomic coordinates and anisotropic atomic displacement parameters were refined. The anisotropy of structural distortion under pressure was shown to be qualitatively different compared with that on cooling (Boldyreva, Kivikoski & Howard, 1997b). The role of the non-covalent interactions, in particular hydrogen bonds, in the anisotropy of structural distortion is discussed.

scholarly journals Redetermination of the crystal structure of R 5Si4 (R = Pr, Nd) from single-crystal X-ray diffraction data

2020 ◽  
Vol 76 (4) ◽  
pp. 510-513
Author(s):  
Kaori Yokota ◽  
Ryuta Watanuki ◽  
Miki Nakashima ◽  
Masatomo Uehara ◽  
Jun Gouchi ◽  
...  
Keyword(s):  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Atomic Displacement ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
X Ray ◽  
Atomic Displacement Parameters ◽  
First Time

The crystal structures of praseodymium silicide (5/4), Pr5Si4, and neodymium silicide (5/4), Nd5Si4, were redetermined using high-quality single-crystal X-ray diffraction data. The previous structure reports of Pr5Si4 were only based on powder X-ray diffraction data [Smith et al. (1967). Acta Cryst. 22 940–943; Yang et al. (2002b). J. Alloys Compd. 339, 189–194; Yang et al., (2003). J. Alloys Compd. 263, 146–153]. On the other hand, the structure of Nd5Si4 has been determined from powder data [neutron; Cadogan et al., (2002). J. Phys. Condens. Matter, 14, 7191–7200] and X-ray [Smith et al. (1967). Acta Cryst. 22 940–943; Yang et al. (2002b). J. Alloys Compd. 339, 189–194; Yang et al., (2003). J. Alloys Compd. 263, 146–153] and single-crystal data with isotropic atomic displacement parameters [Roger et al., (2006). J. Alloys Compd. 415, 73–84]. In addition, the anisotropic atomic displacement parameters for all atomic sites have been determined for the first time. These compounds are confirmed to have the tetragonal Zr5Si4-type structure (space group: P41212), as reported previously (Smith et al., 1967). The structure is built up by distorted body-centered cubes consisting of Pr(Nd) atoms, which are linked to each other by edge-sharing to form a three-dimensional framework. This framework delimits zigzag channels in which the silicon dimers are situated.

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

scholarly journals Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

2021 ◽  
Vol 8 (4) ◽  
pp. 044701
Author(s):  
Zhen Su ◽  
Medhanjali Dasgupta ◽  
Frédéric Poitevin ◽  
Irimpan I. Mathews ◽  
Henry van den Bedem ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Atomic Displacement ◽  
Potential Utility ◽  
X Ray ◽  
Protein X ◽  
Atomic Displacement Parameters

Incommensurate modulation of calcium barium niobate (CBN28 and Ce:CBN28)

2012 ◽  
Vol 68 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Heribert A. Graetsch ◽  
Chandra Shekhar Pandey ◽  
Jürgen Schreuer ◽  
Manfred Burianek ◽  
Manfred Mühlberg
Keyword(s):  
Crystal Structures ◽  
Tungsten Bronze ◽  
Atomic Displacement ◽  
Type Structure ◽  
Formula Unit ◽  
Tetragonal Tungsten Bronze ◽  
First Order ◽  
Oxygen Coordination ◽  
Incommensurate Modulation ◽  
Atomic Displacement Parameters

The incommensurately modulated crystal structures of Ca0.28Ba0.72Nb2O6 (CBN28) and Ce0.02Ca0.25Ba0.72Nb2O6 (Ce:CBN28) were refined in the supercentred setting X4bm(AA0,−AA0) of the 3 + 2-dimensional superspace group P4bm(aa½,−aa½). Both compounds are isostructural with a tetragonal tungsten bronze-type structure. The modulation of CBN28 consists of a wavy distribution of Ba and Ca atoms as well as vacancies on the incompletely occupied Me2 site with 15-fold oxygen coordination. The occupational modulation is coupled with a modulation of the atomic displacement parameters and a very weak modulation of the positional parameters of Me2. The surrounding O atoms show strong displacive modulations with amplitudes up to ca 0.2 Å owing to the cooperative tilting of the rigid NbO6 octahedra. The Me1 site with 12-fold coordination and Nb atoms are hardly affected by the modulations. Only first-order satellites were observed and the modulations are described by first-order harmonics. In Ce:CBN28 cerium appears to be located on both the Me2 and Me1 sites. Wavevectors and structural modulations are only weakly modified upon substitutional incorporation of 0.02 cerium per formula unit of calcium.

scholarly journals Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

2010 ◽  
Vol 67 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Sławomir Domagała ◽  
Parthapratim Munshi ◽  
Maqsood Ahmed ◽  
Benoît Guillot ◽  
Christian Jelsch
Keyword(s):  
Comparative Study ◽  
Charge Density ◽  
Topological Analysis ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Experimental Database ◽  
Figures Of Merit ◽  
Atom Model ◽  
Atomic Displacement Parameters ◽  
Model Approach

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

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