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.

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.

Differences and similarities among hypoxanthinium nitrate hydrate structures

2019 ◽  
Vol 75 (8) ◽  
pp. 1036-1044 ◽  
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Roman Gajda ◽  
Anna Hoser ◽  
Anna Makal ◽  
Paulina Maria Dominiak
Keyword(s):  
Room Temperature ◽  
Temperature Phase ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
X Ray ◽  
Nitrate Hydrate ◽  
Different Temperatures ◽  
Lower Temperature ◽  
Low Temperature Phase ◽  
Nitrate Anions

Crystals of hypoxanthinium (6-oxo-1H,7H-purin-9-ium) nitrate hydrates were investigated by means of X-ray diffraction at different temperatures. The data for hypoxanthinium nitrate monohydrate (C5H5N4O+·NO3 −·H2O, Hx1) were collected at 20, 105 and 285 K. The room-temperature phase was reported previously [Schmalle et al. (1990). Acta Cryst. C46, 340–342] and the low-temperature phase has not been investigated yet. The structure underwent a phase transition, which resulted in a change of space group from Pmnb to P21/n at lower temperature and subsequently in nonmerohedral twinning. The structure of hypoxanthinium dinitrate trihydrate (H3O+·C5H5N4O+·2NO3 −·2H2O, Hx2) was determined at 20 and 100 K, and also has not been reported previously. The Hx2 structure consists of two types of layers: the `hypoxanthinium nitrate monohydrate' layers (HX) observed in Hx1 and layers of Zundel complex H3O+·H2O interacting with nitrate anions (OX). The crystal can be considered as a solid solution of two salts, i.e. hypoxanthinium nitrate monohydrate, C5H5N4O+·NO3 −·H2O, and oxonium nitrate monohydrate, H3O+(H2O)·NO3 −.

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.

Crystal structure and phase transition of thermoelectric SnSe

2016 ◽  
Vol 72 (3) ◽  
pp. 310-316 ◽  
Author(s):  
Mattia Sist ◽  
Jiawei Zhang ◽  
Bo Brummerstedt Iversen
Keyword(s):  
Phase Transition ◽  
High Temperature ◽  
Site Occupancy ◽  
Functional Materials ◽  
Atomic Displacement ◽  
High Temperature Phase ◽  
Temperature Phase ◽  
Lattice Constants ◽  
Temperature Phase Transition ◽  
Atomic Displacement Parameters

Tin selenide-based functional materials are extensively studied in the field of optoelectronic, photovoltaic and thermoelectric devices. Specifically, SnSe has been reported to have an ultrahigh thermoelectric figure of merit of 2.6 ± 0.3 in the high-temperature phase. Here we report the evolution of lattice constants, fractional coordinates, site occupancy factors and atomic displacement factors with temperature by means of high-resolution synchrotron powder X-ray diffraction measured from 100 to 855 K. The structure is shown to be cation defective with a Sn content of 0.982 (4). The anisotropy of the thermal parameters of Sn becomes more pronounced approaching the high-temperature phase transition (∼ 810 K). Anharmonic Gram–Charlier parameters have been refined, but data from single-crystal diffraction appear to be needed to firmly quantify anharmonic features. Based on modelling of the atomic displacement parameters the Debye temperature is found to be 175 (4) K. Conflicting reports concerning the different coordinate system settings in the low-temperature and high-temperature phases are discussed. It is also shown that the high-temperatureCmcmphase is not pseudo-tetragonal as commonly assumed.

Energetic materials: variable-temperature crystal structures of two biguanidinium dinitramides

2003 ◽  
Vol 36 (6) ◽  
pp. 1334-1341 ◽  
Author(s):  
Nadezhda B. Bolotina ◽  
Michaele J. Hardie ◽  
A. Alan Pinkerton
Keyword(s):  
Thermal Expansion ◽  
Crystal Structures ◽  
Energetic Materials ◽  
Variable Temperature ◽  
Atomic Displacement ◽  
Thermal Motion ◽  
Linear Temperature Dependence ◽  
Linear Temperature ◽  
Thermal Displacements ◽  
Atomic Displacement Parameters

The crystal structures of the energetic materials biguanidinium mono-dinitramide C2H8N{}_{5}^{\,+}.N3O{}_{4}^{\,-}, (BIGH)(DN), and biguanidinium bis-dinitramide C2H9N{}_{5}^{\,2+}.2N3O{}_{4}^{\,-}, (BIGH2)(DN)2, have been determined at several temperatures in the range 85–298 K using single-crystal X-ray diffraction techniques. The thermal expansion second-rank tensors have been determined to describe the thermal behavior of the crystals studied. Strongly anisotropic thermal expansion is most important in the direction perpendicular to the least-squares planes of the dinitramide ions in both cases, suggesting that the atomic thermal motion is significantly anharmonic in these crystals. Anharmonicity of thermal motion is also evident from the non-linear temperature dependence of the atomic displacement parameters. Rigid-body analysis of thermal motion both of dinitramide anions and of biguanidinium cations was performed using the libration and translation second-rank tensors. For both compounds, the libration thermal motion is strongly anisotropic with the dominating libration axes oriented in a similar manner in both anions and cations. Although the translation motion of the ions is not strongly anisotropic, the axes of largest thermal displacements are close to the directions of greatest thermal expansion of the crystals.

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.

Online_DPI: a web server to calculate the diffraction precision index for a protein structure

2015 ◽  
Vol 48 (3) ◽  
pp. 939-942 ◽  
Author(s):  
K. S. Dinesh Kumar ◽  
M. Gurusaran ◽  
S. N. Satheesh ◽  
P. Radha ◽  
S. Pavithra ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Three Dimensional ◽  
Web Server ◽  
Data Bank ◽  
Atomic Displacement ◽  
Precision Index ◽  
Client Machine ◽  
Atomic Displacement Parameters ◽  
Temperature Factors ◽  
Coordinate Error

An online computing server,Online_DPI(where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e.atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

DebyeFit: a simple tool to obtain an appropriate model of atomic vibrations in solids from atomic displacement parameters obtained at different temperatures

2019 ◽  
Vol 52 (3) ◽  
pp. 690-692 ◽  
Author(s):  
A. P. Dudka ◽  
N. B. Bolotina ◽  
O. N. Khrykina
Keyword(s):  
Mixed Model ◽  
Characteristic Temperature ◽  
Nonlinear Least Squares ◽  
Atomic Displacement ◽  
Simple Tool ◽  
Atomic Vibrations ◽  
Different Temperatures ◽  
Dynamic Components ◽  
Atomic Displacement Parameters ◽  
Thermal Vibrations

DebyeFit is a simple tool to calculate the Debye or Einstein characteristic temperature of thermal vibrations in crystals from the equivalent atomic displacement parameters (ADPs) of any atom obtained at several temperatures. The ADP values are separated into static and dynamic components to get a best fit to the Debye, Einstein or mixed model. The static term is added to account for possible static disorder. A nonlinear least-squares technique is used to refine the parameters of the model for sets of ADPs observed in multi-temperature structural studies. The program provides a good fit between theoretical and observed ADP values.

Transferability of Empirical Force Fields in Silicates: Lattice-Dynamical Evaluation of Atomic Displacement Parameters and Thermodynamic Properties for the Al2OSiO4 Polymorphs

1997 ◽  
Vol 53 (1) ◽  
pp. 82-94 ◽  
Author(s):  
T. Pilati ◽  
F. Demartin ◽  
C. M. Gramaccioli
Keyword(s):  
Thermodynamic Functions ◽  
Force Fields ◽  
Structure Refinement ◽  
Atomic Displacement ◽  
Poor Quality ◽  
Different Temperatures ◽  
Atomic Displacement Parameters ◽  
Best Fit ◽  
Good Agreement

A Born–von Karman rigid-ion lattice-dynamical model, using empirical atomic charges and valence force fields derived from the best fit to the vibrational frequencies of a group of silicates and oxides, has been applied to andalusite, kyanite and sillimanite, the three naturally occurring Al2OSiO4 polymorphs. For andalusite there is good agreement with the atomic anisotropic displacement parameters (ADP's) derived from accurate crystal structure refinement at different temperatures and with the values of thermodynamic functions, such as the specific heat and entropy. For kyanite, our calculations are successful in reproducing the values of thermodynamic functions, but not the ADP's, almost certainly due to the poor quality of the crystals used in the structure determination. For sillimanite, imaginary frequencies are obtained in a region of the Brillouin zone: such an inadequacy might be ascribed to the presence of fourfold coordinated Al, whose properties are considerably different from those of higher-coordinated Al present in andalusite and kyanite.

scholarly journals Revision of the Li13Si4structure

2013 ◽  
Vol 69 (12) ◽  
pp. i81-i82 ◽  
Author(s):  
Michael Zeilinger ◽  
Thomas F. Fässler
Keyword(s):  
Site Occupancy ◽  
Careful Analysis ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Structure Report ◽  
Diffraction Patterns ◽  
Atomic Displacement Parameters ◽  
A Site

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4(tridecalithium tetrasilicide), the structure of which has been determined previously [Franket al.(1975).Z. Naturforsch. Teil B,30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in theabplane atz= 0 and are strictly separated from the Si–Si dumbbells atz= 0.5.

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