4f-Electron Density Distribution in Crystals of CeB6 at 165 K and its Analysis Based on the Crystal Field Theory

1997 ◽  
Vol 53 (1) ◽  
pp. 143-152 ◽  
Author(s):  
K. Tanaka ◽  
Y. Kato ◽  
Y. Onuki
Keyword(s):  
Field Theory ◽  
Density Distribution ◽  
Electron Density ◽  
Crystal Field ◽  
Electron Density Distribution ◽  
Kondo Effect ◽  
Crystal Field Theory ◽  
X Ray ◽  
Deformation Density ◽  
Density Map

4f-Electron density in single crystals of CeB6, cerium hexaboride, was measured at 165 K by X-ray diffractometry. Significant peaks 2.0 e Å−3 high were found along the \langle100\rangle directions at 0.41 Å from Ce on the deformation density map. Analysis based on the crystal field theory removed the peaks, confirming that they were due to the Ce 4f-electrons on the t 1u -orbital. The deformation density in the B6 octahedron was also markedly improved by the analysis and coincides qualitatively with a theoretical molecular orbital (MO) calculation. It also coincides with the model deformation density map of CaB6 composed of only light atoms. These facts guarantee the accuracy of the intensity measurement for the present study. Since Ce3+ has only one 4f-electron, a highly accurate intensity measurement is necessary to detect its 4f-electron density distribution. A ψ-scan technique was therefore employed to avoid multiple diffraction (MD) and to measure the intensities at ω and χ angles with minimum fluctuation of temperature at the sample position. Relativistic radial functions for orbitals of Ce3+ and the corresponding scattering factors, which take the aspherical electron density distribution of 4f-electrons into account, were used for the analysis. CeB6 is a typical dense Kondo material. The Kondo effect occurs in CeB6 from low temperature to above room temperature. X-ray analysis of the f-electron density based on atomic orbitals (AO) revealed that 1.5 (2) electrons are donated from B6 to Ce and a total of 2.5 (2) electrons localize on the 4f-orbital. κ values are consistent with the 4f-orbitals being highly contracted and thus stabilized. These may be related to the Kondo effect.

scholarly journals Building brain network in electron density map determined by micro-CT

2014 ◽  
Vol 70 (a1) ◽  
pp. C1752-C1752
Author(s):  
Rino Saiga ◽  
Susumu Takekoshi ◽  
Naoya Nakamura ◽  
Akihisa Takeuchi ◽  
Kentaro Uesugi ◽  
...  
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Model Building ◽  
Three Dimensional ◽  
Brain Network ◽  
X Ray ◽  
Density Maps ◽  
Density Map ◽  
Electron Density Map

In macromolecular crystallography, an electron density distribution is traced to build a model of the target molecule. We applied this method to model building for electron density maps of a brain network. Human cerebral tissue was stained with heavy atoms [1]. The sample was then analyzed at the BL20XU beamline of SPring-8 to obtain a three-dimensional map of X-ray attenuation coefficients representing the electron density distribution. Skeletonized wire models were built by placing and connecting nodes in the map [2], as shown in the figure below. The model-building procedures were similar to those reported for crystallographic analyses of macromolecular structures, while the neuronal network was automatically traced by using a Sobel filter. Neuronal circuits were then analytically resolved from the skeletonized models. We suggest that X-ray microtomography along with model building in the electron density map has potential as a method for understanding three-dimensional microstructures relevant to biological functions.

Synchrotron X-ray analysis of the electron density in CoF2 and ZnF2

2001 ◽  
Vol 57 (2) ◽  
pp. 128-135 ◽  
Author(s):  
Nicholas J. O'Toole ◽  
Victor A. Streltsov
Keyword(s):  
Field Theory ◽  
Transition Metal ◽  
Electron Density ◽  
Crystal Field ◽  
Room Temperature ◽  
Crystal Field Theory ◽  
X Ray ◽  
Structure Factors ◽  
Small Crystals ◽  
Multipole Refinement

Accurate structure factors for small crystals of the rutile-type structures CoF2, cobalt difluoride, and ZnF2, zinc difluoride, have been measured with focused λ = 0.8400 (2) Å synchrotron X-radiation at room temperature. Phenomenological structural trends across the full series of rutile-type transition metal difluorides are analysed, showing the importance of the metal atom in the degree of distortion of the metal–F6 octahedra in these structures. Multipole models reveal strong asphericities in the electron density surrounding the transition metals, which are consistent with expectations from crystal field theory and the structural trends in these compounds. Transition metal 3d-orbital populations were computed from the multipole refinement parameters, showing significant repopulation of orbitals compared with the free atom, particularly for CoF2.

A study on α-RuCl3 crystal structure by scanning tunneling microscopy

1989 ◽  
Vol 47 ◽  
pp. 30-31
Author(s):  
H.-J. Cantow ◽  
H. Hillebrecht ◽  
S. Magonov ◽  
H. W. Rotter ◽  
G. Thiele
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Scanning Tunneling Microscopy ◽  
Electron Density ◽  
Structure Determination ◽  
Electron Density Distribution ◽  
Scanning Tunneling ◽  
Monoclinic Space Group ◽  
Tunneling Microscopy ◽  
X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

X-ray emission and X-ray photoelectron studies of electron density distribution in Cu(II) complexes with 2-imidazoline nitroxides

2006 ◽  
Vol 47 (3) ◽  
pp. 558-562 ◽  
Author(s):  
L. N. Mazalov ◽  
S. V. Trubina ◽  
G. K. Parygina ◽  
I. M. Oglezneva ◽  
E. A. Aseeva ◽  
...  
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray

Insight into the Electron Density Distribution in an O,N-Heterocyclic Stannylene by High-Resolution X-ray Diffraction Analysis

2019 ◽  
Vol 2019 (6) ◽  
pp. 875-884 ◽  
Author(s):  
Maxim G. Chegerev ◽  
Alexandr V. Piskunov ◽  
Kseniya V. Tsys ◽  
Andrey G. Starikov ◽  
Klaus Jurkschat ◽  
...  
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Diffraction Analysis ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Insight Into

scholarly journals High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 115-126 ◽  
Author(s):  
E. I. Howard ◽  
B. Guillot ◽  
M. P. Blakeley ◽  
M. Haertlein ◽  
M. Moulin ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Fatty Acid ◽  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Room Temperature ◽  
Water Molecules ◽  
X Ray

Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H...H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

Electron Density Distribution Obtained from X-Ray Powder Data by the Maximum Entropy Method

1991 ◽  
Vol 35 (A) ◽  
pp. 77-83 ◽  
Author(s):  
Makoto Sakata ◽  
Masaki Takata ◽  
Yoshiki Kubota ◽  
Tatsuya Uno ◽  
Shintaro Kuhazawa ◽  
...  
Keyword(s):  
Density Distribution ◽  
Maximum Entropy ◽  
Electron Density ◽  
Diffraction Data ◽  
Electron Density Distribution ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Nuclear Density ◽  
X Ray ◽  
Distribution Maps

AbstractThe electron density distribution maps for CaF2 and TiO2 (rutile) were obtained from profile fitting of powder diffraction data by a Maximum Entropy Method (MEM) analysis. The resultant electron density maps show clearly the nature of the chemical bonding. In order to interpret the results, the nuclear density distribution was also obtained for rutile from powder neutron diffraction data. In the electron density map for rutile obtained by HEM analysis from the X-ray data, both apical and equatorial bonding can be seen. On the other hand, the nuclear density of rutile Is very simple and shows the thermal vibration of nuclei.

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