Modeling electron density distributions from X-ray diffraction to derive optical properties: Constrained wavefunction versus multipole refinement

2013 ◽  
Vol 139 (6) ◽  
pp. 064108 ◽  
Author(s):  
Daniel D. Hickstein ◽  
Jacqueline M. Cole ◽  
Michael J. Turner ◽  
Dylan Jayatilaka
Keyword(s):  
Optical Properties ◽  
Electron Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Distributions ◽  
Multipole Refinement

scholarly journals An analysis of the experimental and theoretical charge density distributions of the piroxicam–saccharin co-crystal and its constituents

RSC Advances ◽  
2016 ◽  
Vol 6 (85) ◽  
pp. 81578-81590 ◽  
Author(s):  
Jonathan J. Du ◽  
Linda Váradi ◽  
Peter A. Williams ◽  
Paul W. Groundwater ◽  
Jacob Overgaard ◽  
...  
Keyword(s):  
High Resolution ◽  
Dft Calculations ◽  
Charge Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Distributions ◽  
Multipole Refinement

Experimental and theoretical charge density of piroxicam, saccharin and their 1 : 1 co-crystal have been determined using high-resolution X-ray diffraction, multipole refinement and DFT calculations

Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data

2008 ◽  
Vol 64 (3) ◽  
pp. 363-374 ◽  
Author(s):  
Christian B. Hübschle ◽  
Birger Dittrich ◽  
Simon Grabowsky ◽  
Marc Messerschmidt ◽  
Peter Luger
Keyword(s):  
Electron Density ◽  
Electron Localization Function ◽  
Electron Localization ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Localization Function ◽  
Intermolecular Contacts ◽  
Multipole Refinement ◽  
First Time

From a high-resolution X-ray data set (sin θ/λ = 1.1 Å−1) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties – about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.

scholarly journals Applications of X-ray Wavefunction Refinement

2014 ◽  
Vol 70 (a1) ◽  
pp. C1343-C1343
Author(s):  
Simon Grabowsky ◽  
Magdalena Woinska ◽  
Joanna Bak ◽  
Dylan Jayatilaka
Keyword(s):  
Experimental Data ◽  
Electron Density ◽  
Defect Density ◽  
Molecular Compound ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
X Ray ◽  
Density Distributions ◽  
Selection Of

X-ray wavefunction refinement (XWR) is a way of modeling the total aspherical electron density from an X-ray diffraction experiment on a single crystal of a molecular compound. It is a combination of existing quantum-crystallographical techniques: In the first step, geometry is determined using Hirshfeld atom refinement,[1] which is based on a stockholder partitioning of quantum-mechanical aspherical electron densities. In the second step, the same wavefunction is fitted to the experimental data to reproduce the diffraction pattern and simultaneously minimize the molecular energy.[2] The XWR protocol involves embedding the molecule into a field of point charges and dipoles as well as termination strategies to avoid overfitting.[3] Results from an X-ray wavefunction refinement are not restricted to the analysis of electron density: the full reconstructed density matrix is available. Therefore, chemical problems can be tackled with suitable tools for any given question including, e.g., experimentally derived bond orders, electron-pair localisation information, or energetics. We will present first applications of this protocol for a selection of organic (hydrogen maleate salts, sulfur-containing protease inhibitors) and inorganic (siloxanes, sulfur dioxide) compounds, for which we measured high-resolution low-temperature X-ray diffraction data at various synchrotron facilities. We will show geometry improvements, anisotropic displacement parameters for hydrogens, anharmonic motion parameters for sulfur and chlorine atoms, and improved total electron-density distributions in comparison to results from multipole modeling. Moreover, we will discuss the contribution of the experimental data to the final constrained wavefunction (defect density) and demonstrate how the experimentally derived orbital-based descriptors assist in solving fundamental chemical problems.

scholarly journals Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 110-118 ◽  
Author(s):  
Agnieszka Poulain ◽  
Emmanuel Wenger ◽  
Pierrick Durand ◽  
Katarzyna N. Jarzembska ◽  
Radosław Kamiński ◽  
...  
Keyword(s):  
Phase Transition ◽  
High Resolution ◽  
Electron Density ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Large Temperature ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Peaks ◽  
Multipole Refinement

The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelschet al.(2011).Acta Cryst.B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called `shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤T≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in thebcell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.

Structural and optical properties of Tin Oxide and Indium doped SnO2 thin films deposited by thermal evaporation technique

2016 ◽  
Vol 12 (3) ◽  
pp. 4394-4399
Author(s):  
Sura Ali Noaman ◽  
Rashid Owaid Kadhim ◽  
Saleem Azara Hussain
Keyword(s):  
Thin Films ◽  
Optical Properties ◽  
Tin Oxide ◽  
Thermal Evaporation ◽  
Pure Sno2 ◽  
X Ray Diffraction ◽  
Structural And Optical Properties ◽  
X Ray ◽  
Evaporation Technique ◽  
Sno2 Thin Films

Tin Oxide and Indium doped Tin Oxide (SnO2:In) thin films were deposited on glass and Silicon  substrates  by  thermal evaporation technique.  X-ray diffraction pattern of  pure SnO2 and SnO2:In thin films annealed at 650oC and the results showed  that the structure have tetragonal phase with preferred orientation in (110) plane. AFM studies showed an inhibition of grain growth with increase in indium concentration. SEM studies of pure  SnO2 and  Indium doped tin oxide (SnO2:In) ) thin films showed that the films with regular distribution of particles and they have spherical shape.  Optical properties such as  Transmission , optical band-gap have been measured and calculated.

scholarly journals Study on the Electrical, Structural, Chemical and Optical Properties of PVD Ta(N) Films Deposited with Different N2 Flow Rates

Coatings ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 937
Author(s):  
Yingying Hu ◽  
Md Rasadujjaman ◽  
Yanrong Wang ◽  
Jing Zhang ◽  
Jiang Yan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Photoelectron Spectroscopy ◽  
Crystal Size ◽  
Silicon Substrates ◽  
X Ray Diffraction ◽  
Dc Magnetron Sputtering ◽  
Flow Rates ◽  
X Ray ◽  
N2 Flow Rate

By reactive DC magnetron sputtering from a pure Ta target onto silicon substrates, Ta(N) films were prepared with different N2 flow rates of 0, 12, 17, 25, 38, and 58 sccm. The effects of N2 flow rate on the electrical properties, crystal structure, elemental composition, and optical properties of Ta(N) were studied. These properties were characterized by the four-probe method, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and spectroscopic ellipsometry (SE). Results show that the deposition rate decreases with an increase of N2 flows. Furthermore, as resistivity increases, the crystal size decreases, the crystal structure transitions from β-Ta to TaN(111), and finally becomes the N-rich phase Ta3N5(130, 040). Studying the optical properties, it is found that there are differences in the refractive index (n) and extinction coefficient (k) of Ta(N) with different thicknesses and different N2 flow rates, depending on the crystal size and crystal phase structure.

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