HAR, TAAM and BODD refinements of model crystal structures using Cu Kα and Mo Kα X-ray diffraction data

2021 ◽  
Vol 77 (1) ◽  
pp. 41-53
Author(s):  
Monika Wanat ◽  
Maura Malinska ◽  
Matthias J. Gutmann ◽  
Richard I. Cooper ◽  
Krzysztof Wozniak
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Quantitative Description ◽  
Systematic Errors ◽  
Limited Information ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Atom Model ◽  
Residual Electron Density

The Independent Atom Model (IAM) of electron density is used in routine X-ray data analysis. However, this model does not give a quantitative description of the electron-density distribution. A better model that allows for modelling of aspherical charge density deformations is introduced by the Hansen–Coppens variant of the multipole model of electron density. However, the application of this model requires crystals of excellent quality and high-resolution XRD data which are quite often difficult criteria to fulfil. Therefore, Mo Kα and Cu Kα data of three model compounds (tricyclic imide, xylitol and methyluracil) were refined using IAM and new methods which enabled the refinement and reconstruction of charge density based on the Cu Kα data. These methods were the Bond-Oriented Deformation Density (BODD) model, Hirshfeld Atom Refinement (HAR) and the Transferable Aspherical Atom Model (TAAM). The final results were compared to the model obtained from neutron diffraction experiments. Our results demonstrated not only that Cu Kα data may be refined using BODD, HAR and TAAM methods, but also revealed systematic errors arising from the use of Cu Kα data. These errors were a result of the limited information in the low-resolution data set that manifested as higher values for the anisotropic displacement parameters (ADPs) and smaller maxima and minima of the residual electron density for the Cu Kα data compared to the Mo Kα data. Notably, these systematic errors were much less significant than those found for the IAM. Therefore, the application of BODD, HAR and TAAM on Cu Kα data has a more significant influence on the final results of refinement than for the Mo Kα data.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

2016 ◽  
Vol 72 (5) ◽  
pp. 775-786 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Mysore S Pavan ◽  
Poomani Kumaradhas
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Topological Characterization ◽  
Data Set ◽  
X Ray ◽  
Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

scholarly journals Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model

2016 ◽  
Vol 72 (1) ◽  
pp. 75-86 ◽  
Author(s):  
Maqsood Ahmed ◽  
Ayoub Nassour ◽  
Sajida Noureen ◽  
Claude Lecomte ◽  
Christian Jelsch
Keyword(s):  
Solar Cells ◽  
Charge Density ◽  
Electron Density ◽  
Organic Solar Cells ◽  
Charge Densities ◽  
Atom Model ◽  
Residual Electron Density ◽  
Derived Properties ◽  
Density Values ◽  
Density Analysis

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

X-Ray Diffraction Study of the Electron Density and Anharmonicity in K2PtCl6

1993 ◽  
Vol 48 (1-2) ◽  
pp. 12-20 ◽  
Author(s):  
Renzo Restori ◽  
Dieter Schwarzenbach
Keyword(s):  
Charge Density ◽  
Room Temperature ◽  
Heavy Atom ◽  
X Ray Diffraction ◽  
Large Core ◽  
Electron Densities ◽  
Core Electron ◽  
Data Set ◽  
X Ray ◽  
Atomic Displacements

Abstract X-ray diffraction data in heavy-atom compounds may be sensitive to anharmonic atomic displacements, since the large core electron densities result in appreciable scattering amplitudes at large reciprocal distances. Since bonding electron densities may also exhibit sharp features affecting high-order reflections, they may be difficult to distinguish from anharmonic effects. We have analyzed an accurate room-temperature single-crystal X-ray data set of K2 PtCl6 using least-squares anharmonic displacement and charge density formalisms. The Hirshfeld charge density formalism, which has successfully been applied to many light-atom structures, fails to parametrize satisfactorily the data, whereas the electron densities at K and CI are easily accounted for by an anharmonic Gram-Charlier expansion to 4th order. Densities around Pt are parametrized only by a combination of anharmonicity and charge density formalisms. If economical parametrizations of the experimental data are preferred to more complicated ones, anharmonicity may be conjectured to play an important rôle while the main bonding feature consists of a preferential occupation of the 5d-orbitals of Pt with t2g symmetry.

scholarly journals Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

2015 ◽  
Vol 71 (4) ◽  
pp. 954-968 ◽  
Author(s):  
Bartosz Zarychta ◽  
Artem Lyubimov ◽  
Maqsood Ahmed ◽  
Parthapratim Munshi ◽  
Benoît Guillot ◽  
...  
Keyword(s):  
Electron Density ◽  
Cholesterol Oxidase ◽  
Optical Resolution ◽  
X Ray Diffraction ◽  
Atom Model ◽  
Bond Density ◽  
Enzymatic Function ◽  
Residual Electron Density ◽  
The Individual ◽  
Model Based Analysis

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein–cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O...H—N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Effect of sintering temperature on the magnetic properties and charge density distribution of nano-NiO

2014 ◽  
Vol 68 (6) ◽  
Author(s):  
Subramanian Saravanakumar ◽  
Ramachandran Saravanan ◽  
Subramanian Sasikumar
Keyword(s):  
Density Distribution ◽  
Charge Density ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Sintering Temperature ◽  
Precipitation Method ◽  
X Ray Diffraction ◽  
Charge Density Distribution ◽  
X Ray ◽  
Distribution Studies

AbstractPhase pure nano nickel oxide was synthesized by the chemical precipitation method and sintered at 200°C, 400°C and 600°C, respectively, to study the effect of sintering on the charge distribution and magnetism. The samples were analyzed by X-ray diffraction for electron density distribution studies, vibrating sample magnetometry for magnetic behavior and by UV-VIS spectrophotometry for optical characteristics. Rearrangement of charge density distribution with respect to sintering temperature was analyzed through the maximum entropy method employed using powder X-ray diffraction data. The observed magnetic transition with respect to the temperature/size effect was analyzed and correlated with electron density distribution studies.

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.

How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine

2009 ◽  
Vol 65 (6) ◽  
pp. 749-756 ◽  
Author(s):  
Birger Dittrich ◽  
Manuela Weber ◽  
Roman Kalinowski ◽  
Simon Grabowsky ◽  
Christian B. Hübschle ◽  
...  
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Room Temperature ◽  
Topological Analysis ◽  
Biologically Active ◽  
Data Set ◽  
Tropical Plants ◽  
X Ray ◽  
Atom Model ◽  
Asian Medicine

Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kα room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree–Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.

scholarly journals On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

IUCrJ ◽  
2020 ◽  
Vol 7 (5) ◽  
pp. 920-933 ◽  
Author(s):  
W. Fabiola Sanjuan-Szklarz ◽  
Magdalena Woińska ◽  
Sławomir Domagała ◽  
Paulina M. Dominiak ◽  
Simon Grabowsky ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Oxalic Acid ◽  
Electron Density ◽  
Structural Information ◽  
Three Dimensional ◽  
Spherical Approximation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Model ◽  
Accuracy And Precision

X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

A synchrotron X-ray study of the electron density in C-type rare earth oxides

1996 ◽  
Vol 52 (3) ◽  
pp. 414-422 ◽  
Author(s):  
E. N. Maslen ◽  
V. A. Streltsov ◽  
N. Ishizawa
Keyword(s):  
Heavy Metal ◽  
Rare Earth ◽  
Electron Density ◽  
Approximate Symmetry ◽  
Data Set ◽  
X Ray ◽  
Metal Atoms ◽  
Structure Factors ◽  
Deformation Electron Density ◽  
Synthetic Crystals

Structure factors for small synthetic crystals of the C-type rare earth (RE) sesquioxides Y2O3, Dy2O3 and Ho2O3 were measured with focused λ = 0.7000 (2) Å, synchrotron X-radiation, and for Ho2O3 were re-measured with an MoKα (λ = 0.71073 Å) source. Approximate symmetry in the deformation electron density (Δρ) around a RE atom with pseudo-octahedral O coordination matches the cation geometry. Interactions between heavy metal atoms have a pronounced effect on the Δρ map. The electron-density symmetry around a second RE atom is also perturbed significantly by cation–anion interactions. The compounds magnetic properties reflect this complexity. Space group Ia{\bar 3}, cubic, Z = 16, T = 293 K: Y2O3, Mr = 225.82, a = 10.5981 (7) Å, V = 1190.4 (2) Å3, Dx = 5.040 Mg m−3, μ 0.7 = 37.01 mm−1, F(000) = 1632, R = 0.067, wR = 0.067, S = 9.0 (2) for 1098 unique reflections; Dy2O3, Mr = 373.00, a = 10.6706 (7) Å, V = 1215.0 (2) Å3, Dx = 8.156 Mg m−3, μ 0.7 = 44.84 mm−1, F(000) = 2496, R = 0.056, wR = 0.051, S = 7.5 (2) for 1113 unique reflections; Ho2O3, Mr = 377.86, a = 10.606 (2) Å, V = 1193.0 (7) Å3, Dx = 8.415 Mg m−3, μ 0.7 = 48.51 mm−1 F(000) = 2528, R = 0.072, wR = 0.045, S = 9.2 (2) for 1098 unique reflections of the synchrotron data set.

Sign in / Sign up

Export Citation Format

Share Document