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.

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.

Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

2017 ◽  
Vol 73 (4) ◽  
pp. 654-659 ◽  
Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
Structure Factors ◽  
Density Analysis ◽  
Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

scholarly journals Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling

2017 ◽  
Vol 73 (4) ◽  
pp. 584-597 ◽  
Author(s):  
Nicola Casati ◽  
Alessandro Genoni ◽  
Benjamin Meyer ◽  
Anna Krawczuk ◽  
Piero Macchi
Keyword(s):  
High Pressure ◽  
Density Distribution ◽  
Charge Density ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Theoretical Work ◽  
Specific Information ◽  
Collection Data ◽  
Modelling Techniques ◽  
Density Analysis

The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casatiet al.(2016).Nat. Commun.7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the speciessyn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

2014 ◽  
Vol 70 (2) ◽  
pp. 331-341 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Hydrogen Bonding ◽  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Bond Critical Point ◽  
Potential Region ◽  
Electrostatic Properties ◽  
Structural And Electronic Properties ◽  
Density Analysis ◽  
Mycobacterial Cell Wall

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed usingCRYSTAL09with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N—N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C—H...N, C—H...O and N—H...N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Fourier Methods and Maximum Entropy Enhancement

1997 ◽  
Author(s):  
Philip Coppens
Keyword(s):  
Fourier Transform ◽  
Charge Density ◽  
Electron Density ◽  
Complex Structure ◽  
Image Formation ◽  
Crystal Structure Analysis ◽  
Space Groups ◽  
Inverse Fourier Transformation ◽  
Density Analysis ◽  
The Fourier Transform

Image formation in diffraction is no different from image formation in other branches of optics, and it obeys the same mathematical equations. However, the nonexistence of lenses for X-ray beams makes it necessary to use computational methods to achieve the Fourier transform of the diffraction pattern into the image. The phase information required for this process is, in general, not available from the diffraction experiment, even though progress has been made in deriving phases from multiple-beam effects. This is the phase problem, the paramount issue in crystal structure analysis, which also affects charge density analysis of noncentrosymmetric structures. For centrosymmetric space groups, the independent-atom model is a sufficiently close approximation to allow calculation of the signs for all but a few very weak reflections. Images of the charge density are indispensable for qualitative understanding of chemical bonding, and play a central role in charge density analysis. In this chapter, we will discuss methods for imaging the experimental charge density, and define the functions used in the imaging procedure. According to Eq. (1.22), the structure factor F(H) is the Fourier transform of the electron density ρ(r) in the crystallographic unit cell. The electron density p(r) is then obtained by the inverse Fourier transformation, or . . . ρ(r)=∫F(H) exp (−2πi H ·r) dH (5.1) . . . in which F(H) are the (complex) structure factors corrected for the anomalous scattering discussed in chapter 1.

Exploring the rare S—H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid

2017 ◽  
Vol 73 (4) ◽  
pp. 626-633 ◽  
Author(s):  
Mysore. S Pavan ◽  
Sounak Sarkar ◽  
Tayur N. Guru Row
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Charge Density ◽  
Interaction Energy ◽  
Electron Density ◽  
Type I ◽  
Weak Hydrogen Bond ◽  
Topological Features ◽  
Density Analysis ◽  
Density Study

Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S—H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S—H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. Thepara-substituted mercaptobenzoic acid depicts a type I S...S interaction.

Transferred multipolar atom model for 10β,17β-dihydroxy-17α-methylestr-4-en-3-one dihydrate obtained from the biotransformation of methyloestrenolone

2016 ◽  
Vol 72 (5) ◽  
pp. 398-404 ◽  
Author(s):  
Muhammad Umer Faroque ◽  
Sammer Yousuf ◽  
Salman Zafar ◽  
M. Iqbal Choudhary ◽  
Maqsood Ahmed
Keyword(s):  
Electron Density ◽  
Structural Modification ◽  
Atom Model ◽  
Derived Properties

Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.

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.

Comparative electronic analysis between hydrogen transfers in the CH4/CH3+, CH4/CH3•, and CH4/CH3− systems: on the electronic nature of the hydrogen (H−, H•, and H+) being transferred

1996 ◽  
Vol 74 (6) ◽  
pp. 1253-1262 ◽  
Author(s):  
Jordi Mestres ◽  
Miquel Duran ◽  
Juan Bertrán
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Hydrogen Transfer ◽  
Correlation Energy ◽  
Topological Analysis ◽  
Electronic Nature ◽  
Density Distributions ◽  
Density Maps ◽  
Density Analysis ◽  
A Charge

A comparative electronic analysis of the generally termed hydrogen transfers between CH4 and the CH3+, CH3•, and CH3− fragments is presented. These systems are taken as simple models of hydride (H−), hydrogen (H•), and proton (H+) transfers between two carbon fragments (in these simple cases being modelized by two CH3+, CH3•, and CH3− fragments, respectively). The study is mainly focused on analysis of the electronic nature of the type of hydrogen being transferred in each system, and for this reason a topological analysis of charge density distributions was performed. Computation of Bader atomic charges and construction of the charge density, gradient vector field, and Appalachian of the charge density maps reveal the specific features of the electronic nature of the transferring H−, H•, and H+. Moreover, characterization of the bond critical points on the charge density surface permits clarification of the differences in atomic interactions between H−, H•, and H+ and the carbon belonging to each CH3+, CH3•, and CH3− fragment, respectively. A charge density redistribution analysis is also performed to quantify the reorganization of the electron density when going from the reactant complex to the transition state. Finally, effects of inclusion of the correlation energy at the MP2 and CISD levels are also discussed. Key words: electron density, hydrogen transfer, topological density analysis, molecular similarity, Bader density analysis.

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