scholarly journals Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye

2012 ◽  
Vol 68 (6) ◽  
pp. 646-660 ◽  
Author(s):  
Yvon Bibila Mayaya Bisseyou ◽  
Nouhza Bouhmaida ◽  
Benoit Guillot ◽  
Claude Lecomte ◽  
Noel Lugan ◽  
...  
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Dipole Moments ◽  
Crystal Form ◽  
Density Peak ◽  
Charge Delocalization ◽  
Molecular Dipole ◽  
Atom Model ◽  
Topological Features ◽  
Coumarin 102

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen–Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C—H...O and C—H...N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.

Biotransformation, spectroscopic investigation, crystal structure and electrostatic properties of 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate studied using transferred electron-density parameters

2018 ◽  
Vol 74 (5) ◽  
pp. 534-541 ◽  
Author(s):  
Ammara Shahid ◽  
Ambreen Aziz ◽  
Sajida Noureen ◽  
Maqsood Ahmed ◽  
Sammer Yousuf ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Van Der Waals Interactions ◽  
Estradiol Valerate ◽  
Spectrometric Analysis ◽  
Spectroscopic Techniques ◽  
Charge Delocalization ◽  
Atom Model ◽  
Network Of Hydrogen Bonds

The biologically transformed product of estradiol valerate, namely 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate, C18H22O3·H2O, has been investigated using UV–Vis, IR, 1H and 13C NMR spectroscopic techniques, as well as by mass spectrometric analysis. Its crystal structure was determined using single-crystal X-ray diffraction based on data collected at 100 K. The structure was refined using the independent atom model (IAM) and the transferred electron-density parameters from the ELMAM2 database. The structure is stabilized by a network of hydrogen bonds and van der Waals interactions. The topology of the hydrogen bonds has been analyzed by the Bader theory of `Atoms in Molecules' framework. The molecular electrostatic potential for the transferred multipolar atom model reveals an asymmetric character of the charge distribution across the molecule due to a substantial charge delocalization within the molecule. The molecular dipole moment was also calculated, which shows that the molecule has a strongly polar character.

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.

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.

scholarly journals Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopentanedione, a compound displaying a resonance-assisted hydrogen bond

2014 ◽  
Vol 70 (2) ◽  
pp. 197-211 ◽  
Author(s):  
Ayoub Nassour ◽  
Maciej Kubicki ◽  
Jonathan Wright ◽  
Teresa Borowiak ◽  
Grzegorz Dutkiewicz ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Density ◽  
Electron Density ◽  
Dipole Moments ◽  
Lone Pair ◽  
Covalent Bonds ◽  
Density Maps ◽  
Structure Factors ◽  
Density Analysis ◽  
Additional Charges

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen–Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O—H...O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C—C=C—OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

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.

Angular terms in the electron density for the phosphine molecule

1956 ◽  
Vol 52 (4) ◽  
pp. 703-711 ◽  
Author(s):  
R. A. Ballinger ◽  
N. H. March
Keyword(s):  
Variational Method ◽  
Charge Density ◽  
Electron Density ◽  
Legendre Polynomials ◽  
Molecular Axis ◽  
Thomas Fermi ◽  
Line Charge ◽  
Density Map ◽  
Circular Line

ABSTRACTAn attempt is made to calculate the first few angular terms in an expansion of the electron density for the phosphine molecule in Legendre polynomials. Such an expansion is appropriate for a model in which the three hydrogen nuclei are smeared to form a circular line charge. The Thomas–Fermi approximation has been used in conjunction with the variational method. The variational density employed includes p and f angular terms. An approximate charge density map is constructed for a plane containing the molecular axis in order to demonstrate the effect of the angular terms.

scholarly journals Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

2010 ◽  
Vol 67 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Sławomir Domagała ◽  
Parthapratim Munshi ◽  
Maqsood Ahmed ◽  
Benoît Guillot ◽  
Christian Jelsch
Keyword(s):  
Comparative Study ◽  
Charge Density ◽  
Topological Analysis ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Experimental Database ◽  
Figures Of Merit ◽  
Atom Model ◽  
Atomic Displacement Parameters ◽  
Model Approach

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

Nonnuclear Maxima in the Charge Density

1993 ◽  
Vol 48 (1-2) ◽  
pp. 127-133 ◽  
Author(s):  
Kenneth E. Edgecombe ◽  
Vedene H. Smith, Jr. ◽  
Florian Müller-Plathe
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Electron Correlation ◽  
Basis Set ◽  
Valence Shell ◽  
Correlation Effects ◽  
Electron Correlation Effects

Abstract Basis-set and electron-correlation effects on the appearance and disappearance of nonnuclear maxima in the electron density are examined in Li2 , Na2 , Na4 and Na5 . It is shown that nonnuclear attractors can be removed in all cases except Li2 . The appearance of a pseudoatom in a lithium molecule correlates remarkably well with the size of the region, in an atomic calculation, of V2r(r) for the valence shell of the atom. This and the fact that the pseudoatom is also present in the promolecule indicate that the pseudoatoms are remnants of, or in fact are portions of, atoms that are not perturbed enough in the molecule to remove an essentially atomic characteristic.

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