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 Charge density studies of energetic material: RDX

2020 ◽  
Vol 2 (1) ◽  
pp. 1-14
Author(s):  
David Stephen A ◽  
Asthana S.N ◽  
Rajesh. B. Pawar ◽  
Kumuradhas P
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Electrostatic Potential ◽  
Topological Analysis ◽  
Energetic Material ◽  
X Ray Diffraction ◽  
Explosive Material ◽  
Cyclotrimethylene Trinitramine ◽  
Density Study ◽  
Experimental Charge Density

Experimental charge density study has been carried out for Cyclotrimethylene-trinitramine (space group Pbca), an explosive material from a low temperature X-ray diffraction experiment. The electron density was modeled using the Hansen-Coppens multipole model and refined to R=0.032 for 6226 unique observed reflections. The electron density, laplacian and electrostatic potential distributions are reported and discussed, especially, the properties of the bond (3,-1) critical points, which are thought to play a key role in the decomposition of the molecule. From the bond topological analysis of all the bonds, it is observed that the N–N bond is the weakest. The dominating nature of the oxygen atoms was clearly well understood from isosurface electrostatic potential of isolated and symmetrically sitting molecules in the crystal.

scholarly journals Charge density analysis of paracetamol, acetotoluidine and methacetin

2014 ◽  
Vol 70 (a1) ◽  
pp. C541-C541
Author(s):  
Dmitry Druzhbin ◽  
Tatiana Drebushchak ◽  
Elena Boldyreva
Keyword(s):  
Charge Density ◽  
Topological Analysis ◽  
Intramolecular Interactions ◽  
Amide Bond ◽  
Electrostatic Energy ◽  
X Ray Diffraction ◽  
Methyl Group ◽  
Point Of Interest ◽  
Density Analysis ◽  
Topological Characteristics

Paracetamol (p-hydroxyacetanilide, Pbca), acetotoluidine (p-methylacetanilide, P21/c) and methacetin (p-methoxyacetanilide, Pbca) contain acetamide group included in molecular fragments, which play an important role in many drugs and proteins. As all of them are derivatives of acetanilide used in medicine, and due to the presence of the amide bond, their charge density analysis is important for better understanding amide infinite peptide chains. Thus, comparing the data obtained for paracetamol with acetotoluidine and with methacetin charge density data can provide deeper insight into NH···O bonding. Another point of interest is the possibility of methyl group rotation that remains to be ambiguous in these acetanilide molecule based compounds. In the present study we have attempted to elucidate these problems using precise X-ray diffraction at 100K with subsequent charge density topological analysis. All charge density refinements were based on the Hansen and Coppens multipolar atom model. The topologies of the inter- and intramolecular interactions are carefully analyzed for compounds. The atomic charges, bond orders, and the electrostatic energy in molecules are discussed. The topological characteristics in the critical point of the NH···O bond of paracetamol, acetotoluidine and methacetin are shown in the table below. In contrast to similarity in NH···O bonds for all studied compounds, intermolecular interactions between the double bonded oxygen atom and the hydrogen of dimer's methyl group are different. In acetotoluidine and methacetin the (3, –1) critical points with the same topological characteristics were detected between these atoms. In comparison to them, paracetamol with disordered methyl group [1, 2] has no such point. That can be related to the absence of the methyl group disorder in acetotoluidine and methacetin.

Doxycycline hydrate and doxycycline hydrochloride dihydrate – crystal structure and charge density analysis

2018 ◽  
Vol 233 (9-10) ◽  
pp. 649-661 ◽  
Author(s):  
Daniel Tchoń ◽  
Anna Makal ◽  
Matthias Gutmann ◽  
Krzysztof Woźniak
Keyword(s):  
Charge Density ◽  
Topological Analysis ◽  
Crystal Form ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
Distribution Models ◽  
Crystal Forms ◽  
Density Analysis ◽  
Resonance Assisted Hydrogen Bond ◽  
Amide Nitrogen Atom

Abstract High-resolution low-temperature X-ray diffraction experiments for doxycycline monohydrate and hydrochloride dihydrate have been performed. Translation-Libration-Screw (TLS) analysis for both crystal forms as well as the data from neutron diffraction experiment for hydrochloride combined with the Hansen-Coppens formalism resulted in precise charge density distribution models for both the zwitterionic monohydrate and a protonated hydrochloride crystal forms. Their detailed topological analysis suggested that the electron structure of doxycycline’s amide moiety undergoes significant changes during protonation due to formation of a very strong resonance-assisted hydrogen bond. A notably increased participation of amide nitrogen atom and hydrogen-accepting oxygen atom in the resonance upon doxycycline protonation was observed. A comparison of TLS- and neutron data-derived hydrogen parameters confirmed the experimental neutron data to be vital for proper description of intra- and inter-molecular interactions in this compound. Finally, calculated lattice and interaction energies quantified repulsive Dox-Dox interactions in the protonated crystal form of the antibiotic, relating with a good solubility of doxycycline hydrochloride relative to its hydrate.

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.

Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K

2005 ◽  
Vol 61 (4) ◽  
pp. 443-448 ◽  
Author(s):  
S. Scheins ◽  
M. Messerschmidt ◽  
P. Luger
Keyword(s):  
Electron Density ◽  
Electron Density Distribution ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Theoretical Studies ◽  
X Ray Diffraction ◽  
X Ray ◽  
Resolution Single ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

2014 ◽  
Vol 70 (3) ◽  
pp. 568-579 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Direct Methods ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Total Electron Density ◽  
Total Electron

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

scholarly journals Structural and Charge Density Properties of Manganese Sulfide

2019 ◽  
Vol 9 (2S2) ◽  
pp. 313-315
Keyword(s):  
Charge Density ◽  
Maximum Entropy Method ◽  
Manganese Sulfide ◽  
Entropy Method ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Structure Factors ◽  
Density Analysis ◽  
Distribution Studies ◽  
Profile Refinement

Single phased Manganese Sulfide was analyzed by powder X-ray diffraction (PXRD) data sets with cubic structure. The simulated XRD data sets were used to analyze the structure of manganese sulfide. The powder profile refinements were done by Rietveld profile refinement technique. The refinement results were subjected to analyze the charge density analysis using structure factors. The chemical bonding nature between Mn and S were analyzed by charge density distribution studies through maximum entropy method. From MEM analsysis, it found that the bonding between Mn and S atoms is ionic in nature.

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.

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.

Experimental and theoretical charge-density study of a tetranuclear cobalt carbonyl complex

2009 ◽  
Vol 65 (6) ◽  
pp. 715-723 ◽  
Author(s):  
Jacob Overgaard ◽  
Jamie A. Platts ◽  
Bo B. Iversen
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Critical Points ◽  
Random Noise ◽  
Topological Analysis ◽  
Carbonyl Complex ◽  
Structure Factors ◽  
Common Motif ◽  
Close Proximity ◽  
Experimental Electron Density

Details of the complex bonding environment present in the molecular centre of an alkyne-bridged dicobalt complex have been examined using a combination of experimental and theoretical charge-density modelling for two compounds which share a central Co2C2 tetrahedral moiety as their common motif. Topological analysis of the experimental electron density illustrates the problem of separating the Co—C bond-critical points (b.c.p.s) from the intervening ring-critical point (r.c.p.), due largely to the flat nature of the electron density in the CoC2 triangles. Such a separation of critical points is immediately obtained from a topological analysis of the theoretical electron density as well as from the multipole-projected theoretical density; however, the addition of random noise to the theoretical structure factors prior to multipole modelling leads to a failure in consistently distinguishing two b.c.p.s and one r.c.p. in such close proximity within the particular environment of this Co2C2 centre.

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