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.

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.

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.

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.

Experimental charge-density analysis towards predictive materials science

2021 ◽  
Vol 4 (03) ◽  
pp. 50-71
Author(s):  
Leonardo Dos Santos ◽  
Bernardo L. Rodrigues ◽  
Camila B. Pinto
Keyword(s):  
Physical Properties ◽  
Charge Density ◽  
Materials Science ◽  
New Materials ◽  
Wide Applicability ◽  
Density Analysis ◽  
Properties Of Materials ◽  
A Charge ◽  
Experimental Charge Density

The ongoing increase in the number of experimental charge-density studies can be related to both the technological advancements and the wide applicability of the method. Regarding materials science, the understanding of bonding features and their relation to the physical properties of materials can not only provide means to optimize such properties, but also to predict and design new materials with the desired ones. In this tutorial, we describe the steps for a charge-density analysis, emphasizing the most relevant features and briefly discussing the applications of the method.

scholarly journals Bonding modes of some labile Si compounds studied by charge density analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1698-C1698
Author(s):  
Daisuke Hashizume
Keyword(s):  
Organic Molecules ◽  
Expansion Method ◽  
Multipole Expansion ◽  
Bond Critical Point ◽  
X Ray Diffraction ◽  
Density Distributions ◽  
Density Maps ◽  
Multipole Expansion Method ◽  
Density Analysis ◽  
Electron Donation

Some organic molecules containing Si atom(s) are very labile, even if the corresponding carbon analogs are very stable. To gain information on bonding modes of such compounds, we analyzed valence density distribution, which play critical roles in chemistry of molecule, by applying multipole expansion method. Very recently, an imine coordinated silacyclopropan-1-one, 1, has synthesized by Baceiredo, Kato and co-workers.[1] To clarify the bonding mode of 1, the electron density distributions of 1 and its precursor have analyzed by a multiple expansion method using single crystal X-ray diffraction data. As shown in static model density maps, bonding electrons of Si-C bonds distribute on the outside of the silacyclopropane ring (Si1-C1-C2 ring) (Fig. 1a) with largely extent, in compared with that of the precursor, indicating an in-plane pi-interaction on the Si1-C1 and Si1-C2 bonds. On the other hand, the C1-C2 bonding electrons distribute on the bond, and the bond critical point (BCP) is located on the inside of the three membered ring. In addition, the C1-C2 bonding electrons elongates inside the ring toward the Si1 atom, indicating electron donation from sigma(C1-C2)-bond to the Si1 (Fig. 1b). Consequently, these maps propose greater contribution of canonical structures in Fig. 1c.

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.

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.

scholarly journals Systematic Experimental Charge Density: Linking Structural Modifications to Electron Density Distributions

2015 ◽  
Vol 44 (1) ◽  
pp. 2-9 ◽  
Author(s):  
Isabelle L. Kirby ◽  
Mateusz B. Pitak ◽  
Simon J. Coles ◽  
Philip A. Gale
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Structural Modifications ◽  
Density Distributions ◽  
Experimental Charge Density
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