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.

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.

Atomic properties and chemical bonding in the pyrite and marcasite polymorphs of FeS2: a combined experimental and theoretical electron density study

2014 ◽  
Vol 5 (4) ◽  
pp. 1408-1421 ◽  
Author(s):  
Mette S. Schmøkel ◽  
Lasse Bjerg ◽  
Simone Cenedese ◽  
Mads R. V. Jørgensen ◽  
Yu-Sheng Chen ◽  
...  
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Chemical Bonding ◽  
Atomic Properties ◽  
Density Analysis ◽  
Density Study

The chemical bonding in the pyrite (left) and marcasite (right) polymorphs of FeS2is investigated by charge density analysis.

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.

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.

Weak intramolecular and intermolecular hydrogen bonding of benzyl alcohol, 2-phenylethanol and 2-phenylethylamine in the adsorption on graphitized thermal carbon black

2015 ◽  
Vol 17 (37) ◽  
pp. 24282-24293 ◽  
Author(s):  
V. V. Varfolomeeva ◽  
A. V. Terentev
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Carbon Black ◽  
Benzyl Alcohol ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Intermolecular Hydrogen Bonding ◽  
Weak Hydrogen Bond ◽  
Graphitized Thermal Carbon Black ◽  
Flexible Molecules

The present paper discusses the contemporary state of the studies of the weak hydrogen bond contribution to the adsorption of flexible molecules. We formulated the problems which can be solved today only using the NCI method and quantum chemical calculations.

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