scholarly journals The nature of the chemical bond in oxyanionic crystals based on QTAIM topological analysis of electron densities

RSC Advances ◽  
2019 ◽  
Vol 9 (21) ◽  
pp. 12020-12033 ◽  
Author(s):  
Dmitry V. Korabel'nikov ◽  
Yuriy N. Zhuravlev
Keyword(s):  
Hydrogen Bonds ◽  
Chemical Bond ◽  
Topological Analysis ◽  
Electron Densities

The QTAIM topological analysis of the calculated electron densities in oxyanionic crystals revealed the covalency criteria for metal–oxygen and hydrogen bonds.

scholarly journals Numerical computation of critical properties and atomic basins from three-dimensional grid electron densities

2003 ◽  
Vol 36 (1) ◽  
pp. 65-73 ◽  
Author(s):  
C. Katan ◽  
P. Rabiller ◽  
C. Lecomte ◽  
M. Guezo ◽  
V. Oison ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Software Package ◽  
Topological Analysis ◽  
Hessian Matrix ◽  
Three Dimensional ◽  
Chemical Bonds ◽  
Critical Properties ◽  
Electron Densities ◽  
Atomic Properties ◽  
Intermolecular Contacts

InteGriTyis a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids. Tricubic interpolation is used to obtain the density, its gradient and the Hessian matrix at any required position. Critical points and integrated atomic properties have been derived from theoretical densities calculated for the compounds NaCl and TTF–2,5Cl2BQ (tetrathiafulvalene–2,5-dichlorobenzoquinone), thus covering the different kinds of chemical bonds: ionic, covalent, hydrogen bonds and other intermolecular contacts.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

scholarly journals Weak Hydrogen Bonds in Some Six- and Five-atom Interactions: An AIM Topological Analysis

2013 ◽  
Vol 2 (6) ◽  
pp. 343-346 ◽  
Author(s):  
Francisco Sánchez-Viesca ◽  
Fernando Cortés ◽  
Reina Gómez ◽  
Martha Berros
Keyword(s):  
Hydrogen Bonds ◽  
Topological Analysis ◽  
Weak Hydrogen Bonds

Charge density study of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex

2018 ◽  
Vol 233 (9-10) ◽  
pp. 745-752
Author(s):  
Peter Herich ◽  
Lenka Kucková ◽  
Jan Moncol ◽  
Jozef Kožíšek
Keyword(s):  
Hydrogen Bonds ◽  
Copper Atom ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Aim Analysis ◽  
Experimental Electron Density ◽  
Density Study ◽  
Imidazole Ligands ◽  
Oxygen Atoms

Abstract An experimental electronic structure of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex, [Cu(cln)2(im)2(EtOH)2] (cln=clonixato, im=imidazole) (1) has been obtained from single-crystal X-ray diffraction data collected at 100 K using an Incoatec IμS Ag microfocus source. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the experimental electron density with the atoms in molecules (AIM) approach. The central copper atom is octahedrally coordinated by two oxygen atoms from two clonixato anions and two nitrogen atoms from two imidazole ligands in equatorial plane. In axial positions are two oxygen atoms from two ethanol molecules. AIM analysis establishes that the central copper atom is bonded more strongly to the clonixato anion that to the imidazole or ethanol molecules. AIM analysis of two intramolecular and one intermolecular hydrogen bonds permits to estimate their strength. We show that the hydrogen bonds are strong enough to protect the molecule from decomposition in solvent media and to disable the more reactive imidazole-Cu-clonixato complex from interacting with e.g. a macromolecule. The electrostatic potential of the complex shows a highly positive value on the central atom, so the complex is highly reactive in an interaction with negative ligands.

A topological analysis of the interion interactions of tetraphenylphosphonium squarate

2006 ◽  
Vol 84 (5) ◽  
pp. 804-811 ◽  
Author(s):  
David Wolstenholme ◽  
Manuel AS Aquino ◽  
T Stanley Cameron ◽  
Joseph D Ferrara ◽  
Katherine N Robertson
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Critical Points ◽  
Topological Analysis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Multipole Refinement ◽  
Diverse Interactions

The tetraphenylphosphonium squarate salt crystallizes with a number of diverse interactions, which all have the potential to be classified as hydrogen bonds. The squarate anions are found as dimers linked by O-H···O interactions. The multipole refinement of the tetraphenylphosphonium squarate was performed using the Hansen–Coppens model followed by topological analysis of its intermolecular interactions. A total of 28 interactions were found among the symmetry related molecules, which include a number of C-H···Cπ, C-H···O, and C-H···H-C interactions, along with the O-H···O interaction. With the criteria for hydrogen bonding proposed by Popelier and Koch, it is possible to determine which of these interactions are hydrogen bonds and which are van der Waals interactions. Both linear and exponentially dependent correlations can be seen for the properties of the bond critical points involving the intermolecular interactions that fulfill these criteria. All this leads to a better understanding of the role that hydrogen bonds play in the formation of small organic compounds.Key words: electron density, multiple refinement, hydrogen bonds.

Preliminary Results of a 20 K X-Ray Study of Citrinin

1993 ◽  
Vol 48 (1-2) ◽  
pp. 99-104 ◽  
Author(s):  
R. Destro ◽  
F. Merati
Keyword(s):  
Dipole Moment ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Topological Analysis ◽  
Coupling Constants ◽  
Molecular Dipole ◽  
X Ray ◽  
A Value ◽  
Quadrupole Coupling ◽  
Asymmetry Parameters

Abstract A total of about 37 000 diffracted intensities has been measured at 20 K for a spherical single crystal of citrinin. Using a multipole formalism to interpret the X-ray data, maps of the charge density and of its Laplacian, as well as for the electrostatic potential have been derived. A value of 7(2) D has been obtained for the magnitude of the molecular dipole moment. A study of the electric field gradient (EFG) at the nuclei has yielded the atomic quadrupole coupling constants (QCC) and asymmetry parameters (η). A topological analysis of the charge density has been performed to characterize the intramolecular covalent and hydrogen bonds.

EDMA: a computer program for topological analysis of discrete electron densities

2012 ◽  
Vol 45 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Lukáš Palatinus ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen
Keyword(s):  
Computer Program ◽  
Electron Density ◽  
Critical Points ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Real Space ◽  
Principal Curvatures ◽  
Electron Densities ◽  
Structure Solution ◽  
Aperiodic Crystals

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

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