Testing the tools for revealing and characterizing the iodine–iodine halogen bond in crystals

2017 ◽  
Vol 73 (2) ◽  
pp. 217-226 ◽  
Author(s):  
Ekaterina Bartashevich ◽  
Irina Yushina ◽  
Kristina Kropotina ◽  
Svetlana Muhitdinova ◽  
Vladimir Tsirelson
Keyword(s):  
Electron Density ◽  
Halogen Bond ◽  
Electron Shell ◽  
Electron Localization Function ◽  
Electron Localization ◽  
Localization Function ◽  
Non Covalent Interactions ◽  
The One ◽  
Covalent Interactions

To understand what tools are really suitable to identify and classify the iodine–iodine non-covalent interactions in solid organic polyiodides, we have examined the anisotropy of the electron density within the iodine atomic basin along and across the iodine–iodine halogen bond using the Laplacian of electron density, one-electron potential and electron localization function produced by Kohn–Sham calculations with periodic boundary conditions. The Laplacian of electron density exhibits the smallest anisotropy and yields a vague picture of the outermost electronic shells. The one-electron potential does not show such a deficiency and reveals that the valence electron shell for the halogen-bond acceptor iodine is always wider than that for the halogen-bond donor iodine along its σ-hole direction. We have concluded that the one-electron potential is the most suitable for classification of the iodine–iodine bonds and interactions in complicated cases, while the electron localization function allows to distinguish the diiodine molecule bonded with the monoiodide anion from the typical triiodide anion.

scholarly journals Reactivity Indices related to DFT Theory, the Electron Localization Function (ELF) and Non-Covalent Interactions (NCI) Calculations in the Formation of the non-Halogenated Pyruvic Esters in Solution

2019 ◽  
Vol 8 (6) ◽  
pp. 476-485 ◽  
Author(s):  
Souad Jorio ◽  
Mohammed Salah ◽  
Hassna Abou El Makarim ◽  
Mohammed Tabyaoui
Keyword(s):  
Topological Analysis ◽  
Electron Localization Function ◽  
Electron Localization ◽  
Localization Function ◽  
Sodium Hydrogen ◽  
Nci Analysis ◽  
Non Covalent Interactions ◽  
The Subject ◽  
Covalent Interactions ◽  
Sulfite Ion

The non-halogenated pyruvic esters are essential compounds, considering that they exhibit particular properties, due to the proximity of two functional groups: carbonyl and ester. These molecules can be obtained from the approach of the Lewis acid MgI2 on the iodinated pyruvic ester by using sodium hydrogen sulfite in aqueous solution, which selectively reduces the carbon-iodine bond of the iodinated pyruvic ester. The sites of attack of hydrogen sulfite of this reaction remained uncertain and were the subject of a debate between the experimenters. Our aim in this work is to determine the more favorable sites of attack by using the local indices (Parr functions). To approve the structure of the reagents, we have conducted a topological analysis of electron localization function (ELF). To reveal the type of interaction in the "ester pyruvic-hydrogen sulfite" complex, we have performed a non-covalent interactions (NCI) calculation. The analysis of local indices and NCI analysis of electron density indicate that the approach of the hydrogen sulfite ion will take place on the iodine atom elucidating the preferable site of the attack.

Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data

2008 ◽  
Vol 64 (3) ◽  
pp. 363-374 ◽  
Author(s):  
Christian B. Hübschle ◽  
Birger Dittrich ◽  
Simon Grabowsky ◽  
Marc Messerschmidt ◽  
Peter Luger
Keyword(s):  
Electron Density ◽  
Electron Localization Function ◽  
Electron Localization ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Localization Function ◽  
Intermolecular Contacts ◽  
Multipole Refinement ◽  
First Time

From a high-resolution X-ray data set (sin θ/λ = 1.1 Å−1) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties – about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.

Topological analysis of the electron density and of the electron localization function of pyrene and its radicals

2005 ◽  
Vol 308 (1-2) ◽  
pp. 181-192 ◽  
Author(s):  
Jesús Hernández-Trujillo ◽  
Isidoro García-Cruz ◽  
José Manuel Martínez-Magadán
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Electron Localization Function ◽  
Electron Localization ◽  
Localization Function

Experimental electron density study of the supramolecular aggregation between 4,4′-dipyridyl-N,N′-dioxide and 1,4-diiodotetrafluorobenzene at 90 K

2004 ◽  
Vol 60 (5) ◽  
pp. 559-568 ◽  
Author(s):  
Riccardo Bianchi ◽  
Alessandra Forni ◽  
Tullio Pilati
Keyword(s):  
Electron Density ◽  
Halogen Bond ◽  
X Ray Diffraction ◽  
One Dimensional ◽  
X Ray ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Experimental Electron Density ◽  
Supramolecular Aggregation ◽  
Density Study

The electron density of the halogen-bonded complex of 4,4′-dipyridyl-N,N′-dioxide (bpNO) with 1,4-diiodotetrafluorobenzene (F4dIb) at 90 K has been determined by X-ray diffraction and analysed. The nature of the I...O intermolecular bond connecting the bpNO and F4dIb molecules into one-dimensional infinite chains, as well as the other non-covalent interactions present in the crystal, such as C—H...O, C—H...F and C—H...I hydrogen bonds and C...C, C...N, C...I and F...F interactions, have been investigated. The integration of electron density over the atomic basins reveals the electrostatic nature of the I...O halogen bond, which is very similar to a previously analysed I...N halogen bond.

WinXPRO: a program for calculating crystal and molecular properties using multipole parameters of the electron density

2002 ◽  
Vol 35 (3) ◽  
pp. 371-373 ◽  
Author(s):  
Adam Stash ◽  
Vladimir Tsirelson
Keyword(s):  
Operating System ◽  
Electric Field ◽  
Computer Program ◽  
Electron Density ◽  
Molecular Properties ◽  
Electron Localization Function ◽  
Electron Localization ◽  
Crystal Potential ◽  
Localization Function ◽  
Kinetic And Potential Energies

The computer programWinXPROenables the calculation of crystal and molecular properties using the multipole parameters of the electron density. The list of properties includes the electron density and its topological and electric field characteristics, the local kinetic and potential energies, the electron localization function, and the effective crystal potential.WinXPROworks under the Windows operating system and can utilize any existing graphics program to display output.

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