Weak interactions in chain polymers [M(μ-X)2 L 2]∞ (M = Zn, Cd; X = Cl, Br; L = substituted pyridine) – an electron density study

2009 ◽  
Vol 65 (5) ◽  
pp. 600-611 ◽  
Author(s):  
Ruimin Wang ◽  
Christian W. Lehmann ◽  
Ulli Englert
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Critical Points ◽  
Weak Interactions ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Density Distributions ◽  
The One ◽  
Experimental Electron Density ◽  
Density Study

The experimental electron-density distributions in crystals of five chain polymers [M(μ-X)2(py)2] (M = Zn, Cd; X = Cl, Br; py = 3,5-substituted pyridine) have been obtained from high-resolution X-ray diffraction data sets (sin θ/λ > 1.1 Å−1) at 100 K. Topological analyses following Bader's `Atoms in Molecules' approach not only confirmed the existence of (3, −1) critical points for the chemically reasonable and presumably strong covalent and coordinative bonds, but also for four different secondary interactions which are expected to play a role in stabilizing the polymeric structures which are unusual for Zn as the metal center. These weaker contacts comprise intra- and inter-strand C—H...X—M hydrogen bonds on the one hand and C—X...X—C interhalogen contacts on the other hand. According to the experimental electron-density studies, the non-classical hydrogen bonds are associated with higher electron density in the (3, −1) critical points than the halogen bonds and hence are the dominant interactions both with respect to intra- and inter-chain contacts.

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.

Experimental electron density study of 1,2,4-triazole at 15 K. A comparison with ab initio-calculations

1997 ◽  
Vol 212 (3) ◽  
Author(s):  
P. Fuhrmann ◽  
T. Koritsánszky ◽  
P. Luger
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Electron Density ◽  
Diffraction Data ◽  
Topological Properties ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Electron Density ◽  
Density Study

AbstractTopological properties and the Laplacian function of the electron density of 1,2,4-triazole have been determined from X-ray diffraction data collected at 15 K. 1,2,4-Triazole, C

scholarly journals Two Tautomers of Thiobarbituric Acid in One Crystal: The Experimental Charge Density Perspective

Materials ◽  
2021 ◽  
Vol 15 (1) ◽  
pp. 223
Author(s):  
Anita M. Grześkiewicz ◽  
Maciej Kubicki
Keyword(s):  
Hydrogen Bonds ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Weak Interactions ◽  
Topological Analysis ◽  
Thiobarbituric Acid ◽  
Polymorphic Form ◽  
X Ray Diffraction ◽  
Geometrical Features

High-quality crystals of a certain polymorphic form of thiobarbituric acid containing both keto and enol tautomers in the asymmetric unit were obtained. High-resolution X-ray diffraction data up to sinθ/λ = 1.0 Å−1 were collected and subsequently successfully used for the refining of the multipolar model of electron density distribution. The use of a crystal containing both ketone and enol forms allowed a direct comparison of the topological analysis results and a closer look at the differences between these two forms. The similarities and differences between the deformation densities, electrostatic potentials, Laplacian maps and bond characteristics of the tautomers were analysed. Additionally, the spectrum of the intermolecular interactions was identified and studied from classical, relatively strong N-H···O and O-H···O hydrogen bonds through weaker N-H···S hydrogen bonds to weak interactions (for instance, C-H···O, C-H···S and N···O). The results of these studies point toward the importance of including both the geometrical features and the details of the electron density distribution in the analysis of such weak interactions.

Electron Density of Paracetamol Metastable Polymorph, Topologycal H-Bonds Analysis

2013 ◽  
Vol 8 (2) ◽  
pp. 109-116
Author(s):  
Dmitriy Druzhbin ◽  
Tatyana Drebushchak ◽  
Elena Boldyreva
Keyword(s):  
Electron Density ◽  
Critical Points ◽  
Experimental Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Orthorhombic Modification ◽  
Experimental Electron Density

The experimental electron density of paracetamol metastable polymorph (orthorhombic, Pbca) was derived from highresolution X-ray diffraction at 100 K. The multipole model was used to refine electron density and for experimental analysis of the features of the critical points for orthorhombic modification. Geometrical H-bonds features were obtained from spherical and multipole models. The current study provides topological H-bonds analysis in orthorhombic paracetamol compared with stable monoclinic paracetamol polymorphs in normal conditions

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.

scholarly journals Experimental Charge Density Analysis and Electrostatic Properties of Crystalline 1,3-Bis(Dimethylamino)Squaraine and Its Dihydrate from Low Temperature (T = 18 and 20 K) XRD Data

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 894
Author(s):  
Riccardo Destro ◽  
Pietro Roversi ◽  
Raffaella Soave ◽  
Arjan Hovestad ◽  
Leonardo Lo Presti
Keyword(s):  
Electron Density ◽  
Theoretical Calculations ◽  
Total Charge ◽  
X Ray Diffraction ◽  
Charge Densities ◽  
Density Distributions ◽  
Distributed Multipole Analysis ◽  
Density Analysis ◽  
Crystal Electron ◽  
Experimental Electron Density

Multipolar refinements of structural models fitting extensive sets of X-ray diffraction (XRD) data from single crystals of 1,3-bis(dimethylamino)squaraine [SQ, C8H12N2O2] and its dihydrate [SQDH, C8H12N2O2·2H2O], collected at very low T (18 ± 1 K for SQ, 20 ± 1 K for SQDH), led to an accurate description of their crystal electron density distributions. Atomic volumes and charges have been estimated from the experimental charge densities using the Quantum Theory of Atoms in Molecules (QTAIM) formalism. Our analysis confirms the common representation (in the literature and textbooks) of the squaraine central, four-membered squarylium ring as carrying two positive charges, a representation that has been recently questioned by some theoretical calculations: the integrated total charge on the C4 fragment is estimated as ca. +2.4e in SQ and +2.2e in SQDH. The topology of the experimental electron density for the SQ squaraine molecule is modified in the dihydrated crystal by interactions between the methyl groups and the H2O molecules in the crystal. Maps of the molecular electrostatic potential in the main molecular planes in both crystals clearly reveal the quadrupolar charge distribution of the squaraine molecules. Molecular quadrupole tensors, as calculated with the PAMoC package using both Stewart and QTAIM distributed multipole analysis (DMA), are the same within experimental error.

Distribution and Topology of the Electron Density in an Aluminosilicate Compound from High-Resolution X-ray Diffraction Data: the Case of Scolecite

1998 ◽  
Vol 54 (6) ◽  
pp. 819-833 ◽  
Author(s):  
S. Kuntzinger ◽  
N. E. Ghermani ◽  
Y. Dusausoy ◽  
C. Lecomte
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Critical Points ◽  
Diffraction Data ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
And Topology ◽  
Experimental Electron Density

The experimental electron density distribution in scolecite, CaAl2Si3O10.3H2O, has been derived from single-crystal high-resolution Ag Kα X-ray diffraction data. A statistical method based on the prediction matrix has been used to discuss the estimation of the valence populations (P val) in the kappa least-squares refinements. The densities on the Si—O—Si and Si—O—Al bridges have been characterized using the topology of the electron density through its Laplacian at the bond critical points. The Si—O and Al—O bond features are related to the atomic environment and to the Si—O—T geometries (T = Si, Al).

An experimental electron density study on “1-zirconacyclopent-3-yne”

2006 ◽  
pp. 1233 ◽  
Author(s):  
Daisuke Hashizume ◽  
Noriyuki Suzuki ◽  
Teiji Chihara
Keyword(s):  
Electron Density ◽  
Experimental Electron Density ◽  
Density Study
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