Topological Analysis of the Experimental Electron Density in Multiferroic Antiferromagnet Ba2MnGe2O7

2021 ◽  
pp. 1-1
Author(s):  
Rajesh Dutta ◽  
Henrik Thoma ◽  
Dmitry Chernyshov ◽  
Balint Nafradi ◽  
Takatsugu Masuda ◽  
...  
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Experimental Electron Density

Atomic interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis

2005 ◽  
Vol 61 (4) ◽  
pp. 418-428 ◽  
Author(s):  
Adam I. Stash ◽  
Kiyoaki Tanaka ◽  
Kazunari Shiozawa ◽  
Hitoshi Makino ◽  
Vladimir G. Tsirelson
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Electronic Energy ◽  
Ligand Interaction ◽  
Atomic Interactions ◽  
Particle Potential ◽  
Density Analysis ◽  
The One ◽  
Electron Density Analysis ◽  
Experimental Electron Density

A topological analysis of the experimental electron density in racemic ethylenebis(1-indenyl)zirconium dichloride, C20H16Cl2Zr, measured at 100 (1) K, has been performed. The atomic charges calculated by the numerical integration of the electron density over the zero-flux atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the atomic interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr—C2 bond paths significantly curved towards the C1—C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the π-electrons of the C1—C2 bond are significantly involved in the metal–ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as η1 with slippage towards η2. The `ligand-opposed' charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski–Mixon bond-order indices calculated directly from the experimental electron density.

Topological analysis of experimental electron densities

1999 ◽  
Vol 32 (2) ◽  
pp. 210-217 ◽  
Author(s):  
Mohamed Souhassou ◽  
Robert H. Blessing
Keyword(s):  
Amino Acid ◽  
Crystal Structures ◽  
Electron Density ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Electron Densities ◽  
Acid Crystal ◽  
Density Distributions ◽  
Amino Acid Crystal ◽  
Experimental Electron Density

Practical computing algorithms are described for analysing the topology of experimental electron density distributions represented as either three-dimensional grid densities or multipolar pseudoatom superpositions. The algorithms are implemented in the programNEWPROP, results from which are illustrated with applications to twoN-acetyl,C-methylamide blocked amino acid crystal structures.

Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K

2005 ◽  
Vol 61 (4) ◽  
pp. 443-448 ◽  
Author(s):  
S. Scheins ◽  
M. Messerschmidt ◽  
P. Luger
Keyword(s):  
Electron Density ◽  
Electron Density Distribution ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Theoretical Studies ◽  
X Ray Diffraction ◽  
X Ray ◽  
Resolution Single ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

Experimental Electron Density of 1-Phenyl-4-nitroimidazole and Topological Analysis of C−H···O and C−H···N Hydrogen Bonds

2002 ◽  
Vol 106 (14) ◽  
pp. 3706-3714 ◽  
Author(s):  
M. Kubicki ◽  
T. Borowiak ◽  
G. Dutkiewicz ◽  
M. Souhassou ◽  
C. Jelsch ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Topological Analysis ◽  
Experimental Electron Density

scholarly journals Is It Conjugated or Not? The Theoretical and Experimental Electron Density Map of Bonding in p-CH3CH2COC6H4-C≡C-C≡C-p-C6H4COCH3CH2

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4388 ◽  
Author(s):  
Przemysław Starynowicz ◽  
Sławomir Berski ◽  
Nurbey Gulia ◽  
Karolina Osowska ◽  
Tadeusz Lis ◽  
...  
Keyword(s):  
Electron Density ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Carbon Chain ◽  
Small Contribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Map ◽  
Electron Density Map ◽  
Experimental Electron Density

The electron density of p-CH3CH2COC6H4-C≡CC≡C-p-C6H4COCH3CH2 has been investigated on the basis of single-crystal X-ray diffraction data collected to high resolution at 100 K and from theoretical calculations. An analysis of the X-ray data of the diyne showed interesting “liquidity” of electron distribution along the carbon chain compared to 1,2-diphenylacetylene. These findings are compatible with the results of topological analysis of Electron Localization Function (ELF), which has also revealed a larger (than expected) concentration of the electron density at the single bonds. Both methods indicate a clear π-type or “banana” character of a single bond and a significant distortion from the typical conjugated structure of the bonding in the diyne with a small contribution of cumulenic structures.

Topological analysis of the electron density in hydrogen bonds

1999 ◽  
Vol 55 (4) ◽  
pp. 563-572 ◽  
Author(s):  
E. Espinosa ◽  
M. Souhassou ◽  
H. Lachekar ◽  
C. Lecomte
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Positive Curvature ◽  
Topological Analysis ◽  
Peptide Bonds ◽  
X Ray ◽  
Systematic Relationships ◽  
Experimental Electron Density

Topological analysis of the experimental electron density ρ(r) in hydrogen-bonding regions has been carried out for a large number of organic compounds using different multipole models and techniques. Relevant systematic relationships between topological properties at the critical points and the usual geometric parameters are pointed out. Results involving X-ray data only and joint X-ray and neutron data, as well as special hydrogen bonding cases (symmetric, bifurcated, peptide bonds, etc.) are included and analysed in the same framework. A new classification of hydrogen bonds using the positive curvature of the electron density at the critical point [\lambda_3({\bf r}_{\rm CP})] is proposed.

scholarly journals Direct air capture of CO2 – topological analysis of the experimental electron density (QTAIM) of the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4

IUCrJ ◽  
2019 ◽  
Vol 6 (1) ◽  
pp. 56-65 ◽  
Author(s):  
Christopher G. Gianopoulos ◽  
Zhijie Chua ◽  
Vladimir V. Zhurov ◽  
Charles A. Seipp ◽  
Xiaoping Wang ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Topological Analysis ◽  
Neutron Data ◽  
X Ray ◽  
Topological Features ◽  
Direct Air Capture ◽  
Air Capture ◽  
Experimental Electron Density ◽  
Carbonate Salt

Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH2 2+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitrogen. The linking hydrogen bonds are approximately perpendicular to the anion–water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,−1) bond critical points. Weaker interactions between the PyBIGH2 2+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.

Topological Analysis of the Experimental Electron Density of Diisocyanomethane at 115 K

1999 ◽  
Vol 5 (11) ◽  
pp. 3413-3420 ◽  
Author(s):  
Tibor Koritsánszky ◽  
Jürgen Buschmann ◽  
Dieter Lentz ◽  
Peter Luger ◽  
Genivaldo Perpetuo ◽  
...  
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Experimental Electron Density

Charge density in crystalline citrinin from X-ray diffraction at 19 K

1996 ◽  
Vol 74 (6) ◽  
pp. 1145-1161 ◽  
Author(s):  
Pietro Roversi ◽  
Felicita Merati ◽  
Riccardo Destro ◽  
Mario Barzaghi
Keyword(s):  
Electron Density ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Bond Path ◽  
Topological Features ◽  
Path Lengths ◽  
The Stability ◽  
Experimental Electron Density

For the fungal metabolite citrinin, C13H14O5, the total experimental electron distribution ρ(r) and its Laplacian [Formula: see text] have been obtained from an extensive set (36 564 measurements) of single-crystal X-ray diffracted intensities at a temperature of 19 ± 2 K. Relevant steps in data collection and processing are reported. The resulting 7698 independent intensity data have been analysed with a multipole (pseudoatoms) formalism. The topological properties of ρ(r) have been determined according to the quantum theory of atoms in molecules. CC and CO bond path lengths have been obtained by numerical integration; their values are found to be well correlated with those of the electron density at the bond critical points. Topological features have been used to characterize the extension of the conjugated system of the molecule, and to confirm the stability of its rings, particularly the two formed by intramolecular H bonds. Maps of [Formula: see text] are presented, showing details in the valence charge distribution and providing a very sensitive tool for analysing dependence of the density on the model adopted to interpret X-ray data. The known chemical reactivity of the molecule towards nucleophiles at a Csp2 atom is confirmed by the shape of the molecular reactive surface (the zero envelope of [Formula: see text]). Key words: experimental electron density, low-temperature X-ray diffraction, topological analysis, Laplacian of ρ.

scholarly journals Experimental and theoretical characterization of the Zn—Zn bond in [Zn2(η5-C5Me5)2]

2007 ◽  
Vol 63 (6) ◽  
pp. 862-868 ◽  
Author(s):  
Juan F. Van der Maelen ◽  
Enrique Gutiérrez-Puebla ◽  
Ángeles Monge ◽  
Santiago García-Granda ◽  
Irene Resa ◽  
...  
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Topological Analysis ◽  
Open Shell ◽  
Synchrotron Diffraction ◽  
Functional Theory ◽  
Metal Metal ◽  
Moller Plesset ◽  
Experimental Electron Density

The existence and characterization of a bond between the Zn atoms in the recently synthesized complex [Zn2(η5-C5Me5)2], as well as between Zn and ligand C atoms is firmly based on neutron diffraction and low-temperature X-ray synchrotron diffraction experiments. The multipolar analysis of the experimental electron density and its topological analysis by means of the `Atoms in Molecules' (AIM) approach reveals details of the Zn—Zn bond, such as its open-shell intermediate character (the results are consistent with a typical metal–metal single bond), as well as many other topological properties of the compound. Experimental results are also compared with theoretical ab initio calculations of the DFT (density functional theory) and MP2 (Møller-Plesset perturbation theory) electron densities, giving a coherent view of the bonding in the complex. For instance, charges calculated from the AIM approach applied to the atomic basin of each Zn atom are, on average, +0.72 e from both the experimental and the theoretical electron density, showing a moderate charge transfer from the metal, confirmed by the calculated topological indexes.

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