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.

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.

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.

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.

Experimental electron density in the triclinic phase of Co2(CO)6(μ-CO)(μ-C4O2H2) at 120 K

2001 ◽  
Vol 57 (5) ◽  
pp. 638-645 ◽  
Author(s):  
Riccardo Bianchi ◽  
Giuliana Gervasio ◽  
Domenica Marabello
Keyword(s):  
Bond Length ◽  
Electron Density ◽  
Closed Shell ◽  
X Ray Diffraction ◽  
X Ray ◽  
Bond Path ◽  
Length Difference ◽  
Triclinic Phase ◽  
Two Phases ◽  
Experimental Electron Density

The experimental electron density (ED) of the triclinic phase of Co2(CO)6(μ-CO)(μ-C4O2H2), μ-carbonyl-μ-5-oxo-2,5-dihydrofuran-2-ylbis(tricarbonylcobalt), has been determined through X-ray diffraction at 120 K. The presence of a `closed shell' Co—Co bond in the title compound, found in an experimental ED study of its orthorhombic form, is confirmed by the Quantum Theory of Atoms in Molecules. However, the two phases show a significant Co—Co bond length difference [triclinic: 2.4402 (2) Å; orthorhombic: 2.4222 (3) Å]. The flat distribution of the experimental ED along the Co—Co bond path and on the two Co2C rings allows for variations of the Co—Co bond length which may be easily induced by the different packing arrangements of the two forms.

Topological analysis of the experimental electron density

1996 ◽  
Vol 74 (6) ◽  
pp. 1171-1179 ◽  
Author(s):  
Vladimir G. Tsirelson
Keyword(s):  
Key Words ◽  
Electron Density ◽  
Diffraction Data ◽  
Topological Analysis ◽  
Crystalline Solids ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Electron Density

Methods of topological analysis of the experimental electron density reconstructed from X-ray diffraction data are described. Their advantages and drawbacks are discussed and the results for organic and inorganic crystalline solids are presented. Key words: topological analysis, experimental electron density.

scholarly journals Topology of the Electron Density and of Its Laplacian from Periodic LCAO Calculations on f-Electron Materials: The Case of Cesium Uranyl Chloride

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4227
Author(s):  
Alessandro Cossard ◽  
Silvia Casassa ◽  
Carlo Gatti ◽  
Jacques K. Desmarais ◽  
Alessandro Erba
Keyword(s):  
Electron Density ◽  
Chemical Bonding ◽  
Topological Analysis ◽  
Theoretical Description ◽  
Basis Functions ◽  
Quantum Mechanical ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Orbitals ◽  
Uranyl Chloride

The chemistry of f-electrons in lanthanide and actinide materials is yet to be fully rationalized. Quantum-mechanical simulations can provide useful complementary insight to that obtained from experiments. The quantum theory of atoms in molecules and crystals (QTAIMAC), through thorough topological analysis of the electron density (often complemented by that of its Laplacian) constitutes a general and robust theoretical framework to analyze chemical bonding features from a computed wave function. Here, we present the extension of the Topond module (previously limited to work in terms of s-, p- and d-type basis functions only) of the Crystal program to f- and g-type basis functions within the linear combination of atomic orbitals (LCAO) approach. This allows for an effective QTAIMAC analysis of chemical bonding of lanthanide and actinide materials. The new implemented algorithms are applied to the analysis of the spatial distribution of the electron density and its Laplacian of the cesium uranyl chloride, Cs2UO2Cl4, crystal. Discrepancies between the present theoretical description of chemical bonding and that obtained from a previously reconstructed electron density by experimental X-ray diffraction are illustrated and discussed.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

2016 ◽  
Vol 72 (5) ◽  
pp. 775-786 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Mysore S Pavan ◽  
Poomani Kumaradhas
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Topological Characterization ◽  
Data Set ◽  
X Ray ◽  
Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

Experimental charge density and electrostatic potential of glycyl-L-threonine dihydrate

2000 ◽  
Vol 56 (1) ◽  
pp. 155-165 ◽  
Author(s):  
Farid Benabicha ◽  
Virginie Pichon-Pesme ◽  
Christian Jelsch ◽  
Claude Lecomte ◽  
Ahmed Khmou
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Electron Density Distribution ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Topological Methods ◽  
X Ray ◽  
Molecular Electron ◽  
Experimental Electron Density ◽  
Experimental Charge Density

The experimental electron density distribution in glycyl-L-threonine dihydrate has been investigated using single-crystal X-ray diffraction data at 110 K to a resolution of (sin θ/λ) = 1.2 Å−1. Multipolar pseudo-atom refinement was carried out against 5417 observed data and the molecular electron density was analyzed using topological methods. The experimental electrostatic potential around the molecule is discussed in terms of molecular interactions. Crystal data: C6H12N2O4.2H2O, Mr = 212.2, orthorhombic, P212121, Z = 4, F(000) = 456 e, T = 110 K, a = 9.572 (3), b = 10.039 (3), c = 10.548 (2) Å, V = 1013.6 (4) Å3, Dx = 1.3 g cm−3, µ = 1.2 cm−1 for λMo = 0.7107 Å.

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

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