Analyzing experimental electron density with the localized-orbital locator

2002 ◽  
Vol 58 (5) ◽  
pp. 780-785 ◽  
Author(s):  
Vladimir Tsirelson ◽  
Adam Stash
Keyword(s):  
Solid State ◽  
Electron Density ◽  
Chemical Bonds ◽  
X Ray Diffraction ◽  
X Ray ◽  
Second Derivatives ◽  
Atomic Interactions ◽  
Different Types ◽  
Localized Orbital ◽  
Experimental Electron Density

The localized-orbital locator, which describes the features of bonding in terms of the local kinetic energy, is approximately expressed as a function of electron density and its first and second derivatives. Calculations based on accurate electron densities derived from X-ray diffraction data are carried out for crystals with different types of chemical bonds. It is demonstrated that the localized-orbital locator reveals the features of atomic interactions in a solid state and allows the covalent, ionic and van der Waals bonds to be distinguished.

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

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

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.

Halogen Bonds in Two Silver(I) Mixed-ligand Supramolecular Frameworks: Synthesis, Structure and Photoluminescence

2011 ◽  
Vol 66 (10) ◽  
pp. 1035-1041 ◽  
Author(s):  
Di Sun ◽  
Rong-Bin Huang ◽  
Lan-Sun Zheng
Keyword(s):  
Solid State ◽  
Ir Spectroscopy ◽  
Room Temperature ◽  
Mixed Ligand ◽  
Methyl Groups ◽  
Halogen Bonds ◽  
Photoluminescence Properties ◽  
X Ray Diffraction ◽  
X Ray ◽  
Different Types

Two silver(I) tetrachlorophthalates incorporating aminopyrimidyl ligands, namely [Ag4(apym)4(tcpta)2]n (1) and [Ag2(dmapym)(tcpta)]n (2), (apym = 2-aminopyrimidine, dmapym = 2-amino-4,6-dimethylpyrimidine, H2tcpta = tetrachlorophthalic acid), were synthesized and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction. Both 1 and 2 form sheets which are assembled into 3D supramolecular frameworks via halogen bonds, hydrogen bonds and π...π interactions. Even adding two more methyl groups to the pyrimidyl ring does not change the dimensions of 1 and 2, but it influences the arrangement of the N- and O-donors in the solid state which in turn results in different types of halogen bonds. The photoluminescence properties of 1 and 2 were investigated in the solid state at room temperature.

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.

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.

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.

VARIATION OF Tc IN SINGLE PHASE Bi2Sr2Ca1Cu2O8−x SYSTEM

1991 ◽  
Vol 05 (24n25) ◽  
pp. 1645-1653
Author(s):  
M. NASIR KHAN ◽  
F.A. KHWAJA ◽  
RAANA FARID
Keyword(s):  
High Temperature ◽  
Solid State ◽  
Electron Density ◽  
Solid State Reaction ◽  
Single Phase ◽  
High Temperature Superconductor ◽  
Nominal Composition ◽  
X Ray Diffraction ◽  
Layer Spacing ◽  
X Ray

The variation of Tc in a single-phase high temperature superconductor Bi 2 Sr 2 Ca 1 Cu 2 O 8−x is studied using techniques like X-ray diffraction, magnetic and electric measurements. The samples of Bi-Sr-Ca-Cu-O (with nominal composition 2212) are synthesized by solid state reaction using appropriate amounts of Bi 2 O 3, SrCO 3, CaCO 3 and CuO powders. The Tc is found to vary from 92 K to 115 K in the quenched samples. These changes in the value of Tc have been related to the changes in the inter-layer spacing. It is concluded that an increase in the electron density due to shortening of the inter-layer increases the attractive interaction between pairs and is thus responsible for the high Tc in these superconductors.

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