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.

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.

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 Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3075
Author(s):  
Riccardo Destro ◽  
Pietro Roversi ◽  
Mario Barzaghi ◽  
Leonardo Lo Presti
Keyword(s):  
Molecular Electrostatic Potential ◽  
X Ray Diffraction ◽  
Distributed Multipole Analysis ◽  
Density Analysis ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Experimental Electron Density ◽  
Temperature Factors

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å−1 are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ–3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long–range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least–squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

2017 ◽  
Vol 73 (4) ◽  
pp. 654-659 ◽  
Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
Structure Factors ◽  
Density Analysis ◽  
Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

scholarly journals Bonding modes of some labile Si compounds studied by charge density analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1698-C1698
Author(s):  
Daisuke Hashizume
Keyword(s):  
Organic Molecules ◽  
Expansion Method ◽  
Multipole Expansion ◽  
Bond Critical Point ◽  
X Ray Diffraction ◽  
Density Distributions ◽  
Density Maps ◽  
Multipole Expansion Method ◽  
Density Analysis ◽  
Electron Donation

Some organic molecules containing Si atom(s) are very labile, even if the corresponding carbon analogs are very stable. To gain information on bonding modes of such compounds, we analyzed valence density distribution, which play critical roles in chemistry of molecule, by applying multipole expansion method. Very recently, an imine coordinated silacyclopropan-1-one, 1, has synthesized by Baceiredo, Kato and co-workers.[1] To clarify the bonding mode of 1, the electron density distributions of 1 and its precursor have analyzed by a multiple expansion method using single crystal X-ray diffraction data. As shown in static model density maps, bonding electrons of Si-C bonds distribute on the outside of the silacyclopropane ring (Si1-C1-C2 ring) (Fig. 1a) with largely extent, in compared with that of the precursor, indicating an in-plane pi-interaction on the Si1-C1 and Si1-C2 bonds. On the other hand, the C1-C2 bonding electrons distribute on the bond, and the bond critical point (BCP) is located on the inside of the three membered ring. In addition, the C1-C2 bonding electrons elongates inside the ring toward the Si1 atom, indicating electron donation from sigma(C1-C2)-bond to the Si1 (Fig. 1b). Consequently, these maps propose greater contribution of canonical structures in Fig. 1c.

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 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.

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