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 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.

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.

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.

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro-3′-(1,2,4,5,7-tetraoxazocane): single-crystal X-ray and theoretical study

2019 ◽  
Vol 75 (10) ◽  
pp. 1439-1447
Author(s):  
Leonard M. Khalilov ◽  
Ekaterina S. Mescheryakova ◽  
Kamil Sh. Bikmukhametov ◽  
Nataliya N. Makhmudiyarova ◽  
Kamil R. Shangaraev ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Topological Analysis ◽  
Chair Conformation ◽  
Considerable Effect ◽  
Intramolecular Interactions ◽  
X Ray ◽  
Topological Parameters ◽  
Dispersion Component ◽  
Hirshfeld Analysis

Single crystals of (2S,5R)-2-isopropyl-5-methyl-7-(5-methylisoxazol-3-yl)cyclohexanespiro-3′-(1,2,4,5,7-tetraoxazocane), C16H26N2O5, have been studied via X-ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6-31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,−1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two-cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*C—O) and vice versa between lpO and σ*C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,−1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H...N and C—H...O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,−1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H...N interactions being electrostatic in origin. The molecules are further stacked due to C—H...O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.

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.

Electron density studies on hydrogen bonding in two chromone derivatives

2010 ◽  
Vol 66 (6) ◽  
pp. 687-695 ◽  
Author(s):  
Magdalena Małecka ◽  
Lilianna Chęcińska ◽  
Agnieszka Rybarczyk-Pirek ◽  
Wolfgang Morgenroth ◽  
Carsten Paulmann
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Topological Analysis ◽  
Bond Energies ◽  
Synchrotron Diffraction ◽  
X Ray ◽  
Chromone Derivatives ◽  
Topological Parameters ◽  
Weak Hydrogen Bonds ◽  
Hydrogen Bond Energies

The experimental electron densities of two chromone derivatives have been determined from X-ray synchrotron diffraction data at low temperature (100 K). Topological analysis of the electron density has been used to analyze the formation of resonance-assisted hydrogen bonds (RAHBs). Geometrical and topological parameters confirm π-electron delocalization within the hydrogen-bonded ring. In addition, weak C—H...O interactions were identified in both structures. Hydrogen-bond energies allowed medium and weak hydrogen bonds to be distinguished.

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.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

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