Charge density study of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex

2018 ◽  
Vol 233 (9-10) ◽  
pp. 745-752
Author(s):  
Peter Herich ◽  
Lenka Kucková ◽  
Jan Moncol ◽  
Jozef Kožíšek
Keyword(s):  
Hydrogen Bonds ◽  
Copper Atom ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Aim Analysis ◽  
Experimental Electron Density ◽  
Density Study ◽  
Imidazole Ligands ◽  
Oxygen Atoms

Abstract An experimental electronic structure of bis(clonixato)bis(ethanol) bis(imidazole)copper(II) complex, [Cu(cln)2(im)2(EtOH)2] (cln=clonixato, im=imidazole) (1) has been obtained from single-crystal X-ray diffraction data collected at 100 K using an Incoatec IμS Ag microfocus source. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the experimental electron density with the atoms in molecules (AIM) approach. The central copper atom is octahedrally coordinated by two oxygen atoms from two clonixato anions and two nitrogen atoms from two imidazole ligands in equatorial plane. In axial positions are two oxygen atoms from two ethanol molecules. AIM analysis establishes that the central copper atom is bonded more strongly to the clonixato anion that to the imidazole or ethanol molecules. AIM analysis of two intramolecular and one intermolecular hydrogen bonds permits to estimate their strength. We show that the hydrogen bonds are strong enough to protect the molecule from decomposition in solvent media and to disable the more reactive imidazole-Cu-clonixato complex from interacting with e.g. a macromolecule. The electrostatic potential of the complex shows a highly positive value on the central atom, so the complex is highly reactive in an interaction with negative ligands.

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.

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.

Carbacylamidophosphates: Synthethis and Structure of N,N'-Tetramethyl-NM-benzoylphosphoryltriamide and Dimorpholido-N-benzoylphosphorylamide

2000 ◽  
Vol 55 (6) ◽  
pp. 495-498 ◽  
Author(s):  
Katerina E. Gubina ◽  
Vladimir A. Ovchynnikov ◽  
Vladimir M. Amirkhanov ◽  
Viktor V. Skopenkoa ◽  
Oleg V. Shishkinb
Keyword(s):  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Sodium Salts ◽  
Space Group ◽  
X Ray ◽  
Centrosymmetric Dimers ◽  
Oxygen Atoms

N,N′-Tetramethyl-N"-benzoylphosphoryltriamide (I) and dimorpholido-N-benzoylphosphorylamide (II), and their sodium salts Nal, Nall were synthesized and characterized by means of IR and 1H, 31P NMR spectroscopy. The structures of I, II were determined by X-ray diffraction: I monoclinic, space group P2i/c with a = 10.162(3), b= 11.469(4), c = 12.286(4) Å , β = 94.04°, V = 1428.4(8) A 3, Z = 4, p(calcd) = 1.187 g/cm3; II monoclinic, space group C2/c with a = 15.503(4), b = 10.991(3), c = 22.000(6) Å, β = 106.39°, V = 3596.3(17) Å3, Z = 8, p(calcd.) = 1.253 g/cm3. The refinement of the structures converged at R = 0.0425 for I, and R = 0.068 for II. In both structures the molecules are connected into centrosymmetric dimers via hydrogen bonds formed by the phosphorylic oxygen atoms and hydrogen atoms of amide groups.

Intermolecular hydrogen bonding H···Cl in crystal structure of palladium(II)-bis(diaminocarbene) complex

2019 ◽  
Vol 234 (3) ◽  
pp. 155-164 ◽  
Author(s):  
Mikhail A. Kinzhalov ◽  
Sergey V. Baykov ◽  
Alexander S. Novikov ◽  
Matti Haukka ◽  
Vadim P. Boyarskiy
Keyword(s):  
Crystal Packing ◽  
Solid Phase ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Intermolecular Contacts ◽  
Organometallic Cations ◽  
Supramolecular Contacts ◽  
Moderate Yield

Abstract The reaction of bis(isocyanide)palladium complex cis-[PdCl2(CNXyl)2] (Xyl=2,6-Me2C6H3) with excess of 4,5-dichlorobenzene-1,2-amine in a C2H4Cl2/MeOH mixture affords monocationic bis(diaminocarbene) complex cis-[PdClC{(NHXyl)=NHC6H2Cl2NH2}{C(NHXyl)=NHC6H2Cl2NH2}]Cl (3) in moderate yield (42%). Complex 3 exists in the solid phase in the H-bonded dimeric associate of two single charged organometallic cations and two chloride anions according to X-ray diffraction data. The Hirshfeld surface analysis for the X-ray structure of 3 reveals that the crystal packing is determined primarily by intermolecular contacts H–Cl, H–H, and H–C. The intermolecular hydrogen bonds N–H···Cl and C–H···Cl in the H-bonded dimeric associate of 3 were studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method, and estimated energies of these supramolecular contacts vary from 1.6 to 9.1 kcal/mol. Such non-covalent bonding means that complex 3 is an anionic receptor for the chloride anions.

Bindung von Metall-Ionen an Dipeptide: Struktur von Thallium(I)-(3-benzyl-6-carboxylatomethyl-2,5-diketopiperazin) / Binding of Metal Ions by Dipeptides: Structure of Thallium(I) 3-Benzyl-6-carboxylatomethyl-2,5-diketopiperazine

1992 ◽  
Vol 47 (7) ◽  
pp. 952-956
Author(s):  
P. Mikulcik ◽  
P. Bissinger ◽  
J. Riede ◽  
H. Schmidbaur
Keyword(s):  
Solid State ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Carbonyl Oxygen ◽  
State Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystalline Product ◽  
Oxygen Atoms

Ester cleavage of aspartame (L-α-aspartyl-L-phenylalanine methylester) (1), by equimolar quantities of thallium ethoxide is accompanied by intramolecular cyclisation to give thallium 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine (2). The solid state structure of the crystalline product was determined by single-crystal X-ray diffraction analysis. The cations were found to form four short and four elongated contacts to seven oxygen atoms and one nitrogen atom of a total of six neighbouring 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine anions. There are inter-anionic hydrogen bonds only between the imino groups and the carbonyl oxygen atoms (O3, O4), featuring a pattern similar to that found for cytosine-guanosine contacts in DNA.

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

The crystal structure of N-[[6-methoxy-5-(trifluoromethyl)thio-1-naphthalenyl]thioxomethyl]-N-methylglycine, C16H14F3NO3S2

1983 ◽  
Vol 61 (9) ◽  
pp. 2137-2140 ◽  
Author(s):  
Kottayil I. Varughese ◽  
Maria Przybylska ◽  
Kazimir Sestanj ◽  
Francesco Bellini ◽  
Leslie G. Humber
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Attractive Interaction ◽  
Monoclinic Space Group ◽  
Intermolecular Hydrogen Bonds ◽  
Space Group ◽  
Block Diagonal ◽  
Oxygen Atoms

The crystals of C16H14F3NO3S2 belong to the monoclinic space group P21/c with a = 11.577(1), b = 12.404(1), c = 12.366(1) Å, β = 90.01(1)°, and Z = 4. The structure was solved by MULTAN 78. The parameters were refined by block-diagonal least-squares to a final R of 0.047 for 2679 observed reflections. Of particular interest is an intramolecular attractive interaction between the sulfur and oxygen atoms with an [Formula: see text] distance of 2.879(2) Å, in which oxygen appears to act as an electrophile. Intermolecular hydrogen bonds between the hydroxyl and keto groups join the molecules related through a centre of symmetry into dimers.

scholarly journals Two Tautomers of Thiobarbituric Acid in One Crystal: The Experimental Charge Density Perspective

Materials ◽  
2021 ◽  
Vol 15 (1) ◽  
pp. 223
Author(s):  
Anita M. Grześkiewicz ◽  
Maciej Kubicki
Keyword(s):  
Hydrogen Bonds ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Weak Interactions ◽  
Topological Analysis ◽  
Thiobarbituric Acid ◽  
Polymorphic Form ◽  
X Ray Diffraction ◽  
Geometrical Features

High-quality crystals of a certain polymorphic form of thiobarbituric acid containing both keto and enol tautomers in the asymmetric unit were obtained. High-resolution X-ray diffraction data up to sinθ/λ = 1.0 Å−1 were collected and subsequently successfully used for the refining of the multipolar model of electron density distribution. The use of a crystal containing both ketone and enol forms allowed a direct comparison of the topological analysis results and a closer look at the differences between these two forms. The similarities and differences between the deformation densities, electrostatic potentials, Laplacian maps and bond characteristics of the tautomers were analysed. Additionally, the spectrum of the intermolecular interactions was identified and studied from classical, relatively strong N-H···O and O-H···O hydrogen bonds through weaker N-H···S hydrogen bonds to weak interactions (for instance, C-H···O, C-H···S and N···O). The results of these studies point toward the importance of including both the geometrical features and the details of the electron density distribution in the analysis of such weak interactions.

scholarly journals ISOLATION AND STRUCTURAL ELUCIDATION OF A NEW DEPSIDE OF LICHEN Everniopsis trulla

2021 ◽  
Vol 87 (2) ◽  
pp. 97-106
Author(s):  
Olivio Nino Castro ◽  
Jesús López Rodilla ◽  
Sofia Pombal ◽  
Francisca Sanz González ◽  
Julio Santiago Contreras
Keyword(s):  
Mass Spectrometry ◽  
Melting Point ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Spectroscopic Data ◽  
Intermolecular Forces ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Uv Visible

In this research, a new depside of the lichen Everniopsis trulla has been isolated. The extraction was carried out to 400 g of dry sample and ground with ethanol for 3 repetitions, then, it was fractionated by applying column chromatography with the CHCl3-MeOH system and purified by recrystallization with MeOH-Acetone (1: 1); Finally, white crystals in the form of needles (solid C) with a melting point of 198 ° C were obtained, whose structure was elucidated based on spectroscopic data (UV-Visible, IR, NMR-H1, NMR-C13, mass spectrometry and single crystal X-ray diffraction). According to the Science Finder databases, it is a new depside, called trullarin, and it is observed that molecular packing is influenced by both intramolecular and intermolecular forces. Intermolecular hydrogen bonds of O - H -O type binds neighboring molecules forming dimers.

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.

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