Electron density of a benzoylated tetrafructopyranose

2022 ◽  
Vol 0 (0) ◽  
Author(s):  
Peter Luger ◽  
Birger Dittrich
Keyword(s):  
Electron Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Properties ◽  
Phenyl Rings ◽  
Structural Database ◽  
Non Covalent Interactions ◽  
Weak Surface ◽  
Average Bond ◽  
Covalent Interactions

Abstract The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge Structural Database (CSD). Bond topological and atomic properties were obtained by application of Bader’s QTAIM formalism. From a large number of 105 C–C bonds in the molecule average bond orders for 33 single and 72 aromatic bonds were calculated yielding values of 1.33 and 1.61. Molecular Hirshfeld and electrostatic potential (ESP) surfaces show that only weak non-covalent interactions exist. The phenyl rings of the benzoyl fragments in the outer regions of the molecule generate a positive ESP shell with repulsive properties between adjacent molecules. Weak surface interactions result in a rather unusual low density around 1.3 g cm−3, which is understandable when compared to other carbohydrates where strong O–H⋯O hydrogen bonds allow a 20% more dense packing with densities >1.5 g cm−3 as determined by single crystal X-ray diffraction.

scholarly journals The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

2010 ◽  
Vol 6 ◽  
Author(s):  
Kari Raatikainen ◽  
Massimo Cametti ◽  
Kari Rissanen
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Halogen Bonding ◽  
Relative Strength ◽  
Supramolecular Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structural Database ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The series of haloanilinium and halopyridinium salts: 4-IPhNH3Cl (1), 4-IPhNH3Br (5), 4-IPhNH3H2PO4 (6), 4-ClPhNH3H2PO4 (8), 3-IPyBnCl (9), 3-IPyHCl (10) and 3-IPyH-5NIPA (3-iodopyridinium 5-nitroisophthalate, 13), where hydrogen or/and halogen bonding represents the most relevant non-covalent interactions, has been prepared and characterized by single crystal X-ray diffraction. This series was further complemented by extracting some relevant crystal structures: 4-BrPhNH3Cl (2, CCDC ref. code TAWRAL), 4-ClPhNH3Cl (3, CURGOL), 4-FPhNH3Cl (4, ANLCLA), 4-BrPhNH3H2PO4, (7, UGISEI), 3-BrPyHCl, (11, CIHBAX) and 3-ClPyHCl, (12, VOQMUJ) from Cambridge Structural Database for sake of comparison. Based on the X-ray data it was possible to highlight the balance between non-covalent forces acting in these systems, where the relative strength of the halogen bonding C–X···A− (X = I, Br or Cl) and the ratio between the halogen and hydrogen bonds [C–X···A− : D–H···A−] varied across the series.

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.

Electron density of a nanohoop [2]rotaxane based on invariom refinement

2021 ◽  
Vol 76 (2) ◽  
pp. 97-102
Author(s):  
Peter Luger ◽  
Birger Dittrich
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Potential Gradient ◽  
Building Blocks ◽  
Pyridyl Ring ◽  
Bond Orders ◽  
X Ray Diffraction ◽  
Phenyl Rings ◽  
Non Covalent Interactions ◽  
Average Bond

Abstract Rotaxanes as well as catenanes are known as potential building blocks of molecular machines. The nanohoop [2]rotaxane investigated is composed of a macrocycle derived from a [6]cycloparaphenylene (CCP, designated as a carbon nanohoop), where one of the six para-linked phenyl rings is replaced by a 2,6-substituted pyridyl ring. This macrocycle is mechanically interlocked with a thread, a linear rod-shaped diyne fragment sitting in the cavity of the macrocycle. Two bulky 3,5-di-t-butyl-phenyl rests as end groups keep the thread fixed. The interplay between macrocycle and thread was examined by means of the electron density distribution (EDD) obtained by application of the invariom formalism, relying on X-ray diffraction data collected earlier. The so-obtained EDD was subjected to topological analysis using the QTAIM formalism. Moreover, molecular Hirshfeld and electrostatic potential (ESP) surfaces were calculated. The 73 C–C bonds were analysed in terms of bond topological properties. For the 46 single and the 22 aromatic bonds, the analysis gave average bond orders of 1.03 and 1.61. The five C–C bonds in the diyne fragment can clearly be distinguished into three types: formal triple bonds with bond orders above 3.0, arene bonds with bond orders of 1.6 and finally bond orders of 1.3 in the adjacent C–C bonds, which indicate a considerable electron delocalization in this fragment. Mapping the ED onto the Hirshfeld surfaces of the macrocycle and the thread does not show strong signals. This shows that in between the molecules only weak non-covalent interactions are present. The electrostatic potentials (ESPs) were mapped onto molecular EDD isosurfaces. For all phenyl rings, small regions of negative ESP are visible on the delocalized π systems. A potential gradient between the mostly positive ESP of the macrocycle and the diyne region of the thread exist, which can be considered the dominant force to hold this rotaxane together.

scholarly journals A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

RSC Advances ◽  
2018 ◽  
Vol 8 (67) ◽  
pp. 38445-38454 ◽  
Author(s):  
Andrea Gionda ◽  
Giovanni Macetti ◽  
Laura Loconte ◽  
Silvia Rizzato ◽  
Ahmed M. Orlando ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Crystal Packing ◽  
Variable Temperature ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Complex Organic Molecule ◽  
Non Covalent Interactions ◽  
Complex Organic ◽  
Covalent Interactions

A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

Dynamic constitutional hybrid materials-toward adaptive self-organized devices

2009 ◽  
Vol 1189 ◽  
Author(s):  
Mihail Barboiu ◽  
Adinela Cazacu ◽  
Simona Mihai ◽  
Yves-Marie Legrand ◽  
Arie van der Lee
Keyword(s):  
Hybrid Materials ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrophobic Silica ◽  
Self Organized ◽  
Non Covalent Interactions ◽  
Covalent Interactions

AbstractDynamic constitutional hybrid materials in which the functional self-organized macrocycles are reversibly connected with the inorganic silica mesopores through hydrophobic non-covalent interactions. Supramolecular columnar self-organized architectures confined within scaffolding hydrophobic silica mesopores can be structurally determined by using X-ray diffraction techniques.

Experimental and theoretical study on the molecular structure, covalent and non-covalent interactions of 2,4-dinitrodiphenylamine: X-ray diffraction and QTAIM approach

2017 ◽  
Vol 1141 ◽  
pp. 53-63 ◽  
Author(s):  
Javier Hernández-Paredes ◽  
Roberto C. Carrillo-Torres ◽  
Ofelia Hernández-Negrete ◽  
Rogerio R. Sotelo-Mundo ◽  
Daniel Glossman-Mitnik ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Theoretical Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Color-tunable phosphorescence of 1,10-phenanthrolines by 4,7-methyl/-diphenyl/-dichloro substituents in cocrystals assembledviabifurcated C—I...N halogen bonds using 1,4-diiodotetrafluorobenzene as a bonding donor

2017 ◽  
Vol 73 (2) ◽  
pp. 247-254 ◽  
Author(s):  
Rui Liu ◽  
Yuan Jun Gao ◽  
Wei Jun Jin
Keyword(s):  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Luminescent Properties ◽  
Halogen Bonds ◽  
X Ray Diffraction ◽  
X Ray ◽  
Color Tunable ◽  
Non Covalent Interactions ◽  
The Impact ◽  
Covalent Interactions

Single-crystal X-ray diffraction reveals a series of phosphorescent cocrystals which were assembled by 1,4-diiodotetrafluorobenzene (1,4-DITFB) and either 4,7-dimethyl-1,10-phenanthroline (DMPhe), 4,7-diphenyl-1,10-phenanthroline (DPPhe) or 4,7-dichloro-1,10-phenanthroline (DClPhe)viaC—I...N halogen bonding. These cocrystals, labeled (1), (2) and (3), respectively, are phosphorescent and a distinct change in phosphorescent color can be observed from orange–yellow, green to yellow–green, with well defined vibrational band maxima at 587, 520 and 611 nm for (1), (2) and (3). Based on the dependence of halogen bonding in sites and strength, we discussed the impact of substituents with different electron-withdrawing effects and steric hindrance on intermolecular noncovalent interactions and phosphorescence. The method of inducing and modulating phosphorescence by halogen bonding and other weak non-covalent interactions through changing the substituent groups of molecules should be significant in both theory and the application of optical function materials with predictable and modulated luminescent properties.

scholarly journals A Comparative Theoretical and Spectroscopic Study of Aminomethylbenzoic Acid Derivatives as Potential NLO Candidates

2020 ◽  
Vol 3 (1) ◽  
pp. 102
Author(s):  
Amani Direm ◽  
Koray Sayın
Keyword(s):  
Nmr Spectra ◽  
Close Agreement ◽  
Molecular Electrostatic Potential ◽  
Structural Parameters ◽  
13C Nmr Spectra ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
X Ray ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Three aminomethylbenzoic acid derivatives were theoretically studied at M062X/6-311++G(d,p) level in a vacuum, namely 2-ammonio-5-methylcarboxybenzene perchlorate (1), 4-(ammoniomethyl) carboxybenzene nitrate (2) and 4-(ammoniomethyl)carboxybenze perchlorate (3). The compounds’ structures were fully optimized and compared with the single-crystal X-ray diffraction results, showing a very close agreement with the experimental structural parameters. Their IR, 1H- and 13C-NMR spectra were calculated and examined in detail. Furthermore, the molecular electrostatic potential (MEP) maps of the studied compounds were investigated and the strength of the non-covalent interactions evaluated. In addition to these results, the NLO properties of the three compounds were predicted.

Attractive halogen···halogen interactions in crystal structure of trans-dibromogold(III) complex

2020 ◽  
Vol 235 (10) ◽  
pp. 477-480 ◽  
Author(s):  
Alexander G. Tskhovrebov ◽  
Alexander S. Novikov ◽  
Andreii S. Kritchenkov ◽  
Victor N. Khrustalev ◽  
Matti Haukka
Keyword(s):  
Self Assembly ◽  
Electron Density Distribution ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Elemental Analyses ◽  
Nmr Techniques ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
C Nmr

AbstractA synthesis of the trans-dibromogold(III) t-Bu-Xantphos complex and its self-assembly into infinite 1-dimensional chain in the solid state is reported. The new complex characterized using elemental analyses (C, H, N), ESI-MS, 1H and 13C NMR techniques and X-ray diffraction analysis. Results of DFT calculations followed by the topological analysis of the electron density distribution within the framework of QTAIM method at the ωB97XD/DZP-DKH level of theory reveal that strength of attractive intermolecular non-covalent interactions Br···Br in the crystal is 1.2–1.6 kcal/mol.

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