scholarly journals The Isocyanide Complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd, Pt; X = Cl, Br) as Tectons in Crystal Engineering Involving Halogen Bonds

Crystals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 799
Author(s):  
Maria V. Kashina ◽  
Daniil M. Ivanov ◽  
Mikhail A. Kinzhalov
Keyword(s):  
Dft Calculations ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Topological Analysis ◽  
Electron Localization ◽  
Halogen Bonds ◽  
Isocyanide Ligands ◽  
1D Chains

The isocyanide complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd; X = Cl, Br; M = Pt; X = Br) form isomorphous crystal structures exhibiting the Cl/Br and Pd/Pt exchanges featuring 1D chains upon crystallisation. Crystal packing is supported by the C–X···X–C halogen bonds (HaBs), C–H···X–C hydrogen bonds (HB), X···M semicoordination, and C···C contacts between the C atoms of aryl isocyanide ligands. The results of DFT calculations and topological analysis indicate that all the above contact types belong to attractive noncovalent interactions. A projection of the electron localization function (ELF) and an inspection of the electron density (ED) and the electrostatic potential (ESP) reveal the amphiphilic nature of X atoms playing the role of HaB donors, HaB and HB acceptors, and a nucleophilic partner in X···M semicoordination.

The role of the Lewis acid−base properties in the supramolecular association of 1,2,5-chalcogenadiazoles

2013 ◽  
Vol 91 (5) ◽  
pp. 338-347 ◽  
Author(s):  
Anthony F. Cozzolino ◽  
Philip J.W. Elder ◽  
Lucia Myongwon Lee ◽  
Ignacio Vargas-Baca
Keyword(s):  
Topological Analysis ◽  
Structural Features ◽  
Lewis Acidity ◽  
Electron Localization ◽  
Dispersion Forces ◽  
Acid Base ◽  
Lewis Bases ◽  
The Individual ◽  
Secondary Bonding

The secondary bonding interactions that link the supramolecular structures assembled by 1,2,5-chalcogenadiazoles were analyzed through explicit orthogonalization of molecular orbitals (NBO), topological analysis of the electron density (AIM), and the electron localization function (ELF). The results of these analyses are consistent with a bonding description that attributes important covalent and electrostatic character to these interactions. Application of these analyses to the individual molecules highlighted the structural features from which each of those contributions originates, namely the polarity and modest strength of the E–N bond. Both of these effects increase along the series S, Se, Te. Perturbations to the heterocycle electronic structure that result in a weaker and more polar E–N bond cause an increase in the Lewis acidity at the chalcogen centre, which in turn leads to stronger secondary bonding interactions with Lewis bases. Additionally, the contribution of dispersion forces is not negligible and is most important in the case of sulfur.

scholarly journals "Organic Fluorine" and its Importance in Crystal Engineering

2014 ◽  
Vol 70 (a1) ◽  
pp. C669-C669
Author(s):  
Angshuman Roy Choudhury ◽  
Gurpreet Kaur ◽  
Maheswararao Karanam ◽  
Sandhya Patel
Keyword(s):  
Crystal Engineering ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Crystal Lattices ◽  
Organic Systems ◽  
Organic Solid ◽  
Group A ◽  
Number Of Publications ◽  
Organic Fluorine

The phrase "Organic fluorine" [1] was introduced by Dunitz and Taylor in 1997 to identify the C–F bonds in organic systems. Different research groups have used the phrase to glorify or deny the influence of C–F bond in crystal lattices. Once Dunitz stated that "Organic Fluorine: Odd Man Out" and Howard et al. questioned the role of "Organic fluorine" in crystal engineering. While some researchers have refuted the role of "organic fluorine" in crystal packing; the others indicated the importance of the interactions involving the same group. A number of publications have shown the importance of "Organic fluorine" in influencing crystal packing. We have been interested in the area of weak interactions in organic solid state chemistry since 1999 [2]; especially interactions involving "Organic fluorine". The study is being conducted following a systematic approach and is still in progress. We have looked at the structures of a number if tetrahydroisoquinoline derivatives, a number of differently substituted imines, phenyleacetanilydes, benzanilides and azobenzenes [3] etc. in order to elucidate the influence of "Organic fluorine" in crystal engineering both in the presence and in the absence of strong hydrogen bonding functional groups present within the molecule. A short summary of our observations will be highlighted in the presentation.

Similarities and differences in the crystal packing of halogen-substituted indole derivatives

2018 ◽  
Vol 74 (4) ◽  
pp. 376-384 ◽  
Author(s):  
Rahul Shukla ◽  
Paramveer Singh ◽  
Piyush Panini ◽  
Deepak Chopra
Keyword(s):  
Quantum Theory ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Topological Analysis ◽  
Indole Derivatives ◽  
Π Interactions ◽  
Supramolecular Motifs ◽  
Exchange Repulsion ◽  
Similarities And Differences

The role of different intermolecular interactions in the crystal structures of halogen-substituted indoles which are fused with six-membered or seven-membered cyclic rings is investigated here. Several crystal structures show isostructural characteristics due to the presence of similar supramolecular motifs. In the absence of any strong hydrogen bonds, the molecular packing of reported structures is primarily stabilized by the presence of non-classical N—H...π and C—H...π interactions in addition to C—H...X (X = F/Cl/Br) interactions. The nature and energetics of primary and secondary dimeric motifs are partitioned into the electrostatics, polarization, dispersion and exchange–repulsion components using the PIXEL method. Short and directional N—H...π interactions are further explored by a topological analysis of the electron density based on quantum theory of atoms in molecules.

scholarly journals Synthon robustness by C-F groups in halogen substituted N-benzylideneanilines

2014 ◽  
Vol 70 (a1) ◽  
pp. C1811-C1811
Author(s):  
Gurpreet Kaur ◽  
Angshuman Roy Choudhury
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Topological Analysis ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor ◽  
The Impact ◽  
Organic Fluorine

The arrangement of the molecules in their crystal structure is controlled by the non-covalent intermolecular interactions other than the effectual space filling. The role of strong hydrogen bonds in guiding the crystal packing is well-known in the literature. But, how significant are the weak interactions in the field of crystal engineering, has yet not been fully understood. Our aim is to comprehend the nature and strength of the weak interactions involving fluorine in guiding the packing of small organic molecules in their respective crystal structure. The reason being the controversies, which are involved regarding the interactions offered by "organic fluorine"[1] and also due to the importance of these interactions in the pharmaceutical industry. Some of the research groups indicate the incapability of interactions offered by fluorine in the formation of supramolecular motifs, whereas other groups have indicated that substantial role is being played by fluorine in constructing the lattice through C-H···F, C-F···F and C-F···π interactions in the presence and absence of strong hydrogen bond donor and acceptor groups. To understand more about these interactions, we have chosen a model system of halogen substituted N-benzylideneanilines[2]. In this system, we have analysed the impact of fluorine mediated interactions on the crystal packing by having fluorine as a substituent on both the phenyl rings. Then the robustness of the synthons offered by organic fluorine has been anticipated in the same system, but with one of the substituent as chlorine or bromine in either of the phenyl ring. It has been observed that the replacement of the non-interacting fluorine by its heavier analogue has not altered the supramolecular motif, which was formed by the other fluorine. But the crystal packing has been found to be completely altered in the molecules where the interacting fluorine was replaced by its heavier analogue. Salient features of our computational studies, which include the calculation of the stabilization energies of the studied dimers using MP2 method and their topological analysis using AIM2000, to support the experimental observations will also be presented to highlight the sturdiness of the synthons formed by so called "organic fluorine".

scholarly journals Crystal engineering with pyrazolyl-thiazole derivatives: Structure-directing role of π-stacking and σ-hole interactions

CrystEngComm ◽  
2021 ◽  
Author(s):  
Muhammad Naeem Ahmed ◽  
Murtaza Madni ◽  
Shaista Anjum ◽  
Saiqa Andleeb ◽  
Shahid Hameed ◽  
...  
Keyword(s):  
Crystal Engineering ◽  
Noncovalent Interactions ◽  
Thiazole Derivatives ◽  
X Ray ◽  
Π Stacking

The synthesis and X-ray characterization of 1-(2-(3-(4-bromophenyl)-5-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)-4-methylthiazol-5-yl)ethanone (7), ethyl 2-(5-(4-bromophenyl)-3-(4-chlorophenyl)-4,5-dihydropyrazol-1-yl)thiazole-4-carboxylate (8) and 2-(5-(4-chlorophenyl)-3-phenyl-4,5-dihydro-1H-pyrazol-1-yl)-N'-(2-hydroxy-3-methoxybenzylidene)thiazole-4-carbohydrazide (10) is described in this manuscript. The structure-directing role of a variety of noncovalent interactions have been...

Structure of the Holliday junction: applications beyond recombination

2017 ◽  
Vol 45 (5) ◽  
pp. 1149-1158 ◽  
Author(s):  
P. Shing Ho
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Noncovalent Interactions ◽  
Three Dimensional ◽  
Essential Element ◽  
Dna Origami ◽  
Holliday Junction ◽  
Dna Assembly ◽  
Halogen Bonds ◽  
Sequence Dependence

The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.

Role of halogen-involved intermolecular interactions and existence of isostructurality in the crystal packing of —CF3 and halogen (Cl or Br or I) substituted benzamides

2018 ◽  
Vol 74 (6) ◽  
pp. 574-591 ◽  
Author(s):  
Pradip Kumar Mondal ◽  
Rahul Shukla ◽  
Subha Biswas ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
X Ray Diffraction ◽  
Substituted Benzamides ◽  
Size Type ◽  
Substituted Benzamide ◽  
Van Der Waals Radii

A total of 23 benzamides are obtained through a simple reaction between chloro-/bromo-/iodoaniline and trifluoromethylbenzoyl chloride and characterized using single-crystal X-ray diffraction. Crystal structures of three series of benzamides based on N-chlorophenyl–trifluoromethyl–benzamide (nine compounds), N-bromophenyl–trifluoromethyl–benzamide (six compounds), and N-iodophenyl–trifluoromethyl–benzamide (eight compounds) are prepared to analyse the halogen-mediated noncovalent interactions. The influences of Cl/Br/I and trifluoromethyl substituents on the respective interactions are examined in the presence of a strong N—H...O hydrogen bond. This exercise has resulted in the documentation of frequently occurring supramolecular synthons involving halogen atoms in the crystal packing of benzamide molecules in the solid state. In the present study, a detailed quantitative evaluation has been performed on the nature, energetics, electrostatic contributions, and topological properties of short and directional intermolecular interactions derived from the electron density on halogenated benzamides in the solid state. Besides these, the occurrence of three-, two- and one-dimensional isostructurality in halogen (Cl or Br or I) substituted benzamide analogues is also investigated. A `region of co-existence' involving halogen-based intermolecular interactions in the vicinity of the sum of the van der Waals radii has been identified. Thus, the nature of the halogen (effective size), type of interaction and the packing characteristics via presence of additional interactions establish the subtle, yet important, role of cooperativity in intermolecular interactions in crystal packing.

Importance of polarization assisted/resonance assisted hydrogen bonding interactions and unconventional interactions in crystal formations of five new complexes bearing chelidamic acid through a proton transfer mechanism

RSC Advances ◽  
2015 ◽  
Vol 5 (89) ◽  
pp. 72923-72936 ◽  
Author(s):  
Masoud Mirzaei ◽  
Hossein Eshtiagh-Hosseini ◽  
Mojtaba Shamsipur ◽  
Mahdi Saeedi ◽  
Mehdi Ardalani ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Dft Calculations ◽  
Coordination Compounds ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Transfer Mechanism ◽  
X Ray ◽  
Hydrogen Bonding Interactions ◽  
Chelidamic Acid

Five new coordination compounds derived from chelidamic acid and amines have been synthesized and X-ray characterized. The noncovalent interactions that govern the crystal packing have been rationalized by means of DFT calculations.

Synthesis, X-ray characterization, DFT calculations and Hirshfeld surface analysis studies of carbohydrazone based on Zn(ii) complexes

CrystEngComm ◽  
2016 ◽  
Vol 18 (1) ◽  
pp. 102-112 ◽  
Author(s):  
Ghodrat Mahmoudi ◽  
Antonio Bauzá ◽  
Antonio Rodríguez-Diéguez ◽  
Piotr Garczarek ◽  
Werner Kaminsky ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
X Ray

Five Zn(ii) complexes based on a N4O core carbohydrazone ligand have been synthesized and X-ray characterized. The noncovalent interactions that govern the crystal packing have been rationalized by means of DFT calculations.

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