Crystal engineering with hydrogen bonds and halogen bonds

CrystEngComm ◽  
2005 ◽  
Vol 7 (58) ◽  
pp. 355 ◽  
Author(s):  
Binoy K. Saha ◽  
Ashwini Nangia ◽  
Mariusz Jaskólski
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Halogen Bonds

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

2014 ◽  
Vol 47 (8) ◽  
pp. 2514-2524 ◽  
Author(s):  
Arijit Mukherjee ◽  
Srinu Tothadi ◽  
Gautam R. Desiraju
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Halogen Bonds

N—H...X (X = Cl and Br) hydrogen bonds in three isomorphous 3,5-dichloropyridinium salts

2017 ◽  
Vol 73 (10) ◽  
pp. 803-809 ◽  
Author(s):  
Ai Wang ◽  
Ulli Englert
Keyword(s):  
Hydrogen Bonds ◽  
Small Molecules ◽  
Crystal Engineering ◽  
Electrostatic Interactions ◽  
Halogen Bond ◽  
Halogen Bonds ◽  
Dipole Orientation ◽  
Halide Ligand ◽  
Van Der Waals Radii ◽  
Short Contacts

Specific short contacts are important in crystal engineering. Hydrogen bonds have been particularly successful and together with halogen bonds can be useful for assembling small molecules or ions into crystals. The ionic constituents in the isomorphous 3,5-dichloropyridinium (3,5-diClPy) tetrahalometallates 3,5-dichloropyridinium tetrachloridozincate(II), (C5H4Cl2N)2[ZnCl4] or (3,5-diClPy)2ZnCl4, 3,5-dichloropyridinium tetrabromidozincate(II), (C5H4Cl2N)2[ZnBr4] or (3,5-diClPy)2ZnBr4, and 3,5-dichloropyridinium tetrabromidocobaltate(II), (C5H4Cl2N)2[CoBr4] or (3,5-diClPy)2CoBr4, arrange according to favourable electrostatic interactions. Cations are preferably surrounded by anions and vice versa; rare cation–cation contacts are associated with an antiparallel dipole orientation. N—H...X (X = Cl and Br) hydrogen bonds and X...X halogen bonds compete as closest contacts between neighbouring residues. The former dominate in the title compounds; the four symmetrically independent pyridinium N—H groups in each compound act as donors in charge-assisted hydrogen bonds, with halogen ligands and the tetrahedral metallate anions as acceptors. The M—X coordinative bonds in the latter are significantly longer if the halide ligand is engaged in a classical X...H—N hydrogen bond. In all three solids, triangular halogen-bond interactions are observed. They might contribute to the stabilization of the structures, but even the shortest interhalogen contacts are only slightly shorter than the sum of the van der Waals radii.

Avoiding “Synthon Crossover” in Crystal Engineering with Halogen Bonds and Hydrogen Bonds

2011 ◽  
Vol 11 (12) ◽  
pp. 5333-5336 ◽  
Author(s):  
Christer B. Aakeröy ◽  
Prashant D. Chopade ◽  
John Desper
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Halogen Bonds

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.

scholarly journals Synthesis of tetrahalide dianions directed by crystal engineering

CrystEngComm ◽  
2015 ◽  
Vol 17 (35) ◽  
pp. 6641-6645 ◽  
Author(s):  
F. Pan ◽  
R. Puttreddy ◽  
K. Rissanen ◽  
U. Englert
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Macrocyclic Compounds ◽  
Halogen Bonds

The analogy between hydrogen bonds and halogen bonds was used to synthesize the unstable [X⋯I–I⋯X]2− species by trapping I2 in the channels of macrocyclic compounds.

Ethynyl hydrogen bonds and iodoethynyl halogen bonds: a case of synthon mimicry

CrystEngComm ◽  
2017 ◽  
Vol 19 (1) ◽  
pp. 11-13 ◽  
Author(s):  
Christer B. Aakeröy ◽  
Dhanushi Welideniya ◽  
John Desper
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Halogen Bond ◽  
Supramolecular Assemblies ◽  
Halogen Bonds ◽  
The Common ◽  
Synthetic Crystal

The common electrostatic features of ethynyl and iodoethynyl hydrogen- and halogen-bond donors, respectively, lead to synthon mimicry which can be employed in synthetic crystal engineering for the construction of identical supramolecular assemblies in the solid-state.

scholarly journals Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 766
Author(s):  
Barbara Bankiewicz ◽  
Marcin Palusiak
Keyword(s):  
Complex Formation ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Electrostatic Interactions ◽  
Dipole Moments ◽  
Main Role ◽  
Halogen Bonds ◽  
Topological Parameters ◽  
Leading Role ◽  
The Impact

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

Intermolecular binding preferences of haloethynyl halogen-bond donors as a function of molecular electrostatic potentials in a family of N-(pyridin-2-yl)amides

2021 ◽  
Author(s):  
Amila M. Abeysekera ◽  
Boris B. Averkiev ◽  
Pierre Le Magueres ◽  
Christer B. Aakeröy
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Halogen Bond ◽  
Electrostatic Potentials ◽  
Halogen Bonds ◽  
Molecular Electrostatic Potentials

The roles played by halogen bonds and hydrogen bonds in the crystal structures of N-(pyridin-2-yl)amides were evaluated and rationalised in the context of calculated molecular electrostatic potentials.

scholarly journals Charge density studies on 1:1 co-crystals of ethenzamide and saccharin

2014 ◽  
Vol 70 (a1) ◽  
pp. C964-C964
Author(s):  
Lucy Mapp ◽  
Mateusz Pitak ◽  
Simon Coles ◽  
Srinivasulu Aitipamula
Keyword(s):  
Hydrogen Bonds ◽  
Charge Density ◽  
Crystal Engineering ◽  
Chemical Properties ◽  
Secondary Level ◽  
Crystal Form ◽  
Monoclinic Space Group ◽  
Stoichiometric Ratio ◽  
Distribution Analysis ◽  
Space Group

The study of multi-component crystals, as well as the phenomenon of polymorphism, both have relevance to crystal engineering. Obtaining a specific polymorph is crucial as different polymorphs usually exhibit different physical and chemical properties and often the origin of this behaviour is unknown. This is especially important in the pharmaceutical industry. Herein, we present results of comparative studies of an analgesic drug, ethenzamide and its co-crystals with saccharin. The co-crystalisation of ethenzamide (2-ethoxybenzamide, EA) with saccharin (1,1-dioxo-,1,2-benzothiazol-3-one, SAC) with a 1:1 stoichiometric ratio resulted in two polymorphic forms of the co-crystal. Form I crystallises in the triclinic P-1 space group, whereas form II crystallises in monoclinic space group P21/n. Previous crystal structure analyses on forms I and II revealed that in both polymorphs the primary carboxy-amide-imide heterosynthon is the same, however the secondary level of interactions which extends the hydrogen bond network is different. Form I consists of extended linear tapes via N-H···O hydrogen bonds, whereas form II is composed of stacks of tetrameric motifs including N-H···O hydrogen bonds and C-H···O interactions. These two forms of EA-SAC can be classified as synthon polymorphs at a secondary level of hydrogen bonding [1]. In our approach an accurate, high resolution charge density distribution analysis has been carried out to obtain greater insight into the electronic structures of both types of the EA-SAC co-crystals and relate differences in electronic distribution with their polymorphic behaviour. To describe the nature and role of inter and intra-molecular interactions in a quantitative manner, the Hansen-Coppens formalism [2] and Bader's AIM theory [3] approach have been applied.

scholarly journals Two New Polyiodides in the 4,4´-Bipyridinium Diiodide/Iodine System

2012 ◽  
Vol 67 (1) ◽  
pp. 5-10
Author(s):  
Guido J. Reiss ◽  
Martin van Megen
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Complex I ◽  
The Other ◽  
Cyclic Dimer ◽  
Water Molecules ◽  
Spectroscopic Methods ◽  
Halogen Bonds ◽  
One Dimensional ◽  
Hydroiodic Acid

The reaction of bipyridine with hydroiodic acid in the presence of iodine gave two new polyiodide-containing salts best described as 4,4´-bipyridinium bis(triiodide), C10H10N2[I3]2, 1, and bis(4,4´-bipyridinium) diiodide bis(triiodide) tris(diiodine) solvate dihydrate, (C10H10N2)2I2[I3]2 · 3 I2 ·2H2O, 2. Both compounds have been structurally characterized by crystallographic and spectroscopic methods (Raman and IR). Compound 1 is composed of I3 − anions forming one-dimensional polymers connected by interionic halogen bonds. These chains run along [101] with one crystallographically independent triiodide anion aligned and the other triiodide anion perpendicular to the chain direction. There are no classical hydrogen bonds present in 1. The structure of 2 consists of a complex I144− anion, 4,4´-bipyridinium dications and hydrogen-bonded water molecules in the ratio of 1 : 2 : 2. The I144− polyiodide anion is best described as an adduct of two iodide and two triiodide anions and three diiodine molecules. Two 4,4´-bipyridinium cations and two water molecules form a cyclic dimer through N-H· · ·O hydrogen bonds. Only weak hydrogen bonding is found between these cyclic dimers and the polyiodide anions.

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