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.

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

Halogen bonds on demand: I...S contacts in cocrystals oftrans-bis(thiocyanato-κN)tetrakis(4-vinylpyridine-κN)nickel(II) and 2,3,5,6-tetrafluoro-1,4-diiodobenzene

2015 ◽  
Vol 71 (11) ◽  
pp. 991-995 ◽  
Author(s):  
Mihaela-Diana Şerb ◽  
Carina Merkens ◽  
Irmgard Kalf ◽  
Ulli Englert
Keyword(s):  
Hydrogen Bonds ◽  
Small Molecules ◽  
Aromatic Ring ◽  
Room Temperature ◽  
Guest Molecule ◽  
Halogen Bond ◽  
Halogen Bonds ◽  
Space Group ◽  
On Demand ◽  
Supramolecular Architectures

Hydrogen bonds are considered a powerful organizing force in designing supramolecular architectures because they are directional, selective and reversible at room temperature.trans-Dithiocyanatotetrakis(4-vinylpyridine)nickel(II) is a popular host for the inclusion of small molecules and 2,3,5,6-tetrafluoro-1,4-diiodobenzene (TFDIB) represents a strong halogen-bond donor. These constituents cocrystallize in a 1:1 stoichiometry, [Ni(NCS)2(C7H7N)4]·C6F4I2, in the tetragonal space groupI41/a. Both residues occupy special positions,i.e.the pseudo-octahedral NiIIcomplex is located on a twofold axis and the TFDIB molecule sits about a crystallographic centre of inversion. The components interactviaa short S...I contact of 3.2891 (12) Å between the thiocyanate S atom of the host and the iodine substituent at the perhalogenated aromatic ring of the smaller guest molecule. This interaction meets the commonly accepted criteria for a halogen bond. Such halogen bonds to sulfur are significantly less common than to smaller electronegative atoms.

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.

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

scholarly journals Design of two series of 1:1 cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine and carboxylic acids

2018 ◽  
Vol 74 (9) ◽  
pp. 1007-1019 ◽  
Author(s):  
Ammaiyappan Rajam ◽  
Packianathan Thomas Muthiah ◽  
Raymond John Butcher ◽  
Jerry P. Jasinski ◽  
Jan Wikaira
Keyword(s):  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Carboxylic Acids ◽  
Halogen Bond ◽  
Single Point ◽  
Carboxyl Group ◽  
Aminobenzoic Acid ◽  
Halogen Bonds ◽  
Large Cage ◽  
Acta Cryst

Two series of a total of ten cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine with various carboxylic acids have been prepared and characterized by single-crystal X-ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton-accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C73, 862–868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine–3-bromothiophene-2-carboxylic acid (1/1), 1, 4-amino-5-chloro-2,6-dimethylpyrimidine–5-chlorothiophene-2-carboxylic acid (1/1), 2, 4-amino-5-chloro-2,6-dimethylpyrimidine–2,4-dichlorobenzoic acid (1/1), 3, and 4-amino-5-chloro-2,6-dimethylpyrimidine–2-aminobenzoic acid (1/1), 4, the carboxyl hydroxy group (–OH) is hydrogen bonded to position N1 (O—H...N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion-related stacked pyrimidines are doubly bridged by the carboxyl groups via N—H...O and O—H...N hydrogen bonds to form a large cage-like tetrameric unit with an R 4 2(20) graph-set ring motif. These tetrameric units are further connected via base pairing through a pair of N—H...N hydrogen bonds, generating R 2 2(8) motifs (supramolecular homosynthon). In the other series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine–5-methylthiophene-2-carboxylic acid (1/1), 5, 4-amino-5-chloro-2,6-dimethylpyrimidine–benzoic acid (1/1), 6, 4-amino-5-chloro-2,6-dimethylpyrimidine–2-methylbenzoic acid (1/1), 7, 4-amino-5-chloro-2,6-dimethylpyrimidine–3-methylbenzoic acid (1/1), 8, 4-amino-5-chloro-2,6-dimethylpyrimidine–4-methylbenzoic acid (1/1), 9, and 4-amino-5-chloro-2,6-dimethylpyrimidine–4-aminobenzoic acid (1/1), 10, the carboxyl group interacts with position N3 and the adjacent 4-amino group of the corresponding pyrimidine ring via O—H...N and N—H...O hydrogen bonds to generate the robust R 2 2(8) supramolecular heterosynthon. These heterosynthons are further connected by N—H...N hydrogen-bond interactions in a linear fashion to form a chain-like arrangement. In cocrystal 1, a Br...Br halogen bond is present, in cocrystals 2 and 3, Cl...Cl halogen bonds are present, and in cocrystals 5, 6 and 7, Cl...O halogen bonds are present. In all of the ten cocrystals, π–π stacking interactions are observed.

THE COOPERATIVITY BETWEEN HYDROGEN AND HALOGEN BONDS

2008 ◽  
Vol 07 (01) ◽  
pp. 13-35 ◽  
Author(s):  
TIMM LANKAU ◽  
YU-CHUNG WU ◽  
JIAN-WEI ZOU ◽  
CHIN-HUI YU
Keyword(s):  
Simple Model ◽  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Halogen Bond ◽  
Computational Method ◽  
Halogen Bonds ◽  
Reasonable Accuracy ◽  
Reference Cluster ◽  
Hybrid Functionals ◽  
Two Parameter

The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y ( X: C2H2, H2O, NH3, HCI, HCN, HF; Y: HF, BrF, Br2 is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X -ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y -ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.

Density Function Theory Study on the Recognition of the Urea-Based Involving Bromine Derivation Receptor for the Halogen Anions

2013 ◽  
Vol 328 ◽  
pp. 850-854
Author(s):  
Kun Yuan ◽  
Hui Xue Li ◽  
Huian Tang ◽  
Yuan Cheng Zhu
Keyword(s):  
Hydrogen Bonds ◽  
Density Function ◽  
Halogen Bond ◽  
Blue Shift ◽  
Nbo Analysis ◽  
Basis Set ◽  
Host Recognition ◽  
Halogen Bonds ◽  
Orbital Theory ◽  
Recognition Mechanism

The recognition mechanism of the urea-based involving Br derivation receptor (A) for the halogen anions through hydrogen bond and halogen bond was discussed by the density function Becke, three-parameter, Lee-Yang-Parr (B3LYP) method. The results showed that the guest-host recognition was performed by using four coordination weak bonds, which include two N-H...X hydrogen bonds and two C-Br...X halogen bonds (X= F-,Cl-,Br- and I-). The calculated interaction energies (ΔECP) with basis set super-position error (BSSE) correction of the four systems are-3.95, -82.43, -70.86 and 992.63 kJmol-1, respectively. So, the urea-based derivation receptor (A) presents the best recognition capable for the Br- and Cl-, and it can not recognize the I- in the same condition. Natural bond orbital theory (NBO) analysis has been used to investigate the electronic behavior and property of the red-shift N-H...X hydrogen bonds and two blue-shift C-Br...X halogen bonds in the A...X- systems.

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