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 Crystal structures of the dioxane hemisolvates ofN-(7-bromomethyl-1,8-naphthyridin-2-yl)acetamide and bis[N-(7-dibromomethyl-1,8-naphthyridin-2-yl)acetamide]

2017 ◽  
Vol 73 (10) ◽  
pp. 1409-1413 ◽  
Author(s):  
Robert Rosin ◽  
Wilhelm Seichter ◽  
Monika Mazik
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Lone Electron Pair ◽  
Electron Pair ◽  
Three Dimensional ◽  
Supramolecular Network ◽  
Halogen Bonds ◽  
Host Interactions ◽  
Compound Ii ◽  
Noncovalent Bonding

The syntheses and crystal structures ofN-(7-bromomethyl-1,8-naphthyridin-2-yl)acetamide dioxane hemisolvate, C11H10BrN3O·0.5C4H8O2, (I), and bis[N-(7-dibromomethyl-1,8-naphthyridin-2-yl)acetamide] dioxane hemisolvate, 2C11H9Br2N3O·0.5C4H8O2, (II), are described. The molecules adopt a conformation with the N—H hydrogen pointing towards the lone electron pair of the adjacent naphthyridine N atom. The crystals of (I) are stabilized by a three-dimensional supramolecular network comprising N—H...N, C—H...N and C—H...O hydrogen bonds, as well as C—Br...π halogen bonds. The crystals of compound (II) are stabilized by a three-dimensional supramolecular network comprising N—H...N, C—H...N and C—H...O hydrogen bonds, as well as C—H...π contacts and C—Br...π halogen bonds. The structure of the substituent attached in the 7-position of the naphthyridine skeleton has a fundamental influence on the pattern of intermolecular noncovalent bonding. While the Br atom of (I) participates in weak C—Br...Oguestand C—Br...π contacts, the Br atoms of compound (II) are involved in host–host interactionsviaC—Br...O=C, C—Br...N and C—Br...π bonding.

scholarly journals Noncovalent Interactions between 1,3,5-Trifluoro-2,4,6-triiodobenzene and a Series of 1,10-Phenanthroline Derivatives: A Combined Theoretical and Experimental Study

Crystals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 140 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Quantum Chemical ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Structural Competition

How many strong C−I⋯N halogen bonds can one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule form in a crystal structure? To answer this question, we investigated in detail the noncovalent interactions between 1,3,5-trifluoro-2,4,6-triiodobenzene and a series of 1,10-phenanthroline derivatives by employing a combined theoretical and experimental method. The results of the quantum chemical calculations and crystallographic experiments clearly show that there is a structural competition between a C−I⋯N halogen bond and π⋯π stacking interaction. For example, when there are much stronger π⋯π stacking interactions between two 1,10-phenanthroline derivative molecules or between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules in the crystal structures, then one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule forms only one C−I⋯N halogen bond with one 1,10-phenanthroline derivative molecule. Another example is when π⋯π stacking interactions in the crystal structures are not much stronger, one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule can form two C−I⋯N halogen bonds with two 1,10-phenanthroline derivative molecules.

Polysulfonylamine, CLXXXVIII [1]. Kristallstrukturen von drei Dimethylammonium-di(4-halogenbenzolsulfonyl)amiden (Halogen = Cl, Br, I) und von Dimethylammonium-di(4-methylbenzolsulfonyl)amid: Eine isotype Reihe mit strukturbestimmenden starken Wasserstoffbrücken und beiläufigen Halogenbrücken/ Polysulfonylamines, CLXXXVIII. Crystal Structures of Three Dimethylammonium Di(4-halobenzenesulfonyl)amides (Halogen = Cl, Br, I) and of Dimethylammonium Di(4-methylbenzenesulfonyl)amide: An Isotypical Series Featuring Strong Structure-determining Hydrogen Bonds and Incidental Halogen Bonds

2010 ◽  
Vol 65 (10) ◽  
pp. 1258-1266 ◽  
Author(s):  
Christoph Wölper ◽  
Alejandra Rodríguez-Gimeno ◽  
Matthias Freytag ◽  
Peter G. Jones ◽  
Armand Blaschette
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Causative Factor ◽  
Monoclinic Space Group ◽  
Halogen Bonds ◽  
Space Group ◽  
Dimethylammonium Chloride ◽  
Hydrogen Bonded

The four title compounds, Me2NH2+·(4-Cl/Br/I/Me-C6H4-SO2)2N-, were obtained by metathesis of dimethylammonium chloride with the corresponding silver di(arenesulfonyl)amides. The products crystallize isotypically in the monoclinic space group Cc (Z = 4, Z´ = 1). In each structure, the ionic entities associate into hydrogen-bonded chains, which propagate along the c axis of the crystals and consist of alternating cations and anions held together by charge-assisted N+-H· · ·N− and N+- H(· · ·O)2 hydrogen bonds. In the three structures containing 4-halobenzenesulfonyl groups, each hydrogen-bonded chain is linked to four neighboring chains by pairs of C-Cl/Br/I· · ·O halogen bonds, which at first sight seem to be the causative factor in the formation of catemeric head-to-tail arrays of anions propagating along the ab face diagonals. On suppressing these halogen bonds by means of halogen-methyl exchange, all essential features of the packing architecture, including the anion headto- tail arrays, are precisely maintained. It may be thus inferred that the halogen bonds occurring in the first three compounds are supportive incidentals, but do not play any structure-determining role.

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.

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.

The Role of Molecular Electrostatic Potentials in the Formation of a Halogen Bond in Furan⋅⋅⋅XY and Thiophene⋅⋅⋅XY Complexes

ChemPhysChem ◽  
2011 ◽  
Vol 12 (6) ◽  
pp. 1080-1087 ◽  
Author(s):  
Yanli Zeng ◽  
Xueying Zhang ◽  
Xiaoyan Li ◽  
Lingpeng Meng ◽  
Shijun Zheng
Keyword(s):  
Halogen Bond ◽  
Electrostatic Potentials ◽  
Molecular Electrostatic Potentials

scholarly journals Crystal structures of 2-[3,5-bis(bromomethyl)-2,4,6-triethylbenzyl]isoindoline-1,3-dione and 2-{5-(bromomethyl)-3-[(1,3-dioxoisoindolin-2-yl)methyl]-2,4,6-triethylbenzyl}isoindoline-1,3-dione

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Manuel Stapf ◽  
Betty Leibiger ◽  
Anke Schwarzer ◽  
Monika Mazik
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Molecular Conformation ◽  
Halogen Bond ◽  
Asymmetric Unit ◽  
Space Group ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions

The title compounds, C23H25Br2NO2 (1) and C31H29BrN2O4 (2), crystallize in the space group P21/n with two (1-A and 1-B) and one molecules, respectively, in the asymmetric unit of the cell. The molecular conformation of these compounds is stabilized by intramolecular C—H...O hydrogen bonds and C—H...N or C—H...π interactions. The crystal structure of 1 features a relatively strong Br...O=C halogen bond, which is not observed in the case of 2. Both crystal structures are characterized by the presence of C—H...Br hydrogen bonds and numerous intermolecular C—H...O hydrogen-bonding interactions.

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.

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