A systematic structural study of halogen bondingversushydrogen bonding within competitive supramolecular systems

As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

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Nontypical iodine–halogen bonds in the crystal structure of (3E)-8-chloro-3-iodomethylidene-2,3-dihydro-1,4-oxazino[2,3,4-ij]quinolin-4-ium triiodide

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229616003934 ◽

2016 ◽

Vol 72 (4) ◽

pp. 341-345 ◽

Cited By ~ 4

Author(s):

E. V. Bartashevich ◽

V. I. Batalov ◽

I. D. Yushina ◽

A. I. Stash ◽

Y. S. Chen

Keyword(s):

Crystal Structure ◽

Rare Case ◽

Halogen Bond ◽

Spectroscopic Properties ◽

Halogen Bonds ◽

X Ray Diffraction ◽

Weakly Bound ◽

X Ray ◽

Raman Spectroscopic

Two kinds of iodine–iodine halogen bonds are the focus of our attention in the crystal structure of the title salt, C12H8ClINO+·I3−, described by X-ray diffraction. The first kind is a halogen bond, reinforced by charges, between the I atom of the heterocyclic cation and the triiodide anion. The second kind is the rare case of a halogen bond between the terminal atoms of neighbouring triiodide anions. The influence of relatively weakly bound iodine inside an asymmetric triiodide anion on the thermal and Raman spectroscopic properties has been demonstrated.

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Halogen Bonds in 2,5-Dihalopyridine-Copper(I) Halide Coordination Polymers

Materials ◽

10.3390/ma12203305 ◽

2019 ◽

Vol 12 (20) ◽

pp. 3305 ◽

Cited By ~ 5

Author(s):

Carolina von Essen ◽

Kari Rissanen ◽

Rakesh Puttreddy

Keyword(s):

Coordination Polymers ◽

Halogen Bond ◽

Halogen Bonding ◽

Halide Ions ◽

Halogen Bonds ◽

Discrete Structure ◽

Electronic Effects ◽

X Ray Diffraction ◽

X Ray ◽

Supramolecular Networks

Two series of 2,5-dihalopyridine-Cu(I)A (A = I, Br) complexes based on 2-X-5-iodopyridine and 2-X-5-bromopyridine (X = F, Cl, Br and I) are characterized by using single-crystal X-ray diffraction analysis to examine the nature of C2−X2···A–Cu and C5−X5···A–Cu halogen bonds. The reaction of the 2,5-dihalopyridines and Cu(I) salts allows the synthesis of eight 1-D coordination polymers and a discrete structure. The resulting Cu(I)-complexes are linked by C−X···A–Cu halogen bonds forming 3-D supramolecular networks. The C−X···A–Cu halogen bonds formed between halopyridine ligands and copper(I)-bound halide ions are stronger than C−X···X’–C interactions between two 2,5-dihalopyridine ligands. The C5−I5···I–Cu and C5−Br5···Br–Cu halogens bonds are shorter for C2-fluorine than C2-chlorine due to the greater electron-withdrawing power of fluorine. In 2,5-diiodopyridine-Cu(I)Br complex, the shorter C2−I2···Br–Cu [3.473(5) Å] distances are due to the combined polarization of C2-iodine by C2−I2···Cu interactions and para-electronic effects offered by the C5-iodine, whilst the long halogen bond contacts for C5−I5···Br–Cu [3.537(5) Å] are indicative that C2-iodine has a less para-electronic influence on the C5-iodine. In 2-fluoro-5-X-pyridine-Cu(I) complexes, the C2-fluorine is halogen bond passive, while the other C2-halogens in 2,5-dihalopyridine-Cu(I), including C2-chlorine, participate in halogen bonding interactions.

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Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction

Molecules ◽

10.3390/molecules26113119 ◽

2021 ◽

Vol 26 (11) ◽

pp. 3119

Author(s):

Sergey V. Baykov ◽

Artem V. Semenov ◽

Eugene A. Katlenok ◽

Anton A. Shetnev ◽

Nadezhda A. Bokach

Keyword(s):

Natural Bond Orbital ◽

Halogen Bond ◽

Lone Pair ◽

Computational Studies ◽

Halogen Bonds ◽

Molecular Electrostatic Potentials ◽

X Ray Diffraction ◽

X Ray ◽

Central Oxygen ◽

Packing Effect

Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs.

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Stoichiomorphic Halogen-Bonded Cocrystals. A Case Study of 1,4-Diiodotetrafluorobenzene and 3-Nitropyridine

Canadian Journal of Chemistry ◽

10.1139/cjc-2021-0245 ◽

2021 ◽

Author(s):

Christelle Hajjar ◽

Tamali Nag ◽

Hashim Al Sayed ◽

Jeffrey S. Ovens ◽

David L. Bryce

Keyword(s):

Halogen Bond ◽

Chemical Shifts ◽

Magic Angle Spinning ◽

Magic Angle ◽

Halogen Bonds ◽

X Ray Diffraction ◽

Pyridyl Nitrogen ◽

Space Group ◽

X Ray ◽

Variable Stoichiometry

The concept of variable stoichiometry cocrystallization is explored in halogen-bonded systems. Three novel cocrystals of 1,4-diiodotetrafluorobenzene and 3-nitropyridine with molar ratios of 1:1, 2:1, and 1:2, respectively, are prepared by slow evaporation methods. Single-crystal X-ray diffraction analysis reveals key differences between each of the nominally similar cocrystals. For instance, the 1:1 cocrystal crystallizes in the P21/n space group and features a single chemically and crystallographically unique halogen bond between iodine and the pyridyl nitrogen. The 2:1 cocrystal crystallizes in the P1- space group and features a halogen bond between iodine and one of the nitro oxygens in addition to an iodine-nitrogen halogen bond. The 1:2 cocrystal crystallizes with a large unit cell (V = 9896 Å3) in the Cc space group and features 10 crystallographically distinct iodine-nitrogen halogen bonds. Powder X-ray diffraction experiments carried out on the 1:1 and 2:1 cocrystals confirm that gentle grinding does not alter the crystal forms. 1H → 13C and 19F → 13C cross-polarization magic angle spinning (CP/MAS) NMR experiments performed on powdered samples of the 1:1 and 2:1 cocrystals are used as spectral editing tools to select for either the halogen bond acceptor or donor, respectively. Carbon-13 chemical shifts in the cocrystals are shown to change only very subtly relative to pure solid 1,4-diiodotetrafluorobenzene, but the shift of the carbon directly bonded to iodine nevertheless increases, consistent with halogen bond formation (e.g., a shift of +1.6 ppm for the 2:1 cocrystal). This work contributes new examples to the field of variable stoichiometry cocrystal engineering with halogen bonds.

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5-Iodo-1-Arylpyrazoles as Potential Benchmarks for Investigating the Tuning of the Halogen Bonding

Crystals ◽

10.3390/cryst10121149 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1149

Author(s):

Denisa Dumitrescu ◽

Sergiu Shova ◽

Isabela C. Man ◽

Mino R. Caira ◽

Marcel Mirel Popa ◽

...

Keyword(s):

Solid State ◽

Small Molecules ◽

Halogen Bond ◽

Halogen Bonding ◽

Halogen Bonds ◽

X Ray Diffraction ◽

Aryl Ring ◽

X Ray ◽

Alkyl Groups ◽

Hirshfeld Analysis

5-Iodo-1-arylpyrazoles are interesting templates for investigating the halogen bond propensity in small molecules other than the already well-known halogenated molecules such as tetrafluorodiiodobenzene. Herein, we present six compounds with different substitution on the aryl ring attached at position 1 of the pyrazoles and investigate them in the solid state in order to elucidate the halogen bonding significance to the crystallographic landscape of such molecules. The substituents on the aryl ring are generally combinations of halogen atoms (Br, Cl) and various alkyl groups. Observed halogen bonding types spanned by these six 5-iodopyrazoles included a wide variety, namely, C–I⋯O, C–I⋯π, C–I⋯Br, C–I⋯N and C–Br⋯O interactions. By single crystal X-ray diffraction analysis combined with the descriptive Hirshfeld analysis, we discuss the role and influence of the halogen bonds among the intermolecular interactions.

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Novel Cd (II) Coordination Polymers Afforded with EDTA or Trans-1,2-Cdta Chelators and Imidazole, Adenine, or 9-(2-Hydroxyethyl) Adenine Coligands

Crystals ◽

10.3390/cryst10050391 ◽

2020 ◽

Vol 10 (5) ◽

pp. 391

Author(s):

Jeannette Carolina Belmont-Sánchez ◽

María Eugenia García-Rubiño ◽

Antonio Frontera ◽

Antonio Matilla-Hernández ◽

Alfonso Castiñeiras ◽

...

Keyword(s):

Density Functional Theory ◽

Coordination Polymers ◽

Density Functional ◽

Molecular Electrostatic Potential ◽

Aqua Ligand ◽

Stacking Interactions ◽

X Ray Diffraction ◽

Functional Theory ◽

X Ray ◽

Mixed Ligands

Three mixed-ligands of Cd(II) coordination polymers were unintentionally obtained: {[Cd(µ3-EDTA)(Him)·Cd(Him)(H2O)2]·H2O}n (1), {[Cd(µ4-CDTA)(Hade)·Cd(Hade)2]}n (2), and {[Cd(µ3-EDTA)(H2O)·Cd(H9heade)(H2O)]·2H2O}n (3), having imidazole (Him), adenine (Hade) or 9-(2-hydroxyethyl)adenine (9heade) as the N-heterocyclic coligands. Compounds 2 and 3 were obtained by working with an excess of corresponding N-heterocyclic coligands. The single-crystal X-ray diffraction structures and thermogravimetric analyses are reported. The chelate moieties in all three compounds exhibit hepta-coordinated Cd centers, whereas the non-chelated Cd center is five-coordinated in 1 and six-coordinated in 2 and 3. Him and Hade take part in the seven-coordinated chelate moieties in 1 and 2, respectively. In contrast, 9heade is unable to replace the aqua ligand of the chelate [Cd (EDTA) (H2O)] moiety in 3. The thermogravimetric analysis (TGA) behavior of [Cd (H2EDTA) (H2O)]·2H2O in 1 and 3 leads to a residue of CdO, whereas the N-rich compound 2 yields CdO·Cd(NO3)2 as a residue. Density functional theory (DFT) calculations along with molecular electrostatic potential (MEP) and quantum theory of atoms-in-molecules computations were performed in adenine (compound 2) and (2-hydroxyethyl)adenine (compound 3) to analyze how the strength of the H-bonding and π-stacking interactions, respectively, are affected by their coordination to the Cd-metal center.

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Acemetacin cocrystal structures by powder X-ray diffraction

IUCrJ ◽

10.1107/s2052252517002305 ◽

2017 ◽

Vol 4 (3) ◽

pp. 206-214 ◽

Cited By ~ 9

Author(s):

Geetha Bolla ◽

Vladimir Chernyshev ◽

Ashwini Nangia

Keyword(s):

Crystal Structures ◽

Molecular Electrostatic Potential ◽

Acid Group ◽

Mutual Orientation ◽

Type I ◽

Type Ii ◽

Melt Crystallization ◽

X Ray Diffraction ◽

X Ray ◽

Hydrogen Bond Interactions

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM),p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthonR32(9)R22(8)R32(9) with three differentsynamides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, beinganti(type I) orsyn(type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O...H, N...H, Cl...H and C...H interactions. The physicochemical properties of these cocrystals are under study.

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Hydrogen bonding patterns in salts of derivatives of aminopyrimidine and thiobarbituric acid

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520615001729 ◽

2015 ◽

Vol 71 (2) ◽

pp. 144-152 ◽

Cited By ~ 1

Author(s):

Sundaramoorthy Gomathi ◽

Jeyaraman Selvaraj Nirmalram ◽

Packianathan Thomas Muthiah

Keyword(s):

Hydrogen Bonds ◽

Thiobarbituric Acid ◽

Water Molecules ◽

X Ray Diffraction ◽

Compound I ◽

Base Pairs ◽

X Ray ◽

Acid And Base ◽

Derivatives Of ◽

Primary Interaction

Three salts, namely 2-amino-4,6-dimethylpyrimidin-1-ium thiobarbiturate trihydrate (I), 2-amino-4,6-dimethoxypyrimidin-1-ium thiobarbiturate dihydrate (II) and 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidin-1-ium thiobarbiturate (III), were synthesized and characterized by IR and X-ray diffraction techniques. The primary interaction between the acid and base happensviaN—H...O hydrogen bonds in (II) and (III), andviawater-mediated N—H...OWand OW—HW...S in (I). The water molecules present in compound (I) form a (H2O)12water clusterviawater–water interactions. In all three compounds (I)–(III), thiobarbiturate anions form self-complementary pairs with a robustR22(8) motifviaa pair of N—H...O/N—H...S hydrogen bonds. They mimic the nucleobase base pairs by utilizing the same groups (thymine/uracil uses N3—H and C4=O8 groups during the formation of Watson–Crick and Hoogsteen base pairs with adenine). Compound (I) forms a water-mediated base pair through N—H...OWhydrogen bonds and forms anR42(12) motif. The formation of N—H...S hydrogen bonds, water-mediated base pairs and water–water interactions in these crystal systems offers scope for these systems to be considered as a model in the study of hydration of nucleobases and water-mediated nucleobase base pairs in macromolecules.

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Halogen Bonding in the Complexes of Brominated Electrophiles with Chloride Anions: From a Weak Supramolecular Interaction to a Covalent Br–Cl Bond

Crystals ◽

10.3390/cryst10121075 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1075

Author(s):

Cody Loy ◽

Matthias Zeller ◽

Sergiy V. Rosokha

Keyword(s):

Bond Strength ◽

Halogen Bond ◽

Covalent Bond ◽

Halogen Bonding ◽

Halogen Bonds ◽

Nucleophilic Reaction ◽

X Ray ◽

Wide Range ◽

Judicious Choice ◽

Range Variation

The wide-range variation of the strength of halogen bonds (XB) not only facilitates a variety of applications of this interaction, but it also allows examining the relation (and interconversion) between supramolecular and covalent bonding. Herein, the Br…Cl halogen bonding in a series of complexes of bromosubstituted electrophiles (R-Br) with chloride anions were examined via X-ray crystallographic and computational methods. Six co-crystals showing such bonding were prepared by evaporation of solutions of R-Br and tetra-n-propylammonium chloride or using Cl− anions released in the nucleophilic reaction of 1,4-diazabicyclo[2.2.2]octane with dichloromethane in the presence of R-Br. The co-crystal comprised networks formed by 3:3 or 2:2 halogen bonding between R-Br and Cl−, with the XB lengths varying from 3.0 Å to 3.25 Å. Analysis of the crystallographic database revealed examples of associations with substantially longer and shorter Br…Cl separations. DFT computations of an extended series of R–Br…Cl− complexes confirmed that the judicious choice of brominated electrophile allows varying halogen Br…Cl bond strength and length gradually from the values common for the weak intermolecular complexes to that approaching a fully developed covalent bond. This continuity of halogen bond strength in the experimental (solid-state) and calculated associations indicates a fundamental link between the covalent and supramolecular bonding.

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Two mononuclear zinc(II) complexes constructed by two types of phenoxyacetic acid ligands: syntheses, crystal structures and fluorescence properties

Zeitschrift für Naturforschung B ◽

10.1515/znb-2019-0147 ◽

2019 ◽

Vol 74 (11-12) ◽

pp. 839-845 ◽

Cited By ~ 9

Author(s):

Jun-Xia Li ◽

Zhong-Xiang Du ◽

Juan Wang ◽

Xun Feng

Keyword(s):

Halogen Bond ◽

Three Dimensional ◽

Luminescent Properties ◽

Phenoxyacetic Acid ◽

Photoluminescence Spectra ◽

X Ray Diffraction ◽

X Ray ◽

Mononuclear Complexes ◽

3D Networks ◽

Oxygen Atoms

AbstractTwo new mononuclear complexes, [Zn(3-Hcpa)2(H2O)4] (1) and [Zn(3,5,6-tcpa)2(H2O)4] [Zn(3,5,6-tcpa)2(H2O)2] (2) (3-H2cpa = 3-carboxy-phenoxyacetic acid, 3,5,6-Htcpa = 3,5,6-trichloro pyridine-2-oxyacetic acid), were synthesized and structurally characterized. The single-crystal X-ray diffraction analysis showed that in 1 the ZnII ion lies on an inversion center of an octahedron formed by four aqua ligands and two carboxy oxygen atoms of two unidentate 3-Hcpa− anions in trans-arrangement. Complex 2 is a co-crystal consisting of two discrete and stereochemically different complexes: one with an octahedrally, and the other a tetrahedrally coordinated zinc center. The six-coordination about the first ZnII ion comprises four oxygen atoms from water (H2O) molecules and two from the carboxy groups of monodentate trans-related 3,5,6-tcpa− ligands. The four-coordination about the second ZnII ion is comprised of two H2O ligands and two unidentate carboxy oxygen atoms from 3,5,6-tcpa− ligands. O–HLO hydrogen bond and/or ClLCl halogen bond interactions play an important part in construction of the three-dimensional (3D) networks for 1 and 2. The photoluminescence spectra reveal that both 1 and 2 display luminescent properties in the violet region.

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