scholarly journals Nature of the Hydrogen Bond Enhanced Halogen Bond

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1885
Author(s):  
Susana Portela ◽  
Israel Fernández

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.

Crystals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 529
Author(s):  
Erik Uran ◽  
Luka Fotović ◽  
Nikola Bedeković ◽  
Vladimir Stilinović ◽  
Dominik Cinčić

In order to study the proclivity of primary amine groups to act as halogen bond acceptors, three aromatic diamines (p-phenylenediamine (pphda), benzidine (bnzd) and o-tolidine (otol)) were cocrystallised with three perfluorinated iodobenzenes (1,4-tetrafluorodiiodobenzene (14tfib), 1,3-tetrafluorodiiodobenzene (13tfib) and 1,3,5-trifluorotriiodobenzene (135tfib)) as halogen bond donors. Five cocrystals were obtained: (pphda)(14tfib), (bnzd)(13tfib)2, (bnzd)(135tfib)4, (otol)(14tfib) and (otol)(135tfib)2. In spite of the variability of both stoichiometries and structures of the cocrystals, in all the prepared cocrystals the amine groups form exclusively I···N halogen bonds, while the amine hydrogen atoms participate mostly in N–H⋯F contacts. The preference of the amine nitrogen atom toward the halogen bond, as opposed to the hydrogen bond (with amine as a donor), is rationalised by means of computed hydrogen and halogen bond energies, indicating that the halogen bond energy between a simple primary amine (methylamine) and a perfluorinated iodobenzene (pentafluoroiodobenze ne) is ca. 15 kJ mol−1 higher than the energy of the (H)NH∙∙∙NH2 hydrogen bond between two amine molecules.


Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1589 ◽  
Author(s):  
Yunwen Tao ◽  
Yue Qiu ◽  
Wenli Zou ◽  
Sadisha Nanayakkara ◽  
Seth Yannacone ◽  
...  

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.


Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1075
Author(s):  
Cody Loy ◽  
Matthias Zeller ◽  
Sergiy V. Rosokha

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.


2017 ◽  
Vol 203 ◽  
pp. 333-346 ◽  
Author(s):  
Sebastiaan B. Hakkert ◽  
Jürgen Gräfenstein ◽  
Mate Erdelyi

We have studied the applicability of15N NMR spectroscopy in the characterization of the very weak halogen bonds of nonfluorinated halogen bond donors with a nitrogenous Lewis base in solution. The ability of the technique to detect the relative strength of iodine-, bromine- and chlorine-centered halogen bonds, as well as solvent and substituent effects was evaluated. Whereas computations on the DFT level indicate that15N NMR chemical shifts reflect the diamagnetic deshielding associated with the formation of a weak halogen bond, the experimentally observed chemical shift differences were on the edge of detectability due to the low molar fraction of halogen-bonded complexes in solution. The formation of the analogous yet stronger hydrogen bond of phenols have induced approximately ten times larger chemical shift changes, and could be detected and correlated to the electronic properties of substituents of the hydrogen bond donors. Overall,15N NMR is shown to be a suitable tool for the characterization of comparably strong secondary interactions in solution, but not sufficiently accurate for the detection of the formation of thermodynamically labile, weak halogen bonded complexes.


Synthesis ◽  
2019 ◽  
Vol 51 (07) ◽  
pp. 1529-1544 ◽  
Author(s):  
Wen-Bo Liu ◽  
Muhammad Usman ◽  
Xiao-Wen Zhang

Recent advances in the use of silicon-tethered frameworks as directing groups for the efficient construction of C–C, C–B, C–O and C–X (X = halogen) bonds are discussed in this short review. In addition, mechanistic insights are briefly discussed. Hence, the goal of this short review is to give an overview of the state of the art in this field, encompassing the reactivity, selectivity and efficiency of different processes.1 Introduction2 Carbon–Carbon Bond Formation2.1 Alkenylation2.2 Arylation2.3 Carbonylation3 Carbon–Boron Bond Formation4 Carbon–Oxygen and Carbon–Halogen Bond Formation5 Conclusion


CrystEngComm ◽  
2020 ◽  
Vol 22 (23) ◽  
pp. 4039-4046 ◽  
Author(s):  
Luka Fotović ◽  
Vladimir Stilinović

Structures of iodopyridinium halogenides have demonstrated why iodide, the weakest halogen bond acceptor among the halogenides, preferentially forms halogen bonds.


Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1147
Author(s):  
Amila M. Abeysekera ◽  
Abhijeet S. Sinha ◽  
Christer B. Aakeroy

Strategies for co-crystal synthesis tend to employ either hydrogen- or halogen-bonds between different molecules. However, when both interactions are present, the structural influence that they may exert on the resulting assembly is difficult to predict a priori. To shed some light on this supramolecular challenge, we attempted to co-crystallize ten aliphatic dicarboxylic acids (co-formers) with three groups of target molecules; N-(pyridin-2-yl)picolinamides (2Pyr-X), N-(pyridin-2-yl)nicotinamides (3Pyr-X), N-(pyridin-2-yl)isonicotinamides (4Pyr-X); X=Cl/ Br/ I. The structural outcomes were compared with co-crystals prepared from the non-halogenated targets. As expected, none of the reactions with 2Pyr-X produced co-crystals due to the presence of a very stable intramolecular N-H···N hydrogen bond. In the 3Pyr series, all six structures obtained showed the same synthons, –COOH···N(py) and –COOH···N(py)-NH, that were found in the non-halogenated parent 3Pyr and were additionally accompanied by structure directing X···O(OH) interactions (X=Br/I). The co-crystals of the unhalogenated parent 4Pyr co-crystals assembled via intermolecular –COOH···N(py) and –COOH···N(py)-NH synthons. Three of the analogues 4Pyr-X co-crystals displayed only COOH···N(py) and –COOH···N(py)-NH interactions. The three co-crystals of 4Pyr-X with fumaric acid (for which no analogues structures with 4Pyr are known) formed –COOH···N(py)-NH and –NH···O=C hydrogen bonds and showed no structure-directing halogen bonds. In three co-crystals of 4Pyr-I in which –COOH···N(py)-NH hydrogen bond was present, a halogen-bond based –I···N(py) synthon replaced the –COOH···N(py) motif observed in the parent structures. The structural influence of the halogen atoms increased in the order of Cl < Br < I, as the size of σ-holes increased. Finally, it is noteworthy that isostructurality among structures of the homomeric targets was not translated to structural similarities between their respective co-crystals.


2020 ◽  
Vol 39 (1) ◽  
pp. 65
Author(s):  
Mustafa Tuğfan Bilkan

In this paper, 4TZDA-DMSO/water complexes formed by hydrogen bonding interactions were investigated by a combined experimental and computational approach. Two conformations of 4TZDA molecule were considered. Seven hydrogen-bonded 4TZDA-DMSO/H2O complexes were characterized in terms of geometries, energies and vibrational frequencies. The optimizations and calculations were performed for the complexes by Density Functional Theory. In the experimental part, the DMSO/H2O solutions of 4TZDA were prepared and infrared spectra of the solutions were recorded. After the solvation process, significant shifts in the existing bands and new band rising were observed in the experimental spectra of 4TZDA. Following results are found from this study: 1) 4TZDA (I) is more stable than 4TZDA (II). 2) Seven 4TZDA-DMSO and 4TZDA-H2O complexes are investigated and it is seen that all nitrogen atoms of 4TZDA are hydrogen bond acceptor and all hydrogen atoms are hydrogen bond donors. 3) Aqueous complexes of 4TZDA are found to form stronger hydrogen bonds compared to DMSO complexes. 4) It is determined that the most stable structures are intermolecular interactions of lpO⋯H-N and lpN⋯H-O type for the complexes. For these interactions, h-bond lengths are calculated as 1.78 and 1.90 Å and interaction energies are -7.10 kJ/mol for 4TZDA-DMSO and -50.5 kJ/mol for 4TZDA-H2O. Because of this energy difference in the complexes, it can be said 4TZDA forms more stable complexes with water molecules compared to DMSO molecules and with this property, it is an ideal molecule for pharmacological purposes.


2018 ◽  
Vol 42 (13) ◽  
pp. 10539-10547 ◽  
Author(s):  
Janaka C. Gamekkanda ◽  
Abhijeet S. Sinha ◽  
John Desper ◽  
Marijana Đaković ◽  
Christer B. Aakeröy

O–H hydrogen-bond donors and R–CC–I halogen-bond donors are close competitors for suitable acceptor sites in solid-state assembly.


2018 ◽  
Vol 74 (4) ◽  
pp. 487-503 ◽  
Author(s):  
Robert Swinton Darious ◽  
Packianathan Thomas Muthiah ◽  
Franc Perdih

Nine salts of the antifolate drugs trimethoprim and pyrimethamine, namely, trimethoprimium [or 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium] 2,5-dichlorothiophene-3-carboxylate monohydrate (TMPDCTPC, 1:1), C14H19N4O3 +·C5HCl2O2S−, (I), trimethoprimium 3-bromothiophene-2-carboxylate monohydrate, (TMPBTPC, 1:1:1), C14H19N4O3 +·C5H2BrO2S−·H2O, (II), trimethoprimium 3-chlorothiophene-2-carboxylate monohydrate (TMPCTPC, 1:1:1), C14H19N4O3 +·C5H2ClO2S−·H2O, (III), trimethoprimium 5-methylthiophene-2-carboxylate monohydrate (TMPMTPC, 1:1:1), C14H19N4O3 +·C6H5O2S−·H2O, (IV), trimethoprimium anthracene-9-carboxylate sesquihydrate (TMPAC, 2:2:3), C14H19N4O3 +·C15H9O2 −·1.5H2O, (V), pyrimethaminium [or 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium] 2,5-dichlorothiophene-3-carboxylate (PMNDCTPC, 1:1), C12H14ClN4 +·C5HCl2O2S−, (VI), pyrimethaminium 5-bromothiophene-2-carboxylate (PMNBTPC, 1:1), C12H14ClN4 +·C5H2BrO2S−, (VII), pyrimethaminium anthracene-9-carboxylate ethanol monosolvate monohydrate (PMNAC, 1:1:1:1), C12H14ClN4 +·C15H9O2 −·C2H5OH·H2O, (VIII), and bis(pyrimethaminium) naphthalene-1,5-disulfonate (PMNNSA, 2:1), 2C12H14ClN4 +·C10H6O6S2 2−, (IX), have been prepared and characterized by single-crystal X-ray diffraction. In all the crystal structures, the pyrimidine N1 atom is protonated. In salts (I)–(III) and (VI)–(IX), the 2-aminopyrimidinium cation interacts with the corresponding anion via a pair of N—H...O hydrogen bonds, generating the robust R 2 2(8) supramolecular heterosynthon. In salt (IV), instead of forming the R 2 2(8) heterosynthon, the carboxylate group bridges two pyrimidinium cations via N—H...O hydrogen bonds. In salt (V), one of the carboxylate O atoms bridges the N1—H group and a 2-amino H atom of the pyrimidinium cation to form a smaller R 2 1(6) ring instead of the R 2 2(8) ring. In salt (IX), the sulfonate O atoms mimic the role of carboxylate O atoms in forming an R 2 2(8) ring motif. In salts (II)–(IX), the pyrimidinium cation forms base pairs via a pair of N—H...N hydrogen bonds, generating a ring motif [R 2 2(8) homosynthon]. Compounds (II) and (III) are isomorphous. The quadruple DDAA (D = hydrogen-bond donor and A = hydrogen-bond acceptor) array is observed in (I). In salts (II)–(IV) and (VI)–(IX), quadruple DADA arrays are present. In salts (VI) and (VII), both DADA and DDAA arrays co-exist. The crystal structures are further stabilized by π–π stacking interactions [in (I), (V) and (VII)–(IX)], C—H...π interactions [in (IV)–(V) and (VII)–(IX)], C—Br...π interactions [in (II)] and C—Cl...π interactions [in (I), (III) and (VI)]. Cl...O and Cl...Cl halogen-bond interactions are present in (I) and (VI), with distances and angles of 3.0020 (18) and 3.5159 (16) Å, and 165.56 (10) and 154.81 (11)°, respectively.


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