scholarly journals Intermolecular Hydrogen and Halogen Bonds in Fluorinated Benzimidazoles

2014 ◽  
Vol 70 (a1) ◽  
pp. C643-C643
Author(s):  
Rosa M Claramunt ◽  
Marta Pérez-Torralba ◽  
M. Ángeles García ◽  
Concepción López ◽  
M. Carmen Torralba ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Bond Distance ◽  
Imidazole Ring ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Molecular Plane ◽  
X Ray ◽  
X Ray Crystallography

After hydrogen bonds (HB) the most studied of related weak interactions are the halogen bonds (XB). The competition between these two interactions as well as their interplay to determine the crystal packing of organic derivatives is a subject of interest. Most the studies related to XB concerns the heaviest halogen atoms, I and Br, less Cl and much less F, because the interaction energy decreases in this order. [1,2] We present here our studies on the structure of five tetrafluorinated benzazoles by X-ray crystallography and solid-state NMR, a powerful synergic mixture of techniques. The compounds are 4,5,6,7-tetrafluoro-1H-benzimidazole (1), 4,5,6,7-tetrafluoro-2-(trifluoromethyl)-1H-benzimidazole (2), 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3), 4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole-2(3H)-one (4), and 4,5,6,7-tetrafluoro-1,3-dimethyl-1H-benzimidazole-2(3H)-one (5). As a common general feature, these compounds are quite planar due to the presence of the two aromatic rings. The existence of the methyl groups as substituent in the nitrogen atoms does not modify the planarity of the molecule. The bond distances and angles are in agreement with the expected ones for this kind of compounds. The presence of the carbonyl group induces some electronic changes in the imidazole ring that is resembled in the lengthening of the C2N3 bond distance and in a higher deviation of C2 atom from the molecular plane. Moreover, all the compounds show one or more interactions by strong linear hydrogen bonds, which lead to the formation of chains that, in some cases, can exhibit additional interactions via pi-pi and/or F···F contacts spreading out the dimensionality of the structure in the crystal. [3] The distribution of the F···F contacts in compounds 1-5 is similar to those of the literature and includes for 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3) one of the shortest F···F distances ever reported [2.596(3) Å]. Two polymorphs of compound 4 are identified.

Substituent position effect on the crystal structures of N-phenyl-2-phthalimidoethanesulfonamide derivatives

2018 ◽  
Vol 74 (1) ◽  
pp. 31-36
Author(s):  
Resul Sevinçek ◽  
Duygu Barut Celepci ◽  
Serap Köktaş Koca ◽  
Özlem Akgül ◽  
Muittin Aygün
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Biological Activities ◽  
Position Effect ◽  
Intermolecular Hydrogen Bond ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
The Impact

In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic. Although the molecules differ from each other only with respect to small substituents and their positions, they crystallized in different space groups as a result of differing intra- and intermolecular hydrogen-bond interactions. The structures of (I), (II) and (III) are stabilized by intermolecular N—H...O and C—H...O hydrogen bonds, while that of (IV) is stabilized by intermolecular O—H...O and C—H...O hydrogen bonds. All four structures are of interest with respect to their biological activities and have been studied as part of a program to develop anticonvulsant drugs for the treatment of epilepsy.

Polysulfonylamine, CLXXXVI [1]. Strukturvielfalt in sechs Cokristallen von Tetramethylharnstoff mit Di(4-X-benzolsulfonyl)aminen (X = F, Cl, Br, I, CH3, NO2) / Polysulfonylamines, CLXXXVI [1]. Structural Diversity in Six Tetramethylurea Di(4-X-benzenesulfonyl) amine Cocrystals (X = F, Cl, Br, I, CH3, NO2)

2008 ◽  
Vol 63 (11) ◽  
pp. 1276-1290 ◽  
Author(s):  
Eva-Maria Zerbe ◽  
Silvia Roca Piñol ◽  
Thomas Hamann ◽  
Matthias Freytag ◽  
Peter G. Jones ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Ion Pairs ◽  
Molecular Complexes ◽  
Structural Diversity ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Competing Interactions ◽  
X Ray Crystallography ◽  
Isomorphic Series ◽  
Carbonyl Function

Abstract Cocrystallization of tetramethylurea (TMU) with one equivalent of either di(4-fluorobenzenesulfo- nyl)amine (FAH), di(4-chlorobenzenesulfonyl)amine (CAH), di(4-bromobenzenesulfonyl)amine (BAH). di(4-iodobenzenesulfonyl)amine (IAH), di(4-methylbenzenesulfonyl)aniine (MAH>, ordi(4- nitrobenzenesulfonyDamine (NAH), using dichloromethane/petroleum ether as the solvent, afforded the molecular complexes (FAH)2 · TMU (1. monoclinic. P21/c,Z' = 1. structure previously reported), CAHTMU, BAH-TMU and IAH-TMU (2-4, isomorphic series, triclinic, P1̅,Z' = 1), MAH · TMU (5, monoclinic. P21, Z' = 1). and the uranium salt TMUH+NA- (6, monoclinic. P21/c,Z' = 2). The structural results obtained by X-ray crystallography at low temperatures indicate that the varying p- substituents of the di(arenesulfonyl)amines exert a decisive influence on (i) the stoichiometry of the cocrystallization reaction (2:1 for 1 vs. 1:1 for 2-6), (ii) the degree of proton transfer between the strongly acidic (SO2)2NH moieties and the basic carbonyl function of TMU (molecular complexes assembled via N-H···O=C hydrogen bonds in 1 -5 vs. two independent ion pairs based upon charge- assisted C-O-H+ ···N- interactions in 6). and (Hi) the conformation of the disulfonylamineZ-amide units as defined by rotations about the S-N bonds (extended forms displaying anticlinal C-S ··· S'- C' torsions for the two molecules in 1 and the two anions in 6 vs. folded forms featuring synperi- planar C-S ···S'-C torsions for the molecules in 2-5). The packing modes of 1-4 underline the well-known correlation between the atomic number of halogen atoms and their propensity to form halogen bonds. Thus, the structure of 1 is devoid of short F···O contacts, whereas the isomorphic co- crystals 2-4 consist of lamellar layers in which the inner lamellae include the TMU molecules and the peripheral regions are built up from CAH, BAH or IAH molecules associated into catemers via C-Hal ··· O=S bonds. The lamellar layers of the non-isomorphic methyl congener 5. although topological^' similar to those of 2-4, are stacked according to a herringbone pattern that does not arise in the structures of 2-4. The most prominent packing feature of the uranium salt 6 are intimate dimers of two independent NA- ions, stabilized by dipolar nitro-nitro interactions and C-H ··· O=S contacts and further connected into monolayers through C-H ··· Onitro contacts. The uranium ions are inserted between these layers and bonded to the anion dimers by the strong hydrogen bonds mentioned above and numerous C-H ··· Onitro contacts. The presence of two independent formula units appears to arise from frustration between several competing interactions, e. g. dipolar nitro attractions, weak hydrogen bonding to sulfonyl and nitro acceptors and π/π stacking of aromatic rings.

Crystal packing and theoretical analysis of halogen- and hydrogen-bonded hydrazones from pharmaceuticals. Evidence of type I and II halogen bonds in extended chains of dichloromethane

2018 ◽  
Vol 74 (6) ◽  
pp. 618-627 ◽  
Author(s):  
Gilles Berger ◽  
Jalal Soubhye ◽  
René Wintjens ◽  
Koen Robeyns ◽  
Franck Meyer
Keyword(s):  
Crystal Packing ◽  
Interaction Strength ◽  
Supramolecular Assembly ◽  
Coupled Cluster ◽  
Type I ◽  
Energy Decomposition ◽  
Halogen Bonds ◽  
Linear Arrangement ◽  
X Ray ◽  
X Ray Crystallography

The supramolecular assembly of halogenated and hydroxyl hydrazones derived from two well known pharmaceuticals, isoniazid (IsX, where X = I, Br, OH) and hydralazine (HyX, where X = I, Br, OH), was studied by X-ray crystallography and theoretical methods. Crystal packing of IsI and HyI shows weak I...N and I...π halogen bonds, whereas the hydrogen bonds are dominant in the brominated scaffolds IsBr and HyBr. Although the calculated I...N interaction strength appears almost three times weaker than the O—H...N contacts in the isoniazid-based hydrazones, the higher directionality of the halogen bonds induces a linear and planar architecture of self-complementary tectons, observed only with the help of a bridging water molecule in the case of IsOH. Finally, the X-ray structure of HyOH is characterized by an unexpected linear arrangement of clathrated dichloromethane molecules bound through type I and II halogen bonds. This rare phenomenon, observed in less than ten structures, was studied by coupled cluster-based energy decomposition.

A combined X-ray crystallography and theoretical study of N—H...OX (X is =P and —C) hydrogen bonds in two new structures with a (C—O)2(N)P(=Y) (Y is O and S) skeleton

2018 ◽  
Vol 74 (12) ◽  
pp. 1610-1621 ◽  
Author(s):  
Banafsheh Vahdani Alviri ◽  
Mehrdad Pourayoubi ◽  
Abolghasem Farhadipour ◽  
Marek Nečas ◽  
Valerio Bertolasi
Keyword(s):  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Software Package ◽  
Theoretical Study ◽  
Natural Bond Orbital ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
X Ray ◽  
X Ray Crystallography ◽  
Hydrogen Bonding Interactions

The crystal structures of N,N′-(cyclohexane-1,4-diyl)bis(O,O′-diphenylphosphoramide), C30H32N2O6P2 or (C6H5O)2P(O)(1-NH)(C6H10)(4-NH)P(O)(OC6H5)2, (I), and N,N′-(1,4-phenylene)bis(O,O′-dimethylthiophosphoramide), C10H18N2O4P2S2 or (CH3O)2P(S)(1-NH)(C6H4)(4-NH)P(S)(OCH3)2, (II), have been investigated. In the structure of (I), with an (O)2(N)P(O) skeleton, two symmetry-independent phosphoramide molecules are linked through N—H...O=P hydrogen bonds. In the structure of (II), with an (O)2(N)P(S) skeleton, the ester O atoms take part in N—H...O—C hydrogen bonds as acceptors; the P=S groups do not participate in hydrogen-bonding interactions. The strengths of these hydrogen bonds were evaluated, using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. For this, LP(O) to σ*(NH) charge transfers were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology, for a three-component cluster of hydrogen-bonded molecules for both structures, including all of the independent N—H...O hydrogen bonds observed in the crystal packing. The details of the intermolecular interactions were studied by Hirshfeld surface maps and two-dimensional fingerprint plots.

Polysulfonylamine, CLXXIII [1]. Intermolekulare Wechselwirkungen in kristallinen Di(organosulfonyl)aminen. – Teil 2 [2]. Strukturvergleich f ¨ur Di(4-X-benzolsulfonyl)amine mit X = Fluor, Chlor, Brom oder Methyl / Polysulfonylamines, CLXXIII [1]. Intermolecular Interactions in Crystalline Di(organosulfonyl) amines. Part 2 [2]. Comparing the Stuctures of Di(4-X-benzenesulfonyl)amines, where X is Fluorine, Chlorine, Bromine, or Methyl

2005 ◽  
Vol 60 (6) ◽  
pp. 645-658 ◽  
Author(s):  
Dagmar Henschel ◽  
Thomas Hamann ◽  
Oliver Moers ◽  
Peter G. Jones ◽  
Armand Blaschette
Keyword(s):  
Hydrogen Bonds ◽  
The Other ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Methyl Group ◽  
X Ray ◽  
Rotation Axes ◽  
Halogen Compounds ◽  
The Face ◽  
Exchange Rule

Low-temperature X-ray structures of the following di(4-X-benzenesulfonyl)amines, HN(SO2-C6H4-X)2, are compared in order to study the effects of the 4-substituents on the molecular packings: X = F (1, monoclinic, C2/c, Z′ = 1), X = Cl (2, monoclinic, C2/c, Z′ = 1/2, N-H bonds lying on twofold rotation axes), X = Me (3, orthorhombic, Pbca, Z′ = 1), X = Br (4A, monoclinic, P21/c, Z′ = 1), X = Br (4B, monoclinic, P21/c, Z′ = 2). As a common feature, the molecules of the halogen compounds, including two polymorphs of 4, are associated into catemers by strong hydrogen bonds of the type N-H···O in 1, 4A and 4B or N-H(···O)2 in 2. These molecular chains are assembled in the crystal structures via different packing modes, which underline the well-known correlation between the atomic number of halogen atoms and their propensity to form halogen bonds. Thus, the structure of 1 is devoid of short C-F···O/N contacts, but close F···F contacts are tolerated, whereas in 2 each catemer is connected to four parallel congeners by long and bifurcated C-Cl(···O)2 bonds, and both polymorphs of 4 display layers in which the molecules are connected by N-H···O bonds in one and by relatively short and approximately linear C-Br···O interactions in the other dimension. Despite the alleged steric equivalence of methyl and chloro substituents (“chloro-methyl exchange rule”), the packing architecture of the methyl compound 3 is not related to any of the preceding structures. In this case, the N-H···O bonding leads to centrosymmetric cyclodimers, which pack in such a way that each methyl group is located between two oxygen atoms and above the face of an aromatic ring in a topology consistent with C-H···O and C-H···C(π) bonding. All the structures are pervaded by weak Car-H···O hydrogen bonds; moreover, 1 displays a short C-H···F hydrogen bond and a C-F···C(π) interaction, and π-stacking of aromatic rings is observed in 1, 3 and 4B

A 3D Chiral Hydrogen Bond Framework Based on Phenanthrolinium Hydrogen 4,5-Dichlorophthalate: Crystal Structure and Luminescent Properties

2012 ◽  
Vol 67 (1) ◽  
pp. 85-88 ◽  
Author(s):  
Bing An ◽  
Yan Bai ◽  
Fan Yang
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Uv Spectroscopy ◽  
Luminescent Properties ◽  
Aromatic Rings ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Face To Face ◽  
X Ray Crystallography ◽  
Intramolecular Hydrogen

A salt with the composition [C12H9N2][C8H3Cl2O4] (1) with 4,5-dichlorophthalic acid and 1,10- phenanthroline (phen) has been synthesized and characterized by IR, UV spectroscopy, elemental analysis, and X-ray crystallography. Compound 1 represents a 3D chiral supramolecular framework containing monohelical chains (21 axis) through multiform C-H· · ·O, O-H· · · O, N-H· · ·N intramolecular hydrogen bonds and C-H· · ·O, N-H· · ·O intermolecular hydrogen bonds. Otherwise, two types of face-to-face π · · ·π interactions between the aromatic rings are found in the solid state. The luminescent properties of compound 1 were investigated in the solid state at room temperature

Polysulfonylamine, CLXXIX [1]. Intermolekulare Wechselwirkungen in kristallinen Di(organosulfonyl)aminen. Teil 4 [2]. Di(4-iodbenzolsulfonyl)amin und zwei Methylpyridinium-di(4-iodbenzolsulfonyl)amide: Iod-Sauerstoff vs. Iod-Iod-Wechselwirkungen / Polysulfonylamines, CLXXIX [1]. Intermolecular Interactions in Crystalline Di(organosulfonyl) amines. Part 4 [2]. Di(4-iodobenzenesulfonyl)amine and Two Methylpyridinium Di(4-iodobenzenesulfonyl) amides: Iodine-Oxygen vs. Iodine-Iodine Interactions

2007 ◽  
Vol 62 (9) ◽  
pp. 1157-1166 ◽  
Author(s):  
Eva-Maria Zerbe ◽  
Matthias Freytag ◽  
Peter G. Jones ◽  
Armand Blaschette
Keyword(s):  
Low Temperature ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
The Other ◽  
Aromatic Rings ◽  
Contrast Structure ◽  
X Ray ◽  
Π Stacking ◽  
Bromo Compound

Low-temperature X-ray structures and crystal packing arrangements are presented for di(4-iodobenzenesulfonyl)amine (4, monoclinic, P21/c, Z ' = 1, isostructural to a previously described dimorph of the corresponding bromo homologue), 2,4-dimethylpyridinium di(4- iodobenzenesulfonyl)amide (5, monoclinic, P21/n, Z ' = 1, isostructural to the corresponding bromo compound), and 3-methylpyridinium di(4-iodobenzenesulfonyl)amide (6, orthorhombic, Pna21, Z '= 1). The packing of 4 consists of non-lamellar layers, in which the molecules are connected by N-H···O hydrogen bonds in one and by Iδ+···Oδ− interactions in the other dimension. Structure 5 involves strands of formula units, whereby the anions form catemers via Iδ+···Oδ− interactions and the cations are isotactically connected to the anion backbone by an N+-H(···O)2 three-centre bond. Short I···I contacts are absent from structures 4 and 5. In contrast, structure 6 displays lamellar layers comprising an inner lamella of cations and N(SO2)2 groups connected by an N+-H···N− two-centre bond, and peripheral regions of 4-iodophenyl rings. Thus, the iodine atoms are efficiently shielded from the oxygen atoms, but in appropriate positions to form Iδ+···Iδ− interlayer contacts. Each structure is reinforced by a parallel-displaced π···π stacking arrangement of aromatic rings and an abundance of short C-H···A contacts (A = acceptor).

Synthesis and structural study of five new phosphoric triamides: interplay between classical and non-classical intermolecular interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Bahar Bakhshipour ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Phosphoric Triamide ◽  
Ft Ir ◽  
Phosphoric Triamides

Abstract Phosphoric triamides are attractive to investigate because of their extensive applications in various fields, especially in medicine. Five new phosphoric triamides with the main parts [N]P(O)[NH]2 and [C(O)NH]P(O)[N]2 have been structurally analyzed by single crystal MoKα/synchrotron-based X-ray diffraction and characterized by spectroscopic methods (FT-IR and 1H, 13C, 31P NMR). Compounds crystallize in orthorhombic (1 with space group Pnma) and monoclinic (2 (P21/a), 3 (C2/c), 4 (P21/n) and 5 (P21/c)) crystal systems. The asymmetric unit of all structures consists of one phosphoric triamide molecule, except for 1 with one half of molecule. X-ray crystallography data reveal that the molecular architectures constructed by classical N—H … O hydrogen bonds are as 1D linear (building the R 2 1 ( 6 ) ${R}\_{2}^{1}(6)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}\_{2}^{2}(10)/{R}\_{2}^{1}(6)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}\_{2}^{2}(8)$ ring motif for 4 and 5). A detailed investigation of the intermolecular interactions using Hirshfeld surface (HS) analysis illustrates that the H … H, O … H/H … O and C … H/H … C contacts for all compounds, and Cl … H/H … Cl and F … H/H … F contacts for 3–5, are the most significant contributors to the crystal packing. Moreover, based on the calculated enrichment ratios (E), the O … H/H … O contacts including the classical N—H … O hydrogen bonds for all structures are considered as favoured contacts.

C−H- - -O Hydrogen Bonds in β-Sheetlike Networks:  Combined X-ray Crystallography and High-Pressure Infrared Study

2003 ◽  
Vol 125 (40) ◽  
pp. 12358-12364 ◽  
Author(s):  
Kwang Ming Lee ◽  
Hai-Chou Chang ◽  
Jyh-Chiang Jiang ◽  
Jack C. C. Chen ◽  
Hsiang-En Kao ◽  
...  
Keyword(s):  
High Pressure ◽  
Hydrogen Bonds ◽  
Infrared Study ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals N′-(3-Hydroxybenzylidene)-4-methylbenzohydrazide

2012 ◽  
Vol 68 (6) ◽  
pp. o1816-o1816
Author(s):  
Ji-Lai Liu ◽  
Ming-Hui Sun ◽  
Jing-Jun Ma
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Compound C ◽  
Centroid Distance ◽  
Benzene Rings

The title compound, C15H14N2O2, was obtained from the reaction of 3-hydroxybenzaldhyde and 4-methylbenzohydrazide in methanol. In the molecule, the benzene rings form a dihedral angle of 2.9 (3)°. In the crystal, N—H...O and O—H...O hydrogen bonds link the molecules into layers parallel to (101). The crystal packing also exhibits π–π interactions between the aromatic rings [centroid–centroid distance = 3.686 (4) Å].

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