The Amine Group as Halogen Bond Acceptor in Cocrystals of Aromatic Diamines and Perfluorinated Iodobenzenes

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.

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Nature of the Hydrogen Bond Enhanced Halogen Bond

Molecules ◽

10.3390/molecules26071885 ◽

2021 ◽

Vol 26 (7) ◽

pp. 1885

Author(s):

Susana Portela ◽

Israel Fernández

Keyword(s):

Hydrogen Bond ◽

Bond Strength ◽

State Of The Art ◽

Halogen Bond ◽

Significant Degree ◽

Halogen Bonds ◽

Hydrogen Atoms ◽

Aryl Group ◽

Hydrogen Bond Acceptor ◽

Orbital Interactions

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.

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The15N NMR chemical shift in the characterization of weak halogen bonding in solution

Faraday Discussions ◽

10.1039/c7fd00107j ◽

2017 ◽

Vol 203 ◽

pp. 333-346 ◽

Cited By ~ 11

Author(s):

Sebastiaan B. Hakkert ◽

Jürgen Gräfenstein ◽

Mate Erdelyi

Keyword(s):

Hydrogen Bond ◽

Chemical Shift ◽

Halogen Bond ◽

Molar Fraction ◽

Halogen Bonding ◽

Relative Strength ◽

Lewis Base ◽

Halogen Bonds ◽

Bonded Complexes

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.

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Halogenide anions as halogen and hydrogen bond acceptors in iodopyridinium halogenides

CrystEngComm ◽

10.1039/d0ce00534g ◽

2020 ◽

Vol 22 (23) ◽

pp. 4039-4046 ◽

Cited By ~ 1

Author(s):

Luka Fotović ◽

Vladimir Stilinović

Keyword(s):

Hydrogen Bond ◽

Halogen Bond ◽

Halogen Bonds

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

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The Impact of Halogen Substituents on the Synthesis and Structure of Co-Crystals of Pyridine Amides

Molecules ◽

10.3390/molecules26041147 ◽

2021 ◽

Vol 26 (4) ◽

pp. 1147

Author(s):

Amila M. Abeysekera ◽

Abhijeet S. Sinha ◽

Christer B. Aakeroy

Keyword(s):

Hydrogen Bond ◽

Halogen Bond ◽

A Priori ◽

Dicarboxylic Acids ◽

Halogen Bonds ◽

Target Molecules ◽

Crystal Synthesis ◽

Py Motif ◽

The Impact ◽

Structural Influence

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.

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Competition between hydrogen bonds and halogen bonds: a structural study

New Journal of Chemistry ◽

10.1039/c8nj00537k ◽

2018 ◽

Vol 42 (13) ◽

pp. 10539-10547 ◽

Cited By ~ 13

Author(s):

Janaka C. Gamekkanda ◽

Abhijeet S. Sinha ◽

John Desper ◽

Marijana Đaković ◽

Christer B. Aakeröy

Keyword(s):

Hydrogen Bond ◽

Solid State ◽

Hydrogen Bonds ◽

Structural Study ◽

Halogen Bond ◽

Halogen Bonds ◽

Hydrogen Bond Donors

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

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Synthesis and absolute structure of (R)-2-(benzylselanyl)-1-phenylethanaminium hydrogen sulfate monohydrate: crystal structure and Hirshfeld surface analyses

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989021010409 ◽

2021 ◽

Vol 77 (11) ◽

Author(s):

H. R. Rajegowda ◽

P. A. Suchetan ◽

R. J. Butcher ◽

P. Raghavendra Kumar

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Solvent Molecule ◽

Shape Index ◽

Hirshfeld Surface ◽

Water Molecules ◽

Hydrogen Sulfate ◽

Hydrogen Atoms ◽

Amine Nitrogen Atom ◽

Amine Nitrogen

A hydrogen sulfate salt, C15H18NSe+·HSO4 −·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 −), of a chiral selenated amine (R)-2-(benzylselanyl)-1-phenylethanamine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT–IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitrogen atom is chiral and in the R configuration, and, the –C—C– bond of the –CH2—CH– fragment has a staggered conformation. In the crystal structure, two HSO4 − anions and two water molecules form an R 4 4(12) tetrameric type of assembly comprised of alternating HSO4 − anions and water molecules via discrete D(2) O—H...O hydrogen bonds. This tetrameric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are interconnected via discrete D(2) N—H...O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 − anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C—H...π interactions between adjacent cations running as chains down the [010] axis. Secondary Se...O [3.1474 (4) Å] interactions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent molecule, was carried out to confirm the presence of various interactions in the crystal structure.

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A redetermination from the original data of the crystal structure of 2-amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016004321 ◽

2016 ◽

Vol 72 (4) ◽

pp. 512-515

Author(s):

Jan Fábry

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Primary Amine ◽

Original Data ◽

Acta Cryst ◽

Amine Groups

The title structure, C6H9.5N3O20.5+·C7H6.5NO20.5−, which might be named schematically as 2-amino-4,6-dimethoxypyrimidine-(μ2-hydrogen)-4-aminobenzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Muthiah & Lynch [Acta Cryst.(2006), E62, o2976–o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally assumed to be planar, as well as in a redetermination of the position of the hydroxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O...N hydrogen bond in two disordered positions with occupancies of 0.5 each.

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Competition and selectivity in supramolecular synthesis: structural landscape around 1-(pyridylmethyl)-2,2′-biimidazoles

Faraday Discussions ◽

10.1039/c7fd00080d ◽

2017 ◽

Vol 203 ◽

pp. 371-388 ◽

Cited By ~ 12

Author(s):

C. A. Gunawardana ◽

J. Desper ◽

A. S. Sinha ◽

M. Ðaković ◽

C. B. Aakeröy

Keyword(s):

Hydrogen Bond ◽

Solid State ◽

Proton Transfer ◽

Halogen Bond ◽

Crystal Formation ◽

Halogen Bonds ◽

Supramolecular Architectures ◽

Hydrogen Bond Interactions ◽

Structure Extension ◽

The Impact

Three isomeric forms of 1-(pyridylmethyl)-2,2′-biimidazole, A1–A3, have been synthesized and subjected to systematic co-crystallizations with selected hydrogen- and halogen-bond donors in order to explore the impact of electrostatics and geometry on the resulting supramolecular architectures. The solid-state supramolecular behavior of A1–A3 is largely consistent in halogen-bonded co-crystals. Only two types of primary interactions, the N–H⋯N/N⋯H–N homomeric hydrogen-bond interactions responsible for the pairing of biimidazole moieties and the I⋯N(pyridine) halogen bonds responsible for the co-crystal formation and structure extension, are present in these systems. The co-crystallizations with hydrogen-bond donors (carboxylic acids), however, lead to multiple possible structural outcomes because of the presence of the biimidazole–acid N–H⋯OC/N⋯H–O heterosynthon that can compete with biimidazole–biimidazole N–H⋯N/N⋯H–N homosynthon. In addition, the somewhat unpredictable nature of proton transfer makes the hydrogen-bonded co-crystals structurally less consistent than their halogen-bonded counterparts.

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Crystal structure of pomalidomide Form I, C13H11N3O4

Powder Diffraction ◽

10.1017/s0885715621000087 ◽

2021 ◽

pp. 1-6

Author(s):

James A. Kaduk ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Powder Diffraction ◽

Density Functional ◽

Double Layers ◽

Carbonyl Groups ◽

Hydrogen Atoms ◽

Powder Diffraction File ◽

Functional Theory ◽

Amine Hydrogen

The crystal structure of pomalidomide Form I has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pomalidomide Form I crystallizes in the space group P-1 (#2) with a = 7.04742(9), b = 7.89103(27), c = 11.3106(6) Å, α = 73.2499(13), β = 80.9198(9), γ = 88.5969(6)°, V = 594.618(8) Å3, and Z = 2. The crystal structure is characterized by the parallel stacking of planes parallel to the bc-plane. Hydrogen bonds link the molecules into double layers also parallel to the bc-plane. Each of the amine hydrogen atoms acts as a donor to a carbonyl group in an N–H⋯O hydrogen bond, but only two of the four carbonyl groups act as acceptors in such hydrogen bonds. Other carbonyl groups participate in C–H⋯O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

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(Z)-3-[2-(2,4-Dinitrophenyl)hydrazin-1-ylidene]isobenzofuran-1(3H)-one dichloromethane hemisolvate

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s1600536814004929 ◽

2014 ◽

Vol 70 (4) ◽

pp. o418-o418

Author(s):

Palak Agarwal ◽

Pragati Mishra ◽

Nikita Gupta ◽

Neelam ◽

Priyaranjan Sahoo ◽

...

Keyword(s):

Hydrogen Bond ◽

Benzene Ring ◽

Dihedral Angle ◽

Title Compound ◽

Crystal Packing ◽

Halogen Bond ◽

Solvent Molecule ◽

Twofold Axis ◽

Bond Interaction ◽

The Mean

In the title compound, 2C14H8N4O6·CH2Cl2, the dichloromethane solvent molecule resides on a crystallographic twofold axis. The mean plane of the phthalisoimide ring is oriented at a dihedral angle of 32.93 (12)° with respect to the nitro-substituted benzene ring. An intramolecular N—H...O hydrogen bond occurs. The crystal packing features a short Cl...O halogen-bond interaction [3.093 (3) Å].

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