scholarly journals 4-Aminobenzoic acid 4-methylpyridine/4-methylpyridinium 4-aminobenzoate 0.58/0.42: a redetermination from the original data

2017 ◽  
Vol 73 (10) ◽  
pp. 1508-1512
Author(s):  
Jan Fábry
Keyword(s):  
Hydrogen Bonds ◽  
Original Data ◽  
Amine Group ◽  
Aminobenzoic Acid ◽  
Hydrogen Atoms ◽  
Acta Cryst ◽  
Methyl Group ◽  
Hydrogen Bond Pattern ◽  
Hydroxyl Hydrogen Atom ◽  
Hydroxyl Hydrogen

The title structure, 4-aminobenzoic acid 4-methylpyridine/4-methylpyridinium 4-aminobenzoate 0.58/0.42, 0.58(C6H7N·C7H7NO2)·0.42(C6H8N+·C7H6NO2−), has been redetermined from the data published by Kumaret al.(2015).Acta Cryst.E71, o125-o126. The improvement of the present redetermination consists in the introduction of disorder of the methyl group over two positions as well as in the correction of the positional parameters of the hydrogen atoms that are involved in the O—H...N or N—H...O hydrogen bonds. After the correction, the hydroxyl hydrogen atom turned out to be disordered over two positions about the centre of the O...N bond, which is relatively long [2.642 (2) Å], while the H atoms of the primary amine group account more realistically for the hydrogen-bond pattern after the removal of the positional constraints. All the O—H...N or N—H...O hydrogen bonds which are present in the title structure are of moderate strength.

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.

Two tautomers in one crystal: 4(5)-nitro-5(4)-methoxyimidazole

2004 ◽  
Vol 60 (2) ◽  
pp. 191-196 ◽  
Author(s):  
Maciej Kubicki
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Imidazole Derivative ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Dimensional Network ◽  
Hydrogen Bond Pattern ◽  
Annular Tautomerism

The case of prototropic annular tautomerism in an imidazole derivative has been found. The crystal structure contains a 50:50 mixture of two tautomers: 4-nitro-5-methoxyimidazole and 5-nitro-4-methoxyimidazole. The X-ray experiment actually shows the superposition of these compounds; it appears as if the structure is centrosymmetric and the N—H hydrogen atoms are disordered over two ring N atoms. Owing to the hydrogen-bond pattern, the values of their site occupation factors have to be exactly equal to 1/2. The molecules are connected into a three-dimensional network by means of N—H...N and C—H...O hydrogen bonds.

Hydrogen bonding in 4-nitrobenzene-1,2-diamine and two hydrohalide salts

2014 ◽  
Vol 70 (7) ◽  
pp. 681-688 ◽  
Author(s):  
David K. Geiger ◽  
Dylan E. Parsons
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Nitro Group ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Planar Geometry ◽  
Amine Group ◽  
Acta Cryst ◽  
Extended Structure ◽  
Hydrogen Bonded

The structures of 4-nitrobenzene-1,2-diamine [C6H7N3O2, (I)], 2-amino-5-nitroanilinium chloride [C6H8N3O2+·Cl−, (II)] and 2-amino-5-nitroanilinium bromide monohydrate [C6H8N3O2+·Br−·H2O, (III)] are reported and their hydrogen-bonded structures described. The amine groupparato the nitro group in (I) adopts an approximately planar geometry, whereas themetaamine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine groupmetato the nitro group is protonated. Compound (I) displays a pleated-sheet hydrogen-bonded two-dimensional structure withR22(14) andR44(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three-dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo-inversion center. The dominant hydrogen-bonding interactions involve the chloride ion and result inR42(8) rings linked to form a ladder-chain structure. The chains are joined by N—H...Cl and N—H...O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to formR42(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternatingR55(15) andR64(24) rings. Ammonium N—H...Br interactions join the sheets to form a three-dimensional extended structure. Energy-minimized structures obtained using DFT and MP2 calculations are consistent with the solid-state structures. Consistent with (II) and (III), calculations show that protonation of the amine groupmetato the nitro group results in a structure that is about 1.5 kJ mol−1more stable than that obtained by protonation of thepara-amine group. DFT calculations on single molecules and hydrogen-bonded pairs of molecules based on structural results obtained for (I) and for 3-nitrobenzene-1,2-diamine, (IV) [Betz & Gerber (2011).Acta Cryst.E67, o1359] were used to estimate the strength of the N—H...O(nitro) interactions for three observed motifs. The hydrogen-bonding interaction between the pairs of molecules examined was found to correspond to 20–30 kJ mol−1.

scholarly journals The crystal structure of BaH6As4O14 redetermined, revealing the localization of the hydrogen atoms

IUCrData ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Matthias Weil
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Hydrogen Atoms ◽  
Acta Cryst ◽  
Bond Lengths ◽  
Precise Data

The crystal structure of barium hexahydrogen cyclo-tetradecaoxidotetraarsenate(V), was redetermined. In comparison with the previous determination [Blum, Durif & Guitel. (1977). Acta Cryst. B33, 3222–3224] the positions of the hydrogen atoms were located, and more precise data in terms of bond lengths and angles were obtained. The crystal structure is composed of an eight-coordinate Ba2+ cation and a condensed oxoarsenate anion with connectivity [As[4](OH)1/1O1/1O2/2As[6](OH)2/1O1/2]2 2–. O—H...O hydrogen bonds between isolated anions consolidate the crystal packing.

Eight Schiff bases derived from various salicylaldehydes: phenol–imine and keto–amine forms, conformational disorder, and supramolecular assembly in one and two dimensions

2018 ◽  
Vol 74 (10) ◽  
pp. 1094-1104 ◽  
Author(s):  
Marisiddaiah Girisha ◽  
Belakavadi K. Sagar ◽  
Hemmige S. Yathirajan ◽  
Ravindranath S. Rathore ◽  
Manpreet Kaur ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Schiff Bases ◽  
Supramolecular Assembly ◽  
Original Data ◽  
Two Dimensions ◽  
Acta Cryst ◽  
Data Set ◽  
Conformational Disorder ◽  
X Ray ◽  
A Chain

Structures are reported for eight Schiff bases derived from various salicylaldehydes: five are newly synthesized and re-investigations are reported for three previously reported structures, leading, in each case, to some revision of previous conclusions. In (E)-N-(3,4-dimethylisoxazol-5-yl)-4-[(2-hydroxybenzylidene)amino]benzenesulfonamide, C18H17N3O4S, (I), and (E)-4-[(5-bromo-2-hydroxy-3-methoxybenzylidene)amino]-N-(3,4-dimethylisoxazol-5-yl)benzenesulfonamide. C19H18BrN3O5S, (II), the isoxazole rings adopt different orientations relative to the rest of the molecules, despite the additional substituents in (II) being in the aryl ring remote from the isoxazole unit. The molecules of both (E)-4-bromo-2-[(2-hydroxyphenylimino)methyl]-6-methoxyphenol, C14H12BrNO3, (III), and (E)-4-bromo-2-methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H14BrNO3, (IV), are both effectively planar; while (III) adopts the phenol–imine constitution, (IV) adopts the keto–amine constitution. (E)-2-Methoxy-6-[(2-methoxyphenylimino)methyl]phenol, C15H15NO3, (V), which was determined previously using powder X-ray data assuming the phenol–imine constitution, has now been refined from single-crystal X-ray data, confirming the phenol–imine constitution. In (E)-3-benzoyl-2-[(5-fluoro-2-hydroxybenzylidene)amino]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H18FNO2S, (VI), the fused carbocyclic ring exhibits conformational disorder; both disorder components, having populations of 0.705 (4) and 0.295 (4), adopt half-chair conformations. The isostructural (E)-3-benzoyl-2-[(2-hydroxybenzylidene)amino)]-4,5,6,7-tetrahydrobenzo[b]thiophene, C22H19NO2S, (VII), which was originally reported as having a fully ordered structure [Kauret al.(2014).Acta Cryst.E70, o476–o477], has been rerefined using the original data set and found to exhibit the same type of disorder as found in (VI), with disordered populations having occupancies of 0.851 (3) and 0.149 (3). The triclinic polymorph of (E)-[(2-hydroxyphenylimino)methyl]phenol, C13H11NO2, (VIII), which crystallizes withZ′ = 2 in the space groupP-1, has been described variously as occurring as the keto–amine tautomer [Maciejewskaet al.(1999).J. Phys. Org. Chem.12, 875–880] and as the phenol–imine tautomer [Tunçet al.(2009).J. Chem. Crystallogr.39, 672–676]. Rerefinement of this structure using one of the original data sets shows that both of the independent molecules exist in the keto–amine form. In the structures of compounds (I), (VI), (VII) and (VIII), hydrogen bonds generate simple chains, while a chain of rings is formed in (V). Sheets are formed by hydrogen bonds in both (II) and (III), while in (IV), the sheet structure is built from aromatic π–π stacking interactions.

scholarly journals A long symmetric N...H...N hydrogen bond in bis(4-aminopyridinium)(1+) azide(1−): redetermination from the original data

2017 ◽  
Vol 73 (9) ◽  
pp. 1344-1347
Author(s):  
Jan Fábry
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Site Occupancy ◽  
Original Data ◽  
Site Symmetry ◽  
Acta Cryst ◽  
Twofold Axis ◽  
Molecular Salt ◽  
Electron Interactions

The structure of the title molecular salt, C10H13N4+·N3−, has been redetermined from the data published by Qian & Huang [Acta Cryst.(2010), E66, o3086; refcode WACMIY (Groomet al., 2016)]. The improvement of the present redetermination consists in a correction of the site-occupancy parameter of the bridging H atom between the pyridine rings, as well as of its position. The present study has shown that the bridging H atom (site symmetry 2) is involved in a symmetric N...H...N hydrogen bond, which is one of the longest ever observed [N...N = 2.678 (3) Å]. In addition, there are also present weaker Nam—H...Nazhydrogen bonds (am = amine and az = azide) of moderate strength and π-electron pyridine...π-electron interactions in the structure. All the azide N atoms also lie on a twofold axis.

Diastereoselective formation of 18-membered ring BINOL-hydrogen phosphonate dimers - Quasi-covalent hydrogen bonds?

2007 ◽  
Vol 85 (7-8) ◽  
pp. 466-474 ◽  
Author(s):  
Hossein A Dabbagh ◽  
Nader Noroozi-Pesyan ◽  
Ali R Najafi-Chermahini ◽  
Brian O Patrick ◽  
Brian R James
Keyword(s):  
Hydrogen Bonds ◽  
Computational Analysis ◽  
Ring Structure ◽  
Membered Ring ◽  
Hydrogen Atoms ◽  
Constrained Geometry ◽  
Decomposition Point ◽  
Point Data ◽  
Hydrolysis Of ◽  
Hydroxyl Hydrogen

Diastereoselective syntheses of the unusual dimers, 4-heptyl-2-(2′-hydroxy-binaphthyl)hydrogen phosphonate (5) and the cyclohexyl analogue (7), are achieved by hydrolysis of 4-(3,5-dioxa-4-phosphacyclohepta[2,1-α;3,4-α′]-dinaphthalene-4-yloxy)heptane (4) and the cyclohexane analogue (6), respectively. Two out of eight possible pairs of monomers units are involved in the stereoselective formation of the dimer 5a of configuration BINOLR-PS:BINOLR-PS; this is determined by X-ray crystallographic data, which reveal a centrosymmetric, 18-membered ring structure with Ci symmetry, consisting of two monomers strongly hydrogen-bonded between the oxygen of P=O units and hydroxyl hydrogen atoms. Mass spectrometric, melting point, and thermal decomposition point data, as well as NMR data, support the presence of strong, quasi-covalent hydrogen bonds. Computational analysis suggests that the diastereoselectivity is controlled by molecularly constrained geometry of the monomer. Compound 7, although not characterized crystallographically, appears to be analogous to 5.Key words: 18-membered ring, phosphonate dimer, diastereoselectivity, hydrogen-bonds, computational analysis.

Crystal structure of pomalidomide Form I, C13H11N3O4

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®).

scholarly journals Crystal structure of bis(azido-κN)bis[2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole-κ2N2,N3]cobalt(II)

2015 ◽  
Vol 71 (5) ◽  
pp. 452-454 ◽  
Author(s):  
Abdelhakim Laachir ◽  
Fouad Bentiss ◽  
Salaheddine Guesmi ◽  
Mohamed Saadi ◽  
Lahcen El Ammari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Title Complex ◽  
Octahedral Coordination ◽  
Maximum Deviation ◽  
Coordination Geometry ◽  
Acta Cryst ◽  
Π Interactions ◽  
The Mean

In the mononuclear title complex, [Co(N3)2(C12H8N4S)2], the cobalt(II) atom is located on an inversion centre and displays an axially weakly compressed octahedral coordination geometry. The equatorial positions are occupied by the N atoms of two 2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole ligands, whereas the axial positions are occupied by N atoms of the azide anions. The thiadiazole and pyridine rings linked to the metal are almost coplanar, with a maximum deviation from the mean plane of 0.0273 (16) Å. The cohesion of the crystal is ensured by weak C—H...N hydrogen bonds and by π–π interactions between pyridine rings [intercentroid distance = 3.6356 (11) Å], forming a layered arrangement parallel to (001). The structure of the title compound is isotypic with that of the analogous nickel(II) complex [Laachiret al.(2013).Acta Cryst.E69, m351–m352].

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

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