Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

ABSTRACT: The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H?N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52?(5) and 0.48?(5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N-H?(O,O) hydrogen bonds. In addition, weak C-H?O hydrogen bonds link inversion-related chains, forming columns along [100].

SUBMITTER: Su P

PROVIDER: S-EPMC4908572 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

Su Ping P Song Xue-Gang XG Sun Ren-Qiang RQ Xu Xing-Man XM

Acta crystallographica. Section E, Crystallographic communications 20160527 Pt 6

The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H⋯N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N- ...[more]

PMID: 27308060

Similar Datasets

Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

Project description:In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C4H5FN3O+·C6H2N3O7-, one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA-) anion. In the crystal, the 5FC+ cation inter-acts with the PA- anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R21(6) and R12(6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

| S-EPMC5347054 | biostudies-literature

Hydrogen-bonding landscape of the carbamoyl-cyano-nitro-somethanide anion in the crystal structure of its ammonium salt.

Project description:The structure of the title salt, ammonium carbamoyl-cyano-nitro-somethanide, NH4 +·C3H2N3O2 -, features the co-existence of different hydrogen-bonding patterns, which are specific to each of the three functional groups (nitroso, carbamoyl and cyano) of the methanide anion. The nitroso O-atoms accept as many as three N-H⋯O bonds from the ammonium cations [N⋯O = 2.688 (3)-3.000 (3) Å] to form chains of fused rhombs [(NH4)(O)2]. The most prominent bonds of the carbamoyl groups are mutual and they yield 21 helices [N⋯O = 2.903 (2) Å], whereas the cyano N-atoms accept hydrogen bonds from sterically less accessible carbamoyl H-atoms [N⋯N = 3.004 (3) Å]. Two weaker NH4 +⋯O=C bonds [N⋯O = 3.021 (2), 3.017 (2) Å] complete the hydrogen-bonded environment of the carbamoyl groups. A Hirshfeld surface analysis indicates that the most important inter-actions are overwhelmingly O⋯H/H⋯O and N⋯H/H⋯N, in total accounting for 64.1% of the contacts for the individual anions. The relatively simple scheme of these inter-actions allows the delineation of the supra-molecular synthons, which may be applicable to crystal engineering of hydrogen-bonded solids containing polyfunctional methanide anions.

| S-EPMC8587992 | biostudies-literature

Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-amino-phenyl-arsonate tetra-hydrate.

Project description:In the structure of the brucinium salt of 4-amino-phenyl-arsonic acid (p-arsanilic acid), systematically 2,3-dimeth-oxy-10-oxostrychnidinium 4-amino-phenyl-ar-son-ate tetra-hydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water mol-ecules of solvation are accommodated between the layers and are linked to them through a primary cation N-H?O(anion) hydrogen bond, as well as through water O-H?O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

| S-EPMC4908506 | biostudies-literature

Crystal structure and halogen-hydrogen bonding of a Delepine reaction inter-mediate.

Project description:The reaction of 1,5-di-bromo-pentane with urotropine results in crystals of the title mol-ecular salt, 5-bromo-urotropinium bromide [systematic name: 1-(5-bro-mo-pent-yl)-3,5,7-tri-aza-1-azoniatri-cyclo-[3.3.1.13,7]decane bromide], C11H22BrN4 +·Br- (1), crystallizing in space group P21/n. The packing in compound 1 is directed mainly by H⋯H van der Waals inter-actions and C-H⋯Br hydrogen bonds, as revealed by Hirshfeld surface analysis. Comparison with literature examples of alkyl-urotropinium halides shows that the inter-actions in 1 are consistent with those in other bromides and simple chloride and iodide species.

| S-EPMC7784050 | biostudies-literature

Hydrogen-Bonded and Halogen-Bonded: Orthogonal Interactions for the Chloride Anion of a Pyrazolium Salt.

Project description:In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the σ-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = 3.1653(11) Å and Cl···I-C = 179.32(6)°. This contact is roughly orthogonal to the N-H···Cl hydrogen bond. An analysis of the electron density according to Bader's Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with ρbcp = 0.129 for the halogen and 0.321eÅ-3 for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the σ-hole contact.

| S-EPMC8272125 | biostudies-literature

Hydrogen-bonded network in the salt 4-methyl-1H-imidazol-3-ium picrate.

Project description:In the title molecular salt, C4H7N2 (+)·C6H2N3O7 (-), the phenolic proton of the starting picric acid has been transferred to the imidazole N atom. The nitro groups are twisted away from the benzene ring plane, making dihedral angles of 12.8?(2), 9.2?(4) and 29.3?(2)°. In the crystal, the component ions are linked into chains along [010] via N-H?O and bifurcated N-H?(O,O) hydrogen bonds. These chains are further linked by weak C-H?O hydrogen bonds into a three-dimensional network. The complex three-dimensional network can be topologically simplified into a 4-connected uninodal net with the point symbol {4.8(5)}.

| S-EPMC4908564 | biostudies-literature

Crystal structure of 2-(morpholino)ethyl-ammonium picrate monohydrate.

Project description:The title compound, C6H15N2O+·C6H2N3O7 -·H2O, was synthesized via slow evaporation of an aqueous solution of picric acid with the substituted morpholine base and crystallized with one cation (C6H15N2O)+, one anion (C6H2N3O7)- and a water mol-ecule in the asymmetric unit. The morpholine ring in the cation adopts a chair conformation. The structure is stabilized by C-H⋯O, O-H⋯O, O-H⋯N and N-H⋯O hydrogen-bonding inter-actions and π-π stacking. The inter-molecular inter-actions of the synthesized compound were qu-anti-fied by Hirshfeld surface analysis.

| S-EPMC9815139 | biostudies-literature

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective.

Project description:We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX???A(-) and the analogous hydrogen-bonded complexes DH???A(-) (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX???A(-) arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO-LUMO interactions between the lone pair of A(-) and the ?* orbital of D-X.

| S-EPMC3922460 | biostudies-literature

Crystal structure of 3-methyl-pyridinium picrate: a triclinic polymorph.

Project description:The title mol-ecular salt, C6H8N(+)·C6H2N3O7 (-) (systematic name: 3-methyl-pyridinium 2,4,6-tri-nitro-phenolate), crystallizes in the triclinic space group P-1. The crystal structure of the monoclinic polymorph (space group P21/n) has been reported [Stilinovic & Kaitner (2011 ▸). Cryst. Growth Des. 11, 4110-4119]. In the crystal, the anion and cation are linked via bifurcated N-H⋯(O,O) hydrogen bonds, enclosing an R 1 (2)(6) graph-set motif. These units are linked via C-H⋯O hydrogen bonds, forming a three-dimensional framework. Within the framework there are π-π inter-actions present, involving inversion-related picrate anions and inversion-related pyridinium cations, with inter-centroid distances of 3.7389 (14) and 3.560 (2) Å, respectively.

| S-EPMC4647397 | biostudies-literature

New Liquid Crystal Assemblies Based on Cyano-Hydrogen Bonding Interactions.

Project description:A new selection of supramolecular liquid crystal complexes based on complementary molecules formed via hydrogen-bonding interactions is reported. All prepared complexes were prepared from 4-n-alkoxybenzoic acid (An) and N-4-cyanobenzylidene-4-n-(hexyloxy)benzenamine (I). FT-IR, temperature gradient NMR, Mass Spectrometer and Chromatography spectroscopy were carried out to confirm the -CN and -COOH H-bonded complexation by observing their Fermi-bands and the effects of the 1H-NMR signals as well as its elution signal from HPLC. Moreover, binary phase diagrams were established for further confirmation. All formed complexes (I/An) were studied by the use of differential scanning calorimetry and their phase properties were validated through the use of polarized optical microscopy Results of mesomorphic characterization revealed that all presented complexes exhibited enantiotropic mesophases and their type was dependent on the terminal lengths of alkoxy chains. Also, the mesomorphic temperature ranges decreased in the order I/A6 > I/A8 > I/A10 > I/A16 with linear dependency on the chain length. Finally, the density functional theory computational modeling has been carried out to explain the experimental findings. The relation between the dimensional parameters was established to show the effect of the aspect ratio on the mesophase range and stability. The normalized entropy of the clearing transitions (∆S/R) was calculated to illustrate the molecular interaction enhancements with the chain lengths.

| S-EPMC8213374 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data