Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure of zwitterionic 4-(ammonio-methyl)-benzoate: a simple mol-ecule giving rise to a complex supra-molecular structure.

ABSTRACT: The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammonio-meth-yl)benzoate zwitterion derived from 4-amino-methyl-benzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15). In the crystal structure, N-H?O hydrogen bonds together with ?-? stacking of the benzene rings [centroid-centroid distance = 3.8602?(18)?Å] result in a strongly linked, compact three-dimensional structure.

SUBMITTER: Atria AM

PROVIDER: S-EPMC4257293 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystal structure of zwitterionic 4-(ammonio-methyl)-benzoate: a simple mol-ecule giving rise to a complex supra-molecular structure.

Atria Ana María AM Garland Maria Teresa MT Baggio Ricardo R

Acta crystallographica. Section E, Structure reports online 20141024 Pt 11

The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammonio-meth-yl)benzoate zwitterion derived from 4-amino-methyl-benzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15). In the crystal structure, N-H⋯O hydrogen bonds together with π-π stacking of the benzene rings [centroid-centroid distance = 3.8602 (18) Å] result in a strongly linked, co ...[more]

PMID: 25484753

Similar Datasets

Crystal structure analysis of the biologically active drug mol-ecule riluzole and riluzolium chloride.

Project description:This study is an investigation into the crystal structure of the biologically active drug mol-ecule riluzole [RZ, 6-(tri-fluoro-meth-oxy)-1,3-benzo-thia-zol-2-amine], C8H5F3N2OS, and its derivative, the riluzolium chloride salt [RZHCl, 2-amino-6-(tri-fluoro-meth-oxy)-1,3-benzo-thia-zol-3-ium chloride], C8H6F3N2OS+·Cl-. In spite of repeated efforts to crystallize the drug, its crystal structure has not been reported to date, hence the current study provides a method for obtaining crystals of both riluzole and its corresponding salt, riluzolium hydro-chloride. The salt was obtained by grinding HCl with the drug and crystallizing the obtained solid from di-chloro-methane. The crystals of riluzole were obtained in the presence of l-glutamic acid and d-glutamic acid in separate experiments. In the crystal structure of RZHCl, the -OCF3 moiety is perpendicular to the mol-ecular plane containing the riluzolium ion, as can be seen by the torsion angle of 107.4?(3)°. In the case of riluzole, the torsion angles of the four different mol-ecules in the asymmetric unit show that in three cases the tri-fluoro-meth-oxy group is perpendicular to the riluzole mol-ecular plane and only in one mol-ecule does the -OCF3 group lie in the same mol-ecular plane. The crystal structure of riluzole primarily consists of strong N-H?N hydrogen bonds along with weak C-H?F, C-H?S, F?F, C?C and C?S inter-actions, while that of its salt is stabilized by strong [N-H]+?Cl- and weak C-H?Cl-, N-H?S, C-H?F, C?C, S?N and S?Cl- inter-actions.

| S-EPMC6690469 | biostudies-literature

3-Ammonio-4-hydroxy-benzoate monohydrate.

Project description:The title compound, C(7)H(7)NO(3)·H(2)O, which crystallized as a hydrate, was obtained from an extraction of the plant species Saussurea atkinsonii of the asteraceae family collected from the hilly area (Ayubia) of Pakistan during the flowering season. The dihedral angle between the benzene ring and the carboxyl-ate group is 25.64?(5)°. In the crystal, the packing is consolidated by N-H?O and O-H?O hydrogen bonds, as well as weak aromatic ?-? stacking [centroid-centroid separation = 3.9365?(9)?Å] and C=O?? inter-actions.

| S-EPMC2969601 | biostudies-literature

4-(Dimethyl-amino)pyridinium tribromide: whole mol-ecule disorder of cation and anion.

Project description:In the title salt, C(7)H(11)N(2) (+)·Br(3) (-), the cation and the near-linear anion [Br-Br-Br = 179.41 (8)°] both show whole-mol-ecule disorder about crystallographic twofold rotation axes. The cation is weakly hydrogen-bonded to the anion by an N-H⋯Br inter-action. The crystal studied was found to be a racemic twin, with a twin component of nearly 50%.

| S-EPMC2969780 | biostudies-literature

Crystal structure of an aryl cyclo-hexyl nona-noid, an anti-proliferative mol-ecule isolated from the spice Myristica malabarica.

Project description:The title compound, C21H26O5, an aryl cyclo-hexyl nona-noid {systematic name: 3,5-dihy-droxy-2-[9-(4-hy-droxy-phen-yl)nona-noyl]cyclo-hexa-2,4-dien-1-one}, extracted from the spice plant Myristica malabarica comprises two ring components, a 4-hy-droxy-phenyl moiety and a 3,5-di-hydroxy-cyclo-hexa-2,4-dienone moiety linked by a nona-noyl chain. The mol-ecule has an extended essentially planar conformation stabilized by an intra-molecular hy-droxy O-H⋯Ocarbon-yl hydrogen bond, giving a dihedral angle between the two ring systems of 6.37 (15)°. The C, O and H atoms associated with one of the hy-droxy groups of the cyclo-hexa-dienone component are disordered over two sets of sites with site occupancies of 0.6972 and 0.3028. In the crystal, hy-droxy O-H⋯O hydrogen bonds to carbonyl O-atom acceptors form large centrosymmetric R22(36) cyclic dimers, which are further extended into supra-molecular one-dimensional ribbon structures along [1-11].

| S-EPMC5050765 | biostudies-literature

Whole-mol-ecule disorder of the Schiff base compound 4-chloro-N-(4-nitro-benzyl-idene)aniline: crystal structure and Hirshfeld surface analysis.

Project description:In the crystal of the title Schiff base compound, C13H9ClN2O2, [CNBA; systematic name: (E)-N-(4-chloro-phen-yl)-1-(4-nitro-phen-yl)methanimine], the CNBA mol-ecule shows whole-mol-ecule disorder (occupancy ratio 0.65:0.35), with the disorder components related by a twofold rotation about the shorter axis of the mol-ecule. The aromatic rings are inclined to each other by 39.3 (5)° in the major component and by 35.7 (9)° in the minor component. In the crystal, C-H⋯O hydrogen bonds predominate in linking the major components, while weak C-H⋯Cl inter-actions predominate in linking the minor components. The result is the formation of corrugated layers lying parallel to the ac plane. The crystal packing was analysed using Hirshfeld surface analysis and compared with related structures.

| S-EPMC7057374 | biostudies-literature

Crystal structure of a 2:1 piroxicam-gentisic acid co-crystal featuring neutral and zwitterionic piroxicam mol-ecules.

Project description:A new 2:1 co-crystal of piroxicam and gentisic acid [systematic name: 4-hy-droxy-1,1-dioxo-N-(pyridin-2-yl)-2H-1?6,2-benzo-thia-zine-3-carboxamide-2-(4-oxido-1,1-dioxo-2H-1?6,2-benzo-thia-zine-3-amido)-pyridin-1-ium-2,5-di-hydroxy-benzoic acid, 2C15H13N3O4S·C7H6O4] has been synthesized using a microfluidic platform and initially identified using Raman spectroscopy. In the co-crystal, one piroxicam mol-ecule is in its neutral form and an intra-molecular O-H?O hydrogen bond is observed. The other piroxicam mol-ecule is zwitterionic (proton transfer from the OH group to the pyridine N atom) and two intra-molecular N-H?O hydrogen bonds occur. The gentisic acid mol-ecule shows whole-mol-ecule disorder over two sets of sites in a 0.809?(2):0.191?(2) ratio. In the crystal, extensive hydrogen bonding between the components forms layers propagating in the ab plane.

| S-EPMC5137592 | biostudies-literature

8-Ammonio-naphthalene-2-sulfonate monohydrate: the zwitterionic hydrate of 1,7-Cleve's acid.

Project description:The structure of 8-amino-2-naphthalene-sulfonic acid monohydrate (1,7-Cleve's acid hydrate), C(10)H(9)NO(3)S·H(2)O, shows the presence of a sulfonate-aminium group zwitterion, both groups and the water mol-ecule of solvation giving cyclic R(3) (3)(8) O-H⋯O and N-H⋯O inter-molecular hydrogen-bonding inter-actions, forming chains which extend down the a axis of the unit cell. Additional peripheral associations, including weak aromatic ring π-π inter-actions [centroid-centroid distance = 3.6299 (15) Å], result in a two-dimensional sheet structure.

| S-EPMC2969967 | biostudies-literature

Ortho-rhom-bic modification of (E)-4-benzyl-idene-2-phenyl-1,3-oxazol-5(4H)-one: whole mol-ecule disorder.

Project description:The title mol-ecule, C(16)H(11)NO(2), is disordered about a pseudo-twofold rotation axis that approximately bis-ects the mol-ecule along the C=O double bond. The two overlapping components are planar [r.m.s. deviation = 0.10?Å in the major 0.537?(4) component and 0.07?Å in the minor component]. The two components are aligned at 1.8?(3)°.

| S-EPMC2977315 | biostudies-literature

6-Isopropyl-3-phenyl-5-(p-tol-yloxy)-3H-1,2,3-triazolo[4,5-d]pyrimidin-7(6H)-one: whole-mol-ecule disorder.

Project description:The title compound, C(20)H(19)N(5)O(2), exhibits whole-mol-ecule disorder the refined ratios of the two components being 0.57?(2):0.43?(2). In the major component, the essentially planar [maximum deviation 0.033?(17)?Å] fused pyrimidine and triazole ring system forms a dihedral angle of 10.5?(3)° with the phenyl ring, while in the minor component of disorder this angle is 27.5?(5)°. The crystal structure is stabilized by ?-? stacking inter-actions between symmetry-related triazole and pyrimidine rings, with centroid-centroid distances of 3.594?(10)?Å.

| S-EPMC2971036 | biostudies-literature

One mol-ecule, three crystal structures: conformational trimorphism of N-[(1S)-1-phenyl-eth-yl]benzamide.

Project description:The title compound, C15H15NO, is an enanti-opure small mol-ecule, which has been synthesized many times, although its crystal structure was never determined. By recrystallization from a variety of solvent mixtures (pure aceto-nitrile, ethanol-water, toluene-ethanol, THF-methanol), we obtained three unsolvated polymorphs, in space groups P21 and P212121. Form I is obtained from aceto-nitrile, without admixture of other forms, whereas forms II and III are obtained simultaneously by concomitant crystallizations from alcohol-based solvent mixtures. All forms share the same supra-molecular structure, based on infinite C 1 1(4) chain motifs formed by N-H⋯O inter-molecular hydrogen bonds, as usual for non-sterically hindered amides. However, a conformational modification of the mol-ecular structure, related to the rotation of the phenyl rings, alters the packing of the chains in the crystal structures. The orientation of the chain axis is perpendicular and parallel to the crystallographic twofold screw axis of space group P21 in forms I and II, respectively. As for form III, the asymmetric unit contains two independent mol-ecules forming parallel chains in space group P212121, and the crystal structure combines features of monoclinic forms I and II.

| S-EPMC7405568 | 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