Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A redetermination from the original data of the crystal structure of 2-amino-4,6-di-meth-oxy-pyrimidin-1-ium 4-amino-benzoate.

ABSTRACT: The title structure, C6H9.5N3O2 (0.5+)·C7H6.5NO2 (0.5-), which might be named schematically as 2-amino-4,6-di-meth-oxy-pyrimidine-(?2-hydrogen)-4-amino-benzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Mu-thiah & 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 hy-droxy 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.

SUBMITTER: Fabry J

PROVIDER: S-EPMC4910325 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A redetermination from the original data of the crystal structure of 2-amino-4,6-di-meth-oxy-pyrimidin-1-ium 4-amino-benzoate.

Fábry Jan J

Acta crystallographica. Section E, Crystallographic communications 20160318 Pt 4

The title structure, C6H9.5N3O2 (0.5+)·C7H6.5NO2 (0.5-), which might be named schematically as 2-amino-4,6-di-meth-oxy-pyrimidine-(μ2-hydrogen)-4-amino-benzoate to indicate a bridging H atom, has been redetermined from the data published by Thanigaimani, Mu-thiah & 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 t ...[more]

PMID: 27375878

Similar Datasets

2-Amino-4,6-dimeth-oxy-pyrimidin-1-ium p-toluene-sulfonate.

Project description:In the title salt, C(6)H(10)N(3)O(2) (+)·C(7)H(7)O(3)S(-), the 2-amino-4,6-dimeth-oxy-pyrimidinium cation inter-acts with the sulfonate group of the p-toluene-sulfonate anion via a pair of N-H?O hydrogen bonds, forming a cyclic hydrogen-bonded R(2) (2)(8) motif, which in the crystal is linked by further intemolecular N-H?O hydrogen bonds, forming supra-molecular chains along the c axis. Furthermore, neighboring chains are inter-linked via weak C-H?O hydrogen bonds and C-H?? inter-actions, forming layers.

| S-EPMC3201388 | biostudies-literature

2-Amino-4,6-dimeth-oxy-pyrimidin-1-ium 2,2-dichloro-acetate.

Project description:In the title salt, C(6)H(10)N(3)O(2) (+)·C(2)HCl(2)O(2) (-), two cations and two anions are linked by N-H?O hydrogen bonds, forming chains along the c axis.

| S-EPMC3379456 | biostudies-literature

Methyl 2-amino-4,5-di-meth-oxy-benzoate.

Project description:The title compound, C10H13NO4, is essentially planar, with an r.m.s. deviation of 0.049?Å. An intra-molecular C-H?O hydrogen bond occurs and the amino group forms an intra-molecular N-H?Oester hydrogen bond; the other H atom forms an inter-molecular N-H?Ocarbon-yl hydrogen bond, leading to the formation of a helical chain that runs along the b-axis direction.

| S-EPMC3885048 | biostudies-literature

2-Amino-4-meth-oxy-6-methyl-pyrimidin-1-ium picrate.

Project description:In the title salt, C(6)H(10)N(3)O(+)·C(6)H(2)N(3)O(7) (-), the dihedral angle between the mean planes of the benzene and pyridine rings is 3.1?(1)°. In the cation, the meth-oxy group is almost coplanar with the pyridine ring [C-O-C-N = -0.6?(2)°]. The p-nitro [C-C-N-O = -1.17?(19)°] and one o-nitro [C-C-N-O = 1.83?(19)°] group in the anion are essentially coplanar with the benzene ring. The other disordered o-nitro group containing the major occupancy [0.868?(6)] O atom is twisted -29.0?(2)° from the mean plane of the benzene ring. A bifurcated N-H?(O.O) hydrogen bond and weak C-H?O intermolecular inter-action between the cation and anion produce a network of infinite O-H?O-H?O-H chains along the c axis in the [101] plane which helps to establish crystal packing. Comparison to a DFT computational calculation indicates that significant conformational changes occur in the free state.

| S-EPMC2979045 | biostudies-literature

2-Amino-4,6-dimethyl-pyrimidin-1-ium chloride.

Project description:In the title compound, C6H10N3(+)·Cl(-), the cation is essentially planar with an r.m.s. deviations of the fitted atoms of 0.008 Å. In the crystal, adjacent ions are linked by weak N-H⋯Cl hydrogen bonds involving the pyrimidine and amine N atoms, forming a three-dimensional network. C-H⋯π inter-actions between the methyl and pyrimidine groups and π-π stacking [centroid-centroid distance = 3.474 (1) Å] between parallel pyrimidine ring systems are also observed.

| S-EPMC3588968 | biostudies-literature

Crystal structures of 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-<i>N</i>-(2,4-di-methyl-phen-yl)acetamide and 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-<i>N</i>-(3-meth-oxy-phen-yl)acetamide.

Project description:In the title compounds, C14H17N5OS (I) and C13H15N5O2S (II), the dihedral angle between the pyrimidine and benzene rings is 58.64 (8)° in (I) and 78.33 (9)° in (II). In both compounds, there is an intra-molecular C-H⋯O hydrogen bond, and in (II) there is also an intra-molecular N-H⋯N hydrogen bond present. In the crystals of both compounds, a pair of N-H⋯N hydrogen bonds links the individual mol-ecules to form inversion dimers with R22(8) ring motifs. In (I), the dimers are linked by N-H⋯O and C-H⋯O hydrogen bonds, enclosing R21(14), R21(11) and R21(7) ring motifs, forming layers parallel to the (100) plane. There is also an N-H⋯π inter-action present within the layer. In (II), the inversion dimers are linked by N-H⋯O hydrogen bonds enclosing an R44(18) ring motif. The presence of N-H⋯O and C-H⋯O hydrogen bonds generate an R21(6) ring motif. The combination of these various hydrogen bonds results in the formation of layers parallel to the (1-11) plane.

| S-EPMC5499277 | biostudies-literature

Methyl 2,6-bis-[(5-bromo-4,6-dimeth-oxy-pyrimidin-2-yl)-oxy]benzoate.

Project description:In the title compound, C(20)H(18)Br(2)N(4)O(8), the inter-planar angle of the pyrimidine rings is 75.1 (2)°. The central benzene ring is inclined at inter-planar angles of 66.5 (2) and 71.9 (2)° with respect to the two pyrimidine rings. In the crystal structure, adjacent mol-ecules are connected into two-mol-ecule-thick arrays parallel to the bc plane via short Br⋯Br [3.5328 (12) Å] and Br⋯O [3.206 (3) and 3.301 (4) Å] inter-actions. A weak inter-molecular π-π aromatic stacking inter-action [centroid-centroid distance = 3.526 (3) Å] is also observed.

| S-EPMC3006963 | biostudies-literature

N-Cyclo-hexyl-N-{[3-(4,6-dimeth-oxy-pyrimidin-2-yl-oxy)pyridin-2-yl]meth-yl}4,6-dimeth-oxy-pyrimidin-2-amine.

Project description:In the title compound, C(24)H(30)N(6)O(5), the cyclo-hexyl ring adopts a chair conformation, while the remainder of the mol-ecule adopts a U-shape. The dihedral angles between the pyridine ring and the pendant pyrimidine rings are 69.04?(12) and 75.99?(9)°. The two pyrimidine rings, however, are nearly parallel to one another, with a dihedral angle of 8.56?(15)° between them. They are also involved in an intra-molecular ?-? stacking inter-action with a distance of 3.6627?(18)?Å between the ring centroids. In the crystal, C-H?O contacts link the mol-ecules into chains along the b axis.

| S-EPMC3344196 | biostudies-literature

2-(4-Amino-benzene-sulfonamido)-4,6-dimethyl-pyrimidin-1-ium 2-carb-oxy-4,6-dinitro-phenolate.

Project description:In the structure of the phenolate salt of the sulfa drug sulfamethazine with 3,5-dinitro-salicylic acid, C12H15N4O2S(+)·C7H3N2O7 (-), the dihedral angle between the pyrimidine and benzene rings of the cation is 59.70?(17)°. In the crystal, cation-anion hydrogen-bonding inter-actions involving pyrim-idine-carb-oxy N(+)-H?O and amine-carb-oxy N-H?O pairs give a cyclic R 2 (2)(8) motif while secondary N-H?O hydrogen bonds between the aniline group and both sulfone and nitro O-atom acceptors give a two-dimensional structure extending in (001).

| S-EPMC3629512 | biostudies-other

2-Meth-oxy-4,6-di-phenyl-nicotino-nitrile.

Project description:In the title compound, C19H14N2O, the phenyl rings form dihedral angles of 10.90?(10) and 42.14?(6)° with pyridine ring and an angle of 35.7?(2)° with each other. The orientation of the meth-oxy group is defined by the C-O-C-N torsion angle of 4.9?(2)°.

| S-EPMC3998366 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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