Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pyramidalization of a carbonyl C atom in (2S)-N-(seleno-acet-yl)proline methyl ester.

ABSTRACT: The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent mol-ecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carb-oxy C atom is expected to be slightly pyramidal due to an n? ?* inter-action, wherein the lone pair (n) of the Se atom overlap with the anti-bonding orbital (?*) of the carbonyl group. Such pyramidalization is observed in one mol-ecule of the title compound but not the other.

SUBMITTER: Guzei IA

PROVIDER: S-EPMC3648325 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Pyramidalization of a carbonyl C atom in (2S)-N-(seleno-acet-yl)proline methyl ester.

Guzei Ilia A IA Choudhary Amit A Raines Ronald T RT

Acta crystallographica. Section E, Structure reports online 20130430 Pt 5

The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent mol-ecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carb-oxy C atom is expected to be slightly pyramidal due to an n→ π* inter-action, wherein the lone pair (n) of the Se atom overlap with the anti-bonding orbital (π*) of the carbonyl group. Such pyramidalization is observed in one mol-ecule of the title comp ...[more]

PMID: 23723945

Similar Datasets

Crystal structure of 4-[(1R,2S,5R)-2-isopropyl-5-methyl-cyclo-hex-yl] 2-methyl (2S,4S,5R)-1-[(2S,3R,5R)-5-meth-oxy-carbonyl-2-(2-methyl-phen-yl)pyrrolidine-3-carbon-yl]-5-(2-methyl-phen-yl)pyrrolidine-2,4-di-carboxyl-ate.

Project description:The title compound, C38H50N2O7, represents a chiral β-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1 Å and adopts a Z configuration along the N-CO bond. In the crystal, the hydrogen atoms of the methyl-ene groups form several short inter-molecular C-H⋯O contacts with the carbonyl oxygen atoms of an adjacent mol-ecule. The only active amino hydrogen atom is not involved in hydrogen bonding.

| S-EPMC6505609 | biostudies-literature

N-But-oxy-carbonyl-5-oxo-l-proline ethyl ester.

Project description:The mol-ecular structure of the title compound, C12H19NO5, may be visualized as made up of two nearly perpendicular planes [dihedral angle = 87.39?(12)°] and its crystal structure is a good example of C-H?O inter-actions assuming significance in optimizing supra-molecular aggregation in crystals in a mol-ecule which is severely imbalanced in terms of donors to acceptor atoms. The pyrrolidine ring adopts a ((3) T 2) twist conformation with puckering parameters Q = 0.2630?(4)?Å and ? = 59?(9)°. The crystal structure features R 2 (4)(10) and R 3 (4)(26) ring motifs formed by four weak C-H?O inter-actions, leading to supra-molecular sheets lying parallel to the bc plane.

| S-EPMC3629616 | biostudies-literature

Methyl 5-(2-bromo-acet-yl)-2-propoxybenzoate.

Project description:The title compound, C(13)H(15)BrO(4), was synthesized from methyl 5-acetyl-2-hydroxy-benzoate. With the exception of the ester group and some H atoms, the molecule is planar, the average deviation from planarity being 0.086?(5)?Å. The dihedral angle between the phenyl ring and the ester group is 41.6?(3)°. Adjacent mol-ecules are inter-connected by C-H?O bonds, generating a layered structure.

| S-EPMC2961638 | biostudies-literature

N-(4-Methyl-phen-yl)-N-{[(2-nitro-phen-yl)acet-yl]-oxy}benzamide.

Project description:In the title mol-ecule, C(22)H(18)N(2)O(5), the nitro-substituted benzene ring makes dihedral angles of 71.56?(1)° with the benzoyl ring and 16.28?(1)° with the methyl-substituted benzene ring. The crystal structure features C-H?O inter-actions, which generate chains.

| S-EPMC3470341 | biostudies-literature

Pyramidalization of backbone carbonyl carbon atoms in proteins.

Project description:The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalization is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alphaR and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.

| S-EPMC2144462 | biostudies-other

1-(2-Hydr-oxy-5-methyl-phen-yl)ethanone [(1H-indol-3--yl)acet-yl]hydrazone.

Project description:The indolyl -NH group of the title Schiff base, C(19)H(19)N(3)O(2), forms a hydrogen bond to the -OH group of an inversion-related mol-ecule, resulting in a hydrogen-bonded dimer; adjacent dimers are further linked through an inter-dimer N-H⋯O hydrogen bond involving the -C(=O)-NH-N=fragment to form a linear ribbon that runs along the a axis.

| S-EPMC2961215 | biostudies-literature

Methyl 2-(N-methoxy-carbonyl-meth-yl-N-methylsulfamo-yl)benzoate.

Project description:In the title compound, C(12)H(15)NO(6)S, the aromatic ring is oriented at dihedral angles of 64.76?(11) and 56.42?(13)° with respect to the planar methyl ester unit and the SO(2) group, respectively. The dihedral angle between the SO(2) group and the planar methoxy-carbonyl-methyl group is 50.42?(14)°. Intra-molecular C-H?O hydrogen bonding results in the formation of an eight-membered ring. In the crystal structure, inter-molecular C-H?O hydrogen bonds link the mol-ecules.

| S-EPMC2968464 | biostudies-literature

(1R,2R,3R,4R,5S)-2,3-Bis[(2S')-2-acet-oxy-2-phenyl-acet-oxy]-4-azido-1-[(2,4-dinitro-phen-yl)hydrazono-meth-yl]bicyclo-[3.1.0]hexa-ne.

Project description:In the title compound, C(38)H(29)N(7)O(12), the five-membered ring adopts an envelope conformation in which the 'flap' is cis to the cyclo-propane group. This conformation is similar to those of other bicyclo-[3.1.0]hexane analogues for which crystal structures have been reported. The absolute configuration of the stereogenic centers on the cyclo-pentane ring, as determined by comparison with the known configurations of the stereogenic centers in the (2S)-2-acet-oxy-2-phenyl-acet-oxy groups, is 1(R), 2(R), 3(R), 4(R) and 5(S). An intramolecular N-H⋯O hydrogen bond is present.

| S-EPMC2960152 | biostudies-literature

(2S)-Methyl 2-(4-chloro-benzene-sulfon-amido)-4-(methyl-sulfan-yl)butanoate.

Project description:The enanti-omerically pure title compound, C(12)H(16)ClNO(4)S(2), contains a pyramidal N atom with an S-N bond length of 1.6306 (15) Å. Mol-ecules are linked to form chains parallel to the a axis by classical N-H⋯O hydrogen bonding involving a sulfonyl O atom, supported by three weak C-H⋯X inter-actions. (X = S, O).

| S-EPMC2969768 | biostudies-literature

Penta-carbon-yl{3-[(2S)-1-methyl-pyrrolidin-2-yl]pyridine}tungsten(0).

Project description:The title compound, [W(C(10)H(14)N(2))(CO)(5)], contains five carbonyl ligands and a nicotine ligand in an octa-hedral arrangement around the tungsten atom. The metal atom shows cis angles in the range 87.30 (16)-94.2 (2)°, and trans angles between 175.2 (2) and 178.1 (4)°. The W-CO bond trans to the pyridine N atom [1.987 (6) Å] is noticeably shorter than the others, which range between 2.036 (3) and 2.064 (3) Å, possibly due to the well-known trans effect. The distance between the W atom and the pyridine N atom is 2.278 (4) Å.

| S-EPMC2983989 | 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