Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts.

ABSTRACT: A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the c i s isomers are lowered by roughly 3 to 4 kcal mol^-1 when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH⋯O, OH⋯S, OH⋯N and OH⋯P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of -41 cm^-1.

SUBMITTER: Smith BE

PROVIDER: S-EPMC6680949 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Photoinduced reactions of cis,trans,cis-[Pt(IV)(N3)2(OH)2(NH3)2) with 1-methylimidazole.

Project description:The photodecomposition of cis,trans,cis-[Pt(IV)(N(3))(2)(OH)(2)(NH(3))(2)] in phosphate buffered saline (PBS), as well as in the presence of 1-methylimidazole (1-MeIm), induced by UVA light (centred at lambda=365 nm) has been studied by multinuclear NMR spectroscopy. We show that photoreduction, photoisomerisation and trans-labilisation pathways are involved. The photodecomposition pathway in PBS, which involves azide release, as detected by (14)N NMR spectroscopy, appears to differ from that in acidic aqueous conditions, under which N(2) is a product. A number of trans-{N-Pt(II)-NH(3)} species were also observed as photoproducts, as well as the release of free ammonia with a corresponding increase in pH. Oxygen was also detected as a product in solution. In the presence of 1-methylimidazole, surprisingly the major photoproduct was the tetra-substituted Pt(II) complex [Pt(II)(1-MeIm-N(3))(4)](2+) (structure confirmed by crystallography), even at a Pt/1-MeIm molar ratio of 1:1, together with cis- and trans-[Pt(II)(NH(3))(2)(1-MeIm-N(3))(2)](2+) as minor products. In these photoinduced 1-MeIm reactions, free ammonia, azide and oxygen were also detected. The results from this study illustrate that photoinduced reactions of platinum complexes can lead to novel reaction pathways, and therefore to new cytotoxic mechanisms in cancer cells.

| S-EPMC2935676 | biostudies-literature

Cis-trans

Project description:Cis-trans

| PRJEB1227 | ENA

LI-cadherin cis-dimerizes in the plasma membrane Ca(2+) independently and forms highly dynamic trans-contacts.

Project description:LI-cadherin belongs to the family of 7D-cadherins that is characterized by a low sequence similarity to classical cadherins, seven extracellular cadherin repeats (ECs), and a short cytoplasmic domain. Nevertheless, LI-cadherins mediates Ca(2+)-dependent cell-cell adhesion and induces an epitheloid cellular phenotype in non-polarized CHO cells. Whereas several studies suggest that classical cadherins cis-dimerize in a Ca(2+)-dependent manner and interact in trans by strand-swapping tryptophan 2 of EC1, little is known about the molecular interactions of LI-cadherin, which lacks tryptophan 2. We thus expressed fluorescent LI-cadherin fusion proteins in HEK293 and CHO cells, analyzed their cell-cell adhesive properties and studied their cellular distribution, cis-interaction, and lateral diffusion in the presence and absence of Ca(2+). LI-cadherin highly concentrates in cell contact areas but rapidly leaves those sites upon Ca(2+) depletion and redistributes evenly on the cell surface, indicating that it is only kept in the contact areas by trans-interactions. Fluorescence resonance energy transfer analysis of LI-cadherin-CFP and -YFP revealed that LI-cadherin forms cis-dimers that resist Ca(2+) depletion. As determined by fluorescence redistribution after photobleaching, LI-cadherin freely diffuses in the plasma membrane as a cis-dimer (D = 0.42 ± 0.03 μm(2)/s). When trapped by trans-binding in cell contact areas, its diffusion coefficient decreases only threefold to D = 0.12 ± 0.01 μm(2)/s, revealing that, in contrast to classical and desmosomal cadherins, trans-contacts formed by LI-cadherin are highly dynamic.

| S-EPMC3478510 | biostudies-literature

Synthesis of cananodine by intramolecular epoxide opening.

Project description:Cananodine is a guaipyridine alkaloid with activity against liver cancer. Cananodine was synthesized using a remarkable intramolecular opening of a trisubstituted epoxide as the key step in construction of the seven-membered carbocycle of the target. The epoxide opening strategy allows all four stereoisomers of cananodine to be prepared.

| S-EPMC5722248 | biostudies-other

Structure of human peptidyl-prolyl cis-trans isomerase FKBP22 containing two EF-hand motifs.

Project description:The FK506-binding protein (FKBP) family consists of proteins with a variety of protein-protein interaction domains and versatile cellular functions. It is assumed that all members are peptidyl-prolyl cis-trans isomerases with the enzymatic function attributed to the FKBP domain. Six members of this family localize to the mammalian endoplasmic reticulum (ER). Four of them, FKBP22 (encoded by the FKBP14 gene), FKBP23 (FKBP7), FKBP60 (FKBP9), and FKBP65 (FKBP10), are unique among all FKBPs as they contain the EF-hand motifs. Little is known about the biological roles of these proteins, but emerging genetics studies are attracting great interest to the ER resident FKBPs, as mutations in genes encoding FKBP10 and FKBP14 were shown to cause a variety of matrix disorders. Although the structural organization of the FKBP-type domain as well as of the EF-hand motif has been known for a while, it is difficult to conclude how these structures are combined and how it affects the protein functionality. We have determined a unique 1.9 Å resolution crystal structure for human FKBP22, which can serve as a prototype for other EF hand-containing FKBPs. The EF-hand motifs of two FKBP22 molecules form a dimeric complex with an elongated and predominantly hydrophobic cavity that can potentially be occupied by an aliphatic ligand. The FKBP-type domains are separated by a cleft and their putative active sites can catalyze isomerazation of two bonds within a polypeptide chain in extended conformation. These structural results are of prime interest for understanding biological functions of ER resident FKBPs containing EF-hand motifs.

| S-EPMC3892300 | biostudies-literature

Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization?

Project description:Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.

| S-EPMC4972606 | biostudies-literature

Cis-trans

Project description:Differential Expression analysis in Drosophila pseudoobscura to identify cis-trans regulation

2014-03-27 | E-MTAB-1424 | biostudies-arrayexpress

Atom-Economical and Metal-Free Synthesis of Multisubstituted Furans from Intramolecular Aziridine Ring Opening.

Project description:Multisubstituted furans were prepared from dialkyl 2-(aziridin-2-ylmethylene)malonate and/or 1,3-dione through aziridine ring opening by the internal carbonyl oxygen with the assistance of BF3·OEt2, followed by aromatization. This synthetic method is free from any metal and is atom-economical with all of the atoms in the starting material retained in the final product.

| S-EPMC6645301 | biostudies-literature

Chiral Bronsted Acid-Catalyzed Asymmetric Synthesis of N-Aryl-cis-aziridine Carboxylate Esters.

Project description:We report a multi-component asymmetric Brønsted acid-catalyzed aza-Darzens reaction which is not limited to specific aromatic or heterocyclic aldehydes. Incorporating alkyl diazoacetates and, important for high ee's, ortho-tert-butoxyaniline our optimized reaction (i.e. solvent, temperature and catalyst study) affords excellent yields (61-98 %) and mostly >90 % optically active cis-aziridines. (+)-Chloramphenicol was generated in 4 steps from commercial starting materials. A tentative mechanism is outlined.

| S-EPMC5502890 | biostudies-literature

Biosynthesis, isolation, and NMR analysis of leukotriene A epoxides: substrate chirality as a determinant of the cis or trans epoxide configuration.

Project description:Leukotriene (LT)A₄ and closely related allylic epoxides are pivotal intermediates in lipoxygenase (LOX) pathways to bioactive lipid mediators that include the leukotrienes, lipoxins, eoxins, resolvins, and protectins. Although the structure and stereochemistry of the 5-LOX product LTA₄ is established through comparison to synthetic standards, this is the exception, and none of these highly unstable epoxides has been analyzed in detail from enzymatic synthesis. Understanding of the mechanistic basis of the cis or trans epoxide configuration is also limited. To address these issues, we developed methods involving biphasic reaction conditions for the LOX-catalyzed synthesis of LTA epoxides in quantities sufficient for NMR analysis. As proof of concept, human 15-LOX-1 was shown to convert 15S-hydroperoxy-eicosatetraenoic acid (15S-HPETE) to the LTA analog 14S,15S-trans-epoxy-eicosa-5Z,8Z,10E,12E-tetraenoate, confirming the proposed structure of eoxin A₄. Using this methodology we then showed that recombinant Arabidopsis AtLOX1, an arachidonate 5-LOX, converts 5S-HPETE to the trans epoxide LTA₄ and converts 5R-HPETE to the cis epoxide 5-epi-LTA₄, establishing substrate chirality as a determinant of the cis or trans epoxide configuration. The results are reconciled with a mechanism based on a dual role of the LOX nonheme iron in LTA epoxide biosynthesis, providing a rational basis for understanding the stereochemistry of LTA epoxide intermediates in LOX-catalyzed transformations.

| S-EPMC3617949 | 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