Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Substituent effect on inter-ring interaction in paracyclophanes.

ABSTRACT: The theoretical calculations, namely multipole-derived charge analysis, quantum theory of atom in molecules, and non-bonding interaction (NCI), were performed for [2.2]paracyclophanes, [2.2]paracyclophane-7,9-dienes, and [3.3]paracyclophanes optimized at B3LYP/6-311++G** level, including dispersion correction. The substituent effect of the electron donor N(Me)₂ and electron acceptor NO₂ group and the influence of the length of bridges joining the aromatic ring on aromatic ring interaction energy (AIE) and strain energy were discussed. The local and electrostatic character of the substituent effect in paracyclophanes was shown. The presence of the weak orbital through-space C···C interaction between the [3.3]paracyclophane ring and weak CH···O hydrogen bonds between the substituents in the different rings was shown.

SUBMITTER: Majerz I

PROVIDER: S-EPMC7033074 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Substituent effect on inter-ring interaction in paracyclophanes.

Majerz Irena I Dziembowska Teresa T

Molecular diversity 20190219 1

The theoretical calculations, namely multipole-derived charge analysis, quantum theory of atom in molecules, and non-bonding interaction (NCI), were performed for [2.2]paracyclophanes, [2.2]paracyclophane-7,9-dienes, and [3.3]paracyclophanes optimized at B3LYP/6-311++G** level, including dispersion correction. The substituent effect of the electron donor N(Me)<sub>2</sub> and electron acceptor NO<sub>2</sub> group and the influence of the length of bridges joining the aromatic ring on aromatic r ...[more]

PMID: 30783945

Similar Datasets

Five-membered ring annelation in [2.2]paracyclophanes by aldol condensation.

Project description:Under basic conditions 4,5,12,13-tetraacetyl[2.2]paracyclophane (9) cyclizes by a double aldol condensation to provide the two aldols 12 and 15 in a 3:7 ratio. The structures of these compounds were obtained from X-ray structural analysis, spectroscopic data, and mechanistic considerations. On acid treatment 12 is dehydrated to a mixture of the condensed five-membered [2.2]paracyclophane derivatives 18-20, whereas 15 yields a mixture of the isomeric cyclopentadienones 21-23. The structures of these elimination products are also deduced from X-ray and spectroscopic data. The sequence presented here constitutes the simplest route so far to cyclophanes carrying an annelated five-membered ring.

| S-EPMC4168897 | biostudies-literature

Zinc(II) Terpyridine Complexes: Substituent Effect on Photoluminescence, Antiproliferative Activity, and DNA Interaction.

Project description:A series of ZnCl2 complexes (compounds 1-10) with 4'-(substituted-phenyl)-2,2':6',2''-terpyridine that bears hydrogen (L1), p-methyl (L2), p-methoxy (L3), p-phenyl (L4), p-tolyl (L5), p-hydroxyl (L6), m-hydroxyl (L7), o-hydroxyl (L8), p-carboxyl (L9), or p-methylsulfonyl (L10) were prepared and then characterized by 1H NMR, electrospray mass-spectra (ESI-MS), IR, elemental analysis, and single crystal X-ray diffraction. In vitro cytotoxicity assay was used to monitor the antiproliferative activities against tumor cells. Absorption spectroscopy, fluorescence titration, circular dichroism spectroscopy, and molecular modeling studied the DNA interactions. All of the compounds display interesting photoluminescent properties and different maximal emission peaks due to the difference of the substituent groups. The cell viability studies indicate that the compounds have excellent antiproliferative activity against four human carcinoma cell lines, A549, Bel-7402, MCF-7, and Eca-109, with the lowest IC50 values of 0.33 (10), 0.66 (6), 0.37 (7), and 1.05 (7) μM, respectively. The spectrophotometric results reveal that the compounds have strong affinity binding with DNA as intercalator and induce DNA conformational transition. Molecular docking studies indicate that the binding is contributed by the π…π stacking and hydrogen bonds, providing an order of nucleotide sequence binding selectivity as ATGC > ATAT > GCGC. These compounds intercalate into the base pairs of the DNA of the tumor cells to affect their replication and transcription, and the process is supposed to play an important role in the anticancer mechanism.

| S-EPMC6943603 | biostudies-literature

Substituent Effect on Porphyrin Film-Gas Interaction by Optical Waveguide: Spectrum Analysis and Molecular Dynamic Simulation.

Project description:Substituent effect on optical gas sensing performance in porphyrin-based optical waveguide detection system was studied by molecular dynamics simulation (MDS), absorption/emission spectrum analysis, and optical waveguide (OWG) detection. The affinities of porphyrin with seven types of substituents (-H, -OH, -tBu, -COOH, -NH2, -OCH3, -SO3-) on para position of meso-phenyl porphyrin toward gas molecules in adsorption process were studied in different size of boxes with the same pressure and concentration. Analyte gases (CO2, H2S, HCl, NO2) were exposed to porphyrin film in absorption spectrophotometer, and in OWG with evanescent field excited by a guiding laser light with 670 nm wavelength. The extent of interaction between host molecule and the guest analytes was analyzed by the number of gas molecules in vicinity of 0.3 nm around substituents of porphyrin molecules. Optical waveguide results reveal that sulfonate porphyrin is mostly responsive to hydrochloride, hydrosulfide gas and nitrogen dioxide gases with strong response intensity. Molecular dynamics and spectral analysis provide objective information about the molecular state and sensing properties. Molecular rearrangements induced by gas exposure was studied by spectral analysis and surface morphology before and after gas exposure taking hydrosulfide gas as an example. Film-gas interaction mechanism was discussed in terms of each gas and substituent group characters.

| S-EPMC7763641 | biostudies-literature

Development of Rhodamine 6G-Based Fluorescent Chemosensors for Al3+-Ion Detection: Effect of Ring Strain and Substituent in Enhancing Its Sensing Performance.

Project description:Four rhodamine 6G-based chemosensors (H 3 L1-H 3 L4) are designed for selective detection of Al3+ ion. They are characterized using various spectroscopic techniques and X-ray crystallography. All absorption and emission spectral studies have been performed in 10 mM N-(2-hydroxyethyl)piperazine-N'-ethanesulfonic acid (HEPES) buffer solution at pH 7.4 in H2O/MeOH (9:1, v/v) at 25 °C. In absorption spectra, chemosensors exhibit an intense band around 530 nm in the presence of Al3+ ion. Chemosensors (H 3 L1-H 3 L4) are nonfluorescent when excited around 490 nm. The presence of Al3+ ion enhances the emission intensity (555 nm) many times. The formation of complexes 1-4 is established with the aid of different spectroscopic techniques. The limit of detection value obtained in the nanomolar range confirms the high sensitivity of the probes toward Al3+ ion. It has been observed that the presence of aliphatic spacers in the diamine part and different halogen substituents in the salicylaldehyde part strongly influences the selectivity of the chemosensors toward Al3+ ion. The propensity of the chemosensors to identify intracellular Al3+ ions in triple-negative human breast cancer cell line MDA-MB-468 by fluorescence imaging is also examined in this study.

| S-EPMC6963915 | biostudies-literature

The inter-ring arrangement of the cytosolic chaperonin CCT.

Project description:The eukaryotic cytosolic chaperonin CCT (chaperonin containing TCP-1) is the most complex of all chaperonins-an oligomeric structure built from two identical rings, each composed of single copies of eight different subunits. The arrangement of the eight subunits within each ring has been characterised for some time, but the phasing between the two rings remains unknown. Here, three-dimensional reconstructions generated by cryoelectron microscopy of complexes between CCT and either of two different monoclonal antibodies that react specifically with the CCTepsilon and CCTdelta subunits have been used to determine the phasing between the two chaperonin rings. The inter-ring arrangement is such that up/down inter-ring communication always involves two different CCT subunits in all eight positions, and the group of subunits concerned with the initiation and completion of the folding cycle cluster together both in the intra- and inter-ring arrangement. This supports a sequential mechanism of conformational changes between the two interacting rings.

| S-EPMC1808031 | biostudies-literature

Substituent Effect in the Cation Radicals of Monosubstituted Benzenes.

Project description:In 30 monosubstituted benzene cation radicals, studied at the ωB97XD/aug-cc-pVTZ level, the phenyl rings usually adopt a compressed form, but a differently compressed form-equivalent to an elongated one-may coexist. The computational and literature ionization potentials are well correlated. The geometrical and magnetic aromaticity, estimated using HOMA and NICS indices, show the systems to be structurally aromatic but magnetically antiaromatic or only weakly aromatic. The partial charge is split between the substituent and ring and varies the most at C(ipso). In the ring, the spin is 70%, concentrated equally at the C(ipso) and C(p) atoms. The sEDA(D) and pEDA(D) descriptors of the substituent effect in cation radicals, respectively, were determined. In cation radicals, the substituent effect on the σ-electron system is like that in the ground state. The effect on the π-electron systems is long-range, and its propagation in the radical quinone-like ring is unlike that in the neutral molecules. The pEDA(D) descriptor correlates well with the partial spin at C(ipso) and C(p) and weakly with the HOMA(D) index. The correlation of the spin at the ring π-electron system and the pEDA(D) descriptor shows that the electron charge supplied to the ring π-electron system and the spin flow oppositely.

| S-EPMC8269098 | biostudies-literature

Ring Structure and Aromatic Substituent Effects on the pK a of the Benzoxaborole Pharmacophore.

Project description:In this work, we present an investigation into the physical properties of a unique class of aromatic boronic acids, the benzoxaboroles. Using spectrophotometric methods, the ionization constants of a family of substituted benzoxaboroles are determined. Heterocyclic ring modifications are examined to determine their effects on the ionization of the boronic acid moiety. It is also shown that the substituent effects about the aromatic ring follow a Hammett relationship with the compounds' measured pK a values. Finally, these substituent effects are also shown to extend to the sugar binding properties of these compounds under physiologically relevant conditions. Combined, these data will inform medicinal chemists wishing to tailor the ionization and/or ability of this class of compound to bind diol-containing biomolecules.

| S-EPMC4025869 | biostudies-other

Supramolecular Complexes of β-Cyclodextrin with Clomipramine and Doxepin: Effect of the Ring Substituent and Component of Drugs on Their Inclusion Topologies and Structural Flexibilities.

Project description:Depression is a global threat. Tricyclic antidepressants (TCAs) are still efficacious in treating depression, albeit with more side effects. Cyclodextrins (CDs) with a suitable nanocavity are potential drug carriers and can enhance the drug bioavailability. Aiming for an atomistic understanding of the CD encapsulation facilitating the improvement of drug stability and the reduction of side effects, a comprehensive study series of the β-CD-TCA inclusion complexes through single crystal X-ray diffraction and density functional theory (DFT) calculation was undertaken. This work reports the supramolecular complexes of β-CD with two pivotal TCAs, clomipramine (CPM; 1) and doxepin (DXP; 2). The different inclusion topologies of the β-CD-TCA complexes were notable. X-ray analysis revealed that, in 1, the CPM B-ring (without chloro group) was entrapped in the β-CD cavity, whereas, in 2, the E-DXP A-ring and the Z-DXP B-ring were disordered in the cavity, yielding energetically favorable complexes primarily maintained by intermolecular C-H⋯π interactions, as indicated by DFT calculation. Because both wings of TCAs were similar, an alternative inclusion scenario of the A-ring was evidenced crystallographically in four other TCA complexes. The enhanced TCA thermodynamic stabilities via CD inclusion complexation helped to reduce the side effects and to increase the bioavailability. Moreover, the scrutinization of six TCAs in different lattice circumstances revealed the greater TCA structural flexibilities for their optimum pharmacological activity while binding with proteins.

| S-EPMC7600898 | biostudies-literature

Selenium halide-induced bridge formation in [2.2]paracyclophanes.

Project description:An addition/elimination sequence of selenium halides to pseudo-geminally bis(acetylene) substituted [2.2]paracyclophanes leads to new bridges with an endo-exo-diene substructure. The reactions have been found to be sensitive to the substitution of the ethynyl group. The formation of dienes with a zig-zag configuration is related to that observed for non-conjugated cyclic diynes of medium ring size.

| S-EPMC4222412 | biostudies-literature

Building complex carbon skeletons with ethynyl[2.2]paracyclophanes.

Project description:Ethynyl[2.2]paracyclophanes are shown to be useful substrates for the preparation of complex, highly unsaturated carbon frameworks. Thus both the pseudo-geminal- 2 and the pseudo-ortho-diethynylcyclophane 4 can be dimerized by Glaser coupling to the respective dimers 9/10 and 11/12. Whereas the former isomer pair could not be separated so far, the latter provided the pure diastereomers after extensive column chromatography/recrystallization. Isomer 11 is chiral and could be separated on a column impregnated with cellulose tris(3,5-dimethylphenyl)carbamate. The bridge-extended cyclophane precursor 18 furnished the ring-enlarged cyclophanes 19 and 20 on Glaser-Hay coupling. Cross-coupling of 4 and the planar building block 1,2-diethynylbenzene (1) yielded the chiral hetero dimer 22 as the main product. An attempt to prepare the biphenylenophane 27 from the triacetylene 24 by CpCo(CO)2-catalyzed cycloisomerization resulted in the formation of the cyclobutadiene Co-complex 26. Besides by their usual spectroscopic and analytical data, the new cyclophanes 11, 12, 19, 20, 22, and 26 were characterized by X-ray structural analysis.

| S-EPMC4168697 | 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