Structure determination of oleanolic and ursolic acids: a combined density functional theory/vibrational spectroscopy methodology.
Ontology highlight
ABSTRACT:
SUBMITTER: Gomez-Pulido LDM
PROVIDER: S-EPMC8170201 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Ursolic and oleanolic acids are secondary plant metabolites that are known to be involved in the plant defence system against water loss and pathogens. Nowadays these triterpenoids are also regarded as potential pharmaceutical compounds and there is mounting experimental data that either purified compounds or triterpenoid-enriched plant extracts exert various beneficial effects, including anti-oxidative, anti-inflammatory and anticancer, on model systems of both human or animal origin. Some of those effects have been linked to the ability of ursolic and oleanolic acids to modulate intracellular antioxidant systems and also inflammation and cell death-related pathways. Therefore, our aim was to review current studies on the distribution of ursolic and oleanolic acids in plants, bioavailability and pharmacokinetic properties of these triterpenoids and their derivatives, and to discuss their neuroprotective effects in vitro and in vivo.
| S-EPMC8124962 | biostudies-literature
Project description:Leaves of Ilex aquifolium L. have been used for their therapeutic properties. In previous studies, components contained in the leaves were first isolated by various chromatographic techniques. Then, quantitation of oleanolic and ursolic acids, which are responsible for the biological and therapeutic activities of the plant, was performed by HPLC, HPTLC, and somewhat by GC-MS. Our objective was to develop a simple method that allows the identification of compounds contained in the leaves of Corsican I. aquifolium and to quantify ursolic and oleanolic acids. Leaves were successively extracted with hexane and dichloromethane. The extracts were chromatographed on silica gel and the fractions of column chromatography submitted to 13C-NMR analysis, following a computerized method developed in the laboratory. 13C-NMR allowed the identification of various triterpenes including ursolic acid and oleanolic acid. Quantitation of both acids was achieved, for the first time, by 1H-NMR after validation of the method (accuracy, precision, linearity, limit of detection and limit of quantitation). Ursolic and oleanolic acids accounted for 55.3% and 20.8% of the dichloromethane extract, respectively. This represents 1.3% and 0.5% of the mass of dried leaves. 1H-NMR spectroscopy appeared as a powerful tool for a rapid quantitation of biologically active compounds from I. aquifolium.
| S-EPMC6930589 | biostudies-literature
Project description:Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd ? 0.5 mM) following a distal Leu16 ? Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ?(Fe-NO2), ?(ONO), and ?s(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}6 and {FeNO}7 states, enabling FTIR measurements to distinguish ?s(NO2) and ?as(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.
| S-EPMC5677563 | biostudies-literature
Project description:We investigate the molecular structure and vibrational properties of perchlorinated hexa-peri-hexabenzocoronene (HBC-Cl) by density functional theory (DFT) calculations and IR and Raman spectroscopy, in comparison to the parent HBC. The theoretical and experimental IR and Raman spectra demonstrated very good agreement, elucidating a number of vibrational modes corresponding to the observed peaks. Compared with the parent HBC, the edge chlorination significantly alters the planarity of the molecule. Nevertheless, the results indicated that such structural distortion does not significantly impair the ?-conjugation of such polycyclic aromatic hydrocarbons.
| S-EPMC4906847 | biostudies-other
Project description:Staphylococcus aureus is an opportunistic pathogen and the major causative agent of life-threatening hospital- and community-acquired infections. A combination of antibiotics could be an opportunity to address the widespread emergence of antibiotic-resistant strains, including Methicillin-Resistant S. aureus (MRSA). We here investigated the potential synergy between ampicillin and plant-derived antibiotics (pentacyclic triterpenes, ursolic acid (UA) and oleanolic acid (OA)) towards MRSA (ATCC33591 and COL) and the mechanisms involved. We calculated the Fractional Inhibitory Concentration Index (FICI) and demonstrated synergy. We monitored fluorescence of Bodipy-TR-Cadaverin, propidium iodide and membrane potential-sensitive probe for determining the ability of UA and OA to bind to lipoteichoic acids (LTA), and to induce membrane permeabilization and depolarization, respectively. Both pentacyclic triterpenes were able to bind to LTA and to induce membrane permeabilization and depolarization in a dose-dependent fashion. These effects were not accompanied by significant changes in cellular concentration of pentacyclic triterpenes and/or ampicillin, suggesting an effect mediated through lipid membranes. We therefore focused on membranous effects induced by UA and OA, and we investigated on models of membranes, the role of specific lipids including phosphatidylglycerol and cardiolipin. The effect induced on membrane fluidity, permeability and ability to fuse were studied by determining changes in fluorescence anisotropy of DPH/generalized polarization of Laurdan, calcein release from liposomes, fluorescence dequenching of octadecyl-rhodamine B and liposome-size, respectively. Both UA and OA showed a dose-dependent effect with membrane rigidification, increase of membrane permeabilization and fusion. Except for the effect on membrane fluidity, the effect of UA was consistently higher compared with that obtained with OA, suggesting the role of methyl group position. All together the data demonstrated the potential role of compounds acting on lipid membranes for enhancing the activity of other antibiotics, like ampicillin and inducing synergy. Such combinations offer an opportunity to explore a larger antibiotic chemical space.
| S-EPMC8615140 | biostudies-literature
Project description:[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeFe]-hydrogenases.
| S-EPMC5699932 | biostudies-literature
Project description:Deltamethrin is widely used in pest prevention and control such as red spiders, aphids, and grubs in strawberry. It is important to accurately monitor whether the deltamethrin residue in strawberry exceeds the standard. In this paper, density functional theory (DFT) was used to theoretically analyze the molecular structure of deltamethrin, gold nanoparticles (AuNPs) and silver nanoparticles (AgNPs) were used to enhance the surface enhanced Raman spectroscopy (SERS) detection signal. As a result, the theoretical Raman peaks of deltamethrin calculated by DFT were basically similar to the measured results, and the enhancing effects based on AuNPs was better than that of AgNPs. Moreover, 554, 736, 776, 964, 1000, 1166, 1206, 1593, 1613, and 1735 cm?1 could be determined as deltamethrin characteristic peaks, among which only three Raman peaks (736, 1000, and 1166 cm?1) could be used as the deltamethrin characteristic peaks in strawberry when the detection limit reached 0.1 mg/L. In addition, the 500?1800 cm?1 SERS of deltamethrin were analyzed by the partial least squares (PLS) and backward interval partial least squares (BIPLS). The prediction accuracy of deltamethrin in strawberry (Rp2 = 0.93, RMSEp = 4.66 mg/L, RPD = 3.59) was the highest when the original spectra were pretreated by multiplicative scatter correction (MSC) and then modeled by BIPLS. In conclusion, the deltamethrin in strawberry could be qualitatively analyzed and quantitatively determined by SERS based on AuNPs enhancement, which provides a new detection scheme for deltamethrin residue determination in strawberry.
| S-EPMC6100570 | biostudies-literature
Project description:Within the framework of the density functional theory (DFT) and the hybrid functional B3LYP by means of the CRYSTAL17 program code, the wavenumbers and intensities of normal oscillations of MgCO3, CaCO3, ZnCO3, CdCO3 in the structure of calcite; CaMg(CO3)2, CdMg(CO3)2, CaMn(CO3)2, CaZn(CO3)2 in the structure of dolomite; BaMg(CO3)2 in the structure of the norsethite type; and CaCO3, SrCO3, BaCO3, and PbCO3 in the structure of aragonite were calculated. Infrared absorption and Raman spectra were compared with the known experimental data of synthetic and natural crystals. For lattice and intramolecular modes, linear dependences on the radius and mass of the metal cation are established. The obtained dependences have predictive power and can be used to study solid carbonate solutions. For trigonal and orthorhombic carbonates, the linear dependence of wavenumbers on the cation radius RM (or M-O distance) is established for the infrared in-plane bending mode: 786.2-65.88·RM and Raman in-plane stretching mode: 768.5-53.24·RM, with a correlation coefficient of 0.87.
| S-EPMC7698329 | biostudies-literature
Project description:The electronic and vibrational structures of trinickel metal string complexes [Ni3(dpa)4X2]1–,0,1+ (X = Cl, NCS) were investigated using both theoretical calculations and spectroscopic methods. We used the density functional theory (DFT) method B3LYP*-D3, including less exact exchange energy and the van der Waals interaction of metal ions, to obtain the geometries and vibrational structures, which were found to be in excellent agreement with the experimental data. The ground state of Ni3(dpa)4X2 is an antiferromagnetic (AF) singlet state, and the next state is a quintet state, which was detected using temperature-dependent Raman spectroscopy under a magnetic field. The vibrational structure of the quintet state is nearly identical to that of the AF state, according to the measured Raman spectra, except that the stretching of Ni–Cl is blue-shifted from 282.5 cm–1 in the AF state to 283.8 cm–1 in the quintet state. Two oxidized Ni3 complexes were found to have [Ni3]7+ cores, the doublet [Ni3(dpa)4]3+ without axial ligands and the quartet [Ni3(dpa)4X2]+. Complex [Ni3(dpa)4X2]?, which was produced from a reduction reaction by gold nanoparticles at room temperature, consists of a quartet state as the ground state and a doublet state lying nearby.
| S-EPMC7331223 | biostudies-literature
Project description:In this study, we revealed that OA and UA significantly inhibited the expression of most genes related to peptidoglycan biosynthesis in S. mutans UA159. To the best of our knowledge, this is the first report to introduce the antimicrobial mechanism of OA and UA against S. mutans.
| S-EPMC4507558 | biostudies-literature