Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts

The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations

This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed.

ROS/pH dual-sensitive emodin-chlorambucil co-loaded micelles enhance anti-tumor effect through combining oxidative damage and chemotherapy

The high level of reactive oxygen species (ROS) at the tumor site has been widely used in the tumor targeted delivery. However, the ROS stimulus-responsive vector itself is also a ROS consumer, and the consumption of endogenous ROS may not be sufficient to maintain sustained drug release. In this study, we designed and synthesized ROS/pH dual-sensitive polymer micelles for the co-delivery of emodin (EMD) and chlorambucil (CLB). The release of quinone methides (QM) can consume glutathione (GSH), on the one hand, it can enhance the chemotoxicity of phenylbutyrate nitrogen mustard, on the other hand, emodin can induce oxidative damage of tumor cells and maintain the sustained targeted release of drugs.

Intramolecular O···H Hydrogen Bonding of Salicylic Acid: Further Insights from O 1s XPS and 1H NMR Spectra Using DFT Calculations

Intramolecular hydrogen bonding (HB) is a complex phenomenon that extends beyond a simple valence event, affecting the core electrons of a molecule. Salicylic acid (SA) and its conformers provide an excellent model compound for studying intramolecular HB as the proton donor (H) and acceptor (O) can be toggled by rotating the C-O and C-C bonds to form up to seven potential conformers through various HB. In this study, we computationally investigated intramolecular interactions in SA conformers with and without such HB, by examining their calculated O 1s core electron-binding energy (CEBE) and ¹H NMR chemical shifts validated using recent measurements. The quantum mechanically stable SA conformers are fully defined by three rotatable bonds in the compound, which are abstracted as SA(η₁η₂η₃) digital structures, where η_i = 0 if the η_i angles match the most stable SA conformer (000) and η_i = 1 otherwise. Our findings suggest that the stability is dominated by the appearance of the intergroup intramolecular HB of H_p···O (where O is in the carboxylic acid functional group and H_p is the phenolic proton in -OH_p), and η₃ serves as a switch of such HB. As a result, the (η₁η₂0) SA conformers containing such H_p···O HB are more stable than other SA conformers (η₁η₂1) without such the H_p···O HB. The present density functional theory calculations reveal that this H_p···O HB results in splitting of the O 1s CEBEs of two hydroxyl groups (-OH) by up to 1 eV and deshielding the H_p proton ¹H NMR (δH_p) up to 11.68 ppm for the (η₁η₂0) conformers. Without such H_p···O HB, the O 1s XPS binding energies of two -OH groups will be closely located in the same band, and the ¹H NMR chemical shift of the H_p atom will be as small as an 4.09 ppm SA conformer [SA-G(101)]. The present study indicates that the O 1s CEBE splitting between two -OH groups serves as an indicator of the presence of the H_p···O HB in SA conformers, which is also supported by the ¹H NMR results.

Density functional theory calculations of δ(13 C) and δ(1 H) chemical shifts and 3 J(13 COO1 H) coupling constants as structural and analytical tools in hydroperoxides: Prospects and limitations of 1 H13 C heteronuclear multiple bond correlation experiments

Density functional theory (DFT) calculations of δ(¹³ C) and δ(¹ H) chemical shifts and ³ J(¹³ COO¹ H) coupling constants of three model hydroperoxides of the naturally occurring cis-11-OOH and trans-9-OOH isomers of oleate and 9-cis, 11-trans-16-OOH endo hydroperoxide of methyl linolenate are reported. The computational δ(OOH) for various functionals and basis sets were found to be nearly identical for the cis/trans geometric isomers. The chemical shifts of the methine CHOOH protons and carbons, on the contrary, are highly diagnostic for the identification of cis/trans geometric isomerism. The chemical shifts of the olefinic protons and carbons strongly depend on the orientation of the hydroperoxide unit relative to the double bond and, thus, of importance in conformational analysis. The results are in very good agreement with the available experimental data. For the various diastereomeric pairs of the model endo-hydroperoxide, the strongly deshielded OOH resonances, due to the presence of an intramolecular hydrogen bond between the hydroperoxide proton and an oxygen of the endo-peroxide ring, along with the δ(CHOOH), are highly diagnostic for identification and structure elucidation of complex erythro- and threo- diastereomeric pairs of endo-hydroperoxides; the computational results are in very good agreement with the available experimental data. The ³ J(¹³ COO¹ H) coupling constants were found to be <  2  Hz for the cis-trans geometric models and <  0.5  Hz for the endo-hydroperoxide and, thus, unimportant in stereochemical analysis. Sharp resonances of the hydroperoxide protons, with Δν_1/2  < 3 Hz, are required for the successful implementation of the ¹ H¹³ C heteronuclear multiple bond correlation (HMBC) technique.

Community composition, bacterial symbionts, antibacterial and antioxidant activities of honeybee-associated fungi

Background

Fungi associated with insects represent one potentially rich source for the discovery of novel metabolites. However, a comprehensive understanding of the fungal communities of Apis mellifera ligustica remains elusive.

Results

Here, we investigated the phylogenetic diversity and community composition of honeybee-associated fungi using combination of culture-dependent and culture-independent approaches. A total of forty-five fungi were isolated and purified from the Apis mellifera ligustica, royal jelly, and honeycomb, which belonged to four classes and eleven different genera. Furthermore, 28 bacterial 16S rRNA gene sequences were obtained by PCR from the fungal metagenome. High-throughput sequencing analyses revealed that the fungal communities were more diverse, a total of 62 fungal genera were detected in the honeybee gut by culture-independent method, whereas only 4 genera were isolated by culture-dependent method. Similarly, 247 fungal genera were detected in the honeycomb, whereas only 4 genera were isolated. In addition, we assessed the antibacterial and antioxidant activities of fungal isolates. Most fungal crude extracts obtained from the cultivation supernatant exhibited antioxidant activities. Only two fungal crude extracts displayed moderate activity against Escherichia coli and Staphylococcus aureus. Chemical analysis of Chaetomium subaffine MFFC22 led to the discovery of three known compounds, including cochliodinol (1), emodin (2), chrysophanol (3). Among them, cochliodinol (1) showed intense DPPH radical scavenging activity with the 50% inhibitory concentration (IC₅₀) of 3.06 μg/mL, which was comparable to that of the positive ascorbic acid (IC₅₀ = 2.25 μg/mL). Compound 2 displayed weak inhibitory activities against Micrococcus tetragenus and S. aureus.

Conclusions

This research provided a fundamental clue for the complex interactions among honeybees, fungi, bacterial symbionts, and the effects on the honeybee. Furthermore, the diversity of honeybee-associated fungi had great potential in finding the resource of new species and antioxidants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02580-4.

Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives

Mono- and polyunsaturated lipids are particularly susceptible to peroxidation, which results in the formation of lipid hydroperoxides (LOOHs) as primary nonradical-reaction products. LOOHs may undergo degradation to various products that have been implicated in vital biological reactions, and thus in the pathogenesis of various diseases. The structure elucidation and qualitative and quantitative analysis of lipid hydroperoxides are therefore of great importance. The objectives of the present review are to provide a critical analysis of various methods that have been widely applied, and more specifically on volumetric methods, applications of UV-visible, infrared, Raman/surface-enhanced Raman, fluorescence and chemiluminescence spectroscopies, chromatographic methods, hyphenated MS techniques, NMR and chromatographic methods, NMR spectroscopy in mixture analysis, structural investigations based on quantum chemical calculations of NMR parameters, applications in living cells, and metabolomics. Emphasis will be given to analytical and structural methods that can contribute significantly to the molecular basis of the chemical process involved in the formation of lipid hydroperoxides without the need for the isolation of the individual components. Furthermore, future developments in the field will be discussed.

Bioguided Isolation of Active Compounds from Rhamnus alaternus against Methicillin-Resistant Staphylococcus aureus (MRSA) and Panton-Valentine Leucocidin Positive Strains (MSSA-PVL)

Despite intensified efforts to develop an effective antibiotic, S. aureus is still a major cause of mortality and morbidity worldwide. The multidrug resistance of bacteria has considerably increased the difficulties of scientific research and the concomitant emergence of resistance is to be expected. In this study we have investigated the in vitro activity of 15 ethanol extracts prepared from Moroccan medicinal plants traditionally used for treatment of skin infections. Among the tested species I. viscosa, C. oxyacantha, R. tinctorum, A. herba alba, and B. hispanica showed moderate anti-staphylococcal activity. However, R. alaternus showed promising growth-inhibitory effects against specific pathogenic bacteria especially methicillin-susceptible Staphylococcus aureus Panton-Valentine leucocidin positive (MSSA-PVL) and methicillin-resistant S. aureus (MRSA). The bioguided fractionation of this plant using successive chromatographic separations followed by nuclear magnetic resonance (NMR) and mass spectrometry (MS) including EIMS and HREIMS analysis yielded the emodin (1) and kaempferol (2). Emodin being the most active with MICs ranging between 15.62 and 1.95 µg/mL and showing higher activity against the tested strains in comparison with the crude extract, its mechanism of action and the structure-activity relationship were interestingly discussed. The active compound has not displayed toxicity toward murine macrophage cells. The results obtained in the current study support the traditional uses of R. alaternus and suggest that this species could be a good source for the development of new anti-staphylococcal agents.

On the molecular basis of H2O/DMSO eutectic mixtures by using phenol compounds as molecular sensors: a combined NMR and DFT study

NMR and DFT studies of phenol compounds as molecular sensors were carried out to investigate H₂O/DMSO eutectic mixtures at a molecular level. The experimental ¹H NMR chemical shifts of the OH groups, δ_exp(OH), of phenol, paracoumaric acid, and vanillic acid show maximum deshielding and, thus, hydrogen bond interactions in the range of mole fractions 0.20 < χ(DMSO) < 0.33. In the mole fractions χ(DMSO) < 0.2, a progressive decrease in δ_exp(OH) was observed which demonstrates a decrease in hydrogen bond interactions at infinite dilution in H₂O, despite the increase in the number of available hydrogen bond acceptor and donor sites. DFT calculated δ_calc(OH) of minimum energy solvation clusters were shown to be in reasonable agreement with the pattern in experimental δ_exp(OH) data. The chemical shift deshielding and, thus, increased hydrogen bond interactions in the natural product + DMSO + nH₂O (n = 2, 3) solvation clusters, relative to complexes in DMSO or H₂O solutions, cannot be attributed to a single structural parameter of the cooperative interactions between H₂O and DMSO molecules with the phenol OH groups of the natural products. The minimum energy conformers of phenol compounds + 2H₂O + DMSO complexes are in excellent agreement with a recent low temperature neutron diffraction experiment of 3D₂O + DMSO and demonstrate a general structural motif of solvation complexes. The combined use of ¹H NMR and DFT studies with emphasis on δ(OH) of phenol compounds, as molecular sensors, can provide an effective method for the study of solute-solvent interactions at the atomic level.

DFT Calculations of 1H NMR Chemical Shifts of Geometric Isomers of Conjugated Linolenic Acids, Hexadecatrienyl Pheromones, and Model Triene-Containing Compounds: Structures in Solution and Revision of NMR Assignments

A DFT study of the ¹H NMR chemical shifts, δ(¹H), of geometric isomers of 18:3 conjugated linolenic acids (CLnAs), hexadecatrienyl pheromones, and model triene-containing compounds is presented, using standard functionals (B3LYP and PBE0) as well as corrections for dispersion interactions (B3LYP-D3, APFD, M06–2X and ωB97XD). The results are compared with literature experimental δ(¹H) data in solution. The closely spaced “inside” olefinic protons are significantly more deshielded due to short-range through-space H^…H steric interactions and appear close to or even beyond δ-values of aromatic systems. Several regularities of the computational δ(¹H) of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest-energy DFT-optimized single conformer for all functionals used and are in very good agreement with experimental δ(¹H) in solution. Examples are provided of literature studies in which experimental resonance assignments deviate significantly from DFT predictions and, thus, should be revised. We conclude that DFT calculations of ¹H chemical shifts of trienyl compounds are powerful tools (i) for the accurate prediction of δ(¹H) even with less demanding functionals and basis sets; (ii) for the unequivocal identification of geometric isomerism of conjugated trienyl systems that occur in nature; (iii) for tackling complex problems of experimental resonance assignments due to extensive signal overlap; and (iv) for structure elucidation in solution.

A holistic strategy for discovering structural analogues of drug residues in meat using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry

A holistic strategy for discovering structural analogs was established using characteristic structural fragments filtering by high-resolution Orbitrap mass spectrometry and successfully employed for discovering potential hazards in meat. The mass spectrometry fragmentation mechanisms of 113 compounds (including sulphonamides, tetracyclines, benzimidazoles, steroid hormones, cephalosporins, β-blockers) were investigated and a new strategy for screening of characteristic fragment ions was proposed. To process the data acquired by two scan modes, firstly an integrated filtering strategy was conducted to facilitate the characterisation of multi-class drugs. The integrated filtering strategy was applied to reduce interference in the raw data, which could help extracting the MS1 characteristics of the homolog-type chemical substances and expand the screening of the compounds as effectively as possible. This strategy was based on a combination of nitrogen rule, neutral loss and multiple characteristic fragment ions filtering. The method was validated by rapid screening and identification of targeted compounds in spiked samples. Particularly, the successful detection of several new compounds indicated that this strategy had significant advantages over individual filtration methods and could be a promising method for screening and identifying newly homolog-type drug residues in complex samples.

NMR and Computational Studies as Analytical and High-Resolution Structural Tool for Complex Hydroperoxides and Diastereomeric Endo-Hydroperoxides of Fatty Acids in Solution-Exemplified by Methyl Linolenate

A combination of selective 1D Total Correlation Spectroscopy (TOCSY) and 1H-13C Heteronuclear Multiple Bond Correlation (HMBC) NMR techniques has been employed for the identification of methyl linolenate primary oxidation products without the need for laborious isolation of the individual compounds. Complex hydroperoxides and diastereomeric endo-hydroperoxides were identified and quantified. Strongly deshielded C-O-O-H 1H-NMR resonances of diastereomeric endo-hydroperoxides in the region of 8.8 to 9.6 ppm were shown to be due to intramolecular hydrogen bonding interactions of the hydroperoxide proton with an oxygen atom of the five-member endo-peroxide ring. These strongly deshielded resonances were utilized as a new method to derive, for the first time, three-dimensional structures with an assignment of pairs of diastereomers in solution with the combined use of 1H-NMR chemical shifts, Density Functional Theory (DFT), and Our N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) calculations.

Multi-spectroscopic monitoring of molecular interactions between an amino acid-functionalized ionic liquid and potential anti-Alzheimer's drugs

Inhibiting the formation of amyloid fibrils is a crucial step in the prevention of the human neurological disorder, Alzheimer's disease (AD). Ionic liquid (IL) mediated interactions are an expedient approach that exhibits inhibition effects on amyloid fibrils. In view of the beneficial role of ILs, in this work we have explored complexation of anti-Alzheimer's drugs (i.e., tacrine and PC-37) and an amino acid-functionalized IL [AIL (4-PyC8)]. Maintaining standard physiological conditions, the binding mechanism, thermo-dynamical properties and binding parameters were studied by employing UV-vis, fluorescence, FTIR, ¹H NMR, COSY and NOESY spectroscopy. The present investigation uncovers the fact that the interaction of anti-Alzheimer's drugs with 4-PyC8 is mediated through H-bonding and van der Waals forces. The Benesi–Hildebrand relation was used to evaluate the binding affinity and PC-37 showed the highest binding when complexed with 4-PyC8. FTIR spectra showed absorption bands at 3527.98 cm⁻¹ and 3527.09 cm⁻¹ for the PC-37 + 4-PyC8 system which is quite promising compared to tacrine. ¹H-NMR experiments recorded deshielding for tacrine at relatively higher concentrations than PC-37. COSY investigations suggest that anti-Alzheimer's drugs after complexation with 4-PyC8 show a 1 : 1 ratio. The cross-peaks of the NOESY spectra involve correlations between anti-Alzheimer's drugs and AIL protons, indicating complexation between them. The observed results indicate that these complexes are expected to have a possible therapeutic role in reducing/inhibiting amyloid fibrils when incorporated into drug formulations.

Ionic liquids mediated interactions are an expedient approach that exhibit inhibition effect on amyloid fibrils which is beneficial for the treatment of Alzheimer's disease.

Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives

We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.

DFT Calculations of 1H- and 13C-NMR Chemical Shifts of Geometric Isomers of Conjugated Linoleic Acid (18:2 ω-7) and Model Compounds in Solution

A density functional theory (DFT) study of the ¹H- and ¹³C-NMR chemical shifts of the geometric isomers of 18:2 ω-7 conjugated linoleic acid (CLA) and nine model compounds is presented, using five functionals and two basis sets. The results are compared with available experimental data from solution high resolution nuclear magnetic resonance (NMR). The experimental ¹H chemical shifts exhibit highly diagnostic resonances due to the olefinic protons of the conjugated double bonds. The "inside" olefinic protons of the conjugated double bonds are deshielded than those of the "outside" protons. Furthermore, in the cis/trans isomers, the signals of the cis bonds are more deshielded than those of the trans bonds. These regularities of the experimental ¹H chemical shifts of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest energy DFT optimized single conformer, for all functionals and basis sets used. The other low energy conformers have negligible effects on the computational ¹H-NMR chemical shifts. We conclude that proton NMR chemical shifts are more discriminating than carbon, and DFT calculations can provide a valuable tool for (i) the accurate prediction of ¹H-NMR chemical shifts even with less demanding functionals and basis sets; (ii) the unequivocal identification of geometric isomerism of CLAs that occur in nature, and (iii) to derive high resolution structures in solution.

Multi-spectroscopic monitoring of molecular interactions between an amino acid-functionalized ionic liquid and potential anti-Alzheimer's drugs

Ionic liquids mediated interactions are an expedient approach that exhibit inhibition effect on amyloid fibrils which is beneficial for the treatment of Alzheimer's disease.

Composition Characterization of Fatty Acid Zinc Salts by Chromatographic and NMR Spectroscopic Analyses on Their Fatty Acid Methyl Esters

To implement EU REACH- (Registration, Evaluation, and Authorization of Chemicals-) like chemical legislations in various countries of which the purpose is human and environment safety, the first step is substance identification followed by the hazard and risk assessments. Although both structural and composition identifications are required, the latter can more importantly result in the essential data to fill out the required substance information such as purity and concentrations of constituents, as well as impurities. With fatty acid zinc salts (FAZSs) as an exemplary industrial chemical of which chromatographic and nuclear magnetic resonance (NMR) analyses were impossible due to their insolubility in water and any organic solvents, the composition characterization was tried by preparing their fatty acid methyl esters (FAMEs) using the conc. HCl/methanol/toluene method. This acid-catalyzed methyl esterification was optimized with zinc stearate as a surrogate substance. Gas chromatography-mass spectrometry (GC-MS) and NMR analyses on methyl-esterified products revealed that the optimum conditions were at 90°C for 10 min or 45°C for 30 min with two equivalent HCl as well as at 45°C for 10 min with five equivalent HCl. Almost all zinc stearates were converted into the corresponding fatty acids with 97-99% conversion rates. Free fatty acids (FFAs) were detected in extracted ion chromatograms of pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) in the methyl-esterified products with incomplete conversions of 73∼79%. The optimized conc. HCl/methanol/toluene method of direct one-step reaction from FAZSs was compared with the two-step NaOH saponification/BF₃-methanol method after acidic hydrolysis of FAZSs. The mechanism of fatty acid zinc salts into free fatty acids and fatty acid methyl esters was suggested with the evidence of the formation of Zn(OH)₂.