GIAO NMR Research Articles

Molecular Networking-Based Screening Led to the Discovery of a Cyclic Heptadepsipeptide from an Endolichenic Xylaria sp.

MS/MS-based molecular networking strain prioritization led to the discovery of a group of cyclic depsipeptides from an endolichenic Xylaria sp. The main component, xylaroamide A (1), was obtained by LC-MS-guided isolation. The planar structure of compound 1 was elucidated via 1D and 2D NMR, as well as MS/MS data. The configurations were fully determined by the combination of advanced Marfey's analysis, partial hydrolysis, Mosher's reaction, and GIAO NMR calculation based on a restricted conformational search. A plausible biosynthetic pathway for xylaroamide A (1) involving a rare trans-acting N-methyltransferase is proposed based on bioinformatics analysis. Xylaroamide A (1) exhibited inhibitory activity against cancer cell lines BT-549 and RKO with IC50 values of 2.5 and 9.5 μM, respectively.

Theoretical, Experimental Studies on Molecular Structure and Vibrational Spectra of 2,6-Dibromo-4-Nitrophenol

Phenol derivatives are interesting molecules for theoretical studies due to their relatively small size and similarity to organic species. 2,6-dibromo-4-nitrophenol was investigated by using density functional theory (DFT). XRD data and optimized DFT studies are found to be in good correspondence with each other. Analysis of title compound was obtained by B3LYP/6-31 + G(d,p) level of theory to explain the vertical transactions. Calculated FT-IR and FT-Raman results are found to be in good agreement with experimental FT-IR and FT-Raman findings. Natural bond theory (NBO) study was also performed using B3LYP/6-31 + G(d,p) method. Correlations between the proton and carbon-13 experimental chemical shifts and the GIAO NMR calculations are in good agreement and these values have been used for the definitive signal assignments to the corresponding structures. Electronic absorption spectra of DBNP has been calculated by using CIS-DFT method based on the B3LYP/6-311++G (d,p) level of the optimized structure in gas phase.

Straightforward green synthesis of indeno-furan carboxylates from ninhydrin and β-ketoesters: X-Ray crystal structure, Hirshfeld and DFT investigations

The diversity of the response of ninhydrin towards β-ketoesters was investigated. Indeno[1,2-b]furan-3-carboxylate 3 was obtained from ethyl acetoacetate via stirring in water for 15 min, whereas, in case of ethyl benzoylacetate afforded the 2-(2‑hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-3-oxo-3-phenylpropanoate 2 in water for longer time about 6 h . Reaction of ninhydrin with ethyl benzoylacetate in a mixture of acetic acid/water/methanol afforded the compound 4. The different types of intermolecular interactions controlling the molecular packing of the studied crystal structures were analyzed using Hirshfeld calculations. The results shed the light on the importance of O…H, H…H and H…C interactions on the crystal stability. The minimum energy structures were predicted using DFT calculations and were found very well matched with the corresponding X-ray structures. The electronic properties HOMO, LUMO, dipole moment, MEP (molecular electrostatic potential) map and the molecular reactivity descriptors were calculated and compared. The GIAO NMR chemical shifts were calculated and the results correlated well with the experimental data and the correlation coefficients were found close to 1.

Characterization of Microbial Degradation Products of Steviol Glycosides

Steviol glycosides were subjected to bacteria present in a soil sample collected from a Stevia plantation in Paraguay. During the incubation experiments, next to the aglycon steviol, steviol degradation products were also formed. X-ray analysis and NMR methods in combination with chemical synthesis and GIAO NMR calculations were used to fully characterize the structure of these compounds as a tricyclic ketone and the corresponding reduced form. They were nicknamed monicanone and monicanol. The latter has the (S)-configuration at the alcohol site.

Absolute Structure Determination and Kv1.5 Ion Channel Inhibition Activities of New Debromoaplysiatoxin Analogues.

Potassium channel Kv1.5 has been considered a key target for new treatments of atrial tachyarrhythmias, with few side effects. Four new debromoaplysiatoxin analogues with a 6/6/12 fused ring system were isolated from marine cyanobacterium Lyngbya sp. Their planar structures were elucidated by HRESIMS, 1D and 2D NMR. The absolute configuration of oscillatoxin J (1) was determined by single-crystal X-ray diffraction, and the absolute configurations of oscillatoxin K (2), oscillatoxin L (3) and oscillatoxin M (4) were confirmed on the basis of GIAO NMR shift calculation followed by DP4 analysis. The current study confirmed the absolute configuration of the pivotal chiral positions (7S, 9S, 10S, 11R, 12S, 15S, 29R and 30R) at traditional ATXs with 6/12/6 tricyclic ring system. Compound 1, 2 and 4 exhibited blocking activities against Kv1.5 with IC50 values of 2.61 ± 0.91 µM, 3.86 ± 1.03 µM and 3.79 ± 1.01 µM, respectively. However, compound 3 exhibited a minimum effect on Kv1.5 at 10 µM. Furthermore, all of these new debromoaplysiatoxin analogs displayed no apparent activity in a brine shrimp toxicity assay.

Forrestiacids A and B, Pentaterpene Inhibitors of ACL and Lipogenesis: Extending the Limits of Computational NMR Methods in the Structure Assignment of Complex Natural Products

AbstractForrestiacids A (1) and B (2) are a novel class of [4+2] type pentaterpenoids derived from a rearranged lanostane moiety (dienophile) and an abietane unit (diene). These unprecedented molecules were isolated using guidance by molecular ion networking (MoIN) from Pseudotsuga forrestii, an endangered member of the Asian Douglas Fir Family. The intermolecular hetero‐Diels–Alder adducts feature an unusual bicyclo[2.2.2]octene ring system. Their structures were elucidated by spectroscopic analysis, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism calculations, and X‐ray diffraction analysis. This unique addition to the pentaterpene family represents the largest and the most complex molecule successfully assigned using computational approaches to predict accurately chemical shift values. Compounds 1 and 2 exhibited potent inhibitory activities (IC50s <5 μM) of ATP‐citrate lyase (ACL), a new drug target for the treatment of glycolipid metabolic disorders including hyperlipidemia. Validating this activity 1 effectively attenuated the de novo lipogenesis in HepG2 cells. These findings provide a new chemical class for developing potential therapeutic agents for ACL‐related diseases with strong links to traditional medicines.

Forrestiacids A and B, Pentaterpene Inhibitors of ACL and Lipogenesis: Extending the Limits of Computational NMR Methods in the Structure Assignment of Complex Natural Products.

Forrestiacids A (1) and B (2) are a novel class of [4+2] type pentaterpenoids derived from a rearranged lanostane moiety (dienophile) and an abietane unit (diene). These unprecedented molecules were isolated using guidance by molecular ion networking (MoIN) from Pseudotsuga forrestii, an endangered member of the Asian Douglas Fir Family. The intermolecular hetero-Diels-Alder adducts feature an unusual bicyclo[2.2.2]octene ring system. Their structures were elucidated by spectroscopic analysis, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism calculations, and X-ray diffraction analysis. This unique addition to the pentaterpene family represents the largest and the most complex molecule successfully assigned using computational approaches to predict accurately chemical shift values. Compounds 1 and 2 exhibited potent inhibitory activities (IC50 s <5 μM) of ATP-citrate lyase (ACL), a new drug target for the treatment of glycolipid metabolic disorders including hyperlipidemia. Validating this activity 1 effectively attenuated the de novo lipogenesis in HepG2 cells. These findings provide a new chemical class for developing potential therapeutic agents for ACL-related diseases with strong links to traditional medicines.

Sensitivity Analysis of DP4+ with the Probability Distribution Terms: Development of a Universal and Customizable Method.

DP4+ is a popular tool for structural elucidation using GIAO NMR calculations. The method was built with 16 statistical parameters [μ,σ,ν], which depend on the level of theory. Herein, we deeply analyzed the sensitivity of DP4+ when using improper [μ,σ,ν] sets, a common situation found in the literature. The results led us to develop a customizable DP4+ methodology that allows preliminary calculations at any desired level of theory using a small set of training molecules.

Opportunities and Limitations for Assigning Relative Configurations of Antibacterial Bislactones using GIAO NMR Shift Calculations.

Four new bislactones, dihydroacremonol (1), clonostachyone (2), acremodiol B (3), and acremodiol C (4), along with one known compound, hymeglusin (5), were isolated from cultures of two fungal strains (MSX59876 and MSX59260). Both strains were identified based on phylogenetic analysis of molecular data as Clonostachys spp.; yet, they biosynthesized a suite of related, but different, secondary metabolites. Given the challenges associated with elucidating the structures and configurations of bislactones, GIAO NMR calculations were tested as a complement to traditional NMR and HRESIMS experiments. Fortuitously, the enantiomer of the new natural product (4) was known as a synthetic compound, and the predicted configuration from GIAO NMR calculations (i.e., for the relative configuration) and optical rotation calculations (i.e., for the absolute configuration) matched those of the synthesis product. These results engendered confidence in using similar procedures, particularly the mixture of GIAO NMR shift calculations coupled with an orthogonal technique, to predict the configuration of 1-3; however, there were important limitations, which are discussed for each of these. The metabolites displayed antimicrobial activities, with compounds 1 and 4 being the most potent against Staphylococcus aureus with MICs of 1 and 4 μg/mL, respectively.

Chlorinated bianthrones from the cyanolichen Nephroma laevigatum

While depsidones, depsides or dibenzofuran-like compounds dominate the chemical composition of lichens, the cyanolichen Nephroma laevigatum affords a diversity of quinoid pigments represented by chlorinated anthraquinones derived from emodin and new bianthrones resulting from the homo- or heterodimerization of monomers. Bianthrones were pointed out from the dichloromethane extract by MS/MS-based molecular networking, then isolated and characterized on the basis of extensive spectroscopic analyzes and GIAO NMR shift calculation followed by CP3 analyzes.

Crystal structure, DFT, antimicrobial, anticancer and molecular docking of (4E)-4-((aryl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one

The Schiff bases (4E)-4-((aryl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one 3 were synthetized by reaction of aromatic aldehydes 1 and 4-aminoantipyrine 2. Compounds 3 were fully characterized by FTIR, 1H, 13C and DEPT-135 NMR spectroscopies, elemental analyses and also by single crystal X-ray diffraction. Hirshfeld surface analysis was used to quantify the intermolecular interactions in the studied compounds. The H⋯H, O⋯H and C⋯H contacts as well as the some π-π stacking interactions are the most important intermolecular forces in their crystal structures. The calculated vibrational frequencies and GIAO NMR chemical shifts were used to describe the FTIR characteristics and NMR spectra. Compound 3b showed better antimicrobial activity than 3a. Further colorimetric assays for assessing cell metabolic activity were utilized to explore the potential of both compounds as anticancer drugs. Our results showed a potential of 3b as an anticancer drug on HeLa cells at high concentrations which is explained by the molecular docking calculation using MOE program.

Cytotoxic Sesquiterpenoid Quinones and Quinols, and an 11-Membered Heterocycle, Kauamide, from the Hawaiian Marine Sponge Dactylospongia elegans.

Several known sesquiterpenoid quinones and quinols (1–9), and kauamide (10), a new polyketide-peptide containing an 11-membered heterocycle, were isolated from the extracts of the Hawaiian marine sponge Dactylospongia elegans. The planar structure of 10 was determined from spectroscopic analyses, and its relative and absolute configurations were established from density functional theory (DFT) calculations of the GIAO NMR shielding tensors, and advanced Marfey’s analysis of the N-MeLeu residue, respectively. Compounds 1 and 3 showed moderate inhibition of β-secretase 1 (BACE1), whereas 1–9 exhibited moderate to potent inhibition of growth of human glioma (U251) cells. Compounds 1–2 and 4–7 were also active against human pancreatic carcinoma (Panc-1) cells.

Further terpenoids from Euphorbia tirucalli

The phytochemical investigation of Euphorbia tirucalli L. (Euphorbiaceae) yielded four new compounds, including a rare cadalene-type sesquiterpene (tirucadalenone), two tirucallane triterpenoids, euphorol L and euphorol M, with the latter being described as an epimeric mixture, and a euphane triterpene, namely, euphorol N, together with 7 known compounds. Their structures and absolute configurations were elucidated from analysis of 1D (1H, J-modulated 13C) and 2D NMR (HSQC, HMBC and NOESY), high-resolution mass spectrometry (HRESIMS), optical rotation, and GIAO NMR shift calculation followed by CP3 analysis, along with comparison with literature reports. All these compounds were tested for cytotoxicity against K562, MCF-7 and/or and HepG2 tumor cell lines. Only tirucadalenone displayed a mild cytotoxic activity.

Irpexolidal Represents a Class of Triterpenoid from the Fruiting Bodies of the Medicinal Fungus Irpex lacteus.

Irpexolidal (1), a triterpenoid with an unprecedented carbon skeleton, along with its biogenetic-related compound irpexolide A (2), were isolated from the fruiting bodies of the medicinal fungus Irpex lacteus. Irpexolidal features a 6/5/6/5/6/5-fused polycyclic skeletal system which arises from the eburicane-type triterpene by a 6,7- seco-6,8- cyclo pattern. The structures of 1 and 2 were established by means of extensive spectroscopic techniques, ECD calculation, and DP4+ probability based on GIAO NMR chemical shift calculations. The plausible biosynthetic pathways for compounds 1 and 2 were proposed. Their biological activities were evaluated.

Computationally aided stereochemical assignment of undescribed bisabolenes from Calea urticifolia

Calea urticifolia (Mill.) DC. (Compositae) is a medicinal plant found in El Salvador. Calea is used in folkloric medicine as a psychoactive principle with calming effect, as well as in the treatment of diarrhea and fever. Three undescribed bisabolenes, named caleanolenes A-C, as well as, three known sesquiterpene lactones 2,3-epoxyjuanislamin, calealactone B, calein C, and the flavonoid acacetin, were isolated from the chloroform extract of the leaves of C. urticifolia. The chemical structures of the isolated compounds were determined on the basis of HRMS, IR, CD, and from 1D and 2D NMR spectroscopic studies. The absolute configurations of the caleanolenes have been partly established using GIAO NMR and ECD calculations. The isolated compounds were evaluated for cytotoxicity against the CA46 and Raji lymphoma, and the MCF7 breast cancer cell lines, with 2,3-epoxyjuanislamin showing the best activity in all cell lines (IC50 value range 2.9–12.3 μM).

Infrared and NMR Spectral Analyses and Computational Studies of 2-amino-3-methylbenzoic acid

Detailed infrared spectrum in gas phase, NMR spectra analyses and theoretical studies of 2-amino-3-methylbenzoic acid were performed with DFT/B3LYP/6-311G+(2d,p) level of method in Gaussian 09W. Ground state molecular geometries of monomeric and dimeric structures were calculated in vacuum and compared to the experimental XRD results. Potential energy surface graphics of the proton transfer and torsional tautomerism process were obtained. Also, HOMA aromaticity chancing graphics were drowned in mentioned process. The IR band assignments and the decompositions of potential energy for each band were done using theoretical calculations. 1H and 13C NMR chemical shifts analyses were performed by using GIAO NMR calculations with SCRF solvent model.

Alashinol H, an epoxylignan with an unusual six-membered cyclic hemiacetal from Syringa pinnatifolia

A new 7, 9′-epoxylignan, alashinol H (1), which features a rare six-membered cyclic hemiacetal, was isolated from the stem barks of Syringa pinnatifolia. The structure was elucidated based on spectroscopic data including HRESIMS and NMR. Its absolute configuration was resolved by GIAO NMR shifts and ECD calculations. A putative biosynthetic pathway of this compound is proposed. Alashinol H showed a moderate inhibitory effect against NO production in BV-2 murine microglia cells.

Antiplasmodial Securinega alkaloids from Phyllanthus fraternus: Discovery of natural (+)-allonorsecurinine

The chemical investigation of the antimalarial plant Phyllanthus fraternus G. L. Webster (Phyllanthaceae) resulted in the discovery of the Securinega alkaloid (+)-allonorsecurinine (1), previously reported as a synthetic compound, together with the known ent-norsecurinine (2), nirurine (3), bubbialine (4), epibubbialine (5) and the lignan phyllanthin (6). The structure and absolute configuration of the new compound were elucidated on the basis of extensive spectroscopic analysis, optical rotation, and GIAO NMR shift calculation followed by CP3 analysis. The antiplasmodial activity of these compounds was evaluated against chloroquine-resistant (W2) and -sensitive (3D7) strains of Plasmodium falciparum. Among them, ent-norsecurinine (2) and (+)-allonorsecurinine (1) showed the strongest activity (IC50: 1.14±0.32 and 2.57±0.53µM) respectively, against W2 but one of the weakest against 3D7.

Tautomerism aspect of thione-thiol combined with spectral investigation of some 4-amino-5-methyl-1,2,4-triazole-3-thione Schiff's bases

Reaction of 4-amino-3-methyl-1,2,4-triazole-5-thione with some substituted benzaldehydes in presence of catalytic amount of hydrochloric acid afforded the respective Schiff's bases 3a-e. Computational studies using DFT incorporating the B3LYP/6-311G(d,p) level of theory is used to predict the stability of the possible tautomers. Molecular modeling, natural charge calculations, NMR, Frontier molecular orbitals and electronic spectra were investigated. Analysis of the thermodynamic parameters of the thione-thiol tautomeric reactions of these derivatives was used to predict the tautomers stability. The thione tautomer is the most favored form in gas phase and in solution whatever the nature of solvent used. The electronic spectra were assigned based on the TD-DFT calculations. The GIAO NMR chemical shifts correlated well with the experimental data.

Antimicrobial Oligophenalenone Dimers from the Soil Fungus Talaromyces stipitatus.

New polyketide-derived oligophenalenone dimers, 9a-epi-bacillisporin E (1) and bacillisporins F-H (2-5), along with the known bacillisporin A (6), were isolated from the fungus Talaromyces stipitatus. Their structures and absolute configurations were determined on the basis of spectroscopic analyses, electronic circular dichroism, and GIAO NMR shift calculation followed by DP4 analysis. The antimicrobial activity of these compounds was evaluated against a panel of human pathogenic bacteria. Among them, bacillisporin H (5) exhibited antimicrobial activity together with modest cytotoxicity against HeLa cells.