NMR Chemical Shift Calculations Research Articles

A new phenol derivative isolated from mangrove-derived fungus Eupenicillium sp. HJ002

A new phenol derivative, 3-chloro-5-hydroxy-4-methoxyphenylacetic acid methyl ester (1), along with five known compounds methyl 4-hydroxyphenylacetate (2), cytosporone B (3), (R)-striatisporolide A (4), (R)-butanedioic acid (5) and ergosterol (6) were isolated from the mangrove-derived fungus Eupenicillium sp. HJ002. Their structures were established by spectroscopic methods, GIAO based 13C NMR chemical shift calculations and comparison with the data of literature. Compounds 1–5 were isolated from Xylocarpus granatum Koening-derived fungus for the first time.

Synthesis and structural elucidation of a phthalide analog using NMR analysis and DFT calculations.

Phtalides are secondary metabolites found in several fungi with a wide range of biological activities. A novel phthalide analog was synthesized by Diels-Alder reaction between cyclopentadiene and 3,4-dichlorofuran-2(5H)-one. Quantum mechanical calculations were used in conjunction with the spectrometric methods to determine the structure of the title compound. The calculated NMR chemical shifts for eight candidate pairs of enantiomers were compared with the experimental NMR chemical shifts applying the DP4 probability and mean absolute errors methodology. DP4 analysis using 1 H and 13 C NMR chemical shifts without assignment of the signals presented 100% probability for the correct candidate structure 3d, proving the consistency of the method even without spectra interpretation. Results from theoretical calculation and NMR spectra interpretation were in agreement to the structure of rac-(3aR,4S,4aS,5R,8S,8aR,9R,9aS)-3a,9a-dichloro-3a,4,4a,5,8,8a,9,9a-octahydro-4,9:5,8-dimethanonaphtho[2,3-c]furan-1(3H)-one.

Three new polyoxygenated bergamotanes from the endophytic fungus Penicillium purpurogenum IMM 003 and their inhibitory activity against pancreatic lipase.

Purpurolides D-F (1-3), three new polyoxygenated bergamotanes bearing a 6/4/5/5 tetracyclic ring system, were isolated from the endophytic fungus Penicillium purpurogenum IMM 003. Their structures were unambiguously elucidated based on extensive spectroscopic data analyses, 13C NMR chemical shifts calculations coupled with the DP4+ probability method, and the calculated and experimental electronic circular dichroism (ECD) spectra. Compounds 1-3 showed significant inhibitory activity against pancreatic lipase (PL). The result highlights that the presence of 3-hydroxylated decanoic acid moiety at C-14 is important for increasing the inhibition potency against PL.

Correction to "Calculation of 15N NMR Chemical Shifts in a Diversity of Nitrogen-Containing Compounds Using Composite Method Approximation at the DFT, MP2, and CCSD Levels".

Correction to "Calculation of 15N NMR Chemical Shifts in a Diversity of Nitrogen-Containing Compounds Using Composite Method Approximation at the DFT, MP2, and CCSD Levels".

Quantum chemical calculations of 31P NMR chemical shifts of P-donor ligands in platinum(II) complexes.

This work aims to find the most suitable method that is practically applicable for the calculation of 31P NMR chemical shifts of Pt(II) complexes. The influence of various all-electron and ECP basis sets, DFT functionals, and solvent effects on the optimized geometry was tested. A variety of combinations of DFT functionals BP86, B3LYP, PBE0, TPSSh, CAM-B3LYP, and ωB97XD with all-electron basis sets 6-31G, 6-31G(d), 6-31G(d,p), 6-311G(d,p), and TZVP and ECP basis sets SDD, LanL2DZ, and CEP-31G were used. Chemical shielding constants were then calculated using BP86, PBE0, and B3LYP functionals in combination with the TZ2P basis. The magnitude of spin-orbit interactions was also evaluated.

Investigation of backbone dynamics and local geometry of bio-molecules using calculated NMR chemical shifts and anisotropies.

Prerequisite for chemical shift (CS) and CS tensor calculations are highly refined structures defining the molecular surroundings of the nuclei under study. Here, we present geometry optimizations with 13C and 15N CS constraints for large bio-molecules like peptides and proteins. The method discussed here provides both, refined structures and chemical shift tensors. Furthermore, since the experimental resonances of aligned systems are related to CS tensors, they strongly depend on the orientation and motion of molecules, their fragments, functional groups and moieties. For efficient CS calculations we apply a semi-empirical approach-the bond polarization theory (BPT). The BPT relies on linear bond polarization parameters and we present a new set of parameters based on ab initio second-order Møller-Plesset perturbation theory calculations. The new parametrization extends the applicability of the BPT approach to a wide range of organic molecules and bio-polymers. Here, the method has been applied to the protein ubiquitin and the membrane-active peptide gramicidin A (dimer) in oriented bilayers. The calculated 13C and 15N CS values of best-refined structures published until now gave a large scatter with respect to the experiment. It will be shown that BPT CS optimizations can reduce these errors to values near the experimental uncertainty. In combination with molecular dynamics with orientational constraints it is possible to study motional dynamics and BPT calculations can provide residual chemical shift anisotropies.

Phenylpropanoid and dibenzofuran derivatives from Crataegus pinnatifida with antiproliferative activities on hepatoma cells

Eleven aromatic compounds, including four pairs of undescribed phenylpropanoids and two undescribed dibenzofurans (1a/1b-4a/4b and 5-6), were isolated from the fruits of C. pinnatifida. Their structures were established by extensive spectroscopic analyses. Their relative and absolute configurations were determined by the assistance of quantum chemical calculations of NMR chemical shifts and electronic circular dichroism (ECD). All isolates were screened for the cytotoxicity against two human hepatoma cell lines, HepG2 and Hep3B. It was found that compound 7 exhibited noticeable cytotoxicity against both cells with the IC50 values of 12.24 (HepG2) and 24.90 (Hep3B) μM. Further Annexin VFITC/ PI staining assay suggested that 7 could induce apoptosis in a concentration-dependent manner to exert antiproliferative activities on hepatoma cells.

Characterization of Leptazolines A-D, Polar Oxazolines from the Cyanobacterium Leptolyngbya sp., Reveals a Glitch with the "Willoughby-Hoye" Scripts for Calculating NMR Chemical Shifts.

The bioactivity-guided examination of a Leptolyngbya sp. led to the isolation of leptazolines A-D (1-4), from the culture media, along with two degradation products (5 and 6). Density functional theory nuclear magnetic resonance calculations established the relative configurations of 1 and 2 and revealed that the calculated shifts depended on the operating system when using the "Willoughby-Hoye" Python scripts to streamline the processing of the output files, a previously unrecognized flaw that could lead to incorrect conclusions.

New norlignan enantiomers from the fruit of Crataegus pinnatifida with neuroprotective activities

(±)-Crataegusnorin A (1a/1b) and B (2a/2b), two pairs of rare 8,9′-epoxy-type norlignan enantiomers featuring a γ-butyrolactone ring, were isolated from the fruit of Crataegus pinnatifida. Their structures were determined via extensive spectroscopic analyses. Gauge-independent atomic orbital (GIAO) NMR chemical shift calculations, combined with the advanced statistical method DP4+ were employed to establish the relative configurations of four compounds. Next, chiral separation was accomplished by chiral chromatographic column and the absolute configurations of the four compounds were unambiguously assigned by comparison between their experimental electronic circular dichroism curves with the quantum-mechanically calculated curves based on time-dependent density functional theory (TDDFT). All the isolates were evaluated for their neuroprotective activities against H2O2-induced cell injury in human neuroblastoma SH-SY5Y cells. The results showed that two pairs of enantiomers 1a/1b and 2a/2b displayed diff ;erent effect on neuroprotective activity. Among them, compound 2a displayed the most potent neuroprotective effect. Further flow cytometry analysis indicated that 2a could protect SH-SY5Y cells from oxidative damage through inhibiting cell apoptosis.

Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins

Quantum mechanics (QM) calculations are applied to examine 1H, 13C, 15N, and 31P chemical shifts of two phosphorylation sites in an intrinsically disordered protein region. The QM calculations employ a combination of (1) structural ensembles generated by molecular dynamics, (2) a fragmentation technique based on the adjustable density matrix assembler, and (3) density functional methods. The combined computational approach is used to obtain chemical shifts (i) in the S19 and S40 residues of the nonphosphorylated and (ii) in the pS19 and pS40 residues of the doubly phosphorylated human tyrosine hydroxylase 1 as the system of interest. We study the effects of conformational averaging and explicit solvent sampling as well as the effects of phosphorylation on the computed chemical shifts. Good to great quantitative agreement with the experiment is achieved for all nuclei, provided that the systematic error cancellation is optimized by the choice of a suitable NMR standard. The effect of the standard reference on the computed 15N and 31P chemical shifts is demonstrated by employing three different referencing methods. Error bars associated with the statistical averaging of the computed 31P chemical shifts are larger than the difference between the 31P chemical shift of pS19 and pS40. The sequence trend of 31P shifts therefore could not be reliably reproduced. On the contrary, the calculations correctly predict the change of the 13C chemical shift for CB induced by the phosphorylation of the serine residues. The present work demonstrates that QM calculations coupled with molecular dynamics simulations and fragmentation techniques can be used as an alternative to empirical prediction tools in the structure characterization of intrinsically disordered proteins.

Assignment of the stereostructures of sesquiterpenoids from the roots of Daphne genkwa via quantum chemical calculations

Five new guaiane-type sesquiterpenoids were obtained from the roots of Daphne genkwa. Their gross structures were established by extensive spectroscopic analyses. Attempts on the assignment of the relative configurations were unsuccessful when based on the NOESY correlations. Therefore, NMR chemical shift calculations based on the gauge independent atomic orbital (GIAO) method in combination with the statistical method DP4+ were employed to establish their relative configurations. Furthermore, the absolute configurations were determined by comparing the experimental and calculated electronic circular dichroism (ECD) using time-dependent density functional theory (TDDFT). The isolated compounds were screened for their cytotoxicity in vitro against two human hepatocellular carcinoma, HepG2 and Hep3B cell lines.

Theoretical calculations of 1H NMR chemical shifts for nitrogenated compounds in chloroform solution

In this work we report DFT and MP2 1H NMR calculations using the GIAO method and TMS as reference, for a series of nitrogenated compounds in chloroform solution to assess the ability of available theoretical models to reproduce experimental 1H NMR spectra measured in CDCl3 solution, focusing on CHn and N-H proton signals which are relevant in conformational analysis studies. The Polarizable Continuum Model (PCM) may not work successfully to predict N-H chemical shifts in solution. Only when a few explicit solvent molecules are used in DFT-PCM-CHCl3 geometry optimizations a good agreement with experimental N-H chemical shifts measured in solution is reached, indicating that this is a reliable computational procedure for the prediction of the full NMR spectra of organic molecules containing N-H group. However, finding adequate DFT optimized solvated solute structures which reproduce well both N-H and CHn proton NMR signals can become a hard-computational task.

Bioactive Polyketide Derivatives from the Mangrove-Derived Fungus Daldinia eschscholtzii HJ004.

Five new tetralones, daldiniones A-E (1-5), three new chromones, 7-hydroxy-5-methoxy-2,3-dimethylchromone (9), 5-methoxy-2-propylchromone (10), and 7-ethyl-8-hydroxy-6-methoxy-2,3-dimethylchromone (11), and two new lactones, helicascolides D and E (16 and 17), together with nine known metabolites (6-8, 12-15, and 18-19) were isolated from the mangrove-derived fungus Daldinia eschscholtzii HJ004. The structures and absolute configurations of the new compounds were determined by analyzing MS and NMR data and utilizing GIAO based 13C NMR chemical shift calculations and quantum chemical electronic circular dichroism (ECD) calculations. Compounds 9, 13, and 18 showed inhibitory activities against α-glucosidase with IC50 values of 13, 15, and 16 μM, respectively.

Chemical constituents of the root bark of Ulmus davidiana var. japonica and their potential biological activities

The root bark of Ulmus davidiana var. japonica (Ulmaceae), commonly known as yugeunpi, has been used as a traditional Korean medicine for the treatment of gastroenteric and inflammatory disorders. As part of continuing projects to discover bioactive natural products from traditional medicinal plants with pharmacological potential, phytochemical investigation of the root bark of this plant was carried out. This led to the successful isolation of a new chromane derivative (1) and 22 known compounds: catechin derivatives (2–5), megastigmane glycoside (6), dihydrochalcone glycosides (7 and 8), flavanone glycosides (9 and 10), coumarins (11 and 12), lignan derivatives (13–17), and phenolic compounds (18–23). The structure of the new compound (1) was determined with 1D and 2D NMR spectroscopy and HR-ESIMS, and its absolute configurations were achieved by chemical reactions and the gauge-including atomic orbital (GIAO) NMR chemical shifts calculations. All the isolated compounds were evaluated for their potential biological activities including neuro-protective, anti-neuroinflammatory, and anti-Helicobacter pylori activities. Among the isolates, compounds 1, 8, and 20 displayed stronger potency by causing a greater increase in the production and the activity of nerve growth factor (NGF) in C6 glioma cells (147.04 ± 4.87, 206.27 ± 6.70, and 143.70 ± 0.88%, respectively), whereas compounds 11, 14, and 19 inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated murine microglial cells (IC50 of 18.72, 12.31, and, 21.40 µM, respectively). In addition, compounds 1, 11, 18, and 20 showed anti-H. pylori activity with MIC values of 25 or 50 µM against two strains of H. pylori 51 and 43504. These findings provide scientific evidence that supports the traditional usage of U. davidiana var. japonica root bark in the treatment of gastroenteric and inflammatory disorders.

Two new secondary metabolites from a mangrove-derived fungus Cladosporium sp. JS1-2

One new pentenoic acid derivative, named 1,1'-dioxine-2,2'-dipropionic acid (1) and a new natural product, named 2-methylacetate-3,5,6-trimethylpyrazine (2), along with six known compounds (3-8), were obtained from the Cladosporium sp. JS1-2, an endophytic fungus isolated from the mangrove Ceriops tagal collected in South China Sea. Their structures were elucidated by detailed analysis of comprehensive spectroscopic data, and the structure of 1 was further determined by X-ray diffraction analyses. 13C NMR chemical shifts of structure 2 was further determined by GIAO based 13C NMR chemical shifts calculations. Compounds 1-4 and 6 showed growth inhibition activities against newly hatched larvae of Helicoverpa armigera Hubner with the IC50 values ranging from 100 to 150 μg ml-1. Compounds 1, 2, 4, 6 and 7 showed moderate antibacterial activities against Staphylococcus aureus with the MIC values of 25.0, 12.5, 6.25, 1.25, and 6.25 μg ml-1, respectively.

Interaction of pseudoephedrine and azithromycin with losartan: Spectroscopic, dissolution and permeation studies.

This study aims at investigating the potential effect of selected cationic drugs (azithromycin (AZN) and pseudoephedrine sulfate (PSD) on the dissolution profile and intestinal permeation of losartan potassium (LOS) that might occur due to ion pair salt formation. DSC, FT-IR and 1H NMR indicated the formation of ion pair salts between LOS and each of AZN and PSD. Based on NMR chemical shifts calculations, utilizing specialized software, the most likely structures of the salt were proposed and revealed interesting structural features. The obtained ion pair products were shown to have lower aqueous solubilities (water and phosphate buffer pH 6.8) and higher apparent partition coefficient values compared to the parent compound. Neither of the cations affected the dissolution of LOS tablet (Cozaar® 100 mg) in the studied media (HCl pH 1.2 and phosphate buffer pH 6.8). Interestingly, AZN significantly increased the dissolution of LOS in phosphate buffer pH 4.5 (f2 = 33), and an explanation based on distinguished association pattern between AZN and LOS (CH/π) was offered. Employing permeation test across Caco-2 cells monolayer, the apparent permeability coefficient (Papp) of LOS increased significantly (from 0.9 × 10-5 cm/s to 1.8 × 10-5 cm/s) in the presence of the selected cations. Therefore, while the employed cationic drugs were not shown to form ion pair salts under the in-vitro dissolution conditions, they may still participate in significant in-vivo interaction with LOS.

Computational Multinuclear NMR of Platinum Complexes: A Relativistic Four-Component Study.

The structures of 16 derivatives of cisplatin and transplatin were optimized at the DFT/dyall.ae2z levels, and their 1H, 15N, and 195Pt NMR chemical shifts were evaluated within the nonrelativistic and four-component relativistic approaches. Reliable correlations of calculated NMR chemical shifts with available experimental data were achieved by taking into account relativistic effects, solvent effects, and vibrational corrections.

Geometries and NMR properties of cisplatin and transplatin revisited at the four-component relativistic level

The equilibrium structures of cisplatin and transplatin were optimized, and their 1H, 15N, and 195Pt NMR chemical shifts were evaluated at both non-relativistic and fully relativistic four-component levels. Reliable correlations with experimental data were achieved at the DFT level with taking into account relativistic effects in calculations of both geometrical parameters and NMR chemical shifts.

Isocoumarindole A, a Chlorinated Isocoumarin and Indole Alkaloid Hybrid Metabolite from an Endolichenic Fungus Aspergillus sp.

Isocoumarindole A (1), a novel polyketide synthetase-nonribosomal peptide synthetase (PKS-NRPS) hybrid metabolite, was isolated from the endolichenic fungus Aspergillus sp. CPCC 400810. The structure of isocoumarindole A (1) was featured by an unprecedented skeleton containing chlorinated isocoumarin and indole diketopiperazine alkaloid moieties linked by a carbon-carbon bond, which was determined by a combination of spectroscopic analyses, Marfey's method, and calculations of NMR chemical shifts, ECD spectra, and optical rotation values. Isocoumarindole A showed significant cytotoxicity and mild antifungal activities.

Theoretical Study of Halogenated B12H nX(12- n)2- (X = F, Cl, Br).

The closoborane and their derivatives have attracted high interest due to their superionic conductivity. Very recently, high ionic conductivities have been reported for compounds containing the closoborane ion B12H122-. In this work, we address halogen-substituted ions B12H nX(12- n)2- ( n = 0-3, 6, 9-12 and X = F, Cl, Br) using DFT calculations to probe the structures, the chemical stability, and the electrochemical stability, as well as spectroscopic properties in view of potential future applications. Considering the theoretical reaction n/12 B12H122- + (12- n)/12 B12X122- → B12H nX(12- n)2-, it appears that for X = Cl and Br the compounds with n = 6 are stabilized by about 100 kJ/mol. The calculation of the vertical detachment energy (which is indirectly related to the electrochemical stability) shows an increasing stability with increasing halogen content. These results suggest that, for practical applications, it is likely that a partially halogenated ion offers the best compromise. The calculations of vibrational properties and NMR chemical shifts also reveal several systematic trends, which are discussed and compared to available literature values.