Novel polycyclic polyprenylated acylphloroglucinols from Hypericum sampsonii

Four new polycyclic polyprenylated acylphloroglucinols with a tricyclo[4.3.1.1^5,7]undecane skeleton, hypersampsones N–Q (1–4), together with four know compounds (5–8), were isolated from the aerial parts of Hypericum sampsonii. Compound 1 bearing a rare 20, 25-epoxy group with the losing of C-21–23 in isopentenyl. An unusual 21, 24-epoxy group was found in the structure of 2. All structures were elucidated by extensive NMR spectroscopic methods. The absolute configurations of new compounds were determined by ECD calculation.     

Bioassay and UPLC-Q-Orbitrap-MS/MS guided isolation of polycyclic polyprenylated acylphloroglucinols from St. John's wort and their neuroprotective activity

St. John’s wort (Hypericum perforatum L.) is a popular dietary supplement ingredient used for the treatment of mild-to-moderate depression in the United States and Germany. Reported studies mainly focused on the biological evaluation and mechanism study of its crude extracts or two main components (namely, hypericin and hyperforin). However, it is unclear whether other phytochemicals including polycyclic polyprenylated acylphloroglucinols (PPAPs) contributed to the neuroprotective effects of H. perforatum. Here, bioassay and ultra performance liquid chromatography–quadrupole orbitrap mass spectrometry (UPLC-Q-Orbitrap-MS/MS) guided isolation were applied to discover bioactive PPAPs from the crude extracts of H. perforatum. A new PPAP, named hyperforen A (2), along with nine known PPAPs (1 and 3–10), were identified from an ethyl acetate extract of H. perforatum. To the best of our knowledge, compound 2 represents the first PPAP with an unprecedented bicyclo[7.3.0]dodecane core. The chemical structures of the isolates were elucidated by extensive spectroscopic analysis and electronic circular dichroism calculations. Moreover, compounds 1–3, 6, and 10 (10 μM) exhibited significant neuroprotective effects against corticosterone-induced injury in PC12 cells. Fingings from the current study suggest that bioactive PPAPs from H. perforatum are promising compouds for the management of depression.     

A new approach for the construction of a highly congested bicyclic system in polycyclic polyprenylated acylphloroglucinols (PPAPs)

A highly congested bicyclo[3.3.1]nonanone core of polycyclic polyprenylated acylphloroglucinols was constructed using a stereoselective Claisen rearrangement and an intramolecular aldol reaction as the key steps. The stereochemistry of C-4 appeared to control the ground state conformation of the cyclohexenone core, which determined the diastereoselectivity in the Claisen rearrangement.     

Qualitative and quantitative analysis of polycyclic polyprenylated acylphloroglucinols from Garcinia species using ultra performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry

Polycyclic polyprenylated acylphloroglucinols (PPAPs) are a group of natural products isolated from different Garcinia species with a wide range of important biological activities. In this study, an ultra performance liquid chromatography (UPLC) coupled to photodiode-array detection and quadrupole time-of-flight mass spectrometry (Q-TOF) method was developed to characterize 16 PPAPs in 10 Garcinia species. In source dissociation techniques based on cone voltage fragmentation were used to fragment the deprotonated molecules and multiple mass spectrometry (MS/MS) using ramping collision energy were used to further break down the resulting product ions. The resulting characteristic fragment ions were generated by cleavage of C1-C5 bond and C7-C8 bond through concerted pericyclic reaction, which is especially valuable for differentiating three types of PPAPs isomers. As such, two new PPAPs isomers present in minor amount in the extracts of Garcinia oblongifolia were tentatively characterized by comparing their tandem mass spectra to the known ones. In addition, an UPLC-Q-TOF-MS method was validated for the quantitative determination of PPAPs. The method exhibited limits of detection from 2.7 to 21.4 ng mL⁻¹ and intra-day and inter-day variations were less than 3.7% and the recovery was in the range of 89-107% with RSD less than 9.0%. This UPLC-Q-TOF-MS method has successfully been applied to quantify 16 PPAPs in 32 samples of 10 Garcinia species, which were found to be a rich source of PPAPs.     

Diagnostic filtering to screen polycyclic polyprenylated acylphloroglucinols from Garcinia oblongifolia by ultrahigh performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry

A novel multistage MS approach, insource collision-induced dissociation (CID) combined with Time Aligned Parallel (TAP) fragmentation, was established to study the fragmentation behavior of polycyclic polyprenylated acylphloroglucinols (PPAPs), which could provide a more reliable fragmentation relationship between precursor and daughter ions. The diagnostic ions for different subtypes of PPAPs and their fragmentation behaviors have been summarized. Moreover, a new and reliable multidimensional analytical workflow that combines ultrahigh performance liquid chromatography (UHPLC), data-independent mass spectrometry (MS^E), and tandem MS with ion mobility (IM) has been optimized and established for the analysis of PPAPs in the plant Garcinia oblongifolia by diagnostic filtering. Diagnostic fragment ions were used to selectively screen PPAPs from extracts, whereas IM coupled to MS was used to maximize the peak capacity. Under the optimized UHPLC-IM-MS^E and UHPLC-IM-MS/MS method, 140 PPAPs were detected from the crude extract of G. oblongifolia, and 10 of them were unambiguously identified by comparing them to the reference compounds. Among those PPAPs, 7 pairs of coeluting isobaric PPAPs that were indistinguishable by conventional UHPLC-HRMS alone, were further resolved using UHPLC-IM-MS. It is anticipated that the proposed method will be extended to the rapid screening and characterization of the other targeted or untargeted compounds, especially these coeluting isomers in complex samples.     

Structural elucidation of dioxa‐cage compounds from tetrahydroisobenzofuran‐1(3H)‐one: analysis of NMR data and GIAO chemical shifts calculations

The polycyclic compounds, especially the dioxa‐cages, have attracted considerable attention in recent years. In our work, a series of 9β‐substituted 3‐oxo‐4,11‐dioxatetracyclo[5.2.1.1^5,8.0^2,6]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3‐hydroxy‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.     

Configurational analysis of the natural product passifloricin A by quantum mechanical C NMR GIAO chemical shift calculations

Quantum chemical calculations at mPW1PW91 level, with full geometry optimization, using the 6-31g(d) basis set, and GIAO (gauge including atomic orbitals) ¹³C NMR chemical shifts using the 6-31g(d,p) basis set, are here utilized as a support to define the configurational features of the natural product passifloricin A, whose previously proposed relative configuration has been recently shown, by synthetic studies, to be incorrect. This study suggests that the relative stereostructure for passifloricin A corresponds to the δ-lactone of the (5R,7R,9S,11R)-tetrahydroxyhexacos-2-enoic acid.     

Perfluoropoly-ether/peroxide compounds: spectroscopic studies and quantum chemical calculations

Perfluoropolyethers (PFPEs) are a class of high performance materials used in a wide range of applications (refrigeration, lubrication, semiconductor industry, etc.). PFPEs containing peroxidic units are intermediate materials for the preparation of commercial end products. In this work we study the spectroscopic properties of ether and peroxides linkages in this class of compounds; nuclear magnetic resonance (NMR) spectra are discussed, FT-Raman data presented. Quantum chemical calculations on model molecules were used as a tool for the interpretation of the Raman experimental data and physical-chemical properties.     

Quantum mechanical calculations of conformationally relevant 1H and 13C NMR chemical shifts of N-, O-, and S-substituted calixarene systems

QM GIAO calculations of (13)C and (1)H chemical shift values of the ArCH(2)Ar group in N-, O-, and S-substituted calixarene systems were performed with a hybrid DFT functional MPW1PW91 and 6-31G(d,p) basis set. A good reproduction of experimental data was obtained for some representative calixarenes and for a series of simplified calixarene models. This allowed the derivation of chemical shift surfaces versus phi and chi dihedral angles. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated.     

Stemmosides C and D, two novel unusual pregnane glycosides from Solenostemma argel: structural elucidation and configurational study by a combined NMR-quantum mechanical strategy

Stemmosides C and D, two novel pregnane glycosides characterized by an unusual C-17 side chain were isolated from the pericarps of Solenostemma argel. In addition, stemmoside D displays an uncommon 14β proton configuration, apparently being the first pregnane isolated from plants known to have a 15 keto, cis CD ring junction. Their structures have been established by ESIMS and NMR experiments. The relative configuration of the molecules was determined using a strategy based on the simulation of ¹H, ¹³C, and J coupling NMR parameters. DFT calculations of ¹H and ¹³C chemical shifts, and of the ¹H homonuclear spin–spin coupling constants were performed with the mPW1PW91 functional using the 6-31G(d,p) basis set on the fully optimized geometries of all the possible stereoisomers.     

1-Boryl-3,4-dimethylphosphole trimer: Synthesis, crystal structure and quantum chemical calculations

A novel cycloadduct of 1-boryl-3,4-dimethylphosphole was prepared by reaction of 3,4-dimethylphospholyl anion with monobromoborane-methylsulfide complex (CH₃)₂S · BH₂Br at −60 °C. It was characterized as a six-membered trimer by spectroscopic means, and its structure confirmed by an X-ray crystal analysis and quantum chemical calculations. Density functional theory calculations (B3LYP) showed that the cyclic trimer is by far more stable than the monomer, dimers or open-chain forms. Various molecular and spectroscopic properties of the borylphosphole monomer and trimer were evaluated. In particular, the changes of the ³¹P NMR chemical shifts upon oligomerization were examined. The six-membered ring was demonstrated to exist preferentially in a chair-like conformation. Computed NMR chemical shifts (¹H, ¹³C and a lesser extent ³¹P) appear to be a highly sensitive analytical tool for distinguishing ring conformations having only small energy differences.     

Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals

We describe the implementation of a parallel, in-core, integral-direct Hartree-Fock and density functional theory code for the efficient calculation of Hartree-Fock wave functions and density functional theory. The algorithm is based on a parallel master-slave algorithm, and the two-electron integrals calculated by a slave are stored in available local memory. To ensure the greatest computational savings, the master node keeps track of all integral batches stored on the different slaves. The code can reuse undifferentiated two-electron integrals both in the wave function optimization and in the evaluation of second-, third-, and fourth-order molecular properties. Superlinear scaling is achieved in a series of test examples, with speedups of up to 55 achieved for calculations run on medium-sized molecules on 16 processors with respect to the time used on a single processor.     

Spectroscopic and structural elucidation of L-tyrosine-containing dipeptides valyl-tyrosine and tyrosyl-alanine: solid-state IR-LD spectroscopy, quantum chemical calculations and vibrational analysis

L-Tyrosine-containing dipeptides valyl-tyrosine (H-Val-Tyr-OH) and tyrosyl-alanine (H-Tyr-Ala-OH) are characterized structurally by means of quantum chemical ab initio calculations and solid-state linear-dichroic infrared (IR-LD) spectroscopy. The IR-characteristic bands are assigned by application of reducing-difference procedure for polarized IR-spectra interpretation. Infrared data obtained are supported as well by the made vibrational analysis. The structures of both peptides are predicted on the basis of conformational analysis and structural information, obtained by the shown IR-spectroscopic tool.     

Facile structural elucidation of imidazoles and oxazoles based on NMR spectroscopy and quantum mechanical calculations

The reaction of 1,2,3-tricarbonyl derivatives with hexamethylenetetramine and ammonium acetate in acetic acid provides an unambiguous approach to the synthesis of imidazoles, whereas the Bredereck reaction of α-haloketones in formamide, yields both imidazoles and oxazoles. Herein we describe a facile methodology for distinguishing between these heterocyclic compounds based on a combination of NMR spectroscopy and quantum mechanical calculations. In the NMR data the oxazole C-2 has a chemical shift of ca. 150 ppm whereas in the imidazoles it is found at ca. 135 ppm, with a ¹J_C-H of ca. 250 Hz for the oxazoles and ca. 210 Hz for the imidazoles. ¹J_C-H values can be easily obtained from a gated-decoupled ¹³C spectrum, and even more trivially, from the separation of the H-2 ¹³C satellites in the ¹H spectra. Additionally, the computed NMR data, obtained from density functional theory, are found to be in good agreement with the experimental data and serve as valuable tools in identifying the products of the Bredereck reaction.     

Structural elucidation,antioxidant and hepatoprotective activities of chemical composition from Jinsi Huangju (Chrysanthemum morifolium) flowers

Six new compounds (huangjusus A-F), including three caffeic acid glycosides (1–3), one quinic acid derivative (4), one dihydroflavone glycoside (11) and one monoterpene (31), together with thirty-eight known compounds (5–10, 12–30, 32–44), were obtained from “Jinsi Huangju” (Chrysanthemum morifolium Ramat.) flowers. Their structures were elucidated on the basis of the data obtained from different spectroscopic techniques. Among these compounds, five new (1–4 and 11) and ten known (5–9, 12, 13, 17, 40, and 42) compounds demonstrated significant 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging effects with IC₅₀ values of 4.22–19.90 μM. Furthermore, three new compounds (1, 11, and 31) and seven known compounds (13, 19, 21, 29, 30, 39, and 41) exhibited potent hepatoprotective activities against N-acetyl-p-aminophenol (APAP)-induced toxicity in HepG2 cells with the cell survival rates of 61.53 %, 63.55 %, 60.01 %, 63.05 %, 59.75 %, 59.15 %, 61.07 %, 62.72 %, 58.86 %, and 58.76 % (positive control bicyclol, 58.41 %), respectively, at a concentration of 10 μM. These results indicate the potency of the flowers against radicals and in hepatoprotections.     

Conformational and thermodynamic analysis of the COXIB scaffold using quantum chemical calculations

Selective cyclo‐oxygenase‐2 inhibitors (COXIBs) are prominent members of the nonsteroidal anti‐inflammatory drugs. The neutral and protonated COXIB scaffold has been subjected to molecular computations in the gas phase and implicit solvent to measure the relative changes in the thermodynamic functions, enthalpy (H_rel), potential energy (U_rel), Gibbs free energy (G_rel) and entropy (S_rel) induced by selected substituents. Conformational analysis of the COXIB scaffold indentified four pairs of atropisomeric conformers (from I, I′ to IV, IV′) associated with a molecular structure containing a double rotor system. All conformers had similar stability. Para‐substitution with substituents that cover a wide range of Hammett sigma values did not alter the geometries of the neutral COXIB conformers; however, the protonated COXIB scaffold was showed an increase in structural and thermodynamic perturbations due to inductive effects. Flexibility and structural resilience of the COXIB scaffold under the conditions studied herein could be an important feature of the COXIBs, especially considering the previously proposed flexibility of the cyclo‐oxygenase binding site. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structural study of 8-azole derivatives of protoberberine alkaloids: experimental and quantum chemical approach

New derivatives of protoberberine alkaloids were prepared by nucleophilic addition of some azoles (differing in bulkiness) to the iminium functionality of the quaternary protoberberine alkaloids. Compounds were structurally characterized mainly by ¹H and ¹³C NMR spectroscopy, and the structure of 8-carbazol-1-yl-7,8-dihydroberberine was determined using single-crystal X-ray diffraction. Additionally, conformational behaviors of five derivatives varying in bulkiness of the azole moiety have been investigated by low temperature NMR spectroscopy and quantum chemical calculations. Ring current effects of pyrrole and carbazole moieties on selected ¹H NMR resonances have been characterized, visualized, and discussed.     

Solid-state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside

Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.     

Structural study of oxalamide compounds: H, C, and DFT calculations

The conformational properties of some N-alkyl, N,N′-dialky, and tetraalkyloxalamides have been investigated, in vacuo and in solvent using DFT methods at the B3LYP/6-31G^∗∗ computational level. Special emphasis has been given on oxalamides with substituents of the type -CH₂CH₂OH. In oxalamides with the N-H group (N-alkyl and N,N′-dialky), the most stable conformations are those in which the oxalamide moiety adopts a planar s-trans arrangement and the amide bonds are trans. A different situation appears in the case of tetraalkyloxalamides, in which the oxalamide moiety always adopts a skewed arrangement and there are conformations with similar energy. A careful study of ¹³C and ¹H NMR spectra together with theoretical calculations (GIAO method) allowed the assignment of the signals of these conformers. The presence of the -CH₂CH₂OH chain produces numerous rotamers. The most stable rotamers, in vacuo, are those with strong intramolecular hydrogen bonds, however in solvent, hydrogen bonds are not crucial to establish the most stable specie and depend on the solvent used.