CD Calculations Research Articles

Isolation and characterization of sesquiterpenes from Celastrus orbiculatus and their antifungal activities against phytopathogenic fungi.

Celastrus orbiculatus is an insecticidal plant belonging to the Celastraceae family. In this survey on the secondary metabolites of plants for obtaining bioactive substances to serve agriculture, the chemical constituents of the fruits of C. orbiculatus were investigated. This phytochemical investigation resulted in the isolation of nine new and one known sesquiterpene. Their structures, especially the complicated stereochemical features, were elucidated on the basis of extensive NMR spectroscopic data analyses, time-dependent density functional theory CD calculations, and the CD exciton chirality method. Biological screenings disclosed that these sesquiterpenes showed antifungal activities against six phytopathogenic fungi. The results of our phytochemical investigation further disclosed the chemical components of C. orbiculatus, and biological screening implied that it may be potentially useful to protect crops against phytopathogenic fungi and the bioactive compounds may be regarded as candidate agents of antifungal agrochemicals for crop protection products.

Five New Acylphloroglucinol Glycosides from the Leaves of Eucalyptus robusta

Five new acylphloroglucinol glycosides, robustasides A-E (1-5), together with a known one (6), were isolated from the leaves of Eucalyptus robusta. The structures were elucidated on the basis of extensive spectroscopic and spectrometric analysis and chemical evidence. The absolute configuration of 1 was further determined by quantum chemical CD calculation.

Chiral/ring closed vs. achiral/open chain triazine-based organogelators: induction and amplification of supramolecular chirality in organic gels.

The purpose of this study is to compare the gelling behavior of two molecules: a chiral compound and its achiral counterpart. The chiral partner is characterized by a rigid, chiral pyrrolidine nucleus, while the achiral one contains a flexible diethanolamine moiety. The chiral compound is an already known good organogelator, but also the achiral compound shows remarkable gelling properties. Very interestingly, a small fraction of the chiral compound induces chirality and strong CD effects in its aggregates with the achiral one. The observed chirality amplification corresponds to a peculiar sergeant-and-soldier effect. Molecular modelling and CD calculations suggested a model for the supramolecular assembly of hetero-aggregates that fits the experimental data.

(+)- and (−)-Cajanusine, a Pair of New Enantiomeric Stilbene Dimers with a New Skeleton from the Leaves of Cajanus cajan

A pair of new enantiomeric stilbene dimers, (+)- and (-)-cajanusine [(+)-1 and (-)-1], with a unique coupling pattern were isolated from the leaves of Cajanus cajan . Their structures including absolute configurations were elucidated on the basis of comprehensive spectroscopic and single-crystal X-ray diffraction analyses, as well as CD calculations. The plausible biogenetic pathway of 1 was also proposed. Additionally, (±)-1, (+)-1, and (-)-1 exhibited inhibitory activities on the growth of human hepatocellular carcinoma cells.

New bhimamycins from Streptomyces sp. AK 671

From the wild-type strain Steptomyces sp. AK 671, three nitrogen-containing octaketides were isolated, bhimamycins F, H and I, besides the known azaanthraquinone utahmycin A and polyketide shunt products SEK 4, SEK 4b, mutactin, dehydromutactin and EM18. The structures were characterized by MS and NMR experiments. The hitherto unknown absolute configuration of the two enantiomers of EM18 was determined by online-CD spectroscopy and quantum-chemical CD calculations. Bhimamycins H and I show weak antibacterial activities, whereas the enzyme phosphodiesterase 4 is strongly inhibited by bhimamycins H and I, which has never been reported for nitrogen-containing octaketides. In addition, bhimamycin H inhibits the enzyme glycogen synthase kinase-3β.

Cis‐Clerodane Diterpenes from the Liverwort Scapania ciliata

Chemical investigation of the Chinese liverwort Scapania ciliata led to the isolation of four new cis-clerodane lactones, named ciliatolides A-D (1-4, resp.), among which compound 1 was found to be a tetranorclerodanoid. Their structures were determined by extensive analysis of spectroscopic data, and, in the case of compound 1, together with a single-crystal X-ray diffraction analysis. The absolute configurations were established by analysis of the CD spectra and by quantum-chemical CD calculations. The cytotoxicities of compounds 1-4 were preliminarily tested against the PC3 and MCF-7 cell lines.

Isolation, Structures, and Biological Activities of Triterpenoids from a Penares sp. Marine Sponge

Six new triterpenoids (1-6) and the previously known penasterone, acetylpenasterol, and ergosta-4,24(28)-dien-3-one were isolated from a Penares sp. sponge collected from Vietnamese waters. Structures of the obtained compounds were established by extensive 1D and 2D NMR spectroscopy and mass spectrometry. Configurations of the triterpene epoxy lactones (1-4) were determined on the basis of NOESY and CD data and calculation of spin coupling constants and confirmed by X-ray crystallographic analysis of compound 2. The isolated triterpenoid 6 was cytotoxic against human leukemia HL-60 cells (IC₅₀ = 9.7 μM).

Asteriscane-Type Sesquiterpenoids from the Soft Coral Sinularia capillosa

Chemical examination of the soft coral Sinularia capillosa collected from the South China Sea resulted in the isolation of 14 new asteriscane-type sesquiterpenoids, namely, capillosananes A-N (1-14), four new seco-asteriscanes, capillosananes O-R (15-18), and (-)-sinularone A and sinularone A. Their structures were determined on the basis of extensive spectroscopic analyses, while the absolute configurations were determined by CD and ECD calculation, Mosher's method, and chemical conversion. This is the first report of asteriscane-type sesquiterpenoids from soft corals, and capillosananes Q (17) and R (18) represent new seco-asteriscane skeletons. Capillosanane A exhibited potent antifouling activity against Balanus amphitrite, with an IC₅₀ value of 9.70 μM, while capillosananes B and I and (-)-sinularone A inhibited inflammation-related TNF-α in vitro.

Cadinane sesquiterpenes from the mushroom Lyophyllum transforme

Two rare cadinane-type sesquiterpenes, lyophyllone A (1) and lyophyllanetriol A (2), were isolated from the mushroom Lyophyllum transforme. The structures were elucidated on the basis of exhaustive NMR techniques, together with MS, UV-Vis and molecular modelling. The absolute configuration of lyophyllone A was determined by ab initio theoretical CD calculation performed by Density Functional Theory (DFT) using the B3PW91/6-31G(d,p) basis set. The experimental CD were found to be in good agreement with the corresponding population-weighted theoretical CD spectra, allowing for the determination of the absolute stereochemistry of the compound.

Oleonin, the first secoiridoid with 1α-configuration from Ligustrum lucidum

The first secoiridoid with unusual 1α-configuration, oleonin (1), was isolated from the fruits of Ligustrum lucidum. The chemical structure and absolute stereochemistry were elucidated on the basis of exhaustive NMR spectral analyses, single crystal X-ray diffraction and quantum chemical CD calculation. The plausible biogenetic pathway of 1 and the evaluation of this mechanism are also described.

Flavonoids from Malus hupehensis and their cardioprotective effects against doxorubicin-induced toxicity in H9c2 cells

Three biflavonoid glycosides along with 12 known flavonoids, were isolated from leaves of Malus hupehensis. The complete structures of two of the compounds were established from analysis of MS, NMR spectroscopic and CD data, as well as DFT CD calculations they were determined to be atropisomeric along a central biaryl axis. The antioxidant activities and protective effects of the compounds against doxorubicin-induced cardiomyopathy in H9c2 cells were also investigated. Amongst all of the isolated compounds, quercetin was the most active radical scavenger with EC(50) values of 3.2 μM and 17.8 μM by the DPPH and ABTS(+) methods, respectively. The results indicated that three of the flavanoids also had a strong protective influence against doxorubicin-induced cell death with EC(50) values of 8.3, 5.2 and 7.6 μM, respectively.

Configurational Assignment of Cyclic Bisbibenzyls by HPLC‐CD and Quantum‐Chemical CD Calculations

AbstractMacrocyclic bisbibenzyls are intriguing natural products that are obtained from liverworts. Recently, they have received growing interest due to the discovery of novel representatives and because of their antitumoral and antifungal activities. Depending on the individual coupling type, these structures can possess one or two biaryl axes, which, with larger ortho substituents or increased ring strain within the macrocycle, leads to the occurrence of configurationally stable atropisomers. Within this work, representatives of the plagiochin and riccardin types, both containing one biaryl unit and one biaryl ether moiety, have been investigated for their stereochemical stabilities and electronic circular dichroism (ECD) by means of HPLC‐UV and HPLC‐CD in combination with quantum‐chemical DFT and ab initio RICC2 calculations. We demonstrate that the computation of the chiroptical properties of such macrocycles is a nontrivial task, because of the presence of charge‐transfer (CT) excitations especially in the riccardin‐type structures, which leads to a failure of DFT methods in the excited‐states calculations, thus necessitating the use of the coupled‐cluster approach for a reliable attribution of the absolute configurations of the enantiomers. In the course of this study, the previous assignments of the absolute configurations of the atropisomers of plagiochin E and riccardin D are revised.

Tokamak coordinate conventions: [formula omitted

Dealing with electromagnetic fields, in particular current and related magnetic fields, yields “natural” physical vector relations in 3-D. However, when it comes to choosing local coordinate systems, the “usual” right-handed systems are not necessarily the best choices, which means that there are several options being chosen. In the magnetic fusion community such a difficulty exists for the choices of the cylindrical and of the toroidal coordinate systems. In addition many codes depend on knowledge of an equilibrium. In particular, the Grad–Shafranov axisymmetric equilibrium solution for tokamak plasmas, ψ, does not depend on the sign of the plasma current Ip nor that of the magnetic field B0. This often results in ill-defined conventions. Moreover the sign, amplitude and offset of ψ are of less importance, since the free sources in the equation depend on the normalized radial coordinate. The signs of the free sources, dp/dψ and dF2/dψ (p being the pressure, ψ the poloidal magnetic flux and F=RBφ), must be consistent to generate the current density profile. For example, RF and CD calculations (Radio Frequency heating and Current Drive) require an exact sign convention in order to calculate a co- or counter-CD component. It is shown that there are over 16 different coordinate conventions. This paper proposes a unique identifier, the COCOS convention, to distinguish between the 16 most-commonly used options. Given the present worldwide efforts towards code integration, the proposed new index COCOS defining uniquely the COordinate COnventionS required as input by a given code or module is particularly useful. As codes use different conventions, it is useful to allow different sign conventions for equilibrium code input and output, equilibrium being at the core of any calculations in magnetic fusion. Additionally, given two different COCOS conventions, it becomes simple to transform between them. The relevant transformations are described in detail.

A new cadinane sesquiterpene from the rhizomes of Alpinia officinarum

AimTo investigate the chemical constituents of the rhizomes of Alpinia officinarum. MethodsCompounds were isolated by various column chromatographic methods, and their structures were identified based on their physicochemical properties and spectral data. ResultsA cadinane sesquiterpene, alpiniaterpene A (1), was isolated. Its structure with absolute configuration was established by means of HR-ESI, NMR, and quantum chemical CD calculation. ConclusionCompound 1 is a new compound.

Antibacterial Spirobisnaphthalenes from the North American Cup Fungus Urnula craterium

Urnucratins A-C (1-3), which possess an unusual bisnaphthospiroether skeleton with one oxygen bridge and one C-C bridge and represent a new subclass of bisnaphthalenes, were isolated from the North American cup fungus Urnula craterium. Their structures, including absolute configurations, were determined by means of HRMS, NMR, and quantum chemical CD calculations. Urnucratin A (1) was found to be active against methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and Streptococcus pyogenes with MIC values of 2, 1, and 0.5 μg/mL, respectively.

Cis-Clerodane diterpenoids from the Chinese liverwort Scapania parva Steph.

Three undescribed cis-clerodane lactones, scapanialides A–C (1–3), and a new cis-clerodane furano-diterpenoid, scaparvin F (4), were isolated from the Chinese liverwort Scapania parva Steph. Scapanialide B (2) is the first cis-clerodane diterpenoid with a bicyclo[5.4.0]undecane skeleton from liverworts. Their structures including the absolute configurations were determined by extensive analysis of multidimensional NMR spectroscopy and TDDFT CD calculations, together with crystal X-ray diffraction measurements. The cytotoxicity of compounds 1–4 was preliminary tested against the Hela and MCF-7 cell lines.

ChemInform Abstract: Leucomidines A—C, Novel Alkaloids from Leuconotis griffithii.

Abstract Two novel indole alkaloids and new quinazoline alkaloids, namely leucomidines A–C ( 1–3 ), were isolated from the barks of Leuconotis griffithii . The structures including the absolute configuration were elucidated on the basis of spectroscopic data, chemical means, and CD calculations. The quinazoline alkaloid, 3 , is proposed to be derived from the same biogenetic precursor as the indole alkaloids 1 and 2 .

Heptaketides with antiviral activity from three endolichenic fungal strains Nigrospora sp., Alternaria sp. and Phialophora sp.

Two new heptaketides, (+)-(2S,3S,4aS)-altenuene (1a) and (−)-(2S,3S,4aR)-isoaltenuene (2a), together with six known compounds, (−)-(2R,3R,4aR)-altenuene (1b), (+)-(2R,3R,4aS)-isoaltenuene (2b), 5′-methoxy-6-methyl-biphenyl-3,4,3′-triol (3), alternariol (4), alternariol-9-methyl ether (5), and 4-hydroxyalternariol-9-methyl ether (6) were isolated from the EtOAc extract of an endolichenic fungal strain Nigrospora sphaerica (No.83-1-1-2). Compounds 1a and 1b were separated from enantiomers 1 by chiral HPLC, and so were 2a and 2b from enantiomers 2. Interestingly, 1–6 were also obtained from other two endolichenic fungal strains Alternaria alternata (No.58-8-4-1) and Phialophora sp. (No.96-1-8-1). The structures of 1–6 were elucidated by means of MS, HR-MS, NMR, and X-ray diffraction. Furthermore, the absolute configurations of 1a–2b were determined by CD experiments and CD calculation. Of these compounds, 4 and 5 showed antiviral activity against herpes simplex virus (HSV) in vitro, with IC50 values of 13.5 and 21.3μM, and with selective index (SI) values of 26.5 and 17.1, respectively.

Investigation of folding patterns in homo-oligomers of (R)-β2,2-amino acids with carbohydrate side chain

The study describes the synthesis of new β2,2-peptides made from geminally disubstituted β2,2-amino acid and their folding propensities. The (R)-C-linked carbo-β2,2-amino acid [(R)-β2,2-Caa] was prepared from d-glucose and converted into the homo-oligomeric di-, tetra-, and hexapeptides. The conformational studies were carried out using NMR (in CDCl3), CD, IR, and MD calculations. These β2,2-peptides were interestingly stabilized by five-membered (mr) inter-residue H-bonds NH(i)⋯O(i-1) (furanoside) and a 6-mr intra-residue H-bond between amide proton (NH(i)) and the oxygen of –OMe(i) at the C3 carbon of the carbohydrate side chain. These results amply demonstrate that the ‘epimerization’ at the spiro carbon center has an effect on the conformational behavior of these peptides. Finding of these, H-bonding patterns, which are not so common to stabilize the folds in this class of β2,2-Caa derived peptides would further facilitate augmentation in the domain of foldamer.

A novel antifouling alkaloid from halotolerant fungus Penicillium sp. OUCMDZ-776

Penispirolloid A (1), a novel alkaloid possessing a unique spiro imidazolidinyl skeleton, was isolated from a halotolerant fungal strain, Penicillium sp. OUCMDZ-776. Its structure was elucidated on the basis of spectroscopic methods and quantum chemical CD calculation. Compound 1 showed significant antifouling activity toward Bugula neritina larvae with EC50 of 2.40μg/ml. Plausible biogenesis of compound 1 was also proposed.