Determination of the absolute configurations of natural products using TDDFT optical rotation calculations: the iridoid oruwacin

A Multiple Stimuli-Responsive Ag/P/S Complex Showing Solvochromic and Mechanochromic Photoluminescence

The reaction of CF₃COOAg, 3-bdppmapy (N,N-bis(diphenylphosphanylmethyl)-3-aminopyridine) and HTZ (1,2,4-triazole-3-thiol) in CH₂Cl₂/MeOH resulted in a dinuclear Ag/P/S complex [Ag₂(TZ)₂(3-bdppmapy)₂]·xSol (1·xSol). Crystals of 1·xSol converted to 1·2MeOH in air at room temperature and further to 1 under vacuum upon heating. The solid-state, room-temperature photoluminescent emission of 1·xSol (510 nm) shifted to 494 nm (1·2MeOH) and 486 nm (1). Grinding solids of 1·2MeOH in air resulted in amorphous 1G characterized by solid-state emission at 468 nm, which converted to 1GR with 513 nm emission upon MeOH treatment. Grinding 1GR in air returned 1G, and this interconversion was reproducible over five cycles. The solid-state photoluminescence of 1G changed in response to vapors containing low-molecular weight alcohols but remained unchanged after exposure to other volatile organic compounds (VOCs) or to water vapor. Test papers impregnated with 1G could detect methanol in vapors from aqueous solutions at concentrations above 50%. Complex 1G is, therefore, an example of a stimuli-responsive molecular sensor for the detection of alcohols.

Ligiamycins A and B, Decalin-Amino-Maleimides from the Co-Culture of Streptomyces sp. and Achromobacter sp. Isolated from the Marine Wharf Roach, Ligia exotica

Streptomyces sp. GET02.ST and Achromobacter sp. GET02.AC were isolated together from the gut of the wharf roach, Ligia exotica, inhabiting the intertidal zone of the west coast of Korea. The co-cultivation of these two strains significantly induced the production of two new metabolites, ligiamycins A (1) and B (2), which were barely detected in the single culture of Streptomyces sp. GET02.ST. The planar structures of ligiamycins A (1) and B (2) were elucidated as new decalins coupled with amino-maleimides by the analysis of various spectroscopic data, including nuclear magnetic resonance (NMR), ultraviolet (UV), and mass (MS) data. The assignment of two nitrogen atoms in amino-maleimide in 1 was accomplished based on 1H-15N heteroatom single quantum coherence spectroscopy (HSQC) NMR experiments. The relative configurations of the ligiamycins were determined using rotating frame Overhauser effect spectroscopy (ROESY) NMR data, and their absolute configurations were deduced by comparing their experimental and calculated optical rotations. Ligiamycin A (1) displayed antibacterial effects against Staphylococcus aureus and Salmonella enterica, while ligiamycin B (2) exhibited mild cell cytotoxicity against human colorectal cancer cells.

Computational prediction of chiroptical properties in structure elucidation of natural products

Covering: up to 2019This review covers the current status of the quantum mechanical prediction of chiroptical properties, such as electronic CD and optical rotation, as needed for stereochemical assignments in new natural products. The reliability of the prediction of chiroptical properties is steadily increasing, with a parallel decrease in the required computational resources. Now, quantum mechanical calculations for a medium-sized natural product can be reliably performed by natural product chemists on a mainstream PC. This review is aimed to guide natural product chemists through the numerous steps involved in such calculations. Through a concise, but comprehensive, discussion of the current computational practice, enriched by a few illustrative examples, this review provides readers with the theoretical background and practical knowledge needed to select the most appropriate parameters for performing the calculations, to anticipate possible problems, and to critically evaluate the reliability of their computational results. Common reasons for mistakes are also discussed; in particular, the importance of the correct evaluation of conformational ensembles of flexible molecules (an aspect often overlooked in current research) is stressed.

Stereo- and Regioselective Synthesis of Molecular Baskets

We describe a stereoselective method for obtaining multigram quantities of molecular basket 1 _syn in overall 11% yield, using inexpensive cyclopentadiene and diethyl fumarate as starting materials. First, an asymmetric synthesis of enantioenriched bromo(trimethylstannyl)alkene (-)-8 was accomplished by the stereoselective bromination of dibromonorbornene (+)-4 guided by anchimeric assistance and subsequent syn- exo-elimination of tetrabromonorbornane (-)-5a as the key steps. Subsequent Cu(I)-catalyzed cyclotrimerization of (-)-8 was optimized to give 1 _{syn/ anti} in 85% yield and 1:1 ratio of diastereomers. Importantly, the results of our mechanistic experiments were in line with the cyclotrimerization occurring in a chain-type fashion with racemization of a Cu(I) homochiral dimeric intermediate, reducing the stereoselectivity of the transformation. Enabled by more facile access to molecular baskets of type 1 _syn, a range of recognition studies can now be completed for producing novel supramolecular catalysts, organophosphorus scavengers, and nanostructured materials.

Establishment of a quantitative and qualitative analysis and isolation method for tetracyclic iridoids from Morinda lucida Bentham leaves

A new high performance liquid chromatography (HPLC) method has been established for quantitative and qualitative analysis of three tetracyclic iridoids: ML-2-3 (1), molucidin (2), and ML-F52 (3), which are responsible for anti-trypanosomal and anti-leishmanial activities of Morinda lucida Bentham leaves. Separation of 1-3 from dried 80% aqueous (aq.) ethanol extract was achieved on a reversed-phase cholester column packed with cholesteryl-bonded silica using an acetonitrile-0.1% aq. formic acid mobile phase system. Ultraviolet-visible (UV-VIS) spectroscopy was employed for detection of compounds, and their contents were determined by measuring absorbance at 254 nm. Depending on the above system, several factors potentially affecting the concentration of tetracyclic iridoids were evaluated resulting in several variation on plant organs, seasonality, variation between individual trees, and branch positions within the trees. Moreover, we developed a simple, quick, and effective method for tetracyclic iridoid isolation from M. lucida leaves that consisted of extraction by sonication into 80% aq. ethanol, basic hydrolysis, acid neutralization, liquid-liquid extraction into an organic solvent, and reverse phase open column chromatography. Employing this method, we have succeeded to obtain 1 as a colorless crystal yielding of 0.23%, which was 28 times higher than that of previous isolation method. Setting up methodology in this paper may be important for future in vitro and in vivo studies of tetracyclic iridoids and moreover for their applications in new drug design and development.

Two pairs of phenolic enantiomers from the leaves of Eucommia ulmoides Oliver

Two pairs of new phenolic enantiomers, (+)-eucophenolic A (1a), (-)-eucophenolic B (1b), (-)-eucophenolic C (2a), (+)-eucophenolic D (2b) were isolated from the leaves of Eucommia ulmodies Oliver by chiral enantiomeric resolution. Their structures were elucidated based on extensive spectroscopic analysis. The absolute configurations of 1a/1b and 2a/2b were determined by empirical method and the calculated ECD and OR. All compounds were tested for Hep G2 tumour cell lines. However, no compounds showed potential cytotoxic activities against Hep G2 in vitro.

Absolute configuration determination through the unique intramolecular excitonic coupling in the circular dichroisms of o,p′-DDT and o,p′-DDD. A combined experimental and theoretical study

Circular dichroisms (CDs) of theo,p′-isomers of 1,1,1-trichloro- and 1,1-dichloro-2,2-bis(chlorophenyl)ethanes (DDTandDDD) were investigated experimentally and theoretically.

Antitrypanosomal Activities and Mechanisms of Action of Novel Tetracyclic Iridoids from Morinda lucida Benth

Trypanosoma brucei parasites are kinetoplastid protozoa that devastate the health and economic well-being of millions of people in Africa through the disease human African trypanosomiasis (HAT). New chemotherapy has been eagerly awaited due to severe side effects and the drug resistance issues plaguing current drugs. Recently, there has been an emphasis on the use of medicinal plants worldwide. Morinda lucida Benth. is a popular medicinal plant widely distributed in Africa, and several research groups have reported on the antiprotozoal activities of this plant. In this study, we identified three novel tetracyclic iridoids, molucidin, ML-2-3, and ML-F52, from the CHCl₃ fraction of M. lucida leaves, which possess activity against the GUTat 3.1 strain of T. brucei brucei. The 50% inhibitory concentrations (IC₅₀) of molucidin, ML-2-3, and ML-F52 were 1.27 μM, 3.75 μM, and 0.43 μM, respectively. ML-2-3 and ML-F52 suppressed the expression of paraflagellum rod protein subunit 2, PFR-2, and caused cell cycle alteration, which preceded apoptosis induction in the bloodstream form of Trypanosoma parasites. Novel tetracyclic iridoids may be promising lead compounds for the development of new chemotherapies for African trypanosomal infections in humans and animals.

A New Trinor-guaiane Sesquiterpene from an Indonesian Soft Coral Anthelia sp

A new trinor-guaiane sesquiterpene has been isolated from an Indonesian soft coral Anthelia sp. The planar structure, possessing an octahydroazulene skeleton, and relative stereochemistry were established by analyzing 1D and 2D NMR data, including NOE experiments. Its absolute stereochemistry was elucidated to be 1 S, 4 S, 7 R, and 10 R by comparing observed and calculated optical rotation values. The new compound showed weak cytotoxicity against NBT-T2 cells.

Tyrosyl-DNA Phosphodiesterase I Inhibitors from the Australian Plant Macropteranthes leichhardtii

Mass-directed isolation of the CH2Cl2/MeOH extract from the bark of an Australian plant, Macropteranthes leichhardtii, resulted in the purification of a new phenylpropanoid glucoside, macropteranthol (1), together with four known analogues (2-5). The structure of compound 1 was elucidated by NMR and MS data analyses and quantum chemical calculations. Compounds 3 and 5 showed inhibitory activity against tyrosyl-DNA phosphodiesterase I with IC50 values of ∼1.0 μM.

New anti-trypanosomal active tetracyclic iridoid isolated from Morinda lucida Benth

Human African trypanosomiasis (HAT), commonly known as sleeping sickness has remained a serious health problem in many African countries with thousands of new infected cases annually. Chemotherapy, which is the main form of control against HAT has been characterized lately by the viewpoints of toxicity and drug resistance issues. Recently, there have been a lot of emphases on the use of medicinal plants world-wide. Morinda lucida Benth. is one of the most popular medicinal plants widely distributed in Africa and several groups have reported on its anti-protozoa activities. In this study, we have isolated one novel tetracyclic iridoid, named as molucidin, from the CHCl3 fraction of the M. lucida leaves by bioassay-guided fractionation and purification. Molucidin was structurally elucidated by (1)H and (13)C NMR including HMQC, HMBC, H-H COSY and NOESY resulting in tetracyclic iridoid skeleton, and its absolute configuration was determined. We have further demonstrated that molucidin presented a strong anti-trypanosomal activity, indicating an IC50 value of 1.27 μM. The cytotoxicity study using human normal and cancer cell lines indicated that molucidin exhibited selectivity index (SI) against two normal fibroblasts greater than 4.73. Furthermore, structure-activity relationship (SAR) study was undertaken with molucidin and oregonin, which is identical to anti-trypanosomal active components of Alnus japonica. Overlapping analysis of the lowest energy conformation of molucidin with oregonin suggested a certain similarities of aromatic rings of both oregonin and molucidin. These results contribute to the future drug design studies for HAT.

Structure and Stereochemical Determination of Hypogeamicins from a Cave-Derived Actinomycete

Culture extracts from the cave-derived actinomycete Nonomuraea specus were investigated, resulting in the discovery of a new S-bridged pyronaphthoquinone dimer and its monomeric progenitors designated hypogeamicins A-D (1-4). The structures were elucidated using NMR spectroscopy, and the relative stereochemistries of the pyrans were inferred using NOE and comparison to previously reported compounds. Absolute stereochemistry was determined using quantum chemical calculations of specific rotation and vibrational and electronic circular dichroism spectra, after an extensive conformational search and including solute-solvent polarization effects, and comparing with the corresponding experimental data for the monomeric congeners. Interestingly, the dimeric hypogeamicin A (1) was found to be cytotoxic to the colon cancer derived cell line TCT-1 at low micromolar ranges, but not bacteria, whereas the monomeric precursors possessed antibiotic activity but no significant TCT-1 cytotoxicity.

Manoyloxide Sesterterpenoids from Salvia mirzayanii

Five new manoyloxide-type sesterterpenes were isolated from aerial parts of Salvia mirzayanii, a species endemic to Iran. The planar structures were established by means of 1D and 2D NMR and HRESIMS. Compounds 1-3 differed only in their configurations at C-13 and C-14. Assignment of relative and absolute configurations was achieved by NOESY experiments and by comparison of experimental and simulated ECD spectra of possible stereoisomers. The absolute configurations of 4 and 5 were established in a similar manner.

Absolute configuration of acremoxanthone C, a potent calmodulin inhibitor from Purpureocillium lilacinum

Bioassay-guided fractionation of an extract prepared from the culture medium and mycelium of Purpureocillium lilacinum allowed the isolation of two calmodulin (CaM) inhibitors, namely, acremoxanthone C (1) and acremonidin A (2). The absolute configuration of 1 was established as 2R, 3R, 1'S, 11'S, and 14'R through extensive NMR spectroscopy and molecular modeling calculations at the DFT B3LYP/DGDZVP level, which included the comparison between theoretical and experimental specific rotation, ³J(C,H), and ³J(H,H) values. Compounds 1 and 2 bind to the human calmodulin (hCaM) biosensor hCaM M124C-mBBr, with dissociation constants (Kd) of 18.25 and 19.40 nM, respectively, 70-fold higher than that of chlorpromazine (Kd = 1.24 μM), used as positive control. Docking analysis using AutoDock 4.2 predicted that 1 and 2 bind to CaM at a similar site to that which KAR-2 binds, which is unusual. Furthermore, a novel, sensible, and specific fluorescent biosensor of hCaM, i.e., hCaM T110C-mBBr, was constructed; this device is labeled at a site where classical inhibitors do not interact and was successfully applied to measure the interaction of 1 with CaM. This is the first report of xanthone-anthraquinone heterodimers in species of Paecilomyces or Purpureocillium genera.

A New Monoterpenoid Oxindole Alkaloid from Hamelia Patens Micropropagated Plantlets

Chemical studies on Hamelia patens (Rubiaceae) micropropagated plantlets allowed production of a new monoterpenoid oxindole alkaloid, named (–)-hameline (7), together with eight known alkaloids, tetrahydroalstonine (1), aricine (2), pteropodine (3), isopteropodine (4), uncarine F (5), speciophylline (6), palmirine (8), and rumberine (9). The structure of the new alkaloid was assigned on the basis of 1D and 2D NMR spectroscopy, mass spectrometry, and molecular modeling.

Tailoring enzymes involved in the biosynthesis of angucyclines contain latent context-dependent catalytic activities

Comparison of homologous angucycline modification enzymes from five closely related Streptomyces pathways (pga, cab, jad, urd, lan) allowed us to deduce the biosynthetic steps responsible for the three alternative outcomes: gaudimycin C, dehydrorabelomycin, and 11-deoxylandomycinone. The C-12b-hydroxylated urdamycin and gaudimycin metabolites appear to be the ancestral representatives from which landomycins and jadomysins have evolved as a result of functional divergence of the ketoreductase LanV and hydroxylase JadH, respectively. Specifically, LanV has acquired affinity for an earlier biosynthetic intermediate resulting in a switch in biosynthetic order and lack of hydroxyls at C-4a and C-12b, whereas in JadH, C-4a/C-12b dehydration has evolved into an independent secondary function replacing C-12b hydroxylation. Importantly, the study reveals that many of the modification enzymes carry several alternative, hidden, or ancestral catalytic functions, which are strictly dependent on the biosynthetic context.

Antimicrobial isopropenyl-dihydrofuranoisoflavones from Crotalaria lachnophora

Two new isopropenyl-dihydrofuranoisoflavones exhibiting antimicrobial properties have been isolated along with eight known compounds from the Cameroonian medicinal plant Crotalaria lachnophora. The structures of the new compounds were elucidated by 1D and 2D NMR spectroscopy and high-resolution mass spectrometry as 7,2',4'-trihydroxy-5''-isopropenyl-4'',5''-dihydrofurano[2'',3'':5,6]isoflavone (1) and 4,8-dihydroxy-2-isopropenyl-2,3-dihydro-5H-[1]benzofuro[2,3-b]furo[3,2-g]chromen-5-one (2). The CH(2)Cl(2)/MeOH (1:1) extract and the compounds isolated were subjected to in vitro antimicrobial assays against a panel of pathogenic microorganisms, including Gram-positive and Gram-negative bacteria and fungi. The new compounds, named lachnoisoflavones A (1) and B (2), showed moderate inhibitory activities against Escherichia coli and Klebsiella pneumoniae.

Stereumins H-J, stereumane-type sesquiterpenes from the fungus Stereum sp

Stereumins H (1), I (2), and J (3), three sesquiterpenes possessing a novel stereumane-type backbone, were isolated from an extract of culture broth of the Basidiomycete Stereum sp. CCTCC AF 207024. The complete structural assignments including the absolute configurations are reported by using X-ray studies and density functional theory at the B3LYP/aug-cc-pVDZ//B3LYP/6-31G(d) level.

Determination of Absolute Configuration of Natural Products: Theoretical Calculation of Electronic Circular Dichroism as a Tool

Determination of absolute configuration (AC) is one of the most challenging features in the structure elucidation of chiral natural products, especially those with complex structures. With revolutionary advancements in the area of quantum chemical calculations of chiroptical spectroscopy over the past decade, the time dependent density functional theory (TDDFT) calculation of electronic circular dichroism (ECD) spectra has emerged as a very promising tool. The principle is simply based on the comparison of the calculated and experimental ECD spectra: the more closely they match, the more reliable conclusion for the AC assignment can be drawn. This review attempts to use several examples representing monomeric flavonoids, rotationally restricted biflavonoids, complex hexahydroxydiphenoyl-containing flavonoids, conformationally flexible and restrained sesquiterpenoids, cembrane-africanene terpenoids, dihydropyranocoumarins, alkaloids, and dihydroxanthones to illustrate the applicability of this approach in determining the AC of structurally diverse natural products. The findings clearly indicate that the TDDFT calculation of ECD spectra can quantify the contribution of individual conformers and the interaction of multiple chromophores, making it possible to determine the AC of complex chiral molecules. The calculated electronic transitions and molecular orbitals provide new insight into the interpretation of ECD spectra at the molecular level.

Compounds from Acorus tatarinowii: determination of absolute configuration by quantum computations and cAMP regulation activity

A new cadinane-type sesquiterpenoid, tatarinowin A (1), two phenylpropanoids, tatarinoids A (2) and B (3), and a trinorlignan, tatarinoid C (4), along with 15 known compounds including two pairs of mixtures were isolated from the rhizome of Acorus tatarinowii. The absolute configurations of 1-4 were established by computation of specific rotation values. The isolated compounds were evaluated for their cAMP regulatory activity by the AlphaScreen assay.

Time-dependent density functional response theory for electronic chiroptical properties of chiral molecules

Methodology to calculate electronic chiroptical properties from time-dependent density functional theory (TDDFT) is outlined. Applications of TDDFT to computations of electronic circular dichroism, optical rotation, and optical rotatory dispersion are reviewed. Emphasis is put on publications from 2005 to 2010, but much of the older literature is also cited and discussed. The determination of the absolute configuration of chiral molecules by combined measurements and computations is an important application of TDDFT chiroptical methods and discussed in some detail. Raman optical activity (ROA) spectra are obtained from normal-mode derivatives of the optical rotation tensor and other linear response tensors. A few selected (ROA) benchmarks are reviewed.