Trigonostemons G and H,dinorditerpenoid dimers with axially chiral biaryl linkage from Trigonostemon chinensis

Trigonostemons G and H, two novel dimeric dinorditerpenoids, were isolated from the stem barks of Trigonostemon chinensis. Their planar structures and relative configurations were established by extensive analysis of spectroscopic data. Trigonostemons G and H possess a homodimeric biaryl skeleton obtained from two rearranged chiral nonracemic abietane-type dinorditerpenes through an axially chiral biaryl 11,11′-linkage. Torsional scan and computation of the transition states were carried out to estimate the rotational energy barrier, and the axial chirality (aS) was determined by time-dependent density functional theory (TDDFT) electronic circular dichroism (ECD) calculations. The positive n-π* ECD transitions of the isolated carbonyl chromophore above 300 nm could be used to determine the central chirality of trigonostemon G independently by ECD calculations of the diastereomers.     

Electronic Circular Dichroism of Chiral Alkenes: B3LYP and CAM‐B3LYP Calculations

Time‐dependent density functional theory (TDDFT) calculations of electronic circular dichroism (ECD) are widely used to determine absolute configurations (ACs) of chiral molecules. Two very popular DFT exchange‐correlation functionals, one hybrid (B3LYP) and one long‐range corrected (CAM‐B3LYP), along with a hierarchical sequence of basis sets were investigated, and the ECD spectra predicted for eight alkenes and compared to gas‐phase experimental spectra. Little variation in predicted ECD spectra was found with the basis set size enlargement, but the sensitivity to the functional is greater. Good agreement was obtained only with the CAM‐B3LYP functional, leading to the conclusion that TDDFT calculations of ECD spectra can routinely provide reliable ACs if and only if an appropriate functional is used. For camphene, twistene, syn‐(E)‐bisfenchylidene, and phyllocladene, solvent effects were estimated. Chirality 27:23–31, 2015. © 2014 Wiley Periodicals, Inc.     

Good Computational Practice in the Assignment of Absolute Configurations by TDDFT Calculations of ECD Spectra

Quantum‐mechanical calculations of chiroptical properties have rapidly become the most popular method for assigning absolute configurations (AC) of organic compounds, including natural products. Black‐box time‐dependent Density Functional Theory (TDDFT) calculations of electronic circular dichroism (ECD) spectra are nowadays readily accessible to nonexperts. However, an uncritical attitude may easily deliver a wrong answer. We present to the Chirality Forum a discussion on what can be called good computational practice in running TDDFT ECD calculations, highlighting the most crucial points with several examples from the recent literature. Chirality 28:466–474, 2016. © 2016 Wiley Periodicals, Inc.     

Spectroscopic Studies on Nicotine and Nornicotine in the UV Region

The UV absorption and electronic circular dichroism (ECD) spectra of (R)‐ and (S)‐nicotine and (S)‐nornicotine in aqueous solution were measured to a significantly lower wavelength range than previously reported, allowing the identification of four previously unobserved electronic transitions. The ECD spectra of the two enantiomers of nicotine were equal in magnitude and opposite in sign, while the UV absorption spectra were coincidental. In line with previous observations, (S)‐nicotine exhibited a negative cotton effect centered on 263 nm with vibronic structure (π–π₁* transition) and a broad, positive ECD signal at around 240 nm associated with the n–π₁* transition. As expected this band disappeared when the pyridyl aromatic moiety was protonated. Four further electronic transitions are reported between 215 and 180 nm; it is proposed the negative maxima around 206 nm is either an n–σ* transition or a charge transfer band resulting from the movement of charge from the pyrrolidyl N lone pair to the pyridyl π* orbital. The pyridyl π–π₂* transition may be contained within the negative ECD signal envelope at around 200 nm. Another negative maximum at 188 nm is thought to be the pyridyl π–π₃* transition, while the lowest wavelength end‐absorption and positive ECD may be associated with the π–π₄* transition. The UV absorption spectra of (S)‐nornicotine was similar to that of (S)‐nicotine in the range 280–220 nm and acidification of the aqueous solution enhanced the absorption. The ECD signals of (S)‐nornicotine were considerably less intense compared to (S)‐nicotine and declined further on acidification; in the far UV region the ECD spectra diverge considerably. Chirality 25:288–293, 2013. © 2013 Wiley Periodicals, Inc.     

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

The optical spectroscopic characterization of γ‐turns in solution is uncertain and their distinction from β‐turns is often difficult. This work reports systematic ECD and vibrational circular dichroism (VCD) spectroscopic studies on γ‐turn model cyclic tetrapeptides cyclo(Ala‐β‐Ala‐Pro‐β‐Ala) ( 1 ), cyclo(Pro‐β‐Ala‐Pro‐β‐Ala) ( 2 ) and cyclo(Ala‐β‐Ala‐Ala‐β‐Ala) ( 3 ). Conformational analysis performed at the 6‐31G(d)/B3LYP level of theory using an adequate PCM solvent model predicted one predominant conformer for 1‐3 , featuring two inverse γ‐turns. The ECD spectra in ACN of 1 and 2 are characterized by a negative n→π* band near 230 nm and a positive π→π* band below 200 nm with a long wavelength shoulder. The ECD spectra in TFE of 1‐3 show similar spectra with blue‐shifted bands. The VCD spectra in ACN‐d₃ of 1 and 2 show a +/?/+/? amide I sign pattern resulting from four uncoupled vibrations in the case of 1 and a sequence of two positive couplets in the case of 2 . A ?/+/+/? amide I VCD pattern was measured for 3 in TFE‐d₂. All three peptides give a positive couplet or couplet‐like feature (+/?) in the amide II region. VCD spectroscopy, in agreement with theoretical calculations revealed that low frequency amide I vibrations (at ～1630 cm^?1 or below) are indicative of a C₇ H‐bonded inverse γ‐turns with Pro in position 2, while γ‐turns encompassing Ala absorb at higher frequency (above 1645 cm^?1). Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

O-Heterocyclic Embeurekols from Embellisia eureka,an Endophyte of Cladanthus arabicus

Three new polyketides (-)-1 , (+)-1 , and 2 ) were isolated from the EtOAc extract of the fungus Embellisia eureka, an endophyte of the Moroccan plant Cladanthus arabicus (Asteraceae). The structures of these new compounds were determined on the basis of one- and two-dimensional NMR spectroscopy as well as by high-resolution mass spectrometry. The absolute configurations of (-)-1 , (+)-1 , and 2 were determined by TDDFT ECD calculations of solution conformers, online HPLC-ECD analysis, and the modified Mosher method. Chirality 25:250–256, 2013. © 2013 Wiley Periodicals, Inc.     

Isolation,Stereochemical Study,and Antioxidant Activity of Benzofuranone Derivatives from a Mangrove‐derived Fungus Eurotium rubrum MA‐150

Enantiomers of a 2‐benzofuran‐1(3H)‐one derivative [(–)‐ 1 and (+)‐ 1 ] and four known analogs ( 2 , 3 , 4 , 5 ) were isolated and identified from the culture extract of Eurotium rubrum MA–150, a fungus obtained from the mangrove‐derived rizospheric soil. Their structures were established by detailed interpretation of nuclear magnetic resonance (NMR) data and the structure of (±)‐ 1 was confirmed by single‐crystal X‐ray diffraction analysis. The absolute configuration of the enantiomers (–)‐ 1 and (+)‐ 1 was determined by means of online high‐performance liquid chromatography – electronic circular dichroism (HPLC‐ECD) measurements and time‐dependent Density Functional Theory – electronic circular dichroism (TDDFT‐ECD) calculations. Compounds (±)‐ 1 as well as 2 and 3 exhibited potent DPPH radical scavenging activities with IC₅₀ values of 1.23, 2.26, and 3.99 μg/mL, respectively. Chirality 28:581–584, 2016. © 2016 Wiley Periodicals, Inc.     

Structural and Stereochemical Studies of Hydroxyanthraquinone Derivatives from the Endophytic Fungus Coniothyrium sp

Four known hydroxyanthraquinones ( 1–4 ) together with four new derivatives having a tetralone moiety, namely coniothyrinones A–D ( 5–8 ), were isolated from the culture of Coniothyrium sp., an endophytic fungus isolated from Salsola oppostifolia from Gomera in the Canary Islands. The structures of the new compounds were elucidated by detailed spectroscopic analysis and comparison with reported data. The absolute configurations of coniothyrinones A ( 5 ), B ( 6 ), and D ( 8 ) were determined by TDDFT calculations of CD spectra, allowing the determination of the absolute configuration of coniothyrinone C ( 7 ) as well. Coniothyrinones A ( 5 ), B ( 6 ), and D ( 8 ) could be used as ECD reference compounds in the determination of absolute configuration for related tetralone derivatives. This is the first report of anthraquinones and derivatives from an isolate of the genus Coniothyrium sp. These compounds showed inhibitory effects against the fungus Microbotryum violaceum, the alga Chlorella fusca, and the bacteria Escherichia coli and Bacillus megaterium. Chirality 25:141–148, 2013. © 2012 Wiley Periodicals, Inc.     

Signatures of n→π* interactions in proteins

The folding of proteins is directed by a variety of interactions, including hydrogen bonding, electrostatics, van der Waals' interactions, and the hydrophobic effect. We have argued previously that an n→π* interaction between carbonyl groups be added to this list. In an n→π* interaction, the lone pair (n) of one carbonyl oxygen overlaps with the π* antibonding orbital of another carbonyl group. The tendency of backbone carbonyl groups in proteins to engage in this interaction has consequences for the structures of folded proteins that we unveil herein. First, we employ density functional theory to demonstrate that the n→π* interaction causes the carbonyl carbon to deviate from planarity. Then, we detect this signature of the n→π* interaction in high‐resolution structures of proteins. Finally, we demonstrate through natural population analysis that the n→π* interaction causes polarization of the electron density in carbonyl groups and detect that polarization in the electron density map of cholesterol oxidase, further validating the existence of n→π* interactions. We conclude that the n→π* interaction is operative in folded proteins.     

Experimental and Calculated CPL Spectra and Related Spectroscopic Data of Camphor and Other Simple Chiral Bicyclic Ketones

UV, circular dichroism (CD), fluorescence and circularly polarized luminescence (CPL) spectra were recorded for a set of four related [2.2.1] bicyclic compounds ((1S,4S)‐and (1R,4R)‐1,7,7‐trimethylbicyclo[2.2.1]heptan‐2‐one, namely (1S)‐ and (1R)‐camphor ( 1 ), (1S,4R)‐4,7,7‐trimethylbicyclo[2.2.1]hept‐5‐en‐2‐one, (1S)‐dehydro‐epicamphor ( 2 ), (1S,4S)‐1,7,7‐trimethylbicyclo[2.2.1]heptane‐2,5‐dione, (1S)‐5‐oxocamphor ( 3 ), (1S,4R)‐ and (1R,4S)‐1,7,7‐trimethylbicyclo[2.2.1]heptane‐2,3‐dione, (1S)‐ and (1R)‐camphorquinone ( 4 )) and a set of three related [2.2.2] bicyclic compounds (1S,4S)‐bicyclo[2.2.2]octan‐2,5‐dione (saturated diketone ( 5 )), (1R,4R)‐bicyclo[2.2.2]oct‐7‐en‐2,5‐dione (unsaturated diketone ( 6 )), ((1S,4S)‐bicyclo[2.2.2]oct‐7‐en‐5(S)‐ol‐2‐one (which we refer to as unsaturated hydroxy‐ketone ( 7 )). For the latter three compounds also mid‐IR vibrational circular dichroism (VCD) spectra were recorded and are presented. Time‐Dependent Density Functional (TD‐DFT) calculations provide a satisfactory interpretation of both absorption and emission chiroptical spectra and permit insight into ground and excited state electronic properties. We discuss the applicability of the octant rule or of other approximated models to rationalize the observed sign of the CPL. Chirality 25:589–599, 2013. © 2013 Wiley Periodicals, Inc.     

Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family

Vibrational circular dichroism spectra (VCD) in the mid‐IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N‐trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines. Chirality 27:907–913, 2015. © 2015 Wiley Periodicals, Inc.     

Three Sesquiterpenoid Dimers from Chloranthus japonicus: Absolute Configuration of Chlorahololide A and Related Compounds

A novel sesquiterpenoid dimer, named multistalide C ( 1 ), together with two known congeners, shizukaols C ( 2 ) and D ( 3 ), was isolated from the whole plant of Chloranthus japonicus Sieb. The structures of compounds 1 , 2 , 3 were elucidated by extensive HR‐ESI‐MS, 1D, and 2D NMR spectroscopic analysis. Compounds 1 , 2 , 3 exhibited significant toxic effects on brine shrimp larvae (Artemia salina). The absolute configuration of 1 was established by CD/TDDFT calculations. The related compound chlorahololide A was also reinvestigated. The previous assignment of the absolute configuration of chlorahololide A and several related sesquiterpenoid dimers, based on an incorrect application of the exciton chirality method, is criticized. Chirality 28:158–163, 2015. © 2015 Wiley Periodicals, Inc.     

Three New Diketopiperazines from the Previously Uncultivable Marine Bacterium Gallaecimonas mangrovi HK‐28 Cultivated by iChip

The in situ application of iChip cultivation in mangrove sediment from Hainan province, China, led to the isolation of a novel bacterial species Gallaecimonas mangrovi HK‐28. The extract of G. mangrovi HK‐28 exhibited antibiotic activity against the aquatic pathogen Vibrio harveyi, and its chemical constituents were further investigated by bioactivity‐guided isolation. Three new diketopiperazines, gallaecimonamides A–C, were accordingly isolated from the AcOEt extract of the fermentation broth of G. mangrovi HK‐28. The planar structures of gallaecimonamides A–C were determined using HR‐ESI‐MS together with 1D‐ and 2D‐NMR. The absolute configurations of gallaecimonamides A–C were assigned by optical rotation, NOESY experiment and TDDFT ECD calculations. The in vitro antibacterial and antimalarial activities of gallaecimonamides A–C were assessed. Gallaecimonamide A was found to display antibacterial activity against V. harveyi with a MIC value of 50 μm . However, gallaecimonamides B and C showed no antibacterial activity against V. harveyi (MIC >300 μm ). In addition, all the isolates did not exhibit any inhibitory activities against V. parahaemolyticus (MIC>300 μm ) and Plasmodium falciparum W2 (EC₅₀>100 μg/mL).     

New Antibacterial Thiodiketopiperazines from the Deep Sea Sediment‐Derived Fungus Epicoccum nigrum SD‐388

Two new antibacterial thiodiketopiperazine derivatives (TDKPs), 7‐dehydroxyepicoccin H and 7‐hydroxyeutypellazine F, along with seven known TDKP analogs, were isolated and identified from Epicoccum nigrum SD‐388, a deep‐sea‐sediment‐derived fungus. The structures of these compounds were elucidated on the basis of detailed spectroscopic analysis. The absolute configuration of 7‐dehydroxyepicoccin H was established by X‐ray crystallographic analysis, while 7‐hydroxyeutypellazine F was determined by ECD experiment and TDDFT‐ECD calculation. The antibacterial activities against human and aquatic pathogens were evaluated. 7‐Dehydroxyepicoccin H and 7‐hydroxyeutypellazine F displayed inhibitory activities against aquatic pathogens Vibrio vulnificus, V. alginolyticus, and Edwardsiella tarda, with MIC values ranging from 4.0 to 8.0 μg/mL.     

Structure and absolute configuration of a secolignan from Peperomia blanda

A secolignan, (−)-2-methyl-3-[bis(3′,4′-methylenedioxy-5′-methoxyphenyl) methyl]butyrolactone (1), with a rare cis configuration was isolated from the aerial parts of Peperomia blanda (Piperaceae). The structure of this compound was elucidated by a combination of spectroscopic methods, including ultraviolet, infrared, 1D- and 2D- nuclear magnetic resonance as well as high resolution mass spectrometry data. The absolute configuration of (−)-1 was determined as (2R,3S) by the comparison of experimental electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TDDFT) calculations.     

Cis-diastereoselectivity in pictet-spengler reactions of L-tryptophan and electronic circular dichroism studies

The diastereoselective synthesis of optically active 1,3‐disubstituted tetrahydro‐β‐carbolines using polar protic Pictet–Spengler cyclization of (S)‐tryptophan methyl ester with five aldehydes RCHO (R═CH₃, C₂H₅, C₃H₇, C₄H₉, and C₆H₅) was studied. As an alternate route, the cyclization of (S)‐tryptophan with the same aldehydes and subsequent methylation of the resulting tetrahydro‐β‐carboline carboxylic acids were also performed for comparison. ¹³C NMR and electronic circular dichroism (ECD) studies and time‐dependent density functional theory ECD calculations data established the relative 1,3 cis/trans and the absolute configuration (1S,3S/ 1R,3S) of the synthesized compounds. The solid‐state and solution ECD study of the prepared compounds, supported by ECD calculation and X‐ray data, afforded a reliable ECD method for the configurational assignment of 1,3‐disubstituted tetrahydro‐β‐carbolines and revealed the stereochemical factors that determine the characteristic ECD data. Chirality 24:789–795, 2012. © 2012 Wiley Periodicals, Inc.     

Absolute Configurations of Four Resorcylic Acid Lactones,Paecilomycins J − M,by CD/TDDFT Calculations

The absolute configurations of four resorcylic acid lactones (RALs), paecilomycins J ? M ( 1 ? 3 and 5 ), were assigned by Time‐Dependent Density‐Functional Theory (TDDFT) calculations of their electronic circular dichroism (CD) spectra. The previously reported structure 4 for paecilomycin M was found to be incorrect and should be changed to structure 5 . Analysis of structure‐spectrum relationship for this group of RALs suggested that V′‐shape conformations give type I CD spectra (two negative Cotton effects around 300 and 260 nm, a positive Cotton effect around 220 nm) while V‐shape conformations yield type II spectra (signs of three Cotton effects were opposite to those in type I). Chirality 26:44–50, 2013. © 2013 Wiley Periodicals, Inc.     

Enantiomeric Neolignans and a Sesquiterpene from Solanum erianthum and Their Absolute Configuration Assignment

One pair of new C‐8–C‐3′/C‐7–O–C‐4′ linked neolignan enantiomers ( 1a / 1b ) and one new guaiane sesquiterpene ( 2 ) first featuring the 1(2),9(10)‐conjugated double bond were isolated from the stems of Solanum erianthum (Solanceae). Their structures were characterized on the basis of extensive spectroscopic analyses, especially from their 2D nuclear magnetic resonance (NMR) spectra. The absolute configurations of 1a / 1b were rigorously elucidated by electronic circular dichroism (ECD) experiments combined with the reversed helicity rule for the 2,3‐dihydrobenzo[b]furan chromophore, and compound 2 is the first report on the sterochemical assignment of a guaiane sesquiterpene by using the allylic axial chirality rule for the conjugated diene chromophore in combination with the calculated ECD spectrum. Chirality 28:259–263, 2016. © 2016 Wiley Periodicals, Inc.     

Exciton coupling between enones: Quassinoids revisited

The electronic circular dichroism (ECD) spectra of two previously reported quassinoids containing a pair of enone chromophores are revisited to gain insight into the consistency and applicability of the exciton chirality method. Our study is based on time‐dependent Density Functional Theory calculations, transition and orbital analysis, and numerical exciton coupling calculations. In quassin ( 1 ) the enone/enone exciton coupling is quasi‐degenerate, yielding strong rotational strengths that account for the observed ECD spectrum in the enone π‐π* region. In perforalactone C ( 2 ) the nondegenerate coupling produces weak rotational strengths, and the ECD spectrum is dominated by other mechanisms of optical activity. We remark the necessity of a careful application of the nondegenerate exciton coupling method in similar cases.     

Stilbene Glycoside Oligomers from the Roots of Polygonum multiflorum

Five new trans‐2,3,5,4′‐tetrahydroxystilbene 2‐O‐β‐d ‐glucopyranoside (TSG)‐based stilbene glycoside oligomers ( 1 – 5 ) were isolated from the roots of Polygonum multiflorum. Their structures were elucidated by comprehensive spectroscopic analyses and chemical evidences. The absolute configurations of 1 , 2 , 4 , and 5 were established by quantum‐chemical electronic circular dichroism (ECD) calculations. Putative biosynthetic pathways of 1–5 were proposed using TSG as the key precursor. In addition, compounds 1 (multiflorumiside H) and 3 (multiflorumiside J) exhibited moderate inhibitory activities against NO production in LPS‐stimulated RAW264.7 cells.