Determination of the absolute configuration of the sugar residues of complex polysaccharides by circular dichroism spectroscopy

Circular dichroism spectroscopy is used to determine the absolute configuration of the constituent sugar residues of bacterial polysaccharides from two strains of Streptococcus sanguis which are important receptors in bacterial coaggregation in the formation of dental plaque. A high-pressure liquid chromatographic method for carbohydrate analysis of glycoproteins, glycolipids, and polysaccharides has been extended to sugar chirality determination by collection of the eluted HPLC fractions and subsequent measurement of their circular dichroism spectra. The method involves methanolysis of the polysaccharide followed by formation of O-benzoyl derivatives and HPLC on reverse-phase columns. Circular dichroism spectra of the collected derivatives in acetonitrile solution in the region 230 nm show large ellipticity bands resulting from "chiral exciton" interaction among the O-benzoyl chromophores which are sensitive to the orientation of hydroxyl groups in the parent sugars. The sensitivity of the method is in the submicrogram range for the absolute configuration of single sugar residues. The circular dichroism of the intact polysaccharide in aqueous solution shows CD bands from the amide chromophore in the region 180 to 220 nm which are sensitive to the chirality of 2-acetamido sugar residues.     

Determination of absolute configuration using vibrational circular dichroism spectroscopy: the chiral sulfoxide 1-thiochromanone S-oxide

We reexamined the absolute configuration (AC) of the chiral sulfoxide 1-thiochromanone S-oxide (1) using vibrational circular dichroism (VCD) spectroscopy. The VCD spectrum of 1 was analyzed using density functional theory (DFT). DFT predicts two stable conformations of 1, separated by <1 kcal/mole. Their VCD spectra were calculated using the DFT/GIAO methodology. The VCD spectrum predicted for the equilibrium mixture of the two conformations of (S)-1 is in excellent agreement with the experimental spectrum of (+)-1. The AC of 1 is therefore definitively R(-)/S(+).     

Determination of the absolute configuration and solution conformation of gossypol by vibrational circular dichroism

Vibrational circular dichroism (VCD) measurements and density functional theory (DFT) calculations were used to obtain the first definitive assignment of the absolute configuration for the polyphenolic binaphpthyl dialdehyde gossypol and a determination of the solution conformation in CDCl(3). VCD spectra recorded for the two resolved enantiomers are near mirror images and excellent agreement between the observed IR and VCD spectra and intensity calculations carried out at the DFT (B3LYP/6-31G*) level establish the absolute configurations of (+)-gossypol as P and (-)-gossypol as M, with two conformations in CDCl(3) solution that differ in isopropyl group orientation.     

Determination of the absolute configuration and solution conformation of a novel disubstituted pyrrolidine acid A by vibrational circular dichroism

Compound A, a novel disubstituted pyrrolidine acid, is a member of a new class of agents that are potentially useful for the treatment of diabetes and dyslipidemia. The absolute configuration of this compound was determined by using vibrational circular dichroism (VCD). The results are in agreement with the assignments based on both X-ray analysis and the stereo-selective chemical synthesis. During VCD analysis, the solution conformation for a portion of compound A in CDCl(3) was also established. The compound is found to associate as an H-bonded carboxylic acid "dimer" in CDCl(3) solution, and VCD calculations on a model dimer fragment were required to establish the absolute configuration.     

The absolute configuration of 1-carboxyethyl substituents on common hexoses by circular dichroism

Determination of the absolute configuration of the 1-carboxyethyl substituent on a monosaccharide by circular dichroism measurements was found to be a sensitive and simple method. It relies on comparison of the spectrum of a 1-carboxyethyl substituted sugar or sugar derivative with the spectra of (R)- and (S)-lactic acid in the region 200-260 nm in which the (R)- and (S)-configuration give negative and positive deltaepsilon, respectively. The oligo- or poly-saccharide containing a 1-carboxyethyl substituted sugar is hydrolyzed to monomers and the 1-carboxyethyl substituted sugar isolated by chromatography. The CD spectrum obtained for the 1-carboxyethyl substituted sugar in water solution at pH 2 is then compared with spectra of (R)- and (S)-lactic acid. The sign for the absorption and a maximum of comparable intensity and appearance around 210 nm, identify the stereochemistry.     

Synthesis and antitumor activity of bicyclo[3.3.1]nonenol derivatives

Various novel bicyclo[3.3.1.]nonenol derivatives were synthesized in an efficient one-pot procedure in a remarkably stereoselective reaction. The title compounds show significant antitumor activity against human cancer cell lines. A variety of cinnamic acid derivatives were linked to the title compounds as side chains in order to enhance the antitumor activity. These compounds were subjected to the in vitro antitumor screening, and the results are discussed. It seems important with respect to antitumor activity to locate an aromatic ring at the C-7 position of the bicyclo[3.3.1]nonane framework.     

Determination of absolute configuration of salvic acid,an ent-labdane from Eupatorium salvia,by vibrational circular dichroism

The relative stereochemistry at C13 and the absolute configuration of salvic acid, a constituent of the leaves of Eupatorium salvia, were established as the 13-(R)-ent-labdane 1. The results follow from vibrational circular dichroism measurements of the derived O-methyl ether methyl ester 3 which were compared to DFT B3LYP/DGDZVP calculated spectra. The relative stereochemistry of salvic acid at C13 was independently verified by single crystal X-ray diffraction measurements of 1, and of its derived diol 4.     

The first intermediates in the bromination of bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane, combination of experiments and theoretical results

Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex and bromonium tribromide, bromonium pentabromide ion pairs. The stoichiometry, formation constants and the electronic spectra of all the species present at equilibrium (pi-complex and bromonium ions), obtained by addition of bromine to alkene 1, have been determined in 1,2-dichloroethane at 25 degrees C and compared with the values that characterize the corresponding aggregates arising from Ad=Ad. The absence of the two bridging CH2 groups in 1 significantly affects all the formation constants. Moreover, at variance with Ad=Ad, olefin 1 reacts with bromine to give, depending on reagent concentration, a substitution product. DFT (B3LYP) and ONIOM computations of 1:1 Br2-olefin complexes for 1 and Ad=Ad confirm that the association energy is larger for the complex 1-Br2. The higher stability of this species seems to be correlated to the greater IP of 1 with respect to Ad=Ad which is able to compensate the reduced polarizability. The experimental value of the formation constant found for the complex 1-Br2, 643 vs 289 M(-1) further supports the primary role exerted by dispersion interactions in alkene-Br2 pi-complexes.     

Determination of the absolute configurations of synthetic daunorubicin analogues using vibrational circular dichroism spectroscopy and density functional theory

The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl₃ solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6‐311G** and 6‐311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Structure and absolute configuration of a visamminol derivative using IR and vibrational circular dichroism

The aerial parts of Arracacia tolucensis (Kunth) Hemsl. (Apiaceae) provided the new visamminol derivative (S)-(+)-4′-O-angeloylvisamminol (1), along with the known angular pyranocoumarin 2. Analysis of HMBC NMR correlations did not allow distinction of the linear dihydrofurochromone 1 from pyranochromone 5. The structure and S absolute configuration of (+)-1 was therefore established by comparison of the IR and vibrational circular dichroism spectra of the natural product with the DFT B3LYP/DGDZVP calculated spectra for (S)-1 and (S)-5. Structural verification followed by single crystal X-ray diffraction of (+)-1 and chemical correlation.     

Determination of the absolute configuration of a key tricyclic component of a novel vasopressin receptor antagonist by use of vibrational circular dichroism

We present the results of a study using vibrational circular dichroism (VCD) for (+)-1, which furnished an unambiguous determination of its absolute configuration as S. The most abundant conformation of (+)-1 in CDCl(3) solution was also established.     

Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques

We have previously reported benzimidazole-based compounds to be potent inhibitors of FabI for Francisella tularensis (FtFabI), making them promising antimicrobial hits. Optically active enantiomers exhibit markedly differing affinities toward FtFabI. The IC₅₀ of benzimidazole (?)-1 is ～100× lower than the (+)-enantiomer, with similar results for the 2 enantiomers. Determining the absolute configuration for these optical compounds and elucidating their binding modes is important for further design. Electronic circular dichroism (ECD) quantum calculations have become important in determining absolute configurations of optical compounds. We determined the absolute configuration of (?)/(+)-1 and (?)/(+)-2 by comparing experimental spectra and theoretical density functional theory (DFT) simulations of ECD spectra at the B3LYP/6-311+G(2d, p) level using Gaussian09. Comparison of experimental and calculated ECD spectra indicates that the S configuration corresponds to the (?)-rotation for both compounds 1 and 2, while the R configuration corresponds to the (+)-rotation. Further, molecular dynamics simulations and MM-GBSA binding energy calculations for these two pairs of enantiomers with FtFabI show much tighter binding MM-GBSA free energies for S-1 and S-2 than for their enantiomers, R-1 and R-2, consistent with the S configuration being the more active one, and with the ECD determination of the S configuration corresponding to (?) and the R configuration corresponding to (+). Thus, our computational studies allow us to assign (?) to (S)- and (+) to (R)- for compounds 1 and 2, and to further evaluate structural changes to improve efficacy.     

Absolute configuration determination of donor-acceptor [2.2]paracyclophanes by comparison of theoretical and experimental vibrational circular dichroism spectra

Vibrational circular dichroism (VCD) spectra were obtained for the assignments of the absolute configurations of diastereomeric 4,7-bis(methoxycarbonyl)-12,15-dimethoxy-[2.2]paracyclophanes (1 and 2), and density functional theory (DFT) calculations were performed at the B3LYP/6-31G(d) level for all possible conformations of both 1 and 2 to give the theoretical VCD spectra. Comparisons of the experimental and theoretical VCD spectra obtained unambiguously established the absolute configurations of the dextrorotatory (+)-enantiomers as (4S(p);12S(p))-1 and (4S(p);12R(p))-2, respectively.     

Stereoselective metabolism of 7-methylbenz[a]anthracene: absolute configuration of five dihydrodiol metabolites and the effect of dihydrodiol conformation on circular dichroism spectra

7-Methylbenz[a]anthracene (7-MBA) was metabolized stereoselectively by rat liver microsomes to form five optically active dihydrodiols as the predominant metabolites. The dihydrodiols were purified by a combination of reversed-phase and normal-phase high performance liquid chromatography (HPLC). By comparison of their circular dichroism (CD) spectra with the corresponding benz[a]anthracene (BA) dihydrodiols of known absolute stereochemistry, the major dihydrodiol enantiomers of 7-MBA have been determined to have 1R,2R-, 3R,4R- and 10R , 11R - absolute configurations, respectively. Due to their quasi- diaxial conformations, the absolute configuration of trans-5,6- and trans-8,9-dihydrodiols, the two most abundant metabolites of 7-MBA, could not be determined by simple comparisons of their circular dichroism spectra with those of the quasidi -equatorial BA 5R, 6R - and 8R , 9R -dihydrodiols. The major enantiomers of the quasi- diaxial trans-5,6- and trans-8,9-dihydrodiol metabolites of 7-MBA were determined by comparison to the CD spectrum of 7-bromo-BA 5R, 6R -dihydrodiol and by the exciton chirality method to have R,R absolute stereochemistry. This study also revealed that the circular dichroism Cotton effects of an enantiomeric dihydrodiol of polycyclic aromatic hydrocarbons can be drastically altered if the conformation (quasi- diaxial vs. quasi di-equatorial ) of the dihydrodiol is changed.     

Solid-state circular dichroism and hydrogen bonding: absolute configuration of massarigenin A from Microsphaeropsis sp

Massarigenin A (1) and papyracillic acids A (2) and B (3) were isolated from the endophytic fungus Microsphaeropsis sp. Their structures were elucidated by multidimensional nuclear magnetic resonance spectroscopy; the structure of massarigenin A (1) was also confirmed by X-ray crystallography. The absolute configuration of massarigenin A (1) was established by means of circular dichroism (CD) spectroscopy and time-dependent density functional theory (TDDFT) calculations. The impact of intermolecular hydrogen bonds detected in the crystal packing of 1 on CD spectra measured in the solid state was also investigated.     

Determination of absolute configuration of conformationally flexible cis-dihydrodiol metabolites: effect of diene substitution pattern on the circular dichroism spectra and optical rotations

Absolute configurations of a number of cis-dihydrodiols (cis-1,2-dihydroxy-3,5-cyclohexadienes), synthetically useful products of TDO-catalyzed dihydroxylations of 1,2- and 1,3-disubstituted benzene derivatives, have been determined by a comparison of calculated and experimental CD spectra and optical rotations and by methods involving X-ray crystallography, 1H NMR spectra of diastereoisomeric derivatives, and by stereochemical correlations. The computations disclosed a significant effect of the substituents on conformational equilibria of cis-dihydrodiols and chiroptical properties of individual conformers. The assigned absolute configurations of cis-dihydrodiols have allowed the validity of a simple predictive model for TDO-catalyzed arene dihydroxylations to be extended.     

Structural properties of arrestin studied by chemical modification and circular dichroism.

A unique conformation of arrestin is crucial for its interaction with phosphorylated photolyzed rhodopsin. Conformational changes in arrestin were investigated using chemical modification and circular dichroism. We studied the kinetics of sulfhydryl modification of bovine arrestin in order to determine whether its conformation is altered by the presence of ligands or salts at different ionic strengths. We found that all three cysteines (stoichiometry was 2.7 +/- 0.06 3-carboxy-4-nitrophenyl sulfide (NbS)/arrestin) are accessible for modification by NbS2. Under pseudo-first-order conditions (30-100-fold excess of NbS2 over arrestin), the modifications of the 3 cysteines are indistinguishable. At higher concentrations of NbS2 (150-300-fold excess), the pseudo-first-order plot is not linear, and the reaction can be resolved into two processes that involve two classes of sulfhydryl groups. Addition of CaCl2, MgCl2, inorganic phosphate, MgATP, or MgGTP had little effect on the rate of modification of the cysteine residues; however, heparin and inositol hexakisphosphate, which have been shown to induce conformational changes in arrestin, block modification of one sulfhydryl group of arrestin and accelerate the modification of the remaining two. Analysis of CD spectra revealed that arrestin has virtually no alpha-helical structure, about 40% beta-structure, about 18% beta-turns, and about 40% other structure. The CD spectrum for arrestin did not change in the presence of heparin. These studies suggest that arrestin exists in equilibrium between two or more conformational states. However, it is proposed that conversion between these conformations occur without altering significantly the secondary structure of arrestin.     

Absolute configuration of 3-hydroxy acids formed by Stenotrophomonas maltophilia: application of multidimensional gas chromatography and circular dichroism spectroscopy.

The soil bacterium Stenotrophomonas maltophilia was found to transform various long-chain fatty acids selectively into 3-hydroxy fatty acids of shorter chain length. Their chiral evaluation was performed by multidimensional gas chromatography (MDGC) on modified cyclodextrin phase comparing the enantiodistribution of 1,3-diol formed without loss of stereochemical information from a representative microbial product with those of synthetic (3RS)- and (3S)-1,3-diols. Enantiomeric excesses of 84-98% (R) were determined for the microbially produced 3-hydroxy acids. In addition, the CD exciton chirality method was applied to determine their absolute configuration. Derivatization with 9-anthryldiazomethane and 2-naphthoylimidazole led to the required bichromophoric structures. Their CD spectra displayed a positive first Cotton effect around 254 nm and a negative second Cotton effect around 237 nm, which confirmed the (R)-configuration of the bacterial products.     

Assignment of the absolute configuration of [n]-ladderanes by TD-DFT optical rotation calculations

In this study, we report theoretical specific rotation values for a series of cis-/trans-alkylated-[5]-ladderanes and cis-/trans-methylated-[n]-ladderanes. Using time-dependent density functional response theory optical rotation calculations, we can assign (+) and (-) optical rotation signs to trans-(S)-alkyl-[5]-ladderane and trans-(R)-alkyl-[5]-ladderane configurations, respectively. In order to qualitatively validate our absolute configuration predictions, we computed optical rotation values at three different levels of theory--B3LYP, RI-BP86, and Hartree-Fock--using the aug-cc-pVDZ basis set. We observe a novel rung-parity-controlled oscillatory optical rotatory phenomenon in our computations, which, to the best of our knowledge, has never been reported or observed before. Furthermore, this preliminary analysis of optical rotation properties in this class of compounds should facilitate the correct absolute stereochemical assignment of natural and synthetic ladderanes, such as the trans-isomer of pentacyclic C(20)-fatty acid methyl ester (pentacycloanammoxic methyl ester), without the need for derivatization, in particular for cases where NMR or X-ray crystal structures are not readily available.     

Experimental and calculated circular dichroism spectra of monoaza[5]helicenes

Circular dichroism (CD) spectra have been measured in the range of 400-200 nm on CH₃OH solutions of both enantiomers for the almost complete series of monoaza[5]helicenes, namely the molecules where the hetero N atom occupies positions 1, 3, 4, 5, 6, and 7, respectively (the 2 isomer is missing due to difficulties in the synthesis). CD spectra recorded at controlled room temperature allow one to define precise racemization rates, that are nicely interpreted on the basis of DFT molecular orbital calculations. Time-dependent DFT methods provide us with calculated CD and UV spectra, that are compared with the corresponding experimental data. We discuss the role of the N atom in determining the height of the racemization barrier and in shaping the appearance of the CD spectra.