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.     

Band structure of electronic circular dichroism spectra and the born-oppenheimer approximation

Theory is presented for determining the effects of band structure on electronic CD spectra. In this development, the effect of the first-order correction to the Born-Oppenheimer approximation is considered. This removes the unrealistic feature of identical CD and absorbance spectral band structures present in previous models. The predicted order of magnitude of this correction is consistent with experimentally observed differences in CD and absorbance band structure. A Green function formalism is used to determine the contribution of the intrinsic CD to the total CD of an aggregate of chromophores. The intrinsic CD can be determined from the monomeric CD that has been corrected for effects of the intermolecular interactions in the aggregate.     

Absolute configuration of an axially chiral sulfonate determined from its optical rotatory dispersion,electronic circular dichroism,and vibrational circular dichroism spectra

The absolute configuration (AC) of an axially chiral sulfonate (aCSO), 3,5‐dimethyl‐2‐(naphthalen‐1‐yl)‐6‐(naphthalen‐1‐yl)benzenesulfonate (labeled as aCSO5), was investigated using optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) spectroscopies. All three methods led to the same conclusion and the AC of aCSO5 is reliably determined to be (−)‐(aR , aR ), or conversely (+)‐(aS , aS ).     

Deconvolution of the circular dichroism spectra of proteins: the circular dichroism spectra of the antiparallel beta-sheet in proteins.

A recently developed algorithm, called Convex Constraint Analysis (CCA), was successfully applied to determine the circular dichroism (CD) spectra of the pure beta-pleated sheet in globular proteins. On the basis of X-ray diffraction determined secondary structures, the original data set used (Perczel, A., Hollosi, M., Tusnady, G. Fasman, G.D. Convex constraint analysis: A natural deconvolution of circular dichroism curves of proteins, Prot. Eng., 4:669-679, 1991), was improved by the addition of proteins with high beta-pleated sheet content. The analysis yielded CD curves of the pure components of the main secondary structural elements (alpha-helix, antiparallel beta-pleated sheet, beta-turns, and unordered conformation), as well as a curve attributed to the "aromatic contribution" in the wavelength range of 195-240 nm. Upon deconvolution the curves obtained were assigned to various secondary structures. The calculated weights (percentages determining the contributions of each pure component curve in the measured CD spectra of a given protein) were correlated with the X-ray diffraction determined percentages in an assignment procedure and were evaluated. The Pearson product correlation coefficients (R) are significant for all five components. The new pure component curves, which were obtained through deconvolution of the protein CD spectra alone, are promising candidates for determining the percentages of the secondary structural components in globular proteins without the necessity of adopting an X-ray database. The CD spectrum of the CheY protein was interesting because it has the characteristic shape associated with the alpha-helical structure, but upon analysis yielded a considerable amount of beta-sheet in agreement with the X-ray structure.     

Evaluation of RNA conformation from circular dichroism and optical rotatory dispersion data

An analysis of optical rotatory dispersion and circular dichroism of RNA is described which leads to an estimate of the degree of base pairing. By the use of new standards for the double-helical parts of the molecule, based on data for two-stranded viral RNA species, a good fit between calculated and observed curves can be achieved. Where data are available the results of analyses of optical rotatory dispersion and circular dichroism in general show satisfactory consistency.     

电子圆二色谱技术在微生物次级代谢产物结构研究中的应用研究进展

微生物次级代谢产物的化学结构十分复杂,对其绝对构型的确定十分困难。近年来,电子圆二色谱(electronic circular dichroism,ECD)由于其用量少、精度高等优点,在测定绝对构型方面的应用越来越多,已经成为研究微生物次级代谢产物结构的重要方法。本文就电子圆二色谱在微生物次级代谢产物结构研究中的应用进行综述,以期为今后的研究奠定基础。     

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.     

Kramers-Kronig transformation of experimental electronic circular dichroism: application to the analysis of optical rotatory dispersion in dimethyl-L-tartrate

When a limited region of the experimental electronic circular dichroism (ECD) spectrum is subjected to Kramers-Kronig (KK) transformation, the resulting optical rotatory dispersion (ORD) may or may not reproduce the experimentally measured ORD in the long-wavelength nonresonant region. If the KK transform of experimentally measured ECD in a limited wavelength region reproduces the experimentally measured ORD in the long-wavelength nonresonant region, then that observation indicates that the ORD in the long-wavelength nonresonant region should be satisfactorily predicted from the correspondingly limited number of electronic transitions in a reliable quantum mechanical calculation. On the other hand, if the KK transform of experimentally measured ECD in a limited region does not reproduce the experimentally measured ORD in the long-wavelength nonresonant region, then it should be possible to identify the ECD bands in the shorter wavelength region that are responsible for the differences between experimentally observed ORD and KK-transformed ECD. This approach helps to identify the role of ECD associated with higher energy-excited states in the nature of ORD in the long-wavelength nonresonant region. These concepts are demonstrated here by measuring the experimental ECD and ORD for dimethyl-L-tartrate in different solvents. While ECD spectra of dimethyl-L-tartrate in different solvents show little variation, ORD spectra in the long-wavelength nonresonant region show marked solvent dependence. These observations are explained using the difference between experimental ORD and KK-transformed ECD. Quantum mechanical predictions of ECD and ORD are also presented for isolated (R, R)-dimethyl tartrate at the B3LYP/aug-cc-pVDZ level.     

Circular dichroism and magnetic circular dichroism spectra of chlorophylls a and b in nematic liquid crystals. II. Magnetic circular dichroism spectra

Absorption and magnetic circular dichroism (MCD) spectra are reported for chlorophyll (Chl) a and Chl b dissolved in nematic liquid crystal solvents. The spectra were measured with the dye molecules oriented uniaxially along the direction of. the magnetic field and measuring light beam. It is significant that under such conditions the MCD spectra recorded in the wavelength region of the Q and Soret bands of the chlorophyll are essentially unchanged with respect to rotation of the sample cell around this axis, even though there is almost complete orientation of the chlorophyll molecules by the liquid crystals. The MCD spectra of Chl a and b in the nematic liquid crystal solvents used in this study are surprisingly similar to the spectra obtained under isotropic conditions. These results illustrate an important technique with which to examine the optical spectra of dyes oriented in liquid crystal matrices in which the anisotropic effects can be reduced the negligible proportions by the application of a strong magnetic field parallel to the direction of the measuring light beam. The first deconvolution calculations are reported that describe the deconvolution of pairs of absorption and MCD spectra, in the Q and B band regions, for both Chl a and b. The spectral analysis to obtain quantitative estimates of transition energies was accomplished by carrying out detailed deconvolution calculations in which the both the absorption and MCD spectral envelopes were fitted with the same number of components; each pair of components had the same hand centres and bandwidth values. This procedure resulted in an assignment of each of the main transitions in the absorption spectra of both Chl a and b. Chl a is clearly monomeric, with Qy, Qx, By and Bx located at 671, 582, 439 and 431 nm, respectively. Analysis of the spectral data for Chl b located Qy, By and Bx, at 662, 476 and 464 nm, respectively.     

Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments

The circular dichroism spectra of membrane particles are distorted by effects of differential absorption flattening, which are a consequence of the nonrandom distribution of chromophores in these samples. We have shown that this phenomenon is not significant in small unilamellar vesicles with high lipid to protein ratios [Mao, D., & Wallace, B. A. (1984) Biochemistry 23, 2667-2673]. It has recently been claimed [Glaeser, R. M., & Jap, B. K. (1985) Biochemistry 24, 6398-6401] that absorption flattening effects are also inconsequential in large membrane fragments with high protein concentrations, such as purple membrane sheets. This paper will demonstrate that absorption flattening is significant in these samples and that it causes substantial distortion of the calculated protein secondary structures derived from the uncorrected circular dichroism data.     

On the analysis of membrane protein circular dichroism spectra

Analysis of circular dichroism spectra of proteins provides information about protein secondary structure. Analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. The reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing CD spectra of soluble proteins. The utility of soluble protein reference sets in analyzing membrane protein CD spectra, however, has been questioned in a recent study that found current reference protein sets to be inadequate for analyzing membrane proteins. We have examined the performance of reference protein sets available in the CDPro software package for analyzing CD spectra of 13 membrane proteins with available crystal structures. Our results indicate that the reference protein sets currently available for CD analysis perform reasonably well in analyzing membrane protein CD spectra, with performance indices comparable to those for soluble proteins. Soluble + membrane protein reference sets, which were constructed by combining membrane proteins with soluble protein reference sets, gave improved performance in both soluble and membrane protein CD analysis.     

Adenine nucleosides in solution: circular dichroism studies and base conformation.

Adenosine, AMP, S-adenosylhomocysteine, S-adenosylmethionine, aristeromycin and 25 other synthetic adenosine analogs modified in the 4' or 5' positions show certain groups of different circular dichroism (CD) spectra. Both positive and negative Cotton effects can occur in the long-wavelength part (250-270 nm) of the spectra. Molar ellipticities [theta] range from -6000 (in adenosine 5'-carboxylate) to +4000 deg. cm2 dmol-1 (in 5'-deoxy-5'iodoadenosine), including some compounds with small, polar 5'-substituents in which low-intensity bands are found in signed pairs. Most of these adenosine derivatives that have the same adenine chromophore and a ribofuranose moiety unsubstituted in the 2' and 3' positions prefer an anti-conformation of the adenine base, as evidenced by proton magnetic resonance spectroscopy. In the majority of cases, electronic perturbations of the chromophore or major alterations of the assymmetric sugar residue can be excluded as sources of the CD variations. Therefore a correlation of the long-wavelength CD bands with the glycosyl torsion angle phiCN is suggested, where the gauche, gauche/anti combination which is typical of AMP in the crystal and in solution (phiCN approximately -40degrees, [theta] negative) is one reference point and a region for phiCN = 0degrees ([theta] positive) is assigned to compounds with space-filling substituents such as S-adenosylmethionine. Both negative and positive Cotton effects can be associated with the anti conformation range. Within this series, the base conformation of novel nucleoside structures could be predicted from CD measurements. The CD spectrum gives no indication, however, of whether a certain torsion angle is the result of a rigid structure (as in AMP) or the average value of a molecule with high rotational freedom (as in 5'-deoxyadenosine). The conformations of aristeromycin and 4'-thioadenosine are discussed in relation to adenosine, and a structure-determining effect of the 4' bridge atom is noted.     

Structural conformation of spidroin in solution: a synchrotron radiation circular dichroism study

Spider silk is made and spun in a complex process that tightly controls the conversion from soluble protein to insoluble fiber. The mechanical properties of the silk fiber are modulated to suit the needs of the spider by various factors in the animal's spinning process. In the major ampullate (MA) gland, the silk proteins are secreted and stored in the lumen of the ampulla. A particular structural fold and functional activity is determined by the spidroins' amino acid sequences as well as the gland's environment. The transition from this liquid stage to the solid fiber is thought to involve the conversion of a predominantly unordered structure to a structure rich in beta-sheet as well as the extraction of water. Circular dichroism provides a quick and versatile method for examining the secondary structure of silk solutions and studying the effects of various conditions. Here we present the relatively novel technique of synchrotron radiation based circular dichroism as a tool for investigating biomolecular structures. Specifically we analyze, in a series of example studies on structural transitions induced in liquid silk, the type of information accessible from this technique and any artifacts that might arise in studying self-assembling systems.     

Wavelength shifts in solid-state circular dichroism spectra: a possible explanation

We have devised an artificial sampling approach generating "absorption flattening" (AF) on the UV-Vis spectrum of a solution of a chiral compound: Tris (ethylendiamine)cobalt(III) chloride (Lambda-Co(en)(3)Cl(3)). We have observed a concomitant red shift of the CD maxima. Related CD and absorption spectra have been calculated from spectra recorded on diluted homogeneous solutions, thus monitoring the effect of AF on both types of data. Experimental data are in good agreement with calculated spectra. Simulations with suitable bandshapes show that the red shift of the CD spectrum is due to AF. On the basis of these results, we conclude that AF is an important cause of distortions in CD spectra for inhomogeneous samples. Plans to compensate or at least to take into account this effect are presented.     

Spectroscopic origin of conformation-sensitive contributions to polysaccharide optical activity: Vacuum-ultraviolet circular dichroism of agarose

The vacuum-uv CD of agarose solid films has been measured to 145 nm and shows a positive band near 180 nm and a larger negative band at around 152 nm. The positive band remains accessible in aqueous solution and has been used to characterize changes in molecular conformation and interaction during the sol–gel transition. The temperature profile of vacuum-uv CD shows sharp, discontinuous changes around the melting and setting points of the gel, which are interpreted in terms of cooperative intermolecular association through double helices, and pronounced hysteresis, which is discussed in terms of helix–helix aggregation.