Dichroism, defined

The question posed above was whether the X-ray structure of the reaction center from Rb. sphaeroides R-26 predicted a linear dichroism consistent with that measured on the single crystals. In order to see if the experimentally observed linear dichroism (defined as a polarization ratio) is consistent with that predicted from the X-ray diffraction data, we shall focus on the spectral features of the bacteriopheophytin Qx transitions near 540 nm. 

Ever since Pasteur s work with enantiomers of sodium ammonium tartrate, the interaction of polarized light has provided a powerful, physical probe of molecular chirality [18]. What we may consider to be conventional circular dichroism (CD) arises from the different absorption of left- and right-circularly polarized light by target molecules of a specific handedness [19, 20]. However, absorption measurements made with randomly oriented samples provide a dichroism difference signal that is typically rather small. The chirally induced asymmetry or dichroism can be expressed as a Kuhn g-factor [21] defined as ... 

Circular dichroism convention. In this chapter, dichroism and asymmetry factors are defined as /icp hep or / =... 

Because of their high molecular weight and their defined structure, dendrimers offer themselves for studying the expression of chirality on a macromolecular level. The construction of configurationally uniform macromolecules is otherwise a complex task but can be achieved more easily with dendrimers because of repetitive synthesis from identical (chiral) building blocks. Comparison of optical rotation values and circular dichroism (CD) spectra should demonstrate what influence there is of the chiral building blocks on the structure of the whole dendrimer. 

Linear Dichroism. In this technique, the DNA molecules are aligned either by an applied electric field pulse or in a flow gradient. The orientation of the aromatic residues of the metabolite model compounds bound to the DNA (either covalently or non-covalently) relative to the orientation of the DNA bases is probed utilizing linearly polarized light. The linear dichroism A A can be either negative or positive, and is defined as... 

The enzymatic activities of O -chymotrypsin in solution and adsorbed at the different surfaces are presented in Fig. 11, where the specific enzymatic activity (defined as activity per unit mass of protein) is plotted as a function of temperature. The enzyme loses activity due to adsorption. On the hydrophobic Teflon and PS surfaces, the activity is completely gone, whereas on the hydrophilic silica surface, or-chymotrypsin has retained most of its biological function. These differences are in agreement with the adsorption isotherms and the circular dichroism spectra. The influence of the hydrophobicity of the sorbent surface on the affinity of the protein for the sorbent surface, as judged from the rising parts of the adsorption isotherms (Fig. 8), suggests that the proteins are more perturbed and, hence, less biologically active when adsorbed at hydrophobic surfaces. Also, the CD spectra indicate that adsorption-induced structural perturbations are more severe at hydrophobic surfaces. 

It was found that In D decays linearly with time [where D is the dichroic ratio defined in Eq. (2)]. The time constant for the decay of the dichroism, r, is plotted vs temperature-1 in Fig. 25. It was shown (Stavola et al., 1988b) that the time constant, r, for a single H jump from one BC site adjacent to the B to another given by r=4r. From the fit to the data shown in Fig. 25 the following expression for the time constant for a single H jump was obtained ... 

Figure 4.8. Calculated value of the rms amplitude or local polar libration (<5e2> /2) that satisfies Eq. (4.60) or Eq. (4.61) versus the assumed equilibrium polar angle (e0). The solid lines are the solutions of Eq. (4.60) for the indicated values of the reduced linear dichroism (LDr). The dashed lines are the solutions of Eq. (4.61) for the indicated values of A when the local angulaT motion of the transition dipole is assumed to be isotropic. The dotted lines are the solutions of Eq. (4.61) for the indicated values of A when the local angular motion of the transition dipole is assumed to be purely polar. The intersection of pairs of curves defines the region allowed" by a particular pair of LDr and A values and a particular assumption about the degree of anisotropy of the local angular motion of the transition dipole. If the LDr lies between -0.92 and -1.02, as indicated by experiment, then for isotropic internal motion, e0 = 70.5°, and 1/2 = 0.122 (7°) fall in the allowed region.

Circular dichroism and optical rotation for particulate media may be operationally defined in terms of the Stokes parameters (2.80), which in the circular polarization representation are written... 

Circular dichroism arises from the same optically active transitions responsible for the Cotton effects observed in ORD curves, but unlike ORD it is an absorption, not a dispersion, phenomenon. Hence, the CD effect is restricted to the region of the transition and can be interpreted more straightforwardly. Both ORD and CD can best be understood if one imagines the incident plane-polarized beam resolved into two in-phase circularly polarized beams whose vectors rotate in opposite directions. A difference in index of refraction between the left and right circularly polarized beams results in rotation of the transmitted plane polarized beam while differential absorption of the two circularly polarized beams results in depolarization of the transmitted beam, so that an incident plane-polarized beam whose frequency is within that of an optically active absorption band becomes both rotated and elliptically polarized upon passage through the sample. This depolarization effect is CD, and the measured parameter is (et — er), the difference in extinction coefficient between the left and right circularly polarized beams. The data is usually recorded as the specific ellipticity, defined as ... 

Figure B3.5.3 The relation of ellipticity to the differential absorption of circularly polarized radiation. The oscillating radiation sine wave, 01, is proceeding out of the plane of the paper towards the viewer. (A) Plane-polarized radiation is made up of left- and right-handed circularly polarized components, OL and OR, respectively. Absorption by a chromophore in a nonchiral environment results in an equal reduction in intensity of each component, whose resultant is a vector oscillating only in the vertical plane—i.e., plane-polarized radiation. (B) Interaction of the radiation with achiral chromophore leads to unequal absorption, so that combination of the emerging vectors, OL and OR, leads to a resultant that describes an elliptical path as it progresses out of the plane of the paper. The ratio of the major and minor axes of the ellipse is expressed by tan 0, thus defining ellipticity. The major axis of the ellipse makes an angle (q) with the original plane, which defines the optical rotation. This figure thus demonstrates the close relation between optical rotation and circular dichroism.

The syntheses of heterostranded coiled coils are presented (Section 13.2.2.4), as are templates and conformationally defined peptide libraries (Sections 13.2.4 and 13.2.4.1). Finally, Section 13.1 concludes with a presentation of the methods for characterization of the coiled coils including circular dichroism, microcalorimetry, size-exclusion chromatography, and analytical ultracentrifugation (Section 13.2.5). 

Triply bridged dinuclear Fe(n) complexes of a bis-N-hydroxy-pyridinone [9.82a] and of bis(bipy) ligands [9.61, 9.82b] possess triple-helical features. A triple-helical arrangement has been assigned to dinuclear Fe(lll) complexes of tripodal ligands on the basis of NMR and circular dichroism (CD) data [9.82c]. The self-assembly of well-defined triple-helical dinuclear cobalt(ll) [9.83] and lanthanide(lll) [9.84] complexes has been achieved. 

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