Circular Dichroism Spectral Profiles Research Articles

Evaluation of optical activities by modern semi‐empirical methods

Modern semi‐empirical molecular orbital methods are applied herein to the direct calculation of the optical rotatory strengths of model molecules. In addition to MNDO, AM1, and PM3 methods, RM1, PM6, and PM7 wavefunctions are used for evaluation of the dipole transition moments. The octant rule for carbonyl compounds is well‐adhered to using the RM1, PM6, and PM7 methods and is reasonably consistent with the charge‐transfer perturbations with regard to the substituents. By using the up‐to‐date methods RM1 and PM7, circular dichroism (CD) spectra of a typical helicene are also well‐reproduced using complete active space configuration interactions. The CD spectral profiles are significantly improved relative to those obtained using conventional CNDO/S or INDO/S levels of theory and are complemented by optical rotatory dispersion spectra. As a platform for analyzing biopolymers, test calculations for polypeptides are also presented. © 2013 Wiley Periodicals, Inc.

Spectroscopic Visualization of Right- and Left-Handed Helical Alignments of DNA in Chiral Vortex Flows

Abstract In a vortex generated by mechanical rotary stirring in an optical cell, DNA molecules in pure water temporarily align helically to the spiral flow, and dynamically display strong induced circular dichroism (CD) and linear dichroism (LD) responses. Although a sample solution without stirring provided the characteristic CD spectral pattern of DNA, an entirely different macroscopic CD spectral pattern with a much larger intensity and LD spectrum appeared upon mechanical rotary stirring of the sample solution. Clockwise (CW) and counterclockwise (CCW) stirring resulted in mirror-image CD spectral profiles and virtually the same LD profiles with different intensities. The CW stirring of the sample solution in LD spectroscopy always resulted in larger spectral intensities than CCW stirring, but the differences became negligible upon addition of NaCl or ethidium bromide. The observed CD and LD responses of the stirred sample solution decreased simultaneously as the double-stranded structure denatures with increasing temperatures. The results obtained in this study indicate that DNA, when it forms a double-stranded structure, can effectively align in the vortex flows, and show hydrodynamic preference to a right-handed vortex than to a left-handed vortex.

Theoretical Modeling of Peptide α-Helical Circular Dichroism in Aqueous Solution

Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors contributing to the CD spectra of the α-helical secondary structure. The dependence on the peptide chain length and also the role of the flexibility and solvent environment were investigated with a model oligopeptide Ac-(Ala)(N)-NH-Me, (N = 1, ..., 18). Both the TDDFT and TDC-like methods suggest that the CD curve typical for the α-helix arises gradually, but its basic characteristic is discernible already for peptides with 4-5 amino acid residues. The calculated dependence was in a qualitative agreement with experimental spectra of short α-helices stabilized by the histidine-metal binding. The TDDFT computations of the CD were found to be unusually sensitive to the basis set and solvent model. Explicit hydration and temperature fluctuations of the peptide geometry, simulated with the aid of molecular dynamics (MD), significantly influenced the CD and absorption spectral shapes. An extensive averaging over MD configurations is thus required to obtain a converged spectral profile in cluster simulations. On the other hand, both the TDDFT and TDC models indicate only a minor influence of the alanine side chains. The CIS and TDC calculations also point toward a relatively small effect of the helix-helix interaction on the CD spectral profiles. For a model system of two helices, the CIS method predicted larger changes in the spectra than TDC. This suggests other than interactions between peptide chains, such as mutual polarization, can have a minor, but measurable, effect on the CD spectrum.

Structural and functional comparisons and production of recombinant crustacean hyperglycemic hormone (CHH) and CHH-like peptides from the mud crab Scylla olivacea

Sco-CHH and Sco-CHH-L (CHH-like peptide), two structural variants of the crustacean hyperglycemic hormone family identified in the mud crab ( Scylla olivacea), are presumably alternatively spliced gene products. In this study, Sco-CHH and Sco-CHH-L were isolated from the tissues using high performance liquid chromatography. Identity of the native peptides was confirmed using mass spectrometric (MS) analyses of purified materials and of trypsin-digested peptide fragments. Additionally, characterizations using circular dichroism (CD) spectrometry revealed that the 2 peptides have similar CD spectral profiles, showing they are composed mainly of α-helices, and are similarly thermo-stable with a melting temperature of 74–75 °C. Results of bioassays indicated that Sco-CHH exerted hyperglycemic and molt-inhibiting activity, whereas Sco-CHH-L did not. Further, recombinant Sco-CHH-Gly (rSco-CHH-Gly, a glycine extended Sco-CHH) and Sco-CHH-L (rSco-CHH-L) were produced using an Escherichia coli expression system, refolded, and purified. rSco-CHH-Gly was further α-amidated at the C-terminal end to produce rSco-CHH. MS analyses of enzyme-digested peptide fragments of rSco-CHH-Gly and rSco-CHH-L showed that the two peptides share a common disulfide bond pattern: C7-C43, C23-C39, and C26-C52. Circular dichroism analyses and hyperglycemic assay revealed that rSco-CHH and rSco-CHH-L resemble their native counterparts, in terms of CD spectral profiles, melting curve profiles, and biological activity. rSco-CHH-Gly has a lower α-helical content (32%) than rSco-CHH (47%), a structural deviation that may be responsible for the significant decrease in the biological activity of rSco-CHH-Gly. Finally, modeled structure of Sco-CHH and Sco-CHH-L indicated that they are similarly folded, each with an N-terminal tail region and 4 α-helices. Putative surface residues located in corresponding positions of Sco-CHH and Sco-CHH-L but with side chains of different properties were identified. The combined results support the notion that Sco-CHH and Sco-CHH-L are functionally different, but resemble each other at higher-level structures. Functional diversity between the 2 peptides is probably due to critical residues located in the C-terminus. The availability of large amounts of recombinant proteins will permit additional functional and structural studies of these CHH family peptides.

Enantioselective DNA binding of iron(II) complexes of methyl-substituted phenanthroline

The enantioselective binding of [Fe(4,7-dmp) 3] 2+ (dmp: 4,7-dimethyl-1,10-phenantroline) and [Fe(3,4,7,8-tmp) 3] 2+ (tmp: 3,4,7,8-tetramethyl-1,10-phenanthroline) to calf-thymus DNA (ct-DNA) has been systematically studied by monitoring the circular dichroism (CD) spectral profile of the iron(II) complexes in the absence and presence of ct-DNA. The effect of salt concentration and temperature on the degree of enantioselectivity of the ct-DNA binding of the iron(II) complexes, i.e. the molar ratio of Δ- to Λ-enantiomer in the solution or vice versa has been rigorously evaluated. It is noticeable that Δ-[Fe(4,7-dmp) 3] 2+ and Λ-[Fe(3,4,7,8-tmp) 3] 2+ are preferentially bound to ct-DNA as reflected in their opposite CD spectral profiles. The preferential binding of the Λ-enantiomer of [Fe(3,4,7,8-tmp) 3] 2+ to ct-DNA compared to that of the Δ-enantiomer is associated with the bulkiness of the ancillary ligands due to substitution of four hydrogen atoms in 1,10-phenanthroline for four methyl groups. The determination of enantiomeric inversion constant ( K inv) at various salt concentrations has revealed that the degree of enantioselectivity is salt concentration dependent, indicating that electrostatic interaction is involved in the enantioselective binding of the iron(II) complexes to ct-DNA. Although [Fe(4,7-dmp) 3] 2+ and [Fe(3,4,7,8-tmp) 3] 2+ exhibit an opposite pattern in the CD spectra, the degree of their enantioselectivity ( K inv) is not different from each other significantly. A thermodynamic study on the enantioselective binding of [Fe(4,7-dmp) 3] 2+ to ct-DNA using the van’t Hoff plot of ln K inv versus 1/ T has demonstrated that the enthalpy change (Δ H°) in the inversion process from the Λ- to Δ-enantiomer of [Fe(4,7-dmp) 3] 2+ ct-DNA is positive, indicating that the process is endothermic and thus entropically driven.

Base-specific and enantioselective studies for the DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2- a:2′,3′- c]phenazine

Base specificity and enantioselectivity for the DNA binding of [Fe(phen) 2(dppz)] 2+ (phen = 1,10-phenanthroline and dppz = dipyrido[3,2- a:2′,3′- c]phenazine) have been studied by determining the equilibrium binding constant ( K b) of the iron(II) complex to calf thymus DNA (ct-DNA), poly[(dA–dT) 2], poly[(dG–dC) 2] and poly[(dI–dC) 2] using spectrophotometric titration and by monitoring the CD spectral profile of the iron(II) complex in the presence and absence of different types of DNA using circular dichroism (CD) spectroscopy, respectively. It has been shown that [Fe(phen) 2(dppz)] 2+ prefers to intercalate into the A–T and I–C sequences of poly[(dA–dT) 2] and poly[(dI–dC) 2] rather than into the G–C sequences of poly[(dG–dC) 2] or into the base pairs of ct-DNA. In contrast to previous reports, it is a surprising observation that the enantioselectivity of the DNA binding for [Fe(phen) 2(dppz)] 2+ is base-dependent in nature. The Δ-enantiomer of [Fe(phen) 2(dppz)] 2+ is preferentially intercalated into the base pairs of poly[(dG–dC) 2] or ct-DNA as indicated by its CD spectral profiles. On the other hand, the Λ-enantiomer of [Fe(phen) 2(dppz)] 2+ is favorably intercalated into poly[(dA–dT) 2] or poly[(dI–dC) 2] as suggested by the opposite CD spectral profile. This preferential binding of Λ-[Fe(phen) 2(dppz)] 2+ for the A–T sequence may be attributed to the fact that the binding site for the A–T sequence is relatively facile and thus the steric effect caused by the ancillary (non-intercalated) phen ligands is alleviated. The degree of enantioselectivity represented by inversion constants ( K inv) decreases as the salt concentration in the solution increases, indicating that electrostatic interaction is also operating in the ct-DNA-binding events of the iron (II) complex.

Specific recognition of chiral amino alcohols via lanthanide coordination chemistry: structural optimization of lanthanide tris(beta-diketonates) toward effective circular dichroism/fluorescence probing.

Lanthanide tris(beta-diketonates) formed stable, 1:1 highly coordinated complexes with amino alcohols, and the resulting complexes exhibited large enhanced fluorescence and intense induced circular dichroism (CD) signals. The stability constants of the highly coordinated complexes were determined for various combinations of lanthanide centers, beta-diketonate ligands, and organic substrates. These revealed that amino alcohol coordinated with the lanthanide center much more strongly than monoamine, monoalcohol, or diol derivative. On the basis of the highly coordinated complexation, several lanthanide tris(beta-diketonates) acted as CD/fluorescence probes specific for amino alcohols. Tris(6,6,7,7,8,8,8-heptafluoro-2,2-dimethyl-3,5-octadionato)europium(III) showed enhanced fluorescence in the presence of amino alcohols, while the corresponding ytterbium complex exhibited chirality-dependent CD signals for amino alcohols. In particular, the observed CD spectral profiles related well with the absolute configuration and optical purity of the bound amino alcohol, indicating that the structural optimization of lanthanide tris(beta-diketonates) offered specific sensing of amino alcohols and precise determination of their enantiomer excess percentages.

DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline

Absorption spectroscopy and circular dichroism (CD) have been used to characterize the DNA binding of [Fe(phen) 3] 2+, [Fe(phen) 2(DIP)] 2+ and [Fe(phen)(DIP) 2] 2+ where phen and DIP stand for 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline, respectively. Both [Fe(phen) 3] 2+ and [Fe(phen) 2(DIP)] 2+ bind weakly to calf thymus DNA (CT-DNA) in an electrostatic mode, while [Fe(phen)(DIP) 2] 2+ binds more strongly to CT-DNA, possibly in an intercalation mode. The hypochromicity, red shift and K b increase in the order [Fe(phen) 3] 2+<[Fe(phen) 2(DIP)] 2+<[Fe(phen)(DIP) 2] 2+ in accordance with the increase in size and hydrophobicity of the iron(II) complexes. The thermodynamic parameters obtained suggest that the DNA binding of both [Fe(phen) 3] 2+ and [Fe(phen) 2(DIP)] 2+ is entropically driven, while that of [Fe(phen)(DIP) 2] 2+ is enthalpically driven. A strong CD spectrum in the UV and visible region develops upon addition of CT-DNA into the racemate solution of each iron(II) complex (Pfeiffer effect). This has revealed that a shift in diastereomeric inversion equilibrium takes place in the solution to yield an excess of one of the DNA-complex diastereomers. The striking resemblance of the CD spectral profiles to those of the pure Δ-enantiomer indicates that the Δ-enantiomer of the iron(II) complexes is preferentially bound to CT-DNA. The mechanism of the development of Pfeiffer CD is proposed on the basis of kinetic studies on the DNA binding of the racemic iron(II) complexes.