Conformational Dependence of the Circular Dichroism Spectrum of α‑Hydroxyphenylacetic Acid: A ChiraSac Study

The conformational dependence of the circular dichroism (CD) spectrum of a chiral molecule, α-hydroxyphenylacetic acid (HPAA) containing phenyl, COOH, OH and H groups around a chiral carbon atom, has been studied theoretically by using the SAC-CI (symmetry adapted cluster–configuration interaction) theory. The results showed that the CD spectrum of HPAA depends largely on the rotations (conformations) of the phenyl and COOH groups around the single bonds. The first band is due to the excitation of electrons belonging to the phenyl region and therefore sensitive to the phenyl rotation. The second band is due to the excitation of electrons belonging to the COOH region and therefore sensitive to the COOH rotation. From the comparison of the SAC-CI CD spectra calculated at various conformations of phenyl, COOH, and OH groups with the experimental spectrum, we could predict the stable geometry of this molecule, which agreed well with the most stable conformation deduced from the energy criterion. We also calculated the Boltzmann averaged spectrum and obtained better agreement with the experiment. Further, we performed preliminary investigations of the temperature dependence of the CD spectrum of HPAA. In general, the CD spectra of chiral molecules are very sensitive to low-energy processes like the rotations around the single bonds. Therefore, one should be able to study the natures of the weak interactions by comparing the SAC-CI spectra calculated at different geometries and conditions with the experimental spectrum using a new methodology we have termed ChiraSac

Circular Dichroism Spectra of Uridine Derivatives: ChiraSac Study

The experimental circular dichroism (CD) spectra of uridine and NH2-uridine that were different in the intensity and shape were studied in the light of the ChiraSac method. The theoretical CD spectra at several different conformations using the symmetry-adapted-cluster configuration-interaction (SAC-CI) theory largely depended on the conformational angle, but those of the anti-conformers and the Boltzmann average reproduced the experimentally obtained CD spectra of both uridine and NH2-uridine. The differences in the CD spectra between the two uridine derivatives were analyzed by using the angle θ between the electric transition dipole moment (ETDM) and the magnetic transition dipole moment (MTDM)

Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study

The helical structure is experimentally determined by circular dichroism (CD) spectra. The sign and shape of the CD spectra are different between B-DNA with a right-handed double-helical structure and Z-DNA with a left-handed double-helical structure. In particular, the sign at around 295 nm in CD spectra is positive for B-DNA, which is opposite to that of Z-DNA. However, it is difficult to determine the helical structure from the UV absorption spectra. Three important factors that affect the CD spectra of DNA are (1) the conformation of dG monomer, (2) the hydrogen-bonding interaction between two helices, and (3) the stacking interaction between nucleic acid bases. We calculated the CD spectra of (1) the dG monomer at different conformations, (2) the composite of dG and dC monomers, (3) two dimer models that simulate separately the hydrogen-bonding interaction and the stacking interaction, and (4) the tetramer model that includes both hydrogen-bonding and stacking interactions simultaneously. The helical structure of DNA can be clarified by a comparison of the experimental and SAC-CI theoretical CD spectra of DNA and that the sign at around 295 nm of the CD spectra of Z-DNA reflects from the strong stacking interaction characteristic of its helical structure

Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC–CI Study

The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC–CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC–CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology