Enantiomeric purity of drugs is essential for their biological activity. In the present study, we investigate the performance of Raman optical activity (ROA) spectroscopy in distinguishing four possible stereoisomers of the synthetic precursor used for the production of taxol from baccatin III. Taxol is one of the best-selling medicaments used in the treatment of ovarian, lung, and breast cancers and Kaposi's sarcoma. In a low yield, it may be isolated from the bark of the Pacific yew tree (Taxus brevifolia); however, its industrial production is largely dependent on the precursor. It is shown that for reliable comparison of the experimental and computed Raman and ROA intensities a large number of conformers had to be averaged, to properly account for molecular flexibility in solution. In addition, if combined with the density functional theory computations, ROA spectra provide convenient and economic means of absolute configuration determination.
A novel descriptor for protein structure is examined here that goes beyond predictions of the average fractional components (FC) of a few conformational types and represents the number and interconnection of segments of continuous, well-defined secondary structural elements such as alpha-helices and beta-sheets. This matrix descriptor can be predicted from optical spectra using neural network methods. The new matrix plus traditional FC descriptors can be quickly and generally obtained to provide a level of detail not previously derived from optical spectra and a discrimination between proteins that might otherwise be viewed as being very similar using just the FC descriptor. As an example of its potential utilization, this matrix descriptor approach was applied to an analysis of both the native state and the reversible thermal denaturation of ribonuclease T1 in H2O. Analyses of the FTIR spectral data indicate initial loss of the major helical segment at 50-55 degrees C but with little accompanying change in the number of sheet segments or the sheet FC values. Circular dichroism (CD) and vibrational CD data are also used to support this interpretation based on FC changes with temperature. Parallel analysis of the corresponding data for this protein in D2O demonstrates that the method is sensitive to the match between the degree of H-D exchange used to prepare samples for the unknown and the reference data set.
Structures of the UCCG and UGCG tetraloops formed in octamer ribonucleotidic hairpin sequences, i.e., 5'-r[GC(UCCG)GC]-3' and 5'-r[GC(UGCG)GC]-3', have been studied in aqueous solution by methods of optical spectroscopy. UV absorption melting profiles of these short hairpins, containing only two closing GC base pairs in the stem, are consistent with a monophasic, completely reversible order-to-disorder transition and clearly confirm their unusual structural stability (with Tm congruent with 50 degrees C). To establish structural characteristics of these tetraloops, Raman and FTIR spectroscopies have been used and vibrational conformation markers arising from the phosphate backbone and various nucleosides have been analyzed. They have been assigned on the basis of known unambiguous vibrational markers established for DNA and RNA chains. Surprisingly, they are easily transferable to short oligonucleotidic sequences. Intensities and wavenumbers of these conformation markers have been monitored in the 0-70 degrees C temperature range, i.e., in going from an ordered to a disordered structure. The main structural features of the UCCG and UGCG tetraloops are similar to those previously found in the UUCG and UACG tetraloops by means of NMR and vibrational spectroscopies, except those of the second nucleosides of the tetraloops (rC and rG, respectively) which adopt a 3'-endo/anti rather than a 2'-endo/anti conformation.
Infrared and Raman spectra of 1 M aqueous solution of tetrahydrofuran (THF) were recorded in the 850−3050 and 560−3050 cm-1 frequency range, respectively. The effects of hydrogen bonding on vibrational spectra of THF were analyzed by comparing spectra of aqueous solution with the spectra of liquid and solid THF reported previously by Cadioli et al. [J. Phys. Chem. 1993, 97, 7844]. More regular band shapes and smaller bandwidths of ring stretching modes indicate that the barrier for pseudorotation of the furanose ring increases in aqueous solution. This finding is in agreement with the results of our ab initio calculations using the Langevin dipoles (LD) solvation model, which predicted that the pseudorotational barrier of gaseous THF increases in aqueous solution by 0.25 ± 0.1 kcal/mol. Considering available gas-phase data, the free energy barrier for the pseudorotation in aqueous solution was estimated to be 0.5 ± 0.2 kcal/mol. The geometric structure and harmonic force fields of the C2 conformer of THF were calculated by using the Hartree−Fock (HE), density functional theory (DFT), and Møller−Plesset perturbation theory of the second order (MP2). The scale factors for the S-VWN, B3-LYP and B-LYP density functional, and HF force constants of THF were determined. These scaled force fields were found to reproduce the observed frequencies with the overall 1% accuracy, with the B3-LYP method providing the most accurate results. The obtained agreement between the calculated and experimental infrared intensities, nonresonant Raman intensities, and depolarization ratios supports the proposed spectral assignment. The scale factors calculated here for THF augment scale factors determined previously for other nucleotide components: dimethyl phosphate and nucleic acid bases. Consequently, reliable ab initio interpretations of the vibrational spectra of nucleic acids in aqueous solution can be obtained in the future by using the concept of the transferability of scale factors from these nucleic acid constituents.
