Takeyuki Tanaka

Conformational preferences of ethyl propionate molecule: Raman, temperature dependent FTIR spectroscopic study aided by ab initio quantum chemical and Car-Parrinello molecular dynamics simulation studies.

The conformational preferences of the industrially significant ethyl propionate (EP) molecule have been investigated from the Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The vibrational signatures of various rotameric forms of the EP molecule have been assigned for the first time from the potential energy distributions (PEDs). The critical analyses of the vibrational signatures reveal the coexistences of the Trans-Trans (TT), Trans-Antigauche (TG(-)) [Trans-Gauche (TG(+))], Antigauche-Trans (G(-)T) [Gauche-Trans (G(+)T)], Antigauche-Antigauche (G(-)G(-)) [Gauche-Gauche (G(+)G(+))], and Gauche-Antigauche (G(+)G(-)) [Antigauche-Gauche (G(-)G(+))] forms of the EP molecule at room and at high temperatures. However, at low temperature (ca. 70 °C), the TT and TG(-) forms of the EP molecule is estimated to be preponderant. The Car-Parrinello molecular dynamics simulation studies of the EP molecule estimated at high, room, and low temperatures are also in harmony with our conjecture as suggested from the vibrational analyses. The ab intio molecular dynamics simulations are observed to be a useful tool for the conformational analyses of the molecule.

Epimerization in peptide thioester condensation

Peptide segment couplings are now widely utilized in protein chemical synthesis. One of the key structures for the strategy is the peptide thioester. Peptide thioester condensation, in which a C‐terminal peptide thioester is selectively activated by silver ions then condensed with an amino component, is a powerful tool. But the amino acid adjacent to the thioester is at risk of epimerization. During the preparation of peptide thioesters by the Boc solid‐phase method, no substantial epimerization of the C‐terminal amino acid was detected. Epimerization was, however, observed during a thioester–thiol exchange reaction and segment condensation in DMSO in the presence of a base. In contrast, thioester–thiol exchange reactions in aqueous solutions gave no epimerization. The epimerization during segment condensation was significantly suppressed with a less polar solvent that is applicable to segments in thioester peptide condensation. These results were applied to a longer peptide thioester condensation. The epimer content of the coupling product of 89 residues was reduced from 27% to 6% in a condensation between segments of 45 and 44 residues for the thioester and the amino component, respectively. Copyright

Influence of Temperature on the Rotameric Forms of the Propyl Acetate Molecule: Raman and FTIR Spectroscopic Studies Aided by ab Initio and Car–Parrinello Molecular Dynamics Simulations

The conformational preferences of the industrially and biologically significant propyl acetate (PA) molecule have been investigated by Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The PA molecule can exist in various rotameric forms at room temperature, trans-trans [TT], trans-gauche [(TG(+))/(TG(-))], gauche-trans [(G(+)T)/(G(-)T)], and gauche-gauche [(G(+)G(-))/(G(-)G(+))], depending upon the rotation about the O3-C4 and C4-C5 bonds of the molecule. The vibrational signatures of different rotameric forms of the PA molecule have been assigned for the first time. Raman and temperature-dependent FTIR spectra of the PA molecule envisage the coexistence of the TT, TG(+)/TG(-), G(+)T/G(-)T, and G(+)G(-)/G(-)G(+) forms of the PA molecule at room temperature. However, at low (ca. -95 °C) and high temperatures (ca. 65 °C), the TG(+) form of the PA molecule is estimated to be preponderant. These results are substantiated by the CPMD simulations, together with the estimation of fwhm values of the vibrational signatures of the PA molecule recorded at high-, room-, and low-temperature domains.