Exploring the Isomer Landscape, Fragment Additivity, and Vibrational Signatures of the Z-Alanine Protected Amino Acid Derivative

The <i>N</i>-benzyloxycarbonyl-l-alanine molecule is a derivative of the l-α-alanine amino acid with a benzyl carbamate protecting group at the N-terminus, more commonly denoted Cbz-Ala or Z-Ala. In this computational investigation, we sought to determine the available isomers of Z-Ala and their distinguishing spectroscopic signatures via quantum-chemistry methods. Sixty-five total isomers were obtained, and coupled-cluster- and perturbation-theory-based relative energies were computed. The two nearly degenerate, lowest-energy isomers were found to differ in their configuration than the lowest-energy form of isolated alanine, suggesting that the protecting group changes the dominant form of Ala. Through comparisons to exhaustive sampling of Ala and benzyl formate isomers, nearly all of the Z-Ala structures could be ascribed to fragment-paired structural motifs, with a few outliers exhibiting new intramolecular interactions between the constituent fragments. Based on this observation, an assessment of the additivity of the two fragments' relative energies was performed for Z-Ala energies. Many of the isomers' energies were reasonably described by such considerations, although backbone strain and hydrogen-bonding interactions altered this energy landscape and led to nonadditive effects for several of the isomers. Comparison to experimental REMPI-based UV/IR ion-dip vibrational spectra in the 90-1822 cm^-1 region indicated that two isomers are dominantly present at the experimental conditions, although signatures of other isomers from the ensemble were also observed. Clear assignments of structural motifs were possible through this experimental comparison. Computed coupled-cluster benchmarks allowed for methodology assessments in this study. The modified opposite-spin MP2 method (MOS-RI-MP2) was found to be particularly accurate, relative to these benchmarks, after minor adjustment of the range-separation parameter. Density functional theory (DFT) methods were found to be variable in their accuracy for both energies and spectra, although a few key functionals performed particularly well for this system in the low-frequency region of the vibrational spectrum. These methodology constraints provided recommendations for similar systems and subsequent anharmonic analyses.