Molecules-in-molecules fragment-based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

• Published in: Chirality (New York, N.Y.) N.Y.), 2016-12, Vol.28 (12), p.755-768
• Main Authors: Jose, K. V. Jovan, Raghavachari, Krishnan
• Format: Article
• Language: English
• Subjects: Alanine - chemistry; Circular Dichroism - methods; density functional theory; infrared spectroscopy; isotopic labeling; linear scaling methods; Models, Molecular; Peptides - chemistry; Raman optical activity; Spectrum Analysis, Raman - methods; Stereoisomerism; vibrational circular dichroism
• ISSN: 0899-0042; 1520-636X
• DOI: 10.1002/chir.22651

The molecules‐in‐molecules (MIM) fragment‐based method has recently been adapted to evaluate the chiroptical (vibrational circular dichroism [VCD] and Raman optical activity [ROA]) spectra of large molecules such as peptides. In the MIM‐VCD and MIM‐ROA methods, the relevant higher energy derivatives of the parent molecule are assembled from the corresponding derivatives of smaller fragment subsystems. In addition, the missing long‐range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM‐VCD and MIM‐ROA fragment‐based methods to explore the evolution of the chiroptical spectroscopic characteristics of 310‐helix, α‐helix, β‐hairpin, γ‐turn, and β‐extended conformers of gas phase polyalanine (chain length n = 6–14). The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size. For a better understanding the site‐specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled 13C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two‐step‐MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets. The chiroptical spectra of α‐(alanine)20 polypeptide obtained using the two‐step‐MIM model, including continuum solvation effects, show good agreement with the full calculations and experiment. This benchmark study suggests that the MIM‐fragment approach can assist in predicting and interpreting chiroptical spectra of large polypeptides.