Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins.

Geometry optimization and vibrational spectra (infrared and Raman spectra) calculations of proteins are carried out by a quantum chemical approach using the EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) method (J. Phys. Chem. A, 2013, 117, 7149). The first and second derivatives of the EE-GMFCC energy are derived and employed in geometry optimization and vibrational frequency calculations for several test systems, including a polypeptide ((GLY)6), an α-helix (AKA), a β-sheet (Trpzip2) and ubiquitin (76 residues with 1231 atoms). Comparison of the present results with those obtained from full system QM (quantum mechanical) calculations shows that the EE-GMFCC approach can give accurate molecular geometries, vibrational frequencies and vibrational intensities. The EE-GMFCC method is also employed to simulate the amide I vibration of proteins, which has been widely used for the analysis of peptide and protein structures, and the results are in good agreement with the experimental observations.