title: Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins.
abstract: 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.
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China. xiaohe@phy.ecnu.edu.cn.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Liu
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.forename: Xiao
authors.initials: X
authors.lastname: He
mesh_terms: D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared; D013059:Spectrum Analysis, Raman; D014732:Vibration
chemical_list: D011506:Proteins