Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 18, Issue 3, Pages 1864-1875Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/c5cp05693d
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Funding
- National Natural Science Foundation of China [21433004, 21303057]
- Shanghai Putuo District [2014-A-02]
- Specialized Research Fund for the Doctoral Program of Higher Education [20130076120019]
- Fundamental Research Funds for the Central Universities
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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 a-helix (AKA), a beta-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.
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