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Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides
Cai, Kaicong; Han, Chen; Wang, Jianping
Source PublicationPHYSICAL CHEMISTRY CHEMICAL PHYSICS
2009
DOI10.1039/b910269h
Volume11Issue:40Pages:9149-9159
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
WOS SubjectChemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS Research AreaChemistry ; Physics
WOS Keyword2-DIMENSIONAL INFRARED-SPECTROSCOPY ; N-METHYLACETAMIDE ; VIBRATIONAL SPECTROSCOPY ; DYNAMICS SIMULATIONS ; BETA-HAIRPIN ; LIQUID WATER ; DIPEPTIDE ; PROTEINS ; SPECTRA ; HELIX
AbstractA molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.
Language英语
WOS IDWOS:000270698900021
Citation statistics
Cited Times:30[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/141578
Collection中国科学院大连化学物理研究所
AffiliationChinese Acad Sci, Inst Chem, State Key Lab Mol React Dynam, Beijing Natl Lab Mol Sci, Beijing 100190, Peoples R China
Recommended Citation
GB/T 7714
Cai, Kaicong,Han, Chen,Wang, Jianping. Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides[J]. PHYSICAL CHEMISTRY CHEMICAL PHYSICS,2009,11(40):9149-9159.
APA Cai, Kaicong,Han, Chen,&Wang, Jianping.(2009).Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides.PHYSICAL CHEMISTRY CHEMICAL PHYSICS,11(40),9149-9159.
MLA Cai, Kaicong,et al."Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides".PHYSICAL CHEMISTRY CHEMICAL PHYSICS 11.40(2009):9149-9159.
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