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题名: Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides
作者: Cai, Kaicong1;  Han, Chen1;  Wang, Jianping1
刊名: PHYSICAL CHEMISTRY CHEMICAL PHYSICS
发表日期: 2009
DOI: 10.1039/b910269h
卷: 11, 期:40, 页:9149-9159
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Physical ;  Physics, Atomic, Molecular & Chemical
研究领域[WOS]: Chemistry ;  Physics
英文摘要: A 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.
关键词[WOS]: 2-DIMENSIONAL INFRARED-SPECTROSCOPY ;  N-METHYLACETAMIDE ;  VIBRATIONAL SPECTROSCOPY ;  DYNAMICS SIMULATIONS ;  BETA-HAIRPIN ;  LIQUID WATER ;  DIPEPTIDE ;  PROTEINS ;  SPECTRA ;  HELIX
语种: 英语
WOS记录号: WOS:000270698900021
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/141578
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Inst Chem, State Key Lab Mol React Dynam, Beijing Natl Lab Mol Sci, Beijing 100190, Peoples R China

Recommended Citation:
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.
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