Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

	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
刊名	physical chemistry chemical physics
	2009
卷号	11 期号:40 页码:9149-9159
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.
WOS标题词	science & technology ; physical sciences
类目[WOS]	chemistry, physical ; physics, atomic, molecular & chemical
研究领域[WOS]	chemistry ; physics
关键词[WOS]	2-dimensional infrared-spectroscopy ; n-methylacetamide ; vibrational spectroscopy ; dynamics simulations ; beta-hairpin ; liquid water ; dipeptide ; proteins ; spectra ; helix
收录类别	SCI
语种	英语
WOS记录号	WOS:000270698900021
公开日期	2015-11-17
内容类型	期刊论文
源URL	[http://159.226.238.44/handle/321008/141578]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
作者单位	Chinese Acad Sci, Inst Chem, State Key Lab Mol React Dynam, Beijing Natl Lab Mol Sci, Beijing 100190, Peoples R China
推荐引用方式 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.