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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
刊名PHYSICAL CHEMISTRY CHEMICAL PHYSICS
2009
DOI10.1039/b910269h
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
关键词[WOS]2-DIMENSIONAL INFRARED-SPECTROSCOPY ; N-METHYLACETAMIDE ; VIBRATIONAL SPECTROSCOPY ; DYNAMICS SIMULATIONS ; BETA-HAIRPIN ; LIQUID WATER ; DIPEPTIDE ; PROTEINS ; SPECTRA ; HELIX
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.
语种英语
WOS记录号WOS:000270698900021
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被引频次:28[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/141578
专题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
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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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