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题名: Treating hydrogen bonding in ab initio calculation of biopolymers
作者: Mei, Y;  Wu, EL;  Han, KL;  Zhang, JZH
通讯作者: 张增辉
关键词: ab initio ;  protein ;  hydrogen bonding ;  alpha-helix ;  beta-sheet ;  polarization
刊名: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
发表日期: 2006-04-05
DOI: 10.1002/qua.20875
卷: 106, 期:5, 页:1267-1276
收录类别: SCI
文章类型: Article
部门归属: 11
项目归属: 1101
产权排名: 2;2
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Physical ;  Mathematics, Interdisciplinary Applications ;  Physics, Atomic, Molecular & Chemical
研究领域[WOS]: Chemistry ;  Mathematics ;  Physics
英文摘要: We present a general scheme to treat backbone hydrogen bonding in protein using the molecular fractionation with conjugate caps (MFCC) approach. In this approach, molecular caps are employed to mimic the hydrogen bonding environment of protein fragments that are calculated individually. Using this scheme in the MFCC method, we carried out explicit numerical calculations for a number of secondary structures of proteins, including the alpha-helix and beta-sheet. The calculated electron densities, electrostatic potentials, and dipole moment are compared with those from the standard full system ab initio calculations. The result shows that the current treatment using the hydrogen bond cap gives an accurate description of the hydrogen bonding effect and accurate dipole moment. In contrast, calculation using the standard force field (FF) approach gives dipole moments that are in huge error (i.e., significantly smaller) than the quantum result for helix structures due to the lack of polarization effect with fixed partial charges. The present study demonstrates that the MFCC approach can quantitatively describe hydrogen bonding in practical ab initio Calculation of proteins. Our result also underscores the importance of the polarization effect in backbone hydrogen bonding of protein. This could have significant implication in studying the electrostatic interaction of proteins, such as protein solvation. (c) 2005 Wiley Periodicals, Inc.
关键词[WOS]: QUANTUM-MECHANICAL CALCULATION ;  INTERACTION ENERGY ;  MOLECULAR-DYNAMICS ;  ELECTRON-DENSITY ;  FORCE-FIELD ;  PROTEIN ;  FRACTIONATION ;  POLYPEPTIDES ;  COMPUTATION ;  PROGRAM
语种: 英语
原文出处: 查看原文
WOS记录号: WOS:000235537700021
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/97315
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.Nanjing Univ, Inst Theoret & Computat Chem, Coll Chem & Chem Engn, Nanjing 210093, Peoples R China
2.Chinese Acad Sci, Ctr Computat Chem, Dalian 116023, Peoples R China
3.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
4.NYU, Dept Chem, New York, NY 10003 USA

Recommended Citation:
Mei, Y,Wu, EL,Han, KL,et al. Treating hydrogen bonding in ab initio calculation of biopolymers[J]. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY,2006,106(5):1267-1276.
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