Citation: CAI Kai-Cong, LIU Shan-Hong, LIU Di-Wen, LIN Shen. Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide[J]. Acta Physico-Chimica Sinica, ;2012, 28(08): 1837-1842. doi: 10.3866/PKU.WHXB201205021 shu

Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide

1.
College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, P. R. China

Received Date: 12 March 2012
Available Online: 2 May 2012
Fund Project: 国家自然科学基金(21103021) (21103021) 福建省自然科学基金(2011J05022) (2011J05022)福建师范大学优秀青年骨干教师培养基金(fjsdjk2012066)资助项目 (fjsdjk2012066)

Ab initio calculation was performed on the model peptide compound alanine dipeptide. The population of the secondary structures and the corresponding potential energies of alanine dipeptide were investigated. Normal mode analysis was performed on the amide vibrational modes, which are known to be quite sensitive to the molecular structure, and the correlation between the vibrational feature and the molecular structure was then revealed. The results show that alanine dipeptide has a minimum potential energy when the backbone dihedral is positioned at Φ/Ψ =-80°/80° , which can be denoted as a C_7eq conformation. It is also possible to form the secondary structures with β sheet, PP_II, C₅, and C₇ conformations for their low potential energies. The vibrational parameters of the 3N-6 vibrational motions were obtained through normal mode analysis. The amide vibrational modes were then assigned by the potential energy distribution analysis. The amide-I mode, mostly consisting of backbone C＝O stretching, was introduced for the prediction of the secondary structure of alanine dipeptide. The correlation between the amide-I vibrational parameters and the molecular structures is then demonstrated. Thus is a new way for the prediction of structural features of peptide and protein systems at the chemical bond level.
- Ab initio calculation,
- Alanine dipeptide,
- Vibrational spectroscopy,
- Amide-I mode,
- Normal mode analysis,
- Potential energy distribution
1. [1]
  
  (1) Krimm, S.; Bandekar, J. Adv. Protein Chem. 1986, 38, 181. doi: 10.1016/S0065-3233(08)60528-8
2. [2]
  (2) Wang, J. P. Chinese Science Bulletin 2007, 52, 1221. [王建平.科学通报, 2007, 52, 1221.]
3. [3]
  (3) Cho, M. Chem. Rev. 2008, 108, 1331. doi: 10.1021/cr078377b
4. [4]
  (4) Zheng, J. R. Physics 2010, 39, 162. [郑俊荣. 物理, 2010, 39,162.]
5. [5]
  (5) Kim, Y. S.; Hochstrasser, R. M. J. Phys. Chem. B 2009, 113,8231. doi: 10.1021/jp8113978
6. [6]
  (6) Wang, J. P. Chin. J. Chem. Phys. 2007, 20, 509. [王建平. 化学物理学报, 2007, 20, 509.] doi: 10.1088/1674-0068/20/05/509-517
7. [7]
  (7) Zhuang,W.; Hayashi, T.; Mukamel, S. Angew. Chem. Int. Edit.2009, 48, 3750. doi: 10.1002/anie.200802644
8. [8]
  (8) Cai, K. C.;Wang, J. P. Acta Phys. -Chim. Sin. 2009, 25, 677.[蔡开聪, 王建平. 物理化学学报, 2009, 25, 677.] doi: 10.3866/PKU.WHXB200904021
9. [9]
  (9) Zhuang,W.; S urakis, N. G.; Li, Z. Y.; Garcia, A. E.;Mukamel, S. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 15687.doi: 10.1073/pnas.1002131107
10. [10]
  (10) Bian, H.;Wen, X.; Li, J.; Chen, H.; Han, S.; Sun, X.; Song, J.;Zhuang,W.; Zheng, J. Proc. Natl. Acad. Sci. U. S. A. 2011, 108,4737. doi: 10.1073/pnas.1019565108
11. [11]
  (11) Cai, K.;Wang, J. J. Phys. Chem. B 2009, 113, 1681. doi: 10.1021/jp8070025
12. [12]
  (12) Barber-Armstrong,W.; Donaldson, T.;Wijesooriya, H.; Silva,R. A. G. D.; Decatur, S. M. J. Am. Chem. Soc. 2004, 126, 2339.doi: 10.1021/ja037863n
13. [13]
  (13) Huang, C. Y.; Getahun, Z.; Zhu, Y.; Klemke, J.W.; DeGrado,W.F.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 2788. doi: 10.1073/pnas.052700099
14. [14]
  (14) Du, D.; Zhu, Y.; Huang, C. Y.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15915. doi: 10.1073/pnas.0405904101
15. [15]
  (15) Lin, Y. S.; Shorb, J. M.; Mukherjee, P.; Zanni, M. T.; Skinner, J.L. J. Phys. Chem. B 2009, 113, 592.
16. [16]
  (16) Roy, S.; Lessing, J.; Meisl, G.; Ganim, Z.; Tokmakoff, A.;Knoester, J.; Jansen, T. L. C. J. Chem. Phys. 2011, 135, 234507.
17. [17]
  (17) Wang, J. Phys. Chem. Chem. Phys. 2009, 11, 5310.
18. [18]
  (18) Cai, K. C.; Han, C.;Wang, J. P. Phys. Chem. Chem. Phys. 2009,11, 9149.
19. [19]
  (19) Wang, J. J. Phys. Chem. B 2008, 112, 4790. doi: 10.1021/jp710641x
20. [20]
  (20) Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B 2006, 110, 3798.doi: 10.1021/jp0530092
21. [21]
  (21) Han, C.;Wang, J. Chin. J. Chem. Phys. 2011, 24, 529.[韩晨, 王建平. 化学物理学报, 2011, 24, 529.] doi: 10.1088/1674-0068/24/05/529-537
22. [22]
  (22) Wang, L.; Middleton, C. T.; Zanni, M. T.; Skinner, J. L. J. Phys. Chem. B 2011, 115, 3713.
23. [23]
  (23) Hermans, J. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3095. doi: 10.1073/pnas.1019470108
24. [24]
  (24) Jamróz, M. H. Vibrational Energy Distribution Analysis VEDA 4,Warsaw, 2004-2010.
25. [25]
  (25) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al . Gaussian 09, Revision A.01; Gaussian Inc.:Wallingford, CT, 2009.
26. [26]
  (26) Wang, Z. X.; Duan, Y. J. Comput. Chem. 2004, 25, 1699. doi: 10.1002/jcc.20092
27. [27]
  (27) Kim, Y. S.;Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B2005, 109, 7511. doi: 10.1021/jp044989d
28. [28]
  (28) Vargas, R.; Garza, J.; Hay, B. P.; Dixon, D. A. J. Phys. Chem. A2002, 106, 3213. doi: 10.1021/jp013952f
29. [29]
  (29) Kim, Y. S.; Hochstrasser, R. M. J. Phys. Chem. B 2005, 109,6884. doi: 10.1021/jp0449511
30. [30]
  (30) Badger, R. M. J. Chem. Phys. 1934, 2, 128. doi: 10.1063/1.1749433
31. [31]
  (31) Badger, R. M. J. Chem. Phys. 1935, 3, 710. doi: 10.1063/1.1749581
1. [1]
  Meiyu Lin , Yuxin Fang , Songzhang Shen , Yaqian Duan , Wenyi Liang , Chi Zhang , Juan Su . Exploration and Implementation of a Dual-Pathway Blended Teaching Model in General Chemistry Experiment Course: A Case Study of Copper Glycine Synthesis and Its Thermal Analysis. University Chemistry, 2024, 39(8): 48-53. doi: 10.3866/PKU.DXHX202312042
2. [2]
  Tianlong Zhang , Rongling Zhang , Hongsheng Tang , Yan Li , Hua Li . Online Monitoring and Mechanistic Analysis of 3,5-diamino-1,2,4-triazole (DAT) Synthesis via Raman Spectroscopy: A Recommendation for a Comprehensive Instrumental Analysis Experiment. University Chemistry, 2024, 39(6): 303-311. doi: 10.3866/PKU.DXHX202312006
3. [3]
  Zhuomin Zhang , Hanbing Huang , Liangqiu Lin , Jingsong Liu , Gongke Li . Course Construction of Instrumental Analysis Experiment: Surface-Enhanced Raman Spectroscopy for Rapid Detection of Edible Pigments. University Chemistry, 2024, 39(2): 133-139. doi: 10.3866/PKU.DXHX202308034
4. [4]
  Jingyi Chen , Fu Liu , Tiejun Zhu , Kui Cheng . Practice of Integrating Ideological and Political Education into Raman Spectroscopy Analysis Experiment Course. University Chemistry, 2024, 39(2): 140-146. doi: 10.3866/PKU.DXHX202310111
5. [5]
  Tianlong Zhang , Jiajun Zhou , Hongsheng Tang , Xiaohui Ning , Yan Li , Hua Li . Virtual Simulation Experiment for Laser-Induced Breakdown Spectroscopy (LIBS) Analysis. University Chemistry, 2024, 39(6): 295-302. doi: 10.3866/PKU.DXHX202312049
6. [6]
  Meijin Li , Xirong Fu , Xue Zheng , Yuhan Liu , Bao Li . The Marvel of NAD⁺: Nicotinamide Adenine Dinucleotide. University Chemistry, 2024, 39(9): 35-39. doi: 10.12461/PKU.DXHX202401027
7. [7]
  Tianlong Zhang , Rongling Zhang , Hongsheng Tang , Yan Li , Hua Li . Exploration on the Integration Mode of Instrumental Analysis with Science and Education under the Background of Artificial Intelligence Era. University Chemistry, 2024, 39(8): 365-374. doi: 10.12461/PKU.DXHX202403014
8. [8]
  Yaqian Duan , Juan Su , Meiyu Lin , Yuxin Fang , Wenyi Liang . Exploration of the Implementation Path of Ideological and Political Education in the “Dual-Track Teaching” Model: a Case Study of Analytical Chemistry Experiment. University Chemistry, 2024, 39(2): 181-188. doi: 10.3866/PKU.DXHX202307024
9. [9]
  Jiaqi Chen , Shuwei Chen , Suocai Ren , Yue Sun , Chunhui Luan , Xu Wu . Exploring the People-Centered Safety Construction Model in Basic Chemistry Laboratories: A Case Study in Analytical Chemistry Laboratories. University Chemistry, 2024, 39(7): 264-271. doi: 10.3866/PKU.DXHX202311009
10. [10]
  Cheng Zheng , Shiying Zheng , Yanping Zhang , Shoutian Zheng , Qiaohua Wei . Synthesis, Copper Content Analysis, and Luminescent Performance Study of Binuclear Copper (I) Complexes with Isomeric Luminescence Shift: A Comprehensive Chemical Experiment Recommendation. University Chemistry, 2024, 39(7): 322-329. doi: 10.3866/PKU.DXHX202310131
11. [11]
  Jia Zhou . Constructing Potential Energy Surface of Water Molecule by Quantum Chemistry and Machine Learning: Introduction to a Comprehensive Computational Chemistry Experiment. University Chemistry, 2024, 39(3): 351-358. doi: 10.3866/PKU.DXHX202309060
12. [12]
  Tingting Yu , Si Chen , Lianglong Sun , Tongtong Shi , Kai Sun , Xin Wang . Comprehensive Experimental Design for the Photochemical Synthesis, Analysis, and Characterization of Difluoropyrroles. University Chemistry, 2024, 39(11): 196-203. doi: 10.3866/PKU.DXHX202401022
13. [13]
  Hao Wu , Zhen Liu , Dachang Bai . ¹H NMR Spectrum of Amide Compounds. University Chemistry, 2024, 39(3): 231-238. doi: 10.3866/PKU.DXHX202309020
14. [14]
  Feiyang Liu , Liuhong Song , Miaoyu Fu , Zhi Zheng , Gang Xie , Junlong Zhao . Tryptophan’s Employment Journey. University Chemistry, 2024, 39(9): 16-21. doi: 10.12461/PKU.DXHX202404037
15. [15]
  Ya-Wen Zhang , Ming-Ming Gan , Li-Ying Sun , Ying-Feng Han . Supramolecular dinuclear silver(I) and gold(I) tetracarbene metallacycles and fluorescence sensing of penicillamine. Chinese Journal of Structural Chemistry, 2024, 43(9): 100356-100356. doi: 10.1016/j.cjsc.2024.100356
16. [16]
  Chun-Lin Sun , Yaole Jiang , Yu Chen , Rongjing Guo , Yongwen Shen , Xinping Hui , Baoxin Zhang , Xiaobo Pan . Construction, Performance Testing, and Practical Applications of a Home-Made Open Fluorescence Spectrometer. University Chemistry, 2024, 39(5): 287-295. doi: 10.3866/PKU.DXHX202311096
17. [17]
  Wei Peng , Baoying Wen , Huamin Li , Yiru Wang , Jianfeng Li . Exploration and Practice on Raman Scattering Spectroscopy Experimental Teaching. University Chemistry, 2024, 39(8): 230-240. doi: 10.3866/PKU.DXHX202312062
18. [18]
  Zhaoyue Lü , Zhehao Chen , Yi Ni , Duanbin Luo , Xianfeng Hong . Multi-Level Teaching Design and Practice Exploration of Raman Spectroscopy Experiment. University Chemistry, 2024, 39(11): 304-312. doi: 10.12461/PKU.DXHX202402047
19. [19]
  Fei Xie , Chengcheng Yuan , Haiyan Tan , Alireza Z. Moshfegh , Bicheng Zhu , Jiaguo Yu . d带中心调控过渡金属单原子负载COF吸附O₂的理论计算研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2407013-. doi: 10.3866/PKU.WHXB202407013
20. [20]
  Chi Li , Jichao Wan , Qiyu Long , Hui Lv , Ying Xiong . N-Heterocyclic Carbene (NHC)-Catalyzed Amidation of Aldehydes with Nitroso Compounds. University Chemistry, 2024, 39(5): 388-395. doi: 10.3866/PKU.DXHX202312016

Get Citation

PDF

XML

Metrics

PDF Downloads(823)
Abstract views(2501)
HTML views(63)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142