Size effect of silk fibroin peptide chains in the growth process

Yang Meng-Shi; Li Xin; Ye Zhi-Peng; Chen Liang; Xu Can; Chu Xiu-Xiang

doi:10.7498/aps.62.236101

Abstract

A theoretical study on 13 oligopeptides of glycine and alanine by density function theory (DFT) is given in this paper. Geometric structures, vibration frequency, average binding energies, dipole moment are studied, and IR spectra of the oligopeptides are examined. Results show that with increasing number of residues the average binding energies tend to a regular pattern, IR frequencies of typical functional groups start to shift, but stretching and bending vibrations of the groups show the opposite trend of red shift and blue shift. It is revealed that the physical and chemical properties of the silk fibroin peptide chain show size effect and anisotropic in the growth process. This phenomenon may come from the coupling effect of the similar groups, and the different effects of intramolecular hydrogen bond on the stretching and bending vibration.

Keywords:

Authors and contacts

1.
School of Engineering, Zhejiang A&F University, Zhejiang Province, Linan 311300, China;
2.
School of Science, Zhejiang A&F University, Zhejiang Province, Linan 311300, China;
3.
Key Lab for Magnetism and Magnetic Materials of Ministry of Education Lanzhou University, Lanzhou 730000, China
Funds: Supported by the National Science Fund for Distinguished Young Scholars (Grant No. 50925103), and the Students Innovation Training Base of Science College, Zhejiang AF University.

References

[1]	Liu H T, Xu W L, Zhao S P, Yang H J, Huang J J, Wang Y L, Ouyang C X 2010 J. Appl. Polym. Sci. 117 235
[2]	Zhou W, Chen X, Shao Z Z 2006 Prog. Chem. 18 1514 (in Chinese) [周文, 陈新, 邵正中 2006 化学进展 18 1514]
[3]	Chen G L, Zheng X, L"u G H, Zhang Z X, Massey S, Smith W, Tatoulian M, Yang S Z 2012 Chin. Phys. B 21 105201
[4]	Liu H T, Xu W L, Huang J J, Zuo D Y, Ke G Z 2009 Polym. Bull. 6 48 (in Chinese) [刘洪涛, 徐卫林, 黄菁菁, 左丹英, 柯贵珍 2009 高分子通报 6 48]
[5]	Smeenk J M, Ayres L, Stunnenberg H G, Hest J C M 2005 Macrom. Symp 225 1
[6]	Jin H J, Park J, Valluzzi R, Cebe P, Kaplan D L 2004 Biomacromolecules 5 711
[7]	Hu A, Zuo B, Zhang F, Zhang H, Lan Q 2013 Oto Neurotol. 34 311
[8]	Yu W B, Liang L, Lin Z J, Ling S L, Haranczyk M, Gutowski M 2009 J. Comput. Chem. 30 589
[9]	Yu W B, Wu Z Q, Chen H B, Liu X, MacKerell A D, Jr, Lin Z J 2012 J. Phys. Chem. B 116 2269
[10]	Yu W B, Xu X, Li H B, Pang R, Fang K, Lin Z J 2009 J. Comput. Chem. 30 2105
[11]	Chen Y, Wang J, Wang W 2007 Chin. Phys. 16 868
[12]	Zhu P, Xu Z Y, Tang X Q 2009 Chin. Phys. B 18 363
[13]	Li W F, Qin M, Tie Z X, Wang W 2011 Phys. Rev. E 84 041933
[14]	Xu C, Cao J, Zhu L F, Gao C Y 2006 Acta Phys. Chim. Sin. 22 445 (in Chinese) [徐灿, 曹娟, 朱莉芳, 高晨阳 2006 物理化学学报 22 445]
[15]	Xu C, Zhang X F, Chen L, Zhu L F, Zhang R J 2007 Acta Phys. Chim. Sin. 23 1733 (in Chinese) [徐灿, 张小芳, 陈亮, 张荣君 2007 物理化学学报 23 1733]
[16]	Zhou G R, Teng X Y, Wang Y, Geng H R, Hur B Y 2012 Acta Phys. Sin. 61 066101 (in Chinese) [周国荣, 滕新营, 王艳, 耿浩然, 徐甫宁 2012 61 066101]
[17]	Wei J, Chen Y J, Xu Z 2012 Acta Phys. Sin. 61 057502 (in Chinese) [魏杰, 陈彦均, 徐卓 2012 61 057502]
[18]	Li C, Hou Q Y, Zhang Z D, Zhang B 2012 Acta Phys. Sin. 61 077102 (in Chinese) [李聪, 侯清玉, 张振铎, 张冰 2012 61 077102]
[19]	Hou G H, Wang H Y, Liu T, Yuan Z, Fang J, Li D H, Qiu Q, Guo S D 2005 Chem. J. Chinese U 26 1277 (in Chinese) [侯光辉, 王慧彦, 刘涛, 袁直, 房杰, 李冬华, 邱奇, 郭世铎 2005 高等学校化学学报 26 1277]
[20]	Li Y, Zhang H J, Liao M X, Liu T 2011 Chem. J. Chinese U 32 1100 (in Chinese) [李晔, 张恒建, 廖明霞, 刘涛 2011 高等学校化学学报 32 1100 ]
[21]	Stewart J J P 1989 J. Comput. Chem. 10 209
[22]	Becke A D 1988 Phys. Rev. A 38 3098
[23]	Lee C, Yang W, Parr R G 1988 Phys. Rev. B 37 785
[24]	Frisch M J, Trucks G W, Schlegel H B 2010 Gaussian 09, Revision C. 01, Wallingford CT: Gaussian, Inc.
[25]	Puente E de la, Aguado A, Ayucla A, Lopez J M 1997 Phys Rev B 56 7607
[26]	Roberts C, Johnston R L 2001 Phys. Chem. Phys. 3 5024
[27]	Santosh K, Amareshwar K R, Singh V B, Rai S B 2005 Spectrochim. Acta A 61 2741
[28]	Malgorzata B, Julien B, Ivan C, Pawel P, Vincenzo B 2012 J. Mol. Struct. 1009 74
[29]	Wolpert M, Hellwig P 2006 Spectrochim. Acta A 64 987
[30]	Barth A 2000 Prog. Biophy. Mol. Bio. 74 141
[31]	Balaj O P, Kapota C, Lemaire J, Ohanessian G 2008 Int. J Mass. Spectrom. 269 196
[32]	Barth A 2007 Biochim. Biophys. Acta 1767 1073
[33]	Rosado M T, Duarte M L T S, Fausto R 1998 Vib. Spectrosc 16 35
[34]	Zhou R M, Shen Y J 1997 J. East China Univ. Sci. Technol. 23 422 (in Chinese) [周瑞明, 沈永嘉 1997 华东理工大学学报 23 422]
[35]	Cao J, Xu C, Zhu L F, Wang X M 2007 Spectrosc. Spect. Anal. 27 1715 (in Chinese) [曹娟, 徐灿, 朱莉芳, 王喜民 2007 光谱学与光谱分析 27 1715]
[36]	Wang C S, Qi X J, Ma Y G, Yang Z Z 2004 Chem. J. Chinese U 25 1111 (in Chinese) [王长生, 齐学洁, 马英格, 杨忠志 2004 高等学校化学学报 25 1111]
[37]	Zhang Y, Wang C S 2007 J. At. Mol. Phys. 24 1166 (in Chinese) [张艳, 王长生 2007 原子与分子 24 1166]
[38]	Yang Y, Zhang W J, Pei S X, Shao J, Huang W, Gao X M 2006 Sci. China Ser. B. 36 218 (in Chinese) [杨颙, 张为俊, 裴世鑫, 邵杰, 黄伟, 高晓明 2006 中国科学 B 辑-化学 36 218]
[39]	Yu W B, Lin Z J, Huang Z J 2006 Chem. Phys. Chem. 7 828
[40]	Clark S A C, Bawagan A O, Brion C E 1989 Chem. Phys. 137 407
[41]	Linder R, Seefeld K, Vavra A, Kleinermanns K 2008 Chem Phys. Lett. 453

Cited By

[1]	Liu H T, Xu W L, Zhao S P, Yang H J, Huang J J, Wang Y L, Ouyang C X 2010 J. Appl. Polym. Sci. 117 235
[2]	Zhou W, Chen X, Shao Z Z 2006 Prog. Chem. 18 1514 (in Chinese) [周文, 陈新, 邵正中 2006 化学进展 18 1514]
[3]	Chen G L, Zheng X, L"u G H, Zhang Z X, Massey S, Smith W, Tatoulian M, Yang S Z 2012 Chin. Phys. B 21 105201
[4]	Liu H T, Xu W L, Huang J J, Zuo D Y, Ke G Z 2009 Polym. Bull. 6 48 (in Chinese) [刘洪涛, 徐卫林, 黄菁菁, 左丹英, 柯贵珍 2009 高分子通报 6 48]
[5]	Smeenk J M, Ayres L, Stunnenberg H G, Hest J C M 2005 Macrom. Symp 225 1
[6]	Jin H J, Park J, Valluzzi R, Cebe P, Kaplan D L 2004 Biomacromolecules 5 711
[7]	Hu A, Zuo B, Zhang F, Zhang H, Lan Q 2013 Oto Neurotol. 34 311
[8]	Yu W B, Liang L, Lin Z J, Ling S L, Haranczyk M, Gutowski M 2009 J. Comput. Chem. 30 589
[9]	Yu W B, Wu Z Q, Chen H B, Liu X, MacKerell A D, Jr, Lin Z J 2012 J. Phys. Chem. B 116 2269
[10]	Yu W B, Xu X, Li H B, Pang R, Fang K, Lin Z J 2009 J. Comput. Chem. 30 2105
[11]	Chen Y, Wang J, Wang W 2007 Chin. Phys. 16 868
[12]	Zhu P, Xu Z Y, Tang X Q 2009 Chin. Phys. B 18 363
[13]	Li W F, Qin M, Tie Z X, Wang W 2011 Phys. Rev. E 84 041933
[14]	Xu C, Cao J, Zhu L F, Gao C Y 2006 Acta Phys. Chim. Sin. 22 445 (in Chinese) [徐灿, 曹娟, 朱莉芳, 高晨阳 2006 物理化学学报 22 445]
[15]	Xu C, Zhang X F, Chen L, Zhu L F, Zhang R J 2007 Acta Phys. Chim. Sin. 23 1733 (in Chinese) [徐灿, 张小芳, 陈亮, 张荣君 2007 物理化学学报 23 1733]
[16]	Zhou G R, Teng X Y, Wang Y, Geng H R, Hur B Y 2012 Acta Phys. Sin. 61 066101 (in Chinese) [周国荣, 滕新营, 王艳, 耿浩然, 徐甫宁 2012 61 066101]
[17]	Wei J, Chen Y J, Xu Z 2012 Acta Phys. Sin. 61 057502 (in Chinese) [魏杰, 陈彦均, 徐卓 2012 61 057502]
[18]	Li C, Hou Q Y, Zhang Z D, Zhang B 2012 Acta Phys. Sin. 61 077102 (in Chinese) [李聪, 侯清玉, 张振铎, 张冰 2012 61 077102]
[19]	Hou G H, Wang H Y, Liu T, Yuan Z, Fang J, Li D H, Qiu Q, Guo S D 2005 Chem. J. Chinese U 26 1277 (in Chinese) [侯光辉, 王慧彦, 刘涛, 袁直, 房杰, 李冬华, 邱奇, 郭世铎 2005 高等学校化学学报 26 1277]
[20]	Li Y, Zhang H J, Liao M X, Liu T 2011 Chem. J. Chinese U 32 1100 (in Chinese) [李晔, 张恒建, 廖明霞, 刘涛 2011 高等学校化学学报 32 1100 ]
[21]	Stewart J J P 1989 J. Comput. Chem. 10 209
[22]	Becke A D 1988 Phys. Rev. A 38 3098
[23]	Lee C, Yang W, Parr R G 1988 Phys. Rev. B 37 785
[24]	Frisch M J, Trucks G W, Schlegel H B 2010 Gaussian 09, Revision C. 01, Wallingford CT: Gaussian, Inc.
[25]	Puente E de la, Aguado A, Ayucla A, Lopez J M 1997 Phys Rev B 56 7607
[26]	Roberts C, Johnston R L 2001 Phys. Chem. Phys. 3 5024
[27]	Santosh K, Amareshwar K R, Singh V B, Rai S B 2005 Spectrochim. Acta A 61 2741
[28]	Malgorzata B, Julien B, Ivan C, Pawel P, Vincenzo B 2012 J. Mol. Struct. 1009 74
[29]	Wolpert M, Hellwig P 2006 Spectrochim. Acta A 64 987
[30]	Barth A 2000 Prog. Biophy. Mol. Bio. 74 141
[31]	Balaj O P, Kapota C, Lemaire J, Ohanessian G 2008 Int. J Mass. Spectrom. 269 196
[32]	Barth A 2007 Biochim. Biophys. Acta 1767 1073
[33]	Rosado M T, Duarte M L T S, Fausto R 1998 Vib. Spectrosc 16 35
[34]	Zhou R M, Shen Y J 1997 J. East China Univ. Sci. Technol. 23 422 (in Chinese) [周瑞明, 沈永嘉 1997 华东理工大学学报 23 422]
[35]	Cao J, Xu C, Zhu L F, Wang X M 2007 Spectrosc. Spect. Anal. 27 1715 (in Chinese) [曹娟, 徐灿, 朱莉芳, 王喜民 2007 光谱学与光谱分析 27 1715]
[36]	Wang C S, Qi X J, Ma Y G, Yang Z Z 2004 Chem. J. Chinese U 25 1111 (in Chinese) [王长生, 齐学洁, 马英格, 杨忠志 2004 高等学校化学学报 25 1111]
[37]	Zhang Y, Wang C S 2007 J. At. Mol. Phys. 24 1166 (in Chinese) [张艳, 王长生 2007 原子与分子 24 1166]
[38]	Yang Y, Zhang W J, Pei S X, Shao J, Huang W, Gao X M 2006 Sci. China Ser. B. 36 218 (in Chinese) [杨颙, 张为俊, 裴世鑫, 邵杰, 黄伟, 高晓明 2006 中国科学 B 辑-化学 36 218]
[39]	Yu W B, Lin Z J, Huang Z J 2006 Chem. Phys. Chem. 7 828
[40]	Clark S A C, Bawagan A O, Brion C E 1989 Chem. Phys. 137 407
[41]	Linder R, Seefeld K, Vavra A, Kleinermanns K 2008 Chem Phys. Lett. 453

[1]	Qiu Zi-Yang, Chen Yan, Qiu Xiang-Gang. Infrared spectroscopic study of topological material BaMnSb₂. Acta Physica Sinica, 2022, 71(10): 107201. doi: 10.7498/aps.71.20220011
[2]	Qiu Zi-Heng, Ahmed Yousif Ghazal, Long Jin-You, Zhang Song. Theoretical studies on molecular conformers and infrared spectra of triethylamine. Acta Physica Sinica, 2022, 71(10): 103601. doi: 10.7498/aps.71.20220123
[3]	Tai Jian-Peng, Guo Wei-Ling, Li Meng-Mei, Deng Jie, Chen Jia-Xin. GaN based micro-light-emitting diode size effect and array display. Acta Physica Sinica, 2020, 69(17): 177301. doi: 10.7498/aps.69.20200305
[4]	Wu Chen-Chen, Guo Xiang-Dong, Hu Hai, Yang Xiao-Xia, Dai Qing. Graphene plasmon enhanced infrared spectroscopy. Acta Physica Sinica, 2019, 68(14): 148103. doi: 10.7498/aps.68.20190903
[5]	Xu Bing, Qiu Zi-Yang, Yang Run, Dai Yao-Min, Qiu Xiang-Gang. Optical properties of topological semimetals. Acta Physica Sinica, 2019, 68(22): 227804. doi: 10.7498/aps.68.20191510
[6]	Zhang Long-Yan, Xu Jin-Liang, Lei Jun-Peng. Size effect on boundary condition at solid-liquid interface in microchannel. Acta Physica Sinica, 2019, 68(2): 020201. doi: 10.7498/aps.68.20181876
[7]	Lin Tong, Hu Die, Shi Li-Yu, Zhang Si-Jie, Liu Yan-Qi, Lv Jia-Lin, Dong Tao, Zhao Jun, Wang Nan-Lin. Infrared spectroscopy study of ironbased superconductor Li0.8Fe0.2 ODFeSe. Acta Physica Sinica, 2018, 67(20): 207102. doi: 10.7498/aps.67.20181401
[8]	Wang An-Jing, Fang Yong-Hua, Li Da-Cheng, Cui Fang-Xiao, Wu Jun, Liu Jia-Xiang, Li Yang-Yu, Zhao Yan-Dong. Simulation of pollutant-gas-cloud infrared spectra under plane-array detecting. Acta Physica Sinica, 2017, 66(11): 114203. doi: 10.7498/aps.66.114203
[9]	Yang Xi-Yuan, Quan Jun. Simulations of the size effect on the elastic properties and the inherent mechanism of metallic nanowire. Acta Physica Sinica, 2015, 64(11): 116201. doi: 10.7498/aps.64.116201
[10]	Gu Zhuo, Ban Shi-Liang. Size and ternary mixed crystal effects on interband absorption in wurtzite ZnO/MgxZn1-xO quantum wells. Acta Physica Sinica, 2014, 63(10): 107301. doi: 10.7498/aps.63.107301
[11]	Ren Dan, Du Ping-An, Nie Bao-Lin, Cao Zhong, Liu Wen-Kui. An equivalent approach to modeling aperture array with considering size effect of apertures. Acta Physica Sinica, 2014, 63(12): 120701. doi: 10.7498/aps.63.120701
[12]	Li Xin, Yang Meng-Shi, Ye Zhi-Peng, Chen Liang, Xu Can, Chu Xiu-Xiang. DFT research on the IR spectrum of glycine tryptophan oligopeptides chain. Acta Physica Sinica, 2013, 62(15): 156103. doi: 10.7498/aps.62.156103
[13]	Zhang Qi, Hou Mei-Ying. Research on size effect of direct shear test. Acta Physica Sinica, 2012, 61(24): 244504. doi: 10.7498/aps.61.244504
[14]	Zhou Guo-Rong, Teng Xin-Ying, Wang Yan, Geng Hao-Ran, Hur Bo-Young. Size effect on the freezing behavior of aluminum nanowires. Acta Physica Sinica, 2012, 61(6): 066101. doi: 10.7498/aps.61.066101
[15]	Liu Xiao-Dong, Tao Wan-Jun, Hagihala Masato, Guo Qi-Xin, Meng Dong-Dong, Zhang Sen-Lin, Zheng Xu-Guang. Mid-infrared spectroscopic properties of geometrically frustrated basic cobalt chlorides. Acta Physica Sinica, 2011, 60(3): 037803. doi: 10.7498/aps.60.037803
[16]	Zhang Chun-Zu, Zhang Ying, Zhou Zhi-Dong. Size effect on phase transition temperature of epitaxial ferroelectric films. Acta Physica Sinica, 2010, 59(9): 6620-6625. doi: 10.7498/aps.59.6620
[17]	Zhang Ran, He Jun, Peng Zeng-Hui, Xuan Li. Molecular dynamics simulation of the rotational viscosity and its odd-even effect of nematic liquid crystals nCB(4-n-alkyl-4′-cyanobiphenyls, n=5—8). Acta Physica Sinica, 2009, 58(8): 5560-5566. doi: 10.7498/aps.58.5560
[18]	Ai Shu-Tao, Cai Yuan-Zhen. Ferroelectric-paraelectric interface dynamics related to latent heat and its finite-size effects. Acta Physica Sinica, 2006, 55(7): 3721-3724. doi: 10.7498/aps.55.3721
[19]	Sun You-Mei, Liu Jie, Zhang Chong-Hong, Wang Zhi-Guang, Jin Yun-Fan, Duan Jing-Lai, Song Yin. Electronic energy loss of the latent track in heavy ion-irradiated polyimide. Acta Physica Sinica, 2005, 54(11): 5269-5273. doi: 10.7498/aps.54.5269
[20]	WANG SONG-YOU, JU XIAO-HUA, LI HE-YIN, XU XU-DONG, ZHOU PENG, ZHANG RONG-JUN, YANG YUE-MEI, ZHOU SHI-MING, CHEN LIANG-YAO. THE SIZE EFFECT ON OPTICAL AND MAGNETO-OPTICAL PROPERTIES IN Fe-Ag GRANULAR FILMS. Acta Physica Sinica, 2001, 50(11): 2252-2257. doi: 10.7498/aps.50.2252

Catalog

Vol. 62, Issue 23 - 2013-12-05

Metrics

Abstract views: 6798
PDF Downloads: 534
Cited By: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

Search

Article

留言板