Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation

doi:10.1088/1674-1056/24/7/073301

中国物理B ›› 2015, Vol. 24 ›› Issue (7): 73301-073301.doi: 10.1088/1674-1056/24/7/073301

• ATOMIC AND MOLECULAR PHYSICS • 上一篇下一篇

Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation

张寒^a, 张朝晖^a, 赵小燕^a, 张天尧^a, 燕芳^a, 申江^b

a Department of Instrumentation Science, School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing 100083, China;
b Institute of Applied Physics, University of Science and Technology Beijing, Beijing 100083, China

收稿日期:2014-11-24 修回日期:2015-03-31 出版日期:2015-07-05 发布日期:2015-07-05
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 61302007 and 60977065), the Fundamental Research Funds for the Central Universities of China (Grant No. FRF-SD-12-016A), and the Engineering Research Center of Industrial Spectrum Imaging of Beijing, China.

Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation

Zhang Han (张寒)^a, Zhang Zhao-Hui (张朝晖)^a, Zhao Xiao-Yan (赵小燕)^a, Zhang Tian-Yao (张天尧)^a, Yan Fang (燕芳)^a, Shen Jiang (申江)^b

a Department of Instrumentation Science, School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing 100083, China;
b Institute of Applied Physics, University of Science and Technology Beijing, Beijing 100083, China

Received:2014-11-24 Revised:2015-03-31 Online:2015-07-05 Published:2015-07-05
Contact: Zhao Xiao-Yan E-mail:zhaoxiaoyan@ustb.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 61302007 and 60977065), the Fundamental Research Funds for the Central Universities of China (Grant No. FRF-SD-12-016A), and the Engineering Research Center of Industrial Spectrum Imaging of Beijing, China.

摘要/Abstract

摘要： The crystal structure of L-glutamine is stabilized by a three-dimensional network of intermolecular hydrogen bonds. We utilize plane-wave density functional theory lattice-dynamics calculations within the generalized-gradient approximation (GGA), Perdew–Burke–Ernzerhof (PBE), PBE for solids (PBEsol), PBE with Wu–Cohen exchange (WC), and dispersion-corrected PBE, to investigate the effect of these intermolecular contacts on the absorption spectra of glutamine in the terahertz frequency range. Among these calculations, the solid-state simulated results obtained using the WC method exhibit a good agreement with the measured absorption spectra, and the absorption features are assigned with the help of WC. This indicates that the vibrational modes of glutamine were related to the combination of intramolecular and intermolecular motions, the intramolecular modes were dominated by rocking or torsion involving functional groups; the intermolecular modes mainly result from the translational motions of individual molecules, and the rocking of the hydrogen-bonded functional groups.

关键词: terahertz vibrational modes, amino acid, plane-wave density functional theory, generalized-gradient approximation

Abstract: The crystal structure of L-glutamine is stabilized by a three-dimensional network of intermolecular hydrogen bonds. We utilize plane-wave density functional theory lattice-dynamics calculations within the generalized-gradient approximation (GGA), Perdew–Burke–Ernzerhof (PBE), PBE for solids (PBEsol), PBE with Wu–Cohen exchange (WC), and dispersion-corrected PBE, to investigate the effect of these intermolecular contacts on the absorption spectra of glutamine in the terahertz frequency range. Among these calculations, the solid-state simulated results obtained using the WC method exhibit a good agreement with the measured absorption spectra, and the absorption features are assigned with the help of WC. This indicates that the vibrational modes of glutamine were related to the combination of intramolecular and intermolecular motions, the intramolecular modes were dominated by rocking or torsion involving functional groups; the intermolecular modes mainly result from the translational motions of individual molecules, and the rocking of the hydrogen-bonded functional groups.

Key words: terahertz vibrational modes, amino acid, plane-wave density functional theory, generalized-gradient approximation

中图分类号: (Vibration-rotation analysis)

33.20.Vq

63.20.-e (Phonons in crystal lattices) 78.55.Kz (Solid organic materials) 87.15.ag (Quantum calculations)

张寒, 张朝晖, 赵小燕, 张天尧, 燕芳, 申江. Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation[J]. 中国物理B, 2015, 24(7): 73301-073301.

Zhang Han (张寒), Zhang Zhao-Hui (张朝晖), Zhao Xiao-Yan (赵小燕), Zhang Tian-Yao (张天尧), Yan Fang (燕芳), Shen Jiang (申江). Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation[J]. Chin. Phys. B, 2015, 24(7): 73301-073301.

参考文献 26

[1]	Smith R M and Arnold M A 2011 Appl. Spectrosc. Rev. 46 636
[2]	Allis D G, Prokhorova D A and Korter T M 2006 J. Phys. Chem. A 110 1951
[3]	Wang W N, Li H Q, Zhang Y and Zhang C L 2009 Acta Phys.-Chim. Sin. 25 2074 (in Chinese)
[4]	Ma S H, Shi Y L, Xu X L, Yan W, Yang Y P and Wang L 2006 Acta Phys. Sin. 55 4091 (in Chinese)
[5]	Wang W N 2009 Acta Phys. Sin. 58 7640 (in Chinese)
[6]	Yamaguchi M, Miyamaru F, Yamamoto K, Tani M and Hangyo M 2005 Appl. Phys. Lett. 86 053903
[7]	Fu R, Li Z, Jin B B, Zhang C H, Dai H, Xue Y H and Chen J 2010 Spectrosc. Spect. Anal. 30 2023 (in Chinese)
[8]	Wang G and Wang W N 2012 Acta Phys.-Chim. Sin. 28 1579 (in Chinese)
[9]	Yamamoto K, Kabir M H and Tominaga K 2005 J. Opt. Soc. Am. B 22 2417
[10]	Wang W N, Li Y B and Yue W W 2007 Acta Phys. Sin. 56 781 (in Chinese)
[11]	Yu B, Zeng F, Yang Y, Xing Q, Chechin A, Xin X, Zeylikovich I and Alfano R R 2004 Biophys. J. 86 1649
[12]	Wang W N, Wang G and Zhang Y 2011 Chin. Phys. B 20 123301
[13]	Zhao X, Su H, Zhang Z, Li Z, Zhang H and Zhang T 2014 Chin. Sci. Bull. 59 2987
[14]	Perdew J P, Ruzsinszky A, Csonka G I, Vydrov O A, Scuseria G E, Constantin L A, Zhou X and Burke K 2008 Phys. Rev. Lett. 100 136406
[15]	Wu Z and Cohen R E 2006 Phys. Rev. B 73 235116
[16]	King M D, Ouellette W and Korter T M 2011 J. Phys. Chem. A 115 9467
[17]	Yan H, Fan W and Zheng Z 2012 Opt. Commun. 285 1593
[18]	Koetzle T F, Frey M N, Lehmann M S and Hamilton W C 1973 Acta Cryst. B 29 2571
[19]	Clark S J, Segall M D, Pickard C J, Hasnip P J, Probert M J, Refson K and Payne M C 2005 Z. Kristallogr. 220 567
[20]	Grimme S 2006 J. Comput. Chem. 27 1787
[21]	Su H, Zhang Z, Zhao X, Li Z, Yan F and Zhang H 2013 Spectrosc. Spect. Anal. 33 921 (in Chinese)
[22]	Li Z, Zhang Z, Zhao X, Su H, Zhang H and Lan J 2013 J. Infrared Millim. TE. 34 617
[23]	Su H, Zhang Z, Zhao X, Li Z, Yan F and Zhang H 2013 Spectrosc. Spect. Anal. 33 3180 (in Chinese)
[24]	THz database (Tera-photonics Laboratory, RIKEN Sendai, date of access) http://www.riken.jp/THzdatabase/
[25]	Li Z, Zhang Z, Zhao X, Su H, Yan F and Zhang H 2012 Appl. Opt. 51 4879
[26]	Lu T and Chen F 2012 J. Comput. Chem. 33 580

Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation

Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation

RichHTML

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献 26

相关文章 5

Metrics

本文评价

推荐阅读 0

[1]	Yan-Hui Li(李彦慧), Zhen-Sheng Zhong(钟振声), and Jie Ma(马杰). Single-molecule mechanical folding and unfolding kinetics of armless mitochondrial tRNA^Arg from Romanomermis culicivorax[J]. 中国物理B, 2021, 30(10): 108203-108203.
[2]	王卫宁, 王果, 张岩. Low-frequency vibrational modes of glutamine[J]. 中国物理B, 2011, 20(12): 123301-123301.
[3]	王向红, 沈瑜, 章林溪. Structural statistical properties of knotted proteins[J]. 中国物理B, 2009, 18(4): 1684-1690.
[4]	葛四平, 赵学应, 盖峥, 赵汝光, 杨威生. Adsorption geometry of glycine on Cu(001) determined with low-energy electron diffraction and scanning tunnelling microscopy[J]. 中国物理B, 2002, 11(8): 839-845.
[5]	赵学应, 王浩, 晏浩, 盖铮, 赵汝光, 杨威生. ADSORPTION BEHAVIOR OF AMINO ACIDS ON COPPER SURFACES[J]. 中国物理B, 2001, 10(13): 84-95.