Please wait a minute...
Chin. Phys. B, 2015, Vol. 24(7): 073301    DOI: 10.1088/1674-1056/24/7/073301
ATOMIC AND MOLECULAR PHYSICS Prev   Next  

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

Zhang Hana, Zhang Zhao-Huia, Zhao Xiao-Yana, Zhang Tian-Yaoa, Yan Fanga, Shen Jiangb
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
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.
Keywords:  terahertz vibrational modes      amino acid      plane-wave density functional theory      generalized-gradient approximation     
Received:  24 November 2014      Published:  05 July 2015
PACS:  33.20.Vq (Vibration-rotation analysis)  
  63.20.-e (Phonons in crystal lattices)  
  78.55.Kz (Solid organic materials)  
  87.15.ag (Quantum calculations)  
Fund: 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.
Corresponding Authors:  Zhao Xiao-Yan     E-mail:  zhaoxiaoyan@ustb.edu.cn

Cite this article: 

Zhang Han, Zhang Zhao-Hui, Zhao Xiao-Yan, Zhang Tian-Yao, Yan Fang, Shen Jiang Assignment of terahertz vibrational modes of L-glutamine using density functional theory within generalized-gradient approximation 2015 Chin. Phys. B 24 073301

[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
[1] Low-frequency vibrational modes of glutamine
Wang Wei-Ning, Wang Guo, Zhang Yan. Chin. Phys. B, 2011, 20(12): 123301.
[2] Structural statistical properties of knotted proteins
Wang Xiang-Hong, Shen Yu, Zhang Lin-Xi. Chin. Phys. B, 2009, 18(4): 1684-1690.
[3] Adsorption geometry of glycine on Cu(001) determined with low-energy electron diffraction and scanning tunnelling microscopy
Ge Si-Ping, Zhao Xue-Ying, Gai Zheng, Zhao Ru-Guang, Yang Wei-Sheng. Chin. Phys. B, 2002, 11(8): 839-845.
[4] ADSORPTION BEHAVIOR OF AMINO ACIDS ON COPPER SURFACES
Zhao Xue-ying, Wang Hao, Yan Hao, Gai Zheng, Zhao Ru-guang, Yang Wei-sheng. Chin. Phys. B, 2001, 10(13): 84-95.
No Suggested Reading articles found!