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A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra

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Abstract

Vibrational optical activity (VOA) spectra, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra, of aliphatic amino acids are simulated using density functional theory (DFT) methods in both gas phase (neutral form) and solution (zwitterionic form), together with their respective infrared (IR) and Raman spectra of the amino acids. The DFT models, which are validated by excellent agreements with the available experimental Raman and ROA spectra of alanine in solution, are employed to study other aliphatic amino acids. The inferred (IR) intensive region (below 2000 cm-1) reveals the signature of alkyl side chains, whereas the Raman intensive region (above 3000 cm-1) contains the information of the functional groups in the amino acids. Furthermore, the chiral carbons of the amino acids (except for glycine) dominate the VCD and ROA spectra in the gas phase, but the methyl group vibrations produce stronger VCD and ROA signals in solution. The C-H related asymmetric vibrations dominate the VOA spectra (i.e., VCD and ROA) > 3000 cm-1 reflecting the side chain structures of the amino acids. Finally the carboxyl and the C(2)H modes of aliphatic amino acids, together with the side chain vibrations, are very active in the VCD/IR and ROA/Raman spectra, which makes such the vibrational spectroscopic methods a very attractive means to study biomolecules.

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References

  1. S.G. Stepanian, I.D. Reva, E.D. Radchenko, L. Adamowicz, J. Phys. Chem. A 102, 4623 (1998)

    Article  Google Scholar 

  2. S.G. Stepanian, I.D. Reva, E.D. Radchenko, L. Adamowicz, J. Phys. Chem. A 103, 4404 (1999)

    Article  Google Scholar 

  3. A.G. Császár, J. Phys. Chem. 100, 3541 (1996)

    Article  Google Scholar 

  4. S. Dokmaisrijan, V.S. Lee, P. Nimmanpipug, J. Mol. Struct. 953, 28 (2010)

    Article  Google Scholar 

  5. L. Gontrani, B. Mennucci, J. Tomasi, J. Mol. Struct. 500, 113 (2000)

    Article  Google Scholar 

  6. M. Pecul, Chem. Phys. Lett. 427, 166 (2006)

    Article  ADS  Google Scholar 

  7. I. Powis, J. Phys. Chem. A 104, 878 (2000)

    Article  Google Scholar 

  8. C.T. Falzon, F. Wang, J. Chem. Phys. 123, 214307 (2005)

    Article  ADS  Google Scholar 

  9. C.T. Falzon, F. Wang, W. Pang, J. Phys. Chem. B 110, 9713 (2006)

    Article  Google Scholar 

  10. A. Ganesan, F. Wang, J. Chem. Phys. 131, 044321 (2009)

    Article  ADS  Google Scholar 

  11. A. Ganesan, F. Wang, C. Falzon, J. Comput. Chem. 32, 525 (2011)

    Article  Google Scholar 

  12. A. Ganesan, F. Wang, M. Brunger, K. Prince, J. Synchrotron Radiat. 18, 733 (2011)

    Article  Google Scholar 

  13. S.G. Stepanian, I.D. Reva, E.D. Radchenko, M.T.S. Rosado, M.L.T.S. Duarte, R. Fausto, L. Adamowicz, J. Phys. Chem. A 102, 1041 (1998)

    Article  Google Scholar 

  14. B. Hernández, F. Pflüger, N. Derbel, J. De Coninck, M. Ghomi, J. Phys. Chem. B 114, 1077 (2009)

    Article  Google Scholar 

  15. J.M. Bakker, L.M. Aleese, G. Meijer, G. von Helden, Phys. Rev. Lett. 91, 203003 (2003)

    Article  ADS  Google Scholar 

  16. I. Compagnon, J. Oomens, G. Meijer, G. von Helden, J. Am. Chem. Soc. 128, 3592 (2006)

    Article  Google Scholar 

  17. J. Oomens, N. Polfer, D.T. Moore, L. van der Meer, A.G. Marshall, J.R. Eyler, G. Meijer, G. von Helden, PCCP 7, 1345 (2005)

    Article  ADS  Google Scholar 

  18. G. von Helden, I. Compagnon, M.N. Blom, M. Frankowski, U. Erlekam, J. Oomens, B. Brauer, R.B. Gerber, G. Meijer, PCCP 10, 1248 (2008)

    Article  ADS  Google Scholar 

  19. Z. Ji, R. Santamaria, I.L. Garzòn, J. Phys. Chem. A 114, 3591 (2010)

    Article  Google Scholar 

  20. G. Zhu, X. Zhu, Q. Fan, X. Wan, Spectrochim. Acta A 78, 1187 (2011)

    Article  ADS  Google Scholar 

  21. B. Andreas, Prog. Biophys. Mol. Biol. 74, 141 (2000)

    Article  Google Scholar 

  22. L.D. Barron, A.R. Gargaro, L. Hecht, P.L. Polavarapu, Spectrochim. Acta 47, 1001 (1991)

    Article  Google Scholar 

  23. D. Chakraborty, S. Manogaran, Chem. Phys. Lett. 294, 56 (1998)

    Article  ADS  Google Scholar 

  24. P. Danecek, J. Kapitan, V. Baumruk, L. Bednarova, V. Kopecky, P. Bour, J. Chem. Phys. 126, 224513 (2007)

    Article  ADS  Google Scholar 

  25. A.R. Gargaro, L.D. Barron, L. Hecht, J. Raman Spectrosc. 24, 91 (1993)

    Article  ADS  Google Scholar 

  26. S. Kumar, A. Kumar Rai, S.B. Rai, D.K. Rai, A.N. Singh, V.B. Singh, J. Mol. Struct. 791, 23 (2006)

    Article  ADS  Google Scholar 

  27. S. Kumar, A.K. Rai, V.B. Singh, S.B. Rai, Spectrochim. Acta A 61, 2741 (2005)

    Article  ADS  Google Scholar 

  28. J. Oomens, J.D. Steill, B. Redlich, J. Am. Chem. Soc. 131, 4310 (2009)

    Article  Google Scholar 

  29. E. Tajkhorshid, K.J. Jalkanen, S. Suhai, J. Phys. Chem. B 102, 5899 (1998)

    Article  Google Scholar 

  30. G.-S. Yu, T.B. Freedman, L.A. Nafie, Z. Deng, P.L. Polavarapu, J. Phys. Chem. 99, 835 (1995)

    Article  Google Scholar 

  31. L.D. Barron, A.D. Buckingham, Chem. Phys. Lett. 492, 199 (2010)

    Article  ADS  Google Scholar 

  32. L.A. Nafie, Annu. Rev. Phys. Chem. 48, 357 (1997)

    Article  ADS  Google Scholar 

  33. R.K. Dukor, L.A. Nafie, in Encyclopedia of Analytical Chemistry (John Wiley & Sons, Ltd, 2006)

  34. L.A. Nafie, M.R. Oboodi, T.B. Freedman, J. Am. Chem. Soc. 105, 7449 (1983)

    Article  Google Scholar 

  35. M. Pecul, Chirality 21, E98 (2009)

    Article  Google Scholar 

  36. B. Nieto-Ortega, J. Casado, E.W. Blanch, J.T. Lòpez Navarrete, A.R. Quesada, F.J. Ramìrez, J. Phys. Chem. A 115, 2752 (2011)

    Article  Google Scholar 

  37. E. Deplazes, W. van Bronswijk, F. Zhu, L. Barron, S. Ma, L. Nafie, K. Jalkanen, Theor. Chem. Acc. 119, 155 (2008)

    Article  Google Scholar 

  38. M.R. Oboodi, B.B. Lal, D.A. Young, T.B. Freedman, L.A. Nafie, J. Am. Chem. Soc. 107, 1547 (1985)

    Article  Google Scholar 

  39. M. Diem, J. Am. Chem. Soc. 110, 6967 (1988)

    Article  Google Scholar 

  40. P. Zhang, P.L. Polavarapu, Appl. Spectrosc. 60, 378 (2006)

    Article  ADS  Google Scholar 

  41. M. Diem, P.L. Polavarapu, M. Oboodi, L.A. Nafie, J. Am. Chem. Soc. 104, 3329 (1982)

    Article  Google Scholar 

  42. M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Comput. Chem. 24, 669 (2003)

    Article  Google Scholar 

  43. J.R. Cheeseman, M.J. Frisch, F.J. Devlin, P.J. Stephens, Chem. Phys. Lett. 252, 211 (1996)

    Article  ADS  Google Scholar 

  44. P.J. Stephens, J. Phys. Chem. 89, 748 (1985)

    Article  Google Scholar 

  45. A.D. Becke, Phys. Rev. A 38, 3098 (1988)

    Article  ADS  Google Scholar 

  46. C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37, 785 (1988)

    Article  ADS  Google Scholar 

  47. E.E. Zvereva, A.R. Shagidullin, S.A. Katsyuba, J. Phys. Chem. A 115, 63 (2010)

    Article  Google Scholar 

  48. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09, Revision A.1 (Gaussian, Inc., Wallingford CT, 2009)

  49. A.G. Császár, J. Mol. Struct. 346, 141 (1995)

    Article  ADS  Google Scholar 

  50. B. Herrera, O. Dolgounitcheva, V.G. Zakrzewski, A. Toro-Labbé, J.V. Ortiz, J. Phys. Chem. A 108, 11703 (2004)

    Article  Google Scholar 

  51. C.H. Hu, M. Shen, H.F. Schaefer, J. Am. Chem. Soc. 115, 2923 (1993)

    Article  Google Scholar 

  52. J.H. Jensen, M.S. Gordon, J. Am. Chem. Soc. 113, 7917 (1991)

    Article  Google Scholar 

  53. A. Lesarri, E.J. Cocinero, J.C. López, J.L. Alonso, Angew. Chem. Int. Ed. 43, 605 (2004)

    Article  Google Scholar 

  54. A. Lesarri, R. Sánchez, E.J. Cocinero, J.C. López, J.L. Alonso, J. Am. Chem. Soc. 127, 12952 (2005)

    Article  Google Scholar 

  55. S. Shirazian, S. Gronert, J. Mol. Struct. 397, 107 (1997)

    Article  Google Scholar 

  56. E.A. Stroev, Biochemistry (Mir Publishers, Moscow, 1989)

  57. F. Tortonda, J. Pascual-Ahuir, E. Silla, I. Tuñón, F. Ramírez, J. Chem. Phys. 109, 592 (1998)

    Article  ADS  Google Scholar 

  58. E.J. Cocinero, A. Lesarri, J.-U. Grabow, J.C. López, J.L. Alonso, Chem. Phys. Chem. 8, 599 (2007)

    Article  Google Scholar 

  59. K. Iijima, K. Tanaka, S. Onuma, J. Mol. Struct. 246, 257 (1991)

    Article  ADS  Google Scholar 

  60. J. Sun, D. Bousquet, H. Forbert, D. Marx, J. Chem. Phys. 133, 114508 (2010)

    Article  ADS  Google Scholar 

  61. A.H. Lowrey, V. Kalasinsky, R.W. Williams, Struct. Chem. 4, 289 (1993)

    Article  Google Scholar 

  62. A.P. Scott, L. Radom, J. Phys. Chem. 100, 16502 (1996)

    Article  Google Scholar 

  63. P.D. Godfrey, S. Firth, L.D. Hatherley, R.D. Brown, A.P. Pierlot, J. Am. Chem. Soc. 115, 9687 (1993)

    Article  Google Scholar 

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Authors and Affiliations

  1. eChemistry Laboratory, Faculty of Life and Social Sciences, Swinburne University of Technology, Melbourne, 3122, Victoria, Australia

    Aravindhan Ganesan & Feng Wang

  2. School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia

    Michael J. Brunger

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  1. Aravindhan Ganesan
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  2. Michael J. Brunger
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  3. Feng Wang
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Correspondence to Feng Wang.

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Contribution to the Topical Issue “Electron and Positron Induced Processes”, edited by Michael Brunger, Radu Campeanu, Masamitsu Hoshino, Oddur Ingólfsson, Paulo Limão-Vieira, Nigel Mason, Yasuyuki Nagashima and Hajime Tanuma.

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Ganesan, A., Brunger, M.J. & Wang, F. A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra. Eur. Phys. J. D 67, 229 (2013). https://doi.org/10.1140/epjd/e2013-40376-x

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