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Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study

  • Received : 2011.03.26
  • Accepted : 2011.05.05
  • Published : 2011.06.20

Abstract

The stable conformers of glycine and the inter-conversions between them were studied theoretically at various levels of theory, B3LYP, MP2, CCSD and CCSD(T), in the gas phase and in aqueous solution. In aqueous solution, the structures examined by use of the conductor-like polarizable continuum model (CPCM) with various cavity models, UA0, UAHF, UAKS, UFF, BONDI and PAULING, and by use of a discrete/continuum solvation model with eight water clusters. The Gibbs free energy differences between the neutral (NE) and zwitterionic conformers (ZW), ${\Delta}G_{Z-N}[=G_{ZW}-G_{NE}]$, in aqueous solution were well reproduced by using the BONDI and PAULING cavity models. However the ${\Delta}G_{Z-N}$ values were underestimated in other cavity models, although the ZW conformers existed as stable species in aqueous solution. In the studies of a discrete/continuum solvation model with eight water clusters, gas phase results are still insufficient to reproduce the experimental findings. However the ${\Delta}G_{Z-N}$ values calculated by use of CPCM method in aqueous solution agreed well with the experimental ones.

Keywords

References

  1. Wolfenden, R.; Andersson, L.; Cullis, P. M.; Southgate, C. C. B. Biochemistry 1981, 20, 849. https://doi.org/10.1021/bi00507a030
  2. Wada, G.; Tamura, E.; Okina, M.; Nakamura, M. Bull. Chem. Soc. Jpn. 1982, 55, 3064. https://doi.org/10.1246/bcsj.55.3064
  3. Slifkin, M. A.; Ali, S. M. J. Mol. Liq. 1984, 28, 215. https://doi.org/10.1016/0167-7322(84)80025-2
  4. Sharp, K. A.; Nicholls, A.; Friedman, R.; Honig, B. Biochemistry 1991, 30, 9686. https://doi.org/10.1021/bi00104a017
  5. Gaffney, J. S.; Pierce, R. C.; Friedman, L. J. Am. Chem. Soc. 1977, 99, 4293. https://doi.org/10.1021/ja00455a015
  6. Godfrey, P. D.; Brown, R. D. J. Am. Chem. Soc. 1995, 117, 2019. https://doi.org/10.1021/ja00112a015
  7. Locke, M. J.; McIver, R. T., Jr. J. Am. Chem. Soc. 1983, 105, 4226. https://doi.org/10.1021/ja00351a017
  8. Suenram, R. D.; Lovas, F. J. J. Am. Chem. Soc. 1980, 102, 7180. https://doi.org/10.1021/ja00544a002
  9. Ramaekers, R.; Pajak, J.; Lambie, B.; Maes, G. J. Chem. Phys. 2004, 120, 4182. https://doi.org/10.1063/1.1643735
  10. Balabin, R. M. J. Phys. Chem. B 2010, 114, 15075. https://doi.org/10.1021/jp107539z
  11. Aikens, C. M.; Gordon, M. S. J. Am. Chem. Soc. 2006, 128, 12835. https://doi.org/10.1021/ja062842p
  12. Bachrach, S. M. J. Phys. Chem. A 2008, 112, 3722. https://doi.org/10.1021/jp711048c
  13. Kundrat, M. D.; Autschbach, J. J. Chem. Theory Comput. 2008, 4, 1902. https://doi.org/10.1021/ct8002767
  14. Takayanagi, T.; Yoshikawa, T.; Kakizaki, A.; Shiga, M.; Tachikawa, M. J. Mol. Struct. (Theochem) 2008, 869, 29. https://doi.org/10.1016/j.theochem.2008.08.016
  15. Fernandez-Ramos, A.; Smedarchina, Z.; Siebrand, W.; Zgierski, M. Z. J. Chem. Phys. 2000, 113, 9714. https://doi.org/10.1063/1.1322084
  16. Balta, B.; Aviyente, V. J. Comput. Chem. 2004, 25, 690. https://doi.org/10.1002/jcc.10422
  17. Tortonda, F. R.; Pascual-Ahuir, J. L.; Silla, E.; Tunon, I. Chem. Phys. Lett. 1996, 260, 21. https://doi.org/10.1016/0009-2614(96)00839-1
  18. Tian, S. X.; Sun, X.; Cao, R.; Yang, J. J. Phys. Chem. A 2009, 113, 480. https://doi.org/10.1021/jp8092594
  19. Tiwari, S.; Mishra, P. C.; Suhai, S. Int. J. Quantum Chem. 2008, 108, 1004. https://doi.org/10.1002/qua.21557
  20. Bonaccorsi, R.; Palla, P.; Tomasi, J. J. Am. Chem. Soc. 1984, 106, 1945. https://doi.org/10.1021/ja00319a008
  21. Balta, B.; Aviyente, V. J. Comput. Chem. 2003, 24, 1789. https://doi.org/10.1002/jcc.10341
  22. Radzicka, A.; Wolfenden, R. Biochemistry 1988, 27, 1664. https://doi.org/10.1021/bi00405a042
  23. Sun, J.; Bousquet, D.; Forbert, H.; Marx, D. J. Chem. Phys. 2010, 133, 114508. https://doi.org/10.1063/1.3481576
  24. Leung, K.; Rempe, S. B. J. Chem. Phys. 2005, 122, 184506. https://doi.org/10.1063/1.1885445
  25. Watanabe, T.; Hashimoto, K.; Takase, H.; Kikuchi, O. J. Mol. Struct. (Theochem) 1997, 397, 113. https://doi.org/10.1016/S0166-1280(96)04942-1
  26. Kiani, F.; Rostami, A. A.; Sharifi, S.; Bahadori, A.; Chaichi, M. J. J. Chem. Eng. Data 2010, 55, 2732. https://doi.org/10.1021/je900975s
  27. Gontrani, L.; Mennucci, B.; Tomasi, J. J. Mol. Struct. (Theochem) 2000, 500, 113. https://doi.org/10.1016/S0166-1280(00)00390-0
  28. Bouchoux, G.; Xuan, R. Chia. Croat. Chem. Acta 2009, 82, 47.
  29. Wood, G. P. F.; Gordon, M. S.; Radom, L.; Smith, D. M. J. Chem. Theory Comput. 2008, 4, 1788. https://doi.org/10.1021/ct8002942
  30. Tunon, I.; Silla, E.; Ruiz-Lopez, M. F. Chem. Phys. Lett. 2000, 321, 433. https://doi.org/10.1016/S0009-2614(00)00365-1
  31. Ke, H.-W.; R. Li.; Xu, X.; Yan, Y.-J. J. Theor. Comput. Chem. 2008, 7, 889. https://doi.org/10.1142/S0219633608004192
  32. Selvarengan, P.; Kolandaivel, P. J. Mol. Struct. (Theochem) 2002, 617, 99. https://doi.org/10.1016/S0166-1280(02)00421-9
  33. Tortonda, F.R.; Pascual-Ahuir, J.L.; Silla, E.; Tunon, I. J. Mol. Struct. (Theochem) 2003, 623, 203. https://doi.org/10.1016/S0166-1280(02)00697-8
  34. Kwon, O. Y.; Kim, S. Y.; No, K. T. Bull. Korean Chem. Soc. 1995, 16, 410.
  35. Yu, D.; Armstrong, D. A.; Rauk, A. Can. J. Chem. 1992, 70, 1762. https://doi.org/10.1139/v92-221
  36. Bykov, S. V.; Myshakina, N. S.; Asher, S. A. J. Phys. Chem. B 2008, 112, 5803. https://doi.org/10.1021/jp710136c
  37. Engelke, R.; Blais, N. C.; Sheffield, S. A. J. Phys. Chem. A 2010, 114, 8234. https://doi.org/10.1021/jp102506k
  38. Falzon, C. T.; Wang, F. J. Chem. Phys. 2005, 123, 214307. https://doi.org/10.1063/1.2133727
  39. Hu, C.-H.; Shen, M.; Schaefer III, H. F. J. Am. Chem. Soc. 1993, 115, 2923. https://doi.org/10.1021/ja00060a046
  40. Jensen, J. H.; Gordon, M. S. J. Am. Chem. Soc. 1995, 117, 8159. https://doi.org/10.1021/ja00136a013
  41. Vishveshwara, S.; Pople, J. A. J. Am. Chem. Soc. 1977, 99, 2422. https://doi.org/10.1021/ja00450a004
  42. Leng, Y.; Zhang, M.; Song, C.; Chen, M.; Lin, Z. J. Mol. Struct. (Theochem) 2008, 858, 52. https://doi.org/10.1016/j.theochem.2008.02.016
  43. Jeon, I.-S.; Ahn, D.-S.; Park, S.-W.; Lee, S.Y.; Kim B. S. Int. J. Quantum Chem. 2005, 101, 55. https://doi.org/10.1002/qua.20269
  44. Cao, X.; Fischer, G. J. Phys. Chem. A 1999, 103, 9995. https://doi.org/10.1021/jp992421c
  45. Bandyopadhyay, P.; Gordon, M. S.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 2002, 116, 5023. https://doi.org/10.1063/1.1433503
  46. Sagarik, K.; Dokmaisrijan, S. J. Mol. Struct. (Theochem) 2005, 718, 31. https://doi.org/10.1016/j.theochem.2004.10.091
  47. Mullin, J. M.; Gordon, M. S. J. Phys. Chem. B 2009, 113, 8657. https://doi.org/10.1021/jp901459y
  48. Osted, A.; Kongsted, J.; Mikkelsen, K. V.; Christiansen, O. Chem. Phys. Lett. 2006, 429, 430. https://doi.org/10.1016/j.cplett.2006.08.060
  49. Tajkhorshid, E.; Jalkanen, K. J.; Suhai, S. J. Phys. Chem. B 1998, 102, 5899. https://doi.org/10.1021/jp9803135
  50. Chuchev, K.; BelBruno, J. J. J. Mol. Struct. (Theochem) 2008, 850, 111. https://doi.org/10.1016/j.theochem.2007.10.026
  51. Kapitan, J.; Baumruk, V.; Kopecky. Jr., V; Bouo, P. J. Phys. Chem. A 2006, 110, 4689. https://doi.org/10.1021/jp060260o
  52. Kang, Y. K.; Byun, B. J.; Kim, Y. H.; Kim, Y. H.; Lee, D. H.; Lee, J. Y. Bull. Korean Chem. Soc. 2008, 29, 1149. https://doi.org/10.5012/bkcs.2008.29.6.1149
  53. Wright, L. R.; Borkman, R. F. J. Am. Chem. Soc. 1980, 102, 6207. https://doi.org/10.1021/ja00540a006
  54. Tortonda, F. R.; Pascual-Ahuir, J.-L.; Silla, E.; Tunon, I. J. Chem. Phys. 1998, 109, 592. https://doi.org/10.1063/1.476596
  55. Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B 1997, 101, 5239. https://doi.org/10.1021/jp970736r
  56. Park, J.-H.; Lee, J.-W.; Park, H. Bull. Korean Chem. Soc. 2010, 31, 1247. https://doi.org/10.5012/bkcs.2010.31.5.1247
  57. MacDermott, J.; Fu, T.; Hyde, G. O.; Nakatsuka, R.; Coleman, A. P. Orig. Life Evol. Biosph. 2009, 39, 407. https://doi.org/10.1007/s11084-009-9161-x
  58. Wyttenbach, T.; Witt, M.; Bowers, M. T. J. Am. Chem. Soc. 2000, 122, 3458. https://doi.org/10.1021/ja992546v
  59. Smith, B. J. J. Comput. Chem. 1999, 20, 428. https://doi.org/10.1002/(SICI)1096-987X(199903)20:4<428::AID-JCC4>3.0.CO;2-1
  60. Dixit, S. B.; Bhasin, R.; Rajasekaran, E.; Jayaram, B. J. Chem. Soc. Faraday Trans. 1997, 93, 1105. https://doi.org/10.1039/a603913h
  61. Kim, J.; Nam, K.-Y.; Cho, K.-H.; Choi, S.-H.; Noh, J. S.; No, K. T. Bull. Korean Chem. Soc. 2003, 24, 1742. https://doi.org/10.5012/bkcs.2003.24.12.1742
  62. Chowdhry, B. Z.; Dines, T. J.; Jabeen, S.; Withnall, R. J. Phys. Chem. A 2008, 112, 10333. https://doi.org/10.1021/jp8037945
  63. Csaszar, A. G.; Perczel, A. Progress in Biophysics & Molecular Biology 1999, 71, 243. https://doi.org/10.1016/S0079-6107(98)00031-5
  64. Kaminsky, J.; Jensen, F. J. Chem. Theory Comput. 2007, 3, 1774. https://doi.org/10.1021/ct700082f
  65. Im, S.; Jang, S.-W.; Lee, S.; Lee, Y.; Kim, B. J. Phys. Chem. A 2008, 112, 9767. https://doi.org/10.1021/jp801933y
  66. Chen, M.; Lin, Z. J. Chem. Phys. 2007, 127, 154314. https://doi.org/10.1063/1.2777161
  67. Bachrach, S. M.; Nguyen, T. T.; Demoin, D. W. J. Phys. Chem. A 2009, 113, 6172. https://doi.org/10.1021/jp901491p
  68. Liu, S.-Z.; Wang, H.-Q.; Zhou, Z.-Y.; Dong, X.-L.; Gong, X.-L. Int J. Quantum. Chem. 2005, 105, 66. https://doi.org/10.1002/qua.20677
  69. Sproviero, E. M.; Newcomer, M.B.; Gascon, J. A.; Batista, E. R.; Brudvig, G. W.; Batista, V. S. Photosynth. Res. 2009, 102, 455. https://doi.org/10.1007/s11120-009-9467-6
  70. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669. https://doi.org/10.1002/jcc.10189
  71. Takano, Y.; Houk, K. N. J. Chem. Theory Comput. 2005, 1, 70. https://doi.org/10.1021/ct049977a
  72. Barone, V.; Cossi, M.; Tomasi, J. J. Comput. Chem. 1998, 19, 404. https://doi.org/10.1002/(SICI)1096-987X(199803)19:4<404::AID-JCC3>3.0.CO;2-W
  73. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 107, 3210. https://doi.org/10.1063/1.474671
  74. Weast, R. C., Ed.; Handbook of Chemistry and Physics, CRC Press: Cleveland, U.S.A, 1981.
  75. Bondi, A. J. Phys. Chem. 1964, 68, 441. https://doi.org/10.1021/j100785a001
  76. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Vreven, T., Jr.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N..; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli. C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision D.02 ed.; Gaussian, Inc., Wallingford CT, 2004.
  77. Weiss, S.; Leroi, G. E. J. Chem. Phys. 1968, 48, 962. https://doi.org/10.1063/1.1668849

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