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Vibrational Spectroscopic and Molecular Docking Studies on N-Carbobenzoxy-L-2-phenylglycine by Density Functional Theory Method

https://doi.org/10.14233/ajchem.2017.20148
M. Sathish
Manonmaniam Sundaranar University, Tirunelveli-627 012, India; Department of Physics, St. Joseph's College of Arts & Science (Autonomous), Cuddalore-607 001, India
G. Meenakshi
Department of Physics, Kanchi Mamunivar Center for Post Graduate Studies and Research, Puducherry-605 008, India
S. Xavier
Department of Physics, St. Joseph's College of Arts & Science (Autonomous), Cuddalore-607 001, India
S. Sebastian
Department of Physics, St. Joseph's College of Arts & Science (Autonomous), Cuddalore-607 001, India
V. Sathana
Department of Physics, St. Joseph's College of Arts & Science (Autonomous), Cuddalore-607 001, India

Corresponding Author(s) : M. Sathish

marysathish2013@gmail.com

Asian Journal of Chemistry, Vol. 29 No. 2 (2017): Vol 29 Issue 2

Abstract

The NLO compound, N-carbobenzoxy-L-2-phenyl glycine (CbzLPG) has been characterized by Fourier transform infrared, Fourier transform Raman and ultraviolet-visible spectrometry. Density functional theory (DFT) calculations has been carried out by performing DFT-B3LYP and M06-2X levels of theories using 6-311+G(d,p) basis set. The geometry of the structure was optimized without any symmetry constraints using the DFT-B3LYP/M06-2X with 6–311+G(d,p) levels of estimations. The targeted interpretation of the vibrational spectra has been prepared on the basis of the calculated potential energy distribution matrix (PED). The vibrational frequencies decided tentatively are contrasted and those acquired hypothetically from DFT computations employing the B3LYP/6–311+G(d,p) and M06-2X/6–311+G(d,p) methods for the optimized geometry of the compound. Utilizing the natural bond orbital (NBO) evaluation stability of the analysis steadiness of the molecule emerging from hyper conjugative interactions, charge delocalization has been examined. In addition, frontier molecular orbitals and molecular electrostatic potential were computed by way of utilizing density functional theory (DFT/B3LYP) using 6-311+G(d,p) basis set. The computed HOMO and LUMO energies demonstrate that charge exchange happens inside of the molecule. The structure-substance reactivity relations of the compound were resolved through global and local reactivity descriptors by conceptual DFT methods. The first order hyperpolarizability (b0) and related properties (b, a0 and Da) of N-carbobenzoxy-L-2-phenyl glycine were calculated. Thermodynamic functions of a label compound were furthermore carried out from B3LYP with basis set 6-311+G(d,p) using Thermo.pl software. As a result, the performances of the B3LYP method with the prediction of the wavenumbers within the molecule were quite close. Molecular docking studies of N-carbobenzoxy-L-2-phenyl glycine has been performed and analyzed.

Keywords

N-Carbobenzoxy-L-2-phenylglycine TD-DFT Natural bond orbital
Sathish, M., Meenakshi, G., Xavier, S., Sebastian, S., & Sathana, V. (2016). Vibrational Spectroscopic and Molecular Docking Studies on N-Carbobenzoxy-L-2-phenylglycine by Density Functional Theory Method. Asian Journal of Chemistry, 29(2), 242–256. https://doi.org/10.14233/ajchem.2017.20148
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References
  1. J.L. Lynch III, P. Honore, D.J. Anderson, W.H. Bunnelle, K.H. Mortell, Ch. Zhong, C.L. Wade, Ch.Z. Zhu, H. Xu, K.C. Marsh, Ch.-H. Lee, M.F. Jarvis and M. Gopalakrishnan, Pain, 125, 136 (2006).
  2. A. Boto, J.A. Gallardo, R. Hernandez, F. Ledo, A. Munoz, J.R. Murguia, M. Menacho Marquez, A. Orjales and C.J. Saavedra, Bioorg. Med. Chem. Lett., 16, 6073 (2006).
  3. O. Angelova, R. Petrova, V. Radomirska and T. Kolev, Acta Crystallogr., 52C, 2218 (1996).
  4. S. Ravichandran, J.K. Dattagupta and Ch. Chakrabarti, Acta Crystallogr., 54C, 499 (1998).
  5. N. Srinivasan, B. Sridhar and R.K. Rajaram, Acta Crystallogr., 57E, 754 (2001).
  6. S. Ramaswamy, B. Sridhar, V. Ramakrishnan and R.K. Rajaram, Acta Crystallogr., 57E, 1149 (2001).
  7. K. Bouchouit, L. Bendheif and N. Benali-Cherif, Acta Crystallogr., 60E, 272 (2004).
  8. S. Bouacida, H. Merazig and P. Benard-Rocherulle, Acta Crystallogr., 62E, o838 (2006).
  9. Y.J. Mast, W. Wohlleben and E. Schinko, J. Biotechnol., 155, 63 (2011).
  10. M. Kusano, K. Yasukawa and K. Inouye, Enzyme Microb. Technol., 46, 320 (2010).
  11. M.M. Ilczyszyn, T. Lis and M. Wierzejewska, J. Mol. Struct., 937, 2 (2009).
  12. M.M. Ilczyszyn, T. Lis, M. Wierzejewska and M. Zatajska, J. Mol. Struct.,919, 303 (2009).
  13. M.A. Palafox, V.K. Rastogi, R.P. Tanwar and L. Mittal, Spectrochim. Acta A, 59, 2473 (2003).
  14. S. Mohan, N. Sundaraganesan and J. Mink, Spectrochim. Acta A, 47, 1111 (1991).
  15. G.N. Ten, V.V. Nechaev, A.N. Pankratov, V.I. Berezin and V.I. Baranov, J. Struct. Chem., 51, 854 (2010).
  16. C. Cirak and N. Koc, J. Mol. Model., 18, 4453 (2012).
  17. M.A. Palafox, G. Tardajos, A. Guerrero-Martínez, V.K. Rastogi, D. Mishra, S.P. Ojha and W. Kiefer, Chem. Phys., 340, 17 (2007).
  18. M. Szczesniak, M.J. Nowak, K. Szczepaniak and W.B. Person, Spectrochim. Acta A, 41, 237 (1985).
  19. J.S. Singh, J. Mol. Struct., 876, 127 (2008).
  20. M.H. Jamróz, J.C. Dobrowolski and R. Brzozowski, J. Mol. Struct., 787, 172 (2006).
  21. C. Cirak, Y. Sert and F. Ucun, Spectrochim. Acta A, 92, 406 (2012).
  22. Y. Zhao and D.G. Truhlar, Theor. Chem. Acc., 120, 215 (2008).
  23. K. Helios, R. Wysokinski, A. Pietraszko and D. Michalska, Vib. Spectrosc., 55, 207 (2011).
  24. J. Gu, J. Wang and J. Leszczynski, Chem. Phys. Lett., 512, 108 (2011).
  25. K.H. Lemke and T.M. Seward, Chem. Phys. Lett., 573, 19 (2013).
  26. E.I. Paulraj and S. Muthu, Spectrochim. Acta A, 108, 38 (2013).
  27. U. Yadava, M. Singh and M. Roychoudhury, Comput. Theor. Chem., 977, 134 (2011).
  28. C.N. Ramachandran and E. Ruckenstein, Comput. Theor. Chem., 973, 28 (2011).
  29. Y. Sert, C. Cirak and F. Ucun, Spectrochim. Acta A, 107, 248 (2013).
  30. M.J. Frisch, et al., Gaussian 09, Revision A.1, Gaussian, Inc., Wallingford CT (2009).
  31. P. Hohenberg and W. Kohn, Phys. Rev., 136, B86 (1964).
  32. A.D. Becke, J. Chem. Phys., 98, 5648 (1993).
  33. C. Lee, W. Yang and R.G. Parr, Phys. Rev. B, 37, 785 (1988).
  34. E. Frisch, H.P. Hratchian, R.D. Dennington II, T.A. Keith, J. Millam, B. Nielsen, A.J. Holder and J. Hiscocks. Gaussian, Inc. GaussView Version 5.0.8 (2009).
  35. M.H. Jamroz, Vibrational Energy Distribution Analysis: VEDA 4 Program, Warsaw, Poland (2004).
  36. Y. Morino and K. Kuchitsu, J. Chem. Phys., 20, 1809 (1952).
  37. W.J. Taylor, J. Chem. Phys., 22, 1780 (1954).
  38. T. Miyazawa, T. Shimanouchi and S. Mizushima, J. Chem. Phys., 29, 611 (1958).
  39. G. Zerbi, J. Overend and B. Crawford, J. Chem. Phys., 38, 122 (1963).
  40. G. Keresztury and G. Jalsovszky, J. Mol. Struct., 10, 304 (1971).
  41. P. Pulay, G. Fogarasi, F. Pang and J.E. Boggs, J. Am. Chem. Soc., 101, 2550 (1979).
  42. L. Lapinski and P. Pongor, PED-Program, Warsaw, Poland (1994).
  43. E.D. Glendening, C.R. Landis, F. Weinhold, WIREs Comput. Mol. Sci., 2, 1 (2011).
  44. D.A. Kleinman, Phys. Rev., 126, 1977 (1962).
  45. S. Shen, G.A. Guirgis and J.R. Durig, Struct. Chem., 12, 33 (2001).
  46. D. Michalska and R. Wysoki’nski, Chem. Phys. Lett., 403, 211 (2005).
  47. D. Michalska, RAINT, A Computer Program for Calculation of Raman Intensities from the Gaussian Outputs, Wroclaw University of Technology, Poland (2002).
  48. K. Dong and Y. Wang, Acta Crystallogr., 70E, o527 (2014).
  49. V. Arjunan, T. Rani, C.V. Mythili and S. Mohan, Spectrochim. Acta A, 79, 486 (2011).
  50. D. Sajan, H.J. Ravindra, N. Misra and I.H. Joe, Vib. Spectrosc., 54, 72 (2010).
  51. N.P.G. Roges, A Guide to the Complete Interpretation of the Infrared Spectra of Organic Structures, Wiley, New York (1994).
  52. A. Fu, D. Du and Z. Zhou, Spectrochim. Acta, 59, 245 (2003).
  53. K. Govindarasu and E. Kavitha, Spectrochim. Acta, 133, 799 (2014).
  54. L.D. Stefano, R. Cioffi and F. Colangelo, J. Anal. Chem., 3, 1 (2012).
  55. L.J. Bellamy, The Infrared Spectra of Complex Molecules, Chapman and Hall, London (1980).
  56. N.B. Colthup, L.H. Daly and S.E. Wiberley, Introduction to Infrared and Raman Spectroscopy, Academic Press, New York (1990).
  57. R.M. Silverstein, G.C. Bassler and T.C. Morril, Spectrometric Identification of Organic Compounds, John Wiley & Sons Inc., Singapore, edn 5 (1991).
  58. A. Spire, M. Barthes, H. Kellouai and G. De Nunzio, Physica D, 137, 392 (2000).
  59. C.Y. Panicker, H.T. Varghese and T. Tansani, Turk. J. Chem., 33, 1 (2009).
  60. A.E. Reed, L.A. Curtiss and F. Weinhold, Chem. Rev., 88, 899 (1988).
  61. J. Henriksson, T. Saue and P. Norman, J. Chem. Phys., 128, 024105 (2008).
  62. J.P. Hermann, D. Ricard and J. Ducuing, Appl. Phys. Lett., 23, 178 (1973).
  63. S. Debrus, H. Ratajczak, J. Venturini, N. Pincon, J. Baran, J. Barycki, T. Glowiak and A. Pietraszko, Synth. Met., 127, 99 (2002).
  64. K. Govindarasu and E. Kavitha, Spectrochim. Acta A, 122, 130 (2014).
  65. R. Parr, L. Szentpaly and S. Liu, J. Am. Chem. Soc., 121, 1922 (1999).
  66. P.K. Chattaraj, B. Maiti and U. Sarkar, J. Phys. Chem. A, 107, 4973 (2003).
  67. R. Parr, R. Donnelly, M. Levy and W. Palke, J. Chem. Phys., 68, 3801 (1978).
  68. R. Parr and R. Pearson, J. Am. Chem. Soc., 105, 7512 (1983).
  69. R.G. Parr and P.K. Chattaraj, J. Am. Chem. Soc., 113, 1854 (1991).
  70. T.A. Koopmans, Physica, 1, 104 (1934).
  71. Z. Ran, D. Baotong, S. Gang and S. Yuxi, Spectrochim. Acta, 75A, 1115 (2010).
  72. W.L. Jorgensen, Science, 303, 1813 (2004).
  73. Chemspider chemical structure database http://www.chemspider.com/Chemical-Structure.715749.html (accessed on 12 December 2015).
  74. D.M.F. van Aalten, R. Bywater, J.B.C. Findlay, M. Hendlich, R.W.W. Hooft and G. Vriend, J. Comput. Aided Mol. Des., 10, 255 (1996).
  75. A.W. Schüttelkopf and D.M.F. van Aalten, Acta Crystallogr. D Biol. Crystallogr., 60, 1355 (2004).
  76. The GlycoBioChem PRODRG2 Server http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/ (accessed on 08 January 2016).
  77. X. Liu, S. Ouyang, B. Yu, Y. Liu, K. Huang, J. Gong, S. Zheng, Z. Li, H. Li and H. Jiang, Nucleic Acids Res., 38(Web Server), W609 (2010).
  78. PharmMapper Server http://59.78.96.61/pharmmapper/ (accessed on08 January 2016).
  79. G. Lange, D. Lesuisse, P. Deprez, B. Schoot, P. Loenze, D. Bénard, J.P. Marquette, P. Broto, E. Sarubbi and E. Mandine, J. Med. Chem., 46, 5184 (2003).
  80. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov and P.E. Bourne, Nucleic Acids Res., 28, 235 (2000).
  81. RCSB The Protein Data Bank http://www.rcsb.org/ (accessed on 08 January 2016).
  82. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew and A.J. Olson, J. Comput. Chem., 19, 1639 (1998).
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