Molecular Structure, Vibrational Spectra and Docking Studies of Abacavir by Density Functional Theory

Solaichamy, R.; Karpagam, J.

doi:10.18052/www.scipress.com/ILCPA.72.9

ILCPA > ILCPA Volume 72 > Molecular Structure, Vibrational Spectra and...

< Back to Volume

Molecular Structure, Vibrational Spectra and Docking Studies of Abacavir by Density Functional Theory

Full Text PDF

Abstract:

In this study, optimized geometry, spectroscopic (FT-IR, FT-Raman, UV) analysis, and electronic structure analysis of Abacavir were investigated by utilizing DFT/B3LYP with 6-31G(d,p) as a basis set. Complete vibrational assignments and correlation of the fundamental modes for the title compound were carried out. The calculated molecular geometry has been compared with available X-ray data of Abacavir. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The molecular stability and bond strength have been investigated by applying the Natural Bond Orbital (NBO) analysis. The computational molecular docking studies of title compound have been performed.

Info:

Periodical:

International Letters of Chemistry, Physics and Astronomy (Volume 72)

Pages:

9-27

DOI:

https://doi.org/10.18052/www.scipress.com/ILCPA.72.9

Citation:

R. Solaichamy and J. Karpagam, "Molecular Structure, Vibrational Spectra and Docking Studies of Abacavir by Density Functional Theory", International Letters of Chemistry, Physics and Astronomy, Vol. 72, pp. 9-27, 2017

Online since:

January 2017

Authors:

R. Solaichamy, J. Karpagam

Keywords:

Abacavir, DFT, FT-IR, FT-Raman, Molecular Docking, NBO

Export:

RIS, BibTeX, Text

Distribution:

Open Access

This work is licensed under a
Creative Commons Attribution 4.0 International License

References:

[1] P. Kommavarapu et al., Simultaneous estimation of degree of crystallinity in combination drug product of abacavir, lamivudine and neverapine using X-ray powder diffraction technique, Journal of Young Pharmacists. 5(4) (2013) 127–132.

DOI: https://doi.org/10.1016/j.jyp.2013.10.003

[2] S.K. Gangwer, A.K. Srivastava, R.B. Singh, Experimental [FT-IR, UV-Visible, NMR] spectroscopy and molecular structure, global reactivity parameters, Fukui Function, NBO, NLO, Homo-Lmo, MESP, and QTAM analysei of abacavir using density functional theory, IOSR-journal of Biotechnology and biochemistry. 2 (2016).

[3] P. Echeverría, E. Negredo, G. Carosi, Similar antiviral efficacy and tolerability between efavirenz and lopinavir/ritonavir, administered with abacavir/lamivudine (Kivexa), in antiretroviral-naïve patients: A 48-week, multicentre, randomized study (Lake Study), Antiviral Research. 85 (2010).

[4] Gaussian Inc., Gaussian 03 Program, Gaussian Inc., Wallingford, (2004).

[5] H.B. Schlegel, Optimization of equilibrium geometries and transition structures, J. Comput. Chem. 3 (1982) 214–218.

[6] A. Frisch, A.B. Nielson, A.J. Holder, Gaussview user manual, Gaussian Inc., Pittsburgh, PA, (2000).

[7] M.H. Jamróz, Vibrational Energy Distribution Analysis, VEDA 4, Warsaw, (2004).

[8] N.C. Handy, P.E. Maslen, R.D. Amos, Study of methane, acetylene, ethene, and benzene using Kohn-Sham theory, J. Phys. Chem. 97 (1993) 4392–4396.

DOI: https://doi.org/10.1021/j100119a023

[9] V. Krishnakumar, R. Mathammal, S. Muthunatesan, FT-IR and Raman spectra vibrational assignments and density functional calculations of 1-naphthyl acetic acid, Spectrochim. Acta A. 70 (2008) 210–216.

DOI: https://doi.org/10.1016/j.saa.2007.06.040

[10] E.D. Glendening et al., NBO Version3. 1, TCI, University of Wisconsin, Madison, (1998).

[11] L. E. Sutton, Tables of interatomic distances, Chemical Society, London, (1958).

[12] K. Govindarasu, E. Kavitha, Vibrational spectra, molecular structure, NBO, NMR, UV, first order hyperpolarizability, analysis of (S)-(−)-N-(5-Nitro-2-pyridyl) alaninol by Density functional theory, Spectrochim. Acta A. 127 (2014) 498–510.

DOI: https://doi.org/10.1016/j.saa.2014.02.107

[13] P.T. Illing et al., Immune self-reactivity triggered by drug-modified HLA-peptide repertoire, Nature. 486 (2012) 554-558.

[14] M.F. Sanner, Python: a programming language for software integration and development, Journal of Molecular Graphics and Modelling. 17 (1999) 57–61.

[15] A.A. Adeniyi, P.A. Ajibade, Inhibitory activities and possible anticancer targets of Ru(II)-based complexes using computational docking method, Journal of Molecular Graphics and Modelling. 38 (2012) 60–69.

DOI: https://doi.org/10.1016/j.jmgm.2012.08.004

[16] R. Thomsen, M.H. Christensen, MolDock: A New Technique for High-Accuracy Molecular Docking, J. Med. Chem. 55 (2012) 623-638.

[17] P. TT. Pham, Abacavir methanol 2. 5-solvate, Acta Crystallographica Section E: Structure Reports Online. 8 (2009) o193.

[18] A.A. Al-Saadi, J. Laane, Ab initio and DFT calculations for the structure and vibrational spectra of cyclopentene and its isotopomers, J. Mol. Struct. 830 (2007) 46–57.

DOI: https://doi.org/10.1016/j.molstruc.2006.06.030

[19] Ismat Fatima et al., 6-Benzylsulfanyl-9H-purine, Acta Cryst. E. 65 (2009) o2994.

[20] C.S.C. Kumara et al., Synthesis, molecular structure, spectroscopic characterization and quantum chemical calculation studies of (2E)-1-(5-chlorothiophen-2-yl)-3-(2, 3, 4-trimethoxyphenyl)prop-2-en-1-one, J. Mol. Struct. 1085 (2015) 63–77.

DOI: https://doi.org/10.1016/j.molstruc.2014.12.052

[21] V. Balachandran, K. Parimala, Automeric purine forms of 2-amino-6-chloropurine (N9H10 and N7H10): Structures, vibrational assignments, NBO analysis, hyperpolarizability, HOMO–LUMO study using B3 based density functional calculations, Spectrochimica Acta Part A. 96 (2012).

[22] K. Parimala, V. Balachandran, Vibrational spectroscopic (FTIR and FT Raman) studies, first order hyperpolarizabilities and HOMO, LUMO analysis of p-toluenesulfonyl isocyanate using ab initioHF and DFT methods, Spectrochim. Acta A. 81 (2011).

DOI: https://doi.org/10.1016/j.saa.2011.07.011

[23] M. Silverstein, G.C. Basseler, T.C. Morrill, Spectrometric identification of organic compound, Wiley, New York, (1981).

[24] G. Socrates, Infrared and Raman characteristic group frequencies, Tables and Charts, Third ed., vol. 2, John Wiley, Chichester, (2001).

[25] N.B. Colthup, L.H. Daly, S.E. Wiberley, Introduction to infrared and Raman spectroscopy, Academic Press, New York, (1990).

[26] I. Fleming, Frontier orbitals and organic chemical reactions, Wiley, London, (1976).

[27] C.H. Choi, M. Kertesz, Conformational information from vibrational spectra of styrene, trans-stilbene, and cis-stilbene, J. Phys. Chem. A. 101 (1997) 3823-3831.

[28] N. Okulik, A.H. Jubert, Theoretical analysis of the reactive sites of non–steroidal anti– inflammatory drugs, Internet Electron J. Mol. Des. 4 (2005) 17-30.

[29] N. Strushkevich, S.A. Usanov, H.W. Park, Structural basis of human CYP51 inhibition by antifungal azoles, J. Mol. Biol. 397 (2010) 1067-1078.

[30] O. Trott, A.J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comput. Chem. 31 (2010) 455-461.

DOI: https://doi.org/10.1002/jcc.21334

Show More Hide

Cited By:

[1] S. Aayisha, T. Renuga Devi, S. Janani, S. Muthu, M. Raja, S. Sevvanthi, "DFT, molecular docking and experimental FT-IR, FT-Raman, NMR inquisitions on “4-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-6-methoxy-2-methylpyrimidin-5-amine”: Alpha-2-imidazoline receptor agonist antihypertensive agent", Journal of Molecular Structure, 2019

DOI: https://doi.org/10.1016/j.molstruc.2019.03.056

[2] D. Milenković, E. Avdović, D. Dimić, S. Sudha, D. Ramarajan, Ž. Milanović, S. Trifunović, Z. Marković, "Vibrational and Hirshfeld surface analyses, quantum chemical calculations, and molecular docking studies of coumarin derivative 3-(1-m-toluidinoethylidene)-chromane-2,4-dione and its corresponding palladium(II) complex", Journal of Molecular Structure, p. 127935, 2020

DOI: https://doi.org/10.1016/j.molstruc.2020.127935

[3] Ž. Milanović, D. Dimić, E. Avdović, D. Milenković, J. Marković, O. Klisurić, S. Trifunović, Z. Marković, "Synthesis and comprehensive spectroscopic (X-ray, NMR, FTIR, UV-Vis), quantum chemical and molecular docking investigation of 3-acetyl-4-hydroxy-2-oxo-2H-chromen-7-yl acetate", Journal of Molecular Structure, p. 129256, 2020

DOI: https://doi.org/10.1016/j.molstruc.2020.129256