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Vol. 37 No. 7 (2025): Vol 37 Issue 7, 2025

Copyright (c) 2025 Jyoti Bhovi, J. Tonannavar, JAYASHREE TONANNAVAR

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MD and DFT Studies of O–H···N Bonded Hordenine Dimer, Aided by Experimental Vibrational Spectroscopy, NBO, AIM and NCI Calculations

https://doi.org/10.14233/ajchem.2025.33894
Jyoti Bhovi
Vibrational Spectroscopy/Molecular Modeling Laboratory, Department of Physics, Karnatak University, Dharwad-580003, India
https://orcid.org/0009-0007-9414-445X
J. Tonannavar
Vibrational Spectroscopy/Molecular Modeling Laboratory, Department of Physics, Karnatak University, Dharwad-580003, India
https://orcid.org/0000-0001-5912-644X
Jayashree J. Tonannavar
Vibrational Spectroscopy/Molecular Modeling Laboratory, Department of Physics, Karnatak University, Dharwad-580003, India
https://orcid.org/0000-0002-3026-8118

Corresponding Author(s) : Jayashree J. Tonannavar

jjtonannavar@kud.ac.in

Asian Journal of Chemistry, Vol. 37 No. 7 (2025): Vol 37 Issue 7, 2025

Abstract

The role of allelopathic and biochemical inhibitor hordenine in many applications may be determined by its potential tendency to the inter–molecular O–H···N bonding among other things. It is of interest to study multi-structural characterizations of the O–H···N bonding interaction to gain insights into the possible functional roles of the bonding, which may be correlated to the diverse application domains. In the present study, we have shown that the O–H···N bonded dimer computed from molecular dynamics (MD) simulation has short-range order and quasi-long range order consistent with the reported XRD results. We computed structural parameters from MD simulation in water yielding radius of gyration, minimum distance and root-mean-square-deviation and radial distribution function values that have been employed to understand the structural behaviour of the dimer. In addition, MD simulation also yielded O–H···O and C–H···N bonds as constituent links in dimer structures. We also combined molecular dynamics (MD) with DFT at B3LYP/6–311++G (d,p) level for computing the afore-mentioned stable structures and associated vibrational and electronic properties. Vibrational IR and Raman spectral features support the O–H···N bonded dimer structure. The orbitals overlap corresponding to the O–H···N bonding interaction has more contributions from s-orbitals of the O–H bond causing its elongation and stretching-mode red shift in the IR. The electron density and its Laplacian values have provided contour maps corresponding to the charge concentration and depletions around the O–H···N bond interaction.

Keywords

Hordenine Molecular dynamics DFT O–H···N bond Non-covalent interactions
(1)
Bhovi, J.; Tonannavar, J.; Tonannavar, J. J. MD and DFT Studies of O–H···N Bonded Hordenine Dimer, Aided by Experimental Vibrational Spectroscopy, NBO, AIM and NCI Calculations. ajc 2025, 37, 1614-1628.
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References
  1. J. Ma, S. Wang, X. Huang, P. Geng, C. Wen, Y. Zhou, L. Yu and X. Wang, J. Pharm. Biomed. Anal., 111, 131 (2015); https://doi.org/10.1016/j.jpba.2015.03.032
  2. S.C. Kim, J.H. Lee, M.H. Kim, J.A. Lee, Y.B. Kim, E. Jung, Y.S. Kim, J. Lee and D. Park, Food Chem., 141, 174 (2013); https://doi.org/10.1016/j.foodchem.2013.03.017
  3. B.P. Mukhopadhyay, J.K. Dattagupta and M. Simonetta, Z. Krist. New Cryst. Struct., 187, 221 (1989); https://doi.org/10.1524/zkri.1989.187.14.221
  4. M. Sobiech, J. Giebultowicz and P. Luliñski, J. Chromatogr. A, 1613, 460677 (2020); https://doi.org/10.1016/j.chroma.2019.460677
  5. J.S. Fitzgerald, Aust. J. Chem., 17, 160 (1964); https://doi.org/10.1071/CH9640160
  6. S. Anwar, T. Mohammad, A. Shamsi, A. Queen, S. Parveen, S. Luqman, G.M. Hasan, K.A. Alamry, N. Azum, A.M. Asiri and M.I. Hassan, Biomedicines, 8, 119 (2020); https://doi.org/10.3390/biomedicines8050119
  7. S. Ghose and J.K. Dattagupta, Z. Kristallogr., 187, 213 (1989); https://doi.org/10.1524/zkri.1989.187.3-4.213
  8. C.J. Barwell, A.N. Basma, M.A.K. Lafi and L.D. Leake, J. Pharm. Pharmacol., 41, 421 (1989); https://doi.org/10.1111/j.2042-7158.1989.tb06492.x
  9. A. Dwivedi, V. Dubey and A.K. Bajpai, Int. J. Chem. Stud., 2, 20 (2015).
  10. M. Parvez and J.F. Malone, Acta Cryst., 293C, 1450 (1991); https://doi.org/10.1107/S0108270190012380
  11. J. Priscilla, D.A. Dhas, I. Hubert-Joe and S. Balachandran, J. Mol. Struct., 1229, 129823 (2021); https://doi.org/10.1016/j.molstruc.2020.129823
  12. R.F.W. Bader, Chem. Rev., 91, 893 (1991); https://doi.org/10.1021/cr00005a013
  13. 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. Aricato, 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 Jr., 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. Cioslowski, J.V. Ortiz and D.J. Fox, Gaussian 09, Revision A.1, Gaussian Inc., Wallingford CT (2009).
  14. M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team, GROMACS User Manual version (2019); http://www.gromacs.org
  15. J. Bhovi, J. Tonannavar and J.J. Tonannavar, J. Mol. Struct., 1299, 137077 (2024); https://doi.org/10.1016/j.molstruc.2023.137077
  16. B. Hess, J. Chem. Theory Comput., 4, 116 (2008); https://doi.org/10.1021/ct700200b
  17. W. Humphrey, A. Dalke and K. Schulten, J. Mol. Graph., 33, 7855, (1996); https://doi.org/10.1016/0263-7855(96)00018-5
  18. T. Lu and F. Chen, J. Comput. Chem., 33, 580 (2012); https://doi.org/10.1002/jcc.22885
  19. M.H. Jamróz, Spectrochim. Acta A Mol. Biomol. Spectrosc., 114, 220 (2013); https://doi.org/10.1016/j.saa.2013.05.096
  20. L. Pallavi, J. Tonannavar and J. Tonannavar, J. Mol. Liq., 352, 118746 (2022); https://doi.org/10.1016/j.molliq.2022.118746
  21. S. Zahn, K. Wendler, L. Delle Site and B. Kirchner, Phys. Chem. Chem. Phys., 13, 15083 (2011); https://doi.org/10.1039/c1cp20288j
  22. Gromacs Manual-2023.3 Documentation, (2023); https://doi.org/10.5281/zenodo.7588711
  23. A. Kantardjiev and P.M. Ivanov, Entropy, 22, 1187 (2020); https://doi.org/10.3390/e22101187
  24. D.H.D. Jong, L.V. Schäfer, A.H. De vries, S.J. Marrink, H.J.C. Berendsen and H. Grubmuller, J. Comput. Chem., 32, 1919 (2011); https://doi.org/10.1002/jcc.21776
  25. A. Rakita, N. Nikolic, M. Mildner, J. Matiasek and A. Elbe-Bürger, Sci. Rep., 10, 1 (2020); https://doi.org/10.1038/s41598-019-56847-4
  26. G.R. Desiraju and T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press: New York (1999).
  27. G. Socrates, Infrared Characteristic Group Frequencies, John Wiley & Sons, New York, London, Sydney, Toronto (1980).
  28. N.B. Colthup, L.H. Daly and S.E. Wiberley, Introduction to Infrared and Raman Spectroscopy, Academic Press Inc., New York and London (1964).
  29. L.J. Bellamy, The Infrared Spectra of Complex Molecules, Chapman and Hall: London, edn. 3 (1975).
  30. M.D. Prabhu, J.T. Yenagi, V. Kamat and J. Tonannavar, J. Mol. Struct., 1218, 128495 (2020); https://doi.org/10.1016/j.molstruc.2020.128495
  31. D. Sajan, J. Binoy, B. Pradeep, K.V. Krishna, V.B. Kartha, I.H. Joe, V.S. Jayakumar, Spectrochim. Acta A Mol. Biomol. Spectrosc., 60, 173 (2004); https://doi.org/10.1016/S1386-1425(03)00193-8
  32. M. Karabacak, Z. Calisir, M. Kurt, E. Kose and A. Atac, Spectrochim. Acta A Mol. Biomol. Spectrosc., 153, 754 (2016); https://doi.org/10.1016/j.saa.2015.09.007
  33. J.P. Merrick, D. Moran and L. Radom, J. Phys. Chem. A, 111, 11683 (2007); https://doi.org/10.1021/jp073974n
  34. E.D. Glendening, C.R. Landis and F. Weinhold, J. WIREs Comput. Mol. Sci., 2, 1 (2012); https://doi.org/10.1002/wcms.51
  35. V. Krishnakumar, D. Barathi, R. Mathammal, J. Balamani and N. Jayamani, Spectrochim. Acta A Mol. Biomol. Spectrosc., 121, 245 (2014); https://doi.org/10.1016/j.saa.2013.10.068
  36. S. Yalagi, J. Tonannavar and J. Tonannavar, Heliyon, 5, e01933 (2019); https://doi.org/10.1016/j.heliyon.2019.e01933
  37. S.S. Malaganvi, J.T. Yenagi and J. Tonannavar, Heliyon, 5, e01586 (2019); https://doi.org/10.1016/j.heliyon.2019.e01586
  38. L.F. Pacios, J. Phys. Chem. A, 108, 1177 (2004); https://doi.org/10.1021/jp030978t
  39. E. Espinosa, I. Alkorta, J. Elguero and E. Molins, J. Chem. Phys., 117, 5529 (2002); https://doi.org/10.1063/1.1501133
  40. P.S.V. Kumar, V. Raghavendra and V. Subramanian, J. Chem. Sci., 128, 1527 (2016); https://doi.org/10.1007/s12039-016-1172-3
  41. S.G. Aziz, A.O. Alyoubi, S.A. Elroby and R.H. Hilal, Mol. Phys., 115, 2565 (2017); https://doi.org/10.1080/00268976.2017.1335896
  42. W. Zierkiewicz, J. Fanfrlík, P. Hobza, D. Michalska and T. Zeegers-Huyskens, Theor. Chem. Acc., 135, 217 (2016); https://doi.org/10.1007/s00214-016-1972-z
  43. I. Rozas, I. Alkorta and J. Elguero, J. Am. Chem. Soc., 122, 11154 (2000); https://doi.org/10.1021/ja0017864
  44. E.R. Johnson, S. Keinan, P. Mori-Sanchez, J. Contreras-García, A.J. Cohen and W. Yang, J. Am. Chem. Soc., 132, 6498 (2010); https://doi.org/10.1021/ja100936w
  45. R. Laplaza, F. Peccati, R.A. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday and J. Contreras-García, J. WIREs Comput. Mol. Sci., 11, e1497 (2020); https://doi.org/10.1002/wcms.1497
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