Theoretical Investigation of Szemaoenoid A with Abietane Skeletone

Abstract

In order to analyze the structure of diterpenes having significant biological activity and predict their chemical properties, the compound of Szemaoenoid A with an abietane skeleton has been examined theoretically. Bond lengths, bond angles, dihedral angles, and 13C-NMR isotropic shielding values were calculated with both ab initio and density functional theory (DFT) methods. The correlations between theoretical and experimental results were examined by statistical analysis works. Vibrational analyses were performed at the B3LYP/cc-pVDZ level of theory. Moreover, the electronic structure (HOMO-LUMO and MEP maps) of title compound was investigated theoretically. By using the energy values of frontier molecular orbitals, the parameters of Szemaoenoid A such as frontier molecular orbital energy differences, chemical hardness and electronegativity were calculated at the B3LYP/cc-pVDZ level. It has been deduced that Szemaoenoid A shows fair chemical stability and reactivity.

Keywords

• Abietane
• DFT
• HF
• NMR
• IR

Abietan İskeletine Sahip Szemaoenoid A Molekülünün Teorik Olarak İncelenmesi

Abstract

Önemli biyolojik aktiviteye sahip olan diterpenlerin yapısını analiz etmek ve kimyasal özellikleri hakkında öngörüde bulunabilmek amacıyla, abietan iskeletine sahip Szemaoenoid A bileşiği teorik olarak incelenmiştir. Abietan bileşiğinin bağ uzunlukları, bağ açıları, dihedral bağ açıları ve 13C-NMR isotropik kayma değerleri, ab initio ve yoğunluk fonksiyoneli teorisi (YFT) yöntemleriyle hesaplanmıştır. Teorik sonuçların deneysel veriler ile korelasyonu, istatistiksel analiz çalışmalarıyla belirlenmiştir. Titreşim analizleri, B3LYP/cc-pVDZ teori düzeyinde gerçekleştirilmiştir. Ayrıca ilgili bileşiğin elektronik yapıları (HOMO-LUMO ve MEP haritaları) teorik olarak incelenmiştir. Sınır moleküler orbitallerinin enerji değerlerini kullanarak, bileşiğin sınır moleküler orbital enerji farkları, kimyasal sertlik ve elektronegatiflik gibi parametreleri B3LYP/cc-pVDZ düzeyinde hesaplanmıştır. Szemaoenoid A bileşiğinin ortalama kimyasal kararlılık gösterdiği ve reaktifliğe sahip olduğu belirlenmiştir.

Keywords

• Abietan
• YFT
• HF
• NMR

References

1. [1] G. Eksi, S. Kurbanoglu, S. A. Erdem, Analysis of diterpenes and diterpenoids, in Recent Advances in Natural Products Analysis, 1st ed., S. Nabavi, M. Saeedi, S. Nabavi, A. S. Silva, Ed. Amsterdam: Elsevier, 2020, pp. 313-345.
2. [2] J. W. Kadereit, The Families and Genera of Vascular Plants, Berlin: Springer, 2004.
3. [3] D. B. Pu, T. Wang, X.-J. Zhang, J.-B. Gao, H.-Y. Wang and W.-L. Xiao, “Isolation, identification and bioactivities of abietane diterpenoids from: Premna szemaoensis.”, RSC Advances, 8, 6425–6435, 2018.
4. [4] S. Habtemariam, “In vitro antileishmanial effects of antibacterial diterpenes from two Ethiopian Premna species: P. schimperi and P. oligotricha.”, BMC Pharmacol., 3, 6-13, 2003.
5. [5] H. Sudo, A. Takushi, E. Hirata, T. Ide, H. Otsuka and Y. Takeda, “Ethnomedicinal uses, phytochemistry and pharmacological aspects of the genus Premna: a review.”, Phytochemistry, 52, 1495–1499, 1999.
6. [6] D. Y. Wang and S. Y. Xu, “Two new xanthones from Premna microphylla”, Nat. Prod. Res., 17, 75–77, 2003.
7. [7] H. Sudo, A. Takushi, T. Ide, H. Otsuka, E. Hirata and Y. Takeda, “Premnethanosides A and B: Phenylethanoids from leaves of Premna subscandens.”, Phytochemistry, 46, 1147–1150, 1997.
8. [8] K. Y. Niu, L. Y. Wang, S. Z. Liu, W. M. Zhao, “New iridoid glycoside and triterpenoid glycoside from Premna fulva.”, J. Asian Nat. Prod. Res., 15, 1–8, 2013.

9. [9] D. Yadav, N. Masood, S. Luqman, P. Brindha, M. M. Gupta,” Antioxidant furofuran lignans from Premna integrifolia.”, Ind. Crops Prod., 41, 397–402, 2013.
10. [10] J. Lin, B. Yang, J. H. Chen, J. Guangxi Med. Univ., 2, 207–208, 2001.
11. [11] N. Narayanan, P. Thirugnanasambantham, S. Viswanathan, M. Kannappa Reddy, V. Vijayasekaran, E. Sukumar, “Antipyretic, antinociceptive and anti-inflammatory activity of Premna herbacea roots.”, Fitoterapia, 71, 147–153, 2000.
12. [12] G. Suresh, K. S. Babu, V. R. S. Rao, M. S. A. Rao, V. L. Nayak and S. Ramakrishna, “Novel cytotoxic icetexane diterpenes from Premna latifolia Roxb.”, Tetrahedron Lett., 52, 1273–1276, 2011.
13. [13] A. W. Salae, A. Rodjun, C. Karalai, C. Ponglimanont, S. Chantrapromma, A. Kanjana-Opas, S. Tewtrakul and H.-K. Fun, “Potential anti-inflammatory diterpenes from Premna obtusifolia”, Tetrahedron, 68, 819–829, 2012.
14. [14] S. R. Ayinampudi, R. Domala, R. Merugu, S. Bathula and M. R. Janaswamy, “New icetexane diterpenes with intestinal α-glucosidase inhibitory and free-radical scavenging activity isolated from Premna tomentosa roots.”, Fitoterapia, 83, 88–92, 2012.
15. [15] A. Azizoglu, Z. Özer, T. Kilic, “An experimental and theoretical study on siderol isolated from sideritis species.”, Collect. Czech. Chem. Commun., 76, 95–114, 2011.
16. [16] H. P. Gümüş ve Y. Atalay, “3-hidroksi-4-hidroksimiinometil-5-hidroksimetil-1,2-dimetilpiridinyum iyodid molekülünün geometrik yapısının incelenmesi.”, Sakarya Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 21, 564-571, 2017.
17. [17] Z. Turhan İrak, M. Poyraz, “[Ni(2-Benzimidazol-ilüre)2 (etanol)2 ][NO3 ]2 Bileşiğinin Yoğunluk Fonksiyoneli Teorisi Kullanılarak Yapılan Bazı Kuantum Kimyasal Hesaplamaları.”, Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 14, 203–212, 2019.
18. [18] D. S. B. Brasil, C. N. Alves, G. M. S. P. Guilhon, A. H. Müller, R. S. Secco, G. Peris, R. Llusar, “Crystal structure and theoretical study of IR and H-1 and C-13 NMR spectra of cordatin, a natural product with antiulcerogenic activity.”, Int. J. Quantum Chem., 108, 2564-2575, 2008.
19. [19] S. Cıtak, Z. Ozer Sagır, S. Carıkcı, T. Kılıç, and A. Azizoglu, “Experimental and theoretical study on linearol isolated from sideritis species.”, Rev. Roum. Chim., 59, 227-234, 2014.
20. [20] S. O. Silva, R. N.S. Peixoto, J. R. A. Silva, C. N. Alves, G.M.S.P. Guilhon, L. S. Santos, and D.S.B. Brasil, “Identification of (-)(E)-N-[2(S)-Hydroxy-2-(4-hydroxyphenyl)ethyl]ferulamide, a Natural Product Isolated from Croton Pullei: Theoretical and Experimental Analysis.”, Int. J. Mol. Sci. 12, 9389-9403, 2011.
21. [21] Z. Özer, T. Kilic, S. Carikci, A. Azizoglu, “Synthesis, Structural Characterization, Spectroscopic Properties, and Theoretical Investigation of Siderol Acetate.”, Russ. J. Phys. Chem. A, 93, 2703–2709, 2019.
22. [22] A. Kaya, “Abietan ve pimaran iskeletine sahip bileşiklerin elektronik, moleküler yapılarının ve titreşim özelliklerinin teorik olarak incelenmesi”, Yüksek Lisans Tezi, Kimya Bölümü, Balıkesir Üniv., Balıkesir, Türkiye, 2020.
23. [23] Gaussian09, rev. A02, Wallingford, CT, USA: Gaussian. Inc., 2016.
24. [24] R. Dennington, T. Keith, J. Millam, GaussView Version 5, Semichem Inc., Shawnee Mission KS. 2009.
25. [25] D. C. Young, Computational Chemistry. New York: Wiley-Interscience, 2011.
26. [26] K. Fukui, Theory of Orientation and Stereoselection, New York: Springer-Verlag, 1975.
27. [27] A. Azizoglu, N. Azizoglu, “A Theoretical Study on The Molecular and Electronic Structure of Halogenated Sumanene”, in Proc. 2nd Int. Aegean Phys. Chem. Days, Ayvalık/Balıkesir, 1, 113, 2004.
28. [28] K. Saraç, “4-Klorometil-6,8-dimetilkumarin Bileşiğinin Sentezi ve Teorik Kimyasal Hesaplamaları.”, BEÜ Fen Bilimleri Dergisi, 7, 311–319, 2018.
29. [29] S. H. Mari, P. C. Varras, A. Wahab, I. M. Choudhary, M. G. Siskos, I. P. Gerothanassis, “Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts, Molecules.”, Molecules, 24, 2290-2309, 2019.
30. [30] M. Balcı, Nükleer Manyetik Rezonans Spektroskopisi. Ankara: ODTÜ Yayıncılık, 2004.
31. [31] R. M. Silverstein, F. X. Webster, Spectroscopic Identification of Organic Compounds. New York: John Wiley & Sons Ltd., 2005.
32. [32] I. Fleming, Molecular Orbitals and Organic Chemical Reactions. New York: John Wiley & Sons Ltd., 2010.
33. [33] M. Rocha, A. D. Santo, D. M. Gil, “Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde.”, Spectrochim. Acta - Part A Mol. Biomol. Spectrosc., 136, 635–643, 2015.
34. [34] A. Azizoglu, “Quantum Chemical Investigation of Monostanna[n]cyclacenes.”, Structural Chemistry, 14, 575-580, 2003.
35. [35] B. Çiçek, U. Çakır, A. Azizoglu, “The associations of macrocyclic ethers with cations in 1,4-dioxane/water mixtures; potentiometric Na+ and K+ binding measurements and computational study.”, J. Inclusion Phenomena and Macrocyclic Chem., 72, 121-125, 2012.
36. [36] T. A. Koopmans, “Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms.”, Physica, 1, 104, 1934.
37. [37] C. B. Yıldız, Z.O. Sagir, T. Kilic, A. Azizoglu, “Computational and experimental study on 7-epicandicandiol isolated from Sideritis Niveotomentosa Huber – Morathii.”, Studia UBB Chemia, LIX, 17–32, 2014.
38. [38] P.C. Mishra, et al., Molecular Electrostatic Potentials: Concepts and Applications, Theoretical and Computational Chemistry Book Series, vol. 3, Amsterdam: Elsevier, 1996.
39. [39] Z. Demircioğlu, C. C. Ersanlı, “(±)-(1SR,8RS,10RS)-9,9,10-Tribromtrisiklo- [6.2.1.02,7]undeka-2,4,6-trien Molekülünün Hesaplamalı Kimya Yöntemiyle Lokal ve Global Kimyasal Aktivite ve DNA Bazları ile Yük Transferinin Tayini.”, Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 14, 165-178, 2019.