Calculations of Charge Transfer with DNA bases and Local and Global Chemical Activity by Computational Chemistry Method of (±)-(1SR,8RS,10RS)-9,9,10- Tribromotricyclo[6.2.1.02,7]undeca-2,4,6-triene

Abstract

All the theoretical calculations of molecular structure were calculated by Gaussian 09 program with B3LYP density functional model with 6-311G(d,p) basis set. The aim of this paper is survey the local and global chemical activity parameters to identify the electrophilic and nucleophilic nature of title compound. Electrophilic and nucleophilic nature is determined by hardness and softness parameters, MEP, net charges (MPA and NPA), Fukui functions. In the molecular systems of quantum chemistry, NBO analyis is used to examine the stabilization energy of E⁽²⁾, conjugate interactions and charge transfer. ECT (electrophilicity-based charge transfer) method examines the electrophilic and nucleophilic nature of the molecule and DNA bases, taking into account their interactions with ΔN, (charge transfer), parameter. Also, the nonlinear optical properties (NLO) were determined by dipol moment, polarizability and first order hyperpolarizibility parameters.

Keywords

• DFT
• Hirshfeld Surface Analysis
• Electrophilic and nucleophilic nature
• DNA&ECT

(±)-(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

Abstract

Moleküler yapıya ait tüm kuramsal hesaplamalar Gaussian 09 program kullanılarak B3LYP yoğunluk fonksiyoneli ve 6-311G(d,p) baz seti ile hesaplanmıştır. Bu çalışmanın amacı lokal ve global kimyasal aktivite parametrelerini inceleyerek yapının elektrofilik ve nükleofilik doğasını anlamaktır. Elektrofilik ve nükleofilik doğa, sertlik ve yumuşaklık parametreleri, MEP, net yükler (MPA ve NPA) ve Fukui fonksiyonları ile belirlenmektedir. Kuantum kimyasına ait moleküler sistemlerde NBO analizi, stabilizasyon enerjisi E⁽²⁾, konjüge etkileşimler veya yük transferini incelemek için etkin bir yöntemdir. ECT (elektrofilik-bazlı yük transferi) yönteminde DNA bazları ve çalışılan molecule ait yük geçişleri ΔN yük transfer parametresi hesaplanarak belirlenmektedir. Bunların yanısıra, yapıya ait lineer olmayan optik, (Non Linear Optical, NLO), özellikler dipol moment, kutuplanabilirlik ve hiperkutuplanabilirlik parametreleri ile belirlenmiştir.

Keywords

• YFK
• HirshfeldYüzeyAnalizi
• Elektrofilik&nükleofilik doğa
• DNA&ECT

References

1. C.C. Ersanlı, U. Çoruh, T. Hökelek, E.M. Va´zquez-Lo´pez and A. Daştan, “(±)-(1SR,8RS,10RS)-9,9,10-Tribromotricyclo[6.2.1.02,7]undeca-2,4,6-triene,” Acta Cryst., E61, o263-o265, 2005.
2. 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. Caricato, 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, J.A. MontgomeryJr., 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, O. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, ve D.J. Fox, Gaussian 09, Revision E.01, Gaussian, Inc., Wallingford CT, 2009.
3. D.J.G.S.K. Wolff, J.J. McKinnon, M.J. Turner, D. Jayatilaka, and M.A. Spackman, CrystalExplorer, 2012, Version3.1.
4. T. Samanta, L. Dey, J. Dinda, S.K. Chattopadhyay, and S.K. Seth, “Structural characterization and Hirshfeld surface analysis of a CoIIcomplex with imidazo [1,2-a] pyridine,” J. Mol. Struct., 1068, 58-70, 2014.
5. N.G. Haress, A. El-Emam, O.A. Al-Deab, C.Y. Panicker, A. Al-Saadi, C. Van Alsenols, and J. Ahmad War, “Vibrational spectroscopic and molecular dockings tudy of 2-benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile, a potential chemo the rapeutic agent,” Spectrochim. Acta A, 137, 569-580, 2015.
6. R.S. Mulliken, “Electronic population analysis on LCAO-MO molecular wave functions. I.,” J. Chem. Phys., 23(10), 1833-1840, 1955.
7. W. Yang and R.G. Parr, “Hardness, softness, and the fukui function in the electronic theory of metals and catalysis,” Proc. Natl. Acad. Sci., 82, 6723-6726, 1985.
8. P.C. Mishra, et al., Molecular Electrostatic Potentials: Concepts and Applications, Theoretical and Computational Chemistry Book Series, vol. 3, Elsevier, Amsterdam, 1996.

9. A. Volkov, C. Gatti, Y. Abramov, and P. Coppens, “On the origin of topological differences between experimental and theoretical crystal charge densities,” Acta Cryst., A56, 252-258, 2000.
10. R.S.J. Mulliken, “Electronic Population Analysis on LCAO–MO MolecularWaveFunctions,” Chem. Phys., 23, 1833-1840, 1955.
11. C.C. Ersanlı, G. Kaya Kantar, and S. Şaşmaz, “Crystallographic, spectroscopic (FTIR and NMR) and quantum computational calculation studies on bis(2-methoxy-4-((E)-prop-1-enyl)phenyl)oxalate,” J. Mol. Struct., 1143, 318-327, 2017.
12. K. Bahgat and S. Fraihat, “Normal coordinateanalysis, molecularstructure, vibrational, electronicspectraand NMR investigation of 4-amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione by ab initio HF and DFT method,” Spectrochim. Acta A, 135, 1145-1155, 2015.
13. M. Çınarlı, Ç. Yüksektepe Ataol, M. Taş and H. Bati, “Synthesis, crystal structure, Hirshfeld surface and DFT studies of([Cu(3-ptp)2(p-TS)2]) from decomposition of tosyl hydrazone,” J. Mol. Struct., 1169, 59-67, 2018.
14. J.P. Foster and F. Weinhold, “Natural hybrid orbitals”, J. Am. Chem. Soc., 102, 7211-7218, 1980.
15. A.E. Reed and F. Weinhold, “Natural bond orbital analysis of near‐Hartree-Fock water dimer,” J. Chem. Phys., 78, 4066-4073, 1983.
16. A.E. Reed and F. Weinhold, “Natural localized molecular orbitals,” J. Chem. Phys,. 83, 1736-1740, 1985.
17. C. Basshard, K. Suttur, P. Pretre, M. Flörsheimer, P. Kaatz, and P. Günter, Organic nonlinear optical materials, 5th ed. John Wiley&Sons, 256, Switzerland, 1995.
18. H.S. Nalwa and S. Miyata, Nonlinear Optics of Organic Molecules And Polymers. CRC Press, p. 896, New York, 1997.
19. H. Alyar, Z. Kantarci, M. Bahat, and E. Kasap, “Investigation of torsional barriers and nonlinear optical (NLO) properties of phenyltriazines,” J. Mol. Struct., 834, 516-520, 2007.