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7-hidroksi-8-[4-metil-piperazin-1-yl)metil]2H-kromen-2-on Molekülünün Kimyasal Aktivite ve Moleküler Kenetlenme Çalışmaları

Year 2022, , 598 - 606, 31.05.2022
https://doi.org/10.31202/ecjse.983751

Abstract

Bu çalışmada7-hidroksi-8-[4-metil-piperazin-1-yl)metil]2H-kromen-2-on molekülünün molekül yoğunluk fonksiyonel kuramı (YFK), B3LYP modeli ve 6-311G(d,p) baz seti kullanılarak optimize edilmiştir. Optimize edilen molekülün kimyasal aktivite parametreleri olan sertlik ve yumuşaklık analizleri, moleküler elektrostatik potansiyeli (MEP) ve Fukui fonksiyon analizleri gerçekleştirildi. İkinci dereceden lineer olmayan optik özellikleri incelenerek optik bir materyal olma eğilimi tartışıldı. Elektrofilik merkezli yük transferi (ECT) yöntemini kullanarak DNA bazları ile incelenen yapının yük transferi etkileşimleri elde edildi. Bunların yanı sıra moleküler kenetlenme yöntemi ile PDB:2YCF proteinin liganda (incelenen molekül) en iyi bağlanma bölgesi tespit edilerek bağlanma enerjisi ve etkileşim durumları incelendi.

References

  • [1]. Kubono, K., Kise, R., Kashiwagi, Y., Tani, K., Yokoi, K., “Crystal structure of 7-hydroxy-8-[(4-methylpiperazin-1-yl)methyl]-2H-chromen-2-one”, Acta Cryst., 2016, E72, 1751–1753.
  • [2]. Frisch M.J. vd. 2009. Gaussian 09, Revision A.02, Gaussian, Inc., Wallingford CT.
  • [3]. Sanner, M.F., “Python: A Programming Language for Software Integration and Development”. J. Mol. Grap. Model., 1999, 17, 57–61.
  • [4]. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson, A.J., “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function”, J. Comp. Chem., 1998, 19, 1639–1662.
  • [5]. Dassault Systèmes BIOVIA. Discovery Studio Modeling Environment, Release 2017. Dassault Systèmes; San Diego, CA, USA.
  • [6]. Mulliken, R.S. “Electronic population analysis on LCAO-MO molecular wave functions”, I. J.Chem.Phys., 1955, 23(10), 1833-1840.
  • [7]. Bahgat, K., Fraihat, S. “Normal coordinateanalysis, molecularstructure, vibrational, electronicspectraand NMR investigation of 4-amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thionebyab initio HF and DFT method”, Spectrochim. Acta A, 2015, 135, 1145-1155.
  • [8]. Uzun S., Demircioğlu Z., Taşdoğan, M., Ağar, E., “Quantum chemical and X-ray diffraction studies of (E)-3-(((3,4-dimethoxybenzyl)imino)methyl)benzene-1,2-diol”, J. Mol. Struc., 2020, 1206, 127749.
  • [9]. Nalwa, H.S., Miyata, S., “Non-linear Optics of Organic Molecules and Polymers” CRC Press, Boca Raton, FL, 1997.
  • [10]. Uzun, S., Koşar, B., Esen, Z., Koç, E., “Kinolin Türevi Biyolojik Aktif Bir Molekülün Farklı Çevrelerde Çizgisel Olmayan Optik Davranışının Yoğunluk Fonksiyoneli Teorisi Kullanılarak İncelenmesi”, AKU J. Sci. Eng., 2016, 16 Özel Sayı, 59-66.
  • [11]. Adant, M., Dupuis, M., Bredas, J.L., “Ab initio study of the nonlinear optical properties of urea: Electron correlation and dispersion effects”, Int. J. Quant. Chem., 1995, 56, 497-507.
  • [12]. Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C.R., Zhang, G., Pommier, Y., Shoemaker, R.H., Waugh, D.S., “Structural Characterization of Inhibitor Complexes with Checkpoint Kinase 2 (Chk2), a Drug Target for Cancer Therapy”, J Struct Biol., 2011, 176, 292.

Chemical Activity and Molecular Docking Studies of 7-hydroxy-8-[(4-methylpiperazin-1-yl)methyl]-2H-chromen-2-one Molecule

Year 2022, , 598 - 606, 31.05.2022
https://doi.org/10.31202/ecjse.983751

Abstract

In this study, the 7-hydroxy-8-[(4-methylpiperazin-1-yl)methyl]-2H-chromen-2-one molecule has been optimized using density functional theory (DFT), B3LYP model and 6-311G(d,p) bases set. Chemical activity parameters of hardness and softness analyzes, molecular electrostatic potential (MEP) and Fukui function analyzes of optimized structure have been performed. The second order nonlinear optical properties have been examined and its tendency to be an optical material is discussed. Using the electrophilic center charge transfer (ECT) method, the charge transfer interactions of the DNA bases and the studied structure have been obtained. In addition, the best binding site of the PDB:2YCF protein to the ligand (studied molecule) examined is determined by molecular docking and the binding energy and interaction states are investigated.

References

  • [1]. Kubono, K., Kise, R., Kashiwagi, Y., Tani, K., Yokoi, K., “Crystal structure of 7-hydroxy-8-[(4-methylpiperazin-1-yl)methyl]-2H-chromen-2-one”, Acta Cryst., 2016, E72, 1751–1753.
  • [2]. Frisch M.J. vd. 2009. Gaussian 09, Revision A.02, Gaussian, Inc., Wallingford CT.
  • [3]. Sanner, M.F., “Python: A Programming Language for Software Integration and Development”. J. Mol. Grap. Model., 1999, 17, 57–61.
  • [4]. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson, A.J., “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function”, J. Comp. Chem., 1998, 19, 1639–1662.
  • [5]. Dassault Systèmes BIOVIA. Discovery Studio Modeling Environment, Release 2017. Dassault Systèmes; San Diego, CA, USA.
  • [6]. Mulliken, R.S. “Electronic population analysis on LCAO-MO molecular wave functions”, I. J.Chem.Phys., 1955, 23(10), 1833-1840.
  • [7]. Bahgat, K., Fraihat, S. “Normal coordinateanalysis, molecularstructure, vibrational, electronicspectraand NMR investigation of 4-amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thionebyab initio HF and DFT method”, Spectrochim. Acta A, 2015, 135, 1145-1155.
  • [8]. Uzun S., Demircioğlu Z., Taşdoğan, M., Ağar, E., “Quantum chemical and X-ray diffraction studies of (E)-3-(((3,4-dimethoxybenzyl)imino)methyl)benzene-1,2-diol”, J. Mol. Struc., 2020, 1206, 127749.
  • [9]. Nalwa, H.S., Miyata, S., “Non-linear Optics of Organic Molecules and Polymers” CRC Press, Boca Raton, FL, 1997.
  • [10]. Uzun, S., Koşar, B., Esen, Z., Koç, E., “Kinolin Türevi Biyolojik Aktif Bir Molekülün Farklı Çevrelerde Çizgisel Olmayan Optik Davranışının Yoğunluk Fonksiyoneli Teorisi Kullanılarak İncelenmesi”, AKU J. Sci. Eng., 2016, 16 Özel Sayı, 59-66.
  • [11]. Adant, M., Dupuis, M., Bredas, J.L., “Ab initio study of the nonlinear optical properties of urea: Electron correlation and dispersion effects”, Int. J. Quant. Chem., 1995, 56, 497-507.
  • [12]. Lountos, G.T., Jobson, A.G., Tropea, J.E., Self, C.R., Zhang, G., Pommier, Y., Shoemaker, R.H., Waugh, D.S., “Structural Characterization of Inhibitor Complexes with Checkpoint Kinase 2 (Chk2), a Drug Target for Cancer Therapy”, J Struct Biol., 2011, 176, 292.
There are 12 citations in total.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Makaleler
Authors

Zeynep Demircioğlu 0000-0001-9538-9140

Publication Date May 31, 2022
Submission Date August 17, 2021
Acceptance Date October 22, 2021
Published in Issue Year 2022

Cite

IEEE Z. Demircioğlu, “7-hidroksi-8-[4-metil-piperazin-1-yl)metil]2H-kromen-2-on Molekülünün Kimyasal Aktivite ve Moleküler Kenetlenme Çalışmaları”, El-Cezeri Journal of Science and Engineering, vol. 9, no. 2, pp. 598–606, 2022, doi: 10.31202/ecjse.983751.
Creative Commons License El-Cezeri is licensed to the public under a Creative Commons Attribution 4.0 license.
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