X-Rays, Spectroscopic and Molecular Docking Studies on Single Crystal Compounds Containing Schiff Base

Yıl 2019, Cilt: 23 Sayı: 2, 505 - 514, 25.08.2019

Tuncay Karakurt , Seher Meral Ayşen Alaman Ağar

https://doi.org/10.19113/sdufenbed.530279

Öz

2,2'-((1E,1'E)-(ethane-1,2-diylbis(azaneylylidene))bis(methaneylylidene))bis(4-(trifluoromethoxy)phenol
single crystal containing Schiff base and thiazole ring was synthesized in this
work. The synthesized crystalline structure was confirmed using IR
spectroscopic and X-ray analysis techniques. It has been found that the
analyzed compound may be two different tautomer forms such as phenol-imine and
keto-amine. All experimental and theoretical studies were made on the two
tautomeric structures. For this purpose, IRC (intrinsic reaction coordinate)
and frontier molecular orbital (FMO) calculations were performed after the
structural parameters of the title compound were optimized using GAUSSIAN 09W
package program and
DFT/B3LYP theory. In the
IRC study, it was observed that the phenol-imine form had lower energy than the
keto-amine form and the energy difference between the two forms was calculated
as -14.71 kj/mol. HOMO energy values of phenol-imine and keto-amine forms was
calculated as -6.31 and -5.77 eV, respectively. Finally,
Molecular Docking study was performed for the 2RKV protein structure to be an
inhibitory agent for the antifungal activity studies of the two tautomer forms. As a
result of this calculation, the affinity values of the phenol-imine and
keto-amine form (Docking score) were obtained as -7.7 and -7.3 kcal / mol,
respectively, and it was observed in our study that the HOMO orbital energies
and the affinity values were proportional.

Anahtar Kelimeler

Gaussian 09W, Phenol–imine, Keto–amine, Molecular docking

Schiff Bazı İçeren Tek Kristal Bileşik Üzerinde X-Işınları, Spektroskopik ve Moleküler Doking Çalışmaları

Öz

Schiff bazı ve tiyazol
halkası içeren 2,2'-((1E,1'E)-(ethan-1,2-dibis(azaneliden))bis(methaneliden))bis(4-(trifloromethoksi)fenol
tek kristali bu çalışmada sentezlenmiştir. Sentezlenen kristalin yapısı, IR
spektroskopik ve X-ışınları analizi teknikleri kullanılarak aydınlatılmıştır. İncelenen
bileşiğin fenol–imin ve keto–amin gibi iki farklı tautomer formda olabileceği
görülmüştür. Deneysel ve teorik tüm çalışmalar iki tautomer yapı üzerinde yapılmıştır.
Bunun içinde bileşiğin yapısal parametreleri, GAUSSIAN 09W paket programı ve
DFT/B3LYP teorisi ile optimize edildikten sonra IRC (intrinsic reaction
coordinate), frontier moleküler orbital(FMO) hesaplamaları yapılmıştır. IRC
çalışmasında fenol-imin formunun keto-amin formuna göre daha düşük enerjiye
sahip olduğu gözlenmiş olup iki form arasındaki enerji farkı -14.71 kj/mol
olarak hesaplanmıştır. Ayrıca, fenol-imin ve keto-amin formlarına ait HOMO
enerji değerleri sırasıyla, -6.31 ve -5.77 eV olarak hesaplanmıştır. Son olarak
da iki tautomer yapının antifungal aktivite çalışmaları için 2RKV protein yapısına inhibitör ajan olabilmesi
yönünde Moleküler Doking çalışması yapılmıştır. Bu hesaplama sonucunda
fenol-imin ve keto-amin formuna ait affinite değerleri (Doking skoru) sırasıyla,
-7.7 ve -7.3 kcal/mol olarak elde edilmiş olup HOMO orbital enerjileri
ile affinite değerlerinin orantılı olduğu çalışmamızda gözlenmiştir.

Anahtar Kelimeler

Gaussian 09W, Fenol–imin, Keto–amin, Moleküler doking

Kaynakça

• [1] Bharti, S.K., Nath, G., Tilak, R., Singh, S. 2010. Synthesis, anti-bacterial and anti-fungal activities of some novel Schiff bases containing 2, 4-disubstituted thiazole ring. European journal of medicinal chemistry, 45 (2010) 651-660.
• [2] Khedr, A.M. Marwani, H.M. 2012. Synthesis, spectral, thermal analyses and molecular modeling of bioactive Cu (II)-complexes with 1, 3, 4-thiadiazole Schiff base derivatives. Their catalytic effect on the cathodic reduction of oxygen. Int J Electrochem Sci, 7 (2012) 10074-10093.
• [3] Ayhan‐Kılcıgil, G., Kus, C., Özdamar, E.D., Can‐Eke, B. Iscan, M. 2007. Synthesis and antioxidant capacities of some new benzimidazole derivatives. Archiv der Pharmazie, 340 (2007) 607-611.
• [4] O’Neil, M.J., Smith, A. Heckelman, P. 2001. The Merck Index, 13th edn. Merck & Co. Inc, Whitehouse Station, NJ, 6596.
• [5] Kus, C., Ayhan-Kilcigil, G. Eke, B.C. 2004. Synthesis and antioxidant properties of some novel benzimidazole derivatives on lipid peroxidation in the rat liver. Archives of pharmacal research, 27 (2004) 156.
• [6] Dega-Szafran, Z., Kania, A., Grundwald-Wyspiańska, M., Szafran, M. Tykarska, E. 1996. Differences between the N· H· O and O· H· O hydrogen bonds in complexes of 2, 6-dichloro-4-nitrophenol with pyridines and pyridine N-oxides. Journal of molecular structure, 381 (1996) 107-125.
• [7] Filarowski, A., Koll, A., Karpfen, A. Wolschann, P. 2004. Intramolecular hydrogen bond in molecular and proton-transfer forms of Schiff bases. Chemical physics, 297 (2004) 323-332.
• [8] Asiri, A., Badahdah, K. 2007. Synthesis of some new anils: part 1. Reaction of 2-hydroxy-benzaldehyde and 2-hydroxynaphthaldehyde with 2-aminopyridene and 2-aminopyrazine. Molecules, 12 (2007) 1796-1804.
• [9] Raczynska, E.D., Kosinska, W. 2005. Tautomeric Equilibria in Relation to Pi-Electron Delocalization. Chem. Rev. 105 (2005) 3561 −3612.
• [10] Seanger, W. 1994. Principles of Nucleic Acid Structure; Springer; New York, 1994.
• [11] Reddy, K.H., Reddy, P.S. Babu, P.R. 2000 Nuclease activity of mixed ligand complexes of copper (II) with heteroaromatic derivatives and picoline. Transition metal chemistry, 25 (2000) 505-510.
• [12] Yu, W., Jia, J., Gao, J., Han, L. Li, Y. 2015. Synthesis, characterization and third-order nonlinear optical properties of symmetrical ferrocenyl Schiff base materials. Chemical Physics Letters, 624 (2015) 47-52.
• [13] Zarei, S.A., Piltan, M., 2015. Hassanzadeh, K., Akhtari, K. & Cinčić, D. Synthesis, characterization, crystal structure and predicting the second-order optical nonlinearity of a new dicobalt (III) complex with Schiff base ligand. Journal of Molecular Structure, 1083 (2015) 82-87.
• [14] Zakerhamidi, M., Nejati, K., Sorkhabi, S.G. Saati, M. 2013. Substituent and solvent effects on the spectroscopic properties and dipole moments of hydroxyl benzaldehyde azo dye and related Schiff bases. Journal of Molecular Liquids, 180 (2013) 225-234.
• [15] Brown, I., Leopold, D., Mohite, S., Sandreczki, T. 1995. Conducting thermoset polymers: A comparative study of Schiff base precursors with different end groups. Synthetic metals, 72 (1995) 269-274.
• [16] Dhahagani, K., Kumar, S.M., Chakkaravarthi, G., Anitha, K., Rajesh, J., Ramu, A. Rajagopal, G. 2014. Synthesis and spectral characterization of Schiff base complexes of Cu (II), Co (II), Zn (II) and VO (IV) containing 4-(4-aminophenyl) morpholine derivatives: Antimicrobial evaluation and anticancer studies. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 117 (2014) 87-94.
• [17] Hanif, M. Chohan, Z.H. 2013. Design, spectral characterization and biological studies of transition metal (II) complexes with triazole Schiff bases. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 104 (2013) 468-476.
• [18] Güngör, Ö., Gürkan, P. 2014. Synthesis and characterization of higher amino acid Schiff bases, as monosodium salts and neutral forms. Investigation of the intramolecular hydrogen bonding in all Schiff bases, antibacterial and antifungal activities of neutral forms. Journal of Molecular Structure, 1074 (2014) 62-70.
• [19] Bruker, A. 2008. APEX2, V2008. 6, SADABS V2008/1, SAINT V7. 60A, SHELXTL V6. 14. Bruker AXS Inc, Madison, Wisconsin, USA, (2008).
• [20] Sheldrick, G.M. 2015. SHELXT–Integrated space-group and crystal-structure determination. Acta Crystallographica Section A: Foundations and Advances, 71 (2015) 3-8.
• [21] Sheldrick, G.M. 2015. Crystal structure refinement with SHELXL. Acta Crystallographica Section C: Structural Chemistry, 71 (2015) 3-8.
• [22] Dolomanov, O.V., Bourhis, L.J., Gildea, R.J., Howard, J.A. Puschmann, H. 2009. OLEX2: a complete structure solution, refinement and analysis program. Journal of Applied Crystallography, 42 (2009) 339-341.
• [23] Frisch, M., Trucks, G., Schlegel, H.B., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. 2009. Gaussian 09, revision a. 02, gaussian. Inc, Wallingford, CT, 200 (2009).
• [24] Becke, A.D. 1993. Density‐functional thermochemistry. III. The role of exact exchange. The Journal of chemical physics, 98 (1993) 5648-5652.
• [25] Lee, C., Yang, W. Parr, R.G. 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical review B, 37 (1988) 785.
• [26] Foresman, J.B., Frisch, A. 1996. Exploring chemistry with electronic structure methods: a guide to using Gaussian.
• [27] Dennington, R., Keith, T., Millam, J., Eppinnett, K., Hovell, W.L. Gilliland, R. 2009. GaussView. Version.
• [28] Dallakyan, S., Olson, A.J. 2015. Small-molecule library screening by docking with PyRx. Chemical Biology: Springer; 2015. p. 243-250.
• [29] Karakurt, T., Cukurovali, A., Subasi, N.T., Onaran, A., Ece, A., Eker, S. Kani, I. 2018. Experimental and theoretical studies on tautomeric structures of a newly synthesized 2, 2’(hydrazine-1, 2-diylidenebis (propan-1-yl-1-ylidene)) diphenol. Chemical Physics Letters, 693 (2018) 132-145.
• [30] Chantrapromma, S., Jansrisewangwong, P. Fun, H.-K. 2010. (1E, 2E)-1, 2-Bis [1-(2-methoxyphenyl) ethylidene] hydrazine. Acta Crystallographica Section E: Structure Reports Online, 66 (2010) 2994-2995.
• [31] Fun, H.-K., Jansrisewangwong, P., Karalai, C. Chantrapromma, S. 2011. (1E, 2E)-1, 2-Bis [1-(3-chlorophenyl) ethylidene] hydrazine. Acta Crystallographica Section E: Structure Reports Online, 67 (2011) 3424-3424.
• [32] Karakurt, T. 2018. Investigation of the molecular structure of 4-(3-methyl-3-phenylcyclobutyl)-2-[2-(3-methylbenzylidene) hydrazinyl] thiazole in the gas and solid phases. Acta Crystallographica Section C: Structural Chemistry, 74 (2018) 1502-1508.
• [33] Karakurt, T., Cukurovali, A., Subasi, N.T. Kani, I. 2016. Molecular structure and computational studies on 2-((2-(4-(3-(2, 5-dimethylphenyl)-3-methylcyclobutyl) thiazol-2-yl) hydrazono) methyl) phenol monomer and dimer by DFT calculations. Journal of Molecular Structure, 1125 (2016) 433-442.
• [34] Tamer, Ö., Avcı, D. Atalay, Y. 2014. Quantum chemical characterization of N-(2-hydroxybenzylidene) acetohydrazide (HBAH): A detailed vibrational and NLO analysis. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 117 (2014) 78-86.
• [35] Atkins, P. Paula J. 2006. Atkins' physical chemistry. New York: WH Freeman and Company; 2006.
• [36] Karakurt, T. 2018. Tiyadiazol Halkası İçeren ‘‘5-(2-Kloro-6-Florobenziltiyo)-1, 3, 4-Tiyadiazol2-Amin’’Tek Kristalinin Moleküler Yapısının Deneysel ve Teorik Yöntemlerle İncelenmesi. Akü Femübid, 18 (2018) 1158-1166.
• [37] Er, M., Ergüven, B., Tahtaci, H., Onaran, A., Karakurt, T. Ece, A. 2017. Synthesis, characterization, preliminary SAR and molecular docking study of some novel substituted imidazo [2, 1-b][1, 3, 4] thiadiazole derivatives as antifungal agents. Medicinal Chemistry Research, 26 (2017) 615-630.