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Investigation of The Crystal and Molecular Structure Of ‘‘5-(2-Chloro-6- Fluorobenzylthio)-1,3,4-Thiadiazol-2-Amine’’ Single Crystal Containing ThiadiazolRingby Experimental and Theoretical Methods

Year 2018, Volume: 18 Issue: 3, 1158 - 1166, 30.12.2018

Abstract

In this work, a single crystal of 5-(2-chloro-6-fluorobenzylthio)-1,3,4-thiadiazol-2-aminecontaining thiadiazole ring was synthesized. The structure of the synthesized crystal was confirmed by 1H-NMR, 13C-NMR and X-ray analysis techniques. Theoretical calculations have been made in order to support experimental results. In this, the geometric parameters of the compound were optimized by the density functional theory(DFT) B3LYP/6-31G(d) method using the gaussian 09 packet program and structural parameters (bond angles, bond lengths and dihedral angles), 1H- and 13C-NMR spectra and frontier molecular orbitals (HOMO-LUMO) of the single crystal have been calculatedtheoretically. Finally, the molecular doking simulation was carried out to inhibit the 2WQY receptor target structure for inhibitor activity study of the synthesized single crystal.

References

  • Atkins P.W., 1992. The elements of physical chemistry (Oxford University Press Oxford United Kingdom).
  • Becke A.D., 1993. Density‐functional thermochemistry. III. The role of exact exchange, The Journal of Chemical Physics, 98, 5648-52.
  • Bruker A., 2008. APEX2, V2008. 6, SADABS V2008/1, SAINT V7. 60A, SHELXTL V6. 14, Bruker AXS Inc., Madison, Wisconsin, USA.
  • Dennington R., Keith, T. and Millam, J., 2009. GaussView, version 5, Semichem Inc., Shawnee Mission, KS.
  • Ditchfield R., 1972. Molecular orbital theory of magnetic shielding and magnetic susceptibility, The Journal of Chemical Physics, 56, 5688-91.
  • Dolomanov O.V., Bourhis, L.J., Gildea, R.J., Howard, J.A. and Puschmann, H., 2009. OLEX2: a complete structure solution, refinement and analysis program, Journal of Applied Crystallography, 42, 339-41.
  • Er M., Işıldak G., Tahtaci H. and Karakurt T., 2016. Novel 2-amino-1,3,4-thiadiazoles and their acyl derivatives: Synthesis,structural characterization, molecular docking studies and comparison of experimental and computational results, Journal of Molecular Structure, 1110, 102-13.
  • Er M., Ergüven B., Tahtaci H., Onaran A., Karakurt T. and 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, 615-30.
  • Er M., Şahin A. and Tahtaci H., 2014. Synthesis and characterization of novel 1,3-thiazole and 2-amino-1,3,4-thiadiazole derivatives, Macedonian Journal of Chemistry and Chemical Engineering, 33, 189-98.
  • Fan S.-H., Zhang, A.-G., Ju, C.-C., Gao, L.-H. and Wang, K.-Z., 2010. A Triphenylamine-grafted imidazo [4, 5-f][1, 10] phenanthroline ruthenium (II) complex: Acid− base and photoelectric properties, Inorganic Chemistry, 49, 3752-63.
  • Frisch M., Trucks, G., Schlegel, H.B., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B. and Petersson, G., 2009. Gaussian 09, revision a. 02, gaussian, Inc., Wallingford, CT, 200.
  • Kim H.S., Jadhav, J.R., Jung, S.-J. and Kwak, J.H., 2013. Synthesis and antimicrobial activity of imidazole and pyridine appended cholestane-based conjugates, Bioorganic & Medicinal Chemistry Letters, 23, 4315-18.
  • Lee C., Yang, W. and Parr, R.G., 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical review B, 37, 785.
  • Macrae C.F., Bruno, I.J., Chisholm, J.A., Edgington, P.R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., Streek, J.V. and Wood, P.A., 2008. Mercury CSD 2.0–new features for the visualization and investigation of crystal structures, Journal of Applied Crystallography, 41, 466-70.
  • Mohamed T.A., Hassan A.E., Shaaban I.A., Abuelela A.M. and Zoghaib W.M., 2017. Conformational stability, spectral analysis (infrared, Raman and NMR) and DFT calculations of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole, Journal of Molecular Structure, 1130, 434-41.
  • Padmavathi V., Kumara C.P., Venkatesh B.C.and Padmaja A., 2011. Synthesis and antimicrobial activity of amido linked pyrrolyl and pyrazolyl-oxazoles, thiazoles and imidazoles, European Journal of Medicinal Chemistry, 46, 5317-26.
  • Rollas S., 1981. Synthesis and spectrometric analysis of some 1, 2, 4-triazoline-5-thiones, J Fac Pharm Istanbul, 17, 155-63.
  • Sancak K., Ünver Y. and Er M., 2007. Synthesis of 2-Acylamino, 2-Aroylamino and Ethoxycarbonyl Imino-1,3,4-thiadiazoles as Antitumor Agents, Turkish Journal Chemistry, 31, 125-34.
  • Sheldrick G.M., 2015a. Crystal structure refinement with SHELXL, Acta Crystallographica Section C: Structural Chemistry, 71, 3-8.
  • Shaaban I.A., Hassan A.E., Abuelela A.M., Zoghaib W.M., and Mohamed T.A., 2016. Infrared, Raman and NMR spectral analysis, vibrational assignments,normal coordinate analysis, and quantum mechanical calculations of 2-Amino-5-ethyl-1,3,4-thiadiazole, Journal of Molecular Structure, 1103, 70-81.
  • Sheldrick G.M., 2015b. SHELXT–Integrated space-group and crystal-structure determination, Acta Crystallographica Section A: Foundations and Advances, 71, 3-8.
  • Singh S.J., Rajamanickam, S., Gogoi, A., and Patel, B.K., 2016. Synthesis of 2-amino-substituted-1, 3, 4-thiadiazoles via 2, 3-dichloro-5, 6-dicyano-1, 4-benzoquinone (DDQ) mediated intramolecular C–S bond formation in thiosemicarbazones, Tetrahedron Letters, 57, 1044-47.
  • Tehranchian S., Akbarzadeh, T., Fazeli, M.R., Jamalifar, H., and Shafiee, A., 2005. Synthesis and antibacterial activity of 1-[1, 2, 4-triazol-3-yl] and 1-[1, 3, 4-thiadiazol-2-yl]-3-methylthio-6, 7-dihydrobenzo [c] thiophen-4 (5H) ones, Bioorganic & Medicinal Chemistry Letters, 15, 1023-25.
  • Trott O., and Olson, A.J., 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455-61.
  • Wang C., Song, H., Liu, W., and Xu, C., 2016. Design, synthesis and antifungal activity of novel thioureas containing 1, 3, 4-thiadiazole and thioether skeleton, Chemical Research in Chinese Universities, 32, 615-20.
  • Wolinski K., Hinton, J.F., and Pulay, P., 1990. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations, Journal of the American Chemical Society, 112, 8251-60.
  • 1- http://accelrys.com(07.12.2016)

Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi

Year 2018, Volume: 18 Issue: 3, 1158 - 1166, 30.12.2018

Abstract

Bu çalışmada, tiyadiazol halka içeren5-(2-kloro-6-florobenziltiyo)-1,3,4-tiyadiazol-2-amin tek kristali sentezlenmiştir. Sentezlenen kristalin yapısı, 1H-NMR, 13C-NMR ve X-ışını analiz teknikleri ile aydınlatılmıştır. Deneysel sonuçlara destek olması amacıyla da teorik hesaplamalar yapılmıştır. Bunun içinde bileşiğin geometrik parametreleri gaussian 09paket programı kullanılarak, yoğunluk fonksiyonel teorisi (DFT) B3LYP/6-31G(d) metodu ile optimize edildi ve yapısal parametreleri (bağ açıları, bağ uzunlukları ve dihedral açıları), 1H- ve 13C-NMR spektrumları vesınır moleküler orbitalleri (HOMO-LUMO) teorik olarak hesaplanmıştır. Son olarak, sentezlenen tek kristalin inhibitör aktivite çalışması için, 2WQY reseptör hedef yapısını inhibe etmek amacıyla moleküler doking simülasyonu yapılmıştır.

References

  • Atkins P.W., 1992. The elements of physical chemistry (Oxford University Press Oxford United Kingdom).
  • Becke A.D., 1993. Density‐functional thermochemistry. III. The role of exact exchange, The Journal of Chemical Physics, 98, 5648-52.
  • Bruker A., 2008. APEX2, V2008. 6, SADABS V2008/1, SAINT V7. 60A, SHELXTL V6. 14, Bruker AXS Inc., Madison, Wisconsin, USA.
  • Dennington R., Keith, T. and Millam, J., 2009. GaussView, version 5, Semichem Inc., Shawnee Mission, KS.
  • Ditchfield R., 1972. Molecular orbital theory of magnetic shielding and magnetic susceptibility, The Journal of Chemical Physics, 56, 5688-91.
  • Dolomanov O.V., Bourhis, L.J., Gildea, R.J., Howard, J.A. and Puschmann, H., 2009. OLEX2: a complete structure solution, refinement and analysis program, Journal of Applied Crystallography, 42, 339-41.
  • Er M., Işıldak G., Tahtaci H. and Karakurt T., 2016. Novel 2-amino-1,3,4-thiadiazoles and their acyl derivatives: Synthesis,structural characterization, molecular docking studies and comparison of experimental and computational results, Journal of Molecular Structure, 1110, 102-13.
  • Er M., Ergüven B., Tahtaci H., Onaran A., Karakurt T. and 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, 615-30.
  • Er M., Şahin A. and Tahtaci H., 2014. Synthesis and characterization of novel 1,3-thiazole and 2-amino-1,3,4-thiadiazole derivatives, Macedonian Journal of Chemistry and Chemical Engineering, 33, 189-98.
  • Fan S.-H., Zhang, A.-G., Ju, C.-C., Gao, L.-H. and Wang, K.-Z., 2010. A Triphenylamine-grafted imidazo [4, 5-f][1, 10] phenanthroline ruthenium (II) complex: Acid− base and photoelectric properties, Inorganic Chemistry, 49, 3752-63.
  • Frisch M., Trucks, G., Schlegel, H.B., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B. and Petersson, G., 2009. Gaussian 09, revision a. 02, gaussian, Inc., Wallingford, CT, 200.
  • Kim H.S., Jadhav, J.R., Jung, S.-J. and Kwak, J.H., 2013. Synthesis and antimicrobial activity of imidazole and pyridine appended cholestane-based conjugates, Bioorganic & Medicinal Chemistry Letters, 23, 4315-18.
  • Lee C., Yang, W. and Parr, R.G., 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical review B, 37, 785.
  • Macrae C.F., Bruno, I.J., Chisholm, J.A., Edgington, P.R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., Streek, J.V. and Wood, P.A., 2008. Mercury CSD 2.0–new features for the visualization and investigation of crystal structures, Journal of Applied Crystallography, 41, 466-70.
  • Mohamed T.A., Hassan A.E., Shaaban I.A., Abuelela A.M. and Zoghaib W.M., 2017. Conformational stability, spectral analysis (infrared, Raman and NMR) and DFT calculations of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole, Journal of Molecular Structure, 1130, 434-41.
  • Padmavathi V., Kumara C.P., Venkatesh B.C.and Padmaja A., 2011. Synthesis and antimicrobial activity of amido linked pyrrolyl and pyrazolyl-oxazoles, thiazoles and imidazoles, European Journal of Medicinal Chemistry, 46, 5317-26.
  • Rollas S., 1981. Synthesis and spectrometric analysis of some 1, 2, 4-triazoline-5-thiones, J Fac Pharm Istanbul, 17, 155-63.
  • Sancak K., Ünver Y. and Er M., 2007. Synthesis of 2-Acylamino, 2-Aroylamino and Ethoxycarbonyl Imino-1,3,4-thiadiazoles as Antitumor Agents, Turkish Journal Chemistry, 31, 125-34.
  • Sheldrick G.M., 2015a. Crystal structure refinement with SHELXL, Acta Crystallographica Section C: Structural Chemistry, 71, 3-8.
  • Shaaban I.A., Hassan A.E., Abuelela A.M., Zoghaib W.M., and Mohamed T.A., 2016. Infrared, Raman and NMR spectral analysis, vibrational assignments,normal coordinate analysis, and quantum mechanical calculations of 2-Amino-5-ethyl-1,3,4-thiadiazole, Journal of Molecular Structure, 1103, 70-81.
  • Sheldrick G.M., 2015b. SHELXT–Integrated space-group and crystal-structure determination, Acta Crystallographica Section A: Foundations and Advances, 71, 3-8.
  • Singh S.J., Rajamanickam, S., Gogoi, A., and Patel, B.K., 2016. Synthesis of 2-amino-substituted-1, 3, 4-thiadiazoles via 2, 3-dichloro-5, 6-dicyano-1, 4-benzoquinone (DDQ) mediated intramolecular C–S bond formation in thiosemicarbazones, Tetrahedron Letters, 57, 1044-47.
  • Tehranchian S., Akbarzadeh, T., Fazeli, M.R., Jamalifar, H., and Shafiee, A., 2005. Synthesis and antibacterial activity of 1-[1, 2, 4-triazol-3-yl] and 1-[1, 3, 4-thiadiazol-2-yl]-3-methylthio-6, 7-dihydrobenzo [c] thiophen-4 (5H) ones, Bioorganic & Medicinal Chemistry Letters, 15, 1023-25.
  • Trott O., and Olson, A.J., 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455-61.
  • Wang C., Song, H., Liu, W., and Xu, C., 2016. Design, synthesis and antifungal activity of novel thioureas containing 1, 3, 4-thiadiazole and thioether skeleton, Chemical Research in Chinese Universities, 32, 615-20.
  • Wolinski K., Hinton, J.F., and Pulay, P., 1990. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations, Journal of the American Chemical Society, 112, 8251-60.
  • 1- http://accelrys.com(07.12.2016)
There are 27 citations in total.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Articles
Authors

Tuncay Karakurt

Publication Date December 30, 2018
Submission Date May 2, 2018
Published in Issue Year 2018 Volume: 18 Issue: 3

Cite

APA Karakurt, T. (2018). Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi, 18(3), 1158-1166.
AMA Karakurt T. Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi. December 2018;18(3):1158-1166.
Chicago Karakurt, Tuncay. “Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel Ve Teorik Yöntemlerle İncelenmesi”. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi 18, no. 3 (December 2018): 1158-66.
EndNote Karakurt T (December 1, 2018) Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi 18 3 1158–1166.
IEEE T. Karakurt, “Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi”, Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi, vol. 18, no. 3, pp. 1158–1166, 2018.
ISNAD Karakurt, Tuncay. “Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel Ve Teorik Yöntemlerle İncelenmesi”. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi 18/3 (December 2018), 1158-1166.
JAMA Karakurt T. Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi. 2018;18:1158–1166.
MLA Karakurt, Tuncay. “Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel Ve Teorik Yöntemlerle İncelenmesi”. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi, vol. 18, no. 3, 2018, pp. 1158-66.
Vancouver Karakurt T. Tiyadiazol Halkası İçeren‘‘5-(2-Kloro-6-Florobenziltiyo)-1,3,4-Tiyadiazol2-Amin’’ TekKristalinin Moleküler YapısınınDeneysel ve Teorik Yöntemlerle İncelenmesi. Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi. 2018;18(3):1158-66.