American Journal of Quantum Chemistry and Molecular Spectroscopy

| Peer-Reviewed |

A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS

Received: 28 July 2019    Accepted: 19 August 2019    Published: 02 September 2019
Views:       Downloads:

Share This Article

Abstract

In this paper we reported the crystal structure of 2-[methylthio(morpholino)methylene]malononitrile (C9H11N3OS). The compound was obtained by crystallization reaction between 2-(bis(methylthio)methylene)malononitrile and morpholine. The structure of compound C9H11N3OS was identified by performing X-ray diffraction analysis. Suitable crystals were grown by slow crystallisation from ethanol for 24h. The compound C9H11N3OS crystallized in an orthorhombic crystal system with a space group of Pna21. In the title compound, C9H11N3OS, the two cyano groups and the morpholinyl ring adopt a cis-trans configuration of the C=C bond, showing an Z, E configuration. The morpholine ring is adopting chair conformation. In the compound C9H11N3OS, the central fragment S1/N3/C2/C9, the morpholine ring O6/N3/O4/C5/C7/C8 and the 1,1-dicyanomethylen fragment N11/N13/C9/C10/C12 are almost planar. The central fragment makes dihedral angle of 23.11 (15)° with the 1,1-dicyano methylen fragment. The morpholine ring is twisted out of the plane of the central fragment as seen in the value of the C8—N3—C2—S1 torsional angle of 33.1 (3)°. The dihedral angle between the central fragment and the morpholine ring is 35.26 (12)°. In the crystal structure a weak intramolecular hydrogen bond C8—H(8 2)…S1 has been observed and intermolecular classical C(4)—H(41)...S(1), C(5—H(52)...S(1) and weak C(8)—(H81)...O(6) hydrogen bonds link the molecules into chains along the a axis.

DOI 10.11648/j.ajqcms.20190301.13
Published in American Journal of Quantum Chemistry and Molecular Spectroscopy (Volume 3, Issue 1, June 2019)
Page(s) 12-16
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Synthesis, Single-crystal X-ray Study, R Factor = 0.0374, wR Factor = 0.0872, Data-to-parameter Ratio = 15.0

References
[1] Wedad M. Al-Adiwish, M. I. M. Tahir, Siti-Noor-Adnalizawati A., Siti Farah Hashim, Nazlina Ibrahim, and W. A. Yaacob. 2013. Synthesis, Antibacterial Activity and Cytotoxicity of New Fused Pyrazolo [1,5-a] pyrimidine and Pyrazolo [5,1-c] [1,2,4] triazine Derivatives from New 5-Aminopyrazoles. European Journal of Medicinal Chemistry 64: 464-476.
[2] Wedad M. Al-Adiwish1, Maryam A. S. Abubakr, Naowara M. Alarafi. 2017 Synthesis of New Pyrazolo [5, 1-c] [1, 2, 4] triazines from 5-Aminopyrazole and Study Biological Activity and Cytotoxicity Cell Biology. 2017; 5 (5): 45-52.
[3] Wedad Melad Al-Adiwish1, Fatma Ali Shtewi1, Munira Muftah Ashrif1, Dalal Mohamed Ibrahim. 2017. Synthesis, Biological Activity and Cytotoxicity of New Fused Pyrazolo [1,5-a] pyrimidine from 5-Aminopyrazole Incorporated with p-Chloroaniline, American Journal of Heterocyclic Chemistry, 2017; 3 (6): 86-94.
[4] Misra, N. C., Panda, K., Ila, H. Junjappa, H. 2007. An Efficient Highly Regioselective Synthesis of 2,3,4-Trisubstituted Pyrroles by Cycloaddition of Polarized Ketene-S,S- and -N,S-Acetals with Activated Methylene Isocyanides. Journal of Organic Chemistry 72 (4): 1246-1251.
[5] Khalil, A., Berghot, M. & Gouda, M. 2009. Synthesis and Antibacterial Activity of Some New Heterocycles Incorporating Phthalazine. European Journal of Medicinal Chemistry 44 (11): 4448-4454.
[6] M. A. Gouda, M. A. Berghot, A. I. Shoeib, A. M. Khalil. 2010. Synthesis and antimicrobial activity of new anthraquinone derivatives incorporating pyrazole moiety, Eur. J. Med. Chem. 45 (2010) 1843–1848.
[7] M. A. Gouda, A. I. Berghot, E. A. Ghada, A. M. Khalil. 2010. Synthesis and antimicrobial activities of some new thiazole and pyrazole derivatives based on 4,5,6,7-tetrahydrobenzo thiophene moiety, Eur. J. Med. Chem. 45, 1338–1345. Loghmani-Khouzani, H., Sadeghi, M. M., Ghorbani, M. H. 2006. A Convenient Synthesis of Some α-Oxoketene-N,S- and -N,N-Acetals. Journal of the Iranian Chemical Society 3 (4): 360-366.
[8] Ma, Y., Wang, M., Li, D., Bekturhun, B., Liu, J. & Liu, Q. 2009. Α-Alkenoyl Ketene S, S-Acetal-Based Multicomponent Reaction: An Efficient Approach for the Selective Construction of Polyfunctionalized Cyclohexanones. The Journal of Organic Chemistry 74 (8): 3116-3121.
[9] Suryawanshi, S. N., Pandey, S., Rashmirathi, Bhatt, B. A., Gupta, S. 2007. Chemotherapy of Leishmaniasis Part Vi: Synthesis and Bioevaluation of Some Novel Terpenyl-S,N- and -N,N-Acetals. European Journal of Medicinal Chemistry 42: 511-516.
[10] Al-Afaleq, E. I. 2001. A Facial Method for the Synthesis of Novel Pyridinone Derivatives Via Ketene-N,S-Acetals. Synthetic communications 31 (22): 3557-3567.
[11] El-Saghiera, A. M., Matoughb, F. S., Farhatb, M. F., Salehb, N. A., Kreddanc, K. M., El-Tierb, S. O. & Hussienc, H. B. 2008. Synthesis and Biological Evaluation of Some New Thienopyridine and Thienopyrimidine Derivatives. Jordan Journal of Chemistry 3 (3): 223-232.
[12] Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). A program for automatic solution of crystal structures by direct methods. J. Appl. Cryst. 27, 435.
[13] Kuwayama, Y. & Kataoka, S. 1965. Reactions of Ketenethioacetals. I. It's Reaction with Some Amines and Active Methylene Compounds]. Yakugaku zasshi: Journal of the Pharmaceutical Society of Japan 85 (5): 387.
[14] Oxford Diffraction, (2006). Expert to Specialist Small Molecule Systems. Gemini User Manual.
[15] Oxford Diffraction. (2010). Data Collection and Processing Software for Agilent X-ray Diffractometers. CrysAlis PRO.
[16] Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. 1987. Tables of Bond Lengths Determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds. Journal of the Chemical Society, Perkin Transactions 2 12: S1-S19.
[17] Cooper, R. I., Thompson, A. L. & Watkin, D. J. (2010). CRYSTALS Enhancements: Dealing with Hydrogen Atoms in Refinement, J. Appl. Cryst. 43, 1100–1107.
[18] Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). SIR92 – a program for automatic solution of crystal structures by direct methods. J. Appl. Cryst. 27, 435.
[19] Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. and Watkin, D. J. (2003) Structural studies and conductivity of [Fe(O3C4)(COO)]·H2O based H4btec (H4btec = 1,2,4,5-benzenetetracarboxylic acid). Software for guided crystal structure analysis. Journal of Applied Crystallography, 36, 1487.
[20] Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON, Chemical Crystallography Laboratory, Oxford, UK.
Author Information
  • Department Chemistry, Faculty of Science, Zawia University, Zawia, Libya

  • Department Chemistry, Faculty of Education, Zawia University, Zawia, Libya

  • Department Chemistry, Faculty of Education, Zawia University, Zawia, Libya

Cite This Article
  • APA Style

    Wedad Melad Al-Adiwish, Mabrouka Mouloud Hamza, Khairi Mohamed Hamza. (2019). A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS. American Journal of Quantum Chemistry and Molecular Spectroscopy, 3(1), 12-16. https://doi.org/10.11648/j.ajqcms.20190301.13

    Copy | Download

    ACS Style

    Wedad Melad Al-Adiwish; Mabrouka Mouloud Hamza; Khairi Mohamed Hamza. A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS. Am. J. Quantum Chem. Mol. Spectrosc. 2019, 3(1), 12-16. doi: 10.11648/j.ajqcms.20190301.13

    Copy | Download

    AMA Style

    Wedad Melad Al-Adiwish, Mabrouka Mouloud Hamza, Khairi Mohamed Hamza. A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS. Am J Quantum Chem Mol Spectrosc. 2019;3(1):12-16. doi: 10.11648/j.ajqcms.20190301.13

    Copy | Download

  • @article{10.11648/j.ajqcms.20190301.13,
      author = {Wedad Melad Al-Adiwish and Mabrouka Mouloud Hamza and Khairi Mohamed Hamza},
      title = {A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS},
      journal = {American Journal of Quantum Chemistry and Molecular Spectroscopy},
      volume = {3},
      number = {1},
      pages = {12-16},
      doi = {10.11648/j.ajqcms.20190301.13},
      url = {https://doi.org/10.11648/j.ajqcms.20190301.13},
      eprint = {https://download.sciencepg.com/pdf/10.11648.j.ajqcms.20190301.13},
      abstract = {In this paper we reported the crystal structure of 2-[methylthio(morpholino)methylene]malononitrile (C9H11N3OS). The compound was obtained by crystallization reaction between 2-(bis(methylthio)methylene)malononitrile and morpholine. The structure of compound C9H11N3OS was identified by performing X-ray diffraction analysis. Suitable crystals were grown by slow crystallisation from ethanol for 24h. The compound C9H11N3OS crystallized in an orthorhombic crystal system with a space group of Pna21. In the title compound, C9H11N3OS, the two cyano groups and the morpholinyl ring adopt a cis-trans configuration of the C=C bond, showing an Z, E configuration. The morpholine ring is adopting chair conformation. In the compound C9H11N3OS, the central fragment S1/N3/C2/C9, the morpholine ring O6/N3/O4/C5/C7/C8 and the 1,1-dicyanomethylen fragment N11/N13/C9/C10/C12 are almost planar. The central fragment makes dihedral angle of 23.11 (15)° with the 1,1-dicyano methylen fragment. The morpholine ring is twisted out of the plane of the central fragment as seen in the value of the C8—N3—C2—S1 torsional angle of 33.1 (3)°. The dihedral angle between the central fragment and the morpholine ring is 35.26 (12)°. In the crystal structure a weak intramolecular hydrogen bond C8—H(8 2)…S1 has been observed and intermolecular classical C(4)—H(41)...S(1), C(5—H(52)...S(1) and weak C(8)—(H81)...O(6) hydrogen bonds link the molecules into chains along the a axis.},
     year = {2019}
    }
    

    Copy | Download

  • TY  - JOUR
    T1  - A Study X-ray Crystal Structure of Compound 2-[Methylthio(morpholino)methylene]malononitrile, C9H11N3OS
    AU  - Wedad Melad Al-Adiwish
    AU  - Mabrouka Mouloud Hamza
    AU  - Khairi Mohamed Hamza
    Y1  - 2019/09/02
    PY  - 2019
    N1  - https://doi.org/10.11648/j.ajqcms.20190301.13
    DO  - 10.11648/j.ajqcms.20190301.13
    T2  - American Journal of Quantum Chemistry and Molecular Spectroscopy
    JF  - American Journal of Quantum Chemistry and Molecular Spectroscopy
    JO  - American Journal of Quantum Chemistry and Molecular Spectroscopy
    SP  - 12
    EP  - 16
    PB  - Science Publishing Group
    SN  - 2994-7308
    UR  - https://doi.org/10.11648/j.ajqcms.20190301.13
    AB  - In this paper we reported the crystal structure of 2-[methylthio(morpholino)methylene]malononitrile (C9H11N3OS). The compound was obtained by crystallization reaction between 2-(bis(methylthio)methylene)malononitrile and morpholine. The structure of compound C9H11N3OS was identified by performing X-ray diffraction analysis. Suitable crystals were grown by slow crystallisation from ethanol for 24h. The compound C9H11N3OS crystallized in an orthorhombic crystal system with a space group of Pna21. In the title compound, C9H11N3OS, the two cyano groups and the morpholinyl ring adopt a cis-trans configuration of the C=C bond, showing an Z, E configuration. The morpholine ring is adopting chair conformation. In the compound C9H11N3OS, the central fragment S1/N3/C2/C9, the morpholine ring O6/N3/O4/C5/C7/C8 and the 1,1-dicyanomethylen fragment N11/N13/C9/C10/C12 are almost planar. The central fragment makes dihedral angle of 23.11 (15)° with the 1,1-dicyano methylen fragment. The morpholine ring is twisted out of the plane of the central fragment as seen in the value of the C8—N3—C2—S1 torsional angle of 33.1 (3)°. The dihedral angle between the central fragment and the morpholine ring is 35.26 (12)°. In the crystal structure a weak intramolecular hydrogen bond C8—H(8 2)…S1 has been observed and intermolecular classical C(4)—H(41)...S(1), C(5—H(52)...S(1) and weak C(8)—(H81)...O(6) hydrogen bonds link the molecules into chains along the a axis.
    VL  - 3
    IS  - 1
    ER  - 

    Copy | Download

  • Sections