Conformational and Topology Analysis of Diphenylthiourea and Diarylhalidethiourea Compounds Using DFT
Nur Najwa-Alyani Mohd Nabil(1), Lee Sin Ang(2*)
(1) Fakulti Sains Gunaan, Universiti Teknologi MARA, 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
(2) Fakulti Sains Gunaan, Universiti Teknologi MARA, Cawangan Perlis, Kampus Arau, 02600 Arau, Perlis Indera Kayangan, Malaysia
(*) Corresponding Author
Abstract
The disubstituted thiourea compounds have shown its reliability on their usages in various industries compared to the thiourea compounds. However, they also show capability to exist in different configurations, which would render them to possess different properties and hence affect their usability by unsuspected users. In this study, investigation was carried out on the polymorphism of five disubstituted thiourea compounds in which the phenyl rings and arylhalide acted as substituents. Using the B3LYP/DEF2–TZVP model chemistry with D3–BJ and gCP correctional schemes, the energetic analysis on the possible structural arrangements of the compounds was performed. The topology analysis of non-covalent interaction and electrostatic potential surfaces was used for understanding the interaction and reactivity of the constitute molecules of the compounds. Energetic results show that for all interested compounds, CT and TT configurations may coexist. Between the two type of substituents, phenyl substituted molecules are more flexible with better capability to be nucleophilic compound. On the other hand, the arylhalide substituted molecules form better electrophilic compounds. The reactive sites of the molecules rotated to the stable new configurations are similar to the molecules in their original configurations observed from experiments.
Keywords
Full Text:
Full Text PDFReferences
[1] Shashidhar, Thiruvenkatam, V., Shivashankar, S.A., Halli, M.B., and Guru Row, T.N., 2006, 1,3-Bis(4-methoxyphenyl)thiourea, Acta Crystallogr., Sect. E: Struct. Rep. Online, 62 (4), o1518–o1519.
[2] Bryantsev, V.S., Firman, T.K., and Hay, B.P., 2005, Conformational analysis and rotational barriers of alkyl- and phenyl-substituted urea derivatives, J. Phys. Chem. A, 109 (5), 832–842.
[3] Phetsuksiri, B., Jackson, M., Scherman, H., McNeil, M., Besra, G.S., Baulard, A.R., Slayden, R.A., DeBarber, A.E., Barry, C.E., Baird, M.S., Crick, D.C., and Brennan, P.J., 2003, Unique mechanism of action of the thiourea drug isoxyl on Mycobacterium tuberculosis, J. Biol. Chem., 278 (52), 53123–53130.
[4] Li, J., Bourne, S.A., de Villiers, M.M., Crider, A.M., and Caira, M.R., 2011, Polymorphism of the antitubercular isoxyl, Cryst. Growth Des., 11 (11), 4950–4957.
[5] Peña, Ú., Bernès, S., and Gutiérrez, R., 2009, (+)-(S,S)-1,3-Bis[(tetrahydrofuran-2-yl)methyl]thiourea, Acta Crystallogr., Sect. E: Struct. Rep. Online, 65 (Pt 1), o96.
[6] Kotke, M., and Schreiner, P.R., 2006, Acid-free, organocatalytic acetalization, Tetrahedron, 62 (2-3), 434–439.
[7] Ramnathan, A., Sivakumar, K., Subramanian, K., Janarthanan, N., Ramadas, K., and Fun, H.K., 1995, Symmetrically substituted thiourea derivatives, Acta Crystallogr., Sect. C: Cryst. Struct. Commun., 51 (11), 2446–2450.
[8] Srivastava, P.C., Dwivedi, S., Singh, V., and Butcher, R.J., 2010, Mono- and bis(dialkyl/aryl dithiocarbamato) complexes of 1,1,2,3,4,5,6-heptahydro-1,1-dihalido telluranes: Synthesis, spectroscopy, structures and cleavage reaction, Polyhedron, 29 (10), 2202–2212.
[9] Štrukil, V., Igrc, M.D., Fábián, L., Eckert-Maksić, M., Childs, S.L., Reid, D.G., Duer, M.J., Halasz, I., Mottillo, C., and Friščić, T., 2012, A model for a solvent-free synthetic organic research laboratory: Click-mechanosynthesis and structural characterization of thioureas without bulk solvents, Green Chem., 14 (9), 2462–2473.
[10] Qin, Y.Q., Jian, F., and Liang, T.L., 2006, 1,3-Bis(4-chlorophenyl)thiourea, Acta Crystallogr., Sect. E: Struct. Rep. Online, 62 (11), o5043–o5044.
[11] Sarojini, B.K., Narayana, B., Swamy, M.T., Yathirajan, H.S., and Bolte, M., 2007, Redetermination of N,N'-bis(4-chlorophenyl)thiourea at 173 K, Acta Crystallogr., Sect. E: Struct. Rep. Online, 63 (9), o3879.
[12] Muhammed, N., Zia-ur-Rehman, Ali, S., and Meetsma, A., 2007, 1,3-Bis(4-bromophenyl)thiourea, Acta Crystallogr., Sect. E: Struct. Rep. Online, 63 (2), o632–o633.
[13] Ramnathan, A., Sivakumar, K., Subramanian, K., Janarthanan, N., Ramadas, K., and Fun, H.K., 1996, 1,3-Bis(2-chlorophenyl)thiourea, Acta Crystallogr., Sect. C: Cryst. Struct. Commun., 52 (1), 134–136.
[14] Yeo, C.I., and Tiekink, E.R.T., 2011, 1,3-Bis(2-chlorophenyl)thiourea: A monoclinic polymorph, Acta Crystallogr., Sect. E: Struct. Rep. Online, 67 (11), o2965.
[15] Lenthall, J.T., Foster, J.A., Anderson, K.M., Probert, M.R., Howard, J.A.K., and Steed, J.W., 2011, Hydrogen bonding interactions with the thiocarbonyl π-system, CrystEngComm, 13 (9), 3202–3212.
[16] Tsuzuki, S., Honda, K., Uchimaru, T., Mikami, M., and Tanabe, K., 2002, Origin of attraction and directionality of the π/π interaction: Model chemistry calculations of benzene dimer interaction, J. Am. Chem. Soc., 124 (1), 104–112.
[17] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery Jr., J.A. Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Keith, T., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., and Fox, D.J., 2013, Gaussian 09, Revision D.01, Gaussian Inc., Wallingford CT.
[18] Castro, M., Cruz, J., Otazo-Sánchez, E., and Perez-Marín, L., 2003, Theoretical study of the Hg2+ recognition by 1,3-diphenyl-thiourea, J. Phys. Chem. A, 107 (42), 9000–9007.
[19] Schäfer, A., Horn, H., and Ahlrichs, R., 1992, Fully optimized contracted Gaussian basis sets for atoms Li to Kr, J. Chem. Phys., 97 (4), 2571–2577.
[20] Peintinger, M.F., Oliveira, D.V., and Bredow, T., 2013, Consistent Gaussian basis sets of triple-zeta valence with polarization quality for solid-state calculations, J. Comput. Chem., 34 (6), 451–459.
[21] Weigend, F. and Ahlrichs, R., 2005, Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy, Phys. Chem. Chem. Phys., 7 (18), 3297–3305.
[22] Grimme, S., Brandenburg, J.G., Bannwarth, C., and Hansen, A., 2015, Consistent structures and interactions by density functional theory with small atomic orbital basis sets, J. Chem. Phys., 143 (5), 054107.
[23] Kruse, H., Goerigk, L., and Grimme, S., 2012, Why the standard B3LYP/6-31G* model chemistry should not be used in DFT calculations of molecular thermochemistry: Understanding and correcting the problem, J. Org. Chem., 77 (23), 10824–10834.
[24] Grimme, S., Ehrlich, S., and Goerigk, L., 2011, Effect of the damping function in dispersion corrected density functional theory, J. Comput. Chem., 32 (7), 1456–1465.
[25] Řezáč, J., 2016, Cuby: An integrative framework for computational chemistry, J. Comput. Chem., 37 (13), 1230–1237.
[26] Řezáč, J., Riley, K.E., and Hobza, P., 2011, S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures, J. Chem. Theory Comput., 7 (8), 2427–2438.
[27] Kruse, H., and Grimme, S., 2012, A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems, J. Chem. Phys., 136 (15), 154101.
[28] Řezáč, J., and Hobza, P., 2016, Benchmark calculations of interaction energies in noncovalent complexes and their applications, Chem. Rev., 116 (9), 5038–5071.
[29] Lu, T., and Chen, F., 2012, Multiwfn: A multifunctional wavefunction analyzer, J. Comput. Chem., 33 (5), 580–592.
[30] Humphrey, W., Dalke, A., and Schulten, K., 1996, Visual Molecular Dynamics, J. Mol. Graphics, 14, 33–38.
[31] Johnson, E.R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A.J., and Yang, W., 2010, Revealing noncovalent interactions, J. Am. Chem. Soc., 132 (8), 6498–6506.
[32] Murray, J.S., and Politzer, P., 2009, Molecular surfaces, van der Waals radii and electrostatic potentials in relation to noncovalent interactions, Croat. Chem. Acta, 82 (1), 267–275.
[33] Dennington, R., Keith, T., and Millam, J., 2009, GaussView, Version 5, Semichem Inc., Shawnee Mission, KS.
[34] Galan, J.F., Germany, E., Pawlowski, A., Strickland, L., and Galinato, M.G., 2014, Theoretical and spectroscopic analysis of N,N'-diphenylurea and N,N'-dimethyl-N,N'-diphenylurea conformations, J. Phys. Chem. A, 118 (28), 5304–5315.
DOI: https://doi.org/10.22146/ijc.40663
Article Metrics
Abstract views : 2434 | views : 2272Copyright (c) 2019 Indonesian Journal of Chemistry
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Indonesian Journal of Chemistry (ISSN 1411-9420 /e-ISSN 2460-1578) - Chemistry Department, Universitas Gadjah Mada, Indonesia.
View The Statistics of Indones. J. Chem.