Computational bases study for complexes containing Cd (II) and biological evaluation in silico
Keywords:Cadmium; In Silico; Computational basis set.
Computational chemistry only gained international recognition after making a significant contribution to the scientific advances that resulted in Nobel prizes. With the technological evolution of the last decades, software was created with the aim of studying, investigating and understanding chemical processes at the molecular level of experimental studies. This promoted research agility and reduced costs with laboratory work. In this work, 5 different sets of computational bases were studied: STO-3G, LAN2DZ, SDD, 3-21G and DGDZVP, using the GaussView 5 and Gaussian 09w software with the DFT and B3LYP functional hybrid method. The distance and angle parameters of the di-u-chloro-bis complex [chlorine (4,7-dimethyl-1,10-phenanthroline) cadmium (II)] were obtained. The RMSD values obtained for each of the bases were observed. Molecular docking test was performed for each base, to verify which one had better parameters. It was noted in this study that the set of SDD bases presented the best results in the tests, being classified as the most suitable for studies of structures containing the element cadmium in its composition.
Alcácer, L. (2012). Introdução à Mecânica Quântica (1a). Editora Livraria da Física.
Amprazi, M., Kotsifaki, D., Providaki, M., Kapetaniou, E. G., Fellas, G., Kyriazidis, I., Perez, J., & Kokkinidis, M. (2014). Structural plasticity of 4- -helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein. Proceedings of the National Academy of Sciences, 111(30), 11049–11054. https://doi.org/10.1073/pnas.1322065111
Bastos, R. S., Sousa, C. S., Oliveira, J. S., Silva, M. V. Da, Lima, F. das C. A., & Rocha, J. A. (2020). Prospecção de proteínas do novo coronavírus covid-2019 e potencial da bioinformática na busca de novas drogas promissoras. Cadernos de Prospecção, 13(2), 347–358. https://doi.org/http://dx.doi.org/10.9771/cp.v13i2%20COVID-19.36008
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235–242.
Braga, J. P. (2007). Fundamentos de Química Quântica. Ed. UFV.
Cao, X., & Dolg, M. (2002). Segmented contraction scheme for small-core lanthanide pseudopotential basis sets. Journal of Molecular Structure: THEOCHEM, 581(1–3), 139–147. https://doi.org/10.1016/S0166-1280(01)00751-5
Casella, G., Ferrante, F., & Saielli, G. (2016). DFT calculation of NMR δ(113Cd) in cadmium complexes. Polyhedron, 117, 48–56. https://doi.org/10.1016/j.poly.2016.05.038
Collins, J. B., von R. Schleyer, P., Binkley, J. S., & Pople, J. A. (1976). Self‐consistent molecular orbital methods. XVII. Geometries and binding energies of second‐row molecules. A comparison of three basis sets. The Journal of Chemical Physics, 64(12), 5142–5151. https://doi.org/10.1063/1.432189
Costa, S., Breno, C., Lopes, S., & Ramos, S. (2018). Validation of Computational Methods Applied in Molecular Modeling of Caffeine With. 41(7), 732–742.
Dobbs, K. D., & Hehre, W. J. (1986). Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third-and fourth-row, main-group elements. Journal of Computational Chemistry, 7(3), 359–378. https://doi.org/10.1002/jcc.540070313
Ferreira, M., Leite, F., Jr, O. de O., & Roz, A. da. (2016). Grandes áreas da nanociência e suas aplicações. Elsevier Brasil.
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., … Fox, D. J. (2009). Gaussian 09w (7.0). Gaussian, Inc.
Hao, X., Siegler, M. A., Parkin, S., & Brock, C. P. (2005). [M(H 2 O) 2 (15-crown-5)](NO 3 ) 2 : A System Rich in Polymorphic and Modulated Phases †. Crystal Growth & Design, 5(6), 2225–2232. https://doi.org/10.1021/cg050312j
Hay, P. J., & Wadt, W. R. (1985). Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. The Journal of Chemical Physics, 82(1), 299–310. https://doi.org/10.1063/1.448975
Horchani, M., Hajlaoui, A., Harrath, A. H., Mansour, L., Ben Jannet, H., & Romdhane, A. (2020). New pyrazolo-triazolo-pyrimidine derivatives as antibacterial agents: Design and synthesis, molecular docking and DFT studies. Journal of Molecular Structure, 1199, 127007. https://doi.org/10.1016/j.molstruc.2019.127007
JAIN, R., AHUJA, B. L., & SHARMA, B. K. (2004). Density-Functional Thermochemistry. III. The Role of Exact Exchange, 43–48.
Kukovec, B.-M., Kodrin, I., Mihalić, Z., & Popović, Z. (2011). Preparation, structural, spectroscopic, thermal and DFT characterization of cadmium(II) complexes with quinaldic acid. Inorganica Chimica Acta, 378(1), 154–162. https://doi.org/10.1016/j.ica.2011.08.050
Lima, D. F. DE. (2015). Investigando mais a fundo as reações de 1,2-dicloro-4,5-dinitrobenzeno e 2,3-dicloro-6,7-dinitroquinoxalina com aminas: estudo sintético e teórico. UNIVERSIDADE FEDERAL DO RIO GRANDE DO NORTE.
Lin, X., Wu, J., Lü, X., Shan, Z., Wang, W., & Huang, F. (2009). Novel antimonate photocatalysts MSb2O6 (M = Ca, Sr and Ba): a correlation between packing factor and photocatalytic activity. Physical Chemistry Chemical Physics, 11(43), 10047. https://doi.org/10.1039/b911352e
Machura, B., Nawrot, I., & Michalik, K. (2012). Synthesis, spectroscopic characterization and X-ray studies of two novel double open cubane-like cadmium(II) complexes. Polyhedron, 31(1), 548–557. https://doi.org/10.1016/j.poly.2011.10.006
Morgon, N. H., & Coutinho, K. (2007). Métodos de Química Teórica e Modelagem Molecular. Editora Livraria da Física.
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
Ramírez, D., & Caballero, J. (2018). Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? Molecules, 23(5), 1038. https://doi.org/10.3390/molecules23051038
Raupp, D., Serrano, A., & Costa Martins, T. L. (2008). A evolução da química computacional e sua contribuição para a educação em Química. Revista Liberato, 9(12), 13–22. https://doi.org/10.31514/rliberato.2008v9n12.p13
Rocha, J. A., Rego, N. C. S., Carvalho, B. T. S., Silva, F. I., Sousa, J. A., Ramos, R. M., Passos, I. N. G., De Moraes, J., Leite, J. R. S. A., & Lima, F. C. A. (2018). Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties. PLoS ONE, 13(6), 1–23. https://doi.org/10.1371/journal.pone.0198476
Sosa, C., Andzelm, J., Elkin, B. C., Wimmer, E., Dobbs, K. D., & Dixon, D. A. (1992). A local density functional study of the structure and vibrational frequencies of molecular transition-metal compounds. The Journal of Physical Chemistry, 96(16), 6630–6636. https://doi.org/10.1021/j100195a022
Steed, K. M., & Steed, J. W. (2015). Packing Problems: High Z ′ Crystal Structures and Their Relationship to Cocrystals, Inclusion Compounds, and Polymorphism. Chemical Reviews, 115(8), 2895–2933. https://doi.org/10.1021/cr500564z
Stratmann, R. E., Burant, J. C., Scuseria, G. E., & Frisch, M. J. (1997). Improving harmonic vibrational frequencies calculations in density functional theory. The Journal of Chemical Physics, 106(24), 10175–10183. https://doi.org/10.1063/1.474047
Vázquez, M. I. N. ., Chiñas, E. M. ., Martínez, F. M. C. ., & Ruvalcaba, R. M. (2016). Algunos Aspectos Basicos de la Quimica Computacional. UNAM.
Warad, I., Al-Ali, M., Hammouti, B., Hadda, T. Ben, Shareiah, R., & Rzaigui, M. (2013). Novel di-μ-chloro-bis[chloro(4,7-dimethyl-1,10-phenanthroline)cadmium(II)] dimer complex: synthesis, spectral, thermal, and crystal structure studies. Research on Chemical Intermediates, 39(6), 2451–2461. https://doi.org/10.1007/s11164-012-0771-y
How to Cite
Copyright (c) 2021 Ruan Sousa Bastos; Joabe Lima Araujo; Maria de Lourde de Aguiar Silva Ferreira; Welson de Freitas Silva; Ionara Nayana Gomes Passos; Francisco das Chagas Alves Lima; Jefferson Almeida Rocha
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
1) Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
2) Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
3) Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.