* Corresponding Author
Basis Set Effects on the Stabilities and Interaction Energies of Small Amide Molecules Adsorbed on Kaolinite Surface
https://doi.org/10.22146/ijc.79795 Najwa-Alyani Mohd Nabil(1*), Lee Sin Ang(2), Shukri Sulaiman(3)
(1) Faculty of Applied Sciences, Universiti Teknologi MARA, Perlis Branch, Arau 02600, Malaysia
(2) Faculty of Applied Sciences, Universiti Teknologi MARA, Perlis Branch, Arau 02600, Malaysia
(3) School of Distance Education, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia
(*) Corresponding Author
Abstract
Adsorptions of small amide molecules, acetamide (AA) and N-methyl-acetamide (NMA) on the surface of kaolinite are investigated in this study. The focus is on the basis set effects towards the stabilities and the interaction energies of the molecules on the Al–O surface. With a fixed B3LYP functional, we increased the size of the basis sets for the single-point calculations, to find the converged interaction energies and obtain the relative stabilities. We found that, under the direct usage of Pople-type and Dunning’s correlation consistent basis sets, it is not possible to achieve the pattern of convergence for the interaction energies and the relative stabilities. Compared to the complete basis set (CBS) extrapolation scheme, the double zeta basis sets deviated the most, in the range of 21 to 27%, while it is from 1 to 7% for the triple zeta basis sets. Based on the results, we suggest using 6-311++G(2df,2pd) or cc-pVQZ for energy-related quantities. Compared to AA, NMA attached more strongly by 0.5 eV on the surface of Al–O.
Keywords
Full Text:
Full Text PDFReferences
[1] Lehtola, S., 2021, Straightforward and accurate automatic auxiliary basis set generation for molecular calculations with atomic orbital basis sets, J. Chem. Theory Comput., 17 (11), 6886–6900.
[2] Coşkun, M., and Ertürk, M., 2022, Double hyperbolic cosine basis sets for LCAO calculations, Mol. Phys., 120 (17), e2109527.
[3] Morgante, P., and Peverati, R., 2020, The devil in the details: A tutorial review on some undervalued aspects of density functional theory calculations, Int. J. Quantum Chem., 120 (18), e26332.
[4] Kirschner, K.N., Reith, D., and Heiden, W., 2020, The performance of Dunning, Jensen, and Karlsruhe basis sets on computing relative energies and geometries, Soft Mater., 18 (2-3), 200–214.
[5] Akbudak, S., Uğur, G., Uğur, Ş., and Ocak, H.Y., 2019, Basis set convergence of binding energy with and without CP-correction utilizing PBEO method: A benchmark study of X2 (X = Ge, As, Se, Sc, Ti, V, Cr, Mn, Co, Cu, Zn), J. Theor. Comput. Chem., 18 (8), 1950034.
[6] Bowman, M.C., Zhang, B.Y., Morgan, W.J., and Schaefer, H.F., 2019, A remarkable case of basis set dependence: The false convergence patterns of the methyl anion, Mol. Phys., 117 (9-12), 1069–1077.
[7] Myllys, N., Elm, J., and Kurtén, T., 2016, Density functional theory basis set convergence of sulfuric acid-containing molecular clusters, Comput. Theor. Chem., 1098, 1–12.
[8] Jensen, F., 2023, Basis set extrapolation of vibrational frequencies, J. Phys. Chem. A, 127 (12), 2859–2863.
[9] Kraus, P., 2021, Extrapolating DFT toward the complete basis set limit: Lessons from the PBE family of functionals, J. Chem. Theory Comput., 17 (9), 5651–5660.
[10] Pansini, F.N.N., Neto, A.C., and Varandas, A.J.C., 2016, Extrapolation of Hartree-Fock and multiconfiguration self-consistent-field energies to the complete basis set limit, Theor. Chem. Acc., 135 (12), 261.
[11] Kupka, T., Buczek, A., Broda, M.A., Gajda, L., and Ignasiak, M., 2018, Convergence of nuclear magnetic shieldings and one-bond (1)J((BH)-B-11-H-1) indirect spin-spin coupling constants in small boron molecules, Magn. Reson. Chem., 56 (5), 338.
[12] Buczek, A., Kupka, T., Broda, M.A., and Żyła, A., 2016, Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn–Sham complete basis set limit, J. Mol. Model., 22 (1), 42.
[13] Kitagawa, Y., Matsui, T., Yasuda, N., Hatake, H., Kawakami, T., Yamanaka, S., Nihei, M., Okumura, M., Oshio, H., and Yamaguchi, K., 2013, DFT calculations of effective exchange integrals at the complete basis set limit on oxo-vanadium ring complex, Polyhedron, 66, 97–101.
[14] Isegawa, M., Neese, F., and Pantazis, D.A., 2016, Ionization energies and aqueous redox potentials of organic molecules: Comparison of DFT, correlated ab Initio theory and pair natural orbital approaches, J. Chem. Theory Comput., 12 (5), 2272–2284.
[15] Vasilyev, V., 2017, Online complete basis set limit extrapolation calculator, Comput. Theor. Chem., 1115, 1–3.
[16] Sacchi, M., and Tamtögl, A., 2023, Water adsorption and dynamics on graphene and other 2D materials: Computational and experimental advances, Adv. Phys.: X, 8 (1), 2134051.
[17] Zhao, N., Tan, Y.X., Zhang, X., Zhen, Z.S., Song, Q.W., Ju, F., and Ling, H., 2023, Molecular insights on the adsorption of polycyclic aromatic hydrocarbons on soil clay minerals, Environ. Eng. Sci., 40 (3), 105–113.
[18] Cheng, Q., Conejo, A.N., Wang, Y., Zhang, J., Zheng, A., and Liu, Z., 2023, Adsorption properties of hydrogen with iron oxides (FeO, Fe2O3): A ReaxFF molecular dynamics study, Comput. Mater. Sci., 218, 111926.
[19] Piela, L., 2014, "Chapter 13 - Intermolecular Interactions" in Ideas of Quantum Chemistry (Second Edition), Elsevier, Oxford, UK, 793–882.
[20] Grabowski, S.J., 2017, New type of halogen bond: Multivalent halogen interacting with π- and σ-electrons, Molecules, 22 (12), 2150.
[21] Dawley, M.M., Scott, A.M., Hill, F.C., Leszczynski, J., and Orlando, T.M., 2012, Adsorption of formamide on kaolinite surfaces: A combined infrared experimental and theoretical study, J. Phys. Chem. C, 116 (45), 23981–23991.
[22] Michalkova Scott, A., Dawley, M.M., Orlando, T.M., Hill, F.C., and Leszczynski, J., 2012, Theoretical study of the roles of Na+ and water on the adsorption of formamide on kaolinite surfaces, J. Phys. Chem. C, 116 (45), 23992–24005.
[23] Song, K., Wang, X., Qian, P., Zhang, C., and Zhang, Q., 2013, Theoretical study of interaction of formamide with kaolinite, Comput. Theor. Chem., 1020, 72–80.
[24] Song, K.H., Zhong, M.J., Wang, L., Li, Y., and Qian, P., 2014, Theoretical study of interaction of amide molecules with kaolinite, Comput. Theor. Chem., 1050, 58–67.
[25] Bish, D.L., 1993, Rietveld refinement of the kaolinite structure at 1.5 K, Clays Clay Miner., 41 (6), 738–744.
[26] Tunega, D., Haberhauer, G., Gerzabek, M.H., and Lischka, H., 2002, Theoretical study of adsorption sites on the (001) surfaces of 1:1 clay minerals, Langmuir, 18 (1), 139–147.
[27] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Petersson, G.A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A., Bloino, J., Janesko, B.G., Gomperts, R., Mennucci, B., Hratchian, H.P., Ortiz, J.V., Izmaylov, A.F., Sonnenberg, J.L., Williams-Young, D., Ding, F., Lipparini, F., Egidi, F., Goings, J., Peng, B., Petrone, A., Henderson, T., Ranasinghe, D., Zakrzewski, V.G., Gao, J., Rega, N., Zheng, G., Liang, W., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Throssell, K., 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., Millam, J.M., Klene, M., Adamo, C., Cammi, R., Ochterski, J.W., Martin, R.L., Morokuma, K., Farkas, O., Foresman, J.B., and Fox, D.J., 2016, Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford CT.
[28] Lu, T., and Chen, F., 2012, Multiwfn: A multifunctional wavefunction analyzer, J. Comput. Chem., 33 (5), 580–592.
[29] Dennington, R., Keith, T.A., and Millam, J.M., 2016, GaussView, Version 6.1, Semichem Inc., Shawnee Mission, KS.
[30] Pettersen, E.F., Goddard, T.D., Huang, C.C., Meng, E.C., Couch, G.S., Croll, T.I., Morris, J.H., and Ferrin, T.E., 2021, UCSF ChimeraX: Structure visualization for researchers, educators, and developers, Protein Sci., 30 (1), 70–82.
[31] Xiao, J., Zhao, Y.P., Fan, X., Cao, J.P., Kang, G.J., Zhao, W., and Wei, X.Y., 2017, Hydrogen bonding interactions between the organic oxygen/nitrogen monomers of lignite and water molecules: A DFT and AIM study, Fuel Process. Technol., 168, 58–64.
[32] Nabil, N.N.A.M., and Ang, L.S., 2022, Selecting suitable functionals and basis sets on the study structural and adsorption of urea-kaolinite system using cluster method, Indones. J. Chem., 22 (2), 361–373.
[33] Emamian, S., Lu, T., Kruse, H., and Emamian, H., 2019, Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory, J. Comput. Chem., 40 (32), 2868–2881.
[34] Humphrey, W., Dalke, A., and Schulten, K., 1996, VMD: Visual molecular dynamics, J. Mol. Graphics, 14 (1), 33–38.
DOI: https://doi.org/10.22146/ijc.79795
Article Metrics
Abstract views : 1391
| 
views : 688
Copyright (c) 2023 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.