Theoretical Study on the Nature and Strength of Interaction of Methylated DNA Nucleobases with Ionic Liquids

Document Type : Research Article


1 Department of Chemical Engineering, Birjand University of Technology, Birjand, I.R. IRAN

2 Department of Physics, Jahrom University, Jahrom, I.R. IRAN


In this research, the interaction of methylated nucleobases of Adenine (m-A), Guanine (m-G), Cytosine (m-C) and Thymine (m-T) with five ionic liquids (ILs) ([Bmim][BF4], [Bpy][BF4], [Ch][BF4], [Bmim][CH3COO] and [Bpy][CH3COO]) was investigated by using Density functional theory (DFT) at the M06-2X level and 6-311++G(d,p) basis set. In this investigation, the nature and strength of interaction between the methylated nucleobases and ionic liquids were analyzed using four analysis methods of natural bond orbital (NBO), atoms in molecules (AIM), reduced density gradient (RDG) surfaces and energy decomposition analysis (EDA). The result of this research showed that the interaction between methylated nucleobases and ionic liquids is electrostatic in nature and is mainly caused by hydrogen bonds. In order to find out the strength of interaction between ionic liquids and methylated nucleobases, the binding energy (ΔEb) values were also evaluated for the ionic liquid…methylated nucleobase complexes. The result of DFT calculations showed that the interaction strength of methylated nucleobases with ionic liquids follows the order of m-G…IL > m-C…IL > A…IL > m-T…IL.


Main Subjects

[1] Pratviel G., Bernadou J., Meunier B., Carbon—Hydrogen Bonds of DNA Sugar Units as Targets for Chemical Nucleases and Drugs, Angew. Chem., 34(7): 746-769 (1995).
[2] Putnam D., Polymers for Gene Delivery Across Length Scales, Nat. Mater., 5(1): 439-451 (2006).
[3] De Pasquale R.J., Uracil. A perspective, Ind. Eng. Chem. Prod. Res. Dev., 17(4): 278-286 (1978).
[4] منصوری ترشیزی ح.، جهانگیری س.، بابایی زارچ م.، خدابخشی کنگان ز.، نزشتی ف.، تهیه، شناسایی، ویژگی‌های ضدتومور، برهم­کنش با DNA و تأثیر بارالکتریکی موجود روی نسبت ­های مولی گوناگون کمپلکس­ های Zn(II):Pd(II) در "ترکیب درمانی" آن‌ها،  نشریه شیمی و مهندسی شیمی ایران، (2)36: 55 تا 67 (1396).
[6] Amo-Ochoa P., Zamora F., Coordination Polymers with Nucleobases: From Structural Aspects to Potential Applications, Coord. Chem., 276(6): 34-58 (2014).
[8] McCleverty J.A., Meyer T.J., “Comprehensive Coordination Chemistry II: From Biology to Nanotechnology”, Elsevier Science, Amsterdam (2003).
[9] Zhao H., DNA Stability in Ionic Liquids and Deep Eutectic Solvents, J. Chem. Technol. Biotechnol., 90(1): 19-25 (2015).
[10] Zielenkiewicz W., Poznański J., Zielenkiewicz A., Partial Molar Volumes of Aqueous Solutions of Some Halo and Amino Derivatives of Uracil, J. Solution Chem., 29(8): 757-757  (2000).
[11] Cardoso L., Micaelo N.M., DNA Molecular Solvation in Neat Ionic Liquids, Chem. Phys. Chem., 12(2): 275-277  (2011).
[12] Maksić Z.B., Kovačević B., Spatial and Electronic Structure of Highly Basic Organic Molecules:  Cyclopropeneimines and Some Related Systems, J. Phys. Chem. A., 103(33): 6678-6684  (1999).
[13] Kaljurand I., Saame J., Rodima T., Koppel I., Koppel I.A., Kögel J.F., Sundermeyer J., Köhn U., Coles M.P., Leito I., Experimental Basicities of Phosphazene, Guanidinophosphazene, and Proton Sponge Superbases in the Gas Phase and Solution, J. Phys. Chem. A., 120(16): 2591-2604 (2016).
[15] Hu X., Zhang B., Dong S., Gao Y., Modification of Thionucleobases in Ionic Liquids, J. Chem., 2014(1): 353797- 353800 (2014).
[16] Welton T., Room-Temperature Ionic Liquids. Solvents for Synthesis and Catalysis, Chem. Rev., 99(8): 2071-2084  (1999).
[18] Yang Z., Pan W., Ionic liquids: Green Solvents for Nonaqueous Biocatalysis, Enzyme Microb. Technol., 37(1): 19-28 (2005).
[19] Berthod A., Ruiz-Angel M., S. Carda-Broch, Ionic Liquids in Separation Techniques, J. Chromatogr. A., 1184(1): 6-18 (2008).
[20] Pârvulescu V.I., Hardacre C., Catalysis in Ionic Liquids, Chem. Rev., 107(6): 2615-2665 (2007).
[21] Sureshkumar M., Lee C. K., Biocatalytic Reactions in Hydrophobic Ionic Liquids, J. Mol. Catal. B Enzymatic, 60(1): 1-12 (2009).
[22] Ferreira I.M.P.L.V.O., Mendes E., Gomes A.M.P., Faria M.A., Ferreira M.A., The Determination and Distribution of Nucleotides in Dairy Products Using HPLC and Diode Array Detection, Food Chem., 74(1): 239-244 (2001).
[23] Blanco López S.L.a., Moal J., San Juan Serrano F., Development of a Method for the Analysis of Nucleotides from the Mantle Tissue of the Mussel Mytilus Galloprovincialis, J. Chromatogra. A., 891(1): 99-107 (2000).
[24] Hua J., Polyakova Y., Row K., Effect of Concentration of Ionic Liquids on Resolution of Nucleotides in Reversed-Phase Liquid Chromatography, Bull. Korean Chem. Soc., 28(4): 601-606 (2007).
[25] Zhang W.-Z., He L.-J., Liu X., Jiang S.-X., Ionic Liquids as Mobile Phase Additives for Separation of Nucleotides in High-Performance Liquid Chromatography, Chin. J. Chem., 22(6): 549-552 (2004).
[26] Yi H., Yao S., Song H., Application of Ionic Liquids in Liquid Chromatography and Electrodriven Separation, J. Chromatogr. Sci., 51(7): 739-752 (2013).
[27] Jin C.H., Koo Y.M., Choi D.-K., Row K.H., Effect of Mobile Phase Additives on Resolution of Some Nucleic Compounds in High Performance Liquid Chromatography, Biotechnol. Bioproc. Eng., 12(5): 525-530 (2007).
[28] Nguyen A.L., Luong J.H.T., Masson C., Determination of Nucleotides in Fish Tissues Using Capillary Electrophoresis, Anal. Chem., 62(22): 2490-2493 (1990).
[29] Vijayaraghavan R., Izgorodin A., Ganesh V., Surianarayanan M., MacFarlane, D.R. Long-Term Structural and Chemical Stability of DNA in Hydrated Ionic Liquids, Angew. Chem. Int. Ed., 49(9): 1631-1633 (2010).
[30] Chandran A., Ghoshdastidar D., Senapati S., Groove Binding Mechanism of Ionic Liquids:
A Key Factor in Long-Term Stability of DNA in Hydrated Ionic Liquids?
, J. Am. Chem. Soc.,  134(50): 20330-20339 (2012).
[31] Araújo J.M.M., Ferreira R., Marrucho I.M., Rebelo L.P.N. Solvation of Nucleobases in 1,3-Dialkylimidazolium Acetate Ionic Liquids: NMR Spectroscopy Insights into the Dissolution Mechanism, J. Phys. Chem. B., 115(36): 10739-10749 (2011).
[32] Araújo J.o.M., Pereiro A.B., Canongia Lopes J.N., Rebelo L.P., Marrucho I.M., Hydrogen-Bonding and the Dissolution Mechanism of Uracil in an Acetate Ionic Liquid: New Insights from NMR Spectroscopy and Quantum Chemical Calculations, J. Phys. Chem. B., 117(15): 4109-4120 (2013).
[33] Norman S.E., Turner A.H., Holbrey J.D., Youngs T.G., Solvation Structure of Uracil in Ionic Liquids, Chem. Phys. Chem., 17(23): 3923-3931 (2016).
[34] Jumbri K., Micaelo N.M., M.B. Abdul Rahman, Solvation Free Energies of Nucleic Acid Bases in Ionic Liquids, Mol. Simul., 43(1): 19-27 (2017).
[35] Dasari S., Mallik, B.S., Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations, J. Phys. Chem. B., 122(42): 9635-9645 (2018).
[36]   Bash P., Singh U., Langridge R., Kollman P., Free Energy Calculations by Computer Simulation, Science, 236(4801): 564-568 (1987).
[37] Young P.E., Hillier I.H., Hydration Free Energies of Nucleic Acid Bases Using an Ab Initio Continuum Model. Chem. Phys. Lett., 215(4): 405-408 (1993).
[38] Orozco M., Colominas C., Luque F.J., Theoretical Determination of the Solvation Free Energy in Water and Chloroform of the Nucleic Acid Bases, Chem. Phys., 209(1): 19-29 (1996).
[40] Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb Ma., Cheeseman J.R., Scalmani G., Barone V., Mennucci B., Petersson G.A., Gaussian 09, Revision C. 01, Gaussian Inc, Wallingford, CT (2009).
[44] Lemke K.H., Seward T.M., Thermodynamic Properties of Carbon Dioxide Clusters by M06-2X and Dispersion-Corrected B2PLYP-D Theory, Chem. Phys. Lett., 573(1): 19-23 (2013).
[45] Izgorodina E.I., Bernard U.L., MacFarlane D.R., Ion-Pair Binding Energies of Ionic Liquids: Can DFT Compete with Ab Initio-Based Methods?, J. Phys. Chem A, 113(25): 7064-7072 (2009).
[46] Wu C., De Visscher A., Gates I.D., Molecular Interactions Between 1-Butyl-3-Methylimidazolium Tetrafluoroborate and Model Naphthenic acids: A DFT Study, J. Mol. Liq., 243(1): 462-471 (2017).
[47] Wu C., De Visscher A., Gates I.D., Interactions of Biodegradable Ionic Liquids with a Model Naphthenic Acid, Sci rep., 8(1): 1-9 (2018).
[49] Marekha B.A., Kalugin O.N., Idrissi A., Non-Covalent Interactions in Ionic Liquid Ion Pairs and Ion Pair Dimers: A Quantum Chemical Calculation Analysis, Phys. Chem. Chem. Phys., 17(26): 16846-16857 (2015).
[50] Zahn S., MacFarlane D.R., Izgorodina E.I., Assessment of Kohn–Sham Density Functional Theory and Møller–Plesset Perturbation Theory for Ionic Liquids, Phys. Chem. Chem. Phys., 15(32): 13664-13675 (2013).
[51] Garcia G., Atilhan M., Aparicio S., Assessment of DFT Methods for Studying Acid Gas Capture by Ionic Liquids, Phys. Chem. Chem. Phys., 17(40): 26875-26891 (2015).
[53] Housaindokht M.R., Sargolzaei M., Bozorgmehr M.R., Ab Initio Study of Ion Replacement in Spinach Plastocyanin Protein, Bulg. Chem., 45(2): 201-206 (2013).
[54] Bader R.F.W., “Atoms in Molecules: A Quantum Theory”, Clarendon Press: Oxford, UK (1990).
[55] Bader R., Biegler-König F., Schönbohm J., AIM2000 Program Package, Ver. 2.0., McMaster University, Hamilton (2002).
[56] Lu T., Chen F., Multiwfn: A Multifunctional Wavefunction Analyzer, J. Comput. Chem., 33(5): 580-592 (2012).
[57] Mulder F., Van-Hemert M., Wormer P.E., A. van der Avoird, Ab Initio Studies of Long Range Interactions Between Ethylene Molecules in the Multipole Expansion, Th. Ch. Ac., 46(1): 39-62 (1977).
[58] Bickelhaupt F.M., Baerends E.J., Density Functional Theory: Predicting and Understanding Chemistry. Rev. Comput. Chem., 15(1): 1-86 (2000).
[60] Baerends E.J., Ziegler T., Autschbach J., Bashford D., Bérces A., Bickelhaupt F.M., Bo C., Boerrigter P.M., Cappelli C.; Cavallo L., Daul C., Chong D.P., Chulhai D.V., Deng L., Dickson R.M., Dieterich J.M., Egidi F., Ellis D.E., van Faassen M., Fan L., Fischer T.H., Förster A., Fonseca Guerra C., Franchini M., Ghysels A., Giammona A., van Gisbergen S.J.A., Goez A., Götz A.W., Groeneveld J.A., Gritsenko O.V., Grüning M., Gusarov S., Harris F.E., van den Hoek P., Hu Z., Jacob C.R., Jacobsen H., Jensen L., Joubert L., Kaminski J.W., van Kessel G., König C., Kootstra F., Kovalenko A., Krykunov M.V., Lafiosca P., van Lenthe E., McCormack D.A., Medves M., Michalak A., Mitoraj M., Morton S.M., Neugebauer J., Nicu V.P., Noodleman L., Osinga V.P., Patchkovskii S., Pavanello M., Peeples C.A., Philipsen P.H.T., Post D., Pye C.C., Ramanantoanina H., Ramos P., Ravenek W., Reimann M., Rodríguez J.I., Ros P., Rüger R., Schipper P.R.T., Schlüns D., van Schoot H., Schreckenbach G., Seldenthuis J.S., Seth M., Snijders J.G., Solà M., Stener M., Swart M., Swerhone D., Tognetti V., te Velde G., Vernooijs P., Versluis L., Visscher L., Visser O., Wang F., Wesolowski T.A., van Wezenbeek E.M., Wiesenekker G., Wolff S.K., Woo T.K., Yakovlev A.L., ADF2013, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, (2014).
[61] Te-Velde G.t., Bickelhaupt F.M., Baerends E.J., Fonseca-Guerra C., van-Gisbergen S.J., Snijders J.G., Ziegler T., Chemistry with ADF, J. Comput. Chem., 22(9): 931-967 (2001).
[63] Shakourian-Fard M., Jamshidi Z., Bayat A., Kamath G., Meta-Hybrid Density Functional Theory Study of Adsorption of Imidazolium-and Ammonium-Based Ionic Liquids on Graphene Sheet, J. Phys. Chem. C, 119(13): 7095-7108 (2015).
[64] Shakourian-Fard M., G. Kamath, Z. Jamshidi, Trends in Physisorption of Ionic Liquids on Boron-Nitride Sheets, J. Phys. Chem. C, 118(45): 26003-26016  (2014).
[65] Johnson E.R., Keinan S., Mori-Sánchez P., Contreras-García J., Cohen A.J., Yang W., Revealing Noncovalent Interactions, J. Am. Chem. Soc, 132(18): 6498-6506 (2010).
[66] Contreras-García J., Johnson E.R., Keinan S., Chaudret R., Piquemal J.-P., Beratan D.N.,Yang W., NCIPLOT: A Program for Plotting Noncovalent Interaction Regions, J. Chem. Theory Comput, 7(3): 625-632  (2011).