A DFT/TD-DFT study on the Molecular Structure Absorption and Fluorescence Spectra of Gas/Solution Phases Adenosine 5’–triphosphate Molecule

Year 2022, , 219 - 233, 01.03.2022

Yavuz Ekincioğlu , Hamdi Şükür Kılıç , Ömer Dereli

https://doi.org/10.35378/gujs.834249

Cited By: 1

Abstract

In this study, the conformational structure of the tetra-protonated Adenosine 5’triphosphate molecule has been investigated using Spartan 08 package program with the molecular dynamics method. Following the conformational analysis; geometry optimization, excited states, absorption and fluorescence (emission) spectra, molecular orbitals, chemical hardness, electronic chemical potential, electronegativity and electrophilicity indexes of the molecule were calculated by using density functional theory and time-dependent density functional theory method with B3LYP functional with 6-311+G (d, p) basis set. All calculations for the tetra-protonated ATP molecule have also been carried out both in the gas phase and in the aqueous solution and then results were compared with the experimental data reported in the literature.

Keywords

ATP, DFT, TD-DFT, Absorption, Emission

Thanks

Authors kindly would like to thanks, - Selçuk University, Department of Physics, 42031, Selçuklu, Konya, Turkey. - Selçuk University, High Technology Research and Application Center, and - University of Selçuk, SULTAN Center, 42031, Selçuklu, Konya, Turkey for supplying with infrastructure.

References

• [1] Nir, E., Imhof, P., Kleinermanns, K., de Vries, M.S., “REMPI Spectroscopy of Laser Desorbed Guanosines”, Journal of the American Chemical Society, 122(33): 8091–8092, (2000).
• [2] Wu, R.R., Yang, B., Berden, G., Oomens, J., Rodgers, M.T., “Gas–phase conformations and energetics of protonated 2'–deoxyadenosine and adenosine: IRMPD action spectroscopy and theoretical studies”, The Journal of Physical Chemistry B, 119(7): 2795–2805, (2015).
• [3] Abraham, E.H., Okunieff, P., Scala, S., Vos, P., Oosterveld, M.J., Chen, A.Y., Shrivastav, B., “Cystic fibrosis transmembrane conductance regulator and adenosine triphosphate”, Science, 275(5304): 1324–1326, (1997).
• [4] Newman, E.A., Zahs, K.R., “Calcium waves in retinal glial cells”, Science, 275(5301): 844–847, (1997).
• [5] Szewczyk, A., Pikula, S., “Adenosine 5'–triphosphate: an intracellular metabolic messenger”, Biochim Biophys Acta, 1365(3): 333–353, (1998).
• [6] Bush, K.T., Keller, S.H., Nigam, S.K., “Genesis and reversal of the ischemic phenotype in epithelial cells”, The Journal of Clinical Investigation, 106(5): 621–626, (2000).
• [7] Ma, C., Chen, H., Han, R., He, H., Zeng, W., “Fluorescence detection of adenosine triphosphate using smart probe”, Analytical Biochemistry, 429(1): 8–10, (2012).
• [8] Neelakandan, P.P., Hariharan, M., Ramaiah, D., “Synthesis of a novel cyclic donor-acceptor conjugate for selective recognition of ATP”, Organic Letters, 7(26): 5765–5768, (2005).
• [9] Crespo–Hernández, C.E., Cohen, B., Hare, P.M., Kohler, B., “Ultrafast excited-state dynamics in nucleic acids”, Chemical Reviews, 104(4): 1977–2020, (2004).
• [10] Burke, R.M., Pearce, J.K., Boxford, W.E., Bruckmann, A., Dessent, C.E., “Stabilization of Excess Charge in Isolated Adenosine 5 ‘–Triphosphate and Adenosine 5 ‘–Diphosphate Multiply and Singly Charged Anions”, The Journal of Physical Chemistry A, 109(43): 9775–9785, (2005).
• [11] Sigel, H., Griesser, R., “Nucleoside 5′–triphosphates: self-association, acid–base, and metal ion-binding properties in solution”, Chemical Society Reviews, 34(10): 875–900, (2005).
• [12] Schinle, F., Crider, P.E., Vonderach, M., Weis, P., Hampe, O., Kappes, M.M., “Spectroscopic and theoretical investigations of adenosine 5'–diphosphate and adenosine 5'–triphosphate dianions in the gas phase”, Physical Chemistry Chemical Physics, 15(18): 6640–6650, (2013).
• [13] Van Outersterp, R.E., Martens, J., Berden, G., Steill, J.D., Oomens, J., Rijs, A.M., “Structural characterization of nucleotide 5'–triphosphates by infrared ion spectroscopy and theoretical studies”, Physical Chemistry Chemical Physics, 20(44): 28319–28330, (2018).
• [14] Amraoui, N.E., Messaoudi, A., Hammoutène, D., “Copper ion Cu (I) interaction effect on DNA nucleotides: DFT study”, Inorganic Chemistry Communications, 119: 108078, (2020).
• [15] Amat, A., Rigau, J., Waynant, R.W., Ilev, I.K., Tomas, J., Anders, J.J., “Modification of the intrinsic fluorescence and the biochemical behavior of ATP after irradiation with visible and near-infrared laser light”, Journal of Photochemistry and Photobiology B Biology, 81(1): 26–32, (2005).
• [16] Van Outersterp, R., “Structural characterization and activation of nature’s fuels of life”, Student Undergraduate Research E-journal, 2, (2016).
• [17] Burke, R.M., Dessent, C.E., “Effect of cation complexation on the structure of a conformationally flexible multiply charged anion: stabilization of excess charge in the Na+·Adenosine 5′–Triphosphate dianion ion-pair complex”, The Journal of Physical Chemistry A, 113(12): 2683–2692, (2009).
• [18] Cercola, R., Matthews, E., Dessent, C.E.H., “Photoexcitation of Adenosine 5'–Triphosphate Anions in Vacuo: Probing the Influence of Charge State on the UV Photophysics of Adenine”, The Journal of Physical Chemistry B, 121(22): 5553–5561, (2017).
• [19] Wu, R., Hamlow, L., He, C., Nei, Y.w., Berden, G., Oomens, J., Rodgers, M., “The intrinsic basicity of the phosphate backbone exceeds that of uracil and thymine residues: protonation of the phosphate moiety is preferred over the nucleobase for pdThd and pUrd”, Physical Chemistry Chemical Physics, 19(45): 30351–30361, (2017).
• [20] Sabat, M., Cini, R., Haromy, T., Sundaralingam, M., “Crystal structure of the alpha, beta, gamma–tridentate manganese complex of adenosine 5'–triphosphate cocrystallized with 2,2'–dipyridylamine”, Biochemistry, 24(26): 7827–7833, (1985).
• [21] Kennard, O., Isaacs, N.W., Coppola, J.C., Kirby, A.J., Warren, S., Motherwell, W.D., Watson, D.G., Wampler, D.L., Chenery, D.H., Larson, A.C., Kerr, K.A., Di Sanseverino, L.R., “Three dimensional structure of adenosine triphosphate”, Nature, 225(5230): 333–336, (1970).
• [22] Akola, J., Jones, R., “ATP hydrolysis in water– a density functional study”, The Journal of Physical Chemistry B, 107(42): 11774–11783, (2003).
• [23] Wang, P., Izatt, R.M., Oscarson, J.L., Gillespie, S.E., “H NMR study of protonation and mg (ii) coordination of AMP, ADP, and ATP at 25, 50, and 70° C”, The Journal of Physical Chemistry, 100(22): 9556–9560, (1996).
• [24] Zhou, J., Lu, G., “Spectroscopy study on the noncovalent interactions in the binary and ternary systems of L–lysine, adenosine 5'–triphosphate and magnesium ions”, Spectrochim Acta A Mol Biomol Spectrosc, 78(4): 1305–1309, (2011).
• [25] Brøndsted Nielsen, S., Sølling, T.I., “Are conical intersections responsible for the ultrafast processes of adenine, protonated adenine, and the corresponding nucleosides?”, ChemPhysChem, 6(7): 1276–1281, (2005).
• [26] Wu, R.R., He, C.C., Hamlow, L.A., Nei, Y.W., Berden, G., Oomens, J., Rodgers, M.T., “N3 Protonation Induces Base Rotation of 2'–Deoxyadenosine–5'–monophosphate and Adenosine–5'–monophosphate”, The Journal of Physical Chemistry B, 120(20): 4616–4624, (2016).
• [27] Wu, R.R., He, C.C., Hamlow, L.A., Nei, Y.W., Berden, G., Oomens, J., Rodgers, M.T., “Protonation induces base rotation of purine nucleotides pdGuo and pGuo”, Physical Chemistry Chemical Physics, 18(22): 15081–15090, (2016).
• [28] Frisch, M.J., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., Petersson, G., “Gaussian 09, Revision D. 01”, Gaussian Inc.: Wallingford, CT, (2009).
• [29] Shao, Y., Molnar, L., Jung, Y., Kussmann, J., Ochsenfeld, C., Brown, S., Gilbert, A., Slipchenko, L., Levchenko, S., O’Neill, D., “Spartan’08, Wavefunction, Inc. Irvine, CA”, Physical Chemistry Chemical Physics, 8: 3172–3191, (2006).
• [30] Dereli, Ö., “Molecular structure and spectral (FT–IR, Raman) investigations of 3–aminocoumarin”, Optics and Spectroscopy, 120(5): 690–700, (2016).
• [31] Miertuš, S., Scrocco, E., Tomasi, J., “Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects”, Chemical Physics, 55(1): 117–129, (1981).
• [32] Tomasi, J., Mennucci, B., Cammi, R., “Quantum mechanical continuum solvation models”, Chemical Reviews, 105(8): 2999–3093, (2005).
• [33] Pakiari, A., Farrokhnia, M., Moradshahi, A., “Quantum chemical analysis of ATP, GTP and related compounds in gas phase”, Journal of the Iranian Chemical Society, 7(1): 51–58, (2010).
• [34] Kennard, O., Isaacs, N.W., Motherwell, W., Coppola, J., Wampler, D., Larson, A.t., Watson, D., “The crystal and molecular structure of adenosine triphosphate”, Proceedings of the Royal Society of London. A. Mathematical Physical Sciences, 325(1562): 401–436, (1971).
• [35] Sugawara, Y., Kamiya, N., Iwasaki, H., Ito, T., Satow, Y., “Humidity-controlled reversible structure transition of disodium adenosine 5'–triphosphate between dihydrate and trihydrate in a single crystal state”, Journal of the American Chemical Society, 113(14): 5440–5445, (1991).
• [36] Dittrich, M., Hayashi, S., Schulten, K., “On the mechanism of ATP hydrolysis in F1–ATPase”, Biophysical Journal, 85(4): 2253–2266, (2003).
• [37] Kurban, M., Gündüz, B., Göktaş, F., “Experimental and theoretical studies of the structural, electronic and optical properties of BCzVB organic material”, Optik, 182: 611–617, (2019).
• [38] Gündüz, B., Kurban, M., “Photonic, spectroscopic properties and electronic structure of PTCDI–C8 organic nanostructure”, Vibrational Spectroscopy, 96: 46–51, (2018).
• [39] Kurban, M., Sertbakan, T.R., Gündüz, B., “A combined experimental and DFT/TD–DFT studies on the electronic structure, structural and optical properties of quinoline derivatives”, Journal of Molecular Modeling, 26: 1–7, (2020).
• [40] Reed, J.L., “Electronegativity: chemical hardness I”, The Journal of Physical Chemistry A, 101(40): 7396–7400, (1997).
• [41] Parr, R.G., Pearson, R.G., “Absolute hardness: companion parameter to absolute electronegativity”, Journal of the American Chemical Society, 105(26): 7512–7516, (1983).
• [42] Pauling, L., “The Nature of the Chemical Bond”, Cornell University Press Ithaca, NY, (1960).
• [43] Koopmans, T., “Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den einzelnen Elektronen eines Atoms”, Physica, 1(1–6): 104–113, (1934).
• [44] Roy, D.R., Parthasarathi, R., Padmanabhan, J., Sarkar, U., Subramanian, V., Chattaraj, P.K., “Careful scrutiny of the philicity concept”, The Journal of Physical Chemistry A, 110(3): 1084–1093, (2006).
• [45] Singh, N.B., Sarkar, U., “Structure, vibrational, and optical properties of platinum cluster: a density functional theory approach”, Journal of Molecular Modeling, 20(12): 2537, (2014).
• [46] Grimme, S., “Calculation of the electronic spectra of large molecules”, Reviews in Computational Chemistry, 20: 153, (2004).
• [47] Dreuw, A., Head–Gordon, M., “Single-reference ab initio methods for the calculation of excited states of large molecules”, Chemical reviews, 105(11): 4009–4037, (2005).
• [48] Varsano, D., Di Felice, R., Marques, M.A., Rubio, A., “A TDDFT study of the excited states of DNA bases and their assemblies”, The Journal of Physical Chemistry B, 110(14): 7129–7138, (2006).
• [49] Adamo, C., Jacquemin, D., “The calculations of excited-state properties with Time-Dependent Density Functional Theory”, Chemical Society Reviews, 42(3): 845–856, (2013).
• [50] Ito, A., Ito, T., “Absorption spectra of deoxyribose, ribosephosphate, atp and dna by direct transmission measurements in the vacuum‐uv (150—190 nm) and far‐uv (190—260 nm) regions using synchrotron radiation as a light source”, Photochemistry and Photobiology, 44(3): 355–358, (1986).
• [51] Hegyi, G., Kardos, J., Kovács, M., Málnási–Csizmadia, A., Nyitray, L., Pál, G., Radnai, L., Reményi, A., Venekei, I., “Introduction to practical biochemistry”, ELTE Faculty of Natural Sciences, (2013).
• [52] Carrasquilla, R., Bueno, O.N., “Time dependent density functional study of the absorption and emission spectra of 1, 3–benzoxazole and three substituted benzoxazoles”, Optica pura y aplicada, 45(3): 287–297, (2012).
• [53] Cervantes–Navarro, F., Glossman–Mitnik, D., “DFT study of the effect of substituents on the absorption and emission spectra of Indigo”, Chemistry Central Journal, 6(1): 70, (2012).
• [54] Noguchi, T., Shiraki, T., Dawn, A., Tsuchiya, Y., Yamamoto, T., Shinkai, S., “Nonlinear fluorescence response driven by ATP–induced self–assembly of guanidinium–tethered tetraphenylethene”, Chemical Communications, 48(65): 8090–8092, (2012).