Theoretical Study of Oxygen Atom Adsorption on A Polycyclic Aromatic Hydrocarbon Using Density-Functional Theory

Mokhammad Fajar Pradipta; Harno Dwi Pranowo; Viny Alfiyah; Aulia Sukma Hutama

doi:10.22146/ijc.53583

Theoretical Study of Oxygen Atom Adsorption on A Polycyclic Aromatic Hydrocarbon Using Density-Functional Theory

https://doi.org/10.22146/ijc.53583

Mokhammad Fajar Pradipta⁽¹⁾, Harno Dwi Pranowo⁽²⁾, Viny Alfiyah⁽³⁾, Aulia Sukma Hutama^(4*)

(1) Austrian-Indonesian Centre (AIC) for Computational Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia
(2) Austrian-Indonesian Centre (AIC) for Computational Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia
(3) Austrian-Indonesian Centre (AIC) for Computational Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia
(4) Austrian-Indonesian Centre (AIC) for Computational Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia
(*) Corresponding Author

Abstract

Potential energy curves (PECs) and energy profiles of atomic O attack on coronene as a model for graphene/graphitic surface and interstellar reaction surface have been computed at the unrestricted B3LYP/cc-pVDZ level of theory to elaborate on atomic O attack mechanism and chemisorption on coronene. The PECs were generated by scanning the O atom distance to the closest carbon atom on "top" and "bridge" positions in the coronene, while fully relaxed geometries in the triplet state were investigated to gain the energy profile. We found that the most favorable geometry as the final product was the chemically bound O on the "bridge" site in the singlet state with an interaction energy of –29.2 kcal/mol. We recommended a plausible mechanism of atomic O attack and chemisorption reaction on coronene or generally graphitic surface starting from the non-interacting O atom and coronene systems into the chemically bound O atom on coronene.

Keywords

graphene oxide; chemisorption; density functional theory

Full Text:

Full Text PDF

References

[1] Geim, A.K., and Novoselov, K.S., 2007, The rise of graphene, Nat. Mater., 6 (3), 183–191.

[2] Johns, J.E., and Hersam, M.C., 2013, Atomic covalent functionalization of graphene, Acc. Chem. Res., 46 (1), 77–86.

[3] Dreyer, D.R., Park, S., Bielawski, C.W., and Ruof, R.S., 2010, The chemistry of graphene oxide, Chem. Soc. Rev., 39 (1), 228–240.

[4] Wang, S., Ang, P.K., Wang, Z., Tang, A.L.L., Thong, J.T.L., and Loh, K.P., 2010, High mobility, printable, and solution-processed graphene electronics, Nano Lett., 10 (1), 92–98.

[5] Becerril, H.A., Mao, J., Liu, Z., Stoltenberg, R.M., Bao, Z., and Chen, Y., 2008, Evaluation of solution-processed reduced graphene oxide films as transparent conductors, ACS Nano, 2 (3), 463–470.

[6] Matyba, P., Yamaguchi, H., Eda, G., Chhowalla, M., Edman, L., and Robinson, N.D., 2010, Graphene and mobile ions: The key to all-plastic, solution-processed light-emitting devices, ACS Nano, 4 (2), 637–642.

[7] Stankovich, S., Dikin, D.A., Piner, R.D., Kohlhaas, K.A., Kleinhammes, A., Jia, Y., Wu, Y., Nguyen, S.T., and Ruoff, R.S., 2007, Synthesis of graphene-based nanosheets via chemical reduction of exfoliated graphite oxide, Carbon, 45 (7), 1558–1565.

[8] Hummers, W.S., and Offeman, R.E., 1958, Preparation of graphitic oxide, J. Am. Chem. Soc., 80 (6), 1339.

[9] Schniepp, H.C., Li, J.L., McAllister, M.J., Sai, H., Herrera-Alonso, M., Adamson, D.H., Prud’homme, R.K., Car, R., Seville, D.A., and Aksay, I.A., 2006, Functionalized single graphene sheets derived from splitting graphite oxide, J. Phys. Chem. B, 110 (17), 8535–8539.

[10] Szabó, T., Berkesi, O., Forgó, P., Josepovits, K., Sanakis, Y., Petridis, D., and Dékány, I., 2006, Evolution of surface functional groups in a series of progressively oxidized graphite oxides, Chem. Mater., 18 (11), 2740–2749.

[11] Gao, W., Alemany, L.B., Ci, L., and Ajayan, P.M., 2009, New insights into the structure and reduction of graphite oxide, Nat. Chem., 1 (5), 403–408.

[12] Li, X., Wang, H., Robinson, J.T., Sanchez, H., Diankov, G., and Dai, H., 2009, Simultaneous nitrogen doping and reduction of graphene oxide, J. Am. Chem. Soc., 131 (43), 15939–15944.

[13] Barinov, A., Malciog, O.B., Fabris, S., Gregoratti, L., Dalmiglio, M., Kiskinova, M., Baris, O., and Sun, T., 2009, Initial stages of oxidation on graphitic surfaces: Photoemission study and density functional theory calculations, J. Phys. Chem. C, 113 (21), 9009–9013.

[14] Nourbakhsh, A., Cantoro, M., Klekachev, A.V., Pourtois, G., Vosch, T., Hofkens, J., van der Veen, M.H., Heyns, M.M., De Gendt, S., and Sels, B.F., 2011, Single layer vs bilayer graphene: A comparative study of the effects of oxygen plasma treatment on their electronic and optical properties, J. Phys. Chem. C, 115 (33), 16619–16624.

[15] Nourbakhsh, A., Cantoro, M., Vosch, T., Pourtois, G., Clemente, F., van der Veen, M.H., Hofkens, J., Heyns, M.M., De Gendt, S., and Sels, B.F., 2010, Bandgap opening in oxygen plasma-treated graphene, Nanotechnology, 21 (43), 435203.

[16] Hossain, M.Z., Johns, J.E., Bevan, K.H., Karmel, H.J., Liang, Y.T., Yoshimoto, S., Mukai, K., Koitaya, T., Yoshinobu, J., Kawai, M., Lear, A.M., Kesmodel, L.L., Tait, S.L., and Hersam, M.C., 2012, Chemically homogeneous and thermally reversible oxidation of epitaxial graphene, Nat. Chem., 4 (4), 305–309.

[17] Vinogradov, N.A., Schulte, K., Ng, M.L., Mikkelsen, A., Lundgren, E., Mårtensson, N., and Preobrajenski, A.B., 2011, Impact of atomic oxygen on the structure of graphene formed on Ir(111) and Pt(111), J. Phys. Chem. C, 115 (19), 9568–9577.

[18] Srinivasan, S.G., and van Duin, A.C.T., 2011, Molecular-dynamics-based study of the collisions of hyperthermal atomic oxygen with graphene using the ReaxFF reactive force field, J. Phys. Chem. A, 115 (46), 13269–13280.

[19] Paci, J.T., Upadhyaya, H.P., Zhang, J., Schatz, G.C., and Minton, T.K., 2009, Theoretical and experimental studies of the reactions between hyperthermal O(³P) and graphite: Graphene-based direct dynamics and beam-surface scattering approaches, J. Phys. Chem. A, 113 (16), 4677–4685.

[20] Morón, V., Martin-Gondre, L., Crespos, C., Larregaray, P., Gamallo, P., and Sayós, R., 2012, Classical dynamics study of atomic oxygen over graphite (0001) with new interpolated and analytical potential energy surfaces, Comput. Theor. Chem., 990, 132–143.

[21] Isborn, C.M., Li, X., and Tully, J.C., 2007, Time-dependent density functional theory Ehrenfest dynamics: Collisions between atomic oxygen and graphite clusters, J. Chem. Phys., 126 (13), 134307.

[22] Steglich, M., Carpentier, Y., Jäger, C., Huisken, F., Räder, H.J., and Henning, T., 2012, The smoothness of the interstellar extinction curve in the UV: Comparison with recent laboratory measurements of PAH mixtures, Astron. Astrophys., 540, A110.

[23] Hammonds, M., Pathak, A., and Sarre, P.J., 2009, TD-DFT calculations of electronic spectra of hydrogenated protonated polycyclic aromatic hydrocarbon (PAH) molecules: Implications for the origin of the diffuse interstellar bands?, Phys. Chem. Chem. Phys., 11 (22), 4458–4464.

[24] Lebouteiller, V., Brandl, B., Bernard‐Salas, J., Devost, D., and Houck, J.R., 2007, PAH strength and the interstellar radiation field around the massive young cluster NGC 3603, Astrophys. J., 665 (1), 390–401.

[25] Biennier, L., Alsayed-Ali, M., Foutel-Richard, A., Novotny, O., Carles, S., Rebrion-Rowe, C., and Rowe, B., 2006, Laboratory measurements of the recombination of PAH ions with electrons: Implications for the PAH charge state in interstellar clouds, Faraday Discuss., 133, 289–301.

[26] Malloci, G., Mulas, G., and Joblin, C., 2004, Electronic absorption spectra of PAHs up to vacuum UV, Astron. Astrophys., 426 (1), 105–117.

[27] Lee, M.W., and Meuwly, M., 2014, Diffusion of atomic oxygen relevant to water formation in amorphous interstellar ices, Faraday Discuss., 168, 205–222.

[28] Dulieu, F., Amiaud, L., Congiu, E., Fillion, J.H., Matar, E., Momeni, A., Pirronello, V., and Lemaire, J.L., 2010, Experimental evidence for water formation on interstellar dust grains by hydrogen and oxygen atoms, Astron. Astrophys., 512 (5), A30.

[29] Goumans, T.P.M., Catlow, C.R.A., Brown, W.A., Kästner, J., and Sherwood, P., 2009, An embedded cluster study of the formation of water on interstellar dust grains, Phys. Chem. Chem. Phys., 11 (26), 5431–5436.

[30] Tachikawa, H., 2017, Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study, Appl. Surf. Sci., 396, 1335–1342.

[31] Tachikawa, H., and Kawabata, H., 2019, Additions of fluorine atoms to the surfaces of graphene nanoflakes: A density functional theory study, Solid State Sci., 97, 106007.

[32] Tachikawa, H., 2020, Mechanism of Li storage on graphene nanoflakes: Density functional theory study, Surf. Sci., 691, 121489.

[33] Hutama, A.S., Hijikata, Y., and Irle, S., 2017, Coupled cluster and density functional studies of atomic fluorine chemisorption on coronene as model systems for graphene fluorination, J. Phys. Chem. C, 121 (27), 14888–14898.

[34] Wang, Y., Qian, H.J., Morokuma, K., and Irle, S., 2012, Coupled cluster and density functional theory calculations of atomic hydrogen chemisorption on pyrene and coronene as model systems for graphene hydrogenation, J. Phys. Chem. A, 116 (26), 7154–7160.

[35] Lee, C., Yang, W., and Parr, R.G., 1988, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B: Condens. Matter, 37 (2), 785–789.

[36] 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., 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, Ö., Foresman, J.B., Ortiz, J.V., Cioslowski, J., and Fox, D.J., 2013, Gaussian-09 Revision D.01, Gaussian, Inc., Wallingford, CT.

[37] Manz, T.A., 2017, Introducing DDEC6 atomic population analysis: Part 3. Comprehensive method to compute bond orders, RSC Adv., 7 (72), 45552–45581.

[38] Manz, T.A., and Limas, N.G., 2016, Introducing DDEC6 atomic population analysis: Part 1. Charge partitioning theory and methodology, RSC Adv., 6 (53), 47771–47801.

[39] Limas, N.G., and Manz, T.A., 2016, Introducing DDEC6 atomic population analysis: Part 2. Computed results for a wide range of periodic and nonperiodic materials, RSC Adv., 6 (51), 45727–45747.

[40] Tachikawa, H., Iyama, T., and Kawabata, H., 2013, Interaction of hydroxyl OH radical with graphene surface: A density functional theory study, Jpn. J. Appl. Phys., 52 (1S), 01AH01.

[41] Tachikawa, H., and Kawabata, H., 2011, Ground and low-lying excited electronic states of graphene flakes: a density functional theory study, J. Phys. B: At. Mol. Opt. Phys., 44 (20), 205105.

[42] Li, J.L., Kudin, K.N., McAllister, M.J., Prud’homme, R.K., Aksay, I.A., and Car, R., 2006, Oxygen-driven unzipping of graphitic materials, Phys. Rev. Lett., 96 (17), 176101.

[43] Blöchl, P.E., 1994, Projector augmented-wave method, Phys. Rev. B, 50 (24), 17953–17979.

[44] Perdew, J.P., Burke, K., and Ernzerhof, M., 1996, Generalized gradient approximation made simple, Phys. Rev. Lett., 77 (18), 3865–3868.

[45] Watanabe, K., Nakatani, N., Nakayama, A., Higashi, M., and Hasegawa, J., 2016, Spin-blocking effect in CO and H₂ binding reactions to molybdenocene and tungstenocene: A theoretical study on the reaction mechanism via the minimum energy intersystem crossing point, Inorg. Chem., 55 (16), 8082–8090.

[46] Kitagawa, Y., Chen, Y., Nakatani, N., Nakayama, A., and Hasegawa, J., 2016, A DFT and multi-configurational perturbation theory study on O₂ binding to a model heme compound via the spin-change barrier, Phys. Chem. Chem. Phys., 18 (27), 18137–18144.

[47] Ma, Z., Ukaji, K., Nakatani, N., Fujii, H., and Hada, M., 2019, Substitution effects on olefin epoxidation catalyzed by Oxoiron(IV) porphyrin π-cation radical complexes: A DFT study, J. Comput. Chem., 40 (19), 1780–1788.

[48] Ma, Z., Nakatani, N., Fujii, H., and Hada, M., 2020, Effect of external electric fields on the oxidation reaction of olefins by Fe(IV)OCl–porphyrin complexes, Bull. Chem. Soc. Jpn., 93 (2), 187–193.

[49] Wang, Y., Qian, H., Wu, Z., and Irle, S., 2017, QM/MD simulations on graphene hydrogenation/deuteration: C_xH/D formation mechanism and isotope effect, J. Phys. Chem. C, 121 (15), 8480–8489.

[50] Fu, B., Han, Y., Bowman, J.M., Leonori, F., and Balucani, N., 2012, Experimental and theoretical studies of the O(³P) + C₂H₄ reaction dynamics: Collision energy dependence of branching ratios and extent of intersystem crossing, J. Chem. Phys., 137 (22), 22A532.

[51] Fu, B., Han, Y.C., Bowman, J.M., Angelucci, L., Balucani, N., Leonori, F., and Casavecchia, P., 2012, Intersystem crossing and dynamics in O(³P) + C₂H₄ multichannel reaction: Experiment validates theory, Proc. Natl. Acad. Sci. U.S.A., 109 (25), 9733–9738.

[52] Hu, W., Lendvay, G., Maiti, B., and Schatz, G.C., 2008, Trajectory surface hopping study of the O(³P) + ethylene reaction dynamics, J. Phys. Chem. A, 112 (10), 2093–2103.

[53] Reed, A.E., Curtiss, L.A., and Weinhold, F., 1988, Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint, Chem. Rev., 88 (6), 899–926.

DOI: https://doi.org/10.22146/ijc.53583