Molecular and dissociative adsorption of tetrachlorodibenzodioxin on M-doped graphenes (M = B, Al, N, P): pure DFT and DFT + VdW calculations

Journal of Molecular Modeling - Tập 26 - Trang 1-12 - 2020
R. Behjatmanesh-Ardakani1,2, A. Heydari1
1Department of Chemistry, Payame Noor University, Tehran, Iran
2Research Center of Environmental Chemistry, Payame Noor University, Ardakan, Iran

Tóm tắt

Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts in adsorbing and dissociating TCDD. P-type and N-type charge carrier effects on the adsorption process are modeled by doping of B/Al and N/P atoms in the graphene. Al-doped graphene, with − 1.27 eV adsorption energy, has the highest possibility to adsorb TCDD. P-type dopants have higher interactions with TCDD in comparing with N-type dopants. Introducing positive and negative charges on the studied complexes shows that in all complexes, the driving force of complexation is π-π stacking except for the Al-doped graphene. Dissociative adsorption studies show that unlike literature data, chlorine atoms on the surface of studied catalysts are not dissociated from TCDD, and instead, C–O bonds in TCDD are dissociated symmetrically and asymmetrically. Data show that Al-doped graphene is the best catalyst for symmetrical dissociation, and pure graphene is the best one for asymmetrical dissociation of TCDD.

Tài liệu tham khảo

Chang RR, Jarman WM, King CC, Esperanza CC, Stephens RD (1990) Bioaccumulation of PCDDs and PCDFs in food animals III: a rapid cleanup of biological materials using reverse phase adsorbent columns. Chemosphere 20(7):881–886. https://doi.org/10.1016/0045-6535(90)90196-Z D. Mackay, WYS, K.C. Ma, Polynuclear aromatic hydrocarbons, (1992) Polynuclear aromatic hydrocarbons, polychlorinated dioxins and dibenzofurans Allinson G, Ueoka M, Morita M (1994) Effect of dietary 1,3,6,8-tetrachlorodibenzo-p-dioxin on the Japanese freshwater fish Oryzias latipes (Medaka) and aquatic snail Indoplanorbis exustus (Indohiramakigai). Chemosphere 28(7):1369–1383. https://doi.org/10.1016/0045-6535(94)90079-5 Marple L, Wasierski T, Throop L (1992) In vitro penetration of 2,3,7,8-tetrachlorodibenzo-p-dioxin through intact human skin. Chemosphere 25(7):1077–1084. https://doi.org/10.1016/0045-6535(92)90110-D Wang L, Kumar M, Deng Q, Wang X, Liu M, Gong Z, Zhang S, Ma X, Xu-Monette ZY, Xiao M, Yi Q, Young KH, Ramos KS, Li Y (2019) 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) induces peripheral blood abnormalities and plasma cell neoplasms resembling multiple myeloma in mice. Cancer Lett 440-441:135–144. https://doi.org/10.1016/j.canlet.2018.10.009 Beatty PW, Vaughn WK, Neal RA (1978) Effect of alteration of rat hepatic mixed-function oxidase (MFO) activity on the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Toxicol Appl Pharmacol 45(2):513–519. https://doi.org/10.1016/0041-008X(78)90113-8 Liwo A (2018) Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: from bioinformatics to molecular quantum mechanics. Springer International Publishing Zhou Q, Su X, Yong Y, Ju W, Fu Z, Li X (2018) Adsorption of 2, 3, 7, 8-tetrachlorodibenzao-p-dioxin (TCDD) on graphane decorated with Ni and Cu: a DFT study. Vacuum 149:53–59. https://doi.org/10.1016/j.vacuum.2017.12.016 Atkinson JD, Hung PC, Zhang Z, Chang MB, Yan Z, Rood MJ (2015) Adsorption and destruction of PCDD/Fs using surface-functionalized activated carbons. Chemosphere 118:136–142. https://doi.org/10.1016/j.chemosphere.2014.07.055 Wang R, Zhang D, Liu C (2017) DFT study of the adsorption of 2,3,7,8-tetrachlorodibenzo-p-dioxin on pristine and Ni-doped boron nitride nanotubes. Chemosphere 168:18–24. https://doi.org/10.1016/j.chemosphere.2016.10.050 Zhao S, Ma X, Pang Q, Sun H, Wang G (2014) Dissociative adsorption of 2,3,7,8-TCDD on the surfaces of typical metal oxides: a first-principles density functional theory study. Phys Chem Chem Phys 16(12):5553–5562. https://doi.org/10.1039/C3CP55048F Fagan SB, Santos EJG, Souza Filho AG, Mendes Filho J, Fazzio A (2007) Ab initio study of 2,3,7,8-tetrachlorinated dibenzo-p-dioxin adsorption on single wall carbon nanotubes. Chem Phys Lett 437(1):79–82. https://doi.org/10.1016/j.cplett.2007.01.071 Zhou Q, Yong Y, Ju W, Su X, Li X, Wang C, Fu Z (2018) DFT study of the adsorption of 2, 3, 7, 8-tetrachlorodibenzofuran (TCDF) on vacancy-defected graphene doped with Mn and Fe. Curr Appl Phys 18(1):61–67. https://doi.org/10.1016/j.cap.2017.10.011 Zhan M-X, Yu M-F, Zhang G, Chen T, Li X-D, Buekens A (2018) Low temperature degradation of polychlorinated dibenzo-p-dioxins and dibenzofurans over a VOx-CeOx/TiO2 catalyst with addition of ozone. Waste Manag 76:555–565. https://doi.org/10.1016/j.wasman.2018.02.049 H-p Z, J-l H, Wang Y, P-p T, Y-p Z, Lin X-y, Liu C, Tang Y (2017) Adsorption behavior of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin on pristine and doped black phosphorene: a DFT study. Chemosphere 185:509–517. https://doi.org/10.1016/j.chemosphere.2017.06.120 Izakmehri Z, Ganji MD, Ardjmand M (2017) Adsorption of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) on pristine, defected and Al-doped carbon nanotube: a dispersion corrected DFT study. Vacuum 136:51–59. https://doi.org/10.1016/j.vacuum.2016.11.025 Wang Q, Ma W, Tong Q, Du G, Wang J, Zhang M, Jiang H, Yang H, Liu Y, Cheng M (2017) Graphene oxide foam supported titanium(IV): recoverable heterogeneous catalyst for efficient, selective oxidation of arylalkyl sulfides to sulfoxides under mild conditions. Sci Rep 7(1):7209. https://doi.org/10.1038/s41598-017-07590-1 Son J, Lee S, Kim SJ, Park BC, Lee H-K, Kim S, Kim JH, Hong BH, Hong J (2016) Hydrogenated monolayer graphene with reversible and tunable wide band gap and its field-effect transistor. Nat Commun 7:13261. https://doi.org/10.1038/ncomms13261 https://www.nature.com/articles/ncomms13261#supplementary-information Rodriguez-Lopez PaK-K, Wilton J. M. and Dalvit, Diego A. R. and Woods, Lilia M. (2018) Nonlocal optical response in topological phase transitions in the graphene family. Phys Rev Materials 2 (American Physical Society):014003. doi:https://doi.org/10.1103/PhysRevMaterials.2.014003 Zeng G, Li W, Ci S, Jia J, Wen Z (2016) Highly dispersed NiO nanoparticles decorating graphene nanosheets for non-enzymatic glucose sensor and biofuel cell. Sci Rep 6:36454. https://doi.org/10.1038/srep36454 https://www.nature.com/articles/srep36454#supplementary-information Hesabi M, Behjatmanesh-Ardakani R (2018) Investigation of carboxylation of carbon nanotube in the adsorption of anti-cancer drug: a theoretical approach. Appl Surf Sci 427:112–125. https://doi.org/10.1016/j.apsusc.2017.08.044 Hesabi M, Behjatmanesh-Ardakani R (2017) Interaction between anti-cancer drug hydroxycarbamide and boron nitride nanotube: a long-range corrected DFT study. Computational and Theoretical Chemistry 1117:61–80. https://doi.org/10.1016/j.comptc.2017.07.018 Behjatmanesh-Ardakani R (2018) Periodic and non-periodic DFT modeling of CO reduction on the surface of Ni-doped graphene nanosheet. Molecular Catalysis 455:239–249. https://doi.org/10.1016/j.mcat.2018.06.008 Yavari F, Koratkar N (2012) Graphene-based chemical sensors. The Journal of Physical Chemistry Letters 3(13):1746–1753. https://doi.org/10.1021/jz300358t Damte JY, S-l L, Leggesse EG, Jiang JC (2018) Methanol decomposition reactions over a boron-doped graphene supported Ru–Pt catalyst. Phys Chem Chem Phys 20(14):9355–9363. https://doi.org/10.1039/C7CP07618E Wang Y, Shen Y, Zhu S (2017) N-doped graphene as a potential catalyst for the direct catalytic decomposition of NO. Catal Commun 94:29–32. https://doi.org/10.1016/j.catcom.2017.02.003 Suzuki A, Selvam P, Kusagaya T, Takami S, Kubo M, Imamura A, Miyamoto A (2005) Chemical reaction dynamics of PeCB and TCDD decomposition: a tight-binding quantum chemical molecular dynamics study with first-principles parameterization. Int J Quantum Chem 102(3):318–327. https://doi.org/10.1002/qua.20396 Blum V, Gehrke R, Hanke F, Havu P, Havu V, Ren X, Reuter K, Scheffler M (2009) Ab initio molecular simulations with numeric atom-centered orbitals. Comput Phys Commun 180(11):2175–2196. https://doi.org/10.1016/j.cpc.2009.06.022 Havu V, Blum V, Havu P, Scheffler M (2009) Efficient O(N) integration for all-electron electronic structure calculation using numeric basis functions. J Comput Phys 228(22):8367–8379. https://doi.org/10.1016/j.jcp.2009.08.008 Yu VW-Z, Corsetti F, García A, Huhn WP, Jacquelin M, Jia W, Lange B, Lin L, Lu J, Mi W, Seifitokaldani A, Vázquez-Mayagoitia Á, Yang C, Yang H, Blum V (2018) ELSI: a unified software interface for Kohn–Sham electronic structure solvers. Comput Phys Commun 222:267–285. https://doi.org/10.1016/j.cpc.2017.09.007 Marek A, Blum V, Johanni R, Havu V, Lang B, Auckenthaler T, Heinecke A, Bungartz HJ, Lederer H (2014) The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science. J Phys Condens Matter 26(21):213201. https://doi.org/10.1088/0953-8984/26/21/213201 Hammer B, Hansen LB, Nørskov JK (1999) Improved adsorption energetics within density-functional theory using revised Perdew-Burke-Ernzerhof functionals. Phys Rev B 59(11):7413–7421. https://doi.org/10.1103/PhysRevB.59.7413 Hauschild A, Karki K, Cowie BCC, Rohlfing M, Tautz FS, Sokolowski M (2005) Molecular distortions and chemical bonding of a large $\ensuremath{\pi}$-conjugated molecule on a metal surface. Phys Rev Lett 94 (3):036106. doi:https://doi.org/10.1103/PhysRevLett.94.036106 Rurali R, Lorente N, Ordejón P (2005) Comment on ``molecular distortions and chemical bonding of a large $\ensuremath{\pi}$-conjugated molecule on a metal surface”. Phys Rev Lett 95 (20):209601. doi:https://doi.org/10.1103/PhysRevLett.95.209601 Tkatchenko A, Scheffler M (2009) Accurate molecular Van Der Waals interactions from ground-state electron density and free-atom reference data. Phys Rev Lett 102(7):073005. https://doi.org/10.1103/PhysRevLett.102.073005 Monkhorst HJ, Pack JD (1976) Special points for Brillouin-zone integrations. Phys Rev B 13(12):5188–5192. https://doi.org/10.1103/PhysRevB.13.5188 Elvins OC, Nash AW (1926) The reduction of carbon monoxide. Nature 118:154 Momma K, Izumi F (2011) VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. J Appl Crystallogr 44(6):1272–1276. https://doi.org/10.1107/S0021889811038970 Neese F (2012) The ORCA program system. WIREs Computational Molecular Science 2(1):73–78. https://doi.org/10.1002/wcms.81 Weigend F, Ahlrichs R (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys Chem Chem Phys 7(18):3297–3305. https://doi.org/10.1039/B508541A Weigend F (2006) Accurate Coulomb-fitting basis sets for H to Rn. Phys Chem Chem Phys 8(9):1057–1065. https://doi.org/10.1039/B515623H Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33(5):580–592. https://doi.org/10.1002/jcc.22885 Lu T, Chen F (2012) Quantitative analysis of molecular surface based on improved marching tetrahedra algorithm. J Mol Graph Model 38:314–323. https://doi.org/10.1016/j.jmgm.2012.07.004 Ehrlich S, Moellmann J, Grimme S (2013) Dispersion-corrected density functional theory for aromatic interactions in complex systems. Acc Chem Res 46(4):916–926. https://doi.org/10.1021/ar3000844 Montejo-Alvaro F, Oliva J, Herrera-Trejo M, Hdz-García HM, Mtz-Enriquez AI (2019) DFT study of small gas molecules adsorbed on undoped and N-, Si-, B-, and Al-doped graphene quantum dots. Theor Chem Accounts 138(3):37. https://doi.org/10.1007/s00214-019-2428-z Goudarzi M, Parhizgar SS, Beheshtian J (2019) Electronic and optical properties of vacancy and B, N, O and F doped graphene: DFT study. Opto-Electronics Review 27(2):130–136. https://doi.org/10.1016/j.opelre.2019.05.002 Esrafili MD (2019) Electric field assisted activation of CO2 over P-doped graphene: a DFT study. J Mol Graph Model 90:192–198. https://doi.org/10.1016/j.jmgm.2019.05.008 Deng D, Pan X, Yu L, Cui Y, Jiang Y, Qi J, Li W-X, Fu Q, Ma X, Xue Q, Sun G, Bao X (2011) Toward N-doped graphene via solvothermal synthesis. Chem Mater 23(5):1188–1193. https://doi.org/10.1021/cm102666r Mahdavian L (2018) DFT study to reduce TCDD by B12N12 nano-cage: a comparison of calculating spectroscopic properties with NMR and NBO. Polycycl Aromat Compd 38(5):445–456. https://doi.org/10.1080/10406638.2016.1238399 Mahdavian L (2018) Computational investigation of 2,3,7,8-tetrachlorodibenzo-para-dioxin (TCDD) adsorption on boron nitride-nanotube (BNNT). Polycycl Aromat Compd:1–8. https://doi.org/10.1080/10406638.2018.1484777 Politzer P, Murray JS, Clark T (2015) Mathematical modeling and physical reality in noncovalent interactions. J Mol Model 21(3):52. https://doi.org/10.1007/s00894-015-2585-5 Sinnokrot MO, Sherrill CD (2004) Substituent effects in π−π interactions: sandwich and T-shaped configurations. J Am Chem Soc 126(24):7690–7697. https://doi.org/10.1021/ja049434a Williams G, Kamat PV (2009) Graphene−semiconductor nanocomposites: excited-state interactions between ZnO nanoparticles and graphene oxide. Langmuir 25(24):13869–13873. https://doi.org/10.1021/la900905h Li X, Shen R, Ma S, Chen X, Xie J (2018) Graphene-based heterojunction photocatalysts. Appl Surf Sci 430:53–107. https://doi.org/10.1016/j.apsusc.2017.08.194 Xie C, Wang Y, Zhang Z-X, Wang D, Luo L-B (2018) Graphene/semiconductor hybrid heterostructures for optoelectronic device applications. Nano Today 19:41–83. https://doi.org/10.1016/j.nantod.2018.02.009 Kao CM, Wu MJ (2000) Enhanced TCDD degradation by Fenton’s reagent preoxidation. J Hazard Mater 74(3):197–211. https://doi.org/10.1016/S0304-3894(00)00161-8