Calculations on the stable structures of ScGe5 cluster on the potential energy surface and its CO adsorption
Main Article Content
Abstract
The structures of the ScGe5 cluster were investigated by a combination of the genetic algorithm (GA) with the density functional theory (DFT) calculations. The structural parameters and relative energy of isomers were reported. These doped germanium clusters were applied to study CO adsorption by calculations with PBE functional. The adsorbed structure, the adsorption energy, and the ELF graphs of CO adsorption were also presented. Results indicated that CO molecule can be adsorbed at many positions of these clusters. The positions around the Sc atom can adsorb CO molecule better than others. The Sc-CO model of adsorption is more advantageous than the Sc-OC model. Scandium doped germanium cluster can be used to produce materials that can treat CO gas by adsorption method.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Keywords
CO, density functional theory, GA-DFT, optimization, ScGe5
References
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Atobe, J., Koyasu, K., Furuse, S., & Nakajima, A. (2012). Anion photoelectron spectroscopy of germanium and tin clusters containing a transition-or lanthanide-metal atom; MGen−(n = 8–20) and MSnn−(n = 15–17)(M = Sc–V, Y–Nb, and Lu–Ta). Phys. Chem. Chem. Phys., 14(26), 9403-9410. http://dx.doi.org/10.1039/c2cp23247b.
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Borshch, N., Pereslavtseva, N., & Kurganskii, S. (2015). Spatial structure and electron energy spectra of ScGen− (n = 6–16) clusters. Russ. J. Phys. Chem. B, 9(1), 9-18. http://dx.doi.org/10.1134/s1990793115010030.
Carolan, D. (2017). Recent advances in germanium nanocrystals: Synthesis, optical properties and applications. Prog. Mater Sci., 90(Supplement C),128-158. http://dx.doi.org/10.1016/j.pmatsci.2017.07.005.
Elsila, J., Allamandola, L. J., & Sandford, S. A. (1997). The 2140 cm−1 (4.673 microns) solid CO band: the case for interstellar O2 and N2 and the photochemistry of nonpolar interstellar ice analogs. Astrophys. J., 479(2), 818. http://dx.doi.org/10.1086/303906.
Feng, R., Glendening, E. D., & Peterson, K. A. (2020). Coupled Cluster Study of the Interactions of AnO2, AnO2(+), and AnO2(2+) (An = U, Np) with N2 and CO. Inorg. Chem., 59(7), 4753-4763. http://dx.doi.org/10.1021/acs.inorgchem.9b03759.s001.
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococcioni, M., Dabo, I., & Dal Corso, A. (2009). QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter., 21(9), 395502. http://dx.doi.org/10.1088/0953-8984/21/39/395502.
Gingerich, K. A., Sai Baba, M., Schmude Jr, R. W., & Kingcade Jr, J. E. (2000). Atomization enthalpies and enthalpies of formation of Ge3 and Ge4 by Knudsen effusion mass spectrometry. Chem. Phys., 262(1), 65-74. http://dx.doi.org/10.1016/s0301-0104(00)00271-8.
Giuseppe, L., Salvatore, M., Arcangelo, M., & Michel, D. (1993). Geometries and energies of small Gen (n = 2-6) clusters: An ab initio molecular orbital study. J. Chem. Soc., Faraday Trans., 89(16), 7. http://dx.doi.org/10.1039/ft9938902961.
Hopper, C. P., Zambrana, P. N., Goebel, U., & Wollborn, J. (2021). A brief history of carbon monoxide and its therapeutic origins. Nitric Oxide, 111-112, 45-63. http://dx.doi.org/10.1016/j.niox.2021.04.001.
Hussein, H. A., & Johnston, R. L., The DFT-genetic algorithm approach for global optimization of subnanometer bimetallic clusters, in Frontiers of Nanoscience, 2019, Elsevier, p. 145-169. http://dx.doi.org/10.1016/b978-0-08-102232-0.00004-x.
Janssens, E., Neukermans, S., Wang, X., Veldeman, N., Silverans, R., & Lievens, P. (2005). Stability patterns of transition metal doped silver clusters: Dopant-and size-dependent electron delocalization. Eur. Phys. J. D, 34(1), 23-27. http://dx.doi.org/10.1140/epjd/e2005-00106-9.
Jennings, P., & Johnston, R. (2013). Structures of small Ti-and V-doped Pt clusters: A GA-DFT study. Comput. Theor. Chem., 1021, 91-100. http://dx.doi.org/10.1016/j.comptc.2013.06.033.
Lu, T., & Chen, F. (2012). Multiwfn: a multifunctional wavefunction analyzer. J. Comput. Chem., 33(5), 580-592. http://dx.doi.org/10.1002/jcc.22885.
Lyakhov, A. O., Oganov, A. R., Stokes, H. T., & Zhu, Q. (2013). New developments in evolutionary structure prediction algorithm USPEX. Comput. Phys. Commun., 184(4), 1172-1182. http://dx.doi.org/10.1016/j.cpc.2012.12.009.
McVey, B. F. P., Prabakar, S., Gooding, J. J., & Tilley, R. D. (2017). Solution synthesis, surface passivation, optical properties, biomedical applications, and cytotoxicity of silicon and germanium nanocrystals. ChemPlusChem, 82(1), 60-73. http://dx.doi.org/10.1002/cplu.201600207.
Nagarajan, V., & Chandiramouli, R. (2017). CO and NO monitoring using pristine germanene nanosheets: DFT study. J. Mol. Liq., 234, 355-363. https://doi.org/10.1016/j.molliq.2017.03.100.
Neese, F. (2012). The ORCA program system. Wiley Interdiscip. Rev. Comput. Mol. Sci, 2(1), 73-78. https://doi.org/10.1002/wcms.81.
Pacchioni, G., & Koutecký, J. (1986). Silicon and germanium clusters. A theoretical study of their electronic structures and properties. J. Chem. Phys., 84(6), 3301-3310. http://dx.doi.org/10.1063/1.450262.
Pápai, I., & Castro, M. (1997). A density functional study of Sc2 and Sc3. Chem. Phys. Lett., 267(5), 551-556. http://dx.doi.org/10.1016/s0009-2614(97)00148-6.
Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Phys. Rev. Lett., 77(18), 3865-3868. http://dx.doi.org/10.1103/physrevlett.77.3865.
Ricks, A. M., Gagliardi, L., & Duncan, M. A. (2010). Infrared Spectroscopy of Extreme Coordination: The Carbonyls of U+ and UO2+. J. Am. Chem. Soc., 132(45), 15905-15907. http://dx.doi.org/10.1021/ja1077365.
Saha, R., Pan, S., Frenking, G., Chattaraj, P. K., & Merino, G. (2017). The strongest CO binding and the highest C-O stretching frequency. Phys. Chem. Chem. Phys., 19(3), 2286-2293. http://dx.doi.org/10.1039/c6cp06824c.
Sajjad, S., Hashmi, M. A., Mahmood, T., & Ayub, K. (2019). Density functional theory study of structural, electronic and CO adsorption properties of anionic Scn− (n = 2–13) clusters. Comput. Theor. Chem., 1163, 112511. http://dx.doi.org/10.1016/j.comptc.2019.112511.
Sajjad, S., Mahmood, T., Ludwig, R., & Ayub, K. (2018). Theoretical insight into structural and electronic properties of cationic Scn+ (n = 2-13): A benchmark study. Solid State Sci., 86, 60-68. http://dx.doi.org/10.1016/j.solidstatesciences.2018.10.002.
Shvartsburg, A. A., Liu, B., Lu, Z.-Y., Wang, C.-Z., Jarrold, M. F., & Ho, K.-M. (1999). Structures of germanium clusters: where the growth patterns of silicon and germanium clusters diverge. Phys. Rev. Lett., 83(11), 2167-2170. http://dx.doi.org/10.1103/physrevlett.83.2167.
Siracusa, R., Schaufler, A., Calabrese, V., Fuller, P. M., & Otterbein, L. E. (2021). Carbon monoxide: from poison to clinical trials. Trends Pharmacol Sci, 42(5), 329-339. http://dx.doi.org/10.1016/j.tips.2021.02.003.
Ugrinov, A., & Sevov, S. C. (2002). [Ge9Ge9Ge9]6−: A linear trimer of 27 germanium atoms. J. Am. Chem. Soc., 124(37), 10990-10991. http://dx.doi.org/10.1021/ja026679j.
Wang, J., & Han, J.-G. (2005). A computational investigation of copper-doped germanium and germanium clusters by the density-functional theory. J. Chem. Phys., 123(24), 244303. http://dx.doi.org/10.1063/1.2148949.
Wang, J., Wang, G., & Zhao, J. (2001). Structure and electronic properties of Gen (n= 2–25) clusters from density-functional theory. Phys. Rev. B, 64(20), 205411. https://doi.org/10.1103/PhysRevB.64.205411.
Wang, Y., Wu, G., Du, J., Yang, M., & Wang, J. (2012). Comparative ab initio study of CO adsorption on Scn and ScnO (n = 2-13) clusters. J. Phys. Chem. A, 116(1), 93-97. http://dx.doi.org/10.1021/jp208314g.
Zhou, S., Yang, X., Shen, Y., King, R. B., & Zhao, J. (2019). Dual transition metal doped germanium clusters for catalysis of CO oxidation. J. Alloys Compd., 806, 698-704. http://dx.doi.org/10.1016/j.jallcom.2019.07.297.
AR, O., AO, L., & M, V. (2011). How Evolutionary Crystal Structure Prediction Work and Why. Acc. Chem. Res., 44(3), 227-237. https://doi.org/10.1021/ar1001318.
AR, O., & CW, G. (2006). Crystal structure prediction using ab initio evolutionary techniques: Principles and applications. J. Chem. Phys., 124(24), 244704–. https://doi.org/10.1063/1.2210932.
Atobe, J., Koyasu, K., Furuse, S., & Nakajima, A. (2012). Anion photoelectron spectroscopy of germanium and tin clusters containing a transition-or lanthanide-metal atom; MGen−(n = 8–20) and MSnn−(n = 15–17)(M = Sc–V, Y–Nb, and Lu–Ta). Phys. Chem. Chem. Phys., 14(26), 9403-9410. http://dx.doi.org/10.1039/c2cp23247b.
Bandyopadhyay, D., & Sen, P. (2010). Density functional investigation of structure and stability of Gen and GenNi (n = 1−20) clusters: validity of the electron counting rule. J. Phys. Chem. A, 114(4), 1835-1842. http://dx.doi.org/10.1021/jp905561n.
Biswas, S., Barth, S., & Holmes, J. D. (2017). Inducing imperfections in germanium nanowires. Nano Res., 10, 1-14. http://dx.doi.org/10.1007/s12274-017-1430-9.
Borshch, N., Pereslavtseva, N., & Kurganskii, S. (2015). Spatial structure and electron energy spectra of ScGen− (n = 6–16) clusters. Russ. J. Phys. Chem. B, 9(1), 9-18. http://dx.doi.org/10.1134/s1990793115010030.
Carolan, D. (2017). Recent advances in germanium nanocrystals: Synthesis, optical properties and applications. Prog. Mater Sci., 90(Supplement C),128-158. http://dx.doi.org/10.1016/j.pmatsci.2017.07.005.
Elsila, J., Allamandola, L. J., & Sandford, S. A. (1997). The 2140 cm−1 (4.673 microns) solid CO band: the case for interstellar O2 and N2 and the photochemistry of nonpolar interstellar ice analogs. Astrophys. J., 479(2), 818. http://dx.doi.org/10.1086/303906.
Feng, R., Glendening, E. D., & Peterson, K. A. (2020). Coupled Cluster Study of the Interactions of AnO2, AnO2(+), and AnO2(2+) (An = U, Np) with N2 and CO. Inorg. Chem., 59(7), 4753-4763. http://dx.doi.org/10.1021/acs.inorgchem.9b03759.s001.
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococcioni, M., Dabo, I., & Dal Corso, A. (2009). QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter., 21(9), 395502. http://dx.doi.org/10.1088/0953-8984/21/39/395502.
Gingerich, K. A., Sai Baba, M., Schmude Jr, R. W., & Kingcade Jr, J. E. (2000). Atomization enthalpies and enthalpies of formation of Ge3 and Ge4 by Knudsen effusion mass spectrometry. Chem. Phys., 262(1), 65-74. http://dx.doi.org/10.1016/s0301-0104(00)00271-8.
Giuseppe, L., Salvatore, M., Arcangelo, M., & Michel, D. (1993). Geometries and energies of small Gen (n = 2-6) clusters: An ab initio molecular orbital study. J. Chem. Soc., Faraday Trans., 89(16), 7. http://dx.doi.org/10.1039/ft9938902961.
Hopper, C. P., Zambrana, P. N., Goebel, U., & Wollborn, J. (2021). A brief history of carbon monoxide and its therapeutic origins. Nitric Oxide, 111-112, 45-63. http://dx.doi.org/10.1016/j.niox.2021.04.001.
Hussein, H. A., & Johnston, R. L., The DFT-genetic algorithm approach for global optimization of subnanometer bimetallic clusters, in Frontiers of Nanoscience, 2019, Elsevier, p. 145-169. http://dx.doi.org/10.1016/b978-0-08-102232-0.00004-x.
Janssens, E., Neukermans, S., Wang, X., Veldeman, N., Silverans, R., & Lievens, P. (2005). Stability patterns of transition metal doped silver clusters: Dopant-and size-dependent electron delocalization. Eur. Phys. J. D, 34(1), 23-27. http://dx.doi.org/10.1140/epjd/e2005-00106-9.
Jennings, P., & Johnston, R. (2013). Structures of small Ti-and V-doped Pt clusters: A GA-DFT study. Comput. Theor. Chem., 1021, 91-100. http://dx.doi.org/10.1016/j.comptc.2013.06.033.
Lu, T., & Chen, F. (2012). Multiwfn: a multifunctional wavefunction analyzer. J. Comput. Chem., 33(5), 580-592. http://dx.doi.org/10.1002/jcc.22885.
Lyakhov, A. O., Oganov, A. R., Stokes, H. T., & Zhu, Q. (2013). New developments in evolutionary structure prediction algorithm USPEX. Comput. Phys. Commun., 184(4), 1172-1182. http://dx.doi.org/10.1016/j.cpc.2012.12.009.
McVey, B. F. P., Prabakar, S., Gooding, J. J., & Tilley, R. D. (2017). Solution synthesis, surface passivation, optical properties, biomedical applications, and cytotoxicity of silicon and germanium nanocrystals. ChemPlusChem, 82(1), 60-73. http://dx.doi.org/10.1002/cplu.201600207.
Nagarajan, V., & Chandiramouli, R. (2017). CO and NO monitoring using pristine germanene nanosheets: DFT study. J. Mol. Liq., 234, 355-363. https://doi.org/10.1016/j.molliq.2017.03.100.
Neese, F. (2012). The ORCA program system. Wiley Interdiscip. Rev. Comput. Mol. Sci, 2(1), 73-78. https://doi.org/10.1002/wcms.81.
Pacchioni, G., & Koutecký, J. (1986). Silicon and germanium clusters. A theoretical study of their electronic structures and properties. J. Chem. Phys., 84(6), 3301-3310. http://dx.doi.org/10.1063/1.450262.
Pápai, I., & Castro, M. (1997). A density functional study of Sc2 and Sc3. Chem. Phys. Lett., 267(5), 551-556. http://dx.doi.org/10.1016/s0009-2614(97)00148-6.
Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Phys. Rev. Lett., 77(18), 3865-3868. http://dx.doi.org/10.1103/physrevlett.77.3865.
Ricks, A. M., Gagliardi, L., & Duncan, M. A. (2010). Infrared Spectroscopy of Extreme Coordination: The Carbonyls of U+ and UO2+. J. Am. Chem. Soc., 132(45), 15905-15907. http://dx.doi.org/10.1021/ja1077365.
Saha, R., Pan, S., Frenking, G., Chattaraj, P. K., & Merino, G. (2017). The strongest CO binding and the highest C-O stretching frequency. Phys. Chem. Chem. Phys., 19(3), 2286-2293. http://dx.doi.org/10.1039/c6cp06824c.
Sajjad, S., Hashmi, M. A., Mahmood, T., & Ayub, K. (2019). Density functional theory study of structural, electronic and CO adsorption properties of anionic Scn− (n = 2–13) clusters. Comput. Theor. Chem., 1163, 112511. http://dx.doi.org/10.1016/j.comptc.2019.112511.
Sajjad, S., Mahmood, T., Ludwig, R., & Ayub, K. (2018). Theoretical insight into structural and electronic properties of cationic Scn+ (n = 2-13): A benchmark study. Solid State Sci., 86, 60-68. http://dx.doi.org/10.1016/j.solidstatesciences.2018.10.002.
Shvartsburg, A. A., Liu, B., Lu, Z.-Y., Wang, C.-Z., Jarrold, M. F., & Ho, K.-M. (1999). Structures of germanium clusters: where the growth patterns of silicon and germanium clusters diverge. Phys. Rev. Lett., 83(11), 2167-2170. http://dx.doi.org/10.1103/physrevlett.83.2167.
Siracusa, R., Schaufler, A., Calabrese, V., Fuller, P. M., & Otterbein, L. E. (2021). Carbon monoxide: from poison to clinical trials. Trends Pharmacol Sci, 42(5), 329-339. http://dx.doi.org/10.1016/j.tips.2021.02.003.
Ugrinov, A., & Sevov, S. C. (2002). [Ge9Ge9Ge9]6−: A linear trimer of 27 germanium atoms. J. Am. Chem. Soc., 124(37), 10990-10991. http://dx.doi.org/10.1021/ja026679j.
Wang, J., & Han, J.-G. (2005). A computational investigation of copper-doped germanium and germanium clusters by the density-functional theory. J. Chem. Phys., 123(24), 244303. http://dx.doi.org/10.1063/1.2148949.
Wang, J., Wang, G., & Zhao, J. (2001). Structure and electronic properties of Gen (n= 2–25) clusters from density-functional theory. Phys. Rev. B, 64(20), 205411. https://doi.org/10.1103/PhysRevB.64.205411.
Wang, Y., Wu, G., Du, J., Yang, M., & Wang, J. (2012). Comparative ab initio study of CO adsorption on Scn and ScnO (n = 2-13) clusters. J. Phys. Chem. A, 116(1), 93-97. http://dx.doi.org/10.1021/jp208314g.
Zhou, S., Yang, X., Shen, Y., King, R. B., & Zhao, J. (2019). Dual transition metal doped germanium clusters for catalysis of CO oxidation. J. Alloys Compd., 806, 698-704. http://dx.doi.org/10.1016/j.jallcom.2019.07.297.
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