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An investigating on the structures of Sc2Ge6 − cluster and its CO adsorption by quantum chemical calculation

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This global minimum structure has the shape of a tetragonal bipyramid having two Sc atoms at two tops of pyramids binding with one edge of Ge-Ge. The ground electronic state of the global minimum isomer is the 2B2 state in the C2v symmetry. The most stable isomer of Sc2Ge6 − has been used to study the CO adsorption. The calculated results indicate that the Sc2Ge6 − cluster has a good interaction with the CO molecule. The adsorption positions are around the Sc atom with two stable models include adsorbing the C atom and adsorbing both the C and O atoms of the CO molecule.

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Nội dung Text: An investigating on the structures of Sc2Ge6 − cluster and its CO adsorption by quantum chemical calculation

Cite this paper: Vietnam J. Chem., 2023, 61(S1), 30-36 Research article DOI: 10.1002/vjch.202200209 An investigating on the structures of Sc2Ge6− cluster and its CO adsorption by quantum chemical calculation Nguyen Minh Thao1,2,3*, Bui Tho Thanh1,2, Phan Trung Cang3, Ly Huy Hoang3, Ho Sy Linh3, Bui Van Thang3, Dang Thi Thu Lieu3, Pham Minh Xuan3, Nguyen Thi Lan Huong4, Nguyen Thi Ngoc Tram5 1 Department of Physical Chemistry, Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, 227 Nguyen Van Cu, District 5, Ho Chi Minh City 70000, Viet Nam 2 Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc City, Ho Chi Minh City 70000, Viet Nam 3 Dong Thap University, 783 Pham Huu Lau, Ward 6, Cao Lanh city, Dong Thap province 81000, Viet Nam 4 Ho Chi Minh University of Natural Resources and Environment, 236, Le Van Sy, Ward 1, Tan Binh District, Ho Chi Minh City 70000, Viet Nam 5 Tra Vinh University, 126 Nguyen Thien Thanh, Ward 5, Tra Vinh city, Tra Vinh province 87000, Viet Nam Submitted November 20, 2022; Revised March 8, 2023; Accepted March 20, 2023 Abstract The structures of the Sc2Ge6− cluster and its CO adsorption have been computational investigated. The density functional theory and couple cluster calculation are used to gether with the genetic algorithm in determine the minimum structures. This global minimum structure has the shape of a tetragonal bipyramid having two Sc atoms at two tops of pyramids binding with one edge of Ge-Ge. The ground electronic state of the global minimum isomer is the 2B2 state in the C2v symmetry. The most stable isomer of Sc2Ge6− has been used to study the CO adsorption. The calculated results indicate that the Sc2Ge6− cluster has a good interaction with the CO molecule. The adsorption positions are around the Sc atom with two stable models include adsorbing the C atom and adsorbing both the C and O atoms of the CO molecule. Scandium doped germanium cluster can be used to produce materials that can treat CO gas by adsorption method. Keywords. GA-DFT, optimization, density functional theory, Sc2Ge6− cluster, CO molecule. 1. INTRODUCTION good adsorption materials and decrease the binding of the CO bond. The dual transitional metal doped Carbon monoxide is an odorless, colorless, and germanium clusters are used to catalyst for tasteless gas with the strongest binding of two atoms transform the CO molecule to product with the and the highest value of the stretching frequency. weaken of the binding between C and O atoms. Carbon monoxide is produced as byproduct of Germanium clusters have been also investigated by combust gasoline, wood, charcoal, or other fuels. their widely application fields. Germanium material Carbon monoxide can cause illness, moreover it can can be used to produce LED devices, the solar cell lead to death when the concentration exceeds the efficiency, the electrode materials for lithium-ion threshold. it’s the toxic and therapeutic origins of batteries with the fast and stable charge-discharge carbon monoxide have been reported in many ability through many cycles. Because germanium publishes.[9,16,19] Because of the strongest bond, so it element is non-toxic and high biocompatibility, so is very difficult to perform the production process. germanium has been used to synthesis the pharmacy Many studies have been performed to to adsorb material.[5] CO gas or to transform CO gas into different The structures of germanium and scandium products by the chemical process[7,13,14,17,21,22] The clusters have been studied in many experimental and CO hydrogenation to methanol can be performed on the theoretical calculation as Gen−/0/+ (n = 2-25).[20], the Cu0-Ce3+ sites of the Cu/CeO2 catalyst.[14] Scn−/0/+ (n = 2-13), ScnO,[17,18,21] ScGen− (n = 6- Scandium, germanium clusters can be used as the 20),[3,4] M2Ge12 (M = Cr, Mn, Fe, Co and Ni).[22] In 30 Wiley Online Library © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH
25728288, 2023, S1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/vjch.202200209 by Readcube (Labtiva Inc.), Wiley Online Library on [01/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Vietnam Journal of Chemistry Nguyen Minh Thao et al. experiment, the mass spectrometric method, the TZVPP basis set. If all harmonic vibrational infrared spectroscopy method, and the photoelectric frequency values of structure are not nagative, that spectroscopy method are employed to study the structure is the stable structure which is the cluster’s structures and properties. In theoretical minimum point of the potential surface energy. If the study, clusters are successfully modelled and harmonic vibrational frequencies include the simulated by quantum chemical calculation to negative value, the structure of that cluster will be understand their structures and properties. reoptimized. A random set of coordination is built Because of the near degeneration of 3d orbitals when the harmonic vibration is performed at that in energy, the scandium doped clusters can have negative frequency. The relative energies are many structural isomers which are the same stability computed with the correctness of the zero-point in energy. In this study, we apply the GA-DFT energy (ZPE) values. The DFT calculation are method which is combined by the genetic algorithm performed by ORCA 4.2.1 code.[12] and the density functional theory calculation to perform the optimization in finding the minimum 3. RESULTS AND DISCUSSION structures of Sc2Ge6− cluster.[10] The genetic algorithm base on the natural selection of the 3.1. The structures of Sc2Ge6− cluster Charles Darwin’s evolutional theory which has advantage in dertermine the dominance individual. The structure, the point group symmetry, the In this study, the structures of Sc2Ge6− cluster are the electronic state, and the relative energies of the individuals in population. The density functional twenty-seven isomers of the Sc2Ge6− cluster are calculation can optimize the structures of cluster in displayed in figure 1 and table 1. As the calculated cheap and fast. The CO molecule adsorption by the results from the PBE/def2-TZVPP method, the Sc2Ge6− cluster is investigated on the most stable global minimum structure of the Sc2Ge6− cluster is isomers. the isomer A1. This structure with the C2v symmetry has the shape of a tetragonal bipyramid having two 2. COMPUTATIONAL METHODS Sc atoms at two tops of pyramids and two last Ge atom in oriented vertical with one Ge-Ge edge. The The geometrical structures of Sc2Ge6− cluster are ground electronic state of isomer A1 is the 2B2 state. determined by the GA-DFT calculation. Firstly, the The relative energy of isomer A2 is 0.19 eV at the random individuals are created with the specific PBE level and 0.14 eV at the ROHF-CCSD(T) level. atoms of two Sc atom and six Ge atoms. The charge Isomer A2 have a shape of the pentagonal bipyramid of structure is set of -1. The optimization process is structure with two Sc tops and one germanium atom performed by the Quantum Espresso 6.0 software.[8] capping a face of bipyramid. The isomer A3 is The low-energy structures are kept in the next higher 0.27 eV by the PBE calculation than the most generation. Some random structures, mutual stable isomer. The ground state of isomer A3 is the 2 structures, and crossing structures are formed to add Aʺ state in the Cs symmetry. to the pool of individuals. The GA-DFT process has The structures of two isomers A4 and A5 are been done until the stop condition is obtained. In both in the C2v symmetry. The ground electronic cluster of eight atoms, the stop condition is set at state of isomer A4 is the 2A1 state which is higher five of the generations which have small different in 0.30 eV than the global minimum A1 in energy. The 2 energy. The GA performance has been run by the B2 state is the ground electronic state of the isomer USPEX 10.3 code.[1,2,11] A5 with the relative energy of 0.41 eV. The relative The obtained structures are reoptimized by the energies of twenty-two isomers A6–A27 are from PBE functional.[17,21] In addition, some structures are 0.45 eV to 2.47 eV. The obtained results show that built from the different references to decrease the the scandium doped-germanium cluster has many loss of minimum structures. To save the cost of isomers with near degeneracy energy. This can be calculation, the geometrical structures are optimized explained by the 3d orbitals of the transitional metal by two basis sets of def2-SVP and def2-TZVPP, Scandium which have the equivalent energy. Many respectively. The most stable structures are used to reports indicate that the germanium cluster’s survey the CO adsorption on the surface of the structures and properties can be modified by doping Sc2Ge6− cluster in two steps with the def2-SVP and the transition metal. In our study, there are twenty- def2-TZVPP basis sets, respectively. seven isomers of the Sc2Ge6− cluster are found. To The harmonic vibrational frequencies of all assess the application of the scandium doped ofisomers are computed with the optimized germanium, some most stable isomers of Sc2Ge6− geometry by the PBE functional and the def2- cluster are used to adsorb the CO molecule by the © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH www.vjc.wiley-vch.de 31
25728288, 2023, S1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/vjch.202200209 by Readcube (Labtiva Inc.), Wiley Online Library on [01/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Vietnam Journal of Chemistry An investigating on the structures of… density functional calculation in combination of the def-TZVPP for reoptimize to obtain the better data PBE functional and the basis sets of def2-SVP for of the structure and energy. The total energies have the initial geometrical optimization, the basis sets of been corrected with the zero point energires. Figure 1: The structural isomers of Sc2Ge6− cluster The one electron detachment process from geometries. The ADE value of the isomer A1 is 2.00 the isomer A1: The adiabatic detachment energy eV from the PBE/def2-TZVPP calculation and 2.08 (ADE) of the isomer A1 is calculated by the eV from the results of the single point energy following formula ADE = Eneutral - Eanionic, where calculation at the level of ROHF-CCSD(T) with the Eneutral and Eanionic are the energy values of the neutral optimized geometries by the PBE functional and the cluster and the anionic cluster with the optimized basis set def2-TZVPP. The equivalent of ADE © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH www.vjc.wiley-vch.de 32
25728288, 2023, S1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/vjch.202200209 by Readcube (Labtiva Inc.), Wiley Online Library on [01/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Vietnam Journal of Chemistry Nguyen Minh Thao et al. values at the PBE/def2-TZVPP level and the gold different reports.[6,15,16] The harmonic vibrational standard of ROHF-CCSD(T) level show that the frequence of CO in references is 2156,[16] 2143,[15] good fitness of the used DFT level. This ADE value 2140 cm-1.[6] These results show that the PBE/def2- is the minimum energy to detach one electron from TZVPP level is a fitness method to obtain a good the highest occupied molecule orbital (HOMO) 28b2 guest of the CO adsorption on the Sc2Ge6− cluster. of the 2B2 state in C2v point group symmetry of the The adsorbed structures and their relative energies Sc2Ge6− cluster to form the Sc2Ge6 cluster at the 1A1 are presented in figure 3. These structures are at the state in C2v point group symmetry. The molecule minima position on the potential energy surface orbital 28b2 is mainly contributed from the atomic because of the negative values of all vibrational orbitals pz of the above Ge atoms. frequencies. Table 1: The structure, the point group symmetry, the electronic state, and the relative energy (RE) of the Sc2Ge6− cluster at the PBE/def2-TZVPP level Isomer Sym State RE (eV) 2 A1 C2v B2 0.00 (0.00)* 2 A2 C1 A 0.19 (0.14)* 2 A3 Cs Aʺ 0.27 2 A4 C2v A1 0.30 2 A5 C2v B2 0.41 2 A6 C1 A 0.45 2 A7 C1 A 0.46 2 A8 Cs Aʹ 0.53 2 A9 Cs Aʹ 0.59 2 A10 Cs Aʹ 0.62 2 A11 Cs Aʹ 0.65 2 A12 C1 A 0.74 2 A13 C1 A 0.90 2 A14 Cs Aʹ 0.92 2 A15 C1 A 0.97 2 A16 Cs Aʹ 1.04 2 A17 C1 A 1.07 2 A18 C1 A 1.09 2 A19 C1 A 1.15 2 A20 Cs Aʹ 1.17 2 A21 C1 A 1.22 2 A22 C2v A2 1.30 2 A23 C2 A 1.34 2 A24 C2 A 1.57 2 A25 C1 A 1.60 2 A26 Cs Aʹ 1.79 2 A27 Cs Aʺ 2.47 * calculated at the ROHF-CCSD(T)/def2-TZVPP. 3.2. The CO adsorption on the most stable isomers of the Sc2Ge6− cluster At the PBE/def2-TZVPP level, the length of the optimized C−O bond is 1.136 Å. This result is good agreement with the result at the couple cluster calculation.[7] The length of the C−O bond in references is 1.117[21] and 1.136 Å.[7] The calculated Figure 2: The one electron detachment process from frequency of the C−O bond by the PBE/def2-TZVPP singly occupied orbital of the isomers A1 of the is 2124.90 cm-1, in good accordance with the Sc2Ge6− cluster © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH www.vjc.wiley-vch.de 33
25728288, 2023, S1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/vjch.202200209 by Readcube (Labtiva Inc.), Wiley Online Library on [01/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Vietnam Journal of Chemistry An investigating on the structures of… Table 2: The bond length (dC-O) and harmonic at C atom. The second model is the CO molecule vibrational frequency (f) of the CO molecule interact with the Sc2Ge6− cluster at O atom. And the third model is the CO molecule interact with the The calculated Reference Sc2Ge6− cluster at both C and O atoms. By the Parameter PBE/def2-TZVPP obtained results from the PBE calculation, the values values structure Ad1 has the lowest relative energy. This dC-O (Å) 1.136 1.136 [7], structure is formed from the isomer A1 of the 1.117 [21] Sc2Ge6− cluster and the CO molecule. The C atom f (cm−1) 2124.90 2140 [6], creates three bonds with one Sc atom and two Ge 2143 [15], atoms. The structures of Ad3, Ad4, Ad5, Ad6, Ad8, 2156 [16] Ad9, Ad10, Ad12, and Ad14 have the same adsorption model with the Ad1. The structures of Ad2, Ad7, Ad11, and Ad13 have the interaction between the Sc2Ge6− cluster and two atoms of the CO molecule. The isomer Ad2 is less stable than the Ad1 by only 0.06 eV at the level of PBE/def2-TZVPP. The complexes of Ad2, Ad3, Ad4, and Ad5 are formed from the isomer A2 of the Sc2Ge6− cluster and the CO molecule in many different positions. The relative energies of Ad3, Ad4, and Ad5 are 0.10, 0.13, and 0.14 eV, respectively. The adsorption structures with higher relative energies are also created by the stable isomers of the Sc2Ge6− cluster with CO molecule. The fifteen structures of two models are reported in a RE range of 0.00 to 0.40 eV. As seen as, there is not the adsorption model with the O atom onto the Sc2Ge6− cluster in this energy range, their relative energies are bigger than the first model and the second model. It means that this model is not an advantage for adsorbing the CO molecule by the Sc2Ge6− cluster. The adsorption energy Eads is calculated by the formula Eadsorption = (Ecomplex – Ecluster – ECO), where Ecomplex, Ecluster, ECO are the total energy of the Sc2Ge6−−CO complex, the Sc2Ge6− cluster, and the CO molecule, respectively. The adsorption energies of the CO adsorption process on two isomers of the Sc2Ge6− cluster are presented in table 3. The adsorption energy of Ad1 and Ad2 are –1.35 eV and –1.47 eV, respectively. These values indicate that these CO adsorption on the Sc2Ge6− cluster are the chemical adsorption as the PBE/def2-TZVPP calculation. The lengths of the CO bond in the Ad1 and Ad2 complexes are 1.179 and 1.285 Å, respectively. These lengths are longer than the length of the C-O bond in the CO molecule. The harmonic vibrational frequencies of the C-O bond are decreased from 2124.90 cm-1 in the CO molecule to 1807.67 cm−1 in the Ad1 and 1295.49 Figure 3: Some optimized structures and relative cm−1 in the Ad2. The images of the electron energies (eV) of the stable Sc2Ge6−−CO complexes localization function (ELF) of the Ad1 and Ad2 are displayed in figure 4. The strength of CO binding is The CO molecule can be adsorbed onto the decreased, the Sc2Ge6− cluster can activate the bond Sc2Ge6− cluster by three models. The first model is between C and O atoms. can be used as the catalyst the CO molecule interacting with the Sc2Ge6− cluster in the chemical processes. © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH www.vjc.wiley-vch.de 34
25728288, 2023, S1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/vjch.202200209 by Readcube (Labtiva Inc.), Wiley Online Library on [01/05/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Vietnam Journal of Chemistry Nguyen Minh Thao et al. Table 3: The length of the C-O bond (dC-O), Acknowledgement. This research is supported by harmonic vibrational frequencies (f), and the the project SPD2021.01.34, Dong Thap University. adsorption energy (Eads) of CO molecule on the Sc2Ge6− cluster REFERENCES Complex dC-O (Å) f (cm-1) Eads (eV) 1. A. R. Oganov, A. O. Lyakhov, M. Valle. How Ad1 1.179 1807.67 – 1.35 evolutionary crystal structure prediction work and why, Acc. Chem. Res., 2011, 44(3), 227-237. Ad2 1.285 1295.49 – 1.47 2. O. AR, G. CW. Crystal structure prediction using ab initio evolutionary techniques: Principles and applications, J. Chem. Phys., 2006, 124(24), 244704 3. J. Atobe, K. Koyasu, S. Furuse, A. Nakajima. 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., 2012, 14(26), 9403-10. 4. N. Borshch, N. Pereslavtseva, S. Kurganskii. Spatial structure and electron energy spectra of ScGe n− (n = 6-16) clusters, Russ. J. Phys. Chem. B, 2015, 9(1), 9- 18. 5. D. Carolan. Recent advances in germanium nanocrystals: Synthesis, optical properties and applications, Prog. Mater Sci., 2017, 90, 128-158. Figure 4: The ELF images of the Sc2Ge6−−CO 6. J. Elsila, L. J. Allamandola, S. A. Sandford. The 2140 complexes (isosurface value = 0.7) cm−1 (4.673 microns) solid CO band: the case for interstellar O2 and N2 and the photochemistry of 4. CONCLUSION nonpolar interstellar ice analogs, Astrophys. J., 1997, 479(2), 818. Twenty-seven structural isomers of the Sc2Ge6− 7. R. Feng, E. D. Glendening, K. A. Peterson. Coupled cluster at the minima positions on the potential Cluster Study of the Interactions of AnO2, AnO2(+), surface energy have been reported from the GA- and AnO2(2+) (An = U, Np) with N2 and CO, Inorg. DFT calculation. The relative energies, the point Chem., 2020, 59(7), 4753-4763. group symmetry, the electronic state, the harmonic 8. P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. vibrational frequencies are calculated by the density Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso. QUANTUM functional theory calculation. The isomer A1 is the ESPRESSO: a modular and open-source software global minimum structure on the potential energy project for quantum simulations of materials, J. Phys. surface. The ground state of isomer A1 of the Condens. Matter., 2009, 21(9), 395502. Sc2Ge6− cluster is the 2B2 state in C2v point group 9. C. P. Hopper, P. N. Zambrana, U. Goebel, J. symmetry. The computed adiabatic detachment Wollborn. A brief history of carbon monoxide and its energy of one electron detachment from the 2B2 state therapeutic origins, Nitric Oxide, 2021, 111-112, 45- of the isomer A1 of the Sc2Ge6− cluster to the 1A1 63. state of the Sc2Ge6 cluster is 2.00 eV at the 10. H. A. Hussein, R. L. Johnston. The DFT-genetic PBE/def2-TZVPP level, 2.08 eV at the ROHF- algorithm approach for global optimization of CCSD(T)/def2-TZVPP calculation. Two levels have subnanometer bimetallic clusters, in Frontiers of Nanoscience, Elsevier, 145-169, 2019. high fitness in study the structure and the energy of 11. A. O. Lyakhov, A. R. Oganov, H. T. Stokes, Q. Zhu. the scandium doped germanium cluster. New developments in evolutionary structure The CO adsorption structures on the some most prediction algorithm USPEX, Comput. Phys. stable isomers of the Sc2Ge6− cluster have been Commun., 2013, 184(4), 1172-1182. studied by the PBE functional. These CO adsorption 12. F. Neese. The ORCA program system, Wiley on the Sc2Ge6− cluster are the chemical adsorption. Interdiscip. Rev. Comput. Mol. Sci, 2012, 2(1). The C-O bond is expanded, the strength of CO bond 13. D. C. Nguyen, T. K. Phung, D. V. N. Vo, T. H. Le, is decreased. It indicates that the Sc2Ge6− cluster can D. Q. Khieu, T. L. M. Pham. Unraveling the effect of active the bond of CO molecule. The Sc2Ge6− cluster Al doping on CO adsorption at ZnO(101̄0), RSC can be a candidate to form the material which can Adv., 2020, 10(67)., 40663-40672. 14. P. Ren, W. Tu, C. Wang, S. Cheng, W. Liu, Z. treat CO molecule by adsorption method. Zhang, Y. Tian, Y.-F. Han. Mechanism and sites requirement for CO hydrogenation to CH3OH over © 2023 Vietnam Academy of Science and Technology, Hanoi & Wiley-VCH GmbH www.vjc.wiley-vch.de 35
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