Master’s thesis Nanotechnology: Quantum simulation of the adsorption of toxic gases on the surface of borophene

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In this study, the adsorption configuration, adsorption energy of toxic gas molecules (CO, NO, CO2, NH3, and NO2) on B12 – borophene was investigated by first – principle calculations using three van der Waals correlation functionals: RevPBE-vdW, optPBE-vdW, and vdW-DF2.

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Nội dung Text: Master’s thesis Nanotechnology: Quantum simulation of the adsorption of toxic gases on the surface of borophene

VIETNAM NATIONAL UNIVERSITY, HANOI VIETNAM JAPAN UNIVERSITY TA THI LUONG QUANTUM SIMULATION OF THE ADSORPTION OF TOXIC GASES ON THE SURFACE OF BOROPHENE MASTER'S THESIS Hanoi, 2019
VIETNAM NATIONAL UNIVERSITY, HANOI VIETNAM JAPAN UNIVERSITY TA THI LUONG QUANTUM SIMULATION OF THE ADSORPTION OF TOXIC GASES ON THE SURFACE OF BOROPHENE MAJOR: NANOTECHNOLOGY CODE: PILOT RESEARCH SUPERVISOR: Dr. DINH VAN AN Hanoi, 2019
ACKNOWLEDGMENT First of all, I sincerely appreciate the great help of my supervisor, Dr. Dinh Van An. Thank you for all your thorough and supportive instructions, your courtesy, and your encouragement. This thesis absolutely could not be conducted well without your dedicated concerns. Second of all, I would like to show my gratefulness to Prof. Morikawa Yoshitada, my supervisor during my internship time at Osaka University. Your guidance helps me a lot to get a more profound insight into my research topic as well as research- related works. Third of all, I want to express my warm thanks to my classmate, Pham Trong Lam. Thanks to you, I got acquaintance more easily with computational material science. Thank you for your willingness to help; it means a lot to me. Last but not least, I also would like to thank Vietnam Japan University and the staff working here for their necessary supports. This research is funded by National Foundation for Science and Technology Development (NAFOSTED) under grant number 103.01-2018.315. i
CONTENTS Page Acknowledgment ......................................................................................................... i CONTENTS ................................................................................................................ii LIST OF TABLES ..................................................................................................... iv LIST OF FIGURES .................................................................................................... v LIST OF ABBREVIATIONS ...................................................................................vii ABSTRACT ............................................................................................................ viii Chapter 1 INTRODUCTION ...................................................................................... 1 1.1 Background of the research ...............................................................................1 1.2 Objectives and subjects of the research .............................................................2 1.2.1 Adsorbent material: Borophene ..................................................................2 1.2.2 Gas molecules..............................................................................................5 1.3 Toxic gases adsorption on two-dimensional materials ......................................7 1.3.1 Gas adsorption on other two-dimensional materials ...................................7 1.3.2 Adsorption application of borophene ..........................................................7 1.4 Thesis outline .....................................................................................................9 Chapter 2 THEORETICAL BASICS AND METHODS ......................................... 11 2.1 Density Functional Theory ..............................................................................11 2.2 Vasp .................................................................................................................15 2.3 Bader charge analysis ......................................................................................16 2.4 Calculation scheme ..........................................................................................17 Chapter 3 RESULTS AND DISCUSSION .............................................................. 20 3.1 Adsorbent characteristics .................................................................................20 3.2 Energetically favorable configurations ............................................................21 3.2.1 CO - borophene .........................................................................................21 3.2.2 CO2 - borophene ........................................................................................22 3.2.3 NH3 - borophene ........................................................................................23 3.2.4 NO2 - borophene ........................................................................................24 3.2.5 NO - borophene .........................................................................................25 3.3 Adsorption energy and reaction length ............................................................26 3.3.1 Adsorption energy and adsorption distance in comparison of vdW- employed functionals .........................................................................................26 3.3.2 Comparison of adsorption energy among gases ........................................30 3.4 Potential energy surface ...................................................................................31 3.5 Electronic characteristic...................................................................................36 3.6 Charge transfer characteristic ..........................................................................39 ii
3.6.1 Charge analysis of the (CO – borophene) system .....................................39 3.6.2 Charge analysis of the (CO2 - borophene) system ....................................40 3.6.3 Charge analysis of the (NO - borophene) system .....................................42 3.6.4. Charge analysis of the (NO2 - borophene) system ...................................43 3.6.5. Charge analysis of the (NH3 - borophene) system ...................................44 CONCLUSION ......................................................................................................... 47 FUTURE PLANS ..................................................................................................... 48 REFERENCES.......................................................................................................... 49 iii
LIST OF TABLES Page Table 1.1. The adsorption energy of CO, CO2, NO2, NO, and NH3 on different two- dimensional materials (eV) .........................................................................................7 Table 3.1 Calculated lattice constants of β12 borophene vs. experimental data .......20 Table 3.2. Bader charge analysis of the (CO - borophene) system ..........................39 Table 3.3. Bader charge analysis of the (CO2 – borophene) system ........................41 Table 3.4. Bader charge analysis of the (NO – borophene) system .........................42 Table 3.5. Bader charge analysis of the (NO2 – borophene) system ........................43 Table 3.6. Bader charge analysis of the (NH3 – borophene) system ........................44 iv
LIST OF FIGURES Page Figure 1.1. Elements predicted to be precursors of synthetic elemental 2D materials and their synthetic methods. ........................................................................................3 Figure 1.2 Borophene assumed to be synthesized on Ag (111) substrate (a) buckled triangular borophene, (b) β12 borophene, and (c) χ3 borophene. .................................4 Figure 2.1. The flow chart of gas absorbing calculations ........................................19 Figure 3.1 The calculated supercell of β12 boron sheet after optimization ..............20 Figure 3.2. Band structure and DOS of the unit cell of β12 borophene ....................21 Figure 3.3. Top view and side view of the most stable configurations of CO on borophene ..................................................................................................................22 Figure 3.4. Top view and side view of the most stable configurations of CO2 on borophene ..................................................................................................................23 Figure 3.5. Top view and side view of the most stable configurations of NH3 on borophene ..................................................................................................................23 Figure 3.6. Top view and side view of the most stable configurations of NO2 on borophene ..................................................................................................................24 Figure 3.7. Top view and side view of the most stable configurations of NO on borophene using 3 different vdW functionals ...........................................................25 Figure 3.8. Adsorption energy change accordingly to the distance of the (a) CO and (b) CO2 molecule and borophene in comparison ......................................................26 Figure 3.9. Adsorption energy change accordingly to the distance of the (a) NH3 and (b) NO2 molecule and borophene .......................................................................28 Figure 3.10. Adsorption energy change accordingly to the distance between NO molecule and borophene ...........................................................................................29 Figure 3.11. Comparison among gases of the shortest distance between gas molecules and substrate (dz), the distance from the massed center of gas molecules to the substrate (dc), and the adsorption energy (Ea) using optPBE-vdW functional ...................................................................................................................................30 Figure 3.12. Potential energy surface of CO adsorbed borophene ..........................31 Figure 3.13. Potential energy surface of CO2 adsorbed borophene .........................32 Figure 3.14. The projected binding energy of NH3 along the surface of borophene ...................................................................................................................................33 Figure 3.15. Potential energy surface of borophene-NO .........................................34 Figure 3.16. Potential energy surface of NO2 – borophene .....................................35 Figure 3.17. Band structure and DOS of CO - borophene .......................................36 Figure 3.18. Band structure and DOS of CO2 - borophene ......................................37 v
Figure 3.19. Band structure and DOS of NH3 - borophene .....................................38 Figure 3.20. Band structure and DOS of NO - borophene .......................................38 Figure 3.21. Band structure and DOS of NO2 - borophene .....................................39 Figure 3.22. Charge density difference after CO adsorption illustrated using isosurface (isosurface level = 0.00034).....................................................................40 Figure 3.23. Charge density difference after CO2 adsorption illustrated using isosurface (isosurface level = 0.00054)....................................................................42 Figure 3.24. Charge density difference after NO adsorption (isosurface level = 0.003).........................................................................................................................43 Figure 3.25. Charge density difference after NO2 adsorption illustrated using isosurface (isosurface level = 0.01) ...........................................................................44 Figure 3.26. Charge density difference after adsorbing NH3 (isosurface level = 0.0012).......................................................................................................................45 Figure 3.27. Charge transfer of CO, CO2, NH3, NO, NO2, and SO2 and borophene ...................................................................................................................................45 vi
LIST OF ABBREVIATIONS 2D Two-dimensional DFT Density Functional Theory VASP Vienna Ab initio Software Package vdW van der Waals DOS Density of state KS Kohn-Sham MO Molecular orbital HF Hartree-Fock 3D Three-dimensional PAW Projector Augmented Wave vii
ABSTRACT 2D materials have attracted significant research interest due to their excellent characteristics. Borophene, a new member of the 2D material family, was proven that it has a unique structure and promising properties by both empirical and theoretical studies. In this study, the adsorption configuration, adsorption energy of toxic gas molecules (CO, NO, CO2, NH3, and NO2) on 12 – borophene was investigated by first – principle calculations using three van der Waals correlation functionals: revPBE-vdW, optPBE-vdW, and vdW-DF2. The most stable configurations and diffusion possibilities of the gas molecules on the 12 – borophene surface were determined visually by using Computational DFT-based Nanoscope [10]. The nature of bonding and interaction between gas molecules and 12 – borophene are also disclosed by using the density of states analysis and Bader charge analysis. The obtained results are not only considerable for understanding gas molecules on borophene but also useful for technological applications of borophene in very near future. Keywords: 12 – borophene, DFT, adsorption, toxic gases viii
CHAPTER 1 INTRODUCTION 1.1 Background of the research In the present society, when industrialization and urbanization are increasing sharply, air pollution becomes a severe global problem. Air pollution can affect human health directly or indirectly. According to WHO (2017) data, air pollution causes 1 in 9 deaths worldwide while ambient air pollution caused 7.6% deaths over the world in 2016, which is included 4.2 million premature deaths. Air pollution might lead to stroke, lung cancer, stroke, chronic obstructive, heart disease and acute respiratory infections in children. Worldwide ambient air pollution accounts for:  29% of deaths and diseases caused by lung cancer  17% of all patients related to acute lower respiratory infection  24% of all deaths from stroke  25% of all deaths and disease from ischaemic heart disease  43% of all deaths and disease from chronic obstructive pulmonary disease [46] To decrease the impacts of air pollution, detecting pollutants is the first work needed to do before carrying out the processing procedure [46]. Hence, the things here is discovering good material which has high sensitivity and selectivity with poisonous gases, which are the significant pollutants causing air pollution, toward creating an effective sensor to detect these pollutants effectively. Overall, low-dimensional materials are potential adsorbents on gas adsorbing applications due to their high surface-to-volume ratio. Borophene is a new noble two-dimensional material, which is newly successfully synthesized [28]. Borophene is expected to have intriguing characteristics like graphene, initially expresses the outstanding mechanical and electronic performance such as existing spin gapless 1
Dirac cone, and supposed to be metallic for most phases [11]. Beside those promising properties, borophene also has a high surface-to-volume ratio due to its two-dimensional existence. Borophene thus is a promising candidate for adsorption of poisonous applications. 1.2 Objectives and subjects of the research Toward developing gas sensor materials, pollutants absorbability of potential materials is investigated by using quantum simulation. This research aims to discover a potential material for filtering or sensing toxic gases in the ambient atmosphere contributing to air pollution mitigation and enhancing community health. As follows, borophene as a potential candidate will be investigated the gas adsorbing performance. The obtained results will be not just for understanding of borophene, a new material, but for the development of gas sensor at the nanoscale as well. Hence, the research subject here is the complex system of toxic gas molecules on the adsorbent material. 1.2.1 Adsorbent material: Borophene As the rising of graphene after the Nobel Prize in Physics to Andre Geim, Konstantin Novoselov in 2010, 2D materials intrigue many interests of scientists worldwide because of their superlative physiochemical characteristics. Moreover, there still exists much unexplored promising information about such nanomaterials. 2D materials are atomically thin sheets that exhibit unique electronic, optical, and mechanical properties with remarkable potential for technological applications and a plethora of unknown fundamental science [29]. Regarding adsorption related problems, 2D materials express as one of the most prospective candidates due to their unique characteristics and its high specific surface area. With tremendous attention from researchers, more and more new 2D materials are synthesized recently. Figure 1.1 shows elements able to form synthetic elemental 2D materials and synthesis methods. 2
Figure 1.1. Elements predicted to be precursors of synthetic elemental 2D materials and their synthetic methods. Adapted from ―Synthesis and chemistry of elemental 2D materials‖, by A. J. Mannix et al., 2017, Nature Reviews Chemistry, 1, 1-15, Copyright [2017] by Macmillan Publishers Limited. Boron is one of the most complicated elements in terms of chemical bond in three- dimensional structure due to its 3-electron outer shell configuration. This fact prevents the fulfillment of the octet rule, leading to irregular ‗electron poor‘ bonding configurations [41]. A striking feature of boron is that B12 icosahedral cages occur as the building blocks in bulk boron and many boron compounds [1]. Regarding its two-dimensional existence, boron also expresses its diversity of polymorphs on different substrates or cultivation conditions [26][13]. Boron 2D sheets, which is so-called borophene, is predicted by first principle calculations to have various allotropes. Notably, these polymorphs of borophene have been predicted to be metallic or semi-metallic where boron in 3D bulk phase is an insulator. [27] Recently, borophene has been successfully synthesized by two independent groups Mannix et al. (2015) and Feng et al. (2016) by chemical vapor deposition method in ultrahigh vacuum conditions on silver (111) substrate [31][12]. From these empirical data, borophene expresses as a metallic material which agrees with 3
previous theoretical predictions. From STM images and LEED diffraction, borophene structures are confirmed to have two main polymorphs when using Ag (111) as a substrate: 12 and 3 (also called as 1/6 and 1/5, respectively) as shown in Figure 1.2. (a) (b) (c) Figure 1.2 Borophene assumed to be synthesized on Ag (111) substrate (a) buckled triangular borophene, (b) β12 borophene, and (c) χ3 borophene. Adapted from ―Two- dimensional boron: Structures, properties and applications‖, by Zhang, Penev, & Yakobson, 2017, Chemical Society Reviews, 46(22), 6746-6763. Copyright [2017] by The Royal Society of Chemistry. Initially, these existences of borophene are controversial; some argued that buckled triangular borophene was experimentally synthesized. The difference between these polymorphs is the number of vacancies in the lattice of theirs. Defining η as the vacancy density, then η is the ratio of the number of vacant sites to the total number of sites (consisting boron sites and vacancies) in one unit cell; it is the number specifying the boron-sheet type from global and local points of view. Accordingly, η is 1/6 in the β12 lattice and 1/5 in the χ3 lattice, while η is zero in buckled borophene. The complex chemical properties accompanying with various geometries, lets borophene become one of the most unpredictable two-dimensional materials. However, borophene itself has an aura of irresistible intriguing properties, which attracts great attention of both theoretical and experimental study groups, so that scientists go to an agreement that 12 and 3 are two kinds of borophene grown 4
on Ag (111) substrate such as Zhang et al. (2016) [50], Campbell et al. (2018) [8] , Peng et al. (2017) [35] and Shukla et al. (2017) [37]. In an attempt to enhance the potential of such unusual material, many experiments and theoretical works related to borophene synthesis and borophene characterization have been conducted recently. As a result, structure and many physiochemical properties are revealed gradually. In 2018, Campbell et al. found out that two types of borophene polymorph (i.e. 12 and 3) can be discrete. They claimed that 12 is dominant in lower temperature (300 C) whereas 3 is mostly formed in higher temperature (400 C) [30]. 12, as a main existence of borophene, has a flat and special symmetry structure which has an alternate arrangement between vacant boron hexagonal row and boron-centered hexagonal row in its lattice. This configuration is assumed that is similar to the honeycomb flat geometry of graphene. However, the alternating of vacant and boron-centered hexagonal even expresses more attractive unique properties. It is the first pure 2D material able to emit the visible and near – infrared light by activating its plasmon [16][4]. Under the microscope, it also exhibits undulations on the STM image, demonstrating its wavy nature [50]. Thus, it can be highly stretched once removed from the substrate, or reattached to a soft on other substrates, which facilitates favorable conditions to borophene applying on electronic devices [14]. Also, this polymorph of borophene has been depicted to have unusual mechanical, electronic, and chemical properties, materializing its potential in practical applications [50]. For example, β12 borophene appears Dirac- fermions or Dirac cones independently explored by both prediction [45] and experiment [11]. 1.2.2 Gas molecules Outdoor air pollution is the result of natural and anthropogenic sources. Adverse health consequences of air pollution can occur as a result of short- or long-term exposure [46]. Herein, this work investigates the adsorbability of 5 pollutants which 5
have strong impacts on human health as well as the earth climate, i.e., global warming. - Carbon monoxide (CO): In normal condition, CO exists as an odorless and colorless gas. At high concentration, CO has severe negative impacts on human health by decreasing the level of oxygen in the blood circulation system. High concentrations of CO are critical for both indoor and outdoor air quality, particularly in developing countries. Moreover, new evidence shows that long-term exposure to low concentrations is also associated with a wide range of health effects [46]. The main sources of ambient CO include motor vehicle exhaust and machinery that burn fossil fuels. - Carbon dioxide (CO2): is the main greenhouse gas affecting global warming and climate change. This gas is emitted from the combusting of fossil fuel originated from vehicles and industrial processes. Accompanying with industrialization and urbanization, the concentration of CO2 in the atmosphere is increasingly higher, contributing to ambient air pollution. - Nitrogen dioxide (NO2): is an important component of particulate matter and ozone depletion. This gas is a by-product of power generating and industrial processes, as well as traffic activities. It affects seriously human health i.e, symptoms of bronchitis, asthma, and lead to respiratory infections and reduced lung function and growth. Evidence also suggests that NO2 may be responsible for a large disease burden, with exposure linked to premature mortality and morbidity from cardiovascular and respiratory diseases. - Nitrogen monoxide (NO): In the atmosphere environment, NO is easily oxidized into NO2. Nitrogen oxides are produced in combustion processes, partly from nitrogen compounds in the fuel, but mostly by direct combination of atmospheric oxygen and nitrogen in flames. Nitrogen oxides are produced naturally by lightning, and also, to a small extent, by microbial processes in soils [3]. 6
- Ammonia (NH3): a colorless gas with a pungent smell. Ammonia is one of the major components of particulate matter which affects more people than any other pollutant. [46] 1.3 Toxic gases adsorption on two-dimensional materials 1.3.1 Gas adsorption on other two-dimensional materials There are many studies on gas adsorption application of 2D materials carried out previously. Overall, these materials have a good sensitivity toward CO, CO2, NO2, NO, and NH3. The adsorption energy of all those gases on buckled borophene, graphene, silicone, phosphorene, germanene, and molybdenum sulfide are summarized in Table 1.1. Table 1.1. The adsorption energy of CO, CO2, NO2, NO, and NH3 on different two- dimensional materials (eV) CO CO2 NO2 NO NH3 Buckled -1.38 -0.36 -2.32 -1.79 -1.75 borophene [24] Graphene -0.01 -0.05 -0.07 -0.03 -0.03 [22, 25] Silicene [18] -0.18 -0.04 -1.37 -0.35 -0.60 Phosphorene -0.32 -0.41 -0.60 -0.86 -0.50 [21] Germanene -0.16 -0.10 -1.08 -0.51 -0.44 [47] MoS2 [52] -0.44 -0.33 -0.14 -0.55 -0.16 1.3.2 Adsorption application of borophene Recently, there are several studies related to sensing application of borophene. However, most of them examined on buckled borophene, which is proven not to be the main existence of borophene. 7
Regarding the gas adsorption on borophene, Valadbeigi, Farrokhpour, and Tabrizchi (2015) utilized DFT with B3LYP functional to investigate the adsorption of small gases (CO, N2, H2O, O2, and NO) on B36 borophene, in which the vacancies to boron atoms ratio is 1:36. They found that the edge of B36 is more active than the area closer to the vacancy. However, this type of borophene B36 has not proved its existence in reality by experiment [44]. Liu et al. studied the adsorption of popular harmful gases (CO, CO2, NH3, NO, NO2 and CH4) on buckled borophene using first principle calculations. They found that all these gases apart from CH4 have a moderately strong interaction with buckled borophene. In particular, CO and CO2 are chemically adsorbed; NH3, NO and NO2 are chemisorbed through covalent bonds; while CH4 physically adsorbed on borophene [24]. Also doing study related to gas adsorption, Shukla et al. researched CO, NO, NO2, NH3 and CO2 adsorbability of buckled borophene monolayer using DFT and non- equilibrium Green‘s function calculations [38]. Similar to Liu‘s group, they found that all buckled borophene has a good adsorbability toward all these gases. The adsorption energy of these gases on borophene are given by -0.18, -0.35, -0.04, - 0.06, -1.37 eV for CO, NO, CO2, NH3 and NO2, respectively. These figures are considerably higher than most of the other 2D materials. Besides, in this case, CO, CO2, NO, and NO2 gas are electron withdrawers; while NH3 gas is electron acceptor. Newly, Hao, Xiaoxing, and Dachang accomplished a study to consider whether buckled borophene has a good adsorbability to SO2 gases using DFT calculation [9]. The SO2 adsorption capacity also was calculated and found to be one supercell of borophene can adsorb maximum 8 SO2 molecules. Nagarajan and Chandiramouli also carried on a theoretical study to predict the interaction of ammonia gas and buckled borophene nanosheets and nanotubes [34]. The Bader charge transfer, the density of state, adsorption configuration, and energy 8
band gap were investigated. Similar to previous studies worked on buckled borophene, this research found that both borophene nanosheets and nanotubes can be used as a chemiresistor to detect NH3 in the ambient atmosphere, in which adsorption energy is -0.951 eV and the charge transfer is 0.494 e. As for gas adsorption on β12 borophene, there exists few studies published related to this topic. Recently, Tan, Tahini, and Smith implemented theoretical research to analyze the capacity of borophene to capture as well as to release CO2 controlled via switching on/off the charges carried on boron sheets [42]. At neutral condition, β12 borophene physically adsorbs CO2 with comparatively small adsorption energy varied from -0.15 to -0.19 eV. Accordingly, the shortest distance from borophene to CO2 is 3.3 Å. This adsorption performance is neither too strong nor too weak facilitating borophene a good sensing material to CO2. Lately, Rana, Meysam, and Sahar studied to analyze how halogen atoms interact with β12 borophene. They found that the electronegativity and the mass of halogen atoms affect to the adsorption behaviors [43]. Thereby, the adsorption energy of all these halogen atoms on borophene is significant high varied from 2.71 to 5.22 eV, increase accordingly to the electronegativity. As follows, the distances from the adsorbent to F, Cl, Br, and I are 1.39, 1.99, 2.18, 2.38 Å, respectively. Also, Alvarez-Quiceno, Schleder, Marinho, and Fazzio (2017) studied the electronic and magnetic characteristics of d-block metals adsorbed on β12 borophene monolayer as well as on silver-supported β12 borophene. They found out that all these transition metals are stably adsorbed on borophene and this stability increased from 3d to 5d elements. Notably, the Ag(111) substrate shows a slight impact on borophene behaviors [2]. 1.4 Thesis outline This thesis ―Quantum simulation of the adsorption of toxic gases on the surface of borophene‖ includes three chapters 9
Chapter 1: Introduction – This chapter includes the research background indicating why we need to conduct this work. It also mentions the research objectives and the research subjects. As a result, the scope of work will be made clear. Chapter 2: Theoretical basics and methods – This chapter presents logically and systematically the brief of theoretical basics related to this work, which are DFT, VASP, and Bader charge analysis. Thereby, the proper foundation of knowledge is built toward being able to understand this work. Also, the framework towards solving the problems of this thesis, the specific utilized method and tools are mentioned carefully in this section. Chapter 3: Results and discussion – This chapter presents and illustrates significant results of this work. The detailed discussions of the adsorption mechanism are given. 10