為了開發高性能的儲氣材料，了解氣體與吸附材料間之相互作用是必須的。本理論
計算研究深究探討了 MOF-74-Ni 對於甲烷儲存能力的吸附機制。在此我們使用凡
德瓦校正之密度泛函理論（ DFT）並在 MOF-74-Ni 的單孔中吸附了 15 個甲烷分子。
在 MOF-74-Ni中不同吸附位點（包括 iSBU（ NiO5）， L（苯接頭）和 P（孔中心）
位點）的逐步計算中，吸附能在-0.3794eV 至-0.1982eV 之間變化。同時我們也觀察
到吸附能量呈現線性趨勢。計算表明，隨著系統的甲烷數達到完全飽和，甲烷在這
些位置上的吸附強度差異開始減小。接著我們通過使用不同的電子分析探討當增加
甲烷負載量時，甲烷分子與 MOF-74-Ni 吸附材料之間的電子結構變化。其中，
partial crystal orbital Hamiltonian population（ PCOHP）分析預測 fermi-level 周圍的骨
架狀態本質上是反鍵合的，暗示即使在電子損失後骨架也將保持穩定。此外基於
DDEC6 的淨電荷分析表明甲烷在 iSBU 和 L 位置上都獲得電子。 Electron density
difference（ EDD）圖顯示甲烷和 L位點之間的電子增加，並且 partial density of state
（ PDOS）分析顯示了甲烷和 iSBU 位置上的氧之間的密度重疊。這些結果分別揭
示了甲烷和 L 以及 iSBU 位置之間的 C-H…pi 和 C-H…O 相互作用。此外部分
DDEC6 結果也顯示甲烷在 iSBU 位置會失去電子， 說明甲烷和 iSBU 位置之間存有
些許 agostic 相互作用。 這些甲烷的增益和失去電子將構築一個電子轉移循環，這
也導致了甲烷吸附的協同效應。這種協同作用可以促進吸附在 MOF-74-Ni 上的甲
烷數量增加。 在此研究的第二部分中， 我們在 MOF-74-Ni 中參入銥金屬。 我們觀
察到銥金屬的聚集比銥金屬在 MOF-74-Ni 中分散略微有利， 其能量差為 0.3184 eV。
相對於純 MOF-74-Ni 上的一個甲烷的吸附能，在成簇的 Ir / MOF-74-Ni 上觀察到甲
烷吸附能會增加，而在分散的 Ir / MOF-74-Ni 上會觀察到其減小。 此研究提供了有
趣的結果，可用於未來的多孔材料開發和催化研究。 此外了解氣體分子與吸附材料
間的相互作用亦將有助於多孔材料性能的改進。

To develop a high-performance gas storage material, an understanding of host-guest and
host-host interactions is essential. This theoretical study highlights the key mechanism
behind the methane storage capacity of MOF-74-Ni. We performed stepwise Van der Waals
corrected density functional theory (DFT) calculations and were able to adsorb fifteen CH4 molecules in a single pore of a unit cell. We identified three adsorption sites, iSBU (NiO5), L (benzene linker), and the P (pore center) site. The adsorption energy at these sites varied between -0.3794 eV to -0.2489 eV with a linear trend of adsorption energy. The calculation showed as the system reaches complete saturation the difference in adsorptive strength of those sites starts to diminish. Variation in adsorbate-adsorbent electronic properties as a function of increased CH4 loading was monitored by using different electronic analysis. Partial crystal orbital Hamiltonian population (PCOHP) analysis predicted that states of framework around fermi level are antibonding in nature, hinting that the framework will remain stable even after electron loss. DDEC6 based net charge analysis demonstrated an interplay of charge gain/loss by CH4 molecules as system approaches to complete saturation. This charge gain/loss makes an electron transfer cycle which results in the cooperative interaction between host-guest and host-host. This cooperative effects can facilitate a high methane storage capacity by MOF-74-Ni. Electron density difference (EDD) maps showed the electrons accumulation between CH4 and framework sites which increases as the CH4 loading increases. Partial density of state (PDOS) analysis displayed the small overlap of host-guest states. The results also indicated the C-H…pi type of interaction between CH4 and L site. In the second part of this study, iridium was introduced in MOF-74-Ni. Clustering of iridium was observed to be slightly favorable by 0.3 eV than the dispersion in the framework. Relative to one CH4 adsorption energy on pure MOF-74-Ni, an increase in adsorption energy was observed on the clustered as well as dispersed Ir/MOF-74-Ni, where dispersed Ir/MOF-74-Ni showing the highest CH4 adsorption energy i.e. -0.4237 eV. This study provides interesting results which can be useful for future porous material development and catalysis studies. Understanding of host-guest interactions will be beneficial in finding improvements in the performance of porous material.

Abstract i
摘要 iii
Contents iv
Index of Tables vi
Index of Figure vii
Chapter 1 – Introduction 1
1.1 Metal Organic Framework 3
1.2 Literature Review 4
1.2.1 Experimental Studies 4
1.2.2 Theoretical Studies 7
1.2.3 Dispersed Heavy Metals in MOFs 11
Chapter 2 – Structure and Computational Detail 14
2.1 Computational Detail 14
2.2 Crystal Structure 15
2.2.1 Characterization 17
2.2.2 Partial crystal orbital hamiltonian population Analysis 20
Chapter 3 – Methane Storage 22
3.1. Flexibility of MOF-74-Ni 23
3.2 Adsorption 26
3.3 Net Charge Analysis 35
3.4 Electron Density Difference (EDD) Analysis 39
3.5 Density of State Analysis 41
3.5.1 Cooperative Interactions 43
3.5.2 CH4-Pi Interactions 44
Chapter 4 – Iridium at MOF-74-Ni 46
4.1 Site Selectivity 48
4.2 Cluster Formation 49
4.2 Methane Adsorption 52
Summary and Future work 54
Chapter 5 References 56

1. Stassen, I.; Burtch, N.; Talin, A.; Falcaro, P.; Allendorf, M.; Ameloot, R., An Updated Roadmap for the Integration of Metal–Organic Frameworks with Electronic Devices and Chemical Sensors. Chemical Society Reviews 2017, 46, 3185-3241.
2. Lin, L.-C., et al., In Silico Screening of Carbon-Capture Materials. Nature Materials 2012, 11, 633.
3. Zhou, H.-C.; Long, J. R.; Yaghi, O. M., Introduction to Metal–Organic Frameworks. Chemical Reviews 2012, 112, 673-674.
4. Furukawa, H.; Cordova, K. E.; O’Keeffe, M.; Yaghi, O. M., The Chemistry and Applications of Metal-Organic Frameworks. Science 2013, 341, 1230444.
5. Suh, M. P.; Park, H. J.; Prasad, T. K.; Lim, D.-W., Hydrogen Storage in Metal–Organic Frameworks. Chemical Reviews 2012, 112, 782-835.
6. Dincǎ, M.; Dailly, A.; Liu, Y.; Brown, C. M.; Neumann, D. A.; Long, J. R., Hydrogen Storage in a Microporous Metal−Organic Framework with Exposed Mn2+ Coordination Sites. Journal of the American Chemical Society 2006, 128, 16876-16883.
7. Poloni, R.; Lee, K.; Berger, R. F.; Smit, B.; Neaton, J. B., Understanding Trends in Co2 Adsorption in Metal–Organic Frameworks with Open-Metal Sites. The Journal of Physical Chemistry Letters 2014, 5, 861-865.
8. Mason, J. A.; Sumida, K.; Herm, Z. R.; Krishna, R.; Long, J. R., Evaluating Metal–Organic Frameworks for Post-Combustion Carbon Dioxide Capture Via Temperature Swing Adsorption. Energy & Environmental Science 2011, 4, 3030-3040.
9. Makal, T. A.; Li, J.-R.; Lu, W.; Zhou, H.-C., Methane Storage in Advanced Porous Materials. Chemical Society Reviews 2012, 41, 7761-7779.
10. Peng, Y.; Krungleviciute, V.; Eryazici, I.; Hupp, J. T.; Farha, O. K.; Yildirim, T., Methane Storage in Metal–Organic Frameworks: Current Records, Surprise Findings, and Challenges. Journal of the American Chemical Society 2013, 135, 11887-11894.
11. Britt, D.; Tranchemontagne, D.; Yaghi, O. M., Metal-Organic Frameworks with High Capacity and Selectivity for Harmful Gases. Proceedings of the National Academy of Sciences 2008, 105, 11623-11627.
12. Dietzel, P. D. C.; Besikiotis, V.; Blom, R., Application of Metal–Organic Frameworks with Coordinatively Unsaturated Metal Sites in Storage and Separation of Methane and Carbon Dioxide. Journal of Materials Chemistry 2009, 19, 7362-7370.
13. Valenzano, L.; Civalleri, B.; Chavan, S.; Palomino, G. T.; Areán, C. O.; Bordiga, S., Computational and Experimental Studies on the Adsorption of Co, N2, and Co2 on Mg-Mof-74. The Journal of Physical Chemistry C 2010, 114, 11185-11191.
14. Yazaydın, A. Ö., et al., Screening of Metal−Organic Frameworks for Carbon Dioxide Capture from Flue Gas Using a Combined Experimental and Modeling Approach. Journal of the American Chemical Society 2009, 131, 18198-18199.
15. Yu, D.; Yazaydin, A. O.; Lane, J. R.; Dietzel, P. D. C.; Snurr, R. Q., A Combined Experimental and Quantum Chemical Study of Co2 Adsorption in the Metal–Organic Framework Cpo-27 with Different Metals. Chemical Science 2013, 4, 3544-3556.
16. Dietzel, P. D.; Blom, R.; Fjellvåg, H., Base‐Induced Formation of Two Magnesium Metal‐Organic Framework Compounds with a Bifunctional Tetratopic Ligand. European Journal of Inorganic Chemistry 2008, 2008, 3624-3632.
17. Zhou, W.; Wu, H.; Yildirim, T., Enhanced H2 Adsorption in Isostructural Metal−Organic Frameworks with Open Metal Sites: Strong Dependence of the Binding Strength on Metal Ions. Journal of the American Chemical Society 2008, 130, 15268-15269.
18. Queen, W. L.; Bloch, E. D.; Brown, C. M.; Hudson, M. R.; Mason, J. A.; Murray, L. J.; Ramirez-Cuesta, A. J.; Peterson, V. K.; Long, J. R., Hydrogen Adsorption in the Metal–Organic Frameworks Fe2(Dobdc) and Fe2(O2)(Dobdc). Dalton Transactions 2012, 41, 4180-4187.
19. Dietzel, P. D.; Morita, Y.; Blom, R.; Fjellvåg, H., An in Situ High‐Temperature Single‐Crystal Investigation of a Dehydrated Metal–Organic Framework Compound and Field‐Induced Magnetization of One‐Dimensional Metal–Oxygen Chains. Angewandte Chemie International Edition 2005, 44, 6354-6358.
20. Dietzel, P. D. C.; Panella, B.; Hirscher, M.; Blom, R.; Fjellvåg, H., Hydrogen Adsorption in a Nickel Based Coordination Polymer with Open Metal Sites in the Cylindrical Cavities of the Desolvated Framework. Chemical Communications 2006, 959-961.
21. Sanz, R.; Martínez, F.; Orcajo, G.; Wojtas, L.; Briones, D., Synthesis of a Honeycomb-Like Cu-Based Metal–Organic Framework and Its Carbon Dioxide Adsorption Behaviour. Dalton Transactions 2013, 42, 2392-2398.
22. Rosi, N. L.; Kim, J.; Eddaoudi, M.; Chen, B.; O'Keeffe, M.; Yaghi, O. M., Rod Packings and Metal−Organic Frameworks Constructed from Rod-Shaped Secondary Building Units. Journal of the American Chemical Society 2005, 127, 1504-1518.
23. Wu, H.; Zhou, W.; Yildirim, T., High-Capacity Methane Storage in Metal−Organic Frameworks M2(Dhtp): The Important Role of Open Metal Sites. Journal of the American Chemical Society 2009, 131, 4995-5000.
24. Wu, H.; Zhou, W.; Yildirim, T., Methane Sorption in Nanoporous Metal−Organic Frameworks and First-Order Phase Transition of Confined Methane. The Journal of Physical Chemistry C 2009, 113, 3029-3035.
25. Lee, K.; Howe, J. D.; Lin, L.-C.; Smit, B.; Neaton, J. B., Small-Molecule Adsorption in Open-Site Metal–Organic Frameworks: A Systematic Density Functional Theory Study for Rational Design. Chemistry of Materials 2015, 27, 668-678.
26. Sillar, K.; Sauer, J., Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal–Organic Frameworks: The Effect of Lateral Interactions for Methane/Cpo-27-Mg. Journal of the American Chemical Society 2012, 134, 18354-18365.
27. Becker, T. M.; Heinen, J.; Dubbeldam, D.; Lin, L.-C.; Vlugt, T. J. H., Polarizable Force Fields for Co2 and Ch4 Adsorption in M-Mof-74. The Journal of Physical Chemistry C 2017, 121, 4659-4673.
28. Hyeon, S.; Kim, Y.-C.; Kim, J., Computational Prediction of High Methane Storage Capacity in V-Mof-74. Physical Chemistry Chemical Physics 2017, 19, 21132-21139.
29. Tan, K.; Zuluaga, S.; Gong, Q.; Gao, Y.; Nijem, N.; Li, J.; Thonhauser, T.; Chabal, Y. J., Competitive Coadsorption of Co2 with H2o, Nh3, So2, No, No2, N2, O2, and Ch4 in M-Mof-74 (M = Mg, Co, Ni): The Role of Hydrogen Bonding. Chemistry of Materials 2015, 27, 2203-2217.
30. Peng, Y.; Huang, H.; Zhang, Y.; Kang, C.; Chen, S.; Song, L.; Liu, D.; Zhong, C., A Versatile Mof-Based Trap for Heavy Metal Ion Capture and Dispersion. Nature Communications 2018, 9, 187.
31. Kresse, G.; Furthmüller, J., Efficient Iterative Schemes for Ab Initio Total-Energy Calculations Using a Plane-Wave Basis Set. Physical Review B 1996, 54, 11169-11186.
32. Kresse, G.; Furthmüller, J., Efficiency of Ab-Initio Total Energy Calculations for Metals and Semiconductors Using a Plane-Wave Basis Set. Computational materials science 1996, 6, 15-50.
33. Perdew, J. P.; Burke, K.; Ernzerhof, M., Generalized Gradient Approximation Made Simple. Physical Review Letters 1996, 77, 3865-3868.
34. Kresse, G.; Joubert, D., From Ultrasoft Pseudopotentials to the Projector Augmented-Wave Method. Physical Review B 1999, 59, 1758-1775.
35. Blöchl, P. E., Projector Augmented-Wave Method. Physical Review B 1994, 50, 17953-17979.
36. Monkhorst, H. J.; Pack, J. D., Special Points for Brillouin-Zone Integrations. Physical Review B 1976, 13, 5188-5192.
37. Poloni, R.; Smit, B.; Neaton, J. B., Co2 Capture by Metal–Organic Frameworks with Van Der Waals Density Functionals. The Journal of Physical Chemistry A 2012, 116, 4957-4964.
38. Kundu, A.; Piccini, G.; Sillar, K.; Sauer, J., Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal–Organic Frameworks. Journal of the American Chemical Society 2016, 138, 14047-14056.
39. Jiří, K.; David, R. B.; Angelos, M., Chemical Accuracy for the Van Der Waals Density Functional. Journal of Physics: Condensed Matter 2010, 22, 022201.
40. Klimeš, J.; Bowler, D. R.; Michaelides, A., Van Der Waals Density Functionals Applied to Solids. Physical Review B 2011, 83, 195131.
41. Bonino, F.; Chavan, S.; Vitillo, J. G.; Groppo, E.; Agostini, G.; Lamberti, C.; Dietzel, P. D. C.; Prestipino, C.; Bordiga, S., Local Structure of Cpo-27-Ni Metallorganic Framework Upon Dehydration and Coordination of No. Chemistry of Materials 2008, 20, 4957-4968.
42. Schoedel, A.; Li, M.; Li, D.; O’Keeffe, M.; Yaghi, O. M., Structures of Metal–Organic Frameworks with Rod Secondary Building Units. Chemical Reviews 2016, 116, 12466-12535.
43. Deng, H., et al., Large-Pore Apertures in a Series of Metal-Organic Frameworks. Science 2012, 336, 1018-1023.
44. Hindocha, S.; Poulston, S., Study of the Scale-up, Formulation, Ageing and Ammonia Adsorption Capacity of Mil-100(Fe), Cu-Btc and Cpo-27(Ni) for Use in Respiratory Protection Filters. Faraday Discussions 2017, 201, 113-125.
45. Queen, W. L., et al., Comprehensive Study of Carbon Dioxide Adsorption in the Metal–Organic Frameworks M2(Dobdc) (M = Mg, Mn, Fe, Co, Ni, Cu, Zn). Chemical Science 2014, 5, 4569-4581.
46. Dronskowski, R.; Bloechl, P. E., Crystal Orbital Hamilton Populations (Cohp): Energy-Resolved Visualization of Chemical Bonding in Solids Based on Density-Functional Calculations. The Journal of Physical Chemistry 1993, 97, 8617-8624.
47. Deringer, V. L.; Tchougréeff, A. L.; Dronskowski, R., Crystal Orbital Hamilton Population (Cohp) Analysis as Projected from Plane-Wave Basis Sets. The Journal of Physical Chemistry A 2011, 115, 5461-5466.
48. Maintz, S.; Deringer, V. L.; Tchougréeff, A. L.; Dronskowski, R., Analytic Projection from Plane-Wave and Paw Wavefunctions and Application to Chemical-Bonding Analysis in Solids. Journal of Computational Chemistry 2013, 34, 2557-2567.
49. Manz, T. A.; Limas, N. G., Introducing Ddec6 Atomic Population Analysis: Part 1. Charge Partitioning Theory and Methodology. RSC Advances 2016, 6, 47771-47801.
50. Limas, N. G.; Manz, T. A., Introducing Ddec6 Atomic Population Analysis: Part 2. Computed Results for a Wide Range of Periodic and Nonperiodic Materials. RSC Advances 2016, 6, 45727-45747.
51. Keller, G.; Bhasin, M., Synthesis of Ethylene Via Oxidative Coupling of Methane: I. Determination of Active Catalysts. Journal of Catalysis 1982, 73, 9-19.
52. Ito, T.; Lunsford, J. H., Synthesis of Ethylene and Ethane by Partial Oxidation of Methane over Lithium-Doped Magnesium Oxide. Nature 1985, 314, 721.
53. Sofranko, J. A.; Leonard, J. J.; Jones, C. A., The Oxidative Conversion of Methane to Higher Hydrocarbons. Journal of catalysis 1987, 103, 302-310.
54. Otsuka, K.; Wang, Y., Direct Conversion of Methane into Oxygenates. Applied Catalysis A: General 2001, 222, 145-161.