REFERENCES
1. Chen J, Min F, Liu L, Liu C. Mechanism research on surface hydration of kaolinite, insights from DFT and MD simulations. Applied Surface Science 2019;476:6-15.
2. Ismadji S, Soetaredjo FE, Ayucitra A. Natural clay minerals as environmental cleaning agents. Clay Materials for Environmental Remediation ;2015:5-37.
3. Bhattacharyya KG, Gupta SS. Adsorption of a few heavy metals on natural and modified kaolinite and montmorillonite: a review. Adv Colloid Interface Sci 2008;140:114-31.
4. Xu Y, Liang X, Xu Y, et al. Remediation of heavy metal-polluted agricultural soils using clay minerals: a review. Pedosphere 2017;27:193-204.
5. Shaikh SM, Nasser MS, Hussein I, et al. Influence of polyelectrolytes and other polymer complexes on the flocculation and rheological behaviors of clay minerals: a comprehensive review. Separation and Purification Technology 2017;187:137-61.
6. Mingqing Z, Jiongtian L, Aiqin S, Han-hu L. Calcium ions adsorption mechanism on clay particles surface in coal slurry. Journal of China Coal Society 2005;30:637-41.
7. Xing Y, Xu X, Gui X, Cao Y, Xu M. Effect of kaolinite and montmorillonite on fine coal flotation. Fuel 2017;195:284-9.
8. Zhao G, Tan Q, Xiang L, et al. Structure and properties of water film adsorbed on mica surfaces. J Chem Phys 2015;143:104705.
9. Kimura K, Ido S, Oyabu N, et al. Visualizing water molecule distribution by atomic force microscopy. J Chem Phys 2010;132:194705.
10. Kobayashi K, Oyabu N, Kimura K, et al. Visualization of hydration layers on muscovite mica in aqueous solution by frequency-modulation atomic force microscopy. J Chem Phys 2013;138:184704.
11. Song S, Peng C, Gonzalez-Olivares MA, Lopez-Valdivieso A, Fort T. Study on hydration layers near nanoscale silica dispersed in aqueous solutions through viscosity measurement. J Colloid Interface Sci 2005;287:114-20.
12. Zhao Y, Yi H, Jia F, et al. A novel method for determining the thickness of hydration shells on nanosheets: a case of montmorillonite in water. Powder Technology 2017;306:74-9.
13. Cheng L, Fenter P, Nagy KL, Schlegel ML, Sturchio NC. Molecular-scale density oscillations in water adjacent to a mica surface. Phys Rev Lett 2001;87:156103.
14. Fenter P, Lee SS. Hydration layer structure at solid-water interfaces. MRS Bull 2014;39:1056-61.
15. Min F, Peng C, Liu L. Investigation on hydration layers of fine clay mineral particles in different electrolyte aqueous solutions. Powder Technology 2015;283:368-72.
16. Peng CL, Min FF, Song SX. Study on hydration of montmorillonite in aqueous solutions. Mining, Metallurgy & Exploration 2015;32:196-202.
17. Casida ME and Chong D. In recent advances in density functional methods. Available from: https://www.researchgate.net/publication/220023836_In_Recent_Advances_in_Density-Functional_Methods [Last accessed on 7 Apr 2022].
18. Nagy Á. Density functional. Theory and application to atoms and molecules. Physics Reports 1998;298:1-79.
19. Geerlings P, De Proft F, Langenaeker W. Conceptual density functional theory. ChemInform 2003:34.
20. Schrödinger E. An undulatory theory of the mechanics of atoms and molecules. Phys Rev 1926;28:1049-70.
22. Fermi E. Un metodo statistico per la determinazione di alcune priorieta dell’atome. Rend Accad Naz. Lincei 1927;6:32. Available from:
23. Dirac PAM. Note on exchange phenomena in the Thomas atom. Math Proc Camb Phil Soc 1930;26:376-85.
24. Teller E. On the stability of molecules in the Thomas-Fermi theory. Rev Mod Phys 1962;34:627-31.
26. Kohn W, Sham LJ. Self-consistent equations including exchange and correlation effects. Phys Rev 1965;140:A1133-8.
27. Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Phys Rev Lett 1996;77:3865-8.
28. Yanai T, Tew DP, Handy NC. A new hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chemical Physics Letters 2004;393:51-7.
29. Hu XL, Michaelides A. Ice formation on kaolinite: lattice match or amphoterism? Surface Science 2007;601:5378-81.
30. Hu XL, Michaelides A. Water on the hydroxylated (001) surface of kaolinite: From monomer adsorption to a flat 2D wetting layer. Surface Science 2008;602:960-74.
31. Peng C, Min F, Liu L, Chen J. A periodic DFT study of adsorption of water on sodium-montmorillonite (001) basal and (010) edge surface. Applied Surface Science 2016;387:308-16.
32. Zhang Y, Meng Y, Liu H, Yang M. First-principles study of water desorption from montmorillonite surface. J Mol Model 2016;22:105.
33. Fonseca CG, Vaiss VS, Wypych F, Diniz R, Leitão AA. Structural and thermodynamic investigation of the hydration-dehydration process of Na + -Montmorillonite using DFT calculations. Applied Clay Science 2017;143:212-9.
34. Sprik M. Computation of the pK of liquid water using coordination constraints. Chemical Physics 2000;258:139-50.
35. Tunega D, Haberhauer G, Gerzabek MH, Lischka H. Theoretical study of adsorption sites on the (001) surfaces of 1:1 clay minerals. Langmuir 2002;18:139-47.
36. Tunega D, Gerzabek MH, Lischka H. Ab Initio Molecular dynamics study of a monomolecular water layer on octahedral and tetrahedral kaolinite surfaces. J Phys Chem B 2004;108:5930-6.
37. Šolc R, Gerzabek MH, Lischka H, Tunega D. Wettability of kaolinite (001) surfaces - Molecular dynamic study. Geoderma 2011;169:47-54.
38. Jorgensen WL, Maxwell DS, Tirado-rives J. Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-36.
39. Weiner PK, Kollman PA. AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J Comput Chem 1981;2:287-303.
40. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, et al. CHARMM: the biomolecular simulation program. J Comput Chem 2009;30:1545-614.
41. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, et al. Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins 1988;4:31-47.
42. Sun H. COMPASS: an AB initio force-field optimized for condensed-phase applications overview with details on alkane and benzene compounds. J Phys Chem B 1998;102:7338-64.
43. Rappe AK, Casewit CJ, Colwell KS, Goddard WA, Skiff WM. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc 1992;114:10024-35.
44. Mayo SL, Olafson BD and Goddard WA. DREIDING: a generic force field for molecular simulations. J Phys Chem 1990;94:8897-909.
45. Cygan RT, Liang J, Kalinichev AG. Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. J Phys Chem B 2004;108:1255-66.
46. Heinz H, Koerner H, Anderson KL, Vaia RA, Farmer BL. Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite. Chem Mater 2005;17:5658-69.
47. Heinz H, Lin TJ, Mishra RK, Emami FS. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field. Langmuir 2013;29:1754-65.
48. Bish DL. Rietveld refinement of non-hydrogen atomic positions in kaolinite. Clays and Clay Minerals 1989;37:289-96.
49. Bish DL. Rietveld refinement and fourier-transform infrared spectroscopic study of the dickite structure at low temperature. Clays and Clay Minerals 1993;41:297-304.
50. Lage MR, Dedzo GK, Stoyanov SR, et al. Computational and experimental investigations of the role of water and alcohols in the desorption of heterocyclic aromatic compounds from kaolinite in toluene. J Phys Chem C 2018;122:10377-91.
51. Fuchs K, Bonjer K, Gajewski D, et al. Crustal evolution of the Rhinegraben area. 1. Exploring the lower crust in the Rhinegraben rift by unified geophysical experiments. Tectonophysics 1987;141:261-75.
52. Demichelis R, De La Pierre M, Mookherjee M, Zicovich-wilson CM, Orlando R. Serpentine polymorphism: a quantitative insight from first-principles calculations. CrystEngComm 2016;18:4412-9.
53. Sun W, Zeng H, Tang T. Synergetic adsorption of polymers on montmorillonite: Insights from molecular dynamics simulations. Applied Clay Science 2020;193:105654.
54. Viani A, Gualtieri AF, Artioli G. The nature of disorder in montmorillonite by simulation of X-ray powder patterns. American Mineralogist 2002;87:966-75.
55. Richardson SM and Richardson JW. Crystal structure of a pink muscovite from Archer’s post, Kenya: implications for reverse pleochroism in dioctahedral micas. American Mineralogist 1982;67:69-75.
56. Xu Y, Liu Y, Liu G. Molecular dynamics simulation of primary ammonium ions with different alkyl chains on the muscovite (001) surface. International Journal of Mineral Processing 2015;145:48-56.
57. Geatches DL, Jacquet A, Clark SJ, Greenwell HC. Monomer Adsorption on Kaolinite: Modeling the Essential Ingredients. J Phys Chem C 2012;116:22365-74.
58. Xi P, Ma R, Liu W. Study on the crystal structure of coal kaolinite and non-coal kaolinite: insights from experiments and DFT simulations. Symmetry 2020;12:1125.
59. Wang Q, Kong X, Zhang B, Wang J. Adsorption of Zn(II) on the kaolinite(001) surfaces in aqueous environment: a combined DFT and molecular dynamics study. Applied Surface Science 2017;414:405-12.
60. Han Y, Liu W, Chen J. DFT simulation of the adsorption of sodium silicate species on kaolinite surfaces. Applied Surface Science 2016;370:403-9.
61. Peng C, Min F, Liu L, Chen J. The adsorption of CaOH+ on (001) basal and (010) edge surface of Na-montmorillonite: a DFT study: DFT study of adsorption of CaOH + on (001) Na-montmorillonite surface. Surf Interface Anal 2017;49:267-77.
62. Peng C, Zhong Y, Min F. Adsorption of alkylamine cations on montmorillonite (001) surface: a density functional theory study. Applied Clay Science 2018;152:249-58.
63. Kasprzhitskii A, Lazorenko G, Yavna V, Daniel P. DFT theoretical and FT-IR spectroscopic investigations of the plasticity of clay minerals dispersions. Journal of Molecular Structure 2016;1109:97-105.
64. Ertan E, Kimberg V, Gel’mukhanov F, et al. Theoretical simulations of oxygen K -edge resonant inelastic x-ray scattering of kaolinite. Phys Rev B 2017:95.
65. Scholtzová E, Tunega D. Prediction of mechanical properties of grafted kaolinite - a DFT study. Applied Clay Science 2020;193:105692.
66. Schoonheydt RA, Johnston CT, Bergaya F. Clay minerals and their surfaces. Surface and Interface Chemistry of Clay Minerals ;2018:1-21.
67. Bish DL. Rietveld Refinement of the Kaolinite Structure at 1.5 K. Clays and Clay Minerals 1993;41:738-44.
68. Chen J, Min F, Liu L, Liu C, Lu F. Experimental investigation and DFT calculation of different amine/ammonium salts adsorption on kaolinite. Applied Surface Science 2017;419:241-51.
69. Zhang Z, Liu J, Yang Y, Shen F, Zhang Z. Theoretical investigation of sodium capture mechanism on kaolinite surfaces. Fuel 2018;234:318-25.
70. Peng C, Zhong Y, Wang G, Min F, Qin L. Atomic-level insights into the adsorption of rare earth Y(OH)3-nn+ (. n ;469:357-67.
71. Chen J, Min F, Liu L, Cai C. Systematic exploration of the interactions between Fe-doped kaolinite and coal based on DFT calculations. Fuel 2020;266:117082.
72. He M, Zhao J. Effects of Mg, Ca, and Fe(II) Doping on the Kaolinite (001) Surface with H < SUB > 2 </ SUB > O Adsorption. Clays Clay Miner 2012;60:330-7.
73. Voora VK, Al-Saidi WA, Jordan KD. Density functional theory study of pyrophyllite and M-montmorillonites (M = Li, Na, K, Mg, and Ca): role of dispersion interactions. J Phys Chem A 2011;115:9695-703.
74. Lavikainen LP, Tanskanen JT, Schatz T, Kasa S, Pakkanen TA. Montmorillonite interlayer surface chemistry: effect of magnesium ion substitution on cation adsorption. Theor Chem Acc 2015:134.
75. Luo Y, Ou L, Chen J, et al. Effects of defects and impurities on the adsorption of H2O on smithsonite (101) surfaces: insight from DFT-D and MD. Colloids and Surfaces A: Physicochemical and Engineering Aspects 2021;628:127300.
76. Wungu TD, Agusta MK, Saputro AG, Dipojono HK, Kasai H. First principles calculation on the adsorption of water on lithium-montmorillonite (Li-MMT). J Phys Condens Matter 2012;24:475506.
77. Du J, Min F, Zhang M, Peng C, Liu C. Mechanism of H2O adsorption on ammonium-illite surface based on density functional theory. Journal of China University of Mining and Technology 2017;46:1349-56.
78. Zhang C, Qi Y, Qian P, Zhong M, Wang L, Yin H. Quantum chemical study of the adsorption of water molecules on kaolinite surfaces. Computational and Theoretical Chemistry 2014;1046:10-9.
79. Croteau T, Bertram AK, Patey GN. Simulation of water adsorption on kaolinite under atmospheric conditions. J Phys Chem A 2009;113:7826-33.
80. Guillaud E. Multiscale experimental and numerical study of the structure and the dynamics of water confined in clay minerals. Available from: https://www.researchgate.net/publication/319791729_Multiscale_experimental_and_numerical_study_of_the_structure_and_the_dynamics_of_water_confined_in_clay_minerals [Last accessed on 7 Apr 2022].
81. Vasconcelos IF, Bunker BA, Cygan RT. Molecular dynamics modeling of ion adsorption to the basal surfaces of kaolinite. J Phys Chem C 2007;111:6753-62.
82. Baek W, Avramov PV, Kim Y. Nuclear magnetic resonance and theoretical simulation study on Cs ion co-adsorbed with other alkali cations on illite. Applied Surface Science 2019;489:766-75.
83. Doi A, Khosravi M, Ejtemaei M, Nguyen TA, Nguyen AV. Specificity and affinity of multivalent ions adsorption to kaolinite surface. Applied Clay Science 2020;190:105557.
84. Greathouse JA, Hart DB, Bowers GM, Kirkpatrick RJ, Cygan RT. Molecular simulation of structure and diffusion at smectite-water interfaces: using expanded clay interlayers as model Nanopores. J Phys Chem C 2015;119:17126-36.
85. Subramanian N, Whittaker ML, Ophus C, Lammers LN. Structural implications of interfacial hydrogen bonding in hydrated wyoming-montmorillonite clay. J Phys Chem C 2020;124:8697-705.
86. Yi H, Jia F, Zhao Y, et al. Surface wettability of montmorillonite (001) surface as affected by surface charge and exchangeable cations: a molecular dynamic study. Applied Surface Science 2018;459:148-54.
87. Pérez-conesa S, Martínez JM, Sánchez Marcos E. Hydration and diffusion mechanism of uranyl in montmorillonite clay: molecular dynamics using an AB initio potential. J Phys Chem C 2017;121:27437-44.
88. Wang X, Huang Y, Pan Z, Wang Y, Liu C. Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations. J Hazard Mater 2015;295:43-54.
89. Heimann JE, Grimes RT, Rosenzweig Z, Bennett JW. A density functional theory (DFT) investigation of how small molecules and atmospheric pollutants relevant to art conservation adsorb on kaolinite. Applied Clay Science 2021;206:106075.
90. Zhang SB, Wei S, Zunger A. Stabilization of ternary compounds via ordered arrays of defect pairs. Phys Rev Lett 1997;78:4059-62.
91. Zhu B, Qi C, Zhang Y, et al. Synthesis, characterization and acid-base properties of kaolinite and metal (Fe, Mn, Co) doped kaolinite. Applied Clay Science 2019;179:105138.
92. Hou J, Chen M, Zhou Y, et al. Regulating the effect of element doping on the CO2 capture performance of kaolinite: a density functional theory study. Applied Surface Science 2020;512:145642.
93. Richard D, Rendtorff NM. Local environments in iron-bearing clay minerals by DFT approaches: the case of structural fe in kaolinite. Applied Clay Science 2021;213:106251.
94. Liao B, Wang J, Han X, et al. Microscopic molecular insights into clathrate methane hydrates dissociation in a flowing system. Chemical Engineering Journal 2022;430:133098.
95. Subramanian N, Nielsen Lammers L. Thermodynamics of ion exchange coupled with swelling reactions in hydrated clay minerals. J Colloid Interface Sci 2022;608:692-701.
96. Parr RG, Yang W. Density-functional theory of the electronic structure of molecules. Annu Rev Phys Chem 1995;46:701-28.
97. Hagler A, Ewig C. On the use of quantum energy surfaces in the derivation of molecular force fields. Computer Physics Communications 1994;84:131-55.
98. Nevins N and Allinger NL. Molecular mechanics (MM4) vibrational frequency calculations for alkenes and conjugated hydrocarbons. Journal of Computational Chemistry 1996;17:730-46.
99. Argyris D, Ho T, Cole DR, Striolo A. Molecular Dynamics Studies of Interfacial Water at the Alumina Surface. J Phys Chem C 2011;115:2038-46.
100. Du H, Miller J. A molecular dynamics simulation study of water structure and adsorption states at talc surfaces. International Journal of Mineral Processing 2007;84:172-84.
101. Wang X, Liu W, Liu W, et al. Understanding adsorption of amine surfactants on the solvated quartz (101) surface by a jointed Dreiding-ClayFF force field. Applied Surface Science 2021;566:150737.
102. Wang X, Liu J, Du H, Miller JD. States of adsorbed dodecyl amine and water at a silica surface as revealed by vibrational spectroscopy. Langmuir 2010;26:3407-14.
103. Pitman MC, van Duin AC. Dynamics of confined reactive water in smectite clay-zeolite composites. J Am Chem Soc 2012;134:3042-53.
104. Senftle TP, Hong S, Islam MM, et al. The ReaxFF reactive force-field: development, applications and future directions. npj Comput Mater 2016:2.
105. Valverde JR. Molecular modelling: principles and applications. Briefings in Bioinformatics 2001;2:199-200.
107. Peng C, Wang G, Qin L, et al. Molecular dynamics simulation of NH4-montmorillonite interlayer hydration: structure, energetics, and dynamics. Applied Clay Science 2020;195:105657.
108. Dünweg B, Kremer K. Molecular dynamics simulation of a polymer chain in solution. The Journal of Chemical Physics 1993;99:6983-97.
109. Xu J, Camara M, Liu J, et al. Molecular dynamics study of the swelling patterns of Na/Cs-, Na/Mg-montmorillonites and hydration of interlayer cations. Molecular Simulation 2017;43:575-89.
110. Ranathunga DTS, Shamir A, Dai X, Nielsen SO. Molecular dynamics simulations of water condensation on surfaces with tunable wettability. Langmuir 2020;36:7383-91.
111. Eremin RA, Kholmurodov K, Petrenko VI, Rosta L, Avdeev MV. Effect of the solute-solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation. J Appl Crystallogr 2013;46:372-8.
112. Belashchenko DK, Rodnikova MN, Balabaev NK, Solonina IA. Investigating hydrogen bonds in liquid ethylene glycol structure by means of molecular dynamics. Russ J Phys Chem 2014;88:94-102.
113. Moultos OA, Orozco GA, Tsimpanogiannis IN, Panagiotopoulos AZ, Economou IG. Atomistic molecular dynamics simulations of H2O diffusivity in liquid and supercritical CO2. Molecular Physics 2015;113:2805-14.
114. Moultos OA, Zhang Y, Tsimpanogiannis IN, Economou IG, Maginn EJ. System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: the case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ethers. J Chem Phys 2016;145:074109.
115. Yeh I, Hummer G. System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions. J Phys Chem B 2004;108:15873-9.
116. Jamali SH, Wolff L, Becker TM, et al. Finite-size effects of binary mutual diffusion coefficients from molecular dynamics. J Chem Theory Comput 2018;14:2667-77.
117. Kikugawa G, Ando S, Suzuki J, et al. Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid. J Chem Phys 2015;142:024503.
118. Yang X, Zhang H, Li L, Ji X. Corrections of the periodic boundary conditions with rectangular simulation boxes on the diffusion coefficient, general aspects. Molecular Simulation 2017;43:1423-9.
119. MacKerell AD, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-616.
120. Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008;4:435-47.
121. Papavasileiou KD, Avramopoulos A, Leonis G, Papadopoulos MG. Computational investigation of fullerene-DNA interactions: Implications of fullerene’s size and functionalization on DNA structure and binding energetics. J Mol Graph Model 2017;74:177-92.
