MINISTRY OF EDUCATION AND TRAINING QUY NHON UNIVERSITY NGUYEN NGOC TRI STUDY ON THE ADSORPTION ABILITY OF ORGANIC MOLECULES ON TiO2 AND CLAY MINERAL MATERIALS USING COMPUTATIONAL CHEMISTRY METHODS DOCTORAL DISSERTATION BINH DINH - 2021 MINISTRY OF EDUCATION AND TRAINING QUY NHON UNIVERSITY Nguyen Ngoc Tri STUDY ON THE ADSORPTION ABILITY OF ORGANIC MOLECULES ON TiO2 AND CLAY MINERAL MATERIALS USING COMPUTATIONAL CHEMISTRY METHODS Major : Physical and Theoretical Chemistry Code No. Pham Tran Nguyen Nguyen Reviewer 2 : Assoc. Tran Van Tan Reviewer 3 : Assoc. Pham Vu Nhat Supervisors: 1. Nguyen Tien Trung 2. Minh Tho Nguyen BINH DINH - 2021 Declaration This thesis was completed at the Department of Chemistry, Faculty of Natural Sciences, Quy Nhon University (QNU) under the supervision of Assoc. Nguyen Tien Trung (QNU, Vietnam) and Prof. Minh Tho Nguyen (KU Leuven, Belgium). I hereby declare that the results presented in this thesis are new and original. While most of them were published in peer-reviewed journals, the other part has not been published elsewhere. Binh Dinh, 2021 Supervisors Ph. Nguyen Tien Trung Prof. Minh Tho Nguyen Nguyen Ngoc Tri Acknowledgements First of all, I would like to express my sincerest thanks to the supervisors, Assoc. Nguyen Tien Trung and Prof. Minh Tho Nguyen, for their patient guidance, genius support, and warm encouragement. I would also like to thank them for their valuable comments, suggestions, and corrections. In fact, without their help, this thesis could not have been achievable. I am grateful to all LCCM members for their help and valuable discussion during my research time. I am very thankful to my friend, Dai Q. Ho, for his help during my graduate study. I would like to thank Prof. Carvalho, University of Evora, Portugal, for his valuable comments, revisions, and computing facilities. I am thankful to Quy Nhon University and KU Leuven for providing me with such a great opportunity to pursue my doctoral program. My thanks are extended to all staff at the Faculty of Natural Sciences, Quy Nhon University and the Department of Chemistry, KU Leuven for their help and supports during my PhD time. My acknowledgements also go to my friends and colleagues for their time and friendship. Furthermore, I would also like to thank the VLIR-TEAM project awarded to Quy Nhon University with Grant number ZEIN2016PR431 (2016-2020) and the VINIF scholarship with code number VINIF.73 for the financial supports during my doctoral studies. Lastly and most importantly, I am forever grateful to my family for all their love and support through the numerous difficulties I have been facing. Binh Dinh, 2021 Nguyen Ngoc Tri TABLE OF CONTENTS List of Symbols and Notations List of Figures List of Tables INTRODUCTION . Object and scope of this study . Novelty, scientific and practical significance . Organic pollutants and antibiotics residues in wastewaters . TiO2 nanomaterial and its applications . Clay minerals and their applications in the treatment of pollutants. Investigations on materials surfaces using computational chemistry . THEORETICAL BACKGROUND AND COMPUTATIONAL METHODS . Quantum chemical approaches . Schrödinger equations . The Born - Oppenheimer approximation and Pauli’s exclusion principle . Born – Oppenheimer approximation . Pauli’s exclusion principle . The variational principle . Slater and Gaussian orbitals. Some popular basis sets . Hartree-Fock approximation . Density functional theory . The Hohenberg-Kohn theorem. Kohn-Sham equations . Local density approximation . General gradient approximation . Van der Waals functionals . Pseudopotential and plane-wave methods . Atoms In Molecules and Natural Bond Orbitals approaches . Atoms In Molecules analysis . Natural Bond Orbitals analysis . Clay mineral systems . Adsorption of organic molecules on kaolinite surfaces . Adsorption of antibiotics on vermiculite surface . Quantum chemical analyses . RESULTS AND DISCUSSION . ADSORPTION OF ORGANIC MOLECULES ON MATERIALS SURFACES. Adsorption of organic molecules on rutile-TiO2 (110) surface . The quantum chemical analysis for the interactions on surface. Adsorption of benzene derivatives on rutile-TiO2 (110) and anatase-TiO2 (101) surfaces . Energetic aspects of the adsorption process . Formation and role of intermolecular interactions . Adsorption of benzene derivatives on kaolinite (001) surface . Energetic aspects of the adsorption process . Formation and role of intermolecular interactions . Adsorption of benzene derivatives on a K+-supported kaolinite (001) surface . AIM and NBO analyses . ADSORPTION OF ANTIBIOTIC MOLECULES ON TiO2 AND VERMICULITE SURFACES . Adsorption of enrofloxacin molecule on rutile-TiO2 (110) surface. Energetic aspects of the adsorption process . Characteristics of interactions on the surface . Adsorption of ampicillin, amoxicillin, and tetracycline molecules on rutile-TiO2 (110) surface. Energetic aspects of the adsorption process . Characteristic properties of intermolecular interactions . Adsorption of ampicillin and amoxicillin molecules on anatase-TiO2 (101) surface . AIM and NBO analyses . Adsorption of chloramphenicol molecule on a vermiculite surface . Adsorption, interaction, and deformation energies . Characteristics of stable interactions upon adsorption process. Adsorption of β-lactam antibiotics on vermiculite surface . Energetic aspects of the adsorption process . Existence and role of different interactions upon complexation .116 CONCLUSIONS AND OUTLOOK .119 LIST OF PUBLICATIONS CONTRIBUTES TO THIS THESIS .121 Appendix LIST OF SYMBOLS AND NOTATIONS Symbol Description 2(ρ(r)) : Laplacian of electron density AIM : Atoms in Molecules theory AP : Ampicillin a-TiO2 : Anatase-TiO2 (101) surface AX : Amoxicillin BCP : Bond critical point BP : Benzylpenicillin CP : Chloramphenicol d : Distance of contact DFT : Density Functional Theory DPE : Deprotonation enthalpy Eads : Adsorption energy EB : Hydrogen bond energy Edef-mol : Deformation energy for molecules Edef-surf : Deformation energy for surfaces EDT : Electron density transfer Eint : Interaction energy ER : Enrofloxacin H(r) : Total of electron density energy H-slab : Hydrogen-rich facet of kaolinite (kaolinite (001) surface) K+-slab : K+-supported kaolinite (001) surface MEP : Molecular Electrostatic Potential NBO : Natural Bond Orbitals O-slab : Oxygen-rich facet of kaolinite (kaolinite (00 1 ) surface) PA : Proton affinity PBE : Perdew–Burke-Ernzerhof (density functional) q : Net charge at atom r-TiO2 : Rutile-TiO2 (110) surface TC : Tetracycline VASP : Vienna Ab initio Simulation Package vdW : Van der Waals α : Bond angle Δr : Change of bond length ρ(r) : Electron density (at BCP) LIST OF FIGURES Page Figure 1. The radial part of the 3s atomic orbit of the Na atom 27 Figure 2. Schematic drawing of a 3s-derived Bloch function of one- 27 dimensional crystals of Na atoms Figure 3. The graph shows the first random substitution for two alkali 28 metals Na, Cs according to Hellmann Figure 4. The slab models of rutile-TiO2 (110) and anatase-TiO2 (101) 33 surfaces Figure 5. The structure of kaolinite surfaces 35 Figure 6. The model slab of vermiculite surface (red, yellow, grey, pink, 36 and white colors displayed for O, Mg, Si, Al, and H atoms, respectively) Figure 1. Stable complexes for the adsorption of organic molecules on 38 rutile-TiO2 (110) surface Figure 1. The charge density between adsorbent and adsorbates in stable 42 complexes Figure 1. The topological analysis for the first-layered structures 42 Figure 1. Stable complexes of adsorption of benzene derivatives on 45 rutile-TiO2 (110) surface Figure 1. Stable structures of adsorption of benzene derivatives on 47 anatase-TiO2 (101) surface Figure 1. MEP maps of benzene derivatives (isovalue = 0.02 au, charge 50 region taken in the range of 2. Topological geometry of the first-layered structures of the most 53 stable complexes for rutile systems Figure 1. Topological geometry of the first-layered structures of the most 53 stable complexes for anatase systems Figure 1. EDT maps of investigated structures for rutile system 53 Figure 1. EDT maps of investigated structures for anatase system 53 Figure 1. Stable structures of adsorption of derivatives on H-slab 57 Figure 1. Topological geometry of the most stable complexes for 62 adsorption of organic molecules on H-slab Figure 1. Schematic of total electron density of complexes at the 64 B3LYP/6-31+G(d,p) level Figure 1. The stable complexes of molecules adsorption on K+-slab 65 Figure 1. The topological geometries of the stable complexes for K+- 68 slab systems Figure 1. The EDT maps of the stable complexes for K+-slab systems 68 Figure 2. Optimized structures of enrofloxacin, rutile-TiO2 (110) surface, 71 and two stable adsorption configurations Figure 2. The topology and electron density transfer maps for the first- 75 layered structures of ER1 and ER2 at the B3LYP/6-31+G(d, p) level Figure 2. Stable complexes for adsorption of antibiotic molecules on 77 rutile-TiO2 (110) surface Figure 2. DOS plot of rutile-TiO2 (110) surface and HOMO, LUMO 84 levels of adsorbed antibiotic molecules Figure 2. a) Topological critical points and b) electronic charge density 85 transfer of the most stable complexes Figure 2. Optimized structures of anatase-TiO2 (101) surface and 87 ampicillin, amoxicillin molecules Figure 2. The optimized structures of ampicillin, amoxicillin adsorbed on 87 anatase-TiO2 (101) surface Figure 2. The topological geometries and EDT maps of the first-layered 90 structures Figure 2. Optimized structures of a) vermiculite surface, and b) 93 chloramphenicol molecule, and c) the MEP map of chloramphenicol (electron density of 0. Stable adsorption configurations of chloramphenicol on the 94 vermiculite surface Figure 2. Topological features for the first layered structures of 99 complexes Figure 2. Total electron density distributions of the first-layered 101 structures Figure 2. Stable complexes of adsorption of AP, AX and BP on a 104 vermiculite surface Figure 2. Molecular electrostatic potential (MEP) of free antibiotic 110 molecules Figure 2. Topological features for the most stable adsorption 112 configurations Figure 2. Total electron density maps of most stable complexes 115 LIST OF TABLES Page Table 1. Charge distribution in molecules at the B3LYP/6-31+G(d,p) 38 level Table 1. Some selected parameters of stable complexes at PBE functional 39 (distance (r) in Å; angle (α) in degree) Table 1. Adsorption, interaction, and deformation energies (all in 40 kcal.mol-1) for the adsorption processes on rutile-TiO2 (110) surface Table 1. The characteristic parameters for topological analysis (all in au) 43 Table 1. Some selected parameters of molecules and TiO2 surfaces 45 Table 1. Interaction distance (d, Å), bond angle (α, o), and changes in 46 length of bonds (r, Å) following the adsorption process for rutile systems Table 1. Distance of intermolecular interactions (d, Å), bonding angle (α, 46 ), and changes of bond length (Δr, Å) upon adsorption process for anatase o systems Table 1. Adsorption, interaction, and deformation energies of adsorption 48 of benzene derivatives on rutile-TiO2 (110) surface (all in kcal. Energetic aspects of adsorption of benzene derivatives on 49 anatase-TiO2 (101) surface (all in kcal. NBO charges at atoms in functional groups involved in 51 interactions in complexes Table 1. Proton affinity (PA) at O and N atoms and deprotonation 52 enthalpy (DPE) of O-H and N-H bonds in functional groups and C-H bonds in the benzene ring of derivatives (in kcal. Characteristic parameters for topological geometry (ρ(r), 54 2(ρ(r)), H(r), in au), EDT (in e) for rutile systems Table 1. Characteristic parameters for topological geometry (ρ(r), 55 2(ρ(r)), H(r), in au), EDT (in e) for anatase systems Table 1. Distances of intermolecular contacts (d), changes in the bond 58 lengths (Δr) involved in interactions in complexes (all in Å) Table 1. Energetic parameters of complexes, molecules and surface 59 upon adsorption processes (in kcal. Characteristics of topological geometries (ρ(r), ρ(r), H(r), in 62 au) and EDT (in e) at the B3LYP/6-31+G(d,p) level Table 1. The adsorption energy of the stable complexes (in kcal. The characteristics for topology analysis and total of electron 69 density transfer (EDT) for K+-slab systems at the B3LYP/6-31+G(d,p) level Table 2. Some selected parameters for two stable complexes using PBE 72 functional Table 2. Energies for adsorption of Enrofloxacin on rutile-TiO2 (110) 73 surface (in kcal. The topological analysis and EDT of investigated structures at 75 the B3LYP/6-31+G(d, p) level Table 2. Some selected parameters for stable adsorption configurations 78 Table 2. Energies for adsorption processes using both PBE and optPBE- 80 vdW functionals (kcal. Some characteristic parameters of the stable complexes 88 Table 2. Adsorption energy (Eads, kcal.mol-1) of stable complexes 89 Table 2.
