Link tải luận văn miễn phí cho ae Kết Nối
Nghiên cứu khả năng hấp phụ một số hợp chất hữu cơ trên các vật liệu tio2 và khoáng sét bằng phương pháp hóa học tính toán
STUDY ON THE ADSORPTION ABILITY OF ORGANIC MOLECULES ON TiO2 AND CLAY MINERAL MATERIALS USING COMPUTATIONAL CHEMISTRY METHODS
Acknowledgements
First of all, I would like to express my sincerest thanks to the supervisors,
Assoc. Prof. 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 Giúp 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. A.J.P. 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 Giúp 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.2019.TS.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 TriTABLE OF CONTENTS
List of Symbols and Notations
List of Figures
List of Tables
INTRODUCTION.....................................................................................................1
1. Motivation ...............................................................................................................1
2. Research purpose ....................................................................................................3
3. Object and scope of this study ................................................................................4
4. Research contents....................................................................................................4
5. Methodology ...........................................................................................................5
6. Novelty, scientific and practical significance .........................................................5
PART 1. OVERVIEW OF LITERATURE ............................................................7
1. Organic pollutants and antibiotics residues in wastewaters....................................7
2. TiO2 nanomaterial and its applications ...................................................................8
3. Clay minerals and their applications in the treatment of pollutants......................10
4. Investigations on materials surfaces using computational chemistry...................12
PART 2. THEORETICAL BACKGROUND AND COMPUTATIONAL
METHODS ..............................................................................................................13
1. Quantum chemical approaches .............................................................................13
1.1. Schrödinger equations........................................................................................13
1.2. The Born - Oppenheimer approximation and Pauli‘s exclusion principle ........15
1.2.1. Born – Oppenheimer approximation ..............................................................15
1.2.2. Pauli’s exclusion principle..............................................................................15
1.3. The variational principle ....................................................................................16
1.4. Basis sets ............................................................................................................17
1.4.1. Slater and Gaussian orbitals...........................................................................17
1.4.2. Some popular basis sets ..................................................................................18
1.5. Hartree-Fock approximation ..............................................................................191.6. Density functional theory...................................................................................20
1.6.1. The Hohenberg-Kohn theorem........................................................................21
1.6.2. Kohn-Sham equations .....................................................................................21
1.6.3. Local density approximation...........................................................................22
1.6.4. General gradient approximation ....................................................................23
1.6.5. Hybrid functionals...........................................................................................24
1.6.6. Van der Waals functionals ..............................................................................25
1.7. Pseudopotential and plane-wave methods .........................................................26
1.8. Atoms In Molecules and Natural Bond Orbitals approaches.............................29
1.8.1. Atoms In Molecules analysis...........................................................................29
1.8.2. Natural Bond Orbitals analysis ......................................................................31
2. Computational methods ........................................................................................33
2.1. TiO2 systems ......................................................................................................33
2.2. Clay mineral systems .........................................................................................35
2.2.1. Adsorption of organic molecules on kaolinite surfaces..................................35
2.2.2. Adsorption of antibiotics on vermiculite surface ............................................35
2.3. Quantum chemical analyses...............................................................................36
PART 3. RESULTS AND DISCUSSION .............................................................38
CHAPTER 1. ADSORPTION OF ORGANIC MOLECULES ON MATERIALS
SURFACES...............................................................................................................38
1.1. Adsorption of organic molecules on rutile-TiO2 (110) surface .........................38
1.1.1. Optimized structures .......................................................................................38
1.1.2. Energetic aspects ............................................................................................40
1.1.3. The quantum chemical analysis for the interactions on surface.....................42
1.1.4. Summary..........................................................................................................44
1.2. Adsorption of benzene derivatives on rutile-TiO2 (110) and anatase-TiO2 (101)
surfaces......................................................................................................................44
1.2.1. Geometrical structures....................................................................................44
1.2.2. Energetic aspects of the adsorption process...................................................481.2.3. Formation and role of intermolecular interactions ........................................50
1.2.4. Summary..........................................................................................................56
1.3. Adsorption of benzene derivatives on kaolinite (001) surface ..........................57
1.3.1. Optimized geometries......................................................................................57
1.3.2. Energetic aspects of the adsorption process...................................................59
1.3.3. Formation and role of intermolecular interactions ........................................61
1.3.4. Summary..........................................................................................................65
1.4. Adsorption of benzene derivatives on a K+-supported kaolinite (001) surface .65
1.4.1. Stable complexes .............................................................................................65
1.4.2. Adsorption energy ...........................................................................................66
1.4.3. AIM and NBO analyses...................................................................................68
1.4.4. Summary..........................................................................................................70
CHAPTER 2. ADSORPTION OF ANTIBIOTIC MOLECULES ON TiO2 AND
VERMICULITE SURFACES ..................................................................................72
2.1. Adsorption of enrofloxacin molecule on rutile-TiO2 (110) surface...................72
2.1.1. Stable structures..............................................................................................72
2.1.2. Energetic aspects of the adsorption process...................................................74
2.1.3. Characteristics of interactions on the surface ................................................75
2.1.4. Summary..........................................................................................................77
2.2. Adsorption of ampicillin, amoxicillin, and tetracycline molecules on rutile-TiO2
(110) surface..............................................................................................................78
2.2.1. Stable complexes .............................................................................................78
2.2.2. Energetic aspects of the adsorption process...................................................81
2.2.3. Characteristic properties of intermolecular interactions ...............................83
2.2.4. Summary..........................................................................................................87
2.3. Adsorption of ampicillin and amoxicillin molecules on anatase-TiO2 (101)
surface .......................................................................................................................88
2.3.1. Stable structures..............................................................................................88
2.3.2. Adsorption energy ...........................................................................................902.3.3. AIM and NBO analyses...................................................................................92
2.3.4. Summary..........................................................................................................94
2.4. Adsorption of chloramphenicol molecule on a vermiculite surface ..................95
2.4.1. Geometrical structures....................................................................................95
2.4.2. Adsorption, interaction, and deformation energies ........................................97
2.4.3. Characteristics of stable interactions upon adsorption process...................100
2.4.4. Summary........................................................................................................104
2.5. Adsorption of β-lactam antibiotics on vermiculite surface..............................105
2.5.1. Stable structures............................................................................................105
2.5.2. Energetic aspects of the adsorption process.................................................109
2.5.3. Existence and role of different interactions upon complexation ..................113
2.5.4. Summary........................................................................................................118
CONCLUSIONS AND OUTLOOK ....................................................................120
1. Conclusions .........................................................................................................120
2. Outlook................................................................................................................122
LIST OF PUBLICATIONS CONTRIBUTES TO THIS THESIS.........................123
REFERENCES........................................................................................................124
AppendixLIST 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 (001) 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 onedimensional crystals of Na atoms
27
Figure 3. The graph shows the first random substitution for two alkali
metals Na, Cs according to Hellmann
28
Figure 4. The slab models of rutile-TiO2 (110) and anatase-TiO2 (101)
surfaces
33
Figure 5. The structure of kaolinite surfaces 35
Figure 6. The model slab of vermiculite surface (red, yellow, grey, pink,
and white colors displayed for O, Mg, Si, Al, and H atoms, respectively)
36
Figure 1.1. Stable complexes for the adsorption of organic molecules on
rutile-TiO2 (110) surface
38
Figure 1.2. The charge density between adsorbent and adsorbates in stable
complexes
42
Figure 1.3. The topological analysis for the first-layered structures 42
Figure 1.4. Stable complexes of adsorption of benzene derivatives on
rutile-TiO2 (110) surface
45
Figure 1.5. Stable structures of adsorption of benzene derivatives on
anatase-TiO2 (101) surface
47
Figure 1.6. MEP maps of benzene derivatives (isovalue = 0.02 au, charge
region taken in the range of 2.10-3 to 0.15 e)
50
Figure 1.7. Topological geometry of the first-layered structures of the
most stable complexes for rutile systems
53
Figure 1.8. Topological geometry of the first-layered structures of the
most stable complexes for anatase systems
53
Figure 1.9. EDT maps of investigated structures for rutile system 53
Figure 1.10. EDT maps of investigated structures for anatase system 53Figure 1.11. Stable structures of adsorption of derivatives on H-slab 57
Figure 1.12. Topological geometry of the most stable complexes for
adsorption of organic molecules on H-slab
62
Figure 1.13. Schematic of total electron density of complexes at the
B3LYP/6-31+G(d,p) level
64
Figure 1.14. The stable complexes of molecules adsorption on K+-slab 65
Figure 1.15. The topological geometries of the stable complexes for K+-
slab systems
68
Figure 1.16. The EDT maps of the stable complexes for K+-slab systems 68
Figure 2.1. Optimized structures of enrofloxacin, rutile-TiO2 (110)
surface, and two stable adsorption configurations
71
Figure 2.2. The topology and electron density transfer maps for the firstlayered structures of ER1 and ER2 at the B3LYP/6-31+G(d, p) level
75
Figure 2.3. Stable complexes for adsorption of antibiotic molecules on
rutile-TiO2 (110) surface
77
Figure 2.4. DOS plot of rutile-TiO2 (110) surface and HOMO, LUMO
levels of adsorbed antibiotic molecules
84
Figure 2.5. a) Topological critical points and b) electronic charge density
transfer of the most stable complexes
85
Figure 2.6. Optimized structures of anatase-TiO2 (101) surface and
ampicillin, amoxicillin molecules
87
Figure 2.7. The optimized structures of ampicillin, amoxicillin adsorbed
on anatase-TiO2 (101) surface
87
Figure 2.8. The topological geometries and EDT maps of the first-layered
structures
90
Figure 2.9. Optimized structures of a) vermiculite surface, and b)
chloramphenicol molecule, and c) the MEP map of chloramphenicol
(electron density of 0.02 au, from -5.10-5 to 0.15 au region).
93
Figure 2.10. Stable adsorption configurations of chloramphenicol on the 94vermiculite surface
Figure 2.11. Topological features for the first layered structures of
complexes
99
Figure 2.12. Total electron density distributions of the first-layered
structures
101
Figure 2.13. Stable complexes of adsorption of AP, AX and BP on a
vermiculite surface
104
Figure 2.14. Molecular electrostatic potential (MEP) of free antibiotic
molecules
110
Figure 2.15. Topological features for the most stable adsorption
configurations
112
Figure 2.16. Total electron density maps of most stable complexes 115LIST OF TABLES
Page
Table 1.1. Charge distribution in molecules at the B3LYP/6-31+G(d,p)
level
38
Table 1.2. Some selected parameters of stable complexes at PBE
functional (distance (r) in Å; angle (α) in degree)
39
Table 1.3. Adsorption, interaction, and deformation energies (all in
kcal.mol-1) for the adsorption processes on rutile-TiO2 (110) surface
40
Table 1.4. The characteristic parameters for topological analysis (all in
au)
43
Table 1.5. Some selected parameters of molecules and TiO2 surfaces 45
Table 1.6. Interaction distance (d, Å), bond angle (α, o), and changes in
length of bonds (r, Å) following the adsorption process for rutile systems
46
Table 1.7. Distance of intermolecular interactions (d, Å), bonding angle
(α, o), and changes of bond length (Δr, Å) upon adsorption process for
anatase systems
46
Table 1.8. Adsorption, interaction, and deformation energies of adsorption
of benzene derivatives on rutile-TiO2 (110) surface (all in kcal.mol-1)
48
Table 1.9. Energetic aspects of adsorption of benzene derivatives on
anatase-TiO2 (101) surface (all in kcal.mol-1)
49
Table 1.10. NBO charges at atoms in functional groups involved in
interactions in complexes
51
Table 1.11. Proton affinity (PA) at O and N atoms and deprotonation
enthalpy (DPE) of O-H and N-H bonds in functional groups and C-H
bonds in the benzene ring of derivatives (in kcal.mol-1)
52
Table 1.12. Characteristic parameters for topological geometry (ρ(r),
2(ρ(r)), H(r), in au), EDT (in e) for rutile systems
54
Table 1.13. Characteristic parameters for topological geometry (ρ(r),
2(ρ(r)), H(r), in au), EDT (in e) for anatase systems
55Table 1.14. Distances of intermolecular contacts (d), changes in the bond
lengths (Δr) involved in interactions in complexes (all in Å)
58
Table 1.15. Energetic parameters of complexes, molecules and surface
upon adsorption processes (in kcal.mol-1)
59
Table 1.16. Characteristics of topological geometries (ρ(r),
2
ρ(r), H(r),
in au) and EDT (in e) at the B3LYP/6-31+G(d,p) level
62
Table 1.17. The adsorption energy of the stable complexes (in kcal.mol-1) 66
Table 1.18. The characteristics for topology analysis and total of electron
density transfer (EDT) for K+-slab systems at the B3LYP/6-31+G(d,p)
level
69
Table 2.1. Some selected parameters for two stable complexes using PBE
functional
72
Table 2.2. Energies for adsorption of Enrofloxacin on rutile-TiO2 (110)
surface (in kcal.mol-1)
73
Table 2.3. The topological analysis and EDT of investigated structures at
the B3LYP/6-31+G(d, p) level
75
Table 2.4. Some selected parameters for stable adsorption configurations 78
Table 2.5. Energies for adsorption processes using both PBE and optPBEvdW functionals (kcal.mol-1) a)
80
Table 2.6. Some characteristic parameters of the stable complexes 88
Table 2.7. Adsorption energy (Eads, kcal.mol-1) of stable complexes 89
Table 2.8. The topological analysis (ρ(r), 2(ρ(r)), H(r), au), electron
density transfers (EDT, e), and hyper-conjugation energies (E2, kcal.mol-1)
91
Table 2.9. Energetic aspects of adsorption of chloramphenicol on the
vermiculite surface (all in kcal.mol-1)
95
Table 2.10. Proton affinity (PA) at O and Cl atoms and vertical deprotonation enthalpy (DPE) of O-H and C-H bonds of chloramphenicol
molecule (in kcal.mol-1)
98
Table 2.11. Topological analysis at the bond critical points (BCPs) of 100intermolecular contacts (in au), hydrogen bond energy (in kcal.mol-1) and
total electron density transfer (EDT, in e) of complexes
Table 2.12. Some selected parameters for optimized complexes shown in
Figure 2.13 (bond distances in Angstrom (Å) and angles in degree (o),
values from DFT computations) *)
105
Table 2.13. Adsorption energies (Eads), interaction energies (Eint) and
deformation energies for antibiotics and vermiculite surface (Edef-mol, Edefsurf) (in kcal.mol-1)
107
Table 2.14. Proton affinity (PA) at atoms or π-ring and deprotonation
enthalpy (DPE) of O(N,C)-H bonds of molecules (kcal.mol-1, obtained
from B3LYP/6-311++G(d,p) computations)*)
111
Table 2.15. Topological analysis (ρ(r), 2(ρ(r)), au) at the bond critical
points (BCPs), hydrogen bond energy (EB, kcal.mol-1) and total electron
density transfer (EDT, e) of most stable complexes at the B3LYP/6-
31+G(d,p) level
1131
INTRODUCTION
1. Motivation
Scientists have constantly been paying considerable attention to problems
related to environmental pollution in which the pollution of water resources remains
a painful global issue [51], [52]. The development of several large-scale industries
leads to a continuous release of toxic compounds into wastewater. They are present
in the environments, gradually accumulated in a significant concentration, and hard
to be biodegraded. Of the pollutants, the derivatives of phenol, carboxylic acids, and
medicinal products are directly and dangerously affecting the organisms‘ lives [5],
[86]. In addition, some antibiotics which are extensively used in shrimp farming and
released in wastewater were found to induce negative effects on both environments
and living organisms [5], [51], [52], [13]. Over the past few decades, experimental
and theoretical studies have been reported on advanced materials and nanomaterials
with high applicability in the fields of science, technology, and environments.
Among nanomaterials, TiO2 has been known as an essential semiconductor and is
widely applied in various fields of energy and health care [32], [43], [121]. Solid
TiO2 is extensively used in the photocatalysis, adsorption, and decomposition of
organic compounds due to its unique surface properties. The processes usually take
place on the TiO2 surfaces and depend on the nature, concentration of the substance,
and the material phases [29], [32], [121], [129]. Notably, the interaction of organic
molecules on surfaces of TiO2 was observed in the initial steps of catalysis, sensors,
drug transmission processes [30], [118], [130]. An insight into the adsorptive
interactions of organic molecules onto surfaces of materials such as TiO2 is the
basis for further understanding the interactions between molecules and ions with
solid-state surfaces. However, research on the fundamental nature and role of
adsorptive interactions and the mechanism of processes that occurred on TiO2
surfaces has not been investigated in detail yet.2
Many previous reports focused on elimination of harmful substances that
cause negative effects on the environment by using nanomaterials or advanced
technologies. Several physical, chemical, and biological solutions were proposed to
achieve the necessary efficiency. Some recent materials have been examined for the
adsorption and treatment capacity of organic pollutants, including activated carbon,
filter membranes, and advanced oxidations. The adsorption of organic molecules
onto surfaces of materials is a suitable way for removing amounts of pollutants
from a specific environment, including antibiotics presented in wastewaters [32],
[121], [122], [136]. However, these approaches require high cost and are too
sophisticated to use [4], [5], [94], [140]. Thus, several studies have been performed
to find out low-cost, environmentally friendly, and highly effective materials to
remove polluted compounds from the environment.
Of the various available materials, scientists have paid a considerable
amount of attention to clay minerals due to their high adsorption capacity,
convenient fabrication, and abundant availability in nature and environmental
friendliness [19], [38], [46], [70], [91], [100], [113], [131], [142], [145]. Clay
mineral materials are characterized by layered structures and a large spatial surface.
The addition or replacement of suitable cations on their surfaces could increase the
adsorption capacity as well as the removal of toxic substances. Investigations of the
adsorption of organic substances and antibiotic residues using clay mineral
materials are feasible and have scientific and practical significances. Notably,
vermiculite is promised to be a potential candidate to treat persistent organic
substances, as it eliminates antibiotic residues in aquatic environments [130].
However, the role of intermolecular interactions and adsorption mechanism on
surfaces of minerals has not fully been understood yet.
Furthermore, to examine the application ability of TiO2 and clay minerals
materials for an efficent treatement of organic pollutants, we must understand the
origin and role of surface interactions, and the inherent stability of geometrical
configurations upon the adsorption process. It is the basis for further understanding3
the interactions between molecules and ions with solid-state surfaces. In recent
years, modeling studies using molecular dynamics and quantum chemical methods
for the surface science field have increasingly been carried out thoroughly [37],
[78], [81], [92]. The development of modern and high-performance computer
systems and efficient computer programs helped scientists significantly in
theoretical studies. Many scientists examined the characteristics of TiO2 and clay
minerals materials, including structural and electronic properties, spectroscopy, and
surface processes [8], [20], [35], [109]. In this context, theoretical investigations on
adsorption and decomposition of organic molecules, incredibly polluted compounds
on materials surfaces by using quantum chemical calculations appear to be an
approach of choice to understand the surface phenomena.
In conclusion, the present theoretical work finds its importance in the
detailed insights and thereby applicability in future experimental studies to find
potential and efficient materials for treating organic pollutants. Hence, a theoretical
investigation with the title: ―Study on the adsorption ability of organic molecules on
TiO2 and clay mineral materials using computational chemistry methods‖ is of high
scientific and practical significance. Our calculated results can be served to orient
subsequent experimental observations and suggest relevant experiments in Vietnam.
2. Research purpose
The purposes of our theoretical studies can be summarized as follows:
i) Determination of the stable structures upon the adsorption of various
organic molecules on material surfaces of TiO2 and clay minerals;
ii) Investigation and examination of the adsorption ability of organic
molecules, antibiotics on TiO2 and clay minerals surfaces;
iii) Obtention of insights into surface interactions, including their formation
and role to the stability of complexes and adsorption processes;
iv) Evaluation of the use of TiO2 and clay minerals materials in future
experimental studies on the adsorption and removal of antibiotics and organic
pollutants in wastewater.4
3. Object and scope of this study
The selected organic molecules and antibiotics include benzene and its
derivatives, ampicillin, amoxicillin, benzylpenicillin, enrofloxacin, and tetracycline.
The material surfaces considered in this work include TiO2 (rutile, anatase),
kaolinite, and vermiculite.
The scope of this study is theoretical investigations of the adsorption ability
of organic compounds, especially antibiotics, on the surfaces of TiO2 (anatase,
rutile) and clay minerals (kaolinite, vermiculite) by using computational chemistry
methods.
4. Research contents
Part 1 gives an overview of previous studies related to this work. A brief
description of quantum chemical approaches in solving the Schrodinger equations is
shown in the first sections of Part 2. In addition, details on computations for
selected systems are also given in the later sections.
Chapters 1 and 2 in Part 3 present the calculations and theoretical results on
adsorptions of organic molecules, especially antibiotics on different material
surfaces of TiO2 and clay minerals. More particularly, the work that are carried out
include i) Optimization of the structures of organic molecules containing different
functional groups (-OH, -COOH, -NH2, -CHO, -NO2, and -SO3H), antibiotics,
materials including TiO2 (rutile-TiO2 (110) and anatase-TiO2 (101) surfaces), clay
minerals (vermiculite and kaolinite); ii) Design and optimization to obtain stable
structures for the adsorption of selected molecules on the surfaces of TiO2 and clay
minerals; iii) Calculations of interesting parameters, energetic parameters following
the adsorption of molecules onto TiO2 and clay minerals surfaces; iv) Analysis and
evaluation of the adsorption ability of organic molecules, antibiotics on different
surfaces of TiO2, clay minerals and the role of intermolecular interactions formed
on the material surfaces in the investigated systems.5
In one of the crucial sections, conclusions and outlook, we summarize the
significant results achieved in the present work and give some outlooks for further
investigations.
5. Methodology
The density functional theory (DFT) methods with suitable and highly
correlated functionals, such as the PBE, optPBE-vdW, vdW-DF-C09 [25], [72],
[104], are considered for the optimization and calculation of characteristic
parameters, such as geometrical and electronic structures of organic molecules,
antibiotics, materials surfaces as well as stable configurations. The energy aspects,
including adsorption, interaction, and deformation energies, are then calculated to
evaluate molecules' adsorption ability on material surfaces.
The VASP, GPAW packages [39], [57], [68], and some visualized software
such as Gaussview, VESTA, and Material Studio are used to simulate the structures
of TiO2, clay minerals materials, and the configurations formed by the adsorption of
molecules onto material surfaces. These programs are also used to calculate
energetic values and other parameters. In addition, to consider the formation and
role of intermolecular interactions, the calculations on DPE, PA, MEP, topological
geometry, and EDT are performed by using Gaussian packages (versions 03 and
09), AIM2000 and NBO 5.G programs [9], [12], [42], [134].
Details of calculations and analyses for the investigated systems are
presented in the computational methods section.
6. Novelty, scientific and practical significance
Scientists in Vietnam and worldwide have not yet paid sufficient attention to
studies on the adsorption ability of organic molecules containing benzene rings onto
TiO2 and clay minerals surfaces, especially theoretical investigations using
computational chemistry. The present results would first provide us with insights
into the adsorption ability of organic molecules and antibiotics on the material
surfaces such as TiO2 and clay minerals. It appears that the results of such research
in surface phenomena can be used to put forward solutions for environmental6
problems. A better understanding of surface interactions is vital for the selection
and use of suitable materials to treat organic pollutants. The results of this work
lead to a good assessment of the adsorption processes that take place on the surfaces
of TiO2 and clay minerals. This study is also an essential investigation for guiding
subsequent experimental studies to remove or decompose pollutants in the
environments.
Our present work results give insights into the adsorption ability of organic
compounds containing different functional groups such as -OH, -COOH, -CHO,
>C=O, NO2, -NH2, -SO3H on the TiO2, kaolinite and vermiculite surfaces.
Remarkably, the role and origin of intermolecular interactions contributing to the
stability of complexes and the adsorption ability of molecules on the material
surfaces can be clarified by using quantum chemical methods. The obtained results
are valuable references for future studies on treatment of polluted compounds in
wastewater sources.
The novelty of this work has been demonstrated by the papers published in
peer-reviewed journals such as Surface Science, Chemical Physics Letters, Vietnam
Journal of Chemistry, Vietnam Journal of Science and Technology, Vietnam
Journal of Catalysis and Adsorption, Quy Nhon University Journal of Science.7
PART 1. OVERVIEW OF LITERATURE
1. Organic pollutants and antibiotics residues in wastewaters
In recent decades, as environmental pollution has emerged as a global and
persistent issue, scientists and policy makers have been paying considerable
attention to its consequences [45], [146], [149]. Because compounds containing
benzene rings were accumulated for a long time in large amounts as part of the
human living conditions [71], it was more and more difficult to completely remove
them from environments. Besides, several antibiotics that are used for various
purposes and released in the wastewaters, induce more negative impacts on the
environments [5], [24], [51], [52], [86], [106], [150]. Antibiotics have been used
extensively not only for treatment of human and animal diseases but also for
industry-scale production of aquatic organisms and in the fields of medicine,
biology, biochemistry, life science, and agriculture [1], [3], [28], [41], [47], [95],
[99], [105], [114], [135], [140]. The uncontrolled use and release of antibioticscontaining waste are continuously causing many environmental and health
problems, such as the pollution of aquatic resources damaging effects on the growth
of living organisms [35], [54].
On the other hand, the growth and export of shrimp and other seafood bring
in high economic values and benefits contributing to the development of the
country. In Vietnam, shrimp farming has been and still is, an essential economic
sector [13]. There has been increasing attention on both the quantity and quality of
shrimp production. Many solutions, models, and advanced technologies were
proposed to achieve the highest results. However, water pollution caused by
farming and processing of shrimp are not still treated thoroughly. In wastewater,
many harmful substances that strongly pollute the environment, are present such as
antibiotic residues, stimulants, nitrogen and phosphorus compounds, and wastes
from the metabolism of food‘s nutrients [27]. Notably, antibiotics such as
tetracycline, penicillins, and quinolones family were, and still are, widely used in8
shrimp farming, especially in Vietnam, but they were, and still are, not strictly
controlled [14], [62]. For the well-being of society, it is imperative to safely remove
pollutants, especially antibiotics, in wastewater discharged from shrimp farming.
2. TiO2 nanomaterial and its applications
Do Drive thay đổi chính sách, nên một số link cũ yêu cầu duyệt download. các bạn chỉ cần làm theo hướng dẫn.
Password giải nén nếu cần: ket-noi.com | Bấm trực tiếp vào Link để tải:
Nghiên cứu khả năng hấp phụ một số hợp chất hữu cơ trên các vật liệu tio2 và khoáng sét bằng phương pháp hóa học tính toán
STUDY ON THE ADSORPTION ABILITY OF ORGANIC MOLECULES ON TiO2 AND CLAY MINERAL MATERIALS USING COMPUTATIONAL CHEMISTRY METHODS
Acknowledgements
First of all, I would like to express my sincerest thanks to the supervisors,
Assoc. Prof. 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 Giúp 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. A.J.P. 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 Giúp 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.2019.TS.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 TriTABLE OF CONTENTS
List of Symbols and Notations
List of Figures
List of Tables
INTRODUCTION.....................................................................................................1
1. Motivation ...............................................................................................................1
2. Research purpose ....................................................................................................3
3. Object and scope of this study ................................................................................4
4. Research contents....................................................................................................4
5. Methodology ...........................................................................................................5
6. Novelty, scientific and practical significance .........................................................5
PART 1. OVERVIEW OF LITERATURE ............................................................7
1. Organic pollutants and antibiotics residues in wastewaters....................................7
2. TiO2 nanomaterial and its applications ...................................................................8
3. Clay minerals and their applications in the treatment of pollutants......................10
4. Investigations on materials surfaces using computational chemistry...................12
PART 2. THEORETICAL BACKGROUND AND COMPUTATIONAL
METHODS ..............................................................................................................13
1. Quantum chemical approaches .............................................................................13
1.1. Schrödinger equations........................................................................................13
1.2. The Born - Oppenheimer approximation and Pauli‘s exclusion principle ........15
1.2.1. Born – Oppenheimer approximation ..............................................................15
1.2.2. Pauli’s exclusion principle..............................................................................15
1.3. The variational principle ....................................................................................16
1.4. Basis sets ............................................................................................................17
1.4.1. Slater and Gaussian orbitals...........................................................................17
1.4.2. Some popular basis sets ..................................................................................18
1.5. Hartree-Fock approximation ..............................................................................191.6. Density functional theory...................................................................................20
1.6.1. The Hohenberg-Kohn theorem........................................................................21
1.6.2. Kohn-Sham equations .....................................................................................21
1.6.3. Local density approximation...........................................................................22
1.6.4. General gradient approximation ....................................................................23
1.6.5. Hybrid functionals...........................................................................................24
1.6.6. Van der Waals functionals ..............................................................................25
1.7. Pseudopotential and plane-wave methods .........................................................26
1.8. Atoms In Molecules and Natural Bond Orbitals approaches.............................29
1.8.1. Atoms In Molecules analysis...........................................................................29
1.8.2. Natural Bond Orbitals analysis ......................................................................31
2. Computational methods ........................................................................................33
2.1. TiO2 systems ......................................................................................................33
2.2. Clay mineral systems .........................................................................................35
2.2.1. Adsorption of organic molecules on kaolinite surfaces..................................35
2.2.2. Adsorption of antibiotics on vermiculite surface ............................................35
2.3. Quantum chemical analyses...............................................................................36
PART 3. RESULTS AND DISCUSSION .............................................................38
CHAPTER 1. ADSORPTION OF ORGANIC MOLECULES ON MATERIALS
SURFACES...............................................................................................................38
1.1. Adsorption of organic molecules on rutile-TiO2 (110) surface .........................38
1.1.1. Optimized structures .......................................................................................38
1.1.2. Energetic aspects ............................................................................................40
1.1.3. The quantum chemical analysis for the interactions on surface.....................42
1.1.4. Summary..........................................................................................................44
1.2. Adsorption of benzene derivatives on rutile-TiO2 (110) and anatase-TiO2 (101)
surfaces......................................................................................................................44
1.2.1. Geometrical structures....................................................................................44
1.2.2. Energetic aspects of the adsorption process...................................................481.2.3. Formation and role of intermolecular interactions ........................................50
1.2.4. Summary..........................................................................................................56
1.3. Adsorption of benzene derivatives on kaolinite (001) surface ..........................57
1.3.1. Optimized geometries......................................................................................57
1.3.2. Energetic aspects of the adsorption process...................................................59
1.3.3. Formation and role of intermolecular interactions ........................................61
1.3.4. Summary..........................................................................................................65
1.4. Adsorption of benzene derivatives on a K+-supported kaolinite (001) surface .65
1.4.1. Stable complexes .............................................................................................65
1.4.2. Adsorption energy ...........................................................................................66
1.4.3. AIM and NBO analyses...................................................................................68
1.4.4. Summary..........................................................................................................70
CHAPTER 2. ADSORPTION OF ANTIBIOTIC MOLECULES ON TiO2 AND
VERMICULITE SURFACES ..................................................................................72
2.1. Adsorption of enrofloxacin molecule on rutile-TiO2 (110) surface...................72
2.1.1. Stable structures..............................................................................................72
2.1.2. Energetic aspects of the adsorption process...................................................74
2.1.3. Characteristics of interactions on the surface ................................................75
2.1.4. Summary..........................................................................................................77
2.2. Adsorption of ampicillin, amoxicillin, and tetracycline molecules on rutile-TiO2
(110) surface..............................................................................................................78
2.2.1. Stable complexes .............................................................................................78
2.2.2. Energetic aspects of the adsorption process...................................................81
2.2.3. Characteristic properties of intermolecular interactions ...............................83
2.2.4. Summary..........................................................................................................87
2.3. Adsorption of ampicillin and amoxicillin molecules on anatase-TiO2 (101)
surface .......................................................................................................................88
2.3.1. Stable structures..............................................................................................88
2.3.2. Adsorption energy ...........................................................................................902.3.3. AIM and NBO analyses...................................................................................92
2.3.4. Summary..........................................................................................................94
2.4. Adsorption of chloramphenicol molecule on a vermiculite surface ..................95
2.4.1. Geometrical structures....................................................................................95
2.4.2. Adsorption, interaction, and deformation energies ........................................97
2.4.3. Characteristics of stable interactions upon adsorption process...................100
2.4.4. Summary........................................................................................................104
2.5. Adsorption of β-lactam antibiotics on vermiculite surface..............................105
2.5.1. Stable structures............................................................................................105
2.5.2. Energetic aspects of the adsorption process.................................................109
2.5.3. Existence and role of different interactions upon complexation ..................113
2.5.4. Summary........................................................................................................118
CONCLUSIONS AND OUTLOOK ....................................................................120
1. Conclusions .........................................................................................................120
2. Outlook................................................................................................................122
LIST OF PUBLICATIONS CONTRIBUTES TO THIS THESIS.........................123
REFERENCES........................................................................................................124
AppendixLIST 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 (001) 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 onedimensional crystals of Na atoms
27
Figure 3. The graph shows the first random substitution for two alkali
metals Na, Cs according to Hellmann
28
Figure 4. The slab models of rutile-TiO2 (110) and anatase-TiO2 (101)
surfaces
33
Figure 5. The structure of kaolinite surfaces 35
Figure 6. The model slab of vermiculite surface (red, yellow, grey, pink,
and white colors displayed for O, Mg, Si, Al, and H atoms, respectively)
36
Figure 1.1. Stable complexes for the adsorption of organic molecules on
rutile-TiO2 (110) surface
38
Figure 1.2. The charge density between adsorbent and adsorbates in stable
complexes
42
Figure 1.3. The topological analysis for the first-layered structures 42
Figure 1.4. Stable complexes of adsorption of benzene derivatives on
rutile-TiO2 (110) surface
45
Figure 1.5. Stable structures of adsorption of benzene derivatives on
anatase-TiO2 (101) surface
47
Figure 1.6. MEP maps of benzene derivatives (isovalue = 0.02 au, charge
region taken in the range of 2.10-3 to 0.15 e)
50
Figure 1.7. Topological geometry of the first-layered structures of the
most stable complexes for rutile systems
53
Figure 1.8. Topological geometry of the first-layered structures of the
most stable complexes for anatase systems
53
Figure 1.9. EDT maps of investigated structures for rutile system 53
Figure 1.10. EDT maps of investigated structures for anatase system 53Figure 1.11. Stable structures of adsorption of derivatives on H-slab 57
Figure 1.12. Topological geometry of the most stable complexes for
adsorption of organic molecules on H-slab
62
Figure 1.13. Schematic of total electron density of complexes at the
B3LYP/6-31+G(d,p) level
64
Figure 1.14. The stable complexes of molecules adsorption on K+-slab 65
Figure 1.15. The topological geometries of the stable complexes for K+-
slab systems
68
Figure 1.16. The EDT maps of the stable complexes for K+-slab systems 68
Figure 2.1. Optimized structures of enrofloxacin, rutile-TiO2 (110)
surface, and two stable adsorption configurations
71
Figure 2.2. The topology and electron density transfer maps for the firstlayered structures of ER1 and ER2 at the B3LYP/6-31+G(d, p) level
75
Figure 2.3. Stable complexes for adsorption of antibiotic molecules on
rutile-TiO2 (110) surface
77
Figure 2.4. DOS plot of rutile-TiO2 (110) surface and HOMO, LUMO
levels of adsorbed antibiotic molecules
84
Figure 2.5. a) Topological critical points and b) electronic charge density
transfer of the most stable complexes
85
Figure 2.6. Optimized structures of anatase-TiO2 (101) surface and
ampicillin, amoxicillin molecules
87
Figure 2.7. The optimized structures of ampicillin, amoxicillin adsorbed
on anatase-TiO2 (101) surface
87
Figure 2.8. The topological geometries and EDT maps of the first-layered
structures
90
Figure 2.9. Optimized structures of a) vermiculite surface, and b)
chloramphenicol molecule, and c) the MEP map of chloramphenicol
(electron density of 0.02 au, from -5.10-5 to 0.15 au region).
93
Figure 2.10. Stable adsorption configurations of chloramphenicol on the 94vermiculite surface
Figure 2.11. Topological features for the first layered structures of
complexes
99
Figure 2.12. Total electron density distributions of the first-layered
structures
101
Figure 2.13. Stable complexes of adsorption of AP, AX and BP on a
vermiculite surface
104
Figure 2.14. Molecular electrostatic potential (MEP) of free antibiotic
molecules
110
Figure 2.15. Topological features for the most stable adsorption
configurations
112
Figure 2.16. Total electron density maps of most stable complexes 115LIST OF TABLES
Page
Table 1.1. Charge distribution in molecules at the B3LYP/6-31+G(d,p)
level
38
Table 1.2. Some selected parameters of stable complexes at PBE
functional (distance (r) in Å; angle (α) in degree)
39
Table 1.3. Adsorption, interaction, and deformation energies (all in
kcal.mol-1) for the adsorption processes on rutile-TiO2 (110) surface
40
Table 1.4. The characteristic parameters for topological analysis (all in
au)
43
Table 1.5. Some selected parameters of molecules and TiO2 surfaces 45
Table 1.6. Interaction distance (d, Å), bond angle (α, o), and changes in
length of bonds (r, Å) following the adsorption process for rutile systems
46
Table 1.7. Distance of intermolecular interactions (d, Å), bonding angle
(α, o), and changes of bond length (Δr, Å) upon adsorption process for
anatase systems
46
Table 1.8. Adsorption, interaction, and deformation energies of adsorption
of benzene derivatives on rutile-TiO2 (110) surface (all in kcal.mol-1)
48
Table 1.9. Energetic aspects of adsorption of benzene derivatives on
anatase-TiO2 (101) surface (all in kcal.mol-1)
49
Table 1.10. NBO charges at atoms in functional groups involved in
interactions in complexes
51
Table 1.11. Proton affinity (PA) at O and N atoms and deprotonation
enthalpy (DPE) of O-H and N-H bonds in functional groups and C-H
bonds in the benzene ring of derivatives (in kcal.mol-1)
52
Table 1.12. Characteristic parameters for topological geometry (ρ(r),
2(ρ(r)), H(r), in au), EDT (in e) for rutile systems
54
Table 1.13. Characteristic parameters for topological geometry (ρ(r),
2(ρ(r)), H(r), in au), EDT (in e) for anatase systems
55Table 1.14. Distances of intermolecular contacts (d), changes in the bond
lengths (Δr) involved in interactions in complexes (all in Å)
58
Table 1.15. Energetic parameters of complexes, molecules and surface
upon adsorption processes (in kcal.mol-1)
59
Table 1.16. Characteristics of topological geometries (ρ(r),
2
ρ(r), H(r),
in au) and EDT (in e) at the B3LYP/6-31+G(d,p) level
62
Table 1.17. The adsorption energy of the stable complexes (in kcal.mol-1) 66
Table 1.18. The characteristics for topology analysis and total of electron
density transfer (EDT) for K+-slab systems at the B3LYP/6-31+G(d,p)
level
69
Table 2.1. Some selected parameters for two stable complexes using PBE
functional
72
Table 2.2. Energies for adsorption of Enrofloxacin on rutile-TiO2 (110)
surface (in kcal.mol-1)
73
Table 2.3. The topological analysis and EDT of investigated structures at
the B3LYP/6-31+G(d, p) level
75
Table 2.4. Some selected parameters for stable adsorption configurations 78
Table 2.5. Energies for adsorption processes using both PBE and optPBEvdW functionals (kcal.mol-1) a)
80
Table 2.6. Some characteristic parameters of the stable complexes 88
Table 2.7. Adsorption energy (Eads, kcal.mol-1) of stable complexes 89
Table 2.8. The topological analysis (ρ(r), 2(ρ(r)), H(r), au), electron
density transfers (EDT, e), and hyper-conjugation energies (E2, kcal.mol-1)
91
Table 2.9. Energetic aspects of adsorption of chloramphenicol on the
vermiculite surface (all in kcal.mol-1)
95
Table 2.10. Proton affinity (PA) at O and Cl atoms and vertical deprotonation enthalpy (DPE) of O-H and C-H bonds of chloramphenicol
molecule (in kcal.mol-1)
98
Table 2.11. Topological analysis at the bond critical points (BCPs) of 100intermolecular contacts (in au), hydrogen bond energy (in kcal.mol-1) and
total electron density transfer (EDT, in e) of complexes
Table 2.12. Some selected parameters for optimized complexes shown in
Figure 2.13 (bond distances in Angstrom (Å) and angles in degree (o),
values from DFT computations) *)
105
Table 2.13. Adsorption energies (Eads), interaction energies (Eint) and
deformation energies for antibiotics and vermiculite surface (Edef-mol, Edefsurf) (in kcal.mol-1)
107
Table 2.14. Proton affinity (PA) at atoms or π-ring and deprotonation
enthalpy (DPE) of O(N,C)-H bonds of molecules (kcal.mol-1, obtained
from B3LYP/6-311++G(d,p) computations)*)
111
Table 2.15. Topological analysis (ρ(r), 2(ρ(r)), au) at the bond critical
points (BCPs), hydrogen bond energy (EB, kcal.mol-1) and total electron
density transfer (EDT, e) of most stable complexes at the B3LYP/6-
31+G(d,p) level
1131
INTRODUCTION
1. Motivation
Scientists have constantly been paying considerable attention to problems
related to environmental pollution in which the pollution of water resources remains
a painful global issue [51], [52]. The development of several large-scale industries
leads to a continuous release of toxic compounds into wastewater. They are present
in the environments, gradually accumulated in a significant concentration, and hard
to be biodegraded. Of the pollutants, the derivatives of phenol, carboxylic acids, and
medicinal products are directly and dangerously affecting the organisms‘ lives [5],
[86]. In addition, some antibiotics which are extensively used in shrimp farming and
released in wastewater were found to induce negative effects on both environments
and living organisms [5], [51], [52], [13]. Over the past few decades, experimental
and theoretical studies have been reported on advanced materials and nanomaterials
with high applicability in the fields of science, technology, and environments.
Among nanomaterials, TiO2 has been known as an essential semiconductor and is
widely applied in various fields of energy and health care [32], [43], [121]. Solid
TiO2 is extensively used in the photocatalysis, adsorption, and decomposition of
organic compounds due to its unique surface properties. The processes usually take
place on the TiO2 surfaces and depend on the nature, concentration of the substance,
and the material phases [29], [32], [121], [129]. Notably, the interaction of organic
molecules on surfaces of TiO2 was observed in the initial steps of catalysis, sensors,
drug transmission processes [30], [118], [130]. An insight into the adsorptive
interactions of organic molecules onto surfaces of materials such as TiO2 is the
basis for further understanding the interactions between molecules and ions with
solid-state surfaces. However, research on the fundamental nature and role of
adsorptive interactions and the mechanism of processes that occurred on TiO2
surfaces has not been investigated in detail yet.2
Many previous reports focused on elimination of harmful substances that
cause negative effects on the environment by using nanomaterials or advanced
technologies. Several physical, chemical, and biological solutions were proposed to
achieve the necessary efficiency. Some recent materials have been examined for the
adsorption and treatment capacity of organic pollutants, including activated carbon,
filter membranes, and advanced oxidations. The adsorption of organic molecules
onto surfaces of materials is a suitable way for removing amounts of pollutants
from a specific environment, including antibiotics presented in wastewaters [32],
[121], [122], [136]. However, these approaches require high cost and are too
sophisticated to use [4], [5], [94], [140]. Thus, several studies have been performed
to find out low-cost, environmentally friendly, and highly effective materials to
remove polluted compounds from the environment.
Of the various available materials, scientists have paid a considerable
amount of attention to clay minerals due to their high adsorption capacity,
convenient fabrication, and abundant availability in nature and environmental
friendliness [19], [38], [46], [70], [91], [100], [113], [131], [142], [145]. Clay
mineral materials are characterized by layered structures and a large spatial surface.
The addition or replacement of suitable cations on their surfaces could increase the
adsorption capacity as well as the removal of toxic substances. Investigations of the
adsorption of organic substances and antibiotic residues using clay mineral
materials are feasible and have scientific and practical significances. Notably,
vermiculite is promised to be a potential candidate to treat persistent organic
substances, as it eliminates antibiotic residues in aquatic environments [130].
However, the role of intermolecular interactions and adsorption mechanism on
surfaces of minerals has not fully been understood yet.
Furthermore, to examine the application ability of TiO2 and clay minerals
materials for an efficent treatement of organic pollutants, we must understand the
origin and role of surface interactions, and the inherent stability of geometrical
configurations upon the adsorption process. It is the basis for further understanding3
the interactions between molecules and ions with solid-state surfaces. In recent
years, modeling studies using molecular dynamics and quantum chemical methods
for the surface science field have increasingly been carried out thoroughly [37],
[78], [81], [92]. The development of modern and high-performance computer
systems and efficient computer programs helped scientists significantly in
theoretical studies. Many scientists examined the characteristics of TiO2 and clay
minerals materials, including structural and electronic properties, spectroscopy, and
surface processes [8], [20], [35], [109]. In this context, theoretical investigations on
adsorption and decomposition of organic molecules, incredibly polluted compounds
on materials surfaces by using quantum chemical calculations appear to be an
approach of choice to understand the surface phenomena.
In conclusion, the present theoretical work finds its importance in the
detailed insights and thereby applicability in future experimental studies to find
potential and efficient materials for treating organic pollutants. Hence, a theoretical
investigation with the title: ―Study on the adsorption ability of organic molecules on
TiO2 and clay mineral materials using computational chemistry methods‖ is of high
scientific and practical significance. Our calculated results can be served to orient
subsequent experimental observations and suggest relevant experiments in Vietnam.
2. Research purpose
The purposes of our theoretical studies can be summarized as follows:
i) Determination of the stable structures upon the adsorption of various
organic molecules on material surfaces of TiO2 and clay minerals;
ii) Investigation and examination of the adsorption ability of organic
molecules, antibiotics on TiO2 and clay minerals surfaces;
iii) Obtention of insights into surface interactions, including their formation
and role to the stability of complexes and adsorption processes;
iv) Evaluation of the use of TiO2 and clay minerals materials in future
experimental studies on the adsorption and removal of antibiotics and organic
pollutants in wastewater.4
3. Object and scope of this study
The selected organic molecules and antibiotics include benzene and its
derivatives, ampicillin, amoxicillin, benzylpenicillin, enrofloxacin, and tetracycline.
The material surfaces considered in this work include TiO2 (rutile, anatase),
kaolinite, and vermiculite.
The scope of this study is theoretical investigations of the adsorption ability
of organic compounds, especially antibiotics, on the surfaces of TiO2 (anatase,
rutile) and clay minerals (kaolinite, vermiculite) by using computational chemistry
methods.
4. Research contents
Part 1 gives an overview of previous studies related to this work. A brief
description of quantum chemical approaches in solving the Schrodinger equations is
shown in the first sections of Part 2. In addition, details on computations for
selected systems are also given in the later sections.
Chapters 1 and 2 in Part 3 present the calculations and theoretical results on
adsorptions of organic molecules, especially antibiotics on different material
surfaces of TiO2 and clay minerals. More particularly, the work that are carried out
include i) Optimization of the structures of organic molecules containing different
functional groups (-OH, -COOH, -NH2, -CHO, -NO2, and -SO3H), antibiotics,
materials including TiO2 (rutile-TiO2 (110) and anatase-TiO2 (101) surfaces), clay
minerals (vermiculite and kaolinite); ii) Design and optimization to obtain stable
structures for the adsorption of selected molecules on the surfaces of TiO2 and clay
minerals; iii) Calculations of interesting parameters, energetic parameters following
the adsorption of molecules onto TiO2 and clay minerals surfaces; iv) Analysis and
evaluation of the adsorption ability of organic molecules, antibiotics on different
surfaces of TiO2, clay minerals and the role of intermolecular interactions formed
on the material surfaces in the investigated systems.5
In one of the crucial sections, conclusions and outlook, we summarize the
significant results achieved in the present work and give some outlooks for further
investigations.
5. Methodology
The density functional theory (DFT) methods with suitable and highly
correlated functionals, such as the PBE, optPBE-vdW, vdW-DF-C09 [25], [72],
[104], are considered for the optimization and calculation of characteristic
parameters, such as geometrical and electronic structures of organic molecules,
antibiotics, materials surfaces as well as stable configurations. The energy aspects,
including adsorption, interaction, and deformation energies, are then calculated to
evaluate molecules' adsorption ability on material surfaces.
The VASP, GPAW packages [39], [57], [68], and some visualized software
such as Gaussview, VESTA, and Material Studio are used to simulate the structures
of TiO2, clay minerals materials, and the configurations formed by the adsorption of
molecules onto material surfaces. These programs are also used to calculate
energetic values and other parameters. In addition, to consider the formation and
role of intermolecular interactions, the calculations on DPE, PA, MEP, topological
geometry, and EDT are performed by using Gaussian packages (versions 03 and
09), AIM2000 and NBO 5.G programs [9], [12], [42], [134].
Details of calculations and analyses for the investigated systems are
presented in the computational methods section.
6. Novelty, scientific and practical significance
Scientists in Vietnam and worldwide have not yet paid sufficient attention to
studies on the adsorption ability of organic molecules containing benzene rings onto
TiO2 and clay minerals surfaces, especially theoretical investigations using
computational chemistry. The present results would first provide us with insights
into the adsorption ability of organic molecules and antibiotics on the material
surfaces such as TiO2 and clay minerals. It appears that the results of such research
in surface phenomena can be used to put forward solutions for environmental6
problems. A better understanding of surface interactions is vital for the selection
and use of suitable materials to treat organic pollutants. The results of this work
lead to a good assessment of the adsorption processes that take place on the surfaces
of TiO2 and clay minerals. This study is also an essential investigation for guiding
subsequent experimental studies to remove or decompose pollutants in the
environments.
Our present work results give insights into the adsorption ability of organic
compounds containing different functional groups such as -OH, -COOH, -CHO,
>C=O, NO2, -NH2, -SO3H on the TiO2, kaolinite and vermiculite surfaces.
Remarkably, the role and origin of intermolecular interactions contributing to the
stability of complexes and the adsorption ability of molecules on the material
surfaces can be clarified by using quantum chemical methods. The obtained results
are valuable references for future studies on treatment of polluted compounds in
wastewater sources.
The novelty of this work has been demonstrated by the papers published in
peer-reviewed journals such as Surface Science, Chemical Physics Letters, Vietnam
Journal of Chemistry, Vietnam Journal of Science and Technology, Vietnam
Journal of Catalysis and Adsorption, Quy Nhon University Journal of Science.7
PART 1. OVERVIEW OF LITERATURE
1. Organic pollutants and antibiotics residues in wastewaters
In recent decades, as environmental pollution has emerged as a global and
persistent issue, scientists and policy makers have been paying considerable
attention to its consequences [45], [146], [149]. Because compounds containing
benzene rings were accumulated for a long time in large amounts as part of the
human living conditions [71], it was more and more difficult to completely remove
them from environments. Besides, several antibiotics that are used for various
purposes and released in the wastewaters, induce more negative impacts on the
environments [5], [24], [51], [52], [86], [106], [150]. Antibiotics have been used
extensively not only for treatment of human and animal diseases but also for
industry-scale production of aquatic organisms and in the fields of medicine,
biology, biochemistry, life science, and agriculture [1], [3], [28], [41], [47], [95],
[99], [105], [114], [135], [140]. The uncontrolled use and release of antibioticscontaining waste are continuously causing many environmental and health
problems, such as the pollution of aquatic resources damaging effects on the growth
of living organisms [35], [54].
On the other hand, the growth and export of shrimp and other seafood bring
in high economic values and benefits contributing to the development of the
country. In Vietnam, shrimp farming has been and still is, an essential economic
sector [13]. There has been increasing attention on both the quantity and quality of
shrimp production. Many solutions, models, and advanced technologies were
proposed to achieve the highest results. However, water pollution caused by
farming and processing of shrimp are not still treated thoroughly. In wastewater,
many harmful substances that strongly pollute the environment, are present such as
antibiotic residues, stimulants, nitrogen and phosphorus compounds, and wastes
from the metabolism of food‘s nutrients [27]. Notably, antibiotics such as
tetracycline, penicillins, and quinolones family were, and still are, widely used in8
shrimp farming, especially in Vietnam, but they were, and still are, not strictly
controlled [14], [62]. For the well-being of society, it is imperative to safely remove
pollutants, especially antibiotics, in wastewater discharged from shrimp farming.
2. TiO2 nanomaterial and its applications
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