MINISTRY OF EDUCATION AND TRAINING QUY NHON UNIVERSITY PHAN DANG CAM TU STUDY ON STABILITY AND NATURE OF INTERACTIONS OF FUNCTIONAL ORGANIC MOLECULES WITH CO2 AND H2O BY USING QUANTUM CHEMICAL METHOD DOCTORAL DISSERTATION BINH DINH - 2022 MINISTRY OF EDUCATION AND TRAINING QUY NHON UNIVERSITY PHAN DANG CAM TU STUDY ON STABILITY AND NATURE OF INTERACTIONS OF FUNCTIONAL ORGANIC MOLECULES WITH CO2 AND H2O BY USING QUANTUM CHEMICAL METHOD Major: Theoretical and Physical Chemistry Code No. Tran Van Man Reviewer 2: Assoc. Ngo Tuan Cuong Reviewer 3: Dr. Nguyen Minh Tam Supervisor: Assoc.
NGUYEN TIEN TRUNG BINH DINH - 2022 DECLARATION This dissertation was done at the Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, Binh Dinh province, under the supervision of Assoc. Nguyen Tien Trung. I hereby declare that the results presented are new and original. Most of them were published in peer-reviewed journals.
For using results from joint papers, I have gotten permissions from my co- authors. Binh Dinh, 2022 Supervisor Ph. Nguyen Tien Trung Phan Dang Cam Tu ACKNOWLEDGEMENT To all the family members, teachers, and friends, I would not complete this dissertation without their help and support. First, I am kindly thankful to my supervisor, Assoc.
Nguyen Tien Trung for his advice and encouragement during my PhD life. I also express thanks to Assoc. Vu Thi Ngan and Prof. Minh Tho Nguyen for their valuable advice and discussing some research problems.
I am thankful to all the past and present members of the LCCM lab for outgoing activities and valuable discussions during my research time. It is a pleasure for me to thank my seniors, Ho Quoc Dai and Nguyen Ngoc Tri for morning coffee chatting and solving all the technical problems. I gratefully acknowledge the lectures of the Department of Chemistry, Faculty of Natural Sciences, and the staff in the Office of Postgraduate Management, Quy Nhon University. I sincerely thank to the Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 104.11; Domestic PhD Scholarship Programme of Vingroup Innovation Foundation (VinIF), Vietnam; and the VLIR-TEAM project awarded to Quy Nhon University with Grant number ZEIN2016PR431 (2016-2020) for the financial support.
I heartily thank my long-time friends, Nhung and Nga, who always are by my side and share with me all the difficulties in life. Thanks should also go to Tran Quang Tue for helping me understand some mathematical aspects in the study of quantum chemistry; and to Nguyen Duy Phi, who encouraged me in the first two years of my PhD. Last but most important, words are never enough to express my gratitude to my parents. To dad, the first person I asked for the decision of doing PhD and the most influential person in my life, I wish you were here, at this moment and proudly smiling to your daughter.
To mom, with your love and endless patience, you make me feel stronger and ready to overcome all challenges. TABLE OF CONTENTS List of symbols and notations. i List of figures. ii List of tables.
iv GENERAL INTRODUCTION. Object and scope of the research. Novelty and scientific significance. Overview of the research.
Objectives of the research. THEORETICAL BACKGROUNDS AND COMPUTATIONAL METHODS. Theoretical background of computational chemistry. The Hartree–Fock method.
The post–Hartree-Fock method. Density functional theory. Computational approaches to noncovalent interactions. Basis set superposition error.
Natural bond orbital theory. Atoms in molecules theory. Symmetry-adapted perturbation theory. Computational methods of the research.
RESULTS AND DISCUSSION. Interactions of dimethyl sulfoxide with nCO2 and nH2O (n=1-2). Geometries, AIM analysis and stability of intermolecular complexes. Interaction and cooperative energies and energy component.
Bonding vibrational modes and NBO analysis. Interactions of acetone/thioacetone with nCO2 and nH2O. Stability and cooperativity. NBO analysis, and hydrogen bonds.
Interactions of methanol with CO2 and H2O. Structures and AIM analysis. Interaction and cooperative energies. Vibrational and NBO analyses.
Interactions of ethanethiol with CO2 and H2O. Structure, stability and cooperativity. Vibrational and NBO analyses. Interactions of CH3OCHX2 with nCO2 and nH2O (X=H, F, Cl, Br, CH3; n=1-2).
Interactions of CH3OCHX2 with 1CO2 (X = H, F, Cl, Br, CH3). Interactions of CH3OCHX2 with 2CO2 (X = H, F, Cl, Br, CH3). Interactions of CH3OCHX2 with nH2O (X = H, F, Cl, Br, CH3; n=1-2). Interactions of CH3OCHX2 with 1CO2 and 1H2O (X =H, F, Cl, Br, CH3).
Interactions of dimethyl sulfide with nCO2 (n=1-2). Geometric structures and AIM analysis. Interaction and cooperativity energy and energetic components. Vibrational and NBO analyses.
Growth pattern of the C2H5OH∙∙∙nCO2 complexes (n=1-5). Structural pattern of the C2H5OH∙∙∙nCO2 complexes (n=1-5). Complex stability, and changes of OH stretching frequency and intensity under variation of CO2 molecules. Intermolecular interaction analysis.
Role of physical energetic components. 132 LIST OF PUBLICATIONS CONTRIBUTING TO THE DISSERTATION. 135 List of symbols and notations AIM Atoms in Molecules aco Acetone acs Thioacetone BCP Bond critical point BSHB Blue-shifting hydrogen bond BSSE Basis set superposition error ChB Chalcogen bond CCSD(T) Coupled-cluster singles and doubles methods DME Dimethyl ether DMSO Dimethyl sulfoxide DMS Dimethyl sulfide DPE Deprotonation energy EDT Electron density transfer Eint Interaction energy Ecoop Cooperative energy HF Hartree Fock method HB Hydrogen bond MEP Molecular electrostatic potential MP2 Second-order Moller-Plesset perturbation method NBO Natural bond orbital NCIplot Noncovalent Interaction plot PA Proton affinity RSHB Red-shifting hydrogen bond SAPT Symmetry-adapted perturbation theory TtB Tetrel bond ZPE Zero-point vibrational energy (r) Electron density 2ρ(r) Laplacian of electron density H(r) Total energy density E(2) Second-order energy of intermolecular interaction Lp Lone pair i List of figures Page Figure 1. Three types of CO2 complexes 7 Figure 1.
Stable geometries of complexes involving CO2 7 Figure 2. The flowchart illustrating Hartree–Fock method 16 Figure 2. Plots of GTO and STO basis functions 23 Figure 2. Perturbative donor-acceptor interaction, involving a filled 30 orbital and an unfilled orbital * Figure 2.
The separation between two atomic basins in HF molecule 31 Figure 2. Molecular graph of H2O, ethane, cyclopropane and cubane 32 at MP2/6-311++G(d,p) Figure 2. a) Representative behaviour of atomic density 34 b) Appearance of a s() singularity when two atomic densities approach each other Figure 2. Difference in geometry of complexes CO2-HCl and CO2- 38 HBr obtained from experimental spectroscopy Figure 3.
Geometries of stable complexes formed by interactions of 47 DMSO with CO2 and H2O Figure 3. A linear correlation between individual EHB and ρ(r) values 49 at BCPs Figure 3. Stable structures of complexes formed by interactions of 60 (CH3)2CZ with CO2 and H2O (Z=O, S) (the values in parentheses are for complexes of (CH3)2CS) Figure 3. The correlation in interaction energies of the most 64 energetically favorable structures in six systems at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p) Figure 3.
SAPT2+ decompositions of the most stable complexes into 68 physically energetic terms: electrostatic (Elst), exchange (Exch), induction (Ind) and dispersion (Disp) at aug-cc- pVDZ basis set Figure 3. Stable geometries of complexes formed by interaction of 74 CH3OH with CO2 and H2O at MP2/6-311++G(2d,2p) Figure 3. Stable geometries of complexes formed by interactions of 81 C2H5SH with CO2 and H2O at MP2/6-311++G(2d,2p) Figure 3. Stable structures of CH3OCHX2∙∙∙1CO2 complexes at 89 MP2/6-311++G(2d,2p) Figure 3.
The difference in interaction energies (with ZPE and BSSE) 91 ii of CH3OCHX2∙∙∙1CO2 complexes Figure 3. Contributions (%) of physical energetic terms 92 Figure 3. Stable structures and topological geometries of complexes 96 CH3OCHX2∙∙∙2CO2 Figure 3. The stable structures of CH3OCHX2∙∙∙nH2O complexes (n = 99 1-2; X = H, F, Cl, Br, CH3) Figure 3.
Stable structures of complexes CH3OCHX2∙∙∙1CO2∙∙∙1H2O 103 (X = H, F, Cl, Br, CH3) Figure 3. Optimized structures and topological geometries of (CH3)2S 108 and nCO2 (n = 1, 2) at MP2/6-311++G(2d,2p) Figure 3. Optimized structures of C2H5OH∙∙∙nCO2 (n=1-2) 116 Figure 3. Optimized structures of C2H5OH∙∙∙nCO2 (n=3-5) 118 Figure 3.
The binding energies per carbon dioxide 123 Figure 3. NCIplot of tetrel model and hydrogen model with gradient 124 isosurface of s=0. MEP surface of monomers including C2H5OH (anti and 127 gauche) and CO2 at MP2/aug-cc-pVTZ Figure 3. Contributions (%) of different energetic components into 128 stabilization energy of C2H5OH∙∙∙nCO2 complexes at MP2/aug-cc-pVDZ iii List of tables Page Table 2.
Characteristics of the common NBO types 29 Table 3. Interaction energy (E) and cooperativity energy (Ecoop) of 51 binary and ternary systems at CCSD(T)/6- 311++G(2d,2p)//MP2/6-311++G(2d,2p) Table 3. The second-order perturbation energy (E(2), kJ.mol-1, MP2/6- 54 311++G(2d,2p)) for transfers in heterodimers and heterotrimers from interactions of DMSO with CO2 and H2O Table 3. Selected results of vibrational and NBO analyses for interaction 56 of DMSO with nCO2 (n = 1-2) (MP2/6-311++G(2d,2p)) Table 3.
Selected results of vibrational and NBO analyses (MP2/6- 57 311++G(2d,2p)) for interaction of DMSO with nH2O (n = 1-2) Table 3. Selected results of vibrational and NBO analyses (MP2/6- 58 311++G(2d,2p)) for interaction of DMSO with CO2 and H2O Table 3. Interaction energy and cooperative energy of complexes of 63 aco/acs and 1,2CO2 and/or 1,2H2O at CCSD(T)/6- 311++G(2d,2p)//MP2/6-311++G(2d,2p) Table 3. Concise summary of interactions between some organic 66 compounds and CO2 Table 3.
Concise summary of interactions of organic compounds and 67 H2O (and CO2) Table 3. Changes of bond length (r(X-H), in mÅ) and stretching 72 frequency ((X-H), in cm-1) of C-H and O-H bonds involved in hydrogen bond Table 3. Selected parameters at the BCPs of intermolecular contacts in 75 complexes of methanol with CO2 and/or H2O at MP2/6- 311++G(2d,2p) Table 3. Interaction energy and cooperative energy of complexes formed 77 by interactions between CH3OH with CO2 and/or H2O at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p) (kJ.
Changes of bond length (r) and corresponding stretching 78 frequency () of C(O)−H bonds involved in HBs along with selected parameters at MP2/6-311++G(2d,2p) Table 3. Interaction energy and cooperative energy of complexes 82 between C2H5SH and CO2 and/or H2O at CCSD(T)/6- 311++G(2d,2p)//MP2/6-311++G(2d,2p) iv Table 3. Selected parameters at the BCPs of intermolecular contacts of 83 complexes between C2H5SH and CO2 and/or H2O at MP2/6- 311++G(2d,2p) Table 3. EDT and E(2) of intermolecular interactions of complexes 85 between C2H5SH and CO2 and/or H2O at MP2/6- 311++G(2d,2p) level Table 3.
Selected results of vibrational and NBO analyses for interaction 87 of C2H5SH with CO2 and H2O Table 3. Intermolecular distances (Å) of CH3OCHX2∙∙∙1CO2 complexes 89 Table 3. Interaction energies corrected ZPE+BSSE of complexes 90 CH3OCHX2∙∙∙nCO2 Table 3. Selected parameters (au) of CH3OCHX2∙∙∙1CO2 complexes 93 (X = H, F, Cl, Br, CH3) Table 3.
EDT and E(2) for CH3OCHX2∙∙∙1CO2 complexes at MP2/6- 95 311++G(2d,2p) level of theory Table 3. Interaction energy and cooperative energy of complexes 97 CH3OCHX2∙∙∙2CO2 (X = H, F, Cl, Br, CH3) at MP2/aug-cc- pVTZ//MP2/6-311++G(2d,2p) Table 3. EDT and E(2) for CH3OCHX2∙∙∙2CO2 complexes at MP2/6- 98 311++G(2d,2p) level of theory Table 3. Selected parameters at BCPs taken from AIM results for 100 complexes of CH3OCHX2 with 1,2H2O at MP2/6- 311++G(2d,2p) Table 3.
Interaction energy and cooperative energy of complexes 101 CH3OCHX2∙∙∙1,2H2O (X = H, F, Cl, Br, CH3) at MP2/aug-cc- pVTZ//MP2/6-311++G(2d,2p) Table 3. Interaction energy and cooperative energy of complexes 104 CH3OCHX2∙∙∙1CO2∙∙∙1H2O (X = H, F, Cl, Br, CH3) Table 3. EDT and E(2) for CH3OCHX2∙∙∙1CO2∙∙∙1H2O (X = H, F, Cl, Br, 106 CH3) at MP2/6-311++G(2d,2p) level of theory Table 3. Changes of bond length C(O)−H (in Å) and stretching 107 frequency ((C/O-H), in cm-1) of C-H and O-H bonds involved in HB of complexes CH3OCHX2∙∙∙1CO2∙∙∙1H2O (X = H, F, Cl, Br, CH3) Table 3.
Selected parameters at the BCPs of intermolecular contacts of 109 (CH3)2S∙∙∙nCO2 (n = 1-2) Table 3. Interaction energies and cooperative energies of complexes 111 DMS∙∙∙nCO2 v Table 3. Contributions of different energetic components into 112 stabilization energy of complexes DMS∙∙∙nCO2 using SAPT2+ approach Table 3. Selected results of vibrational and NBO analysis of complexes 113 DMS∙∙∙nCO2 at MP2/6-311++G(2d,2p) Table 3.
Rotational constant and vibrational frequencies of OH group of 117 isolated ethanol and C2H5OH∙∙∙nCO2 complexes Table 3.