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A Study of Chemical Bonding Through Quantum Chemical Topology

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A Study of Chemical Bonding Through Quantum Chemical Topology Skolkovo Institute of Science and Technology A STUDY OF CHEMICAL BONDING THROUGH QUANTUM CHEMICAL TOPOLOGY Doctoral Thesis by CHRISTIAN TANTARDINI DOCTORAL PROGRAM IN MATERIAL SCIENCES AND ENGINEERING Supervisor Professor Artem R. Oganov Moscow 31-01 2020 © Christian Tantardini 2020 To my father Giuseppe died during my PhD «What does not destroy me makes me stronger» cit. Friedrich Nietzsche The secret of human existence lies not only in living, but also in knowing what we are living for» cit. Fyodor Mihajlovic Dostoevsky CONTENTS 1.0 ABSTRACT………………………………………………………………………………………………………………………2 2.0 PUBLICATIONS……………………………………………………………………………………………………………….3 2.1 Thesis Work…………………………………………………………………………………….……………………….3 2.2 Other Publications………………………………………………………………………………..………………….3 3.0 INTRODUCTION……………………………………………………………………………………………………………..4 4.0 THEORETICAL BACKGROUND……………………………………………………………..………………………...6 4.1 Introduction…………………………………………………………………………………………………………….6 4.2 Bader’s Theory………………………………………………………………………………………………………..6 4.3 Source Function………………………………………………………………………………………………..…..10 4.4 Espinosa Indexes……………………………………………………………………………………………………11 4.5 Delocalization Index……………………………………………………………………………………………….11 4.6 Domain-Averaged Fermi Hole (DAFH)…………………………………………………………………….12 4.7 References……………………………………………………………………………………………………………..14 5.0 OVERVIEW….…………………………………………………………………………………………………………….…18 CHAPTER I…………………………………………………………………………………………………………..….……19 Development of Quantum Chemical Topology. CHAPTER II…………………………………………………………………………………………………………..…….….52 Application of Quantum Chemical Topology in the study of non-covalent interactions within Oxicams. CHAPTER III…………………………………………………………………………………………………………..…..…111 Quantum Chemical Topology applied to Catalysis. CHAPTER IV…………………………………………………………………………………………………………..….…139 Chemical Bonding at High-Pressure. 6.0 CONCLUSION AND FUTURE PROSPECTIVES…………………………………………………………………147 6.1 References……………………………………………………………………………………………………………150 7.0 ACKNOWLEDGMENTS………………………………………………………………………………………………..154 1 | P a g e 1.0 ABSTRACT The chemical behavior of atoms and molecules is entirely defined by the distribution of their electron density. It is by studying the electron density in the field of Quantum Chemical Topology that such key concept as chemical bonding can be used to explain reactivity, atomic hybridization, and the existence of electric multipole moments. In such direction the work here presented is principally focused on development of Quantum Chemical Topology Theory introducing new different concepts, which a new equation style of real gases other that a “energy border” between hydrogen bond and van der Waals interaction with consequent limit of long range interactions, and the investigation of different compounds to investigate the correlations between solubility (oxicams) and reactivity (Dess-martin periodinane) with electronic structure with data supported by literature and experiments. 2 | P a g e 2.0 PUBLICATIONS 2.1 Thesis Work 1_Christian Tantardini* A new equation of state for real gases developed into the framework of Bader’s Theory. Theoretical Chemistry Accounts, 2018, 137, 93. 2_Christian Tantardini*, Sergey G. Arkipov*, Kseniya A. Cherkashina, Alexander S. Kil’met’ev, Elena V. Boldyreva* Synthesis and crystal structure of a meloxicam co-crystal with benzoic acid. Structural Chemistry, 2018, 29 (6), 1867-1874. 3_Christian Tantardini*, Adam A. L. Michalchuk Dess‐martin periodinane: The reactivity of a λ5‐iodane catalyst explained by topological analysis. International Journal of Quantum Chemistry, 2018, 119 (6), e25838. 4_Christian Tantardini* When does a hydrogen bond become a van der Waals interaction? A topological answer. Journal of Computational Chemistry, 2019, 40 (8), 937-943. 5_ Alexey Yu. Fedorov, Tatiana N. Drebushchak and Christian Tantardini* Seeking the best model for non- covalent interactions within the crystal structure of meloxicam. Computational and Theoretical Chemistry, 2019, 1157, 47-53. 6_Sergey G. Arkhipov, Peter S. Sherin*, Alexey S. Kiryutin, Vladimir A. Lazarenk and Christian Tantardini* The Role of S-bond in Tenoxicam Keto-Enolic Tautomerization. CrystEngComm, 2019, 21, 5392-5401. 2.1 Other Publications - Christian Tantardini*, Davide Ceresoli, Enrico Benassi, Source Function and Plane Waves: Toward Complete Bader Analysis, Journal of Computational Chemistry (2016), DOI: 10.1002/jcc.24433. - Christian Tantardini*, Sergey G. Arkhipov*, Ksenya A. Cherkashina, Alexander S. Kil’met’eva and Elena V. Boldyreva*, Crystal structure of a 2:1 co-crystal of meloxicam with acetylendicarboxylic acid, Acta Cryst E (2016), DOI: https://doi.org/10.1107/S2056989016018909. - Christian Tantardini*, Elena V. Boldyreva, and Enrico Benassi*, Hypervalency in Organic Crystals: A Case Study of the Oxicam Sulfonamide Group, J. Phys. Chem. A (2016), DOI: 10.1021/acs.jpca.6b10703. - Christian Tantardini*, Enrico Benassi Topology vs Thermodynamics in Chemical Reactions: The Instability of PH5, Phys. Chem. Chem. Phys. (2017), DOI: 10.1039/C7CP06130G. - Christian Tantardini, Enrico Benassi* Crystal Structure Resolution of a Mott Insulator through Bader’s Theory: The Challenging Case of Cobaltite Oxide Y114, Dalton Transaction (2018), DOI: 10.1039/C8DT00073E * corresponding author 3 | P a g e 3.0 INTRODUCTION The PhD thesis is mainly devoted to the study of fundamental insights on/into chemical bonding within the field of Quantum Chemical Topology using first-principles simulations of different states of matter with both local basis set and plane wave basis set calculations. Some of the chosen systems were investigated not only with a computational approach but also through experimental structural analyses to confirm theoretical results. Great part of the work was focused on non-covalent interactions (NCIs) formulating a new equation of state for describing real gases in the field of theory of atoms in molecules (QTAIM) to overcome the old concept of spherical atoms and in the same field the “energy border” between hydrogen bond (H-bond) and van der Waals (vdW) interaction to fulfill the lacuna of H-bond IUPAC definition based on experimental techniques are not able to discriminate between blurry H-bond and vdW interactions. One important question about the correlation between the intramolecular interactions and the solubility of crystals is also highlighted through first-principles simulations on co-crystals, salts, solvates as compared with pure component solids. In this way, it is possible to explore several issues (i) A first important property to be investigated is the so-called interaction density, i.e. the charge density redistribution that takes place both in the intermolecular region and within the covalent bonding framework of the individual molecules upon 'switching on' their interaction. This charge density rearrangement will be different according to whether cocrystal, salts solvates or pure component crystals are formed. (ii) By applying the topological descriptors that are provided by the wavefunctions, it is possible to explore the different kinds of non-covalent interactions taking place within the examined systems. At the same time, the effect of different crystal fields on the intramolecular interactions can be investigated. Besides the change affecting local properties, also the molecular properties like dipole moments, polarizability and so on, are worth of being monitored when different crystal forms are compared. The role of the symmetry on such properties will be also investigated. It should be noted that molecular properties find their definition in crystals by using topological methods. (iii) As different crystal forms exploit also different thermodynamic stabilities as a function of their environment, how the component molecules vary their energies and their energy decompositions in dependence of the crystal field they experience will be evaluated. It should be noted that energy decomposition may be also afforded in terms of contributions of individual atomic atoms or groups. This is done through QTAIM by exploring the energy landscape through both empirical and quantum mechanical methods eventually gaining insights into thermodynamics of competing polymorphs and with the possibility to predict what kind of structure it will be expected if the crystallization takes place under thermodynamic control. An ulterior employment of QTAIM was focused in order to correlate chemical bonding with molecular reactivity. In the specific case through the study of Dess-Martin periodinane (DMP), which derivatives are popular organic catalysts. DMP is extremely reactive in the presence of alcohols, catalyzing their oxidative conversion into ketones. This work seeks to better understand the intrinsic electronic factors that drive the reactivity of the DMP molecule. 4 | P a g e Furthermore, the chemical bonding was investigated at high pressure through the analysis of one very well-known property: electronegativity, which is a property of bonded atom defined as the capacity of an atom to attract on itself the shared electron cloud in the bond. This property as defined by Pauling represents a definition of ionicity of bond and it is calculated on arbitrarily electronegativity value associated to fluorine of 4.0. During this work such property is evaluated with variation of pressure to understand the hellish chemistry at high pressure. High-Pressure is responsible to modify different atomic properties with repercussion on chemical bonding. The understanding of how pressure modifies chemical
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