Macroscopic and microscopic properties of molecular and solid-state systems are intimately related to the their electronic structure. The electron position and spin densities, which represent the probability distributions to find all or unpaired electrons in the space, contain information concerning several chemical-relevant properties, such as the chemical bonding and the magnetic behaviour. Understanding the fine atomic-level mechanism behind these properties is a key step to design chemical modifications to properly tune and develop materials or molecules with specific features. Topological descriptors can be used to extract information from these electron distributions. In this work, novel applications of the source function descriptor have been developed to gain further insights on the electron and spin density-related properties. These developments, together with other topological descriptors, were used to get further insights on relevant chemical systems. Firstly, the source function reconstruction was enlarged to a multi-dimensional grid of points with a particular focus on the two-dimensional maps. This analysis allows to see the ability of chosen subsets of atoms to reconstruct the density in the selected area within a cause-effect relationship and to rationalise the chemical or magnetic behaviours. The source function partial reconstructed maps depict if in a molecular region the atomic contributions are important, modest or negligible. Besides, they may also be useful for a proper selection of the reference points and for a full understanding of the source function percentages analysis. In fact, the choice of the reference point where to reconstruct the studied density is neither easy nor objective for non-standard situations, such as for the spin density. This novel application was applied to the study of the spin density on a couple of azido Cu complexes. The source function partial reconstructed maps allow to unravel the different role played by the paramagnetic centre Cu and the ligand atoms and to explain the spin transmission mechanism at a molecular level. Moreover, they enable to highlight the nature of the spin density differences between the two complexes and among adopted computational approaches. DFT functionals tend to over-delocalise the spin density towards the ligand atoms introducing a biased spin-polarization mechanism between the Cu and the ligand atoms. The same descriptor was then applied to the study of the hydrogen bonds in the DNA base pairs. The source function reveals the delocalised nature of these interactions, highlighting that distant groups and rings have non-negligible effects on the reconstruction of the electron density in the intermolecular region. Besides, the analysis demonstrates that the purine and pyrimidine bases equally contribute to the reconstruction of the electron density at the hydrogen bond critical points. The source function also reveals that subtle variations of the atomic source contributions occur when the pairs are ionized, revealing that sources and sinks effects redistribution plays an important role in the stabilization of the DNA base pairs. The source function was also used to develop a method to extract full population matrices purely based on the electron density distribution and then amenable to experimental determination. The peculiar features of this descriptor, in particular the cause-effect relationship, assign a profound chemical meaning to the matrix elements in contrast with other population analyses such as the Mulliken's one, where the matrix elements are associated to orbital overlaps. The latest breakthroughs on the development of this method are shown together with some numerical examples on very simple compounds. The full population matrices obtained using the source function descriptor are able to retrieve the major chemical features. A detailed analysis on the intermolecular interactions involved in the in vivo molecular recognition of the antimalarial drug chloroquine with the heme moiety has been carried out using a combined topological-energetic analysis. This work reveals that charged-assisted hydrogen bonds set up between the lateral chains of the chloroquine and the propionate group of the heme are the most important interactions in the drug:substrate recognition process.

TOPOLOGICAL DESCRIPTORS ENABLING NOVEL DISSECTIONS OF ELECTRON POSITION AND SPIN PROPERTIES IN COMPLEX MOLECULAR SYSTEMS / G. Macetti ; Tutor: L. Lo Presti, C. Gatti ; coordinatore: E. Licandro. - : . Università degli Studi di Milano, 2019 Jan 29. ((31. ciclo, Anno Accademico 2018. [10.13130/macetti-giovanni_phd2019-01-29].

TOPOLOGICAL DESCRIPTORS ENABLING NOVEL DISSECTIONS OF ELECTRON POSITION AND SPIN PROPERTIES IN COMPLEX MOLECULAR SYSTEMS

G. Macetti
2019-01-29

Abstract

Macroscopic and microscopic properties of molecular and solid-state systems are intimately related to the their electronic structure. The electron position and spin densities, which represent the probability distributions to find all or unpaired electrons in the space, contain information concerning several chemical-relevant properties, such as the chemical bonding and the magnetic behaviour. Understanding the fine atomic-level mechanism behind these properties is a key step to design chemical modifications to properly tune and develop materials or molecules with specific features. Topological descriptors can be used to extract information from these electron distributions. In this work, novel applications of the source function descriptor have been developed to gain further insights on the electron and spin density-related properties. These developments, together with other topological descriptors, were used to get further insights on relevant chemical systems. Firstly, the source function reconstruction was enlarged to a multi-dimensional grid of points with a particular focus on the two-dimensional maps. This analysis allows to see the ability of chosen subsets of atoms to reconstruct the density in the selected area within a cause-effect relationship and to rationalise the chemical or magnetic behaviours. The source function partial reconstructed maps depict if in a molecular region the atomic contributions are important, modest or negligible. Besides, they may also be useful for a proper selection of the reference points and for a full understanding of the source function percentages analysis. In fact, the choice of the reference point where to reconstruct the studied density is neither easy nor objective for non-standard situations, such as for the spin density. This novel application was applied to the study of the spin density on a couple of azido Cu complexes. The source function partial reconstructed maps allow to unravel the different role played by the paramagnetic centre Cu and the ligand atoms and to explain the spin transmission mechanism at a molecular level. Moreover, they enable to highlight the nature of the spin density differences between the two complexes and among adopted computational approaches. DFT functionals tend to over-delocalise the spin density towards the ligand atoms introducing a biased spin-polarization mechanism between the Cu and the ligand atoms. The same descriptor was then applied to the study of the hydrogen bonds in the DNA base pairs. The source function reveals the delocalised nature of these interactions, highlighting that distant groups and rings have non-negligible effects on the reconstruction of the electron density in the intermolecular region. Besides, the analysis demonstrates that the purine and pyrimidine bases equally contribute to the reconstruction of the electron density at the hydrogen bond critical points. The source function also reveals that subtle variations of the atomic source contributions occur when the pairs are ionized, revealing that sources and sinks effects redistribution plays an important role in the stabilization of the DNA base pairs. The source function was also used to develop a method to extract full population matrices purely based on the electron density distribution and then amenable to experimental determination. The peculiar features of this descriptor, in particular the cause-effect relationship, assign a profound chemical meaning to the matrix elements in contrast with other population analyses such as the Mulliken's one, where the matrix elements are associated to orbital overlaps. The latest breakthroughs on the development of this method are shown together with some numerical examples on very simple compounds. The full population matrices obtained using the source function descriptor are able to retrieve the major chemical features. A detailed analysis on the intermolecular interactions involved in the in vivo molecular recognition of the antimalarial drug chloroquine with the heme moiety has been carried out using a combined topological-energetic analysis. This work reveals that charged-assisted hydrogen bonds set up between the lateral chains of the chloroquine and the propionate group of the heme are the most important interactions in the drug:substrate recognition process.
LO PRESTI, LEONARDO
LICANDRO, EMANUELA
electron density; spin density; topological descriptors; source function; quantum theory of atoms in molecules; azido complexes; intermolecular interactions; hydrogen bonds; DNA base pairs; full population matrix; antimalarial drugs;
Settore CHIM/02 - Chimica Fisica
TOPOLOGICAL DESCRIPTORS ENABLING NOVEL DISSECTIONS OF ELECTRON POSITION AND SPIN PROPERTIES IN COMPLEX MOLECULAR SYSTEMS / G. Macetti ; Tutor: L. Lo Presti, C. Gatti ; coordinatore: E. Licandro. - : . Università degli Studi di Milano, 2019 Jan 29. ((31. ciclo, Anno Accademico 2018. [10.13130/macetti-giovanni_phd2019-01-29].
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/615357
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