Extending the Scope of the Density Overlap Region Indicator

In this thesis, original applications of the Density Overlap Region Indicator (DORI), a density dependent bonding descriptor capable of simultaneously capturing covalent and noncovalent interactions, are discussed. The use of scalar fields, such as DORI, were generally restricted to visualizing bonding situations in static gas phase molecules. Here, DORI is pushed out of its comfort zone and used to probe systems prone to electronic and geometric fluctuations, or those constrained by their condensed phase environments. The applications to challenging chemical systems highlighted within demonstrate the capabilities of DORI as a formidable tool that can be beneficial in many facets of chemistry. Molecules in the excited state are difficult to analyze using popular bonding descriptors, primarily because the required information (orbitals) are not given by standard computational methodologies. DORI, which relies exclusively on the electron density and its derivatives, overcomes previous limitations and permits the characterization of excitation processes (charge transfer, excimer, Rydberg, ...) through visual and numerical signatures. Using DORI, the evolution of covalent and non-covalent excited state interactions where used to rationalize photoemission in BODIPY-derivatives. Certain BODIPY substituents formnon-covalent intramolecular interactions in the excited state, which are crucial for stabilizing the Sx - S0 intersection and prompting nonradiative decay. This application demonstrates that DORI is ideally suited for characterizing excited state phenomena. Dynamical fluctuations represent another domain beyond the standard usage of bonding descriptors. Highly fluxionalmolecules, such as molecular machines or proteins, have complex multi-dimensional conformational spaces that are generally explored using a handful of geometrical collective variables (bond lengths, angles, etc.), or dimensionality reduction algorithms. DORI’s covalent and non-covalent patterns are exploited as alternative sets of descriptors, which are simpler than geometrical parameters because electronic and geometrical fluctuations can be captured by a single-dimensional variable. DORI is also synergistically used alongside dimensionality reduction algorithms to reveal enhanced descriptions of the conformational spaces of a molecular rotor and a photoswitch. Thus, cost effective bonding descriptors are well adapted and beneficial in analyzing electronic and geometrical fluctuations requiring extended mapping of conformational spaces. Finally, DORI allows for simultaneous visualization of covalent and non-covalent interactions, and is thus particularly suited to investigate their interplay, notably present in dense environments of high-pressure crystals and in protein-ligand cavities. Using actual experimental electron densities of an organic crystal, DORI exposes pressure-induced disruptions of intramolecular delocalization and identifies the directional non-covalent interactions that cause these perturbations. Similarly, the scalar field pinpoints the specific non-covalent proteinligand interactions which modify the covalent regions of the ligand and facilitate the reactive process. Overall, the examples presented in this thesis demonstrate the versatility of DORI in translating complex chemical behavior into intuitive representations, greatly extending the range of applications that benefit from visual bonding descriptors.


Advisor(s):
Corminboeuf, Anne-Clémence
Year:
2018
Publisher:
Lausanne, EPFL
Keywords:
Other identifiers:
urn: urn:nbn:ch:bel-epfl-thesis8157-8
Laboratories:




 Record created 2018-01-09, last modified 2019-05-09

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