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. DORIâs 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

Salt-induced thermochromism of a conjugated polyelectrolyte

We report here the photophysical properties of a water-soluble conjugated polythiophene with cationic side-chains. When dissolved in aqueous buffer solution (PBS, phosphate buffered saline), there is ordering of the polymer chains due to the presence of the salts, in contrast to pure water, where a random-coil conformation is adopted at room temperature. The ordering leads to a pronounced colour change of the solution (the absorption maximum shifts from 400 nm to 525 nm). Combining resonance Raman spectroscopy with density functional theory computations, we show a significant backbone planarization in the ordered phase. Moreover, the ratio of ordered phase to random-coil phase in PBS solution, as well as the extent of intermolecular interactions in the ordered phase, can be tuned by varying the temperature. Femtosecond transient absorption spectroscopy reveals that the excited- state behaviour of the polyelectrolyte is strongly affected by the degree of ordering. While triplet state formation is favoured in the random-coil chains, the ordered chains show a weak yield of polarons, related to interchain interactions. The investigated polyelectrolyte has been previously used as a biological DNA sensor, based on optical transduction when the conformation of the polyelectrolyte changes during assembly with the biomolecule. Therefore, our results, by correlating the photophysical properties of the polyelectrolyte to backbone and intermolecular conformation in a biologically relevant buffer, provide a significant step forward in understanding the mechanism of the biological sensing

Fluorescence Quenching in BODIPY Dyes: the Role of Intramolecular Interactions and Charge Transfer

The fluorescence properties of the BODIPY dye and its two meso-substituted derivatives, tert-butyl- and phenyl-BODIPY, are rationalized. The non emissive behavior of the latter two are attributed to the energetically accessible low-lying conical intersection between the ground state and the lowest excited singlet state. Both intramolecular non-covalent interactions and excited state charge transfer character are identified as being crucial for “stabilizing” the intersection and prompting the nonradiative decay. Similar crossing was located in the bare BODIPY dye, however, being energetically less accessible, which correlates well with the high fluorescence quantum yields of the parent dye

Visualizing and Quantifying Interactions in the Excited State

Determining the location and nature of the electron pairs within a molecule provides an intuitive representation of electronic structures. Yet, most of the available theoretical representations are not suitable for describing excited state phenomena. The Density Overlap Region Indicator (DORI) scalar field, which depends only on the density and its derivatives, overcomes previous limitations, while keeping the intuitiveness of popular scalar fields. We here demonstrate its usefulness by pinpointing visual and numerical DORI signatures for both intra- and intermolecular excited state situations

Analyzing Fluxional Molecules Using DORI

The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and non-covalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of π-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH- and - interactions. Finally, DORI serves to examine the fluctuating π-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on post-processing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape

DORI Reveals the Influence of Noncovalent Interactions on Covalent Bonding Patterns in Molecular Crystals Under Pressure

The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid-state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (density overlap region indicator) descriptor, which is capable of simultaneously detecting both covalent patterns and noncovalent interactions from electron density and its derivatives. Using the biscarbonyt[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood-fill-type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrary selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids

DORI Reveals the Influence of Noncovalent Interactions on Covalent Bonding Patterns in Molecular Crystals Under Pressure.

The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid-state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (density overlap region indicator) descriptor, which is capable of simultaneously detecting both covalent patterns and noncovalent interactions from electron density and its derivatives. Using the biscarbonyl[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood-fill-type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrary selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids

Analyzing Fluxional Molecules Using DORI

The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and noncovalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of π-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH-π and π–π interactions. Finally, DORI serves to examine the fluctuating π-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on postprocessing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape

Optical gap and fundamental gap of oligoynes and carbyne

International audienceThe optoelectronic properties of various carbon allotropes and nanomaterials have been well established, while the purely sp-hybridized carbyne remains synthetically inaccessible. Its properties have therefore frequently been extrapolated from those of defined oligomers. Most analyses have, however, focused on the main optical transitions in UV-Vis spectroscopy, neglecting the frequently observed weaker optical bands at significantly lower energies. Here, we report a systematic photophysical analysis as well as computations on two homologous series of oligoynes that allow us to elucidate the nature of these weaker transitions and the intrinsic photophysical properties of oligoynes. Based on these results, we reassess the estimates for both the optical and fundamental gap of carbyne to below 1.6 eV, significantly lower than previously suggested by experimental studies of oligoynes