Les performances optiques non linéaires (ONL) de ligands pi-conjugués à base d’azobenzène et de fragment coordonnant iminopyridine et leurs complexes métalliques de zinc(II), d’argent(I) et de rhénium(I) ainsi que de polymères méthacryliques contenant l’entité styrylquinoline sont étudiées par des techniques complexes mais fiables à savoir THG, SHG ou encore Z-scan. L'indice de réfraction ONL, le coefficient d'absorption ONL, l’hyper-polarisabilité du second ordre et la section efficace d'absorption ONL pour les complexes métallique de zinc(II) et argent(I) ont été obtenus et analysés. L'estimation du facteur de mérite de ces complexes indique que ce sont des composés prometteurs pour les applications dans des dispositifs optiques. Les paramètres ONL améliorés des complexes contenant du Rhénium(I) par rapport à leurs ligands correspondants, confirment le rôle très important de la coordination par des cations métalliques. Cette étude favorise une meilleure compréhension de la relation structure-propriété avec la prédiction possible des propriétés ONL. Les résultats de l'étude ONL (génération de deuxième et troisième harmonique) de films minces de polymères méthacryliques contenant de la styrylquinoline sont également présentés. Une forte dépendance de la réponse ONL en fonction de la structure des polymères a été mise enévidence, qui est liée au transfert de charge plus ou moins important dans les fragments de styrylquinoline. Une bonne compatibilité a été obtenue entre les résultats théoriques et expérimentaux. Le contraste de la réponse ONL après photo-isomérisation trans-cis de ces polymères, les rend intéressants pour les dispositifs photoniques. / The nonlinear optical (NLO) performance of conjugated azo-based iminopyridine complexes with zinc, silver and rhenium metal cations as well as styrylquinoline containing methacrylic polymers are studied by the proven methods of Maker fringe and Z-scan. The NLO refractive index, NLO absorption coefficient, second order hyperpolarizability and NLO absorption cross section for the azo-based iminopyridine zinc(II) and silver(I) complexes were obtained and analysed. The enhanced NLO parameters of the Rhenium(I) containing azo-based iminopyridine complexes as compared to their corresponding ligands confirm the positive role of the metal complexation. This study promotes the better understanding of the structure-property relationship with possible prediction of NLO properties in such metal complexes. The results of the NLO investigation (second and third harmonic generation) of high-quality thin films of styrylquinoline containing methacrylic polymers are presented. Strong dependence of the NLO response upon the structure of the polymers has been found, which is related to a different charge transfer occurring within the styrylquinoline fragments. Good compatibility has been achieved between the theoretical and experimental results. The contrast in NLO response observed after their trans-cis photoisomerization makes them valuable components for photonics devices

Les complexes de ruthénium à ligand nitrosyle sont très connus pour posséder des propriétés photochromes qui résultent des changements de coordination du fragment Ru-NO sous irradiation à basse température. Ce phénomène comporte de nombreuses applications telles que le stockage optique de données. Ces complexes ont aussi la capacité de délivrer l'oxyde nitrique de manière photo-contrôlée. Cela présente un grand intérêt car NO est impliqué dans de très nombreuses réactions physiologiques. Cette thèse est consacrée à l'étude des facteurs qui influencent les propriétés photochromes et la photolibération de NO dans les complexes de nitrosyle de ruthénium avec des ligands pyridine ou bipyridine. Le premier chapitre de cette thèse se concentre sur une étude bibliographique approfondie. Dans le second chapitre, la synthèse et la caractérisation des complexes de nitrosyle de ruthénium avec des ligands pyridine de formule trans(X, NO)-[Ru(R-py)4XNO](PF6)2 (R-py = pyridine, 4-picoline, 3-picoline, 4-vinylpyridine, 3- carboxaldéhydepyridine et 4-chloropyridine, X= Cl, Br, I ou OH) sont étudiés. Dans le troisième chapitre, la synthèse et la caractérisation des complexes de ruthénium nitrosyle avec le ligand bipyridine de formule cis(X, NO)-[Ru(L)2XNO] Y2, (L= 2,2'-bipyridine ou 4,4'-diméthyl-2,2'-bipyridine, X= Cl, NO2 ou Br, Y= PF6 ou Br) sont discutés. Dans le quatrième chapitre, nous présentons les résultats sur l'étude de photoisomérisation des complexes présentés dans les chapitres précédents. La conversion Ru-NO/Ru-ON est estimée par spectroscopie infrarouge après irradiation par une lumière bleue à basse température à l'état solide. Le taux de population Ru-NO/Ru-ON varie entre 1 et 76%. Nous avons étudié les effets de la position cis/trans et de la nature du ligand par rapport au nitrosyle, des substituants (groupe donneur ou attracteur d'électrons) sur le ligand pyridine ou bipyridine sur la réponse photochrome. Des calculs théoriques par DFT ont permis de rendre compte des propriétés photochromes différentes entre le complexe parent avec un ligand pyridine et le ligand 4-chloropyridine. Le cinquième chapitre est consacré à l'étude de la photolibération de NO. Le rendement quantique (NO) se trouve dans la gamme 0.2-0.7. Le test de Griess a confirmé le relargage de NO. / We are interested in the photoactive properties of ruthenium nitrosyl complexes. Ruthenium nitrosyl complexes are well known to possess photochromic properties which arise from the coordination changes of Ru-NO under irradiation at low temperature. This phenomenon has many applications such as high optical data storage and sensors. Ruthenium nitrosyl complexes are also very promising candidates because the photochemical delivery of bioactive small molecules such as nitric oxide (NO•) from ruthenium nitrosyl complexes presents the possibility of controlling the location, timing and dosage of NO• to physiological targets. Nitric oxide photorelease have gained wide attention after the discovery of several nitric oxide physiological functions and its involvement in different cellular processes. This thesis was devoted to studying the factors which affect the photochromic properties and NO photorelease in ruthenium nitrosyl complexes with pyridyl or bipyridyl based ligands. The first chapter of this thesis focuses on a survey of the literature related to both photoisomerization and photorelease phenomena. In chapter 2, the synthesis and characterization of ruthenium nitrosyl complexes with pyridyl based ligands with the formula trans(X,NO)-[Ru(R-py)4XNO](PF6)2, (where R-py is pyridine, 4-picoline, 3-picoline, 4-vinylpyridine, 3-carboxaldhydepyridine and 4-chloropyridine, X=Cl, Br, I or OH) are discussed. In chapter 3, the synthesis and characterization of ruthenium nitrosyl complexes with bipyridyl based ligand with formula cis(X,NO)-[Ru(L)2XNO]Y2, (L= 2,2'-bipyridine or 4,4'-dimethyl-2,2'-bipyridine, X=Cl, NO2 or Br, Y=PF6 or Br) are discussed. In chapter 4, we present the results of our investigations of nitrosyl ligand photoisomerization in Ru-NO with pyridyl and bipyridyl ligands. The conversion of Ru-NO to Ru-ON conformation was estimated by infrared spectroscopy upon irradiation by blue light at low temperature in the solid state. The values are ranged between 1-76%. We studied the effects of cis/trans ligand position to nitrosyl and the nature of substituents on pyridine or bipyridine ligand (electron donating or withdrawing group). We used theoretical calculations (DFT) to explain the different photochromic properties between parent complex with a pyridine ligand and 4-chloropyridine ligand. The fifth chapter is devoted to the study of NO photorelease. The quantum yield (NO) was estimated in the range of 0.2-0.7. Griess test was used to confirm NO delivery.

Les verres moléculaires sont un type de solide amorphe qui ne possèdent pas l’ordre caractéristique d’un cristal. Les verres moléculaires dérivés de l’azobenzène sont le sujet de nombreuses études dû à leur photomobilité, leur capacité à se déplacer sous l'effet de la lumière. Une irradiation à une température inférieure à leur température de transition vitreuse (Tg) produit des cycles d'isomérisation trans-cis-trans à l’échelle moléculaire qui se répercutent en mouvements macroscopiques de la matrice. Ce projet a comme objectif de déterminer si la photomobilité résulte d’une relaxation structurale photoinduite en utilisant le gDR1, un verre moléculaire dérivé du chromophore Disperse Red 1. La spectroscopie UV-visible a été utilisée pour déterminer la fraction d’isomères cis sous irradiation à différentes longueurs d’ondes. Ces longueurs d’ondes ont permis de comparer l’effet d’une irradiation près de l’absorbance maximale de l’un des isomères ou dans les régions peu absorbées par les deux isomères afin de tenir compte de la fraction d'isomère cis et de l’efficacité de l’isomérisation trans-cis-trans. La spectroscopie infrarouge (IR) a ensuite été employée pour mesurer l'impact de l'irradiation sur la température effective locale du groupement azo, de la matrice vitreuse et du groupement espaceur. Malgré une température réelle sous Tg, des augmentations de températures effectives sous irradiation ont été mesurées pour l'azo et l'espaceur. La plus grande augmentation de température effective a été observée pour le groupement azo aux longueurs d’onde d’irradiation provoquant des cycles d'isomérisation efficaces. L’ellipsométrie a permis de mesurer l’expansion photoinduite des films. Les cinétiques de relaxation de la fraction d'isomère cis (UV-vis), des températures effectives (IR) et des changements d’épaisseurs (ellipsométrie) ont ensuite été mesurées pour comparer la relaxation à l'échelle moléculaire et macroscopique du matériau. Finalement, la calorimétrie différentielle à balayage (DSC) a été utilisée pour mesurer des changements enthalpiques du système dus à l’irradiation. Les échantillons ont subi des recuits sous Tg de différentes durées pour leur permettre de tendre vers leur état idéal par une relaxation structurale, ce qui est accompagné par une réduction du volume libre au sein du matériau. L’isomérisation provoquée par l’irradiation a pour effet de produire un excès de volume libre qui est quantifiable en mesurant l’enthalpie associée à la relaxation structurale proche de Tg. Une différence maximale de 1.2 J/g de la relaxation enthalpique en raison d’effets photoinduits a été mesurée, en appui à l'hypothèse voulant que la relaxation structurale contribue au phénomène de photomobilité. Ce projet contribue ainsi à notre compréhension des phénomènes mécaniques photoinduits sous Tg au sein des matériaux amorphes azos. / A molecular glass is a type of amorphous solid that lacks the characteristic molecular order found in a crystal. Azobenzene-derived molecular glasses have been widely studied due to their inherent photomobility. Upon irradiation below their bulk glass transition temperature (Tg), they undergo repetitive trans-cis-trans isomerization on the molecular scale that leads to macroscopic motion known as photoinduced mass transport. This project seeks to explore if photomobility is a result of light-stimulated structural relaxation using gDR1, a molecular glass derived from the Disperse Red 1 chromophore. First, UV-visible spectroscopy was used to measure the minimum cis content reached in the photostationnary state under irradiation at various wavelengths. The wavelengths chosen allowed for irradiation near the maximum absorbance of either isomer or in the regions weakly absorbed by both. In doing so, it was possible to consider the wavelength dependence of the material and the effect of the cycling efficiency. Infrared (IR) spectroscopy was then used to probe the effective temperature at the molecular scale of the azo moiety, spacer group and glassy backbone under irradiation. The results showed that despite the bulk temperature of the sample remaining well below Tg, localized effective temperature increases are felt by the molecule upon irradiation. The increase in effective temperature is greatest near the isomerizing azo group and depends on the irradiation wavelength due to the isomerization cycling efficiency. Ellipsometry measurements were then taken to measure photoexpansion of the films. The kinetics of relaxation of the cis content (UV-vis), effective temperature (IR) and thickness (ellipsometry) were compared to evaluate the relaxation process of the material locally and globally. Finally, differential scanning calorimetry was used to measure the enthalpy change in the system resulting from irradiation. Samples were first annealed below Tg for determined times, allowing the material to structurally relax towards its ideal state and thereby reducing its free volume. Upon irradiation, photoinduced cycling generates excess free volume whose impact can be quantified by measuring the enthalpy associated with structural relaxation near Tg. A comparison of the irradiated and non-irradiated samples showed an enthalpy difference of up to 1.2 J/g due to photoinduced effects, supporting the hypothesis that structural relaxation contributes to the photomobility phenomenon. This work thus contributes to understanding photoinduced mechanical changes below Tg in azo-containing amorphous materials.

Electronic excitation triggered by the absorption of light enables numerous chemical, physical and biological processes and transformations. Accordingly, full control over the processes involving excited molecules requires an in-depth knowledge of electronic UV/vis spectra and potential energy surfaces. Unsurprisingly, most electronic spectra are acquired in the condensed phase in which molecules are dissolved and most transformations occur. However, our knowledge of excitation, transformations and processes at the level of isolated molecules is still limited, partly because such studies require unconventional experimental approaches and equipment. This Thesis describes experimental methods for recording electronic spectra of isolated molecules in the gas phase by ion spectroscopy, which combines mass spectrometry with optical spectroscopy. Using these methods, experimental factors which affect the electronic excitation and therefore the electronic spectra of ions were determined and evaluated for various fluorescent xanthene dyes, iron-containing complexes and molecular pho- toswitches. Furthermore, factors which govern photochemical processes, such as photo- oxidation, photoreduction and photoisomerization, were also analyzed in detail, with surprisingly different outcomes from previous studies...

Neste trabalho foi realizado o estudo do comportamento fotoquímico e fotofísico de complexos mononucleares de rênio do tipo fac-[Re(CO)3(N N)(L)]+(N N = 1,10-fenantrolina, phen, dipirido[3,2-a:2,3-c]fenazina, dppz, L= trans-1,2bis(4-piridil)etileno, trans-bpe, trans-4-estirilpiridina. trans-stpy) e dos complexos binucleares [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+, [(CO)3(phen)Re(trans-bpe)Fe(CN5]2- e [(phen)(CO)3Re(trans-bpe)Os(terpy)(bpy)]3+. O enfoque principal deste trabalho é a investigação das propriedades fotoquímicas dos complexos fac-[ Re(CO)3(phen)(trans-bpe)]+, fac-[Re(CO)3(phen)(trans-stpy)]+ fac-[Re(CO)3(dppz)(trans-bpe)+ e [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+. Observou-se que os compostos em solução de acetonitrila, sob irradiação a 313, 334 ou 365 nm, apresentam variação espectral com definição de pontos isosbésticos, resultante do processo de fotoisomerização trans&#8594;cis do ligante coordenado trans-piridil etileno. Os rendimentos quânticos, &#934;, da reação de fotoisomerização foram calculados com base no decaimento espectral das bandas de absorção das transições eletrônicas. Os valores médios determinados para a fotoisomeriação dos complexos em solução de CH3CN variam de 0,15 - 0,39 sob excitação a 313 nm e de 0,12 - 0,33 sob excitação a 365 nm. As reações de fotoisomerização foram monitoradas também por medidas de emissão e por RMN de 1H. Observou-se um aumento da intensidade de luminescência com o tempo de irradiação dos complexos, consistente com o estado emissivo 3MLCT d&#960;[(Re)&#8594;&#960;*(&#945;-diimina). Após irradiação, as reações de fotoisomerização dos complexos foram monitoradas por RMN de 1H. Os sinais de prótons do isômero trans tiveram um decréscimo gradual, enquanto que a intensidade dos sinais referentes aos prótons da espécie cis aumentaram. Os rendimentos quânticos para o processo de fotoisomerização dos complexos foram calculados através da integração das áreas dos sinais de prótons. Os valores obtidos foram maiores, pelo menos o dobro, que aqueles valores obtidos via espectroscopia UV-Vis. O comportamento fotoquímico dos complexos incorporados em polimetacrilato de metila, PMMA, foi também investigado. A fotólise cios complexos em filmes de PMMA conduz à variação espectral, de absorção e emissão, similar àquela observada em solução de acetonitrila, atribuícla ao processo de fotoisomerização trans &#8594; cis do ligante coordenado. Este estudo mostra que a fotoisomerização do ligante coordenado trans-piridil etileno pode ser promovida também em meio rígido. Essa característica. típica de um dispositivo molecular, pode ser convenientemente explorada no desenvolvimento de fotossensores. As medidas de TRIR mostram que o estado excitado de menor energia para o fac-[Re(CO)3(phen)(trans-bpe)+ é o 3&#960;&#960;*. Para o fac-[Re(CO)3(phen)(cis-bpe)]+ a ordem dos estados excitados aparecem invertidas com o 3MLCT <3&#960;&#960;*, evidenciado pela emissão do complexo cis à temperatura ambiente. Nas espécies binucleares, [(phen) Re(CO)3(trans-bpe)Os(terpy)(bpy)]3+ e [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2-, a fotoisomerização trans &#8594; cis do ligante coordenado trans-bpe, característica da subunidade fac-[Re(CO)3(phen)(trans-bpe)]+, é inibida pela competição de transferência de energia intramolecular. Em meio rígido, em PMMA ou em EPA a 77 K, os máximos de emissão dos complexos fac-[Re(CO)3(phen)(cis-bpe)]+, fac-[Re(CO)3(phen)(cis-stpy)r e [(CO)3(phen)Re(cis-bpe)Re(phen)(CO)3]2+ sofrem um deslocamento hipsocrômico com o aumento da rigidez do meio. As mudanças nas propriedades emissivas, em termos de energia e tempo de vida do estado excitado, são discutidas baseadas no efeito rigidocrômico luminescente. O trabalho mostra uma forma interessante de fotos sensibilizar um substrato orgâmco usando o fato de que a coordenação estende a absorção do ligante a uma região de comprimento de onda maior e promove a fotoisomerização assistida por complexos metálicos em energias menores. / In this work the photochemical and photophysical behavior of rhenium complexes fac-[Re(CO3( N N )(L\')]+N N = 1,10 phenanthroline, phen; dipirido[3,2-a:2\',3\'-c]phenazine, dppz; L\'= trans-1,2bis(4-pyridyl)ethylene, trans-bpe; trans-4-styrylpyridine, trans-stpy) and binuclear complexes [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+, [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2+ and [(phen)(CO)3Re(trans-bpe)Os(terpy)(bpy)]3+ were investigated. The main focus of the work is the investigation of photochemical behavior of fac-[Re(CO)3(phen)(trans-bpe)+, fac-[Re(CO)3(phen)(trans-stpy)+, fac-[Re(CO)3(dppz)(trans-bpe)]+ and [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+ in acetonitrile solution. Photolyses of rhenium completes at 313. 334 or 365 nm led to spectral changes with clear and well defined isosbestic points. These spectral changes are due to the trans &#8594; cis isomerization process of the coordinated pyridyl-ethenyl ligand. Quantum yields, &#934;, for isomerization processes were calculated based on the absorption spectral changes. The average values for the isomerization reactions of the complexes in CH3CN solution are 0.15 - 0.39 at 313 nm excitation and 0.12 - 0.33 at 365 nm excitation. The photoisomerization reactions were also followed by emission and 1H NMR measurements. An increasing luminescence was observed after complexes irradiation which is consistent with an emitting 3MLCT state, d&#960;(Re)&#8594;&#960;*(&#945;.-diimine). Upon irradiation, the photoisomerization reactions for complexes were monitored by 1H NMR spectroscopy. The proton signals of the trans isomer were found to decrease gradually while the cis isomer signals gradually built up in intensity. Quantum yields for the isomerization process were calculated by integratian of the proton signals. The values abtained in this way were higher, twice at least, than those obtained by UV-Vis electronic spectroscopy. The photochemical behavior of the complexes incorporated in poly(methyl methacrilate), PMMA, was also investigated. Photolyses of the complexes in PMMA films lead to UV-Visible and emission changes similar to those observed in solution, due to the trans &#8594; cis isomerization of the coordinated ligand. Therefore the photoisomerization is occurring even in rigid media. This feature, typical for molecular devices, can be conveniently exploited, such as for photosensors. TRIR measurements showed that the lowest lying excited state is a bpe-based 3&#960;&#960;* for the fac-[Re(CO)3(phen)(trans-bpe)]+ complex. For fac-[Re(CO)3(phen)(cis-bpe)]+ the ordering of low-lying states appears to be reversed with 3MLCT < 3&#960;&#960;*, evidenced by emission of the cis complex at room temperature. In the binuclear species. [(phen)Re(CO)3(trans-bpe )Os(terpy)(bpy)]3+ and [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2-, the trans &#8594; cis photoisomerization of the coordinated trans-bpe ligand. characteristic of the Re(CO)3(phen)(trans-bpe)+ subunit, is inhibited by competitive intramolecular energy transfer. In a rigid medium, such as PMMA or EPA at 77 K, the emission maxima of fac-[Re(CO)3(phen)(cis-bpe)+, fac-[Re(CO)3(phen)(cis-stpy)+ and [(CO)3(phen)Re(cis-bpe)Re(phen)(CO)3]2+ complexes exhibit hypsochromic shifts as the medium rigidity increases. Changes in emission properties (energy and lifetime of excited states) are discussed based on the luminescent rigidochromic effect. This work presents an interesting approach to photosensitization of an organic substrate by using the red-shifted absorption of the complex to achieve the photoassisted isomerization by irradiation in the low energy region.

No description available.

Neste trabalho foi realizado o estudo do comportamento fotoquímico e fotofísico de complexos mononucleares de rênio do tipo fac-[Re(CO)3(N N)(L)]+(N N = 1,10-fenantrolina, phen, dipirido[3,2-a:2,3-c]fenazina, dppz, L= trans-1,2bis(4-piridil)etileno, trans-bpe, trans-4-estirilpiridina. trans-stpy) e dos complexos binucleares [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+, [(CO)3(phen)Re(trans-bpe)Fe(CN5]2- e [(phen)(CO)3Re(trans-bpe)Os(terpy)(bpy)]3+. O enfoque principal deste trabalho é a investigação das propriedades fotoquímicas dos complexos fac-[ Re(CO)3(phen)(trans-bpe)]+, fac-[Re(CO)3(phen)(trans-stpy)]+ fac-[Re(CO)3(dppz)(trans-bpe)+ e [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+. Observou-se que os compostos em solução de acetonitrila, sob irradiação a 313, 334 ou 365 nm, apresentam variação espectral com definição de pontos isosbésticos, resultante do processo de fotoisomerização trans&#8594;cis do ligante coordenado trans-piridil etileno. Os rendimentos quânticos, &#934;, da reação de fotoisomerização foram calculados com base no decaimento espectral das bandas de absorção das transições eletrônicas. Os valores médios determinados para a fotoisomeriação dos complexos em solução de CH3CN variam de 0,15 - 0,39 sob excitação a 313 nm e de 0,12 - 0,33 sob excitação a 365 nm. As reações de fotoisomerização foram monitoradas também por medidas de emissão e por RMN de 1H. Observou-se um aumento da intensidade de luminescência com o tempo de irradiação dos complexos, consistente com o estado emissivo 3MLCT d&#960;[(Re)&#8594;&#960;*(&#945;-diimina). Após irradiação, as reações de fotoisomerização dos complexos foram monitoradas por RMN de 1H. Os sinais de prótons do isômero trans tiveram um decréscimo gradual, enquanto que a intensidade dos sinais referentes aos prótons da espécie cis aumentaram. Os rendimentos quânticos para o processo de fotoisomerização dos complexos foram calculados através da integração das áreas dos sinais de prótons. Os valores obtidos foram maiores, pelo menos o dobro, que aqueles valores obtidos via espectroscopia UV-Vis. O comportamento fotoquímico dos complexos incorporados em polimetacrilato de metila, PMMA, foi também investigado. A fotólise cios complexos em filmes de PMMA conduz à variação espectral, de absorção e emissão, similar àquela observada em solução de acetonitrila, atribuícla ao processo de fotoisomerização trans &#8594; cis do ligante coordenado. Este estudo mostra que a fotoisomerização do ligante coordenado trans-piridil etileno pode ser promovida também em meio rígido. Essa característica. típica de um dispositivo molecular, pode ser convenientemente explorada no desenvolvimento de fotossensores. As medidas de TRIR mostram que o estado excitado de menor energia para o fac-[Re(CO)3(phen)(trans-bpe)+ é o 3&#960;&#960;*. Para o fac-[Re(CO)3(phen)(cis-bpe)]+ a ordem dos estados excitados aparecem invertidas com o 3MLCT <3&#960;&#960;*, evidenciado pela emissão do complexo cis à temperatura ambiente. Nas espécies binucleares, [(phen) Re(CO)3(trans-bpe)Os(terpy)(bpy)]3+ e [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2-, a fotoisomerização trans &#8594; cis do ligante coordenado trans-bpe, característica da subunidade fac-[Re(CO)3(phen)(trans-bpe)]+, é inibida pela competição de transferência de energia intramolecular. Em meio rígido, em PMMA ou em EPA a 77 K, os máximos de emissão dos complexos fac-[Re(CO)3(phen)(cis-bpe)]+, fac-[Re(CO)3(phen)(cis-stpy)r e [(CO)3(phen)Re(cis-bpe)Re(phen)(CO)3]2+ sofrem um deslocamento hipsocrômico com o aumento da rigidez do meio. As mudanças nas propriedades emissivas, em termos de energia e tempo de vida do estado excitado, são discutidas baseadas no efeito rigidocrômico luminescente. O trabalho mostra uma forma interessante de fotos sensibilizar um substrato orgâmco usando o fato de que a coordenação estende a absorção do ligante a uma região de comprimento de onda maior e promove a fotoisomerização assistida por complexos metálicos em energias menores. / In this work the photochemical and photophysical behavior of rhenium complexes fac-[Re(CO3( N N )(L\')]+N N = 1,10 phenanthroline, phen; dipirido[3,2-a:2\',3\'-c]phenazine, dppz; L\'= trans-1,2bis(4-pyridyl)ethylene, trans-bpe; trans-4-styrylpyridine, trans-stpy) and binuclear complexes [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+, [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2+ and [(phen)(CO)3Re(trans-bpe)Os(terpy)(bpy)]3+ were investigated. The main focus of the work is the investigation of photochemical behavior of fac-[Re(CO)3(phen)(trans-bpe)+, fac-[Re(CO)3(phen)(trans-stpy)+, fac-[Re(CO)3(dppz)(trans-bpe)]+ and [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+ in acetonitrile solution. Photolyses of rhenium completes at 313. 334 or 365 nm led to spectral changes with clear and well defined isosbestic points. These spectral changes are due to the trans &#8594; cis isomerization process of the coordinated pyridyl-ethenyl ligand. Quantum yields, &#934;, for isomerization processes were calculated based on the absorption spectral changes. The average values for the isomerization reactions of the complexes in CH3CN solution are 0.15 - 0.39 at 313 nm excitation and 0.12 - 0.33 at 365 nm excitation. The photoisomerization reactions were also followed by emission and 1H NMR measurements. An increasing luminescence was observed after complexes irradiation which is consistent with an emitting 3MLCT state, d&#960;(Re)&#8594;&#960;*(&#945;.-diimine). Upon irradiation, the photoisomerization reactions for complexes were monitored by 1H NMR spectroscopy. The proton signals of the trans isomer were found to decrease gradually while the cis isomer signals gradually built up in intensity. Quantum yields for the isomerization process were calculated by integratian of the proton signals. The values abtained in this way were higher, twice at least, than those obtained by UV-Vis electronic spectroscopy. The photochemical behavior of the complexes incorporated in poly(methyl methacrilate), PMMA, was also investigated. Photolyses of the complexes in PMMA films lead to UV-Visible and emission changes similar to those observed in solution, due to the trans &#8594; cis isomerization of the coordinated ligand. Therefore the photoisomerization is occurring even in rigid media. This feature, typical for molecular devices, can be conveniently exploited, such as for photosensors. TRIR measurements showed that the lowest lying excited state is a bpe-based 3&#960;&#960;* for the fac-[Re(CO)3(phen)(trans-bpe)]+ complex. For fac-[Re(CO)3(phen)(cis-bpe)]+ the ordering of low-lying states appears to be reversed with 3MLCT < 3&#960;&#960;*, evidenced by emission of the cis complex at room temperature. In the binuclear species. [(phen)Re(CO)3(trans-bpe )Os(terpy)(bpy)]3+ and [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2-, the trans &#8594; cis photoisomerization of the coordinated trans-bpe ligand. characteristic of the Re(CO)3(phen)(trans-bpe)+ subunit, is inhibited by competitive intramolecular energy transfer. In a rigid medium, such as PMMA or EPA at 77 K, the emission maxima of fac-[Re(CO)3(phen)(cis-bpe)+, fac-[Re(CO)3(phen)(cis-stpy)+ and [(CO)3(phen)Re(cis-bpe)Re(phen)(CO)3]2+ complexes exhibit hypsochromic shifts as the medium rigidity increases. Changes in emission properties (energy and lifetime of excited states) are discussed based on the luminescent rigidochromic effect. This work presents an interesting approach to photosensitization of an organic substrate by using the red-shifted absorption of the complex to achieve the photoassisted isomerization by irradiation in the low energy region.

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L'objectif de ce travail consiste à étudier le mécanisme de photo-isomérisation d'une série de commutateurs moléculaires biomimétiques (IP) inspirés de la Rhodopsine (Rho), par spectroscopie d'absorption transitoire. Ce travail comprend également le développement puis l'utilisation d'une expérience d'absorption transitoire avec des impulsions sub-8 fs dédiée à la mesure des cohérences vibrationnelles concomitantes à la photoréactivité des IPs. [...] La description détaillée des deux montages de type pompe-sonde mis en œuvre pour ce travail, ainsi que le détail des analyses et corrections de données expérimentales effectuée ont été décrits. Les deux montages utilisés ont été alimenté par une même source, un laser Ti: saphir amplifié délivrant des impulsions à 800nm d'une durée de 40 fs. le premier est un montage d'absorption transitoire conventionnel permettant l'acquisition des spectres transitoires sur une large gamme de spectrale à l'aide d'un continuum de lumière blanche, avec une résolution de 70fs. Le second montage pompe-sonde dédié à la mesure de cohérence vibrationnelle a été développé au cours de la thèse. Dans ce dernier les impulsions pompes à 800nm sont comprimés d'une durée de 8fs, à l'aide d'un compresseur composé de fibre creuse contenant du gaz (Néon). Une conversion de fréquence permet de générer une impulsion centrée à 400 nm de largeur spectrale correspondant `a une durée de 8 fs. Un balayage rapide du délai entre la pompe et la sonde est mis en œuvre pour supprimer de manière efficace l’effet dominant du bruit à basse fréquence de l’intensité de la pompe sur les signaux d’absorption transitoire. [...] / The research presented durind this Phd work address one of the paradigms of atomic/molecular physics of modern era, namely the Born-Oppenheimer approximation. The chemical processes on the atomics level has been reliying on the ability to separate fast electron motion from that of heavy nuclei. We focus in the so called conical intersection (CI), whereby molecular isomerization proceed over timescale clearly violating this paradigmatic approximation. Arguably, the most spectacular example of such process is the primary photochemical event in vision. The key aspect of these ultrafast, and often remarkably efficient, transitions is the conversion of optical energy into mechanical energy through coherent channels, that is with negligible loss of energy due to the random dissipation. This work in many aspects expands on the scope and offers a very challenging, et attractive, endeavour into vibrational coherence of complex molecule in solution. Molecular complexity was primarely motivated by wide applicablity of research on synthetic molecules that mimic the photoreaction of Rhodopsin (Rho), to date the fastest and most efficient optomechanical photoswitch. To this end, we have developed and used a state-of-art ultrafast time domain vibrational coherence spectrometer (VCS), allowing sub-10 fs resolution, hence vibration windows up to 3000 cm-1. Such combinaison unlocks to new ways to control over chemical reactions, whereby mechanistic forces precede rather than outpley thermal fluctuations. This concept transcends chemistry, and as a matter pf example, it has only begun to be exploited in material science. [...]

Light is one of the most advantageous stimuli to manipulate functional materials because it can be applied contactless and with high precision. A common strategy to prepare light-responsive physical systems is the embedding of photoswitchable groups such as the dye molecule azobenzene (azo). Upon irradiation with UV light, azobenzene undergoes photoisomerization from the trans to the cis isomer, whereas blue light triggers the inverse conversion. The two isomers differ with respect to their shape, solubility, and light absorption. Up to now, comparatively little research has been focusing on compounds that unite several photoswitchable groups. Such so-called multiphotochromes are promising multi-state molecular systems that can be controlled by light. In this thesis, the object of study is a star-shaped multiphotochromic molecule denoted TrisAzo. It is composed of three azo groups, which are centrally linked by a light-inert BTA group. The molecule has four photoisomers, ranging from the all-trans to the all-cis isomer. Furthermore, TrisAzo is the elementary building block of light-responsive supramolecular aggregates in solution. Previous experimental works report severe morphological changes of the aggregates under UV–Vis light but the underlying molecular mechanisms are still debated. The objective of this thesis is to elucidate the effects of light on TrisAzo – first, concerning its molecular properties and second, regarding the structure and stability of its supramolecular aggregates. In the presented work, the photoisomers of an azobenzene star with a BTA core are studied for the first time via computational methods, particularly using density functional theory and fully atomistic molecular dynamics (MD) simulations. The solvational and optical properties of TrisAzo are quantified as a function of its isomerization state. The solubility of TrisAzo in polar solvents improves with an increasing fraction of the cis-azo arms due to a redistribution of electron density. The absorption spectra of the TrisAzo isomers are nearly linear superpositions of the individual azo arm spectra but with slight deviations. These deviations indicate weak electronic coupling effects between the connected azo groups. Supramolecular aggregates of TrisAzo molecules in water are modeled using fully atomistic MD simulations for extensive investigations on the molecular scale. In equilibrium conditions, it is verified that randomly distributed TrisAzo molecules self-assemble into column-shaped stacks. Simulations of pre-assembled TrisAzo stacks provide detailed insights into their intermolecular interactions. The binding energies are dominated by π-π interactions between conjugated parts of the stacked molecules, especially the azo groups, while hydrogen bonds between the BTA cores play a subordinate but stabilizing role. To implement the effects of light into the simulations, a stochastic model of the repeated photoisomerization of azobenzene is developed. This model reproduces the photoisomerization kinetics of TrisAzo in good agreement with theory and previous experimental results. Based on this approach, light of various intensities and wavelengths is applied on an equilibrated TrisAzo stack. In contrast to prior assumptions, the simulations indicate that a stacked TrisAzo aggregate irradiated by light does not break or disassemble into separate fragments. The stack instead develops defects in the form of molecular shifts and reorientations. As a result, the aggregate eventually loses its columnar shape. The mechanism and driving forces behind these structural changes are clarified based on the simulation results. Thus, this work provides a new interpretation of the experimentally observed morphological changes. The obtained insights on the molecular scale may facilitate the design of light-responsive gels and supramolecular polymers.:Abstract v Kurzfassung vii 1 Introduction 1 2 Properties of Azobenzene and Azobenzene-Containing Materials 5 2.1 Azobenzene 5 2.1.1 Isomers and Photoisomerization 6 2.1.2 The Photostationary State 10 2.2 Multiphotochromic Molecules Based on Azobenzene 10 2.2.1 Azobenzene Stars 11 2.2.2 The Benzene-1,3,5-Tricarboxamide Linker Unit 11 3 Computational Methods and Models 15 3.1 Density Functional Theory 15 3.1.1 Functional and Basis Set 16 3.1.2 Implicit Solvation Models 17 3.1.3 Time-Dependent Density Functional Theory 17 3.2 Molecular Dynamics Simulations 18 3.2.1 All-Atom MD Simulations 18 3.2.2 Force Fields 19 4 Simulation Techniques 23 4.1 Thermodynamic Integration 23 4.1.1 Implementation in Atomistic Simulations 24 4.2 Modeling Photoisomerization in MD Simulations 27 4.2.1 Implementation of the Rotation Pathway 28 4.3 Modeling Light-Irradiated Azo-Materials in MD Simulations 30 4.3.1 The Cyclic Photoisomerization Model 31 5 Photoisomers of an Azobenzene Star 35 5.1 Object of Study: The Molecule TrisAzo 35 5.1.1 Isomers and Conformers 35 5.2 Ground State Properties in the Gas Phase and in Solvents 36 5.2.1 Energies and Standard Enthalpies of Formation 37 5.2.2 Geometry and Shape Properties 38 5.2.3 Dipole Moments 42 5.2.4 Molecular Properties Upon Hydration in Explicit Water 44 5.3 Solubility 47 5.3.1 Influence of Solvent Polarity 48 5.3.2 Influence of Isomerization State 48 5.3.3 Hydration Free Energy 49 5.4 Absorption Spectra and Intramolecular Coupling 51 5.4.1 Influence of the Number of Azo Groups and Their Isomerization State 52 5.4.2 Effect of the Solvent Polarity 54 5.5 Summary 56 6 Equilibrium Properties of TrisAzo Clusters 59 6.1 Supramolecules of Azobenzene Stars in the Experiment 60 6.1.1 Light-Induced Morphological Transition 60 6.2 Self-Assembly Starting from a Random Distribution 62 6.2.1 Radial Distribution Function 63 6.2.2 Cluster Analysis 65 6.3 Intermolecular Energy of a TrisAzo Dimer 69 6.3.1 Total Intermolecular Energy 70 6.3.2 Energy Decomposition 71 6.4 Structural Properties of Columnar TrisAzo Clusters 75 6.4.1 Considered Cluster Arrangements (Cluster Types) 75 6.4.2 Inner Structure of the Clusters 79 6.4.3 Effect of Cluster Size 79 6.5 Intermolecular Energy of Columnar TrisAzo Clusters 82 6.5.1 Total Intermolecular Energy 82 6.5.2 Energy Decomposition 83 6.5.3 The Role of Hydrogen Bonding 88 6.5.4 Rationalizing the Structural Differences of the Considered Cluster Types 91 6.6 Summary 93 7 Columnar TrisAzo Clusters Under UV–Vis Light 97 7.1 TrisAzo Stacks in the Full Photoisomerization Model 97 7.1.1 Cluster Structure Before and After Irradiation 98 7.1.2 Intermolecular Energy 101 7.2 TrisAzo Stacks in the Cyclic Photosomerization Model 104 7.2.1 Photoisomerization Kinetics 104 7.2.2 Cluster Structure Under Irradiation 108 7.2.3 Intermolecular Energy of TrisAzo Stacks Under Irradiation 112 7.2.4 Mechanism of Defect Formation 116 7.2.5 Comparison with Simulations of Comparable Systems 118 7.3 Summary 118 8 Summary and Outlook 121 8.1 Summary 121 8.2 Outlook 123 A Functional Form of the Force Fields 125 A.1 DREIDING Force Field 125 A.2 Polymer Consistent Force Field (PCFF) 129 B Additional Details about Thermodynamic Integration 133 B.1 Derivation of the Formalism 133 B.2 Avoiding Singularities and Instabilities 134 C Details of the Computational Models 137 C.1 DFT and TD-DFT Calculations 137 C.1.1 DFT Calculations 137 C.1.2 TD-DFT Calculations 138 C.2 MD Simulations of TrisAzo Molecules in PCFF 138 C.2.1 Parametrization 139 C.2.2 Preparation of Initial Configurations 139 C.2.3 Simulation Settings 140 C.3 MD Simulations of TrisAzo Molecules in DREIDING 140 C.3.1 Parametrization 141 C.3.2 Preparation of Initial Configurations 141 C.3.3 Simulation Settings 141 C.4 Intermolecular Energy Calculations of TrisAzo Dimers in PCFF and DREIDING 142 C.5 Visualization of Molecular Structures 142 D Equilibrium Properties of TrisAzo Clusters: Additional Material 143 D.1 From Experiments to Simulations 143 D.2 Cluster Analysis for TrisAzo Self-Assembly: Additional Material 144 D.3 Intermolecular Energy of a TrisAzo Dimer: PCFF Results 145 D.3.1 Total Intermolecular Energy 145 D.3.2 Energy Decomposition 145 D.3.3 Estimated Total Intermolecular Energy of TrisAzo-H 148 D.4 Structural Properties of Columnar TrisAzo Clusters: Additional Material 149 D.5 Intermolecular Energy of Columnar TrisAzo Clusters: Additional Material 150 D.5.1 Defect Detection Algorithm 151 D.6 The Role of Hydrogen Bonds: Additional Material 152 E Columnar TrisAzo Clusters Under UV–Vis Light: Additional Material 155 E.1 TrisAzo Stacks in the Full Photoisomerization Model: Additional Material 155 E.2 TrisAzo Stacks in the Cyclic Photosomerization Model: Additional Material 156 F Code Availability 161 Bibliography 163 List of Publications 183 Copyright of Published Articles 187 Acknowledgements / Danksagung 189 List of Abbreviations 191 List of Symbols 193 List of Physical Constants and Unit Conversions 195 Eidesstattliche Erklärung 197 / Licht ist einer der vorteilhaftesten Stimuli für die Manipulation responsiver Funktionsmaterialien, da es berührungslos und mit hoher Präzision angewendet werden kann. Ein weit verbreiteter Ansatz zur Herstellung lichtresponsiver physikalische Systeme ist der Einbau lichtschaltbarer Gruppen wie das Farbstoffmolekül Azobenzol (Azo). Unter UV-Licht vollzieht Azobenzol eine Photoisomerisation vom trans- zum cis-Isomer, während blaues Licht die umgekehrte Umwandlung auslöst. Die beiden Isomere unterscheiden sich vor allem durch ihre räumliche Gestalt, Löslichkeit und Lichtabsorption. Noch unzureichend erforscht sind Moleküle, die mehrere lichtschaltbare Gruppen in sich vereinen. Solche sogenannten Multiphotochrome sind vielversprechende molekulare Mehrzustandssysteme, die durch Licht geschaltet werden können. Untersuchungsobjekt dieser Arbeit ist ein sternförmiges multiphotochromes Molekül namens TrisAzo. Es besteht aus drei Azogruppen, die zentral über eine gegenüber Licht inerte BTA-Gruppe verknüpft sind. Dementsprechend existieren vier Photoisomere dieses Moleküls, vom all-trans- bis zum all-cis-Isomer. Des Weiteren ist TrisAzo der elementare Baustein lichtempfindlicher supramolekularer Aggregate in Lösung. Frühere experimentelle Arbeiten berichten starke morphologische Strukturänderungen der Aggregate unter Lichteinfluss, jedoch sind die zugrundeliegenden molekularen Mechanismen bisher ungeklärt. Ziel dieser Arbeit ist es, die Auswirkungen von Licht auf TrisAzo aufzuklären, erstens in Bezug auf dessen molekulare Eigenschaften und zweitens hinsichtlich der Struktur und Stabilität der supramolekularen Aggregate. In der vorgestellten Arbeit werden erstmals die Photoisomere eines Azosterns mit BTA-Kern auf Basis computerbasierter Methoden untersucht. Eingesetzt werden dabei Dichtefunktionaltheorie und atomistische Molekulardynamiksimulationen (MD). Insbesondere wird die Löslichkeit und das Lichtabsorptionsverhalten von TrisAzo in Abhängigkeit seines Isomerisationszustands analysiert. Die Löslichkeit von TrisAzo verbessert sich mit steigendem Anteil der cis-Azogruppen aufgrund einer damit einhergehenden Umverteilung der Elektronendichte. Die Absorptionsspektren der TrisAzo-Isomere sind in erster Näherung lineare Superpositionen der Einzelspektren jedes Molekülarms, jedoch mit geringen Abweichungen. Diese Abweichungen deuten auf schwache elektronische Kopplungseffekte zwischen den Azogruppen hin. Supramolekularen Aggregate von TrisAzo-Molekülen in Wasser werden für umfangreiche Untersuchungen auf molekularer Ebene in atomistischen MD-Simulationen modelliert. Im thermodynamischen Gleichgewicht bestätigt sich, dass sich zufällig verteilte TrisAzo-Moleküle in säulenförmig gestapelten Aggregaten zusammenfinden. Weitere Simulationen vorgestapelter TrisAzo-Aggregate liefern detaillierte Rückschlüsse auf deren intermolekulare Wechselwirkungen. Die Bindungsenergien werden von π-π-Wechselwirkungen zwischen den konjugierten Bereichen der aufeinanderliegenden Moleküle dominiert. Wasserstoffbrücken zwischen den BTA-Gruppen haben eine untergeordnete, aber stabilisierende Rolle. Um den Effekt von Licht in die Simulationen einzubauen, ist ein stochastisches Modell für die wiederholte Photoisomerisation der Azogruppen entwickelt worden. Dieses Modell reproduziert die Photoisomerisationskinetik von TrisAzo in guter Übereinstimmung mit Theorie und vorigen Experimenten. Basierend auf diesem Ansatz wird Licht verschiedener Intensitäten und Wellenlängen auf die gestapelten TrisAzo-Aggregate angewandt. Entgegen früherer Annahmen zerfallen die Aggregate daraufhin nicht in Einzelfragmente. Stattdessen entwickeln sie Defekte in Form von Molekülumordnungen sowie -reorientierungen und verlieren dadurch ihre säulenartige Form. Der Mechanismus und die Ursachen dieser Strukturänderungen werden anhand der Simulationen aufgeklärt. Damit liefert diese Arbeit eine neue Interpretation der experimentell beobachteten morphologischen Veränderungen. Die gewonnenen Erkenntnisse können die Entwicklung lichtresponsiver Gele und supramolekularer Polymere unterstützen.:Abstract v Kurzfassung vii 1 Introduction 1 2 Properties of Azobenzene and Azobenzene-Containing Materials 5 2.1 Azobenzene 5 2.1.1 Isomers and Photoisomerization 6 2.1.2 The Photostationary State 10 2.2 Multiphotochromic Molecules Based on Azobenzene 10 2.2.1 Azobenzene Stars 11 2.2.2 The Benzene-1,3,5-Tricarboxamide Linker Unit 11 3 Computational Methods and Models 15 3.1 Density Functional Theory 15 3.1.1 Functional and Basis Set 16 3.1.2 Implicit Solvation Models 17 3.1.3 Time-Dependent Density Functional Theory 17 3.2 Molecular Dynamics Simulations 18 3.2.1 All-Atom MD Simulations 18 3.2.2 Force Fields 19 4 Simulation Techniques 23 4.1 Thermodynamic Integration 23 4.1.1 Implementation in Atomistic Simulations 24 4.2 Modeling Photoisomerization in MD Simulations 27 4.2.1 Implementation of the Rotation Pathway 28 4.3 Modeling Light-Irradiated Azo-Materials in MD Simulations 30 4.3.1 The Cyclic Photoisomerization Model 31 5 Photoisomers of an Azobenzene Star 35 5.1 Object of Study: The Molecule TrisAzo 35 5.1.1 Isomers and Conformers 35 5.2 Ground State Properties in the Gas Phase and in Solvents 36 5.2.1 Energies and Standard Enthalpies of Formation 37 5.2.2 Geometry and Shape Properties 38 5.2.3 Dipole Moments 42 5.2.4 Molecular Properties Upon Hydration in Explicit Water 44 5.3 Solubility 47 5.3.1 Influence of Solvent Polarity 48 5.3.2 Influence of Isomerization State 48 5.3.3 Hydration Free Energy 49 5.4 Absorption Spectra and Intramolecular Coupling 51 5.4.1 Influence of the Number of Azo Groups and Their Isomerization State 52 5.4.2 Effect of the Solvent Polarity 54 5.5 Summary 56 6 Equilibrium Properties of TrisAzo Clusters 59 6.1 Supramolecules of Azobenzene Stars in the Experiment 60 6.1.1 Light-Induced Morphological Transition 60 6.2 Self-Assembly Starting from a Random Distribution 62 6.2.1 Radial Distribution Function 63 6.2.2 Cluster Analysis 65 6.3 Intermolecular Energy of a TrisAzo Dimer 69 6.3.1 Total Intermolecular Energy 70 6.3.2 Energy Decomposition 71 6.4 Structural Properties of Columnar TrisAzo Clusters 75 6.4.1 Considered Cluster Arrangements (Cluster Types) 75 6.4.2 Inner Structure of the Clusters 79 6.4.3 Effect of Cluster Size 79 6.5 Intermolecular Energy of Columnar TrisAzo Clusters 82 6.5.1 Total Intermolecular Energy 82 6.5.2 Energy Decomposition 83 6.5.3 The Role of Hydrogen Bonding 88 6.5.4 Rationalizing the Structural Differences of the Considered Cluster Types 91 6.6 Summary 93 7 Columnar TrisAzo Clusters Under UV–Vis Light 97 7.1 TrisAzo Stacks in the Full Photoisomerization Model 97 7.1.1 Cluster Structure Before and After Irradiation 98 7.1.2 Intermolecular Energy 101 7.2 TrisAzo Stacks in the Cyclic Photosomerization Model 104 7.2.1 Photoisomerization Kinetics 104 7.2.2 Cluster Structure Under Irradiation 108 7.2.3 Intermolecular Energy of TrisAzo Stacks Under Irradiation 112 7.2.4 Mechanism of Defect Formation 116 7.2.5 Comparison with Simulations of Comparable Systems 118 7.3 Summary 118 8 Summary and Outlook 121 8.1 Summary 121 8.2 Outlook 123 A Functional Form of the Force Fields 125 A.1 DREIDING Force Field 125 A.2 Polymer Consistent Force Field (PCFF) 129 B Additional Details about Thermodynamic Integration 133 B.1 Derivation of the Formalism 133 B.2 Avoiding Singularities and Instabilities 134 C Details of the Computational Models 137 C.1 DFT and TD-DFT Calculations 137 C.1.1 DFT Calculations 137 C.1.2 TD-DFT Calculations 138 C.2 MD Simulations of TrisAzo Molecules in PCFF 138 C.2.1 Parametrization 139 C.2.2 Preparation of Initial Configurations 139 C.2.3 Simulation Settings 140 C.3 MD Simulations of TrisAzo Molecules in DREIDING 140 C.3.1 Parametrization 141 C.3.2 Preparation of Initial Configurations 141 C.3.3 Simulation Settings 141 C.4 Intermolecular Energy Calculations of TrisAzo Dimers in PCFF and DREIDING 142 C.5 Visualization of Molecular Structures 142 D Equilibrium Properties of TrisAzo Clusters: Additional Material 143 D.1 From Experiments to Simulations 143 D.2 Cluster Analysis for TrisAzo Self-Assembly: Additional Material 144 D.3 Intermolecular Energy of a TrisAzo Dimer: PCFF Results 145 D.3.1 Total Intermolecular Energy 145 D.3.2 Energy Decomposition 145 D.3.3 Estimated Total Intermolecular Energy of TrisAzo-H 148 D.4 Structural Properties of Columnar TrisAzo Clusters: Additional Material 149 D.5 Intermolecular Energy of Columnar TrisAzo Clusters: Additional Material 150 D.5.1 Defect Detection Algorithm 151 D.6 The Role of Hydrogen Bonds: Additional Material 152 E Columnar TrisAzo Clusters Under UV–Vis Light: Additional Material 155 E.1 TrisAzo Stacks in the Full Photoisomerization Model: Additional Material 155 E.2 TrisAzo Stacks in the Cyclic Photosomerization Model: Additional Material 156 F Code Availability 161 Bibliography 163 List of Publications 183 Copyright of Published Articles 187 Acknowledgements / Danksagung 189 List of Abbreviations 191 List of Symbols 193 List of Physical Constants and Unit Conversions 195 Eidesstattliche Erklärung 197