Dissertations / Theses on the topic 'Pi-pi stacking'

Noncovalent interactions are of pivotal importance in many areas of chemistry, biology, and materials science, and the intermolecular interactions involving aromatic rings in particular, are fundamental to molecular organization and recognition processes. The work detailed in this thesis involves the application of state-of-the-art ab initio electronic structure theory methods to elucidate the nature of pi-pi interactions. The binding energies, and geometrical and orientational preferences of the simplest prototype of aromatic pi-pi interactions, the benzene dimer, are explored. We obtain the first converged values of the binding energies using highly accurate methods and large basis sets. Results from this study predict the T-shaped and parallel-displaced configurations of benzene dimer to be nearly isoenergetic. The role of substituents in tuning pi-pi interaction is investigated. By studying dimers of benzene with various monosubstituted benzenes (in the sandwich and two T-shaped configurations), we surprisingly find that all of the substituted sandwich dimers considered bind more strongly than benzene dimer. We also find that these interactions can be tuned by a modest degree of substitution. Energy decomposition analysis using symmetry-adapted perturbation theory (SAPT) reveals that models based solely on electrostatic effects will have difficulty in reliably predicting substituent effects in pi-pi interactions.

Previous studies of the redox states of linear conjugated oligomers as models for polarons and bipolarons in conjugated polymers do not fully address the influence of intermolecular interactions on the electronic structure of conjugated systems in the solid state. Fusion of oligothiophenes onto a bicyclo[4.4.1]undecane core holds the conjugated oligomers in a permanent cofacial stack. One- and two-electron oxidation of the stacked oligomers affords mono(radical cation)s and dications that serve as models for polarons and bipolarons in p-doped conjugated polymers and demonstrates the effect of pi-stacking on the electronic structure of these species. Installation of phenyl-capped and ferrocenyl-capped oligothiophenes allows us to systematically vary pi-stacked oligomers and study intramolecular charge migration in other linear conjugated molecules.

The field of organic electronics has received much attention over the last few years, and engineering of organic crystals to grow with pi-electron systems arranged in a face-to-face motif has been shown to be beneficial in electronic devices. The effects of combining aromatic and perfluorinated aromatic derivatives have shown that the intramolecular stacking pattern can be changed from an edge-to-face arrangement to that of a face-to-face motif. Before the work described herein, there were no reported studies of the supramolecular behavior of fused polycyclic aromatic compounds with partial peripheral fluorination, inducing the desired face-to-face behavior. This is the main focus of the thesis. Furthermore, by exploiting the interactions between the fluorinated and non-fluorinated faces of the molecule, columnar liquid crystalline behavior can be achieved through variations of the alkyl substituents on the molecule.

This work sought to enforce aromatic interactions between compatible π-molecular orbital systems with ionic bonding. In this case the interacting partners are oppositely charged discotic triangulene derivatives. The observed properties of the heterodimeric ion-pairs likely arise due to a hypothetical synergy between electrostatics and π-interactions. The work presented here describes investigation of putative covalency arising from this hypothetical synergy in the electrostatics driven π-stacking. In order to probe this, various hypotheses were made and experiments were designed to test their validity. The results from the experiments show existence of contact ion-pairs and complex solvent-separated discotic ions in solution. The formation of complex ion-pairs arise due to the fact that the electrostatic interaction that brings the discotic ions together is strong, but does not neutralize when the contact is made. So, the dipole created by the monopoles in a dimeric contact ion-pair can attract ions at both termini forming oligomers. This process apparently continues towards highly aggregated states and then to nanometric species and at some point the material precipitates. The propensity to aggregate and form complex-ions limited our approach to the measurement of the energetics of the ion-pairing for two reasons: (1) the observables had a complex dependence on temperature, solvent, concentration and ionic strength; and (2) the mass in solution was undergoing kinetic evolution towards solid states. The turbidimetric effects arising due to aggregate formation further complicated the extraction of weak interactions between the ions and hence effects determination of ion-pairing constants.

Les nucléolipides sont des molécules amphiphiles dont la structure bio-inspirée dérive de celle des acides nucléiques. Leur auto-assemblage en milieu aqueux aboutit à la formation d’objets supramoléculaires de morphologies et structures très diverses. La morphologie a été caractérisée par des techniques complémentaires de microscopie optique et de diffusion de la lumière, tandis que leur structure a été déterminée par la diffusion des rayons X. Il a ainsi été mis en évidence l’existence et le rôle fondamental des interactions faibles entre têtes polaires, au sein des auto-assemblages. La nature de ces interactions faibles a été déterminée par des techniques de spectroscopies IR et UV. Un premier objectif a été de mettre en évidence l’importance de ces interactions, ainsi que leur corrélation avec d’autres facteurs qui régissent le mécanisme d’auto-assemblage, tels que la nature chimique des amphiphiles, ou la morphologie et la structure des objets supramoléculaires en présence.Par ailleurs, la tête polaire nucléotide permet également d’imaginer la formation d’interactions faibles entre les auto-assemblages et un monobrin d’acide nucléique, à l’image des interactions spécifiques entre bases azotées présentes dans l’ADN. Lors de ce travail, nous nous sommes intéressés à une méthode de vectorisation d’acides nucléiques par des objets eux aussi chargés négativement. Contrairement aux approches classiques, l’interaction électrostatique est ici défavorable et l’association repose alors uniquement sur des interactions faibles spécifiques, estimées en spectroscopie. De façon surprenante, la formation des complexes a pu être mise en évidence par des expériences de diffraction des rayons X et un modèle approprié a permis de proposer des mécanismes de formation des complexes. Les propriétés thermodynamiques des différents complexes formés ont été évaluées par la technique de Calorimétrie à Titration Isotherme (ITC). Un point remarquable a été la mise en évidence systématique de trois types de comportements sur l’ensemble des complexes étudiés en fonction de la nature et de la spécificité des interactions mises en jeu. Ceci nous a ainsi permis de proposer différents mécanismes de formation pour chaque type de complexe observé
Nucleolipids are amphiphilic molecules which bio-inspired structure derives from nucleic acid structure. Their self-assembling behaviour in aqueous medium leads to the formation of supramolecular objects of very different morphologies and structures. The morphology has been characterized with optical microscopy and light scattering complementary techniques, whereas their structure has been determined with X-ray scattering. Thus the existence and the fondamental role of weak interactions between polar heads inside the self-assemblies have been highlighted. The nature of these weak interactions has been determined with IR and UV spectroscopies techniques. A first objectif has been to highlight the importance of these interactions, as well as the their correlation with other factors which drive the mechanism of self-assembly, such as the chemical nature of amphiphiles or the morphology and structure of the supramolecular objects.Moreover the nucleotide polar hear also allows to imagine the formation of weak interactions between the self-assemblies and a single-stranded nucleic acid, such as those highlighted in DNA. In this work, we found interest in a nucleic acid vectorisation method with negatively charged objects as well. On the contrary of classic approaches, electrostatic interaction was here defavorable and assembling relies only on specific weak interactions, estimated with spectroscopy methods. Surprisingly, complexes formation could be highlighted with X-ray scattering experiments, and an appropriate model has allowed the proposal of mechanisms for the formation of complexes. Thermodynamic properties of the different complexes formed have been evaluated with Isothermal Titration Calorimetry (ITC) technique. A remarkable point was the systematic highlighting of three types of behaviour on the whole set of complexes studied, depending of the nature and the specificity of the weak interactions implied. This led us to different proposals for the mechanism of formation of each type of complex studied

Thesis (Ph.D.)--University of Mississippi, 2007.
Typescript. Vita. Major professor: Gregory S. Tschumper "May 2007." Includes bibliographical references (leaves [103]-121). Also available online via ProQuest to authorized users.

L’intérêt du greffage moléculaire vis-à-vis des limitations en puissance des batteries et des limitations en énergie des supercondensateurs a été envisagé. Les propriétés morphologiques et électriques résultantes des fonctionnalisations covalente et non covalente de substrats carbonés, ont été évaluées et comparées. Afin de contrôler et d’optimiser le transfert électronique entre les différents constituants d’une électrode de batterie, l’implémentation de jonctions moléculaires à effet tunnel, a été envisagée. Afin d’augmenter l’énergie des supercondensateurs, un nouveau concept a été développé. Il est basé sur l’auto-fonctionnalisation redox nonperturbatrice, de carbones contenus dans des électrodes composites, durant le cyclage électrochimique ou durant l’étape de « calendar life », par un matériau actif redox organique contenu dans l’électrolyte. La diminution de l’épaisseur des électrodes de batteries Li est souvent utilisée comme moyen de compenser les faibles performances en puissance mais au détriment de l’énergie. Une alternative possible serait alors l’utilisation de molécules redox relais du matériau actif, dont la compensation de la charge ne mettrait pas en jeu les ions Li+
The interest of molecular grafting regarding the power limit of Li batteries and the energy limit of the supercapacitors has been considered. Morphological and electrical properties resulting of covalent and non covalent functionalizations of carbon substrates have been evaluated and compared. In order to control and to optimize the electronic conductivity between the different components of a battery electrode, the implementation of tunneling molecular junctions has been investigated. To increase the energy of supercapacitors, a new concept has been developed. It is based on self- and non-disruptive redox fonctionalization of carbon-containing composite electrodes during electrochemical cycling or during calendar life by an organic redox-active material that is contained in the electrolyte. The thickness decrease of Li batteries electrodes is often used as a way to compensate the low power performance but at the expense of the energy. An alternative would be to use redox molecular relay of the active material for which charge compensation occurs without Li+

Bioinorganic chemistry strives to understand the roles of metals in biological systems, whether in the form of naturally occurring or addition of non-essential metals to natural systems. Metal ions play vital roles in many cellular functions such as gene expression/regulation and DNA transcription and repair. The study of metal-protein-DNA/RNA interactions has been relatively unexplored. It is important to understand the role of metalloprotein interactions with DNA/RNA as this enhanced knowledge may lead to better understanding of diseases and therefore more effective treatments. A major milestone in the development of this field was the discovery of the cytotoxic properties of cisplatin in 1965 and its FDA approval in 1978. Since then, two other chemotherapeutic drugs containing platinum, carboplatin and oxaliplatin, have been used in the clinic. These three compounds are all bifunctional with the ligands surrounding platinum In the cis conformation and rearrangement of the ligands to the trans orientation results in a loss of cytotoxic properties due to rapid deactivation through binding to S-containing proteins. This enhanced reactivity yields new opportunities to study the reactions between proteins and DNA. One of the first crosslinking experiments used transplatin to crosslink NCp7 to viral RNA in order to understand how/where the protein bound to RNA. We have studied the interaction between cis and trans dinuclear platinum complexes and the C-terminal zinc finger (ZF). The trans complex reacts at a faster rate than the cis isomer and causes N- terminal specific cleavage of the ZF. The dinuclear structure plays a critical role in the peptide cleavage as studies with transplatin (the mononuclear derivative) does not result in cleavage. Monofunctional trans platinum-nucleobase complexes (MPNs) serve as a model for the binding of transplatin to DNA. This provides an interesting opportunity to study their reactions with S-containing proteins, such as HIV1 NCp7. MPNs have been shown to bind to the C-terminal ZF of HIV1 NCp7, resulting in zinc ejection. This occurs through a two-step process where the nucleobase π-stacks with Trp37 on the ZF, followed by covalent binding at the labile Cl site to Cys. MPNs have also shown antiviral activity in vitro. The labile Cl on MPNs reduces specificity of these compounds, as it leaves an available coordination site on the platinum center for binding to other S-proteins or DNA. Therefore, we have moved to an inert PtN4 coordination sphere, [Pt(dien)L]2+ (dien= diethylenetri- amine). Due to the strong bond between platinum and nitrogen, covalent reactions are highly unlikely to occur at rapid rates. The strength of the pi-stacking interaction between nucleobases (free and platinated) and the aromatic amino acid, tryptophan (Trp), showed an enhanced binding constant for platinated nucleobases. This was confirmed by density functional theory (DFT) calculations as the difference in energy between the HOMO of Trp and the LUMO of the nucleobase was smaller for the platinum complex. The studies were extended to the Trp-containing C-terminal ZF of HIV1 NCp7 and an increase in association constant was seen compared to free Trp. Reaction of PtN4 nucleobases compounds with a short amino acid sequence con- taining either Ala (no pi-stacking capabilities) or Trp (pi-stacking interactions) revealed an enhanced rate of reactivity for the Trp-containing peptide. This result supports the theory of a two-step reaction mechanism where the platinum-nucleobase complex recognizes the pep- tide through a pi-stacking interaction with Trp followed by covalent binding to the platinum center. The [Pt(dien)L]2+ motif allows for systematic modification of the structural elements surrounding platinum in a search for the most effective compound. Methylation of the dien ligand should, in theory, increase lipophilicity of the compounds, however, due to 2+ charge of the compounds, this simple association does not hold true. Analysis of the cellular accumulation profiles showed little change in the uptake with the addition of methyl groups to the dien ligand, in agreement with the non-linear change in lipophilicity. Modification of L using different nucleobases allows for the tuning of the strength of the π-stacking interaction between Trp and the platinum complex. The addition of inosine (which lacks a H-bonding donor/acceptor at the C2 position) resulted in a lower association constant with both N-AcTrp and the C-terminal zinc finger of HIV1 NCp7. Interestingly, the addition of xanthosine resulted in an ehanced pi-stacking interaction with the C-terminal zinc finger of HIV1 NCp7; likely as a results of the addition of a H-bonding donor (double-bonded O) at the C2 position. The ability of PtN4 nucleobase complexes to inhibit formation of the NCp7 complexation with viral RNA was studied by mass spectrometry and gel electrophoresis. Dissociation of the NCp7-RNA complex was seen upon addition of PtN4 compounds. These compounds were also able to retard formation of the NCp7-RNA complex when pre-incubated with the protein. These results have important implications as inhibition of complex formation between NCp7 and viral RNA has negative implications for viral replication. Despite the success of platinum-nucleobase compounds, it is important to evaluate all potential pi-stacking ligands. A series of pyridine- and thiazole-based compounds were evaluated for the strength of the pi-stacking interaction with N-AcTrp and the C-terminal ZF of HIV1 NCp7. There was notable increase in association constant for the platinum- DMAP (4-dimethylaminopyridine) complex compared to other ligands studied. This result highlights the importance of exploring multiple avenues for the design of specifically targeted inhibitors and further confirms the viability of the medicinal chemistry dual approach of target recognition (non-covalent) followed by target fixation (covalent).

Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2005.
Morhan Srinivasarao, Committee Member ; CP Wong, Committee Member ; David M. Collard, Committee Chair ; Marcus Weck, Committee Member ; Laren Tolbert, Committee Member.

Thin-film organic field effect transistors (OFETs) have attracted growing interest in recent years due to their promising electrical, optical and mechanical properties. Especially, oligothiophenes and their derivates are candidates with good prospects for application as the organic semiconducting material in such devices. They possess an extended, polarisable aromatic π-electron system that promotes a high structural arrangement of the molecules. The charge transport in the organic film is realised in the direction perpendicular to the plane of the thiophene rings via a hopping transport mechanism. Thus, a good π-π-overlap and a consequent stacking of the thiophene molecules in the film perpendicular to the gate substrate is essential to achieve excellent electric properties such as high charge carrier mobilities and low resistive losses. The highly polarisable thiophene-based molecules are also very attractive materials that are potentially applicable as the field-sensitive organic semiconducting component of a ferroelectric OFET device. In such a device, the dielectric gate element of a conventional OFET setup is substituted by a ferroelectric substrate. The electric field that is induced by the polarisation of the ferroelectric material serves as gate field and controlls the charge injection and charge density inside the device. In this thesis, thiophene-based molecules are investigated in detail with respect to their application as field-sensitive organic semiconducting component in a ferroelectric OFET device employing quantum-chemical ab initio and DFT-based methods. We demonstrate that the phosphonic acids can bind the organic molecules to the dielectric or ferroelectric material and well-anchored, robust self-assembled monolayers are formed. Furthermore, special focus is put on the influence of the intermolecular interactions among the organic molecules on the technologically relevant structural and electronic properties. It is found that the CN···HC hydrogen bond link the molecules into extended ribbons, but the π-π-stacking-stacking interaction is the main driving force in the self-assembly of the molecules. We also establish in detail the influence of the electric field on the phosphonic acid anchoring molecule and some quarterthiophene derivates. For the latter, the strongest field-sensitivity is obtained for an external electric field aligned parallel to the extension of the thiophene framework. Hence, they are suitable to act as the field-sensitive organic components in devices that take advantage of a band-gap engineering. Moreover, the present results emphasise the importance of the adsorption morphology of the molecules in the film in a π-stacked fashion with their longitudinal axis oriented parallel to the (orthonormal) electric field induced by the ferroelectric substrate.

Weak bonds such as hydrogen bond, pi-pi stacking and van der Waals interaction are much weaker in the strength but play a more important role for the existence of various lives. For example, they are the major intermolecular interactions in the liquid and solid structure of water and determine the 3 dimensional structure of protein and DNA, which are the crucial organic molecules in lives. As a result, studying these weak bonds can lead to the better understanding of fundamental knowledge of lives. Kohn-Sham (K-S) Density Functional Theory (DFT) is an accurate and effect way to investigate the fundamental properties for many-body systems, in which, only the exchange-correlation energy as a functional of electron density need to be approximated. However, weak interaction system is still a challenge problem for KS-DFT. In this dissertation work, several standard density functionals are used to study these weak interactions in the solid state structure ice as long as nucleic bases molecules in the biologic system. It is found that the hydrogen bond can be well described by most semilocal functionals: the mismatch problem of ice Ih and AgI for GGA functional can be solved by using the higher level meta-GGA functionals and the binding length and energy between nucleic bases in DNA can be well described. However, the more accurate dispersion correction is strongly needed for van der Waals interactions and pi stacking for super-high pressure ice phases and large size biologic molecules, where van der Waals interaction takes major role. Finally, the basic structural properties of various phases of ice and DNA can be understood based on the investigation with appropriate functionals.
acase@tulane.edu

碩士
輔仁大學
化學系
96
Abstract Two-state model was introduced to study the electron/hole transfer mechanism in the dipolar π-π stacking systems. Post Hartree-Fork quantum method MP2/6-311g were carried out to evaluate the dipole and π-π coupling interactions in the substituted aniline pairs. Molecular orbital analysis illustrates the evolution of the electronic splitting associated to the HOMO and LUMO levels. According to Marcus and Koopmans’ theorem, the splitting energies can be used to estimate the electronic coupling and excimer effect. The calculated transfer integral of hole against the Hammett parameter of substuient gives a linear relationship. And we also calculated the coupling between ground state and excited state by Generalized Mulliken-Hush method. We found the transfer integral of hole is correlated with the extinction coefficients of brush-like polymers. The interaction and transfer integral between chromophores is dominate its light-harvesting ability in polymer. Our theoretical approach can be applied to the carrier mobility in these brush-like polymers.

Non-covalent interactions are of great interest to chemists and biologists who study the molecular structure and function of biological systems, as well as those who seek to control, undo, or improve upon the efficiency of these systems with man-made chemical tools. The Iverson group has specifically applied noncovalent aromatic donor-acceptor interactions to biotic and abiotic aqueous systems through the use of the electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) moieties. Chapter 1 introduces and reviews the current state of self-assembly research, especially work conducted in aqueous media. Chapter 2 delineates the design and synthesis of a molecule that can self-assemble and form disulfide bonds, with the goal of creating higher-order structure. Chapter 3 comprises the design and synthesis of a series of pendant-NDI bisintercalators of DNA that are distinct from the backbone-incorporated intercalators previously employed in our laboratory. Chapter 4 contextualizes the term of art “pi-stacking,” reviewing the current state of knowledge of specific contributions to this effect and commenting on the putative uniqueness of the interaction. Theoretical and experimental work in the field is summarized. The work discussed in this dissertation serves to expand the scope of programmability of our DNA intercalators, to probe the higher-order assembly behavior of our donor-acceptor pair, and to clarify the term “pi-stacking,” lately overused, that imperfectly describes the interaction that gives both these systems their compelling binding properties.
text

There are currently three known crystal packing motifs of boronsubphthalocyanine derivatives. Each motif is associated with a particular class of BsubPc derivatives, and none are ideal for organic electronic applications according to the criteria we defined for evaluation: having a continuous pathway for charge-carrier conduction in the solid-state, resistance to hydrolysis, good electrochemical and optical properties, and possession of a robust crystal form. In this thesis, we present five methods for altering the crystal packing structure of phenoxy-BsubPc derivatives in order to meet the above four criteria. We find that neither addition of steric bulk to the axial derivative nor changing the symmetry of the compounds is sufficient for creating a new crystal packing motif. We do find that reducing the symmetry of the axial group does increase the solubility greatly, however. We identify a new motif for BsubPc crystals that occurs when the intermolecular interactions between the axial phenoxy segment and the BsubPc ligand are increased. We present two methods for achieving this new motif, one is through addition of a π-Br interaction and the other is through creation of a strong π-acid/ π-base stacking by making the axial phenoxy more π-electron rich. Unfortunately, the p-bromophenoxy-BsubPc forms this new motif as a kinetic product, isolation of which is unreliable. Attaching a naphthol fragment axially to the BsubPc creates a stable version of this new motif. We also synthesized a new class of BsubPc pseudohalides based on sulfonate derivatives. Of the derivatives in this new class, we found that mesylate-BsubPc forms into a crystal packing structure that possesses a one-dimensional pathway for charge carrier mobility, but is still resistant to hydrolysis under the conditions tested. Overall, we show four compounds that meet the criteria for further study as organic electronic materials: p-methoxyphenoxy-BsubPc, α-naphthoxy-BsubPc, β-naphthoxy-BsubPc, and mesylate-BsubPc.

Thin-film organic field effect transistors (OFETs) have attracted growing interest in recent years due to their promising electrical, optical and mechanical properties. Especially, oligothiophenes and their derivates are candidates with good prospects for application as the organic semiconducting material in such devices. They possess an extended, polarisable aromatic π-electron system that promotes a high structural arrangement of the molecules. The charge transport in the organic film is realised in the direction perpendicular to the plane of the thiophene rings via a hopping transport mechanism. Thus, a good π-π-overlap and a consequent stacking of the thiophene molecules in the film perpendicular to the gate substrate is essential to achieve excellent electric properties such as high charge carrier mobilities and low resistive losses. The highly polarisable thiophene-based molecules are also very attractive materials that are potentially applicable as the field-sensitive organic semiconducting component of a ferroelectric OFET device. In such a device, the dielectric gate element of a conventional OFET setup is substituted by a ferroelectric substrate. The electric field that is induced by the polarisation of the ferroelectric material serves as gate field and controlls the charge injection and charge density inside the device. In this thesis, thiophene-based molecules are investigated in detail with respect to their application as field-sensitive organic semiconducting component in a ferroelectric OFET device employing quantum-chemical ab initio and DFT-based methods. We demonstrate that the phosphonic acids can bind the organic molecules to the dielectric or ferroelectric material and well-anchored, robust self-assembled monolayers are formed. Furthermore, special focus is put on the influence of the intermolecular interactions among the organic molecules on the technologically relevant structural and electronic properties. It is found that the CN···HC hydrogen bond link the molecules into extended ribbons, but the π-π-stacking-stacking interaction is the main driving force in the self-assembly of the molecules. We also establish in detail the influence of the electric field on the phosphonic acid anchoring molecule and some quarterthiophene derivates. For the latter, the strongest field-sensitivity is obtained for an external electric field aligned parallel to the extension of the thiophene framework. Hence, they are suitable to act as the field-sensitive organic components in devices that take advantage of a band-gap engineering. Moreover, the present results emphasise the importance of the adsorption morphology of the molecules in the film in a π-stacked fashion with their longitudinal axis oriented parallel to the (orthonormal) electric field induced by the ferroelectric substrate.