abstract: Layered chalcogenides are a diverse class of crystalline materials that consist of covalently bound building blocks held together by van der Waals forces, including the transition metal dichalcogenides (TMDCs) and the pnictogen chalcogenides (PCs) among all. These materials, in particular, MoS2 which is the most widely studied TMDC material, have attracted significant attention in recent years due to their unique physical, electronic, optical, and chemical properties that depend on the number of layers. Due to their high aspect ratios and extreme thinness, 2D materials are sensitive to modifications via chemistry on their surfaces. For instance, covalent functionalization can be used to robustly modify the electronic properties of 2D materials, and can also be used to attach other materials or structures. Metal adsorption on the surfaces of 2D materials can also tune their electronic structures, and can be used as a strategy for removing metal contaminants from water. Thus, there are many opportunities for studying the fundamental surface interactions of 2D materials and in particular the TMDCs and PCs. The work reported in this dissertation represents detailed fundamental studies of the covalent functionalization and metal adsorption behavior of layered chalcogenides, which are two significant aspects of the surface interactions of 2D materials. First, we demonstrate that both the Freundlich and Temkin isotherm models, and the pseudo-second-order reaction kinetics model are good descriptors of the reaction due to the energetically inhomogeneous surface MoS2 and the indirect adsorbate-adsorbate interactions from previously attached nitrophenyl (NP) groups. Second, the covalent functionalization using aryl diazonium salts is extended to nanosheets of other representative TMDC materials MoSe2, WS2, and WSe2, and of the representative PC materials Bi2S3 and Sb2S3, demonstrated using atomic force microscopy (AFM) imaging and Fourier transform infrared spectroscopy (FTIR). Finally, using AFM and X-ray photoelectron spectroscopy (XPS), it is shown that Pb, Cd Zn and Co form nanoclusters on the MoS2 surface without affecting the structure of the MoS2 itself. The metals can also be thermally desorbed from MoS2, thus suggesting a potential application as a reusable water purification technology. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2019

Indiana University-Purdue University Indianapolis (IUPUI) / Gas-phase ion/ion covalent modification was coupled to ion mobility/mass spectrometry analysis to directly correlate the structure of gaseous ubiquitin to its solution structures with selective covalent structural probes. Collision cross-section (CCS) distributions were measured prior to ion/ion reactions to ensure the ubiquitin ions were not unfolded when they were introduced to the gas phase. Ubiquitin ions were electrosprayed from aqueous and methanolic solutions yielding a range of different charge states that were analyzed by ion mobility and time-of-flight mass spectrometry. Aqueous solutions stabilizing the native state of ubiquitin generated folded ubiquitin structures with CCS values consistent with the native state. Denaturing solutions favored several families of unfolded conformations for most of the charge states evaluated. Gas-phase covalent labeling via ion/ion reactions was followed by collision-induced dissociation of the intact, labeled protein to determine which residues were labeled. Ubiquitin 5+ and 6+ electrosprayed from aqueous solutions were covalently modified preferentially at the lysine 29 and arginine 54 residues, indicating that elements of secondary structure, as well as tertiary structure, were maintained in the gas phase. On the other hand, most ubiquitin ions produced in denaturing conditions were labeled at various other lysine residues, likely due to the availability of additional sites following methanol and low pH-induced unfolding. These data support the conservation of ubiquitin structural elements in the gas phase. The research presented here provides the basis for residue-specific characterization of biomolecules in the gas phase.

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This work explores a binary reagent approach to increase the specificity of covalent inhibitors. In this approach, two ligand analogs equipped with inert pre-reactive groups specifically bind a target biopolymer. The binding event brings the pre-reactive groups in proximity with each other. The two groups react, generating active chemical intermediates that covalently modify and inactivate the target. In the present study we compare the new approach with the traditional single-component reagent strategy using DNA polymerase from bacteriophage T4 as a model target biopolymer. We report the design and synthesis of two analogs of deoxythymidine triphosphate, a natural DNA polymerase substrate. Together, the analogs function as a binary nucleotide reagent which is activated by light with wavelengths 365 nm and longer. However, the active analog functions as a traditional single component reagent when activated by light with wavelengths at 300 nm and longer. The traditional single-component reagent efficiently inactivated DNA polymerase. However, in the presence of non-target protein the inactivation efficiency is greatly diminished. Under the same conditions, the binary nucleotide reagent also inactivated DNA polymerase, and the inactivation efficiency is not affected by the presence of the non-target protein. Our results validate that a binary approach can be employed to design highly specific covalent inhibitors. The binary reagent strategy might be useful as a research tool for investigation of ligand-protein interactions in complex biological systems and for drug design

The initial steps involved in the assembly of normally soluble proteins into amyloid fibrils remain unclear, yet over 20 human diseases are associated with proteins that aggregate in this manner. Protein surface modification is a potential means of mapping the interaction sites in early oligomers that precede amyloid formation. This dissertation focuses on the use of covalent labeling combined with mass spectrometry to elucidate the structural features of Cu(II)-induced β-2-microglobulin (β2m) amyloid formation. An improved covalent modification and MS-based approach for protein surface mapping has been developed to address the need for a reliable approach that ensures protein structural integrity during labeling experiments and provides readily detectable modifications. This approach involves measuring the kinetics of the modification reactions and allows any local perturbations caused by the covalent label to be readily identified and avoided. This MS-based method has been used to study human β2m, a monomeric protein that has been shown to aggregate into amyloid fibrils in dialysis patients leading to dialysis-related amyloidosis. Under conditions that lead to β2m amyloid formation, reactions of β2m with three complementary covalent labels have been used to identify the Cu(II) binding site, metal-induced conformational changes, and the oligomeric interfaces. Results confirm that Cu(II) binds to His31 and the N-terminal amine. Binding to these residues causes several structural changes in the N-terminal region and ABED β-sheet which likely enables formation of oligomeric intermediates. The covalent labeling data indicate that the pre-amyloid β2m dimer has an interface that involves the antiparallel arrangement of ABED sheets from two monomers. Moreover, our covalent labeling data allowed us to develop a model for the tetramer in which the interface is mediated by interactions between D strands of one dimer unit and the G strands of another dimer unit. Lastly, the selective covalent modification approach has been used to delineate the structural changes in β2m after interaction with Cu(II), Ni(II), and Zn(II) and their effect on its aggregation. Our covalent labeling data indicates that the unique effect of Cu(II) appears to be caused by the site at which the metal binds the protein and the conformational changes it induces.

This work proposes minimally invasive solutions for spinal cord regeneration after trauma. In particular, injectable biomaterials can be precisely positioned in the lesion site, and eventually repetitively injected until the complete regeneration of the tissue. For this application, a silk fibroin functionalized with collagen type IV and laminin-derived peptides, called bio-inspired multifunctionalized silk fibroin (BMS), possessing piezoelectric properties, has been synthesized. Another approach that avoids damages to the spinal cord is proposed in the thesis as a multilayer hydrogel with piezoelectric properties that acts as a bridge between the healthy parts surrounding the injury. The multilayer hydrogel consists of i) a thin-layer of gelatin and fish collagen functionalized with VEGF for blood vessels formation, which helps the survival of the cells integrating with the pia mater of the spinal cord; ii) a BMS layer, which helps the adhesion, migration of neural stem cells and induces the sprouting of the axons thanks to the presence of Netrin (a chemoattractive protein); and iii) an adhesive layer of polydopamine (PDA) to fix the patch on the injured site. The adhesive patch exhibits a potential larger than an injectable hydrogel that could guarantee a long-term cell survival and help the axons to move towards a direction. The adhesive patch will be located on the surface of the spinal cord and the chemoattractive protein will induce the sprouting of the ascendant or descendant axons in the spinal cord to reach the axons present in the patch, restoring a signal connection. Even if not final, the results indicate that the above strategy could be explored further for the regeneration of the spinal cord.

Nanofluidic is an emerging field of applying fluid properties in nanochannels or nanostructures. The nanoporous channel with a pore size of less than 100 nm will strongly affect the motion of the fluid. Meanwhile, the pore environment, such as hydrophilic and hydrophobic properties, charge density, and host-guest recognition would be crucial for the transportation of molecules and ions in the pore. This thesis is focused on the synthesis, characterization of nanofluidic membranes and their applications to reverse electrodialysis. Chapter 1 focuses on the importance and objective of this work. Chapter 2 gives an overview of nanofluidic and classical nanofluidic structure–covalent organic frameworks (COFs). In Chapter 3, a series of COFs membranes with different surface charge densities were designed by employing a multivariate (MTV) strategy. A volcano-like relationship between the surface charge density and output power density was observed when the membranes were applied for osmotic energy harvesting. Chapter 4 integrates the temperature gradient to the covalent organic frameworks nanofluidic system to further explain the thermophoretic mobility of ions. The recorded osmotic energy production density was obtained while ion concentration polarization was alleviated with increasing hydrodynamic convection effects. In Chapter 5, a coupled photon-electron-ion transport behavior across ionic covalent organic framework membranes with chromophoric porphyrin struts was demonstrated. Photoexcitation-induced ion transmission was developed by converting external light into electric signals. Chapter 6 includes the summary of this thesis.

Photophysical properties of an array of various polyaromatic hydrocarbons were benchmarked with B3LYP, M06 and B97D methods coupled with Pople and CEP-31G(d) basis sets. Results from the benchmark show the importance of diffuse basis sets when modeling the electronic properties of highly conjugated systems and provide qualitative reliable accuracy with certain levels of theory. B97D and M06 are applied to modeling pyrene adducts governed by non-covalent interactions in both gaseous and condensed states to reproduce experimental spectra. DFT calculations with both B97D and M06 functionals show qualitatively and quantitatively that pyrene dimer is a stronger π–base as compared to its monomer. Binding energies coupled with MEP, PCA and Qzz results show that the difference in π-basicity of the monomer and dimer impacts the supramolecular chemistry involved in adducts formed with super π-acidic silver cyclometallic trimer (CTC). Non-covalent interactions between coinage metal CTCs and ammonia/phosphine substrates is reported. Interactions between these substrates and the facial plane of the π-rich gold CTC reveal a novel interaction, where the typical Lewis acid/base roles are reversed for the substrates. Adducts formed through this type of interaction define typical Lewis bases like ammonia and phosphine as Lewis acids, wherein the partially positive hydrogens coordinate to the metallo-aromatic center through dipole-quadrupole interactions. Interactions of ammonia at the side positions is shown to heavily impact the Lewis basicity of the CTC facial plane leading to similar interactions exhibited by the ammonia-gold CTC adducts. Structural and electronic properties of the adducts modeled are examined.

De nos jours, l’élaboration d’objets de dimensions nanométriques constitue un champ de recherches particulièrement prometteur pour la conception de systèmes de petite taille. La possibilité d’exploiter ces systèmes dans des applications telles que l’électronique moléculaire ou la modification des propriétés de surface a suscité l’engouement auprès de la communauté scientifique. Cependant, afin de construire des dispositifs électroniques complexes à partir de molécules organiques, l’assemblage covalent de briques moléculaires sur une surface est primordial. Les recherches menées dans le cadre de cette thèse portent sur l’élaboration de réseaux bidimensionnels à partir de briques moléculaires déposées sur surface. La réalisation de tels réseaux consiste d’une part, en la synthèse des différents précurseurs, et par la suite, au dépôt de ces briques moléculaires sur des surfaces métalliques ou de graphite. La croissance de ces réseaux est contrôlée en variant les conditions de dépôts qui s’opèrent dans un milieu sous-vide ou liquide. Le réseau peut être construit à partir d’un même précurseur, qui réagit dès lors sur lui-même pour former le réseau. Ainsi, des réactions telles que l’auto-condensation, la polymérisation oxydative ou encore la cyclotrimérisation sont abordées. De plus, les réactions entre deux précurseurs de natures différentes sont également décrites. Après la synthèse des briques moléculaires, leur étude sur surface est détaillée dont la caractérisation de réseaux est suivie par microscopie à effet tunnel. / Nowadays, the engineering of nanometer-sized systems is a promising field for the development of little-sized systems. The possibility of extending these systems to applications such as molecular electronics or surface property tuning has attracted much attention to the scientific community. However, in order to construct complex electronic devices from organic molecules, covalent assembly of building blocks on surface is primordial. The researches carried out in this work thesis rest on the construction of two-dimensional frameworks from molecular building blocks deposited on surface. The achievement of such networks consists, first of all, in the synthesis of different precursors and afterwards, in the deposition of these molecular buildingblocks on metallic or graphite surfaces. The growth of such networks is controlled by changing deposition conditions which occurs in ultra-high vacuum or in liquid media. The framework can be built from the precursor itself, which reacts with each other to give rise to the network. Reactions such as self-condensation, oxydative polymerization or either cyclotrimerization are broached. Moreover, reactions between two different precursors are also described. After molecular building block synthesis, on-surface study is detailed which framework characterization is followed by scanning tunneling microscopy.

Le fondaparinux (Arixtra®), anticoagulant de la classe des pentasaccharides de synthèse, est le premier inhibiteur d'origine synthétique, spécifique et indirect du facteur Xa de la coagulation. Il résulte de la synthèse chimique de l'unité pentasaccharidique des héparines, capable de se lier à l'antithrombine, une protéine endogène, inhibitrice de la coagulation. Cependant, son utilisation reste limitée par son administration uniquement possible par voie parentérale.L'objectif de ce travail de thèse est de développer une forme orale du fondaparinux en l'associant à un dérivé squalénique. Le squalène, terpénoïde naturel précurseur de la synthèse du cholestérol, possède une très bonne absorption orale (supérieure à 60 %). Dans ce contexte, deux stratégies d'association ont été développées: la première consistant à associer par liaison covalente le fondaparinux à un dérivé squalénique selon le concept de la « squalénisation » et la deuxième à associer par interactions non covalentes le fondaparinux à un dérivé squalénique cationique.Les travaux expérimentaux ont montré que la première stratégie était délicate à mettre en œuvre en raison d'une part de la difficulté à synthétiser un bioconjugué fondaparinux-squalène et d'autre part de la perte de l'activité anticoagulante du fondaparinux. En raison de ces obstacles, le concept de la « squalénisation » n'est pas adapté à ce type de molécule active. En revanche, la deuxième stratégie s'est montrée très prometteuse. Elle a consisté à formuler des nanoparticules par association non covalente du fondaparinux, chargé négativement, à un dérivé squalénique cationique. Cette approche a permis de mettre en évidence l’excellente capacité d'auto-assemblage en milieu aqueux de ces deux composés, liée à l’établissement de deux types d’interactions, électrostatiques et hydrophobes (entre les molécules de squalène). L'absorption orale du fondaparinux a été considérablement augmentée grâce à ce nouveau système nanoparticulaire. Cette nouvelle approche à base de squalène a ainsi montré son efficacité dans l'amélioration de l'administration orale du fondaparinux et pourrait représenter un système thérapeutique potentiel dans le traitement des maladies thromboemboliques. / Since its introduction in the market in 2002, fondaparinux (Arixtra®) is a drug of choice in the anticoagulant therapy. Its structure corresponds to the heparin pentasaccharide sequence that mediates its interaction with the natural plasma inhibitor of coagulation, antithrombin. However, like heparin, its application is limited due its unique administration by parenteral route. The aim of this project is to develop an efficient oral delivery system for fondaparinux by association with a squalene derivative. Squalene, a natural precursor of cholesterol in sterol biosynthesis, is well-known for its excellent oral absorption (i.e. more than 60 %). In this context, two strategies were investigated. The first consisted in achieving a covalent coupling between fondaparinux and a squalene derivative according to the concept of “squalenoylation”. The second was to associate fondaparinux to a cationic squalenoyl derivative by non-covalent association.Experimental work showed that the first strategy was delicate to implement due to the difficulty to synthesize a fondaparinux-squalene bioconjugate and, the loss of the anticoagulant properties of fondaparinux. Because of these obstacles, the concept of "squalenoylation" was not suitable for this type of active molecule. In contrast, the second strategy has been very promising. It consisted in the formulation of a nanoparticulate delivery system by ion-pairing of fondaparinux and a cationic squalenoyl derivative. This approach permitted to highlight the self-assembly of these two compounds in water as monodisperse nanoparticles thanks to electrostatic and hydrophobic interactions. Furthermore, the oral absorption of fondaparinux was significantly increased with this new nanoparticulate system. This new squalene-based approach has shown its effectiveness in improving the oral administration of fondaparinux and could be a potential delivery system in the treatment of thromboembolic diseases.