Thermoelectric semiconductors can convert temperature differences into electricity or electricity into temperature differences. This offers great potential for the use of wasted heat or cooling. These materials can be used in a variety of fields, from healthcare to space exploration. The effectiveness of the materials is evaluated by their thermoelectric properties such as the Seebeck coefficient, electrical conductivity, and thermal conductivity. The aim of this PhD thesis is to investigate the electronic structure using first-principle methods for potential thermoelectric applications. Materials of interest include Copper and Tin based ternary /quaternary compounds, and monolayers of SnS2, SnSe2 and Janus SnSSe. Density functional theory, ab initio molecular dynamics and Boltzmann transport theory are used to study the electronic and phonon transport properties. In the first part of the thesis, electronic structure calculations were performed on both monoclinic and disordered cubic forms of Cu2SnS3(CTS). The impact of structural disorder on thermoelectric properties was examined through these simulations. The results, obtained through first-principle calculations, revealed the existence of band tails in the electronic density of states for the disordered structure, and low-lying optical modes in the disordered cubic structure. This was found to be caused by a significant variation in Sn bonding, leading to strong anharmonicity as measured by the Grüneisen parameter. The findings from the first principle calculations were supported by Nuclear inelastic scattering experiments. Furthermore, the effect of grain size on Cu2SnS3 was studied using first-principles calculations on various ordered and disordered surfaces. The density of states (DOS) revealed that the surface of CTS is conductive due to the presence of dangling bonds. Furthermore, calculations of the formation energy showed that the stoichiometric CTS, Cu-vacant and Cu-rich systems are energetically more favourable, while the formation of Sn-vacant and Sn-rich systems is less likely. In the subsequent study, the impact of Ag substitution at the Sn site at various concentrations was investigated. The Fermi level for Ag-substituted systems was found to lie deep within the valence band, with the shift of the Fermi level inside the valence band increasing with substitution increasing the carrier concentration. The incorporation of Ag into the system decreases the root mean squared displacement of the other cations and anions, which reduces the scattering of phonons and thereby increases the lattice thermal conductivity. A comparative study of various polymorphs of CTS, Cu2ZnSnS4 and Cu2ZnSnSe4 was done. Ab-initio molecular dynamics was performed on CTS, CZTS and CZTSe. The root mean squared displacement value for the disordered polymorph was higher than for the ordered phase, indicating increased static disorder. This corresponds to the static (temperature-independent) distortion of the crystalline lattice due to the disorder of the cations and is associated with higher anharmonicity and bond inhomogeneity in the disordered phase, which is then directly responsible for the ultra-low thermal conductivity. In the final part of the thesis, thermoelectric properties of dichalcogenide monolayer of SnS2, SnSe2 and Janus SnSSe was performed. Density functional theoretical calculations points out the hexagonal Janus SnSSe monolayer as a potential high-performing thermoelectric material. Results for the Janus SnSSe monolayer show an ultra-low thermal conductivity originating from the low group velocity of the low-lying optical modes, leading to superior zT values of 0.5 and 3 at 300 K and 700 K for the p-type doping, respectively. The successful calculation of properties for materials shows that the computational work done in this thesis can be used for further research into thermoelectricity.

The properties of electrochemical interfaces are studied using Fourier transform infrared spectroscopy. Potential difference infrared spectroscopy (PDIRS) was used in the investigation of carbon monoxide adsorbed on polycrystalline platinum electrodes. It is found that the infrared peak position of adsorbed carbon monoxide is linearly dependent on the applied electrode potential, and that the Stark tuning rate is a function of system temperature. The change in Stark tuning rate is the result of the variation of the interfacial dielectric constant with temperature. Self-assembled alkoxyalkanethiol monolayers were formed on gold substrates as surface modifiers of low dielectric constant designed to influence the interfacial capacitance. Polarization modulation infrared spectroscopy (PMIRS), ellipsometry, interfacial wetting, and cyclic voltammetry were conducted to characterize the modified interfaces. The interfacial capacitance is greatly reduced due to the adsorption of w-mercapto ethers on substrates. It was found that the solvation of the monolayer by solution is capable of improving the mass transport to maintain the Faradaic current while lowering the interfacial capacitance. The oxygen group in w-mercapto ethers at the monolayer-water interface interacts with water molecules to improve the monolayer solubility in water. The w-mercapto ether monolayers were found to be fluid-like in structure, giving better freedom to undergo structural change. The repulsion from the oxygen atoms in adjacent w-mercapto ether molecules adsorbed on the substrate introduces structural disorder to the alkyl chains in the monolayer, allowing better solvent permeation. This relieves some of the current blocking character of long chain alkanethiol monolayers. The interfacial contact angle to water for the w-mercapto ether monolayers is dependent on the oxygen position in the monolayer. 12-Methoxydodecanethiol has the lowest contact angle among all the w-mercapto ethers studied while 12-butoxydodecanethiol through 12-hexoxydodecanethiol have similar contact angles due to the ether oxygen being buried beneath several layers of methylene groups. The film thickness is roughly proportional to the total number of methylene groups in the two alkyl chains on w- mercapto ethers. w-Mercapto ethers that have a longer alkyl chain between the oxygen and thiol tend to form thicker monolayers on the substrates. In situ PMIRS measurements show that w-mercapto ether monolayers do not undergo structural change in the alkyl chains when in contact with either water or acetonitrile. The terminal methyl group, however, suffers from a shift in infrared peak position to lower frequency, and a decrease in peak height as the result of solvent load. / Ph. D.

This study describes the covalent and the electrostatic attachment of molecules, nano-particles, and proteins to patterned self-assembled monolayers. A scanning probe nanografting technique was employed to produce patterns of various sizes, down to 10 nm. Thus, we are able to demonstrate a degree of surface patterning which is an order of magnitude smaller than that used in the semiconductor industry. One efficient strategy for creating chemically specific nanostructures is to use the extraordinary catalytic properties of enzymes. However, as the dimension of a catalyst patch is reduced down to nanometer scale, it is difficult to detect the very low concentration of product. This study resolves the problem by developing a new strategy: the surface trapping of a product generated by a nanometer-scale patch of surface-bound enzyme. An array of proteins finds use when the array contains a number of different proteins. Toward this end, a new and convenient method for immobilizing enzymes is developed, which will allow the preparation of thin films containing several different catalytically-active enzymes on the nanoscale. The disadvantage of scanning probe nanografting technique is that the AFM tip loses resolution through wear during the patterning procedure. This study examines the possibility of developing a new AFM lithographic method to avoid wear: the use of enzymes covalently attached to a tip as a site-specific catalyst. / Ph. D.

The compounds 12-phenoxy-dodecane-1-thiol, 4-dodecyloxymercaptophenol and 3-dodecyloxymercaptophenol have been synthesized using a novel synthesis to investigate the effect that the orientation of the functional group has on surface acidity. 3-dodeycloxymercaptophenol and 4-dodecyloxymercaptophenol differ in that the hydroxyl group is substituted on different carbons of the benzene ring. The difference in substitution patterns should present the hydroxyl group in different orientations in the interface between a self-assembled monolayer of the compound and aqueous solutions buffered over a pH range of 3-13. By preparing self-assembled monolayers of these molecules on gold substrates, the ability of the hydroxyl group to donate its proton was shown to depend on the hydroxyl group substitution pattern on the benzene ring through contact angle titration experiments. 3-dodecyloxymercaptophenol clearly showed plateaus at low and high pH with a broad transition between the two plateaus. 4-dodecyloxymercaptophenol showed a clear plateau at low pH but not at high pH, although a transition was observed. Using infrared spectroscopy, it was further shown that the long molecular axis of the benzene ring in 3-dodecyloxymercaptophenol was tilted from the surface normal by 55°. The short molecular axis of the ring was twisted out of the plane of the surface by 28° for self-assembled monolayers of this molecule on gold substrates. In contrast, the tilt angle of 4-dodecyloxymercatophenol was measured to be 46° and was twisted out of the surface plane by 36°. It was also found from cyclic voltammetry experiments in 0.5 M KOH, that the ionized monolayers of 4-dodecyloxymercaptophenol were 2.3 kJ/mol less stable than monolayers of 3-dodecyloxymercaptophenols. This finding suggests that hydrogen bonding and other intermolecular interactions in 4-dodecyloxymercaptophenol are greater than in 3-dodecyloxymercaptophenol. / Ph. D.

This research focuses on how the structure of modified interfaces influence the behavior of the interface. Two groups of dialkyl sulfides are prepared and studied: a purely hydrocarbon dialkyl sulfide with the structure CH₃(CH₂)₁₇S(CH₂)_nCH₃, where n=7, 9, and 17, and a carboxylic acid containing dialkyl sulfide with the structure CH3₃(CH₂)₁₇S(CH₂)_mCOOH, where m=7, 10, and 15. The structure and the permeability of these monolayers are characterized by <i>ex situ</i> and <i>in situ</i> FTIR, contact angle measurements, and electrochemistry. It is found that the two groups of dialkyl sulfides have different surface structures and different monolayer-solution interfacial behaviors. The presence of a polar group, such as -COOH, within the monolayer structure is found to increase the charge transfer properties of the modified electrode by influencing the interfacial structure. The structure and permeability of monolayers prepared from 15-mercaptopentadecanoic acid, 16-mercaptohexadecanoic acid, and their corresponding ethyl esters are also studied. Infrared spectroscopy and electrochemical permeability measurements indicate that the ester monolayers are ordered and have few differences in their structural and physical properties. Monolayers prepared from 15-mercaptopentadecanoic acid and 16-mercaptohexadecanoic acid, however, are structurally and physically different from the esters and each other. The IR and contact angle results indicate that hydrogen bonding interactions between the terminal groups of the monolayers influence the structural organization and physical properties of the monolayer. The extent of the hydrogen bonding interactions within the ω-mercaptoalkanoic acid monolayers appear to be related to the structure of the interface, suggesting that the orientation of the terminal functional group influences its ability to interact within the monolayer. / Master of Science

Various technologies depend on interfacial events that are influenced by various molecular interactions at a solid-liquid interface. The functionality of a surface plays an important role in many applications such as catalysis, sensing, and bio-compatibility, which can benefit from distinctive chemical and physical surface properties. To create tailor-made functional surfaces, surface host-guest assemblies based on Langmuir-Blodgett and self-assembly technique have been employed as a model system as they may offer the potential ability to regenerate surface properties via intercalation of various functional guest molecules. This thesis ranges over the development and characterization of host-guest assemblies and their feasibilities for the regeneration of surface properties via intercalation of functional guests. In our work, 3-dimensional host structures with cavities are constructed on a targeted solid substrate using Langmuir-Blodgett and self-assembly techniques. In particular, by adopting the fundamental concept of host-guest interaction in supramolecular chemistry, we expect that structurally homologous guest molecules where functional groups are anchored can be intercalated into the cavities between hydrophobe arrays at the liquid-solid interface from solution under well-controlled conditions. This approach offers the potential of separating the functional of the monolayer from the inherent structure of the host. The first part of this thesis details two-dimensional host-guest assemblies consisting of guanidinium (G), octadecylsulfonate (S) and various functional alkane guests at the air-aqueous interface and following deposition onto solid substrates via the Langmuir-Blodgett technique. In particular, we evaluated the stability of the host-guest assemblies and the feasibility of exchanging molecular guests under exposure to various organic solvent environments. Analysis of X-ray reflectivity measurements of the thin films showed that good stability of the host-guest assembly could not be achieved due to weak interactions between the host monoalyer and the solid surface. In addition, no evidence of intercalation of guest molecules into guest-free host-cavities was observed. The second part of this thesis discusses the effective methodologies to prepare low-density self-assembled monolayers (LDSAMs) with cavities on silicon substrates. We employed a step-wise reaction based on hydrolytic or silane chemistry: integral spacer molecules such as anthracene-derivatives were anchored to the Si substrate and then long alkane chains were appended to the spacer molecules. The results showed that LDSAMs using an anthryl spacer are attached at the SAM/Si interface via a Si-O-C linkage, and the films do not exhibit a densely packed monolayer quality as would be expected for a non-sterically hindered alkyltrichlorosilane on Si. Thus, the resulting LDSAMs (with cavities) may be capable of accommodating other guest molecules with hydrocarbon chains through intercalation in order to form host-guest assemblies. The third part of this thesis demonstrates the ability of LDSAMs to produce functional surfaces via the intercalation of various functional guest molecules. Self-assembled monolayers of (10-octadecyl)-9-anthracenethiol (host-SAMs) on Au substrates were prepared. Quartz crystal microbalance with dissipation (QCM-D) measurements was used to demonstrate the capacity of LDSAMs to confine guest molecules in the cavities and to probe the structural changes of the host-guest assembly during guest intercalation from ethanol solution. X-ray photoelectron spectroscopy (XPS) measurements were then used to probe host-guest monolayers formed by immersing the host monolayer in solutions in a variety of other solvents. A combined study of QCM-D and XPS showed that guest molecules were intercalated into host-cavities. The reversibility of the intercalation process allows a guest already situated in a host-cavity to be replaced with second guest under well-regulated solvent conditions. / Ph. D.

L'emploi des agents antibactériens est un moyen important d'une part dans la lutte contre les infections bactériennes et d'autre part pour conserver les produits alimentaires jusqu'à leur consommation. La perte d'efficacité des antibiotiques par le développement de résistance bactérienne ainsi que la toxicité des conservateurs synthétiques rend nécessaire le développement de nouveaux produits antibactériens naturels. Les protéines et les peptides antibactériens agissant sur les membranes bactériennes paraissent une alternative pour limiter l'instauration de résistances bactériennes. L'ovotransferrine est une protéine du blanc d'œuf ayant des propriétés membranotropes responsable entre autre de son activité antibactérienne. L'objectif de cette thèse est d'étudier les mécanismes membranotropes de l'ovotransferrine vis-à-vis des membranes externe et cytoplasmique d'E. coli en utilisant respectivement des monocouches de LPS (lipopolysaccharides) et de phospholipides comme modèles membranaires expérimentales. L'ovotransferrine possède une capacité d'insertion dans la monocouche de LPS qui dépend de la concentration protéique, de la compacité de la monocouche et de la conformation des molécules de LPS. L'ovotransferrine s'adsorbe faiblement à la monocouche de phospholipides. Ainsi, les monocouches sont perturbées par la désorganisation des lipides. L'analyse comparative de l'ovotransferrine chauffée à sec avec la forme native a montré la conservation des structures secondaire et tertiaire avec une augmentation de l'hydrophobie de surface et probablement de la flexibilité et une affinité plus élevée aux interfaces hydrophiles/hydrophobes (eau/air). L'activité membranaire de l'ovotransferrine est accrue après son chauffage à sec. La capacité d'insertion dans la monocouche de LPS est amplifiée avec une affinité plus importante. Une capacité d'insertion dans la monocouche de phospholipides est générée pour la forme chauffée à sec associée à une adsorption plus élevée. L'ovotransferrine chauffée à sec induit des perturbations plus importantes des monocouches à des concentrations protéiques plus faibles. / The use of antibacterial agents is very important, firstly, on the fight against bacterial infections, and secondly, to keep food products until its consumption. The loss of antibiotics effectiveness through the development of bacterial resistance and the toxicity of synthetic preservatives necessitates the development of new natural antibacterial products. Antibacterial proteins and peptides acting on the bacterial membranes appear as an alternative to limit the introduction of bacterial resistances. Ovotransferrin is an egg-white protein with membranotropic properties responsible among other things for its antibacterial activity. The aim of this thesis is to study the membranotropic mechanisms of ovotransferrin towards the outer and cytoplasmic membranes of E. coli using respectively monolayers of LPS (lipopolysaccharides) and phospholipids as experimental membrane models. Ovotransferrin has an insertion capacity in LPS monolayer that is dependent on protein concentration, monolayer compactness, and LPS molecule conformation. Ovotransferrin weakly adsorbs to the monolayer of phospholipids. Thus, the monolayers are disturbed by the disorganization of the lipids. Comparative analysis of dry-heated ovotransferrin with the native form showed conservation of secondary and tertiary structures with an increase of surface hydrophobicity and probably of flexibility and higher affinity to hydrophilic/hydrophobic interfaces (water/air). The insertion capacity in the LPS monolayer is amplified with greater affinity. Insertion capacity in the phospholipid monolayer is generated for the dry heated form associated with higher adsorption. Dry-heated ovotransferrin induces greater disruption of monolayers at lower protein concentrations.

MARCKS-Protein ist in den Signalübertragungsweg der Zelle involviert. Durch einen Adsorptions-/Desorptionszyklus mit der Zellmembran reguliert es die Konzentration bestimmter Botenmoleküle. Im Rahmen dieser Arbeit wurde untersucht, inwieweit strukturelle Änderungen der Membran, verursacht durch die Membran-Protein-Wechselwirkung, mit einem Reaktions-Diffusions-System korrelieren. Die elektrostatische Wechselwirkung von MARCKS-Protein mit negativ geladenen Membranlipiden geschieht an der inneren Seite der Zellmembran. Als Modellsystem lässt sich dies mit einer monomolekularen Lipidschicht an der Wasser-Luft-Grenzfläche realisieren. Anhand von oberflächensensitiven Messungen konnte gezeigt werden, dass die Wechselwirkung von MARCKS mit negativ geladenen Membranlipiden und damit die Adsorption an der Membran, zu einer Änderung der Membrantopologie führt. Damit verbundenen ist auch der partielle Einbau von MARCKS in die Membran, was zu einem größeren molekularen Flächenbedarf führt. Dieser korreliert mit dem Anstieg des lateralen Drucks der Lipidmonoschicht bei konstanter Fläche. Die Desorption von MARCKS kann durch die Wechselwirkung mit PKC induziert werden, detektierbar durch die Reduktion des lateralen Drucks. Bei Vorhandensein eines Reservoirs an MARCKS und PKC oszilliert der laterale Druck, was als zyklische Adsorption und Desorption von MARCKS an bzw. von der Lipidschicht interpretiert wird. Anhand der experimentellen Ergebnisse wurde ein mathematisches Modell entwickelt, dass dieses oszillierende Verhalten als ein Reaktions-Diffusions-System erklärt.

MARCKS-Protein ist in den Signalübertragungsweg der Zelle involviert. Durch einen Adsorptions-/Desorptionszyklus mit der Zellmembran reguliert es die Konzentration bestimmter Botenmoleküle. Im Rahmen dieser Arbeit wurde untersucht, inwieweit strukturelle Änderungen der Membran, verursacht durch die Membran-Protein-Wechselwirkung, mit einem Reaktions-Diffusions-System korrelieren. Die elektrostatische Wechselwirkung von MARCKS-Protein mit negativ geladenen Membranlipiden geschieht an der inneren Seite der Zellmembran. Als Modellsystem lässt sich dies mit einer monomolekularen Lipidschicht an der Wasser-Luft-Grenzfläche realisieren. Anhand von oberflächensensitiven Messungen konnte gezeigt werden, dass die Wechselwirkung von MARCKS mit negativ geladenen Membranlipiden und damit die Adsorption an der Membran, zu einer Änderung der Membrantopologie führt. Damit verbundenen ist auch der partielle Einbau von MARCKS in die Membran, was zu einem größeren molekularen Flächenbedarf führt. Dieser korreliert mit dem Anstieg des lateralen Drucks der Lipidmonoschicht bei konstanter Fläche. Die Desorption von MARCKS kann durch die Wechselwirkung mit PKC induziert werden, detektierbar durch die Reduktion des lateralen Drucks. Bei Vorhandensein eines Reservoirs an MARCKS und PKC oszilliert der laterale Druck, was als zyklische Adsorption und Desorption von MARCKS an bzw. von der Lipidschicht interpretiert wird. Anhand der experimentellen Ergebnisse wurde ein mathematisches Modell entwickelt, dass dieses oszillierende Verhalten als ein Reaktions-Diffusions-System erklärt.

Kovalente organische Frameworks (COFs) haben in den letzten Jahren aufgrund ihrer potenziellen Anwendungen in verschiedenen Bereichen großes Interesse hervorgerufen. Obwohl die Eigenschaften der synthetisierten Materialien empfindlich von den Eigenschaften der entsprechenden organischen Liganden abhängen, ist der Beitrag der einzelnen Bausteine zu den Kristalleigenschaften nicht eindeutig definiert. In dieser Arbeit werden die elektronischen und mechanischen Eigenschaften von einschichtigen zweidimensionalen (2D) COFs untersucht, wobei der Schwerpunkt auf den molekularen Bausteinen liegt. Zunächst wurde die Kristallstruktur als Hooke'sches Federnetzwerk angenommen, und analytische Formeln für 2D-COFs mit quadratischer und hexagonaler Gittertopologie wurden abgeleitet, wobei eine Vorhersage des Kompressionsmoduls aus der Berechnung der Monomer-Federkonstante angestrebt wurde. Alle geschätzten Werte für Moleküle und periodische Strukturen wurden mit der DFTB-Methode (Density Functional based Tight-Binding) berechnet. Benchmarking-Berechnungen mit der Dichtefunktionaltheorie (DFT) wurden eingesetzt, um die Anwendbarkeit der semiempirischen Methode zu überprüfen. In einem zweiten Schritt wurden Methoden vorgeschlagen, um die elektronische Bandstruktur und die elektronischen Eigenschaften von COFs zu verändern, wie z.B. die Änderung von Bindungen oder Linkern, Seitengruppen oder Funktionalisierung und die Erhöhung der Massendichte. Die verschiedenen Methoden ergeben unterschiedliche Eigenschaften der resultierenden Strukturen. Darüber hinaus wurden mehrere Polymere durch periodische Fortsetzung in einer oder zwei Dimensionen auf der Grundlage derselben molekularen Bausteine modelliert. Es wurde ein zweistufiges System auf der Grundlage des Tight-Binding-Ansatzes vorgeschlagen, und dessen Parameter wurden mit Hilfe der Bandoberkante des Valenzbandes und der Bundunterkante des Leitungsbandes abgeschätzt. Ein maschinelles Lernverfahren wurde eingesetzt, um die elektronische Bandlücke auf der Grundlage der gleichen Kernmonomere vorherzusagen. Interessanterweise erbt das 2D-COF die elektronische Lücke von der monomeren Einheit mit der niedrigeren elektronischen Energiedifferenz zwischen besetztem und unbesetztem Band. Schließlich wurde die Protonentautomerisierung in zwei sehr häufig verwendeten Kernmonomeren für 2D-COFs, Porphyrin und Phthalocyanin, und ihren Derivaten untersucht. Die Freie-Energie-Oberfläche wurde mit Quanten-Molekulardynamik-Simulationen durch Kombination von DFTB und Metadynamik berechnet. Durch die Analyse der Potenzialporträts werden die strukturellen Symmetrien des Moleküls in Protonentransferreaktionen widergespiegelt. Ich erwarte, dass die Ergebnisse dieser Arbeit Einsichten für die Synthese von 2D COFs geben werden, welche auf optimierte elektronische Eigenschaften mit hoher struktureller Stabilität abzielt.:ABSTRACT ZUSAMMENFASSUNG 1. INTRODUCTION Motivation Nomenclatures Experimental characterization and computational studies Objectives and outline 2. THEORETICAL AND COMPUTATIONAL BACKGROUND Many-body system Density Functional Theory (DFT) Kohn-Sham auxilary approach and the computational application of DFT Exchange-correlation functional Hybrid functionals Basis-set Pseudo-potentials Tight-binding model Density Functional based Tight-binding model (DFTB) Slater-Koster approach Slater-Koster sets in DFTB Molecular Dynamics and Metadynamics Classical Molecular Dynamics (MD) Quantum Molecular Dynamics (QMD) Metadynamics(MTD) 3. PREDICTING THE BULK MODULUS Conceptualization Equivalent spring constant Two dimensional bulk modulus Computational details COFs with square lattice type Models Molecular Spring constant Single layer 2D COFs COFs with hexagonal lattice type Models Single layer 2D COFs Synopsis 4. ENGINEERING THE ELECTRONIC PROPERTIES Computational details COFs with square lattice type Models Benchmarking of different methods π -conjugated COFs COFs with hexagonal topology Models π -conjugated COFs Synopsis PREDICTING THE ELECTRONIC BAND GAP Conceptualization Models Computational protocol 1D- and 2D-polymer Comparing the cores Predicting the gap Synopsis 6 SIMULATING THE PROTON TAUTOMERIZATION Models Collective variables (CVs) Computational protocol FES portraits and energy barriers Synopsis 7 CONCLUSIONS AND OUTLOOK APPENDIX A APPENDIX B APPENDIX C BIBLIOGRAPHY SCIENTIFIC OUTPUT ACKNOWLEDGEMENTS