A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.

Harnessing bacterial signals for suppression of biofilm formation in the nosocomial fungal pathogen Aspergillus fumigatus

Faced with the continued emergence of antibiotic resistance to all known classes of antibiotics, a paradigm shift in approaches toward antifungal therapeutics is required. Well characterized in a broad spectrum of bacterial and fungal pathogens, biofilms are a key factor in limiting the effectiveness of conventional antibiotics. Therefore, therapeutics such as small molecules that prevent or disrupt biofilm formation would render pathogens susceptible to clearance by existing drugs. This is the first report describing the effect of the Pseudomonas aeruginosa alkylhydroxyquinolone interkingdom signal molecules 2-heptyl-3-hydroxy-4-quinolone and 2-heptyl-4-quinolone on biofilm formation in the important fungal pathogen Aspergillus fumigatus. Decoration of the anthranilate ring on the quinolone framework resulted in significant changes in the capacity of these chemical messages to suppress biofilm formation. Addition of methoxy or methyl groups at the C5–C7 positions led to retention of anti-biofilm activity, in some cases dependent on the alkyl chain length at position C2. In contrast, halogenation at either the C3 or C6 positions led to loss of activity, with one notable exception. Microscopic staining provided key insights into the structural impact of the parent and modified molecules, identifying lead compounds for further development.