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This master thesis deals with preparation of cyclodextrin (CD) derivatives that are suitable for bonding on solid surfaces such as dopamine polymer and gold. The nucleophilic attack of 6I -O-p-toluenesulfonyl--CD (6-tosyl-β-CD) by dithiols created derivatives with substituents bound to CD skeleton by one of the sulphur atom while keeping a free terminal sulphanyl group. Despite initial problems caused by oxidation of the thiols to disulfides, CDs were modified by alkyl or oligoethylene glycol spacers prepared in 60 - 88% yields. The same reaction was used for preparation of derivatives of β-CD with amino group at the end of the tether that was linked to CD by nitrogen atom. For these purposes were used corresponding diamines and reactions proceeded smoothly reaching up to 92% isolated yield. Next, also the chemoselectivity of the reaction with an ambident spacer bearing both amino and sulphanyl functional group was studied and by 2D NMR experiments was proved that substituent was bound to CD through sulphur atom. It was demonstrated on the case of preparation of CD derivative with dimethylene linker that was prepared in 84% yield. A complete set of yet other CD-oligoethylene glycol derivatives with spacers linked to CD skeleton through the sulphur atom and terminated by amino group was prepared by...

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Biofouling is the attachment and biofilm formation that leads to negative repercussions such as persistent post-harvest infections, infections obtained from medical implants and continual surface contamination of food processing plants. Much of the problem lies with the resistance that develops against conventional treatments due to the formation of mature biofilms. Thus the focus has shifted from the removal of biofilms to the prevention of initial attachment of organisms. This entails the use of antimicrobial surfaces that either have an inherent antimicrobial activity, e.g. certain metals, or surfaces that are modified by the attachment of antimicrobial agents. The attachment of antimicrobial agents can either be through covalent bonding or adsorption, depending on the intended use of the surface as well as the mode of action of the antimicrobial agent. Antimicrobial peptides (AMPs) are ubiquitous in nature, tend to have a broad spectrum of activity, are very stable and have been shown to maintain activity when covalently bound to solid surfaces. Tyrocidines (Trcs), antimicrobial peptides produced by Bacillus aneurinolyticus, are cyclodecapeptides with a broad spectrum of activity against Grampositive bacteria, fungi, yeasts and the human malaria parasite, Plasmodium falciparum. The aim of this study was to determine the antimicrobial activity of surfaces treated with a tyrocidine extract, under which conditions the activity remained stable and to look into possible applications of these peptide-treated surfaces. The study focussed on different solid surfaces namely mixed cellulose, polyvinylidene fluoride, polycarbonate, cellulose acetate, cellulose (paper)(CL) and high density cellulose packing material (HDC), as a pilot study to assess the antimicrobial activity of Trc and gramicidin S (GS) treated solid surfaces. Peptide desorption and subsequent analysis by mass spectrometry was used to confirm the presence and integrity of the Trcs adsorbed. Scanning electron microscopy was utilised to show that the adsorbed peptides did not affect the structural integrity of the treated filters. However, it was shown that the adsorbed peptides changed the hydrophobic/hydrophilic character by means of a wettability assay. A cell viability assay and erythrocyte assay were developed from existing methodologies to determine the biological activity of the AMP-functionalised polymeric material. Seven of the AMP treated solid surfaces showed antimicrobial activity when challenged with >105 Micrococcus luteus cells/cm2. Although the polycarbonate filter lost antimicrobial activity at the high cell concentrations, it was shown to have potent antimicrobial activity at lower cell concentrations. Complete inhibition of M. luteus growth was observed for both the gramicidin S and tyrocidine extract treated high density cellulose and cellulose filters. Stability tests showed that the tyrocidines remained adsorbed to cellulose filters and biologically active when exposed multiple water washes, water washes at different temperatures (25°C - 100°C) and pH changes (pH 1-12). The antimicrobial activity was only affected after exposure to the water wash of pH 13 which is possible due to susceptibility of the CL filters to high pH solvents. A preliminary study on the effect of Trcs treated CL filters on the sterilization, germination and effect on tomato seedlings was conducted. It was found that Trcs had no effect on the germination and did not fully sterilise the seeds or environment against fungi. However, it was observed that 5 μg/mL Trcs treated filters promoted root length opposed to the toxic effect seen with filters treated with higher Trc concentrations. It is hypothesised that Trcs prefer to bind to hydrophilic surfaces exposing the hydrophobic residues and the cationic residue of the peptide to interact with the bacterial membrane to elicit its antimicrobial response. The exposed residues contain some of the hydrophobic residues and the cationic Orn9/Lys9, which are crucial to the antimicrobial activity of the peptides. Hydrophobic interaction is particularly important for the haemolytic activity which is currently the only viable method of detection of the adsorbed Trcs. Trcs also have a preference for adsorption onto cellulose and cellulose analogues which points to possible application in protective food wrapping and wood surface protection. Trcs maintains its antimicrobial activity regardless of adsorption to solid surfaces. It can therefore be concluded that Trcs treated solid surfaces hold great potential in preventing the initial bacterial colonization and subsequent biofilm formation. Antimicrobial peptide enriched solid surfaces can thus be developed and tailored to a specific application such as filters, catheters and packaging materials. / AFRIKAANSE OPSOMMING: Biovervuiling is die aanhegting en vorming van biofilms met negatiewe gevolge soos aanhoudende na-oes infeksies, infeksies op mediese inplantings en voortdurende oppervlak besoedeling van voedselverwerkings fabrieke. Die probleem lê grotendeels by die weerstand wat ontwikkel word teen konvensionele behandelings as gevolg van die vorming van volwasse biofilms. Die fokus het gevolglik verskuif vanaf die verwydering van biofilms na die voorkoming van aanvanklike aanhegting van organismes aan oppervlaktes. Dit behels die gebruik van antimikrobiese oppervlaktes wat of 'n inherente antimikrobiese aktiwiteit het, bv. sekere metale óf oppervlaktes wat aangepas is deur die aanhegting van antimikrobiese middels. Die aanhegting van antimikrobiese agente kan of deur kovalente binding óf adsorpsie plaasvind, afhangende van die beoogde gebruik van die oppervlak, sowel as die metode van werking van die antimikrobiese agent. Antimikrobiese peptiede (AMPe) is alomteenwoordig in die natuur, is geneig om 'n breë spektrum van aktiwiteit te hê, is baie stabiel en het getoon dat aktiwiteit in stand gehou word wanneer dit kovalent gebind word op soliede oppervlaktes. Tirosidiene (Trcs), antimikrobiese peptiede wat deur Bacillus aneurinolyticus geproduseer word, is siklodekapeptiede met 'n breë spektrum van aktiwiteit teen Gram-positiewe bakterieë, swamme, giste en die menslike malaria parasiet Plasmodium falciparum. Die doel van hierdie studie was om die antimikrobiese aktiwiteit te bepaal van oppervlaktes wat met 'n tirosidien ekstrak behandel is, te bepaal onder watter omstandighede die aktiwiteit stabiel bly en om te soek na moontlike toepassings van hierdie peptied-behandelde oppervlaktes. Die studie het gefokus op verskillende soliede oppervlaktes naamlik gemengde sellulose, polyvinylidene fluoried, polikarbonaat, sellulose asetaat, sellulose (papier)(CL) en 'n hoë digtheid sellulose verpakkings materiaal (HDC), as 'n loodsstudie om die antimikrobiese aktiwiteit van die Trcs en gramisidien S (GS) behandelde soliede oppervlaktes te ondersoek. Peptied-desorpsie en daaropvolgende ontleding deur massaspektroskopie is gebruik om die teenwoordigheid en integriteit van die geadsorbeerde Trcs te bevestig. Skandering elektronmikroskopie is gebruik om aan te toon dat die geadsorbeerde peptiede geen invloed op die strukturele integriteit van die behandelde filters het nie. Daar is egter getoon dat die geadsorbeerde peptiede die hidrofobiese / hidrofiliese karakter verander. „n Lewensvatbaarheid selgebaseerde toets en eritrosiet toets is ontwikkel uit bestaande metodes om die biologiese aktiwiteit van die AMP-gefunktionaliseerde polimeriese materiaal te bepaal. Sewe van die AMP behandel soliede oppervlaktes het antimikrobiese aktiwiteit getoon wanneer dit met > 105 Micrococcus luteus selle/cm2 gedaag is. Hoewel die polikarbonaat filter antimikrobiese aktiwiteit met hoë sel konsentrasies verloor het, is dit getoon dat dit wel uitgeproke antimikrobiese aktiwiteit het teen laer konsentrasies selle. Volledige inhibisie van M. luteus groei is waargeneem vir beide die hoë digtheid sellulose en sellulose filters wat met GS en tirosidien ekstrak behandel is. Stabiliteit toetse het getoon dat die tirosidiene geadsorbeer en biologies aktief op sellulose filters bly nadat dit blootgestel is aan verskeie water was-stappe, waterwasse by verskillende temperature (25 °C -100 °C) en pH veranderinge (pH 1-12). Die antimikrobiese aktiwiteit was net beïnvloed ná blootstelling aan die water met 'n pH 13, wat moontlik is te danke aan die vatbaarheid van die CL filters by hoë pH oplosmiddels is. 'n Voorlopige studie is gedoen om die uitwerking van Trcs behandelde CL filters op die sterilisasie, ontkieming en tamatiesaailinge te bepaal. Daar is gevind dat Trcs geen effek op die ontkieming het nie, maar dat dit nie volledig die sade en omgewing steriliseer vir fungiese groei nie. Daar is egter waargeneem dat 5 μg/mL Trcs behandelde filters wortel lengte van die saailinge bevorder teenoor die giftige uitwerking soos waargeneem vir die filters wat met hoër konsentrasies Trcs behandel is. Dit word gepostuleer dat Trcs verkies om aan hidrofiliese oppervlaktes te bind wat die van die hidrofobiese aminosure en die kationiese residu van die peptied blootstel om aan die bakteriële membraan te bind om gevolglik antimikrobiese reaksie te ontlok. Die blootgestelde deel bevat sommige van die hidrofobiese residue en positiewe Orn9/Lys9 wat noodsaaklik vir die antimikrobiese aktiwiteit van die peptiede. Die hidrofobiese interaksies is veral belangrik vir die hemolitiese aktiwiteit wat tans die enigste bruikbare metode van opsporing van die geadsorbeerde Trcs is. Trcs het ook 'n tendens vir adsorpsie op sellulose en sellulose analoë wat dui op die moontlike toepassing in beskermende voedselverpakking en die beskerming van houtoppervlaktes. Trcs handhaaf hul antimikrobiese aktiwiteit, ongeag van adsorpsie aan soliede oppervlaktes. Dit kan dus afgelei word dat Trcs-behandelde soliede oppervlaktes die potensiaal het om die aanvanklike kolonisasie van bakterië te voorkom en die daaropvolgende biofilm vorming. Antimikrobiese peptied verrykde soliede oppervlaktes kan dus ontwikkel en aangepas word vir gebruik in spesifieke toepassing soos in filters, kateters en verpakkingsmateriaal.

In this thesis I concentrate on the description of electron transport properties of microscopic objects, including molecular junctions and nano junctions, in particular, inelastic electron tunneling in surface-adsorbate systems are examined with more contemplations. Boosted by the rapid advance in experimental techniques at the microscopic scale, various electric experiments and measurements sprung up in the last decade. Electric devices, such as transistors, switches, wires, etc. are expected to be integrated into circuit and performing like traditional semiconductor integrated circuit (IC). On the other hand, detailed information about transport properties also provides new physical observable quantities to characterize the systems. For molecular electronics, which is in the state of growing up, its further applications demands more thorough understanding of the underlying mechanism, for instance, the effects of molecular configuration and conformation, inter- or intra-molecular interactions, molecular-substrate interactions, and so on. Inelastic electron tunneling spectroscopy (IETS), which reflects vibration features of the system, is also a finger print property, and can thus be employed to afford the responsibility of single molecular identification with the help of other experimental techniques and theoretical simulations.There are two parts of work presented in this thesis, the first one is devoted to the calculation of electron transport properties of molecular or nano junctions: we have designed a negative differential resistance (NDR) device based on graphene nanoribbons (GNRs), where the latter is a star material in scientific committee since its birth;The transport properties of DNA base-pair junctions are also examined by theoretical calculation, relevant experimental results on DNA sequencing have been explained and detailed issues are suggested.The second part focused on the simulation of scanning tunneling microscope mediated IETS (STM-IETS). We have implemented a numerical scheme to calculate the inelastic tunneling intensity based on Tersoff-Hamann approximation and finite difference method, benchmark results agree well with experimental and previous theoretical ones; Two applications of single molecular chemical identification are also presented following benchmarking. / QC20100630

This dissertation, studies two specific topics related to the research of surface science by employing the molecular dynamics (MD) approach, that of a water droplet deposited on a poly (methyl methacrylate) (PMMA) substrate and that of a single tricarboxylic acid derivative, 1, 3, 5-tri(carboxymethoxy) benzene (TCMB, C6H3(OCH2COOH)3 ) adsorbed on gold (100) and (110) surfaces. These can help engineers clarify the characteristics and phenomena of physical adsorption of the molecule, as well as contributing to the application of surface science. This work is divided into two parts. Effect of droplet size on the structural and dynamical behavior of a water droplet spreading on a PMMA amorphous surface: note that most experts prefer to consider a rigid model as the substrate in research of surface wetting because it is more efficient to run the MD simulation such that a long simulation can be accomplished in a short time. The results verify that the rigid model is not suitable to act as the PMMA substrate in simulation because it prevents the diffusion of PMMA molecules, which then affects the penetration behavior of water molecules in the droplet upon impact with the PMMA surface. Several sizes of water droplets are considered in order to understand the size influence of the droplet on the properties of water molecules and on the PMMA surface. The penetrated water molecules and the local roughness increase with a decrease in the size of the droplet, which also leads to a smaller contact angle of the water droplet on the PMMA substrate. When the droplet is composed of more than 1000 water molecules, the contact angle shows agreement with experimental results. As regarding the structure of the water molecule in the droplet on PMMA substrate, the average number of hydrogen-bonded penetrating water molecules is in inverse proportion to the size of the droplet By examining the velocity field, the regular motion of the water droplet is found during the equilibrium process and after the droplet reaches the equilibrium state. The diffusion of the water molecules shows a significant decrease for the penetrated water molecules and an increase as it gradually approaches the vapor/liquid interface. Finally, calculations at different regions are made for the vibration spectrum of the oxygen atom, life time, and the relaxation time of the hydrogen bond. The changes of the hydrogen-bond dynamics of the hydrogen bond are consistent with the change of the distribution of the hydrogen bond angle. Effect of surface structure on the structural and dynamical behavior of a tricarboxylic acid derivative molecule on Au surfaces: the dynamical behavior of the single tricarboxylic acid derivative, 1, 3, 5-tri(carboxymethoxy) benzene (TCMB, C6H3(OCH2COOH)3 ) on Au (100) and (110) surfaces by molecular dynamics simulation approach is studied to provide better understanding of surface diffusion. Four possible conformations of the adsorbed TCMB molecule on the Au surface are found, with differences arising from different numbers of CH2 groups adsorbed on the Au substrate. Both the number of CH2 groups in the TCMB molecule that interact with Au surface and the different geometric relationship between the TCMB molecule and the Au surface strongly affect the translational motion, rotational motion, interaction energy and the Lock-and-Key behaviors of the TCMB molecule. A poor complementarity between the TCMB molecule shape and atomic structure of the surface results in significant migration of the molecule and is therefore an unstable adsorption. These results will be useful for the design of a molecular monolayer.

La présence de surfaces solides peut modifier l'organisation et le comportement dynamique d'espèces chargées en solution. Dans ce cadre, nous étudions des systèmes chargés de complexité croissante au voisinage d'une surface d'argile par des méthodes numériques. Il convient de choisir une échelle de description appropriée selon les propriétés que l'on cherche à obtenir, tout en limitant le temps de calcul. Modéliser le transport d'ions dans un échantillon d'argile demande de décrire sa structure complexe mais également les interactions entre les particules mobiles considérées comme ponctuelles et les parois solides. Nous proposons un modèle mésoscopique composé d'un système à deux milieux dans lequel le déplacement des ions obtenu par dynamique brownienne est conditionné par la localisation de l'espèce diffusante, les coefficients de diffusion étant extraits de simulations atomiques de dynamique moléculaire. Pour des espèces chargées non ponctuelles comme un polyélectrolyte, le système peut être simplifié en construisant un modèle à gros grains qui permet d'avoir accès aux échelles de temps adaptées à la diffusion par dynamique de Langevin. Deux cas sont envisagés, avec une description explicite ou non des contre-ions, et les paramètres sont calibrés sur des simulations atomiques. En revanche, pour des molécules chargées complexes comme les nucléotides, une description tout atome est nécessaire pour tenir compte des interactions spécifiques qui émergent de la structure locale de la molécule. Les simulations de métadynamique permettent alors d'accéder aux grandeurs liées aux phénomènes « rares » comme l'adsorption des molécules sur la surface d'argile. / The presence of solid surfaces can modify the organization and the dynamics of charged species in solution with potential applications from the transport of polluants to formation of the firt biopolymers. We study charged systems with increasing complexity in the vicinity of a clay surface by numerical methods. The level of description should be adapted according to the relevant properties while limiting calculation times. Modeling the transport of ions in a clay sample requires to describe its complex structure but also the interactions between the mobile particles considered as punctual and the solid walls. We propose a mesoscopic model composed of a two-media system in which the displacement of the ions obtained by Brownian dynamics is conditioned by the localization of the diffusing species whith the diffusion coefficients being extracted from atomic simulations of molecular dynamics. For non-punctual species such as polyelectrolytes, the system can be simplified by constructing a coarse-grained model that allows to gain access to time scales adapted to diffusion phenomenon thanks to Langevin dynamics simulations. Two cases are considered, with an explicit or non-explicit description of the counter-ions, and the parameters are calibrated on atomic simulations. However, for complex charged molecules such as nucleotides, an atomic description is necessary to take into account the specific interactions emerging from the local structure of the molecule. Then, metadynamics simulations give quantities related to "rare" phenomena such as the adsorption of molecules on the surface of clay.

The aim of the diploma thesis was to prepare and characterize fluorescence sensor systems based on fluorophores and supramolecular components - cyclodextrins - attached to solid supports. In this work, functionalized 75 µm glass beads and two types of Nafion membranes were used as negatively charged solid surfaces. Derivatives of naphthalimide with a positively charged part allowing the attachment to surfaces were synthesized. The positively charged naphthalimide derivative was then attached on negatively charged surfaces via electrostatic interactions and the binding to the solid supports was examined using UV-VIS spectroscopy. Alternatively, the positively charged β-cyclodextrin derivative was also attached to the surface in an equimolar ratio with PNI-HEMPDA. The focus of the work were measurements of fluorescence sensor responses in the gas and liquid phase to linear alcohols - methanol to n-hexanol - for all sensor systems. For the studied sensor systems, the selected sensor parameters were determined - sensitivity, the limit of detection, linear dynamic range and a sensor response time constant. A practical application of the novel sensor system for the detection of ethanol in gasoline was examined. Fluorescence sensor response measurements of the prepared systems based on naphthalimide and...

As compared with the concentration in sample when the detection limit of analyte is low, a preconcentration method can be used. In this study, cloud point extraction (CPE) was used as the preconcentration method. The aqueous solutions of nonionic and zwitterionic surfactant materials become cloudy when its temperature reaches the cloud point temperature and analyte collapses with surface active material. The volume of surfactant rich phase is much smaller than the solution volume and therefore a way high preconcentration factor was obtained. For the cloud point extraction of selenite, a fluorimetric ligand, 2,3-diminonaphthalene (DAN) was used and the hydrophobic Se(IV)-DAN complex formed (4,5-benzopiazselenol) was extracted with Triton X-114. The effects of pH, complexation period, reaction temperature, DAN concentration and surfactant concentration on the extraction efficiency were investigated. The extraction efficiency at the optimized conditions was 98 percent. Spectrofluorimetric determination of selenium was performed at excitation and emission wavelegths of 379 nm and 582 nm, respectively. The detection limit, established as 3s /slope where s is the standard deviation of 9 measurements of 0.020 mg/L Se (IV)-DAN complex after 10 fold preconcentration was 3.7 &micro / g/L Se. By using solid surface fluorescence measurements detection limit could be reduced down to 1.2 &micro / g/L. The obtained detection limits (3.7 and 1.2 &micro / g/L) were sufficiently low for detecting selenite in diverse samples. The accuracy of the method was confirmed by the analysis of trace elements in waste water Standard reference material (EnviroMAT- Waste Water LOW EU-L-1). The interference effects of some anions and cations were also tested.