Synthesis and characterisation of polyacrylonitrile and its derived carbon materials

Carbon is a versatile material which is composed of different allotropes, and also come in with different structures. Carbon nanofibres (CNFs) is one dimensional carbon nanomaterials, which have exhibited superior mechanical properties, great specific area, good electrical conductivity, good biocompatibility, and ease of modification. In addition to the lower cost associated to compare with carbon nanotubes (CNTs), CNFs have been attracted in numerous applications, such as reinforcement materials, filtrations, Li-ion battery, supercapacitor as well as tissue engineering, just to list a few. Therefore, it is a great deal to understand the relationship between the fabrication conditions and the characteristics of the resulted CNFs. In this project, electrospun PAN NFs were used as precursor material to fabricate carbon nanofibres. In order to produce CNFs with good morphology, the processing parameters of PAN nanofibres by electrospinning was optimized toward to the morphology at solution concentration of 12 wt%. The optimized processing parameters at given concentration were 16 kV, 14 cm and 1.5 mL/h, which led to the formation of PAN NFs with average fibre diameter of approximately 260 nm. Along with the effect of processing parameter study, the effect of concentration on the morphology was also carried out at optimized processing parameters. It was found that by increasing concentration of PAN solution from 2 to 16%, the resulted PAN transformed from beads only, to beaded fibres and finally to smooth fibres. With further increasing concentration the morphology of smooth fibres remain with increase in the fibre diameter. Electrospun PAN NFs with average fibre of 306 nm was selected to be converted into CNFs by using standard heating procedures, stabilisation in air at 280 °C and carbonization in N2. The effect of carbonization temperature ranging from 500 to 1000 °C was investigated, by using SEM, FTIR, Raman, and Impedance spectroscopy. With increasing carbonization temperature from 500 to 1000 °C, the diameter of NFs was decreased from 260 to 187, associated with loss of almost all functional groups of NFs. It was indicated by Raman results, that the graphitic crystallite size was increased from 2.62 to 5.24 nm, and the activation energy obtained for this growth was 7570 J/mol. Furthermore, impedance results (i.e. Cole-Cole plot) revealed that the electrical characteristic of CNFs transitioned from being insulating to electrically conducting in nature, suggested by the different electrical circuits extracted from Cole-Cole plots with carbonization temperature from 500 to 800 °C. The carbonization on PAN NFs with diameter of ~431nm was carried out by using novel route, microwave plasma enhance chemical vapour deposition (MPECVD) process. To compare with carbonized PAN NFs by using conventional route, MPECVD was not only able to facilitate carbonization process, but more interestingly can form carbon nanowalls (CNWs) grown on the surfaces of carbonized PAN NFs. Suggested by the unique morphology, the potential applications for the resulted carbon fibrous hybrid materials are supercapacitor electrode material, filtrations, and etc., The method developed in this project required one step less, compared with other literature. Therefore, using MPECVD on stabilised PAN NFs is proposed as economical, and straightforward approach towards mass production of carbon fibrous hybrid materials containing CNWs.

Comprehensive characterization of Napier grass as a feedstock for thermochemical conversion

Study on Napier grass leaf (NGL), stem (NGS) and leaf and stem (NGT) was carried out. Proximate, ultimate and structural analyses were evaluated. Functional groups and crystalline components in the biomass were examined. Pyrolysis study was conducted in a thermogravimetric analyzer under nitrogen atmosphere of 20 mL/min at constant heating rate of 10 K/min. The results reveal that Napier grass biomass has high volatile matter, higher heating value, high carbon content and lower ash, nitrogen and sulfur contents. Structural analysis shows that the biomass has considerable cellulose and lignin contents which are good candidates for good quality bio-oil production. From the pyrolysis study, degradation of extractives, hemicellulose, cellulose and lignin occurred at temperature around 478, 543, 600 and above 600 K, respectively. Kinetics of the process was evaluated using reaction order model. New equations that described the process were developed using the kinetic parameters and data compared with experimental data. The results of the models fit well to the experimental data. The proposed models may be a reliable means for describing thermal decomposition of lignocellulosic biomass under nitrogen atmosphere at constant heating rate.

Pd/C catalysts based on synthetic carbons with bi- and tri-modal pore-size distribution:applications in flow chemistry

Two new types of phenolic resin-derived synthetic carbons with bi-modal and tri-modal pore-size distributions were used as supports for Pd catalysts. The catalysts were tested in chemoselective hydrogenation and hydrodehalogenation reactions in a compact multichannel flow reactor. Bi-modal and tri-modal micro-mesoporous structures of the synthetic carbons were characterised by N2 adsorption. HR-TEM, PXRD and XPS analyses were performed for characterising the synthesised catalysts. N2 adsorption revealed that tri-modal synthetic carbon possesses a well-developed hierarchical mesoporous structure (with 6.5 nm and 42 nm pores), contributing to a larger mesopore volume than the bi-modal carbon (1.57 cm3 g-1versus 1.23 cm3 g-1). It was found that the tri-modal carbon promotes a better size distribution of Pd nanoparticles than the bi-modal carbon due to presence of hierarchical mesopore limitting the growth of Pd nanoparticles. For all the model reactions investigated, the Pd catalyst based on tri-modal synthetic carbon (Pd/triC) show high activity as well as high stability and reproducibility. The trend in reactivities of different functional groups over the Pd/triC catalyst follows a general order alkyne ≫ nitro > bromo ≫ aldehyde.

Climate change and plankton phenology in freshwater: current trends and future commitments

A solid body of empirical, experimental and theoretical evidence accumulated over recent years indicated that freshwater plankton experienced advance in phenology in response to climate change. Despite rapidly growing evidence for phenological changes, we still lack a comprehensive understanding of how climate change alters plankton phenology in freshwater. To overcome current limitations, we need to shed some light on trends and constraints in current research. The goal of this study is to identify current trends and gaps based on analysis of selected papers, by the help of which we can facilitate further advance in the field. We searched the literature for plankton phenology and confined our search to studies where climate change has been proposed to alter plankton phenology and rates of changes were quantified. We did not restrict our search for empirical ontributions; experimental and theoretical studies were considered as well. In the following we discuss the spatio-temporal setting of selected studies, contributions of different taxonomic groups, emerging methodological constraints, measures of phenological trends; and finally give a list of recommendations on how to improve our understanding in the field. The majority of studies were confined to deep lakes with a skewed geographical distribution toward Central Europe, where scientists have long been engaged in limnology. Despite these findings, recent studies suggest that plankton in running waters may experience change in phenology with similar magnitude. Average rate of advancement in phenology of freshwater plankton exceeded those of the marine plankton and the global average. Increasing study duration was not coupled either with increasing contribution of discontinuous data or with increasing rates of phenological changes. Future studies may benefit from i) delivering longterm data across scientific and political boundaries; ii) extending study sites to broader geographical areas with a more explicit consideration of running waters; iii) applying plankton functional groups; iv) increasing the application of satellite data to quantify phytoplankton bloom phenology; v) extending analyses of time series beyond the spring period; vi) using various metrics to quantify variation in phenology; vii) combining empirical, experimental and theoretical approaches; and last but not least viii) paying more attention to emergence dynamics, nonresponding species and trophic mismatch.

Functionalized carbon micro/nanostructures for biomolecular detection

Advancements in the micro-and nano-scale fabrication techniques have opened up new avenues for the development of portable, scalable and easier-to-use biosensors. Over the last few years, electrodes made of carbon have been widely used as sensing units in biosensors due to their attractive physiochemical properties. The aim of this research is to investigate different strategies to develop functionalized high surface carbon micro/nano-structures for electrochemical and biosensing devices. High aspect ratio three-dimensional carbon microarrays were fabricated via carbon microelectromechanical systems (C-MEMS) technique, which is based on pyrolyzing pre-patterned organic photoresist polymers. To further increase the surface area of the carbon microstructures, surface porosity was introduced by two strategies, i.e. (i) using F127 as porogen and (ii) oxygen reactive ion etch (RIE) treatment. Electrochemical characterization showed that porous carbon thin film electrodes prepared by using F127 as porogen had an effective surface area (Aeff 185%) compared to the conventional carbon electrode. To achieve enhanced electrochemical sensitivity for C-MEMS based functional devices, graphene was conformally coated onto high aspect ratio three-dimensional (3D) carbon micropillar arrays using electrostatic spray deposition (ESD) technique. The amperometric response of graphene/carbon micropillar electrode arrays exhibited higher electrochemical activity, improved charge transfer and a linear response towards H2O2 detection between 250&mgr;M to 5.5mM. Furthermore, carbon structures with dimensions from 50 nano-to micrometer level have been fabricated by pyrolyzing photo-nanoimprint lithography patterned organic resist polymer. Microstructure, elemental composition and resistivity characterization of the carbon nanostructures produced by this process were very similar to conventional photoresist derived carbon. Surface functionalization of the carbon nanostructures was performed using direct amination technique. Considering the need for requisite functional groups to covalently attach bioreceptors on the carbon surface for biomolecule detection, different oxidation techniques were compared to study the types of carbon-oxygen groups formed on the surface and their percentages with respect to different oxidation pretreatment times. Finally, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor oncoprotein detection on functionalized three-dimensional carbon microarrays platform was demonstrated. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5 pmol.

The investigation of photocatalysts and iron based materials in the oxidation and adsorption of toxic organic and chromium materials

The presences of heavy metals, organic contaminants and natural toxins in natural water bodies pose a serious threat to the environment and the health of living organisms. Therefore, there is a critical need to identify sustainable and environmentally friendly water treatment processes. In this dissertation, I focus on the fundamental studies of advanced oxidation processes and magnetic nano-materials as promising new technologies for water treatments. Advanced oxidation processes employ reactive oxygen species (ROS) which can lead to the mineralization of a number of pollutants and toxins. The rates of formation, steady-state concentrations, and kinetic parameters of hydroxyl radical and singlet oxygen produced by various TiO2 photocatalysts under UV or visible irradiations were measured using selective chemical probes. Hydroxyl radical is the dominant ROS, and its generation is dependent on experimental conditions. The optimal condition for generation of hydroxyl radical by of TiO2 coated glass microspheres is studied by response surface methodology, and the optimal conditions are applied for the degradation of dimethyl phthalate. Singlet oxygen (1O2) also plays an important role for advanced processes, so the degradation of microcystin-LR by rose bengal, an 1O2 sensitizer was studied. The measured bimolecular reaction rate constant between MC-LR and 1O2 is ∼ 106 M-1 s-1 based on competition kinetics with furfuryl alcohol. The typical adsorbent needs separation after the treatment, while magnetic iron oxides can be easily removed by a magnetic field. Maghemite and humic acid coated magnetite (HA-Fe3O4) were synthesized, characterized and applied for chromium(VI) removal. The adsorption of chromium(VI) by maghemite and HA-Fe3O4 follow a pseudo-second-order kinetic process. The adsorption of chromium(VI) by maghemite is accurately modeled using adsorption isotherms, and solution pH and presence of humic acid influence adsorption. Humic acid coated magnetite can adsorb and reduce chromium(VI) to non-toxic chromium (III), and the reaction is not highly dependent on solution pH. The functional groups associated with humic acid act as ligands lead to the Cr(III) complex via a coupled reduction-complexation mechanism. Extended X-ray absorption fine structure spectroscopy demonstrates the Cr(III) in the Cr-loaded HA-Fe 3O4 materials has six neighboring oxygen atoms in an octahedral geometry with average bond lengths of 1.98 Å.

Results of an isotope tracer experiment with arctic deep-sea nematodes

A stable isotope (13C)-labeling experiment was performed to quantify the importance of bacterial carbon as a food source for an Arctic deep-sea nematode community. Bacterial functional groups were isotopically enriched with 13C-glucose, 13C-acetate, 13C- bicarbonate, and 13C-amino acids injected into sediments collected from 1280 m depth at 79uN, 6uE, west of Svalbard. Incorporation of the 13C label into bacterial phospholipid-derived fatty acids (PLFAs) and nematodes in the top 5 cm of the sediment was monitored over a 7-d period. The 13C dynamics of nematodes was fitted with a simple isotope turnover model to derive the importance of the different bacterial functional groups as carbon sources for the nematodes. The different substrates clearly labeled different bacterial groups as evidenced by differential labeling of the PLFA patterns. The deep-sea nematode community incorporated a very limited amount of the label, and the isotope turnover model showed that the dynamics of the isotope transfer could not be attributed to bacterivory. The low enrichment of nematodes suggests a limited passive uptake of injected 13C-labeled substrates. The lack of accumulation suggests that the injected 13C-labeled dissolved organic carbon compounds are not important as carbon sources for deep-sea nematodes. Since earlier studies with isotopically enriched algae also found limited uptake by nematodes, the food sources of deep-sea nematodes remain unclear.

Spatial and temporal stability of soil microbial properties in the Jena Experiment (Germany) from 2003-2014

The study was carried out on the main plots of a large grassland biodiversity experiment (the Jena Experiment). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. We tracked soil microbial basal respiration (BR; µlO2/g dry soil/h) and biomass carbon (Cmic; µgC/g dry soil) over a time period of 12 years (2003-2014) and examined the role of plant diversity and plant functional group composition for the spatial and temporal stability (calculated as mean/SD) of soil microbial properties (basal respiration and biomass) in bulk-soil. Our results highlight the importance of plant functional group composition for the spatial and temporal stability of soil microbial properties, and hence for microbially-driven ecosystem processes, such as decomposition and element cycling, in temperate semi-natural grassland.

Efeito da seca na dinâmica dos grupos funcionais fitoplanctônicos em reservatórios eutróficos do semiárido

Reservoirs are the main sources of surface water in Brazil´s semiarid region. The majority of these water supplies, however, are compromised by eutrophication. A severe drought in 2012 contributed to significant losses in water volume, influencing the availability of resources (nutrients and light) for phytoplankton. The aim of this study is to understand the dynamics of the functional groups of phytoplankton and the factors that affect them during a severe drought in the semiarid reservoirs of the northeast. We therefore studied the Dourado, Gargalheiras and Passagem das Traíras reservoirs in Rio Grande do Norte from January 2012 to January 2013. The effect of drought favoured homogeneity within the reservoir, in relation to biotic and abiotic variables, notably the absence of water supply given the lack of flow from its tributaries (intermittent river). The phytoplankton functional groups of bloomforming cyanobacteria (SN, S1 and M) dominated throughout the year 2012, in both the shallow and deep areas of the three reservoirs studied. The groups were related to high concentrations of volatile solids, total phosphorus and ammonia, and high turbidity. Cylindrospermopsis raciborskii (SN group) was the species with the greatest biomass in the three reservoirs. M group (Sphaerocavum brasiliense) performed better in shallow waters with more available phosphorus. Our data showed that high concentrations of nutrients and low availability of light, besides the stability of the water column due to lack of flow and the system´s high residence time, favoured the dominance of bloom-forming cyanobacteria groups, especially those tolerant to shadow

Estudo da capacidade de remoção de óleo solúvel, em águas produzidas, por bentonitas hidrofobizadas

In this study we evaluated the capacity removal of PAHs in an oily solution between the bentonite hydrofobized with linseed oil and paraffin with natural bentonite. Analyses of natural bentonite and hydrofobized were made by the characterization techniques: (1) Thermogravimetric Analysis (TGA), which aimed to evaluate the thermal events due to mass loss, both associated with the exit of moisture and decomposition of clay as due to hidrofobizante loss agent. (2) Analysis of X-ray diffraction (XRD) in order to determine the mineralogical phases that make up the structure of clay and (3) Spectrophotometry in the infrared region used to characterize the functional groups of both the matrix mineral (bentonite) and the hidrofobizantes agents (linseed oil and paraffin). We used a factorial design 24 with the following factors; hidrofobizante, percent hidrofobizante, adsorption time and volume of the oily solution. Analyzing the factorial design 24 was seen that none of the factors apparently was more important than the others and, as all responses showed significant values in relation to the ability of oil removal was not possible to evaluate a difference in the degree of efficiency the two hidrofobizantes. For the new study compared the efficiency of the modified clay, with each hidrofobizante separately in relation to their natural form. As such, there are four new factorial designs 23 using natural bentonite as a differentiating factor. The factors used were bentonite (with and without hydrophobization), exposure time of the adsorbent material to the oily solution and volume of an oily solution, trying to interpret how these factors could influence the process of purifying water contaminated with PAHs. Was employed as a technique for obtaining responses to fluorescence spectroscopy, as already known from literature that PAHs, for presenting combined chains due to condensation of the aromatic rings fluoresce quite similar when excited in the ultraviolet region and as an auxiliary technique to gas chromatography / mass spectrometry (GC-MS) used for the analysis of PAHs in order to complement the study of fluorescence spectroscopy, since the spectroscopic method only allows you an idea of total number of fluorescent species contained in the oil soluble. The result shows an excellent adsorption of PAHs and other fluorescent species assigned to the main effect of the first factor, hydrophobization for the first planning 23 BNTL 5%, for 93% the sixth stop in the second test (+-+),factorial design 23 BNTL 10%, the fourth test (++-) with 94.5% the third factorial design 23 BNTP 5%, the second test (+--) with 91% and the fourth and final planning 23 BNTP 10%, the last test ( + + +) with 88%. Compared with adsorption of bentonite in its natural form. This work also shows the maximum adsorption of each hidrofobizante

O impacto da remoção de peixes sobre a dinâmica e estrutura dos grupos funcionais fitoplanctônicos em um lago raso tropical durante uma seca severa

The artifi cial eutrophication is one of the biggest t h reat for the quality of aquatic ecosystems in the whole world. The expectations for the future climatic scenarios in arid and semi - arid regions are intense and frequent droughts enhancing the risk of eutrophicati on and cyanobacterial blooms. Restoration techniques of eutrophic lakes were proposed to reduce nutrient loading and improve the water quality. A successful technique used in temperate regions is the biomanipulation by benthivorous fish removal . Our hypoth esis is that the benthivorous fish removal reduces phytoplankton total biomass and change the composition of phytoplankton functional groups, improving water quality. The aim of the study was evaluate the impact of biomanipulation on phytoplankton function al groups and in the water quality. We applied the technique of biomanipulation in the artificial lake ESEC, in a semi - arid region of Brazil and analyzed the physical and chemical variables and the dynamic of phytoplankton functional groups monthly during November 2012 to August 2013. With the removal of benthivorous fish we observed a significant increase of the euphotic depth, phytoplankton richness and the recruitment of green algae (groups F and J ), indicators of good water quality. However, we did not observe significant differences on total phosphorous concentration and on phytoplankton biomass and diversity. The drought effect in the region during the study was evident , promoting a drastic reduction on water level which influenced the availability of resource and affected phytoplankton community before the biomanipulation. To evaluate the effect of severe drought on the dynamic of phytoplankton functional groups and test if the drought periods are favorable to dominance of cyanobacterial groups, we stu died two artificial neighbors lakes (ESEC and Pocinhos) in a semi - arid tropical region during May 2012 to February 2013. We observed a temporal differentiation of biotic and abiotic variables caused by drought. Both lakes presented reduction of 2 meters of water level and increase on conductivity, turbidity, nutrients concentration and a reduction on water transparency, during the severe drought. The deeper lake (Pocinhos) increased phytoplankton total biomass and presented cyanobacterial functional group d ominance (group S N ) and the shallower lake (ESEC) reduced phytoplankton total biomass and presented dominance of mixotrophic and flagellate functional groups (groups W 1 e W 2 ). Summarizing, the knowledge of the effects of benthivorous fish removal in semi - a rid tropical lakes still unknown and this study had limitations caused by the impact of drought. Thus, it is necessary a long term monitoring to investigate the real effects of biomanipulation on the functioning of the studied ecosystems. Otherwise, period s of drought could have opposite effects (increase or reduction) on total biomass and composition of phytoplankton functional groups. Drought not always leads to dominance of cyanobacterial groups.

Influência da seca extrema na dinâmica fitoplanctônica de um reservatório da região tropical semiárida: uma abordagem morfofuncional

Droughts are climatic phenomena whose frequency has increased in the last decades and also compromised drinkable water supplies in semiarid regions. The lack of rain combined with high evaporation rates promotes a significant reduction of the volume of reservoirs in these regions. Shallower conditions favors nutrients concentration and phytoplankton overgrowth, including potentially toxic cyanobacteria blooming. Therefore, there is a tendency to the intensification of eutrophication in those reservoirs during drought periods. Phytoplankton can respond quickly to environmental conditions related to light and nutrient availability by changes in algal biomass and composition, therefore it is considered a good predictor of environmental variables. Two functional approaches - Reynolds’s Functional Groups (FG) and Kruk’s Morphologically Based Functional Groups (MBFG) - were used to assess which environmental variables were responsible for phytoplankton dynamics, in addition to compare which functional approach explains environmental changes better. This study highlights that the reduction of 90% in the volume of a tropical reservoir of Brazilian semi-arid region, as well as light limitation and nutrient increase, can promote phytoplankton overgrowth. Multivariate analyses using both functional approaches indicated a clear separation between high volumes and low volumes conditions, showing that light and nutrient availability were the main variables that better explained the combination of functional groups. The composition of phytoplankton assemblage changed from species of meso-eutrophic habitats (FG: F and J; MBFG: VI), to organisms of eutrophic and turbid environments (FG: SN and M; MBFG: VIII and VII) during shallower conditions. Both ecological approaches described properly the phytoplankton dynamics according to light and trophic state alterations related to the water volume reduction, therefore they can be considered as equivalent approaches for using in similar environments.

Water temperature, salinity, DOC content and THNS concentration in samples taken during POLARSTERN cruise to the Fram Strait and Greenland Sea

Dissolved organic matter (DOM) was isolated with XAD-2 and 4 resins from different water masses of the Greenland Sea and Fram Strait. The contribution of XAD-extractable dissolved organic carbon (DOC), operationally defined as 'recalcitrant' or humic substances, to total DOC was in the range of 45 ± 9% in surface waters and 60 ± 6% in deep waters. The carbohydrate concentration and composition were determined using the l-tryptophan/sulfuric acid method (for the bulk carbohydrate concentration, TCHO) and high performance anion-exchange chromatography after sulfuric acid hydrolysis (for the distribution of total hydrolysable neutral sugars, THNS). Carbohydrates contributed up to 6.8% to both total and recalcitrant DOC. TCHO contribution to total DOC decreased with depth from on average 4.1 ± 1.2% in surface waters to 2.2 ± 1.0% in deep waters, whereas the THNS contribution was similar in both layers, accounting for 2.5 ± 1.6% (surface) and 2.4 ± 0.2% (at depth). TCHO contribution to XAD-extractable DOC also decreased with depth from 4.5 ± 1.7% to 2.1 ± 1.0%, whereas THNS contribution was almost constant, with yields of 0.5 ± 0.3% for surface samples and 0.6 ± 0.1% at depth. The molecular size distribution of the recalcitrant DOM showed for all fractions a clear trend towards small molecules in the deep sea. More than half of the XAD-extractable carbohydrates of surface samples and more than 70% of deep sea samples were found in the nonpolar fraction from XAD, which was eluted with methanol. Glucose was the dominant carbohydrate in the surface water samples, whereas in the deep sea the composition was more uniform. In the XAD extracts, the compositions were less variable than in the original samples. The neutral sugar composition, in particular glucose and the deoxysugars, is indicative of the diagenetic state of the extracted DOM. The molar ratio (fucose + rhamnose)/(arabinose + xylose) was lowest for deep sea extractable DOM, indicating a high contribution of material modified by microorganisms. The THNS composition and distribution reveal that "recalcitrant" carbohydrates are heteropolysaccharides, carbohydrate units incorporated into a framework of a highly nonpolar structure with a lack of functional groups.

Effect of reaction mechanism on precursor exposure time in atomic layer deposition of silicon oxide and silicon nitride

Atomic layer deposition (ALD) of highly conformal, silicon-based dielectric thin films has become necessary because of the continuing decrease in feature size in microelectronic devices. The ALD of oxides and nitrides is usually thought to be mechanistically similar, but plasma-enhanced ALD of silicon nitride is found to be problematic, while that of silicon oxide is straightforward. To find why, the ALD of silicon nitride and silicon oxide dielectric films was studied by applying ab initio methods to theoretical models for proposed surface reaction mechanisms. The thermodynamic energies for the elimination of functional groups from different silicon precursors reacting with simple model molecules were calculated using density functional theory (DFT), explaining the lower reactivity of precursors toward the deposition of silicon nitride relative to silicon oxide seen in experiments, but not explaining the trends between precursors. Using more realistic cluster models of amine and hydroxyl covered surfaces, the structures and energies were calculated of reaction pathways for chemisorption of different silicon precursors via functional group elimination, with more success. DFT calculations identified the initial physisorption step as crucial toward deposition and this step was thus used to predict the ALD reactivity of a range of amino-silane precursors, yielding good agreement with experiment. The retention of hydrogen within silicon nitride films but not in silicon oxide observed in FTIR spectra was accounted for by the theoretical calculations and helped verify the application of the model.

Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.