Polymer Supported Optical Biosensors

The use of various polymer supports adhering phospholipid multibilayers to an internal reflection element have been investigated. The polymer supports studied range from polystyrene (PS), and 100 nm wide PS nanospheres to triethylaminated poly(vinyl benzyl chloride) (PVBC). The PS nanospheres showed the most promise as an adhesion layer since they appear to be the most robust with repeated washings. They also appear to stabilize their adjacent phospholipid multibilayer by increasing the lipid melting temperature. The triethylaminated DVBC also provided an increase of lipid melting temperature, but not quite to the same degree as the PS nanospheres. The cooperativity of such systems is much greater than without an adhesion layer. It is believed that in the case of PS nanospheres, a slight negative charge interacts with the polar head groups of the phospholipid multibilayer, thus leading to an increase in cooperativity. The triethylaminated DVBC is believed to interdigitate between the phospholipid molecules in a way such that the positively charged nitrogen atom interacts directly with the negatively charged phosphate group located on the phospholipid molecules, thus giving rise to its relatively high cooperativity and lower melting temperature than the uncharged polymers and nanobeads. The PS nanosphere polymer support was shown to be an effective platform for biosensors. Myoglobin based biosensors, using PS nanosphere supports, showed that myoglobin retains its native ligand binding ability

Structural and Thermodynamic Properties of Transition Metal Ions in Room Temperature Ionic Liquids

openRoom temperature ionic liquids (RTILs) are salts made by an organic cation and an organic or inorganic anion, which are at the liquid state at 25 °C. RTILs have attracted much attention as new sustainable solvents owing to some unique properties they usually possess, such as a practically negligible vapor pressure, non-flammability, high thermal stability, wide electrochemical windows, good solvation ability and supposed low toxicity. These features make RTILs good candidates for the substitution of classical organic solvents in many technological applications. For these reasons, they are currently studied as new media for chemical separations, electrodepositions, electrolytes for batteries and supercapacitors, catalysis and pharmaceutical research. Several of these applications also involve the presence of metal ions as solvated species in RTILs. In this field, structural and thermodynamic data about single-ion solvation are fundamental quantities that need to be known to improve new technologies. However, this fundamental knowledge still lacks for many metal species in several ionic liquids. The aim of this thesis is to obtain a complete description of metal ions solvation in RTILs both from a structural and thermodynamic point of view. Molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) experiments have been performed to study solutions of metal ions of industrial, environmental and economic interest such as Zn2+, Co2+, Ag+ in widely used RTILs like those based on the [Tf2N]- (bis(trifluoromethylsulfonyl)imide) and [BF4]- (tetrafluoroborate) anions within the [Cnmim]+ (1-alkyl-3-methylimidazolium) cation. MD simulations have been carried out on Zn2+ in [Cnmim][Tf2N] (n = 2, 4) and [C4mim][BF4]. The obtained thermodynamic data are in good agreement with literature experimental values and indicate the goodness of the employed protocol. The calculated Gibbs free energies of transfer (ΔGtrans) from water to the [Cnmim][Tf2N] RTILs suggest that Zn2+ is more favorably solvated in aqueous solution than in this class of ionic liquids, while the opposite is found for [C4mim][BF4]. The obtained single-ion solvation enthalpies and entropies provided an interpretation of the different contributions to the calculated free energies. In addition, XAS experimental results allowed to understand the coordination of Zn2+ in water-saturated [C4mim][Tf2N], representing the real-operating condition in a liquid-liquid extraction. A similar picture has been obtained for Co2+ in [C4mim][Tf2N]. MD calculated ΔGtrans showed that the metal ion is still more favorably solvated in water than in the RTIL because of an unfavorable entropic contribution. XAS experiments and data-fitting allowed to obtain Co2+ coordination in dry [C4mim][Tf2N]. The metal resulted to be bound by six monodentate anions forming the [Co(Tf2N)6]4- octahedral species. In addition, water is found to preferentially coordinate the metal when present at high concentrations in the RTIL, as provided by UV-Vis data. As regards the study about Ag+ in RTILs, a totally different picture with respect to Zn2+ and Co2+ has been obtained. MD results showed that this ion is more favorably solvated both in [C4mim][Tf2N] and [C4mim][BF4] with respect to water, and this encourages the employment of these RTILs as extracting phase for this metal. Ag+ resulted coordinated by four or five RTILs anions, depending on the employed interaction potential. However, when considering the transfer of Ag+ from water to the RTILs, great care must be taken because of a possible change in the coordination number. Indeed, preliminary XAS data suggest a linear coordination for this metal ion in aqueous solution, differently from the tetrahedral model that is usually accepted and reproduced by the current classical potentials. Ab initio MD simulations with the Car-Parrinello method seemed to confirm this observation.Dottorato di ricerca in Scienze dell'ingegneria energetica e ambientaleopenBusato, Matte

Reactivity of a Low Valent Gallium Compound

The work described in this thesis is conducted to expand the reactivity of the β-diketiminate gallium(I) compound, NacNacGa (NacNac=[ArNC(Me)HC(Me)NAr]−, Ar=2,6-iPr2C6H3). The reactivity of NacNacGa towards various unsaturated compounds is studied. In particular, reaction between NacNacGa and phenyl isothiocyanate resulted in the oxidative addition of the C=S bond under ambient conditions, leading to the isolation cyclization product NacNacGa(κ2-S2CNPh) and sulfide isocyanide-bridged dimer (NacNacGa)2(μ-S)(μ-CNPh). Additionally, a [1+4] cycloaddition with a conjugated aldehyde (methacrolein) and a [1+2+3] cycloaddition with isocyanate and carbodiimide are presented. The oxidative cleavage of P=S bond of triphenylphosphine sulfide at increased temperatures gave the previously reported sulfide bridged gallium dimer. In situ oxidation of NacNacGa in the presence of substrates featuring donor sites led to the C-H activation reactions. As such, C-activation of pyridine N-oxide, pyridine, cyclohexanone, DMSO, and Et3P=O by a transient NacNacGa=O resulting in the corresponding gallium hydroxides is demonstrated. DFT calculations suggested initial formation of adducts between substrates and NacNacGa=O followed by a C-H bond abstraction from the substrate. Similarly, a transient gallium imide NacNacGa=NSiMe3, generated from the reaction of NacNacGa with trimethylsilyl azide, is shown to cleave C-H bonds of pyridine, cyclohexanone, ethyl acetate, DMSO, and Et3P=O with the formation of gallium amides. In an attempt to isolate a gallium alkylidene, NacNacGa was treated with trimethylsilyl(diazomethane). Instead, a monomeric gallium nitrilimine and a metalated diazomethane were obtained. The gallium nitrilimine undergoes 1,3-addition reaction with phenylsilane and catecholborane forming gallium hydrazonides. Its reaction with diborane resulted in the formal nitrene insertion into the B-B bond to produce a gallium diborylamide. DFT calculations revealed intermediate gallium alkylidene formation from the reaction of NacNacGa with diazomethane that upon reaction with the second equivalent of diazomethane leads to a gallium nitrilimine

Structural geometry and controlling factors for a rock slope failure area at Hompen/Váráš, Signaldalen, Troms, North Norway

Abstract This thesis uses a multidisciplinary approach to investigate factors affecting the origin and evolution of a rock slope failure (RSF) at Hompen (Varas) in Troms, Northern Norway. These factors include internal existing structures in the bedrock, external factors such as glacial unloading, and changes in fluid pressure affecting the RSF. The study combines bedrock geology, structural geology, geomorphology, and satellite data and dGPS measurements to analyze and classify the area. Detailed field work, analyses of field data, DEM models and aerial photos are employed to interpret the RSF. The area has been divided into two domains based on observed structures. Domain I show classical RSF morpho-structures: a major scarp striking NW-SE, lateral scarps striking NE-SW, counter scarps and transfer structures. Domain II is stable but show clear pre-rock slope failure structures, e.g. major tensile fractures, which potentially may enlarge the main RSF area. Among interpreted movement mechanism, creep occurs at present towards SSW (7-10 mm/year) as indicated by dGPS data. There is also clear evidence of toppling as a failure mechanism, shown by the major graben area filled with toppled rock material. The detachment surface is assumed to be of ramp-flat geometry with several sliding planes, affected by fractures working their way down to a basal detachment. The initiation of the RSF is likely linked to pre-existing fracture systems inherited from Mesozoic-Cenozoic tectonic regimes, release of stress regimes in the bedrock after de-glaciation. Other factors such as permafrost melting and water drainage may have caused changes in the pore fluid pressure in the area. Today the Hompen RSF can be classified as a complex RSF field and classifies under the deep seated gravitational slope deformations (DSGSD)

Description of Gallium Phosphide Epitaxy Growth by Computational Chemistry

The following research goals were achieved supporting the development of novel III/V semiconductor materials and their integration in optoelectronic devices. (i) For triethylgallane (TEGa), tert-butylphosphine (TBP) and related precursors, the decomposition networks were comprehensively elaborated and the most likely pathways were identified by thermodynamic and kinetic data. (ii) The β-hydrogen elimination mechanism for group 15 compounds was identified as dominant decomposition channel and was described in detail for the first time. (iii) A quantum-chemical descriptor for the prediction of decomposition rates of TBP, TBAs and related sources was proposed based on the findings on the β-hydrogen mechanism. It enables the design of new compounds based on their ability to stabilize the elimination’s transition state. (iv) The reactivity of TBP on the Si(001) surface was investigated and a kinetic reasoning for sub-monolayer adsorption patterns was delivered next to β-hydrogen elimination barriers of P(C4H9))H and Ga(C2H5)H adsorbates. (v) Essential growth processes of GaP epitaxy were determined by results from TEM and kinetic modeling. On the basis of kinetic as well as thermodynamic data , computed with DFT, the resulting GaP-Si interface morphology was explained. (vi) Intrinsic III/V-Si interface formations were described by absolute energies of a large set of atomic configurations. Electrostatic and mechanical properties of those were calculated providing a rationale for the stabilities found and valuable insight into the relation between electronic and atomic structure at the interfaces

On the Use of the Linear Interaction Energy Method to Predict Affinities of Charged Aromatic Ammines to Naturally Occurring Clay Minerals

This study presents the use of the linear interaction energy (LIE) method as a predictive tool to approximate the free energies of sorption of organic cations to naturally occurring clay mineral montmorillonite. One objective of this thesis is to explore the applicability and the accuracy of LIE, originated in the biochemistry field, as a predictive tool to estimate the free energies of sorption of organic cations to naturally occurring aluminosilicates. For this purpose, a set of charged aromatic amines sorbing to a prototypical homoionic clay montmorillonite (MMT) with calcium ions were modeled using molecular dynamics (MD) simulations. As the LIE method enables the inclusion of both electrostatic and van der Waals interactions of the sorbate (organic cation) with the negatively charged aluminosilicate (sorbent), it provided a major improvement over existing predictive models which underestimates the sorption free energies due to exclusion of electrostatic interactions. Moreover, Use of MD simulations and electronic structure calculations provided atomistic level insight into the orientation of different organic cations inside the clay and their charge distribution. This thesis also explores the transferability of the derived LIE parameters as a function of different interlayer ions: Ca+2 and Na+ in MMT

Exploring the World of Helix Association: Disease Mechanism, Basic Folding and Novel Design

Helix association provides an efficient model for studying the fundamental principles behind protein folding. It also serves as a suitable template for the design of proteins with novel functions. This thesis begins by investigating the role of transmembrane helix association in protein folding, where a novel “protein-folding-centric” viral fusion model has been proposed here to explain the membrane-fusion process of paramyxovirus. Furthermore, the forces driving membrane helix association, which determine both affinity and orientation, have been quantitatively studied using a model membrane peptide MS1. Finally, two examples are discussed that illustrate the application of helix association in novel protein design. A pH-switchable drug delivery system for the endosomal escape of biomacromolecular therapeutics has been designed using the helix-association model. The sequence is designed to form a stable water-soluble helix bundle at pH 7.4 and to insert in membrane at lower pH to promote endosomal escape. The most successful sequence shows selective release for biomacromolecule (ATP and miRNA) at lower pH (pH 5.4). The assembly of the designed peptide has been studied in aqueous buffer, detergent micelle and model lipid bilayer using the most successful sequence. Also, the paradigm of helix association has been applied to the design of a membrane metalloprotein, which can serve as a template for further design of membrane metalloenzymes. In summary, the work in this thesis has established an efficient model for helix association that can be used to solve problems in both basic and applied research

Biological Systems Workbook: Data modelling and simulations at molecular level

Nowadays, there are huge quantities of data surrounding the different fields of biology derived from experiments and theoretical simulations, where results are often stored in biological databases that are growing at a vertiginous rate every year. Therefore, there is an increasing research interest in the application of mathematical and physical models able to produce reliable predictions and explanations to understand and rationalize that information. All these investigations are helping to overcome biological questions pushing forward in the solution of problems faced by our society. In this Biological Systems Workbook, we aim to introduce the basic pieces allowing life to take place, from the 3D structural point of view. We will start learning how to look at the 3D structure of molecules from studying small organic molecules used as drugs. Meanwhile, we will learn some methods that help us to generate models of these structures. Then we will move to more complex natural organic molecules as lipid or carbohydrates, learning how to estimate and reproduce their dynamics. Later, we will revise the structure of more complex macromolecules as proteins or DNA. Along this process, we will refer to different computational tools and databases that will help us to search, analyze and model the different molecular systems studied in this course