Understanding the effects of uncertainty on modeling has seen an increased focus as engineering disciplines rely more heavily on computational modeling of complex physical processes to predict system performance and make informed engineering decisions. These computational methods often use simplified models and assumptions with models calibrated using uncertain, averaged experimental data. This commonplace method ignores the effects of uncertainty on the variation of modeling output. Qualitatively, uncertainty is the possibility of error existing from experiment to experiment, from model to model, or from experiment to model. Quantitatively, uncertainty quantification (UQ) methodologies seek to determine the how variable an engineering system is when subjected to variation in the factors that control it. Often performed in conjunction, sensitivity analysis (SA) methods seek to describe what model factor contributes the most to variation in model output. UQ and SA methodologies were employed in the analysis of the Modified Embedded Atom Method (MEAM) model for a pure aluminum, a microstructure sensitive fatigue crack growth model for polycarbonate, and the MultiStage Fatigue (MSF) model for AZ31 magnesium alloy. For the MEAM model, local uncertainty and sensitivity measures were investigated for the purpose of improving model calibrations. In polycarbonate fatigue crack growth, a Monte Carlo method is implemented in code and employed to investigate how variations in model input factors effect fatigue crack growth predictions. Lastly, in the analysis of fatigue life predictions with the MSF model for AZ31, the expected fatigue performance range due to variation in experimental parameters is investigated using both Monte Carlo Simple Random Sampling (MCSRS) methods and the estimation of first order effects indices using the Fourier Amplitude Sensitivity Test (FAST) method.

The growing interest of renewable fuel and energy sources has steadily increased over time due to climate changes. Research is being made around the world to find solutions for the different problems; one possible solution is to produce hydrogen gas to help phase out the usage of fossil fuels. So far, the technology for the hydrogen gas production is expensive for various reasons, one of the challenges is to minimize the energy usage for the production. Hydrogen could be used in fuel cells which can be used to fuel an electric car. In a fuel cell, hydrogen and oxygen gas are mixed to produce electrical energy as the main product, but it also forms thermal energy and water. Hydrogen gas can be produced from the reversed reaction; by electrolysis of water. This reaction requires energy and one way to minimize the energy usage for this is by using acatalyst. The goal with this master thesis was to see how the reaction rate of the oxygen evolution reaction can be affected by different single atom catalyst systems. The main structure for this catalyst in this thesis is aporphyrin molecule where different transition metals were tried as the active site. Different modifications on the structure were also made by exchanging some of the structures atoms and by adding different ligands.The purpose of this is to see how these modifications change the activity of the catalyst. The catalysts were optimized and calculated in a computational chemistry program called Gaussian 16. The calculations was made by using the DFT functional PBE0 and the basis sets Def2svp and Def2tzvpp. The results show that different modifications do affect the activity of the catalyst. The biggest variations in activity are from placing ligands under the active site while exchanging hydrogens to other substituents on the outer radial position can fine tune the results. The best active sites for this system came by using iridium, rhodium and cobalt which are all elements in group 9 of the periodic table. The lowest overpotential of 0.513 V was given by an iridium based system with four hydrogens exchanged by fluorides. / Runt om i världen finns ett ökat intresse för förnyelsebara energi och bränslekällor för att tackla klimat förändringarna. Stor del av forskningen som görs idag har i syfte att hitta nya lösningar för att minska klimatpåverkan i olika områden. Ett av forskningsområderna är hitta vägar till en miljövänligare vätgasproduktion där vätgasen skulle kunna användas i bränsleceller. Dessa celler kan sättas i elbilar och på så sätt fasa ut användingen av fossila bränslen. En av utmaningarna för vätgasproduktionen är att den idag är kostsam och kräver mycket energi. Forskare försöker hitta olika katalysatorer som kan minska energiåtgången som krävs vid elektrolys av vatten där syrgas och vätgas produceras. Målet med det här examensarbetet är att se hur en single atom catalyst kan påverka reaktionskinitiken för den syrgasbildande reaktionen vid elektrolys av vatten. Huvudstrukturen för katalysatorn som beräkningarna är gjorda på är en porphyrinmolekyl där olika övergångsmetaller kommer testas som det aktiva sätet i katalysatorn. Olika ligander kommer även tillsättas systemet samt utbyte av några väteatomer till olika substituenter i porfyrinstrukturen. Katalysatorn optimerades i det kvantkemiska beräkningsprogrammet Gaussian 16 med funktionalen PBE0 med basset Def2svp och Def2tzvpp. Resultaten visade att olika modifikationer på systemet hade en påverkan på katalysatorns aktivitet. Den största påverkan hade de olika liganderna som placerades under det aktiva sätet jämfört med de olika substituenterna. De bästa metallerna för katalysatorn var iridium, rhodium och kobolt vilket alla ligger i grupp nio i det periodiska systemet. Den lägsta överpotentialen på 0.513 V gavs av iridium systemet med fyra utbyta väten till fluor.

Research was performed to improve the procedures for testing performance parameters of vapor cells for a nuclear-magnetic-resonance gyroscope. In addition to summarizing the theoretical infrastructure of the technology, this research resulted in the development and successful implementation of new techniques to characterize gyro cell performance. One of the most important parameters to measure for gyro performance is the longitudinal spin lifetime of polarized xenon atoms in the vapor cell. The newly implemented technique for measuring these lifetimes matches results from the industry standard method to within 3.5% error while reducing the average testing time by 76% and increasing data resolution by 54%. The vapor cell test methods were appended with new software to expedite the analysis of test data and to investigate more subtle details of the results; one of the two isotopes of xenon in the cells tends to exhibit troublesome second-order effects during these tests due to electric-quadrupole coupling, but now the added analysis capabilities can accurately extract relevant results from such data with no extra effort. Some extraneous lifetime measurement techniques were explored with less substantial results, but they provided useful insight into the complex workings of the gyro cell test system. New criteria were established to define the signal to noise ratio on a consistent basis from cell to cell across various parameters such as cell volume, temperature, and vapor pressure. A technique for measuring gas pressures inside the sealed cells helped link cell performance to cell development processes. This led to informed decisions on filling and sealing methods that consistently yielded cells with better performance in the last few months of this work. When this research began, cells with xenon lifetimes over ten seconds were rare in our lab; by the end, anything under 30 seconds was a disappointment. Not only did the test procedures improve, but so did the parameters being tested, and quite significantly at that. At the same time, many new avenues for continued progress have been opened; the work presented here, while instrumental, is only the beginning.

The inductively coupled plasma - mass spectrometer (ICP-MS) is the analytical instrument of choice for trace element detection and quantification. Despite the popularity of ICP-MS, significant degradation in sensitivity and precision occurs as the result of matrix and instrument-induced effects. The sources of these effects are not well understood, characterized, or correlated to particular plasma operating condition settings or matrix compositions and involve both neutral and charged species. The purpose of this study is to characterize the behavior of metastable Ar (I) atom and Ca (II) ion through the measurement of Doppler velocities and fluorescence line width "temperatures." For the characterization of Ar (I), axial and radial velocity and temperature profiles were collected as a function of nebulizer rate, incident ICP power and matrix composition to establish a behavioral baseline for neutral species in the first vacuum stage expansion of an ICP-MS. Velocities were determined from the Doppler shift of laser-induced Ar (I) fluorescence compared to stationary population wavelength reference. Unambiguous evidence of a thick Mach disk forming 10-12 mm downstream and persisting through 17-18 mm downstream, under standard ICP conditions, conflicts with the widely held view of a thin Mach disk located between 15-17 mm downstream. Characterization of Ca (II) ion focused on the effect of changing ICP conditions and matrix composition on calcium ion Doppler velocity and temperature profiles in the first vacuum stage expansion. Evidence of the plasma potential acceleration of ions through the interface was found as a higher Ca (II) terminal velocity than that of Ar (I) under standard ICP conditions. Additionally, the effect of a lithium matrix on Ca (II) velocity and temperature profiles was generally opposite than on Ar (I) velocity and temperature profiles.

The structure and dynamics of membranes are crucial to ensure the proper functioning of cells. There are some compounds used in therapeutics that show nonspecific interactions with membranes in addition to their specific molecular target. Among them, two compounds recently used in therapeutics against COVID-19, remdesivir and favipiravir, were subjected to molecular dynamics simulation assays. In these, we demonstrated that the compounds can spontaneously bind to model lipid membranes in the presence or absence of cholesterol. These findings correlate with the corresponding experimental results recently reported by our group. In conclusion, insertion of the compounds into the membrane is observed, with a mean position close to the phospholipid head groups.

<p>This work focused on grafting water-soluble polymers with well-controlled properties such as tuneable polymer chain length and high graft density to improve the biocompatibility of polymer surfaces via surface-initiated atom transfer radical polymerization (s-ATRP); and on gaining improved fundamental understanding of the mechanisms and factors (e.g., graft chain length and surface density of monomer units) in protein resistance of the water-soluble grafts.</p><p>Protein-resistant polyurethane (PU) surfaces were prepared by grafting watersoluble polymers including poly(oligo(ethylene glycol) methacrylate) (poly(OEGMA)) and poly(l-methacryloyloxyethyl phosphorylcholine) (poly(MPC)) via s-ATRP. A typical three-step procedure was used in the ATRP grafting. First, the substrate surface was treated in an oxygen plasma and reactive sites (-OH and -OOH) were formed upon exposure to air. Second, the substrate surface was immersed in 2-bromoisobutyryl bromide (BffiB)-toluene solution to form a layer of ATRP initiator. Finally, target polymer was grafted from the initiator-immobilized surface by s-ATRP with Cu(I)Br/2bpy complex as catalyst. The graft chain length was adjusted by varying the molar ratio of monomer to sacrificial initiator in solution. The modified PU surfaces were characterized by water contact angle, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM).</p><p>Protein adsorption experiments were carried out to evaluate the protein resistance of the surfaces. Adsorption from single and binary protein solutions as well as from plasma decreased significantly after poly(OEGMA) grafting, and decreased with increasing poly(OEGMA) main chain length. Fibrinogen (Fg) adsorption on the most resistant surfaces (chain length 200 units) was in the range of 3-33 ng/cm^2, representing a reduction of more than 96% compared to the control surfaces.</p><p>OEGMA monomers with three different molecular weights (MW 300, 475, 1100 g/mol) were used to achieve different side chain lengths of poly(OEGMA). Fibrinogen (Fg) and lysozyme (Lys) were used as model proteins in adsorption experiments. The effects of side chain length as well as main chain length were then investigated. It was found that adsorption to the poly(OEGMA)-grafted PU (PU/PO) surfaces was protein size dependent. Resistance was greater for the larger protein. For grafts of a given side chain length, the adsorption of both proteins decreased with increasing polymer main chain length. For a given main chain length, the adsorption of Fg, the larger protein, was independent of side chain length. Surprisingly, however, Lys (the smaller protein) adsorption increased with increasing side chain length. A reasonable explanation is that graft main chain density decreased as monomer size and footprint on the surface increased. Protein size-based discrimination suggests that the chain density was lower than required to form layers in the "brush" regime in which protein size is expected to have little effect on protein adsorption.</p><p>In order to achieve high surface densities of ethylene oxide (EO) units, we used a sequential double grafting approach whereby the surface was grafted first with poly(2-hydroxyethyl methacrylate) (HEMA) by s-ATRP. OEGMA grafts were then grown from the hydroxyl groups on HEMA chains by a second ATRP. The effect of EO density on protein-resistant properties was then investigated. Protein adsorption on the sequentiallygrafted poly(HEMA)-poly(OEGMA) surfaces (PU/PH/PO) was not only significantly lower than on the unmodified PU as expected, but also much lower than on the PU/PO surfaces with the same poly(OEGMA) chain length. Moreover, protein adsorption decreased with increasing EO density for these grafts. On the PU/PH/PO surface with a poly(OEGMA) chain length of 100, the adsorption of Ls and Fg were reduced by ~98% and >99%, respectively, compared to the unmodified PU. Binary protein adsorption experiments showed that suppression of protein adsorption on the PU/PH/PO surfaces was essentially independent of protein size. The double-grafted OEG layers resisted both proteins equally.</p><p>The general applicability of this approach which combines oxygen plasma treatment and ATRP grafting was also studied. Various kinds of polymers such as PU, silicone hydrogel, and polydimethylsiloxane (PDMS) were chosen as substrates. Poly(MPC) grafts with different chain lengths were achieved by the three-step ATRPgrafting procedure. It was found that protein adsorption levels on the poly(MPC) grafts were significantly lower than on the respective unmodified surfaces. Protein adsorption decreased with increasing poly(MPC) chain length. Among the surfaces investigated, PU/MPC showed the highest protein resistance for a given chain length.</p> / Thesis / Doctor of Philosophy (PhD)

The development of the semi-empirical atomistic potential called the embedded atom method (EAM) has allowed for the efficient modeling of solid-state environments, at a lower computational cost than afforded by density functional theory (DFT). This offers the capability of EAM to model the energetics of solid-state phases of varying coordination, including defects, such as vacancies and self-interstitials. This dissertation highlights the development and application of two EAMs: a Ti potential constructed with the multi-state modified embedded atom method (MS-MEAM), and a Ni potential constructed with the fragment Hamiltonian (FH) method. Both potentials exhibit flexibility in the description of different solid-states phases and applications. This dissertation also outlines two applications of DFT. First, a study of structure and stability for solid-state forms of NixCy (in which x and y are integers) is investigated using plane-wave DFT. A ground state phase for Ni2C is elucidated and compared to known and hypothesized forms of NixCy. Also, a set of correlation consistent basis sets, previously constructed using the B3LYP and BLYP density functionals, are studied. They are compared to the well-known to the correlation consistent basis sets that were constructed with higher-level ab initio methodologies through computations of enthalpies of formation and combustion enthalpies. The computational accuracy with regard to experiment is reported.

No description available.

<p>  </p> <p>Alkyl radicals are powerful intermediates for the generation of carbon-carbon bonds, which play an indispensable role in the synthesis of natural products, pharmaceuticals, and pesticides. Traditionally, there are two main methods for the generation of alkyl radicals. The first is C-H bond functionalization via hydrogen-atom-transfer (HAT). HAT processes have been used as an effective approach for selectively activating C-H bonds via radical pathways. The other strategy to explore the generation of alkyl radicals is C-X bond functionalization via halogen-atom-transfer (XAT). Alkyl halides are one of the largest classes of building blocks in synthesis and they can be obtained from the corresponding alcohols. The most straightforward and effective way to form such alkyl radicals is the direct homolytic cleavage of C-X bonds. In past decades, photoredox catalysis has emerged as a powerful and greener tool for the synthesis of radicals under mild reaction conditions, which has brought tremendous attention. Although remarkable success has been made in this field, some methods still require costly transition metal catalysts or toxic reagents. Herein, we display a series of visible light-induced approaches under transition-metal free conditions or using earth-abundant metals. These novel photo-induced transformations and corresponding mechanistic work will be discussed in the following order:</p> <p>We will first present our work on metal-free visible-light-promoted C(sp3)-H functionalization of aliphatic cyclic ethers using trace O2.  This reaction uses a trace amount of aerobic oxygen as the sole green oxidant under blue light at room temperature to achieve the synthesis of sulfone and phosphate derivatives in good to excellent yields using cyclic ethers and vinyl sulfones. Then, we report on a photo-induced C(sp3)-H chalcogenation of amide derivatives and ethers via a ligand-to-metal charge-transfer. This reaction converts secondary and tertiary amides, sulfonamides, and carbamates into the corresponding amido-<em>N,S</em>-acetal derivatives in good yields, using an earth abundant metal catalyst under mild conditions.</p> <p>Finally, we present a photoredox polyfluoroarylation of alkyl halides via halogen atom transfer. This method converts primary, secondary, and tertiary unactivated abundant alkyl halides into the corresponding polyfluoroaryl compounds in good yields and has good functional group compatibility.</p>

Dipolar (3+2) cycloadditions are extensively utilized by synthetic chemists for accessing important 5-membered heterocyclic structures. After the pioneering work by Rolf Huisgen in the early 1960s, the field greatly matured and found applications in a variety of fields of chemistry. Worthy of mention, the discovery by Meldal, Sharpless, and Folkin of copper-catalyzed azide alkyne cycloadditions (CuAAC), also referred to as a “Click” reaction, was awarded the Nobel Prize in 2022. The finding of this ideal CuAAC reaction originated from the reliability of dipolar (3+2) cycloaddition reactions, whose transformation was rendered extremely kinetically favorable and stereospecific with the use of copper-catalysis. It is therefore of high importance to continue finding novel (3+2) cycloadditions, despite the apparent maturity of the field. The research described in this thesis presents the efforts towards the synthesis of fused pyrroles and thiophenes by means of (3+2) cycloaddition cascades using ynamides and alkynyl sulfides as isoelectronic species to 1,3-dipoles. In Chapter 2, the exploration of different strategies to bridge the in-situ synthesis of alkyne tethered ynamide and our group’s previously described thermally induced (3+2) cycloaddition cascade was investigated. Many challenges were faced when attempting to design one-pot procedures including the unprecedented degradation of yne-ynamides under metal-containing reaction conditions. This impeded the use of copper-catalyzed cross-coupling reactions as a general retrosynthetic disconnection for the in-situ formation of the ynamide functionality. Even an attempt to functionalize an ynamide precursor containing a tethered terminal alkyne by a Sonogashira cross-coupling was unsuccessful. With the aim to find an efficient way of synthesizing these diynes while limiting the use of stoichiometric reagents, the use of a previously unreported ynamide substituted propynal building block was explored. These aldehyde synthons were easily synthesized from accessible ynamide substituted propargyl alcohols using Dess-Martin Periodinane as the oxidant. Upon mixing these propynal derivatives with primary propargyl amines, a rapid condensation reaction takes place as long as the removal of water is done. These in-situ formed yne-ynamides then undergo (3+2) cycloaddition cascades towards fully substituted fused pyrroles at temperatures ranging from 60 to 100 oC. While the method was found to be limited to [3.3.0] fused pyrroles and moderate yields were observed (22-55% yields, 8 examples), this one-pot method permitted an extremely rapid growth of molecular complexity. Collectively, the work described in this chapter further accentuates the utility of ynamides as building blocks for densely functionalized pyrrole heterocycles. In Chapter 3, the reactivity of analogous alkyne tethered alkynyl sulfides (thioalkynes) was investigated. Alkynyl sulfides are an important class of heteroatom-substituted alkynes, whose alkynyl carbons are weakly polarized in contrast to ynamines (N-alkynyl amines) derivatives. While thioalkynes display superior stability in contrast to ynamides, both X-alkynyl species share similar reactivities. Upon heating of S-ester substituted yne-alkynyl sulfides, fully substituted thiophenes were obtained indicating that the reactivity observed with ynamides (as 4 cycloaddition partner) was transferable to thioalkynes. When S-alkyl substituted yne-thioalkynes are used, 5-unsubstituted thiophenes are formed instead. The use of S-tert-butyl substituted alkynyl sulfides enabled a broad scope of 5-unsubstituted fused thiophenes to be obtained via an intramolecular (3+2) cycloaddition and dealkylation cascade. The transient thiophenium ylide cycloadducts formed as a result of (3+2) cyclization were also efficiently trapped with electrophiles generating complex functionalized thiophenes. The use of S-n-propyl substituted yne-alkynyl sulfide was necessary in this case to provide control over product selectivity and to permit the electrophilic trapping to occur before dealkylation. Collectively, the reactivity cascades of thermally formed thiophenium ylides cycloadducts were studied in detail revealing a modulable and controllable reactivity by judicious choice of alkynyl sulfide substitution and reaction condition. In Chapter 4 the use of coinage metals for catalyzing the (3+2) cycloaddition of yne-alkynyl sulfides at room temperature was presented. Our group established that metal-induced low-energy pathways are accessible when alkynyl sulfides are tethered with terminal alkynes. Application of the new set of reaction conditions to an S-phenyl substituted yne-thioalkyne substrate revealed the formation of a thiophenium cycloadduct intermediate. The screening of alternative reaction conditions enabled the successful isolation of this S-phenyl thiophenium cycloadduct by precipitation from the reaction crude enabling structure confirmation by NMR and X-ray crystallography. The reactivity of this previously undescribed S-phenyl thiophenium salt was also evaluated under thermolysis and (metallo)photoredox conditions. The synthesis of S-(hetero)aryl yne-thioalkynes derivatives was first tackled revealing an incompatibility of the current methods described in the literature for a broad range of (hetero)aryl substituted alkynyl sulfides. Despite the numerous challenges encountered, the synthesis of para-substituted electron-poor and rich phenyl derivatives was successfully achieved using sulfur umpolung methods. A one-pot strategy was applied to these S-phenyl derivatives involving the in-situ formation of thiophenium cycloadducts which readily underwent a [1,5]-sigmatropic rearrangement and aromatization upon mild heating (70 oC) towards 2-aryl substituted fused thiophenes. Lastly, the compatibility of the S-phenyl thiophenium cycloadduct in (metallo)photoredox transformations for new CPh-C bond formation was evaluated. In contrast to electrophilic S-aryl sulfonium reagents commonly employed, this first generation of thiophenium salt was not efficient in providing high yields for the desired cross-coupled products. It was postulated that undesired HAT side reactivity was detrimental to the reaction efficacy. These preliminary studies allowed us to gain crucial insight into the inherent reactivity of an S-phenyl thiophenium salt with the hope to guide the next generation of potentially useful electrophilic reagents.