Browsing by Subject "chemistry"

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  • Mukherjee, A.B.; Bhattacharya, P. (NRC Research Press, 2001)
  • Salmi, Emma (Helsingin yliopisto, 2015)
    Corrosion is a major global challenge with both economical and technological impacts. The total world-wide costs of corrosion have been evaluated to rise to over 2 000 000 million euros annually. While several methods exist for corrosion protection, atomic layer deposited (ALD) coatings have an advantage in applications where thin, fully conformal, highly precise and well-defined coatings both in composition and thickness are needed. In this work the corrosion protection properties of ALD Al2O3 and Ta2O5 based coatings on low alloy steel were studied. The aim was to increase the general understanding on factors affecting the protective properties and failure mechanisms of the ALD coatings. The protective performance of ALD coatings on steel was improved by focusing on three topics: substrate pre-treatment, optimisation of the ALD coating architecture, and combination of the optimised ALD coatings with layers deposited by other methods. The substrate surface was found to significantly influence the ALD coating performance. Improved protective properties were found on steel samples that were mechanically polished to a lower surface roughness, and efficiently cleaned with H2-Ar plasma in addition to the traditional degreasing with an organic solvent. The smoother surface finish was concluded to be beneficial due to decreased defect formation after the coating deposition upon detachment of loose particles or mechanically fragile sites. The H2-Ar plasma removed organic residues from the steel surface, therefore improving the quality of the first layers of the ALD coating. The performance of the ALD coatings themselves was found to improve when Al2O3 and Ta2O5 were combined to produce Al2O3-Ta2O5 nanolaminate and AlxTayOz mixture coatings. In these coatings Al2O3 provided sealing properties and Ta2O5 the chemical stability, therefore resulting in coatings with better long-term performance than could be achieved with either material alone. Optimisation of the Al2O3-Ta2O5 nanolaminate and AlxTayOz mixture coating architectures further enhanced the protective properties. To further improve the coating-steel interface and to widen the application areas for the ALD based protective coatings, the optimised ALD coating processes were combined with layers deposited with other methods. Firstly, thin filtered cathodic arc sublayers were used to separate the ALD process from the steel surface. This enabled a more precise control of the coating-steel interface and led to improved durability of the ALD coatings. Secondly, pinhole defects in physical vapour and plasma-enhanced chemical vapour deposited hard coatings were sealed with ALD to afford coatings with both good corrosion protection performance and resistance against mechanical wear.
  • Blanquart, Timothee (Helsingin yliopisto, 2013)
    The atomic layer deposition process (ALD) is an alternative to the chemical vapour deposition (CVD) method that is universally appreciated for its unique advantages such as excellent repeatability, conformity and thickness control at the atomic level. ALD precursor chemistry has mainly been based on homoleptic compounds such as, but not limited to, metal halides, alkylamides or alkoxides. However, these precursors have drawbacks such as possible halide contamination and low thermal stabilities with respect to the alkylamides and alkoxides. Consequently, heteroleptic precursors were investigated as alternatives to the existing homoleptic counterparts, which have led to the development of several advantageous processes. Nevertheless, no thematic review dedicated to heteroleptic precursor and their properties exists and it seems that no coherent strategy has been adopted for the development of heteroleptic precursors. This thesis gives a brief description of ALD and presents studies on the deposition of thin films of groups 4 and 5 metal oxide films using ALD. A description of the general ALD properties of homoleptic precursors in addition to a review on the thermal ALD of groups 4 and 5 metal oxides from heteroleptic precursors is provided. Trends in the properties of heteroleptic ALD precursors based on a literature review and new experimental data are discussed. Several novel heteroleptic compounds were evaluated for the ALD of thin films of TiO2, ZrO2, Nb2O5 and Ta2O5. The characteristics of these processes were evaluated and the film properties of these oxides were investigated by means of various characterization approaches. The effects of oxygen source, water or ozone, on the film growth characteristics and properties of ZrO2, Nb2O5, and Ta2O5, were also investigated. Mixed alkoxide-alkylamide and alkoxide-amidinate titanium compounds are liquid at room temperature. They are highly volatile, have excellent reactivity towards water and have high thermal stability. The deposited films exhibit high purity and conformability on high aspect ratio substrates. The growth of thin films of ZrO2 from a heteroleptic alkylamide-guanidinate zirconium precursor was notable in that the films grew in the high permittivity cubic phase and the ozone-based process had a high growth rate. Thin films of VOx were deposited from the homoleptic vanadium alkylamide precursor,vanadium tetraethylmethylamide. It was found that the structure and oxidation state of the films could be tuned from an amorphous mixture of VO2 and V2O5 to crystalline VO2 or V2O5. This was accomplished by simply exposing the films to heat treatment in different atmospheres, namely air or N2. Finally, alkylamide-imide precursors were investigated for the ALD of Nb2O5 and Ta2O5 thin films. These precursors are liquid at room temperature, and exhibited high thermal stabilities compared with the earlier known niobium and tantalum ALD precursors. The alkylamide-imide precursors studied had high volatility and excellent reactivity towards both water and ozone. The deposited films were smooth, uniform, and contained only low amounts of impurities.
  • Sibaouih, Ahlam (Helsingin yliopisto, 2015)
    Catalytic transformation of carbon dioxide into useful organic compounds has attracted much attention due to its economic and environmental benefits. In addition, other reasons are also taken into account, such as the possible utilization of CO2 as a renewable source chemical and the growing concern of the greenhouse effect. CO2 is an abundant, cheap, and safe C1 building block in organic synthesis. However, due to the inert nature of CO2, efficient catalytic processes of its chemical fixation remain a significant challenge. In this work, we have studied a possible pathway for practical utilization of CO2. The reaction of CO2 with epoxides giving cyclic carbonates, has been investigated. New catalyst systems based on cobalt capable of catalyzing the chemical transformation of carbon dioxide are described in detail. Oxygen is a cheap, readily available and environmentally friendly natural oxidant. The catalytic activation of molecular oxygen has great potential in a variety of applications. Catalysis and reactions, which are based on molecular oxygen, can also be considered to be ecologically benign processes. Moreover, catalytic reactions in water are highly desirable in terms of green chemistry. In this context, our purpose was to develop an environmentally friendly catalytic systems, suitable for oxidation of alcohols with molecular oxygen in water solution. In this part of the work, efficient catalysts, based on copper complexes have been synthesized and studied in the presence of TEMPO for the oxidation of benzyl and aliphatic alcohols with molecular oxygen in aqueous and nonaqueous medium.
  • Holding, Ashley John (Helsingin yliopisto, 2016)
    In this thesis, the synthesis and application of tetraalkylphosphonium-based ionic liquids towards the dissolution of cellulose (and lignocellulose) is explored. Ionic liquids were synthesised from trialkylphosphines by quaternisation with alkyl halides or dimethylcarbonate and subsequent anion exchange reactions. The ionic liquids were used to dissolve lignin, and were found only to dissolve cellulose upon addition of a polar aprotic molecular solvent, such as DMSO (dimethylsulfoxide). The cellulose dissolution capabilities of a range of these phosphonium ionic liquids in combination with DMSO was studied. It was found that these organic electrolyte solutions were very effective solvents for cellulose, with a high molar dissolution capacity. At the greatest extent, only one mole of ionic liquid per glucose units in cellulose is needed to dissolve cellulose. The role of the cation and anion in the dissolution process is explored, with the aid of solvent parametisation techniques and NMR studies. Other solvents, including GVL (gamma-valerolactone), were explored as greener replacements for DMSO. For the shorter chain phosphonium ionic liquids with DMSO and GVL, upper critical solution temperature behaviour was observed and explored in more detail. In these solutions, cellulose is only soluble at high temperatures, and reforms at low temperatures to form a gel with a spherical micro-particle morphology. The phase behaviour of hydrophobic phosphonium ionic liquids, DMSO, and water was studied and applied to the recovery of the ionic liquid after cellulose dissolution in the electrolyte solutions. Ternary phase diagrams of three of the hydrophobic ionic liquids in combination with DMSO and water were constructed. Finally, phosphonium ionic liquid and deuterated DMSO electrolytes were studied and successfully used for the NMR analysis of high molecular weight cellulose materials. Future work in this area is expected to focus further on the theoretical understanding of cellulose dissolution in phosphonium ionic liquid-based organic electrolyte solutions - with expanded NMR measurements, and other experimental techniques, in tandem with molecular dynamics modelling. Additionally, it is expected that techniques for the solution-state NMR of cellulose will be applied at extended range of analytes, including but not limited to, whole biomass, modified and unmodified nano-celluloses, and high molecular weight cellulose derivatives. The thermo-responsive behaviour (UCST-type) phase-separation of cellulose will continue to be explored especially in its application to new materials, included fibres and shaped spherical particles.
  • Rico del Cerro, Daniel (Helsingin yliopisto, 2021)
    The overall aim of this thesis is to understand the chemistry of different types of ionic liquids (ILs) and their application in cellulose processing, as well as in the chemical analyses of pulp. ILs are applied either on their own or as electrolytes with dimethyl sulfoxide (DMSO) or gamma valerolactone (GVL) as co-solvents. All of the ILs utilised in this work were synthesised in our laboratory via Menshutkin reaction followed by metathesis to different counter anions or via acid-base chemistry. The beginning of our work focused on the investigation of the C2 chemistry of imidazolium ionic liquids (IMILs), one of the first class of ionic liquids utilised in biomass processing, resulting in the understanding of the C2 chemistry of IMILs under neutral and acidic conditions, which complete the comprehension on the mechanistic scenario of the C2 chemistry of IMILs. In this investigation, the importance of the quality of the ILs is remarked. The studies continued to investigate the activation of the chemical reactivity of pulps using tetrabutylphosphonium acetate ([P4444][OAc]), a more thermal stable ionic liquid. The non-dissolving pre-treatment of pulps by [P4444][OAc] demonstrated a reduction in the crystallinity of the pulp to be directly related to its chemical reactivity enhancement. Additionally, [P4444][OAc]:d6-DMSO (20:80 wt.%) was also investigated in both the regioselectivity studies of acetylation reactions and the oxidised nanocellulose nuclear magnetic resonance (NMR) analyses. Quantitative heteronuclear single quantum correlation (HSQC) NMR was a suitable experiment for the quantitation of the oxidation level achieved in the nanocellulose, demonstrating the potential of this method for cellulose analyses. Finally, the research concluded with the studies on other cellulose solvent systems, such as 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) with dimethylsulphoxide (DMSO), which resulted on the discovery of the unexpected reactivity of 1,1,3,3-tetramethylguanidinium acetate ([TMG][OAc]). Furthermore, this investigation led us to the design and synthesis of a novel task-specific ionic liquid (TSIL), so called ‘TMG2SA’. This IL was investigated with regard to cellulose chemical modification, resulting in the high yield production of nanocellulose-type materials by a low demanding energy step, with a different approach than previously reported.
  • Muha, Villo; Williamson, Ritchie; Hills, Rachel; McNeilly, A.D.; McWilliams, T.G.; Alonso, Jana; Schimpl, Marianne; Leney, Aneika C.; Heck, Albert J.R.; Sutherland, Calum; Read, Kevin D.; McCrimmon, Rory J.; Brooks, S.P.; Van Aalten, Daan M.F. (2019)
    O-GlcNAcylation is an abundant post-translational modification in the nervous system, linked to both neurodevelopmental and neurodegenerative disease. However, the mechanistic links between these phenotypes and site-specific O-GlcNAcylation remain largely unexplored. Here, we show that Ser517 O-GlcNAcylation of the microtubule-binding protein Collapsin Response Mediator Protein-2 (CRMP2) increases with age. By generating and characterizing a Crmp2S517A knock-in mouse model, we demonstrate that loss of O-GlcNAcylation leads to a small decrease in body weight and mild memory impairment, suggesting that Ser517 O-GlcNAcylation has a small but detectable impact on mouse physiology and cognitive function. © 2019 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License, which permits unrestricted use, provided the original author and source are credited.
  • Iashin, Vladimir (2020)
    C-H activation is a challenging problem in modern organic chemistry. Direct C–H borylation is one of the widely growing subclasses of C–H activation. As a rule, these reactions are performed by transition metal catalysis. However, recently a metal-free approach towards C-B boron bond formation has been growing intensively. Usually, metal-free borylations are performed with a boron compound as a Lewis acid component and a Lewis base as a proton acceptor, which may or may not be preorganized for this transformation. Usually, such reactions require the use of boranes with high Lewis acidity such as B(C6F5)3, BCl3, BBr3, etc. At the same time, the chemistry of the less acidic boron trifluoride, BF3, as a borylating species is unprecedented. This work is aimed at uncovering the reactivity of BF3 towards C-H borylation of Csp–H and Csp2–H bonds. In this respect, the following factors were studied in the work: • Formation of BF3 adducts with various amines and their reactivity in Csp2–H and Csp–H borylation reactions • Scope of borylation: influence of the substrates’ electronic structure and various functional groups’ compatibility • Controlling the formation of mono-, bis-, tris-, and tetrakisorganoborates from BF3, amine, and Rsp–H/Rsp2–H substrate. • Reactivity difference between BF3·SMe2, BF3·OEt2, and BF3-1,2,2,6,6-pentamethylpiperidine (BF3·PMP) with respect to alkyne borylation Because organoboranes are often unstable reactive species, they were converted to fluoroborates by tetramethylammonium fluoride. In this respect, competing reactions of protodeborylation and fluorination of organofluoroboranes were studied. The literature review consists of two parts: metal-free borylation of triple bonds and double bonds. For triple bonds, the review is preferably limited to terminal acetylenes because internal alkynes cannot undergo Csp–H activation. The influence of each component of a Lewis pair as well as its structure’s selectivity for C–H borylation, 1,2-addition, and carboboration is discussed. The second part uncovers the topic of C-H borylation of Csp2–H bonds. It includes both concerted borylations and borylations by reactive borenium cations. There is a special accent on the chemistry of haloboranes. In order to limit the size of the review, the use of hydroboranes for C–H activation is reviewed least in this book.
  • Vesterinen, Veli-Matti (Helsingin yliopisto, 2012)
    Nature of science (NOS) describes what science is, how it works, how scientists operate, and the interaction between science and society. As a crucial element of scientific literacy, knowledge about NOS is widely recognized as one of the key aims of chemistry education. To enhance students understanding of NOS, teachers need adequate understanding of NOS as well as sufficient pedagogical content knowledge related to NOS for translating their understanding of NOS into classroom practice. This thesis reports an educational design research project on the design and development of a pre-service chemistry teacher education course on NOS instruction. Educational design research is the systematic study of the design and development of educational interventions for addressing complex educational problems. It advances the knowledge about the characteristics of designed interventions and the processes of design and development. The thesis consists of four interconnected studies and documents two iterative design research cycles of problem analysis, design, implementation, and evaluation. The first two studies describe how NOS is presented in the national frame curricula and upper secondary school chemistry textbooks. These studies provide a quantitative method for analysis of representations of NOS in chemistry textbooks and curricula, as well as describe the components of domain-specific NOS for chemistry education. The other two studies document the design, development, and evaluation of the goals and instructional practices used on the course. Four design solutions were produced: (i) description of central dimensions of domain-specific NOS for chemistry education, (ii) research group visits to prevent the diluting of relevance to science content and research, (iii) a teaching cycle for explicit and structured opportunities for reflection and discussion, and (iv) collaborative design assignments for translating NOS understanding into classroom practice. The evaluations of the practicality and effectiveness of the design solutions are based on the reflective essays and interviews of the pre-service teachers, which were collected during the course, as well as on the four in-depth interviews of selected participants, collected a year after they had graduated as qualified teachers. The results suggest that one critical factor influencing pre-service chemistry teachers commitment to teach NOS was the possibility to implement NOS instruction during the course. Thus, the use of collaborative peer teaching and integrating student teaching on NOS instruction courses is suggested as a strategy to support the development of the attitudes, beliefs, and skills necessary for teaching NOS. And even though the outside forces of school culture (e.g. school community, curriculum, textbooks) tend to constrain rather than support novice teachers efforts to implement new practices, the results also demonstrate that a pre-service teacher education course can be successful in producing innovators or early adopters of NOS instruction. Thus it might be one of the first steps in the challenging task of injecting NOS instruction into the chemistry curriculum for enhancing students understanding of NOS and strengthening their scientific literacy.
  • Losilla Fernández, Sergio A (Helsingin yliopisto, 2013)
    In this thesis, several numerical methods for electronic structure calculations are presented. The first is a quadrature scheme for the accurate and efficient computation of electrostatic potentials. The quadrature is applied to calculations on real-space grids, and to Coulomb integrals over Gaussian-type orbitals. Second, we introduce a real-space representation for three-dimensional scalar functions encountered in electronic structure calculations. In this representation, each function is partitioned into numerical atom-centred parts (the bubbles), and the remainder is represented on a three-dimensional Cartesian grid. The algorithms to carry out the required operations are discussed, along with benchmarks of their computer implementations. The presented methods are all of a divide-and-conquer nature, breaking the problem into simple pieces which are suitable for execution in emerging massively parallel computer architectures, such as general-purpose graphics processing units.
  • Asmi, Eija; Neitola, Kimmo; Teinila, Kimmo; Rodriguez, Edith; Virkkula, Aki; Backman, John; Bloss, Matthew; Jokela, Jesse; Lihavainen, Heikki; De Leeuw, Gerrit; Paatero, Jussi; Aaltonen, Veijo; Mei, Miguel; Gambarte, Gonzalo; Copes, Gustavo; Albertini, Marco; Perez Fogwill, German; Ferrara, Jonathan; Elena Barlasina, Maria; Sanchez, Ricardo (2018)
    Aerosol particle optical properties were measured continuously between years 2013-2015 at the Marambio station in the Antarctic Peninsula. Annual cycles of particle scattering and absorption were studied and explained using measured particle chemical composition and the analysis of air mass transport patterns. The particle scattering was found elevated during the winter but the absorption did not show any clear annual cycle. The aerosol single scattering albedo at lambda = 637 nm was on average 0.96 +/- 0.10, with a median of 0.99. Aerosol scattering Angstrom exponent increased during summer, indicating an increasing fraction of fine mode particles. The aerosol was mainly composed of sea salt, sulphate and crustal soil minerals, and most of the particle mass were in the coarse mode. Both the particle absorption and scattering were increased during high wind speeds. This was explained by the dominance of the primary marine sea-spray and wind-blown soil dust sources. In contrast, the back-trajectory analysis suggested that long-range transport has only a minor role as a source of absorbing aerosol at the peninsula.
  • Kiessling, Andreas R.; Malik, Anchal; Goldman, Adrian (2020)
    Adhesion is the initial step in the infection process of gram-negative bacteria. It is usually followed by the formation of biofilms that serve as a hub for further spread of the infection. Type V secretion systems engage in this process by binding to components of the extracellular matrix, which is the first step in the infection process. At the same time they provide protection from the immune system by either binding components of the innate immune system or by establishing a physical layer against aggressors. Trimeric autotransporter adhesins (TAAs) are of particular interest in this family of proteins as they possess a unique structural composition which arises from constraints during translocation. The sequence of individual domains can vary dramatically while the overall structure can be very similar to one another. This patchwork approach allows researchers to draw conclusions of the underlying function of a specific domain in a structure-based approach which underscores the importance of solving structures of yet uncharacterized TAAs and their individual domains to estimate the full extent of functions of the protein a priori. Here, we describe recent advances in understanding the translocation process of TAAs and give an overview of structural motifs that are unique to this class of proteins. The role of BpaC in the infection process of Burkholderia pseudomallei is highlighted as an exceptional example of a TAA being at the centre of infection initiation.
  • Witos, Joanna (Helsingin yliopisto, 2015)
    This doctoral thesis describes the development of novel miniaturized analytical tools applicable to in situ nanoscale studies for a deeper understanding of biomolecular interactions. Capillary electrophoresis (CE), atomic force microscopy (AFM), quartz crystal microbalance (QCM) measurements, and partial filling affinity capillary electrophoresis (PF-ACE) were utilized to study the separation of lipoproteins and their interactions with extracellular matrix (ECM) components. The major focus of the study was on low and high density lipoprotein particles (LDL and HDL), which are the main vehicles of cholesterol transport in human circulation. Lipoproteins are involved in specific interactions with proteoglycans (PGs) and collagens, structural components of ECM of the arterial wall. The interactions lead to the development and progression of atherosclerosis and diabetes. The first step of the work was to clarify, by AFM, the structural and molecular properties of collagens I and III under physiological conditions. Study was made of the effect of decorin on the fibril formation of collagen, which promotes and enhances the binding of collagen with LDL. Moreover, the immobilized collagen I surface was exposed to in situ glycation, and the adsorption pattern of the glycated collagen was elucidated. In addition to AFM, QCM was used to examine characteristics of the interaction between collagens and apolipoprotein B-100 (apoB-100), the major protein of LDL. Values of the dissociation constant were then estimated by evaluating the differences in strength of the binding process. To avoid strong and unwanted adsorption of lipoprotein particles on the inner wall of the capillary, the effect of five different sugars on the separation of lipoproteins was studied by CE in uncoated capillary at physiological pH 7.4. In addition, the effect of the sugars on the size of the lipoproteins was elucidated by asymmetrical flow field-flow fractionation (AsFlFFF) and dynamic light scattering (DLS) measurements. Molecular dynamics (MD) simulations were employed to discover the influence of sugars on the structures of apolipoprotein E (apoE) of HDL and apoB-100 of LDL. In another attempt to eliminate the adsorption of positive analytes and allow their separation, a polycationic coating was developed and covalently bound to the inner wall of the fused silica capillary. The immobilization of the coating was achieved in a three-step procedure during on-line polymerization. The stability study of the coating in wide pH range 3 8 demonstrated the suitability of the coating for the separation of small proteins and -blockers. Finally, PF-ACE technique was used to evaluate in detail the interactions involved in the binding of the most common isoforms of apoE with the major glycosaminoglycan (GAG) chain of PGs, viz., chondroitin-6-sulfate (C6S). As is well known, PF-ACE enables the evaluation of affinity constants only for single-type interactions, and adsorption energy distribution (AED) calculations were introduced to widen its application. AED allowed characterization of the heterogeneity of interactions and permitted evaluation of differences in the binding process strengths. The key contributions of the work are the promising and reliable tools developed for separation and interaction studies of biological processes occurring in the ECM.
  • Al-Rashed, F.; Ahmad, Z.; Iskandar, M.A.; Tuomilehto, J.; Al-Mulla, F.; Ahmad, R. (2019)
    Background/Aims: TNF-α-mediated pro-inflammatory phenotypic change in monocytes is known to be implicated in the pathogenesis of metabolic inflammation and insulin resistance. However, the mechanism by which TNF-α-induces inflammatory phenotypic shift in monocytes is poorly understood. Since long-chain acyl-CoA synthetase 1 (ACSL1) is associated with inflammatory monocytes/macrophages, we investigated the role of ACSL1 in the TNF-α-driven inflammatory phenotypic shift in the monocytes. Methods: Monocytes (Human monocytic THP-1 cells) were stimulated with TNF-α. Inflammatory phenotypic markers (CD16, CD11b, CD11c and HLA-DR) expression was determined with real time RT-PCR and flow cytometry. IL-1β and MCP-1 were determined by ELISA. Signaling pathways were identified by using ACSL1 inhibitor, ACSL1 siRNA and NF-κB reporter monocytic cells. Phosphorylation of NF-κB was analyzed by western blotting and flow cytometry. Results: Our data show that TNF-α induced significant increase in the expression of CD16, CD11b, CD11c and HLA-DR. Inhibition of ACSL1 activity in the cells with triacsin C significantly suppressed the expression of these inflammatory markers. Using ACSL-1 siRNA, we further demonstrate that TNF-α-induced inflammatory markers expression in monocytic cells requires ACSL1. In addition, IL-1b and MCP-1 production by TNF-α activated monocytic cells was significantly blocked by the inhibition of ACSL-1 activity. Interestingly, elevated NF-κB activity resulting from TNF-α stimulation was attenuated in ACSL1 deficient cells. Conclusion: Our findings provide an evidence that TNF-α-associated inflammatory polarization in monocytes is an ACSL1 dependent process, which indicates its central role in TNF-α-driven metabolic inflammation. © 2019 The Author(s).