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Chemistry in Progress

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Displaying theses 1-10 of 710 total
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V. Hafych
Master programme: Atomic Scale Modelling of Physical, Chemical and Bio-Molecular Systems (ATOSIM), Physics / Chemistry February 20th, 2019
Institute: Other Research group: CECAM Graduation thesis Supervisor: Evert Jan Meijer
photo of the author
Quantum Free Energy Calculations via Langevin-guided Monte Carlo
The free energy is a quantity which plays a crucial role in physics, chemistry, and biology. It allows one to analyze the stability of systems, describe phase transitions and chemical reactions for classical and quantum systems. A lot of research has been conducted recently to develop precise and computationally efficient algorithms for the free energy reconstruction. The main focus of the vast majority of scientific papers is the efficient exploration of the configuration space, which allows to overcome the problem of rare event sampling. In this thesis, the problem of the free energy reconstruction is considered from slightly different perspective, motivated by the search for an efficient scheme to compute quantum free energies. Namely, a proof of principle is provided here that one can compute the mean forces which act on the auxiliary variable by performing a Hybrid Monte Carlo in which the proposal moves are generated by evolving Langevin trajectory. The obtained mean forces can be used to reconstruct the free energy landscape by performing a variational fitting procedure. The method has been developed both for classical free energies, where several efficient alternatives exist, and later extended to the quantum case, for which considerably less work has been done.
picture that illustrates the research done
Scientific abstract (pdf 32K)   For more info or full text, mail to: E.J.Meijer@uva.nl

C. Tantiwong
Master programme: Chemistry - Molecular Simulation and Photonics February 20th, 2019
Institute: Other Research group: Institut de Biologie et Chimie des Protéines Graduation thesis Supervisor: Evert Jan Meijer
PHYSICS OF LIPID DROPLET BUDDING: INSIGHT FROM COARSE-GRAINED SIMULATIONS
Lipid droplets (LDs) are the organelles regulating energy metabolism in cells. Their structure is similar to oil emulsions in water, with a core consisting of hydrophobic lipids surrounded by a monolayer consisting of amphipathic lipids. We used molecular simulations at the coarse-grained level, to explore the relationship between the shape of nascent LDs (i.e., oil clusters embedded in lipid bilayer membranes) and their chemical and physical properties. We performed simulations of nascent LDs with different size (various number of oil molecules), different chemical composition, and different temperature, using the MARTINI coarse-grained model. All these results are in qualitative agreement with the theory. We also investigated if LD budding has a preferential site. In eukaryotic cells, LDs form in the endoplasmic reticulum (ER), a membrane-bound organelle with both flat and highly curved regions; it is currently unknown if nascent LDs form preferentially in flat or curved regions of the ER. We generated membranes with variable curvature by buckling very large bilayers. We then inserted multiple oil droplets in the buckled membrane, and observed their dynamic evolution and their preferential localization. Still, preliminary results suggest that nascent droplet prefer to localize in regions of high curvature of the lipid bilayer.
picture that illustrates the research done
Scientific abstract (pdf 3K)   For more info or full text, mail to: E.J.Meijer@uva.nl

M.A. Ramzan
Master programme: Atomic Scale Modelling of Physical, Chemical and Bio-Molecular Systems (ATOSIM), Physics / Chemistry February 20th, 2019
Institute: Other Research group: none Graduation thesis Supervisor: Dr. Evert Jan Meijer
Correlations Between Friction Coefficient and Interfacial Thermal Conductance in DWCNTs Using Green-Kubo Formalism and NEMD
Carbon nanotubes (CNTs) are low dimensional materials with properties that make them ideal for many nanoscale thermoelectromechanical devices. However, the concepts of sliding friction and interfacial thermal conductance in CNT base materials need to be investigated for the better implementation of these materials in nanodevices. Using equilibrium (Green-Kubo) and NEMD simulations, we investigated the correlations between the friction coefficient Γ and the interfacial thermal conductance G in the radial direction of three different double-walled CNTs of different commensurability, each of length 10 nm.
picture that illustrates the research done
Scientific abstract (pdf 51K)   For more info or full text, mail to: E.J.Meijer@uva.nl

M.W. ten Harmsen van der Beek
Bachelor programme: Scheikunde February 1st, 2019
Institute: VU / Chem. & Pharm.Sc. Research group: VU Analytical Chemistry and Applied Spectroscopy Graduation thesis Supervisor: Rob Haselberg
Hemoglobin aggregate analysis using Size Exclusion Chromatography in ammonium acetate buffer.
Size Exclusion chromatography is a method which is capable of separating big molecules, among which proteins, based on its size. Diluted into a aqueous solution, the proteins are being pressured (up to 70 bar) into the SEC column. Small proteins will fit better inside the columns pores than bigger ones, which causes the small proteins to stick better inside the column than its bigger counterparts. In other words; smaller proteins will have a bigger retention time (and retention volume) than the bigger ones, which makes effective separation possible. By analyzing proteins from which the molecular weight is already known, one is able to make a calibration curve. By making this curve it will be possible to estimate the molecular weight of a unknown protein, given a certain retention volume. One should consider however, that this is always a estimation, since SEC separates proteins not based on its weight, but on its size. And since those two properties do not correlate exactly one-to-one, one could only speak of a rough approximation of the size of the protein.
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Scientific abstract (pdf 2K)   For more info or full text, mail to: r.haselberg@vu.nl

B.J. van Enter
Master programme: Science for Energy and Sustainability - Physics / Chemistry January 31st, 2019
Institute: VU / Physics & Astr. Research group: Hybrid Solar Energy Conversion Graduation thesis Supervisor: Elizabeth von Hauff
Towards accurate glucose sensing: Determining the effect of pH on glucose detection
Diabetes is a worldwide epidemic that can cause severe medical complications. There are limitations on accuracy and practicality with the current technologies used for diabetes management, so research on improving techniques and on new technologies is prevalent. One of the technologies with great potential for glucose detection is Raman spectroscopy. Raman Spectroscopy is a useful analytical tool that can be applied to study glucose properties and concentrations in physiologically relevant (i.e. aqueous) solutions. Glucose is a unique organic molecule and thus has a unique Raman spectrum. In this MSC research project glucose was dissolved in aqueous solutions under varying acidity (pH 3 – 8), and measured with Raman spectroscopy, enzymatic test-strips and NMR. This way it was possible to measure the proposed change of equilibrium as well as checking the potential for Raman spectroscopy to reliably detect glucose under varying circumstances.
picture that illustrates the research done
Scientific abstract (pdf 2K)   For more info or full text, mail to: e.l.von.hauff@vu.nl

A.V. Panteleev
Bachelor programme: Scheikunde January 30th, 2019
Institute: HIMS Research group: Heterogeneous Catalysis and Sustainable Chemistry Graduation thesis Supervisor: dr. N.R. Shiju
Dehydration of glucose to 5-hydroxymethylfurfural using WO3-doped Nb2O5 Catalysts
The increasing concern over the use of fossil fuels has resulted in increasing focus on the development of sustainable feedstocks for chemicals and fuels. Biomass is a promising candidate for this due to its abundance. Lignocellulose is the biomass that cannot be used as food, making it especially suitable as a feedstock. The glucose in lignocellulose can be dehydrated to hydroxymethylfurfural (HMF), a platform chemical that can be used for the carbon neutral synthesis of biofuels and important chemicals. To effectively gain HMF from biomass, an effective catalyst for the conversion of glucose to HMF is necessary. Niobium(V)oxide (Nb2O5) possesses the right characteristics for this. For transition metal oxides like Nb2O5 it is known that addition of tungsten(VI)oxide (WO3) results in more active acid sites, potentially improving yield. This study found the highest HMF-yield when the catalyst contained 30% WO3 and was calcined at 300°C. This is because WO3 has a different ratio of Lewis and Brönsted acid sites, so its addition can optimize the ratio for this reaction. Calcination at higher temperatures reduces the amount of available acids, causing the HMF-yield to decrease.
picture that illustrates the research done
Scientific abstract (pdf 1K)   For more info or full text, mail to: n.r.shiju@uva.nl

Y. Boeije
Bachelor programme: Scheikunde January 28th, 2019
Institute: HIMS Research group: Molecular Photonics Group Graduation thesis Supervisor: Fred Brouwer
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Deep Ultraviolet Photochemistry of a Tin-oxo Cage
Nowadays, everybody is making use of microchips. To make more efficient laptops and mobile phones, the patterns in microchips should be made smaller. To achieve that, it is important to know how these patterns are created. With photolithography, a photoresist is exposed to light, which leads to a difference in solubility. Unfortunately, it is not well known how the solubility changes of most photoresists. The aim of this research was to discover what happens if a tin-oxo cage, which is a potential photoresist, is exposed to light. In this research, we got to know more about the photochemistry, by exposing a solution of the tin-oxo cage with a laser at 225 nm and analyzing with spectroscopic techniques. It was discovered that tin-carbon bonds split after the exposure, after which radicals are formed. The butyl radical converts to 1-butene, 1-butanol and 1,1-dimethoxybutane.
picture that illustrates the research done
Scientific abstract (pdf 2K)   For more info or full text, mail to: a.m.brouwer@uva.nl

J.J. Peek
Master programme: Chemistry - Molecular Science January 25th, 2019
Institute: HIMS Research group: Homogeneous, supramolecular and bio-inspired catal Literature thesis Supervisor: dr. ir. J.I. van der Vlugt
Current Developments in Immobilised Homogeneous CO2 Electrocatalysts in Intrinsically Electron Conducting Metal-Organic-Frameworks and Concepts for Electrocatalytic Systems
In this review, we will describe the scientific efforts towards an integrated electrochemical CO2 reduction system with homogeneous catalysts immobilised on intrinsically conducting metal-organic frameworks. To do this, we examine the research frontiers in electro-conducting MOFs, homogenous catalysis in CO2 reduction and catalyst implementation strategies in MOFs. An up-to-date description of the current challenges, progressions and future prospects will be presented. With the aim of giving a detailed account of the fast pace developments in this exciting multidisciplinary research area for CO2 reduction. A research question was composed to set a clear boundary on the focus of this review; What are the current developments for immobilised homogeneous CO2 electrocatalysts in intrinsically electron conducting metal-organic-frameworks and which concepts are essential for a good electrocatalytic system? To find an in dept and satisfactory answer, this question is further broken down into smaller issues which will be discussed separately.
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Scientific abstract (pdf 4K)   For more info or full text, mail to: J.I.vanderVlugt@uva.nl

E. Blokker
Master programme: Chemistry - Molecular Science January 17th, 2019
Institute: VU / Chem. & Pharm.Sc. Research group: VU Division of Theoretical Chemistry Graduation thesis Supervisor: Prof. Dr. F.M. Bickelhaupt
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Bonding Mechanisms of C-C, Si-Si and SiO-OSi Bonds – A Theoretical Study
In this thesis, we have studied the bonding properties of various selected single element-element, with the use of density functional theory (DFT) at BLYP-D3(BJ)/TZ2P. An elaborated analysis of the bonding mechanisms of R3AAR3 (A = C, Si, OSi) systems reveals the underlying physical factors that determine structure and stability of single bonds in the model systems and beyond.
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Scientific abstract (pdf 0K)   For more info or full text, mail to: f.m.bickelhaupt@vu.nl

M.L.A. Hakkennes
Bachelor programme: Scheikunde January 17th, 2019
Institute: HIMS Research group: Synthetic Organic Chemistry Graduation thesis Supervisor: Dr. M.A. Fernádez Ibáñez
C-H olefination of 1,2,3,4-tetrahydroquinolines promoted by a S,O-ligand
Tetrahydroquinolines are abundant in natural products and bioactive compounds, but often require a multistep synthesis. In the last few decades functionalization of carbon hydrogen bonds has been a solution to bypass this problem. A new catalytic system developed by Fernández-Ibáñez et al., and based on palladium and a bidentate S,O-ligand, showed a greater acceleration on the C-H olefination of simple arenes. Furthermore, the catalytic system proved to be efficient for the selective para-C-H olefination of anilines. Herein, we report the C-H olefination of 8-substituted-1,2,3,4-tetrahydroquinolines using the Pd/S,O-ligand catalytic system.
picture that illustrates the research done
Scientific abstract (pdf 1K)   For more info or full text, mail to: M.A.FernandezIbanez@uva.nl

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