Indium nitride has many applications as a semiconductor. High quality films of indium nitride can be grown using Chemical Vapour Deposition (CVD) and Atomic Layer Deposition (ALD), but the availability of precursors and knowledge of the underlaying chemical reactions is limited. In this study the gas phase decomposition of a new indium precursor, N,N-dimethyl-N',N''-diisopropylguanidinate, has been investigated by quantum chemical methods for use in both CVD and ALD of indium nitride. The computations showed significant decomposition at around 250°C, 3 mbar indicating that the precursor is unstable at ALD conditions. A computational study of the surface chemical mechanism of the adsorption of trimethylindium and ammonia on indium nitride was also performed as a method development for other precursor surface mechanism studies. The results show, in accordance with experimental data, that the low reactivity of ammonia is a limiting factor in thermal ALD growth of indium nitride with trimethylindium and ammonia.

As the demand for clean and renewable energy sources continues to grow, much attention has been given to solid oxide fuel cells (SOFCs) due to their efficiency and low operating temperature. However, the components of SOFCs must still be improved before commercialization can be reached. Of particular interest is the solid electrolyte, which conducts oxygen ions from the cathode to the anode. Samarium-doped ceria (SDC) is the electrolyte of choice in most SOFCs today, due mostly to its high ionic conductivity at low temperatures. However, the underlying principles that contribute to high ionic conductivity in doped ceria remain unknown, and so it is difficult to improve upon the design of SOFCs. This thesis focuses on identifying the atomistic interactions in SDC which contribute to its favourable performance in the fuel cell. Unfortunately, information as basic as the structure of SDC has not yet been found due to the difficulty in experimentally characterizing and computationally modelling the system. For instance, to evaluate 10.3% SDC, which is close to the 11.1% concentration used in fuel cells, one must investigate 194 trillion configurations, due to the numerous ways of arranging the Sm ions and oxygen vacancies in the simulation cell. As an exhaustive search method is clearly unfeasible, we develop a genetic algorithm (GA) to search the vast potential energy surface for the low-energy configurations, which will be most prevalent in the real material. With the GA, we investigate the structure of SDC for the first time at the DFT+U level of theory. Importantly, we find key differences in our results from prior calculations of this system which used less accurate methods, which demonstrate the importance of accurately modelling the system. Overall, our simulation results of the structure of SDCagree with experimental measurements. We identify the structural significance of defects in the doped ceria lattice which contribute to oxygen ion conductivity. Thus, the structure of SDC found in this work provides a basis for developing better solid electrolytes, which is of significant scientific and technological interest. Following the structure search, we perform an investigation of the electronic properties of SDC, to understand more about the material. Notably, we compare our calculated density of states plot to XPS measurements of pure and reduced SDC. This allows us to parameterize the Hubbard (U) term for Sm, which had not yet been done. Importantly, the DFT+U treatment of the Sm ions also allowed us to observe in our simulations the magnetization of SDC, which was found by experiment. Finally, we also study the SDC surface, with an emphasis on its structural similarities to the bulk. Knowledge of the surface structure is important to be able to understand how fuel oxidation occurs in the fuel cell, as many reaction mechanisms occur on the surface of this porous material. The groundwork for such mechanistic studies is provided in this thesis.

It is well established that the morphology and physical properties of an organic semiconducting (OSC) material regulate its electronic properties. However, structure-function relationships remain difficult to describe in polymer-based OSC, which are of particular interest due to their robust mechanical properties. If relationships among the molecular and bulk levels of structure can be found, they can aid in the design of improved materials. To explore and detail important structure-function relationships in polymer-based OSC, this work employs molecular dynamics (MD) simulations to study various π-conjugated polymers in different environments. Two independent investigations are discussed in this work. One investigation examines how the purposeful disruption of the π-conjugated backbone to increase the chain flexibility impacts the chain structure and packing in the condensed phase. This is done by adding a conjugation break spacer (CBS) unit of one to ten carbons in length into the monomer structure of diketopyrrolopyrrole-based polymers. It is found that trends in the folding and glass structure follow the increase and the parity (odd versus even) of the CBS length. The second investigation analyzes a variety of polymers and small molecule acceptor (SMA) blends to observe the effects of changing the shape of either component and the physical properties of the material, as well as the structure of the polymer chains. It is found that the conjugated core, the side chains, and the planarity or sphericity each influence the density and diffusion of the materials made.

abstract: Single-layer pentagonal materials have received limited attention compared with their counterparts with hexagonal structures. They are two-dimensional (2D) materials with pentagonal structures, that exhibit novel electronic, optical, or magnetic properties. There are 15 types of pentagonal tessellations which allow plenty of options for constructing 2D pentagonal lattices. Few of them have been explored theoretically or experimentally. Studying this new type of 2D materials with density functional theory (DFT) will inspire the discovery of new 2D materials and open up applications of these materials in electronic and magnetic devices.In this dissertation, DFT is applied to discover novel 2D materials with pentagonal structures. Firstly, I examine the possibility of forming a 2D nanosheet with the vertices of type 15 pentagons occupied by boron, silicon, phosphorous, sulfur, gallium, germanium or tin atoms. I obtain different rearranged structures such as a single-layer gallium sheet with triangular patterns. Then the exploration expands to other 14 types of pentagons, leading to the discoveries of carbon nanosheets with Cairo tessellation (type 2/4 pentagons) and other patterns. The resulting 2D structures exhibit diverse electrical properties. Then I reveal the hidden Cairo tessellations in the pyrite structures and discover a family of planar 2D materials (such as PtP2), with a chemical formula of AB2 and space group pa ̄3. The combination of DFT and geometries opens up a novel route for the discovery of new 2D materials. Following this path, a series of 2D pentagonal materials such as 2D CoS2 are revealed with promising electronic and magnetic applications. Specifically, the DFT calculations show that CoS2 is an antiferromagnetic semiconductor with a band gap of 2.24 eV, and a N ́eel temperature of about 20 K. In order to enhance the superexchange interactions between the ions in this binary compound, I explore the ternary 2D pentagonal material CoAsS, that lacks the inversion symmetry. I find out CoAsS exhibits a higher Curie temperature of 95 K and a sizable piezoelectricity (d11=-3.52 pm/V). In addition to CoAsS, 34 ternary 2D pentagonal materials are discovered, among which I focus on FeAsS, that is a semiconductor showing strong magnetocrystalline anisotropy and sizable Berry curvature. Its magnetocrystalline anisotropy energy is 440 μeV/Fe ion, higher than many other 2D magnets that have been found. Overall, this work not only provides insights into the structure-property relationship of 2D pentagonal materials and opens up a new route of studying 2D materials by combining geometry and computational materials science, but also shows the potential applications of 2D pentagonal materials in electronic and magnetic devices. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2020

Recent research has shown that small hydrogen bonding catalysts can catalyze the hetero Diels-Alder reaction. In this thesis such hydrogen bonding catalysts in conjunction with varying functional groups and their effect on the hetero Diels-Alder reaction have been investigated. The influence of the different solvents has been investigated as well. The activation barriers for the different region- and stereo isomeric pathways have been compared in order to determine the stereo specificity of the reactions. These calculations have been done using the B3LYP functional for the geometry optimizations and then M06-2X for single point calculations. For the solvated cases the cPCM model and the M06-2X functional were used. It was shown that for the catalyzed systems bulkier groups in the endo position tend to have a lower activation barrier, allowing for control over the stereoselectivity. Electron withdrawing groups have an activating effect and are also synergistic with the hydrogen bonding catalysts. The solvent with the lowest dielectric constant gave the lowest activation barrier.

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Light or photons can excite electrons in a molecule, leading to creation of electronically excited states. Such processes are ubiquitous in nature, such as, vision, photo-protection of DNA/RNA nucleobases, light harvesting, energy and charger transfer etc. This photoexcitation induces nuclear motion on the excited states, leading the excess energy to dissipate either non-radiatively via internal conversion back down to the ground state, isomerization, and dissociation, or radiatively via fluorescence and phosphorescence. In this dissertation, we investigate the non-radiative processes in organic chromophores that ensue in an ultrafast manner, mediated via conical intersections (CoIn). Description of such excited state processes generally require multi-reference treatment because of quasi-degeneracy near CoIns. Hence, most insight about these processes is typically gained by constructing potential energy surface (PES) using multi-reference electronic structure methods along important reaction coordinates. Nonetheless, the aforementioned static treatment fails to provide any dynamical information, such as, excited state lifetime, state populations, branching ratio, quantum yield etc. In this dissertation, we have gone beyond the static treatment by undertaking computationally expensive non-adiabatic excited state molecular dynamics simulations employing trajectory surface hopping (TSH) methodology on PESs created on-the-fly using multi-reference electronic structure methods. This allows us to compare theoretical results to experimental observables, when possible, strengthening the explanations underlying those processes. Our goal is to examine the effect of structure, and of electronic structure methods on the excited state dynamics. We have examined the non-adiabatic excited state dynamics of cis,cis-1,3-cyclooctadiene (cc-COD), a cyclic diene, in an effort to systematically compare and contrast the dynamics of cc-COD to that of other well studied conjugated molecules. Such exploration is very significant, since the majority of the molecules involved in natural photoexcited processes, include an ethylenic double bond or alternating double bonds creating conjugation. Our calculations have revealed ultrafast sub-ps decay for cc-COD, and have illustrated that the internal conversion dynamics is facilitated by CoIns, dominated by twisting of one of the double bonds and pyramidalization of one of the carbons of that double bond, similar to trans-1,3-butadiene and unlike 1,3-cyclohexadiene (CHD). Our high-level electronic structure calculations have also explained the features in the experimental time-resolved photoelectron spectrum of cc-COD. Another molecule of biological importance, uracil, was also investigated using TSH simulations, by systematically increasing dynamical correlation. We have found that the inclusion of dynamical correlation for uracil leads to an almost barrierless PES on S2, leading to a faster decay and no population trap on this state. Uracil also contains a double bond and the simulations have revealed that the ultrafast relaxation is dominated by an ethylenic twist and pyramidalization of a carbon of that bond, increasing importance of such nuclear motion in photoexcited molecular dynamics. A comparison of the molecules studied have illustrated that the rigid molecules, such as uracil, CHD, have a very local CoIn seam space, whereas cc-COD, which is flexible having many low frequency degrees of freedom, has a non-local or extended CoIn seam space. Overall, the work performed in this dissertation, elucidates the significance of structure and conjugation, in the photoinduced coupled electron-nuclear dynamics in organic molecules. / Chemistry

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Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...

Water molecules play a significant role in biological process and are directly involved with bio-molecules and organic compounds and ions. Recent research has focused on the thermal dynamics and kinetics of water molecules in solution, including experimental (infrared spectroscopy and Raman spectroscopy) and computational (Quantum Mechanics and Molecular Dynamics) approaches. The reason that water molecules are so unique, why they have such a profound influence on bio-activity, why water molecules show some anomalies compared to other small molecules, and where and how water molecules exert their influence on solutes are some of the areas under study. We studied some properties of hydrogen bond networks, and the relationship of these properties with solutes in water. Molecular dynamics simulation, followed by an analysis of “water bridges”, which represent protein-water interaction have been carried out on folded and unfolded proteins. Results suggest that the formation of transient water bridges within a certain distance helps to consolidate the protein, possibly in transition states, and may help further guide the correct folding of proteins from these transition states. This is supporting evidence that a hydrophilic interaction is the driving force of protein folding. Biological membranes are complex structures formed mostly by lipids and proteins. For this reason the lipid bilayer has received much attention, through computation and experimental studies in recent years. In this dissertation, we report results of a newly designed pH sensitive lipid MORC16, through all-atom and coarse-grained models. The results did not yield a MORC16 amphiphile which flips its conformation in response to protonation. This may be due to imperfect force field parameters for this lipid, an imperfect protonation definition, or formation of hydrogen bond does not responsible for conformation flip in our models. Despite this, some insights for future work were obtained.