Low energy electron (LEE) driven chemistry underpins a wide range of interdisciplinary fields, including radiation biology, redox chemistry, astrochemistry and biomaterial design. A growing interest in the chemistry of LEEs concerns the radiative damage to DNA. Studies have found that LEEs can induce single and double-strand breaks in DNA by forming a negative ion resonance (NIR). These processes are remarkably site-specific and have been utilized to synthesize radiosensitizers, which aid in identifying target cells in hypoxic tumors in radiation therapy. Despite the prevalence of LEE-induced reactions, computational studies of such processes are limited compared to thermal and photochemical reactions. The relative scarcity in computational studies of LEE-induced reactions stems from the difficulties in the theoretical treatment of NIRs. In our work, we report new developments on the application of quantum chemical methods to NIRs. We demonstrate that the combination of approaches developed for resonances with multi reference electronic structure methods enables the computation of various types of NIRs in a single calculation. Additionally, we show that multi-reference methods can also quantify the mixing between NIRs. It is observed that the mixing between resonances can have significant consequences on their lifetimes. We also report the development of a new technique, the continuum remover Feshbach projection operator approach, which uses the conventional methods developed for bound states to characterize resonances. We show that this new approach is straightforward to implement with standard electronic structure packages, it is efficient, and provides promising results. / Chemistry

Molecules in the ‘X-C≡N’ chemical family serve as markers for chemical processes happening in various regions of space and are members of the prebiotic molecular pool, which makes them important in astrochemistry and astrobiology. Although these kinds of molecules have been identified in the interstellar medium, cometary comae, plumes of Enceladus, meteorites, and around young stellar objects, it is not clear which mechanisms are responsible for their formation. However, it has been suggested that they may serve as precursors to prebiotically important compounds, such as amino acids and nucleobases. In this work, a theoretical computational study was conducted using quantum mechanical approaches to predict properties of sixteen astrochemically relevant ‘X-C≡N’ molecules. To perform this study, General Atomic and Molecular Electronic Structure System (GAMESS(US)) and AutoGAMESS software were used to calculate optimized geometries, harmonic vibrational frequencies, infrared intensities, and Raman activities of each molecule using density functional theory (BLYP, B3LYP, PBE, and PBE0) and second order Møller-Plesset perturbation theory (MP2, SCS-MP2) paired with several basis sets (6-311++G(d,p), def2QZVPD, Sadlej-pVTZ, and aug-cc-pVQZ). Geometries and frequencies were additionally calculated using coupled cluster approaches (CCSD, CCSD(T), and CCSD(2)T) to help assess accuracy and reliability of the other calculations. For many of these species, experimentally and computationally determined Raman activities have not been reported in the literature. We assess the reliability of our calculations in comparison to previous works and discuss how the implementation of both Raman and infrared spectroscopy can offer new insights into potential reaction mechanisms linking these prebiotically relevant compounds.

<p dir="ltr">Chemical reaction networks govern polymer degradation and contain critical design information regarding specific susceptibilities, degradation pathways, and degradants. However, predicting reaction pathways and characterizing complete reaction networks has been hindered by high computational costs because of the vast number of possible reactions at deeper levels of network exploration. In the first section, an exploration policy based on Dijkstra's algorithm on YARP using the reaction rate as a cost function was shown to provide a tractable means of exploring the pyrolytic degradation network of a representative commodity polymer, PEG. The resulting network is the largest reported to date for this system and includes pathways out to all degradants observed in earlier mass spectrometry studies. The initial degradation pathway predictions were validated by complementary experimental analysis of pyrolyzed PEG samples by ESI-MS. These findings demonstrate that reaction network characterization is reaching sufficient maturity to be used as an exploratory tool for investigating materials degradation and interpreting experimental degradation studies.</p>

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The Diels-Alder is an important reaction that is one of the primary tools for synthesizing cyclic carbon structures, while simultaneously introducing up to four stereocenters in the resulting product. Not only is it a widely explored reaction in organic chemistry, but a vital tool in industry to construct novel compounds for pharmacological applications. Still, a remaining concern is the fact that upon the introduction of stereogenic carbons, the possibility of stereoselective control is greatly diminished. A common solution to the problem of undesirable stereoisomers is to employ chiral auxiliaries and ligands as means to increase the yield of a certain stereoisomer. However, incorporating these types of compounds in order to obtain an enantiomerically pure product increases the amount of synthetic steps to be regulated, implying that one or more purification steps are necessary to obtain the desired result. An accompanying thought leans toward the environmental aspect, as the principles of green chemistry are of great importance. This thesis presents the attempts to explore the possibility of engineering an enzyme that can catalyze an asymmetric Diels-Alder reaction through the use of molecular modeling. Based on previous work, the catalytically proficient enzyme ketosteroid isomerase had been deemed a probable candidate as a Diels-Alderase. To evaluate the enzyme thoroughly, a set of compounds was scored against the active binding site where the best hits against the wild type were saved and evaluated repeatedly after the introduction of rational mutations. Although no conclusive indication of an optimal design could be obtained at the end of this work, valuable insight was retrieved on plausible design strategies, which eventually could help lead to the first catalytically proficient Diels-Alderase. / Diels-Alder är en viktig reaktion då den är ett redskap för att syntetisera cykliska kolstrukturer, samtidigt som uppemot fyra stereocentra introduceras i den resulterande produkten. Reaktionen används inte enbart inom organisk kemi, utan är även ett viktigt redskap inom industriella sammanhang för att ta fram nya preparat som direkt kan tillämpas inom farmakologi. En återstående problematik är faktumet att introduktionen av nya stereogena kol bidrar till att drastiskt minska möjligheten att bibehålla en stereoselektiv kontroll. En vanlig lösning för att undvika oönskade stereoisomerer är att nyttja kirala hjälpmolekyler och ligander för att öka utbytet av en specifik stereoisomer. Dock innebär införandet av dessa hjälpmolekyler i strävan att erhålla en enantiomeriskt ren produkt ett ökat antal syntes-steg att hantera, vilket antyder att ett eller flera reningssteg är nödvändiga för att uppnå önskat resultat. Ur en miljösynpunkt är detta värt att ha i åtanke, då principerna för grön kemi är viktiga. Detta arbete utforskar möjligheterna att konstruera ett enzym som kan katalysera en asymmetrisk Diels-Alder-reaktion, med hjälp av molekylär modellering. Baserat på tidigare arbeten har enzymet ketosteroid isomeras valts ut som en potential kandidat till ett Diels-Alderase. För att noggrant evaluera enzymet så screenades ett set av substrat mot dess aktiva säte, där de bästa träffarna gentemot vildtypen sparades och återevaluerades allteftersom rationella mutationer kontinuerligt introducerades. Trots avsaknaden av klara indikationer på att en optimal design har kunnat tas fram vid slutet av detta arbete, så erhölls värdefull insikt på möjliga design-strategier, vilket skulle kunna bistå sökandet av det första katalytiskt effektiva Diels-Alderase.

Geometry optimization is a key step in the computational modeling of chemical reactions because one cannot model a chemical reaction without first accurately determining the molecular structure, and electronic energy, of the reactants and products, along with the transition state that connects them. These structures are stationary points— the reactant and product structures are local minima, and the transition state is a saddle point with one negative-curvature direction—on the molecular potential energy surface. Over the years, many methods for locating these stationary points have been developed. In general, the problem of finding reactant and product structures is relatively straightforward, and reliable methods exist. Converging to transition states is much more challenging. Because of the difficulty of transition-state optimization, researchers have designed optimization methods specifically for this problem. These methods try to make good choices for the initial geometry, the system of coordinates used to represent the molecule, the initial Hessian, the Hessian updating method, and the step-size. The transition-state optimization method developed in this thesis required considering all of these methods. Specifically, a new method for finding an initial guess geometry was developed in chapter 2; good choices for a coordinate system for representing the molecule were explored in chapters 2 and 6; different choices for the initial Hessian are considered in chapter 5; chapters 3 and 4 present, and test, a sophisticated new method for updating the Hessian and controlling the step-size during the optimization. iv The methods created in the process of this research led to the development of Saddle, a general-purpose geometry optimizer for transition states and stable structures, with and without constraints on the molecular coordinates. Saddle can be run in conjunction with the Gaussian program or almost any other quantum chemistry program, and it converges significantly more often than the other traditional methods we tested. / Thesis / Doctor of Science (PhD)