The Langevin equation is a stochastic differential equation frequently used in molecular dynamics for simulating systems with a constant temperature. Recent developments have given rise to wide uses of Langevin dynamics at different levels of spatial resolution, which necessitate time step and friction parameter choices outside of the range for which many existing temporal discretization methods were originally developed. We first study the GJ--F, BAOAB and BBK numerical algorithms, originally developed for atomistic simulations, on a coarse-grained polymer melt, paying close attention to the large time step regime. The results of this study then inspire our search for new algorithms and lead to a general class of velocity Verlet-based time-stepping schemes designed to perform well for all parameter regions, by ensuring that they faithfully reproduce statistical quantities for the case of a free particle and harmonic oscillator. This family of methods depends on the choice of a single free parameter function and we explore some of the methods defined for certain choices of this parameter on realistic coarse-grained and atomistic molecular systems relevant in material and bio-molecular science. In addition, we provide an equivalent splitting formulation of this one-parameter family which allows for enhanced insight into the hidden time scaling induced by the choice of the free parameter in the Hamiltonian and stochastic time scales. / Mathematics

<p> The organic ions studied in this thesis were generated in the rarefied gas phase of the mass spectrometer by electron ionization of selected precursor molecules. The characterization of their structure and reactivity was probed by using a variety of tandem mass spectrometry techniques. These include metastable ion spectra to probe the dissociation chemistry of the low energy ions and collision experiments to establish the atom connectivity of the ions. The technique of neutralization-reionization mass spectrometry (NRMS) was used to probe the structure and stability of the neutral counterparts of the ions. Computational results involving the CBS-QB3 model chemistry formed an integral component in the interpretation of the experimental findings.</p> <p> The above approach was used to study proton-transport catalysis in the formaldehyde elimination from low energy 1,3-dihydroxyacetone radical cations. Solitary ketene-water ions, CH2=C(=O)OH2·+, do not readily isomerize into its more stable isomer, CH2=C(OH)2·+. A mechanistic analysis using the CBS-QB3 model chemistry shows that metastable 1,3-dihydroxyacetone radical cations will rearrange into hydrogen-bridged radical cations [CH2C(=O)O(H)-H•••OCH2]·+, where the CH2=O will catalyze the transformation of CH2=C(=O)OH2·+ into CH2=C(OH)2·+.</p> <p> Metastable pyruvic acid radical cations, CH3C(=O)COOH·+, have been shown to undergo decarboxylation to yield m/z 44 ions, C2H4O·+, in competition with the formation of CH3C=O+ + COOH· by direct bond cleavage. Collision induced dissociation experiments agree with an earlier report that oxycarbene ions CH3COH·+ are formed but they also suggest the more stable isomer CH3C(H)=O·+ may be co-generated. Using the CBS-QB3 model chemistry, a mechanism is proposed to rationalize these results.</p> <p> Next, the isomeric ions CH3O-P=S·+ and CH3S-P=O·+ were characterized and differentiated by tandem mass spectrometry. Metastable CH3O-P=S·+ and CH3S-P=O·+ ions both spontaneously lose water to yield m/lz 74 cyclic product ion [-S-CH=]P·+. Using the CBS-QB3 model chemistry a mechanism is proposed for the water loss from CH3O-P=S·+ and CH3S-P=O·+. Our calculations also show that these two isomers communicate via a common intermediate, the distonic ion CH2S-P-OH·+, prior to the loss of water.</p> <p> The final component of this work details the computational study addressing the long standing question on the mechanism for the water elimination from metastable ethyl acetate radical cations. The CBS-QB3 results show that low energy ethyl acetate ions isomerize into ionized 4-hydroxy-2-butanone prior to the loss of water.</p> / Thesis / Master of Science (MSc)

Computational studies have become an essential tool in biochemistry, providing detailed insight into biological systems alongside experimental studies. Molecular simulation can predict protein conformational dynamics and the impact of mutations, enabling rapid and low-cost investigation of potential therapeutic targets and better understanding of biological systems. Molecular dynamics (MD) is a computational method able to model ensembles of biomolecular conformations in solution by simulating atomic motion at high temporal resolution. The principle limitation of MD is the ability to collect sufficient data for equilibrium sampling. However, with the progression of high-performance computing (HPC) clusters and distributed computing platforms, timescales previously inaccessible to MD can be reached and relevant protein parameters can be extracted using modeling. From these simulations, Markov state models (MSMs) are used extract system-relevant kinetic and thermodynamic information. An MSM represents a series of memoryless, probabilistic transitions between discrete states in a kinetically meaningful way. The obtained information is used to understand the relationships between relevant protein conformations, thus enabling a comprehensive understanding of the modelled system in a human-readable format. Recent advancements in model scoring and hyper-parameterization moved MSM construction away from anecdotal, case-by-case basis to a highly systematic approach that focuses on optimization and validity. Thus, modern MSMs are employed to investigate protein properties, and predict experimental observables using system-representative ensembles of conformations. Additionally, a comprehensive MSM can be combined with sparse experimental data to generate an improved interpretation of the system. My work focuses on performing all-atom massively-parallel MD simulation using the Folding@home distributed computing platform in order to build comprehensive MSMs that are used in improving simulation accuracy and protein design. This work results in the development of an unbiased framework for MSM building that is used to lend insight into simulation parameters, extract novel system behavior and enable clear comprehension of a target function, such as impact of mutations or emphasis of rare events. / Chemistry

Serine/threonine protein kinases (STKs) are extremely ancient and ubiquitous signaling enzymes; despite their common name “eukaryotic protein kinases”, these protein domains are also present in archaea and bacteria suggesting their presence in the last universal common ancestor 3-4 billion years ago. It is known that tyrosine kinases (TKs) descended from this lineage much later, just prior to the emergence of the first metazoans. TKs share a great deal of structural homology with even the most distantly related STKs, however their ability to phosphorylate Tyr instead of Ser and Thr along with their unique domain organizations sets them apart from STKs in both sequence and function. This thesis explores the distinct conformational “landscapes” of these two important protein families, dealing with a ~20 residue long “activation loop” which has multiple inactive conformations but only one active conformation. By employing a statistical energy Potts Hamiltonian model of protein sequences and using molecular dynamics free-energy simulations, major sequence features of the catalytic domain were determined which control the shape of the free-energy landscape i.e., the relative depths of the “active” and “inactive” basins, a quantity termed the reorganization free-energy ΔG_reorg. A key finding from this approach is the marked divergence in the conformational landscapes of TKs from STKs that is encoded in the sequences of extant family members, which was detected by threading their Potts sequence energies over the active “DFG-in” (catalytic “Asp-Phe-Gly motif oriented “in”) basin relative to an inactive “DFG-out” basin where the activation loop is “folded up” by ~20 Å. This free-energy basin autoinhibits the kinase because the activation loop behaves as a pseudo-substrate in cis. The Potts couplings threaded over the active and inactive basins suggest that TKs evolved to have a smaller free-energy difference between the active and inactive basins compared with STKs, by 4-6 kcal/mol. The sequence and structural basis for this effect was explored in detail by decomposing the threaded Potts Hamiltonian into pairwise interactions and analyzing the statistical energy effects of natural sequence variation at evolutionary divergent positions in the sequence. These effects were then verified by performing mutations of amino acid sidechains using FEP (Free Energy Perturbation) molecular dynamics simulations in both the active and inactive conformational states and comparing the results with analogous sequence-based calculations by making mutations in the Potts model. The results are highly consistent (Pearson correlation of 0.81) suggesting that the Potts model is comparable to FEP in its ability to capture the physical free-energy balance of amino acid sidechain interactions between two different conformational basins and validates the Potts model-predicted evolutionary divergent landscapes of TKs and STKs. This divergence can in part be attributed to autoinhibitory pseudo-substrate interactions involving the activation loop; the evolved peptide-substrate specificity of TKs compared with STKs, and the functional surfaces that have been evolutionarily molded to complement Tyr vs Ser/Thr-containing peptides, appear to have energetic feedback with the propensity of the kinase’s own activation loop to “fold” against these surfaces when the DFG is flipped from “in” to “out”, and TKs have evolved to exploit this as a means of regulation. / Chemistry

This dissertation focuses on the assessment and development of heterogeneous catalysts for the deperoxidation of cyclohexyl hydroperoxide and oxidation of cyclohexane, which will be based in metal oxides and gold nanoparticles. For this endeavour a multidisciplinary approach will be used combining theoretical chemistry, kinetic studies and synthesis and characterisation of materials. The starting choice for the catalyst to carry out the process is supported gold nanoparticles. The approach of this dissertation is to first model the mecha- nism of cyclohexyl hydroperoxide decomposition and oxidation of cyclohexane on gold nanoparticles by theoretical calculations, and use these findings to synthesise efficient heterogeneous catalysts which will be subsequently tested and optimised experimentally. But as it will be seen, some metal oxides are active rather than acting as mere supports, which will also be studied both theoretical and experimentally. Each chapter has a specific focus and constitutes a strand of the overall goal: Chapter 1 provides an introductory background on the topics that this dissertation lies upon: oxidation of cyclohexane, heterogeneous catalysis and catalysis by gold and metal oxides. Chapter 2 outlines the objectives of the thesis, formulating the relevant hypotheses of this research and the subsequent validation tests. Chapter 3 exposes the methodology with a brief conceptual background that has been used to carry out this work. Chapter 4 is the first chapter dealing with results. It consists in a theoretical study using density functional theory of the reaction mechanism over different models of gold nanoparticles, in order to study the influence of several parameters on their catalytic activity: the particle size, atom coordination, and presence of additional species like oxygen atoms and water. Chapter 5 uses the findings found in chapter 4 to drive the synthesis of supported gold nanoparticles. It consists in a experimental study of gold-based catalysts, which is combined with a theoretical study which takes into account an additional variable: the support. Chapter 6 exploits one of the findings of chapter 5. One of the supports used for anchoring the gold nanoparticles is active by itself, namely cerium oxide. This chapter comprises an experimental work about its activity, studying parameters like particle size, morphology and the effect of doping. Chapter 7 continues with the catalytic activity of cerium oxide-based materials, but now from a theoretical point of view. It first presents a systematic study of the parameters relevant for the proper quantum mechanical description of cerium oxide, which is followed by a mechanistic study on different models. Chapter 8 outlines the conclusions obtained in this dissertation, present- ing them in a summarised way. Even though each chapter presents its corresponding conclusions at its end, this chapter groups them all in a structured way for the reader's convenience, so a global view of the project can be swiftly grasped. The results herein further the knowledge of heterogeneous catalysis for the oxidation of cyclohexane, one of the most important industrial reactions, and which continues to be a challenge. Although the ultimate goal is to develop an industrial catalyst, the dissertation also aims to show how computational chemistry can drive the design of novel materials, and how it can help to understand catalytic reactions at the atomic level. / El presente trabajo se centra en el estudio y desarrollo de catalizadores heterogéneos para la desperoxidación de ciclohexil hidroperóxido y la oxidación de ciclohexano, basados en óxidos metálicos y nanopartículas de Au. Para lograr tal objetivo se ha usado un enfoque multidisciplinar, que combina química teórica y estudios cinéticos, a la vez que síntesis y caracterización de materiales. El candidato inicial para llevar a cabo el proceso consiste en partículas de Au soportadas. El camino a seguir pasa primero por modelizar el mecanismo de descomposición de ciclohexil hidroperóxido y oxidación de ciclohexano mediante cálculos teóricos, y utilizar el conocimiento generado por este estudio para dictar la síntesis de catalizadores heterogéneos, comprobando y optimizando posteriormente su actividad de forma experimental. Sin embargo, como será visto a lo largo de este trabajo, algunos óxidos metálicos dejan de lado su papel como mero soporte físico para las partículas de Au y son activos por sí mismos. Tal hecho será estudiado tanto teórica como experimentalmente. Cada capítulo tiene un objetivo específico, y es a su vez una parte del objetivo global de esta investigación: El capítulo 1 provee al lector de una breve introducción a los temas sobre los que yace este trabajo: oxidación de ciclohexano, catálisis heterogénea y catálisis mediante Au y óxidos metálicos. El capítulo 2 expone de una forma breve y concisa los objetivos de esta investigación, formulando la hipótesis de partida y los correspondientes experimentos para su validación. El capítulo 3 describe la metodología utilizada junto a una explicación de los fundamentos en los que se basa cada técnica. El capítulo 4 es el primer capítulo que discute los resultados obtenidos en esta investigación. Se trata de un estudio usando la teoria del funcional de densidad para investigar el mecanismo de reacción del proceso sobre diferentes modelos teóricos de Au, con el objetivo de comprender la influencia de diversos factores en la actividad catalítica, tales como el tamaño de partícula, la coordinación de los á'tomos de Au y la presencia de especies adicionales como átomos de O y agua. El capítulo 5 hace uso de los resultados obtenidos en el estudio anterior, y los utiliza para dirigir la síntesis de nanopartículas soportadas de Au. Se trata de un estudio experimental en el que se investigan diversos factores que pueden afectar a su actividad catalítica. Este estudio se combina a su vez con uno de tipo teórico en el que se tiene en cuenta la influencia del soporte en la actividad catalítica de las particulas de Au. El capítulo 6 se basa en uno de los resultados obtenidos en el capítulo 5. Uno de los soportes utilizados para anclar las partículas de Au resulta de por sí activo: el CeO2. Su notable actividad para catalizar este proceso exige un estudio en mayor profundidad, el cual se lleva a cabo en este capítulo. Parámetros como el tamaño de particula, la morfología de superficie y el dopaje entre otros se investigan en este punto. El capítulo 7 sigue la estela del trabajo anterior sobre CeO2, pero ahora desde el punto de vista de la química teórica. Presenta primero un estudio sistemático de parámetros relacionados con la mecánica cuá'ntica que afectan al CeO2, con el objetivo de alcanzar una descripción satisfactoria de los modelos teóricos para este óxido. Tras esto, se lleva a cabo un estudio del mecanismo de reacción en dichos modelos de CeO2, a fin de comprender el origen de su actividad catalítica. El capítulo 8 presenta de forma estructurada y concisa todas las conclusiones que se han sacado a raíz de los resultados obtenidos. Aún a pesar de que cada capítulo presenta sus correspondientes conclusiones al final, aquí se presentan de una forma agrupada a comodidad del lector, para que pueda obtener de forma ágil una visión global de los resultados de esta investigación. / Aquest treball es centra en l'estudi i desenvolupament de catalitzadors hetero- genis per a la desperoxidació de ciclohexil hidroperòxid i la oxidació de ciclohexà, basats en òxids metàl·lics i nanopartícules de Au. Per aconseguir aquest objectiu s'ha utilitzat un enfocament multidisciplinari, en el qual es combinen química teòrica i estudis cinètics amb síntesi i caracterització de materials. El candidat inicial per dur a terme el procés consisteix en partícules de Au suportades. El camí a seguir passa primer per modelitzar el mecanisme de descomposició del ciclohexil hidroperòxid i la oxidació de ciclohexà mitjançant càlculs teòrics, i utilitzar el coneixement generat per aquest estudi per dirigir la síntesi de catalitzadors heterogenis, comprovant i optimitzant posteriorment la seua activitat de forma experimental. No obstant això, com es veurà al llarg d'aquest treball, alguns òxids metàl·lics deixen de costat el seu paper com a suport físic de les partícules de Au y són actius per si mateixos. Aquest fet s'ha estudiat tant teòrica com experimentalment. Cada capítol té un objectiu específic i és al mateix temps una part de l'objectiu global d'aquesta recerca: El capítol 1 proporciona al lector una breu introducció als temes tractats en aquest treball: oxidació de ciclohexà, catàlisi heterogènia i catàlisi mitjançant Au i òxids metàl·lics. El capítol 2 exposa d'una forma breu i concisa els objectius d'aquesta investigació, formulant la hipòtesi inicial i els corresponents experiments per a la seua validació. El capítol 3 descriu la metodologia utilitzada conjuntament amb una explicació dels fonaments en els quals es basa cada tècnica. El capítol 4 és el primer capítol que discuteix els resultats obtinguts en aquesta investigació. Es tracta d'un estudi usant la teoria del funcional de densitat per investigar el mecanisme de reacció del procés en diferents models teòrics de Au, amb l'objectiu de comprendre la influència en l'activitat catalítica de diversos factors, com ara la grandària de partícula, la coordinació dels àtoms de Au i la presencia d'espècies addicionals, com àtoms de O i aigua. El capítol 5 fa ús dels resultats obtinguts en l'estudi anterior, i els utilitza per dirigir la síntesi de nanopartícules suportades de Au. Es tracta d'un estudi experimental en el qual s'investiguen diversos factors que poden afectar a la seua activitat catalítica. Aquest estudi es combina amb un altre de caràcter teòric en el qual es té en compte la influència del suport en la activitat catalítica de les partícules de Au. El capítol 6 es basa en un dels resultats obtinguts en el capítol 5. Un dels suports utilitzats per fixar les partícules de Au resulta de per si actiu: el CeO2. La seua notable activitat per catalitzar aquest procés demana un estudi de major profunditat, el qual es duu a terme en aquest capítol. Paràmetres com la grandària de partícula, la morfologia de superfície i el dopatge, entre altres, s'investiguen en aquest punt. El capítol 7 continua l'estudi anterior sobre el CeO2, però ara des del punt de vista de la química teòrica. Presenta en primer lloc un es- tudi sistemàtic de paràmetres relacionats amb la mecànica quàntica que afecten al CeO2, amb l'objectiu d'aconseguir una descripció satisfactòria pels models teòrics d'aquest òxid. Després, es duu a terme un estudi del mecanisme de reacció en aquests models de CeO2, a fi de com- prendre l'origen de la seua activitat catalítica. El capítol 8 presenta de forma estructurada i concisa totes les conclusions que s'han extret arran dels resultats obtinguts. Encara que cada capí- tol presenta les seues corresponents conclusions al final, ací es presenten d'una forma agrupada per a la comoditat del lector, per què puga obtindre de forma àgil una visió global dels result d'una forma agrupada per a la comoditat del lector, per què puga obtindre de forma à / López Auséns, JT. (2016). From Quantum Mechanics to Catalysis: Studies on the oxidation of alkanes by gold and metal oxides [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/76806

Kovalente Inhibition stellt einen effektiven Weg dar, die Verweildauer des Liganden innerhalb einer Bindetasche zu erhöhen. In dieser Arbeit wurden theoretische Methoden angewendet, um die Reaktivität und den nichtkovalenten Zustand vor der Reaktion zu modellieren. Im Rahmen einer Fallstudie zu Cathepsin K wurden nichtkovalente Modelle von kovalenten Inhibitoren generiert. Für verschiedene Komplexe aus Cathepsin K und einem kovalent gebundenem Liganden wurde der Zustand vor der Reaktion modelliert und dessen Stabilität im Rahmen einer klassischen MD-Simulation überprüft. Die Stabilität des Warheads in der Bindetasche hing hauptsächlich vom gewählten Protonierungszustand der katalytischen Aminosäuren ab. Für eine Reihe von Inhibitoren der ChlaDUB1 wurde ein Protokoll aus quantenmechanischen Rechnungen genutzt, um die Reaktivität verschiedener Warheads abzuschätzen. Die erhaltenen Aktivierungsenergien korrelierten mit experimentell bestimmten Raten zur Inaktivierung des Enzyms. Im Rahmen eines Wirkstoffdesign-Projektes zur Deubiquitinase USP28 wurden von unpublizierten Kristallstrukturen ausgehend erste Docking-Experimente durchgeführt. Es konnte gezeigt werden, dass ein literaturbekannter Inhibitor von USP28 mit einem Warhead so modifiziert werden kann, dass die reaktive Einheit in direkter Nachbarschaft zu einem Cystein positioniert wird. Für diese Warheads wurden ebenfalls quantenmechanische Rechnungen zur Bestimmung der Aktivierungsenergie durchgeführt. Um besser nachvollziehen zu können, warum bei einem Photoswitch-Inhibitor der Butyrylcholin-Esterase der cis-Zustand des Moleküls besser inhibiert als der trans-Zustand, wurde eine Docking-Studie des Zustandes vor der Reaktion durchgeführt. Es konnte ein qualitatives Modell aufgestellt werden, das zeigt, dass der trans-Zustand aufgrund seiner längeren Form mit wichtigen Aminosäuren am Eingang der Bindungstasche kollidiert. / Covalent inhibition is an effective way to increase the residence time of a ligand within the active site. In this work theoretical methods were used to model the reactivity and the noncovalent pre-reaction state. Noncovalent models of covalent inhibitors were generated as part of a case study of Cathepsin K. Several complexes of Cathepsin K and a covalently bound ligand were modeled in their state before the reaction, and their stability was assessed by classical molecular dynamics simulations. In most cases the warhead was positioned in close proximity to the catalytic unit, remaining there for up to several hundred nanoseconds. This stable positioning was largely dependent on the protonation state of the catalytic amino acids. To estimate the reactivity of a series of ChlaDUB1 inhibitors, a protocol of quantum mechanical calculations was adapted. The obtained activation energies correlated with experimentally obtained rate constants of enzyme inactivation. Using unpublished crystal structures, first design steps for the inhibition of the deubiquitinase USP28 were performed. Docking studies showed that modification of a literature-known inhibitor of USP28 with a warhead allowed to place this reactive unit close to a cysteine. Activation energies were also obtained for these structures via quantum mechanical calculations. To better rationalize the differences in inhibition between the cis- and trans-state of a photoswitch inhibitor of butyrylcholine esterase, a docking study of the noncovalent state was performed. The different ring conformers and stereochemical properties of the photoswitch were critical for a sensible model of the ligand. A qualitative model could be obtained which explains that the cis-isomer is more active than the trans-isomer due to a steric clash of the latter with amino acids at the entrance of the pocket.

Inkjet additive manufacturing is the next step toward ubiquitous manufacturing by enabling multi-material printing that can exhibit various mechanical, electronic, and thermal properties. These characteristics are realized in the careful formulation of the inks and their functional materials, but there are many constraints that need to be satisfied to allow optimal jetting performance and build quality when used in an inkjet 3-D printer. Previous research has addressed the desirable rheology characteristics to enable stable drop formation and how the metallic nanoparticles affect the viscosity of inks. The contending goals of increasing nanoparticle-loading to improve material deposition rates while trying to maintain optimal flow dynamics is the closely held trade secret in formulating these inkjet compositions. We use data from previous experiments and the CRC Handbook of Chemistry and Physics to train machine learning regression models to predict the relevant factors of inkjet printability at a standardized temperature of 25ºC: viscosity, surface tension, and density. These models were used to predict the rheological factors of the main components of a UV-curable inkjet ink formulation: UV-curable monomers and oligomers, photoinitiators, dispersants, and humectants. This paper compares the relative performance of five machine learning algorithms to assess the effectiveness of each approach for chemoinformatics regression tasks.

Computational methods were employed to investigate catalytic processes. First, DFT calculations predicted the important geometry metrics of a copper–nitrene complex. MCSCF calculations supported the open-shell singlet state as the ground state of a monomeric copper nitrene, which was consistent with the diamagnetic character deduced from experimental observations. The calculations predicted an elusive terminal copper nitrene intermediate. Second, DFT methods were carried out to investigate the mechanism of C–F bond activation by a low-coordinate cobalt(I) complex. The computational models suggested that oxidative addition, which is very rare for 3d metals, was preferred. A π–adduct of PhF was predicted to be a plausible intermediate via calculations. Third, DFT calculations were performed to study ancillary ligand effects on C(sp3)–N bond forming reductive elimination from alkylpalladium(II) amido complexes with different phosphine supporting ligands. The dimerization study of alkylpalladium(II) amido complexes indicated an unique arrangement of dative and covalent Pd-N bonds within the core four-membered ring of bimetallic complexes. In conclusion, computational methods enrich the arsenal of methods available to study catalytic processes in conjunction with experiments.

This dissertation focuses on the computational investigation of gold(I) acyclic diaminocarbene (ADC) complexes and their application in homogeneous gold(I) catalysis. Chapter 2 is an in-depth computational investigation of the σ- and π-bonding interactions that make up the gold-carbene bond. Due to the inherent conformation flexibility of ADC ligands, distortions of the carbene plane can arise that disrupt orbital overlap between the lone pairs on the adjacent nitrogen atoms and the empty p-orbital of the carbene. This study investigated the affect these distortions have on the strength of the σ- and π-bonding interactions. This investigation demonstrated that while these distortions can affect the σ- and π-bonding interactions, the ADC ligand have to become highly distorted before any significant change in energy of either the σ- or π-bonding interactions occurs. Chapter 3 is a collaborative investigation between experimental and computational methods, DFT calculations were employed to support the experimental catalytic results and determine the role that steric effects have in controlling the regioselectivity of a long-standing electronically controlled gold(I)-catalyzed tandem 1,6-enyne cyclization/hydroarylation reaction with indole. This study demonstrated that by sterically hindering nucleophilic attack of indole at the favored position, nucleophilic attack would occur at a secondary position leading to the selective formation of the electronically unfavored product. Chapter 4 is a collaborative investigation between experimental and computational methods. DFT calculations were employed to investigate and rationalize the importance of secondary non-covalent interactions and their influence on the enantioselectivity of a gold(I)-catalyzed intramolecular hydroamination of allene reaction. Through computational investigation of the enantiodetermining step, and the non-covalent interactions present between 2′-aryl substituent and the rest of the catalyst, it was determined that the presence of CF3 group on the 3,5-position of the 2′-aryl ring is crucial to maintaining a more rigid chiral pocket leading to higher enantiomeric excesses in this dynamic system. This increased rigidity is believed to be attributable to the several weak non-covalent interactions that arise between the allene substrate or diisopropyl N-substituent and the fluorine atoms of the CF3 groups.

Thesis advisor: Junwei Bao / The mysteries in chemistry could be reveals by utilization of innovative computational methods and the creative application of advanced modeling techniques. The limitation or difficulties of experimental methods sometimes makes it hard to study the mechanism behind the reaction energy, so computational chemistry could play an important role to investigate and analyze the detailed reaction mechanism and elementary reaction pathways behind a complexed, multi-step chemical reaction. Also, it is important to develop robust and accurate theoretical methods to perform computational and simulation works. We applied multiple computational or simulation models to study various chemical systems, which provided us valuable insights to understand the chemical reactions happened in our daily life. Chapter 1 explores an advanced Gaussian Process (GP)-based optimization approach for the efficient geometry optimization of polypeptides, focusing on reducing computational costs associated with single-point energy (SPE) evaluations in traditional methods. By employing Gaussian Process Regression (GPR) as a surrogate model, the optimization steps are minimized through a surrogate potential energy surface (PES) generated from quantum mechanical data. The study assesses the performance of four kernel types—Matern, squared exponential, rational quadratic, and periodic—within multiple coordinate frameworks, including redundant and non-redundant internal coordinates and Coulombic coordinates. Results indicate that the periodic kernel combined with non-redundant delocalized internal coordinates is the most effective in reducing optimization steps, particularly suited to handle molecular structures with periodic characteristics. Additionally, the rational quadratic kernel shows promise when used with Coulombic coordinates, offering flexibility for functions with varying smoothness. Implemented in the mad-GP framework, this study provides insights into optimizing large biomolecules, such as polypeptides, with significant implications for computational chemistry and biomolecular modeling. We also compared the GP-optimized structures with the AlphaFold-predicted structures to assess their respective effectiveness in accurate structure prediction. This comparison provides insight into the reliability and applicability of each method for modeling polypeptide conformations. Chapter 2 investigates the interaction energies and energy decomposition of van der Waals (vdW) complexes between N6-methyladenosine (m6A) and tryptophan residues in YTH proteins, the readers of m6A modifications on mRNA. Given the role of m6A in cellular processes, structural insights into its interaction with YTH proteins could facilitate therapeutic advancements. We examined the effects of various chemical modifications on tryptophan residues (W465 and W470) in the YTH binding pocket, with the aim of enhancing the CH-π interactions with m6A through modified electron density. Using Density Functional Theory (DFT) and Symmetry-Adapted Perturbation Theory (SAPT), we explored the vdW interactions into electrostatic, dispersion, induction, and Pauli exchange components and identified London dispersion and electrostatics as dominant stabilizing forces. Correlations of these components with molecular descriptors such as polarizability and multipole moments further highlighted the effects of electronic properties on binding. Our results suggest that optimized tryptophan modifications could strengthen m6A recognition, potentially guiding the design of enhanced m6A-binding proteins for applications in RNA biology. Chapter 3 presents a computational analysis of reaction pathways and energy barriers on LiCoO₂ and TiO₂ surface models, exploring their role in promoting reactions critical to lithium-ion battery (LIB) performance and catalytic applications. For LiCoO₂, we examine the dissociation of H₂O₂. Using density functional theory (DFT) and climbing-image nudged elastic band (CI-NEB) calculations, we identified and characterized the elementary steps in the dissociation mechanism, and indicated that the reaction barriers are reduced in the presence of organic species. For TiO₂, we model the adsorption and dissociation of a Li(DME)₃ complex, exploring solvent dissociation and solvent exchange mechanisms in the context of DME ligands. Results show that the TiO₂ surface aids in stabilizing Li⁺ ions after solvent dissociation, and it favors a solvent-exchange pathway with a lower reaction barrier. These insights provide valuable mechanistic detail that help the design of materials. / Thesis (MS) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.