Structures, Energetics, and Reaction Barriers for CH_x Bound to the Nickel (111) Surface

To provide a basis for understanding and improving such reactive processes on nickel surfaces as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we report quantum mechanics calculations (PBE flavor of density functional theory, DFT) of the structures, binding energies, and reaction barriers for all CH_x species on the Ni(111) surface using periodically infinite slabs. We find that all CH_x species prefer binding to μ3 (3-fold) sites leading to bond energies ranging from 42.7 kcal/mol for CH_3 to 148.9 kcal/mol for CH (the number of Ni-C bonds is not well-defined). We find reaction barriers of 18.3 kcal/mol for CH_(3,ad) → CH_(2,ad) + H_(ad) (with ΔE = +1.3 kcal/ mol), 8.2 kcal/mol for CH_(2,ad) → CH_(ad) + H_(ad) (with ΔE = -10.2 kcal/mol) and 32.3 kcal/mol for CH_(ad) → C_(ad) + H_(ad) (with ΔE = 11.6 kcal/mol). Thus, CH_(ad) is the stable form of CH_x on the surface. These results are in good agreement with the experimental data for the thermodynamic stability of small hydrocarbon species following dissociation of methane on Ni(111) and with the intermediates isolated during the reverse methanation process

Computational Study of Acid-Catalyzed Reactions in Zeolites

Aldol condensation is a very important reaction in organic synthesis because it leads to the formation of C-C bonds. Because of that, the use of different catalysts and in particular the use of zeolites for the catalysis of this reaction has been previously studied. The first step of aldol condensation is the the acid- catalyzed keto-enol tautomerization of the aldehyde or ketone. In this thesis, we study all the possible locations of BA sites in the vicinity of each of the defined inequivalent T site positions in FER and MOR zeolites and establish the most stable location of proton siting at force field and periodic DFT level. The reactions involving the small carbonyl compounds, acetaldehyde and acetone, are studied at the specific acid site locations in both zeolites in order to discover which are the active sites that can stabilize the reactants and therefore how the existing catalyst can be improved. Besides the H-bonding and other interactions, the confinement effect are of equal importance in the determination of factors that influence the reactivity of these complexes. In order to understand the keto-enol tautomeric mechanism in zeolites and identify the transition states, constrained geometry optimizations were performed of acetaldehyde in FER and MOR using periodic DFT. From this we determined the formation of enol product via and an one and two-step concerted mechanism. The calculations reveal that C-β deprotonation is the kinetic bottleneck for enol formation. The concerted mechanism was performed at each of the inequivalent T position in both zeolites. We found that proton transfer is a consequence of a cooperation between the acid site and its total environment acting on the molecular adsorbate. The adsorption and stability of the intermediates is dependent upon the heterogeneity of acid sites and their local geometry, the pore channels and cavities and interactions such as dispersive and H-bonding that do not reflect, and are often independent of, acid strength. Thirdly, we studied the keto-enol tautomerization of acetaldehyde in FER and MOR in the presence of a single water or methanol molecular and found the activation barriers to reduce further with an increase in stability of the adsorbed enol form with larger reverse barriers in the larger pores of FER. We establish the importance of the specific role of the H-bonding using these solvent molecules. In the smaller pores of MOR, the presence of a solvent supresses the catalytic interconversion due to steric repulsion. Lastly, we explored the location of monovalent alkali ions in FER and found that the most stable location of the cations is in the FER cavity and dependent upon the Al position. We studied the effect of hydration on the mobility of the cesium ion in the cavities of FER using static DFT calculations supplemented with ab initio molecular dynamics. We estabished the cesium ion prefers to coordinate with the framework oxygens of the zeolite rather than oxygen atoms of the water molecules as well as the position of the cesium ion is affected by the Al siting. The coordination number of cesium is ~ 10 with the ion interacting with only 1-3 water molecules. In addition, we identified a self-organization of water molecules across the channels forming a H-bonding network

Minimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis

From a theoretical standpoint, the accurate description of potential energy surfaces for bond breaking and the equilibrium structures of metal-ligand catalysts are distinctly similar problems. Near degeneracies of the bonding and anti-bonding orbitals for the case of bond breaking and of the partially-filled d-orbitals for the case of metal-ligand catalyst systems lead to strong non-dynamical correlation effects. Standard methods of electronic structure theory, as a consequence of the single-reference approximation, are incapable of accurately describing the electronic structure of these seemingly different theoretical problems. The work within highlights the application of multi-reference methods, methods capable of accurately treating these near-degeneracies, for describing the bond-breaking potentials in several small molecular systems and the equilibrium structures of metal-salen catalysts. The central theme of this work is the ability of small, compact reference functions for accurately describing the strong non-dynamical correlation effects in these systems.Ph.D.Committee Chair: C. David Sherrill; Committee Member: Jean-Luc Bredas; Committee Member: Mostafa El-Sayed; Committee Member: Peter J. Ludovice; Committee Member: Thomas Orland

Importance of Electrostatically Driven Non-Covalent Interactions in Asymmetric Catalysis

Computational chemistry has become a powerful tool for understanding the principles of physical organic chemistry and rationalizing and even predicting the outcome of catalytic and non-catalytic organic reactions. Non-covalent interactions are prevalent in organic systems and accurately capturing their impact is vital for the reliable description of myriad chemical phenomena. These interactions impact everything from molecular conformations and stability to the outcome of stereoselective organic reactions and the function of biological macromolecules. Driven by the emergence of density functional theory (DFT) methods that can account for dispersion-driven noncovalent interactions, there has been a renaissance in terms of computational chemistry shaping modern organic chemistry. DFT Studies of the origins of stereoselectivity in asymmetric organocatalytic reactions can not only provide key information on the mode of asymmetric induction, but can also guide future rational catalyst design. We start with an overview of weak intermolecular interactions and aromatic interactions. Special emphasis is given to the methods that one can use to study these ephemeral interactions. We next provide a brief account how computational chemistry has aided our understanding of chiral phosphoric acid (CPA) catalyzed reactions. Thereafter, three case studies showcasing the importance of non-covalent interactions in chiral NHC catalysis, CPA catalysis, and chiral nucleophilic catalysis has been elaborated. Each of these studies highlights the importance of electrostatically-driven non-covalent interactions in controlling reactivity and selectivity. Moreover, unprecedented activation modes are identified and new predictive selectivity models developed that can be used to rationalize the outcome of future reactions. Studying these reactions using state of art DFT methods, we aimed not only to contribute to the understanding of their selectivity and the importance of noncovalent interactions in catalysis, but also to bring a sound understanding that will enable the design of new reactions and better catalysts. Overall, this dissertation highlights the underappreciated role of electrostatic interactions in controlling reactivity and selectivity in asymmetric catalysis

Quantum nuclear effects on surfaces and dispersion bonded systems

Computer simulation methods are established as extremely useful approaches for understanding physical and chemical processes. Density functional theory is one of the most popular theoretical methods used to study a variety of systems, from gas phase molecules to bulk materials and surfaces. However despite its success, there remain challenges that must be resolved before density functional theory is generally applicable across all system types. In particular long range van der Waals dispersion forces and quantum nuclear effects are typically ignored by standard calculations, however as algorithms have matured and fast parallel computing resources are now more widely available it is possible to include these in simulations. We use state of the art methods to include van der Waals dispersion and quantum nuclear effects on a range of well defined model systems. By comparing with experiment whenever possible we provide new insight into how quantum tunnelling, zero point motion and long range dispersion forces can affect physical processes

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

The current state of the art of Quantum Mechanical/molecular mechanical (QM/MM) molecular dynamics approaches in ground and electronically excited states and their applications to biological problems is reviewed. For a complete description of quantum phenomena, the quantum nature of both electrons and nuclei has to be taken into account. Most of the current QM/MM applications are based on adiabatic dynamics in the electronic ground state. However, for dynamics in electronically excited states, the coupling between states, which is mediated via the nuclear motion, can be sizable, and nonadiabatic effects have to be taken into account. Configuration Interaction Singles (CIS) is a popular method in QM/MM applications due to its computational expedience that allows for the treatment of several hundred atoms. Since the 1990s, the Modified Neglect of Differential Overlap (MNDO) method has been further extended to a d orbital basis. This MNDO/d extension allows for the treatment of heavier elements. By using feature selection algorithms348 to identify the most appropriate subset of relevant variables that describe a certain phenomenon, the high-dimensionality of QM/MM data can be reduced and used for further analysis with causal inference algorithms to establish unique cause-effect relationships

Computational Investigations into Nucleic Acid-Related Chemistry

Nucleic acids are biopolymers of nucleotides, which are composed of a phosphate, nucleobase and ribose sugar. In addition to acting as the genetic carrier, nucleic acids play a variety of other important roles in biological systems. In this thesis, nucleic acid-related chemistry is investigated using computational methods. Chapter 1 presents an overview of the problems addressed in this thesis, whereas Chapter 2 discusses various theoretical methods. Then, Chapter 3 investigates the feasibility of using the phosphate oxygens as the general base to catalyze the aminoacyl transfer reaction in histidyl-tRNA synthetase. Three possible mechanisms with different phosphate oxygens acting as the base to abstract the 3\u27-OH group of A76 were examined and compared. Chapter 4 elucidates the catalytic mechanism of the repair of an alkylated nucleobase by the enzyme AlkB. It was found that this mechanism consists of four stages and that our calculated barrier for the rate-controlling step is in good agreement with experimental studies. Chapter 5 addresses the catalytic mechanism of the HDV ribozyme. Both cytosine and hydrated Mg2+ ion were found to be involved in the reaction with the former acting as the acid and the latter as the base. Chapter 6 studies the protonation of guanine quartets and quartet stacks. Each quartet plane was found to be able to accept maximally two protons. Chapter 7 deals with the interactions of metal ions with ribose and locked ribose. Four metal ions, Na+, K+, Mg2+ and Cd2+ were chosen and their properties upon interacting with ribose and locked ribose were compared. Chapter 8 presents the influences of the selection of computational methods and chemical models on the amide bond formation as catalyzed by the ribosome. Two proton transfer processes involving four- and six-membered transition structures were systematically examined using a variety of methods. Finally, Chapter 9 summarizes the main conclusions and possible extensions of the current work

First Principles-Based Microkinetic Modeling of Ethanol from Syngas on Bimetallic Co-Pd Catalysts

In the future, the availability of reliable alternative fuels will be crucial for any country to become energy independent. One such alternative is ethanol as it can be used both as a fuel and as a fuel additive. Most of the ethanol produced in the world today is derived from biomass. The biomass feedstocks and fermentation broths used in ethanol production both contain high amounts of water and therefore, the energy efficiency of the process is lessened by product separation processes (azeotropic separation of water and ethanol) that are non-trivial and highly inefficient (due to the evaporation of water). An alternative route to produce ethanol, which negates the need for costly distillation processes, is via the catalytic conversion of syngas (CO and H2) generated from biomass. Syngas is a mixture of carbon monoxide and hydrogen, which results from the reforming of natural gas, as well as the gasification of coal, biomass, and solid wastes. In theory, syngas can be readily converted to ethanol using chemical catalysts, but to-date no high efficiency, low-cost catalyst has been found. In this work, sub-nanometer size, bimetallic cobalt-palladium particles are found to be active and selective catalysts for the desired reaction as the particles contain two metals having different CO dissociation capabilities. The reaction mechanism considered for this study includes forty-six reversible reactions, including Fischer-Tropsch reactions. We used Density Functional Theory (DFT) coupled with nudged elastic band methods to determine the activation barrier heights and enthalpy change with reactions for the full reaction pathway needed for ethanol production from syngas. To lessen the computational burden, linear Bronsted-Evans –Polanyi (BEP) relations, for association and dissociation reactions, are developed. A microkinetic model is built using the reaction information derived from combined DFT and BEP studies, which is used to examine if there is a synergistic effect between Co and Pd favoring the production of ethanol. Coverage dependent sticking coefficients are used to examine the effects of surface coverage on reactivity. It also incorporates diffusion of intermediate species between the sites. One of the first and important steps in the syngas to ethanol conversion process is carbon monoxide (CO) adsorption on the metal catalyst. Therefore, computational models were developed to help understand CO adsorption energetics as well as surface coverage effects on a Co7Pd6 catalyst. From these initial studies, we determined the adsorption energies of CO on both cobalt and palladium as a function of CO surface coverage (where the number of CO species on the catalyst surface was varied from 1 to 6). Further, we calculated the infrared spectra for adsorbed CO species and key bond lengths (metal–carbonyl carbon and adsorbed CO bond lengths) using DFT. Results from the DFT simulations compared favorably with experimental values. Separate microkinetic models results on Co, CoPd and Pd sites indicate that ethanol formation happens only on CoPd bimetallic sites indicating the synergetic effect of Co and Pd to make ethanol from syngas. A batch reactor is modeled and 24 ordinary differential equations are solved simultaneously to obtain time evolution of products and intermediates. The pathway for ethanol production is identified as: CO* →HCO*→CH2O*→CH3O*→CH3CO*→CH3CHO*→CH3CH2O*→CH3CH2OH. Further, the microkinetic model was modified to include diffusion reactions. Ratio of number of sites of cobalt, cobalt-palladium and palladium is altered to study CoxPdy catalysts of different cobalt and palladium ratios