Browsing by Subject "Density functional theory"

Now showing 1 - 6 of 6
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    Computational Modeling and Predictive Design of Metal-organic Frameworks for Catalysis and Adsorption
    (2023-08) Chheda, Saumil
    Metal-organic frameworks (MOFs) are structurally well-defined nanoporous materials built from inorganic metal oxide nodes connected by organic linkers. The high porosity, surface area, and chemical and thermal stability of MOFs have attracted interest to use these materials in catalysis, gas adsorption and storage, and separation. Furthermore, the modularity of MOFs allows to tailor their nanoscale pore environment for enhanced performance in a desired application. This thesis utilizes different computational modeling techniques to provide fundamental mechanistic insights into catalysis and adsorption phenomena occurring in MOFs which can be used to design better-performing systems. Chapter 1 highlights the suitability of MOFs for catalysis and adsorption and briefly discusses the computational methods useful for modeling MOFs for these applications. In Chapter 2, the reactivity of CAU-1, an Al-based MOF, is investigated for the dehydration of methanol to dimethylether. Density functional theory (DFT) studies in conjuction with experimental reactivity measurements are used to elucidate the reaction mechanism occurring on active sites constituted by the nodes and linkers of the MOF. In Chapter 3 and Chapter 4, the catalytic activity of several single-atom transition metals deposited on the nodes of UiO-66 (a Zr-based MOF) through post-synthetic modifications (Mn+-UiO-66), is investigated for the dimerization of 1-butene to linear octenes. The Cossee-Arlmann reaction mechanism is found to be the energetically most favorable reaction mechanism occurring on the undercoordinated metal sites of Mn+-UiO-66 catalysts investigated with Ni-UiO-66 outperforming the other metalated catalysts. Chapter 5 and Chapter 6 demonstrate the use of Al-rod-based MOFs for adsorption-assisted atmospheric water harvesting (AWH). In Chapter 5, insights into the primary adsorption sites and water uptake mechanism in MOF-303 obtained from periodic DFT optimization and ab initio molecular dynamics (MD) simulations in concert with single crystal X-ray diffraction measurements are used to design a linker-variate analogue of MOF-303, MOF-333, with increased water throughput. Furthermore, the water adsorption behavior predicted in these MOFs using force-field-based Gibbs ensemble Monte Carlo (GEMC) simulations are shown to achieve good agreement with experimental data after a careful choice of the rigid framework structures and force field parameters used for the MOF. In Chapter 6, a novel linker extension strategy in MOFs is used to enhance the water harvesting characteristics of MOF-303. Remarkably, the new MOF, MOF-LA2-1, shows a 50% increase in the water uptake capacity compared to MOF-303. Finally, in Chapter 7, the effect of the structural flexibility of IRMOFs on the adsorption and self-diffusion behavior of DMF is investigated using GEMC and MD simulations in the constant-stress ensemble using flexible force fields for the MOF.
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    First principles simulations of hydrocarbon conversion processes in functionalized zeolitic materials
    (2013-05) Mazar, Mark Nickolaus
    With increasing demand for chemicals and fuels, and finite traditional crude oil resources, there is a growing need to invent, establish, or optimize chemical processes that convert gasifiable carbon-based feedstocks (e.g., coal, natural gas, oil sands, or biomass) into the needed final products. Catalysis is central to almost every industrial chemical process, including alkane metathesis (AM) and the methanol-to-hydrocarbons (MTH) process, which represent final steps in a sequence of hydrocarbon conversion reactions. An in depth understanding of AM and MTH is essential to the selective production of the desired end products. In this dissertation, ab initio density functional theory simulations provide unique mechanistic and thermodynamic insight of specific elementary steps involved in AM and MTH as performed on zeolite supports. Zeolites have been employed throughout the petroleum industry because of their ability to perform acid-catalyzed reactions (e.g., cracking or MTH). The crystalline structure of zeolites imparts regular microporous networks and, in turn, the selective passage of molecules based on shape and functionality. Many different elements can be grafted onto or substituted into zeolites, resulting in a broad range of catalytic behavior. However, due to the variety of competing and secondary reactions that occur at experimental conditions, it is often difficult to extract quantitative information regarding individual elementary steps. ab initio calculations can be particularly useful for this purpose. Alkane metathesis (i.e., the molecular redistribution or chain length averaging of alkanes) is typically performed by transition metal hydrides on amorphous alumina or silica supports. In Chapter 3, the feasibility of AM in zeolites is assessed by using a grafted Ta-hydride complex to explore the full catalytic cycle in the self-metathesis of ethane. The decomposition of a Ta-metallacyclobutane reaction intermediate that forms during olefin metathesis is responsible for the largest activation energy of the catalytic cycle. This assessment is similar to the findings of alkane metathesis studies on alumina/silica supports and indicates that the entire AM cycle can be performed in zeolites by isolated single-atom transition metal hydrides. Performed over acid form zeolites, MTH is used in the conversion of methanol into a broad range of hydrocarbons, including alkenes, alkanes, and aromatics. For reasons that are not yet rigorously quantified, product selectivities vary dramatically based on the choice of catalyst and reaction conditions. The methylation of species containing double bonds (i.e., co-catalysts) is central to the overall process. Distinct structure-function relationships were found with respect to the elementary steps in the methylation and β-scission of olefins. In Chapter 4, the role of zeolite topology in the step-wise methylation of ethene by surface methoxides is investigated. Elementary steps are studied across multiple frameworks (i.e., BEA, CHA, FER, MFI, and MOR) constituting a wide variety of confinement environments. The reaction of surface methoxides with ethene is found to require a transition state containing a primary carbocation. The barrier height is found to decrease nearly monotonically with respect to the degree of dispersion interactions stabilizing the primary carbocationic species in the transition state. In addition, quantification of the ``local'' dispersion energy indicates that confinement effects can not be simply correlated to pore size. The β-scission of olefins plays an important role in the product selectivities of many important chemical processes, including MTH. In Chapter 5, β-scission modes involving C6 and C8 isomers are investigated at a single, isolated Bronsted acid site within H-ZSM-5. We find that the relative enthalpic barriers of β-scission elementary steps can be rationalized by the substitution order of the two different carbocationic carbon atoms that are present in the reactant (C+) and transition states (βC). In fact, the increase in charge required by the βC atom to go from the physi/chemi-sorbed reactant state to the β-scission transition state (+0.23e-0.33e) is found to correlate almost linearly with the intrinsic activation energy (89-233 kJ mol-1). The charge of the βC atom depends, to a large extent, on the substitution order of both the C+ and βC atoms and, therefore, each $beta$-scission mode is a sub-category onto itself. Isomerization reactions, which are fast with respect to β-scission, enable reactant hydrocarbons to explore and find low barrier β-scission pathways. Selectivities predicted on the basis of the relative barrier heights of β-scission modes accessible to C6 and C8 species indicate general agreement with experimental observations.
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    Mechanistic Insights into Controlling the Molecular Transformations of Oxygenates
    (2019-07) Chemburkar, Ashwin
    The detrimental environmental impact of excessive use of petroleum and fossil-fuel has motivated efforts to manufacture chemicals and fuels from biomass, a renewable feedstock. In addition, a large emphasis has been placed on developing chemistries that are not only atom-efficient, but also involve one-pot synthesis, green solvents, and easy separations, thereby, driving next generation technologies towards sustainability and green manufacturing. To that effect, this dissertation elucidates reaction mechanisms of such new chemistries, identifies catalytic features that enable fast, yet selective chemical transformations, as well as explores the complex role of greener solvents in mediating reactions, in a series of collaborative studies involving density functional theory (DFT) simulations and experiments. Biomass-derived precursors are shown to possess chemical and structural flexibility to generate a novel slate of structurally diverse intermediates that can be used as scaffolds in the synthesis of current chemical feedstocks as well as new molecules with advanced functionality for the design of new chemical and materials intermediates. Chemical diversification is demonstrated by using heterogeneous catalysts together with solvents to achieve high reactivity and selectivity. The results presented in this dissertation aim to guide the design of more active, selective, stable and cheaper catalytic materials, as well as synthesis of new molecules and establish new strategies to control the specific products that are formed. A significant part of this dissertation focusses on chemically diversifying coumalic acid (CMA)- a bio-privileged molecule, using a selective, one-pot Diels-Alder-decarboxylation-dehydrogenation domino sequence to generate a library of aromatic compounds. Not only petroleum-derived aromatics, but also a host of novel structures can be synthesized using this approach. These new aromatics have functionalities and structures inaccessible via petroleum and have applications as pharmaceuticals, insecticides, and antimicrobials. Here, we combine in-situ NMR, DFT, and solid-state NMR to guide one-pot synthesis of aromatics from biomass, thus, providing a sustainable means to access these compounds. Our efforts lie at engineering the reactivity by identifying the rate-limiting step in the domino sequence and then subsequently catalyzing it using a heterogeneous catalyst. Selectivity is fine-tuned by esterification of CMA as well as by screening different solvents. Finally, during synthesis of more complex aromatics, structure-reactivity relationships are developed to guide stereo-selective synthesis. This dissertation also discusses aldol condensation and esterification, reactions that are can be utilized to make longer molecules from bio-derived oxygenates to synthesize fuel-grade precursors and additives respectively. Previous studies have shown that these reactions can be catalyzed when pre-equilibrated mixture of alcohol-aldehyde-H2 is fed over metallic Cu catalysts. Here, we reveal the nature of active sites on metallic Cu that enable C-C and C-O bond formation reactions that traditionally been thought to require explicit base or acid assistance. DFT simulations, together with kinetic analyses show the prevalence of Lewis-basic alkoxide sites as well as Lewis-acidic aldehyde sites that co-operatively carry out proton and hydride transfer reactions that enable C-C and C-O bond formation reactions. The studies not only demonstrate the use of greener, earth-abundant transition metals such as Cu in biomass processing, but also opens opportunities to utilize active sites unique to Cu, and possibly other coinage metals, in reduction reactions that selectively require hydrides (for example, C-H formation). Reactions that allow for selective C-O bond hydrogenolysis are central to biomass upgradation. This dissertation also reports hydrogenolysis of fatty acid over bimetallic rhenium oxide catalysts promoted by Pd. Such bimetallic catalysts allow for near-atmospheric pressure operations, contrary to commercial processes. The role of the constituent metals is elucidated here through DFT and multiple experimental probes including steady state and transient rate measurements, extensive characterization, and kinetic isotope effects. The results demonstrate a synergistic role of Pd and Re; while Pd directly provides hydrides (electrons) for C-H formation, Re catalyzes dehydration reactions by providing protons via Brønsted acid sites (ReOH). These results can be extended to over oxophilic metals to screen more selective, cheap and durable materials in the processing of fatty acids and other oxygenates. The last part of this dissertation highlights the role of protic solvents in mediating reduction reactions of oxygenates. Reduction reactions are not only at the heart of biomass upgradation, but also are involved in a host of important applications such as organic and pharmaceutical synthesis. The use of greener solvents such as water, methanol or their mixtures instead of organic solvents is of critical importance from an environmental viewpoint. Here we combine DFT, kinetic isotope effects, flow reactor measurements, and in operando X-ray spectroscopy to show that protic solvents directly participate in hydrogenation reactions over transition metal surfaces. Protic solvents are shown to activate characteristically different routes that can enable transfer of hydrogens as protons and electrons in proton coupled electron transfer (PCET) reactions that favor the formation of O-H bonds on oxygenates. In such reactions, solvent molecules react with co-adsorbed hydrogen atoms on the metal catalyst as well as enable proton-shuttling, while the metal catalyst is found to conduct electrons. In addition, we present evidence for the prevalence of heterogeneous mediator-based chemistry that governs reduction reactions when the protic solvent can decompose on the host catalyst. The structure and reactivity of these heterogeneous surface mediators are found to resemble well-known solution-phase mediators such as TEMPOH (in organic synthesis) and NADPH (in biology). These results demonstrate the ability to impact selectivity during hydrogenation of oxygenates and perhaps other unsaturated compounds by tuning the metal and the protic solvent.
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    Static and Dynamic Charge and Energy Transport in Organic Electronics
    (2018-06) Ghosh, Soumen
    Organic electronic materials are a new generation of materials that have the potential to move our society to clean and renewable energy sources, but the efficiency of these materials has only recently become competitive with that of their inorganic counterparts. One of the major challenges to increasing the efficiency of organic materials is our present inability to understand in detail the mechanisms of energy and charge transport within them. Computational modeling can play a very important role in understanding such mechanisms and discovering new materials. However, accurate modeling of charge and energy transfer processes remains challenging for many electronic structure methods. Often it is not enough to just model static properties of these systems, and charge and energy transfer dynamics need to be studied as well. Considering the large size of these systems, such modeling is still not practical with ab-initio electronic structure methods and current computational power. Herein, I report studies of the charge-transport properties of both small organic electronics and molecular wires. We have tried to understand structure-function relationships in these materials and suggest how chemical modification may affect charge-transport mechanisms. We have also tested multiconfiguration pair-density functional theory, which is a very accurate electronic structure method for recovering both static and dynamic electron correlation, for ground- and excited-state charge transfer. Finally, we have developed a new method for modeling electronic dynamics in chemical systems by combining semiempirical Hartree-Fock theory with real-time dynamics. We have used this method to calculate UV/Vis spectra of medium and large organic systems. We have developed a new approach to characterize different peaks in real-time spectra, and we have also developed a new approach for modeling exciton dynamics using real-time approaches.
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    Theoretical Investigations Into The Effects Of Reaction Environment On Acid-Catalyzed Dehydration Of Biomass-Derived Oxygenates
    (2020-04) Sanpitakseree, Chotitath
    The growing concerns over greenhouse gas emissions and the limited fossil fuel resources has driven the development of alternative carbon-neutral energy sources. Lignocellulosic biomass is considered an attractive option as they are renewable and are available in abundance at low cost. However, these feedstocks possess relatively low carbon/oxygen ratio and thus making the oxygen removal necessary to increase the energy density. The chemical treatment of biomass in aqueous phase typically involves initial decomposition of sugar polymers into individual sugar monomers followed by a series of acid-catalyzed dehydration steps. The intermediate products that from include 5-hydroxymethylfurfural (HMF), 2-furfuraldehyde (furfural), levulinic acid, and formic acid which can be further upgraded to liquid fuel. These processes are relatively cost-efficient as they can be carried out in aqueous phase at low temperature. Despite its economic potential, very little is known about the effects of solvent on the dehydration kinetics. In this work, we utilized ab initio quantum chemical methods to examine the underlying principles that control the reactivity and selectivity of biomass conversion reactions, especially Brønsted acid-catalyzed dehydration of biomass-derived oxygenates in organic solvent/water mixtures. Recent experimental studies have shown that the rate of acid-catalyzed dehydration of sugars increases by up to two orders of magnitude when the reaction is carried out in polar aprotic solvent/water mixtures such as DMSO/water mixtures and acetonitrile/water mixtures in comparison to water solvent. Furthermore, the addition of metal halides such as chloride anion into the reaction media has been shown to significantly improve the reactivity and selectivity towards the desired HMF product. In order to develop better understandings of these observations, we used ab initio molecular dynamics (AIMD) together with classical molecular dynamics simulations to explore the effects of reaction environment in liquid phase on the dehydration reactions of biomass-derived oxygenates. Our calculations suggest that the rate of Brønsted acid catalyzed dehydration in polar aprotic solvent/water mixtures is governed by the relative stability between reactants in comparison to transition state in the rate determining step. This difference in the stability is in turn controlled by the different extent of solvation for these reactive species in different solvents which explains the reactivity trend observed experimentally. The molecular dynamics trajectories for organic solvent/water systems reveal that the solvent-solute as well as solvent-solvent interactions result in the reorganization of solvent molecules around the solvated species, leading to the formation of hydrophilic domain on the reactive polyol hydroxyl groups in which the acidic proton and other hydrophilic species reside. The localization of these reactive species in close vicinity facilitates the dehydration reaction, stabilizes the charged transition state, and lowers the activation free energy of dehydration. The investigation is also extended to different reaction paths leading to the formation of humins side products to elucidate the effects of solvent on the selectivity of dehydration reactions toward HMF. In the second part of this thesis, we focus on the use of heterogeneous catalyst for dehydration reactions. The use of heterogeneous catalyst is favored over homogeneous catalyst due to the ease of catalyst recovery. However, the ab initio computational investigation of liquid-phase reactions in microporous catalyst is challenging as the result can be sensitive to the number of solvent molecules and reactive species available in the zeolite pore. In this work, we thus focused on developing an atomistic model to predict the adsorption properties of water molecules in industrially common Faujasite and Mordenite zeolites. The model features a new ‘cluster swap’ Monte Carlo move that allows simultaneous simulation of cation siting and aluminum distribution within the zeolite framework. The simulation results were found to satisfactorily reproduce the cationic siting in Faujasite as well as aluminum occupancy of the framework T-sites in Mordenite over a broad range of Si/Al ratios. The obtained parameters can be further improved to include the adsorption affinity for each solvent and solvated species.
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    Toward Simulation of Complex Reactive Systems: Development and Application of Enhanced Sampling Methods
    (2018-03) Fetisov, Evgenii
    redictive modeling of fluid phase and sorption equilibria for reacting systems presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions representing the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. This thesis showcases some of my efforts in developing and applying advanced simulation methods to a variety of important systems. Chapters 2 and 3 describe how a novel Monte Carlo method (reactive first principles Monte Carlo or RxFPMC) can be used to overcome some limitations of existing methods for simulation of reactive systems. Chapter 4 shows how advanced sampling techniques in combination with sophisticated interatomic potentials can be used to elucidate nucleation pathways. Chapters 5 and 6 manifest how first principles simulations can be leveraged to understand liquid structure of novel complex solvents as well as reactive processes in such solvents. Finally, the last chapter discusses the use of smart sampling algorithms to study chemisorption of mixed ligands on nanoparticles.