Browsing by Subject "DFT"

Now showing 1 - 10 of 10
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    Computational Studies of the Chemical Properties of Complex Metalloenzyme Systems and Transition Metal Catalysis using Electronic Structure Methods
    (2021-06) McGreal, Meghan
    Computational chemistry is a useful tool for studying the aspects of chemistry that cannot be wholly studied in a laboratory setting, such as mechanisms, electronic structure, reaction barriers, and other various chemical and physical properties. In this dissertation, computational chemistry methods, specifically Density Functional Theory (DFT), is utilized to study complex catalytic systems. These systems include transition-metal based metalloenzymes and molecular catalysts that were studied utilizing electronic structure methods. Chapters 2, 3, and 4 focus on elucidation of catalysis, structural features, function, and other various properties of the [NiFe]-hydrogenase enzyme system. Specifically, the mechanism of catalysis was studied, appropriate models for the study of this bimetallic enzyme active site were determined (Chapter 2), the effect of mutation of highly conserved residues were analyzed (Chapter 3), and the influence biomimetic-inspired changes to the active site were assessed (Chapter 4). Chapter 5 focuses on elucidating the structure and function of the non-heme Fe chlorination enzyme, SyrB2, in collaboration with the Bhagi-Damodaran Group. Chapter 6 is a study of titanium-catalyzed nitrene transfer of diazenes to isocyanides for carbodiimide synthesis in collaboration with the Tonks Group. Finally, Chapter 7 is computational determination of the chemical hardness of various anions, as well as the effect of stability of anion impact, selectivity and affinity for Gd-containing complexes in collaboration with the Pierre Group.
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    An investigation into the electronic structure of light-harvesting macrocycles using UV-Vis and MCD spectroscopy as well as DFT and TDDFT computational methods
    (2016-05) Rhoda, Hannah
    An electronic structure investigation was done on three separate types of light-harvesting macrocycles using UV-visible (UV-vis) and magnetic circular dichroism (MCD) spectroscopy as well as density functional theory (DFT) and time-dependent DFT (TDDFT) computational methods. The choice of the macrocycle compounds was such that a large range of non-traditional porphyrin analogues was covered including subpthalocyanines, corroles, and reduced porphyrins. It has been found that small changes in structure of these result in large changes in the optical and redox properties of these compounds.
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    Leveraging Linear Polymer Affinity Agents and Surface-enhanced Raman Scattering for the Detection of Food Contaminants
    (2022-04) Rodriguez, Rebeca
    This thesis focuses on leveraging linear polymer affinity agents and surface- enhanced Raman scattering (SERS) for the detection of food contaminants. First, I discuss the different sensing techniques and methodology that exist for food contamination detection: UV-visible spectroscopy, immuno- and lateral flow assays, liquid and gas chromatography, field-effect transistors, and SERS. I address the need for relatively facile and inexpensive multiplex detection and how linear polymer affinity agents can address these needs. The first experimental work focuses on optimization of SERS substrates for biosensing applications and initial work with anchored polymer chain lengths for the detection of the food allergen and protein soybean agglutinin with a glycopolymer. I then focus on optimization of linear polymer affinity agents for the detection of mycotoxins, which are small molecule food toxins that are naturally produced by fungi. I determined that attachment order, attachment chemistry, and polymer chain length all play a role in small molecule sensing. These optimization studies led me to be able to do multiplex detection of two small molecule toxins with linear polymer affinity agents and formulate conclusions on how polymers and small molecules bind through hydrogen bonding. I did this by combining SERS experimental studies and computational modeling of these small molecules to label what vibrational modes are being observed in the multiplexed spectra. In an effort to use linear polymer affinity agents for another class of food contaminants, bacteria, we work to optimize and use a linear glycopolymer for the detection of Listeria monocytogenes. Although the previous work with small molecules concluded that small to mid-length polymers performed best for capture and detection, this work has shown that longer polymer chain lengths work best to promote binding between polymer and Listeria. This gives insight on how to move forward with linear polymer affinity-enabled detection of different classes of food contaminants and pathogens. Overall, this work demonstrates optimization of SERS sensing to achieve limits of detection comparable to current detection methods with a simpler and more flexible signal transduction mechanism, providing an opportunity for future applications to multiplex at low-cost.
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    Modeling Homo- and Heterogeneous Catalysis with Applications Ranging from Hydrocarbon Activation to the Synthesis of Sustainable Polymers
    (2020-08) Mandal, Mukunda
    The diverse chemical properties of compounds containing metal atoms are inherently highly tunable. In terms of size, they may be small molecular complexes consisting of only 1 or 2 metal atoms or, at the other extreme of scale, they may be crystalline solids with clusters of metal ions periodically dispersed in the structure of a metal–organic framework (MOF). In both cases, relevant chemistries can be tailored to fit specific needs, especially with respect to catalytic reactivity. For a molecular catalyst, the combination of metal atom and its ancillary ligand can be chosen carefully to optimize selectivity and activity, while in three-dimensional MOFs, the metal clusters (called nodes) and connecting organic molecules (called linkers) can be ‘mixed and matched’ to best suit a particular application. Because of the inherent complexity of these systems, experimental characterization of structure/activity relations can often be challenging. Starting from a set of reactants, obtaining a mechanistic picture of the steps leading to the product formation is also demanding since isolation of an intermediate does not necessarily guarantee involvement of the species in the ‘productive’ pathway of the mechanism. Theory and computation can be immensely helpful in these instances to gain molecular-level understanding of the reaction mechanism(s). One can explore multiple pathways that yield the product and then evaluate the feasibility of each pathway by comparing computed energetics. Mechanistic knowledge can then be exploited to establish a structure/property relation, thereby fostering the design of subsequent generations of the catalytic species, ideally having improved performance, and helping to further refine the overall model. This dissertation demonstrates the use of computational methodologies, primarily quantum mechanical density functional theory, to explore the electronic structures of various metal-organic systems and the roles they play in carrying out targeted catalytic processes. In particular, computational modeling efforts are presented that illuminate (i) mechanisms of sustainable polymer production and principles for designing new catalysts (Chapter 2), (ii) site-selective C–H bond functionalization having relevance in drug discovery and chemical biology (Chapter 3) (iii) C–H activation reactions in light hydrocarbons using bio-mimetic copper-complexes having the potential to address challenges in fuel liquefaction (Chapter 4), and (iv) MOF-based single-site heterogeneous catalysts capable of oxidation reactions having industrial relevance (Chapter 5).
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    Raman spectroscopy data and phonon calculations for ScV6Sn6 in P6/mmm and R-3m structures, 2023
    (2023-06-27) Ritz, Ethan T; Birol, Turan; Gu, Yanhong; Musfeldt, Janice L; eritz@umn.edu; Ritz, Ethan T; Birol Research Group, University of Minnesota; Musfeldt Group, University of Tennessee Knoxville
    We use density functional theory (DFT) to calculate the phonon frequencies and the distortions associated with them in the compound ScV6Sn6 in the P6/mmm and R-3m space groups, then compute the overlap between the Raman-active phonons in each structure. This data includes scripts to generate the DFT submission files, the results of those simulations, as well as MATLAB scripts to plot the results. We also include experimental Raman spectroscopy data at temperatures from 5.5 K to 300 K.
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    Strain effect on the ground-state crystal structure of Sr2SnO4 Ruddlesden-Popper oxides
    (2022-09-08) Yun, Hwanhui; Gautreau, Dominique; Mkhoyan, K. Andre; Birol, Turan; yunxx133@umn.edu; Yun, Hwanhui; Theoretical Materials Physics Group
    Simulation data for a manuscript 'Strain effect on the ground-state structure of Sr2SnO4 Ruddlesden-Popper oxides'. Key data including structures and input files for structural relaxation and phonon calculation of various phases in Sr2SnO4 are included.
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    Synthesis and characterization of copper zinc tin sulfide nanoparticles and thin films.
    (2012-07) Khare, Ankur
    Copper zinc tin sulfide (Cu2ZnSnS4, or CZTS) is emerging as an alternative material to the present thin film solar cell technologies such as Cu(In,Ga)Se2 and CdTe. All the elements in CZTS are abundant, environmentally benign, and inexpensive. In addition, CZTS has a band gap of ~1.5 eV, the ideal value for converting the maximum amount of energy from the solar spectrum into electricity. CZTS has a high absorption coefficient (>104 cm-1 in the visible region of the electromagnetic spectrum) and only a few micron thick layer of CZTS can absorb all the photons with energies above its band gap. CZT(S,Se) solar cells have already reached power conversion efficiencies >10%. One of the ways to improve upon the CZTS power conversion efficiency is by using CZTS quantum dots as the photoactive material, which can potentially achieve efficiencies greater than the present thin film technologies at a fraction of the cost. However, two requirements for quantum-dot solar cells have yet to be demonstrated. First, no report has shown quantum confinement in CZTS nanocrystals. Second, the syntheses to date have not provided a range of nanocrystal sizes, which is necessary not only for fundamental studies but also for multijunction photovoltaic architectures. We resolved these two issues by demonstrating a simple synthesis of CZTS, Cu2SnS3, and alloyed (Cu2SnS3)x(ZnS)y nanocrystals with diameters ranging from 2 to 7 nm from diethyldithiocarbamate complexes. As-synthesized nanocrystals were characterized using high resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, and energy dispersive spectroscopy to confirm their phase purity. Nanocrystals of diameter less than 5 nm were found to exhibit a shift in their optical absorption spectra towards higher energy consistent with quantum confinement and previous theoretical predictions. Thin films from CZTS nanocrystals deposited on Mo-coated quartz substrates using drop casting were found to be continuous but highly porous. Annealing CZTS nanocrystal films at temperatures as low as 400°C led to an intense grain growth; however, thin films from CZTS nanocrystals cracked on annealing due to their high porosity. Although quantum confinement in CZTS is only accessible in nanocrystals of diameters less than 5 nm, the high volume of the ligands as compared to the volume of the nanocrystals makes it a challenge to deposit continuous compacted thin films from small nanocrystals. Films deposited from thermal decomposition of a stoichiometric mix of metal dithiocarbamate complexes were found to be predominantly CZTS. These films from complexes were found to be continuous but microporous. The diameter of the spheres making up the microporous structure could be changed by changing the anneal temperature. The structural composition of the final film could be altered by changing the heating rate of the complexes. CZTS exists in three different crystal structures: kesterite, stannite, and pre-mixed Cu-Au (PMCA) structures. Due to the similarity in the crystal structures, it is extremely difficult to distinguish them based on X-ray diffraction. We computed the phonon dispersion curves for the three structures using ab-initio calculations, and found characteristic discontinuities at the Γ-point which can potentially be used to distinguish the three. In addition, the Γ-point phonon frequencies, which correspond to the Raman peak positions, for the three structures were found to be shifted from each other by a few wavenumbers. By deconvoluting the experimental Raman spectra for both CZTS and Cu2ZnSnSe4 (CZTSe) using Gaussian peaks, we observed that the most intense Raman scattering peak in both CZTS and CZTSe is a sum of two different peaks which correspond to scattering from their respective kesterite and stannite phases. The electronic, structural, and vibrational properties of a series of CZTS-CZTSe alloys (CZTSSe) were studied using ab-initio calculations. The S-to-Se ratio and the spatial distribution of the anions in the unit cell were found to determine the energy splitting between the electronic states at the top of the valence band and the hole mobility in CZTSSe alloys and solar cells. X-ray diffraction patterns and phonon distribution curves were found to be sensitive to the local anion ordering. The predicted Raman scattering frequencies and their variation with x agree with experimentally determined values and trends.
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    Synthesis and characterization of ferrocenyl-containing porphyrins and tetraazaporphyrins
    (2013-08) Purchel, Anatolii
    Nano-sized molecular-based platforms provide a promising approach to materials which can be used in optoelectronics, switchable redox-driven devices, and dye-sensitized solar cells (DSSC), as well as other technological applications. Poly(ferrocene)-containing compounds with accessible mixed-valence properties at low potentials and broad absorption spectra in the UV-vis-NIR region represent an important class of organometallics which have potential for use in light-harvesting, photocatalysis, and molecular electronics. Target compounds were prepared using previously developed procedures, and characterized using UV-vis-NIR, MCD, and NMR methods. A variety of solvents and electrolytes were used to investigate the redox properties of these poly(ferrocene)-containing porphyrins and tetraazaporphyrins analogues in order to determine their influence on long-range metal-metal coupling. The spectroscopic signatures of the redox-active species were investigated using spectroelectrochemical methods which were well correlated with Density Functional Theory calculations. The mixed valence properties and electronic communication observed in obtained compounds relate to those desired in molecular electronics applications and for use in DSSC's.
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    Understanding the role of local condensed phase environments in pyrolytic and catalytic biomass conversion
    (2021-05) Maliekkal, Vineet
    Biomass conversion generally involves two major sets of chemical transformations – (1) thermal breakdown of macromolecules in the feedstock, such as cellulose, to smaller sugars and oxygenates via fast pyrolysis followed by (2) catalytic upgrading to the desired fuels or precursor chemicals. These reactions of biomass conversion usually occur in the condensed phase – either in the melt phase for pyrolytic reactions or in the solvent phase for catalytic upgrading reactions. The work in this thesis sheds light on the molecular complexity of such condensed phase environments. Explicit molecular modeling of these condensed phase environments coupled with first-principles simulation techniques such as density functional theory (DFT) and ab initio molecular dynamics (AIMD) are used to elucidate the influence of such environments on the kinetics of biomass conversion reactions. Examples from cellulose pyrolysis and hydrogenation chemistry are studied to demonstrate the critical importance of considering the role of condensed phase environments in biomass conversion.Using DFT calculations, constrained AIMD and experimental kinetics from the Pulsed Heated Analysis of Solid Reactions (PHASR) set-up, it is shown that vicinal hydroxyl groups which are present in the cellulose matrix in abundance can directly participate in the activation of cellulose by promoting facile proton transfer as well as stabilizing transition states through hydrogen bonding. The kinetic influence of calcium ions, naturally present in such feedstocks, is also examined in this thesis. It is shown that calcium interacts with cellulosic melt environment such that the native hydrogen bonding is disrupted. Such disruption of the hydrogen bonding network coupled with Lewis acid stabilization of the transition states leads to dual catalytic cycles for cellulose activation and second order rate dependence on calcium. Explicit modeling of the cellulosic environment is critical towards capturing such kinetic behavior. Furthermore, the influence of hydroxyl groups, calcium ions and more generally the cellulosic condensed phase environment, is examined more broadly and extended to other ring opening and fragmentation pathways that lead to glycolaldehyde, a side product of pyrolysis. The work from this part of the thesis helps establish the ubiquitous involvement of the local condensed phase environment in mediating biomass pyrolysis reactions. Finally, aqueous phase hydrogenation of C=C bonds in phenol over Pt particles inside zeolites is studied as a model reaction to demonstrate the importance of solvent environment in catalytic upgrading. Through explicit modeling of local water clusters around the reaction centers, it is shown that increasing the acidity of the zeolite supports can alter the local acidity of the water clusters. This in turn is shown to not just open up proton coupled electron transfer (PCET) pathways but also improve the efficacy of such mechanisms for hydrogenation. Thus, this study helps demonstrate that one can alter the solvent environment to enhance reactions of biomass conversion, especially those that involve proton transfer. More generally, the collective body of work in this thesis could act as a framework for future studies that seek to understand the role of condensed phase environments in biomass conversion as well as to develop strategies that use such environments for improved reactivity and selective chemical transformations.
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    UV-Vis and MCD Spectroscopy and TDDFT investigations into N-Confused porphyrins and properties of mono-functionalized tetraferrocenyl porphyrins in solution and on a gold surface
    (2014-08) Erickson, Nathan Robert
    N-confused porphyrin (NCP) and its externally methylated variant (MeNCP) were investigated using UV-visible and magnetic circular dichrosim (MCD) spectroscopies. In addition to evaluating the spectroscopy of the neutral compounds, the acid/base chemistry of these macrocycles was examined by the same methods. NCP exhibits two tautomeric states depending on the polarity of the solvent, and their protonation/deprotonation chemistries also differ depending on solvent polarity. DFT and TDDFT calculations were employed to evaluate the observed spectroscopic changes. Using both experimental and calculated results, we were able to determine the sites of protonation/deprotonation for both tautomeric forms of NCP. Inspection of the MCD Faraday B terms for all of the macrocycles presented in this report showed that the ΔHOMO > ΔLUMO condition is maintained in all cases and these observations were in good agreement with the DFT calculations. Various methylated N-confused tetraphenylporphyrins (MeNCTPP) were investigated using UV-Vis and magnetic circular dicrhoism (MCD) spectroscopy in polar and apolar solvents as well as the protonation and deprotonation of the compounds. The MeNCTPPs were also investigated using time-dependent density functional theory (TDDFT) methods in the gas phase. Experimentally, the MCD spectra showed that all the molecules investigated had transitions with the ΔHOMO > ΔLUMO. TDDFT results confirmed these energy gaps. TDDFT calculations also showed that nearly all low energy transitions were from the HOMO to the LUMO and LUMO+1, except in the case of 2c, 5a, and 5c. Otherwise, results show that the addition of a methyl group to the N-confused tautomer of tetraphenylporphyrin effectively regulates the proton tautomerization of the N-confused tautomer. MeNCTPPs are unaffected by the polarizability of the solvent. Two unsymmetric meso-tetraferrocenyl-containing porphyrins of general formula H2Fc3Fc(COR)P [Fc = ferrocenyl, R = -CH3 or -(CH2)5Br, P = porphyrin(2-)] have been prepared and characterized by variety of spectroscopic methods, while their redox properties were investigated using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) approaches. Spectroscopic signature of the mixed-valence [H2Fc3Fc(COR)P ]n+ (n = 1, 3) were investigated using spectroelectrochemical as well as chemical oxidation methods and corroborated with DFT and TDDFT calculations. Inter-valence charge-transfer (IVCT) transitions in [H2Fc3Fc(COR)P ]+ were analyzed using band deconvolution analysis in the borders of Hush model. The resulting data from the mixed-valence [H2Fc3Fc(COR)P ]+ derivatives matched very closely to the previously reported MTFcP and metal-free poly(ferrocenyl)porphyrins complexes and were assigned as Robin and Day Class II mixed-valence compounds. Following previous results indicating the ability of gold supported TFcP monolayers in photo-catalytic reduction of dioxygen, self-assembled monolayers (SAMs) of a thioacetyl derivative (H2Fc3Fc(CO(CH2)5SCOCH3)P) were also prepared and characterized using UV-vis spectroscopy and CV methods. Photoelectrochemical properties of SAMs in different electrolyte systems were investigated by electrochemical techniques and photocurrent generation experiments, showing that the choice of electrolyte is critical for efficiency of redox-active SAMs.