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Ab Initio and Density Functional Investigation of the Conformer Manifold of Melatonin and a Proposal for a Simple Dft-based Diagnostic for Nondynamical Correlation

Description: In this work we address two problems in computational chemistry relevant to biomolecular modeling. In the first project, we consider the conformer space of melatonin as a a representative example of “real-life” flexible biomolecules. Geometries for all 52 unique conformers are optimized using spin-component scaled MP2, and then relative energies are obtained at the CCSD (T) level near the complete basis set limit. These are then used to validate a variety of DFT methods with and without empirical dispersion corrections, as well as some lower-level ab initio methods. Basis set convergence is found to be relatively slow due to internal C-H…O and C-H…N contacts. Absent dispersion corrections, many DFT functionals will transpose the two lowest conformers. Dispersion corrections resolve the problem for most functionals. Double hybrids yield particularly good performance, as does MP2.5. In the second project, we propose a simple DFT-based diagnostic for nondynamical correlation effects. Aλ= (1-TAE [ΧλC]/TAE[XC])/λ where TAE is the total atomization energy, XC the “pure” DFT exchange-correlation functional, and ΧλC the corresponding hybrid with 100λ% HF-type exchange. The diagnostic is a good predictor for sensitivity of energetics to the level of theory, unlike most of the wavefunction-based diagnostics. For GGA functionals, Aλ values approaching unity indicate severe non-dynamical correlation. The diagnostic is only weakly sensitive to the basis set (beyond polarized double zeta) and can be applied to problems beyond practical reach of wavefunction ab-initio methods required for other diagnostics.
Date: August 2013
Creator: Fogueri, Uma

Baeyer-Villiger Oxidation of 1,7- & 1,9-dibromopentacyclo[5.4.0.02,6.03,10.05,9]undecane-8,11-dione

Description: Baeyer-Villiger oxidation of 1,9-dibromopentacyclo[5.4.0.02,6.03,10.05,9]undecane-8,11-dione (1,9-dibromo-PCU-8,11-dione) was performed by using an excess amount of m-chloroperbenzoic acid (3 equivalents) and resulted in the formation of the corresponding monolactone. The reaction would not proceed to the dilactone stage. The structure of the reaction product was established unequivocally via single crystal X-ray diffraction. Baeyer-Villiger oxidation of 1,9-dibromo-PCU-8,11-dione using ceric ammonium nitrate (CAN) was also performed and afforded a mixture of lactones. Only one of these lactones, which also contained an alkene functionality, could be isolated and characterized. 1,7-dibromo-PCU-8,11-dione was also reacted with CAN, yielding the mono-lactone, which has also been characterized.
Date: May 2004
Creator: Akinola, Adeniyi O.

Design, Synthesis and Screening of Homoleptic and Heteroleptic Platinum(ii) Pyridylazolate Complexes for N-type Semiconducting and Light-emitting Devices

Description: A series of heteroleptic and homoleptic platinum(II) complexes has been synthesized and characterized towards their use in thin film devices such as organic light-emitting diodes (OLEDs) and organic thin film transistors (OTFTs). Pyridylpyrazolate- and pyridyltetrazolate-containing ligands were selected due to their structural rigidity and ease of functionalization. Single-crystal x-ray diffraction studies of two selected heteroleptic complexes show strong aggregation with preferential stacking into vertical columns with a varying degree of overlap of the neighboring square planar molecular units. It is shown that the close proximity of the molecules to one another in the stack increases semiconducting character, phosphorescence quantum yields, and shorter radiative lifetimes. The potential for these materials towards incorporation into high-efficiency doping free white OLEDs (DFW-OLEDs) for solid-state lighting and display applications has been realized and will be expanded upon by present and future embodiments of materials in this thesis.
Date: August 2012
Creator: Oswald, Iain William Herbert

Diphosphine Ligand Substitution in H4Ru4(CO)12: X-ray Diffraction Structures and Reactivity Studies of the Diphosphine Substituted Cluster Products

Description: The tetraruthenium cluster H4Ru4(CO)12 has been studied for its reactivity with the unsaturated diphosphine ligands (Z)-Ph2PCH=CHPPh2, 4,5-bis (diphenylphosphino)-4-cyclopenten-1,3-dione, bis(diphenyphosphino)benzene and 1,8- bis(diphenyl phosphino)naphthalene under thermal, near-UV photolysis, and Me3NO-assisted activation. All three cluster activation methods promote loss of CO and furnish the anticipated substitution products that possess a chelating diphosphine ligand. Clusters 1, 2, 3 and 4 have been characterized in solution by IR and NMR spectroscopies, and these data are discussed with respect to the crystallographically determined structures for all new cluster compounds. The 31P NMR spectral data and the solid-state structures confirm the presence of a chelating diphosphine ligand in all four new clusters. Sealed NMR tubes containing clusters 1, 2, 3 and 4 were found to be exceeding stable towards near-UV light and temperatures up to ca. 100°C. The surprisingly robust behavior of the new clusters is contrasted with the related cluster Ru3(CO)10(bpcd) that undergoes fragmentation to the donor-acceptor compound Ru2(CO)6(bpcd) and the phosphido-bridged compound Ru2(CO)6 (µ-PPh2)[µ-C=C(PPh2)C(O)CH2C(O)] under mild conditions. The electrochemical properties have been investigated in the case of clusters 1 and 2 by cyclic voltammetry, and the findings are discussed with respect to the reported electrochemical data on the parent cluster H4Ru4(CO)12.
Date: December 2006
Creator: Kandala, Srikanth

Effects of Web-based Instruction in High School Chemistry.

Description: The intent of this study is to identify correlations that might exist between Web-based instruction and higher assessment scores in secondary education. The study framework was held within the confines of a public high school chemistry classroom. Within this population there were students identified as gifted and talented (GT) as well as those without this designation. These two classifications were examined for statistically higher assessment scores using a two-tailed t-test. Results indicated that females outperformed males on pre- and post- instructional unit tests. All subgroups improved their logical-thinking skills and exhibited positive attitudes towards Web-based instruction. In general, Web-based instruction proved beneficial to improving classroom performance of all GT and non-GT groups as compared to traditional classroom instruction.
Date: May 2003
Creator: Stratton, Eric W.

Electrochemical Deposition of Zinc-Nickel Alloys in Alkaline Solution for Increased Corrosion Resistance.

Description: The optimal conditions for deposition of zinc-nickel alloys onto stainless steel discs in alkaline solutions have been examined. In the past cadmium has been used because it shows good corrosion protection, but other methods are being examined due to the high toxicity and environmental threats posed by its use. Zinc has been found to provide good corrosion resistance, but the corrosion resistance is greatly increased when alloyed with nickel. The concentration of nickel in the deposit has long been a debated issue, but for basic solutions a nickel concentration of 8-15% appears optimal. However, deposition of zinc-nickel alloys from acidic solutions has average nickel concentrations of 12-15%. Alkaline conditions give a more uniform deposition layer, or better metal distribution, thereby a better corrosion resistance. Although TEA (triethanolamine) is most commonly used to complex the metals in solution, in this work I examined TEA along with other complexing agents. Although alkaline solutions have been examined, most research has been done in pH ≥ 12 solutions. However, there has been some work performed in the pH 9.3-9.5 range. This work examines different ligands in a pH 9.3-9.4 range. Direct potential plating and pulse potential plating methods are examined for optimal platings. The deposits were examined and characterized by XRD.
Date: December 2009
Creator: Conrad, Heidi A.

Electrodeposition of adherent copper film on unmodified tungsten.

Description: Adherent Cu films were electrodeposited onto polycrystalline W foils from purged solutions of 0.05 M CuSO4 in H2SO4 supporting electrolyte and 0.025 M CuCO3∙Cu(OH)2 in 0.32 M H3BO3 and corresponding HBF4 supporting electrolyte, both at pH = 1. Films were deposited under constant potential conditions at voltages between -0.6 V and -0.2 V vs Ag/AgCl. All films produced by pulses of 10 s duration were visible to the eye, copper colored, and survived a crude test called "the Scotch tape test", which stick the scotch tape on the sample, then peel off the tape and see if the copper film peels off or not. Characterization by scanning electron microscopy (SEM), energy dispersive X-ray (EDX) and X-ray photon spectroscopy (XPS) confirmed the presence of metallic Cu, with apparent dendritic growth. No sulfur impurity was observable by XPS or EDX. Kinetics measurements indicate that the Cu nucleation process in the sulfuric bath is slower than in the borate bath. In both baths, nucleation kinetics do not correspond to either instantaneous or progressive nucleation. Films deposited from 0.05 M CuSO4/H2SO4 solution at pH > 1 at -0.2 V exhibited poor adhesion and decreased Cu reduction current. In both borate and sulfate baths, small Cu nuclei are observable by SEM upon deposition at higher negative overpotentials, while only large nuclei (~ 1 micron or larger) are observed upon deposition at less negative potentials.
Date: May 2004
Creator: Wang, Chen

Exploring Inorganic Catalysis with Electronic Structure Simulations

Description: Organometallic catalysis has attracted significant interest from both industry and academia due to its wide applications in organic synthetic transformations. Example of such transformations include the reaction of a zinc carbenoid with olefins to form cyclopropanes. The first project is a computational study using both density functional and correlated wavefunction methods of the reaction between ethylene and model zinc carbenoid, nitrenoid and oxenoid complexes (L-Zn-E-X, E = CH2, NH or O, L = X = I or Cl). It was shown that cyclopropanation of ethylene with IZnCH2I and aziridination of ethylene with IZnNHI proceed via a single-step mechanism with an asynchronous transition state. The reaction barrier for the aziridination with IZnNHI is lower than that of cyclopropanation. Changing the leaving group of IZnNHI from I to Cl, changes the mechanism of the aziridination reaction to a two-step pathway. The calculation results from the epoxidation with IZnOI and ClZnOCl oxenoids suggest a two-step mechanism for both oxenoids. Another important example of organometallic catalysis is the formation of alkyl arenes from arenes and olefins using transition metal catalysis (olefin hydroarylation). We studied with DFT methods the mechanism of a novel Rh catalyst (FlDAB)Rh(TFA)(η2–C2H4) [FlDAB = N,N’ -bis(pentafluorophenyl)-2,3-dimethyl-1,4-diaza-1,3-butadiene; TFA = trifluoroacetate] that converts benzene, ethylene and air-recyclable Cu(II) oxidants to styrene. Possible mechanisms are discussed.
Date: May 2016
Creator: Karbalaei Khani, Sarah

Incorporating Electrochemistry and X-ray Diffraction Experiments Into an Undergraduate Instrumental Analysis Course

Description: Experiments were designed for an undergraduate instrumental analysis laboratory course, two in X-ray diffraction and two in electrochemistry. Those techniques were chosen due their underrepresentation in the Journal of Chemical Education. Paint samples (experiment 1) and pennies (experiment 2) were characterized using x-ray diffraction to teach students how to identify different metals and compounds in a sample. in the third experiment, copper from a penny was used to perform stripping analyses at different deposition times. As the deposition time increases, the current of the stripping peak also increases. the area under the stripping peak gives the number of coulombs passed, which allows students to calculate the mass of copper deposited on the electrode surface. the fourth experiment was on the effects of variable scan rates on a chemical system. This type of experiment gives valuable mechanistic information about the chemical system being studied.
Date: May 2012
Creator: Molina, Cathy

Layered Double Hydroxides and the Origins of Life on Earth

Description: A brief introduction to the current state of research in the Origins of Life field is given in Part I of this work. Part II covers original research performed by the author and co-workers. Layered Double Hydroxide (LDH) systems are anion-exchanging clays that have the general formula M(II)xM(III)(OH)(2x+2)Y, where M(II) and M(III) are any divalent and trivalent metals, respectively. Y can be nearly any anion, although modern naturally occuring LDH systems incorporate carbonate (CO32-), chloride (Cl-), or sulfate (SO42-) anions. Intercalated cobalticyanide anion shows a small yet observable deviation from local Oh symmetry causing small differences between its oriented and non-oriented infrared spectra. Nitroprusside is shown to intercalate into 2:1 Mg:Al LDH with decomposition to form intercalated ferrocyanide and nitrosyl groups of an unidentified nature. The [Ru(CN)6]4- anion is shown to intercalate into layered double hydroxides in the same manner as other hexacyano anions, such as ferrocyanide and cobalticyanide, with its three-fold rotational axis perpendicular to the hydroxide sheets. The square-planar tetracyano-nickelate(II), -palladate(II), and platinate(II) anions were intercalated into both 2:1 and 3:1 Mg:Al layered double hydroxides (LDH). The basal spacings in the 2:1 hosts are approximately 11 Å, indicating that the anions are inclined approximately 75 degrees relative to the hydroxide layers, while in the 3:1 hosts the square-planar anions have enough space to lie more nearly parallel to the LDH cation layers, giving basal spacings of approximately 8 Å. It has been found that the LDH Mg2Al(OH)6Cl catalyzes the self-addition of cyanide, to give in a one-pot reaction at low concentrations an increased yield of diaminomaleonitrile and in addition, at higher ($0.1M) concentrations, a purple-pink material that adheres to the LDH. We are investigating whether this reaction also occurs with hydrotalcite itself, what is the minimum effective concentration of cyanide, and what can be learned about the products ...
Date: May 2001
Creator: Brister, Brian

Modeling wild type and mutant glutathione synthetase.

Description: Glutathione syntethase (GS) is an enzyme that belongs to the ATP-grasp superfamily and catalyzes the second step in the biosynthesis of glutathione. GS has been purified and sequenced from a variety of biological sources; still, its exact mechanism is not fully understood. Four highly conserved residues were identified in the binding site of human GS. Additionally, the G-loop residues that close the active site during catalysis were found to be conserved. Since these residues are important for catalysis, their function was studied computationally by site-directed mutagenesis. Starting from the reported crystal structure of human GS, different conformations for the wild type and mutants were obtained using molecular dynamics technique. The key interactions between residues and ligands were detected and found to be essential for enzyme activity.
Date: August 2004
Creator: Dinescu, Adriana

An NMR Study of 2-Ethylbutyllithium/Lithium 2-Ethyl-1-butoxide Mixed Aggregates, Lithium Hydride/Lithium 2-Ethyl-1-butoxide Mixed Aggregates, n-Pentyllithium Aggregates, and n-Pentyllithium/Lithium n-Pentoxide Mixed Aggregates

Description: A 13C and 6Li variable temperature NMR study of 2-ethylbutyllithium/lithium 2-ethyl-1-butoxide mixed aggregates formed from reacting 2-ethyl-1-butanol with 2-ethylbutyllithium in two O/Li ratios of 0.2/1 and 0.8/1. The 0.2/1 sample resulted in two 2-ethylbutyllithium/lithium 2-ethyl-1-butoxide mixed aggregates and seven lithium hydride/lithium 2-ethyl-1-butoxide mixed aggregates. The lithium hydride mixed aggregates were also studied using selective 1H decoupling experiments. The 0.8/1 sample resulted in six 2-ethylbutyllithium/lithium 2-ethyl-1-butoxide mixed aggregates and five lithium hydride/lithium 2-ethyl-1-butoxide mixed aggregates. A low temperature 13C NMR spectroscopy study of n-pentyllithium indicated three aggregates, most likely a hexamer, an octamer, and a nonamer. A low temperature 13C NMR study of an 0.2/1 O/Li ratio sample of n-pentyllithium mixed with 1-pentanol resulted in three n-pentyllithium/lithium n-pentoxide aggregates mixed aggregates along with the three n-pentyllithium aggregates. 13C NMR data for this mixture gave inconclusive results whether or not lithium hydride/lithium alkoxide mixed aggregates were present in the sample.
Date: December 2005
Creator: Sellers, Nicole

An NMR Study of Trimethylsilylmethyllithium Aggregates and Mixed Trimethylsilylmethyllithium/Lithium trimethylsilylmethoxide Aggregates

Description: An NMR spectroscopy study of trimethylsilylmethyllilthium, TMSM-Li, indicates that TMSM-Li exists as two different aggregates in cyclopentane solution. Using previously reported colligative properties of TMSM-Li in different solutions in connection with new 13C and 6Li NMR data collected in this study, aggregation states were assigned as octamer and hexamer. Low temperature 13C and 6Li NMR peak intensities indicated an equilibrium exists between the two aggregates that shifts toward the octamer as the temperature decreases. ΔH was calculated to be 5.23 + 0.15 kcal/mol and ΔS was calculated to be 17.9 + 0.6 eu for the hexamer/octamer equilibrium system. Samples of TMSM-Li were mixed with TMSM-OH in attempts to form mixed alkyllithium/lithium alkoxide aggregates. 13C NMR data for these mixtures gave inconclusive results whether or not these compounds formed, which is different from other primary alkyllithium compounds studied in the past. A study of neopentyllithium, NpLi, indicates only one aggregate in solution with the aggregation state unknown using low temperature 13C NMR spectroscopy.
Date: December 2004
Creator: Medley, Marilyn S.

Passivation effects of surface iodine layer on tantalum for the electroless copper deposition.

Description: The ability to passivate metallic surfaces under non-UHV conditions is not only of fundamental interests, but also of growing practical importance in catalysis and microelectronics. In this work, the passivation effect of a surface iodine layer on air-exposed Ta for the copper electroless deposition was investigated by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Although the passivation effect was seriously weakened by the prolonged air exposure, iodine passivates the Ta substrate under brief air exposure conditions so that enhanced copper wetting and adhesion are observed on I-passivated Ta relative to the untreated surface.
Date: May 2004
Creator: Liu, Jian

Preparation and characterization of praseodymium oxide films and powders.

Description: Nanocrystalline praseodymium oxide films have been successfully generated on stainless steel substrates. The electrochemical deposition was performed in the cathode compartment of a divided electrochemical cell with a regular three-electrode configuration. The green films obtained by electrodeposition were then annealed at high temperatures for 1-3 hours. X-ray diffraction revealed the fluorite structure of Pr6O11 and the crystallite size was calculated. X-ray photoelectron spectroscopy was employed to study the composition of the oxide films and also the oxidation state of Pr. Scanning electron microscopy was utilized to study the surface texture and microstructure of deposits. Fourier transform infrared spectrometery was used to investigate the composition of the films. The effects of different conditions on the green films were also studied such as different pH values of the electrolyte solution, different deposition modes, different supporting electrolytes and different applied current densities. Sintering experiments were conducted to investigate the properties of the green films. Praseodymium oxide powders were also successfully prepared by combining electrochemical methods with sintering processes. The praseodymium oxide powders were characterized by X-ray diffraction and Fourier transform infrared spectroscopy. The crystallite sizes of the powders were evaluated.
Date: May 2004
Creator: Shang, Yajuan

Synthesis and Properties of Novel Cage-Annulated Crown Ethers

Description: Three cage-functionalized polyoxacrown ethers (9, 10 and 12) and four novel cage-functionalized polyoxamonoazacrown ethers (18, 20, 25 and 29) that contain 3,5-disubstituted-4-oxahexacyclo[5.4.0.02,6.03,10.05,9.08,11]dodecane ("oxahexacyclic") moiety have been synthesized and their respective alkali metal picrate extraction profiles along with that of three analogues 13, 14 and 21 have been obtained. The observed avidities and selectivities of the host molecules toward complexation and transport of alkali metal picrates can be related to the size and shape of their respective macrocyclic cavity and the number of donor atoms. The effect of N-alkyl substitution on the complexation properties of azacrown ethers has been studied. The avidity of N-Et azacrown ethers toward complexation with alkali metal cations is generally higher than that of the corresponding non-N-alkylated hosts. However, the presence of an N-Et group appears to have a negligible effect upon their relative selectivities in their regards. The effect of pH on extraction process was studied; it was thereby determined that the alkali metal picrate extraction experiments are best performed at high pH (ca. 11-12).
Date: May 2003
Creator: Huang, Zilin

Synthesis and X-ray Diffraction Structure of 8,9-Dichloropyrrolo[1,2-a]perimidin-10-one

Description: Treatment of dichloromaleic anhydride and 1,8-diaminonaphthalene in either benzene or toluene under refluxing conditions gives low yields of the new heterocyclic compound 8,9-dichloropyrrolo[1,2-a]perimidin-10-one. This product has been isolated and characterized in solution by NMR, IR, and UV/vis spectroscopies, and the solid-state structure of 8,9-dichloropyrrolo[1,2-a]perimidin-10-one has been established by X-ray crystallography. The nature of the HOMO and LUMO levels of 8,9-dichloropyrrolo[1,2-a]perimidin-10-one has been studied by extended Hückel molecular orbital calculations.
Date: August 2003
Creator: Chen, Tao

Synthesis, Characterization and Catalytic Studies of Chiral Gold Acyclic Diaminocarbene Complexes

Description: Chiral gold complexes have been applied in homogeneous catalytic reactions since 1986, in some cases with high enantioselectivity. Acyclic diaminocarbene (ADC) ligands are acyclic analogues of N-heterocyclic carbenes (NHCs) that have larger N-CCarbene-N angles and stronger donating ability. ADCs have been developed as alternatives to phosphine and NHC ligands in homogeneous gold catalysis. In 2012, a new series of chiral gold(I) ADCs were first developed by Slaughter's group and were shown to give remarkable enantioselectivities in some reactions. Because of the hindered rotation of the N-CCarbene bonds of ADC, chiral ADC substituents can easily get close to the metal center in some conformations, although two rotameric structures are formed if the chiral amine is nonsymmetric. The selective of specific ADC conformations was the initial focus of this study. Formational selectivity of one diastereomer of an ADC ligand during synthesis was examines by measuring the relative rates of diastereomer formation in a 1H NMR kinetic study. The potential for converting multiple conformational isomers of ADCs into a single conformation, or at least a simpler mixture, was examined. This study used the analogy that anti- isomer has electronic and structural similarity with urea/thiourea, raising the possibility that 1,8-naphthyridine can be used to favor certain conformations through a self-assembled hydrogen-bonding complex. Gold(I) is a soft carbophilic Lewis acid able to active C-C π bonds to nucleophilic attack, and ADC-gold complexes are potentially useful in this regard. Therefore, biaryl gold(I) ADC complexes were examine with silver salt additives in catalytic 1,6-enyne cyclization reaction. A detailed study found that the counteranion affects the regioselectivities of these reactions more than substituents on the ancillary ADC ligands.
Date: August 2016
Creator: Zhang, Xiaofan

Synthesis of Tethering Group on Borylazadipyrromethene Dyes to Apply to Photogalvanic Dye-sensitized Solar Cells

Description: This is my thesis research on the preparation of borylazadipyrromethene (azaBODIPY) dyes bearing an anchoring group, such as a carboxylic acid group, at the β-pyrrolic position of the azadipyrromethene scaffold. Carboxylate groups form covalent bonds to oxide semiconductors such as TiO2 (n-type) or Cu2O (p-type) in dye-sensitized solar cells (DSCs) or photogalvanic dye-sensitized solar cells (P-DSCs). Oxide-binding azaBODIPY dyes can be used to investigate the rate and mechanism of electron injection from the dyes to the semiconductors. Two different types of azaBODIPY (difluoroboryl and dialkynylboryl) were prepared by following previously developed methods. To convert difluoroborylazaBODIPY to the final dyes having a carboxylic acid in the β-pyrrolic position, several distinct synthetic routes were designed, adopting various reactions, such as halogenation, Sonogashira coupling, Knoevenagel condensation, Grignard reagents, Vilsmeir-Haack, and Steglich esterification. Some of these reactions were successful, but the overall synthesis to the targeted final molecule couldn’t be accomplished. Even though further studies on the synthesis of oxide-binding azaBODIPYs are needed, at least my thesis research suggests what reactions can be implemented to complete this synthesis in the future. Proton NMR (nuclear magnetic resonance) and carbon NMR were commonly used to confirm the synthesized compounds, and sometimes crystallographic information was obtained by XRD (X-ray diffraction) whenever crystals of sufficient size and quality were grown. NMR spectra, interpreted by SpinWorks 3 software, and crystal structures will be introduced in each chapter.
Date: August 2014
Creator: Park, Eunsol