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.
The regulations of many food products in the United States have been made and followed very well but unfortunately some products are not put under such rigorous standards as others. This leads to products being sold, that are thought to be healthy, but in reality contain unknown ingredients that may be hazardous to the consumers. With the use of several instrumentations and techniques the detection, characterization and identification of these unknown contaminates can be determined. Both the AZ-100 and the TE2000 inverted microscope were used for visual characterizations, image collection and to help guide the extraction. Direct analyte-probed nanoextraction (DAPNe) technique and nanospray ionization mass spectrometry (NSI-MS) was the technique used for examination and identification of all adulterants. A Raman imaging technique was than introduced and has proven to be a rapid, non-destructive and distinctive way to localize a specific adulterant. By compiling these techniques then applying them to the FDA supplied test samples three major adulterants were detected and identified.
The continuously increasing demand for innovation in the miniaturization of microelectronics has driven the need for ever more precise fabrication strategies for device packaging, especially for printed circuit boards (PCBs). Subtractive copper etching is a fundamental step in the fabrication process, requiring very precise control of etch rate and etch factor. Changes in the etching chemical equilibrium have significant effects on etching behavior, and CuCl2 / HCl etching baths are typically monitored with several parameters including oxidation-reduction potential, conductivity, and specific gravity. However, the etch rate and etch factor can be difficult to control even under strict engineering controls of those monitoring parameters. The mechanism of acidic cupric chloride etching, regeneration and recovery is complex, and the current monitoring strategies can have difficulty controlling the interlocking chemical equilibria. A complimentary tool, thin-film UV-Vis spectroscopy, can be utilized to improve the current monitoring strategies, as UV-Vis is capable of identifying and predicting etching behavior that the current standard methodologies have difficulty predicting. Furthermore, as a chemically-sensitive probe, UV-Vis can investigate the complex changes to the chemical equilibrium and speciation of the etch bath, and can contribute overall to significant improvements in the control of the copper etching system in order to meet the demands of next-level design strategies.
Density functional theory is an efficient and useful method of solving single-reference computational chemistry problems, however it struggles with multi-reference systems. Modifications have been developed in order to improve the capabilities of density functional theory. In this work, density functional theory has been successfully applied to solve multi-reference systems with large amounts of non-dynamical correlation by use of modifications. It has also been successfully applied for geometry optimizations for lanthanide trifluorides.
The growth of single and multilayer BN films on several substrates was investigated. A typical atomic layer deposition (ALD) process was demonstrated on Si(111) substrate with a growth rate of 1.1 Å/cycle which showed good agreement with the literature value and a near stoichiometric B/N ratio. Boron nitride films were also deposited by ALD on Cu poly crystal and Cu(111) single crystal substrates for the first time, and a growth rate of ~1ML/ALD cycle was obtained with a B/N ratio of ~2. The realization of a h-BN/Cu heterojunction was the first step towards a graphene/h-BN/Cu structure which has potential application in gateable interconnects.
Experimental data were obtained for the computation of mole fraction solubilities of three dichloronitrobenzenes in organic solvents at 25oC, and solubility ratios were obtained from this data. Abraham model equations were developed for solutes in tributyl phosphate that describe experimental values to within 0.15 log units, and correlations were made to describe solute partitioning in systems that contain either "wet" or "dry" tributyl phosphate. Abraham model correlations have also been developed for solute transfer into anhydrous diisopropyl ether, and these correlations fit in well with those for other ethers. Abraham correlations for the solvation of enthalpy have been derived from experimental and literature data for mesitylene, p-xylene, chlorobenzene, and 1,2-dichlorobenzene at 298.15 K. In addition, the enthalpy contribution of hydrogen bonding between these solutes and acidic solvents were predicted by these correlations and were in agreement with an established method. Residual plots corresponding to Abraham models developed in all of these studies were analyzed for trends in error between experimental and calculated values.
A novel application of ionic liquid as a charge carrier for the analysis and detection of neutral organometallic complexes using a mass spectrometer has been presented. The mass spectrometer detects only charged compounds which raise a difficulty in analyzing a neutral molecule that lacks a basic site to associate with charge. Therefore, an effective way of providing charge has always been an area of keen interest in the field of mass spectrometry. Ionic liquids have a very fascinating property of forming a cation-? interaction with other molecules to give a charged complex. In order to take advantage of this, it is important to know the geometric structure of the complex. Advanced methodologies like hydrogen-deuterium exchange and computational calculations have been used assisting in better understanding of the structure of the ionic liquid complexes.
This work focuses on finding the complete iodine and nitrogen nuclear electric quadrupole coupling tensors for fluoroiodoacetonitrile using chirped-pulse Fourier transform microwave spectroscopy. Fluoroiodoacetonitrile contains two hyperfine nuclei, iodine (I=5/2) and nitrogen (I=1) and the spectra were observed with great resolution. A total of 499 transitions were observed for this molecule. The a, b and c rotational constants were obtained. A study of chloropentafluoroacetone was also done using chirped-pulse Fourier transform microwave spectroscopy. The two chlorine isotopes for this molecule, Cl-35 and Cl-37 were observed and 326 and 170 transitions were recorded, respectively.
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.
Portable mass spectrometry has become an important analytical tool for chemical detection and identification outside of a lab setting. Many variations and applications have been developed to benefit various fields of science. Membrane inlet mass spectrometry is used to allow certain analytes to pass into the mass spectrometer without breaking vacuum or letting in large particulate matter. These two important analytical tools have been applied to the detection of harmful chemicals in the air. Earth-based separations and reverse gas stack modelling are useful mathematical tools that can be used to locate the source of a chemical release by back calculation. Earth-based separations studies the way different molecules will diffuse and separate through the air. Reverse gas stack modelling refers to the concentration differences of a chemical in relation to its distance from its source. These four analytical techniques can be combined to quickly and accurately locate various harmful chemical releases. The same system can be used for many applications and has been tested to detect harmful chemicals within and air-handling system. The monitoring of air-handling systems can greatly reduce the threat of harm to the building occupants by detecting hazardous chemicals and shutting off the air flow to minimize human exposure.
The Abraham solvation parameter model is a good approach for analyzing and predicting biological activities and partitioning coefficients. The general solvation equation has been used to predict the solute property (SP) behavior of drug compounds between biological barriers. Gas chromatography (GC) retention time can be used to predict molecular descriptors, such as E, S, A, B & L for existing and newly developed drug compounds. In this research, six columns of different stationary phases were used to predict the Abraham molecular descriptors more accurately. The six stationary phases used were 5% phenylmethyl polysiloxane, 6% cyanopropylphenyl 94% dimethylpolysiloxane, 5% diphenyl 95% dimethylpolysiloxane, 100% dimethylpolysiloxane, polyethylene glycol and 35% diphenyl 65% dimethylpolysiloxane. Retention times (RT) of 75 compounds have been measured and logarithm of experimental average retention time Ln(RTexp) are calculated. The Abraham solvation model is then applied to predict the process coefficients of these compounds using the literature values of the molecular descriptors (Acree Compilation descriptors). Six correlation equations are built up as a training set for each of the six columns. The six equations are then used to predict the molecular descriptors of the illegal drugs as a test set. This work shows the ability to extract molecular information from a new compound by utilizing commonly used GC columns available with the desired stationary phases. One can simply run the new compound in GC using these columns to get the retention time. Plugging in the retention time into the developed equations for each of the column will predict the molecular descriptors for the test compound and will give some information about the properties of the compound.
In this experiment, more than one hundred volatile organic compounds were analyzed with the gas chromatograph. Six capillary columns ZB wax plus, ZB 35, TR1MS, TR5, TG5MS and TG1301MS with different polarities have been used for separation of compounds and illicit drugs. The Abraham solvation model has five solute descriptors. The solute descriptors are E, S, A, B, L (or V). Based on the six stationary phases, six equations were constructed as a training set for each of the six columns. The six equations served to calculate the solute descriptors for a set of illicit drugs. Drugs studied are nicotine (S= 0.870, A= 0.000, B= 1.073), oxycodone(S= 2.564. A= 0.286, B= 1.706), methamphetamine (S= 0.297, A= 1.570, B= 1.009), heroin (S=2.224, A= 0.000, B= 2.136) and ketamine (S= 1.005, A= 0.000, B= 1.126). The solute property of Abraham solvation model is represented as a logarithm of retention time, thus the logarithm of experimental and calculated retention times is compared.
An investigation of luminescent sensing has been presented. Neutral Red, a common pH luminescent sensor, was shown to be an effective carbon dioxide sensor for the first time. Sensing experiments were performed both through fluorometric and fluorescent microscopy studies, giving rise to the possibility of carbon dioxide sensing for biological applications. Neutral Red was benchmarked against the well-established carbon dioxide sensor Pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt), HPTS. Neutral Red was shown to have improved response times and higher consistency within the sensing drift compared to HPTS. Trinuclear Au(I) complexes have previously shown to sense metal ions through changes in their luminescent properties. A computational study on d10-d10 interactions, which exist in complexes where Cu+, Ag+, and Au+ are intercalated with [Au(μ-C2,N3-ethylImidazolate)]3 in the form of both half and full sandwich adducts. Binding energies, total density plots, and Morse and Dunham analyses of potential energy surfaces are employed to better understand the metal-metal interactions and the effects of electron correlation, basis set superposition error, and dispersion of metallophilic interactions of the adduct complexes. As metal-metal interactions within these types of complexes become better understood, the tuning of trinuclear Au(I) complexes for luminescent sensing of metals becomes increasingly possible.
NiSi is an attractive material in the production of CMOS devices. The problem with the utilization of NiSi, is that there is no proper method of cleaning the oxide on the surface. Sputtering is the most common method used for the cleaning, but it has its own complications. Dry cleaning methods include the reactions with radicals and these processes are not well understood and are the focus of the project. Dissociated NF3 and NH3 were used as an alternative and XPS is the technique to analyze the reactions of atomic fluorine and nitrogen with the oxide on the surface. A thermal cracker was used to dissociate the NF3 and NH3 into NFx+F and NHx+H. There was a formation of a NiF2 layer on top of the oxide and there was no evidence of nitrogen on the surface indicating that the fluorine and hydrogen are the reacting species. XPS spectra, however, indicate that the substrate SiO2 layer is not removed by the dissociated NF3 and NiF2 growth process. The NiF2 over layer can be reduced to metallic Ni by reacting with dissociated NH3 at room temperature. The atomic hydrogen from dissociated ammonia reduces the NiF2 but it was determined that the atomic hydrogen from the ammonia does not react with SiO2.
The optimal conditions for deposition of nickel coating and Ni-layered double hydroxide metal matrix composite coatings onto stainless steel discs in a modified all-sulfate solutions have been examined. Nickel films provide good general corrosion resistance and mechanical properties as a protective layer on many metallic substrates. In recent years, there has been interest in incorporation nano-dimensional ceramic materials, such as montemorillonite, into the metal matrices to improve upon the corrosion and mechanical properties. Layered double hydroxides have been used as corrosion enhancer in polymer coatings by increasing mechanical strength and lowering the corrosion rate but until now, have not been incorporated in a metal matrix by any means. Layered double hydroxides can be easily synthesized in a variety of elemental compositions and sizes but typically require the use of non-polar solvents to delaminate into nanodimensional colloidal suspensions. The synthesis of a Zn-Al LDH has been studied and characterized. The effects of the non-polar solvents dimethylformamide and n-butanol on the deposition and corrosion resistance of nickel coatings from a borate electrolyte bath have been studied, a nickel-LDH nanocomposite coating has been synthesized by electrochemical deposition and the corrosion resistance has been studied. Results indicate an improvement in corrosion resistance for the coatings with minimal change in the nickel matrix's internal strain and crystallite size.
Cyclic voltammetry experiments were performed to compare the electrodeposition characteristics of bismuth on ruthenium. Two types of electrodes were used for comparison: a Ru shot electrode (polycrystalline) and a thin film of radio-frequency sputtered Ru on a Ti/Si(100) support. Experiments were performed in 1mM Bi(NO3)3/0.5M H2SO4 with switching potentials between -0.25 and 0.55V (vs. KCl sat. Ag/AgCl) and a 20mV/s scan rate. Grazing incidence x-ray diffraction (GIXRD) determined the freshly prepared thin film electrode was hexagonally close-packed. After thermally oxidizing at 600°C for 20 minutes, the thin film adopts the tetragonal structure consistent with RuO2. a hydrated oxide film (RuOx?(H2O)y) was made by holding 1.3V on the surface of the film in H2SO4 for 60 seconds and was determined to be amorphous. Underpotential deposition of Bi was observed on the metallic surfaces and the electrochemically oxidized surface; it was not observed on the thermal oxide.
Kinetics and thermodynamics of bismuth (Bi) underpotential deposition (UPD) on ruthenium (Ru) and on electrochemically formed Ru oxide are studied using electrochemical quartz crystal microbalance technique. The Bi UPD and Bi bulk deposition are observed both on Ru and on electrochemically formed Ru oxide electrodes. The anodic peak potential of Bi UPD shifts slightly to positive potential as the scan rate increases. The peak current ratio (IAnode/ICathode) of Bi UPD and Bi bulk increases as the scan rate increases. Bi monolayer coverage calculated from mass (MLMass) and from charge (MLCharge) with scan rates dependent are compared both in Bi UPD region and in Bi bulk region. Stability and oxidation time effects are also investigated. Bi UPD on Ru and on electrochemically formed Ru oxide are quasi-reversible, scan rate independent, oxidation time dependent, and have higher plating efficiency on Ru. However, Bi bulk deposition on Ru and on electrochemically formed Ru oxide are quasi-reversible, scan rate dependent, oxidation time independent, and have higher plating efficiency on electrochemically formed Ru oxide. Both Bi UPD adatoms and Bi bulk are unstable in 0.5M H2SO4.
The experiment successfully established the mathematical correlations between the logarithm of retention time of illegal drugs with GC system and the solute descriptor L from the Abraham model. the experiment used the method of Gas Chromatography to analyze the samples of illegal drugs and obtain the retention time of each one. Using the Abraham model to calculate and analyze the sorption coefficient of illegal drugs is an effective way to estimate the drugs. Comparison of the experimental data and calculated data shows that the Abraham linear free energy relationship (LFER) model predicts retention behavior reasonably well for most compounds. It can calculate the solute descriptors of illegal drugs from the retention time of GC system. However, the illegal drugs chosen for this experiment were not all ideal for GC analysis. HPLC is the optimal instrument and will be used for future work. HPLC analysis of the illegal drug compounds will allow for the determination of all the solute descriptors allowing one to predict the illegal drugs behavior in various Abraham biological and medical equations. the results can be applied to predict the properties in biological and medical research which the data is difficult to measure. the Abraham model will predict more accurate results by increasing the samples with effective functional groups.
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.
Presented in this thesis are two methods that are coupled to the instrumentation for the recovery and analysis of ultra-trace illicit drug residues. The electrostatic dust lifting process is coupled with nanomanipulation-nanospray ionization to retrieve drug particles off of hard surfaces for analysis. For the second method, drug residues from fingerprint impressions are extracted followed by analysis. The methodology of these hyphenated techniques toward forensic science applications is applied as to explore limits of detection, sensitivity, and selectivity of analytes as well as immediacy and efficiency of analysis. The application of nanomanipulation-coupled to nanospray ionization-mass spectrometry toward forensic science based applications is considered as future improvements to trace and ultra-trace analysis.
This research proposed to evaluate whether homework or daily quizzes were better for academic success within high-school pre-AP chemistry or if differences in the two methods were detectable. The study involved two years of data where homework was assigned and graded and one year of data where homework was suggested but daily quizzes provided the assessment. The mean of each of the unit tests were evaluated and t-tests were calculated. The results showed that over two-thirds of the units had statistically significant data when daily quizzes were utilized.
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.
The reactions of atomic hydrogen with methanethiol and that of atomic hydrogen with carbon disulfide were studied experimentally using flash-photolysis resonance-fluorescence techniques. Rate constants were determined over a range of temperatures and pressures, and through analysis and comparison to theoretical work details of the reactions were ascertained.
The kinetics of the reaction of atomic sulfur and nitrogen dioxide have been investigated over the temperature range 298 to 650 K and pressures from 14 - 405 mbar using the laser flash photolysis - resonance fluorescence technique. The overall bimolecular rate expression k (T) = (1.88 ± 0.49) x10-11 exp-(4.14 ± 0.10 kJ mol-1)/RT cm3 molecule-1 s-1 is derived. Ab initio calculations were performed at the CCSD(T)/CBS level of theory and a potential energy surface has been derived. RRKM theory calculations were performed on the system. It is found that an initially formed SNO2 is vibrationally excited and the rate of collisional stabilization is slower than the rate of dissociation to SO + NO products by a factor of 100 - 1000, under the experimental conditions.
The kinetics of the gas-phase reactions of chlorine atoms with fluoromethane (CH3F) and fluoromethane-d3(CD3F) were tested experimentally. The relative rate method was applied by using CH4 as the reference compound for fluoromethane (CH3F) and CH4 and CH3F as the reference compound for fluoromethane-d3(CD3F). The rate constants for H-abstraction from CH3F and D-abstraction from CD3F were measured at room temperature and a total pressure of 920 Torr using Ar as a diluent. The rate constants are described by the expressions: kH= (3.50±0.52) x 10-13 cm3 molecule-1 s-1 and kD=(5.0±0.51) x 10-14 cm3 molecule-1 s-1. The kinetic isotope effect, equal to the ratio kH/kD, was found to be 7.0±1.2 at room temperature.
The kinetics of the reaction of atomic sulfur with acetylene (S (3P) + C2H2) were investigated experimentally via the flash photolysis resonance fluorescence method, and the theoretical potential energy surface for the reaction CN + SO was modeled via the density functional and configuration interaction computational methods. Sulfur is of interest in modern chemistry due to its relevance in combustion and atmospheric chemistry, in the Claus process, in soot and diamond-film formation and in astrochemistry. Experimental conditions ranged from 295 – 1015 K and 10 – 400 Torr of argon. Pressure-dependence was shown at all experimental temperatures. The room temperature high-pressure limit second order rate constant was (2.10 ± 0.08) × 10-13 cm3 molecule-1 s-1. The Arrhenius plot of the high-pressure limit rate constants gave an Ea of (11.34 ± 0.03) kJ mol-1 and a pre-exponential factor of (2.14 ± 0.19) × 10-11 cm3 molecule-1 s-1. S (3P) + C2H2 is likely an adduct forming reaction due to pressure-dependence (also supported by a statistical mechanics analysis) which involves intersystem crossing. The potential energy surface for CN + SO was calculated at the B3LYP/6-311G(d) level and refined at the QCISD/6-311G(d) level. The PES was compared to that of the analogous reaction CN + O2. Notable energetically favorable products are NCS + O, CO + NS, and CS + NO. The completed PES will ultimately be modeled at the CCSD(T) level (extrapolated to infinite basis set limit) for theoretical reaction rate analysis (RRKM).
Laser Ablation Inductively coupled plasma mass spectrometry (LA-ICP-MS) and Raman spectroscopy are both powerful imaging techniques. Their applications are numerous and extremely potential in the field of biology. In order to improve upon LA-ICP-MS an in-house built cold cell was developed and its effectiveness studied by imaging Brassica napus seeds. To further apply LA-ICP-MS and Raman imaging to the field of entomology a prong gilled mayfly (Ephemeroptera: Leptophlebiidae) from the Róbalo River, located on Navarino Island in Chile, was studied. Analysis of both samples showcased LA-ICP-MS and Raman spectroscopy as effective instruments for imaging trace elements and larger molecules in biological samples respectively.
The reaction of the chelating ligand 4-[4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazin-2-yl]-N,N-diethyl-benzenamine, L, with pentacarbonylchlororhenium by conventional heating method produces the complexes fac-[ReL(CO)3Cl2] and fac-[Re2L(CO)6Cl2] in a period of 48 hours. The use of microwaves as the source of heat and the increase in the equivalents of one of the reactants leads to a more selective reaction and also decreases the reaction time to 1 hour. After proper purification, the photophysical properties of fac-[ReL(CO)3Cl] were analyzed. The solid-state photoluminescence analysis showed an emission band at 628 nm independent of temperature. However, in the solution studies, the emission band shifted from 550 nm in frozen media to 610 nm when the matrix became fluid. These results confirm that this complex possess a phenomenon known as rigidochromism.
Examinations of the effects of (a.) alkyl carbon chain length and (b.) perfluorination of acyl chlorides; propionyl chloride, butyryl chloride, valeroyl chloride, and perfluorinated acyl chlorides; perfluoropropionyl chloride and perfluorobutyryl chloride, are reported and compared using CP-FTMW spectroscopy. All of these molecules are already published in various journals except for valeroyl chloride. The chapters are organized by molecule alkyl chain length and include some background theory. Conformational stability, internal rotation, helicity, and ionic character of the C-Cl bond via the nuclear electric quadrupole coupling constant (χzz) are analyzed. Results show syn, syn-anti/syn-gauche, and syn-anti-anti/syn-gauche-anti stable conformations. Internal rotation was only seen in propionyl chloride. Helicity was not observed. (χzz) was observed to be inert to alkyl chain length, ~ 60 MHz and ~ 65 MHz for the nonfluorinated and fluorinated acyl chlorides. Partial fluorination and varying functional groups are recommended.
The potential use of polymeric, functionalized nanoparticles (NPs) as drug delivery vectors was explored. Covalent conjugation of albumin to the surface of NPs via maleimide chemistry proved problematic. However, microwave assisted synthesis of NPs was not only time efficient, but enabled the exploration of size control by changing the following parameters: temperature, microwave power, reaction time, initiator concentration, and percentage of monomer used. About 1.5 g of fluorescently-labeled, carboxylic acid-functionalized NPs (100 nm diameter) were synthesized for a total cost of less than $1. Future work will address further functionalization of the NPs for the coupling of albumin (or other targeted proteins), and tests for in vivo biodistribution.
Two aluminum spherical mirrors with radii of 203.2 mm and radii of curvature also of 203.2 mm have been used to construct a tunable Fabry-Perót type resonator operational at frequencies as low as 500 MHz. The resonator has been incorporated into a pulsed nozzle, Fourier transform, Balle-Flygare spectrometer. The spectrometer is of use in recording low J transitions of large asymmetric molecules where the spectra are often greatly simplified compared to higher frequency regions. The resonators use is illustrated by recording the rotational spectra of bromobenzene and iodobenzene. In related experiments, using similar equipment, the pure rotational spectra of four isotopomers of SrS and all three naturally occurring isotopomers of the actinide-containing compound thorium monoxide have been recorded between 6 and 26 GHz. The data have been thoroughly analyzed to produce information pertaining to bond lengths and electronic structures.
Preparative mass spectrometry is an important method for the synthesis of new materials. Recently, soft landing mass spectrometry has been used to land ions on surfaces to coat or otherwise alter them. Commercial soft landing instruments do not yet exist, and the physical phenomenon of soft landing has not yet been fully described. For future ion mobility soft landing research, the theory of ion mobility, ion optics and soft landing is discussed, and 2 soft landing instruments have been built and described, along with proof of concept experiments for both instruments. Simulations of the process of ion mobility and ion optics for use in these instruments, as well as some preliminary results for the optics are included. Surfaces described include copper on mica and iron on silicon. Self assembly of soft landed ions is observed on the surfaces. The instruments constructed will be useful for future soft landing research, and soft landing can be used for future materials research with special attention focused on the self-assembly of the landed ions.
Six peripherally meso-modified Zn (II) porphyrin sensitizer dyes are designed and their J-V performance in dye sensitized solar cell (DSSC) evaluated. Electron-donating groups including phenothiazine, carbazole and pyrene are used to modify the porphyrin macrocycle at the meso-carbon position(s). To compare the effect of donor substitution on the performance of the cells in terms of short circuit current (Jsc), light harvesting efficiency (LHE) and power conversion efficiency (η), two sets of sensitizers with different degrees of substitution are synthesized. One set of dyes (mono-substituted) have one electron donor at trans-position to the acceptor, while the second set (tri-substituted) dyes have three of the same type electron donor groups at 5, 10 and 15 meso-carbon positions making all the six dyes push-pull type sensitizers incorporating 4'-carboxyphenyl as an electron-acceptor/anchor group. Different spectroscopic and electrochemical methods are used to study the photophysical and electrochemical properties of the dyes, while the photovoltaic performance of their cells under 1.5 A.M is studied using solar simulator. Meso-substitution of Zinc (II) porphyrin with these small donor molecules is shown to improve the light harvesting character of the Zinc (II) porphyrin macrocycle in the UV-Vis absorption while at same time improving its fluorescence quantum yield, excited-state life time and electron donating potential. All these factors combined make these meso-modified dyes better sensitizers with suitable Δ0 Δ0, and much improved power conversion efficiencies (PCE) compared to unsubstituted Zn (II) porphyrin. In particular, as a result of the peripheral modification, a doubling in efficiency in the mono- substituted series (RA-200-Zn; η=^M 4.2%, Jsc= -13.13 mA cm-2, Voc=0.54 ) and tripling in the tri-substituted series ( tri-phenothiazine Zn (II) Porphyrin; η= 7.3%, Jsc= -18.15 mA cm-2, Voc= 0.55 ) compared to unsubstituted Zn (II) porphyrin (η= 2.11%, Jsc= -5.7 mA cm-2, Voc= 0.53 V) has been accomplished.
Photoinduced electron transfer in self-assembled via axial coordination porphyrin-fullerene dyads is investigated. Fullerene functionalized with imidazole and fullerenes functionalized with pyridine are chosen as electron acceptors, while zinc pophyrin derivatives are utilized as electron donors. The electron withdrawing ability of halogen atoms make the porphyrin ring electrophilic, which explained the binding of (F20TPP)Zn with fullerene derivatives having the highest binding constant around 105M-1. Another important observation is that the fullerene imidazole binding to zinc pophyrin had higher stability than fullerene pyridine-porphyrin dyad. Computational DFT B3LYP-21G(*) calculations are used to study the geometric and electronic structures. The HOMO and LUMO was found to be located on the porphyrin and fullerene entities, respectively. Photoinduced electron transfer is investigated by the steady-state absorption and emission, differential pulse voltammetry, and nanosecond and femtosecond transient absorption studies. The measurements provided the same conclusion that the increasing number of the halogen atoms on the porphyrin ring leads to the higher binding of porphyrin-fullerene supramolecular dyads and efficient charge separation and charge recombination processes.
The world is facing a tough challenge regarding fulfilling human energy needs. Scientists are motivated to find alternative ways to the fossil fuel at a lower cost with little or no environmental pollution. Among the available renewable resources, the solar energy is an alternative energy to fossil fuel. Scientists are engaged in mimicking the photosynthesis to create the new energy devices such as dye sensitized solar cells. The fundamental theory and properties of the dye sensitized solar cells is given in the first chapter. In this research, the application of the different methods for surface alteration of SnO2 with water soluble porphyrins and phthalocyanine is studied. Using optical absorbance and steady state fluorescence studies, the formation of porphyrins and phthalocyanine discuss on the SnO2 surface is shown. Moreover, the different results of photoelectrochemical cells are show on chapter 2 to understand the porphyrin and phthalocyanine modified on SnO2 as electron injector. In summary, the application porphyrin and phthalocyanine of dimers as a broad band capturing photosensitized dye is discussed.
The details of dye sensitized solar cells was explained and phenothiazine and porphyrin based dyes were synthesized for use in DSSCs. DSSCs offer a unique and cost effective method of renewable energy. DSSCs are characterized through various tests, with the overall efficiency, η, bearing the greatest importance. Incident photon to current conversion efficiency, or IPCE, is also another important characterization of DSSCs. Effect of positioning of the cyanoacrylic acid anchoring group on ring periphery of phenothiazine dye on the performance of dye sensitized solar cells (DSSCs) is reported. The performances of the cells are found to be prominent for solar cells made out of Type-1 dyes compared to Type-2 dyes. This trend has been rationalized based on spectral, electrochemical, computational and electrochemical impedance spectroscopy results. Free-base and zinc porphyrins bearing a carboxyl anchoring group at the para, meta, or ortho positions of one of the meso-phenyl rings were synthesized for DSSCs. Photoelectrochemical studies were performed after immobilization of porphyrins onto nanocrystalline TiO2. The performance of DSSCs with the porphyrin anchoring at the para or meta position were found to greatly exceed those in the ortho position. Additionally, zinc porphyrin derivatives outperformed the free-base porphyrin analogs, including better dye regeneration efficiency for the zinc porphyrin derivatives and for the meta and para derivatives through electrochemical impedance spectroscopy studies. The overall structure-performance trends observed for the present porphyrin DSSCs have been rationalized based on spectral, electrochemical, electrochemical impedance spectroscopy and transient spectroscopy results.
The reaction between the formamidine ligand PriN=CHNHPri and the activated cluster Os3(CO)10(MeCN)2 has been studied. A rapid reaction is observed at room temperature, yielding the hydride clusters HOs3(CO)9[μ-OCNPriC(H)NPri] and HOs3(CO)10[μ-NPriC(H)NPri] as the principal products. The spectroscopic data and X-ray diffraction structures of those formamidinate-substituted clusters will be present. The thermal reactivity of the clusters has been investigated, with the face-capped cluster HOs3(CO)9[μ-NPriC(H)NPri] found as the sole observable product. The relationship between these three clusters has been established by kinetic studies, the results of which will be discussed.
A set of five new C3-symmetric phosphites were synthesized and tested in palladium-catalyzed asymmetric Suzuki coupling. The observed reactivity and selectivity were dependent upon several factors. One of the phosphites was able to achieve some of the highest levels of enantioselectivity in asymmetric Suzuki couplings with specific substrates. Different hypotheses have been made for understanding the ligand effects and reaction selectivities, and those hypotheses were tested via various methods including DOSY NMR experiments, X-ray crystallography, and correlation of catalyst selectivity with Tolman cone angles. Although only modest enantioselectivities were observed in most reactions, the ability to synthesis these phosphites in only three steps on gram scales and to readily tune their properties by simple modification of the binaphthyl 2´-substituents makes them promising candidates for determining structure-selectivity relationships in asymmetric transition metal catalysis, in which phosphites have been previously shown to be successful. A series of novel chiral oxazoline-based carbodicarbene ligands was targeted for synthesis. Unfortunately, the chosen synthetic route could not be completed due to unwanted reactivity of the oxazoline ring. However, a new and efficient route for Pd-catalyzed direct amination of aryl halides with oxazoline amine was developed and optimized during these studies. Chiral binaphthyl based Pd(II) ADC complexes with different substituent groups have been synthesized and tested in asymmetric Suzuki coupling reactions. Although only low enantioselectivities were observed in Suzuki coupling, this represents a new class of chiral metal-ADC catalysts that could be tested in further catalytic.
Polymeric nanoparticles were synthesized and loaded with Cu²⁺ to explore the therapeutic potential for catically active transition metal ions and complexes other than cisplatin. Two types of nanoparticles were synthesized to show the potential for polymer based vectors. Copper loading and release were characterized via inductively coupled plasma mass spectrometry (ICP MS), energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), and elemental analysis. Results demonstrated that Cu could be loaded to the nano-sized carriers in an aqueous environment, and that the release was pH-dependent. The toxicity of these particles was measured in HeLa cells where significant toxicity was observed in vitro via dosing of high Cu-loaded nanoparticles. No significant toxicity was observed in cells dosed with Cu-free nanoparticles.
In the development of covalent organic frameworks (COFs), often the scaffold linkers are assumed to be electro- and photoinactive, and this was also to be the case for 2,3,6,7,10,11-hexahydroxytriphenylene, a tritopic linker. However, as demonstrated in the present study, the reaction product of this linker, hexaoxatriphenylene, is electron rich and when connected to a suitable photosensitizer engages itself in an efficient excited-state charge separation process. In the present study, we have employed BF2-chelated dipyrromethenes (BODIPYs) as sensitizers, which are connected to hexaoxatriphenylene through the center boron, rendering paddle-wheel-type structures. Systematic photophysical, electrochemical, computational, and photochemical studies involving pump-probe femtosecond transient spectroscopy have been performed to establish efficient charge separation in these novel supramolecular structures.
This study expands the role of polythiophenes as an electron donating chromophore within energy harvesting milti-modular donor-acceptor systems. The polythiophene moiety would act as an electron donating spacer group between the donor and acceptor entities, viz., phenothiazine and fulleropyrrolidine, respectively, in the newly synthesized supramolecular triads. The triads 10-{[2,2';5',2"] terthiophene-5-fulleropyrrolidine} phenothiazine and 10-{[2,2'] bithiophene-5-fulleropyrrolidine} phenothiazine were synthesized and characterized through electrochemical and spectroscopic methods to ascertain their structural integrity. the componets of the triads were selected for their established redox parameters. Phenothiazine would act as a secondary donor and would facilitate hole-transfer from the polythiophene primary electron donor, due to its ease of oxidation and yield a long-lived charge separated state. Fulleropyrrolidine would act as an acceptor for ease of reductive capabilities and its ability to hold multiple charges. Finally, occurrence of photoinduced electron transferleading to the anticipated charge separated states is established from advanced transient spectroscopic techniques on these novel supramolecular systems.
Combinatorial libraries are used in the search for ligands that bind to target proteins. Fmoc solid-phase peptide synthesis is routinely used to generate such libraries. Microwave-assisted peptide synthesis was employed here to decrease reaction times by 80-90%. Two One-Bead-One-Compound combinatorial libraries were synthesized on 130μm beads (one containing 750 members and the other 16, 807). The use of smaller solid supports would have many important practical advantages including; increased library diversity per unit mass, smaller quantities of library needed to generate hits, and screening could be conducted by using a standard flow cytometer. To this end, a miniaturized peptide library was synthesized on 20 μm beads to demonstrate proof of principle. A small sample from the 16,807-member library was screened against transferrin-AlexaFluro 647, a protein responsible for iron transport in vivo. A number of hits were identified and sequenced using techniques coupling nanomanipulation with nanoelectrospray mass spectrometry.
The efficiency and mechanism of electron- and energy transfer events occurring in both in natural and synthetic donor-acceptor systems depend on their distance, relative orientation, and the nature of the surrounding media. Fundamental knowledge gained from model studies is key in building efficient energy harvesting and optoelectronic devices. Faster charge separation and slower charge recombination in donor-acceptor systems is often sought out. In our continued effort to build donor-acceptor systems using near-IR sensitizers, in the present study, we report ground and excited state charge transfer in newly synthesized, directly linked, tetrads featuring bisdonor (donor = phenothiazine and ferrocene), BF2-chelated azadipyrromethane (azaBODIPY) and C60 entities. The tetrads synthesized using multi-step synthetic procedure revealed strong charge transfer interactions in the ground state involving the donor and azaBODIPY entities. The near-IR emitting azaBODIPY acted as a photosensitizing electron acceptor along with fullerene while the phenothiazine and ferrocene entities acted as electron donors. The triads (bisdonor-azaBODIPY) and tetrads revealed ultrafast photoinduced charge separation leading to D•+-azaBODIPY•–-C60 and D•+-azaBODIPY-C60•– (D = phenothiazine or ferrocene) charge separated states from the femtosecond transient absorption spectral studies in both polar and nonpolar solvent media. The charge separated states populated the triplet excited state of azaBODIPY prior returning to the ground state.
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.
Syntheses of diphosphine gold (I) complexes from gold THT and two ligands, 4, 5-bis (diphenylphosphino)-4-cyclopenten-1, 3-dione (BPCD) and 2,3-bis(diphenylphosphino)-N-phenylmaleimide (BPPM), were done separately. The reactions happened under ice conditions followed by room temperature conditions and produced two diphosphine gold (I) complexes in moderated yield. Spectroscopic results including nuclear magnetic resonance (NMR) and X-ray crystallography were used to study and determine the structures of the products formed. Moreover, X-rays of all newly synthesized diphosphine gold (I) complexes were compared with the known X-ray structures of other phosphine and diphosphine gold (I) complexes. There were direct resemblances in terms of bond length and angle between these new diphosphine gold (I) complex structures and those already published. For instance, the bond lengths and angles from the newly prepared diphosphine gold (I) complexes were similar to those already published. Where there were some deviations in bond angles and length between the newly synthesized structures and those already published, appropriate explanation was given to explain the deviation. Heterocyclic ligands bearing acetylacetonate (ACAC) side arm(s) were prepared from ethyl malonyl chloride and the heterocyclic compounds 8-hydroxylquinoline, Syn-2-peridoxyaldoxime, quinoxalinol and 2, 6-dipyridinylmethanol. The products (heterocyclic ACAC ligands) from these reactions were screened with transition metal carbonyl compounds in thermolytic reactions. The complexes formed were studied and investigated using NMR and X-ray crystallography. Furthermore, the X-ray structures of the heterocyclic ACAC ligand or ligand A and that of rhenium complex 1 were compared with similar published X-ray structures. The comparison showed there were some similarities in terms of bond length and bond angles.
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.
While computational chemistry methods have a wide range of applications within the set of traditional physical sciences, very little is being done in terms of expanding their usage into other areas of science where these methods can help clarify research questions. One such promising field is Forensic Science, where detailed, rapidly acquired sets of chemical data can help in decision-making at a crime scene. As part of an effort to create a database that fits these characteristics, the present work makes use of computational chemistry methods to increase the information readily available for the rapid identification and scheduling of drugs to the forensic scientist. Ab initio geometry optimizations, vibrational spectra calculations and ESI-MS fragmentation prediction of a group of common psychedelics are here presented. In addition, we describe an under development graphical user interface to perform ab initio calculations using the GAMESS software package in a more accessible manner. Results show that the set of theoretical techniques here utilized, closely approximate experimental data. Another aspect covered in this work is the implementation of a boiling point estimation method based on group contributions to generate chemical dispersion areas with the ALOHA software package. Once again, theoretical results showed to be in agreement with experimental boiling point values. A computer program written to facilitate the execution of the boiling point estimation method is also shown.
The growth of Co (0001) films and Cr2O3 (0001)/Co (0001) has been investigated using surface analysis methods. Such films are of potential importance for a variety of spintronics applications. Co films were directly deposited on commercial Al2O3 (0001) substrates by magnetron sputter deposition or by molecular beam epitaxy (MBE), with thicknesses of ~1000Å or 30Å, respectively. Low Energy Electron Diffraction (LEED) shows hexagonal (1x1) pattern for expected epitaxial films grown at 800 K to ensure the hexagonally close-packed structure. X-ray photoemission spectroscopy (XPS) indicates the metallic cobalt binding energy for Co (2p3/2) peak, which is at 778.1eV. Atomic force microscopy (AFM) indicates the root mean square (rms) roughness of Co films has been dramatically reduced from 10 nm to 0.6 nm by optimization of experiment parameters, especially Ar pressure during plasma deposition. Ultrathin Cr2O3 films (10 to 25 Å) have been successfully fabricated on 1000Å Co (0001) films by MBE. LEED data indicate Cr2O3 has C6v symmetry and bifurcated spots from Co to Cr2O3 with Cr2O3 thickness less than 6 Å. XPS indicates the binding energy of Cr 2p(3/2) is at 576.6eV which is metallic oxide peak. XPS also shows the growth of Cr2O3 on Co (0001) form a thin Cobalt oxide interface, which is stable after exposure to ambient and 1000K UHV anneal.
The focus of this thesis is on C-O bonds activation by transition metal atoms. Lignin is a potential alternative energy resource, but currently is an underused biomass species because of its highly branched structure. To aid in better understanding this species, the oxidative cleavage of the Cβ-O bond in an archetypal arylglycerol β-aryl ether (β–O–4 Linkage) model compound of lignin with late 3d, 4d, and 5d metals was investigated. Methoxyethane was utilized as a model molecule to study the activation of the C-O bond. Binding enthalpies (ΔHb), enthalpy formations (ΔH) and activation enthalpies (ΔH‡) have been studied at 298K to learn the energetic properties in the C-O bond cleavage in methoxyethane. Density functional theory (DFT) has become a common choice for the transition metal containing systems. It is important to select suitable functionals for the target reactions, especially for systems with degeneracies that lead to static correlation effects. A set of 26 density functionals including eight GGA, six meta-GGA, six hybrid-GGA, and six hybrid-meta-GGA were applied in order to investigate the performance of different types of density functionals for transition metal catalyzed C-O bond cleavage. A CR-CCSD(T)/aug-cc-pVTZ was used to calibrate the performance of different density functionals.
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