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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.
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Date: August 2013
Creator: Fogueri, Uma

Accuracy and Efficiency in Computational Chemistry: The Correlation Consistent Composite Approach

Description: One of the central concerns of computational chemistry is that of efficiency (i.e. the development of methodologies which will yield increased accuracy of prediction without requiring additional computational resources – RAM, disk space, computing time). Though the equations of quantum mechanics are known, the solutions to these equations often require a great deal of computing power. This dissertation primarily concerns the theme of improved computational efficiency (i.e. the achievement of greater accuracy with reduced computational cost). Improvements in the efficiency of computational chemistry are explored first in terms of the correlation consistent composite approach (ccCA). The ccCA methodology was modified and this enhanced ccCA methodology was tested against the diverse G3/05 set of 454 energetic properties. As computational efficiency improves, molecules of increasing size may be studied and this dissertation explored the issues (differential correlation and size extensivity effects) associated with obtaining chemically accurate (within 1 kcal mol-1) enthalpies of formation for hydrocarbon molecules of escalating size. Two applied projects are also described; these projects concerned the theoretical prediction of a novel rare gas compound, FKrOH, and the mechanism of human glutathione synthetase’s (hGS) negative cooperativity. The final work examined the prospect for the parameterization of the modified embedded atom method (MEAM) potential using first principles calculations of dimer and trimer energies of nickel and carbon systems. This method of parameterization holds promise for increasing the accuracy of simulations for bulk properties within the field of materials science.
Date: August 2011
Creator: Wilson, Brent R.

Advancements in Instrumentation for Fourier Transform Microwave Spectroscopy

Description: The efforts of my research have led to the successful construction of several instruments that have helped expand the field of microwave spectroscopy. The classic Balle-Flygare spectrometer has been modified to include two different sets of antenna to operate in the frequency ranges 6-18 GHz and 18-26 GHz, allowing it to function for a large range without having to break vacuum. This modified FTMW instrument houses two low noise amplifiers in the vacuum chamber to allow for the LNAs to be as close to the antenna as physically possible, improving sensitivity. A new innovative Balle-Flygare type spectrometer, the efficient low frequency FTMW, was conceived and built to operate at frequencies as low as 500 MHz through the use of highly curved mirrors. This is new for FTMW techniques that normally operate at 4 GHz or higher with only a few exceptions around 2 GHz. The chirped pulse FTMW spectrometer uses horn antennas to observe spectra that span 2 GHz versus the standard 1 MHz of a cavity technique. This instrument decreases the amount of time to obtain a large spectral region of relative correct intensity molecular transitions. A Nd:YAG laser ablation apparatus was attached to the classic Balle-Flygare and chirped pulse FTMW spectrometers. This allowed the study of heavy metal containing compounds. The instruments I constructed and the techniques I used have allowed the discovery of further insights into molecular chemistry. I have seen the effects of fluorinating an alkyl halide by determining the geometry of the carbon backbone of trans-1-iodoperfluoropropane and observing a ΔJ = 3 forbidden transition caused by a strong quadrupole coupling constant on this heavy molecule. The quadrupole coupling tensors of butyronitrile, a molecule observed in space, have been improved. The nuclear quadrupole coupling tensor of difluoroiodomethane was added to a list of variably fluorinated methyl ...
Date: August 2011
Creator: Dewberry, Christopher Thomas

Application of the Correlation Consistent Composite Approach to Biological Systems and Noncovalent Interactions

Description: Advances in computing capabilities have facilitated the application of quantum mechanical methods to increasingly larger and more complex chemical systems, including weakly interacting and biologically relevant species. One such ab initio-based composite methodology, the correlation consistent composite approach (ccCA), has been shown to be reliable for the prediction of enthalpies of formation and reaction energies of main group species in the gas phase to within 1 kcal mol-1, on average, of well-established experiment, without dependence on experimental parameterization or empirical corrections. In this collection of work, ccCA has been utilized to determine the proton affinities of deoxyribonucleosides within an ONIOM framework (ONIOM-ccCA) and to predict accurate enthalpies of formation for organophosphorus compounds. Despite the complexity of these systems, ccCA is shown to result in enthalpies of formation to within ~2 kcal mol-1 of experiment and predict reliable reaction energies for systems with little to no experimental data. New applications for the ccCA method have also been introduced, expanding the utility of ccCA to solvated systems and complexes with significant noncovalent interactions. By incorporating the SMD solvation model into the ccCA formulation, the Solv-ccCA method is able to predict the pKa values of nitrogen systems to within 0.7 pKa unit (less than 1.0 kcal mol-1), overall. A hydrogen bonding constant has also been developed for use with weakly interacting dimers and small cluster compounds, resulting in ccCA interaction energies for water clusters and dimers of the S66 set to within 1.0 kcal mol-1 of well-established theoretical values.
Date: May 2015
Creator: Riojas, Amanda G

Chirped-Pulse Fourier Transform Microwave Spectroscopy of Fluoroiodoacetonitrile and Chloropentafluoroacetone

Description: 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.
Date: December 2010
Creator: Kadiwar, Gautam

The One Electron Basis Set: Challenges in Wavefunction and Electron Density Calculations

Description: In the exploration of chemical systems through quantum mechanics, accurate treatment of the electron wavefunction, and the related electron density, is fundamental to extracting information concerning properties of a system. This work examines challenges in achieving accurate chemical information through manipulation of the one-electron basis set.
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Date: May 2016
Creator: Mahler, Andrew

Photophysics and Photochemistry of Copper(I) Phosphine and Collidine Complexes: An Experimental/Theoretical Investigation

Description: Copper(I) complexes have been studied through both experimental and computational means in the presented work. Overall, the work focuses on photophysical and photochemical properties of copper(I) complexes. Photophysical and photochemical properties are found to be dependent on the geometries of the copper(I) complexes. One of the geometric properties that are important for both photochemical and photophysical properties is coordination number. Coordination numbers have been observed to be dependent on both ligand size and recrystallization conditions. The complexes geometric structure, as well as the electronic effects of the coordination ligands, is shown both computationally as well as experimentally to affect the emission energies. Two-coordinate complexes are seen to have only weak emission at liquid nitrogen temperature (77 K), while at room temperature (298 K) the two-coordinate complexes are not observed to be luminescent. Three-coordinate complexes are observed to be luminescent at liquid nitrogen temperature as well as at room temperature. The three-coordinate complexes have a Y-shaped ground (S0) state that distorts towards a T-shape upon photoexcitation to the lowest lying phosphorescent state (T1). The geometric distortion is tunable by size of the coordinating ligand. Luminescence is controllable by limiting the amount of non-radiative emission. One manner by which non-radiative emission is controlled is the amount of geometric distortion that occurs as the complex undergoes photoexcitation. Bulky ligands allow for less distortion than smaller ligands, leading to higher emission energies (blue shifted energies) with higher quantum efficiency. Tuning emission and increasing quantum efficiencies can be used to create highly efficient, white emitting materials for use in white OLEDS.
Date: August 2011
Creator: Determan, John J.

Quantum Chemistry Calculations of Energetic and Spectroscopic Properties of p- and f-Block Molecules

Description: Quantum chemical methods have been used to model a variety of p- and f-block chemical species to gain insight about their energetic and spectroscopic properties. As well, the studies have provided understanding about the utility of the quantum mechanical approaches employed for the third-row and lanthanide species. The multireference ab initio correlation consistent Composite Approach (MR-ccCA) was utilized to predict dissociation energies for main group third-row molecular species, achieving energies within 1 kcal mol-1 on average from those of experiment and providing the first demonstration of the utility of MR-ccCA for third-row species. Multireference perturbation theory was utilized to calculate the electronic states and dissociation energies of NdF2+, providing a good model of the Nd-F bond in NdF3 from an electronic standpoint. In further work, the states and energies of NdF+ were determined using an equation of motion coupled cluster approach and the similarities for both NdF2+ and NdF were noted. Finally, time-dependent density functional theory and the static exchange approximation for Hartree-Fock in conjunction with a fully relativistic framework were used to calculate the L3 ionization energies and electronic excitation spectra as a means of characterizing uranyl (UO22+) and the isoelectronic compounds NUO+ and UN2.
Date: August 2016
Creator: South, Christopher James

Transition Metal Catalyzed Oxidative Cleavage of C-o Bond

Description: 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.
Date: May 2015
Creator: Jiaqi, Wang