Doctor of Philosophy (PhD), Ohio University, 2024, Chemistry and Biochemistry (Arts and Sciences)

In this dissertation, the gas-phase fragmentation chemistries of deprotonated carbohydrates were characterized. Tandem mass spectrometry and density functional theory (DFT) reaction pathway calculations were applied to rationalize the gas-phase fragmentation mechanisms. The fragmentation behavior of singly charged deprotonated glucose-α-glucose positional isomers: b,b-trehalose and isomaltose was investigated. The gas-phase chemistry of two other glucose-α-glucose positional isomers was studied: kojibiose and nigerose. The fragmentation mechanisms of singly deprotonated glucose- 1,4-glucose stereochemistry isomers α/β for maltose and cellobiose, respectively were examined. Finally, the fragmentation chemistry of acidic glycan galacturonic acid is studied, both singly and doubly deprotonated precursor ions were individually fragmented, and theoretical modeling was used to compare the charge-state effect on the fragmentation behavior of digalacturonic acid.

Committee: Benjamin Bythell Mr (Advisor); Howard Dewald Mr (Committee Member) Subjects: Chemistry

Doctor of Philosophy, The Ohio State University, 2023, Chemistry

Algebraic diagrammatic construction (ADC) theory has been found to be a relatively low-cost method with attractive features for the study of photochemical problems. However, because the original formulation of ADC is formulated with a single Slater determinant approximating the ground-state wavefunction, it is insufficient in reproducing accurate photochemical results for systems that exhibit strong correlation effects. In this thesis, I present new approximations in multireference algebraic diagrammatic construction (MR-ADC) theory for simulating electronic excitations of strongly-correlated molecular systems. First, I present the theory and implementation of new strict and extended second-order MR-ADC methods (MR-ADC(2) and MR-ADC(2)-X, respectively) and benchmark these methods for low-lying excited states in several small molecules, including the carbon dimer, ethylene, and butadiene. Next, I present an implementation of MR-ADC methods that incorporates the core-valence separation (CVS) approximation, providing efficient access to simulating core-excited states. The potential of CVS-MR-ADC for systems with multiconfigurational electronic structure is examined by calculating the K-edge XAS spectrum of the ozone molecule and the dissociation curve of core-excited molecular nitrogen. I conclude with an efficient implementation of CVS-MR-ADC, reformulated in terms of spin-free quantities, and present preliminary data on core-excitations in large chemical systems that were not computationally feasible using spin-orbital quantities.

Committee: Alexander Sokolov (Advisor); Bern Kohler (Committee Member); John Herbert (Committee Member) Subjects: Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2016, Chemistry

We discuss the development and application of a number of fragmentation methods focused on understanding of intermolecular interactions in different systems. The advantage of fragmentation methods is to avoid the exponential growth of required computational power for the most advanced and accurate quantum chemistry theories which preclude the application in systems with large number of atoms and molecules. In those fragmentation methods, the full chemical system is partitioned into different subsystems, circumventing the exponential scaling computational cost. How this partitioning is performed and applied appropriately is the principal emphasis of this work. One of the fragmentation methods developed by our group, called extended XSAPT, combines an efficient, iterative, monomer-based approach to computing many-body polarization interactions with a two-body version of symmetry-adapted perturbation theory (SAPT). The result is an efficient method for computing accurate intermolecular interaction energies in large non-covalent assemblies such as molecular and ionic clusters, supramolecular complexes, clathrates, or DNA--drug complexes. As in traditional SAPT, the XSAPT energy is decomposable into physically-meaningful components. Dispersion interactions are problematic in traditional low-order SAPT, and the empirical atom-atom dispersion potentials are introduced here in an attempt to improve this situation. Comparison to high-level ab initio benchmarks for biologically-related dimers, water clusters, halide--water clusters, supremolecular complexes, methane clathrate hydrates, and a DNA intercalation complex illustrate both the accuracy of XSAPT-based methods as well as their limitations. The computational cost of XSAPT scales as third to fifth order with respect to monomer size, depending upon the particular version that is employed, but the accuracy is typically superior to alternative ab initio methods with similar scaling. Moreover, the monomer-based nature of (open full item for complete abstract)

Committee: John Herbert (Advisor); Sherwin Singer (Committee Member); Marcos Sotomayor (Committee Member) Subjects: Chemistry; Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2012, Chemistry

We discuss the development and application of a number of theoretical physical models focused on improving our understanding of quantum chemical phenomena in condensed phase environments, especially aqueous solutions. The large number of atoms and molecules present in such systems precludes the application of the most advanced and accurate quantum chemistry theories available due to their exponential growth of required computational power with respect to the number of electrons in a system. As a feasible alternative, we opt to take a ``multi-layer" approach, wherein the full chemical system is partitioned into different layers treated with varying levels of approximation, circumventing the exponential scaling computational cost. How this partitioning is performed and applied appropriately is the principal emphasis of this work. Our main chemical system of interest is aqueous DNA and its excited electronic states. We examine applications of mixing quantum mechanics and classical molecular mechanics models, a multi-layer approach known as ``QM/MM," to simulate the electronic absorption spectrum of aqueous uracil as computed with Time-Dependent Density Functional Theory (TDDFT). We encounter a major issue of spurious charge-transfer (CT) states in TDDFT even at small uracil--water clusters. Applying Long-Range Corrected TDDFT (LRC-TDDFT), however, alleviates this issue and allows us to investigate the absorption spectrum of aqueous DNA systems of up to as much as 8 nucleobases, providing some important clues to the initial dynamics of aqueous DNA excited by ultraviolet light and its possible ensuing damage. Then, to overcome certain computational limitations in modeling solvent by QM/MM alone, we turn to the methodology of polarizable continuum models (PCMs), which can be added on top of the QM/MM multi-layer approach as an ``implicit" solvent model (in the sense that the average solvent charge density is approximated as a dielectric medium). We find that several extan (open full item for complete abstract)

Committee: John Herbert PhD (Advisor); Sherwin Singer PhD (Committee Member); Terry Miller PhD (Committee Member) Subjects: Molecular Physics; Physical Chemistry

Master of Arts, The Ohio State University, 1973, Graduate School

Committee: Not Provided (Other) Subjects:

Doctor of Philosophy, The Ohio State University, 2021, Chemistry

In the following work, we discuss the development and application of efficient techniques either aimed at extending the applicability of the currently available methods in the liquid phases to larger system sizes, or at eliminating the artifacts with the existing techniques for several open-shell systems encountered in condensed phases. First, we have investigated the local solvation structure of aqueous hydroxyl radical and absorption spectrum by employing both the mixed quantum mechanics\slash molecular mechanics (QM/MM) framework and periodic density functional theory (DFT) framework. Theoretically, the presence of a hemibond (a two-center, three-electron bond) in this system has been debated for a long time. This structural motif has been explained as either an artifact arising from the self-interaction error (SIE) in DFT or an artifact because of the finite-size effects of the simulation cell but shown to play an important role in the absorption spectrum based on some theoretical studies on smaller representative clusters. Our investigations based on simulations with various DFT simulations suggest that a pseudo-hemibonded motif still persists in this system. We have also demonstrated that the population of hemibonds is extremely sensitive to the amount of exact Hartree-Fock (HF) exchange employed in the simulation. However, we have concluded that these hemibonded motifs play an outsized role in the absorption spectrum, even when present as a rare configuration, due to an intense charge-transfer transition in the hemibonded structures. To eliminate the artifacts arising from this SIE, we have then implemented the density-corrected DFT (DC-DFT) formalism along its analytical gradient, which has been proven to be powerful for the systems with larger density-driven errors. Afterward, we have applied this technique for studying the electronic structure descriptions of the hole defects in Al-doped silica and electron-polarons in anatase titanium oxide where most of (open full item for complete abstract)

Committee: John M. Herbert (Advisor); Marcos Sotomayor (Committee Member); Alexander Y. Sokolov (Committee Member) Subjects: Chemistry; Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2015, Chemical Physics

Astrochemistry studies chemical reactions that occur in the interstellar medium. Most astrochemical studies focus on the detection of interstellar molecules via rovibrational spectroscopy or the interpretation of their abundance using reaction dynamics. This thesis is divided into two parts, and in each of them we address one of the two aspects from the perspective of theoretical chemistry. In the first part we propose the synthetic route for propene (CH3-CH=CH2), which has a surprisingly high abundance as the most saturated organic molecule in the extremely cold and thin gas-phase medium. Based on the reaction rates obtained from experiments and ab initio calculations for all three reactions in this route, we simulate the time-evolution for the abundance of propene and find that our synthetic route is able to reproduce part of the observed propene abundance. In the second part we discuss the spectroscopy and the dynamics of H5+, aiming to decipher its role as the intermediate of the astrochemically important proton transfer reaction, H3+ + H2 -> H5+ -> H2 + H3+. The large amplitude motions (LAM's) in H5+ allow the protons to permute between H3+ and H2 and result in products that have different nuclear spins and rovibrational states from the reactants. These LAM's introduce challenges to the theoretical studies of H5+ because the conventional harmonic oscillator and rigid rotor approximation is no longer valid. Diffusion Monte Carlo and its extensions are used to capture the couplings between LAM's and other rovibrational modes in H5+. Specifically, we focus on three LAM's: the proton transfer vibration, the H2-H2 torsion, and the internal rotation of H3+ about its C3 symmetry axis. For selected states of H5+, we evaluate energies and wave functions as well as the reaction paths for the above-mentioned proton transfer process. In the spectroscopic studies, we find that the proton transfer vibration has a significant mixing with the dissociation vibration, (open full item for complete abstract)

Committee: Anne McCoy (Advisor); Terry Miller (Committee Member); John Wilkins (Committee Member) Subjects: Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2011, Chemistry

Using Diffusion Monte Carlo, vibrational and rotational excited states of CH5+ and its deuterated isotopologues are evaluated and analyzed. A method for evaluating anharmonic corrections to energies along a minimized energy path for the reaction CH3+ + H2 → CH5+ → CH3+ + H2 is also discussed. For the vibrational excited states, the fundamentals in the five modes for CH5+ and CD5+ are calculated. The fundamentals are generated by requiring that the wave functions change sign at specified values of the five Symmetry Adapted Linear Combinations (SALC's) of the CH or CD bond lengths. While the definitions of these modes are based on displacements of the CH or CD bond lengths, the frequencies are found to be low compared to previously calculated CH vibrational frequencies of CH5+. The totally symmetric mode, with A1+ symmetry, has a calculated frequency of 2164 and 1551 cm-1 for CH5+ and CD5+. The frequencies of the four fundamentals that arise from excitation of the four SALC's that transform under G1+ symmetry have frequencies that range from 1039 to 1383 and 628 to 893 cm-1 in CH5+ and CD5+, respectively. The origins of the broken degeneracy are investigated and are found to reflect extensive coupling to the two low-frequency modes that lead to isomerization of CH5+. For the rotational excited states, the J=1, |K|=0,1 rotationally excited states of CH5+ and its deuterated isotopologues are calculated. The calculated J=1, |K|=0,1 rotationally excited state energies are high in energy when compared to the rotational energies calculated from vibrationally averaged rotational constants. The energy of a low-lying inversion mode that corresponds to a low-energy tunneling doublet is also calculated. When the inversion energy is subtracted from that of the J=1, |K|=0,1 rotational energy, the energies are in good agreement with those calculated from the vibrationally averaged rotational constants. The low-lying inversion mode cannot be removed from the calculations because of (open full item for complete abstract)

Committee: Anne McCoy PhD (Advisor); Terry Gustafson PhD (Committee Member); Sherwin Singer PhD (Committee Member) Subjects: Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2010, Chemistry

The spectroscopy and dynamics of various van der Waals complexes have been in- vesitgated. The electronic spectra resulting from the (B-X) transitions in He-Br2 and He-I2 were calculated and compared to each other and to experiment. Differences in the higher energy spectral feature in both the experimental and calculated spectra led to the question of the origin of its structure. To investigate this difference, the He-Br2 spectrum using the parameters from the He-I2 B-state potential surface, and the He-I2 spectrum using the B-state potential parameters of He-Br2 were calculated. It was determined that the features within the spectra are dictated by the rotational structure of the I2/Br2 rather than the anisotropies in the potential surface. This theory was further tested by approximating the He-I2 B-state surface as a simplified elliptical potential which further demonstrated that the spectral structure of these systems, initially believed to be very complex, can be described with simple models that are relatively insensitive to the details of the potential surface. Excited-state probability amplitudes and their corresponding energies have been calculated for the H2-I2 and D2-I2 systems to gain insights into the nature of the excited states. Due to the nature of the van der Waals bond between the H2/D2 and the I2 and the relative insensitivity of these rare gas-dihalogen complexes to the details of the excited-state surfaces, it was assumed that there is little dependence on the orientation of the H2/D2 axis relative to the I2, and the H2/D2 were treated as spherical. The calculations of the H2-I2 and D2-I2 intermolecular vibrational energies within the H2/D2 + I2(B,v'=20) potential energy surface (PES), using a scaled potential model based on the He + I2(B,v'=20) were performed, and the resulting energies were compared to experiment to help in the assignment of spectral features. To investigate the dynamics of van der Waals species, hydrogen-transfer reactions wer (open full item for complete abstract)

Committee: Anne McCoy PhD (Advisor); Terry Miller PhD (Committee Member); Russell Pitzer PhD (Committee Member); Scott Sheer PhD (Committee Member) Subjects: Chemistry