First Advisor

Theresa M. McCormick

Term of Graduation

Summer 2022

Date of Publication


Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Chemistry







Physical Description

1 online resource (xxiii, 176 pages)


Molecular modeling is a useful tool in the field of catalyst design for various processes. The use of Density Functional Theory (DFT) is routine in almost every discipline of chemistry. This allows for a deeper understanding of a molecular system even in situations where implementation of an experimental technique is unfeasible. However, without the right choice of theory and insufficient description, the model becomes susceptible to produce ambiguous results. This often leads to poor correlation with experimental findings hence an incomplete understanding of the system under study. Hence, to acquire a thorough knowledge of the intricacies involved in a system, a judicious survey of the molecular model is necessary.

Explored herein are embodiments of four catalytic systems, combining computational and experimental techniques, to better understand the structure-function relationship. The systems of choice include twelve homoleptic, and two heteroleptic Ni(II) tris-pyridinethiolate water splitting catalysts, an organo-photocatalyst for aerobic oxidation of benzylic alcohols, and finally a series of eighteen diarylhalonium salts and diarylchalcogenides.

The first chapter describes a detailed study on homoleptic water splitting catalysis that demonstrates the impact of intramolecular hydrogen bonding (H-bonding) on the pKa of octahedral tris-(pyridinethiolato)nickel (II), [Ni(PyS)3]-, commonly referred to as Ni(II) tris-pyridinethiolate. Protonation is a key step in catalytic proton reduction to produce hydrogen gas, and thus optimizing the catalyst's pKa is critical for catalyst design. DFT calculations on a Ni(PyS)3]- catalyst, and eleven derivatives, demonstrate geometric isomer formation in the protonation step of the catalytic cycle. Through Quantum Theory of Atoms in Molecules (QTAIM), we show that the pKa of each isomer is driven by intramolecular H-bonding of the proton on the pyridyl N to a S on a neighboring thiopyridyl (PyS-) ligand. Experimental measurements used to determine the pKa and reduction potential (E0) of the catalysts support the formation of the geometric isomers upon protonation, although the isomers complicate understanding the experimental results. This work demonstrates that ligand modification via the placement of electron-donating (D) or electron-withdrawing (W) groups may have unexpected effects on the catalyst's pKa due to intramolecular H bonding. This work suggests the possibility that modification of substituent placement on the ligands to manipulate H bonding in homogeneous metal catalysts could be explored as a tool to simultaneously target both desired pKa and E0 values in small molecular catalysts.

In the subsequent chapter a strategy to fine-tune the efficiency of a water splitting Ni(PyS)3]- catalyst through heteroleptic ligand design was explored using a computational investigation of the complete catalytic mechanism. DFT calculations supported by topology analyses using QTAIM, show introduction of electron donating (D) -CH3 and electron withdrawing (W) -CF3 groups on the PyS- ligands of the same complex can tune the pKa and E0, simultaneously. Computational modeling of two heteroleptic nickel(II) tris-pyridinethiolate complexes with 2:1 and 1:2 ED and EW -CH3 and -CF3 group containing PyS- ligands, respectively, suggests that the ideal combination of EW to ED groups is 2:1. This work also outlines the possibility of formation of a large number of isomers after the protonation of one of the pyridyl N atoms as observed in the homoleptic catalysis, and suggests that it is important to carefully account for all possible geometric isomers in order to obtain unambiguous computational results. This work provides a roadmap for synthetic chemists to achieve a better water splitting catalyst that could work in elevated pH media with lower overpotential.

The next chapter describes a novel reaction pathway to photochemically oxidize a benzylic alcohol using an organocatalyst, N-hydroxyphthalimide (NHPI), and allows for the simultaneous access to hydrogen peroxide (H2O2) as a value-added byproduct under metal-free conditions. Photocatalytic oxidation of alcohols using oxygen often proceeds through excitation of oxygen from its triplet ground state to the singlet excited state where, singlet oxygen (1O2) is produced by using a photosensitizer to excite oxygen. Through computational and experimental investigation of the process, we have evaluated that the process utilizes 1O2 as the oxidant, that converts NHPI to the active radical intermediate phthalimide-N-oxyl (PINO). PINO initiates the oxidation on the organic motif by the abstraction of a H atom. Understanding the process in greater detail using computational methodologies will allow for the design of more efficient photocatalysts that are capable of carrying out more complicated aerobic oxidations using greener methods which is of immense interest for both laboratory and industrial scale reactions.

Finally, a series of diarylhalonium salts and isoelectronic diarylchalcogenides were studied. This chapter entails the deviation of the structural parameters of these compounds from the well-accepted three center-four electron (3c-4e) bonding model. The existing 3c-4e model describes the bonding in λ3-iodanes accurately, however, fails to account for any structural deviation based on the periodic trends for hypervalent halogens and chalcogens. To provide a better understanding of the bonding and properties such as halogen bonding, and Lewis acidity, a major restructuring of the existing bonding theory was required. That was achieved by the inclusion of computed s- /p- orbital mixing on the molecular orbitals directed toward the incoming substituents, based on qualitative Bent's rule. The introduction of orbital mixing along with the electronegativity of the substituents in the revised bonding could account for both experimentally observed thermodynamic and kinetic reactivity of a series of halonium salts.

This work entails the exploration of different chemical systems that utilizes appropriate molecular model using computational methodologies. The calculated results were compared with the experimental investigations and a good correlation was observed. The molecular models described herein can be extrapolated to structurally allied systems to gain a better understanding of the underlying structure-function relationships.


© 2022 Avik Bhattacharjee

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Available for download on Tuesday, June 20, 2023