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Articles 1 - 10 of 10
Full-Text Articles in Computational Chemistry
Computational Quantum Chemistry Studies Of The Stabilities Of Radical Adducts Formed During The Oxidation Of Melatonin Derivatives, James Horne
Electronic Theses and Dissertations
Melatonin is a natural antioxidant that has been investigated for properties as a potential spin trap to identify short-lived free radicals. Computational quantum chemistry studies have been performed for the oxidation of melatonin to N1-acetyl-N2-formyl-5-methoxykynuramine. This research focused on modification of melatonin into derivatives and analyzing the change in total molecular energy from melatonin to its oxidation product, as well as the corresponding derivatives. Each of the molecular geometries were optimized at the DFT/B3LYP/6-31G(d), DFT/B3LYP/cc-pVXZ (X = D, T), HF/6-31G(d), HF/cc-PVXZ (X = D, T), MP2/6-31G(d), and MP2/cc-PVXZ (X = D, T) levels of theory. …
Computational Investigations Of Bond Breaking Processes Using Dft And Td-Dft Approaches., Saurav Parmar
Computational Investigations Of Bond Breaking Processes Using Dft And Td-Dft Approaches., Saurav Parmar
Electronic Theses and Dissertations
The efficient application of DFT and TD-DFT has been harnessed to study bond-breaking processes in some molecules which play a prominent role in enzymatic reactions. The first application includes Radical S-adenosyl methionine (SAM) enzymes which are fundamentally important sources of organic radicals to initiate diverse radical reactions. Recently a bio-organometallic intermediate (Ω) that contains an Fe‒C bond has been characterized and shown to be a common feature of radical SAM enzymes. The strength of Fe‒C bond in Ω has been computed using broken-symmetry density functional theory (BS‒DFT). Additionally, Fe‒C bond dissociation energy (BDE) in Ω has been compared to that …
Quantum Mechanical Studies Of Water Splitting Reaction With (Zno)3 Nanoclusters As Catalysts, Duwage C. Perera
Quantum Mechanical Studies Of Water Splitting Reaction With (Zno)3 Nanoclusters As Catalysts, Duwage C. Perera
Electronic Theses and Dissertations
With the current energy crisis, H2 production through the water-splitting reaction has drawn attention recently. In this thesis, I studied the structural (geometry) and electronic properties (vertical detachment energy and electron affinity) of ZnO monomers and dimers using density functional theory. ZnO is a metal oxide with a 3.37 eV band gap and can be a commercially cheaper photocatalyst in hydrogen (H2) production. The B3LYP/DGDZVP2 pair was selected after investigating different pairs of exchange functionals and basis sets to study the hydration, hydrolysis, and water-splitting reaction. The singlet-triplet energy gaps of small (ZnO)n clusters (n=1-6) of …
Development Of Nonorthogonal Wavefunction Theories And Application To Multistate Reaction Processes., Emily Kempfer
Development Of Nonorthogonal Wavefunction Theories And Application To Multistate Reaction Processes., Emily Kempfer
Electronic Theses and Dissertations
Many prominent areas of technological development rely on exploiting the photochemical response of molecules. An application of particular interest is the control of molecular switches through a combination of different external stimuli. However, despite significant advances in theoretical approaches and numerous cases of successful application of theory, simulating photochemical reactions remains a computational challenge. Theoretical methods for describing excited states can be broadly divided into single-reference response methods and multireference methods. Single reference methods provide reliable semiquantitative results for single excitations. However, these methods cannot describe double-excited states, systems with strongly correlated ground states, or regions of degeneracy on the …
Biophysical Insights Into Peptide And Alcohol Perturbations On Biomimetic Membranes, Michael Hai Nguen
Biophysical Insights Into Peptide And Alcohol Perturbations On Biomimetic Membranes, Michael Hai Nguen
Electronic Theses and Dissertations
Biological membranes exist in every domain of life. Life exists due to the presence of these special structures for which we take for granted. They are composed of fatty lipids and workhorse proteins and act as the premier interface of biological processes. Due to the sheer quantity and complexity within their thin boundary, studying their actions and properties pose challenges to researchers. As a result, simplified biomembrane mimics are employed regularly. We will use several types of biomembrane mimics to understand fundamental properties of membranes. In the present thesis, we also attempt to move beyond the canonical structure-based theories upon …
Gold (I) Tetrathiomolybdate Clusters: Synthesis, Characterization, Computational Studies, And Reactivity With Thiophenol And Selenophenol, Dhirgam Humaidy
Gold (I) Tetrathiomolybdate Clusters: Synthesis, Characterization, Computational Studies, And Reactivity With Thiophenol And Selenophenol, Dhirgam Humaidy
Electronic Theses and Dissertations
This thesis describes the synthesis and reactivity of heterometallic complexes containing medicinally active Au(I) and tetrathiomolybdate, [MoS4]2-. The research is motivated by the idea of multifunctional drugs, which are designed to treat diseases through two or more mechanisms of action. Five clusters of the general form, [MoS4(AuL)2] were prepared: C-1 (L=IPr), C-2 (L=IBzMe), C-3 (L=IMes), C-4 (L=PPh3), and C-5 (L=PEt3). The clusters with NHC ligands, C-1, C-2, and C-3 were prepared for the first time and thoroughly characterized by 1H NMR,13C{1H} …
Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez
Electronic Theses and Dissertations
Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …
Turning Ligands On Their Side: Computational Investigation Into The Binding Of N2o And N2 In Transition Metal Complexes, Cole Donald
Electronic Theses and Dissertations
Common greenhouse gas nitrous oxide (N2O) is a thermodynamically potent and environmentally benign oxidant, making it a desirable target for metal center activation. Unfortunately, N2O is a poor ligand for transition metals due to its weak sigma-donating and pi-accepting properties; as a result, few transition metal complexes capable of interacting with N2O have been found. As the primary source of all nitrogen in organisms, abundant gas dinitrogen (N2) is a crucially important tiny molecule and an essential part of daily existence. However, due to its inertness, it has limited practical uses in …
Theory Of Aqueous Solvation: Uninterrupted, Cyclic Hydrogen-Bonding Essential For Accurate Keto-Enol Energies And Grotthuss Tautomerism Of Acetone, Mark Recznik
Electronic Theses and Dissertations
Keto-enol tautomerization (KET) is a fundamental process impacting a range of molecular phenomena in organic and biochemistry. However, the accurate computation of solution-phase KET energies remains a challenge, even for prototypical acetone.
In Part I, keto-enol tautomers of acetone were incorporated into solvent clusters that interact via uninterrupted, cyclic hydrogen-bonding (UCHB) networks. An empirical model was created to predict accurate KET energies, Etaut, of simple carbonyl compounds. Based on the availability of experimental data and structural simplicity, acetone was selected as a prototype. A discrete-continuum strategy was employed – accounting simultaneously for local noncovalent interactions and bulk-phase effects …
Computational Enzymology On Sulfur-Containing Enzymes: From Method To Application, Paul Meister
Computational Enzymology On Sulfur-Containing Enzymes: From Method To Application, Paul Meister
Electronic Theses and Dissertations
Sulfur-containing biomolecules display incredible functional diversity. Indeed, in addition to thiols and thioethers, S-nitrosothiols, 3,4-coordinate, sulfoxides, persulfides and now even polysulfides are commonly observed intermediates. Unfortunately, however, their biological synthesis and roles remain poorly understood. In addition, sulfur-containing species can access a broad range of oxidation states and thus can act as either an electrophile or nucleophile giving rise to an even more diverse set of sulfur-derived functional groups. However, these unique properties can lead to difficulties in characterizing such compounds experimentally and reinforces the need for computational studies to reliably predict their structural and energetic properties. In this dissertation, …