For many pre-health and graduate programs, organic chemistry is often the most difficult prerequisite course that students will take. To alleviate this difficulty, an intelligent tutoring system was developed to provide valuable feedback to practice problems within organic chemistry. This paper focuses on the design and use of an intelligent input parser for nomenclature questions within this system. Students in Dr. Gould's Fall 2014 organic chemistry class used this system and their data was collected to analyze the effectiveness of the input parser. Overall the students' feedback was optimistic and there was a positive relationship between test scores and student use of the system.

Photophysical Studies of the DNA Microenvironment and Small Molecule-DNA Interactions
The photophysical properties of ethidium in a variety of organic solvents, as well as several dsDNAs, were measured. We report that the fluorescence quantum yield of intercalated ethidium is .30(.03), which falls between previous stated measurements of .14 and .60. We believe this to be the most accurately measured fluorescence quantum yield to date, as verified by Strickler-Berg analyses, which exhibit excellent agreement with experimental fluorescence lifetimes. A marked hypochromism upon binding to DNA is noted due to interactions of the dye’s and nucleobases’ respective π-stacks. This more than counteracts the expected increase in transition dipole due to increased conjugation caused by twisting of the phenyl moiety upon intercalation.
The reduced volume cylinder model was tested by the quenching of the fluorescence of an intercalator (ethidium bromide) by a groove binder (methyl viologen). We report that the model is not accurate over a relevant range of DNA concentrations.

The ability to manipulate the interaction between small molecules and biological macromolecules towards the study of disease pathogenesis has become a very important part of research towards treatment options for various diseases. The work described here shows both the use of DNA oligonucleotides as carriers for a nicotine hapten small molecule, and the use of microsomes to study the stability of compounds derived to treat mitochondrial diseases.

Nicotine addiction is a worldwide epidemic because nicotine is one of the most widely used addictive substances. It is linked to early death, typically in the form of heart or lung disease. A new vaccine conjugate against nicotine held within a DNA tetrahedron delivery system has been studied. For this purpose, several strands of DNA, conjugated with a modified dTpT having three or six carbon atom alkynyl linkers, have been synthesized. These strands have later been conjugated to three separate hapten small molecules to analyze which conjugates formed would be optimal for further testing in vivo.

Mitochondrial diseases are hard to treat, given that there are so many different variations to treat. There is no one compound that can treat all mitochondrial and neurodegenerative diseases; however, improvements can be made to compounds currently under study to improve the conditions of those afflicted. A significant issue leading to compounds failing in clinical trials is insufficient metabolic stability. Many compounds have good biological activity, but once introduced to an animal, are not stable enough to have any effect. Here, several synthesized compounds have been evaluated for metabolic stability, and several showed improved stability, while maintaining biological activity.

Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications.

Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to functionalize AFM tips. For multiplexed recognition imaging, recognition heads based on a C3 symmetrical three arm linker with azide functionalities at its ends were synthesized and the chemistry to attach them to AFM tips was developed, and these recognition heads were used in detecting multiple proteins simultaneously using AFM.

A bis-Angiopeptide-2 conjugate with this three-arm linker was synthesized and this was conjugated with anti-West Nile virus antibody E16 site specifically to target advanced West Nile virus infection in the Central Nervous System. The bis-Angiopeptide-2 conjugate of the antibody shows higher efficacy compared to a linear linker-Angiopeptide-2 conjugate of the antibody in in vitro studies and currently the efficacy of this antibody conjugate in studied in mice. Surface Plasmon Resonance imaging (SPRi) results indicate that the conjugation does not affect the antigen binding activity of the antibody very significantly.

A Y-shaped bisbiotin ligand was also prepared as a small sized antibody mimic. Compared to a monovalent biotin ligand, the y-Bisbiotin can cooperatively form a significantly more stable complex with streptavidin through intramolecular bivalent interactions, which were demonstrated by gel electrophoresis, SPR and AFM. Continuing on these lines, a four-arm linker was synthesized containing three single chain variable fragments (scFv) linked to the scaffold to form a tripod base, which would allow them to concomitantly interact with a trimeric Glycoprotein (GP) spike that has a “chalice” configuration. Meanwhile, a human IgG1 Fc is to be installed on the top of the tetrahedron, exerting effector functions of a monoclonal antibody.

The manipulation of biological targets using synthetic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that act either as probes for studying protein conformational changes or DNA–protein interaction, or as multifunctional radical quenchers.

Fluorescent labeling is of paramount importance to biological studies of proteins. For the development of new extrinsic small fluorophores, a series of tryptophan analogues has been designed and synthesized. Their pdCpA derivatives have been synthesized for tRNA activation and in vitro protein synthesis. The photophysical properties of the tryptophan (Trp) analogues have been examined, some of which can be selectively monitored even in the presence of multiple native tryptophan residues. Further, some of the Trp analogues form efficient FRET pairs with acceptors such as acridon-2-ylalanine (Acd) or L-(7-hydroxycoumarin-4-yl)ethylglycine (HCO) for the selective study of conformational changes in proteins.

Molecules which can bind with high sequence selectivity to a chosen target in a gene sequence are of interest for the development of gene therapy, diagnostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Stereoselective synthesis of different alanyl nucleobase amino acids is described. Their pdCpA derivatives have been synthesized for tRNA activation and site-specific incorporation into the DNA-binding protein RRM1 of hnRNP LL. It is proposed that the nucleobase moieties in the protein may specifically recognize base sequence in the i-motif DNA through H-bonding and base-stacking interactions.

The mitochondrial respiratory chain accumulates more oxidative damage than any other organelle within the cell. Dysfunction of this organelle is believed to drive the progression of many diseases, thus mitochondria are an important potential drug target. Reactive oxygen species (ROS) are generated when electrons from the respiratory chain escape and interact with oxygen. ROS can react with proteins, lipids or DNA causing cell death. For the development of effective neuroprotective drugs, a series of N-hydroxy-4-pyridones have been designed and synthesized as CoQ10 analogues. All the analogues synthesized were evaluated for their ability to quench lipid peroxidation and reactive oxygen species (ROS).

For reading DNA bases more accurately, a series of nitrogen-containing aromatic heterocycles have been designed and synthesized as candidates of universal reader to interact with all naturally occurring DNA nucleobases by hydrogen bonding interaction and eventually is used to read DNA by recognition tunneling. These recognition molecules include 6-mercapto-1H-benzo[d]imidazole-2-carboxamide, 5-(2-mercaptoethyl)-1H-imidazole-2-carboxamide, 5-(2-mercaptoethyl)-4H-1,2,4-traizole-3-carboxamide and 1-(2-mercaptoethyl)-1H-pyrrole-3-carboxamide. Their formation of hydrogen bonding complexes with nucleobases was studied and association constants were measured by proton NMR titration experiments in deuterated chloroform at room temperature. To do so, the mercaptoethyl chain or thiol group of these reading molecules was replaced or protected with the more lipophilic group to increase the solubility of these candidates in CDCl3. The 3' and 5' hydroxyl groups of deoxyadenosine (dA), deoxyguanosine (dG), deoxycytidine (dC) and thymidine (dT) were protected with tert-butyldimethylsilyl (TBDMS) to eliminate hydrogen bonding competition from the hydroxyl protons with these candidates as well as to increase the solubility of the nucleosides in CDCl3 for NMR titration experiment. Benzimidazole and imidazole containing readers exhibited the strongest H-bonding affinity towards DNA bases where pyrrole containing reader showed the weakest affinity. In all cases, dG revealed the strongest affinity towards the readers while dA showed the least.

The molecular complex formation in aqueous solution was studied by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry. The formation of both 1:1 and 2:1 complexes between one or two reading molecules and a DNA nucleotide were observed by ESI mass. A series of amino acids and carbohydrates were also examined by mass spectrometry to show the formation of non-covalent complexes with imidazole reader in aqueous solution. The experimental results were compared by calculating energies of ground state conformers of individual molecules and their complexes using computer modeling study by DFT calculations. These studies give insights into the molecular interactions that happen in a nanogap during recognition tunneling experiments.

Biomolecules can easily recognize its corresponding partner and get bound to it, resulting in controlling various processes (immune system, inter or intracellular signaling) in biology and physiology. Bonding between two partners can be a result of electrostatic, hydrophobic interactions or shape complementarity. It is of great importance to study these kinds of biomolecular interactions to have a detailed knowledge of above mentioned physiological processes. These studies can also open avenues for other aspects of science such as drug development. Discussed in the first part of Chapter 1 are the biotin-streptavidin biomolecular interaction studies by atomic force microscopy (AFM) and surface plasmon resonance (SPR) instrument. Also, the basic working principle of AFM and SPR has been discussed.

The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.

To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.

In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.

Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base.

First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory.

Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations.

Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases.

The energy required in a eukaryotic cell is provided by mitochondria. Mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation generates ATP. During electron transport, electron leakage from the ETC produces reactive oxygen species (ROS). In healthy cells, there are preventive and defense mechanisms in place to manage ROS. Maintaining a steady balance of ROS is very important because overproduction of ROS can lead to several pathological conditions. There are several strategies to prevent ROS production. Addition of external antioxidants is widely used among them. Discussed in the first part of Chapter 1 is the mitochondrial ETC, ROS production and antioxidant strategies.

The second part of Chapter 1 is concerned with ribosomal protein synthesis in bacteria. Ribosome, the organelle that synthesizes proteins with exceptional fidelity, has a strong bias for α-L-amino acids. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome could enable the incorporation of both α-D-amino acids and β-amino acids into full length protein.

Oxidative stress is a common cause of various neurological disorders such as Alzheimer’s disease and Parkinson’s disease. Antioxidative strategies are used widely for the treatment of these disorders. Although several antioxidants demonstrated positive results in vitro as well as in in vivo models, none of them have been effective in clinical settings. Hence, there is an ongoing search for effective neuroprotective drugs. Described in Chapter 2 is the synthesis and biological evaluation of several methylene blue analogues as potentially effective antioxidants for the treatment of pathologies related to oxidative stress.

In Chapter 3, the synthesis and ribosomal incorporation of several rationally designed dipeptidomimetic analogues are discussed. The dipeptidomimetic analogues are structurally similar to the GFP chromophore and, therefore, highly fluorescent. In addition, the backbone of the dipeptidomimetic analogues resemble the peptide backbone of a dipeptide, due to which they can be incorporated into protein by modified ribosomes selected for the incorporation of dipeptides.

Discussed in Chapter 4 is the synthesis of the pdCpA derivatives of several β-amino acids. The pdCpA derivatives were ligated to tRNA-COH and were used as probes for studying the regio- and stereoselectivity of modified ribosomes.

The growing use of Learning Management Systems (LMS) in classrooms has enabled a great amount of data to be collected about the study behavior of students. Previously, research has been conducted to interpret the collected LMS usage data in order to find the most effective study habits for students. Professors can then use the interpretations to predict which students will perform well and which student will perform poorly in the rest of the course, allowing the professor to better provide assistance to students in need. However, these research attempts have largely analyzed metrics that are specific to certain graphical interfaces, ways of answering questions, or specific pages on an LMS. As a result, the analysis is only relevant to classrooms that use the specific LMS being analyzed.

For this thesis, behavior metrics obtained by the Organic Practice Environment (OPE) LMS at Arizona State University were compared to student performance in Dr. Ian Gould’s Organic Chemistry I course. Each metric gathered was generic enough to be potentially used by any LMS, allowing the results to be relevant to a larger amount of classrooms. By using a combination of bivariate correlation analysis, group mean comparisons, linear regression model generation, and outlier analysis, the metrics that correlate best to exam performance were identified. The results indicate that the total usage of the LMS, amount of cramming done before exams, correctness of the responses submitted, and duration of the responses submitted all demonstrate a strong correlation with exam scores.