Other Chemistry Commons^™

From Small Molecules To Infinite Crystals: Probing Noncovalent Interactions Through Vibrational Spectroscopy, Sadisha Nanayakkara

Chemistry Theses and Dissertations

During my four years in the CATCO group supervised by Dr. Kraka, I have been exposed to various topics targeted to address a multitude of chemical problems, broadening our knowledge of modern chemistry research as we know it. In undertaking the age-old problem of understanding the nature of chemical bonding, I could modestly contribute with my work, using in-house tools based on vibrational spectroscopy.

First part of my dissertation is focused on inventing new methods and tools to efficiently investigate chemical bonding, followed by the study of some non-covalent interactions, imperative in catalysis and solid-state chemistry. This includes analysis of …

Crystal Structure Of 2-(2,6-Diisopropylphenyl)-N,Ndiethyl- 3,3-Dimethyl-2-Azaspiro[4.5]Decan-1- Amine: A Diethylamine Adduct Of A Cyclic(Alkyl)- (Amino)Carbene (Caac), Roxanne A. Naumann, Joseph W. Ziller, Allegra Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The structure of the title compound, C₂₇H₄₆N₂, at 93 K has monoclinic (P2₁/n) symmetry. The title compound was prepared by treatment of 2-(2,6-diiso­propyl­phenyl)-3,3-dimethyl-2-aza­spiro­[4.5]dec-1-en-2-ium hydrogen dichloride with two equivalents of lithium di­ethyl­amide. Characterization of the title compound by single-crystal X-ray diffraction and ¹H and ¹³C NMR spectroscopy is presented. Formation of the di­ethyl­amine adduct of the cyclic(alk­yl)(amino)­carbene (CAAC) was unexpected, as deprotonation using lithium diiso­propyl­amide results in free CAAC formation.

Stimuli Responsive Dye-Containing Peg-Pla Block Copolymer Micelles And Computationally Assisted Design Of A Stapled Peptide Bundle, Tyler L. Odom

Graduate Theses/Dissertations

In this thesis, I report the preparation and characterization of dye-containing PEG-b-PLA block copolymer micelles and the computational design of a novel coiled-coil peptide bundle. The PEG-b-PLA micelles encapsulate hydrophobic molecules into their core and have strong potential as nanocontainers or delivery vesicles. In theory, these internalized molecules can be released upon exposure to mechanical forces that disrupt the micellar structures. This force-responsive nature is one of the inherent properties of micellar systems. However, there is a stark lack of research that utilize this property in applications. Along those lines, I have studied the behavior of …

Biomaterials With Structural Hierarchy And Controlled 3d Nanotopography Guide Endogenous Bone Regeneration, Shixuan Chen, Hongjun Wang, Valerio Luca Mainardi, Giuseppe Talò, Alec Mccarthy, Johnson V. John, Matthew J. Teusink, Liu Hong, Jingwei Xie

Department of Chemistry: Faculty Publications

Biomaterials without exogenous cells or therapeutic agents often fail to achieve rapid endogenous bone regeneration with high quality. Here, we reported a class of three-dimensional (3D) nanofiber scaffolds with hierarchical structure and controlled alignment for effective endogenous cranial bone regeneration. 3D scaffolds consisting of radially aligned nanofibers guided and promoted the migration of bone marrow stem cells from the surrounding region to the center in vitro. These scaffolds showed the highest new bone volume, surface coverage, and mineral density among the tested groups in vivo. The regenerated bone exhibited a radially aligned fashion, closely recapitulating the scaffold’s architecture. The organic …

Aromatic Substitution: Another View, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

Electrophilic substitution on substituted benzenes is reviewed in terms of molecular orbitals. The HOMO falls into two classes. For all meta director C-X groups, a node passes through the ring and through the substituent C-X bond. With ortho/para director C-X groups, a node perpendicular to the one described above, passes through the ortho-meta bonds.

Gate-Tunable Optical Extinction Of Graphene Nanoribbon Nanoclusters, Erin Sheridan, Gang Li, Mamun Sarker, Shan Hao, Ki-Tae Eom, Chang-Beom Eom, Alexander Sinitskii, Patrick Irvin, Jeremy Levy

Department of Chemistry: Faculty Publications

We investigate the optical response of graphene nanoribbons (GNRs) using the broadband nonlinear generation and detection capabilities of nanoscale junctions created at the LaAlO₃/SrTiO₃ interface. GNR nanoclusters measured to be as small as 1–2 GNRs in size are deposited on the LaAlO₃ surface with an atomic force microscope tip. Time-resolved nonlinear optical probes of GNR nanoclusters reveal a strong, gate-tunable second and third harmonic response, as well as strong extinction of visible to near-infrared light at distinct wavelengths, similar to previous reports with graphene.

Computational Analysis Of Type 3 Iodothyronine Deiodinase: Potential Inhibitors, Substrate Binding, And Dimer Structure, Eric Scott Marsan

Chemistry & Biochemistry Theses & Dissertations

Thyroid hormones (THs) in mammalian tissues are crucial for development and maintaining metabolic homeostasis. Iodothyronine deiodinases (Dios) remove iodines from THs by a selenocysteine (Sec) residue, which either activates or inactivates them. Halogen bonding (XB) has been proposed to describe the interaction between the Se and I atoms of the T4-Dio complex. Disruption of TH homeostasis by xenobiotics, such as polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) can cause deleterious effects on the endocrine system. Experimental studies have indicated that PBDEs and PCBs could disrupt TH homeostasis by inhibiting Dio through XB formation. However, no current quantitative study exists …

Ultrafast Adsorbate Excitation Probed With Subpicosecond-Resolution X-Ray Absorption Spectroscopy, Elias Diesen, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Tony F. Heinz, Frank Abild-Pedersen, Johannes Voss, Alan C. Luntz, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We use a pump-probe scheme to measure the time evolution of the C K-edge x-ray absorption spectrum from CO/Ru(0001) after excitation by an ultrashort high-intensity optical laser pulse. Because of the short duration of the x-ray probe pulse and precise control of the pulse delay, the excitation-induced dynamics during the first picosecond after the pump can be resolved with unprecedented time resolution. By comparing with density functional theory spectrum calculations, we find high excitation of the internal stretch and frustrated rotation modes occurring within 200 fs of laser excitation, as well as thermalization of the system in the picosecond …

A Bacterial Inflammation Sensor Regulates C-Di-Gmp Signaling, Adhesion, And Biofilm Formation, Arden Perkins, Dan A. Tudorica, Raphael D. Teixeira, Tilman Schirmer, Lindsay Zumwalt, O. Maduka Ogba, C. Keith Cassidy, Phillip J. Stansfeld, Karen Guillemin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacteria that colonize animals must overcome, or coexist, with the reactive oxygen species products of inflammation, a front-line defense of innate immunity. Among these is the neutrophilic oxidant bleach, hypochlorous acid (HOCl), a potent antimicrobial that plays a primary role in killing bacteria through nonspecific oxidation of proteins, lipids, and DNA. Here, we report that in response to increasing HOCl levels, Escherichia coli regulates biofilm production via activation of the diguanylate cyclase DgcZ. We identify the mechanism of DgcZ sensing of HOCl to be direct oxidation of its regulatory chemoreceptor zinc-binding (CZB) domain. Dissection of CZB signal transduction reveals that …

Assessing Competitive Reaction Rates In The Nitration Of 2-Methylbiphenyl, Biphenyl, And Toluene To Determine Steric Restriction In Resonance-Stabilized Planarization Of The Carbocation Intermediates, Victor A. Hanson, Tristan Wine, Kevin Bartlett, Joshua Padilla, Alessandro Rizzi

Honors Projects

Electrophilic aromatic substitution (EAS) reactions have long been a fundamental addition to sophomore-level organic chemistry classes, allowing students the opportunity to explore the electron donating and withdrawing effects of electrons contained in the substituents of the aromatic reactant. In this paper we present preliminary findings on the nitration of methylated biphenyls using kinetic and regioselective assessments to analyze steric influences on the planarization of 2-methylbiphenyl after EAS nitration. Our preliminary findings show that nitration favors the methylated phenyl ring of 2-methylbiphenyl, indicating that the steric influence of the methyl group restricts planarization of the carbocation intermediate. Furthermore, a competition nitration …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

A Theoretical Study Of Synchronous Proton Transfer In (Hf)N, (H2O) N, And (Hcl) N Where N = 3, 4, 5, Johnny Yang

Honors Theses

For (HF)_n, (H₂O)_n, and (HCl)_n (n = 3 − 5), we have rigorously characterized the structures for the minima and transition states for synchronous proton transfer (SPT) with the CCSD(T) method and aug-cc-pVTZ basis set. The electronic barrier heights (∆E^†) associated with these transition states have also been computed with the explicitly correlated CCSD(T)-F12 method and the aug-cc-pVQZ-F12 basis set (abbreviated aQZ-F12). (HCl)_n (n = 3 − 5) SPT transition states have not been previously identified to the best of our knowledge, and they have been found …

Water Purification And The Industries It Supports, Zeljka Zec, Kj Bell

Symposium of Student Scholars

Water Purification and the Industries It Supports

Zeljka Zec and KJ Bell

Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Ga 30144

Clean and readily available water plays a crucial role in daily societal functions. The dynamic research of water purification involves the process of removing undesired chemical or biological contaminants that affect our use of fresh, consumable water. Depending on desired applications, purification quality is adjusted for use in medical settings, manufacturing, agriculture or personal use in households. Several methods and techniques have been used in the water purification process. Those processes are coagulation, flocculation, sedimentation, and filtration. …

Using Eye-Tracking Data To Determine What Biochemistry Students Attend To When Completing A Revised Three-Dimensional Modeling Activity, Hailey Knoeferl

Symposium of Student Scholars

In biochemistry, three-dimensional models are being used to help students comprehend advanced topics within the subject. Because a greater cognitive load is often related to three-dimensional models, learning what raises the cognitive load is critical. From there, measures can be taken to help lower the cognitive load and make the material easier for students to understand. To understand cognitive load in relation to models, students were presented with three-dimensional serine protease models and their substrates and asked to match the clear surface plate to the backbone, and then the substrate to the surface plate. On the substrates, students were asked …

Computational Investigation Of Stellar Cooling, Noble Gas Nucleation, And Organic Molecular Spectra, Jax Dallas

Honors Theses

Since the advent and optimization of the Hartree-Fock method, quantum chemistry has been utilized to investigate systems operating on timeframes and environments traditionally unavailable to bench-top chemistry. As computational methods have grown more robust and less time consuming, quantum chemistry has been utilized to investigate a range of fields, including the steadily growing discipline of computational astrochemistry. Through the lens of computational astrochemistry, chemistry that occurred billions of years ago can be explored with equal clarity to that which is currently happening in the cosmos. The work presented throughout this thesis is a series of investigations into different timeframes of …

Oriented External Electric Field (Oeef) Tuning Of Unsubstituted Azoheteroarene Photoswitching Performance., Irma Avdic

College of Arts & Sciences Senior Theses

Azoheteroarenes are relatively new photoswitchable compounds, where one of the phenyl rings of an azobenzene molecule is replaced by a heteroaromatic five-membered ring. Although few studies have been performed, recent findings on methylated azoheteroarenes show that these photoswitches have great potential in various optically addressable applications. Thermal stability of molecular switches is one of the primary factors considered in the design process. For the purposes of quick information transmission in materials science, the thermal (Z – E) relaxation process should be as short as possible. On the other hand, molecular memory storage devices prefer long Z - E relaxation times. …

A Conductivity Analysis Of A Newly Synthesized Poly(Ethylene Glycol) Methyl Ether Hydroxide Electrolyte, Sarah Marie Peterson

Honors Theses

This thesis investigates the synthesis and conductive properties of a Poly (ethylene glycol) methyl ether-based polymer electrolyte. The goal of the synthesis is to enhance the hydroxide ion conduction properties of the polymer with its cationic groups attached. The MePEG backbone contained seven ethylene glycol groups and was modified to substitute the hydroxide group in the MePEG with trimethylamine. In addition, the bromide added in the synthesis was exchanged for hydroxide ions to allow for the transportation of hydroxide ions in polymeric electrolytes that can be used in Anion Exchange Membrane Fuel Cells. The newly synthesized polymer was compared to …

Structure Formation And Coupling Reactions Of Hexaphenylbenzene And Its Brominated Analog, Jacob D. Teeter, Paulo S. Costa, Christoph Dobner, Mamun Sarker, Alexander Sinitskii, A Enders

Department of Chemistry: Faculty Publications

The on-surface coupling of the prototypical precursor molecule for graphene nanoribbon synthesis, 6,11-dibromo-1,2,3,4-tetraphenyltriphenylene (C₄₂Br₂H₂₆, TPTP), and its non-brominated analog hexaphenylbenzene (C₄₂H₃₀, HPB), was investigated on coinage metal substrates as a function of thermal treatment. For HPB, which forms non-covalent 2D monolayers at room temperature, a thermally induced transition of the monolayer’s structure could be achieved by moderate annealing, which is likely driven by π-bond formation. It is found that the dibrominated carbon positions of TPTP do not guide the coupling if the growth occurs on a substrate at temperatures that …

Studies Of The Rectification Behavior Of The Pdt Ligand And The Active Site Of Msrp, Laura J. Ingersol

Chemistry and Chemical Biology ETDs

Molybdenum (Mo) is an essential element that plays an important role in global nitrogen, carbon, and sulfur cycles with a critical role in human metabolism and ecological balance. It becomes catalytically active when complexed with the pyranopterin dithiolene ligand (PDT), forming the nearly ubiquitous molybdenum cofactor (Moco). The complex biosynthetic pathway of Moco, its presence in all three domains of life, and its role as a constituent cofactor in the last universal common ancestor (LUCA) all point toward the importance of the PDT in the development of life on Earth. Molybdoenzymes catalyze the two-electron oxidation or reduction of substrates that …

Dibenzophosphole Synthesis From 4-4’-Ditertbutyl-1,1’-Biphenyl By Double C-P Bond Formation, Annette Echevarria

Campus Research Month

No abstract provided.