Physical Sciences and Mathematics Commons^™

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Identification Of Chemical Structures And Substructures Via Deep Q-Learning And Supervised Learning Of Ftir Spectra, Joshua D. Ellis

MSU Graduate Theses

Fourier-transform infrared (FTIR) spectra of organic compounds can be used to compare and identify compounds. A mid-FTIR spectrum gives absorbance values of a compound over the 400-4000 cm^-1 range. Spectral matching is the process of comparing the spectral signature of two or more compounds and returning a value for the similarity of the compounds based on how closely their spectra match. This process is commonly used to identify an unknown compound by searching for its spectrum’s closes match in a database of known spectra. A major limitation of this process is that it can only be used to identify …

Emergent Photophysics In Diketopyrrolopyrrole Superstructures, Andrew Levine

Dissertations, Theses, and Capstone Projects

Organic semiconductors have received substantial attention as active components in optoelectronic devices because of their processability and customizable electronic properties. Tailoring the organic active layer in these devices to exhibit desirable optoelectronic properties requires understanding the complex and often subtle structure-property relationships governing their photophysical response to light. Both structural organization and frontier molecular orbitals (FMO) play pivotal roles in energy relaxation processes, and complex interplay between organization and orbital energies are difficult to anticipate based upon the molecular structure of the components alone, especially in systems comprised of multiple components. In pursuit of design rules, there is a need …

Cu-Promoted C-H Bond Hydroxylation Inspired By Cu-Dependent Metalloenzymes, Rachel Trammell

Chemistry Theses and Dissertations

From 2003 to 2015, Schӧnecker and Baran proposed a dinuclear Cu/O₂ species in their mechanistic proposal for the hydroxylation of sp³ C-H bonds within their systems (proposed based on yields). Inspired from the site selectivity of this methodology and poor analysis of the mechanism, the first project was inspired to re-examine the sp³ C-H bond hydroxylation by Schrӧnecker and Baran and perform an intensive investigation into understanding how Cu/O₂ interact which led us to propose a new mechanism based on the evidence collected (i.e., LCu^II-hydroperoxide species that undergoes homolytic O-O bond cleavage). From there …

Applications Of Sodium Azide In The Synthesis Of Tetrazines And Hydrolysis Reactions, My Le

Honors Theses

The inverse electron demand Diels−Alder cycloadditions of heterocyclic azadienes have provided a robust methodology for synthesizing highly substituted and functionalized heterocycles. It is widely used in organic synthesis and the pharmaceutical industry in the divergent construction of screening libraries and bioorthogonal conjugation. Each heterocyclic azadiene was found to possess a unique reactivity toward different classes of dienophiles, display predictable modes of cycloaddition, and exhibit substantial substituent electronic effects impacting their intrinsic reactivity and cycloaddition regioselectivity. Synthesis of 1,2,4,5-tetrazine has been reported in the literature since the late 19th century, showing scientists' tremendous interest in its application.

Herein we attempt to …

Synthesis Of A Dd-Π-Aa Organic Dye For Dye-Sensitized Solar Cells, Hope Lovell

Honors Theses

This project investigates the synthesis of a DD-π-AA (dual donor/dual acceptor) organic dye as a potential sensitizer for dye-sensitized solar cells (DSCs). The design of this dye was based off previous research that found dual donor/dual acceptor dyes exhibited promising results when used in a DSC. The donor groups, acceptor groups, and π-bridge were chosen for their stability, ability to absorb in the near-infrared (NIR) region, and intramolecular charge transfer (ICT) abilities.

While many components of the dye were synthesized, the final stages of the synthetic scheme were not completed due to the loss of time from COVID-19. Had the …

Synthesis Of A Zinc Dipyrrin Complex For Photocatalytic Reduction Of Co2, Sylvia Meredith

Undergraduate Honors Theses

Zinc dipyrrin complexes have the potential to act as cheap, effective photosensitizers. Synthesizing and studying different types could lead to more efficient solar energy harvesting processes, especially the production of solar fuel. Here, two attempts to synthesize 1,3,7,9-tetraphenyl-5-mesityldipyrromethene are reported and discussed. According to ¹H NMR, the first synthesis attempt was not successful. The second synthesis attempt was not purified effectively, so ¹H NMR produced inconclusive results. Further purification strategies or alternate synthesis methods are required.

The Synthesis Of Photoswitchable Triptan Derivatives, Chelsea Sainsbury

Honors College

Serotonin has various functions throughout the body and directly effects many neurological diseases/disorders, like depression, that are linked to the dysregulation of serotonin. Triptans are indole containing drugs that bind to a subset of serotonin receptors (5-HT1Band 5-HT1D) and are used to treat migraines. In this project, the synthesis of anindole intermediate is attempted. Ideally, an azobenzene would have been added to the 5th position (replacing the primary amine). Azobenzenes are compounds composed of 2 benzene rings connected by a nitrogen-nitrogen double bond that can switch between cis and trans conformations by absorbing different wavelengths of light. The transformation of …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …