Chemistry Commons^™

Game-Based Learning In Science: Can Video Games Simplify Organic Chemistry?, Rachel Israel

Senior Honors Theses

Organic chemistry has been taught in the same way for decades, and students still have difficulty understanding and comprehending the subject material. Perhaps it is time to change the methods by which this subject is taught. Video games have been successfully used in education to create learning environments that increase student motivation and engagement as well as challenge students and promote collaboration. It is difficult for students to maintain a growth mindset in organic chemistry within the classroom. However across different genres, video games create a unique environment where an individual is encouraged to try again when they fail. This …

The Application Of Machine Learning In Analyzing Organic Compounds From Nmr Spectral Data, Nicole Maia Powell

Senior Independent Study Theses

Nuclear magnetic resonance (NMR) is used in organic chemistry to identify unknown organic compounds. The data obtained from an NMR spectrometer are typically shown in the form of a spectrum, which is then analyzed by an analytical chemist. The action of analyzing a spectrum, especially one of a large and complex molecule, is a long and tedious process. In this project, Python is used to implement hierarchical clustering on NMR data obtained from an NMR spectrometer at the College of Wooster to explore its application in NMR analysis. MATLAB is used to build a decision tree from the same data, …

Peppytides, Dave Zwicky

2019 Symposium on Electronic Theses and Dissertations

Lightning talk for Symposium on Electronic Theses and Dissertations (ETD) at Purdue University on May 23, 2019.

Hartree-Fock Implementation For Pedagogical & Research Purposes, Gary Zeri, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Often during the process of innovation and scientific advancement, experimentation is the key to increasing the current knowledge of body. Unfortunately, experimentation can often require extended periods of time as well as monetary resources to perform. The use of computational chemistry can increase the rate of scientific advancement by simulating experimental results, allowing researchers to focus on experiments whose computational counterparts show the greatest promise. Students new to the sciences are often not exposed to these methods due to their complexities. The purpose of this project is to implement the Hartree-Fock method, one type of computational chemistry method, whose programming …

Spidr: Small-Molecule Peptide-Influenced Drug Repurposing, Matthew D. King, Thomas Long, Daniel L. Pfalmer, Timothy L. Andersen, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Background: Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which compounds that have already gone through some level of clinical testing are examined for efficacy against diseases divergent than their original application. Repurposing of existing drugs circumvents the time and considerable cost of early stages of drug development, and can be accelerated by using software to screen existing chemical databases to identify suitable drug candidates.

Results: Small-molecule Peptide-Influenced Drug Repurposing (SPIDR) was developed to identify small molecule …

Excitonic And Logic Gates On Dna Brick Nanobreadboards, Brittany L. Cannon, Donald L. Kellis, Paul H. Davis, Jeunghoon Lee, Wan Kuang, William L. Hughes, Elton Graugnard, Bernard Yurke, William Knowlton

Chemistry and Biochemistry Faculty Publications and Presentations

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

Homology Modeling And Molecular Docking For The Science Curriculum, Owen M. Mcdougal, Nic Cornia, Chris Mallory, Julia Thom Oxford, Tim Andersen

Chemistry and Biochemistry Faculty Publications and Presentations

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular structure creation, ligand binding calculations, and visualization of docking results. A student procedure is provided that illustrates the use of DockoMatic to create a homology model for the amino propeptide region (223 amino acids with two disulfide bonds) of collagen α1 (XI), followed by molecular docking of the commercial drug Arixtra^® to the …

Accessible High-Throughput Virtual Screening Molecular Docking Software For Students And Educators, Reed B. Jacob, Tim Andersen, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK …

Dockomatic - Automated Ligand Creation And Docking, Casey W. Bullock, Reed B. Jacob, Owen M. Mcdougal, Greg Hampikian, Tim Andersen

Chemistry and Biochemistry Faculty Publications and Presentations

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user …

Undergraduate Research Opportunities In Microelectronics At Boise State University, S. Burkett, J. Lusth, D. Russell, W. B. Knowlton, S. Parke

Chemistry and Biochemistry Faculty Publications and Presentations

Several opportunities exist for undergraduates in the Microelectronics area at Boise State University. This paper will describe the Research Experience for Undergraduates (REU) program funded by the National Science Foundation and other opportunities that have resulted for undergraduates due to external support. BSU became a NSF REU site for Microelectronics research in 1999. Each year 10 students are recruited nation-wide from various engineering and science disciplines to come to BSU for 8 weeks. The students work intensively with various faculty advisors and graduate student mentors. Another unique feature of our program is the tie to local industry. In 1999-2001, three …