Quantum mechanical simulation of fluorine-containing biomolecules

Project Title: Quantum mechanical simulation of fluorine-containing biomolecules
Program:
CAREERS (323)

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Tags:
quantum-mechanics (281)

Status: Complete
Project Leader
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Project Leader:
Fang Wang

Email: fangwang@uri.edu
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Project Personnel
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Mentor(s):
Fang Wang (18689)

Student-facilitator(s):
Matthew Paolella (18707)

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Project Information
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Project Description:
Biologists and medicinal chemists have long been interested in fluorine-containing amino acids due to their unique biological activities and pharmaceutical properties. In this project, we will conduct quantum mechanical calculations on a library of fluorine-containing amino acids that act as mimics of naturally occurring counterparts. Facilitated by high-performance computing resources available through CAREERS, we will compute the physicochemical properties of these fluorinated molecules using high-level density-functional theory (DFT). We will further compare the simulation results with experimental observations from the literature as well as from our group, from which we will establish a model allowing for correlating calculations with experimental results. We anticipate that this data-driven, computational experiment hybrid approach will enable the accurate prediction of important properties of fluorine-containing amino acids for drug design purposes at the molecular level.


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Project Institution: University of Rhode Island
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Anchor Institution: CR-University of Rhode Island
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Start as soon as possible.: No
Project Urgency: Already behind3Start date is flexible
Expected Project Duration (in months): 6
Launch Presentation: https://support.access-ci.org/system/files/webform/project/3947/20231008%20Careers-project-launch_Matt%20Paolella.pdf
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Wrap Presentation: https://support.access-ci.org/system/files/webform/project/3947/20240416%20Careers-project-wrap_Matt%20Paolella.pdf
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Project Milestones:
- Milestone Title: Milestone #1
  Milestone Description: HPC and software familiarization, launch presentation, literature reading, initial calculation setup, GitHub setup. 
  Completion Date Goal: 2023-10-31
- Milestone Title: Milestone #2
  Milestone Description: Establish a library of reported molecules for calculation, create a database with calculated results and reported experimental data.
  Completion Date Goal: 2023-11-30
- Milestone Title: Milestone #3
  Milestone Description: Expand molecule library to include new molecules, expand the database.
  Completion Date Goal: 2023-12-31
- Milestone Title: Milestone #4
  Milestone Description: Explore solvent effects, correlate predicted properties with experimental observations. 
  Completion Date Goal: 2024-01-31
- Milestone Title: Milestone #5
  Milestone Description: Calculate spectroscopic properties, correlate predicted spectra with experimental spectra. 
  Completion Date Goal: 2024-02-28
- Milestone Title: Milestone #6
  Milestone Description: Finalize project documentation and GitHub, finish presentation, initiate manuscript preparation, wrap presentation.
  Completion Date Goal: 2024-03-31

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Final Report
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What is the impact on the development of the principal discipline(s) of the project?:
This research has the opportunity to be built upon by other researchers in the chemistry field. Our findings may provide answers to some questions, but they also open the door to a lot more questions for future studies in this exciting field. Once our manuscript on this project is published, the results will be available for all those in the chemistry field who are interested in this area to reference.

What is the impact on other disciplines?:
Our research has findings that are useful to fields such as the pharmaceutical industry, where drugs are constantly being developed for new and existing conditions. Developers must first understand the chemical properties of a compound before even considering if/how it could effectively interact in a biological system. The data we are publishing on the ability of these molecules to be hydrogen bond donors could prove useful in the future of drug development.

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Lessons Learned:
One of the biggest lessons I learned from this project was how to effectively problem solve when faced with challenges. Experimental procedures would often have to be modified or adjusted in several ways as we obtained certain results. This is something that is not only applicable to my future research, but also to life in general. I also made tremendous progress learning how to use Unity and harnessing the power of the HPC system to work on this project.

Overall results:
The findings of this project are currently being prepared for publication in a peer reviewed journal. Overall, we were able to show that some of our fluorine containing molecules can participate in hydrogen bonding interactions, which was our main hypothesis.