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Quantum mechanical simulation of fluorine-containing biomolecules
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Submission information
Submission Number:
176
Submission ID:
3947
Submission UUID:
c5e2fb05-9a2a-454e-ae96-f82272eba08b
Submission URI:
/form/project
Created:
Mon, 08/21/2023 - 13:01
Completed:
Mon, 08/21/2023 - 13:01
Changed:
Thu, 06/13/2024 - 06:28
Remote IP address:
104.28.39.94
Submitted by:
Gaurav Khanna
Language:
English
Is draft:
No
Webform:
Project
Project Title
Quantum mechanical simulation of fluorine-containing biomolecules
Program
CAREERS
Project Image
{Empty}
Tags
quantum-mechanics (281)
Status
Complete
Project Leader
Project Leader
Fang Wang
Email
fangwang@uri.edu
Mobile Phone
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Work Phone
{Empty}
Project Personnel
Mentor(s)
Fang Wang
Student-facilitator(s)
Matthew Paolella
Mentee(s)
{Empty}
Project Information
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.
Project Information Subsection
Project Deliverables
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Project Deliverables
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Student Research Computing Facilitator Profile
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Mentee Research Computing Profile
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Student Facilitator Programming Skill Level
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Mentee Programming Skill Level
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Project Institution
University of Rhode Island
Project Address
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Anchor Institution
CR-University of Rhode Island
Preferred Start Date
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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
20231008 Careers-project-launch_Matt Paolella.pdf
(532.5 KB)
Launch Presentation Date
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Wrap Presentation
20240416 Careers-project-wrap_Matt Paolella.pdf
(840.82 KB)
Wrap Presentation Date
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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
Github Contributions
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Planned Portal Contributions (if any)
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Planned Publications (if any)
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What will the student learn?
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What will the mentee learn?
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What will the Cyberteam program learn from this project?
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HPC resources needed to complete this project?
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Notes
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Final Report
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.
Is there an impact physical resources that form infrastructure?
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Is there an impact on the development of human resources for research computing?
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Is there an impact on institutional resources that form infrastructure?
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Is there an impact on information resources that form infrastructure?
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Is there an impact on technology transfer?
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Is there an impact on society beyond science and technology?
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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.