Computational Quantum Chemistry Project Proposal

To earn a B or higher (454) or C or higher (550), you propose a computational quantum chemistry project and give a satisfactory presentation it. To earn a B or higher (454) or an A (550), you must also complete a satisfactory report about it. As mentioned in the syllabus, an unsatisfactory presentation or report may be revised with 2 tokens.

Research

The research project includes the following steps:

  • Search for and select a set of molecules to do further research on.
  • Download and at least partially read at least three references related to your molecules.
  • Build a molecular model and perform an energy minimization on at least three of the molecules.

Presentation

In the presentation, you should address the following questions:

  • Why are your molecules interesting? Are they common in nature? Do they have a (potential) technological purpose?
  • What can you learn about the molecules through computational chemistry?
  • What computational chemistry calculations, if any, have already been done? What level of theory and basis sets were used? Would you do anything differently?
  • What experiments could corroborate your calculations? Have they already been conducted?

The presentation should be 7 minutes long, followed by 3 minutes for questions.

As a visual aid to your presentation, you should prepare a series of slides that present evidence for your answers based on your own work as well as data and figures from other sources. Data and figures from other sources should be properly cited. Citations should be numbered/named on individual slides and an ACS-style bibliography included at the end of the slide slow. The slide show should be in Apple Keynote (.key), Microsoft Powerpoint (.ppt/,pptx), Google Slides (.gslides), or Portable Document Format (.pdf) format. Before the first student presents, your slides should be saved in a folder within your class folder as ComputationalQC/ComputationalQCPresentation.XXX, where XXX is the file extension. To expedite transitions between presentations, students will all present using the instructor’s laptop.

A satisfactory presentation will

  • address all of the questions with sufficient evidence for the answers,
  • include the required calculations,
  • cite references properly, and
  • be clear and concise, within the specified time slot

Report

The report is a written version of the presentation. You should address the same questions and present evidence in the text and in figures and tables. The report should be at least three pages long and saved as a document in Apple Pages (.pages), Microsoft Word (.doc/.docx), Google Document (.gdoc), or Portable Document Format (.pdf) format.

Before 1:50pm on the due date, your report should be saved in a folder within your class folder as ComputationalQC/ComputationalQCReport.XXX, where XXX is the file extension.

A satisfactory report will meet the same criterion as the presentation except for the last. Instead, the report should be clearly written with proper English spelling and grammar.

Final Project

To pass this class, you must work in teams of up to 3 members to complete one of the research projects proposed by a team member. The project should use some of the computational chemistry methods that we have learned about in this class to study a chemistry problem. Your team must also give a final presentation and write a final report. Finally, to earn a C or higher, you must write a report that describes your individual contributions to the project.

Research

Your team should propose, design, and perform a rational series of calculations involving the selected set of molecules. To earn a B or higher, your project should have a clear contribution to science - to explain an experimental observation, to make predictions about the molecules, or both. I strongly encourage you to talk to me about the feasibility of your planned calculations.

Presentation

Your presentation should have the following sections that address specific questions:

  • Introduction. What was the motivation for your calculations?
  • Results. What data were produced by your calculations? Data could include optimized structures and calculations of energetic, thermochemistry, spectroscopic, or other properties. They could be visualized in various types of figures and tables. If helpful, you may present data from project proposal. What do the calculations explain or predict about the set of molecules?
  • Discussion. How do your results fit in with the scientific literature? Are they consistent or contradictory? Were the results expected or unexpected?
  • Future Directions. What additional calculations or experiments could potentially be done? Would would you expect to learn from them?
  • Conclusion. Based on all your results and in the context of the scientific literature, what did you learn?
  • Methods. What calculations did you perform and how did you do them? You may not actually present this section, but you should have slides in case there are questions about it.

In general, the sections should be in this order. However, if the Methods are not standard, you may want to include them between the Introduction and Results.

The presentation should be 15 minutes long, including questions.

As with the project proposal, you should prepare a series of slides to accompany your presentation. Data and figures that you did not generate should be properly cited. Citations should be numbered/named on individual slides and an ACS-style bibliography included at the end of the slide slow. The slide show should be in Apple Keynote (.key), Microsoft Powerpoint (.ppt/,pptx), Google Slides (.gslides), or Portable Document Format (.pdf) format. Before the first team presents, your slides should be saved in a folder within your class folder as FinalProject/FinalPresentation.XXX, where XXX is the file extension. To expedite transitions between presentations, students will all present using the instructor’s laptop.

A presentation that enables the team to pass the class will

  • address all of the questions with sufficient evidence for the answers,
  • include the required calculations,
  • cite references properly, and
  • be clear and concise, within the specified time slot

A presentation that enables the team to earn an A or B will describe a clear contribution to science. To enable the team to earn an A, the presentation must have the polish of a conference presentation. Conference presentations are well-organized and smoothly delivered. Moreover, presenters are knowledgable about the background and are able to answer most questions intelligently.

Report

The final report should capture the team’s project work in the format of a scientific journal. Fortunately, the sections of the presentation reflect this format; as with the project proposal presentation and report, the report is a written version of the presentation. You should address the same questions and present evidence in the text and in figures and tables. Unless approved for another journal, the document should be prepared for submission to the Journal of Chemical Information and Modelling according to the journal’s author guidelines. It should be saved as a document suitable for submission to the journal. If there is a clear scientific contribution, the team may be encouraged to actually submit the paper for publication.

Before 1:50pm on the due date, your report should be saved in a folder within your class folder as FinalProject/FinalReport.XXX, where XXX is the file extension.

A satisfactory report will meet the same criterion as the presentation except for the last. Instead, the report should be clearly written with proper English spelling and grammar.

A report that enables the team to earn an A or B will describe a clear contribution to science. To enable the team to earn an A, the presentation must have the polish of a journal article. Journal articles are well-organized and written logically with citations for every claim that is not common knowledge. Figures and table should clearly convey information that is discussed in the text. All conclusions should be clearly supported by the data. Submitted manuscripts that do not meet these requirements are likely to be rejected or require major revision. If I deem the article acceptable as is or with only minor revisions, then the team will have the opportunity to earn an A.

Individual contribution summary and project portfolio

To earn a C or higher, you must write a report (1 page or longer) that includes two sections:

  • an individual contribution summary and
  • a project portfolio.

In the individual contribution summary, you should summarize how you contributed to the final project. For some examples of ways that you may have contributed to the project, see the PLOS guidelines for author contributions. The PLOS guidelines were developed for a journal article. Additional ways that you can contribute are preparing the presentation slides or poster before the class.

For the project portfolio, you should describe the skills that you have developed over the course of the project. These skills could be technical skills related to the calculations. They could also be “soft” skills related to teamwork, project management, interpersonal relationships, communication, presentation, and writing. Preparing this project portfolio could help you answer job interview questions in the future.

This report will be a major factor in your “Individual contribution to final project” grade.