192192 organic chemistry lab: Lab report

Lab report 9 instructions:

Complete the lab assignment and craft a lab report containing all of the necessary sections; refer to Module 3’s “Writing a Lab Report” for guidance as needed. The lecture details what to include for photos as well as specific questions to help guide your observation and results/ discussion sections.

I) Title

II) Stated Objective (5 points)

III) Overall Reaction (5 points)

IV) Mechanism: hand drawn with proper arrow pushing (20 points)

V) Procedure/Methods (10 points)

VI) Your observations: Include photographs or screenshots of your real experimental set-up (30 points)

VII) Results/Discussion (25 points)

For this lab, your reaction will be the thia-Michael Addition to your chosen compound (hand drawn).

For the methods, please describe the steps you took to open and investigate your chosen compound on PyMol. Please write it as a step-by-step guide others could reference to use PyMol.

Remember to include figure numbers and detailed descriptions on your screenshots.

Points of discussion for Results and Discussion:

• What is PyMol and why is it useful?
• What is your chosen compound, include PDB number. What is its history, why is it important, and why is it interesting to you?
• Conclusion on the impact it has had as a medicine

Please include in-text citations and add your references list at the end of your lab report.

Lab reports that show only BTK will receive a 0.

Please include the name (Nicholas Pro with today’s date) in any photos or images created to write the lab report.

Lab report guidelines:

Instructions for writing a lab report: Lab Reports should include the following sections:

Title:

• Be sure to include basic information such as
  • Your name
  • Date the Experiment was performed / completed
  • You may include a Title page with this information if you desire

Stated Objective:

• Why did you perform this experiment?
• What was your hypothesis?
• What specific outcomes were you seeking? Why?

Overall Reaction (as applicable):

• The overall reaction drawn as a chemical equation (A+B –> C+D) will be required for lab assignments where a chemical reaction is taking place

Mechanism (as applicable):

• The mechanism drawn with electron pushing will be required for lab assignments where a chemical reaction is taking place
• Mechanisms need to be hand drawn and show all necessary steps

Methods (Procedures) & Materials:

• A well-detailed account of what you did written in the past tense. Someone should be able to use your methods section as guide to performing / replicating the experiment themselves without needing to reference the lab manual.
• References to any established protocols that you are following
• Materials used
  • including specific volumes, temperature values, pHs of buffers, concentrations of chemicals used, etc. that you used as applicable
    • Do not blindly copy and paste the lab manual instructions. For example, if the protocol calls for “5 g” of material to be used, but you measured out and used “4.5 g,” state that you used 4.5 g in your methods, not 5 g.
• Mention any deviations or changes from an established protocol and why
  • For example, changed or unexpected cooling/heating times, material substitutions, measurement errors, omitting or forgetting steps or materials, etc.)
• Results are not mentioned in Methods sections

Stoichiometry Tables (as applicable):

• Stoichiometry Tables are organizational tools that help you plan and document chemical reactions using reactant quantities and product yields. These will be included in reports for experiments that involve chemical reactions. (More details to come)

Observations:

• This will Include photographs or screenshots of your real experimental set-up.
  • All lab reports will require photos for proof that the lab was completed, whether specifically mentioned in the lab manual / template or not.
  • Photographs need to be clear
    • Lab reports that do not contain real experimental photos will not receive credit
  • All photos in the lab report must contain your name and date to be graded
• Note observations from your experiment

Results/Discussion (Conclusions):

This should be 3-4 paragraphs with a background on the scientific technique, highlight key learning objectives that were covered with this lab experiment, an analysis and/or deeper discussion about the experiment, and a conclusion summarizing your findings. The discussion should be technical, scientific writing.

Ideas for your Discussion section:

• Analysis of successful and unsuccessful aspects of the experiment
  • personal challenges with the experiment
• Identification of potential sources of error as applicable
• Suggestions for improvements or future experiments as applicable
• Discussion of significant observations or unexpected results as applicable
• Real world applications / implications

Lab reports that only summarize the results in the Discussion section will not receive full points.

References (as applicable):

• A separate Reference section should be included with citations for articles and other information sourced to complete your report.
• Include in-text citationsKeep in mind that accurate and credible references strengthen your work, foster peer-learning, support scientific reasoning and analysis, and enhance the overall quality of research reporting. The use of improper, fabricated, or missing citations in coursework misleads the reader and therefore cannot be credited/scored. If you are unable to provide the source of your citation (link, pdf) or use incorrect/ fabricated citations, this will result in reduced or no credit/ grade for the assignment.

Additional Data Tables and Questions

• Some of the Lab Manuals used in this course will provide Data tables and questions for you to answer. Please include these tables and fill them out for full credit.
• Some of the Lab Manuals will have additional questions to be answered. Please include these questions in their own section and answer them for full credit.

Additional:

All Figures (photos) need to have a figure number and a short description with every image, for example, “Figure 1. TLC before applying acetone mobile phase.” All tables need to have a number and Title, for example, “Table 1. List of Rf values observed.” Points will be taken off for missing Figure / Table numbers and missing Figure / Table descriptions.

Please submit your lab report as a PDF file saved with the following naming convention: Last Name_First Name_Lab#_due date.pdf Points will be taken off for reports not submitted as PDF.

Points will be taken off for mechanisms that are not hand-drawn.

Photos that do not include your name and date will not be graded

Experimental details and results do not have to be perfect as this is a learning experience. If you perform an experiment and do not achieve the intended results, you can reach out with any questions and/or concerns and, in these cases, I will be looking for your thoughts in the Discussion section as to why the experimental results could have varied.

Data or claims that are scientifically inaccurate will have points taken off.

Example of Photos in Lab Reports:

Figure X. The materials needed to perform experiment Y, including a, b, and c, were gathered.

Note on Deviations: Documenting deviations from a procedure is crucial for reproducibility and future experimentation. For example, if a specific modification (e.g., extending a cooling time) led to a significant improvement in results, this information should be clearly noted and discussed, and indication of whether to include if the experiment is repeated. The impact of deviations can be explored in the Discussion section.

Note on the use of AI and other online sources: All online sources MUST be referenced; you must provide references (both in-text citations and listed references) to published articles to support your statements. This includes claims that are paraphrased, quotes used, photos of equations or data that may be included to support your claims (see references section).

Immediately following a statement, you should include a superscript Arabic numeral correlating with the order of which reference is cited first or (Author Last Name, year) correlating to the author’s last names and date of a published citation. The citation indicates which reference the information came from. You must then provide the full reference at the end of your post/ report with a corresponding link to the article. Please use the APA style citation format. DO NOT USE AI GENERATED CITATION MACHINES (easybib, Scribbr) as they result in multiple mistakes. Please consult UCSD library guide on citation & attribution for more information and examples.

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