Organic Chemistry Laboratory

Guidelines for Writing a Scientific Laboratory Report (50 pts)

Academic honesty is expected of all students taking the Organic Chemistry Laboratory course at Columbia. You are
responsible for writing your report and generating your structures, diagrams, figures, and/or reaction mechanisms
using ChemDraw. Copying of structures, diagrams, figures, and/or reaction mechanisms from an online or any other
source is strictly prohibited. You are not allowed to write any portion of a report with a classmate, submit another
student’s work or that found on the internet as your own. Failure to adhere to these policies will result in the
disciplinary action as described in the syllabus and will result in loss of all points associated with the assignment.

Submission Details
Lab reports are due at 11:59pm, the night before your lab day, on the due date specified in the syllabus. The report
must be uploaded to Canvas. Late assignments will be penalized 1 point per day and may not be graded by your TA by
the projected release date of the grades.
The following must be e-mailed to your TA:
r word docx file (including annotated UV-Vis, IR, 1H NMR spectra), pdf file (including annotated spectra), and
ChemDraw file of any generated structure(s), diagram(s), figure(s), and/or reaction mechanism(s).
The following must be uploaded to Canvas linked to [Link]:
r complete pdf file (including annotated spectra and ChemDraw)
Failure to adhere to these specifications will results in a loss of 5 pts. Use the docx template to avoid formatting
issues. Hard copies of the report, labeled spectra, or reaction mechanisms will not be accepted and/or graded.

General Information
These guidelines provide a general outline and specific discussion points and/or questions that should be included in
each report. Please note that an excellent lab report will go above and beyond to demonstrate an in depth
understanding of the experiment and background material. Although you are asked to write the report according to a
rigid format, there is space for you to apply your own unique voice and interpretations of the experiment. Use clear
simple prose, write in the past tense, refer to yourself in the first person, and avoid the passive voice where possible
(except in the procedure section). That said, since you are writing a scientific lab report and not an essay for an English
class, you should also avoid any opinion statements (“overall, the experiment went smoothly”). Simply outline the
facts, and state how they support your interpretation of the experiment. View the published journal articles and the
sample lab report for examples of the expected writing style for each section. Do not use bullet points in your report
(this will result in a loss of 5 pts), but do use transition paragraphs. Reports should:
r Include a descriptive title that clearly and succinctly describes the outcome of the experiment. E.g.: Observation of
a mechanism change from E2 to E1 in the dehydration of a mixture of cis- and trans-2-methylcyclohexanol
r Include a heading: Last, First Name; Lab Partner’s Last, First Name; Experiment Number; Due Date; TA’s Last, First
Name; Lecture Section; Lab Section.
r Be succinct and written in clear, grammatically correct language.
r Not exceed a 3300 word limit using 12-point Times New Roman with 1.15 line spacing and one-inch margins. The
word count should be obtained in the word document (docx). The word limit excludes the References. Failure to
adhere to the word limit or formatting rules will result in a loss of 5 pts.
r Include ChemDraw figures that are neat, organized, and easy to read.
r The following headings should appear in your final report: (1) Abstract, (2) Introduction, (3) Discussion and
Conclusion, (4) Experimental Procedure, (5) Results, (6) References. Each section has a checklist of information
that should be included in order for that section to be considered complete. Please keep in mind that you must
include all of the required information within the appropriate section. For example, just because you briefly
introduce a mechanism in your Introduction does not mean it will be counted toward your Discussion &
Conclusion, which is why you may not merit the points you worked so hard to achieve.
r Your TA will assign a score for each section based on its thoroughness and execution. Please view the sample lab
report and the sample experimental procedure for examples of the expected writing style.

1. Abstract (5 points)
The abstract should be concise and provide a one-paragraph summary of the purpose of the experiment and its results.
In the Abstract you should:

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r Provide the composition of tomato paste. State what was isolated and in which step (do not include quantities of
reactants), the type of reaction(s), and any important techniques utilized (e.g.: solid/liquid and liquid/liquid
extraction/wash, column chromatography, isomerization, UV-Vis spectroscopy, etc.).
r Provide a brief summary of the actual results, key UV-Vis data, and the appearance of isolated pigments. Comment
on major characterizations. Cite lmax of lycopene and cis isomerization value from the addition of I2.

2. Introduction (5 points)
The introduction section is meant to provide the reader with general background information on the experiment. It
should not be more than 2-4 paragraphs in length. You will not be penalized for having too much information or "fluff,"
but please be mindful of the word count limit. This section should include information about the technique/chemistry
you are studying; historical information is a great lead-in, but ultimately the chemistry of the reaction—qualities of
reagents, general mechanism, and applications of the technique/reaction in chemistry—should be your focus. You do
not need to get into details about your specific experiment like how you washed, filtered, or extracted your product or
what substituents you used for the reaction. Ask, in general, why is this technique/reaction useful? What makes it
unique? Knowing this may save you all some space to be used elsewhere in the write-up. In the Introduction you
should:
r Include citations from relevant scientific literature. It is standard practice within the chemical literature to use
numerical superscripts and numbered references—look up a peer-reviewed paper for comparison. This segues
nicely into the next sub-point: use at least one paper related to the experiment from the peer-reviewed, academic
literature. Include some outside sources, whether it be a paper, or a textbook/manual not used by this course.
Please do not limit your Introduction sections to what is provided in the lab manual or in the
supplements. Something we are looking for in your Introduction is both a firm grasp of the reaction in question as
evidenced by knowing more than what is in your standard textbook. Citing at least one paper related to what you
are writing about shows you have done your research. Similarly, a good paper should help give you good, on topic,
facts to discuss in your Introduction. The final sub-point is to cite the important content only. Do not give a
citation that shows that acetic acid has a bad odor; we will take you at your word; however, when you start
mentioning equilibrium coefficients, melting points, boiling points, densities, or any other sort of data that you
yourself did not derive from the experiment, cite it J
r Introduce extraction to isolate pigments, column chromatography, isomerization with I2, UV-Vis.
r Relate the information in the introduction to the experiment performed. A brief summary of the experiment should
end the section.

3. Discussion and Conclusion (28 points)

This is the most important section of your lab report. You should discuss any and all results in detail, specifically
answering two fundamental questions: (1) were the pigments successfully isolated from the tomato paste? (2) Were
the pigments successfully purified via a column? (3) What is the % of all trans-lycopene? (4) What % of lycopene was
isomerized? Looking at all data discuss whether or not the experiment was successful and if you were able to isolate
pure product(s). How does the spectral data show this? Include information about the reaction mechanism and
experimental outcomes. In the Discussion and Conclusion section you should:
r Include ChemDraw structures of all relevant molecules, a reaction scheme and mechanism for the acid-
base reaction utilized (citric acid) for the wash, and a reaction scheme (no mechanism) for the conversion of trans-
lycopene to cis-lycopene with I2.
r Show an overall reaction diagram. Use ChemDraw. Include a caption.
r Show a detailed arrow-pushing reaction mechanism and refer to it in discussing your results. Use ChemDraw.
Include a caption.
r Looking at all data discuss whether the isolation and isomerization of lycopene was successful. Determine if UV-Vis
spectral data are consistent with the literature content posted on Canvas.
r Discuss results by referring to procedural steps and making the connection between your data and the product(s)
obtained. In general, it is not enough to assume that the isolated product is what you expect it to be; try to work
backwards by showing how each piece of evidence proves that you have isolated the compound(s) that you say you
have. Use UV-Vis data to discuss and confirm % of trans-lycopene and its isomerization to cis. Annotate (lmax and
cis peak) and paste the UV-Vis spectrum as an image into your report.
r Discuss potential consequences of any mistakes/mishaps. Account for any unusual observations.
r After your results have been discussed, briefly state any conclusions that can be drawn from the experiment.

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Specific Discussion Points:
Extraction of Pigments from Tomato Paste:
ü Partitioning of pigments from tomato paste with acetone/hexanes system.
ü Use of aq. 10% K2CO3 and aq. saturated NaCl.
ü Use of MgSO4 and importance of concentrating the organic layer to dryness.

Separation & Isolation of Lycopene:

ü Importance of the following packing order: cotton, sand, alumina, sand.
ü Use of hexanes to saturate the alumina column.
ü Importance of not letting the top of the column run dry.
ü Driving factor of separating solutes in column chromatography.
ü Polarity of the mobile phase to elute each pigment and its significance.
ü Relative polarity of each pigment.
ü Observations of pigments as they elute out of the column and success of separation.

Spectral Analysis & Isomerization of Lycopene:

ü Effect of conjugation on molecules and what makes them absorb in the visible region of the electromagnetic
spectrum. Comment on the energy difference between HOMO and LUMO (p -> p transition). Comment on
differences in lmax values of the two pigments.
ü Estimate % of all trans-lycopene present in the original tomato paste and after isomerization with I2.
(calculations must already be included in the notebook).
ü Effect of isomerization (blue shift, hypsochromic, vs. red shift, bathochromic).
ü Compare 13-cis isomer to 15-cis, 9-cis, and 5-cis isomers.

Sources of Error (Technical Mistakes):

ü Overloading the column and an uneven surface top.
ü Air bubbles and hairline fractures in a dry column.
ü How would residual water in the round bottom flask that contains the pigments impact the results of
separation via column?

4. Experimental Procedure (5 points)

Describe the procedure as it was performed and as if you were explaining it to a fellow chemist. You can say: “the
organic layer was extracted with 25 mL of 1M HCl,” or “the product was recrystallized from 1.5 mL water to yield 15
mg (0.11 mmol, 23%) yellow, needle-shaped crystals.” In the Experimental Procedure section you should:
r Not plagiarize the procedure from the textbook.
r Use passive voice and past tense.
r Describe the steps in the order they were performed.
r Include pertinent information of temperatures and observations (turbidity and color change).
r Include modifications made to the experimental procedure while in lab.
r Note any mistakes that occurred during the procedure (e.g.: “half of the liquid spilled from the separatory funnel
during work-up.”) Discussion of consequences should appear in the Discussion and Conclusion.
r Include the mass/volume of each reagent, solvent used and the mmol amounts of each starting material. Identify
the limiting reagent (e.g.: “x mL (y mmol, limiting reagent) of A was dissolved in 25 mL DCM in a round-bottom
flask). A solution of x mg (y mmol) B in 5.0 mL DCM was added drop-wise to the solution of A via an addition
funnel over five minutes.”
r Include mass, % yield, physical description of the final product (e.g.: “C was obtained in x mg (y mmol, 38%) as a
white, crystalline solid.”)

5. Results (5 points)
The Results section is where you outline all data obtained during the experiment. Do not include any calculations,
these should be done in your notebook. In the Results section you should:
r Save any discussion for the Discussion and Conclusion portion of your write-up.
r Summarize analytical and spectroscopic data (e.g.: UV-Vis, % yield, melting point, etc.) in a table. Include captions
for tables and figures.
r Paste annotated spectra as an Appendix. All spectra should be attached, with each on their own page.

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Scanners are available in the Northwest Corner Building Science and Engineering Library. You may use a smartphone
to take pictures of your annotated spectra. Genius Scan or Microsoft Office Lens apps are free and will help with taking
acceptable pictures of the spectra. Save the spectra as an image (not pdf) and insert them as pictures in your report.

6. References (2 points)
Reference any source used for the report write-up. Remember that you need to cite everything that is not common
knowledge. Remember that failure to cite is considered cheating. Where did you get the procedure from? Where did
you get information in your Introduction from? Where did you get melting point and molar mass values from? At the
very least, you should be citing the lab manual, procedure, and/or physical data. In the References section you should:
r Include citations from relevant scientific literature. You are required to include at least one reference from a peer-
reviewed, academic journal.
r Include literature sources that list the physical properties of known compounds. Listing the observed value
without including a literature source is unacceptable.
r List references with corresponding numerical superscripts. References should be numbered in a consecutive series
in the order that they were noted in the text.
r Use the standard American Chemical Society format for references:

1Journal: (#) Author last name, author first and middle initials; author last name, author first and middle initials. Title
of Journal Abbrev. Year of publication, volume, page referenced.
(1) Payne, M. M.; Parking, S. R.; Anthony, J. E.; Jackson, T. N. J. Am. Chem. Soc. 2005, 127, 4986.
2Journal Accessed Online: (#) Author last name, author first and middle initials; author last name, author first and

middle initials. Title of Journal Abbrev. Year of publication, volume, page referenced. URL (accessed month, day, year)
3Book: (#) Author last name, author first and middle initials. Title of Book, publisher: city of publication, year of

publication, page referenced.

4Supplemental Readings: (#) Ghurbanyan, A.G.; Sedbrook, D.F. Title of Supplement, Columbia University, Organic

Chemistry Lab, Semester (accessed month day, year)

5ChatGPT: ChatGPT. OpenAI. Accessed on month day, year.

Here is a list of web databases (Pubmed, Web of Science, SciFinder [to register for SciFinder]) you can use to search for
articles. Below is a comprehensive list of common academic journals where you might expect to find useful
information (Wikipedia is not an acceptable source). To access databases, journals off-campus, use
.[Link] after .com/.org in the web address:
[Link] ® [Link] /journal/jacsat

Chemistry Journals
Journal of the American Chemical Society, Journal of Chemical Education, Journal of Organic Chemistry, Organic
Letters, Journal of Medicinal Chemistry, Angewandte Chemie International Edition, Chemical, Science, Tetrahedron,
Tetrahedron Letters, Science, Nature, PNAS, Nature Chemistry, Synthesis, SynLett.

ChemDraw Information
Generating structure(s), diagram(s), figure(s), and/or reaction mechanism(s), TLC plates in an electronic format using
ChemDraw is an absolute requirement.

Download Instructions
Download the software through the Columbia libraries free of charge. The link will take you to the CambridgeSoft
website; you will be asked to enter your Columbia e-mail address to download the software. Licensing information will
be sent to you in a separate e-mail. If you do not receive the serial number for the software, log in to your Perkin-
Elmer account using the Columbia email address you used when you registered for the serial number. Once you sign
up, click on: “PLEASE NOTE: If you are looking for SERIAL NUMBERS for your downloaded software, they can be found
under My Downloads. If your serial number is not listed under the My Downloads link, you may have to go through the
authentication and registration process again for the activation code.

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Online Tutorials
You are expected to learn how to use the software on your own. To assist you, use the links to tutorials provided by
CambridgeSoft. There are several independent tutorials that can be found on YouTube (ChemDraw Wizard has several
engaging and useful videos on his channel).

#Extra Tips
For the best-looking structures, use the object setting “ACS Document 1996.” This setting will allow your structures
look the best when copied and pasted into Word. Set this before drawing any mechanisms!
To do this, draw any object in ChemDraw and select it. In the main toolbar, select Object > Apply Object Settings from >
ACS Document 1996. If the structures look too small, zoom in (on a Mac type "command >").
type "command >").