4.4.1: Prelaboratory Assignment

📅 Due: This assignment must be completed before 1:00 PM on your scheduled lab meeting day (see syllabus schedule).

🕒 Time: Plan at least two hours to complete this assignment. 

🎯 Purpose: This pre-meeting assignment is designed to help you arrive to our first meeting prepared to complete course-specific MatLab training.

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This module includes Wet Lab work, thus you should prepare for your meeting by dressing appropriately for lab and bringing your own safety eyewear.  In addition, for this and all following meetings, there is a written pre-lab assignment as described below.  Because all experimental modules require similar preparation, the pre-lab assignment is divided into a "General" assignment that should be completed for each module and a "Specific" assignment for each meeting.

GENERAL Pre-Lab Assignment

A template file for preparing your pre-lab assignment is available (click).
Read the module in canvas and in the lab manual, follow the instructions within, then write a brief introduction to the experiment and an experimental plan using the following outline:

1. Experiment Introduction: In your own words, briefly describe the underlying theory and explain the principle upon which the experiment is based. Keep it concise; lengthy discussions or derivations of equations are unnecessary.
   1. Background (importance/relevance): A brief description and justification of the importance of the topic, with references to source material. What is the topic and why is it interesting and important? This is meant to "hook" the reader so they want to read about the topic.
   2. Theory: A concise paragraph or more describing the general theory for the method/technique used; this section should contain a reference to the appropriate pages of the textbook, or other source material from the literature.
   3. Goals/Purpose: Brief statement of purpose, which should indicate what is analyzed and the technique used. Limit to three to five sentences.
2. Experimental Plan: a short summary of the specific things that you would need to know in order to do the experiment without having access to your lab manual, with the understanding that you will always have a TA available to teach you how to use the instrument.
   
   The best way to approach this task is to thoroughly read the procedure for the experiment. While reading, take notes on the specifics of the work. What chemicals will you use? If you have to make solutions, what solutions do you need to make and of what concentration? How will you prepare them? What instrument will you use, and what specific instrument settings will you need to input (sometimes you will find this information in the Appendices that discuss the use of the instruments)? How many runs of each sample will you do; and over what wavelength, or temperature, etc. range? You do not need to write down how to use the instrument; we will teach you that. Bottom Line: we want you to write down only that pertinent information about samples, sample preparation, instrument and instrument parameters, numbers of runs, and other things, that you will need to know in order to do your work.

 In addition to the general pre-lab assignment, please complete the specific tasks listed below. Your assignment must be submitted on Canvas before the deadline.

SPECIFIC Pre-Lab assignment for Absorption Spectra of Conjugated Dyes

1. Complete the general pre-lab assignment.
2. Find structures and literature values for \( { \lambda }_{max} \) for the four dyes to be studied in this experiment. This information is readily available on the Sigma-Aldrich web site (http://www.sigmaaldrich.com) by searching for the name of each dye. Enter a copy of each dye structure and its \( { \lambda }_{max} \) value(s) in the ELN. If more than one  \( { \lambda }_{max} \) value is listed, record all of them in your notebook. Cite your sources.
   • Dye #1: 1,1’-diethyl-2,2’-cyanine iodide
   • Dye #2: 1,1’-diethyl-2,2’-carbocyanine chloride
   • Dye #3: 1,1’-diethyl-2,2’-dicarbocyanine iodide
   • Dye #4: 1,1’-diethyl-4-4’-carbocyanine iodide
     
     Some additional resources for more precise \( { \lambda }_{max} \) values are:
     • Hamer, F.M., A Comparison of the Absorption Spectra of Some Typical Symmetrical Cyanine Dyes, Proceedings of the Royal Society of London, Series A, 154 (883), 1936, pps. 703-723 (doi: 10.1098/rspa.1936.0078)
     • And/or find other sources for these values by searching for the dye names in Web of Science.
3. Use your knowledge of HOMO and LUMO to answer the questions below.
   1. Give a definition of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO).
   2. How are HOMO and LUMO related to UV-Vis absorption spectroscopy, specifically in the context of the \( { \lambda }_{max} \) values of these dyes?
   3. How does the HOMO-LUMO energy gap change as the length of a conjugated \(\pi\) system increases? (consider your knowledge from organic chemistry)
4. Examine the structure of each dye (specifically the length of the conjugated chain between the N atoms).  What trend do you expect in the \( { \lambda }_{max} \) values of this series of dyes? Is your hypothesis consistent with the literature values?
5. Using your knowledge of Beer's Law, draw absorbance spectra in the range of 400 - 800 nm (example blank plot axes provided below). 
   1. On plot A and B, sketch the spectrum of a dye molecule that absorbs light with \( { \lambda }_{max} = 700\) nm at absorbance of 0.8 A.U.
   2. On plot A, add the spectrum of the same dye at half of the original concentration.  
   3. On plot B, add the spectrum of a second dye that has \( { \lambda }_{max} = 500 nm\). 
   4. On plot B, in a separate color or line thickness, show the spectrum that would occur if the two original dye solutions were mixed together in equal portions.
   5. Provide a concise justification of your predicted spectra; specifically justify your prediction for how the spectrum changes upon dilution (plot A) and how the spectrum changes upon mixing (plot B).

      

      Figure \(\PageIndex{1}\): Predicted Absorption Spectra of Dyes. A) Shows a Dye with \( { \lambda }_{max} = 700\) at two different concentrations.  B) Shows predicted spectra of two dyes before and after mixing. (CC-BY-NC-SA; Kathryn Haas 2025)

6. Read one of the following (Duke students click here):
   • Change, R., Physical Chemistry for the Chemical Sciences, University Science Books, CA, 2014 (Section 10.9)
   • Chang, R., Physical Chemistry for the Chemical and Biological Sciences, University Science Books, CA, 2000 (Section 14.8)

Additional reminders

Since this is the first time you will be going into lab, we recommend reviewing the Safety Manual and the Orientation Module.  Here are some reminders:

Wear Protective Clothing: As always, please dress appropriately for a laboratory environment. You must wear close-toes shoes and clothing must cover your body from your upper arms to your knees. You should also have your own pair of protective eyewear, bring them to lab, and wear them the entire time you are in lab. Safety eye wear can be purchased from the Graduate Chemistry Council (GCC). If lab attire is not jiving with your wardrobe, please purchase a lab coat and bring it with you so that you can cover up in lab. No student should be in lab without wearing protective eyewear and appropriate protective clothing.

Prepare by completing the Pre-Lab Assignment: It is absolutely essential that each student be prepared for lab meetings by reading the appropriate module in this manual, and completing the specified pre-laboratory assignments. The pre-laboratory assignments are designed to prepare you to operate efficiently and safely during the experimental module.  You will not be allowed to conduct experiments if the pre-lab assignment is not completed before your lab meeting. If there is an extenuating circumstance that prevents your preparation, please inform your instructors as soon as possible.

The pre-lab assignment must be submitted as a single pdf document on Canvas before the scheduled lab meeting. Pre-lab assignments should be legible and preferably typed if your handwriting is not clear to others. If you prefer to write out equations by hand, they should be neat and inserted as an image in the appropriate place (please note that handwritten equations are not accepted for formal reports). If you need advice for how to insert equations or images into your documents, please ask for help at least 48 hours before the assignment is due; an in-person (or zoom) meeting is most appropriate for this issue.

Late pre-laboratory work will not be accepted and will receive a score of zero. Your TA will evaluate the work and return it no later than the beginning of your lab section. Your preparedness will also be evaluated by your answers to oral questions pertaining to the laboratory from the TA and other lab instructors. The pre-lab and preparation accounts for 10 points of each experiment requiring a pre-lab.