4.1: Pre-lab 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 the meeting prepared to engage in thoughtful discussion and to conduct the experimental work.

---

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. Description of the Experiment: In your own words, briefly introduce the topic, describe the theory upon which the experiment is based, and state the goals for this experiment. 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 at least two references to source material (do not use the lab manual as a reference). Describe the topic, and describe why is it interesting, important, and worth your time to learn. 
   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 Chemistry Department Safety Manual and the Orientation Module.  Here are some critical reminders:

• Wear Protective Clothing: As always, please dress appropriately for a laboratory environment. You will not be permitted to enter lab, and thus will lose the opportunity to participate in the course assignments, if you fail to dress appropriately.
• 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 by completing the specified pre-laboratory assignments. The pre-lab assignment must be submitted as a single pdf document on Canvas before the scheduled lab meeting. 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.
• Your preparedness will be evaluated by the quality of your work on pre-lab assignments, your answers to oral questions pertaining to the laboratory from the instructors, and/or your responses to unannounced quizzes and skills checks.