Lab 7
Lab techniques: vacuum filtration, pH testing.
Lab notes:
This lab is difficult. There are many steps where things can go wrong, and you should read the procedure very closely. Monitoring the pH requires some care because the solution is so strongly pigmented and will need to be diluted. The theoretical aspect of this lab is also non-trivial. Unfortunately, this week seems very packed with midterms for many of you, but please put extra effort into the pre-lab and preparation for this week's lab.
Thought question: Why is keeping track of the pH so important for this lab?
Feedback on various assignments.
Formal report:
This was a hard assignment. Don't be discouraged if you got a bad grade, because others did poorly as well. This assignment is difficult because technical writing is difficult. There are two such assignments left, each worth more points, and you can definitely improve by taking the time to identify what you're doing wrong and fixing it. To this end, I will host additional office hours for the next lab report on Wednesday 11/14 from 5:40 pm to 7:10 pm. Let me know if you want to attend but have schedule conflicts at this time. Bring your first drafts and any questions that you have. The more prepared you are, the more helpful I will be. I plan on going over common mistakes from the first formal report, addressing general questions, and then having you work on an activity where you design a rubric and grade part of each other's report. During this time, I will answer individual questions.
- The procedure section was written poorly in general. Many students focused on superfluous details and did not touch on the salient points of the experiments. In particular, no student described the appearance or state of the plant mixture at important points in the procedure.
- A few students only addressed the flame test aspects of the flame test experiment, without talking about the copper nitrate serial dilutions, unknown solutions, or the use of a spectroscope. Even though the discussion questions do not cover this material, these should still be mentioned in the procedure.
- Many students mentioned observing the flame color in the flame test experiment or recording the volume of a solution. These are inappropriate details for a formal report. Measuring and observing things during your experiment should be obvious and not explicitly stated. Instead, you should write your measurements and observations indirectly in your procedure. (See rubric for example. "To a 250 mL Erlenmeyer flask was added 0.5 g contaminated Mammoth sunflower sample," not "0.5 g of contaminated Mammoth sunflower sample was measured. The sample was added to a 250 mL Erlenmeyer flask.")
- Many students mentioned sending their final sample to the stockroom for analysis. This also does not belong in a formal report. Focus on the experiment that was done, not who did what. However, data that is not yours (like the control data that Prof. Berns created) should be cited and referenced: "Control data obtained from V. Berns [1]," and cite the lab manual as Ref. 1, for example.
- Several students had figure labels as well as a figure caption. Don't do this. Instead, label all figures in their captions: "Figure 1. ICP-AES calibration curve for Cu at a wavelength of 220.32 nm. Six standard solutions were prepared with concentrations 0.005, 0.01, 0.05, 0.1, 0.5, and 1 ppm Cu."
- Many students did not have descriptive captions. Make sure they are more descriptive. See above.
- All figures and tables should be cited in the text itself. See rubric.
- Most students answered questions in order. While this was acceptable for this lab because the questions followed a natural progression, this might not be the case for future lab reports and you may be penalized in the future. The questions need not be answered sequentially.
- Make sure all discussion questions are explicitly addressed, however. Many students lost easy points by not addressing possible sources of error fully, not suggesting modifications to the experiment to fix these errors, and not explaining how these errors would affect their results.
- Very specific statements---for example, discussing phytoremediation---should be cited. Note that you can, in fact, cite a lab manual or a lab lecture.
- Some students tried to cite external sources. This is a good idea, but make sure you do it properly. Follow ACS format (see below).
- Citations. I expect ACS-style citations in your formal reports. You can look up JACS papers and see how citations are handled there as example. In-text citations are required, and these should involve a superscripted number ยน or non-superscripted number in brackets [1]. Again, look up papers for examples. All citations should be stated in full at the end of your report. There are some browser extensions that can help you with this. I like the Google Scholar extension.
Notes for the next formal report. There will be new sections to write (the introduction) and a small addition to one section (procedures and methods). You have gone over the introduction section in lab lecture. In the procedures and methods section, you should not only describe the experimental procedure but also discuss why the procedure works (i.e. what the purpose of all the reagents you're using is). Finally, note that screenshots of spectra are not sufficient for report figures. You need to make your own figures using the data exported from the spectrometer software.
Lab notebook:
Decent, for the most part. Please make sure you have enough observations in general.
Post-lab for WebMO lab:
Unfortunately, this assignment also did not go very well. Presumably this was due to a confluence of factors: (i) midterm the next day, (ii) post-lab rubric this time was quite strange, (iii) MOs are hard.
Also, please note that you should be using the post-lab template on Canvas, not LabArchives. Canvas is more up-to-date, and my numbering scheme follows the Canvas questions.
- Q1.a: A very common mistake was not mentioning the double-bond character or calculating or approximating the bond order in the given compounds.
- Q1.b: Note the difference between electron domain geometry and molecular geometry.
- Q3: Many students stated that the F atoms in SF6 are not equivalent. They are!
- Q4: Several students did not note formal charges on their resonance structures. Also, while no points were taken off here, I expect you to always rationalize your answer, even if you are not explicitly asked to do so, particularly when you're asked to compare two things. A few students did attempt an explanation using Lewis structures, but I did not find them satisfying. The best approach at this level is likely to talk about how the p orbitals in N, C, and O must be planar to allow for the greatest electron delocalization (and hence stabilization), using valence bond theory.
- Q5.b: Many, many students missed this question. A surprising number simply did not sketch the NBOs in the WebMO computation. I apologize that I did not clarify this question well in advance, because it is worded somewhat confusingly. You were supposed to state that, while the lone pair orbitals themselves did not look the same (and hence are clearly not equivalent and don't match the VSEPR prediction), the molecular geometry still did.
- Q6: You should have mentioned something about molecular shape, bond angles, resonance, and electron domains or lone pairs on the central atom.
Post-lab for silver nanoprisms:
Nothing major here. Note that the reason nano is such a buzzword is because nanomaterials behave very differently from bulk materials, and we should not expect an "infinitely large nanoprism"---that is, a bulk material---to behave the same way as does a (nanoscale) nanoprism.
Lab 5-6
Lab techniques: micropipette use, venting, UV/vis spectrophotometry, cleanliness.
Lab notes:
(Week 1.) Nanoparticle synthesis requires very clean glassware, so be sure you do not introduce any contaminants into your solution. You will be picking up clean glassware from the stockroom. In addition, the colors of the nanoparticle solutions will be very sensitive to the volumes of reagents measured out, so take care with that also. Follow the Experimental Information section of the LabArchives notebook closely. If your absorption spectra have a weird flatlining at an absorbance around 3.0, you need to dilute your sample more.
(Week 2.) This week's experiment is relatively straightforward---you'll be making calibration curves for one of your nanoprism solutions from last week, as well as making silver-coated vials. Remember to clean your vial with ethanol beforehand, or the silver will not coat the inner surface of the vial properly.
Thought question: Can you explain the different colors of your nanoparticle solutions using MO theory?
Lab 4
Lab techniques: None.
Lab notes: You are welcome to start work on this lab at home, but you must still attend lab.
Here are some more details about what I'm looking for in terms of your lab report. Please also look at Lab 2 feedback below for more guidance. You should go to my office hours if you have specific questions or want me to provide (limited) feedback on your lab report before it's due. Bring a paper copy of your report.
Turn your lab reports in on time! Late lab reports are worth half credit if turned in up to a day late and no credit if turned in later.
- Challenge. If you are intending to become a scientist, this is a great opportunity to learn how to prepare professional-looking documents in \(\LaTeX\), a typesetting system. This is less important for students in engineering and other disciplines, but you are welcome to learn as well. Send me an e-mail if you're interested, and I'd be happy to help get you started. I love \(\LaTeX\)!
- Purpose statement. Note that this is not your hypothesis. You might want to write it last after finishing every other part of your lab report---the discussion questions should give you a sense as to the purpose of this set of experiments.
- Procedure. There are many, many experimental papers (I recommend JACS, but you are free to choose your favorite journal) with example procedures that you should look at. Consider especially their style and content---what information are they putting in their procedures, and what information are they leaving out? Also refer to Lab 2 feedback. These are easy points, so don't lose them!
- Results. This should not just be a list of figures and tables. You should describe your results in the context of your experiments not just in figure captions, but also in the main text. Refer explicitly to your figures and tables ("Table 1 lists the data from ICP-AES analysis..."). All figures and tables must have captions. Figure captions go at the bottom of a figure, and table captions at the top.
- Discussion. Do not treat the discussion questions as a list of questions to be addressed in order. Instead, you should divide the discussion questions into broad categories and address each category in its own paragraph, within the context of your experiment. The discussion questions should meld with your explanation of the data. You should address your hypothesis here also.
This is not an easy assignment. But it is part and parcel of scientific work, and I encourage you to treat this as though you were communicating your results to a fellow scientist, instead of just an annoying assignment you have to complete.
Thought question: How would you construct the molecular orbital diagram for \(\mathrm{BeH_2}\)? For \(\mathrm{BH_3}\)?
Lab 3
Lab techniques: Vacuum filtration, syringe filtration.
Lab notes: There is significant downtime during this lab while waiting for your plant sample to be digested. During this time, we will discuss how to write a good lab report, and everyone should leave with at least a good hypothesis written describing a prediction regarding the trace metal content of the poisoned sunflower relative to the normal sunflower and explaining the rationale behind such a prediction. I also suggest, but will not require, that everyone work on writing their procedure for their lab report. Note that the discussion questions should be answered as a narrative in the discussion section of the lab report, not as an isolated list of questions and answers.
- You'll have heard more about this in the lab lecture, but the goal of your lab report is to convey your work to another scientist. Why is your work important? Why are you doing this experiment (or, alternatively, why do you think this experiment is part of your curriculum)? Writing a lab report is meant to consolidate your knowledge about the experiment in order to present it to a peer, and you should be thinking about it from this perspective.
- During lab, we will have some time to talk about writing down good hypotheses and good procedures. If you want to work ahead, come to lab with a good hypothesis and a sample written procedure, and I can give you feedback on it during the lab period. You should follow the template provided on Canvas closely.
- Hypothesis: Your hypothesis should be a one-sentence response to the following two questions. What trends do you think the data should show between the sunflower watered with pure water and the one with contaminated water? Why?
- Procedures: You are writing for a fellow scientist, not, for example, your younger sibling, who might not know about any lab techniques. You don't have to explain things like making serial dilutions---your reader knows to make these solutions in volumetric flasks and to invert them 25 times to get even mixing and so on. But you do want to make your procedure descriptive enough that your fellow scientist can replicate your experiment just based on the procedure alone.
Thought question: The spectra obtained from an ICP-AES instrument are very clean, and the emission lines quite discrete. What distinguishes the ICP-AES spectra from, say, UV-Vis absorbance spectra, which are instead continuous?
Feedback from last lab:
Pre-lab:
A lot of you lost easy points because you did not show explicit dilution calculations for all your copper nitrate solutions, as was required. Please read and follow the directions for the pre-lab more carefully.
Lab notebook:
Overall, I'm pretty happy with the state of all your lab notebooks, and am confident that all of you now know how to take good observations. As a result, starting from this week's lab, you no longer have to show me your lab notebook before you leave lab. I will, however, still be grading you on your observations.
Common mistakes in the lab notebook included
- not being thorough regarding the spectrum you saw through the spectroscope, and
- not stating that the spectroscope would replace the diffraction grating observations.
Post-lab:
Note that the energy levels can only be characterized by just one quantum number, n, when all orbitals have the same energy, as is the case with hydrogenic (one-electron) atoms. In this case, however, Li, Na, and K are all multi-electronic species, and the orbitals have different energies. It's therefore not appropriate to say that the ground state is n=2---instead, it's the 2s orbital---or that the excited state is n=2---instead, it's the 2p orbital. And so on.
Lab 2
Lab techniques: Bunsen burner, flame test, spectroscope, dilutions.
Lab notes:
- The diffraction gratings don't work well, so the entire lab section will be sharing a spectroscope. To use the spectroscope, squint and look into the opening in one eye. To the right will be a spectrum with markings to measure hundreds of nanometers. Compare the spectrum from a background observation and from observing the flame, in terms of the location, brightness, and color of each line in the spectrum.
Thought question: What is fire?
Feedback from last lab:
Lab notebook:
I was not very clear regarding my expectations for the lab notebook, and I apologize. I graded last week's work more leniently to account for this. I will only grade things written in your lab notebook while you are in lab. When I grade your lab notebooks, I look at the last version of your notebook saved during the lab period. If you edit your lab notebook after lab, that's fine, but it will not affect your grade. All observations, measurements, and data must be taken and recorded during lab.
For observations, I expect at least six to eight sentences or bullet-point equivalents. Many of you asked what observations to write down. You should record
- any changes you make to the procedure, or any missing details. For example, a lot of you had written that you would use 50 mL volumetric flasks for the serial dilution. If you ended up using 10 mL or 25 mL volumetric flasks, that should be recorded. You can either modify your procedure directly or write this down as an observation. If you modify your procedure directly, please make it clear---for example, use bold or underlined text, or text of a different color.
- any instrument readings. This includes things like the weight of copper nitrate used for making each solution. Most of you calculated how much to use beforehand (good!), but did not actually record how much copper nitrate you weighed out.
- key points mentioned in the procedure. For example, the procedure asked you to discuss with your lab partner how to calculate the molar absorptivity constant \(\epsilon\) and what units it should have. This should be recorded in your lab notebook.
- potential sources of error, such as instrumental error, and how you dealt with these sources of error. Many balances were not working very well, and some of you observed large fluctuations when weighing copper nitrate. Write this down!
Common mistakes in the lab notebook included
- not stating, or having the wrong units for, \(\epsilon\),
- not recording the mass of copper nitrate weighed,
- having any other set of missing units or unlabeled data tables. Please make sure all measurements are recorded with the proper units and that all data tables are labeled.
- not stating a value for the path length \(b\),
- not stating, either in the procedure or observations, the volume of the volumetric flask used to perform serial dilutions.
Procedure:
Your procedure is for you. Write it in a way that will help you during lab. If the procedure tells you to weigh or measure something, have a blank line in that step of the procedure to remind you to record measurements. If there are important or time-sensitive steps, bold them. You can even write down all the glassware you need at the top of the procedure and get them all ready at the start of lab. Read through the post-lab questions beforehand, and think about what you need to pay attention to in lab.
A few of you decided to take multiple absorbance readings for each sample. This takes more time, but is a good idea in general. If you have extra time, all of you should consider doing this, especially for the upcoming written reports where having good data is more important.
Post-lab:
Individual feedback is included in the post-lab grading that you'll be able to view by Monday at the latest. Many of you did not include the equation for the best-fit line in the graph itself and did not show full calculations for every question. You should also pay attention to significant figures, although I did not mark you down for them this lab.
There were two different methods available to calculate the absorbance---to use the value of \(\epsilon\) obtained from the slope of the best-fit line, or to use the equation for the best-fit line directly. In principle, the best-fit line is preferable, because it represents your data best. Using the value of \(\epsilon\) corresponds to arbitrarily shifting the best-fit line up or down so the intercept is at the origin. In addition, whenever you are asked to compare two results (here, in Q7), you should be prepared to explain any discrepancy observed.
Lab 1
The first day of lab is Thursday, 10/4.
☞ Before your first day of lab, you must obtain lab goggles and a lab coat. See the relevant announcement on Canvas. You must wear close-toed shoes and long pants to lab, or I cannot let you in. Clothes made of synthetic fibers, like yoga pants or leggings, should not be worn to lab.
☞ You must also obtain a copy of Microsoft Excel or similar graphing software. Google Sheets is not accepted.
☞ In addition, you must complete the online safety quiz perfectly and academic integrity agreement by midnight of 10/3.
☞
You must complete all pre-lab questions before you can begin lab! The pre-lab is due an hour before lab starts.
☞ Tech is hard to navigate, so be prepared. You can try using
this site. Don't be late for lab, because I have to give a lab lecture to everyone before we can start.
Lab schedule for week 2: Lab tour. Safety. Lab equipment and locker inspection. Lab. All labs will be performed in pairs, which have been randomly assigned. I will let you know who your lab partner is on the first day of lab.
Lab techniques: measurement, serial dilution, UV-Vis spectrophotometry, calibration curves, regression and data analysis.
Lab notes:
☞ Volumetric flasks have to be obtained from the stockroom. Every pair should pick up one 50 mL volumetric flask and one other (hopefully smaller) volumetric flask.
☞ Balances aren't very good, so the calibration curve won't be accurate due to the large uncertainty in concentration.
☞ Copper nitrate is deliquescent, which means that it absorbs moisture from the air and becomes sticky and hard to transfer. If the copper nitrate containers are left uncapped, the resulting copper nitrate will be hydrated and lead to inaccuracy in the concentration of your solution. Make sure you keep all copper nitrate containers capped at all times.
☞ Write about a full paragraph (6-8 sentences) for observations---for example, you can describe what solid copper nitrate looks like, what it looks like when you dissolve it, and what happens to the color when doing serial dilution, and so on. This lab isn't very exciting, so writing observations may be harder here. Note that observations are due by the end of lab, before you leave.
☞ If you run the spectrophotometry software on your computer and you get a sensor error, hold down the power button on the spectrometer until a blue light starts flashing, then let go. Close and reopen the spectrophotometry software. Some computers don't actually have this software, and in this case you should switch to a different computer.
☞ Calibrate dark means calibration without a cuvette in the spectrometer. Calibrate reference means calibration with a cuvette with DI water in the spectrometer. You should do both.
Thought question: Molecular excitations occur among discrete energy levels with well-defined energies. Why, then, is the absorbance spectrum continuous rather than discrete?