All posts by Anna Grace

I am a middle school science teacher and the science department chair at Hogg MS. During the day I work to foster relationships with students and urge them to think beyond what is expected. With this philosophy I teach a little bit of all of the sciences.

New Week a New Protocol


This week the lab was considerably quieter. With our undergrad still sick and my mentor working on a manuscript at home I had a lot of time in the lab by myself. I continued to work on the old protocol and start writing and refining my abstract. I continue to look at the same papers that I have read about ATPE and try to find new ones that use different molecular weights of the polymers that form the two phases. I have gotten to a place where I have almost mastered the oxidation protocol using TCCA to separate semi-metallic SWCNTs from metallic SWCNTs. It’s weird that my separation works better after incubating over night so I will be looking into why this may be by changing the centrifugation next week.

All SWCNTs are in the top phase before the addition of TCCA.
After the addition of TCCA the semi-metallic SWCNTs are found in the top phase. While the bottom phase has no clear properties.
After waiting overnight there is a clear separation of phases with an aggregate at the interphase.
Semi-metallic SWCNTs rich top phase is in the cuvette on the left while metallic SWCNTs rich bottom phase is in the cuvette on the right.


I run my cuvettes containing samples in the spectroscopy machine. During the weekly meeting we went over my results. I am now getting a much better sample of semi-metallics than before. The absorbance, however, looks off. So next week I will be working on getting a clearer bottom phase, currently it looks cloudy. I also will be looking into why the separation works better if I let the eppendorf tube incubate over night.

Reading the data as it is collected with the NS1 machine.


I’ve mentioned that I was using different molecular weights which resulted in poor separation. It turns out that the new molecular weights are supposed to be used with DNA wrapped SWCNTs rather than surfactant wrapped SWCNTs. Knowing this, I was given a new protocol to use with the molecular weights. I have only run one trial with this new protocol. It uses a VERY small amount of substances because DNA is much more expensive than the surfactants that I had been using.

First attempt of separating DNA wrapped SWCNTs using Dx 250 and PEG 1.5 following a new procedure.

New Weights New Results

This week was spent in the lab working to create a new protocol to complete a more successful separation of carbon nanotubes. I also was able to visit labs this week.


I had a wonderful time visiting labs this week. Now, I am able to better understand everyone’s research. Amazing, how everyone is working on such different projects. Sarah’s mentor did a great job of explaining their carbon nanotube lab to us. It was really cool seeing the possible applications of carbon nanotubes. Just like a fascinating look into the future.

The BRC labs were in a much more open space with collective sharing of equipment, very different than my self enclosed lab. Most members had a machine and process ready to present to us.


After our weekly meeting I was assigned a new task. To work with the new molecular weights to create an aqueous two phase separation of carbon nanotubes. I was having success following the protocol correctly with the original molecular weights. Using the new molecular weights affects the two phase separation in a large way. Following my original protocol there was no phase separation of the polymers. I tried reading more papers about different molecular weights. There were only a few available and even fewer articles about two phase separation of carbon nanotubes.

All SWCNT are in the top phase.
Added TCCA and it helped create an aggregate at the interphase but not SWCNT are in the bottom phase.


My mentor pushed me to list all of the parameters that could possible affect my separation. I created a list of about 15 different variables. It’s a hard challenge to try to create a protocol and only change one thing. What makes it difficult is that you see that it didn’t work so you want to start to make bigger changes.  Later I learned that there are no protocols using these molecular weights and that it was recently uncovered. This is making the challenge even more difficult. I’m now trying to work out the new protocol.


  • sometimes there are no papers to help you
  • think of ALL of the small parameters that can be change
  • change one small thing at a time
  • use not only math but also your observations
  • sometimes it’s okay to go with your instincts

SUCCESS… kind of


All of the SWCNT are in the top phase. This can mean that the bottom phase has too high of a molecular weight or that not enough oxidizer TCCA was added. If there is a clear difference in color between the top and bottom phase then a successful separation has been performed.

We have weekly meetings to share what we have accomplished and to help give feedback to the other people in our lab.  I was able to say “I learned what nanotubes are and I started working on the aqueous two phase extraction except, I have not had success.” The follow up questions helped me to realize that the polymers that I am using come in different molecular weights. These molecular weights  indicate how large the polymer is. The larger the molecular weight the bigger the polymer is and the harder for the single walled carbon nanotubes (SWCNTs) to move in that solution. I think of it like trying to swim through water (low molecular weight) compared to trying to swim through through honey (big molecular weight).

Aqueous two phase extraction (ATPE) relies on the movement of SWCNT between the top phase (layer) and bottom phase (layer) to create a separation of SWCNTs. My large molecular weight of the bottom phase was preventing any SWCNT from moving into the bottom phase to separate from the top phase. This means I was not extracting a specific group of SWCNTs.

Aqueous two phase separation before SWCNTs are added. There is a faint line separating the top PEG polymer) and bottom dextran) phase.


I decided to run the same protocol but with the molecular weight of the polymers indicated in various articles. I also created a more concentrated solution of SWCNTs in a 2% sodium cholate solution.

Me trying to measure out SWCNT to use in my dispersion.
SWCNT before tip sonification and centrifuge. SWCNT have iron impurities in them and are hydrophobic before the tip sonification process.
Tip sonification allows the mixture of the SWCNT with the surfactant sodium cholate. The surfactant surrounds the SWCNT to make it hydrophilic and able to dissolve. The iron will not be surrounded by the surfactant.
After using the centrifuge. The solid leftover contains most of the impurities while the supernatant (liquid) that is collected contains dispersed usable SWCNTs.

Much to the relief of the undergraduate whose protocol I have been using.  Success! A “blue” top phase and “red/brown” bottom phase.

Top phase has a blue tint while the bottom phase has a different tint. The color comes from the optical properties of the SWCNT that is isolated. Semimetallic SWCNT from this batch of SWCNTs have a blue tint. Metallic SWCNTs have a red/brown tint.

Riding my high horse I showed my sample to my mentor. She reminded me that just because the appearance seems right doesn’t mean that I have the correct result. Time to go get some data using the spectroscopy machine. Also, how cool is it that the professor in charge of the lab works on creating this machine! I analyzed my data with the help of the undergraduate student in the lab. It looks like I am doing an “okay” job of separating the semi-metallic SWCNT but not a great job of separating the metallic SWCNT.

Time to problem solve: I was probably extracting the bottom phase incorrectly getting part of the interphase with the bottom phase, my TCCA might have decomposed or be the wrong concentration necessary, the pH could have changed, or the solutions were not properly “mixed” before using the centrifuge.

Testing the pH to see if using the old Dextran has created a more acidic solution. Looks like the pH is relatively the same.

After you problem solve you jump back in and try it again. It is important to have multiple successful trials before making conclusions and moving on.



  • I created a carbon nanotube dispersion on my own
  • Independently I was able to correctly identify the solute and the molecular weight to create stock solutions
  • I used articles to inform decisions
  • I asked questions to clarify how to read the spectroscopy data
  • I had some success and failures using the EXACT same protocol


How do you separate something “invisible”?
SWCNT diagram (1)

Going into this RET experience I had a semester of undergraduate research experience in 2010 working with the genetics of a beet plant. Skip forward through my undergrad and 5 years of teaching to the summer of 2018. Now I’m working in a chemistry lab isolating single walled carbon nanotubes aka SWCNT using the chemical and physical properties of the SWCNTs. SWCNTs are less than 100 nm, made of only carbon and have the appearance of a tube. Just a little, okay maybe more than a little different than working with a beet plant.Good thing I have a positive attitude and love to learn! Plus carbon nanotubes are cooler than plants and less messy.


When I arrived to the lab I was given my own station with a stack of articles and a computer. I read through the articles, took notes, and used the computer to look up more articles and information. Most of the articles that I read didn’t include their protocols (procedures) within the paper so I would have to look somewhere else for that. The papers focus mostly on the theory of why the chemistry should work. I was perfectly content reading and thinking and reading some more, but my mentor and the rest of the people in the lab were ready for me to actually do something. This is a small lab of 5 people including myself and the professor. My goal is to sort the SWCNT sample by the properties of the SWCNT. By influencing the solubility of the SWCNT I can isolate the semi-metallic SWCNT in a hydrophobic solution while the metallic SWCNT will be in the hydrophilic solution.

Phase Extraction (2-4)

My mentor Yu took me into the lab and helped me to start my stock solutions. Let’s just say I have room to grow or rather to slow down and be more gentle. I was surprised by just how fluffy and light the SWCNT sample was. They went flying as I tried to reach my scapula in. That’s when I learned that using weighing paper to get your substance is actually easier. All of the solutions have an easy to follow “recipe” because their concentration is determined by using the mass. LOVE THAT MATH! <– I do my students …. let’s just say formulas are their best friends.

Weighing is Difficult!

I will quickly summarize the steps that I took to create my unsuccessful separation. 1. Disperse SWCNT 2.  Combine Correct Amounts of Solutions Into Eppendorf Tube 3. Centrifuge the Eppendorf Tube 4. Pipette Out Your Top Layer of Semi-metallic SWCNTs!

1. Disperse
2. Combine Solutions
3. Centrifuge
4. Pipette SemiMetallic SWCNTs

I would give myself a solid 2.5/4. I have followed 3 different protocols to isolate the semi-metallic SWCNTs from the metallic SWCNTs and each protocol has not been successful. Instead of separating the semi-metallic SWCNT from the metal SWCNT I’m just separating all of the SWCNT from the bottom phase of Dextran.

No one in the lab is surprised though, they are supportive and have assured me that it takes a while to figure out how to correctly separate the SWCNT using this particular protocol. Also, the tiniest of mistake in a measurement can lead to an unsuccessful trial.

My takeaway: I need to learn more about the surfactants and how they interact with the oxidizing agent. I will look for articles about the basics of dispersion and review oxidation of SWCNTs. Translated: I need to understand my ingredients better and how they affect my SWCNT



2, 3.

4. Redox Sorting of Carbon Nanotubes

Hui Gui, Jason K. Streit, Jeffrey A. Fagan, Angela R. Hight Walker, Chongwu Zhou, and Ming Zheng
Nano Letters 2015 15 (3), 1642-1646

DOI: 10.1021/nl504189p