Sunday, July 25, 2010

Field Trips Galore!

This week, we had two field trips back to back. On Thursday, we went to PPG's Monroeville branch. We were able to see some of the projects they are working on, such as photochromics and Teslin paper. Later, a chemical engineer came to talk to us about different jobs you can have with a chemistry degree, something very helpful to all of us SEED students. It was such a wonderful experience.

On Friday, all of the senior SEED students took a trip to Washington and Jefferson College. One of the admissions counselors talked to us about applying for student aid, and what colleges look for. This is very helpful, as all of us will be applying to colleges in just a few short months. From there, we had a tour guide take us on a walking tour of campus. Sydney and I immediately fell in love with it. Next was our amazing lunch, and finally a tour of the brand new science building, fully equipped with all the newest technology. The trip was great. I now have a new college to consider! and to think I would have never known about Washington and Jefferson if it wern't for Project Seed!

Wednesday, July 21, 2010

Symposium Stress

Many Sto-Rox kids are going to be leaving for band camp next week, (actually all the Sto-Rox kids will be leaving for band camp except me). They are really stressed out, because they have to get their posters, and panels finished by this Friday, but I believe in them. At first, I didn't really care, because I still have a week to do my PowerPoint and panels, but yesterday when I started working on my panels I realized that this is a big deal to me, and started feeling the pressure. I'm really sad that the symposium is so soon, and my results aren't turning out how they would if they were right. My lab sent my mutations for sequencing to find out if the mutation worked, and when we received the paper showing our DNA sequence it didn't seem like my mutations worked, but it was hard to tell. We decided to send them back, because they could have worked in the reverse so now I have to wait to find out that. Also, I can't do anymore mutations right now, because we ran out of plates and they didn't come in yet. This is just a bad week for me. Hopefully I will get some good news to put into my symposium panels and Power Point by the end of this week, or at least before the symposium. I also hope the plates come in soon, but who knows. I'm trying to stay positive. as they would say in Japanese, "Ganbatte!!"

Monday, July 19, 2010

Mandatory Blog Challenge. Due August 2nd

Choose a graduate student or professor and discuss with them their career path and the road they traveled to arrive in their current position. Ask them what they would do differently. Ask them what their greatest successes and failures were along the way. Be insightful and thought provoking. Posts will be judged for depth of content, how well your writing engages the reader, and creativity. Pictures and videos always get you bonus points. This is not just a mandatory challenge, but it is also a big reward challenge.

Trial and Error

Last week, I found out that all my data was wrong, because I did not check the concentration of my salt box. I later found out that I was adding the wrong number of ions to my salt box. My equation gave me the number 16...there was confusion whether that meant 16 anions and 16 cations, or 8 anions and 8 cations to add to the box. We later found out that it meant 16 of each. Now, I'm back on track. I've equilibrated and minimized 4 boxes, NaCl and KCl 0.2 and 2.0M. Now all we have to do is run them on our super, TeraGrid computer, and I'll finally have some results. (:

Friday, July 16, 2010

Opitmization and Parameterization of IR and GC for Simple Reaction Mixture Analysis in ATRA

ATRA was discovered in 1937 by Karasch, but had low product yields at the time. Later, Minisci discovered metal catalyzed ATRA through his experiments and found this to have a much higher product yield. ATRA is a process by which carbon-carbon bonds are formed by means of a metal catalyst with products of small molecules that are used to create complex organic compounds and pharmaceuticals. The reason that I'm studying this is to achieve a more efficient way to run this mechanism.

In ATRA an alkyl halide reacts with a copper (l) catalyst to form a primary radical and copper (ll). The radical reacts with an alkene forming a secondary radical which abstracts a halogen atom from copper (ll) to regenerate copper(l) and form a monoadduct. Recent advances in this field have found that addition of a reducing agent can be used to dramatically reduce copper concentrations, making this method more attractive to synthetic chemists. Traditionally, analysis has been conducted via 1H NMR spectroscopy, which is inaccessible to smaller research facilities. I'm studying this mechanism with the application of gas chromatography and infrared spectroscopy to analyze these reactions.

My first week here I spent learning what all I would be doing. This included how to calculate the amounts of how much AIBN, internal standard, alkene, alkyl halide and solvent I would put into my test tubes to run. It was all a bunch of stoichiometry problems that were simple enough once I got the hang of it. Then the next few days were spent learning how to use the gas chromatographer (GC) and read the scans that it spit out. The first thing to do is turn on the gas tanks; first nitrogen, then air, then helium and finally to light the machine. The machine should always be purged before using it, to clean out anything that may have been left inside the column. To do this the GC is set to run at 180 degrees Celsius for 20 minutes, or until the scans look clean. Then the parameters are set for the sample; initial temperature, initial time, amount of degrees to ramp per minute (rate), final temperature, and final time. Sometimes this also includes changing the ramp time. Then the parameters on the integrator are set, which is the machine connected to the GC, and prints out the scans. The only parameters that are changed it the attenuation, which is how much the graph is zoomed in or out of the scan, and the stop time, which is how long the integrator should run for. The stop time is calculated by this formula: finial temp - initial temp / rate + initial time + final time = total time. Then .2 micro liters is injected into the column simultaneously while pressing start on both the GC and the integrator. As the machine runs, the sample moves through the column and the substances in the sample will shoot out of the column around their boiling point, as recorded by different sizes peaks on the integrator scan. Sometimes part of a sample will shoot out of the column at a significant time before or after it's boiling point and add and extra unknown peak to the scan. In that case, another scan is run again. At least two scans of every sample is run to confirm that the scan is quantitative. Though, since the machine is old it doesn't always work right and sometimes time is needed to purge again.

The second week I moved to the infrared spectrometer (IR). This machine measures the bonds in samples. First, a background is always collected before using the machine, so that it can tell the difference between what should be recorded, and what shouldn't. Then two drops of the sample is placed between two salt plates and put into the machine. After the IR runs it displays a spectra of the sample, which it obtained by shooting a photon of light through the sample. The light photon causes the connected atoms to vibrate about their bonds and different bonds absorb different amounts of energy, which are displayed in the spectra. The spectras can be checked against the SDBS database for confirmation.

The experiments we did at first were to check if the two machines were quantitative. On the IR we first ran Octene, Methanol, Acetonitrile, CCl4, Styrene, Methyl Acrylate, and Methyl Methacrylate. Then a mystery sample was made of two samples that I had already ran and were mixed together for me to identify what it was. Looking at the scans that I had already done of our materials and comparing the different peaks in the scans did this. If the peaks matched, it meant that the sample did as well. On the GC I ran all of our starting materials a few times, to check that they always came out at the expected time, in the right amounts. This week we've started running our solutions with AIBN, internal standard, alkene, alkyl halide and solvent through the GC. AIBN is our reducing agent and the reason this is used is because it gives a higher product yield than the other reducing agent, ascorbic acid, even though it's more environmentally friendly. We've ran four different scans all with differing ingredients and all but the first one came out okay, but we've yet to figure out why.

Next week the other IR head might be back, the one that's more quantitative, since the one we have now isn't and I might run some samples on that if it does.

Next week's gonna be rough

Next week is the last week for me to work on my project before the symposium. I feel like I haven't done that much, but when I look at all my data and scans I sort of wonder where all the time went. I lost my flash drive...which means I might have to redo my first power point, but at least I didn't lose the flash drive with all my data saved on it. My undergrad comes back next week, and that's when I'll probably be locked up in the lab running my experiments all day long. Then I need to finish my poster by Friday at the latest...It's all a tight deadline. At least we got paid today though, and that makes all the hard work worth it.

My Cells Grew!!!

Recently, I have been very busy, and happy, because my cells grew! Although, I had plated six cells to grow, only one of them grew how they were supposed to. That's okay though, because I'm still happy that I have data. Yesterday, I finally had the chance to do my first miniprep, and received data from sequencing, so I now have results that I can put in my power point to tell everyone about. I'm still not sure if my cells grew with the mutation, but the fact that they grew makes me happy. Now, I will continue to work hard and try to do more mutations, and succeed again!

Joseph Glorioso

Today we went to listen to a professor talk about his work in microbiology. It was really informative, but I guess not too interesting for me since that's not really a field I'm looking into. Most of it was biology related, but I learned that a lot of scientists will make a stretch to get funding for their research. A lot of the information on the internet isn't always as accurate as scientists make it seem. I also learned that when you get you PhD and start doing your own research, that that's exactly what it is your research. It's all your responsibility to figure out what you're doing, who's doing it with you, what you need, and how to fund all of it. Being in charge is also the good part though, because you do get to make all those choices and you end up being you're own motivation(and boss) and in the end it can lead to a lot of opportunities.


I kind of feel like I do the same thing every day: run scans on the GC. I guess it's pretty easy, so I shouldn't complain, but it doesn't always work right. At first it was pretty horrendous, but now it's actually okay.

Dr. Aitken Returns

Yesterday came the return of Dr. Aitken, the person responsible for bringing us here. She was out on maternal leave with the expectant arrival of the new baby (who was really cute). She stopped by for just a few hours to see everyone and it was nice to see her. She says she will be back for the symposium so I better get working to make her proud.

Thursday, July 15, 2010

Busy, Busy, Busy

Things are really starting to roll here. Along with all of our projects we have tons of other things to do. It seems like every day we have some kind of extra thing to do from SEED group meetings every Wednesday(along with our own Lab group meetings at various times) to field trips starting next week to PPG and Washington and Jefferson. It is really exciting though. I can't wait to go to all of these places. It is really nice to get out of the lab every once in a while (even though I enjoy that too).

Your Friendly Neighborhood Spiderman

Wednesday, July 14, 2010

So much to do, so little time!

Well, it's that time again. This is when things start to get hard. As the days go by, it gets closer and closer to the symposium. Since I have band camp, I have to have my poster done by next week. This means that I really need to get to work. I'm still in need of results and i'm hoping to have them soon. This is where things get somewhat stressful. Doing work, getting results and getting drafts for my poster done are alot to do in the little time that I have. On the plus side, I can't wait to see how the next few weeks turn out. Us SEED kids have some field trips to attend. It's going to be so much fun. The symposium is going to be a good experience for all of us as well. It will allow us to meet new people and show them the hard week we've done over the past few weeks.

Monday, July 12, 2010

It's Crunch Time!

There are so many things planned for this week, it's hard to keep up! We have everything from our abstracts being due tomorrow, to seminars and guest speakers. Not to mention only 2 and a half weeks til the symposium! I can't wait to see how this week unfolds.

Friday, July 9, 2010

Chris came to visit! =)

Today, Chris Sidun, a former SEED student and current Duquesne student, came to visit and share his experience with us. He talked about his time in the SEED program, what he's doing currently, what he would have done differently in the past and any advice that he could give to us. Overall, I found it very beneficial. Hearing the perspective of someone who was once in the spot that I'm in now really helped me. It really got me to think about what I want to do and where I want to be.

Page Views...

Guys, we hit 1000 blog views! Awesome! :)

Rough Draft of Abstract Due 7/9/2010 (Today)

Please read the formatting rules carefully before you begin writing your abstract for the symposium.

Wednesday, July 7, 2010


The field of microfluidics is relatively new to Chemistry. It has only been around for a couple of decades, but it's popularity has increased in not only the the chemistry department, but engineering and physics as well. Microfluidics is the observation and controlling of fluids at microscopic levels. The benefits of microfluidics include its cheaper cost and the unique ability to obtain the necessary results in mere seconds.

The objectives of my project includes trying various ratios to obtain continuous droplet flow using the microfluidic process. The ratios are from both the Oil and Aqueous Phase machines that is connected to syringes. The Oil Phase machine has a syringe filled with three milliliters filled with oil. As for the Aqueous Phase machine, three syringes are used. Two of them are filled with three milliliters of methanol. As for the other syringe, three milliliters of water is used mixed with food coloring dye. These syringes are attached to wire tubes that are connected to the microfluidic chip with droplets that I'm trying to form.

Once the preparation process is completed, I set ratios for the Phases to run. During the runs, it is normal for the run to come to an abrupt halt due to stalling. Stalling occurs when there is too much pressure on the Aqueous phases. Which will cause the droplet making to come to a halt as well. Ways that I can prevent stalling includes using new syringes with new methanol, and just using as many ratios as I can hoping that I can achieve my goals for this summer.

Ian's Project

Hi everyone, Alright, well my project has a long and complicated title... don't believe me?

It's called the Synthesis and Characterization of Copper and Cobalt Complexes with Dithione Ligands.

Ok, well now that that is out of the way... Let's explain what in the world this means. A ligand is just a molecule that binds to a metal like copper, cobalt, or molybdenum. The two types of ligands are dithiolene and dithione. The differences between the two are just how the elements are bonded together. Sometimes there are single bonds and sometimes double bonds. On the dithione, the double bonds let the extra hydrogen go away.

These ligands containing sulfur are found often in the body bonded to m
olybdenum. My project is to create copper and cobalt version of the man-made form of the molybdenum complex and compare the three using Ultraviolet-visible spectroscopy(UV-Vis), Infrared spectroscopy(IR), and Nuclear magnetic resonance spectroscopy(NMR).
My Experiment So Far:
Alright, so now that you have some background info, let's get into what I am actually doing...

1. 2. 3.

First I took N,N diisoproyl ethylene diamine(1.) and reacted it with diethyl oxalate (2.) to get the1,4-diisoproyl – 2,3- piperazinedione (3.) and from there we reacted it with Lawesson's reagent to create number 4. which is the dithione ligand. This reaction can be very random sometimes because the Lawesson's reagent can form many different things. In order to get only the ligand we had to do something called column chromatography. The white and yellow parts are just some random things that are waste. We only wanted the dark brown portion which is the ligand.

From here we recrystallized the ligand using hot ethanol then letting it sit in the fridge for the night. Once we got the ligand we were able to use it to create the copper complex. We first had to react copper (I) oxide in acetonitrile with perchloric acid to create [Cu(CH3CN)4][CLO4]. The[Cu(CH3CN)4][CLO4] reacts with air so we had to do the experiment in the dry box which is filled with nitrogen instead of air.
From here we reacted it with the ligand to create the final product, the copper dithione complex. The next things we need to do are create the cobalt dithione complex in much the same way as how we created the copper dithione complex. We also need to characterize the ligand and complexes using the UV-Vis, NMR, and IR.

And lastly, just some random thing that i had to learn in order to be able to do some of these reaction is dispensing liquid nitrogen. It is actually really simple... as long as you wear gloves because it can get a little cold.

Thursday, July 1, 2010

Blog Challenge #2

Post a complete summary of your research to date. Include experiments you performed, training you've received, and the future direction of your project. Spelling and grammar count. The most thorough and error free wins the swag.