Weeks Four, Five and Six
Again, I apologize for the delay in posting about my fellowship experience. The past few weeks have been very busy. Because I can’t remember all of the details of these weeks, I will be compressing them into one post.
I’m sad to say that my research hasn’t progressed much in the past few weeks. I understand this is the nature of research, but its still a bummer. In week four, I was attempting the protection reaction on the batches of porphyrin I had. We started to run low on our batches, so needed to make more. Dr. Balaz assigned this task to me and another grad student, but none of our reactions to make the porphyrin were working (less than 2% yield).
Dr. Balaz had the other grad student go back to his own research and we started troubleshooting. First, he observed me setting up and running the reactions to see if I was doing a systematic error. I trained the other grad student in the porphyrin synthesis, so any mistakes I could be making he may be as well. Nothing appeared to be wrong here, so we moved onto the possibility of contamination in my reagents or solvent.
This required us running multiple reactions, only changing one part at a time. In the sixth week, we narrowed down the contamination to one reagent – dipyrrole methane. If you recall from my earlier posts, this reagent is something I synthesized myself from pyrrole and formaldehyde. This reagent is light sensitive so I have to store it in vials covered with black electrical tape in a dark freezer. I’m not certain how it may have been contaminated, but it was and it set me back at square one.
Dr. Balaz also observed me setting up and running the dipyrrole methane reaction. He noticed an error – I wasn’t quenching the reaction or isolating my product properly, which can significantly decrease the yield and purity. Apparently I’m suppose to perform a precipitation after the Kugelrohr distillation. It was a little frustrating because they way I had been running this reaction is the way it was shown to me by a grad student who trained me. Please understand that I’m not blaming the grad student. I was frustrated that I had not asked more questions during my training to get a bigger picture and understand the reasons behind each step I took.
This is a common recommendation Dr. Balaz recites from day to day: ask as many questions as possible, then ask some more. He says that undergraduates struggle to do this because we like to be independent and great from the start, and we should not feel any shame for asking questions. He also says a lot of our mistakes do not come from a lack of knowledge, rather a lack of experience. I’m sure this is not the first time I’ve heard these comments, it was just the first time it sunk in.
If I remember correctly, Dr. Carroll also told my classmates and I that she doesn’t expect us to know of particular techniques because we don’t have the experience – we have never been introduced to them. She also ensured us that this shouldn’t be taken as a failure as a student, and encouraged us to continually ask questions. If we were to read about a technique in a scientific journal and didn’t know about it, to do more research and find out.
Now that we have narrowed down what sources were contaminated, we should be able to get a fresh start. For week seven and part of week eight, Dr. Balaz will be away on a conference and meeting with collaborators for his research. I’m a little nervous, because I would like to get something done and done well while he is away.
In Preparation for my Senior Comp
A part of my graduation requirements in the chemistry program, I will be giving a presentation to the department (as well as any public that choose to attend) on my research at Nazareth. Many of you may already know that I have been doing biodiesel research for Dr. Hartmann for quite some time, and the specific project I have been focusing on has lasted for the past year and will continue into my senior year.
The research course that sets the guidelines for my work requires that I give several presentations and reports varying in degree of depth. I have also completed a course focused on grant writing in which I wrote a mock grant proposal and defense presentation for my research. As a result, I have had a lot of practice over the past year presenting on my research.
During my second week of my fellowship, Dr. Balaz asked me to give a 20-40 minute presentation on my research at Nazareth to him and his graduate students. I said yes, but began to feel nervous almost immediately. This would be my first time presenting my research to group of people who are not familiar with what I am doing and also have much more expertise in chemistry than I do. There are a lot of advantages to this situation, because Dr. Balaz and his students are a set of fresh eyes and ears that can point areas of improvement or what was good. I was still afraid of opening my work up to harsh criticism. I understand that the criticism is not about me as a person, rather the work that could be better. However, as a student it is difficult to be told I fail on producing quality work after putting in so much effort. I probably hate failure as much as the next student.
When the day of my presentation came, I got up early, dressed business casual and headed off to the conference room. There was a small delay in my presentation because neither I nor anybody in the department had the adapter needed to plug the projector into my Mac Book. Apparently just about every model of Mac has a different type/fit of a projector port, and the adapters are not cheap.
During the presentation, I made eye connection with each person in the room and spoke clearly. Every person in Dr. Balaz’s lab speaks English as a second language, even though they all speak very well, it is easy for my to slip up on some words and cause confusion. At the end they all had good things to point out, recommendations for slides that were confusing, and minor formatting considerations. Dr. Balaz said my introduction was “fantastic” and I made my goals and objectives very clear. The group told me I did a good job and Dr. Balaz said I’m a very smart student (he has since made this comment multiple times when I surprise him with my knowledge about concepts like anisotropy).
I have several people to thank for success in presenting my research. When I first entered college, I had a lot of trouble presenting in front of groups and would feel intense stage fright to the point of my knees buckling and almost tossing my cookies. The only way this fear and feeling ever went away was through practice. Several of my courses required me to present multiple times through out a semester and some focused on critiquing my skills. Both of the courses (Chemistry Seminars) I have taken with Dr. Alicia Carroll have been focused scientific writing for journal articles and grants and presenting on my research. My research courses, advised by Drs. Carroll, Hartmann and Knoerzer also required presentations in front of peers and faculty.
The experiences in these courses offered a lot advice and insight about many aspects of a presentation. For example, the presentations in my research courses allowed for great peer review of my work and insight into what type of questions to expect. Dr. Carroll has been especially helpful, because even though her tough critiques seemed discouraging at times, it is the only way I progressed.
I have to thank Dr. Richard Hartmann for allowing me to do research for him and all of his advisement along the way. He has helped me greatly in finding what area of chemistry is my passion. He was also the person to recommend the University of Wyoming REU to me!
We will all miss Dr. Timm Knoerzer this next year. It is strange to think what Organic Chemistry lab is going to be with out him! I have to thank him for all of his advice and suggestions he offered during my presentations and whenever I dropped by his office, and not to forget all the skills he taught during lab. There was a time in my undergraduate career that I wasn’t sure if I could continue on due to tragedy in my family. Dr. Timm stepped up and helped me get back on track in my academics, encouraged me, and ensured me that I’m a great student. Dr. Carroll also played a large role in helping me during this hard time.
If I could offer any advice to undergraduate students in any of the science programs at Nazareth, it would be to participate early and often in research and take courses (if possible) with Dr. Alicia Carroll. Yes – she will give a tough critique, but it is honest and straightforward. You may be aware that the seminars she offers are only worth 1 or 2 credits, which doesn’t seem to represent the amount of work you will do, but its worth it. At this stage in your career, you need a professor like her to push you.
Thank you all for reading along, and I’m sorry for the delay in posts. I promise I have more coming!
Week Three
As of the second week, several batches of my starting material were synthesized. In a previous entry I mentioned that introducing new functionalities to the reactive sites (called meso positions) is difficult because they are all equal. The goal of my research is to determine if is possible to introduce a functionality known as a protection group to only one site, and then to remove it when desired. The third week is when I started to attempt the protection group reaction.
The purpose of the protection group is to temporarily occupy one of the reactive sites, not allowing anything else to be introduced to that specific site, but allowing other functionalities to be introduced to other sites. The protection group should also have the ability to be easily removed by changing the conditions of the reaction like introducing a new catalyst or changing the acidity.
Here’s an analogy for the non-scientific audience: think of the protecting group as a bouncer and the reactive sites as doors. The bouncer is standing at door A in which he doesn’t allow anybody to pass and party with the rock stars behind that door, but he doesn’t care about the equivalent door B nearby that people are interested in passing through (reacting with) to hang out (bind with) with those rock stars.
Later on, the bouncer’s boss (the researcher changing the catalyst or condition) tells him to go home for the day and stop protecting the door (removing the protection group), which now allows for people to pass through the door (new reactions with that site, different than previous reactions with the other sites).
Developing a system that allows for the introduction and removal of a protection group whenever desired gives the researcher the ability to manipulate porphyrin synthesis in time and space. This will take quite sometime and from now on out, I will most likely be repeating the same reactions over and over, slightly changing conditions.
The protection group addition is a time consuming reaction as well. The reaction itself will run for at least 4 hours, and that doesn’t include set up and the time it takes me to perform tests that monitor the reaction such as thin layer chromatography (TLC) and mass spectrometry (MS). Once the reaction is done, I have to isolate all of the products using column chromatography, which can take several hours depending on the conditions of the column.
Because this reaction that I am focusing on is so time consuming Dr. Balaz has requested that one of his grad students, Urice, to help me by making batches of starting material. The batches he will be making will be various types of porphyrins, so we may be able to show that this reaction is applicable to multiple types, not just limited to the porphyrin I have been working with. For the non-scientific audience: different types of porphyrins mean there are various functionalities already attached to two of the reactive sites on the porphyrins. Those functionalities can have different effects on the compound as a whole and can alter the reactivity of the remaining sites. That is why it is important to test this reaction on multiple types of porphyrins.
Every so often there is down time. There are always things to do during down time, such as cleaning glassware, reading literature, and preparing schemes and data sets for presentations. At the end of the ten weeks, I am required to give a formal presentation on the work I have done, similar to my senior comp presentation that I will be giving next spring.
I have good news about my presentation skills that I somehow forgot to report on. During my second week, Dr. Balaz asked me to give a formal presentation to him an his students on the research I have been doing at Nazareth. Overall, it was good. To give you more detail, I’ll write another entry.
Hiking a Mountain
As advertised, the REU program includes several trips for sight seeing, hiking and camping. This includes camping in Yellowstone National Park, visiting local coalmines (one of Wyoming’s primary exports), and the National Renewable Energy Laboratory in Golden, Colorado. All of those trips will be scattered through out the month of July.
On Saturday (June 5th), the group drove to Greyrock Mountain about 20 miles outside of Fort Collins, Colorado. Greyrock stands out from all of the other surrounding mountains because of its height and the summit is all … grey rocks.
The mountain starts out at about 5,000 feet above sea level, and reaches over 7,400 feet (slightly higher than Laramie). At the bottom of the mountain is the Cache La Poudre River where many professional kayaker and rafters travel down the rapids (it looked to be about a 3 on the 1-5 scale). There are two trails, varied in walking distance, that meet just before the steep climb to the very top. Both trails are considered a “moderate” challenge.
Cache La Poudre River
Because the trails started out at a lower elevation, the temperature was fairly high (around 90 °F), unfortunately some of the other students thought long pants and wool socks would be appropriate. The heat at the beginning of the trail was tough. I think on a cooler day I would’ve considered the trail to be very manageable otherwise.
The whole trail was beautiful, very scenic, and as the elevation increased the view became breathtaking (it was either the view or weather, hard to tell). Some of us did not anticipate how long the trail and how hot it would be, some students did not bring enough water with them. Fortunately, the park rangers walking the trail carry extra bottles of water for hikers.
Once both trails met up again just before the summit climb, it became difficult to determine where the path actually was. In these cases where the trail isn’t obvious, it is marked with small stacks of rocks.
"Up" is a trail.
It took about three hours to get to the top, and we spent a good hour at the summit before hiking back down the mountain. At the top, there are several scenic ponds and the view included snow cap mountains, nearby mountains, hills and cities (Fort Collins was visible). There was also cell phone reception!
The hike back down was relaxing, but a little rough on the ankles and it took about 3 hours. In total we hiked from around 11 AM to 6 PM. Afterward we went to a local professor’s house for a barbeque and a game of bocce ball (seriously, what is up with chemists and bocce ball?). I’m sad to say that my team (full of mostly central/east coast people) lost miserably.
At the end of the bbq, the host pointed out the mountain we climbed off in the distance. The whole day felt rewarding and even though it might not have been the most challenging hike, I was still proud of myself for dedicating the whole day to climbing a mountain.
The bump to the left of the garage roof is Greyrock Mountain
My Second Week
My second week in the laboratory consisted of porphyrin synthesis from the dipyrrole methane I had previously made and a selection of benzaldehydes to generate batches of my starting material. As I mentioned before, porphyrins are highly colored compounds so determining the progress of the reactions is simple and column chromatography allows for easy isolation due to variation in color for each product.
About an hour into porphyrin synthesis
Final product - deep purple
So far, I’ve used techniques I am already familiar with, but I’m improving on them. For example, I’ve improved a lot on my spotting for TLC plates and determining eluent systems. I also have improved my lab notebook keeping and other minor skils in the lab. I know they are small, but there is always room for growth on old skills.
As far as analysis goes, I’ve done MS and NMR. The University has three NMR instruments, the one I used was 400 MHz and has a lot of the same controls as Nazareth’s old 200 MHz NMR. This NMR has the shimming dial, which I have to say – I don’t miss it.
The NMR (AKA - Giant Magnet)
Each student in the program has been placed with a PhD in the Chemistry Department and has their own project to work on. The types of chemistry varies from analytical, physical, photo, and organic. As you may have already guess, I am working in organic synthesis. During the day I don’t see much of the other students, because we are all working in our labs anywhere from 7 – 10 hours a day.
I work in Balaz’s Dark Lab that is designed to allow the researcher to work with light sensitive compounds. The dark lab is much like a dark room for photographers, when the lights are out we work underneath a red light. So far, none of the reactions I’ve completed are so sensitive to require the red light; instead I keep my flasks covered with tin foil (high tech, right?)
The Dark Lab
Through out the day I work pretty independently unless I am using a new technique or doing a new reaction. In those cases Dr. Balaz or one of his students will coach me through the process and give me advice from their experiences.
On my blog account, I receive statistics about how many people are viewing my entries. Just yesterday, I had 55 hits! Thank you for all of your support and I look forward to hearing from you and seeing all of you again in the fall!
Vedauwoo
On Saturday afternoon (May 29th), all of the REU students and three of the advisors drove out to the Vedauwoo campgrounds just outside of Laramie, WY. Vedauwoo is a large rocky outskirt of Laramie, with a slightly higher elevation (around 8,000 feet).
Rocks!
We didn’t have proper climbing equipment, so we only hiked the Turtle Rock trail. The whole trail only took about two to three hours to complete and afterward we barbequed hot dogs on one of the public grills.
The trail was nice, very easy and scenic (parts of it still had snow). We didn’t see much wildlife besides birds and chipmunks. Apparently mountain lions and moose inhabit the area. I’ve seen many moose while living in Northern Maine for my last two years of high school, but never a mountain lion. I was told if I see one, its best to intimidate it, and they are easy to scare away. Unfortunately we never saw one, but many of the other hiking areas and mountains we will be visiting have them.
More rocks!
At dinner, there was a very trusting chipmunk that wandered into our gazebo and would eat the trail mix we dropped. We named him Happy Cheeks.
Our friend, Happy Cheeks.
My first week
Tuesday, the 25th, was my first real day in the lab. Dr. Balaz introduced me to the graduate students and the project I will be working on. His students are all international, from South Korea, Cameroon, and Armenia. If you are advantageous enough to learn about what his research team does, Google Dr. Milan Balaz, his website is the first result.
My first assignment was to follow one of his students around the lab to learn where every thing was location and to get my feet wet. I followed Fidelis Ngwa, one of two students from Cameroon. I practiced techniques with Fidelis, all of which I have learned before in Organic Chemistry, but I was slightly rusty on. I couldn’t quite remember all the steps to packing a column, but I got there.
My desk
Ultra-cool leather bound lab notebook!
That night, Dr. Balaz treated his research team and I to a sushi dinner at a local restaurant (I can never turn down sushi). It was delicious and meeting all of the students was fun. We exchange a lot of questions about our hometowns and universities and it was interesting learning about their experiences. All of the students speak English very well, so communication is not difficult. At times, some of the students from Cameroon will speak their version of broken English to each other, which is a mixture of English and German. If I listen closely enough I can recognize words and understand the basic theme of the conversation. Some of the students told me that I was not a typical American. I wasn’t quite sure what they meant by this, and they said it was because I am a young female that enjoys science and I’m not lazy. At times, I don’t think I would agree about my level of laziness, but I took it as a compliment.
A boat load of sushi!
My project is a branch from Gevorg’s research (found on Dr. Balaz’s website). In simplest terms for my non-scientific audience: I am trying to find/develop synthesis methods for manipulating porphyrin synthesis. What are porphyrins? They are highly colored and naturally existing compounds found in blood cells and chlorophyll (two of many places) and cause the red and green pigmentations observed, respectively. The simplest porphyrin is porphine, and that structure is considered the “backbone” of every porphyrin structure. Porphine can be synthesized, but trying to further add to the backbone to make other porphyrin compounds is very difficult because the all of the reactive sites are equal. For example, if you would like to introduce a new functionality to only one of the sites, you are likely to introduce that functionality to multiple or all of the sites. In other words, selectivity is hard to control. My job is to work on reaction conditions that Dr. Balaz has proposed and determine if they allow for selective synthesis, and what are the optimal conditions.
Porphine
The rest of the week, I jumped straight into synthesis. Fidelis and Dr. Balaz tested my knowledge on mechanisms by having me draw out the entire mechanism for a triflouroacetic acid catalyzed synthesis of dipyrrole methane from pyrrole and formaldehyde. I impressed them, thanks to Dr. Timm and my experience as a workshop leader for Organic Chem.
In the actual synthesis of dipyrrole methane, I used a new technique I had never heard of. Once I quenched (stopped the reaction) my reaction mixture, I had to distill a solid from my solution. This is done with a Kugelrohr distillation apparatus. The night before, I read about the set up from an article in the Journal of Chemical Education. It is a bulb-to-bulb distillation: my mixture rotates in a glass bulb that is placed inside a heat chamber that reaches higher temperatures than attainable with a rotary evaporator or hot plate. All of the glass bulbs are also under a high vacuum. The first glass bulb is connected through a second glass bulb that sits outside the heat chamber and on an ice bath. As my mixture rotates in the first bulb, my desired product (which conveniently has the lowest boiling point of all products made) evaporates and travels upward into the second bulb and condenses due to the lower temperature. And voila! I have my isolated product, a white crystalline solid.
A modern version of the Kugelrohr distillation apparatus.
The brown stuff is all the crap I don't want, the white stuff it what I'm isolating from it.
Due to the shortened week (thanks to safety classes and introductions), I did not complete much work. That Memorial Day weekend, the entire group of REU students and a few of the advisors (mine included) took a trip to Vedauwoo, a rock-climbing and hiking site just outside of Laramie. The next entry will be about the Vedauwoo experience.
The Journey to Laramie, WY
I left Rochester around 7 AM on May 20th and started driving to Mahomet, Illinois. The drive with all the stops included took about 12 hours, and I crossed over into the Central Time Zone (one hour behind the Eastern Time Zone). The longest part of the trip was driving through Ohio. Many times I was tempted to drive off to Cleveland to see what Drew Carey was so excited about, but I stayed on track. Indiana is where the land started flattening out, and there were an abundance of road signs telling me to repent for my sins.
My Aunt Lydia, her husband, and children live in Mahomet and offered to let me stay the night at their home. Once I arrived in Mahomet, my Aunt graciously took the family and I out to a sushi dinner. Both of Lydia’s children work for a private company that develops packaging and bottles for beverage companies. It was great catching up with the Brazier side of the family, and I will be stopping in Mahomet again on my way back. The next morning, I left for Omaha, Nebraska.
Just beyond the Iowa boarder is the World’s Largest Truck Stop, also called Iowa 80. They weren’t kidding. This place had a regular restaurant, five fast food restaurants, a gas station, convenience store, and large gift shop bigger than the gift shop at Corning Museum of Glass. The place was packed with people.
The gift shop
Eight and a half hours later, I arrived in Omaha, Nebraska. My second cousin, David, and his wife and three children live in Omaha where David works from home for a steel company (optimizing their production line using classic physics) and his wife works as a pathologist (along with many other titles) at a near by hospital. David and I talked a lot about grad school and his experience. David is a Doctor of Physics and proudly gave me a copy of his dissertation titled “Hydrogen and Deuterium in the Cosmic Ray Flux,” and told me to enjoy some light reading. Lets hope he doesn’t quiz me on it at the next family reunion.
The eight-hour drive between Omaha and Laramie was probably the worst leg of the trip. Nebraska is very flat and hot until the western part of the state where the time zone changed and I started to see tumbleweed and plateaus. Once I crossed the state boarder and drove through Cheyenne, I could see the Rocky Mountains. Having never seen landscapes and desert like nature before in my life, I was pretty excited to say the least.
Plateaus!
The REU program provides room and board. More specifically I’ve been place in a double occupancy room in McIntyre Hall on campus. McIntyre is 12 floors high and is considers Wyoming’s tallest building. Meals are offered in the building next door, in a fairly large café with plenty of entrée options. The campus also offers many other services such as the recreational center (RC). In the RC there is a pool, gym, various courts (racquet, volley, etc), dance rooms, general exercise room, and a HUGE climbing wall open for bouldering and climbing. The RC also has a great outdoor program which you can repair your bike with their tools, rent a bike for the summer (I rented one myself, $20 for the summer), and equipment for almost any outdoor activity (mountain bikes, tents, hiking gear, etc).
Laramie is considered a city with a population around 27,000. However, it is really isolated, making it seem very small in comparison to Rochester. To me, it is odd what businesses exist in Laramie and what ones don’t. The only department store here is Walmart and then there are several fast food places and restaurants that cater to college student appetites, such as the mythical Sonic. I call it mythical because I have only seen commercials for Sonic, never the actual restaurant. Behold! Laramie has one. Also there is this bar across the street from our dorm called The Library (Karen, I know you would love this.)
The bar across the street from the dorms.
On that Sunday (the 23rd) all of the students met and we enjoyed an indoor barbeque (due to 40 mph winds) at Dr. Hoberg’s house. The next day Dr. Hoberg gave us a tour of the campus to show us where to go, introduce us to our advisors, and provide more information about our stay and potential trips. I didn’t notice until we were doing a lot of walking and climbing stairs that I felt out of breath and a headache coming on. Most of the other students were in the same boat, and Dr. Hoberg explained that it was due to the altitude which roughly 7,200 feet above sea level and estimated there was bout 20% less oxygen in the atmosphere. He also explained that Laramie is considered an elevated desert. Rochester, NY is at about 550 ft and my hometown in Maine is 85 ft.
For lunch we had a pizza and met our advisors. My advisor is Dr. Milan Balaz (pronounced with a soft ‘g’ at the end), an organic chemist who focuses most of his research on DNA. You are probably saying to yourself “Hey, isn’t this REU focused on alternative energy development?” Yes, it is, but I will get into that in a later entry. The rest of the afternoon was filled with safety training courses.
This sums up the traveling experience and introduction to Laramie.
Introduction
My name is Jenna, as many of my targeted readers should know, and I’m a rising senior in the chemistry program at a liberal arts college in upstate New York. Recently, I was accepted into a ten week Research Experience for Undergraduate program (REU) funded by the National Science Foundation (NSF) and the Department of Defense at the University of Wyoming. This REU is focused on alternative energy research. In this program are nine other students, hailing from Jamaica and various parts of the United States including Pennsylvania, Georgia, North Dakota, Wisconsin, Colorado, Iowa, Minnesota, and Maine (my home state).
Many of my friends, family, coworkers, and professors have asked a lot of questions about this REU and requested that I send e-mails and pictures about how things are going. I decided rather than sending out mass e-mails that may flood boxes, people can choose to follow this blog. For ten weeks I will attempt to keep up a blog about my summer experience with my peers and mentors, and try to come out with new entry once a week.
I hope you all enjoy my updates, and I also hope to hear from you as the summer progresses!
-Jenna
