The moment had arrived -- the moment that we would each be expected to submit an 8-12 page paper and a group presentation documenting our research over the Interim period. When I first received the assignment, it really didn't seem that daunting or challenging. I served as an intern to the Department of Energy over the summer, which required a 5000-word professional publication with at least fifteen references and a 10-minute presentation in front of the entire program. After that experience, I was confident that I could tackle any project thrown my way in record time.
Which is why I procrastinated until the night before to start my research paper. Bad idea.
The issue was not writing the paper. I easily reached the 8-12 page minimum a few hours after I started. The problem was getting all my information into the paper, along with appropriate images and citations. That process took me most of the next day.
It resulted in 19 pages, excluding the title page and references. Yeah. Over-achiever. But it was a really good paper.
The presentation process lasted only about half the time, which was fortunate. I am now running through my presentation notes so that I can provide good information to my audience tomorrow morning.
Maybe I'll post a link to my paper and presentation later.
Wish me luck!
Tuesday, January 29, 2013
Friday, January 25, 2013
Day Sixteen: Everything That Could Go Wrong
It probably didn't help that the sleet started to fall on my uncovered head as I walked to Milliken this morning.
On the other hand, I had a voucher for free coffee and ordered a large one. The Pop-Tart and Oreos were good, too.
Anyways.
I was feeling quite productive as I wandered into the laboratory this morning, having set my large coffee in the hallway where it would be protected from chemicals. I quickly spotted three TLC plates with samplings of my thirty-five test tubes from yesterday and prepared a new solvent chamber to develop them while I drank my coffee. Unfortunately, things don't always go according to plan. The solvent touched my samples immediately instead of gradually in the absorbance process, and the plate was left in the chamber for too long, rendering the test useless.
However, all was not lost, as I realized that I wanted to test a larger sampling of my test tubes and prepared a new set of TLC plates: one for the original, and then four sets of every three. They developed uniformly and displayed great results under the UV light. I happily documented my results in my notebook.
Everything went downhill from there.
Dr. Bass and I decided that we would attempt to oxidize my impure 2-benzylcyclohexanol product and see what results we could get. So while my TLC plates were developing, I scrounged through his old laboratory for a three-necked flask, West condenser, separatory funnel, and thermometer adapter that would be the appropriate side for about 15 mL of reagents. The final apparatus was actually quite adorable:
The unfortunate part occurred when the supposedly half-hour reaction took an hour and a half to complete. And when I had to constantly adjust the heat setting to maintain a warm temperature. And when I left an important TLC plate in the chamber for too long.
Yeah. That's how the day ended. We can only hope that Monday will be more successful. There is still a distillation to complete.
Have a wonderful weekend!
On the other hand, I had a voucher for free coffee and ordered a large one. The Pop-Tart and Oreos were good, too.
Anyways.
I was feeling quite productive as I wandered into the laboratory this morning, having set my large coffee in the hallway where it would be protected from chemicals. I quickly spotted three TLC plates with samplings of my thirty-five test tubes from yesterday and prepared a new solvent chamber to develop them while I drank my coffee. Unfortunately, things don't always go according to plan. The solvent touched my samples immediately instead of gradually in the absorbance process, and the plate was left in the chamber for too long, rendering the test useless.
However, all was not lost, as I realized that I wanted to test a larger sampling of my test tubes and prepared a new set of TLC plates: one for the original, and then four sets of every three. They developed uniformly and displayed great results under the UV light. I happily documented my results in my notebook.
Everything went downhill from there.
Dr. Bass and I decided that we would attempt to oxidize my impure 2-benzylcyclohexanol product and see what results we could get. So while my TLC plates were developing, I scrounged through his old laboratory for a three-necked flask, West condenser, separatory funnel, and thermometer adapter that would be the appropriate side for about 15 mL of reagents. The final apparatus was actually quite adorable:
The unfortunate part occurred when the supposedly half-hour reaction took an hour and a half to complete. And when I had to constantly adjust the heat setting to maintain a warm temperature. And when I left an important TLC plate in the chamber for too long.
Yeah. That's how the day ended. We can only hope that Monday will be more successful. There is still a distillation to complete.
Have a wonderful weekend!
Thursday, January 24, 2013
Day Fifteen: Chromatography
It is at this point in the process, with Interim swiftly coming to a close, that I should say our polymerization will not be happening by the end of the month. There is a good chance that my colleagues will be able to continue their syntheses over the next semester, but since I will be studying abroad, I won't get to complete it myself.
In light of these developments, we spent today learning useful separation techniques in an attempt to isolate our products from the Grignard reaction. The first technique we explored was thin-layer chromatography (TLC). Essentially, a plastic-backed paper is coated with a polar compound - in this case, a silicon oxide. A drop of product is placed about one centimeter from the bottom of the paper, and the paper is set in a container with a small amount of solvent. This solvent is absorbed onto the TLC paper and catches the drop of product as it travels. Depending on the attractions between the solvent and the product, the product will move a certain distance along the paper, until the paper overcomes that attraction. If multiple components exist in the solution, they will separate based on their polarities. Analysis of the TLC is possible using UV radiation (if the product contains pi bonds) or solid iodine.
The purpose of the TLC was to determine what composition of solvent would best serve to separate our compounds in the product solution. In my case, I was attempting to separate 2-benzylcyclohexanol, some 2-chlorocyclohexanol, and a small amount of bibenzyl. Out of some varied combinations of hexane (nonpolar) and ethyl acetate (fairly polar), we determined that a 4:1 ratio was optimal overall.
The second technique we utilized was column chromatography. Assembling the column itself was probably the most interesting part of the process. First, we stuffed the bottom of the column right above the stopcock with a swab of cotton and poured in about 3 cm of hexane. Next, we measured enough silica gel powder to fill 20 cm of the column, dissolved it in hexane, and poured it into the column with excess hexane. After draining out the hexane and removing any air bubbles by tapping the column with a rubber hose, I poured a sample of my product dissolved in hexane and ethyl acetate into the column and let it settle into the silica layer. After that, it was a matter of preparing 50-mL hexane and ethyl acetate solvents of varying compositions - lower to higher concentrations of ethyl acetate.
We let the liquid elute for almost two hours, catching 5-10 mL at a time in test tubes and replacing the solvent when necessary. I tested for eluting product by placing small dots on TLC paper but not developing it, rather relying on UV radiation to confirm the presence of a benzyl product. There was no visible dot left by the end of the column chromatography process.
In the morning, I will develop TLC plates for every fourth test tube out of a total thirty-five and run appropriate gas chromatography samples from today's separation.
In light of these developments, we spent today learning useful separation techniques in an attempt to isolate our products from the Grignard reaction. The first technique we explored was thin-layer chromatography (TLC). Essentially, a plastic-backed paper is coated with a polar compound - in this case, a silicon oxide. A drop of product is placed about one centimeter from the bottom of the paper, and the paper is set in a container with a small amount of solvent. This solvent is absorbed onto the TLC paper and catches the drop of product as it travels. Depending on the attractions between the solvent and the product, the product will move a certain distance along the paper, until the paper overcomes that attraction. If multiple components exist in the solution, they will separate based on their polarities. Analysis of the TLC is possible using UV radiation (if the product contains pi bonds) or solid iodine.
The purpose of the TLC was to determine what composition of solvent would best serve to separate our compounds in the product solution. In my case, I was attempting to separate 2-benzylcyclohexanol, some 2-chlorocyclohexanol, and a small amount of bibenzyl. Out of some varied combinations of hexane (nonpolar) and ethyl acetate (fairly polar), we determined that a 4:1 ratio was optimal overall.
The second technique we utilized was column chromatography. Assembling the column itself was probably the most interesting part of the process. First, we stuffed the bottom of the column right above the stopcock with a swab of cotton and poured in about 3 cm of hexane. Next, we measured enough silica gel powder to fill 20 cm of the column, dissolved it in hexane, and poured it into the column with excess hexane. After draining out the hexane and removing any air bubbles by tapping the column with a rubber hose, I poured a sample of my product dissolved in hexane and ethyl acetate into the column and let it settle into the silica layer. After that, it was a matter of preparing 50-mL hexane and ethyl acetate solvents of varying compositions - lower to higher concentrations of ethyl acetate.
We let the liquid elute for almost two hours, catching 5-10 mL at a time in test tubes and replacing the solvent when necessary. I tested for eluting product by placing small dots on TLC paper but not developing it, rather relying on UV radiation to confirm the presence of a benzyl product. There was no visible dot left by the end of the column chromatography process.
In the morning, I will develop TLC plates for every fourth test tube out of a total thirty-five and run appropriate gas chromatography samples from today's separation.
Wednesday, January 23, 2013
Days Thirteen and Fourteen: Where's the Product?
It has been a long two days of IR, GC, NMR, and attempting to isolate our desired first product from unreacted materials still in solution. Thus far, it's been somewhat unsuccessful. Although it's clear from the spectra that 2-benzylcyclohexanol is in high abundance in my product solution, we haven't been able to purify it by vacuum distillation and aren't sure that we'll be able to perform the oxidation reaction as is. Tomorrow, we plan to use TLC spotting and column chromatography in a last shot at obtaining pure product prior to oxidation.
Unfortunately, this setback means that none of our monomers will be ready in time to polymerize at College of Charleston, which has been the source of some tension. I'm trying to remind myself that, in the real world, there isn't really a time-limit on research - even with the pressure to submit papers for certain journals and symposiums with deadlines - so I shouldn't be worried that three weeks of experimental work didn't yield the results that we had hoped for.
I expect that my group will have its work cut out for us during the upcoming semester.
Unfortunately, this setback means that none of our monomers will be ready in time to polymerize at College of Charleston, which has been the source of some tension. I'm trying to remind myself that, in the real world, there isn't really a time-limit on research - even with the pressure to submit papers for certain journals and symposiums with deadlines - so I shouldn't be worried that three weeks of experimental work didn't yield the results that we had hoped for.
I expect that my group will have its work cut out for us during the upcoming semester.
Monday, January 21, 2013
Day Twelve: Long but Good
Hello, after what I hope was a wonderful weekend!
I suppose that I could document my day's activities. However, there isn't much new information to report. We characterized our Grignard reaction and decided to run it again, keeping me in the lab from 8:50 - 6:30...not the longest day I've spent in a laboratory, but definitely unexpected.
What I'd rather do is reflect on how this day of work affected my attitude toward the future.
There are a lot of cool Interim projects on campus this year: Latin dance, knitting, yoga and rock-climbing. I was recommended to quite a few of these, and would gladly have participated in any of them. After spending my last two Interim terms out of the country - first in Chile, then in Italy - it might have made sense to pick a project that was more relaxing, especially considering that I leave for my semester abroad a week after Interim ends. I knew, though, that this might be my only chance to garner research experience this academic year. Not only that, if I couldn't travel and explore new cultures, I couldn't see myself anywhere other than in a chemistry laboratory.
I won't lie and say that watching a half-hour reflux is the most enjoyable task. It's actually somewhat tedious, all things considered. But I found myself comforted in the knowledge that I could have a reflux running in one hood, a GC sample being scanned in the other lab, and be setting up a new apparatus or washing glassware all at once. I enjoyed wandering back and forth and comparing my reaction process to my lab mates'. In comparison to last week's trial, today's experiment proceeded without a hitch, so it was nice to lean back and observe without significant stress.
Another wonderful aspect about the day was affirming my desire to attend graduate school and being able to hash out my ideas with another chemistry major. As of now, I still don't know where I'm headed, but I am confident that organic chemistry is a viable option for me. I love the work that I've done this Interim and can't wait to pursue chemical research for the next few years!
I suppose that I could document my day's activities. However, there isn't much new information to report. We characterized our Grignard reaction and decided to run it again, keeping me in the lab from 8:50 - 6:30...not the longest day I've spent in a laboratory, but definitely unexpected.
What I'd rather do is reflect on how this day of work affected my attitude toward the future.
There are a lot of cool Interim projects on campus this year: Latin dance, knitting, yoga and rock-climbing. I was recommended to quite a few of these, and would gladly have participated in any of them. After spending my last two Interim terms out of the country - first in Chile, then in Italy - it might have made sense to pick a project that was more relaxing, especially considering that I leave for my semester abroad a week after Interim ends. I knew, though, that this might be my only chance to garner research experience this academic year. Not only that, if I couldn't travel and explore new cultures, I couldn't see myself anywhere other than in a chemistry laboratory.
I won't lie and say that watching a half-hour reflux is the most enjoyable task. It's actually somewhat tedious, all things considered. But I found myself comforted in the knowledge that I could have a reflux running in one hood, a GC sample being scanned in the other lab, and be setting up a new apparatus or washing glassware all at once. I enjoyed wandering back and forth and comparing my reaction process to my lab mates'. In comparison to last week's trial, today's experiment proceeded without a hitch, so it was nice to lean back and observe without significant stress.
Another wonderful aspect about the day was affirming my desire to attend graduate school and being able to hash out my ideas with another chemistry major. As of now, I still don't know where I'm headed, but I am confident that organic chemistry is a viable option for me. I love the work that I've done this Interim and can't wait to pursue chemical research for the next few years!
Friday, January 18, 2013
Day Eleven: Pyrotechnics and Argon
Dawned the morning of our scaled-up Grignard reaction. Fortunately, it was sunny and low in humidity, so keeping moisture out of the lab was a much more feasible goal. However, we still had to dry our glassware prior to starting the reaction, and we wanted to do what we could to maintain the dryness throughout the experimental run.
Enter a hair dryer, a flame torch, and a large tank of argon gas.
Even after removing my glassware from the oven, there was a significant amount of water in my round-bottomed flask. Before assembling my reflux apparatus, I clamped the flask aloft and ran a hair dryer in a swirling motion below it. Once most of the moisture was gone, I added the remaining pieces of glassware and stoppered the ends with dessicant tubes. Then, I ignited a small flame torch and ran it lightly from bottom to top outside the apparatus, watching the condensation move up into the dessicant tubes:
After that, we connected gas tubing where the dessicant tubes had previously been via syringe needles poked through rubber septa. It took some adjusting to infuse all three apparatuses with argon, but it was effective once we got it to work. The problem that arose then was the amount of pressure due to the argon, even with the outlet tube. Since my alkyl halide, benzyl chloride, is quite volatile, the reflux process caused a lot of my reaction solution to spit out of the RB flask instead of condensing and falling back down. We promptly removed the argon and the heat from my apparatus, though, and the rest of the experiment proceeded without any other disruptions.
The product has been left to stir over the weekend and will be characterized and oxidized on Monday!
Enter a hair dryer, a flame torch, and a large tank of argon gas.
Even after removing my glassware from the oven, there was a significant amount of water in my round-bottomed flask. Before assembling my reflux apparatus, I clamped the flask aloft and ran a hair dryer in a swirling motion below it. Once most of the moisture was gone, I added the remaining pieces of glassware and stoppered the ends with dessicant tubes. Then, I ignited a small flame torch and ran it lightly from bottom to top outside the apparatus, watching the condensation move up into the dessicant tubes:
After that, we connected gas tubing where the dessicant tubes had previously been via syringe needles poked through rubber septa. It took some adjusting to infuse all three apparatuses with argon, but it was effective once we got it to work. The problem that arose then was the amount of pressure due to the argon, even with the outlet tube. Since my alkyl halide, benzyl chloride, is quite volatile, the reflux process caused a lot of my reaction solution to spit out of the RB flask instead of condensing and falling back down. We promptly removed the argon and the heat from my apparatus, though, and the rest of the experiment proceeded without any other disruptions.
The product has been left to stir over the weekend and will be characterized and oxidized on Monday!
Thursday, January 17, 2013
Day Ten: Humidity Problems
Very little to report today. With the non-stop rain in upstate South Carolina, lab conditions weren't really optimal for performing another Grignard reaction today. We decided to perform the calculations necessary for a scaled-up experiment (2 mL cyclohexene oxide to 10 mL) and prepare the glassware and reagents to run our reaction tomorrow. Since my compound, benzyl chloride, is volatile, I completed an experiment of Dr. Bass's during normal lab time, which included a GC scan and a simple distillation. After placing our glassware in the oven to dry, we called it a day!
Hopefully there will be more to do and say tomorrow.
Hopefully there will be more to do and say tomorrow.
Wednesday, January 16, 2013
Day Nine: Step One is a Success!
Hello, Blogger world (and Dr. Pittman).
Once again, I must apologize for posting my daily blog one day late. In my defense, yesterday was a very long day and today I did not work in the lab because I accompanied another Interim group to Duke Energy in Seneca, which was a fantastic experience and has given me some things to consider for my future. Educational opportunities are everywhere.
Yesterday's process was slow but valuable. We began by preparing GC samples of our Grignard products - in my case, 2-benzylcyclohexanol. (Note that this is fairly similar to the standard cyclohexanol that we reacted last week.)
Once again, I must apologize for posting my daily blog one day late. In my defense, yesterday was a very long day and today I did not work in the lab because I accompanied another Interim group to Duke Energy in Seneca, which was a fantastic experience and has given me some things to consider for my future. Educational opportunities are everywhere.
Yesterday's process was slow but valuable. We began by preparing GC samples of our Grignard products - in my case, 2-benzylcyclohexanol. (Note that this is fairly similar to the standard cyclohexanol that we reacted last week.)
We added water to our reaction flasks, and two separable layers - liquid and solid - formed. We decanted the top layer into a new RB flask, using a sample of that liquid for our GC scan. The precipitate was left in the flask.
From the first scan of our samples, we determined that all of the cyclohexene oxide had reacted, because the known peak for that compound was not present in the spectrum. After that, we ran the same samples through the GC but performed mass spectrometry, as well. My top match for the product mass was the desired compound - yay!
Having concluded that my product solution contained 2-benzylcyclohexanol, I set the purified solution to dry with magnesium sulfate and turned my attention to the leftover, untested product. Since we believed that some product might have been trapped in the precipitate, I removed the unreacted magnesium by vacuum filtration and treated the solution with 6-M hydrochloric acid until the solution was no longer basic. This was to ensure that all of the alcohol was indeed protonated and to make it more ether-soluble than aqueous. I rinsed the solution with ether and separated the organic product from aqueous. Tomorrow, we will determine if the two solutions match.
Thus far, the most frustrating part about research is having to wait for results before moving on. It would have been much more time-efficient to perform the acid workup while the first GC scans were in progress, but then, we may have done more work than was necessary if there hadn't actually been desired product in our samples. There is a lot of trial and error involved, as well, which is distinctly more nerve-wracking than following a set procedure. On the other hand, taking notes and modifying what we've been given is a very exciting process! It's cool that we can somewhat customize this research experience - from the number of Keck clips we use on our apparatuses to the compounds we've selected to study.
Monday, January 14, 2013
Day Eight: I Had to Wear Legit Goggles
Because the alkyl halide used in forming my Grignard reagent is benzyl chloride:
To the observer who has not taken organic chemistry, this structure means very little and certainly couldn't be dangerous, if it's been entrusted to college students. In actuality, benzyl chloride is an incredibly volatile liquid that doesn't mind becoming airborne as a vapor. When that happens, it's very easy for this vapor to localize on one's eyes and cause an irritation - hence, it is called a lachrymate.
Unfortunately, benzyl chloride also reacts very willingly with water to form an alcohol. One of water's protons is released during this process and can react with the chloride anion that resulted from the substitution. Hydrogen + chloride = hydrochloric acid...a dangerous chemical to have in one's eye.
For this reason, any time that I worked with benzyl chloride, I kept the fume hood mostly closed and wore legitimate laboratory goggles for protection, rather than glasses.
Aside from that, the Grignard reflux was fairly straightforward. Granted, every piece of glassware had to be dried in an oven at 100 degrees Celsius for an hour to remove any excess water, but once set up, we were able to mix the alkyl halide with magnesium and ether to form the Grignard agent and then add cyclohexene oxide for the Grignard reaction.
We'll find out how it went when we characterize our products tomorrow!
To the observer who has not taken organic chemistry, this structure means very little and certainly couldn't be dangerous, if it's been entrusted to college students. In actuality, benzyl chloride is an incredibly volatile liquid that doesn't mind becoming airborne as a vapor. When that happens, it's very easy for this vapor to localize on one's eyes and cause an irritation - hence, it is called a lachrymate.
Unfortunately, benzyl chloride also reacts very willingly with water to form an alcohol. One of water's protons is released during this process and can react with the chloride anion that resulted from the substitution. Hydrogen + chloride = hydrochloric acid...a dangerous chemical to have in one's eye.
For this reason, any time that I worked with benzyl chloride, I kept the fume hood mostly closed and wore legitimate laboratory goggles for protection, rather than glasses.
Aside from that, the Grignard reflux was fairly straightforward. Granted, every piece of glassware had to be dried in an oven at 100 degrees Celsius for an hour to remove any excess water, but once set up, we were able to mix the alkyl halide with magnesium and ether to form the Grignard agent and then add cyclohexene oxide for the Grignard reaction.
We'll find out how it went when we characterize our products tomorrow!
Sunday, January 13, 2013
Day Seven: LOTS of Separations
This post is two days late, for which I apologize. Everything that follows is written from Friday's point of view.
I never knew before this morning that so many different separations could take place to isolate an organic product. We treated the solution that had been stirred overnight with three solids: sodium bisulfite to reduce the oxidizing agents, bleach and m-CPBA; sodium bicarbonate to neutralize the carboxylic acid formed in the reaction; and sodium chloride to extract any remaining water from the dichloromethane component of the solution. The process involved a good number of runs through the separatory funnel and one vacuum filtration, and some of the layers looked rather interesting:
There were originally three layers in this particular separation. The portion of the solution that resembles a cloud was in-between the organic and aqueous layers. We believe that this center layer formed because the composition was both dichloromethane- and water-soluble, so the cloud was trying to exist in both layers at once. By the time we performed the last separation, only two layers remained. The organic solution was left to dry with sodium sulfate and will be characterized on Monday.
Additionally, we began to make preparations for our Grignard reaction of cyclohexene oxide, which will also take place on Monday. We distilled "anhydrous" ether over a period of about four hours in this rather impressive apparatus:
We used a 5-L three-necked round-bottomed flask, a condensation column, a distilling head, a West condenser, a vacuum filter, and three receiving flasks, two of which were 1-L teardrop-shaped flasks. Our apparatus also included a coiled copper tube immersed in ice to ensure that the water entering the condenser was as cold as possible. This tube, along with the condensation column, was important to be sure that only ether and not water was distilling into the receiving flask. We will use this more anhydrous ether to make our Grignard reagent.
Hopefully soon, I will provide on this blog the procedure used for the Baeyer-Villiger oxidation and the reference for our standard workup. Enjoy the rest of the weekend!
I never knew before this morning that so many different separations could take place to isolate an organic product. We treated the solution that had been stirred overnight with three solids: sodium bisulfite to reduce the oxidizing agents, bleach and m-CPBA; sodium bicarbonate to neutralize the carboxylic acid formed in the reaction; and sodium chloride to extract any remaining water from the dichloromethane component of the solution. The process involved a good number of runs through the separatory funnel and one vacuum filtration, and some of the layers looked rather interesting:
There were originally three layers in this particular separation. The portion of the solution that resembles a cloud was in-between the organic and aqueous layers. We believe that this center layer formed because the composition was both dichloromethane- and water-soluble, so the cloud was trying to exist in both layers at once. By the time we performed the last separation, only two layers remained. The organic solution was left to dry with sodium sulfate and will be characterized on Monday.
Additionally, we began to make preparations for our Grignard reaction of cyclohexene oxide, which will also take place on Monday. We distilled "anhydrous" ether over a period of about four hours in this rather impressive apparatus:
Hopefully soon, I will provide on this blog the procedure used for the Baeyer-Villiger oxidation and the reference for our standard workup. Enjoy the rest of the weekend!
Thursday, January 10, 2013
Day Six: Tying Loose Ends
Time can be very valuable if it is used to wrap up one project and make preparations for the next one. Today, my group tested our individual cyclohexanone samples from the oxidation experiment, performed the next portion of the Baeyer-Villiger oxidation, and set up the apparatus for a Grignard reaction.
From the IR spectrum of my cyclohexanone sample, the OH peak has significantly reduced from the last experimental run. Since the GC suggests that no more cyclohexanol remains in the solution, we suspect that there is still water in the system or that some the cyclohexanone has been converting to its enol form. We will extract the liquid from the vial containing drying agent prior to our next run of the Baeyer-Villiger reaction.
The workup following the Baeyer-Villiger reflux involved transferring the contents of the reaction flask to an Erlenmeyer flask, using 30 mL of dichloromethane to make a qualitative transfer. After that, the solution was left to stir with 30 mL of water. Adding 0.15 g of sodium bisulfite and 10 mL of 10% sodium bicarbonate solution formed two separate layers in the reaction mixture after vigorous fizzing. We will complete the reaction tomorrow, once the mixture has been stirred through the night.
The apparatus we set up is, in one word, AWESOME, and I will post a picture of it tomorrow...brace yourselves....
From the IR spectrum of my cyclohexanone sample, the OH peak has significantly reduced from the last experimental run. Since the GC suggests that no more cyclohexanol remains in the solution, we suspect that there is still water in the system or that some the cyclohexanone has been converting to its enol form. We will extract the liquid from the vial containing drying agent prior to our next run of the Baeyer-Villiger reaction.
The workup following the Baeyer-Villiger reflux involved transferring the contents of the reaction flask to an Erlenmeyer flask, using 30 mL of dichloromethane to make a qualitative transfer. After that, the solution was left to stir with 30 mL of water. Adding 0.15 g of sodium bisulfite and 10 mL of 10% sodium bicarbonate solution formed two separate layers in the reaction mixture after vigorous fizzing. We will complete the reaction tomorrow, once the mixture has been stirred through the night.
The apparatus we set up is, in one word, AWESOME, and I will post a picture of it tomorrow...brace yourselves....
Wednesday, January 9, 2013
Day Five: Multi-tasking
It was one of those days that I arrived at 8 a.m. and monitored as many as four processes at once. That isn't to say that I didn't enjoy the work; I love being in the lab and performing reactions that I understand on a basic level. I am, however, quite tired and hopeful that today's experiments will yield good results tomorrow.
I began my day setting up a simple reflux apparatus for the addition of m-CPBA to cyclohexanone in dichloromethane:
Originally, Dr. Bass and I added heat to the reaction flask and deposited the m-CPBA solid through the West condenser. On review of the procedure, however, we realized that the m-CPBA was to be added prior to setting the heat. We also found that the solid tended to clump inside the condenser, though we were able to force the solid through by adding more dichloromethane. The next time we run this reaction, we will add the solid straight to the reaction flask rather than through the narrow tube. This mixture was left to reflux until about 5:00 this afternoon.
My second reaction was the re-run of the oxidation of cyclohexanol. Following my notes from the previous day made adjusting the reaction conditions much easier, so that the solution stayed within the proper temperature range the entire time that bleach was being added dropwise. Actually, the bleach was sufficient to maintain the heat without a mantle, and I removed the outside heat source once the mixture reached 40 degrees, even though that slowed the overall process. I also used two 80-mL portions of bleach instead of 72-mL.
In the case that bleach was in excess, I prepared 100 mL of saturated sodium bisulfite solution, just as I did the other day. This reaction was performed during the 20-minute stirring period after the addition of bleach was complete.
Halfway through the experiments, after the 20 minutes, I prepared a GC sample to test for unreacted cyclohexanol. I extracted a 2-mL sample from the reaction flask into a small Erlenmeyer flask. A potassium iodide starch paper test revealed that the sample contained excess bleach, so I added a few drops of the prepared sodium bisulfite to neutralize it. Afterwards, I transferred the sample to a vial and added 2 mL of ether, capping the bottle and shaking until two separable layers formed. The top (ether) layer was extracted into another vial, and ether was added by the same procedure as yesterday.
The GC scan confirmed formation of cyclohexanone and absence of cyclohexanol, signifying a complete reaction. (YAY.)
The rest of the experiment proceeded as modified after the first run, except for one key point. After the addition of solid sodium chloride on Monday, some of the salt crystals transferred into the separatory funnel and clogged the stop-cock area. To avoid this, I performed a vacuum distillation of the salted solution to extract the hydrated crystals and be left with two clean layers. Extracting the organic layer was much simpler, and it is being left to dry with solid magnesium sulfate.
Tomorrow's focus will be characterization of the product and a closer look at the Baeyer-Villiger oxidation!
--
Now, for your viewing pleasure: what chemists do before, during, and after reactions...multiple times...sometimes more often than actually running experiments.
In case anyone wondered, we wash glassware. A lot. My roommates wonder why I put off washing dishes after a meal. It's just a reality of the industrial and researching world that I will enjoy for quite awhile.
I began my day setting up a simple reflux apparatus for the addition of m-CPBA to cyclohexanone in dichloromethane:
Originally, Dr. Bass and I added heat to the reaction flask and deposited the m-CPBA solid through the West condenser. On review of the procedure, however, we realized that the m-CPBA was to be added prior to setting the heat. We also found that the solid tended to clump inside the condenser, though we were able to force the solid through by adding more dichloromethane. The next time we run this reaction, we will add the solid straight to the reaction flask rather than through the narrow tube. This mixture was left to reflux until about 5:00 this afternoon.
My second reaction was the re-run of the oxidation of cyclohexanol. Following my notes from the previous day made adjusting the reaction conditions much easier, so that the solution stayed within the proper temperature range the entire time that bleach was being added dropwise. Actually, the bleach was sufficient to maintain the heat without a mantle, and I removed the outside heat source once the mixture reached 40 degrees, even though that slowed the overall process. I also used two 80-mL portions of bleach instead of 72-mL.
In the case that bleach was in excess, I prepared 100 mL of saturated sodium bisulfite solution, just as I did the other day. This reaction was performed during the 20-minute stirring period after the addition of bleach was complete.
Halfway through the experiments, after the 20 minutes, I prepared a GC sample to test for unreacted cyclohexanol. I extracted a 2-mL sample from the reaction flask into a small Erlenmeyer flask. A potassium iodide starch paper test revealed that the sample contained excess bleach, so I added a few drops of the prepared sodium bisulfite to neutralize it. Afterwards, I transferred the sample to a vial and added 2 mL of ether, capping the bottle and shaking until two separable layers formed. The top (ether) layer was extracted into another vial, and ether was added by the same procedure as yesterday.
The GC scan confirmed formation of cyclohexanone and absence of cyclohexanol, signifying a complete reaction. (YAY.)
The rest of the experiment proceeded as modified after the first run, except for one key point. After the addition of solid sodium chloride on Monday, some of the salt crystals transferred into the separatory funnel and clogged the stop-cock area. To avoid this, I performed a vacuum distillation of the salted solution to extract the hydrated crystals and be left with two clean layers. Extracting the organic layer was much simpler, and it is being left to dry with solid magnesium sulfate.
Tomorrow's focus will be characterization of the product and a closer look at the Baeyer-Villiger oxidation!
--
Now, for your viewing pleasure: what chemists do before, during, and after reactions...multiple times...sometimes more often than actually running experiments.
In case anyone wondered, we wash glassware. A lot. My roommates wonder why I put off washing dishes after a meal. It's just a reality of the industrial and researching world that I will enjoy for quite awhile.
Tuesday, January 8, 2013
Day Four: Characterization
Today's primary objective was characterization of our cyclohexanone samples. We began with IR scans, since we are more familiar with the technique. The scan showed a clear carbonyl peak near 1700 cm-1, which confirmed the formation of a C=O functional group; however, a prominent OH peak was present at 3500 cm-1. Initially, we assumed that the product had not finished drying and added extra drying agent to our samples for about half an hour.
To determine whether the peak was due to excess water or unreacted cyclohexanol, we prepared samples to test by gas chromatography in the following steps:
Based on these results, we decided to perform the oxidation reaction again tomorrow. We plan to use fresher bleach reagent and attempt to better stay within the desired temperature range of 40-45 degrees Celsius. Because my temperature dropped below 40 degrees for longer than ten minutes, I believe that my reaction rate slowed over the 30-minute reaction period such that the reaction did not proceed to completion - hence the need for sodium bisulfite to neutralize the unreacted bleach.
Additionally, we plan to begin a Baeyer-Villiger oxidation reaction of standard cyclohexanone tomorrow. From the procedure given by Dong Tian, et. al. (see below), the cyclohexanone, m-CPBA, and dichloromethane reagents will be in reflux for 15 hours, so we will start the process early in the morning and spend the rest of the day with the regular oxidation reaction.
Here's to another day of research, hopefully with fewer set-backs!
--
References:
Tian, Dong, Philippe Dubois, Christian Grandfils, and Robert Jerome. "Ring-Opening Polymerization of 1,4,8-Trioxaspiro[4.6]-9-undecanone: A New Route to Aliphatic Polyesters Bearing Functional Pendent Groups." Macromolecules 30 (1997): 406-409. Print.
To determine whether the peak was due to excess water or unreacted cyclohexanol, we prepared samples to test by gas chromatography in the following steps:
- Insert a glass pipet into the liquid product to extract a small amount (just a tip-full)
- Fill a plastic pipet with ether solvent
- Push the ether through the glass pipet so that a mixture of product and ether collects in a sample vial
Based on these results, we decided to perform the oxidation reaction again tomorrow. We plan to use fresher bleach reagent and attempt to better stay within the desired temperature range of 40-45 degrees Celsius. Because my temperature dropped below 40 degrees for longer than ten minutes, I believe that my reaction rate slowed over the 30-minute reaction period such that the reaction did not proceed to completion - hence the need for sodium bisulfite to neutralize the unreacted bleach.
Additionally, we plan to begin a Baeyer-Villiger oxidation reaction of standard cyclohexanone tomorrow. From the procedure given by Dong Tian, et. al. (see below), the cyclohexanone, m-CPBA, and dichloromethane reagents will be in reflux for 15 hours, so we will start the process early in the morning and spend the rest of the day with the regular oxidation reaction.
Here's to another day of research, hopefully with fewer set-backs!
--
References:
Tian, Dong, Philippe Dubois, Christian Grandfils, and Robert Jerome. "Ring-Opening Polymerization of 1,4,8-Trioxaspiro[4.6]-9-undecanone: A New Route to Aliphatic Polyesters Bearing Functional Pendent Groups." Macromolecules 30 (1997): 406-409. Print.
Monday, January 7, 2013
Day Three: Practice Reaction
There are days that I wonder if I truly want to pursue chemistry as a profession. Then there are days like today that confirm how much I LOVE working in the lab. My group performed our first reaction today: the oxidation of cyclohexanol to cyclohexanone, given by the procedure in Mohrig's Modern Projects and Experiments. The first portion of the reaction, including set-up, lasted about three hours; the second portion took another three hours. We had a very productive day! (Thank goodness for 96.1 FM!)
The apparatus for the first portion was designed to measure temperature, add reagent dropwise, and prevent evaporation by keeping part of the flask cool. Our assembly of three-necked round-bottomed flask, thermometer (right), addition funnel (left), and West condenser (center) is shown below:
The flask was set in a heating mantle mounted atop a stirring motor.
The objective was to add approximately 150 mL bleach to the reaction flask of cyclohexanol and acetic acid over a period of 30 minutes...while maintaining a temperature between 40 and 45 degrees Celsius. Our biggest struggle during this reaction was staying within those boundaries. Fortunately, we picked up a few tips along the way that will help when we repeat this reaction with our own compounds.
We found that setting the heating mantle to level 20 (out of 100 - slightly ambiguous) and lowering the heat to level 5 once reaching the desired temperature range was the best method for regulating temperature. Increasing the addition rate of bleach is helpful in reaching this temperature range more quickly. Additionally, when the liquid mixture temperature exceeded 45 degrees, moving the flask to an ice water bath for no longer than ten seconds was sufficient to return to the temperature range without significantly dropping in temperature. (A temperature lower than 40 degrees could slow the reaction rate and lower percent yield of the final product.) After the 30-minute addition period, the mixture is left to stir for 20 minutes at maintained heat, during which time the solution forms a foamy, yellow-colored ring at the surface.
Another small set-back occurred when we realized that we didn't have the necessary saturated sodium bisulfite solution to neutralize the excess bleach. The solubility of sodium bisulfite crystal is 42 g / 100 mL, and we decided to prepare a 50-mL sample in a small flask by swirling. For the next run-through, we plan to prepare this solution during the 20-minute stirring period.
Adding thymol blue indicator turned the entire solution a golden yellow. About 17 mL concentrated sodium hydroxide were required to reach pH 9, at which time the solution had become royal blue in color.
For the second portion, a simple distillation apparatus was assembled, this time incorporating a Claisen adapter, a distillation head, and a small round-bottomed receiving flask:
The objective was to separate the organic cyclohexanone product by steam distillation. Interestingly, because so much water is produced during this reaction, an azeotrope of cyclohexanone and water forms with a boiling point of 95 degrees Celsius. This is primarily due to hydrogen bonding between the two compounds. Once this azeotrope is distilled into the receiving flask, solid sodium chloride is added to attract the water away from the cyclohexanone and form a more distinctive aqueous layer for separation.
Though this process should have been simple and straightforward, we encountered trouble during the drying process. Some salt remained in solution, so while the drying agent was effective in removing the water, the organic solution was not pure. We solved this issue by pipetting the liquid into a glass pipet stuffed at the bottom with cotton - the cotton allowed the pure liquid to seep through but captured the salt. After the liquid was transferred into a sample vial, we added more drying agent and left the product to sit overnight. We will characterize our product in the morning.
Overall, I am optimistic about tomorrow's results and have enjoyed the process thus far. I will be interested to see how the reaction proceeds when I test my own compound.
The apparatus for the first portion was designed to measure temperature, add reagent dropwise, and prevent evaporation by keeping part of the flask cool. Our assembly of three-necked round-bottomed flask, thermometer (right), addition funnel (left), and West condenser (center) is shown below:
The flask was set in a heating mantle mounted atop a stirring motor.
The objective was to add approximately 150 mL bleach to the reaction flask of cyclohexanol and acetic acid over a period of 30 minutes...while maintaining a temperature between 40 and 45 degrees Celsius. Our biggest struggle during this reaction was staying within those boundaries. Fortunately, we picked up a few tips along the way that will help when we repeat this reaction with our own compounds.
We found that setting the heating mantle to level 20 (out of 100 - slightly ambiguous) and lowering the heat to level 5 once reaching the desired temperature range was the best method for regulating temperature. Increasing the addition rate of bleach is helpful in reaching this temperature range more quickly. Additionally, when the liquid mixture temperature exceeded 45 degrees, moving the flask to an ice water bath for no longer than ten seconds was sufficient to return to the temperature range without significantly dropping in temperature. (A temperature lower than 40 degrees could slow the reaction rate and lower percent yield of the final product.) After the 30-minute addition period, the mixture is left to stir for 20 minutes at maintained heat, during which time the solution forms a foamy, yellow-colored ring at the surface.
Another small set-back occurred when we realized that we didn't have the necessary saturated sodium bisulfite solution to neutralize the excess bleach. The solubility of sodium bisulfite crystal is 42 g / 100 mL, and we decided to prepare a 50-mL sample in a small flask by swirling. For the next run-through, we plan to prepare this solution during the 20-minute stirring period.
Adding thymol blue indicator turned the entire solution a golden yellow. About 17 mL concentrated sodium hydroxide were required to reach pH 9, at which time the solution had become royal blue in color.
For the second portion, a simple distillation apparatus was assembled, this time incorporating a Claisen adapter, a distillation head, and a small round-bottomed receiving flask:
The objective was to separate the organic cyclohexanone product by steam distillation. Interestingly, because so much water is produced during this reaction, an azeotrope of cyclohexanone and water forms with a boiling point of 95 degrees Celsius. This is primarily due to hydrogen bonding between the two compounds. Once this azeotrope is distilled into the receiving flask, solid sodium chloride is added to attract the water away from the cyclohexanone and form a more distinctive aqueous layer for separation.
Though this process should have been simple and straightforward, we encountered trouble during the drying process. Some salt remained in solution, so while the drying agent was effective in removing the water, the organic solution was not pure. We solved this issue by pipetting the liquid into a glass pipet stuffed at the bottom with cotton - the cotton allowed the pure liquid to seep through but captured the salt. After the liquid was transferred into a sample vial, we added more drying agent and left the product to sit overnight. We will characterize our product in the morning.
Overall, I am optimistic about tomorrow's results and have enjoyed the process thus far. I will be interested to see how the reaction proceeds when I test my own compound.
Friday, January 4, 2013
Day Two: To Design an Experiment
Today was the perfect reminder that this research project is much more concerned about the process than the product. I love being part of a collaborative group that is happy to progress at an even but not hurried pace. It gives us the opportunity to focus on preparation, what we're attempting to accomplish, and how the work can be divided to simultaneously challenge us, highlight our strong points, and complete our tasks in an efficient manner.
As I mentioned yesterday, we did learn to operate the IR and NMR instruments today. We will certainly practice more in the future, but it was helpful to get an overview of these instruments' functions and review how to read the spectra that they produce. These spectra will be essential in determining whether or not our reactions proceed as we expect.
Since a big component of our project deals with monomers that we aren't even sure will polymerize, Dr. Bass suggested that we carry out a practice reaction with materials that we have and that have been evaluated in the literature before we attempt to synthesize our target compounds. This process will also familiarize us with the procedures on a general level. As it turns out, preparation methods aren't necessarily right on-hand, and some research and modifications are needed before beginning the process.
The first procedure that we modified was the oxidation of cyclohexanol to cyclohexanone:
The process was relatively simple, as we had a method outlined for this process (1) and simply wanted to scale down from 16 mL of starting material (cyclohexanol) to 10 mL. The only concern that we've encountered thus far has to do with the apparatus. The article calls for a three-necked 500-mL round-bottomed flask with an addition funnel, a West condenser, and a thermometer inserted in the three necks. However, it may be simpler for us to use materials already accessible in the student organic chemistry laboratory - namely, a 250-mL round-bottomed flask, a distillation head, and alternating uses of the addition funnel and thermometer at the top portion of the distillation head. We will find out what Dr. Bass suggests when we return on Monday.
Our next step involved searching for methods describing the Baeyer-Villiger oxidation of cyclohexanone to caprolactone and general Grignard reactions of cyclohexene oxide:
We found a method for the Baeyer-Villiger oxidation in Synthetic Communications via the SciFinder database (2). The reaction with cyclohexanone is expected to proceed over the course of thirty minutes with 100% yield. The Grignard procedure will be detailed in later posts.
So far, it has been a thoroughly enjoyable process, and we look forward to beginning our first series of reactions next Monday morning!
--
References:
As I mentioned yesterday, we did learn to operate the IR and NMR instruments today. We will certainly practice more in the future, but it was helpful to get an overview of these instruments' functions and review how to read the spectra that they produce. These spectra will be essential in determining whether or not our reactions proceed as we expect.
Since a big component of our project deals with monomers that we aren't even sure will polymerize, Dr. Bass suggested that we carry out a practice reaction with materials that we have and that have been evaluated in the literature before we attempt to synthesize our target compounds. This process will also familiarize us with the procedures on a general level. As it turns out, preparation methods aren't necessarily right on-hand, and some research and modifications are needed before beginning the process.
The first procedure that we modified was the oxidation of cyclohexanol to cyclohexanone:
The process was relatively simple, as we had a method outlined for this process (1) and simply wanted to scale down from 16 mL of starting material (cyclohexanol) to 10 mL. The only concern that we've encountered thus far has to do with the apparatus. The article calls for a three-necked 500-mL round-bottomed flask with an addition funnel, a West condenser, and a thermometer inserted in the three necks. However, it may be simpler for us to use materials already accessible in the student organic chemistry laboratory - namely, a 250-mL round-bottomed flask, a distillation head, and alternating uses of the addition funnel and thermometer at the top portion of the distillation head. We will find out what Dr. Bass suggests when we return on Monday.
Our next step involved searching for methods describing the Baeyer-Villiger oxidation of cyclohexanone to caprolactone and general Grignard reactions of cyclohexene oxide:
We found a method for the Baeyer-Villiger oxidation in Synthetic Communications via the SciFinder database (2). The reaction with cyclohexanone is expected to proceed over the course of thirty minutes with 100% yield. The Grignard procedure will be detailed in later posts.
So far, it has been a thoroughly enjoyable process, and we look forward to beginning our first series of reactions next Monday morning!
--
References:
- Mohrig, Jerry R., Christina Noring Hammond, Paul F. Schatz, and Terence C. Morrill. "Green Chemistry: Oxidation of Cyclohexanol Using Sodium Hypochlorite." Modern Projects and Experiments in Organic Chemistry: Miniscale and Williamson Microscale. 2nd ed. W.H. Freeman and Company, 2002. 107-14. Print.
- Alam, M. Mujahid, Ravi Varala, and Srinivas R. Adapa. "Bi(OTf)3-Catalyzed Baeyer-Villiger Oxidation of Carbonyl Compounds with m-CPBA." Synthetic Communications 33.17 (2003): 3035-3040. http://web.ebscohost.com/
ehost/pdfviewer/pdfviewer?sid= c39ae472-aa6e-4a8c-b2fc- 1c33e5172b38%40sessionmgr104& vid=2&hid=119.
Thursday, January 3, 2013
Day One: Intro to Polymers!
Well, it has certainly been an informative and productive first day of polymer research! Arrived on the third floor of Milliken at precisely 9:13 this morning to meet with my advisor - the great Dr. Bass - and determine my group's goals for the immediate future. Though we certainly have a plan of what we hope will transpire over the course of the month of January, we also realize that our schedule will need to be flexible based on the success of our syntheses and reaction mechanisms.
Fortunately, there are a few things that we can say right off the bat.
So let's begin with...definitions!
- Polymer: Taken from the Greek polus ("many") and meros ("parts"), a chemical compound consisting of repeating structural units. Examples include rubber, cellulose, nylon, PVC, and silicone.
- Monomer: The structural unit.
- Polymerization: The process of linking monomers to make a polymer.
Those were hopefully fairly straightforward, but the remaining definitions are very specific and technical.
- Ester: An organic compound characterized by one carbon connected to a carbon and an oxygen by single bonds and another oxygen by a double bond.
- Lactone: A cyclic ester.
- Caprolactone: A lactone formed from caproic acid (also known as hexanoic acid). Contains six carbons in its backbone.
- Ring-opening polymerization: The polymerization process facilitated by opening the cyclic structure and connecting monomers at the break point.
- Substituent: An additional group attached to the primary compound.
At this point in the process, it would be beneficial to mention how these vocabulary terms are connected. The goal of this project is to synthesize four substituted caprolactones and separately polymerize them. According to current research being conducted at College of Charleston under Dr. Van Horn and other publicized studies (see below), rate of polymerization - and polymerization in general - could be impacted by the bulkiness of the substituent on the ring. Essentially, the bigger the lactone, the slower the rate of polymerization. In order to test this hypothesis, each member of my group will be synthesizing one of these four monomers.
The monomer I will be investigating is 7-benzyloxepan-2-one. In order to synthesize this molecule, I will begin with simple cyclohexanone and lithium diisopropylamide (LDA). The important thing to know about these reagents is that an incredibly strong base will form as a result, which will react quite nicely with the compound chlorotoluene (more commonly, benzyl chloride). The desired monomer, minus the additional oxygen that makes it a lactone, should result.
From there, a reaction called the Baeyer-Villager oxidation will be employed to convert 2-benzylhexanone into 7-benzyloxepan-2-one, and a catalyst will be added to the reaction vessel to begin the polymerization process.
In later entries, I will detail the techniques and apparatuses that my group uses to carry out these reactions. Tomorrow, we plan to learn how to operate the infrared radiation (IR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy instruments that will be used to characterize our compounds as we go along. Until next time!
Publications:
Martello, Mark T., Adam Burns, and Marc Hillmyer. "Bulk Ring-Opening Transesterification Polymerization of the Renewable δ-Decalactone Using an Organocatalyst." ACS Macro Letters 1 (2012): 131-134.
Wang, Cui, Yan Xiao, Andreas Heise, and Meidong Lang. "Organometallic and Enzymatic Catalysis for Ring Opening Copolymerization of ε-Caprolactone and 4-methyl-ε-Caprolactone." Journal of Polymer Science 49 (2011): 5293-5300.
Peeters, Joris W., Oscar van Leeuwen, Anja R. A. Palmans, and E. W. Meijer. "Lipase-Catalyzed Ring-Opening Polymerizations of 4-Substituted ε-Caprolactones: Mechanistic Considerations." Macromolecules 38 (2005): 5587-5592.
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