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Prof Friesen's LabBlog

Page history last edited by jbfriesen 16 years, 1 month ago

This Blog has now been entirely moved to

http://ochemonline.wordpress.com/

March 1

Week 7:

Identification of a Conjugated Diene from Eucalyptus Oil

1) Source(s)

This experiment was adapted by a group of 4 students from: Lehman, J. W., Lehman, J. W., Operational organic chemistry, & 3rd. (2004). Microscale operational organic chemistry : A problem-solving approach to the laboratory course. Upper Saddle River, N.J: Pearson Prentice Hall. This was an interesting find, I thought. I have done a couple of different Diels Alder experiments over the years: maleic anhydride and cyclopentadiene, as well as maleic anhydride and anthracene. I liked working with anthracene much more that cyclopentadiene.

2) Changes to published procedure

The amount of diene in the essential oil is very small. I ended up spiking the Eucalyptus oil with phellandrene from Aldrich. The experiment, as written, gives no indication of how much diene to expect from the essential oil. We did the experiment with 6 grams of essential oil and a great excess of maleic anhydride. Recrystallization was done with ethanol.

3) Positive

+The Diels-Alder reaction is one of those quintessential reactions that should be emphasized in the OChem curriculum.

+I liked the interface with natural products as well as the inquiry potential. The experiment presents four possible dienes in Eucalyptus oil. The essential oil is reacted with maleic anhydride and identification of the product by melting point reveals which diene was prevalent in Eucalyptus oil.

+Smells nice.

4) Neutral

±Not much new as far as technique here. The technical part comes with the methods of characterizing the product.

5) Negative

-The use of ether as a solvent is less-than-ideal here. We had a small fire in the lab when a student removed the round bottom from the reflux condenser.

-Melting point is a mundane way to characterize a product. GC or even IR are more appropriate here.

6) Inquiry & Extension ideas.

●This could possibly be done as a “solventless” reaction. The cineole in Eucalyptus oil could play the part of solvent.

●The inquiry aspect could be transferred to a “unknown” format. An unknown diene is reacted with maleic anhydride and the product characterized to reveal the structure of the diene.

February 24

Week 6: Oxidation of Cinnamyl Alcohol using Pyridinium Chlorochromate:

1) Source(s)

The experiment was adapted by a group of four students from: Experiment #14 in Mohrig, J. R. “Modern projects and experiments in organic chemistry: Miniscale and standard taper microscale.” (2003) New York; Basingstoke: W.H. Freeman; Palgrave Macmillan.

2) Changes to published procedure

○We did not visualize the TLC with p-anisaldehyde.

○We did not pre-mix the PCC, NaOAc, and molecular sieves.

○We stopped the reaction after one hour.

○We used hexane instead of pentane in the column chromatography solvent mixture.

3) Positive

+This is a reaction we are learning in the lecture section.

+The reactant and product smell nice.

+Column chromatography is an important technique

4) Neutral

±The lab is very TLC intensive. The TLC solvent system should be optimized to give clear indication of what it happening.

±Could a substitute for ethyl ether in the reaction work-up be used?

±GC chromatogram shows that there is an appreciable amount of unreacted alcohol present.

5) Negative

6) Inquiry & Extension ideas.

●Versatile reaction: Many different substrates can be envisioned such as benzyl alcohol, hydrocinnamyl alcohol, or substituted cinnamyl alcohol derivatives.

●Could be explored by leaving out reagents such as NaOAc or molecular sieves. What would be the effect of running the reaction longer or refluxing?

●Could be compared and contrasted with other oxidation methods.

Synthesis of a Tertiary Alcohol Using a Pre-Made Grignard Reagent

1) Source(s)

The experiment was adapted by a group of four students from a recent JCE article: Michael A. G. Berg and Roy D. Pointer. J. Chem. Educ. 2007, 84, 483.

2) Changes to published procedure

○We changed the configuration of the reaction vessel. Instead of a three-neck round bottom, we used a single-neck round bottom with a Claisen adapter to accommodate a separatory funnel and condenser.

○We had no special treatment of the Grignard reagent other than measuring it from the bottle with a syringe.

○We had no special treatment of the dried glassware.

○We set the addition time to 30 minutes.

○We gave more specific directions for acidification, extraction with ether, back extraction of ether with sodium bicarbonate, drying, and recrystallization.

3) Positive

+We are learning this reaction in the lecture section. The acid work-up is especially instructive since this concept comes up a lot in reactions.

+Using a commercially available pre-made Grignard is a great idea.

+The reaction turns pink! Very nice. Is it the Mg(OH)₂?

+experience with an air & water sensitive reaction is important.

4) Neutral

±Is a there a possibility of using an alternative to ethyl ether for the extracions?

±Triphenylmethanol has poor solubility in practically every solvent.

±Triphenylmethanol is difficult to remove from the round bottom.

±Determining if the two-phase aqueous work-up is a little tricky.

±TLC system should be optimized.

5) Negative

-Grignard solution is unstable. Buy a fresh bottle for each lab period.

6) Inquiry & Extension ideas.

●Versatile reaction: Many different carbonyl substrates can be envisaged. The JCE article suggests acetophenone and 4-chlorobenzophenone in addition to benzophenone.

●Further modification of the alcohol could be performed.

●Qualitative test to confirm the presence of a tertiary alcohol.

February 17:

Chemistry is the art of seeing what is invisible. Many students came up to me or the laboratory aide and pronounced that their spice steam distillation had produced “nothing.” What they meant was they could not detect anything in their beaker with their eyesight. Their noses, however, could detect the odor of their essential oil. From this we can conclude that the olfactory sensory apparatus is a more sensitive chemical detector in some instances that the optic sensory organ. It occurs to me that a lot of what we do in chemistry is sensing something that is not visible to the naked eye. Chemists use an array of chemical analysis methods to separate (chromatography) and detect (spectroscopy) individual chemical compounds. Interestingly, for natural product extracts, it seems like the more sensitive the detection method – the more compounds are detected. This brings up the philosophical question: “With and infinitely sensitive detection method with we observe and infinite number of compounds?” Even in this age of metabolomics research, the number of compounds contained, or potentially contained, in a living organism is difficult to determine. Hundreds of compounds can be detected with GC with a very low level of separation. At the end of more separation steps will there be thousands? My graduate advisor, the late Edward Leete, once said, “every plant contains every compound.” It is just a matter of improving the separation and detection to prove his statement right or wrong. I would also extend this concept to chemical reactions. If we were to look as closely at reaction mixtures as we do natural extracts we would find a myriad of “side products” present in every reaction mixture.

February 17

Week 5: This week we took a break from our Peer Developed Peer Lab experiment project in order for the students to firm up the final copies of their experiment handouts and webpages. We did the “Steam Distillation of Essential Oils” experiment this week. It may be better described a “hydrodistillation” rather than steam distillation since we simply put the ground up spices in water and, boil the concoction, and collect the condense steam. The classic version of this experiment used cloves. Cloves smell nice and give a fair amount of essential oil. From cloves, I have expanded to anise, caraway, cumin and cinnamon. I like the steam distillation lab because of its application to natural products chemistry, my specialty. This year we have the benefit of analyzing the samples by GC-FID. Other years we have done the analysis with UV, IR, and, or course, TLC. These methods do not show the blend of compounds that typically constitute essential oils. It seems like most steam distilled essential oils are made up a one or two major compounds with several minor components that would be detectable only with a technique like GC. This year we were able to detect both the “trees” and the “grass.” Using several spices instead of one, allows students to contrast and compare their results with others. I put up representative GC chromatograms for each spice on the internet as well as a few standard compounds. Please see our steam distillation page for an expanded discussion of this experiment.

February 9

Why do we repeat experiments? Don’t Repeat Yourself, “DRY” may be central tenet of computer programming doctrine, but is it not part of the chemist’s credo. Scientists spend a significant amount of time repeating procedures and even experiments in the quest to push back the frontiers of human knowledge. If we want to create and discover new knowledge, why do we spend so much time repeating what has been done before? There are several good reasons why experiments need to be repeated:

1) The first reason to repeat experiments is simply to verify results. Different science disciplines have different criteria for determining what good results are. Biological assays, for example must be done in at least triplicate to generate acceptable data. Science is built on the assumption that published experimental protocols are repeatable.

2) The next reason to repeat experiments is to develop skills necessary to extend established methods and develop new experiments. “Practice make perfect” is true for the concert hall and the chemical laboratory.

3) Refining experimental observations is another reason to repeat. Maybe you did not follow the progress of the reaction like you should have.

4) Another reason to repeat experiments is to study and/or improve them in way. In the synthetic chemistry laboratory, for example, there is always a desire to improve the yield of a synthetic step. Will certain changes in the experimental conditions lead to a better yield? The only way to find out is to try it! The scientific method informs us that it is best to only make one change at a time.

5) The final reason to repeat an extraction, chromatographic or synthetic protocol is to produce more of your target substance. This is sometimes referred to scale-up.

February 9

Week 4. This week, most of the seven groups repeated their experiment. For a couple, this week was the first time their experiment yielded acceptable results. For others, they had a chance to fine-tune already acceptable experimental results from Week 3. Several groups adjusted the scale of their experiment. We are working with “macroscale” glassware. Working with too small amounts it is rather easy to “lose” the product and end the experiment with disappointment. On the other hand, working with too large amounts is wasteful in time, money, and materials. Another issue, beside scale, that comes up often in synthetic experiments is, “How long should we run the reaction?” In my experience, an hour reflux is about the maximum that is reasonable for a Sophomore Organic Chemistry Laboratory experiment. Even an hour seems excessive at times. I assume that often we are working with “the law of diminishing returns.” The law of diminishing returns, in this case, informs us that most of the action is taking place at the beginning of the process. For example, a reaction may be %50 complete in 15 minutes, %90 complete in 30 minutes and %100 complete at the end of one hour. Is the extra half-hour worth the %10? Of course, the only way to really know what is going on in that reaction mixture is to monitor the progress of the reaction by TLC or some other means.

February 3:

Why do we do Sophomore Organic Chemistry Labs? Traditionally course laboratories are designed to reinforce and complement classroom instruction at the same time that students acquire laboratory skills commensurate with their level. In Sophomore Organic Chemistry (SOC) concepts taught in the lecture sections usually have to do with reaction chemistry and spectroscopic techniques such as ultraviolet-visible (UV-vis), Infrared (IR), and Nuclear Magnetic Resonance (NMR). Laboratory skills introduced and practices in SOC laboratory sections are chromatography techniques, suction filtrations, recrystallization, reflux, distillation, melting point, refractive index, and liquid-liquid separation. Safe practices for handling dangerous and unstable compounds are also practiced as well as more advanced instrumental techniques in chromatography (GC-FID, GC-MS, HPLC, etc…) and spectroscopy (UV-vis, IR, NMR, etc…) as they are available. What else is there? Laboratory sections provide a unique opportunity for kinetic learning. Some students enjoy laboratory work simply because they like working with their hands. Laboratory sections also lend themselves to various forms of group work. Developing skills in observation and notebook taking are also key proficiencies developing in SOC laboratory sections, though these are hardly unique to Organic Chemistry. Learning and practicing the “scientific method” may be another outcome, though this is usually not as intentional as it could be. Hopefully, working in the lab arouses and encourages a student’s natural curiosity to know more about the physical universe as well as giving them skills with which to discover it.

February 1:

We did some real chemistry this week. Almost too real, if you know what I mean. If you don’t know what I mean, read on. Students did the published experimental procedures that they found and selected the first two weeks of lab period. Students soon discovered that 1) significant modifications are sometimes needed to adapt the experiment to the equipment available in our particular laboratory, 2) sometimes the published directions are unclear or incomplete and certain informed guesses need to be made to complete the procedure, and 3) sometimes things don’t work out as indicated. Then, of course, there is the excitement (and sometimes disbelief) when the experiment does yield interesting and useful results. I think that the students discovered that it’s a little different performing an experiment in order to develop it into a classroom experiment as opposed to simply “getting it done” in a one-shot deal. They also realized that there are a lot of mechanical things like measuring procedures and handling techniques that need to be thought through. Further improvisation: the ice machine was broken on Wednesday. The students had to go outside and collect snow for their ice baths! The fun part for me is that I am not “the expert” here. I am discovering these experiments along with my students. Some groups need to go “back to the drawing board” and trouble-shoot their procedure, other groups have a successful experimental procedure in their hands. Real chemistry gets a little messy in more ways than one.

January 27:

Experimentation is a Scientist's Highest Calling: I consider myself an education innovator. From the very beginning, I have eschewed the use of textbook experiments in my labs. Instead, I write a handout for each lab that adapted a published procedure to the specifications that I felt best suited our facilities and our students. That way, each year I write suggestions in the margins of the lab handout that I will incorporate into next year’s handout. My intention is that the experiment evolves each year, to a more concise student-friendly venture. Let’s face it, I’m a scientist and happen to employ the scientific method in my pedagogical efforts. I like to try things to “see what happens” both while working on the lab bench and while teaching a course. I can always adjust my hypothesis if things don’t work out as planned. Fortunately, education is a game of second chances for both students and professors. If we don’t get it right the first time around, we can always come back at it from another angle with the benefit of experience. Not every line of work is so generous to give you second (and multiple) chances to learn from your mistakes. That doesn’t mean that instructors should be deliberately sloppy, it just means that we have some freedom to explore and experiment with our pedagogical approach. Science instructors should take the adage "Live and Learn" very seriously.

Week 2: The winners please! My comments in red.

1) “Oxidation of Cinnamyl Alcohol using Pyridinium Chlorochromate” Experiment #14 in Mohrig, J. R. “Modern projects and experiments in organic chemistry: Miniscale and standard taper microscale.” (2003) New York; Basingstoke: W.H. Freeman; Palgrave Macmillan. Looks good! Has a column chromatography step. Why cinnamyl alcohol? Does it matter?

2) “Vanillin Synthesis from 4-Hydroxybenzaldehyde.” Douglass F. Taber, Shweta Patel, Travis M. Hambleton, and Emma E. Winkel, J. Chem. Educ. 2007, 84, 1158.

Two-step synthesis experiment. Uses bromine and sodium ethoxide – potentially nasty stuff. Has a column chromatography step

3) “Preparation of Banana Oil (Isoamyl Acetate)” (any number of lab manuals and websites) A Classic! I did this one as an undergrad. We were excited to find a microwave version of the experiment. However, we were quickly disappointed to find it needed rather specialized equipment.

4) “Identification of a Conjugated Diene from Eucalyptus Oil” Lehman, J. W., Lehman, J. W., Operational organic chemistry, & 3rd. (2004). Microscale operational organic chemistry : A problem-solving approach to the laboratory course. Upper Saddle River, N.J: Pearson Prentice Hall. The Diels-Alder Reaction of a Conjugated Diene in Eucalyptus Oil. Very intriguing – the text does not even give away which will be the major diene in eucalyptus oil.

5) “Synthesis and Recrystallization of Adipic Acid” Experiment 5, Doxsee, K. M., & Hutchison, J. E. (2004). Green organic chemistry : Strategies, tools, and laboratory experiments Southbank, Vic., Australia ; United States: Thomson-Brooks/Cole. I like the Doxsee & Hutchuson Green Chemistry book. They have a nice companion website that gives advice and discusses each experiment. http://greenchem.uoregon.edu/gems.html

6)“Using a Premade Grignard Reagent to Synthesize Tertiary Alcohols in a Convenient Investigative Organic Laboratory Experiment,” Michael A. G. Berg and Roy D. Pointer. J. Chem. Educ. 2007, 84, 483. My first Grignard in long time. Wish us luck!

7)“Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students,” Duarte, Robert; Nielsen, Janne T.; Dragojlovic, Veljko. J. Chem. Educ. 2004, 81, 1010. I’ve had this one in my “idea” file for awhile. A challenging experiment. Hopefully we can sort this out. Potentially expensive. I ordered a dozen new chemicals for this one.

Week 1: There are 26 students in my class. We divided into 7 groups. Five groups meet Monday afternoon, two groups meet on Wednesday afternoon. Each group received one second-semester organic chemistry topic: 1) Alcohols, 2) Diels-Alder, 3) Aldehydes/Ketones, 4) Esters, and 5) Carboxylic Acids. That’s the order of appearance of these topics in the semester. The students dove right in a started finding experiment candidates in my collection of lab manuals, online, and on the Journal of Chemical Education search. I realize that it was a stretch for students to be looking at experiments that covered topics that they have not “covered” yet in OChem. They did well, navigating the maze of chemical equations, unfamiliar names, and experimental protocols. I liked the “anything goes” attitude they had about picking experiments that seems interesting. I am already too prejudice when I look through experiments, “We can’t do that one because…” It will definitely be interesting. I was surprised that there were a lot of experiments available on the internet. If you take an experiment title out of a lab manual and Google it, you are likely to get several hits from instructors who have posted their experiments online.

January 21, 2008

More with Less: Current pedagogical research also tells us that often “less is more” when it comes to content and learning: less content can engender more learning. A good discussion of this may be found in “What to do When you Stop Lecturing” by Kersey Black JCE 1993 70(2) 140-144. It is tough for a classically trained professor to let go of even the slightest bit of content. This is especially true for standard courses like Sophomore Organic Chemistry that are taught in every college and university in the world. How embarrassing for me if an alumni from Cal. Tech. asks one of my former students if they studied the Bayer-Villager reaction and my former student answers, “I never even heard of that one!” On the other hand, I realize that I expend a lot of effort driving my students to “learn” an ever-increasing flood of content that they could not possibly understand at more than a superficial level – if at all. The same goes for lab, a full-scale organic chemistry lab complete with prelab preparation and laboratory report every week is a very intense task and does not promote much real interaction with and understanding of what they are actually doing at the lab bench. This last semester (Fall 2007) I had my student extend the traditional “Isolation of Caffeine from Tea” experiment an extra week by bringing in their own caffeine source and extracting the caffeine. Several students really seemed to get buzzed about this little gesture to engage them. This Peer-Developed Peer-Led approach seems like an opportunity for students to get excited about at least one lab in the semester.

January 19, 2008

Week One: There are 24 students in my class. We divided into 7 groups. Five groups meet Monday afternoon, two groups meet on Wednesday afternoon. Each group received one second-semester organic chemistry topic: 1) Alcohols, 2) Diels-Alder, 3) Aldehydes/Ketones, 4) Esters, and 5) Carboxylic Acids. That’s the order of appearance of these topics in the semester. The students dove right in and started finding experiment candidates in my collection of lab manuals, online, and on the Journal of Chemical Education search. I realize that it was a stretch for students to be looking at experiments that addressed topics that they have not “covered” yet in OChem. They did well, navigating the maze of chemical equations, unfamiliar names, and experimental protocols. I liked the “anything goes” attitude they had about picking experiments that seemed interesting. I am already too prejudice when I look through experiments, “We can’t do that one because…” It will definitely be interesting. I was surprised that there were a lot of experiments available on the internet. If you take an experiment title out of a lab manual and Google it, you are likely to get several hits from instructors who have posted their experiments online. Also, microwave-assisted experiments seem to be very fashionable.

January 15, 2008

My Inspiration: This semester the organic chemistry class is dividing into groups of four students or less and planning a lab. They will have 4 weeks to find an appropirate experiment, order chemicals, try it out, and write up a lab handout for the experiment. Then the class will perform each other’s experiments.The inspiration for this endeavor is a recent article in the Journal of Chemical Education, by Lorena Tribe & Kim Kostka. The article is entitled, “Peer-Developed and Peer-Led Labs in General Chemistry” 2007, 84(6), 1031-1034. The basic premise is that students were asked to divide into groups to research, develop, and prepare general chemistry experiments that would be performed by their peers. The first phase took 5 weeks to do. The result was that students took ownership of the laboratory process and they thought through the scientific method in a much deeper way that they would have if they would have shown up each week to follow the directions. It pushed a lot of buttons for me. “The students were present, more actively engaged, more enthusiastic, and very cooperative.” I had always envied my colleagues who do an individual synthesis project as a second semester organic chemistry laboratory project. I saw this article as describing a similar engagement of students’ creativity and originality that didn’t involve running 27 simultaneous experiments. This approach seems manageable with a great potential for satisfaction.

January 9, 2008

Why? What if Sophomore Organic Chemistry Lab was the best three hours of the week?! That is my quest. I would like to make the three hours of contact time with my students in the lab and make it the best learning experience possible for them. I want them to be enthusiastic, engaged, inquisitive, and (who knows) even happy. I know that I am the envy of my Liberal Arts colleagues. What humanities professor would not jump at the chance to challenge and engage their students an extra three hours a week? Not only is there the attraction of spending more quality time with the students, there is also the kinetic learning aspect of labs. Not everyone learns well by sitting in a lecture taking notes. (In fact, current pedagogical research suggests that no one learns well that way.) I am a chemist primarily because I like my hands and my intellect to work together. I feel more affinity for an art teacher than I do a history teacher in that regard. If I didn’t have an opportunity to get my hands dirty in the lab, it would be similar to being slowly roasted over hot coals, i.e. becoming an administrator! Not wanting my students to grow up to become administrators, I want to share my passion for chemical experimentation with them.