Posts in: CH250

Organic Chemistry is Alkynes of Fun

As week three comes to a close, the Orgo I students finished up their last experiments and checked out of lab. The foundations of organic structures and configurations have already been established in the first two weeks of class leading up to the final full week where concepts are expanded to reagents and mechanisms of reactions. Learning the multitude of reagents and understanding mechanisms is challenging and overwhelming at times, but allowing these two concepts to become a way of thinking instead of memorization is one of the keys to success in organic chemistry (along with hard work and plenty of chemistry jokes of course). With the introduction of mechanisms and reagents, students are now able to propose and conduct different synthesis routes to produce a desired final compound, which is exactly what occurred in lab. The lab this week was spread out over two days, with each day dedicated to one of the two steps of the synthesis of diphenylacetylene, a compound containing two phenyl groups attached by an alkyne or carbon-carbon triple bond.

The first day, students performed an addition reaction to add two bromine atoms to a carbon-carbon double bond. To determine if the bromines were added syn (on the same side) or anti (on opposite sides), a melting point of the product stilbene dibromide was taken. The high melting point of the product indicated that the anti addition occurred to form a meso compound incapable of rotating plane polarized light. In addition to melting point, students worked through the mechanism of this reaction to provide an explanation for why the anti addition occurred.

A new theme in all organic chemistry classes at Colorado College is the use of green or environmentally benign reagents as alternatives to typical procedures requiring the use of extremely toxic or hazardous chemicals. To eliminate the use of corrosive liquid bromine as a reagent to brominate the starting material trans-stilbene, bromine was produced in situ (in the reaction mixture) by the use of pyridinium tribromide, which exists in equilibrium with pyridinium bromide and elemental bromine (Br2). As the elemental bromine is used up in the reaction, the equilibrium is pushed further to the right as explained by Le Châtelier’s principle to replace the reacted bromine, therefore providing a continuous “slow release” of bromine. Thus the reaction is able to proceed to produce the desired product and avoid the use of hazardous liquid bromine. Although it’s sometimes exciting to add a bit of danger to one’s life, this is definitely a case where the use of an alternative, safer procedure is greatly appreciated by both students and professors.

Safety first! Students make sure to use hot hands when working with heated reactions.

Safety first! Students make sure to use hot hands when working with heated reactions.

After students isolated stilbene dibromide using vacuum filtration, the samples were analyzed using Nuclear Magnetic Resonance (NMR). The NMR instrument, by far my favorite form of analysis in organic chemistry, detects signals of different atom isotopes depending on the specifications of the study being run. This time, everyone ran a proton NMR, which detects the spin signals (up or down) given off by neighboring protons. Where the signal for a proton appears on the spectrum depends on the electronegativity of the surrounding atoms.

The more electronegative or de-shielded the environment of a proton, the more downfield or to the left the signal will appear. In contrast, the more shielded a proton is, the more upfield or to the right of the spectrum a signal will appear. Analysis of a spectrum can provide a chemist with information regarding connectivity, structure, and composition of a particular compound. Pretty amazing if you ask me! Although the students seemed a bit more impressed with the pressurized sample loading system than the actual mode of action of the instrument, NMR data collecting went smoothly and it was onto the final step of the synthesis.

Students get psyched to do the last step of the synthesis.

Students get psyched to do the last step of the synthesis.

On day two of the synthesis, students worked on a double dehydrohalogenation of stilbene dribomide, or the formation of a carbon-carbon triple bond to produce the desired product diphenylacetylene. To isolate and purify the final product, students practiced a new technique: recrystallization. This technique is based on the principle of solubility, specifically that solubility increases with temperature. Using the minimal amount of a hot solvent to dissolve the crude product caused the impure crystals to deform and allow new, pure crystals to form as the solution cooled down and solid begun to crash out of solution. These pure crystals were separated from the liquid containing impurities by vacuum filtration and then analyzed by Infrared Spectroscopy (IR) and NMR.

Dissolving the crude product with a minimal amount of solvent to produce pure crystals-- perhaps the most intense part of lab.

Dissolving the crude product with a minimal amount of solvent to produce pure crystals– perhaps the most intense part of lab.

So excited to recrystallize their product!

So excited to recrystallize their product!

Although this blog was filled with quite a bit of organic chemistry jargon, I hope I made it accessible to everyone, even those students who took chemistry in high school and decided it was not their cup of tea. Hopefully the joy of accomplishing a synthesis or understanding a new concept was expressed through the pictures and my rambling about the procedure. If you can’t tell, I find the whole synthesis process quite fascinating. Stay tuned for Organic Chemistry jeopardy (yes it exists and is the only kind of jeopardy where I can actually answer any of the questions) and a wrap up of the final three days of class!

Lab is alkynes of fun!

Lab is alkynes of fun!

Adventures of Organic Chemistry I

The organic chemistry I students have been hard at work this block learning the foundations of organic structures and reactions. With lecture in the morning and lab most afternoons, the class keeps up an intimidating reputation. This blog, however, will hopefully illustrate that organic chemistry can also be an enjoyable and rewarding experience. I may be a bit biased as organic chemistry is my favorite subject, but it’s hard to argue with some of the pictures I was able to snap of the students this week completing a substitution versus elimination lab and the famous food pairing activity.

The first lab this week was focused on determining which type of reaction was occurring: substitution or elimination. The students worked with condensers for the first time, heating the solvent to its boiling point and then cooling it back down with a water-cooling system to ensure no product was lost by evaporation. To conclude which type of reaction occurred, gas chromatography mass spectroscopy was used to identify the product. A product with a carbon-carbon double bond would indicate an elimination reaction had taken place, while a product with the loss of a leaving group and replacement of that group with a new moiety would indicate substitution. Once all the reactants and solvents were added to a round bottom flask, students heated their mixtures to reflux (boiling) temperature and prepared to time the reaction for exactly 25 minutes.

Students time reaction for 25 minutes.

Students time the reaction for 25 minutes.

Perfecting the reflux set-up under the hood.

Perfecting the reflux set-up under the hood.

Posing with the product mixture. The reaction was a success!

Posing with the product mixture. The reaction was a success!

The next lab involved pairing different foods based on the structure of predominate flavor molecules. After studying the structures of the flavor molecules of selected products and identifying key functional groups, students filled out a food-pairing sheet and began to try different combinations. Many were happily surprised when they found foods with structurally similar flavor molecules paired well together. Some of the students’ favorite unusual combinations were thyme and strawberry, cilantro and clementine, and chili and chocolate.

Preparing to pair flavors.

Preparing to pair flavors.

Thyme and strawberry tastes great!

Thyme and strawberry tastes great!

Unusual combinations don't always work out...

Unusual combinations don’t always work out…

After selectively pairing foods, students were offered the option of trying a miracle berry. These natural products suppress the proton detectors on taste buds, inhibiting one’s ability to taste sour foods, which are acidic (have high proton concentration), and instead replace the sour taste with sweet.

Once the miracle berries had dissolved, students set out trying different sour foods including lemon, clementine, and even vinegar! Although the vinegar tasted strangely sweet, it was still vinegar and didn’t become a class favorite. Lemon, however, was found to taste like delicious lemonade and a whole bag of lemons, previously untouched during the food pairing, quickly disappeared. In all, this week has been great fun and I hope it will continue into third and fourth week! Stay tuned and be prepared for more pictures and perhaps even a video or two of the exciting activities the Orgo I students will be up to this block!

Two brave students try the vinegar.

Two brave students try the vinegar.

It might be sweet, but it's still vinegar. Luckily lemon was provided help with the after taste.

It might be sweet, but it’s still vinegar. Luckily lemon was provided to help with the after taste.

CO2 Dance

In case you missed the CO2 dance last week, here it is!

Safety First!


All geared up for lab!

Chromatography and the NMR

Students started week two of organic chemistry with their first major test.  They didn’t get much rest time after though, as they jumped right back into lab the next day.  This week students will be leaning how to use NMR spectroscopy as another tool for identifying organic compounds.  NMR (nuclear magnetic resonance) treats the nucleus of different atoms as tiny magnets and subjects them to an oscillating external magnetic force. The nuclei will resonate differently depending on how the are bonded to their neighbors and what their neighbors are.  If you’ve ever had an MRI at the doctors, you’ve experienced a type of NMR.   Students will be given an unknown compound and asked to identify it using the NMR and IR.

Students will also learn about different types of chromatography this week. Chromatography is a general term referring to lab techniques that are used to separate compounds from one another. They first will use column chromatography to separate ferrocene and acetyl ferrocene.

ferrocene                                                ferricebe


Both molecules contain iron and two five member rings, but acetyl ferrocene also contains an additional functional group. This functional group will allow acetyl ferrocene to move through a silica gel column at a different speed than the ferrocene. The originally dark orange solution of a combination of the two compounds will come out in two bands, a yellow one and a light orange one.

Students will then use thin-layer chromatography (TLC) to compare the separation on their own compounds against pure standards.  With TLC, students dot small drops of their sample on silica coated plastic. The plastic is then placed in a small amount of liquid and the liquid will carry the dots up the plate at different rates depending on the structure of the compound.


On this sample TLC plate, the mixed sample is spotted in the the middle and a pure samples lay on either side.




Week One

Welcome to Chemistry 250: Structures of Organic Molecules!

We have hit the ground running full speed ahead in Orgo 1. Already students have dived into the first three (yes 3 !) chapters of their text books.  They are learning how to draw organic molecules and identify different functional groups. Functional groups are characteristic groups of bonded atoms that have predictable properties.  For example, alcohols are one type of functional group. They consist of an oxygen atom and a hydrogen atom bonded together at the end of a chain of carbons atoms.  Wood alcohol (methanol), alcohol for consumption (ethanol), rubbing alcohol (iso-propyl alcohol) and even cholesterol all have this C—O-H bond.


The students will begin their lab work tomorrow by extracting caffeine molecules from tea leaves. During this lab they will learn basic organic techniques such as separation, filtration, recrystallization and melting point determination. This week students will also be utilizing infrared spectroscopy. IR spectroscopy is a useful tool for identifying functional groups on organic molecules.  Molecules are subjected to wavelengths of infrared light and different types of bonds will absorb the light and be excited in different ways.

If you want to learn all of the ways bonds exhibit vibrational excitation come stop by the lab at 1 on Wednesday for our awesome IR dance!