Introduction to Organic Laboratory

The laboratory course in organic chemistry provides a “hands on” environment that is crucial for developing your understanding of theoretical concepts and reactions. Much of the experience obtained in a lab course is nearly impossible to communicate within a lecture format. For example, it is one thing to learn about the polarity of different molecules based on their structural formulas sketched on the blackboard but quite another to actually observe the separation of a mixture of polar compounds during a chromatography experiment. Furthermore, the chromatography technique learned in the lab is a useful one that then becomes part of an organic chemist’s repertoire.

The other important realm of a laboratory course is to expose the student to the safe handling of many different types of chemicals as well as to the myriad of apparatus and equipment used in the lab. The laboratory experience also helps the student to understand and interpret experimental procedures.

Laboratory Experiments

The laboratory experiment is usually not a true scientific experiment in the sense that a hypothesis is formulated, experiments are planned to test the hypothesis, data is collected and analyzed and ultimately a conclusion is reached which supports or contradicts the hypothesis. In other words, all of the tenets of the scientific method are not addressed routinely in a laboratory experiment. What a chemist means by the word “experiment” can often be regarded as one of two major types, investigative experiments and preparative experiments. An investigative experiment is one in which the student learns how to perform a particular technique such as how to correctly obtain a melting point for a solid or how to set up equipment for a distillation and then actually do a distillation. A “prep” experiment involves the conversion of one substance into another, in other words, an actual chemical reaction is performed, the product is isolated and purified and a percent yield is calculated. Bear in mind that the procedures required for a prep experiment are carried out by using the techniques and operations learned from investigative experiments.

It stands to reason that the student must master some common laboratory techniques prior to carrying out even a simple prep experiment. For this reason, the first semester of organic lab introduces several different types of investigative experiments. These experiments are designed to teach the three basic operations required to perform most organic reactions in the lab: isolation, purification and identification of various substances. These are the operations that are done after the chemical reaction is complete. In other words, “doing the reaction” is often only half the job; what the chemist does to the reaction mixture after the reaction is complete constitutes a major part of any experiment involving a chemical transformation.

Think about actually performing a preparative experiment; the process is generalized in the next few paragraphs and diagrammed in a flowchart.

Flowchart for a Hypothetical Organic Reaction

Running a reaction is often the easiest part of an experiment.

First, the reagents are mixed together in an organic solvent according to the stoichiometry of the reaction and the reaction is stirred (perhaps heated or cooled as stated in the procedure) for the allotted time period or until the reaction is deemed finished.

Many reactions require a work up to isolate the product.

Next, the product must be isolated from the reaction mixture. However, the organic reaction product at this point may not exist in molecular form. For example, in the synthesis of an alcohol, the product may be in the form of the corresponding alkoxide. Therefore, a “work up” is needed to convert the alkoxide into the desired product alcohol. Typically the work up involves adding an aqueous phase which may be acidic or basic depending upon the requirements of the species involved For example, in this case, an acidic aqueous phase would protonate the alkoxide to give the alcohol.

Consider intermolecular forces for a moment and recall the adage “likes dissolve likes”. The addition of an aqueous phase is necessary for the work up but also serves to solubilize the inorganic by-products and any salts formed in the reaction. Since water and organic solvents are generally not miscible, two layers form and the desired organic product remains in the organic phase. A separatory funnel can be used to separate the organic phase from the aqueous phase. The result is that the product has been separated from most of the other components in the reaction mixture and the organic solvent can be removed by evaporation or some form of distillation to provide the crude (unpurified) product. Hence, isolation is achieved.

The “art” of organic chemistry often lies in the ability to purify the product.

Purification is the next step. Solids can sometimes be purified by recrystallization, liquids (or oils) may be purified by distillation. Chromatography is often used to purify both solids and liquids if other techniques are not successful. Gas chromatography would be a logical choice for purification of gases, although few of your products are gases.

You may recall from general chemistry another purification technique, selective effusion, which was used to purify the isotopic mixture of uranium hexafluorides, 235UF6 and 238UF6. These are just a few of the choices chemists have in their arsenal for purification challenges.

Instrumentation has become an integral part of modern chemistry.

The last step in a prep experiment is to identify the reaction product. Many traditional, classical methods are still used. A melting point may serve to identify a solid, a boiling point could be used to identify a liquid and a density measurement could be used for a gas. Also, there exists several qualitative tests that can be used to identify certain functional groups in a molecule. By far the most useful modern techniques used for identification purposes include NMR, IR and mass spectrometry. Used in conjunction with classical approaches, these methods can unambiguously determine the entire molecular structure of your reaction product.

Performing organic reactions in the lab enables one to study the chemical properties of various substances. However, the student should also begin thinking about the notion that it is the physical properties of a compound which are exploited in order to isolate, purify and identify that substance. Several different techniques will be introduced in this course including a description of each operation and the physical basis for each.

Miniscale versus Microscale

A laboratory course in organic chemistry conjures up stereotypical images for many students: fragile glassware and complicated equipment, goofy eyewear, unpleasant odors, even the occasional fire, to name a few. While some of these impressions may be difficult to eliminate, the organic lab experience has changed considerably within the last few decades. In particular the nature of doing experiments has changed from the classical approach involving several grams of starting material to a scaled-down operation that can be performed successfully using much smaller quantities of material.

Historically, the classical organic experiment was done on a fairly large scale using ten to twenty grams of starting material or even larger amounts. The reaction vessels utilized for these experiments included round bottom flasks with capacities ranging from 100-mL up to 1-L. Liquid reagents were often measured using 100-mL graduated cylinders or beakers, and masses were measured using a standard triple-beam balance. Big capacity Erlenmeyer flasks and filter flasks were required for working up the reaction and large columns and condensers were needed for operations that involved reflux or distillation. This is the type of equipment often shown when a chemist or “mad scientist” is portrayed in film and television.

Semimicro is between mini and microscale. The distinction is not always clear from one scale to the next. It is important for the student to learn which type of glassware is appropriate for a particular experiment.

Miniscale is the term used for reactions that are done using smaller amounts of material, typically one or two grams. The glassware used for miniscale is very much the same as those used for larger scale except the size of the “pots and pans” is a bit smaller. For example, a reaction that uses, say 15 grams of starting material, may require a 500-mL round bottom flask and several large Erlenmeyer flasks for work up. The same reaction done on miniscale (1 gram) may be carried out in a 25 or 50-mL round bottom flask.

Microscale is the term used for reactions that use very small amounts of material, perhaps 10 to 200 milligrams. Microscale glassware is different from the conventional glassware used for miniscale and larger. Conical shaped vials are used in place of round-bottom flasks. The surface area is minimized in a conical vial which alleviates the problem of compounds adhering to the glass. Imagine mixing 100 milligrams of solid in one or two milliliters of solvent in a 25-mL round bottom flask. When the mixture is stirred, much of the solid will work its way up the side of the reaction vessel away from the reaction medium. Using a conical vial is simply more efficient. Microscale glassware in general is designed to minimize surface area and eliminate the transfer of tiny amounts of substances from one container to another.

The drive towards small scale experiments has several benefits such as reduced cost of materials, less environmental waste and shorter reaction times. The safety issues are often attenuated due to the smaller amounts of material used. One drawback of small-scale reactions is that students often cannot observe what a tiny sample looks like; the quantities can be so small that it is difficult to make visual observations about the physical nature of compounds. Unfortunately, this adds a mysterious aspect to organic chemistry. Thus, there is a need to balance small scale operations against the classical approaches that have been used for decades to introduce laboratory techniques.