Chemistry

Organic chemistry is an art-form and a craft. In research, we often talk about candidates that “have it”, the “magic touch” to get a compound analytically pure, or solve a very difficult synthetic challenge. In this chapter we will go through some common techniques that you will encounter in the organic chemistry labs. The aim of this chapter is not to give you a comprehensive introduction in the theory behind these techniques, but to highlight technical aspects to make sure you also develop this “magic touch.” We will discuss recrystallization, distillation, liquid-liquid extraction, TLC, chromatography and lastly sublimation.

At PSU, it is required to use and keep a notebook. This notebook will be used both in the preparation of the experiment, and during the experiment itself. We will focus on how to use the notebook in the prepara- tion phase of an experiment. In chapter 4.4 we will discuss the use of the notebook during the experiment.

When stepping into the lab, your notebook should contain the following:

1. A title and a balanced reaction scheme, if a synthesis is planned. If not, the relevant chemical structures of the compounds of interest should be shown.
2. A flow-diagram that outlines the experiment, where you have included the most relevant information.
3. A table or overview that shows all chemicals handled, and their risk and hazard statements.
4. A synthesis table that shows the quantities of the reagents/reactants that you plan to use, with room to fill in the quantities you actually used.
5. A table that shows the properties of the reagents/reactants and reaction solvents used in the procedure.

Table 2. Example of a synthesis table for reagent(s), reactant(s) and product(s)

* The values for benzyl alcohol is based on the procedure, that states that a yield of 65.6% is expected.

The table for physical properties is used not only for the reagent(s), reactant(s) and product(s), but also reaction solvent, work-up chemicals and others. This table is very handy in the lab, as the physical properties of the chemicals play a large part in the work-up of any reaction.

Table 3. Example of a table for physical data

Laboratory courses can be magical. They can be enlightening experiences that open your eye to a big picture. A laboratory experience should work in tandem with a lecture course, and fully realize concepts, techniques and reactions that you have heard of. Unfortunately, they can also be discouraging experiences. One of the key factors that dictates which experience you will have, is preparation.

A rewarding aspect of a well-prepared experiment is that it can firmly cement the information that you have obtained through studying in a way that is far superior to simply reading about it. Your knowledge evolves beyond routine memorizing to real understanding, because you have seen the reaction and principles with your own eyes. The synergy between a lecture course and a lab component should not be underestimated.

In this chapter I outline a systematic way of preparing for any organic chemistry experiment to ensure that you succeed in the laboratory and that you leave with an optimal experience. Seeing, after all, is believing. I discuss how to make and use the flow diagrams, how to obtain relevant safety information about the chemicals you are handling, and how to use your note-book to prepare efficiently.

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