Laboratory Techniques in Organic Chemistry

Laboratory Techniques in Organic Chemistry are some methods used to execute an experiment in lab. In organic chemistry lab various reactions or functional group transformations are performed by using numerous chemicals and instruments. 

Hi Friends, in this article we will see some important lab techniques and protocols while performing the experiment in organic laboratory.

Key words: Laboratory experiments, Practical techniques, Lab report, Small scale laboratory experiments.

The experiment in organic lab meaning that there is certain reaction is performed for the purpose of chemical transformation. There are some important aspects we need to consider before and after the completion of reaction, they are listed below;

Planning

Every experiment in the lab requires proper plan. This reduces the time and efforts while performing the experiment. Hence plan the experiment a day before or at least few hours. Confirm whether the required chemicals, apparatus and instruments are in good condition or not. If not then don’t use it.  Set up the experiment at least 1 hr before leaving the lab so that any changes or leakage in the reaction flask can be noted,

Safety

Safety is the most important aspect we need to keep in mind while performing the experiment. For every chemical compound there is a manual available called as Material Safety Data Sheet (MSDS). It is easily available on internet. The safety data sheet includes properties, storage and safe handling protocols. Read the above document carefully and use the chemicals accordingly.

Set up

Every experiment requires specific set up. The reaction must be carried out in three neck flask. The flask should be tightly fixed to a stand. A nitrogen balloon is fixed at one end by using vacuum adapter whereas other two ends are used for reagent addition. The reactions which are carried out at room temperature should be performed in secondary container. The reaction mixture is stirred by magnetic stirrer.

Figure 1: A set up for room temperature reaction

There are some reactions which require heating condition it is done by using paraffin oil bath. Required temperature is achieved by heating regulator. Internal and external temperature is monitored by two thermometers. A condenser is fixed at one end of the flask to condense the vapours.

Figure 2: A set up for reaction under heating condition

The reactions under cooling conditions are done in ice bath. There are some reaction which are carried out below 0 °C temperature, they are done is special chillers.

Figure 3: A set up for reaction under cooling condition

Observations

While performing the experiment we must record all the changes that occurred during the course of reaction. There may be change in colour or temperature of the reaction. Sometimes appearance of the reaction mixture changes from clear solution to precipitate. All the changes must be observed carefully and write in the record book.

Monitoring the reaction

Usually progress of the reaction is checked by thin layer chromatography (TLC). It is the cheapest and easy method to confirm progress of the reaction. In the method a small aluminium plate with coating of silica is taken. Then at the base of place three points are marked as starting material, co spot and reaction mixture. Then on the respective points, solution of above material is deposited by using capillary. After that in a glass chamber solvent mixture is added. This mixture is made from polar and non-polar solvent. Then the TLC is dipped in to the solvent and solvent allowed to rise up to the top of TLC. Then the TLC removed from chamber and observed under UV light. The TLC also dipped in various stains and charred to visualize various spots. This gives idea about whether the stating material is consuming or not also any new spot formation in the reaction mixture.

Quenching

After confirmation of completion of reaction it needs to be stopped. This process is called as quenching the reaction. In this method reactive species are neutralized by adding aqueous acidic or basic solution. The reactions which are performed in acidic medium, they are quenched be adding aqueous sodium bicarbonate solution. And the basic medium reactions are quenched by addition of aqueous HCl solution. Sometimes basic medium reactions are quenched by addition of aqueous NH₄Cl (ammonium chloride) solution, it produces mild acidic solution. As a result of quenching there is formation of biphasic solution; that is organic and aqueous phase.

Work up / Extraction

Work up or extraction is the process by which organic compound from the biphasic mixture that is formed after quenching the reaction. In this process the biphasic mixture is transferred to separating funnel. Usually the organic compounds are extracted by using solvents such as ethyl acetate, dichloromethane or ether.  So the solvent is then added to the separating funnel and shacked carefully to form two layers. The organic layer is collected and above process is repeated twice or thrice.

Figure 4: Extraction of organic compound

Then all the organic fractions are collected and some amount of sodium sulphate (Na₂SO₄) is added to remove traces of water. Finally the solvent is filtered and concentrated to get crude compound.

Purification

The crude compounds consist of impurities of side products and un-reacted reagents. Hence it needs to be purified for the purpose of analysis and for the use in next step of synthesis. There are various methods are preferred for the isolation or purification. Most frequently used method is column chromatography. We have discussed available methods of purification in previous article.

Yield of Reaction

After getting pure compound from crude compound, yield of the reaction is calculated. Yield of the reaction is expressed in percentage. We have discussed about calculation of yield of reaction in previous article.

Analysis

The pure compound is analyzed on the basis of appearance, melting / boiling point, NMR spectroscopy, IR spectroscopy and Mass spectrometry. These four methods confirm the structure of given compound. In general to record NMR spectrum 10-15 mg of compound is required. The NMR method is non-destructive that means the compound can be recovered after experiment. The given compound is dissolved in deuterated solvents such as chloroform-d, DMSO-d6 to record NMR spectrum. To record IR spectrum 2-5 mg compound is required and this can not be recovered. To record Mass spectrum 1-3 mg compound is used and it can not be recovered. The chiral compounds as needs to be confirm by specific optical rotation value.  Structure of the crystalline compound is studied by crystal structure of compound.

Lab Report

The lab report is generally written in lab note book. It is the final document which includes date of experiment, reaction structure, reaction condition, procedure, isolation methods and analysis of the compound. All the observations and safety measures are written in the lab report, so that any unknown person can perform the given experiment with minimum difficulties. The lab report must consist of final conclusion whether the experiment is successful or not. It is also written that if any changes are required in the procedure or isolation method.

To summarize this article, proper planning is required to perform the experiment safely in lab. After performing the experiment, pure compound is isolated and analysed by various methods. Finally all the observations and findings are documented in lab note book.

That's all for this topic. If you have any questions please feel free to ask me in the comment box. Thank you..!