Organic Chemistry Laboratory a Physical Approach Chapter 1 Introduction to Working in the Laboratory Very few introductory science courses

es are offered simply as a lecture series. In nearly all cases, an accompanying laboratory course is required. In the coming year, your lecture instructor will ask you take many of his or her statements for granted. Naturally, the statements made by your professor are grounded in two hundred years of organic chemistry research conducted by countless hard working individuals. Nonetheless, because the laws of chemistry are grounded in empirical observation it stands to reason that conducting such inquiries ones self should be an integral part of any organic chemistry course. Your laboratory course is a chance to test some of the rules set forth by your lecture professor. It is an opportunity to develop sound organizational skills, time management, diligent preparation habits and thoughtful critical analysis skills. In doing so, the students goal should be to better understand how the body of chemical knowledge is created, expanded and even corrected from time to time. If you are taking an organic chemistry laboratory course, chances are that you are no stranger to the teaching lab environment. What sets the organic chemistry laboratory apart from others is the level of risk associated with its contents. Flammable, toxic, carcinogenic and environmentally dangerous materials abound in the organic chemistry laboratory. When not respected, these materials can present a significant health, safety or environmental hazard. When treated properly, however, the lab can be a safe and fun place to learn and explore the practice of science. For this reason, the first step to becoming an effective lab chemist is to understand these risks and how to minimize them. Safety in the Laboratory Personal Protective Equipment Short of preventing accidents themselves, Personal Protective Equipment (also referred to as PPE) is one of the most effective safeguards available to protect those working in a laboratory. PPE is defined as any specialized equipment or garment designed to protect the wearer from health and safety hazard in the laboratory. Although PPE cannot prevent lab accidents, it can significantly reduce the consequences of one! Safety Glasses Eye protection in the form of safety glasses or chemical splash goggles should be worn by everyone in the laboratory whenever anyone in the laboratory is working with chemicals or evacuated/pressurized glassware. Remember that is does not have to be your accident to cost you your vision! The best protection is afforded by chemical splash goggles, which form a seal around the eyes and prevent any liquid or solid material from reaching the eyes. As an alternative, safety glasses are sometimes used provided that they meet three important criteria:

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1. They must be impact resistant so that a shard of glass doesnt become multiple shards of glass and plastic when it reaches your eyewear! 2. They must have an articulated brow to help prevent splashes from coming over the glasses. 3. They must have side splash guards to help prevent splashes from coming around the side of the glasses. Gloves The use of gloves in the organic chemistry laboratory at all times is highly recommended. They are essential when strong mineral acids, strong bases or organic solvents are being used. It should be noted that gloves are made of many different materials, the two most common being latex and nitrile. Each of these materials offer differing levels of protection from various types of solvents. Consult a glove compatibility chart if you are uncertain which gloves afford the best protection. Proper Attire The best way to protect your skin in the laboratory is simple. Cover it! Remember that the tops of your feet are the only horizontal part of your body below the benchtop. This means that when something spills or falls, it is most likely to end up on your feet! For this reason, shoes of a non-woven material which cover the feet should always be worn in the lab. Additionally, clothing which is excessively loose should not be worn.

Know the Location of Safety Equipment All modern laboratories are equipped with a number of items which, if properly used in an emergency, can significantly reduce the risk and/or impact of lab accidents. As a student, it is your responsibility to be familiar with the location and operation of this equipment. Safety showers are for use when a large amount of chemical or solvent has spilled on a worker in the lab, or when clothing is on fire. Pulling the handle releases a very large flow of water, so these devices should only be used when a large-scale accident has taken place. Eyewash stations are for use when a chemical or solvent has contacted the eye of a worker in the lab. Affected eyes should be rinsed with the eyewash for no less than 15 minutes. Fire extinguishers will always be nearby. In the case of very small fires (for example ether igniting in a beaker) it is best to simply cover the container and allow it to extinguish from lack of oxygen. Before 2 Dr. Ron Davis, Jr., Ph.D. - 2010

taking the responsibility of attempting to fight a large chemical fire with an extinguisher, one should be absolutely certain that the fire extinguisher used is designed for the type of fire being fought. As a student, if you are uncertain then it is best to leave the fire fighting to your instructor. Chemical fume hoods will be provided for work with volatile, flammable or particularly reactive materials. Most modern fume hoods are equipped with a movable sash. The sash may be raised to facilitate setting up a glassware apparatus, but must be lowered to the operating height when chemicals are present!

Disposing of Chemical Waste Chemical waste must always be segregated for several reasons. First, compatibility of all chemicals in a waste container must be assured for the safety of those in the lab and those responsible for removing the waste containers. Second, certain types of chemical waste are particularly harmful to the environment and are disposed of using a special (and expensive!) method. Naturally, segregating this type of waste can save a great deal of money in the waste removal budget for your lab. Wastes are generally sorted into several classifications. Your lab will have its own system for identifying and segregating chemical waste, so defer to your lab instructors policy when in doubt. The sink Only soap and water should ever be sent down the drains of the laboratory sink. Very weakly acidic or basic aqueous solutions (pH 6-8) are usually allowed, but nothing else may be disposed of in this way. The drains from most lab sinks lead to the common drain for the building, and water handling plants are not expecting to receive chemical waste for treatment! To best ensure that chemicals do not reach the sink drain, it is recommended that all glassware be triple-rinsed into an appropriate waste container before washing with soap and water in the sink. The Trash Can All labs will be equipped with trash cans for non-chemical waste. Frequently they are the receptacle for paper towels, uncontaminated disposable lab equipment such as parafilm, protective gloves and little else. Liquid Chemical Waste Solvent and solution waste will be collected in one or more containers placed in a chemical fume hood. Due to the complex and potentially reactive nature of liquid 3 Dr. Ron Davis, Jr., Ph.D. - 2010

chemical wastes, your disposal plan may differ from experiment to experiment. Always be certain that you are disposing of the waste in the proper container. Solid Chemical Waste Solid waste is sometimes segregated from liquid waste to facilitate disposal. Solid chemicals and significantly contaminated disposable items such as filter paper go here. Broken Glass Containers Special containers for broken glass are provided to ensure the safety of those responsible for its removal. These containers have a very thick liner inside to protect anyone handling the waste after it has accumulated. Uncontaminated broken glass, pipettes, capillaries, etc. may be placed in this container. If your waste glass is significantly contaminated with chemical reagents, seek assistance from your instructor. Incompatible waste may react within the container and cause a very dangerous situation to develop! Working with Chemicals Know Your Reagents Any company which manufactures a reagent or solvent for laboratory use is required by law to produce and publish a document known as its M.S.D.S. (Material Safety Data Sheet). The MSDS of a reagent contains a wealth of useful information, including: The chemical name and other common synonyms used for it Hazard information such as toxicity, flammability, etc Instructions for proper storage Chemical and physical properties such as formula, appearance, molar mass, melting point and boiling point Transportation and disposal considerations

In short, the MSDS is an excellent resource for any chemist to begin familiarizing his/herself with a new chemical before using it in the lab. The MSDS of most compounds can be found in the laboratory containing the compound or at the manufacturers website. Know the rules for heating organic material Preventing solvent fires

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Many organic solvents are highly flammable. Heating such materials inappropriately poses significant risk of fire breaking out. In order for a fire to start in the lab (or anywhere else, for that matter) three components must be brought into contact with one another: 1. A fuel 2. An oxidizer 3. An ignition source

As you have probably guessed, organic solvents often can act as fuels, and atmospheric oxygen is usually a sufficiently strong oxidant to allow such fuel to burn. In the laboratory, the most common source of ignition is heat or spark from the device being used to boil and stir solvents. Most organic compounds have what is known as an auto ignition point, which is a temperature at which the compound will spontaneously ignite in the presence of oxygen. For this reason, it is crucial to carefully safeguard organic solvents from simultaneous exposure to oxygen and excessive heat or spark. To accomplish this, several general rules are always followed when heating organic solvents (Figure 2.1). 1. Never heat an open container of organic solvent directly on a heat source The surfaces of heat sources can reach temperatures well in excess of those needed to spontaneously ignite certain solvents. Placing these devices under open containers of solvents brings together the three ingredients needed to start a solvent fire! Instead, use a water or oil bath to moderate the temperature of heat source in contact with the solvent container. 2. Always clamp the lowest piece of glassware in an apparatus in place and set the heat source on a lab-jack with sufficient room to lower the heat source away from the apparatus. In the event that overheating takes place, complex synthesis setups can be cumbersome to move away from a heat source. Therefore, it is better to set up your apparatus so that the heat source can be lowered. 3. Containers of organic solvent may be heated directly on a heat source if the opening to the apparatus is distant from the heat source.

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When the opening of an apparatus to the atmosphere is far away from the solvent and heat source, oxygen cannot reach the boiling liquid, reducing the risk of ignition. In this specific case, organic solvents may be heated directly on a heat source.

Figure 2.1 Safe Heating of Organic Solvents (A) Never heat an open container of organic solvent directly on a hotplate. (B) Instead, clamp the lowest piece of glassware in the apparatus and use a lab jack to raise a heating bath up to the solvent. (C) Direct heating of a system which has an opening at great distance from the heat source is acceptable, since oxygen cannot reach the heated solvent vapor. Preventing flash boiling or bumping An additional hazard associated with heating of organic solvents is the phenomenon commonly known as bumping. Bumping of a solvent occurs when a local pocket of heat causes a region of the solution to boil suddenly (and sometimes violently). The large vapor bubbles created in this process can cause a container of solvent to froth, foam or even spit solvent out of the confines of the container. Naturally, this presents a safety hazard in the laboratory. Bumping is avoided by the addition of a deterrent which either decreases vapor bubble size or promotes even heating of the sample. In general, three types of bumping deterrents are used in the lab. Boiling stones or chips which are later removed by filtration or decanting Boiling sticks which may be removed by simply pulling them out of the container A magnetic spin bar which continuously stirs the solution and can be removed with the aid of a magnetic spin bar retrieval stick

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Proper Documentation At the heart of any scientific project is the paper documentation of the experiment and its outcome. For this reason, there are a number of time-tested documentation rules which have been followed by scientists for centuries. As modern technology pushes documentation into the digital arena, rules have had to change slightly but the general principle remains that a complete, real-time, indelible account of a researchers activities and observations must be made if their work is to be considered credible. Now lets review a few ways in which laboratory scientists maintain their experimental records appropriately. The record of the experiment must be complete. For this reason, all observations and actions are recorded in a bound laboratory notebook. Comb or spiral binding is not acceptable, since removal of a page from these types of books could be concealed. Additionally, the notebook pages are pre-numbered serially to make any page removal evident. All entries into the notebook are made as the experiment is being carried out and placed on the lowest numbered available page using indelible ink. Erroneous entries are stricken through with a single line leaving them legible. Scratching out entries, using white-out, black markers or other methods to redact entries is strictly prohibited. Scientific documentation is filled with mistakes, but to attempt to conceal these mistakes is to cast suspicion on the integrity of an experimental record. Your laboratory instructor will almost certainly have additional documentation rules for your experimental records. These may seem arbitrary, redundant, excessive or even downright paranoid, but one should keep in mind that the mere appearance of impropriety in scientific documentation can be harmful regardless of the actual intent of the author!

Interpreting Scientific Data A proper analysis of scientific data is not complete without an analysis of what the data are able to tell us with certainty. It is a common misconception that scientists engaged in research are out to find a data set which will prove their hypothesis. In fact, scientific research is quite the opposite. Scientists spend their days in the laboratory trying to prove themselves wrong! If extensive testing fails to disprove a hypothesis, then the hypothesis is considered valid. If extensive testing disproves all other reasonable explanations but the hypothesis, then (and only then) is the hypothesis considered proven. This concept is best conveyed using a simple example. If one were to hold a tennis ball out at arms length and release it, what is the expected result? Naturally, one would hypothesize that the ball will fall downward in accordance with the law of gravity. If after many dozens, hundreds or thousands of trials the ball has fallen downward each time, one might conclude that the law of gravitational attraction has been proven. But has it really been immutably proven? After any number of trials, 7 Dr. Ron Davis, Jr., Ph.D. - 2010

could one ever say with absolute confidence that the next attempt would not be the one in which the ball falls upward due to some yet-to-be understood force? The answer in our simple example is no! Of course, after many trials it becomes reasonably certain that the law of gravity applies because we were unable to disprove it (not because we proved it definitively!). A more classical scientific example is that of Newtonian mechanics, which stood as physical law for centuries. Throughout the 18th and 19th centuries physicists observed the world around them operating in apparent accordance with Newtons laws of motion. Several hundred years after their creation, however, more sophisticated measurement techniques made it possible to disprove Newtons assumption that time is constant, and the most basic laws of physical motion needed to be re-written!

What do the Data Really Tell Us? The results of a soundly designed, hypothesis-driven experiment can tell a researcher one of several things: The data can disprove a theory if it is in direct conflict with the original hypothesis. The data can support a theory if it is consistent with the hypothesis, but other reasonable explanations for the observation exist. The data can prove a theory if there is no other reasonable interpretation of the observations. Recall that it is never possible to prove a theory with absolute certainty. Scientists must instead make a judgment about when they feel reasonably certain that a theory is proven.

It is not uncommon for data sets to appear to be self-contradictory when considered within the framework of a particular hypothesis or theory. The temptation in such a situation is to consider the data unreliable or erroneous. Although this can sometimes be the case, no analysis of a problematic data set is complete without an attempt to modify the hypothesis to fit the empirical observation. Willingness to abandon or modify a hypothesis is an essential trait in an effective researcher.

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