Organic Chemistry

This collection features techniques routinely used in the organic chemistry lab, focussing on regulating temperature and atmosphere during chemical reactions and post-reaction refinement.

  • Organic Chemistry

    Introduction to Catalysis

    Source: Laboratory of Dr. Ryan Richards — Colorado School of Mines

    Catalysis is among the most important fields of modern technology and presently accounts for approximately 35% of the gross domestic product (GDP) and sustenance of approximately 33% of the global population through fertilizers produced via the Haber process.1 Catalysts are systems that facilitate chemical reactions by lowering the activation energy and influencing the selectivity. Catalysis will be a central technology in addressing the energy and environmental challenges of modern times.

  • Organic Chemistry

    Assembly of a Reflux System for Heated Chemical Reactions

    Source: Laboratory of Dr. Philip Miller — Imperial College London

    Many chemical experiments require elevated temperatures before any reaction is observed, however heating solutions of reactants can lead to loss of reactants and/or solvent via evaporation if their boiling points are sufficiently low. In order to ensure no loss of reactants or solvent, a reflux system is used in order to condense any vapors produced on heating and return these condensates to the reaction vessel. 

  • Organic Chemistry

    Conducting Reactions Below Room Temperature

    Source: Laboratory of Dr. Dana Lashley - College of William and Mary

    Demonstration by: Matt Smith

    When new bonds are formed in the course of a chemical reaction, it requires that the involved species (atoms or molecules) come in very close proximity and collide into one another. The collisions between these species are more frequent and effective the higher the speed at which these molecules are moving. A widely used rule of thumb, which has its roots in the Arrhenius equation1, states that raising the temperature by 10 K will approximately double the rate of a reaction, and raising the temperature by 20 K will quadruple the rate: (1) Equation (1) is often found in its logarithmic form: (2) where k is the rate of the chemical reaction, A is the frequency factor (relating to frequency of molecular collisions), Ea is the activation energy required for the reaction, R is the ideal gas constant, and T is the temperature at which the reaction is taking place. A higher temperature therefore means a reaction is completed much faster. Nonetheless, in some cases it is desirable to carry out reactions at low temperatures, in spite of the lowering effect on the rate of the reaction. A few scenarios in this regard are elaborated upon further below. When it is useful to run a reaction below room temperature, chemists use cooling baths to maintain a certain temperature or tem

  • Organic Chemistry

    Schlenk Lines Transfer of Solvents

    Source: Hsin-Chun Chiu and Tyler J. Morin, laboratory of Dr. Ian Tonks—University of Minnesota Twin Cities

    Schlenk lines and high vacuum lines are both used to exclude moisture and oxygen from reactions by running reactions under a slight overpressure of inert gas (usually N2 or Ar) or under vacuum. Vacuum transfer has been developed as a method separate solvents (other volatile reagents) from drying agents (or other nonvolatile agents) and dispense them to reaction or storage vessels while maintaining an air-free environment. Similar to thermal distillations, vacuum transfer separates solvents by vaporizing and condensing them in another receiving vessel; however, vacuum transfers utilize the low pressure in the manifolds of Schlenk and high vacuum lines to lower boiling points to room temperature or below, allowing for cryogenic distillations. This technique can provide a safer alternative to thermal distillation for the collection of air- and moisture-free solvents. After the vacuum transfer, the water content of the collected solvent can be tested quantitatively by Karl Fischer titration, qualitatively by titration with a Na/Ph2CO solution, or by 1H NMR spectroscopy.

  • Organic Chemistry

    Degassing Liquids with Freeze-Pump-Thaw Cycling

    Source: Laboratory of Dr. Neil Branda — Simon Fraser University

    Degassing refers to the process by which dissolved gases are removed from a liquid. The presence of dissolved gases such as oxygen or carbon dioxide can impede chemical reactions that utilize sensitive reagents, interfere with spectroscopic measurements, or can induce unwanted bubble formation.

    A number of different techniques are available for degassing liquids; some of these include heating, ultrasonic agitation, chemical removal of gases, substitution with inert gas by bubbling and freeze-pump-thaw cycling. Freeze-pump-thaw cycling is a common and effective method for small scale degassing, and will be demonstrated here in more detail.

  • Organic Chemistry

    Preparing Anhydrous Reagents and Equipment

    Source: Laboratory of Dr. Dana Lashley - College of William and Mary Demonstrated by: Timothy Beck and Lucas Arney

    Many reactions in organic chemistry are moisture-sensitive and must be carried out under careful exclusion of water. In these cases the reagents have a high affinity to react with water from the atmosphere and if left exposed the desired reaction will not take place or give poor yields, because the reactants are chemically altered. In order to prevent undesired reactions with H2O these reactions have to be carried out under an inert atmosphere. An inert atmosphere is generated by running the reaction under nitrogen gas, or in more sensitive cases, under a noble gas such as argon. Every component in such a reaction must be completely anhydrous, or free of water. This includes all reagents and solvents used as well as all glassware and equipment that will come into contact with the reagents. Extremely water-sensitive reactions must be carried out inside of a glovebox which provides a completely sealed off anhydrous environment to work under via a pair of gloves which protrudes out to one of the sides of the chamber.

  • Organic Chemistry

    Purifying Compounds by Recrystallization

    Source: Laboratory of Dr. Jimmy Franco - Merrimack College

    Recrystallization is a technique used to purify solid compounds.1 Solids tend to be more soluble in hot liquids than in cold liquids. During recrystallization, an impure solid compound is dissolved in a hot liquid until the solution is saturated, and then the liquid is allowed to cool.2 The compound should then form relatively pure crystals. Ideally, any impurities that are present will remain in the solution and will not be incorporated into the growing crystals (Figure 1). The crystals can then be removed from the solution by filtration. Not all of the compound is recoverable — some will remain in the solution and will be lost. Recrystallization is not generally thought of as a separation technique; rather, it is a purification technique in which a small amount of an impurity is removed from a compound. However, if the solubility properties of two compounds are sufficiently different, recrystallization can be used to separate them, even if they are present in nearly equal amounts. Recrystallization works best when most impurities have already been removed by another method, such as extraction or column chromatography. Figure 1. The general scheme for recrystallization.

  • Organic Chemistry

    Separation of Mixtures via Precipitation

    Source: Laboratory of Dr. Ana J. García-Sáez — University of Tübingen

    Most samples of interest are mixtures of many different components. Sample preparation, a key step in the analytical process, removes interferences that may affect the analysis. As such, developing separation techniques is an important endeavor not just in academia, but also in industry. 

    One way to separate mixtures is to use their solubility properties. In this short paper, we will deal with aqueous solutions. The solubility of a compound of interest depends on (1) ionic strength of solution, (2) pH, and (3) temperature. By manipulating with these three factors, a condition in which the compound is insoluble can be used to remove the compound of interest from the rest of the sample.1

  • Organic Chemistry

    Solid-Liquid Extraction

    Source: Laboratory of Dr. Jay Deiner — City University of New York

    Extraction is a crucial step in most chemical analyses. It entails removing the analyte from its sample matrix and passing it into the phase required for spectroscopic or chromatographic identification and quantification. When the sample is a solid and the required phase for analysis is a liquid, the process is called solid-liquid extraction. A simple and broadly applicable form of solid-liquid extraction entails combining the solid with a solvent in which the analyte is soluble. Through agitation, the analyte partitions into the liquid phase, which may then be separated from the solid through filtration. The choice of solvent must be made based on the solubility of the target analyte, and on the balance of cost, safety, and environmental concerns.

  • Organic Chemistry

    Rotary Evaporation to Remove Solvent

    Source: Dr. Melanie Pribisko Yen and Grace Tang — California Institute of Technology

    Rotary evaporation is a technique most commonly used in organic chemistry to remove a solvent from a higher-boiling point compound of interest. The rotary evaporator, or "rotovap", was invented in 1950 by the chemist Lyman C. Craig. The primary use of a rotovap is to dry and purify samples for downstream applications. Its speed and ability to handle large volumes of solvent make rotary evaporation a preferred method of solvent removal in many laboratories, especially in instances involving low boiling point solvents.

  • Organic Chemistry

    Fractional Distillation

    Source: Laboratory of Dr. Nicholas Leadbeater — University of Connecticut 

    Distillation is perhaps the most common laboratory technique employed by chemists for the purification of organic liquids. Compounds in a mixture with different boiling points separate into individual components when the mixture is carefully distilled. The two main types of distillation are "simple distillation" and "fractional distillation", and both are widely used in organic chemistry laboratories. Simple distillation is used when the liquid is (a) relatively pure (containing no more than 10% liquid contaminants), (b) has a non-volatile component, such as a solid contaminant, or (c) is mixed with another liquid with a boiling point that differs by at least 25 °C. Fractional distillation is used when separating mixtures of liquids whose boiling points are more similar (separated by less than 25 °C). This video will detail the fractional distillation of a mixture of two common organic solvents, cyclohexane and toluene.

  • Organic Chemistry

    Growing Crystals for X-ray Diffraction Analysis

    Source: Laboratory of Dr. Jimmy Franco - Merrimack College

    X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms in a crystalline solid, which allows for the determination of the three-dimensional shape of a molecule or complex. Determining the three-dimensional structure of a compound is of particular importance, since a compound's structure and function are intimately related. Information about a compound's structure is often used to explain its behavior or reactivity. This is one of the most useful techniques for solving the three-dimensional structure of a compound or complex, and in some cases it may be the only viable method for determining the structure. Growing X-ray quality crystals is the key component of X-ray crystallography. The size and quality of the crystal is often highly dependent on the composition of the compound being examined by X-ray crystallography. Typically compounds containing heavier atoms produce a greater diffraction pattern, thus require smaller crystals. Generally, single crystals with well-defined faces are optimal, and typically for organic compounds, the crystals need to be larger than those containing heavy atoms. Without viable crystals, X-ray crystallography is not feasible. Some molecules are inherently more crystalline than others, thus the difficulty of obtaining X-ray quality crystals can vary between compounds. The growth of

  • Organic Chemistry

    Performing 1D Thin Layer Chromatography

    Source: Laboratory of Dr. Yuri Bolshan — University of Ontario Institute of Technology

    Thin layer chromatography (TLC) is a chromatographic method used to separate mixtures of non-volatile compounds. A TLC plate consists of a thin layer of adsorbent material (the stationary phase) fixed to an appropriate solid support such as plastic, aluminum, or glass1. The sample(s) and reference compound(s) are dissolved in an appropriate solvent and applied near the bottom edge of the TLC plate in small spots. The TLC plate is developed by immersing the bottom edge in the developing solvent consisting of an appropriate mobile phase. Capillary action allows the mobile phase to move up the adsorbent layer. As the solvent moves up the TLC plate, it carries with it the components of each spot and separates them based on their physical interactions with the mobile and stationary phases.

  • Organic Chemistry

    Column Chromatography

    Source: Laboratory of Dr. Jimmy Franco - Merrimack College

    Column chromatography is one of the most useful techniques for purifying compounds. This technique utilizes a stationary phase, which is packed in a column, and a mobile phase that passes through the column. This technique exploits the differences in polarity between compounds, allowing the molecules to be facilely separated.1 The two most common stationary phases for column chromatography are silica gel (SiO2) and alumina (Al2O3), with the most commonly used mobile phases being organic solvents.2 The solvent(s) chosen for the mobile phase are dependent on the polarity of the molecules being purified. Typically more polar compounds require more polar solvents in order to facilitate the passage of the molecules through the stationary phase. Once the purification process has been completed the solvent can be removed from the collected fractions using a rotary evaporator to yield the isolated material.

  • Organic Chemistry

    Nuclear Magnetic Resonance (NMR) Spectroscopy

    Source: Laboratory of Dr. Henrik Sundén – Chalmers University of Technology

    Nuclear magnetic resonance (NMR) spectroscopy is a vital analysis technique for organic chemists. With the help of NMR, the work in the organic lab has been facilitated tremendously. Not only can it provide information about the structure of a molecule but also determine the content and purity of a sample. Compared with other commonly encountered techniques for organic chemists — such as thermal analysis and mass spectrometry (MS) — NMR is a non-destructive method that is valuable when recovery of the sample is important. One of the most frequently used NMR techniques for an organic chemist is proton (1H) NMR. The protons present in a molecule will behave differently depending on its surrounding chemical environment, making it possible to elucidate its structure. Moreover, it is possible to monitor the completion of a reaction by comparing NMR spectra of the starting material to that of the final product. This video exemplifies how NMR spectroscopy can be used in the everyday work of an organic chemist. The following will be shown: i) preparation of an NMR sample. ii) Using 1H NMR to monitor a reaction. iii) Identifying the product obtained from a reaction with 1H NMR. The reaction that will be shown is the synthesis of an E-chalcone (3) from an aldehyde (1) and a ketone (2) (Scheme 1).1