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Books: Organic Synthesis - Organic Chemistry Portal

So I about Donald Batesky, the 85-year-old synthetic organic chemist at the University of Rochester who recently in the Journal of Organic Chemistry. He contacted me afterwards, and I ended up talking to him for quite a while about his career, which has been long (clearly!) and varied. With his permission, I’m doing an entire blog post just on that – a tour through both his own experiences and through some interesting chemistry as well.

For instance, if the target compound was the base in the system, the extraction with HCl should be performed first. Whatever remains in the organic layer is not of interest anymore afterwards, unless one of the other compounds has to be isolated from this layer as well. If the target compound was an acid, the extraction with NaOH should be performed first. This strategy saves steps, resources and time, and most of all, greatly reduces waste.

Practical Aspects of an Extraction

An extraction can be carried out in macro-scale or in micro-scale. In macro-scale, usually a separatory funnel (on details how to use it see end of this chapter) is used. Micro-scale extractions can be performed in a conical vial or a centrifuge tube depending on the quantities. Below are several problems that have been frequently encountered by students in the lab:



Synthesis of cyclopentanes - Organic Chemistry Portal

Advanced Organic Chemistry Francis A

Microscale Organic Laboratory: with Multistep and Multiscale Syntheses, …

Acknowledgements Components of a Microscale Organic Kit Microscale vs. Macroscale Procedures for Safety Equipment Emergency Procedures for CHE: 206 Emergency Procedures for CHE: 219 Keeping a Laboratory Notebook Format for a Lab Notebook Experiment #1 – Distillation Using the Hickman Still Experiment #2 – Gas Chromatography (Gas-LiquidChromatography): Analysis of a Mixture Experiment #3 – Thin Layer Chromatography (TLC) Experiment #4 – Recrystallization Experiment #5 – Stereochemistry Experiment #6 – Extraction Experiment #7 – Synthesis of n-butyl bromide (SN2 Reaction)Experiment #8 and #9 – Elimination: E1 and E2 Reactions Experiment #10 – Addition Polymers Experiment #11 – Diels-Alder Reaction Experiment #12 – Competitive Aromatic Nitration Experiment #13 – Solubility and solution Experiment #14a – Infrared Spectroscopy Experiment #14b – NMR Spectroscopy Experiment #15 – Williamson Ether Synthesis Experiment #16 – Sodium Borohydride Reduction Of ketoneExperiment #17 – Grignard Reaction Experiment #18– Fischer Esterification Experiment #19 – Dye-Coupling and Diazo-Imaging Experiment #20 – Preparation of an α,β-Unsaturated KetoneExperiment #21 – Condensation Polymers or Step-GrowthPolymers: Nylon and Polyester

After separation of the organic and the aqueous layer, the amine can be recovered by addition of a strong base like NaOH or KOH to the acidic extract i.e., lidocaine synthesis. Note that amides are usually not basic enough to undergo the same protonation (pKa of conjugate acid: ~ -0.5).




Most neutral compounds cannot be converted into salts without changing their chemical nature. Many of these neutral compounds tend to react in undesired ways i.e., esters undergo hydrolysis upon contact with strong bases or strong acids. One has to keep this in mind as well when other compounds are removed. For instance, epoxides hydrolyze to form diols catalyzed by acids and bases. Ketones and aldehydes undergo condensation reactions catalyzed by both, acids and bases. Esters also hydrolyze to form carboxylic acids (or their salts) and the corresponding alcohol. In order to separate these compounds from each other, chromatographic techniques are often used, where the compounds are separated based on their different polarities (see Chromatography chapter).




Based on the discussion above the following overall separation scheme can be outlined. Which sequence is the most efficient highly depends on the target molecule. There is obviously no reason to go through the entire procedure if the compound sought after can be isolated in the first step already. Note that many of these steps are interchangeable in simple separation problems.

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Unraveling Surface Plasmon Decay in Core–Shell Nanostructures toward Broadband Light-Driven Catalytic Organic Synthesis
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Molecular Co-Catalyst Accelerating Hole Transfer for Enhanced Photocatalytic H2 Evolution
Atomic-Layer-Confined Doping for Atomic-Level Insights into Visible-Light Water Splitting
Visible-Light Photoexcited Electron Dynamics of Scandium Endohedral Metallofullerenes: The Cage Symmetry and Substituent Effects
A Unique Semiconductor–Metal–Graphene Stack Design to Harness Charge Flow for Photocatalysis
Integration of an Inorganic Semiconductor with a Metal–Organic Framework: A Platform for Enhanced Gaseous Photocatalytic Reactions
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Fishpond United States, Microscale Organic Laboratory with Multistep and Multiscale Syntheses by Ronald M Pike Dana W Mayo

After a reaction is completed, the solution often times does not only contain the desired product, but also undesired byproducts of the reaction, unreacted starting material(s) and the catalyst (if it was used). These compounds have to be removed in the process of isolating the pure product. A standard method used for this task is an extraction or often also referred to as . Strictly speaking, the two operations are targeting different parts in the mixture: while the extraction removes the target compound from an impure matrix, the washing removes impurities from the target compound i.e., water by extraction with saturated sodium chloride solution. Washing is also used as a step in the recrystallization procedure to remove the impurity containing mother liquor adhering to the crystal surface.

Many liquid-liquid extractions are based on acid-base chemistry. The liquids involved have to be immiscible in order to form two layers upon contact. Since most of the extractions are performed using aqueous solutions (i.e., 5 % NaOH, 5 % HCl), the miscibility of the solvent with water is a crucial point as well as the compatibility of the reagent with the compounds and the solvent of the solution to be extracted. Solvents like dichloromethane (=methylene chloride in older literature), chloroform, diethyl ether, or ethyl ester will form two layers in contact with aqueous solutions if they are used in sufficient quantities. Ethanol, methanol, tetrahydrofuran (THF) and acetone are usually not suitable for extraction because they are completely miscible with most aqueous solutions. However, in some cases it is possible to accomplish a phase separation by the addition of large amounts of a salt (“salting out”). Commonly used solvents like ethyl acetate (8.1 %), diethyl ether (6.9 %), dichloromethane (1.3 %) and chloroform (0.8 %) dissolved up to 10 % in water. Water also dissolves in organic solvents: ethyl acetate (3 %), diethyl ether (1.4 %), dichloromethane (0.25 %) and chloroform (0.056 %). Oxygen containing solvents are usually more soluble in water (and vice versa) because of their ability to act as hydrogen bond donor and hydrogen bond acceptor. The higher water solubility lowers the solubility of weakly polar or non-polar compounds in these solvents i.e., wet Jacobsen ligand in ethyl acetate. Other solvents such as alcohols increase the solubility of water in organic layers significantly because they are miscible with both phases and act as a mediator. This often leads to the formation of emulsions.

The most important point to keep in mind throughout the entire extraction process is which layer contains the product. For an organic compound, it is relatively safe to assume that it will dissolve better in the organic layer than in most aqueous solutions unless it has been converted to an ionic specie, which makes it more water-soluble. If a carboxylic acid (i.e., benzoic acid) was deprotonated using a base or an amine (i.e., lidocaine) was protonated using an acid, it would become more water-soluble because the resulting specie carries a charge. Chlorinated solvents (i.e., dichloromethane, chloroform) exhibit a higher density than water, while ethers, hydrocarbons and many esters possess a lower density than water (see solvent table), thus form the top layer . One rule that should always be followed when performing a work-up process:

Never dispose of any layer away until you are absolutely sure (=100 %) that you will never need it again. The only time that you can really be sure about it is if you isolated the final product in a reasonable yield, and it has been identified as the correct compound by melting point, infrared spectrum, etc. Keep in mind that it is always easier to recover the product from a different layer in a beaker than from the waste container or the sink. In this context it would be wise to label all layers properly in order to be able to identify them correctly later if necessary.

In order to separate compounds from each other, they are often chemically modified to make them more ionic i.e., convert a carboxylic acid into a carboxylate by adding a base. Standard solutions that are used for extraction are: 5 % hydrochloric acid, 5 % sodium hydroxide solution, saturated sodium bicarbonate solution (~6 %) and water. All of these solutions help to modify the (organic) compound and make it more water-soluble and therefore remove it from the organic layer. More concentrated solutions are rarely used for extraction because of the increased evolution of heat during the extraction, and potential side reactions with the solvent.





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NMR Chemical Shifts of Common Laboratory Solvents …

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