One or more chemists will be assigned to the project full-time. Progress of the work is communicated at regular intervals, typically in written weekly or monthly reports. Samples of intermediate compounds are available on request at any stage of the synthesis. The project can be stopped at any time.
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Most phenols are weak acids (pKa= ~10) and do not react with sodium bicarbonate, which is a weak base itself (pKa(H2CO3)=6.37, 10.3). However, they do react with a strong base like NaOH. This difference in acidity can be exploited to separate carboxylic acids and phenols from each other in an organic layer. While many phenols dissolve poorly in water (8.3 g/100 mL at 20 oC, log Kow=1.46), phenolates dissolve very well in aqueous solutions. After the extraction, the phenol can be recovered by adding a mineral acid to the basic extract.
Which of the two reagents should be used depends on the other compounds present in the mixture. Sodium hydroxide is usually easier to handle because it does not evolve carbon dioxide as a byproduct. In addition, the concentration can be increased significantly if is needed. However, if compounds were present that are sensitive towards strong bases or nucleophiles (i.e., esters, ketones, aldehydes, etc.), sodium bicarbonate should be used. It does not react with these compounds because it is a weaker base and a weak nucleophile (due to its resonance stabilization). Note that the formation of carbon dioxide as a byproduct causes a pressure build-up in the separatory funnel, the centrifuge tube or the conical vial. Thus, additional precautions (i.e., frequent venting) have to be taken to prevent any accidents resulting from the pressure build up in the extraction vessel. The target compound can subsequently be recovered by adding a mineral acid to the basic extract i.e., benzoic acid in the Grignard experiment in Chem 30CL.
Depending on the chain length, amines might or might not be soluble in water i.e., propylamine is miscible with water (log Kow=0.48), triethylamine displays a limited solubility at room temperature (17 g/100 mL, log Kow=1.44), while tributylamine hardly dissolves at all (0.37 g/100 mL, log Kow=4.60). Amines are basic and can be converted to ammonium salts using mineral acids i.e., hydrochloric acid. The resulting salts dissolve in water. However, the solubility of the ammonium salts decreases as the number and size of R-groups increases. Ammonium salts from primary amines are much more soluble in water than salts from tertiary amines due the increased ability to form hydrogen bonds [(H3NEt)Cl: 280 g/100 g H2O, (H2NEt2)Cl: 232 g/100 g H2O, (HNEt3)Cl: 137 g/100 g H2O (all at 25 oC)].
In order to remove an acidic compound from a mixture, a base like NaOH or NaHCO3 is used. The carboxylic (or mineral) acid and the base react to form a sodium salt, which is usually exhibits a higher solubility in aqueous solutions due to its negative charge and higher polarity (as indicated by a more negative log Kow value i.e., CH3COOH: -0.17, Na+CH3COO-: -3.72).
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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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.