Reaction Workup Planning: A Structured Flowchart Approach

Article pubs.acs.org/jchemeduc

Reaction Workup Planning: A Structured Flowchart Approach, Exemplified in Difficult Aqueous Workup of Hydrophilic Products George B. Hill*,†,§ and Joseph B. Sweeney*,‡ †

Oncology Innovative Medicines, AstraZeneca PLC, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TF, United Kingdom Department of Chemistry and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield, West Yorkshire HD1 3DH, United Kingdom

‡

S Supporting Information *

ABSTRACT: Reaction workup can be a complex problem for those facing novel synthesis of difficult compounds for the first time. Workup problem solving by systematic thinking should be inculcated as mid-graduate-level is reached. A structured approach is proposed, building decision tree flowcharts to analyze challenges, and an exemplar flowchart is presented for aqueous workup of awkwardly hydrophilic products. Its use is illustrated with real synthetic compounds and model examples.

KEYWORDS: Graduate Education/Research, Problem Solving/Decision Making, Continuing Education, Inquiry Based/Discovery Learning, Organic Chemistry

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INTRODUCTION Reaction workup is a science that can be the key to success. Yet it is one little studied or taught in the generic sense, unlike either mechanistic reaction design or equipment training. This becomes noticeable when more difficult novel synthesis begins around mid-graduate-level, and also in early pharmaceutical research training at the same age. This paper is aimed at those at, and supervising at, these levels. Why? Because reaction workup is largely an orphan science. At no stage of laboratory training is workup formally taught, for understandable reasons. Reaction workup planning seems trivial nearly to irrelevance in organic undergraduate labs. At this stage, when obedience does not achieve success, comparison usually does. A simple organic product can be isolated by analogy with the wealth of precedent in Organic Syntheses or Scif inder. At early graduate-level, the analogue may be an in-house one; but a workup “known in the art” from similar chemistry should still succeed. From mid-graduate-level, the challenges become compound specific. A young chemist gains experience in narrow areas, but seeing general principles of workup is not within their targets. Similarly, supervisors focus on hands-on learning. In addition (and remarkably), no current journal is devoted to generic organic workup. Systematic workup selection in novel synthesis appears unconsidered. Only certain techniques or situations are addressed by existing publications, such as in chromatography and process chemistry. These offer detail often of little practical use for synthesizers of one-off compounds with © 2014 American Chemical Society and Division of Chemical Education, Inc.

unfamiliar properties. In contrast, chemical education journals mostly focus on well-defined lessons. In the general literature, innumerable workups appear, but searching by workup to locate good models is hard for atypical compounds. Generic recommendations are scarce and confined to strategy rather than tactics, e.g., preparing boronic esters as reagents for use in Suzuki reactions (instead of hydrophilic boronic acids).1 There is, therefore, a hiatus both in the syllabus and in the literature. When precedent is unhelpful, or is unattractive due to safety or other considerations, young experimentalists can struggle. Their approach to a workup problem might only be an educated guess. Personal support is then critical as they are helped (or occasionally hindered!) by others offering anecdotal advice, intuition, guesswork or even prejudice. In industry, the rapid current loss of experienced senior chemists from the bench is a further problem, as found by one of us [G.B.H.], who has spent nearly 35 years in novel synthesis. Could more systematic training be given? Should reaction workup not be an intimate part of the synthetic strategy? A reasoned plan for workup needs to be in place when one embarks upon synthesis. A flowchart basis for this is proposed.

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AIMS AND CONTEXT The laboratory process of workup can be more challenging than what it follows (i.e., the reaction). So, more advice on applying Published: November 5, 2014 488

dx.doi.org/10.1021/ed500580p | J. Chem. Educ. 2015, 92, 488−496

Journal of Chemical Education

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adding the resultant brew to an acidic resin would have resulted in a safety issue. An action taken without foresight had misfired. Planning may also both help morale and rebuke foolishness. A rigorous approach to workup, when a product has awkward properties (hydrophilicity, polarity, low MW, visualization problems, volatility), should cut frustration, a significant error driver for even the most patient scientist. It also adds weight to reprimand, as of one irresponsible student described to one us [G.B.H.], who (without taking advice) carried out no less than 40 diethyl ether extractions to remove a compound from an aqueous quench, still with only 70% recovery!

logical rigor to workup selection could usefully be given to all students starting novel synthesis of difficult products. In this context, it should be noted that the different lab environments of academic and industrial target audiences (particularly in their levels of access to technology) are part of the theme: experimentalists may have to cross such boundaries, and in any case should understand how workup principles direct the technology. Thus, this paper: 1. Explains the need for structure in workup problem analysis; 2. Examines the need for the learner to learn good habits; 3. Selects a decision tree approach for the purpose; 4. Identifies hazards associated with providing instructions in generic form; 5. Recommends a procedure to prepare and populate a suitable flowchart; 6. Lists likely benefits to trainers and learners in novel research; 7. Mentions key practical learning points necessary to gain maximum benefit; 8. Uses a key problem area (i.e., aqueous workup) to exemplify the approach; 9. Presents a series of real examples and model workups of very hydrophilic compounds to illustrate the flowchart.

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LEARNING GOOD HABITS IN PROBLEM ANALYSIS Structured problem solving is a cornerstone of scientific training. The best approach is to teach a novice to identify concepts and generic approaches, rather than describing all possible angles. In the laboratory, training must quickly establish the good habits that underpin successful (i.e., productive) work. For synthetic chemists, the reaction is only part of the experimental process and can only be considered a success once an experimenter has obtained, characterized and identified the pure product. Yet young chemists nowadays appear in the training environment (university or industrial) with a considerably reduced palette of skills following inadequate exposure to challenging chemistry. A research supervisor then has to discourage a “follow this recipe” approach, in favor of an “understand these methods” purview. This is particularly necessary in workup, for the postsynthesis process remains a black-box problem. Workup theory is little explored and practical classes emphasize only the content of the experiment, not of an experimenter’s subsequent mindset! Moreover, early practical work is designed to be successful and compounds usually made are well-behaved, largely hydrophobic species whose isolation is straightforward. Learners are little prepared to deal with workup difficulties such as phase issues, or polarity mismatches, or unfamiliar physical properties. This lack of breadth in isolation techniques, carried forward into later postgraduate work, means that experimenters may have to ad lib their separation protocol, or give up. Problem workups are sometimes avoided, of course, by telescoping of reaction sequences (not isolating intermediates between reactions) until an easily handled product is reached. This can work well in simple chemistry, but is risky in a difficult synthesis where delicate reactions may require pure starting mixtures and is of little help if the target itself is a problem compound. Once acquired, good workup reasoning will quickly become second nature, and will develop the habits of interrogative thinking that best empower a practical chemist.

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STRUCTURE IN WORKUP PROBLEM ANALYSIS The pedagogical principles for practical chemistry should be no different to those for theoretical chemistry: learning should be instilled in a logical way. “Open learning” inquiry based experiments that do not merely confirm a known outcome have value, but their lack of structure allows students to acquire misconceptions leading to discouragement,2 e.g., when a poor test suggests that a slightly soluble compound is hopelessly insoluble. A logical scaffolding is, therefore, important.3 An irrational choice of a workup technique (such as trying to extract an obviously hydrophilic compound out of aqueous solution) is bad news. Not only can time be lost (often unexpectedly), but also expensive resources can be consumed and unnecessary waste generated. A good experimental scientist will understand the value of contingency planning. The simplest contingency would anticipate the need for workup flexibility using available techniques. The most extreme contingency plan would be to rewrite the prequel: to redesign the synthetic route to avoid problems in advance. Where the latter is impossible, the bench chemist can be faced with a stark choice: improve the workup or abandon the pursuit of the compound. In either case, thinking ahead deserves more attention. At the very least, thinking about the workup as an experiment in itself can mitigate both against misunderstandings (for example, of the best pH at which to isolate an amphoteric compound) and against unnecessary errors (most commonly, over- or under-additions of workup additives). On one occasion where G.B.H. was consulted, a hydrophilic boronic acid was “trapped” in a quantity of salt-laden aqueous quench. Flowchart analysis predicted that the use of a high-loading sulfonic acid ionexchange resin was the obvious workup to choose, until the experienced scientist who had brought the problem remembered that (for a reason hard to remember!), a large amount of aqueous sodium bicarbonate had previously been introduced. Clearly,

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DECISION TREES IN REACTION WORKUP: PRECEDENTS AND TYPES Most structured approaches to workup improvement are published in process chemistry, e.g., the ranking of purification techniques by their ecological value.4 A friendlier form of structuring is a decision tree, which this paper presents in flowchart form. Various sorts of tree could be designed; in practical chemistry answers are required that can immediately be applied in order to decide what happens next. Therefore, a decision tree is used whose suggestions are generic rather than exact, but can easily be tested (rather than, say, a 489



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(b) a consistent house style, using colored boxes, panels or (our terminology) “tiles”.

dichotomous key leading to an already defined answer set, or a predictive tree whose answers cannot easily be tested). This type of tree, widely used in medicine, has been used in chemistry for prediction of optimum parameters for chromatography systems.5 Such a tree has two benefits. First, it allows a student to be trained to interrogate systematically a reaction mixture, a quenched mixture or a crude product, in order to choose the optimal workup for it. This gives an experimenter information, e.g., likely useful solvents. Second, a guide of this type can present a broader range of options than might immediately be obvious to a single experimentalist.

Insert the Title and First Tiles

These should comprise the following: (a) clear safety warnings at the start and where needed on applying generic techniques to novel mixtures; (b) advice to use any technique or facility you have in your lab, and otherwise to follow the chart to the next option; (c) a “catch-all” and user-friendly Start Tile to confirm the initial state. These points are illustrated in Figure 1 (the techniques named are described later).

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HAZARDS: SAFETY CONSIDERATIONS Any new compound could present unspecified danger. Generic approaches to novel chemistry techniques cannot include specific hazard prediction. It is therefore important not to assume that a flowchart can offer any safe suggestion for any particular case. A common error in using identification keys, for example, is the assumption that the correct result is even included in that key at all; similarly, in workup selection it may be that none of the options presented may be safe (or indeed useful) for a chemist to use. A decision tree flowchart can only offer suggestions, not instructions, to which supervisors and learners must both apply their normal laboratory skills, responsibilities, risk assessment and judgment. It must therefore warn inexperienced experimentalists to treat its output as guidelines, not rigid rules.

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STYLE: PROCEDURE FOR DESIGNING A FLOWCHART The following process is recommended, which is exemplified later:

Figure 1. Examples of safety, advice, and start tiles.

Identify the Area of Enquiry

Exclude Triviality

Use of flowchart decision trees is worth considering where: (a) the aim is to obtain pure useful product from a challenging mixture; (b) many choices could be made, or the best one is not obvious; (c) practical skill is the focus; (d) experienced chemist trainers have much to impart; but (e) knowledge is difficult to convey or reconvey; (f) advice will depend on the case in question; (g) no existing guide is available.

Provide an “Escape Tile” to exclude trivial problems for which the flowchart is hardly necessary (e.g., compounds thought only mistakenly to be very hydrophilic) (Figure 2).

Define the Purpose

A flowchart may guide a chemist through any of the following: (a) a spectrum of options (e.g., for very hydrophilic compounds); (b) a technique with several forms (e.g., in chromatography); (c) options within a specific technique (e.g., in extraction).

Figure 2. Escape tile to exclude trivial problems.

Make a Rough Design

Color-Code the Subsequent Tiles

A first sketching should be done on paper, but as soon as text boxes need to be moved around, it becomes easier on screen (rather than using scissors!).

Thus, (a) Different tiles should indicate questions; instructions; Information Check tiles with tests to carry out (such as, check the pH); and Technique Tiles to apply (and to seek more information on). Figure 3 et seq. are representative. (b) Tiles should present all the relevant scenarios a chemist conceivably could face, with suggestions to help; and arrow labels should be clear (Figure 4).

Choose the House Style of the Components

Drawing a flowchart for a specific purpose should involve the following: (a) suitable software. Commercial software is expensive; Powerpoint is fine; 490



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solid phase extraction (SPE) separation; awkward byproducts such as salts soluble in organic solvents.

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RESULT AND ASSESSMENT Successful use of a flowchart designed and used after structured thinking is sufficient result. When students obtain a pure product, they will remember it, how they did it and how a flowchart assisted them. Assessment should take the form of a presentation explaining the decisions taken, with challenging peer review.

Figure 3. Tiles color-coded by function.

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LEARNER RESEARCHER BENEFIT What could a learner researcher learn from using and perhaps preparing such a chart? (a) The need for safety right from the start of workup as well as during the reaction; (b) The value and habit of approaching all workup problems systematically; (c) How to interrogate an unfamiliar chemical mixture informatively; (d) The importance of consistency whatever happens in workup; (e) The importance of testing and of data; (f) The existence of techniques not yet learnt or even heard about; (g) Sound practical advice in novel organic synthesis.

Figure 4. Tile presenting all likely scenarios.

Mark a Successful Outcome Clearly

There should be a clear success marker so far as the flowchart’s expectation goes (here, a green asterisk). This does not necessarily mean a bottled final product but an available one (Figure 5).

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TRAINER BENEFIT How could a trainer gain from such a chart? (a) A chart itself could be used to train or assist other experimentalists; (b) Practical skills requiring further training may well be highlighted.

Figure 5. Tile anticipating a successful outcome.

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Content: Drawing a TreeCriteria

KEY PRACTICAL LEARNING POINTS Best practice in workup will also become plain. The main mental gain is resilience (learning to make decisions and learning from mistakes). The main practical learning point is the importance of smallscale trials. Challenging reaction workups should proceed via constant testing. This is the necessary implication of structured thinking and a learner should see this. At no point should bulk mixture or material be compromised. This is essential in order not to limit the options remaining thereafter. Experimentalists are always reluctant to spend time on small-scale trials. Yet without these, any “errors” that arise may restrict which further “trials” can be made. A flowchart’s first and most important use is to determine that tests are needed and which tests they are. Even a milligram of crude material can sometimes reveal critical information without prejudice to the main batch. A connected lesson is the need to locate (or predict) any helpful data that can reduce the range of options to be considered, e.g., pKa, and to indicate its significance.

All resulting problem mixtures that could be envisaged should first be listed. Then, the first criterion is safety. After that, the logical criteria are necessity and then increasing complexity. A flowchart should guide a chemist using these three criteria. The entire process above is illustrated later by an exemplar case of “A Flowchart for Aqueous Workup of Very Hydrophilic Compounds”. Test and “Sanity Check” The Route

Every reasonably conceivable path should reach a foolproof (and not merely logical) answer. An instruction given by one person can be misunderstood by another in a way the first had never imagined possible or even imagined at all. We have all failed while following instructions that at first appeared clear to us, as well as their author. For any outcome, a chemist must be presented with the right questions. An extraction gives two layers: which is the aqueous one? Can this be changed? How? Practical tips may be added. In fact, these are good reasons for preparing a flowchart in the first place; if it is not an experience transferring vehicle, it is no more than an encouragement to think. Even this is, of course, of value, but the aim should be to develop practical as well as mental resource. Problems or opportunities afforded by particular functional groups or expected side products may need highlighting, e.g., amphoteric product issues; the amenability of amine bases to

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PROBLEMS OF A SELECTED KEY AREA: HIGHLY HYDROPHILIC COMPOUND WORKUP Our example area can be hard work, typically when a reaction has required an aqueous quench. When isolation by simple extraction or precipitation fails, a structured approach should be considered. 491



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Figure 6. A flowchart to guide aqueous workups.

Hydrophilic species are increasingly required across organic

Academia is increasingly involved in making drug-like molecules through joint enterprises with industry, where low logP and logD (partition-coefficient and distribution-coefficient) properties make molecules compatible with biological systems. Surveys show that the industry trend is clearly toward final

chemistry in both academia and industry, in challenging purity and scale. Even general organic chemistry sometimes needs very hydrophilic intermediates. 492



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products whose hydrophilicity makes them harder to purify.6 Yet a mini-review by Churcher et al. at GlaxoSmithKline7 stated that “much synthetic methodology is unintentionally predisposed to producing molecules with poorer drug-like properties.” The authors noted that organic synthesis succeeds more often in making less hydrophilic molecules (“LogP drift in array synthesis”) because “the more polar products in an array tend to systematically fail more often in synthesis.” Three of the five likely causes they identified, namely, insolubility, poor extraction, and problems in chromatography, are all troublesome with very hydrophilic and/or polar products.

discussed in turn and illustrated by the real Examples shown. Also described are Model Workup ideas using trivial compounds. The latter are representative suggestions only, with no experimental quantities or details; and are only demonstration models, although full safety procedures should still be observed. All hazards must be eliminated or taken fully into account as indicated above before any workup option is applied. Abbreviations

The following are used to help decide what options are practical: [STD] = a standard and often common workup; [SOA] = a “state-of-the-art” workup that may or may not be economic or available on the scale required.

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A FLOWCHART FOR AQUEOUS WORKUP OF VERY HYDROPHILIC COMPOUNDS This section expands on the criteria listed earlier.

Purification

Some workups described (e.g., Workups 1−4 below) may not give pure product but should give water-free crude product that can then be purified easily, e.g., by chromatography. Evaporation, when necessary, is normally by a rotary evaporator, but safety and stability issues must be assessed beforehand, as must the potential loss of a volatile product unless distilled or efficiently condensed.

Safety

A reaction mixture MUST be quenched into an aqueous state if safety requires it, or if an experimentalist is not sure. Necessity

Such a flowchart should help a chemist to discover the best workup while not endangering the product, that is, not adding a new problem. It should also confront common difficulties. One is the presence of high boiling solvents because many reactions are diluted with water to assist removal of these. (The alternative of distilling them off has several problems: it may concentrate a hazard; it may damage a thermally fragile product; and it does not remove organic salt byproducts that can complicate chromatography.) However, such solvents can only be removed by several water washes of a product solution in ethyl acetate (EtOAc) (or preferably diethyl ether (Et2O)), but so will such a product! This presents a dilemma, for the state-of-the-art answer is SPE. Should a student be told about techniques that may not easily be available to them (e.g., SPE sorbents)? Yes, because the point is education and the principle should be understood in any case, since it was probably invented in academia. Also, collaboration or in-house synthesis of materials can then be justified.

Escape Tile

This is for compounds mistakenly assumed to be difficult. This is combined with Workup 1. Workup 1: “Conversion to Free Form” [STD]. The flowchart’s first nonsafety instruction is also an “Escape Tile” in case the problem compound is not actually a serious workup challenge (e.g., is not very hydrophilic and its properties have been guessed wrongly, such as a slightly water-soluble alcohol). This workup applies to any product that is an organic acid or base (but not both). Take a small sample of the solution. Determine the pH. If the product might still be a salt at that pH, begin by acidifying (a salt of an acid) or basifying (a salt of an amine) with dilute aq HCl or NaOH to give the free form. Filter off any precipitate of product. Then agitate the sample well with EtOAc. Next, run TLC and/or NMR on the organic layer to see if product (or more product) can be obtained. If not and workup is clearly not going to be trivial, begin to progress through the flowchart. Model Workup: A carboxylic acid such as isophthalic acid can be precipitated with excess inorganic acid from an aqueous solution of its sodium salt. Workup 2: “Enhanced Extraction” [STD]. This workup applies only to a neutral compound with no ionizable groups or to a salt converted to its free form as in Workup 1. Extraction with a single solvent (EtOAc) has “failed”. If normal extraction gives only a little product, can we make it more effective? For single water-immiscible solvents, the power of a solvent to extract a compound out of water generally increases in the order Et2O < dichloromethane (DCM) < EtOAc < 2methyltetrahydrofuran. If the test extraction above gave poor (rather than zero) recovery, repeat Workup 1 but now: (a) extract three times with a mixture of 15% of isopropyl alcohol (IPA) or of tetrahydrofuran (not 2-methyltetrahydrofuran) in EtOAc. Then/or: (b) do as in (a) using 15% IPA in DCM. These methods are superior to the common practice of adding of brine or excess solid NaCl (or in acid mixtures, ammonium sulfate) to the mixture. This adds little to the efficiency of (a) or (b) which should be first choice. It can help to break up emulsions and to separate layers, but with highly hydrophilic

Complexity

The expected workup challenges should be listed in order of increasing difficulty. In aqueous workup mixtures this might be: (a) one containing a product thought wrongly to be very hydrophilic and difficult; (b) one containing a product that can be extracted but only with an “enhanced” technique, i.e., one using a suitable miscible additive (such as isopropanol); (c) one containing only an unwanted cation or anion, i.e., a simple salt of the product; (d) one in which only the product (and easily removed material) can ionize; (e) one for which chromatography of some sort would be practicable and the first choice (but appears impossible unless water can be removed); (f) one containing an amphoteric product in salt form; (g) very difficult cases. Applying the criteria above gives the exemplar flowchart shown in Figure 6.

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EXAMPLES AND MODEL WORKUPS In this section, the flowchart in Figure 6 is followed and the workups shown on the numbered green Technique Tiles are 493



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(i.e., all solvent and neutral waste) is washed through. The column is washed with clean methanol; then the product is eluted using ammonia solution. (Excess ammonia displaces the product from the column by mass action even when the product is a base of up to tertiary amine strength.) This can also be a good way of separating from a nonvolatile solvent (e.g., dimethyl sulfoxide (DMSO) or N,N-dimethylformamide (DMF)). A key difference between Workup 4 and Workup 3 is that silica rather than polystyrene resin is the material supporting the ion exchanging (acid or basic) groups. One reason for this is because trapped organic materials are easier to free from silica sorbents than from lipophilic resins. Example: After amination of 4 by 5 (Scheme 3), the hydrophilic amine product 6 was retained on strong cation exchanger (SCX) silica. Then, after washing, the product was washed off with ammonia/methanol mixture.

compounds, if extraction still fails, it adds large amounts of inorganics to the problem! Example: The chemical literature describes many “enhanced extractions”. The hydrophilic molecule theophylline, 1, (which occurs naturally in trace amounts in tea) requires chloroform/ isopropyl alcohol, or dichloromethane/isopropyl alcohol for efficient extraction from an aqueous mixture (Scheme 1).8 Scheme 1. A Product Obtained More Efficiently by “Enhanced Extraction”

Scheme 3. A Product Isolated by Solid-Phase Extraction

Model Workup: Compare the extraction of a 5% aqueous solution of maleic acid with EtOAc, without and with addition of 15% IPA, testing each layer using TLC/UV. Workup 3: “Resin-Based Ion Exchange”Deionization [STD/SOA]. This is now the standard option for isolating a free compound from a simple salt of it. (Traditional precipitation methods using toxic metal salts are now obsolete.) Typically, sodium cations are removed from the sodium salt of a simple organic acid by filtering the mixture through a column containing beads of a suitable (reusable) strong acid ionexchange resin. The corresponding resin for removing anions from an amine is MP-carbonate resin (macroporous polymer supported hydrogen carbonate). In each case, a very small excess of reagent (e.g., residual NaOH after a hydrolysis in the former case) can usefully be removed too. Example: After hydrolysis9 of the diester 2 (Scheme 2), the whole mixture was passed through an acidic ion-exchange resin.

Model Workup: Ordinary flash silica can be used to show a crude SPE-like effect. Thus, picoline elutes readily in 5% DCM/ MeOH, while the stronger base 4-dimethylaminopyridine (DMAP) is essentially retained and requires 0.5% aqueous ammonia added to the eluent to elute it. Workup 5: “Preparative RPLC” (Reverse Phase Liquid Chromatography) [SOA]. This workup is chromatography on a form of silica (“reverse phase” silica) that works in the opposite way to normal silica. But it is not always realized that very hydrophilic compounds can be purified by “prep” RPLC when loaded in pure water containing virtually no organic solvent. The theory of RPLC is not further described here; nevertheless, although reverse phase silica sorbent is expensive it can be synthesized even for undergraduate use, as previously described in this Journal.10 Example: After amination of the disubstituted 2-chloropyrimidine 711 with diethanolamine 8 (Scheme 4), the IPA solvent was evaporated and a solution of the highly hydrophilic product 9 in water was purified by prep RPLC. Workup 6: “Low Aqueous Quench” [STD]. This workup is simply common sense. If only a slight excess of water is needed to quench a reaction safely and fully and if the product is organic soluble (in EtOAc), then follow the quench by adding excess solvent and excess drying agent. Workup 7 : “Dry-Loading” [STD]). In dry-loading, a solution is mixed with 2−5 times its weight of silica and evaporated to dryness. Then the loaded silica is added to the top of a preconditioned chromatography column (Workup 8) and more solvent is added as usual. This workup is generally done because the product is poorly soluble. But it can be used for mixtures containing water if the silica is first fully dried, e.g., by

Scheme 2. A Product Isolated by Resin-Based Ion Exchange (I.E.)

This trapped all sodium ions from both the product and from the unreacted alkali left. The diacid 3 passed through the column without being trapped and was obtained pure on evaporation. Model Workup: The hydrolysis of dimethyl or diethyl malonate, leading (by use of a suitable resin) to isolation of free malonic acid, could be used to illustrate this workup. Workup 4: “Solid Phase Extraction” (SPE)Product Capture and Release [SOA]. If all waste material cannot be trapped as a solid, then perhaps all of an ionizable product can. This workup is usually used to isolate mild amine bases containing no acid groups. Typically, a reaction mixture is diluted (if necessary) with water or methanol (MeOH) and added to a small column of special SPE silica, which has ion-exchanging groups attached (via alkyl chains) to the silica particles. All material except the product 494



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Scheme 4. A Product Purified by RPLC

Scheme 6. A Product Isolated by Conversion to Its Free Form

(a) advanced “enhanced extraction” using n-butanol (which has unusual properties14 but is difficult to remove); (b) “Continuous Extraction” using special liquid−liquid extraction glassware [SOA]; (c) trapping a neutral compound on special “desalting resin” [SOA] then releasing it; (d) “Freeze Drying” [SOA]; (e) evaporation of a bulk aqueous solution slowly to dryness on a rotary evaporator (if safe) then washing the dry residue with a solvent [STD]; (f) separating by classic pH-controlled ion exchange [SOA]; (g) precipitating the product as a salt [STD]; (h) derivatizing the compound in situ or reacting it further while crude [STD].

“azeotroping” the silica twice (e.g., adding excess toluene and distilling it off again) before adding to the column. If the product is highly polar, continue to Workup 8. Example: The workup example in Scheme 5 is from a published reaction.12 After a Grignard reaction on an aldehyde

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Scheme 5. A Product Purified after “Dry-Loading”

CONCLUSION AND FURTHER SCOPE Decision trees have not obviously been applied in novel reaction workup15 previously. We recommend their use and exemplify it in difficult aqueous workup.

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ASSOCIATED CONTENT

S Supporting Information *

was quenched with aqueous NH4Cl, the solvent mixture of diethyl ether and water was simply evaporated and the whole residue including the NH4Cl was mixed with silica, added to a chromatography column, and eluted to give the product 10. Workup 8: “Normal (Phase) Silica Chromatography with Very Polar Additives” [STD]. Once water has been excluded, a polar hydrophilic compound can often be columned on ordinary flash silica in solvents such as dichloromethane containing 3−20% of methanol plus 1−2% of aqueous ammonia (for bases) or of acetic acid (for acids). The solvent mixture must first be eluted through the column to precondition it f ully before starting. Workup 9: “Free Form Isolation of Amphoteric Compounds” [STD]. If the compound is amphoteric (both an acid and a base), plan to precipitate or extract it when it is not a salt (i.e., as the free compound). To do this, estimate (using pKa tables) the pKa values in water of the weakest proper acidic and basic groups. Calculate the midpoint (the compound’s isoelectric point) and adjust to this pH. Example: Hydrolysis of the nitrile imine 1113 (Scheme 6) gives the amino acid 12 which precipitates best (in 92% yield) on acidifying to pH 3. Model Workup: A simple example is the amino acid tyrosine, which precipitates best at pH 5.63 from a solution of it in either acid or alkali.

Experimental procedures for compounds 3, 5, 9, and 12. This material is available via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. Present Address §

2 Marriott Road, Wheelock, Sandbach, Cheshire, CW11 3LU, U.K. Notes

The authors declare no competing financial interest.

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REFERENCES

(1) Wong, K.; Chien, Y.; Liao, Y.; Lin, C.; Chou, M.; Leung, M. Efficient and Convenient Nonaqueous Workup Procedure for the Preparation of Arylboronic Esters. J. Org. Chem. 2002, 67 (3), 1041− 1044. (2) Kirschner, P. A.; Sweller, J.; Clark, R. E. Why Minimal Guidance During Instruction Does Not Work: An Analysis of the Failure of Constructivist, Discovery, Problem-based, Experiential, and InquiryBased Teaching. Educ. Psychol. 2006, 41 (2), 75−86. (3) Hmelo-Silver, C. E.; Duncan, R. G.; Chinn, C. A. Scaffolding and Achievement in Problem-based and Inquiry Learning: A Response to Kirschner, Sweller, and Clark (2006). Educ. Psychol. 2007, 42 (2), 99− 107. (4) Van Aken, K.; Strekowski, L.; Patiny, L. EcoScale, a SemiQuantitative Tool to Select an Organic Preparation Based on Economical and Ecological Parameters. Beilstein J. Org. Chem. 2006, 2, No. 3.

Techniques for Extreme Cases

Further techniques could be added as a single final flowchart tile. In aqueous workup, methods for very difficult cases include the following: 495



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(5) Hubert, P.; Chiap, P.; Moors, M.; Bourguignon, B.; Massart, D. L.; Crommen, J. Knowledge-Based System for the Automated Solid-Phase Extraction of Basic Drugs from Plasma Coupled with Their Liquid Chromatographic Determination: Application to the Biodetermination of β-Receptor Blocking Agents. J. Chromatogr., A 1994, 665 (1), 87−99. (6) Leeson, P. D.; St-Gallay, S. A. The Influence of the ‘Organizational Factor’ on Compound Quality in Drug Discovery. Nat. Rev. Drug Discovery 2011, 10 (10), 749−765. (7) Nadin, A.; Hattotuwagama, C.; Churcher, I. Lead-Oriented Synthesis: A New Opportunity for Synthetic Chemistry. Angew. Chem., Int. Ed. 2012, 51 (5), 1114−1122. (8) Pirrung, M. C. The Synthetic Organic Chemist’s Companion; John Wiley & Sons, Inc.: Hoboken, NJ, 2007; p 109. (9) Cunliffe, C. J.; Franklin, T. J.; Hales, N. J.; Hill, G. B. Novel Inhibitors of Prolyl 4-Hydroxylase. 3. Inhibition by the Substrate Analog N-Oxaloglycine and Its Derivatives. J. Med. Chem. 1992, 35 (14), 2652− 2658. (10) Ortega, F.; Velez, E.; Somanathan, R. Synthesis and Use of Reverse-Phase Silica Gel for HPLC in Undergraduate Chemistry. J. Chem. Educ. 1996, 73 (2), A26−A27. (11) Morris, J. J.; Pike, K. G. Trisubstituted Pyrimidine Derivatives for the Treatment of Proliferative Diseases (AstraZeneca UK Limited) WO2009007748A2, 2009. (12) Jung, M. H.; Park, J.; Yang, K. J.; Lee, M. Synthesis and Muscarinic Activity of 1,2,3,4-Tetrahydropyrimidine Derivatives. Arch. Pharm. (Weinheim, Ger.) 2001, 334 (3), 79−85. (13) Mortlock, A. A.; Keen, N. J. Therapeutic Quinazoline Derivatives (AstraZeneca UK Limited), WO-2001021597, 2001. (14) Stephenson, R. M. Mutual Solubilities: Water-Ketones, WaterEthers, and Water-Gasoline-Alcohols. J. Chem. Eng. Data 1992, 37 (1), 80−95. (15) “Workup”; or, less frequently in the literature, “work-up”. In searches, also note the verb, “work up”.

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Reaction Workup Planning: A Structured Flowchart Approach

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