Reaction101 and Yield101: Two mobile apps with pedagogical value


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We describe the use of two mobile apps, Reaction101 and Yield101, in the context of a learning environment. Reaction101 includes features for learning to balance reactions. Yield101 assists with calculating quantities that are relevant for a laboratory preparation. While both apps have capabilities that are useful to synthetic chemists at all stages of career development, they have been designed to be specifically useful to students learning chemistry at high school and undergraduate level. These mobile apps also facilitate communication of chemical data, in both digitally interpretable forms and presentation-ready formats.

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Reaction101 and Yield101: Two mobile apps with pedagogical value

  1. 1. Reaction101 and Yield101: Two mobile apps for chemistry with pedagogical valueAuthors:Alex M. Clark (corresponding author) Molecular Materials Informatics, Inc. Montréal, Québec, Canada H3J2S1 http://molmatinf.comMaurizio Bronzetti, Steven M. Muskal Eidogen-Sertanty, Inc. 3460 Marron Road, Suite 103-475, Oceanside, CA 92056 http://eidogen-sertanty.comAbstract:We describe the use of two mobile apps, Reaction101 and Yield101, in the context of a learningenvironment. Reaction101 includes features for learning to balance reactions. Yield101 assists withcalculating quantities that are relevant for a laboratory preparation. While both apps have capabilitiesthat are useful to synthetic chemists at all stages of career development, they have been designed to bespecifically useful to students learning chemistry at high school and undergraduate level. These mobileapps also facilitate communication of chemical data, in both digitally interpretable forms andpresentation-ready formats.
  2. 2. distinct component. Reaction componentsIntroduction consist of a chemical structure sketch, name,Mobile apps have become prevalent within an and in the case of reactants and products,incredibly broad segment of the population, stoichiometry. The reaction editor is derivedincluding education at all levels. A modern from the Mobile Molecular DataSheet app (8),smartphone, music player or tablet computer the and the structure diagram sketcher is describedsize of a small book now delivers high in detail in the literature (9).performance graphics, storage, computational Reaction101 is supplemented by useful reactioncapacity and access to the Internet. A growing aids that are provided by server side contentnumber of educational institutions are adopting from Eidogen-Sertanty. A public collection ofmobile devices as classroom tools (1). There are common generic reactions, organized by name,an increasing number of apps designed for is available, and any one of them can be viewedchemists at varying stages of professional for reference purposes, or used as a startingdevelopment, from high school students to point for drawing a new reaction. Also,graduates and beyond (2). individual reaction components can be obtainedA recent review (3) describes a large number of by searching the Mobile Reagents (10) apps for chemistry, many of them Searching can be done by name, formula, exactfocused on education. There are also online structure, substructure, and structural similarity.resources, such as SciMobileApps (4), which When a reaction is displayed onscreen, it isprovides a living resource that is regularly checked to verify whether it is balanced. Bothupdated by the community. sides of the reaction - reactants and products -In this article we describe two apps: are tallied up by multiplying the molecularReaction101 (5) and Yield101 (6), which were formula for each component by itscreated with the needs of students in mind. Both stoichiometry. For each element whose countsof these apps are available for iOS based are not equal on both sides, the excess is addeddevices, specifically the iPhone, iPod and iPad to the opposite side. In this way, it is made very(7). clear at a glance that a reaction is not balanced. When a reaction is not balanced, it is because ofReaction101 some combination of missing components,Reaction balancing is a vital skill for students incorrect stoichiometries, or incorrectly drawnwho intend to pursue any branch of chemistry, reactants or products. Figure 1 and Figure 2and it has traditionally been practiced by show screen captures for two reactions, wheredrawing out reactions on paper. Verifying 1(a) and 2(a) are not balanced, and the display iswhether a reaction is balanced is a relatively annotated with the excess atoms on either side.tedious calculation, and is prone to mistakes. The screen captures shown in Figures 1(b) andComplementing this approach with a computer- 2(b) show the analogous reactions, with all theassisted solution that provides real-time components included, and balanced. In thesefeedback adds an important and valuable extra cases, the element counts match, and so nodimension to learning. excess atoms are denoted.Addressing this challenge is one of the primarymotivations for designing Reaction101, amobile app centered around the drawing andrendition of a single chemical reaction. Areaction is represented as a set of reactants,reagents and products, each of which is a
  3. 3. (a) (b) Figure 1. Unbalanced (a) and balanced (b) representations of a perchlorination reaction (11) (a) (b) Figure 2. Unbalanced (a) and balanced (b) representations of a deacylation/methylation reaction (12).This concise feedback can be thought of as a result. While this may seem like a way tokind of checksum for the correctness of a shortcut the learning process, it is only effectivereaction, i.e. a balanced reaction is not if the actual components are correctly specified.necessarily correct, but a non-balanced reactionis definitely wrong or incomplete. Often the Yield101leftover element counts make missing When setting up a reaction in a lab, thecomponents quite obvious, for example calculations that go into adding up molecularelimination of small molecule byproducts such weight, interconverting mass and volume byas water. The student is free to experiment by density or concentration etc., are not particularlytinkering with the reaction components and difficult, but they must be learned by repetition.stoichiometric equivalents, and obtain real-time Students need to focus on observing thefeedback as to the extent to which the reaction is experiment as it progresses, learning how to usebalanced. the equipment, thinking about the actualThe app also features an automatic balancing chemistry that is occurring, recordingfeature, which attempts to guess the experimental notes legibly, scheduling timing instoichiometry of each component by picking the order to workaround availability of sharedcoefficients that lead to the most balanced resources, getting the experiment finished
  4. 4. (a) (b) Figure 3. Yield scheme for a silylation reaction (13). Values that are highlighted in turquoise are actual values, provided by the user, while non-highlighted values are calculated. (a) shows the scheme before the reaction is complete, where the yield has been set to 100% in order to trigger calculation of the mass of the theoretical maximum (8.06 g). (b) shows the scheme after the reaction is complete, with the actual yield specified explicitly (4.73 g, 59%).before the deadline, and all the while paying - mass and molar mass are related viaattention to laboratory safety protocols. molecular weightDevoting too much time to quantity - mass and volume are related by densityinterconversion may take attention away from (for pure substances)the learning experience. As with reactionbalancing, introducing a tool that performs these - mass and volume are related byinterconversions automatically provides a real- concentration (for diluted substances)time answer key. It can be used in conjunction When there is more than one reactant, one ofwith a manual calculation, to confirm the them should be marked as being primary. Byanswer and build confidence. using the primary reactant as a reference point,The Yield101 app has a similar interface to the following relationships between componentsReaction101, as both apps present an individual apply:reaction as the central object, but its focus is on - molar mass of reactants and products canthe physical quantities that make up an be derived from the molar mass of theindividual laboratory preparation. Each of the primary reactant, scaled by the ratio ofreactants and products are characterized by, in their stoichiometryaddition to structure, stoichiometric equivalents,mass, molar mass, volume, density and - yield of products can be derived from theconcentration. The purpose of the app is to make expected molar mass (fromuse of the relationships between these stoichiometry) relative to the observedproperties. The user needs to provide the actual molar massmeasurements. The algorithm will then calculate By applying these relationships iteratively, aany of the missing quantities that are implied by few key experimental measurements providedactual data. by the user can allow many of the remainingWithin an individual component, the following quantities to be derived, ultimately providing arelationships apply: percentage yield for the reaction, once the products have been measured. - molecular weight is derived from structure
  5. 5. The app can be used to enter actual values as Besides calculating the quantities of reactantsthey become available, or it can be used in a and products involved in an experiment,more speculative way, e.g. by entering a value Yield101 also introduces a calculated quantityof 100% for a yield, the calculations will be called process mass intensity (PMI). This is andone in reverse, and the theoretical maximum index that is often promoted in the context ofquantities will be filled out instead, as is green chemistry (14). The calculation is veryillustrated in Figure 3(a). In Figure 3(b), the simple: total mass of all reactants divided byactual yield for the reaction has been entered. total mass of desired products. Water is typically excluded from both sides of theSome quantities can be codependent, e.g. reaction, and non-aqueous solvents are added toproviding mass, volume and density is allowed, the product side only if they are recovered. Thebut it introduces the possibility of inconsistency. ideal "green reaction" has a PMI value of 1,If the calculated and provided values do not which means that there are no unusedmatch up, they are all highlighted in red, byproducts other than water, and non-aqueousindicating that a mistake has been made, andsome correction is required. solvents were either not used or recovered, and the yield was 100%. While the PMI values forThe app also has the ability to print out a two different reactions are not usuallyquantity scheme (or create a PDF file), which is comparable, smaller values are more desirablea useful pre-laboratory exercise (see Figure 4). from the point of view of waste andPrior to beginning the experiment, the known environmental side effects.quantities and properties can be entered, which Yield101 displays the PMI calculation at theprovides information on quantities of reaction bottom of the screen, as shown in Figure 5, andequivalents and theoretical yields. Once the also displays the relative contribution for eachexperiment is completed, actual values can be of the components, in the form of a percentageapplied to produce a second scheme, either or sidebar. Calculation of these metrics is notboth of which can be attached to the laboratory typically a high priority in the laboratoryreport, if this is allowed as part of the exercise. environment, and so the always-on automatic calculation of these properties is a way to encourage students to start thinking about the environmental implications of chemical Figure 5. Yield scheme for a mercuration reaction (15). All solvents are included onFigure 4. Print-ready display of a reaction the reaction side. The calculated PMI isyield scheme. 6.836.
  6. 6. reactions early on in their careers, which is attachments, either originating by email or fromlikely to become an increasingly important skill. a browser download, can be opened with either app, if they are of a recognized format, whichCommunication includes the industry standard MDL RXN andBoth Reaction101 and Yield101 have strong RDfiles (17). The ability to share reaction datadata sharing capabilities. App-to-app sharing allows both of these apps to participate in thecan be accomplished via the open-with realm of cheminformatics, as they can bothfunctionality: both Reaction101 and Yield101 create and consume content.are capable of sending and receiving reaction Reaction images can be copied to the clipboardcontent, so they can pass reaction schemes in bitmap form, which allows them to be pastedbetween each other. The same applies for any into other apps on the device, e.g. Keynote (18).other installed app that registers itself As previously mentioned, Yield101 can be usedappropriately (16). to generate a PDF file of the reaction/quantityBoth apps are capable of storing content on a scheme, which can be viewed, printed or sent bycloud-hosted server, which is associated with email.the device. Reactions or yield schemes can berecalled for later use, and Yield101 is capable of Conclusionopening reactions stored by Reaction101, which Both apps have features that are useful forbinds them together in a logical workflow: professional chemists, but they have particular value in a learning environment. Interactive - use Reaction101 to draw and balance a reaction balancing calculations and automatic reaction calculation of related physical quantities - use Yield101 to fill in quantity data, once provides feedback and encourages learning by for each experiment trial and error. Determination of process massReactions and yield schemes can be sent by intensity (PMI) for reaction schemes encouragesemail. An outgoing email message includes a students to consider the environmentalpicture of the reaction, and the actual data. If the implications of each chemical reaction. Therecipient of the email message is running either ability to create presentation quality graphicsof these apps, the content can be automatically and communicate data encourages students toextracted and opened within the selected app. If collaborate and share, and also provides anthe recipient is using a generic email client, the entrypoint into the wealth of digitized chemistryattachment content can be downloaded and used data that is available on the any compatible software. Incoming
  7. 7. References1. (a); (b); (c); (d); (e) (accessed 20 September 2011).2. Williams, A.J.; Pence, H.E. J. Chem. Educ. 2011, 88, 683-686.3. Williams, A.J.; Ekins, S.; Clark, A.M.; Jack, J.J.; Apodaca, R.L. Drug Discov. Today 2011, in press.(doi:10.1016/j.drudis.2011.09.002)4. Scientific Mobile Applications wiki: (accessed 19 September 2011).5. (accessed 19 September 2011).6. (accessed 19 September 2011)7. Both of these apps are available on the Apple iTunes AppStore, which is the standard delivery mechanism for all iOSbased devices.8. (accessed 19 September 2011).9. Clark, A.M. J. Cheminf. 2010, 2:8.10. (accessed 19 September 2011).11. (a) ChemSpider Synthetic Pages, (accessed 19 September 2011). (b)Rosevear, J.; Wilshire, J.F. Aust. J. Chem. 1980, 33, 843-852.12. (a) ChemSpider Synthetic Pages, (accessed 19 September 2011). (b)Locksley, H.D.; Murray, I.G. J. Chem. Soc. C 1970, 392-398.13. Lettan, R.B.; Milgram, B.C.; Scheidt, K.A. Org. Synth. 2007, 84, 22.14. (a) Jimenez-Gonzalez, C.; Ponder, C.S.; Broxterman, Q.B.; Manley, J.B. Org. Proc. Res. Dev. 2011, 15, 912-917. (b) (accessed 20 September 2011).15. Clark, A.M.; Oliver, A.G.; Rickard, C.E.F.; Wright, L.J.; Roper, W.R. Acta Cryst. C 2000, 56, 26-27.16. (accessed 19 September 2011).17. (accessed 19 September 2011).18. Keynote for iOS: (accessed 19 September 2011).