Overview

Specifying Reactions

Using Reaction101

Editing Reactions with Yield101

Providing Quantities

Compound Availability

Sharing Data

Store and Recall

Print Preview

Email

New Features

Process Mass Intensity

Solvent Selection

Summary

Overview

Yield101 is an app for iOS, which runs on Apple iPhone, iPod and iPad devices. It is built from the same technology as the Mobile Molecular DataSheet (MMDS). Yield101 is the result of an ongoing collaboration between Molecular Materials Informatics, Inc., and Eidogen-Sertanty.

Yield101 has a lot in common with its companion application, Reaction101, except that it is designed explicitly to be used by practical synthetic chemists. Both apps have as their focus a single chemical reaction, but the features of Yield10 are geared toward providing data input fields for the quantities of reactants and products:

In this flowchart, the synthesis of aspirin is shown. The structures of the reactants and products are available. If the mass of salicylic acid is provided (top left), it is possible to use the calculated molecular weight to obtain the molarity. Mass and molar mass can be interconverted with volume if density or concentration is available. If the stoichiometry of the reactants is known, it is possible to calculate the molarity of the other reactant, acetic anhydride (top right), and also the molarity of the product, acetylsalicylic acid (aspirin) (bottom). From the molar mass of the product, the theoretical maximum yield can be calculated. When the actual quantity is provided, the yield can be derived.

This is what Yield101 does, in a nutshell. It requires each reaction component to have a structure and a stoichiometry. Once this is provided, you can enter whatever quantity information you have available, and anything that can be derived from it will be calculated and displayed.

Calculating quantities for laboratory synthesis experiments can now be done without having to add up molecular weights, or repeatedly checking to make sure that the arithmetic is correct. Just check that the structures are right, and that the input quantities are correct, and the rest is ready to use.

For a video introduction: Yield101 tutorial, Introductory white-paper: Alex M. Clark; Maurizio Bronzetti; Steven M. Muskal: "Reaction101 and Yield101: Two mobile apps for chemistry with pedagogical value", White-paper (2011) link

Specifying Reactions

Before any quantity calculations are possible, it is necessary to define the reaction: at least one reactant and one product are required, and each of them needs a structure diagram and stoichiometry. The best way to define reactions for use in Yield101 is by using the Reaction101 app to define the reaction and store it in your personal collection, then load it with Yield101 and fill out the quantity details. Yield101 also has structure editing capabilities, so reactions can be drawn within the app itself. It is also integrated with email and web attachments, which can be used to pass data in and out.

Using Reaction101

Switch tasks and run the Reaction101 app:

Use Reaction101 to draw the three components:

Submit the reaction, preferably with an identifying name:

Now switch tasks back to Yield101, and activate the Recall action:

The list of reactions will show reactions that you have stored using Reaction101, as well as reactions with yield schemes stored from within Yield101. Select the reaction of interest, in this case aspirin synthesis:

Select the reaction to bring it into Yield101:

The reaction is now ready for the quantity values to be provided.

Editing Reactions with Yield101

Yield101 supports editing of reactants and products using a similar interface to Reaction101. Components can be added, deleted, copied and pasted, and multi-level undo/redo is available. Structures can be edited conveniently by double-tapping.

Providing Quantities

Each of the reaction components supports 7 properties in addition to the structure.

All of these quantities are co-dependent, which means that once the user enters one datum, it is possible that other values may be able to be calculated. Tap the Mass data entry bubble for the first reactant, and provide a value of 10 grams:

Now the screen has update to show that there are 10g of salicylic acid. This value is shown with bright turquoise background, to indicate that it is user-entered data.

Note that the Moles field also has a value, but that it is displayed without the turquoise background: this is because it is a calculated quantity. It is derived from knowing the mass and the molecular weight, which is in turn derived from the structure. If you were to enter the value for moles, instead of mass, then the opposite calculation would be done: moles would be the user-entered quantity, and mass would be calculated.

Now tap the data entry bubble for Density, and provide the value for salicylic acid:

Observe that that density field is displayed, with a turquoise background to signify user-entered data, and that the Volume has now been calculated:

The equivalence between mass and volume, via density, works in both directions. A similar equivalence exists between moles and volume, via concentration. Concentration is always expressed in molar units (such as mol/L). Note that density should only be used for pure substances, while concentration should only be used for mixtures.

This reaction involves two reactants, salicylic acid is the primary reference point in terms of determining the yield of the product, since the othe reactant, acetic anhydride, is typically used in excess. Tap the data entry bubble for Primary:

Firstly, the field itself is marked with an asterisk. Secondly, some of the data has been filled in for the other (non-primary) reactant. This indicates that for the 1:1 stoichiometry of the reaction, at least 0.0724 moles, or 7.39 grams, of acetic anhydride will be needed for the reaction to go to completion. The actual data for the quantities used in the experiment can be entered at any time, and will override the values calculated based on the stoichiometry.

When the reaction is finished and the products have been worked up, it is time to enter the quantities obtained. If the aspirin synthesis provided 11.5 grams of finished product:

As can be seen, the calculated yield is just over 88%.

For products, the same relationships between quantities are preserved (mass to volume, etc.). The number of moles required for a theoretical yield of 100% is calculated by looking up the molarity of the primary reactant, and the stoichiometry ratios.

Compound Availability

Whenever a structure is modified, Yield101 does a quick check to see if the compound can be found in the Mobile Reagents collection. If there are any hits, this means that the compound is commercially available. You will see an icon displayed below or to the side of the component:

If no matches were found, the icon is deactivated:

This feature allows you to tell at a glance which of your reactants and products are commercially available from a known source. Tapping on the icon will launch the Mobile Reagents app, and instruct it to lookup the corresponding structure and display the results. Being able to check for commercial sources of reactants is useful if stocks are running low, but knowing that a product is available for purchase may be even more so: you may not even need to do the reaction at all!

Attempting to launch Mobile Reagents when it is not installed will instead direct to the AppStore. The download is free.

Sharing Data

Yield101 can be used at the lab bench, which means that in some use case scenarios it is sufficient to simply have quantity data displayed onscreen, but there are more things that can be done with the data. When the reaction and quantity scheme is complete, activate the Finished button, and select one of the options:

Store and Recall

The Store Scheme action submits the current scheme to a cloud-hosted personal collection, which is associated with the current device. The data can be recalled for later use. Before submitting a scheme, you will be prompted to enter a name, which will help to identify it later:

Previously submitted schemes can be browsed and loaded using the Recall button:

The list includes content from 3 different sources: schemes submitted from Yield101 are shown first, and they are differentiated by including the yield percentages in the name; reactions submitted from Reaction101 are shown next, followed by a list of common named reactions, which can be used as templates for drawing new reactions.

Print Preview

Yield101 can format the current scheme on a page using PDF format. This can be previewed by selecting the View PDF button, which will display the PDF version of the reaction:

If your device is connected to a printer, you can use the Print button, and optionally attach the page to a lab notebook. Otherwise, PDF files can be exported via email...

Email

The most comprehensive way to export data is by selecting the Email Scheme action, which will compose an outgoing email containing a variety of information:

In the text part of the email, right at the top, is a link to rxn101.com, which can be used to access the reaction content. It is stored online indefinitely, so it can be hard-linked, used for sharing via social media, etc.

Two data attachments are included: yield.ds and yield.rxn. The first attachment contains a complete record of the reaction scheme with quantity data. If the recipient of the email has Yield101 installed, the attachment can be opened directly with Yield101. The RXN file is also included for use with third party sketchers, although this file format does not allow storing of the quantity information.

The third attachment is a PDF version of the data, which is the same as the PDF preview described earlier. In the screenshot shown above, the iPad email client is displaying the PDF as an inline graphic.

New Features

Version 1.0.2 of Yield101 introduced a new features: process mass intensity (PMI) calculation, and solvent selection.

Process Mass Intensity

The process mass intensity (PMI) of a reaction is defined as the total mass of the reaction inputs divided by the total mass of the desired products obtained. The value is a useful indicator of the greenness of a reaction, because a lower number is consistently desirable according to green chemistry principles.

When the masses of all the reactants and products are available, the PMI is calculated automatically, and displayed along the bottom of the scheme:

This example shows a Diels-Alder reaction being carried out neat, i.e. with no solvent. The PMI value shown is 1.053, which is almost perfect. The absence of a solvent, 100% atom efficiency and high yield are the reasons for this excellent score.

The contributions of each component to the PMI are also shown, as grey bars; 2,3-dimethylbutadiene accounts for 36% of the weight of the inputs, while the alkene diester makes up 64%.

Most reactions involve solvents, reagents and catalysts, and generate byproducts, and often have low yields - all of these factors contribute to raising the PMI value. The following example is a reaction which does not fare so well:

The main contributor to the high PMI score (34.842) is the toluene solvent, which contributes 83% of the mass of the reaction inputs, and is not recovered. Although the reaction has a reasonably high yield (82%), it is hindered by the fact that the reagent, vinyltributyl tin, has a high molecular weight, and the byproducts include tin and bromine atoms.

Solvent Selection

Including solvents in the yield scheme is necessary for the PMI calculation to be meaningful. Solvents can conveniently be added by activating the Add Solvent button:

A list of common solvents will appear:

The solvents are listed in alphabetical order. Select Add or double tap to include in the scheme. Solvents are automatically given a stoichiometry coefficient of 0, since they are not an intrinsic part of the reaction.

Summary

Yield101 is a useful addition to the mobile chemistry app series, and a time-saving tool for bench chemists. Yield schemes can be prepared quickly and reliably ahead of time, then updated as the experiment progresses. Output and sharing tools ensure that the data can be made use of, and integration with compound searching provides a convenient reference point for commercial availability.

The automatic calculation of process mass intensity makes the app useful for determining an important parameter for optimising a reaction from a green chemistry perspective.

See Also

Mobile Molecular DataSheet (iOS), Mobile Reagents App with Embedded MMDS, Products, Reaction101, iProtein App with Embedded MMDS