Overview

Drawing Reactions

Getting Started

Adding components

Mobile Reagents

Stoichiometry

Using Reactions

Personal Storage

Reaction Recall

Email Attachments

Clipboard

Summary

Overview

Reaction101 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). Reaction101 is the result of an ongoing collaboration between Molecular Materials Informatics, Inc., and Eidogen-Sertanty. Reaction101 interfaces with serverside technology from Eidogen-Sertanty, which includes the Mobile Reagents data collection.

The focus of Reaction101 is a chemical reaction, which can be viewed, edited, stored, recalled, emailed or exported as graphics. Reactions are made up of components: reactants, products and reagents, which are described by chemical structure, name and stoichiometry. The interface is a scaled down and simplified version of the Mobile Molecular DataSheet, to which have been added features to make the app more accessible to students learning organic or inorganic chemistry.

For a video introduction: Reaction101 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

Drawing Reactions

The following sections describe reaction drawing using Reaction101. The reaction editor is analogous to the feature found in the Mobile Molecular DataSheet: Introduction to Reactions (iPhone).

Getting Started

When Reaction101 is opened for the first time, a blank reaction will be shown. Depending on the form-factor of your device, and the orientation, the initial state will resemble one of the following:

iPhone/iPod		iPad

The initial blank reaction is prompting for new reaction components to be provided. The Reaction101 app, as with the Mobile Molecular DataSheet, stores reactions as a collection of distinct components. Consider the following simple Diels-Alder reaction:

There are 4 components to this reaction: 2 reactants, 1 reagent and 1 product.

The most important component types are reactants and products. A reaction is not fully specified until at least one of each has been provided. Reactants and products have three properties associated with them:

• structure
• name
• stoichiometry

Reactants and products should always have a structure associated with them. This is the primary display property, as is usual for representation of chemical reactions. The reactant and product components are intended to be used mainly for stoichiometric ingredients, and there is an additional stoichiometry field that can be used when the ratios are not 1:1, which will be described later.

Reagent components are intended to be used for ingredients which are not stoichiometric, which includes a broad variety of possibilities: catalysts, solvents, reagents used in excess, resins, etc. Unlike reactants and products, reagents are primarily displayed by name. It is possible to record their chemical structure as well, but for most display modes, only the name will be shown.

Adding components

To recreate the Diels-Alder reaction shown above, the 4 components of the reaction need to be specified. The starting state for a new reaction provides a prominent clue as to how to go about this:

Double-tapping on the reactant placeholder will open up the structure editor. Alternatively, tap the reactant box just once to select it, then activate the edit structure command button, which will accomplish the same thing:

Use the structure editor to draw butadiene. For an introduction to structures, see: Introduction to Drawing (iPhone).

Once the structure has been specified, the butadiene molecule is now the first reactant:

There are now quite a few more things going on with the display. The reactant is highlighted in green because it is selected. Not only is the structure shown in the main box, but there are extra annotations. The number "1" is displayed in a turquoise box, which is the stoichiometry. Reactants and products always default to a stoichiometry of 1, which will be described in more detail later. Underneath the structure is a box with "?", which is the name of the component. It can be edited, either by double tapping on the box, or by activating the edit name command button. Underneath that is the molecular formula that is implied by the structure.

Note that on the right hand side, underneath the product placeholder, the formula is repeated. This is an indicator of the reaction balance: butadiene is currently the only reactant, and it has 4 carbons and 6 hydrogens. Since there is no product defined, there is an excess of these 10 atoms on the left hand side. The residual is displayed on the opposite side, i.e. adding a product which had the formula C₄H₆ is one way in which the reaction could be balanced. Stoichiometry and reaction balancing will be described in more detail later.

Now that the diene is specified, the dienophile has to be added as the second reactant. Now we do not have a placeholder for this reactant, so we need to add a new one:

Activating this command will create a blank reagent. This time instead of double-tapping on the structure area, either double tap on the "?" name placeholder, or activate the edit name command button. An opportunity to edit the name will be presented:

Enter 1,4-benzoquinone as the name, and press Accept. Now that the name has been provided, we are going to use that to lookup the structure within the Mobile Reagents data collection. Activate the MORE command button on the bottom right:

Select Name Search:

The search matches just one structure:

Select it, in order to import the component:

Specifying the structure for products is analogous. Double-tap the product placeholder to draw the structure of the adduct.

Adding reagents requires first activating the add reagent command button:

A new blank reagent will be created. Double-tapping on the blank placeholder will allow the name to be edited. Enter the name of the Lewis base catalyst: aluminium trichloride. The structure can also be provided, but this is nonessential.

Mobile Reagents

Mobile Reagents is an independent app which provides access to a growing collection of commercially available chemicals. The search functionality of Mobile Reagents is directly available from within the Reaction101 app.

Searching Mobile Reagents for a chemical species involves the following steps:

1. Create a new component
2. Specify either a structure or a name, depending on what kind of search is desired
3. Select the component, and select the search type

The following search types are available:

• Name Search: the name field for the component is used to locate a chemical with the same exact name.
• Similar Name Search: as for the Name Search, except that chemicals with similar names are returned. This search can take slightly longer, since it needs to process more data.
• Formula Search: retrieves all chemicals with the same molecular formula. If the component has a structure defined, the formula that is used to perform the search is computed from the structure. Otherwise, it is necessary to enter a name for the component that is a valid molecular formula, and this will be used for the search.
• Substructure Search: uses the currently defined chemical structure, and searches for all chemicals which contain this structure fragment. When searching for chemicals using substructure fragments, it is highly recommended that the fragment be as large and specific as possible, since this increases the probability of finding the desired result. Very common fragments (e.g. benzene) will match too many chemicals to be useful.
• Similarity Search: uses the currently defined structure to look for all chemicals which have a similar structure. The results are arranged so that the most similar results are shown first.

When a search successfully obtains at least one result, a list of results is shown. In each case the chemical structure and name are available. Selecting a result will replace the structure and name for the currently selected component.

The following searches show results based on 1-naphthoic acid:

Molecular Formula	Substructure	Structure Similarity

Stoichiometry

Each of the reactant and product components has a stoichiometry value, which defaults to 1, which is not normally displayed in the reaction diagram. Stoichiometry values can be expressed in several forms, which have several interpretations:

• Blank or 1: no stoichiometry is the same as a stoichiometry of 1.
• 0: zero is a special value, which means that the component is not stoichiometric, i.e. it should be ignored when determining whether or not the reaction is balanced.
• counting numbers: values of 2, 3, 4, etc., imply that this many equivalents is involved in each reaction.
• ratios: an expression of two numbers in fraction form, e.g. "1/2", "3/4", "5/2", etc., may be used. Rational fractions are the preferred way to specify non-integral stoichiometry.
• decimals: any positive floating point number may be specified as the stoichiometry, e.g. "3.142". This notation should be avoided unless there is a good reason, e.g. indicating the experimentally observed ratio of product isomers.

Consider the following reaction, which is clearly not balanced:

The first step toward balancing this reaction is to select the phenyl lithium component, and open the stoichiometry button bank:

Three equivalents of phenyl lithium are required. Select the command button labelled "3":

Now that the reactants both have the correct stoichiometry, the reaction is almost balanced. On the product side, the screen indicates that there are 3 chlorine and 3 lithium atoms leftover:

To balance the reaction completely, add a second product for lithium chloride, and change the stoichiometry to "3".

Reactions can be balanced manually, as described above, using the residual atoms as a hint. Alternatively, there is an automatic balancer feature available within the stoichiometry sub-menu:

Pressing the button labelled "?" will cause Reaction101 to try combinatorial permutations of reaction equivalents in order to find the stoichiometry values which result in the least atoms leftover. This usually produces the correct answer when the major reaction components have all been specified, and the leftover species are byproducts with few atoms (such as water, salts, or organic fragments with few atoms). If any of the principal reaction components have been omitted, the result will probably not be useful.

Using Reactions

The previous section described the basic process of specifying a chemical reaction using Reaction101. Once a reaction is defined, it can be used for a variety of purposes, besides viewing.

Personal Storage

Reaction101 only allows editing of one reaction at a time. The current reaction is stored locally, so it will not be lost when the app quits, but if you need to edit a new reaction without losing the current data, it is necessary to submit the reaction to Eidogen-Sertanty's cloud-based server, which will allow the reaction to be recalled at a later date.

To store your reaction, activate the finished command button:

From the options that follow, select Store Reaction. Before submitting the reaction, you will be prompted for an opportunity to name the reaction. Reaction names are optional but recommended:

The reaction will be uploaded in the background. You can continue to work with the app while the submission process takes place.

Reaction Recall

The recall feature can be used to retrieve a personal reaction that you have stored previously, or to obtain access to a collection of common named reactions:

Once the server has been contacted, a list will be shown, which has two parts:

The first part is a list of recently stored reactions. Selecting any of these will replace the current reaction with the one shown in the list.

Following the list of personal reactions is a list of groups, each of which contains some number of representative examples of common named reactions. Tapping the chevron, or double-tapping, on any of these group rows will replace it with the individual reactions, e.g. for Birch reductions:

These named common reactions can be retrieved in the same way as personal reactions, and used as reaction templates.

Email Attachments

To send the current reaction via email, activate the finished command button:

From the menu, select Export... then Email Reaction:

The outgoing email is populated with 3 attachments: one is a high resolution graphical image, while the other two contain data. The attachment entitled reaction.ds stores the reaction data using the native XML format used by MMDS and Reaction101, while reaction.rxn is encoded using the industry standard MDL RXN format, which can be opened by a number of popular sketcher applications.

Reaction101 is also capable of reading email attachments, which makes it possible for users of Reaction101 to pass data back and forth via email. This capability is also shared with MMDS, which is capable of reading the same formats.

Clipboard

The Export... option mentioned above also offers to place the reaction data onto the clipboard, either as an image or as data. An image of the reaction can be pasted into any other iOS app that makes use of the clipboard, e.g. Keynote or Pages. Data is pasted onto the clipboard as plain text XML, which can be read by other applications which understand the native reaction format: this currently includes MMDS and the Reaction101 app. When reaction data is available on the clipboard, the content will be listed in the list that is shown when the recall dialog is in process.

Summary

Reaction101 is an independent app which combines the technical strengths of the Mobile Molecular DataSheet with the serverside features of Mobile Reagents and the ease of use of a single-purpose product.

See Also

Mobile Molecular DataSheet (iOS), Mobile Reagents App with Embedded MMDS, Products, Yield101, iProtein App with Embedded MMDS