The reaction editing capabilities of MMDS are described in the form of a short tutorial. A new reaction datasheet is createad, and a single reaction is added to it.
As of version 1.2, MMDS for iOS supports drawing and viewing of chemical reactions. Reactions are stored in a specially marked-up datasheet, which is referred to as a reaction datasheet. A reaction datasheet is presented just like a normal datasheet, except that each row features a reaction rather than a molecular structure:
Reactions are stored in a structured format that delineates each component as a separate entity:
In this case, A and B are reactants, C and D are reagents, E and F are products. Each component has a name and a structure associated with it.
NOTE: There are two common ways of storing reactions in general use: structure-separated and freeform. The freeform approach is typically used with desktop sketcher applications, in which the user is allowed to add reaction symbols, such as arrows, "+", annotation text, etc., as drawing glyphs. The structure-separated approach requires that each component be defined separately. MMDS reactions are structure-separated.
Reaction datasheets are for the most part treated the same way as normal datasheets. The editing process uses the reaction editor, which allows the reaction components to be specified. Reaction datasheets can be imported and exported using the same methods that are available for normal datasheets.
The remainder of this tutorial describes the steps involved in creating a reaction datasheet, then adding and editing a reaction. For a live introduction, see Video Demo: Reaction Drawing Tutorial.
The first step to accessing reaction functionality is to create a reaction datasheet.
Creating a Reaction DataSheet
Open the main menu by tapping or holding the logo on the top left, and selecting the New ReactionSheet entry:
Or alternatively, press the button entitled New Reactions:
Both of these access points will bring up the New ReactionSheet dialog:
Enter a name for the reaction datasheet, then press the Accept button. A new reaction datasheet will be created, and positioned directly below the Scratch Sheet:
The newly created reaction datasheet is empty. The screenshot above shows one of the icons on the left hand side of the datasheet is framed with a white rectangle. This is in fact flashing, which is a cue: tap on this icon to add a new entry to the datasheet.
Adding a Reaction
After tapping the add reaction icon, the reaction editor screen appears, and starts out with a blank reaction:
Since all reactions have at least one reactant and product, an entry has been added for both sides of the reaction: a blank reactant, and a blank product.
Note that the screenshot above applies to the iPhone/iPod resolution, for which MMDS only allows portrait mode. The reaction arrow is drawn downward, in order to make best use of the available screen space.
When viewing a reaction on an iPad in landscape mode, the reaction arrow is shown in the left-right direction:
As an example reaction, this tutorial will be using the Hiyama coupling reaction:
Hatanaka, Y.; Hiyama, T.: "Cross-coupling of organosilanes with organic halides mediated by a palladium catalyst and tris(diethylamino)sulfonium difluorotrimethylsilicate", J. Org. Chem.53, 918-920 (1988) link
Defining the First Reactant
The starting point shown above, with a blank reactant and a blank product, indicates its readiness to be edited with the message double tap to edit displayed. As it suggests, double-tapping on the first of these two boxes will go directly to the editing screen for the reactant.
Alternatively, select the reactant by tapping it just once, which will highlight it:
Then select the edit molecular structure command from the button bank.
The molecular structure editing screen will be presented, starting from scratch. For an introduction to drawing structures with MMDS, see: Introduction to Drawing (iPhone). Draw the structure of 1-iodonaphthalene:
Save the diagram to return to the reaction editor, which should now look like:
Now that we have defined the structure, we may choose to name it as well. Notice that the selected reactant has a small question mark symbol underneath the structure:
Either double click on it, or activate the edit name of component command in the buttonbank:
This will bring up the naming panel. Enter the name, then press the Accept button.
The name of the reactant will now be displayed underneath the structure whenever it is selected.
Defining the Product
The product from this reaction is 1-vinylnaphthalene, which is similar to the starting material, so it is easier to start drawing the product by duplicating the reactant. Make sure the reactant is selected, then activate the copy command:
This will copy both the structure and name onto the clipboard.
Now select the product, and activate the paste command:
The product is now defined to have the same structure and name as the reactant. Edit the product structure, either by double-tapping the structure, or using the edit molecular structure command, and modify the structure so that the iodide substituent is replaced by a vinyl group. Edit the name as well:
Adding a Second Reactant
The second reactant is vinyltrimethylsilicon, which needs to be added to the scheme. Activate the add reactant command to create a second reactant:
The second reagent will appear as a blank entity:
Edit the structure and name:
The key components of the reaction have been defined, but the reagents are still missing. MMDS does not define any scientific difference between a reactant and a reagent, since the definition of these two concepts is highly circumstantial. There is just one distinction you need to be aware of: reactants and products are usually represented by structure, and reagents are usually represented by name.
Reagents are typically used for non-stoichiometric components such as solvents, catalysts and reactants that are used in excess, or species which are just not exotic enough to justify being drawn by structure.
Activate the add reagent command:
This will create a new blank reagent:
Reagents are shown in the general vicinity of the reaction arrow. Edit the name of the reagent, either by double-tapping on the text part, or selecting the edit component name command. The name should be changed to allylpalladium chloride. For bonus points, draw the structure of the reagent, which is a dimer:
Note that for reagents, the structure is only shown when the reagent is selected. This is because the name is the primary characteristic, which is the opposite of the case for reactants and products. For most reaction drawings, the reagent structure is not shown. Omitting the structure for a reagent is quite valid under some circumstances. If the reaction is only intended to be presented visually, drawing reagent structures is potentially unnecessary. For informatics purposes, though, all reaction components should have both structure and name whenever possible.
The second reagent, tris(dimethylamino)sulfonium difluorotrimethylsilicate, can be named by its common abbreviation: TASF. Once again, drawing the structure is optional, though certainly recommended for purposes of thoroughness:
Save the reaction:
The reaction editor will be closed, and control returned to the opening screen, which now shows the newly created reaction:
Stored reactions are displayed with three possible styles. The style used by the reaction editor shows all of the components, and interactively provides more information for the selected component. The style used by the main screen, shown above, is ultra miminalistic, due to size constraints: only the reactant and product structures are shown.
A medium level of detail is displayed when using the datasheet detail viewer. Click on the magnifying-glass icon for the reaction datasheet:
The entries are presented in a vertical top-down list, which currently includes just one reaction:
The reaction which was just completed shows the molecular structures for the reactants and products, and text annotations above and below the reaction arrow for reagents.
Once a reaction datasheet has been defined and populated with content, it can be used in the same way as for normal datasheets. Rows can be added, edited, inserted, deleted, moved, copied and pasted. The same interoperability features are available for reaction datasheets: when exported or emailed, a reaction datasheet will be encoded using the native XML format, as well as the MDL RDF format, which can be read by a number of third party programs. When applied to just a single row from a reaction datasheet, the MDL RXN format is also included. For incoming email or content downloaded from websites, the MDL RDF format can be imported by opening with MMDS.
Reactions can be described in MMDS by creating a reaction datasheet, then using the reaction editor to define the components of each reaction. A reaction consists of reactants, reagents and products, which are stored as distinct entities, each of which has a molecular structure and a name. Reaction datasheets behave in the same way as normal datasheets, except with a different editor and rendering scheme.