Path View

By default, the analysis opens in Path View, where the pathways are presented individually in a list and ranked by path score.

Path Rank

The result pathways are ranked by path score, from the lowest score to the highest. Path scores are calculated by scoring functions governed by the criteria selected to run the analysis. Scoring functions assign penalties for undesirable elements in pathways. Therefore, lower scores are more desirable.

Each pathway is then assigned a unique invariable number, the path rank, starting from 1, and increasing in order of increasing path score. Path rank can be found on top of each pathway, in the lavender header. The number of steps is also listed next to the path rank. 

Building Blocks View

By default, the result pathways for automatic retrosynthesis analyses are presented in Building Blocks View. Building Blocks View allows a quick assessment of the disconnection pattern that has been used to build the pathway. 

The target molecule is displayed on the left. The bonds that are formed during the synthesis are colored in black and marked by a hashtag sign next to them. The other bonds are colored in sections representing the contribution of the different building blocks to the construction of the molecule. The starting materials corresponding to each building blocks are listed on the right of the target molecule and colored in matching colors. 

When a starting material is commercially available, the price per gram is displayed on top of the structure. Price per gram is based on buying research quantities and calculated as the median of the pricing for all catalogue entries. In case the starting material is also a Greener Alternative Product, a green icon is displayed next to the price.
>> Greener Products & Solutions

Click any starting material to open the corresponding molecule card. (See “Molecule Cards” for more details.)

Click the target molecule to open the disconnection card for the corresponding pathway, and see which reaction is used to form each of the disconnected bonds. Hover over a disconnected bond to see the reaction name. Alternatively, you can select a reaction name from the list on the right to have it displayed next the corresponding bond disconnection.

The Path Rank and the number of steps for the pathway can be found on top of the target molecule tile. You can navigate to the previous or next path in the list by using the arrows in the control at the lower right of the target molecule. The order of the pathways is determined by the sorting order and filters used in path view before expanded path view was opened.

Close the disconnection card by clicking on the ‘X’ at the top right of the window, or by pressing the ‘Escape’ key.

Pathway View

Pathway View is the second option to view the list of result pathways under the Path tab. In this view, full reaction schemes are displayed for each pathway. Pathway View can be enabled by clicking on the toggle above each pathway. Alternatively, clicking on the toggle in the white header on top of the pathway list will activate it for all pathways. 

Each pathway is presented as a reaction scheme from the starting materials to the target compound. The reaction name and typical conditions are shown above the reaction arrow. Links for illustrative references are displayed under the reaction arrow for published reactions originated from the SPRESI and Enzyme-catalysed reaction databases. Price per gram is displayed below the structure of commercially available compounds.

Additional tags provide further information on compounds and reactions. See the “Path View Legend” section below for more details.

You can move the reaction scheme using your mouse to drag it in any direction, or use you mouse wheel to zoom in and out. Click on any molecule or a reaction name to open the molecule or reaction card. (See “Molecule Cards” or “Reaction Cards” for more details.)

Hover over any colored reaction arrow to see a label indicating whether the reaction is nonselective or diastereoselective only (red arrows), or whether it is suggested as part of a Strategy or Power Search option (green arrows). 

Expanded Path View

Expanded Path View can be accessed either from Building Block View or from Pathway View, by clicking the Expanded Path View icon, at the top right of each pathway. 

Expanded Path View gives you a close-up detailed view of one individual pathway. The pathway is presented exactly as it is presented in Pathway View.

The path rank is listed on the upper left of the screen, next to the ‘Shop now’ icon, which allows you to add the commercial compounds in the pathway into your Shopping List (See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy). 
>> Shopping List

As in Pathway View, you can move the reaction scheme using your mouse to drag it in any direction. Zoom in and out using the controls at the lower right of the screen or your mouse wheel. Click the ‘Reset’ icon to return to the default view.

You can navigate to the previous or next path in the list by using the arrows in the control at the upper right of the screen. The order of the pathways is determined by the sorting order and filters used in path view before expanded path view was opened.

Close expanded path view by clicking on the ‘X’ at the top right of the screen, or by pressing the ‘Escape’ key.

Path View Legend

Click the ‘Legend’ icon to open a panel which shows the key for the pathway tags.

Similar reactions

The book tag under reaction arrows indicates that published reactions similar to the suggested reaction in the pathway have been found. The number of stars in the book specify how closely similar the published reactions are to the suggested reaction.

• Three stars and a ‘100’ badge: the suggested reaction is a published reaction or has a matching published reaction
• Two stars: most similar reactions have a similarity score of 0.5 or over
• One star: most similar reactions have a similarity score under 0.5 

Click the book tag to open the Similarity tab of the Reaction Card. (See “Reaction Cards” for more details.)

Add to Shopping List

For commercially available compounds, click ‘Shop now’ to add the compound into your Shopping List (See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy). 

Reaction arrows

Hover over any colored reaction arrow to see a label indicating whether the reaction is nonselective or diastereoselective only (red arrows), or whether it is suggested as part of a Strategy or Power Search option (green arrows). 

Add to Shopping List

For commercially available compounds, click ‘Shop now’ to add the compound into your Shopping List (See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy). 

Reaction arrows

Hover over any colored reaction arrow to see a label indicating whether the reaction is nonselective or diastereoselective only (red arrows), or whether it is suggested as part of a Strategy or Power Search option (green arrows). 

Compound tags

Compound tags are hexagon shaped and give additional information about the compounds in a quick glance. 

Published Molecules: A Book tag next to a compound indicates that the compound is included in our databases of published compounds. The number in the badge is the popularity score of the compound, or the number of times it has been included in a published reaction. It is possible for a published compound to have a popularity score of 0, if it has been described in scientific literature but not in a synthesis (examples: metabolites, isolated natural compounds, virtual compounds claimed in a patent). Compounds included in our commercial databases also display their price per gram below their structure.

Protection Requirement: Compounds displaying a Shield tag require protection of at least one of their functional groups for the suggested reaction to proceed. Click on the molecule to open the Molecule Card and find more information on protection requirements.

Regulated Substances: Compounds with a Warning tag are included in one of the lists of regulated substances from governmental agencies. Click on the molecule to open the Molecule card and find which agencies are listing the compound.

• Australia group: list of controlled chemical weapons precursors
• Department of Homeland Security: list of chemicals of interest monitored by the DHS for counter-terrorism purposes
• Environmental Protection Agency: list regulated substances that may cause serious adverse effects to human health or the environment if accidentally released
• Environmental Protection Agency List of Lists: consolidated list of hazardous chemicals subject to reporting requirements

Inventory Compounds: Compounds available in a custom on the user’s site are marked with a Chemistry Glassware Set tag. For more information on custom inventories, please refer to the "Inventory" section.
>> Inventory

Path View Settings

In the Settings panel, you can enable the path score to be displayed next to the number of steps for each pathway. 

Path scores are calculated by scoring functions governed by the criteria selected to run the analysis. Scoring functions assign penalties for undesirable elements in pathways. Therefore, lower scores are more desirable.

Path View Preferences

There are a few options allowing you to customize how you see your results in Path View.

Pathway Options

Open the Pathway Options dropdown menu to select how much information you want to see displayed in your Pathway View or Expanded Pathway View. 

Sort Pathways

Use the Sort By menu to select one of the following options to sort your pathways:

• Path rank
• Number of steps (protection and deprotection steps will not be considered in the total number of steps)
• Number of protection steps
• Similarity to published reactions
   

You can toggle between ascending or descending order by clicking the ‘Sorting Order’ icon.

Pathway Actions

You can find a series of pathway actions at the right of the ‘Pathway View’ toggle in each pathway header.

Favorite pathway: Click the ‘Favorite’ icon to save this pathway as a favorite. 

Download pathway: To export a pathway, open the three-dot menu, select Download, and choose your preferred format from the menu.

• Report (PDF): Generates a PDF report including the analysis parameters, the pathway node scheme, and a description of each reaction (reaction scheme, protection requirements, typical conditions, and illustrative references)
• Image (SVG): Saves an image of the pathway as it is displayed in Pathway View
• Reactions (RDF): Generates a Reaction Data File (RDF), which saves reactions in mol file format with all associated data

Add to Shopping List: Open the three-dot menu and select ‘Add to shopping List’ to add the commercial compounds in the pathway to your shopping list.

Note: See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy. You can then either export your list as a csv file, or directly to your Sigma-Aldrich® catalog e-commerce account. 
>> Shopping List