Getting Started Using Synapse
Applicability: Synapse

Welcome to Synapse !

Synapse is our chemical product design software package. With Synapse you can design new chemicals and new mixtures that possess specific physical properties.

This page provides a quick tour of some of Synapse's capabilities. Because Synapse contains all of the capabilities of Cranium, we recommend you also look through the Cranium introductory documentation: Getting Started Using Cranium.

Because you will be creating new entities, entering data and estimating properties, it is very important that you create and use a copy of a knowledge base.

Video: Designing Chemical Products

Tip: No copying needed in Reader version

The Reader version of Synapse does not allow you to make copies of documents. If you are using the Reader version you can edit the original document. The Reader version does not save any changes.

Example: Create a copy of a chemical design document
  1. Start the Synapse application. Synapse displays a welcome dialog.
  2. Press the welcome dialog’s Done button. Synapse will then display the Open file dialog.
  3. Select a chemical design document and press the Open button. You can choose the MKS Chemical Design Examples document that comes with the Synapse application. Synapse will open and display the selected design document.
  4. Choose the 'Save a Copy' command from the File menu. Synapse displays the Save As dialog.
  5. Choose a location and enter a name for the knowledge base copy, e.g., "MKS Chemical Design Examples - Work".
  6. Finally press the dialog’s Save button.

Synapse will save a copy of the current design document. Use the File menu's Open command to open this new copy.

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The 'mkscdd' extension denotes a Molecular Knowledge Systems Chemical Design document.
Tip: Use Save Copy command to make backups

The Save a Copy command is useful for quickly making a backup of your current document. Before you make significant changes to a document, you should consider using the Save a Copy command to make a backup.

Example: Go to the page displaying a specific function
  1. Click the left mouse button on the Functions Chapter tab located at the top of the window. Synapse displays a page of the Functions Chapter. (See documentation for the Chemical Function Chapter for details.)
  2. Choose the Navigation menu’s Goto command or press ctrl-g. Synapse displays the Go To Function dialog. (See documentation for the Navigation Menu and the Go To Entity Dialog for details.)
  3. Click the left mouse button on the "Vapor Pressure at 125°C [kPa]" function and press the OK button. Synapse turns to the page displaying the function's properties. (If you chose to work with another design document that does not contain the vapor pressure function, simply choose another function.)
Designing Chemicals

The goal of a chemical design is to assemble molecular structures that have physical properties that satisfy a set of design constraints. In a graphical design, the designer assembles the molecular structure manually while Synapse performs all the calculations needed to determine if its properties satify the design constraints. In a combinatorial design, the process is similar except that Synapse conceives of and assembles the molecular structures automatically.

Example: Graphically design a new chemical
  1. Click the left mouse button on the Graphicals Chapter tab located at the top of the window. Synapse displays a page of the Graphicals Chapter. (See documentation for the Graphical Chemical Design Chapter for additional details.)
  2. Navigate to the "Example Graphical Chem Design 001" design. (It may be the first design.)
  3. Scroll down to the Design Structures Section and the Constraints Section. These two sections provide the key inputs to the graphical design process.
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    Design Elements: this are the elements used to create new molecular structures.
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    Design Bond Types: this are the bonds that can be used to connect design elements.
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    Constraints Section: these are the physical property constraints that will be checked for each newly designed molecular structure.
  4. Click the left mouse button on the Commands menu and select the Design Candidates command. Synapse displays the Chemical Candidate design dialog.
  5. Draw the chemical structure for n-pentane. Push the atom button (large letter A) and click the left mouse arrow in the structure pane in five different places. Then push the bond button (diagonal line) and connect pairs of atoms together. Click the left mouse button on the first atom and then again on the second atom. (See the documentation for the Chemical Structure Edit Dialog for details on entering and editing molecular structure.)
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    Push the atom button (large "A") to add atoms to the editor pane.
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    Click the left mouse button on the editor pane to add atoms. Use the Element control to change the element of the atoms being created.
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    Push the bond button (diagonal line) to bond pairs of atoms together.
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    Click the left mouse button on the first atom of the pair and then on the second atom. Use the Bond control to change the bond's type.
  6. Press the Update button. Synapse will estimate the physical properties of the drawn structure, use these values to calculate the result of each design function and then use these function results to evaluate each design constraint. Design constraints and their values for the current structure are shown in the Constraints group.
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    Push the Update button to evaluate each design constraint.
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    For each design constraint, the dialog displays the constraint's name, range of valid values, goal value (blue diamond) and value for the current chemical candidate (green rectangle). A red arrow is displayed if the current value is lower or higher than the limits of the constraint's valid range.
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    If you check the Auto Update button, Synapse will automatically evaluate the design contraint whenever you draw a valid molecular structure in the edit pane.

    The constraint values (shown as green rectangles) for the boiling point and vapor pressure at 25°C are satisfactory - the values are between the lower and upper limits specified for these constraints. The value for the vapor pressure at 125°C is not satisfactory. The red arrow at the left of the contraint's axis indicates that the value is too low.

  7. Since some, but not all, of the constraints are satisified, we will save the current structure as an intermediate candidate. (An intermediate candidate does not need to satisfy all constraints. A final candidate must satisfy all constraints.)
  8. Press the Add button in the Intermediate Candidates control group. Synapse will activate the Candidate Name dialog.
  9. Press the Default button to insert the default name, add a comment in the Comment control and then press the OK button. Synapse add the new candidate to the list of intermediate candidates.
  10. Use the Element control to change the current element to fluorine.
  11. Add two fluorines to pentane's end carbon atom. If the Auto Update button is checked, Synapse will automatically reevaluate the constraints and redisplay their resulting values. If the Auto Update button is not checked, press the Update button.
  12. Synapse will redisplay the design constraints. All constraints are now satisified. Thus, 1,1-difluoropentane can now be added to the final candidates list.
  13. Continue trying additional structural varitions to identify additional intermediate and final candidates. When you are done, press the dialog's Save button. Synapse will store these candidates into the current design document.
Example: Combinatorially design chemicals

In a combinatorial design, the Synapse will automatically create molecular structures and perform all the calculations needed to evaluate their feasiblity.

  1. Click the left mouse button on the Combinatorials Chapter tab located at the top of the window. Synapse displays a page of the Combinatorials Chapter. (See documentation for the Combinatorial Chemical Design Chapter for details on this chapter.)
  2. Navigate to the "Example Combinatorial Chem Design 001" design.
  3. Click the left mouse button on the Commands menu and select the Design Candidates command. Synapse displays the Combinatorial Chemical design dialog. (See documentation for the Combinatorial Chemical Design Dialog for details on this dialog.)
  4. Simply press the Start button. Synapse generates molecular structures, estimates physical properties, calculates function results, evaluates constraints and presents these results graphically in the design dialog.
  5. Once the combinatorial design is complete, press the Save button. Synapse will store the list of updated final candidates into the current design document.
Related Documentation

Please follow the links below for additional documentation on editing molecular structures and designing chemicals: