Plan Options

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The default options for retrosynthesis plans are:

Synthetic Depth

Synthetic depth limits the number of synthetic steps allowed in a retrosynthesis plan by setting a maximum of four steps for the longest pathway. The retrosynthesis analysis along a synthetic pathway terminates when it reaches either a starting material or the synthetic depth limit. All retrosynthesis plans, whether they terminated at starting materials or reached the synthetic depth limit, will be shown. Setting the parameter's value higher increases the likelihood of finding synthetic pathways that arrive at starting materials at all pathways, but it also gives rise to longer search times.

The default synthetic depth of three steps is a good starting point as it offers a balance between realistic synthetic requirements and computational costs.

SF-Retrosynthesis-PlanOptions-SyntheticDepth.png

It should be noted that some plans may show a synthetic depth greater than the depth you specified; this is because intermediate structures may be found in another retrosynthetic pathway or in other search trees. Thus, the retrosynthesis plan found previously will be reused and sometimes expanded.

Break and Protect Bonds

Bond-breaking restrictions are a useful means to submit more concrete retrosynthesis queries to prune the proposed pathways and to guide the search and control the size of the solutions space. You may break a single bond or protect multiple bonds in the target molecule.

To break a specific bond:

  1. Click the Break Bond button.
  2. Click the bond in the structure to break. The bond selected to break appears highlighted in green.

    SF-Retrosynthesis-PlanOptions-BreakAndProtectBonds.pngNote: To select a different bond, click the Clear All Bond Selections link or click the highlighted bond in the structure.

To protect bonds:

  1. Click the Protect Bond button.
  2. Click the bond(s) in the structure to protect. The protected bonds appear highlighted in red.

    SF-Retrosynthesis-PlanOptions-BreakAndProtectBonds-Protect.png

Notes:

  • To clear all selections, click the Clear All Bond Selections link.
  • To clear a single selection, click the highlighted bond in the structure.

Important: A protected bond will not be broken completely during the retrosynthesis analysis, but the bond order may still change.

Rules Supporting Predicted Reactions

Reaction rules are triggered according to the number of literature examples supporting them:

  • Common rules include reaction types that are frequently used in the lab. They are considered both robust and versatile, and are supported by many literature examples.
  • Uncommon or Rare rules are supported by fewer examples, but may potentially expose more novel synthetic approaches.

Note: Your search speed could decrease by selecting Uncommon or Rare rules.

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Starting Material Cost Limit

For each step in the plan, the retrosynthetic search compares precursors to commercially available compounds. A plan terminates when it reaches either a starting material's cost limit or the synthetic depth limit. The default limit is $1,000 USD/mol or $10 USD/g.

Note: The cost limit at which a plan is run is retained for further plan generation.

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