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Molkit

Mechanism Arrows

Mechanism arrows show electron movement in a reaction: the tail starts at an electron source and the head points at where the electrons end up. Molkit’s arrow tool snaps both endpoints to chemically meaningful targets and bows the arrow automatically, so a usable curved arrow comes out of a single drag.

Drawing a mechanism arrow

  1. Press A or pick the arrow tool, then choose Curved Arrow from its flyout menu.
  2. Press down near an electron source. The start point snaps to the nearest valid target within range.
  3. Drag to the destination and release. The end point snaps the same way, and the arrow bows into a curve on its own.

Valid snap targets, checked in this priority order:

  • Lone pairs, snapped to the exact dot position
  • Radical electrons (single dots)
  • Bond midpoints, using the visual midpoint of the drawn bond, not the raw atom-to-atom midpoint
  • Text annotation edges
  • Atoms

Snap tolerance scales with zoom, so targets stay clickable when you zoom out. While you drag near a target, the candidate highlights with a dashed ring, and small dots mark the available anchor points on nearby atom labels. Hold Shift to suppress snapping entirely and place a free endpoint; without a snap target, the drag angle snaps to 15 degree increments instead.

Auto-curving

Any arrow whose endpoint lands on a lone pair or radical is upgraded to a curved spline automatically, even if a straight type was selected. Bond-anchored arrows are also upgraded, except reaction-class types (reaction, equilibrium, retrosynthesis, double harpoon, arc) which keep their rigid stem geometry for bond attachments.

At creation, Molkit computes the curve’s control handles from the attachment geometry: the arrow leaves a lone pair or radical radially, exits a bond perpendicular to it, and bows between the two. You see this live during the drag preview. One special case is user visible: a reaction-class arrow anchored to a lone pair or radical still curves, because a straight stem would bury the arrowhead in the dot cluster.

Because endpoints store attachments (which lone pair, which bond) rather than fixed coordinates, the arrow follows its source and target when you move atoms or reposition lone pairs.

Full head vs. half head (harpoon)

By convention, a full arrowhead means a two-electron (pair) movement and a half-head harpoon means a one-electron (radical) movement.

Press H to cycle the arrowhead style: filled, harpoon up, harpoon down, then back to filled. This works on selected arrows (including multi-selection) or, with nothing selected and the arrow tool active, on the tool’s current configuration. With no arrow context, H switches to the pan tool instead.

The flyout menu also offers dedicated Curved Harpoon Up and Curved Harpoon Down entries. While the arrow tool is active, number keys pick types directly: 3 curved arrow, 4 straight harpoon up, 5 straight harpoon down (the straight harpoons become curved automatically when anchored to a lone pair or radical).

Adjusting the curve

After drawing, select the arrow to expose its control handles and reshape the bow; see Curved Arrows for handle editing and waypoints, and Arrow Beautification for the right-click auto-shaping actions (Beautify, Auto S-Curve, Symmetrize, Straighten, and others). Two quick fixes:

  • Press F with a single curved arrow selected to flip the bow to the other side of the chord.
  • Right-click the arrow for shape actions that recompute the curve while respecting the endpoint attachments.

See also