Lone Pairs
Lone pairs render as a pair of dots next to an atom. Molkit places them automatically in the open space between bonds, and you can override the angle by dragging. Lone pairs are also the highest-priority snap target for mechanism arrows, so adding them first makes electron-pushing diagrams easier to draw.
Adding lone pairs
Select the Electrons tool in the toolbar (the two-dot icon) or press L. The button has a flyout with two subtypes; pick Lone Pair (the other is Radical).
Click an atom to add one lone pair. Each click adds another, up to the atom’s electron-domain limit:
- Period 2 elements (C, N, O, F, B, Be, Li) allow 4 domains total, following the octet rule.
- All other elements allow 6 domains, permitting expanded octets.
The maximum lone pair count is the domain limit minus the number of bonds. Clicking again once the atom is full cycles the count back to zero, so you can clear an atom by clicking through the maximum.
Clicking empty canvas with the tool creates a standalone lone pair annotation you can position freely. This is useful for diagrams where the dots are not tied to a drawn atom.
Automatic placement
In the default auto mode, positions are computed at render time. Molkit finds the gaps between the atom’s bond directions (an implicit hydrogen label also counts as occupied space) and places each lone pair at the center of the largest gap. On an atom with no bonds, pairs start at the top and spread evenly. Because positions are recomputed on every render, lone pairs move out of the way when you add, delete, or rotate bonds.
Manual angle override
To set the angle yourself, press on the atom with the Electrons tool and drag outward more than a few pixels. A preview follows the cursor and, when Smart Guides are on, shows snapping to VSEPR-style angles (the bisectors of the gaps between bonds). On release the angle always snaps unless you hold Shift, which commits the free angle. Releasing switches the atom to manual mode; lone pairs already placed in auto mode keep their current positions.
Removing lone pairs
Use the Eraser tool and click a lone pair to remove it; see Eraser. On a manually placed atom this removes the specific dot pair you clicked. In auto mode it lowers the count by one. You can also select lone pairs with the Select tool and press Delete.
Mechanism arrows
When you draw a curved mechanism arrow, lone pairs are checked before radicals, bonds, and atoms as snap targets. An arrow anchored to a lone pair stays attached when the atom moves, and its endpoint handle aligns radially so the arrow leaves the dots in a natural arc. See Mechanism Arrows.
Display and styling
Structure, then Display, has a Show Lone Pairs toggle that hides or shows all lone pairs without deleting them (on by default). With a lone pair selected, the properties panel offers a style choice (Dots, Lines, or Lobes), size, dot spacing, distance from the label, and color modes including element color and per-dot custom colors.