Radicals
A radical is an unpaired electron, drawn as a single dot next to an atom. The Radical tool adds dots one at a time in the largest open gap around the atom, and you can drag a dot to a custom angle. Radical dots also serve as start and end anchors for mechanism arrows.
To draw the methyl radical, place a carbon, press . for the Radical tool, and click the carbon once. The carbon now counts three implicit hydrogens instead of four.
Activating the tool
Click the Electrons button in the toolbar and choose Radical from the flyout (the same flyout holds Lone Pair), or press . (period).
Adding radicals
Click an atom to add one radical electron. Each click adds another dot, up to the atom’s available electron domains: bonds and lone pairs count against the same budget (4 domains for period 2 elements such as C, N, O, and F; 6 for heavier elements). Clicking past the maximum resets the atom to zero dots.
Clicking empty canvas places a standalone radical dot that is not attached to any atom. Use this for free electrons in a scheme.
Placement angle
New dots are placed automatically in the largest open gap between the atom’s bonds and lone pairs. On a bare atom, dots distribute evenly starting from the top.
To set the angle yourself, press on the atom and drag outward more than a few pixels. The dot follows the cursor and snaps to suggested angles based on the atom’s geometry; a snap circle previews the candidate positions. Hold Shift while dragging for free placement with no snapping. Once any dot has a manual angle, the atom keeps manual angles for all its dots.
Clicking an existing dot with the Radical tool cycles its fine position between centered on the angle and offset to either perpendicular side.
Removing radicals
Click a dot with the Eraser tool to remove only that electron, or select a dot with the Select tool and press Delete. Cycling an atom past its maximum also clears all of its dots.
Structure > Display > Show Radicals toggles radical visibility document-wide without deleting anything.
Radicals in Molkit’s chemistry
The chemistry engine counts radical dots as electrons. Each one takes the place of an implicit hydrogen, counts as a non-bonding electron in the formal charge (valence electrons minus bonds minus lone-pair electrons minus radical electrons), and counts toward the octet. A methyl radical drawn as a carbon with one dot is therefore CH3, not CH4.
For geometry, each unpaired electron counts as one non-bonding electron domain. The nitrogen of nitrogen dioxide (two bonds to oxygen, one unpaired electron, no lone pair) has three domains, so it is sp2 and bent. A single electron repels less than a bonding pair, so the O-N-O angle opens past 120 degrees; Molkit uses the measured NO2 angle of about 134 degrees. See Geometry and Hybridization.
Radicals and mechanism arrows
When you draw a mechanism arrow near a radical dot, the endpoint snaps to the dot and stays attached as the molecule moves. Arrows anchored to a dot curve out radially from the atom, which matches the convention for single-electron (fishhook) movement. See Mechanism arrows for arrow types and attachment editing.