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Molkit

Functional Groups & Abbreviations

Molkit ships two libraries of common chemistry shorthand: functional groups (OH, COOH, NO2, …) and abbreviations (Me, Ph, Boc, …). You can place either as a compact text label or as a fully drawn structure, and you can collapse any group you have already drawn into a label and expand it back later.

Picker buttons

The element picker on the right edge of the canvas has two shorthand rows below the element buttons:

  • Functional groups: OH, NH2, CH3, COOH, NO2, CN
  • Abbreviations: Me, Et, Ph, OMe, tBu, Ac

Clicking any of these selects it as the active group and switches you to the Bond tool if you are not already on it (the Ring tool is also kept). Labels on the buttons are colored by their primary element, matching how they will render on the canvas.

The More flyouts

Each row ends with a More button that opens a flyout with the full library:

  • Functional groups (13): OH, NH2, SH, CH3, COOH, CHO, NO2, CN, OCH3, COCH3, CF3, SO3H, CONH2
  • Abbreviations (25): Me, Et, nPr, iPr, tBu, Ph, Bn, OMe, OEt, Ac, Bz, Boc, Cbz, Fmoc, TMS, TBS, TIPS, Ts, Ms, Tf, PPh3, OAc, NMe2, CO2Me, CO2Et

Hover an abbreviation to see its full name (Boc shows “tert-Butoxycarbonyl”, and so on). Close the flyout with Esc or by clicking anywhere else.

Label vs. structure: the Abc/Str toggle

The Abc / Str toggle above the group buttons controls what placement produces:

  • Abc (label, the default): the group is placed as a single atom carrying a formatted text label. Click an existing atom to relabel it; click empty space or drag from an atom to create a new labeled atom. Labels mirror automatically based on bond direction, so CH3 becomes H3C when the bond comes in from the right, keeping the bonded element next to the bond.
  • Str (structure): the group is placed as real atoms and bonds. Clicking an existing atom grows a new bond at the best open angle and attaches the full group. Clicking empty space drops the group standalone. Single-atom groups like OH simply set the element and let implicit hydrogens handle the display.

Collapsing and expanding drawn groups

You can convert between drawn structure and label at any time with the right-click menu:

  • Collapse: select two or more atoms, right-click, and choose Collapse to Abbreviation…. Enter a label (for example Ph, OMe, Boc). Molkit picks the attachment atom automatically (the selected atom that bonds to the rest of the molecule), stores the hidden atoms on it, and rewires any external bonds to the labeled atom.
  • Expand: select a collapsed atom, right-click, and choose Expand “label”. The stored atoms and bonds are recreated at their original positions relative to the attachment atom, and external bonds are reconnected.

Each collapse or expand is a single undo step.

Formula and weight caveat

The status-bar formula readout counts only the atoms that actually exist on the canvas. A collapsed label contributes just its attachment atom (plus implicit hydrogens); the hidden atoms inside the label are not counted. The same applies to groups placed in Abc label mode. Expand the group first if you need an accurate formula or molecular weight.

See also