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Molkit

Functional Groups & Abbreviations

Molkit ships two libraries of chemistry shorthand: functional groups (OH, COOH, NO2 and others) and abbreviations (Me, Ph, Boc and others). You can place either as a compact text label or as a fully drawn structure, and you can collapse a 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:

RowButtons
Functional groupsOH, NH2, CH3, COOH, NO2, CN
AbbreviationsMe, Et, Ph, OMe, tBu, Ac

Clicking one makes it the active group and switches you to the Bond tool if you are not already on it (the Ring tool is also kept). Each button’s label is colored by its primary element, as it will render on the canvas.

The More flyouts

Each row ends with a More button that opens a flyout with the full library. The functional-group flyout lists 13 groups (OH, NH2, SH, CH3, COOH, CHO, NO2, CN, OCH3, COCH3, CF3, SO3H, CONH2); the abbreviation flyout lists 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”, OEt shows “Ethoxy”. Close the flyout with Esc or by clicking anywhere else.

Label or structure: the Abc/Str toggle

The Abc / Str toggle above the group buttons decides what placement produces.

With Abc (the default), the group becomes a single atom carrying a formatted text label. Click an existing atom to relabel it, or click empty space or drag from an atom to create a new labeled atom. Labels mirror to suit the bond direction, so CH3 becomes H3C when the bond comes in from the right and the bonded element stays next to the bond.

With Str, the group is placed as atoms and bonds. Clicking an existing atom grows a new bond at the best open angle and attaches the whole group; clicking empty space drops the group on its own. Single-atom groups such as OH only set the element, and implicit hydrogens complete the display.

Collapsing and expanding drawn groups

The right-click menu converts between a drawn group and a label at any time.

  • To collapse, select two or more atoms, right-click, and choose Collapse to Abbreviation…. Type a label (for example Ph, OMe or Boc) and confirm. Molkit uses the selected atom that bonds to the rest of the molecule as the attachment atom, stores the hidden atoms on it, and rewires any external bonds to the labeled atom.
  • To expand, select a collapsed atom, right-click, and choose Expand “label” (for example Expand “OEt”). The stored atoms and bonds come back at their original positions relative to the attachment atom, and external bonds are reconnected.

Each collapse or expand is one undo step. Expand appears only on a group you collapsed yourself. A label placed in Abc mode has no stored atoms, so it cannot be expanded; place the group in Str mode if you want the atoms.

To collapse and expand an ethoxy group

  1. Draw benzene, set the toggle to Str, open the abbreviation More flyout, and choose OEt.
  2. Click a ring carbon. An O-CH2-CH3 chain grows from it, giving ethoxybenzene.
  3. Select the oxygen and the two chain carbons, right-click, choose Collapse to Abbreviation…, type OEt, and confirm. The chain becomes a single atom labeled OEt.
  4. Right-click that atom and choose Expand “OEt”. The three atoms return where they were.

Formula and weight with collapsed groups

The status-bar formula readout counts only the atoms that exist on the canvas. A collapsed label contributes its attachment atom (plus implicit hydrogens) and none of the hidden atoms inside it, and the same is true of a group placed as an Abc label. Expand the group first when you need the correct formula or molecular weight.

See also