Chemical symbols and orbitals

Implementation notes and historical checks. Open the visual guide →.

Chemical symbols add charges, radicals, lone pairs and other marks to atoms or to the page. Orbitals are editable drawing shapes that can snap to an atom.

Use it

Add a mark to an atom

1. Open the Chemical symbols palette button and choose a symbol. It offers 20 choices: circled and plain charges, radicals and diradicals, lone pairs and bars, radical ions, H-dot and H-dash, attachment diamond, star, wave and bead, single and double daggers, and partial positive (δ+) and partial negative (δ−).
2. With Attach to atoms on, click an atom to add the mark. The symbol tool stays active for more placements; press Escape or choose another tool to stop. Drag from the atom to choose its side: the mark orbits the atom in 15° steps, just outside the label with the same gap a click uses. Hold Option/Alt or Shift to place it at any offset.
3. To adjust marks later, select the atom and choose Position atom marks. Drag a mark’s handle to move it around the same orbit; Option/Alt or Shift frees it. While dragging, a dashed line shows the orbit and dots show the 15° positions it can take. Rotate turns a mark by 45°, and Remove deletes it.

A lone pair or bar always turns across the line from the atom, so its two dots sit side by side around the label, also when placed freely. Charges and radicals stay upright.

Charges and radicals change the atom’s chemistry, and ReShiki refreshes its hydrogen label and unpaired electrons. Lone pairs, bars and partial charges are annotations only. Partial charges leave formal charge and valence unchanged; choose them explicitly when a figure needs to emphasize charge distribution. Marks move, copy and transform with their atom, take the atom label’s color, and each edit is one Undo step. Rotating or flipping a molecule turns its lone pairs with it; formal and partial charges stay upright. Diradical dots have a wider separation than lone-pair dots.

Draw an orbital

1. Open the Orbitals palette button and choose s, sigma, single lobe, p, sp³ hybrid, dxy or dz².
2. Drag from the node to set size and direction; Shift keeps the direction at 15° steps. A click uses one default bond length.
3. Choose outline, solid or flat-gray phases in Properties. Multi-lobe orbitals can reverse their phases.

Snap to atoms in the context row snaps the orbital’s node to the nearest atom. A green ring marks the chosen atom. Hold Option/Alt to place an orbital freely. An orbital stays a drawing object; group it with the molecule when they should move together. Orbital lobes are always drawn whole. An atom label that a lobe reaches is drawn on top of the orbital inside a thin halo of the paper color, so the label stays readable over filled lobes.

Limits

• Lone pairs do not change valence, electron counts or orbital occupancy.
• H-dot, H-dash and attachment markers are free symbols. They do not define hydrogen stereo, R-groups, polymers or reaction attachment points. Draw an explicit H atom and a stereo bond for hydrogen stereochemistry.
• Very crowded drawings may still need lone pairs placed by hand.
• Gray fill is flat, not gradient shading. Gradient-shaded orbitals cannot be imported.
• Some marks need a .rsk file or SVG, PDF or PNG; CDXML export rejects them. See Persistence and exchange.

Implementation notes

JACS / ACS remains the default: Arial 10 pt, black, 14.4 pt bonds and 0.6 pt lines. New restores those settings even after changing tool styles. Properties previews the actual styled geometry. Free symbols are ordinary selectable graphics. Charge changes release imported implicit-label hydrogen counts so ammonium can become ammonia again. Removing a mark clears its represented charge or radical state.

Click-created lone pairs and bars sit just outside the visible label ink, with a modest gap scaled to its font size. New placements try the top, left, bottom and right sides, avoiding nearby label ink, bonds and existing atom marks. Pairs beside the label turn vertically. Click-created charges and radicals keep their usual side when it is clear; otherwise they try the nearest 15° steps, avoiding bond ink, nearby labels and existing marks after the changed charge’s hydrogens are refreshed. Saved marks keep their exact offsets. A dragged mark’s orbit follows the label at the same gap a click uses, measured from the label’s outline: each glyph counts as a rounded rectangle fitted to its outline (O is nearly round, while N and H keep the corners their stems reach), and the glyphs together form one convex shape, so OH reads as one rounded label with its hydrogen. The mark counts as one shape too, so a lone pair keeps the gap like the box a click measures. The gap therefore stays even all the way round, and straight up is exactly where a click puts a pair. Steps where the mark would touch one of the atom’s bonds are skipped: the drag lands on the nearest clear step, and the guide leaves those steps out. Other marks are not avoided, so dragging one mark onto another is allowed. A free (Option/Alt or Shift) drag keeps the exact requested offset, bonds included; existing saved marks do not move when labels or styles change.

Snap to atoms controls orbital node snapping independently of chemical-symbol attachment. The choice stays selected when switching tools in the current document; New restores snapping. Option/Alt places freely inside the snap radius, and the drag preview names the snapped target or free placement.

Orbital fills and outlines are never cut around atom labels. When a lobe’s fill or outline comes within 1 pt of visible atom-label ink (including hydrogen, isotope and charge labels), that atom’s label and its attached marks are drawn above the orbital inside a halo in the paper color. The halo follows the glyphs: each glyph is filled and stroked 1 pt wider, and the middle of each glyph’s ink box is covered too, so the inside of an O stays clear. The rule is the same for the orbital’s own atom and for neighboring atoms, and for orbitals behind molecular content (the default) or in front of it. A label reached only by orbitals behind the molecule keeps its usual place above the bonds. Otherwise each reached label is drawn right above the topmost front orbital that reaches it, so graphics stacked above that orbital still cover it, and a click on the label selects what is drawn on top. Clicking these visible labels selects their atom through a foreground orbital. The atom positions, orbital node, axes and layer remain exactly as placed, and the halo follows later label edits. Bonds, text captions and other annotations keep their ordinary layering against orbitals.

The canvas and exports with a background (SVG, PDF, PNG and EMF files) paint the halo in the canvas background color. Transparent output, such as copied SVG, PDF and PNG, paints no paper: the halo shape is knocked out of everything drawn beneath the label (an SVG mask, a soft mask in PDF), so whatever lies behind the pasted drawing shows through and the surround stays transparent. EMF has no soft masks, so a transparent EMF paints the halo in the canvas background color instead. SVG readers that ignore masks show the label over the whole lobe without a halo.

Persistence and exchange

• Document format 8 keeps orbital parameters, phases and atom-owned marks; earlier document versions still open.
• Canvas, SVG, PDF and PNG use shared vector geometry, including differently filled orbital lobes and rotated marks.
• SMILES/MOL/CDXML keep supported one/two-unpaired-electron chemistry; molecular formats omit drawing annotations.
• An atom with two nonbonding electrons is a triplet unless Atom details → Spin state marks it singlet. .rsk, MOL (RAD 1/RAD 3, V2000 and V3000) and CDXML (Radical="Singlet"/"Triplet") keep the spin state; SMILES and InChI cannot. Both states draw the same two dots, and Molecular properties counts a singlet as 0 unpaired electrons.
• Partial charges export to CDXML/CDX as uninterpreted δ+ / δ− text. An attached partial charge becomes a free caption in those formats; .rsk retains its atom attachment. A stretched or mirrored free partial charge exports as upright, unstretched text.
• Other free symbols and orbitals export to CDXML/CDX as grouped editable vector curves with whole lobes. A front orbital that reaches an atom label is stacked just behind the molecule, so the reading application draws the labels (and, unlike the canvas, the bonds) over it, and a re-import places the curves behind the molecule too. No halo shapes are written: they would become stray editable objects. Importing those vectors keeps their appearance, but not their parametric orbital/symbol controls or the halo.
• CDXML plain/solid orbital and supported free-symbol objects import as editable ReShiki objects. Gradient-shaded orbitals are rejected explicitly.
• CDXML atom-owned single charges, radical dots and supported lone pairs use represent ownership links. Carbon lone-pair annotation export is rejected because an external drawing application interprets it as diradical chemistry. Positioned multiple-charge marks, combined radical-ion marks, bars and colored attached marks require .rsk/SVG/PDF/PNG; unsupported per-symbol CDXML overrides are rejected. External saves can discard ownership of distant marks, so export requires marks within 1.05 label sizes of their owner’s label ink (of the atom itself when it has no label), so orbited marks beside hydrogens still export, and closer to that atom than any other atom. A visible atom label and hydrogen count are written explicitly.
• Template attachment rejects marked or radical anchor atoms; free insertion of these templates keeps their full drawing.

This is a bounded drawing/chemistry subset, not complete chemical-symbol or orbital parity. Arbitrary mark colors/sizes in the inspector, gradient shading, orbital fixed-length constraints and 3D orbital semantics remain incomplete.

Records

The original symbol checks record the first build’s fixtures, desktop checks and tests.