Views and Resonance

A single species can be drawn several ways: a Lewis structure, a VSEPR sketch with wedges and dashes, a condensed formula, a bond-line drawing, or a Fischer projection. In Molkit you can tag each drawing with the kind of view it is (its category), have the missing views drawn for you, and group related drawings into resonance sets and visual sets. The commands are in the Structure menu and the right-click canvas menu.

Every command here works on the current selection. Most need exactly one connected structure with at least two atoms selected. In the Structure menu, an item that does not apply is dimmed and its tooltip gives the reason, for example “Select a single structure to derive another view.” The right-click menu shows only the items that apply to what you have selected.

Set Category

Structure > Set Category tags the selected structure with one of Lewis, VSEPR, Condensed, Bondline, or Fischer. Clear Category removes the tag and is dimmed when the structure has none. The tag appears right away as a small blue label at the top-left of the drawing, such as LEWIS or VSEPR.

The right-click Set category submenu offers the same choices plus two Lewis layouts:

Lewis (square): a schematic Lewis structure drawn on a 90 degree grid. The label reads LEWIS (SQUARE).
Lewis (angled): a Lewis structure drawn with realistic bond angles. For a planar species the label reads LEWIS (ANGLED) + VSEPR, because a flat drawing with real angles already shows the shape.
Lewis + VSEPR (planar): offered only when the species is planar (water, nitrate, BF3). The label reads LEWIS + VSEPR.

The active category has a check mark. Clicking the checked entry again removes the tag.

Derive View

Structure > Derive View draws a new copy of the selected structure in another view. The new structure is tagged with its category, and the whole operation is one undo step. The right-click Derive view submenu offers the same views plus Orbital picture.

Where the copy goes depends on the source:

A loose structure gets the copy to its right, top-aligned. Deriving the same view again places the new copy to the right of the earlier one instead of on top of it.
A structure in a named group (a named selection, or a set holding two or more forms) gets the copy at the group’s right end, level with the source and at the spacing the group already uses, and the copy joins the group as a new form. A named molecule that a derived view joins becomes a visual set, with the source as its first form.

Nothing else on the canvas is moved out of the way, so a copy can land on top of other drawings.

To derive a Lewis structure of acetic acid

Draw acetic acid in bond-line form (CH3-COOH, with the OH written as a label or drawn as an atom).
With the Select tool, drag a box around the whole structure.
Choose Structure > Derive View > Lewis.

A second drawing appears to the right of the first. Every hydrogen is drawn as an atom, a label such as OH is expanded into its atoms, and a blue view label at its top-left marks it as a Lewis structure. Press Ctrl+Z once to remove it.

The views you can derive

Menu item	When it is offered	What it draws
Lewis	Always.	Condensed labels such as `OH` or `CH3` are expanded and every hydrogen is drawn. A label that cannot be expanded (`R`, `Ts`, `Boc`) stays as written and gets no extra hydrogens or lone pairs. The hydrogens of a CH2 or CH3 group sit on the angles the bond tool snaps to. The Structure menu gives the angled layout; the right-click menu offers `Lewis (angled)` and `Lewis (square)` separately when the structure, with its labels expanded, has no ring and no atom with more than four neighbours, and a single `Lewis` otherwise (so a `Ph` label gets no square layout).
VSEPR	When the selection does not already look like a VSEPR drawing.	A 3D geometry drawn with wedge and dash bonds, with terminal groups folded into labels such as `CH3` and `OH`.
Condensed, Bondline	When there is a carbon skeleton: two or more carbons, or one carbon bearing hydrogens or bonded to another heavy atom. Water and ammonia do not qualify.	The condensed formula or the bond-line drawing. A label you wrote, such as `R`, `Ph`, `COOH` or `OTs`, stays as written. Deuterium stays drawn in bond-line and reads `CD3` in condensed. Condensed formulas place every branch and write a left-hand methyl as `H3C`.
Orbital picture (right-click only)	When one structure is selected.	A copy with an orbital picture built on it, labelled `ORBITALS`. A structure with hydrogens that are not drawn is copied as its Lewis structure, so the hydrogens get orbitals. If there is nothing to draw (p orbitals only on a structure with no pi bond), no copy is left.
Fischer Projection	When there is an open (acyclic) carbon chain, at least one heteroatom and a stereocenter. For an achiral molecule such as ethanol, a message says there is no stereocenter to depict and nothing is added.	A Fischer projection with terminal methyls written as `CH3` and no lone pairs.
All Applicable	When at least two views would be drawn.	Every applicable view not already present, in one row to the right (orbital pictures are not included). The original and the new drawings are then grouped into one visual set (see below) and selected, so you can drag the set into place. For a structure already in a named group, the new views join that group instead. A planar species gets no separate VSEPR drawing, because the angled Lewis structure already shows its shape.

The angled Lewis and bond-line views keep each double bond cis or trans as drawn, and bond-line keeps each stereocentre’s R or S however the source was drawn. A stereocentre marked only by a wedged or dashed hydrogen keeps its mark on a heavy bond when bond-line removes the hydrogen.

Whether a species counts as planar decides whether it gets a separate VSEPR drawing. Allene, hydrogen peroxide and disulfides are not treated as planar, and an atom with no drawn lone pairs counts the pairs its valence leaves, so a bare NH3 is not read as trigonal planar.

VSEPR and Fischer derivations need the 3D chemistry engine to load. If it cannot build a 3D geometry (for example, a structure with generic R groups), you get a warning and nothing is added.

Resonance sets

A resonance set tells Molkit that several drawings are resonance contributors of one species.

Marking a resonance set by hand

Draw two or more contributors as separate structures with a double-headed straight arrow between them. Select the structures and the arrows, right-click, and choose Mark as Resonance Set. The arrow is required: it is what asserts the resonance. Molkit draws a violet box around the set with a bold Res tag, and suggests a weight for each form (equivalent, major, or minor) from standard rules: complete octets, fewer and smaller formal charges, and negative charge on the more electronegative atom. These are qualitative rankings, not percentages. To undo the grouping without deleting anything, select the set and choose Unmark Resonance Set; the box stays as a plain named selection.

The resonance arrow checkbox

When you select a straight arrow with a head on both ends, the shape properties panel shows a Resonance arrow checkbox. It flags the arrow as a resonance arrow without changing how it looks. Marking a resonance set checks it for you.

Generate Resonance Forms

Select one symmetric ion with a single delocalized pi bond, such as carbonate, nitrate, nitrite, a carboxylate, phosphate, or ozone, and choose Structure > Generate Resonance Forms. Your drawing becomes the first form; Molkit adds the others in a row to its right, each with its own copy of your brackets and charge label, joins them with double-headed arrows, and marks them as an equivalent resonance set. Ions with more than one pi bond on the central atom (for example sulfate drawn with two S=O bonds) are not handled.

Generate Octet Resonance Forms

Select an expanded-octet species such as SF6, PF5, XeF4, or ClF3 and choose Structure > Generate Octet Resonance Forms. Molkit writes the octet-respecting ionic forms, in which some bonds are replaced by a fluoride ion so the central atom has only four electron domains: SF6 gives 15 forms (SF4 2+ with two F-), PF5 gives 5, XeF4 gives 6. The forms are laid out in a grid, five per row, and copy the geometry of the drawing you selected, so select your VSEPR drawing if you want wedged forms.

If the drawing you generate from already belongs to a visual set, the new forms are added to that set; otherwise they form their own Res set.

Visual sets

A visual set groups different views of one species, for example its Lewis structure and its VSEPR sketch. Select the drawings, right-click, and choose Group as Visual Set. The selection must contain drawings in more than one view, or a single planar structure. Each drawing keeps the category you gave it with Set category, and drawings that share a category become resonance forms within that view. The set gets a violet box with a bold Vis tag. A drawing that carries an orbital picture is an ORBITALS view; Set category does not offer it, because it follows from the picture. A set can hold several orbital pictures, and they are alternative pictures rather than resonance forms. If you leave the set unnamed, Molkit looks the species up on PubChem and, when a match comes back, uses the lowercase name as the set’s name.

Unmark Visual Set splits a set with several views back into its individually tagged drawings. A set with only one view is removed instead. Your drawings are not changed either way.

For a planar resonance set such as nitrate, the right-click menu offers Show under Lewis & VSEPR (planar), which turns it into a visual set whose forms count as both the Lewis and the VSEPR depiction. Show under Lewis only turns it back into a resonance set. A non-planar set cannot do this, because its VSEPR drawing differs from its Lewis structure; draw the VSEPR forms separately and group them.

Seeing and managing sets

Every named selection, resonance set and visual set is outlined by a labelled box on the canvas, and you can rename one in place by double-clicking the name at its top-left. A single structure that only carries a category shows its view label without a box. The boxes and view labels are screen aids and do not appear in exported images.

View > Named Selections shows or hides the Named Selections panel, which lists every named selection, with a Vis or Res tag on the sets. Click a row to select that set on the canvas, double-click to rename, use the pencil to edit its details (including resonance weights), and the X to delete it. Deleting can be undone.

Why the category matters for lone pairs

Molkit normally works out lone pairs from the electron count, so an atom with no drawn lone pairs still gets the ones it needs. That suits bond-line drawings, where the oxygen of an -OH group shows none but has two.

A structure tagged Lewis (a visual-set form in the Lewis view) or any form of a resonance set is treated as a complete Lewis structure, so a drawn lone-pair count of 0 means zero. If you leave lone pairs off an atom in such a drawing, Molkit reports the formal charge your drawing implies instead of quietly filling them in. Every other drawing keeps the automatic behavior.