Geometry and Hybridization
For every atom in a structure, Molkit works out how many electron domains surround it, its hybridization, its VSEPR geometry and an ideal bond angle. You never request this directly. Clean Up Structure uses it to straighten angles, the Orbital tool uses it to recommend hybrid orbitals, the 3D viewer uses it to shape central atoms, and SVG export writes it into each atom’s data. The rules below tell you what Molkit will report for a given drawing and why.
Counting electron domains
An electron domain is a region of electron density around an atom. Molkit counts one domain for each of these:
- each bonded neighbour, with a double or triple bond counting once, as in VSEPR theory
- each implicit hydrogen, so a skeletal CH3 carbon has four domains even though its hydrogens are not drawn
- each lone pair (see How lone pairs are counted)
- each unpaired electron (a radical dot)
Neighbours and implicit hydrogens are bonding domains; lone pairs and unpaired electrons are non-bonding domains.
Hybridization
The total number of domains gives the hybridization:
| Domains | Hybridization |
|---|---|
| 2 | sp |
| 3 | sp2 |
| 4 | sp3 |
| 5 | sp3d |
| 6 | sp3d2 |
The one exception is a nitrogen or oxygen whose lone pair is delocalized into a neighbouring pi bond; see Lone pairs next to a pi bond.
To read the hybridization of formamide’s nitrogen
Molkit has no hybridization readout on the canvas, but the atom’s right-click menu shows the value it computed.
- Draw formamide, HC(=O)NH2, in bond-line form: a carbon double-bonded to O and single-bonded to N.
- With the Select tool, click the nitrogen so that it is the only thing selected.
- Right-click it and open the Orbitals submenu. The entry Fill with sp² (recommended) is marked, because the nitrogen’s lone pair is delocalized into the C=O bond.
- Try the same on the nitrogen of methylamine, CH3NH2. There the recommended entry is Fill with sp³.
Choosing an entry places hybrid orbitals on the atom (see Orbital tool).
Geometry and ideal angles
The geometry name describes the shape made by the bonded atoms (the molecular geometry), so it depends on how many of the domains are lone pairs or unpaired electrons:
| Domains | Non-bonding | Geometry | Ideal angle |
|---|---|---|---|
| 2 | 0 | linear | 180 |
| 3 | 0 | trigonal planar | 120 |
| 3 | 1 | bent | 117 |
| 4 | 0 | tetrahedral | 109.5 |
| 4 | 1 | trigonal pyramidal | 107 |
| 4 | 2 | bent | 104.5 |
| 5 | 0 | trigonal bipyramidal | 90 and 120 |
| 5 | 1 | seesaw | 90 and 120 |
| 5 | 2 | T-shaped | 90 |
| 5 | 3 | linear | 180 |
| 6 | 0 | octahedral | 90 |
| 6 | 1 | square pyramidal | 90 |
| 6 | 2 | square planar | 90 |
For bent and trigonal pyramidal atoms Molkit uses typical measured angles (water 104.5, ammonia 107) in place of the idealized 109.5, because lone pairs push the bonded atoms closer together.
How lone pairs are counted
The lone pairs Molkit uses depend on how the structure is tagged.
In a Lewis depiction or a resonance form, the lone pairs you drew are taken literally, and an atom drawn with none has none. A structure is a Lewis depiction when you tag it with Set Category > Lewis (or one of the Lewis variants); every form in a resonance set also counts. See Views and resonance.
Everywhere else, including skeletal (bond-line) and condensed drawings and any untagged structure, an atom with no drawn lone pairs gets them from its electron count: valence electrons, minus charge, minus bonds, minus implicit hydrogens, minus unpaired electrons, divided by two. A skeletal -OH oxygen therefore has its two lone pairs even though you did not draw them. If you do draw lone pairs on an atom, the drawn count is used.
The difference matters for octet-rule sulfate. Its sulfur has four single bonds and no lone pairs, with the 2- charge on the bracket. Tagged as Lewis, it is read as drawn: four domains, tetrahedral. Untagged, Molkit would derive a lone pair from the electron count and report a seesaw shape. A Lewis structure with a missing lone pair reports what the drawing implies, and the pair is not filled in for you.
Lone pairs next to a pi bond
A nitrogen or oxygen that has only single bonds, at least one lone pair, and a neighbour carrying a double or triple bond can delocalize that lone pair into the pi bond. The pair then occupies a p orbital and the atom becomes sp2. The domain count stays at four, because the pair is still there; only the hybridization changes, and for some nitrogens the geometry too.
Molkit applies this three ways, matched to measured structures:
| Atom | Result | Covers |
|---|---|---|
| Amide-type and pyrrole-type nitrogen | sp2, trigonal planar, 120 degrees | a nitrogen bonded to a C=O or C=S carbon (amides, peptides, ureas, carbamates; formamide is the textbook case) and a nitrogen with two pi-bearing neighbours (the ring nitrogen of pyrrole, diarylamines) |
| Oxygen next to a pi bond | labelled sp2, geometry unchanged | the single-bonded oxygen of a carboxylic acid, ester or phenol; it stays bent with the angle from the table above, because the measured angles (about 106 to 115 degrees) do not open to 120 |
| Aniline and enamine nitrogen | unchanged: sp3, trigonal pyramidal | aniline’s nitrogen is measurably pyramidal |
An alcohol oxygen or an amine nitrogen bonded only to sp3 carbons is never affected. Sulfur is excluded, because its larger 3p lone pairs overlap poorly with a 2p pi bond.
Radical centres
An unpaired electron counts as one non-bonding domain, so the nitrogen of nitrogen dioxide (two bonds, one unpaired electron, no lone pair) has three domains and is sp2 and bent.
A single electron repels less than a bonding pair, so it opens the angle past 120 degrees. For an atom with three domains, two bonds, one unpaired electron and no lone pair, Molkit uses the measured NO2 angle of 134 degrees in place of the table’s 117. Other radical centres get the right geometry class with an approximate angle.
Generic placeholders
A generic placeholder such as R, X or A has no defined valence, so Molkit reports no lone pairs, hybridization or geometry for it.
Where this information is used
Clean Up Structure uses the ideal angle when it evens out the angle at an atom with two neighbours. The Orbital tool uses each atom’s hybridization to pick sp, sp2 or sp3 labels and to place a p orbital perpendicular to the bonds. The 3D viewer draws textbook VSEPR shapes for a single central atom.
SVG export writes each atom’s hybridization, geometry, ideal angles and domain counts into the file as data-mk-hybridization, data-mk-geometry, data-mk-vsepr-angles, data-mk-domains-bonding and data-mk-domains-nonbonding, and marks atoms whose lone pair is delocalized into a pi bond. See SVG metadata.