VSEPR placement
Each atom's electron domains are its bonded neighbours (a double or triple bond counts once) plus its lone pairs. Lone pairs come from the electron count: valence electrons − formal charge − bonds, divided by 2. New atoms and lone pairs go to the ideal positions for that steric number, with lone pairs equatorial in a trigonal bipyramid and trans in an octahedron. Second-row atoms (B–F) are limited to an octet. Si, P, S, Cl, Br and I can expand to five or six domains. Adding a fourth bond to N or O, or to B, sets the formal charge automatically (NH₄⁺, H₃O⁺, BH₄⁻).
| Steric no. | Electron geometry | Shapes (0, 1, 2, 3 lone pairs) |
|---|
| 2 | linear · sp | linear |
| 3 | trigonal planar · sp² | trigonal planar, bent |
| 4 | tetrahedral · sp³ | tetrahedral, trigonal pyramidal, bent, linear |
| 5 | trigonal bipyramidal | trig. bipyramidal, seesaw, T-shaped, linear |
| 6 | octahedral | octahedral, square pyramidal, square planar |
From a 2D drawing
A drawing from the Sketch (or any 2D .mol file) is scaled to real bond lengths; atoms on wedge bonds are lifted toward you and atoms on hashed bonds pushed away; rings start puckered; hydrogens and lone pairs are added. The structure is then relaxed while each wedged stereocentre is held to the handedness you drew, and finally the conformer search runs. The search rejects any move that would invert a stereocentre, so R/S, cis/trans and E/Z stay as drawn. Text, arrows and elements other than the twelve listed are not converted.
Energy minimization
A deliberately simple force field with four terms: bond stretching (harmonic, toward covalent-radius bond lengths, shortened for double and triple bonds); electron-domain repulsion (each pair of domains around an atom repels, more strongly when a lone pair or multiple bond is involved, so lone pairs squeeze bond angles: H₂O ≈ 102°, NH₃ ≈ 106°, SF₄ equatorial ≈ 106°); torsion (keeps groups on a double bond coplanar and gives a small staggering preference about sp³–sp³ bonds); and steric repulsion between atoms three or more bonds apart (ε(σ/r)¹², from van der Waals radii). Minimize energy does more than slide downhill: it relaxes the structure (FIRE algorithm), then searches for better conformers by trying a chair flip of each ring, a corner flip of each ring atom (boat → chair), and a ±120° rotation about each rotatable single bond, relaxing each try and keeping any that lowers the energy until nothing helps. Ring flips keep every substituent on its own face of the ring, so axial ↔ equatorial swap while cis/trans and R/S stay the same: an axial methyl moves equatorial (≈1.9 model units, A-value 1.7 kcal/mol), and diaxial cis-1,3-dimethylcyclohexane becomes diequatorial (≈4.0; experiment ≈5.4). Red dashed lines mark the worst contacts between atoms four or more bonds apart. Energies are in model units, useful for comparing shapes of the same molecule, not real thermochemistry. Resonance, hyperconjugation, hydrogen bonding and electrostatics are not included, so an amide N is treated as pyramidal and angles are typically within about 5° of experiment.