How this site is made

The figure library

Every picture here is generated from code at build time. This page lists the generators, each rendered at its defaults.

No figure on this site is a drawing that was made once and saved. Each one is a function: it takes parameters and returns SVG, so the same generator produces the p4 plate and the p6m plate without either being redrawn.

That is the reason the collection can keep growing without the illustrations drifting apart. A generator is written once, checked once, and every essay that calls it inherits the same line weights, the same colour roles, and the same behaviour in dark mode. There are 15 of them so far.

angle-table

The angles each arrangement givesEvery distinct angle subtended at the centre, for each number of sites, measured off the minimised arrangement. Five is the case with three distinct angles, which is the arithmetic signature of sites that are not all equivalent.sitesshapeangles measured2linear180.0°×13trigonal planar120.0°×34tetrahedral109.5°×65trigonal bipyramidal90.0°×6 120.0°×3 180.0°×16octahedral90.0°×12 180.0°×3each row is a separate minimisation

contour-choice

One orbital, three contoursThe same orbital drawn at three enclosed fractions, all at one scale. The pictures differ substantially, and a caption that says only "the orbital" does not distinguish them — which is why every figure on this site states its level.50% of the density|ψ| = 1.48e-190% of the density|ψ| = 3.94e-299% of the density|ψ| = 8.44e-31slevels solved for by integration, drawn at one scale

enclosed

Choosing a contour for 1sThe fraction of the density enclosed by a contour, against the contour's level. Picking a level is picking a point on this curve, and the usual practice of picking one that looks right is picking a point without knowing which.0%25%50%75%100%50% enclosed|ψ| = 1.48e-190% enclosed|ψ| = 3.94e-299% enclosed|ψ| = 8.44e-3contour level |ψ|fraction of the density enclosedevery level here was solved for, not chosen1s

five-sites

Five sites are not five of a kindThe minimised arrangement of five points, with the two axial sites marked apart from the three equatorial ones. Their neighbour angles differ, so the two kinds of position are genuinely different places — which the shape's name does not convey.axial — 2 sitesneighbours at 90°, 90°, 90°, 180°equatorial — 3 sitesneighbours at 90°, 90°, 120°, 120°the two are not equivalentneighbour angles measured, not assumed5 sites

hybrid

sp3 hybridsThe directions the hybrids point, with the angle between them computed from the coefficients rather than quoted. The set is an orthogonal transformation of the atomic orbitals, so it describes the same space in different coordinates.sp3109.471°between every pair4 hybridsworst off-diagonal 0e+0an orthogonal transformation of the atomic orbitalsone electron

hybrid-matrix

The sp3 transformationEach row is one hybrid, written in the basis of the atomic orbitals it is made from. The rows are orthonormal, so the matrix is a rotation — and a rotation of a basis changes no observable quantity whatever.spₓp_yp_zhybrid 10.50000.50000.50000.5000hybrid 20.50000.5000-0.5000-0.5000hybrid 30.5000-0.50000.5000-0.5000hybrid 40.5000-0.5000-0.50000.5000every row normalised and every pair orthogonal to 0e+0a change of basis, and nothing moresp3

mo-levels

Splitting goes with overlapFor each pair, the atomic levels on the outside and the combinations they form in the middle, with the splitting drawn in proportion to the computed overlap. A pair that symmetry forbids does not split at all, because its overlap is exactly zero.1s-1sσ overlapS = 0.39002pz-2pzσ overlapS = 0.45852px-2pxπ overlapS = 0.75291s-2pxsymmetry forbids itS = 0 exactlyno splittingoverlaps computed at 2.8 bohr, levels in proportionone electron

molecule

water — C2vThe molecule with the point group found from its coordinates rather than looked up: every candidate operation was applied and kept when it permuted the atoms among themselves.HHOC2vprincipal axis C22 mirror planesno inversion centremay be polarcannot be chiralgroup recovered from the coordinates3 atoms

orbital

The 2pz orbitalThe 2pz orbital at the contour enclosing 90 per cent of its density — a level solved for by integration rather than chosen. The two colours are the two signs of the wavefunction, which is what distinguishes a bonding interaction from an antibonding one.2pzencloses 90% of the densitycontour at |ψ| = 9.48e-30 radial nodes1 angular nodecontour solved for by integrating the density1 shell · one electron

orbital-set

Orbitals at the 90 per cent contourSeveral orbitals drawn at the same enclosed fraction and, unless stated otherwise, at the same scale — so the sizes on the page are the sizes. Each contour was solved for separately by integrating that orbital's own density.one scale across the plate1s0 radial · 0 angular2s1 radial · 0 angular2pz0 radial · 1 angular3dz20 radial · 2 angulareach level solved for separately90% · one electron

overlap

1s with 1s at 2.8 bohrThe two orbitals in the plane containing both nuclei, with the regions where their product is positive and negative shown faintly. The overlap integral is the signed volume of that product, and where symmetry makes the two regions mirror images it comes out exactly zero.1s · 1sS = 0.38997sigma interactionseparation 2.8 bohrcontours at 50% of each densitythe signed product integrated over all spaceone electron

overlap-curve

Overlap against separationHow the overlap integral falls as two atoms are pulled apart, for several pairs of orbitals. Where a closed form exists it is drawn over the computed curve, so the integrator is checked rather than trusted.1234561s-1ssigma1s-2pzsigma2px-2pxpidots: the closed formoverlap Sseparation / bohrintegrated numerically, checked against the exact resultone electron

polar-chiral

What the group settlesFor each molecule, the point group found from its coordinates and the two properties that follow from the group alone. Neither column required knowing anything about the bonds.moleculegroupmay be polarmay be chiralwaterC2vyesno2 σcarbon dioxideD∞hnonohas iammoniaC3vyesno3 σmethaneTdnono6 σboron trifluorideD3hnono4 σhydrogen peroxideC2yesyesbromochlorofluoromethaneC1yesyesboth columns derived from the symbol, not from the bonds

radial

The radial function of 2sThe radial part of the wavefunction, which changes sign at each node, and the radial distribution, which is the probability of finding the electron in a shell at that radius. The second vanishes at the nucleus and the first does not.node 2.00most probable radius 5.24 a₀R(r)and 4πr²R²r / bohrmeasured off the computed function1 radial node · one electron

vsepr

4 sites, minimisedThe arrangement of 4 points on a sphere that minimises their mutual repulsion. The angles printed were measured off the result rather than quoted, and the shape was not assumed.tetrahedral109.47° × 6repulsion minimised, angles measured off the result4 sites