Molecular Geometry & Bonding
what the shape decides
Concept

Wavefunction — where it appears

The function whose square gives the probability of a configuration, and from which every observable follows. Its sign carries the bonding information a density cannot, and it is not itself measurable.

Named by 16 essays across 3 fields — each of them below, with the objects they name alongside it.

1s with 1s at 2.8 bohr. The 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. Contours drawn: 1s at 50% of its density, |ψ| = 1.48e-1; 1s at 50% of its density, |ψ| = 1.48e-1.

Overlap decides

Two orbitals interact in proportion to how much they overlap, and the sign of the overlap decides which of the two combinations is the lower in energy. It is one integral, and almost everything about bonding follows from it.

bonding · Overlap The 2pz orbital. The 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. Contours drawn: 2pz at 90% of its density, |ψ| = 9.48e-3.

What an orbital is

Not a region the electron occupies, not a path it follows, and for any atom but hydrogen not an exact anything. An orbital is a one-electron wavefunction, and almost every difficulty in this subject comes from forgetting that.

orbitals · Orbital Orbitals at the 90 per cent contour. Several 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. Contours drawn: 1s at 90% of its density, |ψ| = 3.94e-2; 2s at 90% of its density, |ψ| = 7.40e-3; 2pz at 90% of its density, |ψ| = 9.48e-3.

Orbitals are not where the electron is

A many-electron atom has no exact orbitals at all. The orbital picture is a basis for an approximation — an extremely good one — and treating it as a description of reality is the source of most of the confusion in this subject.

wrong · Approximation Choosing a contour for 3s. The 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. Contours drawn: 3s at 50% of its density, |ψ| = 6.24e-3; 3s at 90% of its density, |ψ| = 2.64e-3; 3s at 99% of its density, |ψ| = 7.15e-4.

Say what it encloses

An orbital picture is a contour at a level somebody chose, and almost no source says which. Two textbooks can draw the same orbital at visibly different sizes with the same caption, and both be printed in good faith.

orbitals · Contour sp3 hybrids. The 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.

Hybrids are a basis

An sp³ hybrid set is an orthogonal matrix applied to the atomic orbitals. Rotating a basis changes no observable, so asking whether the electrons are really in hybrids is asking which coordinate system nature prefers.

bonding · Hybrids The radial function of 3s. The 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.

Nodes

An orbital with quantum numbers n and l has exactly n−l−1 radial nodes and l angular ones. That is a count, it is exact, and it is the fastest way to catch a drawing that is wrong.

orbitals · Orbital The radial function of 1s. The 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.

Where the electron is

The wavefunction is largest at the nucleus, the electron is most likely to be found a bohr out, and the ninety-per-cent contour is at 2.66. Three numbers, all correct, all answering different questions.

orbitals · Orbital Four measures of size for 6 orbitals. The most probable radius, the mean radius, the root-mean-square radius and the radius of the sphere holding ninety per cent of the density, for 1s, 2s, 2pz, 3s, 3dz2, 4s. All four are computed from the same radial function, all four are correct, and they are not the same number.

How big is an orbital

Four measures of size, all computed from the same radial function, all correct, and spanning a factor of two and a half for a 1s orbital. The one that governs chemistry is a fifth, and it is not a measure of size at all.

orbitals · Contour 1s, 2s, 2pz, 3s, 3dz2, 4s at one level and at one fraction. The orbitals 1s, 2s, 2pz, 3s, 3dz2, 4s, each with the contour level that encloses 90 per cent of its own density, and beside it what each one encloses when they are instead all drawn at 1s's level. The first column is a set of pictures that can be compared; the second is what a plate drawn at a single contour value actually shows. Contours drawn: 1s at 90% of its density, |ψ| = 3.94e-2; 2s at 90% of its density, |ψ| = 7.40e-3; 2pz at 90% of its density, |ψ| = 9.48e-3; 3s at 90% of its density, |ψ| = 2.64e-3; 3dz2 at 90% of its density, |ψ| = 3.60e-3; 4s at 90% of its density, |ψ| = 1.24e-3.

One level is not one comparison

A plate of orbitals drawn at a single contour value looks like a comparison and is not one. At the level that encloses ninety per cent of a 1s, a 2s encloses four per cent, a 3s under one, and a 3d has no surface at all — its wavefunction never reaches that value anywhere in space.

orbitals · Contour The exponent the molecule chooses, and what it buys. The 1s exponent that minimises the energy of a one-electron diatomic, against the separation of the nuclei, with the binding curves at that exponent and at the free atom's. Held at ζ = 1 the bond comes out at 2.49 bohr and binds 0.0648 hartree; with the exponent free it comes out at 2.00 bohr at ζ = 1.238 and binds 0.0865. The exact answer for this molecule is 2.00 bohr and 0.1026.

The atom does not bring its own orbital

Build a one-electron diatomic from two hydrogen 1s functions and it comes out 25 per cent too long and 37 per cent too weakly bound. Let the molecule choose how large those functions are and the bond length is right to three figures, at an exponent of 1.238 — the orbital contracts by a quarter when the bond forms.

orbitals · Orbital The wrong shape, fitted as well as it can be. The exact hydrogen 1s orbital and the best sums of one, two, three and six Gaussians, each with its exponents optimised for the energy. Three of them already reproduce the exact function to 99.94 per cent by overlap, which is why the method works at all — and the two places it goes wrong, at the nucleus and far out, are exactly where the other faces of this figure look.

A Gaussian is the wrong shape

Sixty years of molecular calculation are built on functions that get the two ends of an orbital wrong. A Gaussian has no cusp at the nucleus and dies too fast far away, and no number of them fixes either — while three of them already reproduce hydrogen's 1s to better than 99.9 per cent by overlap, and that is why the method works.

orbitals · Basis Where the electron is, and how fast it is going. The radial distribution in position on the left and in momentum on the right, for the same orbitals. The two run opposite ways: the 1s is the most compact in space and the widest in momentum, and every excited orbital that spreads out in one narrows in the other. Both are normalised, both are the same function, and neither is more fundamental than the other — the transform loses nothing and adds nothing.

The orbital in momentum space

Every orbital has a second picture as complete as the first and almost never drawn. Nothing is added by taking it — it is the same function in the other variable — but the uncertainty product falls out of it, and the functions quantum chemistry is built from turn out to be the only ones that attain the bound.

orbitals · Orbital The Compton profile, exact and fitted. The momentum density integrated over the two perpendicular directions, for the exact 1s and for three fitted bases. The exact curve is 8/3π(1 + q²)³ in closed form; the fitted ones are sums of Gaussians and are cusped differently at the origin, which is the position-space cusp showing up as a shape in momentum.

The measurement a basis was not fitted to

Six Gaussians reproduce hydrogen's energy to eleven parts in a hundred thousand and its Compton profile to three parts in a thousand — twenty-five times worse, on a quantity an X-ray scattering experiment measures directly. The gap between the two errors widens as the basis is improved, because the energy is the one property a variational fit is best at.

orbitals · Basis The ionic weight against how much ionic structure is in the wavefunction. The percentage each convention calls ionic, at a fixed structure overlap, as the amount of ionic structure in the wavefunction is raised from none to the molecular orbital value. They meet at both ends of the sweep and disagree everywhere between. Every curve is a weight and every set sums to one.

A weight that depends on how it is weighed

The ionic character of a two-electron bond is quoted as a percentage. For one wavefunction at hydrogen's bond length, three conventions in the literature give 18.73, 34.74 and 5.88 per cent — a factor of six — and on a wavefunction with no ionic structure in it at all, one of them still reports a quarter.

bonding · Models The same count in both pictures, and no rule between them. Every hydrogenic orbital with a radial node, drawn twice: its position nodes on the left axis and its momentum nodes on the right, at the same nuclear charge. The counts are identical and exact — n − l − 1 in each — because the two radial functions are polynomials of the same degree. The positions are unrelated: a node three quarters of the way out in one picture is not three quarters of the way out, or anywhere in particular, in the other.

The nodes in the other variable

An orbital has n − l − 1 radial nodes, and it has exactly that many in momentum too — the two radial functions are polynomials of the same degree. Nothing pairs one node with another: they are zeros of two different classical families. What is exact is the product over all of them, which is a ratio of factorials and does not depend on the nuclear charge at all.

orbitals · Orbital A bond is a cosine in momentum space. The two factors a two-centre bonding orbital's momentum density is made of. One is the atomic momentum density, unchanged by the bond and falling as the eighth power of the momentum. The other is cos²(q·R/2), the interference between the two centres, whose period is fixed by the bond length and by nothing else. Everything that distinguishes a bond from two atoms in this picture is that cosine — and it has zeros where the atomic factor has none.

Oblate in the picture nobody draws

Every drawing of a σ bond shows a density stretched along the bond, and the position-space calculation agrees: the second moment along the axis is twice the one across it. In momentum the same orbital is flattened in the same direction, because the interference between the two centres cuts the distribution off at π over the bond length — and that cut-off is a zero a measurement could find.

orbitals · Orbital

Named alongside it

The objects these essays reach for when they reach for this one.

NodeProbability densityBasisContour levelExpectation valueEnclosed probabilityOne-electron modelsApproximationConventionOverlap integralRadial distributionClosed form

All concepts