Molecular Geometry & Bonding
what the shape decides
Concept

Eigenvector — where it appears

The vector an operator returns a multiple of, which carries the shape of the state. Bond orders, mode compositions and orbital coefficients are all read from eigenvectors rather than from the eigenvalues beside them.

Named by 13 essays across 5 fields — each of them below, with the objects they name alongside it.

Hückel levels of three-centre four-electron. The orbital energies of the pi system, computed as the eigenvalues of the molecule's adjacency matrix. Degenerate levels share a line. The electrons are placed by aufbau with Hund's rule, so a half-filled degenerate shell shows as two unpaired spins.

Three-centre bonding, computed

Three orbitals in a line and four electrons: a bonding level, a level with exactly zero amplitude on the central atom, and an empty antibonding one. The middle atom never exceeds an octet, and the ligands carry the charge — which is why every molecule that needs this arrangement has electronegative ligands.

beyond · Hypervalency π bond orders in naphthalene. Each bond drawn with a thickness set by its computed pi bond order, and the number printed beside it. The orders come from the eigenvectors and cost nothing extra once the matrix is diagonalised.

Bond order from the eigenvectors

Having diagonalised the matrix, the coefficients are already there. Two sums over them give every bond's order and every atom's charge, and naphthalene's three kinds of bond come out in the order the measurements find them.

bonding · Delocalisation π bond orders in benzene. Each bond drawn with a thickness set by its computed pi bond order, and the number printed beside it. The orders come from the eigenvectors and cost nothing extra once the matrix is diagonalised.

What one pair can hold together

Put a single electron pair into a ring of any size and it supplies a total bond order of exactly two and a π energy of exactly 4β — three atoms, eight atoms or six hundred. Spreading a pair over more centres divides the bonding among them; it neither creates nor destroys any.

beyond · Multicentre The state on a defect at site 31 of 60. The amplitude of one eigenvector at each site of a 60-site chain whose site 31 has its energy raised by 1.6β. The two colours are the two signs. A state belonging to the whole chain would reach across it; this one does not.

A defect is a level in the gap

Change one site's energy in a chain of a hundred and sixty and a level leaves the band, carrying a state that lives on a handful of atoms. In one dimension it happens for any change however small — the threshold measured on chains of forty, eighty and a hundred and sixty halves with every doubling, so there is no threshold at all.

solids · Defect The state on the end of a chain of 60. The amplitude of one eigenvector at each site of a 60-site chain whose site 1 has its energy raised by 0.6β. The two colours are the two signs. A state belonging to the whole chain would reach across it; this one does not.

The end is the hardest place to bind

A site in the middle of a chain traps a state for any energy difference however small. The site at the end demands a whole β before it traps anything — measured at 1.025, 1.013 and 1.006 on chains of forty, eighty and a hundred and sixty, converging on exactly one. The intuition runs the other way and is wrong.

solids · Defect Three orbitals in a line, four electrons in them. The three levels of a linear three-centre system, with the two lowest filled. The lower one is bonding across all three centres; the second has exactly zero amplitude on the middle atom, by symmetry rather than by arithmetic, so the two electrons in it sit entirely on the ends. That is where the charges come from: -0.5 on each end and +1 in the middle. Each of the two bonds has an order of 0.7071, which is 1/√2 and not the half the electron count suggests.

Hypervalency is about the ligands

The three-centre four-electron bond is offered as the reason sulfur hexafluoride needs no d orbitals. Read it forwards instead of backwards and it is a requirement rather than a permission — the arrangement puts half an electron onto each ligand before any electronegativity difference is applied, which is why the hypervalent compounds are fluorides and SH₆ is not a compound.

beyond · Hypervalency Two answers from one projector: E1g. The E1g projection operator of benzene, applied to the pz function on one atom and then to the one on its neighbour. Both results belong to the same two-dimensional representation and span the same subspace; neither is more correct than the other; and they are different pictures, overlapping by 0.500. The circle areas are the coefficients and the two colours are their signs.

The projector is unique, the basis is not

A reduction says how many times each representation appears. It cannot say which combinations of orbitals they are — that takes a projection operator, and for a degenerate representation the operator returns a different pair of orbitals depending on which function it is handed first. Both pairs are correct, they span the same space, and every energy computed from either is identical.

symmetry · Representation H₂O: 3 distinct modes. The displacement of every atom in 3 normal modes of H₂O, drawn from the eigenvectors of the mass-weighted Hessian. Under each is the internal coordinate with the largest share of the motion and how large that share is; where no coordinate holds nine tenths, the mode is not a motion of one bond or one angle and is labelled so.

The six motions that are not modes

Three N minus six is quoted in every textbook and the six are almost never computed. Diagonalising a mass-weighted Hessian gives six eigenvalues at arithmetic noise, and projecting their vectors onto the three translations and three rotations written down from the geometry alone accounts for every one of them.

spectra · Normal mode A 6×5 patch with one site missing. A 6 by 5 patch of a square structure with one site removed, the two colours of the bipartite structure drawn differently. The disc areas show where the level at zero has its amplitude: entirely on one colour.

A vacancy is not an impurity

An impurity is a site whose energy has been changed, and everything about the level it produces depends on by how much. A vacancy is a site that is not there, and the levels it leaves sit at exactly zero for a reason that cannot be tuned, weakened or moved — the count of them is a difference between two numbers of atoms, and two vacancies do not split however far apart they are put.

solids · Defect seven sets of parameters, one spectrum. Benzene's π levels from seven sets of the three Hückel parameters, each fitted to reproduce the two measured ionisation energies exactly. The two occupied levels sit at the same energy in every column, because that is what was fitted. The empty level moves from -3.15 to 4.69 electronvolts across the family, and the resonance integral from -3.05 to -7.66.

One spectrum, a line of models

Hückel theory has three parameters and benzene's photoelectron spectrum supplies two numbers, so the fit has a curve of solutions rather than a point. Along it the resonance integral runs from −3.05 to −7.66 electronvolts, the empty level moves by eight, the terminal-to-central bond order ratio in butadiene goes from 2.000 to 2.671 — and the delocalisation energy is 6.100 electronvolts in every member.

bonding · Models Which numbers survive a change of frame, and which are coordinates. Every quantity this field quotes, against the four things that can be changed without changing the molecule: the zero of energy, the unit, the reference state a stabilisation is measured from, and what a "per" quantity is divided by. A filled mark is a quantity that moves. three of the 9 survive all four, and every one of them is a property of the eigenvectors rather than of the energies. The first two changes are exact symmetries of the model, so a quantity that moves under either is a coordinate and not a quantity at all.

Which numbers carry a frame

A Hückel calculation is written in two numbers nobody computes and quoted against reference states nobody measures, so every quantity it prints is a quantity in a frame. Nine of them, tested against four changes of frame: three survive all four, and the one that survives both exact symmetries and looks safest — a dimensionless ratio between two molecules — is the most fragile of all, because against one reference its denominator is exactly zero.

bonding · Delocalisation One pi energy, two delocalisation energies. For each of six rings: the computed pi energy, the energy of the same atoms with one bond deleted, and the delocalisation energy that follows from each of the two reference states. Every entry is an eigenvalue sum; the two right-hand columns differ only in what was subtracted from the second column.

The frame that was allowed to relax

Four changes of frame were tested on nine quantities and none of them could move a bond order, because a bond order is a property of the eigenvectors and every change left the eigenvectors alone. Letting the geometry answer back does move them — butadiene's central bond falls from 0.4472 to 0.3676 — and it moves naphthalene's the other way, because its weakest bond is the one two rings share and relaxation strengthens it.

bonding · Delocalisation The unpaired electron's level stays put while its spin moves to the far end. Above, the trio's three levels as the overlap of A with C is raised from 0.25 to 0.45 while B's stays at 0.25. The lowest falls from -16.26 to -17.07 eV and the highest rises from -8.02 to -2.78 eV; the middle one, which holds the radical's unpaired electron, stays at −13.6 eV. Below, the spin on A and on B over the same change: from a half each to 0.236 on A and 0.764 on B, with the ratio of squared overlaps drawn as open circles on top.

The spin the count does not hold

Three orbitals in a row keep one level at the free-atom energy however the overlap of one end is changed, and at three electrons that level holds the radical's unpaired electron. Its energy does not move. Its spin does: from half on each end to 0.236 and 0.764 as one overlap goes from 0.25 to 0.45, exactly the squared ratio of the two overlaps, at every energy of the middle orbital. A coupling between the ends moves the level and cannot move the spin. The energy and the spin are answering to different things.

bonding · Overlap

Named alongside it

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

Bond orderHückel theoryDelocalisationConventionBands in a solidEigenvalueElectron-deficient bondingHOMO–LUMO gapLocalisationModel limitNon-bonding orbitalsThree-centre bonding

All concepts