Molecular Geometry & Bonding
what the shape decides
Concept

Perturbation — where it appears

A small addition to a Hamiltonian whose effect is expanded in powers of its size. The first-order term vanishes by symmetry for any non-totally-symmetric distortion of a non-degenerate state, which is why the interesting cases are second order.

Named by 11 essays across 7 fields — each of them below, with the objects they name alongside it.

Two is the ordinary answer, and one is a different kind of correlation. The local exponent of the correlation energy in the repulsion, against the repulsion, for three systems at half filling. The two closed-shell systems tend to two as the repulsion vanishes, which is ordinary perturbation theory. The ring of four tends to one, at repulsions fifty times smaller than the hopping.

A third kind of correlation

The two-site model gave an exact identity — the power of the correlation energy in the repulsion equals the occupation of the bonding natural orbital — and asked whether anything like it survives with more orbitals. It does not, and the way it fails is better than the identity was: a ring of four gives a power of one where every closed-shell system gives two, at repulsions fifty times weaker than the hopping, because its reference was never a single state.

beyond · Correlation The total energy against the distortion, at several gaps. The elastic cost plus the second-order lowering, for five gaps between the ground state and the excited state it mixes with. The critical gap is 1.00: above it the symmetric structure is the minimum, below it the minimum has moved off zero, and nothing about the molecule is degenerate in either case.

A distortion needs two states

A degenerate electronic state cannot survive — that is the Jahn–Teller theorem, and it can be computed. A closed shell can fail to survive too, and the condition is a number: the symmetric structure holds only while the nearest excited state of the right symmetry lies above 2λ²/k, and one of ten symmetry species in an octahedron is the right one.

applied · Peierls distortion The bonding follows the overlap over, and turns where it turns. The stabilisation of three pairs of orbitals against how far apart they are, each scaled to its own largest, with the coupling taken from the computed overlap. Two orbitals with no radial node are stabilised less at every separation further out; the two with one turn over — and the maximum of the bonding is at exactly the separation of maximum overlap, to five decimal places, because a coupling proportional to the overlap makes the stabilisation a strictly increasing function of it.

The same overlap, a different bond

A 1s and a 2s change their overlap by two thirds between two and seven bohr, and change what they are bonded by by 0.154 per cent. The overlap turns over and the bonding turns over with it, at exactly the same separation to five decimal places — the arithmetic refused the expectation that the secular denominators would move it — and what separates one pair from another is not where the maximum is but how little of it there is.

wrong · Overlap How anisotropic a structure has to be. The fourth moment of a layered band, divided by the square of its second so that the width drops out, against the coupling between layers. The curve is the closed form that follows from adding cumulants — 3 − 3(2 + λ⁴)/(2(2 + λ²)²) — with nothing fitted; the points are eigenvalues. At λ = 1 it is the three-dimensional value 2.5 and at λ = 0 the two-dimensional 2.25, and it is halfway between them at λ = 0.47 — so the question of when a band is effectively two-dimensional has a number rather than an opinion.

Two bands, and the shape of each

A band's shape has a closed form when the structure it belongs to factorises. Put a second band beside it and the form survives exactly while the two do not talk, and fails as the square of the coupling once they do. Make one direction weaker instead and the form survives everywhere — 3 − 3(2 + λ⁴)/(2(2 + λ²)²), agreeing with eigenvalues to nine decimal places — so how anisotropic a structure has to be before its band is two-dimensional is a number: λ = 0.46518.

solids · Bands in a solid An effect that cannot distort a molecule, deciding how far it distorts. The energy along one distortion coordinate, three times. With only the first-order term the minimum is at 0.6; with only the second-order term there is no minimum away from zero at all, because the gap of 1.5 is above the critical 1 for a closed shell on its own. With both, the molecule distorts to 1.06 — well past the first-order answer — and gains 0.09 more than the two separate stabilisations add up to.

Two distortions in one coordinate

A second-order Jahn–Teller effect that cannot distort a molecule by itself — its gap is half again above the critical value — nearly doubles the distortion when a first-order effect is already acting. The molecule goes to 1.075 instead of 0.600 and gains twice the energy, and it does it while the gap the second-order term divides by is opening rather than closing.

shape · Peierls distortion Two curves that cross, and two that do not. Every pair of parameters that reproduces one measured number, for three numbers, with the true system marked at Δ = 12 and t⊥ = 0.06. The lower band's shape is a function of the ratio of the two, so its curve is a straight line through the origin; the excess gap is a function of the coupling squared over the separation, so its curve bends. The two cross at one point. The upper band's shape draws a line almost on top of the first, because it is a function of the same ratio — a second measurement lying along the first fixes nothing the first had not already fixed.

Two ways of being second order

A band's shape and a band's gap are both second order in the coupling that mixes two bands, which sounds like a reason to measure only one of them. They are second order in different ways — one goes as the square of the ratio and the other as the square over the separation — and that single difference of one power is what turns a curve of possible answers into a point.

solids · Bands in a solid A length that keeps growing, and one that stops. The fitted decay length of the ring-current response, against the number of rings. The bare acene's runs 1.397, 1.669, 1.896, 2.104, 2.302 — up by a factor of 1.65 and still climbing — while its own gap falls from 0.590 to 0.1102. With a gap held open the same measurement gives 0.678, 0.642, 0.636, 0.636, 0.639, which has stopped moving by the third molecule. There is a magnetic reach, and an acene is too nearly gapless to have one.

A reach that has no length

A ring current's response to a neighbouring ring falls with distance, which invites asking for the length. Every acene computed gives a longer one — 1.397, 1.669, 1.896, 2.104, 2.302 rings — because the gap that would set the length is closing at the same time. Give the same molecule a gap that stays open and the number settles at 0.636 by the third one and does not move.

symmetry · Aromaticity The pair's regime is not a property of the pair. How much the pair's bonding responds to its own overlap — the ratio of what it is bonded by at an overlap of 0.4 to what it is bonded by at 0.1 — with and without a third orbital coupled to both. Alone it is 11.83, which is the regime in which bonding tracks overlap. With a third orbital present it falls to 1.46, 0.92, 0.74 — and two of those are below one, meaning a fourfold increase in the overlap between the two atoms buys them less bonding rather than more. The coupling comes from the overlap by the Wolfsberg–Helmholz rule with K = 1.75, which is fitted rather than derived. Every stabilisation here inherits that; the shape of the curve against separation does not, because K is a constant.

A regime that belongs to the neighbours

Two orbitals at the same energy are bonded in proportion to their overlap and two far apart are barely bonded at all — two regimes, and the natural question is whether the regime is a property of the pair. It is not. Put a third orbital beside them and the pair's response to its own overlap falls from twelvefold to less than one: more overlap buys less bonding.

wrong · Overlap 6 rings fused two ways. Two catacondensed chains of 6 hexagons: the linear one, where every fusion continues the line, and the angular one, where the fusions alternate. They have the same formula and the same number of bonds and they are not the same graph. Ring centres are numbered; in the linear molecule two rings k steps apart have centres 1.7321k units apart and in the angular one they do not, which is the whole reason this pair can be asked the question.

Neither of the two separations

A linear acene cannot pose the question, because the number of fusions between two rings and the distance between their centres are the same variable there. Bending the molecule pulls them apart — and the response follows neither. Two pairs of rings the same distance apart differ by two thirds, and the larger one is at the greater distance.

symmetry · Aromaticity Two bands, square below, triangular above. The 128 levels of a structure carrying two orbitals on every one of its 64 sites, where the lower orbitals hop on a square net and the upper ones on a triangular net, separated by 12 and coupled at 0.06. The two bands have different widths and different shapes before anything mixes, which is the situation a single net cannot construct. Every level here is also reproduced by a two-by-two problem, one per mode, to 3e-13.

The constant that belonged to one net

Divide one second-order departure by another and the coupling cancels, leaving one constant times the gap — which reads as arithmetic. It was arithmetic about a square net. On a triangular one — the same graph for both bands, nothing else changed — the quotient drifts by a hundred and twenty-eight per cent.

solids · Bands in a solid One heteroatom, and how far the relaxation carries it. The change every ring's bonds undergo when one carbon of the end ring is given a site energy, on a chain of 12 fused hexagons with its gap held open. The upper curve measures each molecule's couplings from its own mean bond order, which is what this collection's relaxation has always done; it stops falling at 4.48e-5 and stays there. The lower curve measures both from the same mean and keeps falling to 7.89e-9. Nothing about the molecule differs between them.

The floor was in the bookkeeping

A heteroatom in one ring of a fused chain is a perturbation with a place, and the relaxation carries it along the molecule. Measured directly, the response stops falling after five rings and sits at four hundredths of a millionth for ever. That floor is not the molecule. It is the relaxation measuring each system's couplings from its own mean, and removing it recovers nine orders of magnitude.

bonding · Delocalisation

Named alongside it

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

Model limitClosed formConventionBand gapEigenvalueHOMO–LUMO gapLeast-squaresBands in a solidBand widthDegeneracyDelocalisationGraph

All concepts