Molecular Geometry & Bonding
what the shape decides
The collection

Every essay — page 6

Page 6 of 36, continuing through the fields in the same order.

Orbitals Where the atoms go Bonding models What symmetry decides Beyond the octet What a spectrum settles When the molecule does not stop What the shape is for What is taught wrongly Series Named objects Orbitals Refutations Search

Beyond the octet

Hypervalency without d orbitals, delocalisation, aromaticity, and the structures the first-year rules quietly cannot describe.

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.

4 figures benzene: what alternation costs and gains. The π energy of benzene as its bonds are alternated by β(1 ± δ), the elastic cost of alternating them at a stated stiffness, and the sum. The π curve falls quadratically in δ, which is measured here and is the whole difference between a molecule that distorts and one that does not. The stiffness is a stated parameter, so where the minimum falls is not a claim; which power of δ each curve goes as is.

The hexagon is the frame's doing

Benzene's delocalisation energy is quoted as 2β and read as the reason its bonds are equal. Let the bonds alternate and the π energy goes down, not up — at every ring size, for 4n+2 as much as for 4n. The π electrons are not what keeps the hexagon regular; the σ frame is, and the margin between them is uncomfortably thin.

5 figures How far the ground state is from being one determinant. The occupations of the two natural orbitals of the Hubbard dimer against the repulsion. At zero they are two and nothing, which is a single determinant exactly. As the repulsion grows they converge on one and one, which is a state no single determinant has — the failure is in the description rather than in the number. The entropy of the occupations rises to ln 2, one bit: the two determinants of the singlet.

Two kinds of correlation, and only one is small

Correlation energy is defined as a subtraction, and the definition hides that the thing subtracted is not one thing. In the two-site model the local power of the correlation energy in the interaction falls from two to one — and at every interaction strength it equals, exactly, the occupation of the bonding natural orbital.

7 figures One carbon, three lithiums, and no way to make it two. The four localised orbitals of the tetramer, with the share of each pair on each of the eight framework atoms. Each sits on exactly four: one carbon and the three lithiums of the face that carbon caps, which was not put in anywhere. The four shares are not equal — about 59 per cent of the pair is on the carbon — so the participation number comes out near 2.5 rather than at four. A bond over four centres is not a bond divided into four.

Four centres, and the pair that will not localise

The occupied orbitals of a molecule can be mixed freely without changing anything observable, and the freedom is usually spent on making them as local as possible. For the methyllithium tetramer the answer is four centres — one carbon and the three lithiums of the face it caps — and no mixing of the four pairs reduces it.

4 figures Strong outside, weak inside. The bond orders along each chain. A three-centre system has two equal bonds of 0.707 — not the one half the electron count suggests — and every longer chain alternates, strong at the ends and weak in the middle. The spread grows with the chain: 3:0.000, 5:0.211, 7:0.271, 9:0.296. Nothing here is about iodine.

Hypervalency does not stop at three centres

The three-centre four-electron bond is written up everywhere as an arrangement peculiar to hypervalent molecules. It is the first member of a family — five centres and six electrons, seven and eight — and the family predicts alternating bond strengths that the polyiodide crystal structures have.

7 figures 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.

5 figures The two figures, per electron. For each ring, the delocalisation energy against isolated double bonds and against the same ring with one bond deleted, divided by the number of pi electrons. The upper bar of each pair is the usual reference; the lower one is the cycle's own contribution, and the two are nowhere proportional.

A stabilisation is measured from somewhere

Benzene's delocalisation energy is 2β against three isolated double bonds and 1.0121β against the same six carbons with one bond deleted. Cyclobutadiene's is exactly zero against the first reference and −0.4721β against the second, so one of the two references records the most famously destabilised ring in the subject as neutral.

10 figures The error, against the repulsion it is an error about. The energy a mean field misses, for two electron counts on 4 sites, against the strength of the repulsion. Each is a straight line at large repulsion and the dashed line through it is not a fit: its slope is the count of coincidences a uniform density forces, computed from the electron number and the site number alone.

A mean field cannot get out of the way

The energy a mean field misses grows without limit as the repulsion rises — 27.82 at U = 32 for four electrons on four sites, against an exact energy of −0.2946, so the error is ninety-four times the answer. The rate it grows at is not an energy at all: it is n²/4N, a count of the coincidences a spread-out density cannot avoid.

8 figures One exact state, two correlation energies. The energy each of two mean fields misses, against the repulsion, for one system whose exact energy is a single smooth curve. Below U = 2 the unrestricted search returns the restricted answer and the two definitions agree to the last bit. Above it they part: at U = 32 the restricted reference reports -27.82 and the unrestricted one -0.11, a factor of 259.43, and one is growing while the other falls.

The reference decides the correlation

The correlation energy of one exact state, measured against two references that are both called Hartree–Fock, is −27.82 and −0.107 at the same repulsion — a factor of 259, on a system whose exact energy is a single smooth curve. Below the instability at U = 2 the two agree to the last bit; above it one grows without limit while the other falls, and the reference that reports almost no correlation has ⟨S²⟩ = 1.99 where a singlet is zero.

5 figures Four, however many ligands there are. For each molecule, the number of ligand σ combinations that find a partner among the central atom's four s and p orbitals, against the number of ligands and lone pairs it has. The matched count rises along the diagonal and then stops at four, because there are four orbitals; everything above the ceiling is a pair with nowhere on the central atom to go, and that is what the word hypervalent names.

Four is all that s and p can match

Reduce the ligand σ set of ten molecules in each one's own point group and ask how many of its components transform as one of the central atom's four valence orbitals. The answer is never more than four — not by arrangement, in every geometry from linear to octahedral — and what is left over is n + L − 4, with exactly twice that many electrons in excess of an octet.

6 figures How many centres, by two measures that do not agree. For each of eight systems, the number of atoms one localised pair has real amplitude on, and its participation number — which weights those atoms by how much of the pair each holds. Where the sharing is even the two coincide; where it is not they differ by more than a whole centre, and that gap is what electron deficiency looks like from the inside. one of the systems has more than one localisation, so for it neither number is an answer.

One scale, from two centres to a cage

How many centres a pair of electrons holds together is two different numbers, and they separate exactly where the bonding is most deficient: the methyllithium tetramer's pairs sit on four atoms each and have a participation number of 2.54. Run the same measurement up the scale and the twelve-vertex borane refuses it — its localisation has at least ten maxima differing by six parts in a thousand, so the number of centres is not an output for it at all.

7 figures Ten answers, and none of them is another one turned round. Every localised description the search found for a twelve-vertex cage, placed by the value of the functional it maximises. There are 10 of them, spanning 0.02, and the two closest differ by 0 — far more than the 10⁻¹³ the sweep converges to, so they are different maxima rather than one maximum reached to different precision. Each has its own multiset of participation numbers, and a symmetry of the cage permutes sites without changing that multiset, so no two of these are related by one. The controls above find one answer each.

How many descriptions a cage has

A localisation is a maximisation, and running it once reports the maximum it reached rather than the maximum there is. Run to exhaustion on a twelve-vertex borane it finds ten answers and then three batches of twelve starts in a row that find nothing new — and none of the ten is another one seen from a different side, because a symmetry of the cage cannot change a multiset of participation numbers and all ten multisets differ.

5 figures