Molecular Geometry & Bonding
what the shape decides
Concept

Localisation — where it appears

A unitary transformation of the occupied orbitals into combinations concentrated on bonds and lone pairs. It changes no observable at all, which is why the resulting picture is a choice of description rather than a discovery.

Named by 35 essays across 6 fields — each of them below, with the objects they name alongside it.

methane — Td. The 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.

Hybridisation does not explain

Methane's photoelectron spectrum has two bands, not one. Four equivalent sp³ bonding orbitals cannot produce that, and the resolution is that hybridisation was never a claim about what a measurement would find.

wrong · Hybrids What the group settles. For 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.

The dipole is not a sum of bonds

Adding bond dipoles as vectors gets the easy cases right and rests on a quantity with several incompatible definitions. The symmetry argument is exact, needs no electronegativities, and says when the answer must be zero.

wrong · Dipole Splitting goes with overlap. For 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.

Molecular orbital and valence bond

Two frameworks, taught as rivals, describing the same molecules. One starts from delocalised orbitals and localises; the other starts from localised bonds and delocalises. Pushed far enough they meet.

bonding · Models Four bonds, or one a₁ and three t₂. The same four occupied orbitals written in two bases. On the left each orbital sits on one bond; on the right one is shared over all four hydrogens and three follow the Cartesian directions. The transformation between them is orthogonal, so the density is unchanged.

The localisation transformation, demonstrated

Four equivalent bonds or one a₁ and three t₂ — two descriptions of methane's bonding electrons that disagree about everything except the electron density, which they agree about to the last bit a double can hold.

bonding · Hybrids 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 How far two hybrids are from orthogonal. The overlap between two equivalent s–p hybrids of a stated label, against the angle between them. Each curve crosses zero at exactly one angle — sp3 at 109.47°, sp2 at 120.00°, sp at 180.00° — and a molecule whose measured angle is not that angle has hybrids that overlap. The largest here is cyclopropane at 0.63.

Hybrids that were never orthogonal

Two sp³ hybrids are orthogonal at 109.47° and nowhere else. Water's are drawn at 104.5° and overlap by 0.062; cyclopropane's are drawn at 60° and overlap by 0.625, which is not a small correction to a basis but a description that has stopped being one.

shape · Hybrids 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 ammonia: 3 valence bands. The measured valence photoelectron bands of ammonia, each labelled with the symmetry species of the orbital it comes from, and beside them the species the valence basis spans — the central atom's s and p functions and one s on each ligand, reduced in the molecule's own group. A band carrying a species the reduction does not produce would stop this figure being drawn.

Fewer bands than electrons

Methane has eight valence electrons and two photoelectron bands. Ammonia has eight and three; water has eight and four. The count is not of electrons, not of bonds and not of orbitals — it is of the symmetry species the occupied orbitals fall into, and it falls as the symmetry rises.

spectra · Photoelectron Two impurities at 2 to 14 sites apart. The splitting between the two levels a pair of impurities of strength -2β pulls out of a chain of 61, against how far apart they are, on a logarithmic scale. It falls by a constant factor per site of separation, and that factor is the decay of the isolated bound state computed from its energy alone. The two levels close on the single impurity's level as the pair separates.

Two defects, and the level between them

One impurity pulls a level out of a band at exactly −√(h²+4). Two of them pull out a pair, split by an amount that falls by a factor of 0.41421 for every site of separation — which is √2 − 1, predicted from the isolated level's energy alone and measured to six figures.

solids · Defect 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.

beyond · Multicentre H₂O with 1→D: what each mode is made of. H₂O with 1→D. Each row is one distinct frequency and each column one internal coordinate; the bar is the share of the motion in that coordinate. A mode whose largest share reaches nine tenths is a motion of one bond or one angle and is named for it. 3 of 3 here are.

When a mode becomes a bond stretch

Water's two stretching modes are each exactly half in one O–H bond and half in the other, which is why neither of them belongs to a bond. Change one hydrogen to deuterium and the same force field at the same geometry gives two modes that are 99.5 and 99.7 per cent in a single bond each. Nothing about the bonding changed; a mass did.

spectra · Normal mode One double bond, two descriptions. A carbon–carbon double bond drawn twice in the plane perpendicular to the molecule: as a σ orbital along the axis with a π orbital above and below it, and as two equivalent bent bonds tilted 50.8 degrees either side of the axis. The two descriptions are related by a rotation and have the same density everywhere.

Two bent bonds, or a σ and a π

A carbon–carbon double bond is drawn two ways and the two look like rival claims about what is there. They are one occupied space in two bases, related by a rotation of exactly forty-five degrees: the density is identical to the last bit a double holds, the bent pair are sp⁵ hybrids at 50.77° to the axis, and their charge sits 0.235 Å off the plane of the molecule where neither canonical orbital's does.

bonding · Hybrids 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 One impurity is a level; many are a band. The impurity levels of a ring of 160 with sites of depth -3, drawn as a bar from the lowest to the highest, against the fraction of sites that are impurities. At the lowest concentration every level is at the same energy and the bar has no height at all. By 30 per cent the levels span 2.44 and have closed to within 0.25 of the host band, which is shaded.

One defect is a level, many are a band

A single deepened site in a chain pulls one state out of the band to −√(h² + 4), exactly, and holds it on 1.42 sites. Put in more and the levels spread: at one site in ten they span 1.45 in the same units and have closed to within 0.69 of the host band, and above one site in eight the count of levels stops matching the count of defects, because two defects on neighbouring sites push one of their pair back into the band.

solids · Defect How many sites a state occupies, and whether that depends on the ring. The participation ratio of the states at the middle of the band — the number of sites a state occupies — against the width of the disorder, for rings of 50, 100, 200 sites. With no disorder the three curves are three different numbers, each two thirds of its own ring. At the right they have converged: 7.47 sites on a ring of 50 and 9.82 on a ring 4 times larger.

The third way to be an insulator

A ring of two hundred sites with a half-filled band has its levels crowding together as 1/n, which is the usual electronic-structure criterion for a metal, and it goes on holding at every disorder tested. Meanwhile the states at the middle of the band go from occupying 127 sites to occupying 10 — and at that disorder the number stops depending on how large the ring is at all.

wrong · Metal 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.

beyond · Multicentre Three bent bonds, at a hundred and one degrees to each other. A carbon–carbon triple bond in its localised description: three equivalent bent bonds, spaced by 101.54 degrees, each tilted 63.43 degrees off the axis and each carrying 0.17 of an s orbital — an sp⁵ hybrid. Its charge sits 0.32 ångström off the axis, where every canonical orbital's sits on it. The mixing that makes the three equivalent is a rotation in the three-dimensional occupied space, so the density is untouched.

Three bent bonds, and the same hybrid

A triple bond localises into three bent bonds at 101.537 degrees to one another, each an sp⁵ hybrid with exactly one sixth s character. A double bond's two bent components are sp⁵ hybrids at 101.537 degrees. The two are the same hybrid, built out of different frameworks and in different numbers, and the reason is that a third of a half is a half of a third.

shape · Hybrids 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.

beyond · Multicentre A state in the gap is a particle in a box the alloy happened to make. The participation ratio of the 40 levels nearest the gap centre, over 5 chains of 400 sites, against the length of the run of like sites each one sits on. The line is 2(L+1)/3, the participation ratio of the ground state of an isolated chain of L sites, with nothing fitted. 38 of 40 lie on it to within 3.1 per cent. The ones above it are states shared between two runs close enough to talk, which is a defect band beginning.

A particle in a box the alloy made

A random alloy's gap is set by the longest run of like sites. What sits at the edge of that gap turns out to be the simplest state in quantum mechanics: a particle in a box of L sites, occupying 2(L+1)/3 of them, to within three per cent and with nothing fitted — except for the two states in forty that found a second run to share.

solids · Defect A functional with no interior maximum. The Boys functional against the mixing angle for a carbonyl, evaluated directly at a hundred and eighty-one angles. It is a quadratic in cos²θ − ½ with no linear term, so it is symmetric about forty-five degrees and its maximum is at the middle or at the ends and nowhere else. Here the coefficient is positive, so the best is at 0° — the canonical σ and π. There is no angle to search for, however unsymmetrical the molecule is.

The angle that does not have to be searched for

A carbonyl's two bent components have no symmetry making them equivalent, so the mixing that best localises them looks like something to search for and their s characters look like two different numbers. Neither happens. The localisation functional is a quadratic with no linear term, so its maximum is at forty-five degrees or at the ends — bent bonds or canonical ones, decided by one inequality, with nothing in between.

bonding · Hybrids The count is a curve, and the curve flattens. How many distinct localised descriptions of a twelve-vertex cage had been found after each batch, out of 4,000 random starts. The last new one appears at start 124; the remaining 3,876 add nothing. The dashed curve is what the basin sizes measured here predict — the chance of having hit each description at least once — and it is a closed form rather than a fit to the points.

Where the count stops being an effort

A cage's localised descriptions were counted by a search that stopped when it stopped finding new ones, which makes the count a property of the stopping rule. Run to four thousand starts the count is fourteen and the last new description appears at start 124 — after which three thousand eight hundred and seventy-six starts add nothing. The four rarest are found six times in a thousand, which is what says nothing rarer is hiding.

beyond · Multicentre Where the coupling overtakes the spacing. Two quantities that both depend on the chain length, for runs of 6. The coupling is the splitting of the closest pair of runs, which rises as the chain grows because a longer chain brings some pair closer together. The spacing is the mean separation of the gap levels in energy, which falls as the chain grows because there are more of them. They cross at 8,675 sites, and a set of levels coupled more strongly than they are spaced is a band.

The length at which levels become a band

Two runs of low sites share a state when they are close enough, and the splitting falls exponentially over two sites. A longer chain brings some pair closer while spreading its levels thinner, so the two quantities run against each other and cross — at about a thousand sites for runs of four and eighty thousand for runs of eight. Chains of four hundred sites are far below that, which is why every gap state on them is a box.

solids · Defect The inequality, decided twice. The quantity the localisation criterion compares — the centroid separation over twice the off-axis dipole — computed with hydrogenic radial functions and with Slater ones at the same effective charges. Below one the localised description is a pair of bent components; above it, σ and π. The hydrogenic answer is 1.8090 and the Slater answer is 0.3937, and they are on opposite sides.

The node that decided a picture

A hydrogenic calculation cannot say whether formaldehyde's localised description is two bent components or σ and π, because the integral that decides it came out at 0.00718 where it should be the largest in the molecule. Replacing the hydrogenic radial functions with nodeless Slater ones moves that overlap by a factor of ninety-seven, leaves the π overlap identical to the last bit, and flips the answer: the description is bent.

bonding · Hybrids Three basin populations from one search. The share of 4000 random starts landing on each localised description, in rank order, on a logarithmic axis, for three cages and fillings. a twelve-vertex cage at twelve electrons gives 14 descriptions and two groups with a gap; a nine-vertex cage at eight electrons gives 63 descriptions and a smooth tail; a twelve-vertex cage at twenty electrons gives 15 descriptions and one basin and dust. Only the first is the twelve-vertex shape, and the rule it suggests is a rule about that shape.

Three shapes from one search

A cage's fourteen localised descriptions fell into two groups with a factor of five between them and nothing in the gap, which made counting the big basins look like a stopping rule. Two more cases from the same family give a smooth tail over sixty-three descriptions and a single basin holding ninety-eight per cent. One search, one family, three shapes.

beyond · Multicentre The coupling at the closest pair, and at the typical one. For runs of four to eight low sites at half concentration: the splitting between two runs one site apart, which is the largest coupling any chain can produce, and the splitting at the separation two runs typically have. Both on a logarithmic axis spanning 173 decades. A band width taken from the second is not a small number; it is not a number.

A band that is a hundred and seventy decades of nothing

The chain length at which a defect's levels become a band can be located by asking when the coupling between the closest pair exceeds the level spacing. A band also has a width, and a width is set by the typical coupling rather than the closest one. For runs of eight at half concentration those two numbers differ by a hundred and seventy-three orders of magnitude.

solids · Defect What a rotation group buys over a single angle. The Boys functional at the canonical orbitals, at the best mixing of the two bonds with the lone pair left alone, and at the maximum over the whole three-dimensional rotation group. The first step is 11.70 per cent and the second, which no two-orbital treatment can reach, is a further 2.50.

An interior maximum a third orbital allows

Two orbitals related by a mirror plane give a Boys functional with no linear term, so it has no interior maximum and no angle is ever searched for. Add the oxygen lone pair and the search over a three-dimensional rotation group finds one — eight and a half degrees of lone pair mixed into two bent bonds, worth a further two and a half per cent that no pair of orbitals could reach.

bonding · Hybrids Three cages, three answers, and none of them reassuring. For each cage: how many descriptions the search finds, what share the commonest takes, how far the whole set spreads in the functional, whether the commonest is the best, and the verdict. A search that always agrees with itself is agreeing about a choice that does not matter; a search whose descriptions genuinely differ does not return the best one.

Fifty descriptions of one molecule

A search whose largest basin takes ninety-eight per cent of its starts will report one description however long it is run, and nobody runs four thousand starts when the first fifty agree. Whether the rare ones are worse descriptions or merely rarer is one number per description, already computed and never looked at. On two of three cages they are not worse — they are the same answer, to parts per million.

beyond · Multicentre The count, for five run lengths. The fraction of runs whose nearest neighbour of the same length is coupled more strongly than a threshold, against how many decades below the closest possible coupling that threshold sits. Every curve is a straight line over this range, because the fraction is small and the geometric tail is linear in the separation there. The slope is what the next figure is about: it is the whole content of the distribution, and it is a product of two numbers.

A count rather than an average

Two couplings quoted from one distribution sit a hundred and seventy decades apart. Neither is a summary of it. The quantity that decides how much of a spectrum near a box level is resonant pairs is a count of pairs above a threshold — and it has a closed form, which is a density times a reach times the logarithm of ten.

solids · Defect How many descriptions, against how much they differ. Every cage-and-filling pair, by the number of distinct descriptions its localisation finds and by how far apart they are in the functional. If the count measured ambiguity the points would rise from left to right. The case with the most descriptions — 44 of them — has a spread of two parts in a hundred thousand, and sits at the bottom right.

Counting was right except where it mattered

A cage whose localisation gives dozens of descriptions that are all the same answer raises a worry: if degeneracy is common across the family, counting descriptions is the wrong measure of ambiguity. Across forty-eight cage-and-filling pairs it is the right measure on eleven of the thirteen that have anything to count — and it fails on the one leaned on hardest.

beyond · Multicentre The criterion is the reciprocal of the p amplitude. The two lone pairs' mixing criterion — twice the dipole between them over the separation of their centroids — against the p fraction of the outward hybrid. The curve is 1/√(p fraction), written down rather than fitted; the marks are the numerical integrals. They agree to 15 parts in a million at every hybrid, and the criterion never falls to one, so the mixed description wins at every s character there is.

The five figures were an identity

Two lone pairs satisfy the two-orbital mixing criterion by a margin of 1.732128, against √3 = 1.732051 — agreement to five figures on a number assembled from three integrals over a numerical grid. It is exact. The criterion is the reciprocal of the p amplitude of the outward hybrid, and everything else in the molecule cancels out of it.

bonding · Hybrids Five pairs, one boundary, and every case anybody asked about on one side. The mixing criterion's margin for every pair of orbitals available from the carbonyl and from ethene. Above one the mixed description wins. Three pairs were put to the criterion and all three clear the line; two more come from the same three orbitals and the same dipole matrices, and both fail it. The instrument discriminates — the selection did not.

The criterion that has never said no

The two-orbital mixing criterion is a tautology on a carbonyl's lone pairs, and it is tempting to contrast that with the double bond, where the criterion seems to discriminate. Both halves are wrong. The double bond's margin is wider, ethene's is infinite because symmetry puts both centroids at the same point, and the criterion has never returned a negative on any case it is usually put to — though the same three orbitals supply two pairs it refuses outright.

bonding · Hybrids Both criteria leave a gap, and Boys leaves a chasm. Every non-zero relative spread under each criterion, on one logarithmic axis, with the largest empty stretch shaded. Pipek–Mezey's runs a factor of 206; Boys's runs 2.8e+7 — seven decades, from numerical zero to a real spread with nothing between. So the bimodality belongs to the cages rather than to the functional, and under the second criterion the threshold matters even less.

A second criterion left a gap too

The localisation spreads are bimodal — an empty factor of two hundred around the degeneracy threshold — and the gap might belong to the criterion rather than to the cages. Boys localisation leaves a gap of seven decades on the same forty-eight pairs, so it belongs to the cages. But the two criteria disagree about six of them, in both directions, and the family's most ambiguous cage under one is exactly degenerate under the other.

beyond · Multicentre Six pairs off the diagonal, and every one of them on an axis. Each cage-and-filling pair's Pipek–Mezey spread against its Boys spread, both logarithmic, with the two thresholds drawn. Agreements sit in the two opposite corners: spreads that are zero in both, or large in both. The six disagreements do not sit between them — they sit on the axes, with one coordinate at the floor. A criterion-dependent cage is not one the two criteria half-agree about; it is one where the difference between its descriptions is invisible to one of them entirely.

The cage is on both sides

Two localisation criteria classify six cage-and-filling pairs differently, and a symmetry explanation for the six is the natural first guess. The icosahedron's graph has a hundred and twenty automorphisms, the most in the family, and supplies three of the six disagreements and nine of the agreements. What the six do have in common is sharper than a symmetry: in every one, one criterion's spread is not small but zero.

beyond · Multicentre Forty-eight rows, thirty-three calculations. Every cage-and-filling pair the family survey covers, one cell per pair, with cells that hand the localisation the same set of orbitals joined. A localisation here selects its occupied orbitals by asking which have any occupation at all, and Hund's rule puts one electron into each member of a degenerate shell before pairing any of them — so adding two electrons to a half-filled shell pairs a spin and changes nothing the search can see. Fifteen of the forty-eight rows repeat an input already in the table.

Six disagreements and three calculations

Two localisation criteria classified six of the family's forty-eight cage-and-filling pairs differently, and three of the six were consecutive fillings of one icosahedron with spreads identical to three figures. They are not three coincidences and not one degeneracy being filled: they are one calculation, because the survey's forty-eight rows are thirty-three distinct questions.

beyond · Multicentre The boundary falls inside a shell, and the shell has no inside. The 12-vertex cage at 10 electrons: its Hückel levels, with each degenerate shell drawn as its members and the occupied ones filled. The occupied set takes 2 of the 5 members of one shell — and the members of a degenerate shell are not distinguishable. Whichever combinations the eigenvalue routine happened to return are the ones that get occupied, so the density being localised is a choice made by a diagonaliser rather than a property of the cage.

The basis a diagonaliser happened to return

Six of the cage family's thirty-three inputs have their occupied set cut through the middle of a degenerate shell, and the members of a degenerate shell are interchangeable. Re-orienting the shell changes nothing about the cage, the filling or the criterion — and it moves the best localisation functional by up to twenty-one per cent, moves the count of descriptions from ten to fourteen, and flips the degeneracy label on three of the six.

beyond · Multicentre

Named alongside it

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

Model limitUnitary transformationDegeneracyClosed formApproximationCanonical orbitalsBands in a solidMulticentre bondingParticipation ratioTight-binding modelsBasisConvention

All concepts