Molecular Geometry & Bonding
what the shape decides
Concept

Molecular orbital — where it appears

An orbital spread over a whole molecule rather than one bond. It is the natural description for a spectrum and the wrong one at dissociation, where it forces the electrons to remain paired however far the atoms separate.

Named by 31 essays across 8 fields — each of them below, with the objects they name alongside it.

Chains of 2, 4, 8, 16, 40: the levels crowd, the edges do not move. Every level of a chain of 2, 4, 8, 16, 40 sites, drawn at its computed energy on one axis. Adding sites adds levels inside a fixed interval rather than widening it, which is what makes the large system a band rather than a wider molecule.

A solid is a molecule that did not stop

Diagonalise a chain of two atoms, then four, then forty. Nothing new happens at any point, and by forty the levels are a band. The passage from molecule to solid is not a change of subject; it is the same matrix at a different size, and every step of it can be watched.

solids · Bands in a solid 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 benzene — D6h. 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.

Delocalisation

Benzene does not alternate between two structures. It has one structure, and the two Kekulé forms are basis functions in a description of it — which is a different and much less exciting claim than the one usually made.

beyond · Delocalisation 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 Overlap against separation, Z = 3.25. How the overlap integral falls as two atoms are pulled apart, for several pairs of orbitals. Where a closed form exists it is drawn over the computed curve, so the integrator is checked rather than trusted.

A double bond is not two single bonds

Carbon's single bond is 348 kilojoules a mole and its double is 614, which is not twice anything. The two halves are different integrals over different orbitals with different distance dependence, and computing them shows why no arithmetic could have made them add.

wrong · Overlap 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 The Td character table. The irreducible representations of the molecule's point group. The class headings carry the number of operations found by generating the group from the coordinates, and those counts were produced before this table was opened.

Degeneracy is a group theorem

How many orbitals can share an energy is decided before any energy is computed. The dimensions of a group's irreducible representations are the only degeneracies it permits, and a molecule with no representation larger than one cannot have a degenerate level at all.

symmetry · Representation Two orbitals, 4 electrons, S = 0 and S = 0.25. Two interacting orbitals with 4 electrons in them, drawn twice: once with the overlap set to zero and once with it kept at 0.25. Dropping the overlap makes the two shifts equal, which is the picture usually taught; keeping it makes the upper level rise by more than the lower falls, which is why four electrons in two orbitals is a repulsion.

The antibonding level goes up more

The two-level diagram every course draws is symmetric, and the symmetry is an artefact of setting the overlap to zero. Keep it, and the upper level rises further than the lower one falls — which is why helium has no molecule and why closed shells push each other apart.

bonding · Overlap methane: 2 valence bands. The measured valence photoelectron bands of methane, 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.

What a photoelectron spectrum measures

The bands of a photoelectron spectrum are routinely read off as orbital energies. They are ionisation energies, which is a different quantity — and the identification rests on two errors of about an electronvolt each that happen to have opposite signs.

wrong · Photoelectron water: 4 valence bands. The measured valence photoelectron bands of water, 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.

Water's lone pairs are not a pair

Every course draws two equivalent lone pairs on water, pointing away from the hydrogens like a pair of ears. Its photoelectron spectrum shows the two bands they would produce at 12.6 and 14.7 electronvolts, two point one apart, in different symmetry species.

bonding · Photoelectron Two orbitals, 2 electrons, S = 0 and S = 0.2. Two interacting orbitals with 2 electrons in them, drawn twice: once with the overlap set to zero and once with it kept at 0.2. Dropping the overlap makes the two shifts equal, which is the picture usually taught; keeping it makes the upper level rise by more than the lower falls, which is why four electrons in two orbitals is a repulsion.

Overlap is not interaction

Two orbitals interact by the square of their coupling divided by the distance between them in energy. A coupling half again as large, with a gap four times worse, buys a third less stabilisation — so the pair that overlaps best is often not the pair that bonds best.

applied · Overlap How often two electrons are in the same place. Double occupancy per site in the exact ground state of a chain of 2, against the repulsion. It starts at the independent-electron quarter and falls to nearly nothing. The second curve is what the state actually pays in repulsion, which peaks and then falls because the electrons have stopped meeting.

Where molecular orbital theory dissociates

The molecular orbital description of a two-electron bond puts both electrons on the same atom half the time — at every bond length, including infinite. The exact answer falls from a half to 0.0039 as the atoms separate, and the point where the two standard models are equally wrong is exactly U = 4t.

bonding · Models The valence-bond and molecular-orbital directions in one plane. The valence-bond function and the molecular-orbital function as two directions, at the angle their overlap requires — 45.0°, since they overlap by 0.7071. The exact ground state lies in the plane they span at every repulsion, to twelve decimal places, and swings from one to the other as the repulsion grows without ever arriving. Neither picture is a special case of the other and the answer is not either of them.

Two pictures, one plane

Molecular orbital theory and valence bond theory are taught as rival descriptions of a two-electron bond. In a model small enough to solve exactly they are two vectors in a two-dimensional space, the exact answer lies in the plane they span at every repulsion, and it is neither of them at any repulsion but two.

bonding · Models A σ contour at 90 per cent, and the two atomic ones. The section through both nuclei of the surface enclosing 90 per cent of the bonding orbital's density at 2 bohr, with circles marking where two atomic contours of the same stated fraction would be. The two pictures are different shapes and enclose different amounts, and the atomic pair encloses 91.70 per cent of the molecular orbital's density. Contours drawn: 1s at 90% of its density, |ψ| = 3.94e-2.

A bond is not two atoms overlapping

The surface enclosing ninety per cent of a σ orbital's density is one closed surface with both nuclei inside it, at a level of 0.0359. The two atomic surfaces usually drawn instead sit at 0.0394, are a different shape, and enclose 91.70 per cent of the same orbital — and whether the molecular one is one object or two is decided by the fraction the caption claims, anywhere between 2.1 and 5.2 ångström.

orbitals · Contour 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 Three lines, then a hundred. The exact removal spectrum of a 6-site Hubbard ring at half filling: every final state of the ion, at the energy it costs to reach and with the intensity the matrix element gives it. With no repulsion there are 3 lines and they are the occupied orbital energies. At U = 8 there are 100, on a molecule with 6 orbitals — so the spectrum cannot be read as a list of orbital energies, because there are more bands in it than there are orbitals to name.

More bands than there are orbitals

A photoelectron spectrum is read as a list of orbital energies, one band per occupied orbital. Computed exactly for a six-orbital ring, it has three bands with no repulsion and a hundred with eight — and by then fifty-three per cent of the intensity is in lines that no orbital corresponds to. The total intensity is three at every repulsion, exactly, because that is a sum rule and not a fit.

spectra · Photoelectron The test that works until it does not. How many times stronger the weakest fundamental is than the strongest satellite, against the repulsion, on a half-filled ring of six. It starts at 23.8 and falls to 1.15 — a spectrum whose tallest satellite is as tall as its shortest band. The marked repulsion is where the other test fails as well: satellites start appearing inside the range the fundamentals span, so neither height nor position sorts the spectrum.

A hundred lines and no way to sort them

A spectrum with a hundred lines has six fundamentals in it somewhere. Sorting by height works until the tallest satellite is as tall as the shortest band, and sorting by position works until satellites start arriving between the bands — and on a ring of six both stop working at the same repulsion.

spectra · Photoelectron The metal's charge is a coordinate, and the count is not. The metal's charge in an octahedral d6 complex, against how much of each shared pair the ligand is given. Half each is Mulliken's rule and the whole to the ligand is the assumption an oxidation state makes; the answer runs over 2.06 electrons between them. The oxidation state itself is 0, which is off the end of the range, and the electron count is the same number at every point on it.

An integer nobody measured

The oxidation state of chromium in the hexacarbonyl is zero. Its charge, computed from the same wavefunction, is anywhere between −3.04 and −0.98 depending on how the shared electrons are divided — and the integer sits outside that whole range. The electron count, meanwhile, is eighteen at every point on it.

applied · Electron count Two molecules, one eigenvalue, and 1.27 eV between them. Six alternant hydrocarbons placed by the Hückel eigenvalue of their highest occupied level — computed by diagonalising each molecule's own adjacency matrix — against the measured first π ionisation energy. Ethene and benzene share an eigenvalue of exactly 1 and their measurements differ by 1.27 eV; butadiene and naphthalene share 0.618 and differ by 0.94. A model that reads only the eigenvalue is a function of it, so it must give each pair one answer, and the two vertical pairs are the whole of its error.

A parameter that never finds a value

Show a two-parameter model six measurements instead of two and it stops being underdetermined and starts being wrong. Adding the third parameter improves the fit by one part in eighty, moves the resonance integral by a factor of four, and never finds a best value at all — because nine tenths of the error is a term the model does not have.

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 answer a search is most likely to give

If a cage has ten equally good localised descriptions, why does the literature agree about its picture? The hoped-for answer was that one basin is very large. Counting four hundred and eighty starting points says it is not: two independent searches agree one time in ten, and the description they most often return is not the best one.

beyond · Multicentre The current does not divide equally between equal rings. The current each ring of an acene carries under a uniform field, ring by ring, for four acenes. Naphthalene's two rings are equal by symmetry; anthracene's middle ring carries 1.180 times what its outer ones do, and tetracene's inner rings 1.222 times. Every ring has the same area and the same six carbons, and the response is a matrix rather than a set of parallel loops.

The current does not divide

A fused ring system's response was computed from the areas of its rings, and the obvious next question was whether the current divides between them the way it divides between two resistors. Giving each ring its own flux and taking the second derivatives says no: the response is a matrix, its off-diagonal entries are nearly half its diagonal ones, and anthracene's middle ring carries 1.18 times what its outer rings do.

symmetry · Aromaticity However hard the π channel is driven, the counted orbital stays the metal's. The metal's share of the filled T₂g orbital against the π coupling, with the eighteen-electron count drawn beside it. The share falls from 1 to 0.5467 across a coupling range of 80,000 cm⁻¹ and approaches a half from above without reaching it: the lower eigenvector of a two-level problem always carries more of the lower basis function, whatever the coupling. The count is eighteen at every point.

The count that cannot be broken by strength

Back-donation puts electrons into orbitals that are not the metal's, and the eighteen-electron rule counts the metal's nine. Turning the π channel up as far as it will go never breaks it: the counted orbital's metal share falls from 100 per cent to 54.67 and approaches a half from above without reaching it. What does flip it is not strength but order.

applied · Electron count 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 Ten molecules, twenty-six arrangements, three disagreements. Every arrangement of every one of the ten molecules, with the point group recovered from the arrangement's own coordinates and the ligand σ set reduced in it. 27 of them can be worked in a tabulated group; the formula n + L − 4 is right for 23 and wrong for 4. Every failure is a planar arrangement of four or more ligands, and every one of them is a molecule that does not adopt that arrangement.

The square that wastes an orbital

The orphan count that prices hypervalency was treated as a property of a molecule's composition — ligands plus lone pairs minus four. Run on twenty-six arrangements of the same ten molecules it is right for twenty-three and wrong for three, and all three are flat. A planar arrangement gives a main-group centre three usable orbitals rather than four, so the count is a property of the shape.

beyond · Hypervalency The filled orbital at 3 bohr, with a node in the middle of the bond. The combination the two-level model puts lower at 3 bohr, drawn as contours of the wavefunction with the two signs in the two colours. The overlap here is 0.4825, so the interaction is of the sign that fills the plus combination. There is a nodal plane through the midpoint: the pair the model calls bonded has no density at all between its nuclei.

A bond with nothing in the middle

Two head-on 2p functions have an overlap that changes sign at 5.03 bohr, and the picture of what that means is worth drawing. Below that separation the combination the model fills has a nodal plane through the midpoint of the bond, so two electrons in it put exactly nothing between the nuclei; above it the same model fills the other one. Which picture a bonding orbital has is decided by a separation.

bonding · Overlap 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 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 One geometry, four electron counts, four answers. The bond order between two orbitals with exactly no overlap and no resonance integral, as the third orbital's energy is swept, at every count the trio can hold. With none it is identically zero. With two it is positive and rises past one. With four it is negative and reaches -0.954. With six it is a horizontal line — the third orbital's energy stops mattering entirely.

A filled shell is not an empty statement

A bond order of −0.954 between two orbitals with no overlap and no resonance integral invites the prediction that at six electrons — every level occupied, the sum over a complete set — it would be exactly zero. It is exactly one seventh, and the reason is that a complete set in a non-orthogonal basis sums to the inverse of the overlap matrix, which has entries where the overlap has none.

wrong · Overlap An antibonding occupation fills the zero and moves the minimum. The profile along the bond near π/R, per electron, on a logarithmic scale, for five antibonding occupations of the same two orbitals. With nothing in the antibonding orbital the profile is exactly zero at π/R = 1.573. Two hundredths of an electron leave a minimum at 1.608, which reads the separation as 1.954 bohr instead of 1.997. At 0.104 the minimum becomes a flat shoulder, and the Heitler–London bond, at 0.236, has none.

The zero belongs to one determinant

A bonding orbital's momentum profile along the bond is exactly zero at π/R, and that zero reads a bond length with nothing fitted. It is a property of putting every electron into that one orbital. Any antibonding occupation fills it in linearly and drags the minimum outward, a tenth of an electron erases it, and the valence-bond wavefunction built from the same two functions never has one at any separation.

orbitals · Orbital The zero at π/R follows parity, not bonding. The bonding and antibonding combinations of three atomic functions on nitrogen, each along the bond and each normalised to its own largest value, against momentum in units of π/R. For 2s the bonding combination is zero at π/R and the antibonding one is not. For 2p along the bond it is the other way round: the σ bond carries a sine, is zero at the origin and near its largest at π/R, and the antibonding combination carries the cosine. For 2p across the bond the π bond carries the cosine again. The factor is a cosine exactly when the orbital's inversion parity matches the atomic function's.

The zero is a parity, not a bond

A hydrogen-like σ bond has a momentum profile along its axis that vanishes at π/R, and it is natural to read that zero as a bond's signature. Built from 2p functions pointing along the axis, the σ bond carries a sine instead and sits at 83 per cent of its peak there. Which factor an orbital carries is decided by whether its inversion parity matches its atom's, and bonding has nothing to do with it.

orbitals · Orbital Folding the ring off its plane never gives the orbital back. For rings of four to eight ligands round a centre with no lone pair, the orphan count minus the formula n + L − 4, at polar angles from 60° to 120°. The upper dot in each row is the bare ring and the lower the same ring with a ligand on the axis. The bare ring is one over the formula at every angle, including 90°, where the ring is flat and its group is D₄ₕ, D₅ₕ or D₆ₕ; there is no table here for D₇ₕ or D₈ₕ. The capped ring agrees with the formula at every angle, 90° included, where the ring is exactly flat and the apex alone keeps its group C₄ᵥ to C₈ᵥ.

Folding the ring does not give the orbital back

Three arrangements break the orphan count n + L − 4, all flat, and the reason given was flatness: the p orbital perpendicular to the ring has no ligand combination of its species. Fold the ring into an umbrella at any angle and that orbital becomes totally symmetric — and the count stays wrong by exactly one, for rings of four to eight. The ring offers one symmetric combination to a centre with two symmetric orbitals. Writing C₅ᵥ to see it also counts the pentagonal pyramid at last, and the formula holds there.

beyond · Hypervalency

Named alongside it

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

Model limitOverlap integralBasisEigenvalueAntibondingClosed formConventionDegeneracyOne-electron modelsApproximationElectron correlationIonisation energy

All concepts