Molecular Geometry & Bonding
what the shape decides
Concept

Closed-shell configurations — where it appears

A configuration in which every occupied level is full, leaving no partly filled degenerate set. It gains nothing from a first-order distortion, which is why closed-shell molecules keep their symmetry unless a low-lying excited state takes it away.

Named by 25 essays across 7 fields — each of them below, with the objects they name alongside it.

Eighteen electrons, from a reduction. The ligand σ orbitals of an octahedral complex reduced in Oh (A₁g ⊕ Eg ⊕ T₁u), matched against the metal's nine valence orbitals by species, and counted. 6 bonding and 3 non-bonding orbitals hold 18 electrons.

Eighteen is a count

The eighteen-electron rule is usually justified by adding up an s, three p and five d orbitals. That is a restatement rather than a reason. Reduce the ligand orbitals in the complex's own point group, match them against the metal's by symmetry, and the number that comes out is the count of orbitals lying below a gap — which is eighteen for an octahedron, sixteen for a square plane, and eighteen again for a tetrahedron for a different reason.

applied · Electron count 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.

Counting electrons in an extended structure

The octet rule, Hückel's 4n + 2 and the 8 − N rule that predicts the structures of the main-group elements are one rule counted three ways. Each says the same thing — close the shell — and each stops being reliable at exactly the point where closing it becomes impossible.

solids · Metal 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 Orbitals at the 90 per cent contour. Several orbitals drawn at the same enclosed fraction and, unless stated otherwise, at the same scale — so the sizes on the page are the sizes. Each contour was solved for separately by integrating that orbital's own density. Contours drawn: 2px at 90% of its density, |ψ| = 9.49e-3; 2py at 90% of its density, |ψ| = 9.49e-3; 2pz at 90% of its density, |ψ| = 9.48e-3.

A filled shell has no shape

Sum the angular densities of a complete p shell and the answer is 3/4π in every direction, to sixteen decimal places. A filled d shell gives 5/4π. The lobes are in the decomposition and not in the density, and nothing that measures a closed-shell atom can see them.

orbitals · Contour The largest angle each ring size can have. The ceiling on a bond angle in a closed ring of equal bonds, 180°(n−2)/n, which is the interior angle of the regular planar polygon and follows from a closed curve having to turn through a full circle. The line at 109.47° is the tetrahedral angle: rings of 3, 4, 5 atoms cannot reach it at any geometry whatever, and every larger ring can, by leaving the plane.

The angle a ring cannot have

A closed ring of equal bonds has to turn through a full circle, so its bond angles cannot average more than 180°(n−2)/n. Three, four and five atoms are below the tetrahedral angle at every geometry whatever; six is above it, and reaches it only by leaving the plane.

shape · Strain How often two electrons are in the same place. Double occupancy per site in the exact ground state of a chain of 4, against the repulsion. It starts at the independent-electron quarter and falls to nearly nothing. The second curve is how the neighbouring spins line up in the same wavefunction, which is already -0.0750 at no repulsion at all — that part is exchange — and deepens as the electrons are kept apart.

The hole that is not repulsion

Two electrons in a bond keep out of each other's way, and the obvious reason is that they repel. Setting the repulsion to zero and computing the spin correlation exactly gives −0.125 rather than nothing, and the number is reproduced to nine decimal places by a determinant with no repulsion in it at all.

beyond · Correlation Two sites, two electrons, every level exactly. The four states of a two-site Hubbard model against the on-site repulsion, in units of the hopping. The left-hand edge is the one-electron answer — -2t — and the dashed line is the lowest state with the spins parallel, which cannot hop at all and so does not move with U.

The smallest many-electron calculation

A Hückel energy comes from a model with one electron in it. Add a single term — a cost for two electrons on the same site — and the problem stops being a matrix of size n and becomes a matrix over configurations. Four sites give thirty-six of them, which is small enough to solve exactly, and the answers correct two things the one-electron model got wrong.

bonding · Correlation Why d⁸ is square planar and nothing else is. The ligand field energy a square plane buys over a tetrahedron, for every d^n, each geometry in its own ground state. The maximum is at d⁸ (1.73 in units of eσ), it is exactly zero for an empty shell and a full one, and d⁸ is one of only two fillings where the plane is diamagnetic and the tetrahedron is not.

VSEPR does not reach a transition metal

Four ligands minimising their repulsion give a tetrahedron, whatever the metal. Half the four-coordinate complexes of the platinum group are square planar, which has larger repulsion, and the term that overrules it is largest at d⁸ and exactly zero at d⁰ and d¹⁰ — which is where the repulsion rule works again.

wrong · VSEPR The bonds are what is left over. Thirteen carbonyls and clusters, with the total valence electron count, the number of metal–metal bonds that leaves over from eighteen per metal, and the number the crystal structure has. They agree for every cluster up to five metals. At six they disagree by one, in both entries tested — and the skeletal count in the last column, which is the rule boranes are analysed with, comes out at n + 1 for both, meaning a closed deltahedron, which an octahedron is.

The bonds are what is left over

Every metal wants eighteen electrons and a metal–metal bond gives one to each of its partners, so the number of bonds in a cluster is what is left over after the counting. It works for every carbonyl cluster up to five metals and fails at six by exactly one bond — where the other counting rule, the one boranes are analysed with, is right.

applied · Electron count A ring of 60: binding against filling. The occupied-level sum per site of a ring of 60, swept from an empty band to a full one. It rises to a maximum at half filling, falls symmetrically, and reaches exactly zero when every level is occupied. The thin curve is the closed form the finite sum approaches, and the second trace is the same sweep for the structure with ends.

Half filled is as bonded as it gets

Sweep a band from empty to full and the binding it supplies rises to a maximum at half filling and returns to exactly zero when every level is occupied. A completely filled band holds a solid together no more than a filled shell holds two helium atoms together, and for the same reason.

solids · Bands in a solid Which count closes a shell, ligand by ligand. For each ligand the spectrochemical series has parameters for: its π parameter, the two gaps, and which electron count the deeper one sits above. The π donors close at twelve and the π acceptors at eighteen, and the ligand's charge predicts neither.

The count that is not always eighteen

The eighteen-electron rule is a shell closure, and an octahedral level diagram has two of them — one at twelve electrons and one at eighteen. Which is deeper is decided by the sign of one parameter: with a π acceptor the gap above eighteen is 3.720 and above twelve 2.280, and with a π donor the two swap over exactly.

applied · Electron count Where two He atoms stop, with no contact distance put in. The repulsion between two He atoms, computed from the overlap of their filled valence orbitals — four electrons in a bonding and an antibonding pair, of which the antibonding one rises further — against London's dispersion attraction from the measured polarisability and ionisation energy. The minimum is at 3.14 ångström where the tabulated van der Waals contact is 2.8, and nothing anywhere in the calculation is a length.

The radius that was tabulated

A van der Waals radius is a fitted number that every structural argument in chemistry uses. Computing it instead — a repulsion taken from computed overlap integrals, an attraction taken from two measured scalars, and no length anywhere — puts helium's contact at 3.140 ångström against a tabulated 2.80, neon's at 3.226 against 3.08 and argon's at 3.996 against 3.76. And the surface two atoms actually stop at encloses 99.4 per cent of the density, not ninety.

orbitals · Contour How many times more a metal carries, and when. The ratio of the carriers in a uniform ring to those in an alternating one of the same size, at four sizes and six temperatures. Down the left-hand column the two are indistinguishable, because a ring of 42 at kT = 0.002 has a level spacing larger than the temperature and is no more a metal than the gapped one is. Along the bottom row they are indistinguishable again, because the temperature is larger than the gap. The word only means anything in the middle.

The metal a thermometer cannot find

A metal is a system with excitations of arbitrarily small energy, which is a claim about a sequence of finite systems rather than about any one of them. Put a temperature on it and the claim needs a second limit, and the two do not commute: a uniform ring of forty-two at kT = 0.002 carries exactly as much as an alternating one, and at kT = 0.1 a ring of three hundred and twenty-two carries only four times as much.

wrong · Metal The fraction a table encloses is not one number. For each ion, the fraction of its own electron density that lies inside its tabulated radius. Along each isoelectronic series the answer runs over eight percentage points, where three neutral atoms at their contact distances spanned three tenths of one. And it peaks at the neutral rather than falling through it, because a van der Waals radius is fitted to the distance between two atoms that are not bonded and an ionic radius is one term of a sum fitted to the distance between two that are.

The surface a table draws

Three noble gases stop at a surface enclosing between 99.38 and 99.75 per cent of their density — a near-constant, and an argument that a contour is a real boundary. Charge the atoms and it collapses. Across ten electrons the tabulated radius encloses anything from 94.4 to 99.98 per cent, it peaks at the neutral rather than trending through it, and radii built at a fixed enclosure do not add up to a single measured separation.

orbitals · Contour A mixture is not the average of its ends. The binding per site of a square net whose sites are of two kinds, against how many of each. The straight line is arithmetic rather than a fit: a structure of one kind only has every level shifted by ±δ, so the two ends and the line between them are known before anything is diagonalised. Every mixture lies above it — more bound — by as much as 0.43 per site at the middle, and that departure is the whole of what makes an ordered compound worth forming.

A mixture is not the average of its ends

Half of a structure's sites raised and half lowered, and the line between the two pure ends is arithmetic — no diagonalisation needed. Every mixture lies below it, by 0.42987 per site for the ordered arrangement and 0.23690 for the segregated one at the same composition, so composition fixes neither the binding nor the gap. And the departure is not quadratic in the contrast: it grows as its 1.79 power in a chain and its 1.28 power on a square net.

solids · Cohesion 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 Every arrangement, and the winner is not the one with the most unlike bonds. All 1820 ways of raising 4 of 16 sites on a wrapped square net, at a contrast of 4, each placed by its count of unlike bonds against the binding it gives. The best arrangement has 12 unlike bonds where 16 is available, and it binds at 1.103953 against 1.080031 for the best of those that do have the most. The count and the spectrum are two different orderings.

The arrangement a count cannot pick

Three arrangements of one composition came out ordered by their count of unlike bonds, which looked like a rule. Enumerating every arrangement instead of three shows it is not one: it holds at every composition on a square net at a small contrast, fails at four of them at a large contrast, and fails on a triangular net at any contrast at all.

solids · Cohesion A ninety per cent surface with a neighbour beside it. The contour enclosing 90 per cent of a one-electron ion's density at an effective charge of 1.6, drawn with no field as a circle and in a field of 0.05 atomic units as the closed curve. The surface moves out by 47.3 millibohr on the side the field pulls the density towards and in by the same amount on the far side — 2.84 per cent of its own radius. What the sphere encloses does not change to first order; only where the surface is does.

The surface a neighbour moves

An ion in a crystal sits in the field of the ion next to it, and that field moves its contour. The displacement has a closed form, it is checked against the polarisability it implies, and it turns out to be almost perfectly anti-correlated with the discrepancy it was proposed to explain — the pairs that need the most correction get the least.

orbitals · Contour A control that ranked better than the mechanism. Rank correlations against the additivity shortfall, over eight ion pairs. The overlap of the two closed shells ranks at 0.8571 — but the cation's formal charge, which cannot be a mechanism, ranks at 0.9524, so the set is confounded: its eight pairs split four and four by charge and everything else rises with it. Held fixed within a charge group the overlap still ranks at 0.80 — and so does the softness, at -1.00. Four pairs cannot separate two candidates.

A control that outranked the mechanism

Ruling polarisation out left one candidate, and the closed-shell overlap ranks at 0.857 against the additivity shortfall — which looked like the answer until the control was read. The cation's formal charge, which cannot be a mechanism, ranks at 0.9524. Eight pairs split four and four by charge cannot separate anything, and within a charge group two candidates both rank perfectly.

orbitals · Contour Eight wells, and where each one puts its pair. The total energy of each pair against separation, with the measured distance marked on every curve. The wells are deep and their minima are in the right region — tenths of an ångström from the measurements — which is what makes the comparison worth making. What they are not is closer to the measurements than the sum of two tabulated radii, and that is the result.

A size a confound cannot supply

A rank correlation of 0.857 was beaten by a control that cannot be a mechanism, so a size is the next thing to ask for: does a closed-shell repulsion of the computed magnitude displace two ions by the tenths of an ångström the additive radii are wrong by. It does not. The balance of a Madelung attraction against six computed repulsions predicts six separations to 0.242 ångström where adding two tabulated radii predicts them to 0.183, and the displacement it produces ranks at 0.14 against the shortfall it was proposed to explain.

orbitals · Contour 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 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 Two conditions, and one factor that nearly meets both. The mean error of each group of pairs as the third-row p exponents alone are contracted, with the second-row pairs untouched by construction. One factor has to bring both other groups onto them. The pairs with one third-row ion arrive at 1.376 and potassium chloride at 1.346, 2.2 per cent apart — a test that could have produced two factors nowhere near each other, and did not.

One contraction for two conditions

The ionic model's errors run with the row of the periodic table, and the test proposed for that — stiffen the repulsion and watch for second-row pairs moving out and third-row pairs moving in — produces exactly that pattern from a repulsion that knows nothing about shells. The test that can fail contracts the third-row shells alone and asks one factor to bring two different groups of pairs onto the second-row ones. The two factors needed are 1.35 and 1.38.

orbitals · Contour Three ions with the same shell, and three different contractions. Each pair with one third-row ion, its error plotted against a contraction of that ion's p exponents alone. Sodium chloride's error falls to the second-row pairs' mean when chloride is contracted by 1.302, potassium fluoride's when potassium is contracted by 1.387, and calcium oxide's when calcium is contracted by 1.441. The single factor that contracts every third-row shell at once, 1.376, is drawn faint: it sits between the three, and the three span 10.7 per cent.

Three contractions for one shell

One contraction of the third-row p shells removed the row pattern from an ionic model's errors, with two conditions met by factors 2.2 per cent apart, and left the order of three pairs untouched. Taken ion by ion, chloride needs 1.302, potassium 1.387 and calcium 1.441 — the pairs' own order — and potassium chloride, fitted on nothing, lands among the second-row pairs. The single factor's two conditions agreed because both were averages of these three.

orbitals · Contour 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

Named alongside it

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

Model limitOverlap integralConventionEffective nuclear chargeOne-electron modelsProbability densityAntibondingContour levelCoordination complexDegeneracyElectron countFilling

All concepts