Molecular Geometry & Bonding
what the shape decides
Concept

Probability density — where it appears

The square of the wavefunction, which is what a measurement of position would sample. It has no sign, so a picture of it throws away the distinction between a bonding and an antibonding combination.

Named by 25 essays across 6 fields — each of them below, with the objects they name alongside it.

The 2pz orbital. The 2pz orbital at the contour enclosing 90 per cent of its density — a level solved for by integration rather than chosen. The two colours are the two signs of the wavefunction, which is what distinguishes a bonding interaction from an antibonding one. Contours drawn: 2pz at 90% of its density, |ψ| = 9.48e-3.

What an orbital is

Not a region the electron occupies, not a path it follows, and for any atom but hydrogen not an exact anything. An orbital is a one-electron wavefunction, and almost every difficulty in this subject comes from forgetting that.

orbitals · Orbital 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: 1s at 90% of its density, |ψ| = 3.94e-2; 2s at 90% of its density, |ψ| = 7.40e-3; 2pz at 90% of its density, |ψ| = 9.48e-3.

Orbitals are not where the electron is

A many-electron atom has no exact orbitals at all. The orbital picture is a basis for an approximation — an extremely good one — and treating it as a description of reality is the source of most of the confusion in this subject.

wrong · Approximation Choosing a contour for 3s. The fraction of the density enclosed by a contour, against the contour's level. Picking a level is picking a point on this curve, and the usual practice of picking one that looks right is picking a point without knowing which. Contours drawn: 3s at 50% of its density, |ψ| = 6.24e-3; 3s at 90% of its density, |ψ| = 2.64e-3; 3s at 99% of its density, |ψ| = 7.15e-4.

Say what it encloses

An orbital picture is a contour at a level somebody chose, and almost no source says which. Two textbooks can draw the same orbital at visibly different sizes with the same caption, and both be printed in good faith.

orbitals · Contour The radial function of 1s. The radial part of the wavefunction, which changes sign at each node, and the radial distribution, which is the probability of finding the electron in a shell at that radius. The second vanishes at the nucleus and the first does not.

Where the electron is

The wavefunction is largest at the nucleus, the electron is most likely to be found a bohr out, and the ninety-per-cent contour is at 2.66. Three numbers, all correct, all answering different questions.

orbitals · Orbital Four measures of size for 6 orbitals. The most probable radius, the mean radius, the root-mean-square radius and the radius of the sphere holding ninety per cent of the density, for 1s, 2s, 2pz, 3s, 3dz2, 4s. All four are computed from the same radial function, all four are correct, and they are not the same number.

How big is an orbital

Four measures of size, all computed from the same radial function, all correct, and spanning a factor of two and a half for a 1s orbital. The one that governs chemistry is a fifth, and it is not a measure of size at all.

orbitals · Contour 1s, 2s, 2pz, 3s, 3dz2, 4s at one level and at one fraction. The orbitals 1s, 2s, 2pz, 3s, 3dz2, 4s, each with the contour level that encloses 90 per cent of its own density, and beside it what each one encloses when they are instead all drawn at 1s's level. The first column is a set of pictures that can be compared; the second is what a plate drawn at a single contour value actually shows. Contours drawn: 1s at 90% of its density, |ψ| = 3.94e-2; 2s at 90% of its density, |ψ| = 7.40e-3; 2pz at 90% of its density, |ψ| = 9.48e-3; 3s at 90% of its density, |ψ| = 2.64e-3; 3dz2 at 90% of its density, |ψ| = 3.60e-3; 4s at 90% of its density, |ψ| = 1.24e-3.

One level is not one comparison

A plate of orbitals drawn at a single contour value looks like a comparison and is not one. At the level that encloses ninety per cent of a 1s, a 2s encloses four per cent, a 3s under one, and a 3d has no surface at all — its wavefunction never reaches that value anywhere in space.

orbitals · Contour 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 One isovalue, many fractions — and one fraction, many isovalues. What each of 4 conventional isovalues encloses, for 7 orbitals of hydrogen, and in the last column the level each one needs to enclose 90 per cent. At 0.02 atomic units the fractions run from 0.4 to 96.2 per cent, and the levels in the last column differ by a factor of 32. A plate of orbitals drawn at one value is not a comparison of sizes. Contours drawn: 1s at 90% of its density, |ψ| = 3.94e-2; 2s at 90% of its density, |ψ| = 7.40e-3; 2pz at 90% of its density, |ψ| = 9.48e-3; 3s at 90% of its density, |ψ| = 2.64e-3; 3pz at 90% of its density, |ψ| = 3.03e-3; 3dz2 at 90% of its density, |ψ| = 3.60e-3; 4s at 90% of its density, |ψ| = 1.24e-3.

The isovalue nobody chose

Every program that draws an orbital asks for a number, and almost every user accepts the default. At 0.02 atomic units that default encloses 96 per cent of hydrogen's 1s, 52 per cent of its 2s and four tenths of one per cent of its 4s — three pictures drawn to one rule, meaning three completely different things.

orbitals · Contour The surface-honest curve and the page-honest curve. The 2pz orbital in its xz plane, drawn twice. The outer curve is the contour whose SURFACE encloses 90.0 per cent of the density in space — the claim every orbital figure here makes — and in this plane it encloses 96.7 per cent. The inner curve is the one that encloses 90 per cent in the plane, which is what a reader looking at a flat picture would take the caption to mean. The two levels differ by a factor of 1.87 and the curves differ visibly; the caption does not. Contours drawn: 2pz at 90% of its density, |ψ| = 9.48e-3.

A slice is not the surface

The page is flat, so every printed orbital is a slice through a contour rather than the contour itself — and a curve that leaves a tenth of the density outside it in space leaves about a thirtieth outside it on the page. Both claims are true of the same picture and only one of them is ever stated.

orbitals · Contour Where the electron is, and how fast it is going. The radial distribution in position on the left and in momentum on the right, for the same orbitals. The two run opposite ways: the 1s is the most compact in space and the widest in momentum, and every excited orbital that spreads out in one narrows in the other. Both are normalised, both are the same function, and neither is more fundamental than the other — the transform loses nothing and adds nothing.

The orbital in momentum space

Every orbital has a second picture as complete as the first and almost never drawn. Nothing is added by taking it — it is the same function in the other variable — but the uncertainty product falls out of it, and the functions quantum chemistry is built from turn out to be the only ones that attain the bound.

orbitals · Orbital 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 One of these is guaranteed to improve, and it is not the one anybody measures. The relative error in the energy and in four properties of the fitted function, against the number of Gaussians. The energy falls at every step, because that is what the variational principle promises. The mean radius is exact for the single-function basis and 332 thousand times worse for the two-function one, and the density at the nucleus is still 6.2 per cent wrong where the energy is wrong by 0.011 per cent.

The property that gets worse

One Gaussian fitted to hydrogen gets the mean radius exactly right — 1.500000, against an exact 1.5. Two Gaussians get it wrong by 1.4 per cent, which is three hundred and thirty-two thousand times further out, while the energy improves fivefold. The variational principle bounds one number and says nothing whatever about any other, and the sequence of errors in everything else need not even be monotone.

orbitals · Basis Three bands of one spectrum, and the bond length behind each. Nitrogen's three photoelectron bands, drawn as the vibrational intensity distributions computed from the measured bond lengths and vibrational constants of the three states of the ion. Each band's lines add to one. The middle band is spread over five lines because the electron removed came out of a strongly bonding orbital and the bond lengthened by 77.22 thousandths of an ångström; the outer two keep 92 and 88 per cent of their strength in a single line.

The width of a band is a bond length

Nitrogen's three photoelectron bands are one sharp line, a progression of five, and a line with a shoulder. Computed from the measured bond lengths of the three states of the ion, the intensities come out at 0.917, 0.263 and 0.880 in the first line of each — because removing a weakly bonding electron lengthens the bond by 18.7 thousandths of an ångström, a strongly bonding one by 77.2, and an antibonding one shortens it by 23.7.

spectra · Photoelectron The part of the bond that is outside the picture. The share of the overlap integral between two 1s orbitals that lies outside both of their 90 per cent contours, against how far apart the atoms are. At a bond length it is 8.3 per cent; by 7 bohr it is 53.4. The two drawn surfaces stop touching at 5.32 bohr, where the overlap is still 0.08 — so the picture separates well before the interaction does.

The tenth that is not drawn

A ninety per cent contour of a hydrogen 1s orbital is a sphere of radius 2.661 bohr, and two of them stop touching at 5.322 bohr — where the overlap between the two orbitals is still 0.0768 and rising in importance. At a three-ångström contact, 36.9 per cent of the overlap integral lies outside both drawn surfaces, and holding nine tenths of it inside the picture would take a contour enclosing 97.28 per cent.

orbitals · Contour 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 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 Where the electrons are, without subtracting anything. The opposite-spin pair distribution of a half-filled ring of 6 at six repulsions, by separation, each divided by what uncorrelated electrons of the same density would give. At no repulsion it is one everywhere; at a repulsion of 16 the chance of finding two electrons on one site is 0.0430 of that, and what is missing has turned up next door. Nothing here is a difference between two calculations.

Where the electrons are, without subtracting anything

A correlation energy is an exact energy less a mean-field one, so the answer depends on which mean field was picked — by a factor of 259. The pair distribution says the same thing with no subtraction in it, and two systems matched to the same correlation energy turn out to have electrons in visibly different places.

beyond · Correlation 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 The same hole, priced three ways. The correlation hole of a ring of 6 at a repulsion of 8, weighted by three interactions. With an on-site interaction the answer is 100 per cent at separation zero — as an identity, since the interaction is zero everywhere else. With one that reaches a neighbour, the enhancement at separation one costs rather than pays, and gives back 44.0 per cent of the on-site saving; with a Coulomb tail, 46.9. Everything beyond one neighbour is worth under a twentieth of the on-site term.

Half of it is given back at one bond

The correlation hole of a ring removes 1.2653 pairs from zero separation and puts 1.1126 of them one site away. With an on-site repulsion that second number costs nothing, because the interaction is zero there — but with anything that reaches a neighbour it costs 44 per cent of what the hole saved, and with a Coulomb tail 46.9.

beyond · Correlation 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 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 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 Four ways of predicting the same six separations. How far each model's predicted separation is from the measured one, pair by pair. The best additive model misses by 0.0098 ångström on average, the tabulated radii by 0.0237, radii read off the ions' own densities by 0.1828, and the balance of a Madelung attraction against a computed repulsion by 0.2421.

The residue that is two numbers

Is a shortfall between a sum of radii and a measured separation a property of the pairs, or of the compromise a universal table makes? The eight separations are two complete two-by-two blocks, so what no assignment of radii can reproduce is not a residual at all — it is an alternating sum, computed by subtraction, and it comes to three hundredths of an ångström and six.

orbitals · Contour The same count in both pictures, and no rule between them. Every hydrogenic orbital with a radial node, drawn twice: its position nodes on the left axis and its momentum nodes on the right, at the same nuclear charge. The counts are identical and exact — n − l − 1 in each — because the two radial functions are polynomials of the same degree. The positions are unrelated: a node three quarters of the way out in one picture is not three quarters of the way out, or anywhere in particular, in the other.

The nodes in the other variable

An orbital has n − l − 1 radial nodes, and it has exactly that many in momentum too — the two radial functions are polynomials of the same degree. Nothing pairs one node with another: they are zeros of two different classical families. What is exact is the product over all of them, which is a ratio of factorials and does not depend on the nuclear charge at all.

orbitals · Orbital A bond is a cosine in momentum space. The two factors a two-centre bonding orbital's momentum density is made of. One is the atomic momentum density, unchanged by the bond and falling as the eighth power of the momentum. The other is cos²(q·R/2), the interference between the two centres, whose period is fixed by the bond length and by nothing else. Everything that distinguishes a bond from two atoms in this picture is that cosine — and it has zeros where the atomic factor has none.

Oblate in the picture nobody draws

Every drawing of a σ bond shows a density stretched along the bond, and the position-space calculation agrees: the second moment along the axis is twice the one across it. In momentum the same orbital is flattened in the same direction, because the interference between the two centres cuts the distribution off at π over the bond length — and that cut-off is a zero a measurement could find.

orbitals · Orbital

Named alongside it

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

Model limitContour levelConventionEnclosed probabilityClosed formOne-electron modelsWavefunctionIsosurfaceExpectation valueNodeRadial distributionApproximation

All concepts