Molecular Geometry & Bonding
what the shape decides
Concept

Bond length — where it appears

The separation between two bonded nuclei, which is several different numbers. The minimum of the potential, the average in the ground vibrational state and the value a rotational constant implies differ by more than a hundredth of an ångström for a bond to hydrogen.

Named by 27 essays across 7 fields — each of them below, with the objects they name alongside it.

d⁹: what a tetragonal distortion is worth. The electronic energy of d⁹, the elastic cost of the distortion, and their sum, against the fractional elongation of the axial bonds. The best distortion is at 0.14 and it is worth 0.54 in units of eσ; d⁶ in the same field gains 0, which is nothing.

Copper is never quite octahedral

A d⁹ ion in an octahedral field has three electrons in a doubly degenerate pair, which cannot be shared evenly. The energy it gains by distorting is linear in the distortion and the elastic cost is quadratic, so no stiffness holds the symmetric structure — and the four configurations with an even occupation gain exactly nothing.

applied · Peierls distortion carbonyl sulfide: a linear. The principal axes of carbonyl sulfide drawn at its centre of mass, with the moment of inertia about each. Which kind of top this makes it is decided by comparing three numbers, and the point group forces the same answer independently: an axis of order infinity means a linear molecule, with one moment at zero forbids an asymmetric top.

The rotational spectrum is a moment of inertia

Every line in a microwave spectrum sits at a multiple of one number, and that number is a conversion constant divided by a sum of mass times distance squared. No bonding argument appears anywhere in it.

spectra · Rotation A structure out of a spectrum. Two rotational constants and two bond lengths, three times over, from three pairs of carbonyl sulfide isotopologues. Above them, the same inversion run on moments computed from a known structure, which returns it to twelve figures. The measured pairs disagree with one another by 7.4 milliangstrom, which is the difference between a ground-state average and an equilibrium geometry.

A bond length out of a spectrum

A linear triatomic has two bond lengths and one moment of inertia, so one measurement cannot determine it. Substituting an isotope gives a second measurement on the same structure, and two equations in two unknowns have a solution — which comes out differently depending on which isotope is used.

spectra · Rotation 6 fitted force fields. Every valence force field fitted here, ordered by the size of its bond stretching constant, with the stretching frequencies of the molecule beside it. The two orders are not the same, which is the whole of what separates a force constant from a frequency. The last two columns say how many constants were fitted to how many observed frequencies, and a field with as many of the first as the molecule has distinct frequencies fits exactly and reports nothing.

The frequency is not the bond strength

Sulfur dioxide's S–O force constant is larger than water's O–H constant, and its stretching bands sit at a third of the frequency. A vibrational frequency carries a mass as well as a force, and the two cannot be separated by looking at a spectrum.

wrong · Normal mode 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 The exponent the molecule chooses, and what it buys. The 1s exponent that minimises the energy of a one-electron diatomic, against the separation of the nuclei, with the binding curves at that exponent and at the free atom's. Held at ζ = 1 the bond comes out at 2.49 bohr and binds 0.0648 hartree; with the exponent free it comes out at 2.00 bohr at ζ = 1.238 and binds 0.0865. The exact answer for this molecule is 2.00 bohr and 0.1026.

The atom does not bring its own orbital

Build a one-electron diatomic from two hydrogen 1s functions and it comes out 25 per cent too long and 37 per cent too weakly bound. Let the molecule choose how large those functions are and the bond length is right to three figures, at an exponent of 1.238 — the orbital contracts by a quarter when the bond forms.

orbitals · Orbital 7 molecules, three moments each. The principal moments of inertia of water, sulfur dioxide, formaldehyde, boron trifluoride, ammonia, methane, hydrogen peroxide, in u Ų, with the inertial defect and the asymmetry parameter beside them. The defect vanishes exactly for a planar structure and does not for any other, so three numbers computed from the coordinates decide planarity with no model anywhere in the argument. Every classification is checked against the one the molecule's point group forces.

The moment that is the sum of the other two

Three numbers computed from the coordinates and the masses decide whether a molecule is flat. For water, sulfur dioxide, formaldehyde, benzene and every other planar structure here the largest moment of inertia is the sum of the other two exactly; for ammonia it misses by 0.76 and for methane by 3.18.

spectra · Rotation The cost of a ratio decided somewhere else. Four bases containing exactly the same six primitives, differing only in how many of the linear coefficients the calculation may choose. The horizontal axis is the effective nuclear charge, which is this one-electron problem's only knob for a different environment; the contraction was fitted at one. At 1.238 — the exponent H₂⁺ chooses when a bond forms — the fully contracted basis is 0.0283 hartree above what the same six functions could give, and one freed coefficient removes most of it.

A contraction is a decision made once

Every published basis set freezes its primitive functions into fixed combinations, on an isolated atom, before any molecule is in sight. Freeing one coefficient recovers three quarters of what that costs — and freeing it at the other end of the basis recovers one per cent.

orbitals · Basis Which site a long bond takes, and it is not the one the rule says. The energy of the axial placement minus the energy of the equatorial one, against the odd bond's length. Above the line the equatorial placement wins and below it the axial one does. The textbook sentence is that a bulkier group goes equatorial where there is more room; given a longer bond and nothing else, the repulsion model puts it AXIAL, at every length, by a margin that grows. A site pushed further out interacts with everything less, so what is left to decide is the arrangement of the four sites left behind — and three equatorial with one axial is the better set of four.

The sites are not the same size

Every arrangement in this collection puts its sites on one sphere, which is an assumption about bond lengths made silently. Give the repulsion model a bond length and it predicts that the long bond goes axial — the opposite of the rule the model is always cited for.

shape · VSEPR The twist the ring forces on the bond. For each ring size, the largest torsion about the double bond that the ring will close on — 180° being a flat trans arrangement and 90° being a π bond broken outright. The six-ring will not close at any torsion tested. The eight-ring reaches 139.3°, against 136° measured in trans-cyclooctene by diffraction: a model with bond lengths and bond angles in it and no energy anywhere agrees with the crystal to a few degrees.

The double bond a ring cannot hold

A trans double bond needs a ring of nine carbons to sit flat, and the eight-ring will hold one twisted by 40.7 degrees — against 136 degrees measured in trans-cyclooctene. The same eight-ring threshold, applied by counting ring sizes, sorts nine bridgehead alkenes correctly with no bridgehead anywhere in the argument.

shape · Strain A microwave constant predicted from an infrared one. For four diatomics: the rotational constant and the stretching frequency, both measured, and the centrifugal distortion constant predicted from them by 4B³/ω² — then the constant a microwave spectroscopist fits to the line positions. The prediction and the fit agree within a few per cent across three orders of magnitude in the quantity, and nothing connects the two measurements except the assumption that the bond stretching under rotation is the same bond that vibrates.

The rotor that stretches

A rigid rotor's lines are evenly spaced, and a real molecule's are not — it pulls itself apart as it spins. How much is not a fitting parameter: it follows from the stretching frequency by one relation, and the prediction agrees with the measured constant to a few per cent across four molecules spanning three orders of magnitude.

spectra · Rotation water, drawn with its nuclei the size they are. The molecule with a disc round each nucleus whose radius is the computed root-mean-square displacement of that nucleus in the vibrational ground state. The hydrogens' discs are a substantial fraction of the bond length, and this is at no temperature at all.

The atoms are not at the points

Every structure in this collection is a set of points, and every bond angle it argues about is a property of that set. Computed from the fitted force fields it already has, water's hydrogens are 0.094 Å from where they are drawn and its bond angle has a spread of 8.9 degrees — larger than the difference between 104.5 and the tetrahedral value that half the essays here are about. This is at no temperature at all.

shape · Approximation H³⁵Cl: the well, its states and their averages. The Morse potential built from H³⁵Cl's measured vibrational constants, with the lowest four states drawn at their computed energies and the average separation of each marked. Every average lies to the right of the minimum, because the well is not symmetric — and they move outward as the state rises.

The bond length that depends on the isotope

Hydrogen chloride and deuterium chloride have the same potential energy curve, and their measured equilibrium lengths agree to three hundredths of a milliångström. Their average bond lengths differ by 4.34 mÅ — a hundred times more — because a lighter atom explores more of a well that is not symmetric.

wrong · Approximation 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 A photoelectron band is a filter, and the group chooses the filter. The Huang–Rhys factor of every vibration of five molecules under a change of geometry that lengthens every bond alike — which is what removing an electron from a non-degenerate orbital does. On a logarithmic scale spanning sixteen decades, eight modes carry the whole of it and the rest sit on the floor at arithmetic noise. Which ones is decided by the point group: only a totally symmetric vibration can appear, whatever the size of the change.

A band is a filter on the modes

A photoelectron band's vibrational structure reports the frequencies of a few of the ion's vibrations and is silent about the rest, and which few is decided by the point group before any geometry is known. Under a change of shape that lengthens every bond alike, methane's totally symmetric stretch gets a Huang–Rhys factor of 0.905 and its other eight modes get between 10⁻²⁸ and 10⁻³⁵.

spectra · Photoelectron The splitting against the square of one computed overlap. five chromium(III) complexes: the measured ligand-field splitting against the square of the metal–ligand σ overlap, computed from Slater-type functions at the measured bond lengths. The angular overlap model says the splitting is proportional to that square and to no other power, and the line drawn through the origin is that proportionality with nothing fitted but its slope. Across a series in which the splitting doubles, the ratio varies by 30.75 per cent.

The splitting against something structural

The angular overlap model says a ligand field splitting is proportional to the square of one overlap integral and to no other power. Computing that integral from Slater functions at the measured bond lengths, for five chromium complexes whose splittings run from 13,600 to 26,700 wavenumbers, the ratio varies by thirty-one per cent with nothing fitted. And a power law on the donor's effective charge, at an exponent nobody predicted, does slightly better.

applied · Ligand field One pi energy, two delocalisation energies. For each of six rings: the computed pi energy, the energy of the same atoms with one bond deleted, and the delocalisation energy that follows from each of the two reference states. Every entry is an eigenvalue sum; the two right-hand columns differ only in what was subtracted from the second column.

The frame that was allowed to relax

Four changes of frame were tested on nine quantities and none of them could move a bond order, because a bond order is a property of the eigenvectors and every change left the eigenvectors alone. Letting the geometry answer back does move them — butadiene's central bond falls from 0.4472 to 0.3676 — and it moves naphthalene's the other way, because its weakest bond is the one two rings share and relaxation strengthens it.

bonding · Delocalisation Two errors, opposite signs, four orders of magnitude apart. A finite basis makes H₂⁺'s binding too large by letting each atom borrow the other's functions, and too small by describing the molecule incompletely. Both are computed here against the exact binding of 0.102634 hartree. The second is thousands of times the first at every basis size, and it is the first that counterpoise removes — so the corrected number is further from the true one than the uncorrected at every row of this table.

The basis the other atom lent

Two atoms in a molecule are described in each other's functions and the separated atoms are not, so the molecule is treated better than the pieces and the binding comes out too large. That is the basis set superposition error, it is removed by a standard correction, and for H₂⁺ in four Gaussians a centre it is six tenths of a microhartree against an incompleteness error of twelve millihartree — a factor of eighteen thousand the other way.

orbitals · Basis A correction computed at 3 bohr and used everywhere. Three binding curves for H₂⁺ in 2 Gaussians a centre: uncorrected, properly counterpoise corrected at every separation, and corrected once at 3 bohr with that value subtracted throughout. The frozen curve is the uncorrected one shifted down by a constant, so its minimum sits at 2.2270 bohr — exactly where the uncorrected minimum is, and 4.2 millibohr from where the full correction puts it. The depth moves and the structure does not.

A correction computed at one length

The counterpoise correction is expensive, so it is evaluated once at a reference geometry and subtracted across a whole potential surface. A constant does not move a minimum — so a frozen correction returns the uncorrected bond length exactly, at every reference geometry and in every basis, and everything the correction does to a structure is the part that has just been thrown away.

orbitals · Basis A ratio that measures a distortion, and squares it first. How far ammonia's depolarised bands come off three quarters against how far one of its bonds has been stretched. Undistorted the departure is 3.1e-8, which is the rounding in the stored coordinates rather than a physical effect; at 0.1 Å it is 0.04239, and the slope is 1.999 — the departure goes as the square of the distortion, so a ratio measured to three decimals fixes a length to one and a half.

A ratio that squares what it measures

A depolarised Raman band sits at exactly three quarters because symmetry says its mean polarisability derivative is zero. Distort the molecule and it comes off — by 4.5 × 10⁻⁴ for a hundredth of an ångström and 0.042 for a tenth, going as the square of the distortion, which makes a ratio measured to three decimals a length known to one and a half.

spectra · Spectrum The shared bond's response falls and reverses, at every coupling. How far the relaxation moves the most interior cross bond of an acene, against the number of rings, at three couplings. Every series falls monotonically and every one changes sign — at λ = 0.2 between 3 and 4 rings, at λ = 0.4 between 3 and 4 rings, at λ = 0.6 between 4 and 5 rings. Where it crosses is a property of the coupling; that it crosses is not. The natural reading — that the effect grows with the number of rings feeding a bond — is refused by every one of these curves.

An anomaly that is not the first of a series

Naphthalene's shared bond behaves differently when the geometry is allowed to answer back, and the obvious reading is that two rings feeding one bond is what does it. Run it up the acenes and the effect falls at every step and changes sign: +0.02036 for two rings, +0.00678 for three, −0.00029 for four, −0.00603 for five. Two rings feeding a bond is not the beginning of anything.

bonding · Delocalisation The two halves change places. What fraction of the counterpoise correction belongs to the lighter of two unlike atoms, against their separation. At a bonding distance it is 1.26 per cent — essentially the whole correction is the heavier atom's — and by 9.0 bohr it is 67. The two change places at 6.29 bohr. A symmetric pair's share is exactly a half everywhere, which is what makes one frozen number a complete description there and nowhere else.

A correction that is two functions

A symmetric pair's counterpoise correction splits exactly in half, at every separation, to the last digit — which is why one frozen number describes it. Give the two atoms different charges and the split runs from 0.03 per cent to 67, changing places at 6.29 bohr: the correction a single number was standing in for is two functions of different shapes.

orbitals · Basis Twelve hydrogen bonds, four tables. The bond dipole of hydrogen against each partner, in debye, on each of the four tables after all four are anchored to the same hydrogen–fluorine separation. Positive is hydrogen at the positive end. A bond whose marks straddle the axis is one the tables disagree about the direction of, and there are 3 of them.

Four tables and one molecule to disagree about

A molecule of two elements is provably safe from the choice of electronegativity table, and a series down a group should land where the tables do disagree. It does. All four agree that hydrogen iodide is the exception — and they disagree about what its dipole is by 1.245 debye, which is two and a half times the 0.448 that was measured.

shape · Dipole The two terms in a vibrationally averaged rotational constant. A rotational constant averages 1/r², not r², so the moment it reports carries +2⟨Δr⟩/rₑ from the anharmonicity and −3⟨Δr²⟩/rₑ² from the harmonic spread. The two have opposite signs in every molecule here, and the anharmonic one — which is exactly zero in any symmetric well and therefore absent from every harmonic force field — is larger by a factor of 1.94 to 2.58.

The term a harmonic field cannot produce

The usual zero-point correction to a moment of inertia comes from a harmonic force field, which contains the mean square displacement and nothing else. A rotational constant does not average that. It averages one over r squared, whose leading correction is the mean displacement — zero in any symmetric well — and which enters with the opposite sign and about twice the size.

spectra · Rotation Water's two hydrogens are closer than platinum's chlorine. For each molecule, the longest pair that is a bond and the shortest pair that is not, on a logarithmic length axis. A cutoff on the length has to sit to the right of every filled mark and to the left of every open one, and it cannot: the longest bond in the collection is 2.3200 ångström and the shortest non-bond is 1.5144. The two populations overlap by a factor of 1.53, so the rule in use is not a rule with a badly chosen number in it — it is a rule with no number that works.

No length separates them

A bond list here is one distance cutoff with a clause about hydrogen, added when peroxide came back with five bonds instead of three. The clause repaired one molecule. Across the twenty-three molecules drawn here, the longest bond is 2.32 ångström and the shortest pair that is not a bond is 1.51 — so no cutoff can work at all, and five molecules currently come back with no bonds.

symmetry · Point group 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 A long bond goes axial at five and equatorial at seven. The energy of the odd site placed axially minus placed equatorially, against the odd bond's length relative to the others, for the trigonal bipyramid and the pentagonal bipyramid. Above zero the equatorial site is preferred. At five a longer bond goes axial and a shorter one equatorial; at seven, from 0.7 to 1.3, every sign is reversed — a shorter bond axial, a longer one equatorial. An open marker is a placement that is not a minimum: at seven the site each bond avoids is one it would slide out of.

The long bond goes to the crowded site

Given one bond longer than the others, the repulsion model puts it axial in a trigonal bipyramid — against the rule it is usually cited for. The reason is a crowding count, and at seven sites the count reverses: the pentagonal bipyramid's crowded site is equatorial, so a long bond goes equatorial and a short one axial. PF₅'s long bonds are axial and IF₇'s are equatorial. And at seven the site a bond avoids is not even a minimum.

shape · VSEPR

Named alongside it

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

Model limitApproximationConventionClosed formHarmonic approximationExpectation valueMoment of inertiaOverlap integralReduced massReference stateRotational constantBasis

All concepts