Molecular Geometry & Bonding
what the shape decides
Concept

Intermolecular force — where it appears

An attraction or repulsion between whole molecules rather than within one. Its leading term depends on which multipole moments each molecule has, so a molecule with no dipole can still interact strongly through its quadrupole.

Named by 10 essays across 3 fields — each of them below, with the objects they name alongside it.

What holds matter together, per pair. Four kinds of interaction between two units of matter, each computed from the model named beside it, on a logarithmic energy scale. The range from top to bottom is a factor of several hundred, which is the number behind why a molecular solid melts hundreds of degrees below a covalent one.

What holds a solid together

Four kinds of interaction between two units of matter, each computed from a stated model and put on one logarithmic scale. The ordering is not the one usually taught — an ion pair at contact beats a shared pair, which is a fact about the comparison rather than about the numbers.

solids · Cohesion What holds matter together, per pair. Four kinds of interaction between two units of matter, each computed from the model named beside it, on a logarithmic energy scale. The range from top to bottom is a factor of several hundred, which is the number behind why a molecular solid melts hundreds of degrees below a covalent one.

The lattice sum that depends on the order of adding

An ionic solid's binding is the sum of every pair of charges in it, and the series does not converge absolutely — rearranged, it gives a different answer. That is a genuine mathematical difficulty rather than a technicality, and it is the clearest example of something a real-space, neighbour-by-neighbour method cannot compute at all.

solids · Cohesion Face to face repels, edge to face attracts. Two benzene molecules 5 Å apart, one turned against the other, with only the quadrupole interaction between them. Stacked, the two negative faces meet and the energy is +8.8 kJ/mol; perpendicular, one molecule's positive rim meets the other's negative face and it is -4.6. The sign changes on the way, so the preference is not that one arrangement is weaker — it is that they are opposite. This is a molecule with no dipole moment at all.

Zero dipole is not no interaction

Benzene's dipole moment is exactly zero at every origin, and its quadrupole moment is large enough to decide a crystal structure. Two benzenes face to face repel by nine kilojoules a mole; edge to face they attract, and the sign changes on the way between.

shape · Dipole The same angles, the same torsions, and not the same molecule. twelve closed conformers of a ring of 10 at a bond angle of 111.5 degrees. Every one has exactly the same bond angles, so an account built from angles and torsions places them all on the horizontal axis alone. The vertical axis is the closest approach of two atoms four or more bonds apart, which no term in that account mentions: two of these differ by 0.08 kilojoules in torsional energy and by 0.75 ångström in how close they come.

The atoms that meet across a ring

Twelve closed conformers of a ten-membered ring at one bond angle, so every one has identical angle strain by construction. Two of them differ by 0.026 kilojoules a mole in torsional energy and by 0.80 ångström in how close two atoms on opposite sides of the ring come — 2.331 against 3.131, where two carbons are in contact at about 3.4. An account built from angles and torsions calls those two structures the same.

shape · Strain 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 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 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 The ceiling rises and the measurements fall, so they cross. The largest acceleration the rotamer account can produce, against the ring being closed, with the measured gem-dimethyl accelerations on the same axis. Closing a bigger ring means freezing more rotations, so the ceiling rises steeply; the measurements go the other way. The five-membered ring's 250-fold acceleration is above its own ceiling of 36.5 and the six-membered ring's tenfold one is far below its 121 — so the account is refused at one size and sufficient at the next.

A ceiling that rises where the measurements fall

The rotamer account of the gem-dimethyl effect has a largest possible acceleration, which looks like a limitation. It is a prediction: the ceiling is a closed form in the number of rotations a closure freezes, it rises steeply with ring size, and the measurements fall — so the account is refuted for the five-membered ring and more than sufficient for the six.

shape · Strain 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 The trimer's correction, and the sum of its pairs. The counterpoise correction of a three-fragment system computed directly — each fragment's energy alone less its energy in the whole trimer's basis — against the sum of the three pairwise corrections, on a logarithmic axis. The sum is the larger everywhere the difference is above the solver's noise: 30.4 per cent at 1.6 bohr and nothing by six.

The assembly that counts one share twice

A counterpoise correction is divided unequally between its two centres, and the first place that matters is a three-fragment system, where the pairwise corrections are added up and the assembly must double-count one share and undercount another. It does: the heavy centre is over-corrected by seventeen per cent and the light ones under-corrected by two and a half, and the two do not cancel.

orbitals · Basis

Named alongside it

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

Model limitLong-range interactionClosed formContour levelEnclosed probabilityApproximationClosed-shell configurationsCohesionConventionEffective nuclear chargeIonic bondingLattice energy

All concepts