Molecular Geometry & Bonding
what the shape decides
The collection

Every essay — page 22

Page 22 of 42, continuing through the fields in the same order.

Orbitals Where the atoms go Bonding models What symmetry decides Beyond the octet What a spectrum settles When the molecule does not stop What the shape is for What is taught wrongly Series Named objects Orbitals Refutations Search

Where the atoms go

VSEPR as a repulsion minimisation rather than a table, the angles that fall out of it, and the case where five sites are not all alike.

One number separates the disputed bonds from the agreed ones. Every bond in the collection, ordered by how big its electronegativity difference is as a fraction of each table's range. The six the tables disagree about are all below 0.0507; the 25 they agree about are all above 0.0584. Nothing lies between, and which elements a bond joins does not enter — a dispute is what happens when the difference is small enough that the tables' own disagreement about it is larger.

A dispute is a small difference

Four electronegativity tables disagree about the direction of a quarter of a set of hydrogen bonds, and the interhalogens look like the natural test: five compounds with no hydrogen in them, to say whether the disagreement is about one awkward element or about the whole idea. All four tables agree about every interhalogen. They agree because the differences are large, and that is not a fact about halogens.

6 figures The measurement is not a horizontal line. The rotamer ceiling against temperature, with the measured tenfold drawn four ways: flat, and as a rate ratio whose two activation energies differ by 3, 5.31 and 8 kJ/mol. Flat, it is crossed at 312.1 K, which is the flat-rotor answer. At 5.31 kJ/mol the two curves are parallel and never meet. At 8 they meet on the other side, and it is cooling rather than heating that refutes the account.

One number decides which way it breaks

The six-membered verdict gives way at 312.1 K, and that is a statement about the ceiling rather than a prediction about the ratio — because a real rate ratio has a temperature dependence the model has no term for. Putting that term in moves the crossing, and at 5.308 kJ/mol it removes it entirely.

6 figures The gap closed when the other hundred and twenty-two pairs arrived. Every pair sorted by the size of its normalised electronegativity difference: the 31 common bonds on the left, all 153 pairs the four tables cover on the right. Filled marks are pairs the four tables put on different sides of zero. On the small set they are the 6 smallest with nothing in between; on the full set 27 uncontested pairs sit below the largest contested one.

A gap that was a choice of bonds

One number separates every disputed bond from every agreed one with nothing in between — on thirty-one bonds, which is enough to see a gap and not enough to know it is real. It is not real. The line is in the same place on all one hundred and fifty-three pairs the four tables cover, and twenty-seven agreed pairs now sit below the largest disputed one.

6 figures The five-membered ring would need more rotors than its chain has bonds. For each measured acceleration, the least rotor count whose ceiling reaches it, against the most rotors any convention gives that ring and against the number of bonds the chain has at all. The five-membered cases need five and eight rotors from a chain with four bonds, so they are refused by supply rather than by a margin — a refutation that needs no convention to be chosen, because every convention is below the requirement.

The count that was never written down

The rotamer ceiling for a ring closure needs a count of frozen rotations, and the counts in use disagree in direction: one gives the six-membered ring more frozen rotations than the five, another fewer. Every measured verdict survives all three defensible conventions unchanged — and the margins move by a factor of eleven, which is why a verdict decided by ten per cent was worth being nervous about.

7 figures Two quantities, and the best straight line between the two kinds of pair. Every pair the four electronegativity tables all cover, by how much the two elements differ and by how much the tables disagree about them. Filled points are pairs whose sign the tables dispute. The line is the boundary that misclassifies fewest — 3 of 153, against 6 for the best rule using the difference alone. It slopes upward, which is the mechanism: more dispute buys a larger difference and still leaves the sign in doubt.

Two numbers caught what one could not

No single threshold on the electronegativity difference separates the bond pairs whose polarity the four tables dispute from those they agree on — the best misses six of a hundred and fifty-three. Adding how much the tables disagree halves that to three and catches every disputed pair. And three is what four coin-flips produce: the rule flags nineteen pairs, an eighth of which should look agreed for no reason at all, which is 2.375 against the three observed.

7 figures NH₃: four states in a well the molecule does not sit at the bottom of. The umbrella coordinate of NH₃ — the signed distance of the N atom from the plane of its three H atoms — with the quartic well that has its minima at the measured 0.3816 ångström and its barrier at the quoted 2020 wavenumbers. The lowest 4 states are drawn at their computed energies. The lowest sits 587 wavenumbers above the bottom, which is 29.1 per cent of the way up the barrier, so the state is far from the harmonic bottom that a drawing of a pyramid implies.

A barrier is not what a splitting measures

Ammonia's inversion barrier is quoted everywhere as 2020 wavenumbers. Put that number into the simplest double well its own measured geometry allows and the ground-state splitting comes out at 1.3508 against a measured 0.7935, and the excited one at 68.37 against 35.81. Both are too large because a splitting is an area under a barrier and a height is only one of its two dimensions.

7 figures One per cent on the barrier is 3.6 per cent on the splitting. The ground inversion splitting of NH₃'s quartic well against the barrier height, both logarithmic, with the geometry and the reduced mass held at their measured values. The curve is visibly bent: its local slope is -3.56 at the published barrier and steepens either side, so a power law is a tangent to it rather than a description of it. The measured 0.7935 wavenumbers is reached at 2330, which is 15.3 per cent above the quoted 2020 — so a splitting wrong by a factor of 1.70 is a barrier wrong by a sixth. The same derivative read the other way is what makes a barrier quoted to ten per cent useless for predicting a splitting.

The exponent that runs both ways

How hard does a splitting depend on a barrier? Locally, as the power −3.5628 — and the local slope runs from −2.53 to −6.15 across the same sweep, so there is no power law. What is exact is stranger: rescaling the equation forces the mass exponent to be one below the barrier's and the geometry exponent to be twice the mass's, so the model's three sensitivities are one number and the arithmetic reproduces both identities to six decimals.

7 figures The mass is worth a factor of 1.6, and the other two 1e+4 and 9e+4. Ammonia's umbrella well, with each of phosphine's three differences substituted into it one at a time and then all together. The reduced mass is 11 per cent larger and costs a factor of 1.61. The pyramid is 2.01 times taller and costs 9.6e+3; the barrier is 6.1 times higher and costs 9.4e+4. Phosphine's own splitting is below what the arithmetic resolves, so it is drawn at that bound.

It was never the mass

Phosphine does not invert, and the reason given is that phosphorus is heavier than nitrogen. Three things about phosphine differ from ammonia. Substituting each into ammonia's own well one at a time, the reduced mass costs a factor of 1.61, the pyramid height costs 9,600 and the barrier 94,000 — and the mass is the smallest of the three by four orders of magnitude.

7 figures Three constructions of one number, spanning a factor of 5.6. The reduced mass of NH₃'s umbrella coordinate under each construction, against position along the coordinate. Two of the three are constants and the third is not: if the bonds are held at their measured length, the ligands must slide outward as the apex descends, and their radial motion adds to the mass. It runs from 2.4866 at the plane to 2.9874 at the pyramid — 20 per cent — and the coordinate itself stops existing at one bond length, which is where the curve ends.

The mass nobody chose

Every one-dimensional treatment of ammonia's inversion needs a mass, and the measurement does not supply one. Three constructions are defensible and they give 1.35075, 0.94420 and 0.0000055 wavenumbers. The honest one is not a constant at all, and it moves the answer thirty per cent towards the measurement — which means the usual choice is the wrong one.

6 figures The ceiling moves by 8.7-fold across the gauche energy's own reported range. The rotamer ceiling against butane's gauche energy, for the rotor counts each convention assigns to a five-membered and a six-membered closure, with the three measured accelerations drawn as horizontal lines. Across the reported range the ceiling moves by up to 8.70-fold, and two of the nine verdicts cross a measurement during the sweep. The natural prediction is that this input would be the smaller lever of the two; it is the larger.

The lever that was supposed to be smaller

Sweeping the rotor conventions leaves every verdict unmoved, and suggests that the other quoted input will be a smaller lever. It is a larger one. Sweeping butane's gauche energy over its reported range moves the ceiling by 8.7-fold, flips the six-membered verdict at 3.630 kilojoules a mole — inside the quoted error bar — and takes the five-membered refutation with it at 4.422.

6 figures Two sweeps, and one of them covers 28 per cent less ground than the other. What each of the two sweeps reaches, measured in the one variable the rotamer ceiling has: g/RT. The temperature sweep lies entirely inside the gauche sweep, so it explored no arrangement the other does not. Their widths are 0.581 and 0.807, their union is 0.807, and treating them as independent would have credited them with 1.387.

Two sweeps and one lever

The rotamer ceiling depends on the gauche energy and on the temperature only through their ratio, so a sweep of either traces the same curve. Measured in that one variable, the temperature sweep lies entirely inside the gauche sweep — it covered no ground the other does not, and the whole reported spread in one energy is worth a temperature swing from 196 to 353 kelvin.

5 figures The orderings in use move the splitting by 0.47 per cent between them. The change in NH₃'s ground inversion splitting under each ordering of the kinetic operator, relative to BenDaniel–Duke, with the bond-conserving mass throughout. The bars are exact solves and the ticks are first-order perturbation theory. The five span 0.469 per cent, from −0.407 to 0.060; the change from a constant mass to the bond-conserving one, in the same well and box, is 43.1 per cent, 92 times as large.

An ordering worth half a per cent

A mass that varies along a coordinate has no unique quantum kinetic energy, and the choice among the Hermitian orderings in use was the one thing left that could undo a forty-three per cent correction to ammonia's splitting. It cannot. The five orderings anybody uses span 0.47 per cent between them, a ninety-second of the correction, and the family only reaches the measurement at exponents three times larger than any of them.

7 figures