Molecular Geometry & Bonding
what the shape decides
Concept

Symmetry breaking — where it appears

Adopting a state with less symmetry than the Hamiltonian that produced it. A mean field can lower its energy this way — putting spin density on a molecule whose exact state has none — and so buys a better number attached to a worse picture, which is the sharpest form of the warning that an energy is not a measure of a wavefunction.

Named by 32 essays across 8 fields — each of them below, with the objects they name alongside it.

Four fillings, four periods. four fillings of a ring of 120, and for each of them what a distortion of every available period is worth. Every period pays the same elastic cost, so the bars compare what the electrons give back and nothing else. The winner is one over the filling in every case.

The distortion the filling chooses

A half-filled chain of equal bonds is unstable and alternates — long, short, long, short. That is the case everyone is shown, and it is one case. Fill the chain a third of the way instead and the alternation is worthless: what wins is a pattern that repeats every three bonds, and the period is one over the filling at every filling tried.

solids · Peierls distortion The error, against the repulsion it is an error about. The energy a mean field misses, for two electron counts on 4 sites, against the strength of the repulsion. Each is a straight line at large repulsion and the dashed line through it is not a fit: its slope is the count of coincidences a uniform density forces, computed from the electron number and the site number alone.

A mean field cannot get out of the way

The energy a mean field misses grows without limit as the repulsion rises — 27.82 at U = 32 for four electrons on four sites, against an exact energy of −0.2946, so the error is ninety-four times the answer. The rate it grows at is not an energy at all: it is n²/4N, a count of the coincidences a spread-out density cannot avoid.

beyond · Correlation One distortion, resolved into the species of the group it left. An arbitrary displacement of benzene, projected onto each symmetry species of D6h. The weights add to 1, which is the check that the projectors resolve the whole of it: the largest is E2g at 35.0 per cent, and the totally symmetric part — 3.4 per cent here — is the part that changes every distance and no symmetry at all.

How far, and along which coordinate

A continuous symmetry measure returns one number: how far a structure is from a shape. Projecting the same displacement onto the twelve symmetry species of benzene's group turns it into a list that sums to 1.000000000000, says which coordinates the structure left along, and shows that the totally symmetric part — 3.4 per cent of this one — moves every atom by 0.0200 ångström and lowers the symmetry measure by nothing at all.

symmetry · Point group One exact state, two correlation energies. The energy each of two mean fields misses, against the repulsion, for one system whose exact energy is a single smooth curve. Below U = 2 the unrestricted search returns the restricted answer and the two definitions agree to the last bit. Above it they part: at U = 32 the restricted reference reports -27.82 and the unrestricted one -0.11, a factor of 259.43, and one is growing while the other falls.

The reference decides the correlation

The correlation energy of one exact state, measured against two references that are both called Hartree–Fock, is −27.82 and −0.107 at the same repulsion — a factor of 259, on a system whose exact energy is a single smooth curve. Below the instability at U = 2 the two agree to the last bit; above it one grows without limit while the other falls, and the reference that reports almost no correlation has ⟨S²⟩ = 1.99 where a singlet is zero.

beyond · Correlation 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 An effect that cannot distort a molecule, deciding how far it distorts. The energy along one distortion coordinate, three times. With only the first-order term the minimum is at 0.6; with only the second-order term there is no minimum away from zero at all, because the gap of 1.5 is above the critical 1 for a closed shell on its own. With both, the molecule distorts to 1.06 — well past the first-order answer — and gains 0.09 more than the two separate stabilisations add up to.

Two distortions in one coordinate

A second-order Jahn–Teller effect that cannot distort a molecule by itself — its gap is half again above the critical value — nearly doubles the distortion when a first-order effect is already acting. The molecule goes to 1.075 instead of 0.600 and gains twice the energy, and it does it while the gap the second-order term divides by is opening rather than closing.

shape · Peierls distortion The shallowest slope, and the steepest. For three molecules, the softest and stiffest vibrations, the species each belongs to, and what a unit distortion along each costs. The cost is not taken from the frequency: it is computed by resolving the distortion onto the normal coordinates in the mass-weighted metric and adding up ω²q². That it comes back as the frequency is the identity the whole comparison rests on — the species decomposition uses only the coordinates and the group, and the cost uses only the masses and the force constants, and the two have to agree on this case before they can be asked to disagree on any other.

The coordinate it was already soft along

A distorted structure can be resolved into the symmetry species of its ideal group, and that resolution cannot say which coordinate a molecule fell down by itself and which one something outside pushed it along. The force field answers that, and the two halves agree on the case where they must — a unit distortion along a normal mode costs exactly that mode's frequency, to a part in a million, computed from masses and force constants by one side and from coordinates and characters by the other.

symmetry · Point group A correction that stops belonging to the system it is added to. The exact ground state of a four-site Hubbard ring, the unrestricted mean field's, and the composite: the mean field plus the correlation correction computed on the symmetric molecule. At ε = 0 the two systems are the same one and the composite is exact. As the sites are made unlike, the transferred correction stops being the right one — the exact correlation energy shrinks towards nothing while the transferred number does not — and the last rows are the recipe adding a correction almost as large as the error it is meant to remove.

The correction that was computed somewhere else

Every composite method rests on one assumption: that an expensive correction computed on a small case can be added to a cheap calculation on a large one. Tested on four sites where both answers are exact, it removes 99.74 per cent of the cheap method's error near the reference and −1450 per cent of it further away — at which point the recipe is fifteen times as wrong as the calculation it was improving.

wrong · Approximation The whole difference lives at the two ends. The energy difference between the two dimerisations of an open chain, held at the same distortion, multiplied by the number of sites. It settles on a constant — 1.09 in units of the hopping — so the difference per site falls as one over the length, with a fitted exponent of -1. An end is a bond that is not there, and it is worth the same amount whatever it is attached to.

The distortion the ends decide

A chain of an even number of sites has an odd number of bonds, so its two dimerisations are different molecules rather than one molecule translated. Held at the same distortion they differ by 1.08715 in units of the hopping, whatever the length — a fixed amount of energy living at the two ends, with the per-site difference falling as one over the length at a fitted exponent of −0.99986. And below a hundred and twenty-eight sites the second dimerisation does not exist at all.

applied · Peierls distortion How nearly a broken symmetry survives. A screened potential splits the n = 2 shell and destroys the degeneracy the linear Stark effect depends on. The field needed to overcome the splitting and restore the linear behaviour runs from 4.3e+4 volts a centimetre at a quantum defect of 0.00040 to 2.9e+7 at a defect of 0.208. The dipole between the states is 3.000 throughout, so the field is exactly the splitting divided by twice it.

How nearly a broken symmetry survives

The hydrogen shell's extra symmetry is what makes its Stark effect linear, and a real atom does not have it. Screening splits the shell, and the field needed to overcome the splitting and restore the linear behaviour is a curve — from forty thousand volts a centimetre at a quantum defect of 0.0004 to thirty million at a defect of 0.21.

symmetry · Representation A cheap number that predicts an expensive failure. Thirty-two systems. Along the bottom, how far the mean field's own symmetry breaking has moved between the reference and the target — a quantity available before any exact calculation. Up the side, how wrong the transferred correction turns out to be. They rank together at 0.902, and the open marks are the systems whose broken solution has collapsed entirely, which is where the diagnostic stops being a scale and becomes a warning.

The warning a cheap calculation gives

A correlation correction computed on one system and carried to another works until it does not, and nothing in the scheme says in advance which. The mean field's own symmetry breaking says: it collapses at a definite field, and the transfer fails where it goes. Across thirty-two systems the two rank together at 0.90.

wrong · Approximation How fast the three quarters goes, along each coordinate. The coefficient of the square, for every non-symmetric mode of three molecules, against the mode's own frequency. A single measurement takes one of these — along a bond stretch — and reports the exponent rather than the size. The sizes span a factor of thirty within methane alone, and the coordinates a molecule is softest along are not systematically the most sensitive: ammonia's stiff pair is five times more sensitive than its soft one.

One number was one direction

The departure of a depolarisation ratio from three quarters goes as the square of a distortion, and the exponent was first measured along one bond stretch. Computed along every non-symmetric coordinate the exponent is always two and the coefficient is not: it spans a factor of thirty inside methane. And the ratio is not preferentially sensitive to the coordinates a molecule is soft along — in two molecules of three the stiffest coordinate is the most sensitive.

spectra · Spectrum A ring of 6 as the neighbour repulsion is turned up. At an on-site repulsion of 8, three quantities against the nearest-neighbour repulsion: the alternating structure factor, the double occupancy, and the nearest-neighbour opposite-spin pair distribution. The rise is steepest at V = 4.5, which is 0.563 times the on-site repulsion. Far past it the ring is charge ordered — nearly every electron paired on alternate sites, which is what a double occupancy approaching a half means.

The give-back that turned into a saving

Take a wavefunction optimised for an on-site repulsion, weight its correlation hole with an interaction that reaches one neighbour, and the enhancement at one bond gives back forty-four per cent of the on-site saving. Putting that neighbour term into the Hamiltonian and solving exactly does not shrink the give-back. It reverses its sign.

beyond · Correlation Two events, not one — and both below the n = 2 shell's. The field at which each coupled pair's shift stops being quadratic and starts being linear, for the n = 3 shell and for the n = 2 shell. The n = 3 shell has two, a factor of 3.66 apart, and both are far below n = 2's single one — so the linear effect returns is two events in a shell with a d, and it happens at a field thirty times weaker than in a shell without one.

Two events where there was one

A broken symmetry returns at a field where the coupling matches the gap it has to overcome, and in a shell with two levels that field is a single number. The next shell up has three, two gaps and two dipoles — so there are two crossovers, a factor of 3.66 apart, both of them below the single one of the shell below, and the exponent takes more than a decade of field to travel between them.

symmetry · Representation 6 rings fused two ways. Two catacondensed chains of 6 hexagons: the linear one, where every fusion continues the line, and the angular one, where the fusions alternate. They have the same formula and the same number of bonds and they are not the same graph. Ring centres are numbered; in the linear molecule two rings k steps apart have centres 1.7321k units apart and in the angular one they do not, which is the whole reason this pair can be asked the question.

Neither of the two separations

A linear acene cannot pose the question, because the number of fusions between two rings and the distance between their centres are the same variable there. Bending the molecule pulls them apart — and the response follows neither. Two pairs of rings the same distance apart differ by two thirds, and the larger one is at the greater distance.

symmetry · Aromaticity Two bands, square below, triangular above. The 128 levels of a structure carrying two orbitals on every one of its 64 sites, where the lower orbitals hop on a square net and the upper ones on a triangular net, separated by 12 and coupled at 0.06. The two bands have different widths and different shapes before anything mixes, which is the situation a single net cannot construct. Every level here is also reproduced by a two-by-two problem, one per mode, to 3e-13.

The constant that belonged to one net

Divide one second-order departure by another and the coupling cancels, leaving one constant times the gap — which reads as arithmetic. It was arithmetic about a square net. On a triangular one — the same graph for both bands, nothing else changed — the quotient drifts by a hundred and twenty-eight per cent.

solids · Bands in a solid Every crossover a shell has. The field at which each coupled pair's linear behaviour returns — the gap between the two levels divided by twice the dipole joining them — on a logarithmic axis. The n = 3 shell has 3 distinct fields rather than four, because its m = ±1 half is a two-level ladder with one coupled pair. All three are below the n = 2 shell's single one.

Three events, and a ratio of two dipoles

The m = 0 half of a shell has two crossovers because it has three levels and two coupled pairs. The other half has two levels and one, so the whole shell has three distinct fields rather than four — and two of the three share a gap exactly, which makes the ratio between them a ratio of two dipoles, 2/√3.

symmetry · Representation Where the broken solution appears. The mean field's spin polarisation against the on-site repulsion, at half filling and no site-energy modulation, for three systems. Two of them are symmetric below a threshold and polarised above it — 1.672 for a chain of four and 2.355 for a ring of six. The third is polarised at every repulsion tested, because its half-filled shell is degenerate and the symmetric solution is unstable however small the repulsion is.

The half of the square a ring of four cannot show

There is a warning that says in advance whether a transferred correction will hold: the mean field's own symmetry breaking, which collapses at a definite site-energy modulation and takes the transfer with it. The other axis of the same square has a threshold too — on the other side — and the ring of four it was all measured on is the one system with no threshold to find.

wrong · Approximation Folding two ligands makes the gap bigger before it makes it smaller. The gap above eight electrons as two of the four ligands fold to the same side. It rises first, to 2.0938eσ at 20°, before falling. The four-ligand path only ever closes it, so the direction the gap moves is not a property of bending — it is a property of which ligands bend.

The distortion that opens the gap

Two distortions close the sixteen-electron gap — one by bending all four ligands, one by adding a fifth. Folding two of the four makes it larger, by five per cent, before it makes it smaller. And it costs the exactness at the first degree, while the gap is still growing, so the size of a gap and whether it is exact are not one measurement.

applied · Electron count Tilting the field raises the count, and then lowers it again. How many distinct fields the shell has an event at, against the angle between the field and the z axis. Along either axis there are 3; at a general tilt every one of the 6 coupled pairs has its own field and there are 6. In between the count comes back down at four angles where two events coincide, and at forty-five degrees two separate coincidences happen at once.

Four angles the shell chooses

A field along one axis gives a shell of nine functions three fields with an event, and tilting the field should separate the coincident ones and raise the count towards the number of coupled pairs. It does — from three to six. But not monotonically: at four angles two events collide again, and every one of those angles is the arctangent of a ratio of the shell's own angular integrals.

symmetry · Representation One crossing, and the six fields that are not one. Open marks: every two-state crossover field, at each tilt. Filled line: the field at which the exact spectrum's one avoided crossing actually sits. The estimates scatter over a factor of four to twenty; the real crossing moves by a factor of 1.34 across the whole ninety degrees, and passes the four coincidence angles — the dashed verticals — without any feature at all.

None of the six was a crossing

Counting events in a tilted field finds the count rising from three to six, dropping again at four angles that are exact arctangents of the shell's own integrals. Every one of those statements is true of the two-state estimates. Diagonalising the five-level problem exactly finds one avoided crossing at every tilt, in a field that moves by a third across ninety degrees, and no feature whatever at any of the four angles.

symmetry · Representation Six distortions, and the one the ratio cannot see at all. How far a depolarised band of boron trifluoride comes off three quarters when the bonds are stretched in six different combinations, all at the same size. Five move it. The one that stretches every bond by the same amount moves it by nothing whatever — not a small amount, exactly none — because that distortion keeps every symmetry operation the molecule had, and the band sits at three quarters by its species.

The distortion the ratio cannot see

A depolarisation ratio can be made into a structural probe: break a molecule's symmetry and a band fixed at three quarters comes off it by an amount that depends on the distortion. The question is whether two distortions the ratio can see separately might cancel into one it cannot. They do — and the cancellation is exact, at any size, because the blind direction is the one that keeps the symmetry.

spectra · Spectrum How often a random start reaches the best of them. The share of random starts that reach the best arrangement found, against the fraction of sites raised, for two nets at two contrasts. Every curve dips in the middle of its left half and recovers: the hard compositions are between a quarter and a third, and the half-filled one — the rightmost point of each curve — is among the easiest. The hardest points are 5 of 16, 6 of 16, 9 of 36, 12 of 36.

The composition that is hard is not the full one

A landscape of arrangements measured at one composition on each of two nets raises the question of where the hardest one sits — and the natural guess is the half-filled one, where there is most to arrange. It is the easiest. On thirty-six sites at a contrast of one, half filling has one local optimum and nine billion arrangements, and a quarter filling has six optima and a hundredth as many.

solids · Cohesion The second number is the first one, rearranged. The composite's error against the change in the correlation energy, at every point on both axes of the square. They lie on the diagonal because they are the same quantity: the composite is the target's mean field plus the reference's correlation energy, so its error is the reference's correlation energy minus the target's. The largest departure across 20 points is 2.2e-16, which is the arithmetic's own precision and not a measurement.

The second number is the error, rearranged

A cheap diagnostic for a composite method leaves a scatter it cannot explain, and the number that ought to close it is the change in the correlation energy, already computed at every point, so the test is arithmetic rather than a calculation. It is arithmetic, and the arithmetic is the answer. The composite's error is that change with a sign on it.

wrong · Approximation A thirty-four per cent variation that is entirely the truncation. The field at which the one avoided crossing sits, against the tilt, computed in the five functions a field in the xz plane couples and in the whole nine-function shell. The truncated answer runs from 1.6435e-5 to 2.2014e-5 — a factor of 1.34. The whole shell's is 2.0876e-5 at every direction, and equals the truncated answer at zero tilt, where the truncation is exact because the field is along z and the excluded functions genuinely do not couple.

The variation was the basis

Solved in the five functions a field in one plane couples, the tilted Stark problem has one avoided crossing at every tilt and a crossing field that moves by a third across ninety degrees. Solved in the whole nine-function shell the field does not move at all — the same number at every direction, to eleven decimal places — and the thirty-four per cent was the truncation.

symmetry · Representation The reading is a function of direction, with a sixty-degree period. The departure of a depolarised band from three quarters, for distortions of equal magnitude pointing all the way round the plane of stretches that sum to zero. It is not one number: it runs from 8.177e-6 to 1.617e-5, a factor of 1.978. The minima are at one bond against another and the maxima at two bonds against one, and the pattern repeats every sixty degrees.

One number was a direction too

The depolarisation probe is exactly blind to the totally symmetric direction, which suggests it reads the distortion's component outside that species. What is left is a plane, and over a circle in it the reading varies by a factor of 1.98 — smallest for one bond against another, largest for two bonds against one, repeating every sixty degrees.

spectra · Spectrum One fold opens it, two close it, and the antisymmetric one does neither. The gap along three directions out of the square plane: folding one pair, folding both equally, and — from a symmetric point ten degrees out — folding one pair further while unfolding the other by as much. The first rises, the second falls, and the third leaves at zero slope. That third direction is the one the question asked for.

The direction the gap cannot see

A two-ligand fold opens the sixteen-electron gap and a four-ligand bend closes it, so a distortion mixing the two must pass through a direction the gap does not move along. It does, and the direction is the antisymmetric fold — one pair of trans ligands up, the other down. Its blindness is exact, because exchanging the two pairs is a symmetry of the arrangement.

applied · Electron count The sum is flat and the maximum is not. Both readings round the circle, each divided by its own average so the two can be drawn together. The maximum varies by 98 per cent; the sum over all four depolarised bands varies by 0.038. A sum cannot be changed by reordering, so if each band's departure is an isotropic quadratic form the sum must be constant — and to four parts in ten thousand it is.

The sum was flat all along

The depolarisation reading varies by a factor of two round a circle in the non-symmetric plane, and the anisotropy may belong to taking a maximum over four bands rather than to the physics. Summing the four instead gives a reading constant to four parts in ten thousand, against a maximum that varies by ninety-eight per cent.

spectra · Spectrum Two levels of different symmetry, closest at 0.0399865. The lowest m = 0 level and the lowest |m| = 1 level of the zero-defect shell, in units of the s–p gap, against the field in the same units. Both fall. Their separation is smallest at 0.039986525, where it is 0.97648 of the zero-field gap, and they never meet. The field along z commutes with the angular momentum about z, the two levels belong to different values of it, and no element of the field connects them.

The crossing nothing couples

A tilted Stark shell's one avoided crossing settled at 0.04000 of the zero-field gap, and the natural guess was a ratio of angular integrals. With the quantum defect taken out the limit is 0.0399865, not four hundredths — and the two levels at that minimum belong to different symmetries about the field, which no element of the field connects. It was never an avoided crossing. The one minimum between levels that do interact sits at half the field, behind a level of the other kind.

symmetry · Representation The gap is flat along it everywhere, and the repulsion is flat only where a symmetry says so. At each distorted geometry, how far the sixteen-electron gap and the ligand–ligand repulsion move along the direction the gap is blind to, over 5 degrees. On the symmetric line the repulsion moves by about a tenth of a per cent and downward, and its own null direction is the same one; off it the repulsion climbs by up to 1.30 per cent and its null direction is elsewhere. A blindness a symmetry produces is inherited by every function of the arrangement; one a gradient search produces is inherited by nothing.

A blindness that is inherited

There is a direction the sixteen-electron gap does not move along, and it is tempting to call it the one a complex is softest along without paying for it. That second half is a claim about an energy the gap model has no term for. Put the ligand repulsion on the same family and the answer splits: where a symmetry fixes the blind direction the repulsion is blind to it too, exactly, and slightly downhill — and where no symmetry fixes it, the two are nearly perpendicular.

applied · Electron count One net has a two-colouring and the other cannot. Sixteen sites wrapped into a square net and into a triangular one, with the wrapping bonds left undrawn. The square net is bipartite: its sites split into two classes with every bond running between them. The triangular net is not, and the obstruction is a triangle — three sites in a cycle of odd length cannot be two-coloured. It has thirty-two of them, two per site, and forty-eight bonds against the square net's thirty-two.

A net with no two-colouring

Half filling is the easiest composition to search and the reason given was the two-colouring: on a bipartite net it is the unique arrangement with every bond unlike, so the optimum has nothing competing with it. A triangular net has no two-colouring, its half-filled composition is reached by every one of two hundred starts, and its best arrangement is two bonds short of what counting allows.

solids · Cohesion Each half has an integer exponent and the mixture does not. On logarithmic axes against the amplitude: the combined residual, the even half's anisotropy and the odd half relative to the mean. The even half is a straight line of slope 2.005. The odd half has slope 0.981 below 0.04 and then bends over. The combined residual, fitted as one power, gives 1.248 — an average of two integers weighted by where the sweep happens to sit, with the halves crossing at 0.084.

Two integers made one exponent

A sum over boron trifluoride's depolarised bands is nearly isotropic, and its residual scaled as the amplitude to the 1.248 — no integer, and a two-term fit left a pattern it could not remove. Averaging each distortion with its reverse splits the residual exactly into an even half that scales as the square, to 2.005, and an odd half that scales as the first power until a fifth-order term turns it over. And the sum was a stand-in: what an unresolved pair of bands would actually show is twenty times less flat.

spectra · Spectrum

Named alongside it

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

Model limitDegeneracyExact diagonalisationReference stateIrreducible representationsApproximationCorrelation energyHubbard modelClosed formConventionElectron correlationNormal mode

All concepts