Theme

The theme: From the diffraction back

Nobody has seen a space group. They are inferred from where a crystal scatters and, just as informatively, from where it does not.

$A lattice and its reciprocal. The reciprocal lattice is where a crystal scatters. A long axis in the crystal gives closely spaced spots and a short one gives widely spaced spots, so the diffraction pattern is the structure turned inside out.$ How it is known

The reciprocal lattice

Nobody has seen a space group. Crystals are read from where they scatter, and where they scatter is a second lattice in which long has become short and short has become long.

$What pg scatters. The diffraction pattern computed from the atom positions alone. Where a glide plane is present, alternate reflections along a row cancel exactly — and those missing spots are how the glide is identified in an experiment, since the glide itself is never seen.$ How it is known

Systematic absences

The most informative part of a diffraction pattern is the part that is not there. A glide plane cancels alternate reflections along a row, exactly, and those missing spots are how a symmetry nobody can see is identified.

$A diffraction pattern with tenfold symmetry. Sharp spots, arranged with a symmetry that no periodic crystal can have. When the ten-fold case was measured in 1982 the immediate reaction was that the sample must be a twinned crystal, because the alternative was that a theorem with a one-line proof had a case nobody had considered. The star of reciprocal vectors is a parameter here, so the eight- and twelve-fold patterns that were found afterwards come out of the same call.$ Order without repetition

Order is not periodicity

For most of a century the two words were used interchangeably, because every known ordered structure repeated. A diffraction pattern measured in 1982 forced them apart, and the definition of a crystal was rewritten.

$The phase problem. The same structure rebuilt from its diffraction three ways: with the true amplitudes and phases, with the phases scrambled, and with the amplitudes discarded but the phases kept. The atoms survive the loss of the amplitudes and do not survive the loss of the phases, which is what an experiment throws away.$ How it is known

The phase problem

A detector records how much light arrives and not when it arrives, so half of every diffraction measurement is thrown away before it is written down. The half that is lost turns out to be the half that carries the structure.

One lattice, two cells, and the absences the choice creates. The same set of points described on a centred rectangular cell and on its primitive rhombic cell, with what the centred description scatters. Half the reflections vanish, and they vanish because of how the cell was drawn rather than because of anything the crystal does.

Lattices

Centring, and why cm is not pm

A centred cell has a lattice point in the middle and twice the area it needs, and crystallography prefers it anyway. The preference has a price, and the price is paid in reflections that vanish for reasons that have nothing to do with the crystal.

{100} offered to 5 classes: one form between them — the shape names none of the 5. The same face, {100}, handed to 5 crystal classes — m3̅m, m3̅, 432, 4̅3m, 23 — with the orbit each one returns drawn as a stereogram. Filled marks are poles in the upper hemisphere and open ones their partners below. The face counts are 6, 6, 6, 6, 6, taking 1 distinct value; the sets of faces take 1, which is the number that matters, since two classes can return the same count and different faces. Here every class returns the identical set, so a crystal bounded by this form alone has said nothing about which of them grew it.

Symmetry at work

Five classes grow the same cube

A crystal's shape is the most obvious thing about it and the least informative. Five of the thirty-two classes produce an identical cube, diffraction cannot see an inversion centre and so collapses the thirty-two to eleven, and the measurements that finally separate them are etch pits, optical rotation and a heated crystal attracting ash.

How it is known

What a powder pattern loses

Grind a crystal up and every orientation is present at once, so a two-dimensional pattern of spots collapses onto a single axis. Reflections that had their own places arrive together, and some of the coincidences are exact and have nothing to do with symmetry.

$What p3 scatters, and what the scattering shows. The structure on the left has point group 3, of order 3. The intensities it scatters, on the right, have point group 6, of order 6 — more symmetric than the thing that produced them. Reversing the sign of both indices conjugates every term in the sum and leaves the modulus alone, so a diffraction pattern always acquires a centre of symmetry, and in the plane a centre is a half turn. Both numbers are measured: the left from the operations, the right by testing each candidate against the computed intensities.$ How it is known

The symmetry diffraction adds

A diffraction pattern is always more symmetric than the crystal that made it. The extra symmetry is not a mistake in the experiment and no care removes it — it is a property of what a detector records, and it collapses the seventeen groups onto six.

p4m, displaced and then measured. Every atom of a p4m pattern moved by up to 1.2 per cent of a cell edge, and the resulting positions examined at 26 tolerances. At zero tolerance only the identity survives, so the structure has no exact symmetry whatever. Between 0.021 and 0.094 the count sits at 8, which is the group that was displaced. Above that it climbs to 15, accepting operations no version of this pattern has. The climb is not even steady: at 4 of the 25 steps the count falls as the tolerance is loosened, because operations accepted separately at one threshold merge into one at the next. The correct answer is a step on a staircase and nothing in the coordinates says which step.

How it is known

Near-symmetry, and the tolerance that is not here

Every claim on this site is decided by integer arithmetic, so no threshold is ever chosen. Measured coordinates do not arrive that way, and the moment a tolerance is introduced the answer stops being a fact about the structure and becomes a fact about the threshold.

A 5-fold cluster in a crystal that has no 5-fold axis. A cluster of 10 points with an exact 5-fold axis at the centre of each cell, repeated by the lattice. Two measurements, on the same points. The cluster is carried onto itself by a turn of 72° to within 2e-16 of a cell — exact, as far as the arithmetic goes. The pattern is not: applying the same turn about a lattice point sends some atoms 1.19 of a cell from the nearest atom, which is most of the way across it. Both are true at once. The axis is a symmetry of the contents of one cell and not of the crystal, which is what non-crystallographic symmetry means and why a virus with a sixty-fold capsid can crystallise in an ordinary space group.

What a lattice forbids

A fivefold axis in an ordinary crystal

A virus with sixty-fold symmetry crystallises in a space group that has none of it. The restriction forbids a fivefold axis to the lattice and says nothing about what sits inside one cell — so the axis is exact, the crystal genuinely lacks it, and both statements are measurable on the same set of atoms.

Building the reciprocal lattice from spacings. Each family of lattice rows has a spacing, and each contributes one reciprocal point: perpendicular to the rows, at the inverse of the spacing. The points built that way were compared against the algebraic definition and agree exactly.

Lattices

The dual lattice, as a construction

The reciprocal lattice is usually introduced as a formula and then used as a fact. Building it instead — one point per family of lattice rows, at the inverse of the spacing — makes every property it has obvious rather than memorable.

What Shechtman measured

A diffraction pattern with sharp spots and tenfold symmetry, in April 1982. Sharpness meant order and tenfold meant no lattice, and the two had been believed inseparable — so the interesting question is what the observation had to rule out before it could mean anything.

$The eleven Laue classes. Adjoining the inversion to each of the thirty-two crystal classes collapses them onto 11 groups. Friedel's law says a diffraction experiment sees the crystal and its inverse alike, so this — and not the crystal class — is what a diffraction pattern's symmetry reports. The highlighted symbol in each row is the class that is already its own Laue class, which is to say the centrosymmetric one.$ What symmetry decides

The eleven a diffraction pattern reports

A diffraction experiment cannot tell a crystal from its inverse. So the thirty-two classes collapse to eleven before a single reflection is indexed, and a structure determination begins by answering a different question from the one it was asked.

Lattices

Why the bigger cell wins

A centred cell has twice the area it needs and crystallography prefers it anyway. The preference is not conservatism — it buys operations that read as whole numbers along the axes, and the price is a set of reflections that vanish for reasons having nothing to do with the crystal.

The h0l layer of P2₁/c. The h0l reflections of P2₁/c out to 4 in each index, with each spot decided by summing the structure factor over the group's operations: 44 survive and 36 vanish identically, whatever the atoms are. The pattern of holes is the condition h0l: l even, read back off the spots rather than imposed on them.

How it is known

The reflections that are not there

A screw axis and a glide plane leave no mark on the intensity of any reflection. What they do is delete some, exactly, for every possible arrangement of atoms — and the pattern of deletions is computed here from the sum a crystallographer writes down, rather than read from a table.

$p3, single and twinned. Left, the diffraction pattern of a single crystal of p3. Right, the same crystal twinned, with 50 per cent of it in one orientation. Not one spot has moved — the twin law is a symmetry of the lattice, so the two reciprocal lattices lie exactly on top of one another — and 72 of the 81 reflections drawn have changed intensity. At a fifty-fifty twin the pattern acquires the full symmetry of the lattice's point group and is indistinguishable from a crystal that genuinely has it.$ Symmetry at work

A merohedral twin moves no spot at all

The twin law is a symmetry of the lattice, so the two individuals have reciprocal lattices lying exactly on top of one another. Nothing splits, nothing appears in a new place, and the only thing that changes is that pairs of intensities which were different have been averaged — which produces a diffraction pattern with a symmetry the crystal does not have and no sign that anything is wrong.

$A chain modulated at q = 0.211. The lower row is the lattice: 34 sites, evenly spaced. The upper row is the structure: the same sites displaced by a wave of amplitude 0.12 of a spacing and wavevector 0.211, drawn through them. Because 0.211 is not a ratio of small whole numbers, no cell of any size holds the structure — the displacement pattern never repeats — and yet the atoms are nowhere near random: each one is exactly where a single sine wave says it should be. That is what an incommensurately modulated crystal is, and its diffraction pattern is sharp.$ Order without repetition

The satellites that need a second integer

A crystal whose atoms are displaced by a wave of the wrong wavelength has no unit cell at all, and diffracts to sharp spots anyway. Indexing them takes two integers per reflection instead of one — and the intensities of the extra spots are Bessel functions, which is a check the arithmetic can be made to pass.

$A structure, and the vectors between its atoms. On the left, 4 atoms in a cell. On the right, every one of the 16 vectors between them, each drawn from a common origin: 13 distinct positions, with the 4-fold peak at the origin being each atom paired with itself. That right-hand picture is what a Patterson map shows, and it is the thing a diffraction experiment gives without phases. It has more peaks than the structure has atoms — n² against n — which is why interpreting one is hard, and why it is always symmetric about its centre.$ How it is known

The map that needs no phases

A diffraction experiment measures intensities and loses phases, so the electron density cannot be computed from it. One map can be: the transform of the intensities, whose peaks are not atoms but the vectors between them — every ordered pair, brought to a common origin.

$What each group extinguishes. The extinction conditions of 9 space groups, each derived by summing the structure factor over that group's own operations and reading the surviving rule off the result: P1 — nothing; P1̅ — nothing; P2 — nothing; Pm — nothing; P2/m — nothing; P222 — nothing; Pmm2 — nothing; P4 — nothing; P23 — nothing. 9 of the 9 extinguish nothing at all, and diffraction alone cannot distinguish those from each other.$ How it is known

Where the experiment runs out

Absences narrow the space group down and often not to one. Two groups can extinguish exactly the same reflections and scatter with exactly the same symmetry, and telling them apart needs something the diffraction pattern does not contain.

P2₁2₁2₁: the sections its symmetry forces. The Patterson cell of P2₁2₁2₁ with the sections marked. Each operation (M, t) sends an atom at x to Mx + t, so the vector between them is (I − M)x − t; where I − M is singular that vector cannot leave a plane, and the plane's equation comes from the left null space in integers. This group has 3 such operations, giving the sections w = 0.5, u = 0.5, v = 0.5. A heavy atom's vector to its own image is somewhere on one of them, which is what made structure solution possible before computers: a plane can be searched by eye and a volume cannot.

How it is known

Where symmetry stacks the vectors

A Patterson map of a real structure is a blur with thousands of overlapping peaks. A screw axis rescues it: the vectors between symmetry-related atoms cannot leave a plane, so the search for a heavy atom is a search of a section rather than of a volume — and which plane it is falls out of the operation's matrix in integers.

$An antiphase boundary in p4. Where two antiphase states meet. Above the line the species alternate one way and below it the other, so at the boundary two cells of the same species sit next to one another and the ordering is out of step. This is a domain wall with no change of orientation across it: the crystal is not twinned, its lattice is undisturbed, and diffraction sees it only in the width of the superlattice reflections.$ Symmetry at work

The domains a lost translation makes, which nothing optical can see

An ordering transition can leave the crystal class untouched and take away translations instead. The domains that result have the same orientation, the same shape and the same optical properties as each other, and where two of them meet the ordering is simply out of step — a boundary with no change of direction across it and no way to find it except by looking at the ordering itself.

$Friedel's law, as an equality rather than a resemblance. Each pair of bars is a reflection and its opposite for a structure of three atoms in no particular arrangement. They are the same height, and not approximately: with real scattering factors, negating the indices conjugates the structure factor, and conjugation does not change a modulus. The test behind this figure requires the largest difference over 40 pairs to be below 10⁻⁹ and it comes back exactly zero. This is why a diffraction pattern is centrosymmetric whatever the crystal is, and why the thirty-two classes collapse to eleven before a structure is even proposed.$ How it is known

The law that hides handedness

With real scattering factors, negating the indices conjugates the structure factor and leaves the intensity exactly alone — so every diffraction pattern is centrosymmetric whatever the crystal is. The escape is an imaginary component that the negation does not touch, and it is how the handedness of a molecule is measured.

Which inflation factors a tiling may have. Every distinct inflation factor produced by a two-letter substitution whose matrix has entries up to 4, plotted against its algebraic conjugate. The two grey lines are the unit circle, which in the quadratic case is the pair of values ±1. A factor whose conjugate lies strictly inside is a Pisot number and the chain it grows has sharp Bragg peaks; 39 of the 77 factors here lie outside and cannot. The golden ratio is the smallest of them all, which is the arithmetic reason it turns up in every quasicrystal anybody has drawn.

Order without repetition

Which inflation factors exist

A tiling grown by substitution has an inflation factor, and it is an eigenvalue of an integer matrix — so it is an algebraic integer, and sharp diffraction demands that its conjugates be small. That condition is an inequality between two integers, and it explains why the golden ratio turns up in every quasicrystal anybody has drawn.

How it is known

Solving from the vector set

A Patterson map contains a copy of the structure laid over every atom in turn. Shift it by one interatomic vector, take the pointwise minimum with itself, and the copies that fail to coincide are cut away — leaving the structure, together with its inverse, from a measurement that carries no phases at all.

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