Crystallography & Symmetry
patterns derived from their groups
Concept

Friedel law — where it appears

That negating a reflection's indices conjugates its structure factor and leaves the intensity alone, so every diffraction pattern is centrosymmetric. The escape is an imaginary scattering component that the negation does not touch, and it is how the handedness of a structure is measured.

Named by 12 essays across 4 fields — each of them below, with the objects they name alongside it.

{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.

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.

applied · Forms 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.

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.

diffraction · Accidental symmetry Which classes can twin by merohedry, and how many ways. Every crystal class, with the number of twin laws its own lattice offers it. The index of the class in the point group of its lattice is the number of orientations available; 25 of the thirty-two have more than one, and the 7 holohedral classes have exactly one — their crystal already has every symmetry their lattice has, so there is nothing left over to twin by. The names along the right are the old mineralogical ones: hemihedral for half, tetartohedral for a quarter.

Twenty-five of the thirty-two can twin, and seven cannot

The number of twin laws available to a crystal is the index of its class in the point group of its lattice, minus one. Doing that arithmetic for all thirty-two classes takes a moment and produces a census with a sharp edge on it — the seven classes that cannot twin this way are exactly the seven that already use everything their lattice has.

applied · Twinning 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.

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.

point-groups · Diffraction 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.

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.

applied · Twinning 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.

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.

diffraction · The Patterson function 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.

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.

diffraction · Diffraction Everything measurable at λ = 1.54 Å, and it is a finite set. A section through the reciprocal lattice of a cubic cell of 10 Å, with the limiting sphere drawn. Bragg's law reaches a reflection only if its spacing is at least half the wavelength, so the measurable reflections are the lattice points inside a sphere of radius 2/λ and the points outside it are not merely unmeasured — no experiment at this wavelength can reach them. In this section 516 points lie inside; in the full sphere there are 9,092.

How many reflections there are

The reciprocal lattice is infinite and a measurement is not. A wavelength cuts a sphere out of it, the number of points inside is the sphere's volume times the cell's, and symmetry then removes all but a fraction — though never quite the fraction a division would give.

diffraction · Resolution p4m: 4 and 4. The standard motif — three points in no particular arrangement — repeated by p4m, with each copy coloured by the sign of the area of the triangle it makes. 4 copies have one sign and 4 the other, because the group contains an operation that reverses orientation. A structure built from one enantiomer cannot sit here: the group would put its mirror image in the same crystal. The colours were computed from the coordinates rather than assigned.

The groups a single hand may sit in

A protein is built from one enantiomer of every amino acid, and a crystal of it contains nothing else. That single fact deletes most of the classification at a stroke: any operation reversing orientation would put the other hand in the same crystal. The criterion is one line of arithmetic, and in the plane the enumeration is complete — five of the seventeen.

space-groups · Chirality pmg: 80 of 80 restricted. The reflections of pmg inside a window of ±4, with the ones whose phase symmetry restricts to two values picked out. Every solid spot has a structure factor that must be real up to a fixed rotation — a sign, in effect — whatever the atoms turn out to be, and the pale ones have a phase symmetry says nothing about. The 4 palest spots carry two incompatible restrictions at once, which leaves them nothing to be but zero. Which spots these are was computed from the operations, before any structure existed.

The zones that behave as if there were a centre

The phase problem is usually stated as though symmetry had nothing to say about phases. It is true of most reflections and false of some, and which is decidable from the group alone: where an operation carries a reflection onto its own negative, the phase is confined to two values half a turn apart, computed from that operation's translation.

diffraction · Statistics The same structure, mapped from intensities and from differences. Left, the ordinary Patterson map of the structure: 14762 interatomic vectors, a continuous field of overlapping peaks, and the two vectors between the anomalous scatterers — circled — nowhere among its strongest. Right, the map from squared Bijvoet differences over the same reflections: two peaks after the origin, and they are those two vectors. The difference map is 7381 times smaller a problem to read.

A map of the atoms that break the law

Feed a Patterson synthesis the differences between the two halves of each Friedel pair instead of the intensities, and the map that comes back holds the vectors between the anomalous scatterers and nothing else. Two atoms among a hundred and twenty-two: 14,762 vectors become two.

diffraction · The Patterson function Two symmetric structures a diffraction pattern cannot separate. Two arrangements of 6 atoms on a 6 × 6 torus, each invariant under the plane group p6m, drawn beside the Patterson they share. No translation and no inversion carries one onto the other, so they are different structures; every one of the thirty-six interatomic vector counts is the same, so every diffracted intensity is the same and no measurement at any resolution separates them. Of the 4 structures with this symmetry and this many atoms, there are only 3 Pattersons — so imposing the most symmetric of the seventeen plane groups has not removed the ambiguity.

Symmetry does not rescue a Patterson

Every homometric pair found so far sits on a bare ring with no operations imposed, and a real crystal sits in a space group. Impose one and the ambiguity does not go away: 12 of the 13 groups searched still have pairs, and at six atoms the hexagonal groups are indistinguishable two to three times as often as the general position.

diffraction · Homometry

Named alongside it

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

Structure factorLaue classCentrosymmetricCrystal classThe Patterson functionPhase problemSystematic absenceAnomalous scatteringChiralityDiffractionMeasurementPoint group

All concepts