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 19 essays across 6 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 Two hundred and thirty groups on a hundred and twenty-two diffraction symbols. Every space group placed in a column for its diffraction symbol — Bravais lattice, Laue group and systematic absences — with the columns grouped by lattice. There are 122 symbols. 50 of them name one group; 44 are shared by two, 23 by three, 2 by four and 3 by five.

Every ambiguity in a diffraction pattern, sorted by its cause

A diffraction pattern shows a lattice, the symmetry of its intensities and the reflections that are missing, and the 230 space groups show 122 different combinations of the three. Fifty of those name a single group. For the rest, each pair of groups that share one can be sorted by why they do, and there are five reasons. Four of them are ambiguities some further measurement resolves. The fifth, two groups with the same operations in the same places except for where their axes cross, happens exactly twice, and nothing but a solved structure decides it.

classification · Cohomology The worst edge pair is the two most anomalous wavelengths. For each pair of the four wavelengths, and for the peak, inflection and high remote together, the median error of the phase difference between the whole structure and its anomalous atoms, recovered from both Friedel mates at each wavelength with a 1% error on every intensity. Beside each, the spread of f′ across the chosen wavelengths. The pairs that include a remote wavelength and one on the edge phase to seven or eight degrees; the peak and the inflection together, the two with the largest anomalous effect, to eighteen; the two remotes to fifty-five.

The two most anomalous wavelengths are the wrong pair

A MAD experiment measures both Friedel mates at two wavelengths near an absorption edge and solves for a phase. The obvious choice is the two wavelengths where the anomalous effects are largest, the peak of f″ and the dip of f′. Of all the pairs that use the edge, it is the worst. The sine of the phase is carried by f″, but the cosine is carried by how much f′ changes between the two wavelengths, and two points on the same edge barely change it.

diffraction · Friedel's law Three difference maps of one substructure, and the map they approximate. Patterson syntheses over 1,681 reflections of a structure with 120 light atoms and two anomalous scatterers, from squared Bijvoet differences at one wavelength, squared dispersive differences between two wavelengths, and the two normalised and summed; the fourth panel is the Patterson of the anomalous atoms' own intensities. Circles mark the two vectors between the anomalous atoms. Each map's correlation with the exact one is printed beneath it: Bijvoet 0.775, dispersive 0.838, combined 0.999.

A second wavelength completes the map

The Bijvoet difference carries the anomalous substructure's intensity times the sine squared of a phase; the dispersive difference between two wavelengths carries it times the cosine squared. Normalised and added, the two make the substructure's own Patterson, correlation 0.999. It needs no fewer reflections than either half, because the threshold was never the average. What the dispersive half brings is a way of failing the Bijvoet half cannot have: two datasets, and a scale between them.

diffraction · The Patterson function Almost no homometric pair on the torus is a reversed factor. For ten plane groups at several numbers of atoms on a 6 × 6 torus, the structures, the pairs of structures sharing one Patterson, how many of those pairs reversing one factor of a sumset explains, and how many are a patchwork of Galois classes. Factor reversal explains 2 of 3522; the patchwork explains all 3522.

A homometric twin is the structure moved class by class

On a ring, every homometric pair a small search found came from one construction: factor the structure as a sumset and reverse one factor. Imposing a plane group on a torus made homometry more common, and the obvious guess was that symmetry makes structures easier to factor. Tested pair by pair, factor reversal explains two of 3,522 homometric pairs on a 6 × 6 torus, and none at all at six atoms. What explains all 3,522 is a different mechanism: the partner is the structure's own Fourier transform moved independently on each Galois class of characters, by a shift, a sign or an inversion.

diffraction · Homometry Where the third wavelength should go. The median Cramér–Rao bound on the phase difference for two hundred reflections, measured at the inflection and the high remote and at a third wavelength whose energy runs across the edge, twice: with f′ known everywhere, and with f′ at the edge energies refined from the data. Known, the best third sits 1 eV above the edge at 6.26°, and a repeat of either wavelength is nearly as good. Refined, both repeats determine nothing, and the best third moves to +2 eV at 6.30°.

The third wavelength is there to measure the edge

A three-wavelength MAD experiment is usually justified as more anomalous signal: a third look at the edge, placed where the first two left the most out. Counted with the scattering factors known, a third wavelength buys nothing a longer look at the best pair would not buy better. Its real job appears only when f′ at the edge has to be found from the data, which it always does. Two wavelengths then carry one equation too few, and any third energy that is not a repeat supplies it, for two hundredths of a degree.

diffraction · Friedel's law No triple of wavelengths is best for both the phase and the edge. Every triple of energies on a grid across a model selenium edge, placed by two Cramér–Rao bounds with the edge's position and white line refined from the data: the median phase error across, and the error in the edge's position up, on a logarithmic scale. The front of triples that no other beats on both runs from +1, +2, +150 eV (6.15°, ±0.066 eV) to -120, -1, +3 eV (7.54°, ±0.022 eV). The classic peak, inflection and high remote sits on it, at 6.42° and ±0.026 eV.

The wavelengths that phase best do not find the edge

A MAD experiment refines the anomalous atom's scattering factors so that it can solve for the phases, and those same factors report where the absorption edge sits and how tall its white line stands, which is chemistry. Scored for the edge instead of the phase, the best triple of wavelengths moves: two straddling the step and one far below it, where the phase-best triple put two on the step and one far above. No triple is best at both, and the textbook peak, inflection and remote turns out to be the compromise between them.

diffraction · Friedel's law Three-species arrangements whose sums are parallel at every spot, with and without a centre. Every arrangement of three species, all present, on a cyclic cell of four to nineteen sites. The third column counts those whose two phase sums are parallel at every superlattice spot, the fourth those among them with a centre of inversion, the fifth those without one, and the last how many kinds the exceptions make up to translation, inversion, relabelling the spots and renaming the species. Primes are shaded. At 5, 7 and 11 sites every parallel arrangement has a centre; at 13 sites 936 do not, and they are all one arrangement; at 17 there are 17 kinds and at 19 there are 48.

Thirteen sites obey Friedel's law without a centre

At five and seven sites the earlier census found that a three-species structure has a contrast that darkens a spot exactly when it has a centre, and asked whether that is a theorem. It is not. The two phase sums are parallel exactly when the A–B pairs are as common at every separation forwards as backwards, and exactly when no anomalous scatterer can produce a Bijvoet difference anywhere in the pattern. At 5, 7 and 11 sites only a centre achieves that. At 13 sites one arrangement does it without one.

operations · Counting

Named alongside it

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

Structure factorPhase problemAnomalous scatteringLaue classThe Patterson functionCentrosymmetricCrystal classSystematic absenceBijvoet differenceHomometryLeast squaresResolution

All concepts