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Lecture 2: Crystal Symmetry. Crystals are made of infinite number of unit cells. Unit cell is the smallest unit of a crystal, which, if repeated, could generate the whole crystal. .

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Lecture 2: Crystal Symmetry


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slide2

Crystals are made of infinite number of unit cells

Unit cell is the smallest unit of a crystal, which, if repeated, could generate the whole crystal.

A crystal’s unit cell dimensions are defined by six numbers, the lengths of the 3 axes, a, b, and c, and the three interaxial angles, ,  and .

slide3

A crystal lattice is a 3-D stack of unit cells

Crystal lattice is an imaginative grid system in three dimensions in which every point (or node) has an environment that is identical to that of any other point or node.

miller indices
Miller indices

A Miller index is a series of coprime integers that are inversely proportional to the intercepts of the crystal face or crystallographic planes with the edges of the unit cell. 

It describes the orientation of a plane in the 3-D lattice with respect to the axes.

The general form of the Miller index is (h, k, l) where h, k, and l are integers related to the unit cell along the a, b, c crystal axes.

slide5

Miller Indices

Rules for determining Miller Indices:

1. Determine the intercepts of the face along the crystallographic axes, in terms of unit cell dimensions.

2. Take the reciprocals

3. Clear fractions

4. Reduce to lowest terms

An example of the (111) plane (h=1, k=1, l=1) is shown on the right.

slide6

Another example:

Rules for determining Miller Indices:

1. Determine the intercepts of the face along the crystallographic axes, in terms of unit cell dimensions.

2. Take the reciprocals

3. Clear fractions

4. Reduce to lowest terms

slide7

Where does a protein crystallographer see the Miller indices?

  • Common crystal faces are parallel to lattice planes
  • Each diffraction spot can be regarded as a X-ray beam reflected from a lattice plane, and therefore has a unique Miller index.
slide8

Symmetry

A state in which parts on opposite sides of a plane, line, or point display arrangements that are related to one another via a symmetry operation such as translation, rotation, reflection or inversion.

Application of the symmetry operators leaves the entire crystal unchanged.

slide9

Symmetry Elements

Rotation

turns all the points in the asymmetric unit around one axis, the center of rotation. A rotation does not change the handedness of figures. The center of rotation is the only invariant point (point that maps onto itself).

slide12

Symmetry Elements

Translation

moves all the points in the asymmetric unit the same distance in the same direction. This has no effect on the handedness of figures in the plane. There are no invariant points (points that map onto themselves) under a translation.

slide13

Symmetry Elements

Screw axes (rotation + translation)

rotation about the axis of symmetry by 360/n, followed by a translation parallel to the axis by r/n of the unit cell length in that direction. (r < n)

slide14

120 rotation

1/3 unit cell translation

slide16

Symmetry Elements

Inversion, or center of symmetry

every point on one side of a center of symmetry has a similar point at an equal distance on the opposite side of the center of symmetry.

slide17

Symmetry Elements

Mirror plane or Reflection

flips all points in the asymmetric unit over a line, which is called the mirror, and thereby changes the handedness of any figures in the asymmetric unit.

The points along the mirror line are all invariant points (points that map onto themselves) under a reflection.

slide19

Symmetry Elements

Glide reflection (mirror plane + translation)

reflects the asymmetric unit across a mirror and then translates parallel to the mirror. A glide plane changes the handedness of figures in the asymmetric unit. There are no invariant points (points that map onto themselves) under a glide reflection.

symmetries in crystallography
Symmetries in crystallography
  • Crystal systems
  • Lattice systems
  • Space group symmetry
  • Point group symmetry
  • Laue symmetry, Patterson symmetry
crystal system
Crystal system
  • Crystals are grouped into seven crystal systems, according to characteristic symmetry of their unit cell.
  • The characteristic symmetry of a crystal is a combination of one or more rotations and inversions.
slide24

7 Crystal Systems

orthorhombic

hexagonal

monoclinic

trigonal

cubic

tetragonal

triclinic

Crystal System External Minimum Symmetry Unit Cell Properties

Triclinic None a, b, c, al, be, ga,

Monoclinic One 2-fold axis, || to b (b unique) a, b, c, 90, be, 90

Orthorhombic Three perpendicular 2-folds a, b, c, 90, 90, 90

Tetragonal One 4-fold axis, parallel c a, a, c, 90, 90, 90

Trigonal One 3-fold axis a, a, c, 90, 90, 120

Hexagonal One 6-fold axis a, a, c, 90, 90, 120

Cubic Four 3-folds along space diagonal a, a, ,a, 90, 90, 90

lattices
Lattices

Auguste Bravais

(1811-1863)

  • In 1848, Auguste Bravais demonstrated that in a 3-dimensional system there are fourteen possible lattices
  • A Bravais lattice is an infinite array of discrete points with identical environment
  • seven crystal systems + four lattice centering types = 14 Bravais lattices
  • Lattices are characterized by translation symmetry
tetragonal lattices are either primitive p or body centered i
Tetragonal lattices are either primitive (P) or body-centered (I)

C centered lattice

=

Primitive lattice

point group symmetry
Point group symmetry
  • Inorganic crystals usually have perfect shape which reflects their internal symmetry
  • Point groups are originally used to describe the symmetry of crystal.
  • Point group symmetry does not consider translation.
  • Included symmetry elements are rotation, mirror plane, center of symmetry, rotary inversion.
n fold axes with n 5 or n 6 does not occur in crystals
N-fold axes with n=5 or n>6 does not occur in crystals

Adjacent spaces must be completely filled (no gaps, no overlaps).

laue class patterson symmetry
Laue class, Patterson symmetry
  • Laue class corresponds to symmetry of reciprocal space (diffraction pattern)
  • Patterson symmetry is Laue class plus allowed Bravais centering (Patterson map)
slide35

Space groups

The combination of all available symmetry operations (32 point groups), together with translation symmetry, within the all available lattices (14 Bravais lattices) lead to 230 Space Groups that describe the only ways in which identical objects can be arranged in an infinite lattice. The International Tables list those by symbol and number, together with symmetry operators, origins, reflection conditions, and space group projection diagrams.

slide37

Identification of the Space Group is called indexing the crystal.

The International Tables for X-ray Crystallography tell us a huge

amount of information about any given space group. For instance,

If we look up space group P2, we find it has a 2-fold rotation axis and the following symmetry equivalent positions:

X , Y , Z

-X , Y , -Z

and an asymmetric unit defined by:

0 ≤ x ≤ 1

0 ≤ y ≤ 1

0 ≤ z ≤ 1/2

An interactive tutorial on Space Groups can be found on-line in Bernhard Rupp’s Crystallography 101 Course: http://www-structure.llnl.gov/Xray/tutorial/spcgrps.htm

space group p1
Space group P1

Point group 1 + Bravais lattice P1

space group p1bar
Space group P1bar

Point group 1bar + Bravais lattice P1

space group p2
Space group P2

Point group 2 + Bravais lattice “primitive monoclinic”

space group p2 1
Space group P21

Point group 2 + Bravais lattice “primitive monoclinic”,

but consider screw axis

coordinate triplets equivalent positions
Coordinate triplets, equivalent positions

r = ax + by + cz,

Therefore, each point can be described by its fractional coordinates, that is, by its coordinate triplet (x, y, z)

space group determination
Space group determination
  • Symmetry in diffraction pattern
  • Systematic absences
  • Space groups with mirror planes and inversion centers do not apply to protein crystals, leaving only 65 possible space groups.
slide46

Asymmetric unit

Recall that the unit cell of a crystal is the smallest 3-D geometric figure that can be stacked without rotation to form the lattice. The asymmetric unit is the smallest part of a crystal structure from which the complete structure can be built using space group symmetry. The asymmetric unit may consist of only a part of a molecule, or it can contain more than one molecule, if the molecules not related by symmetry.

matthew coefficient
Matthew Coefficient
  • Matthews found that for many protein crystals the ratio of the unit cell volume and the molecular weight is between 1.7 and 3.5Å3/Da with most values around 2.15Å3/Da
  • Vm is often used to determine the number of molecules in each asymmetric unit.
  • Non-crystallographic symmetry related molecules within the asymmetric unit