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3. Crystals. What defines a crystal? Atoms, lattice points, symmetry, space groups Diffraction B-factors R-factors Resolution Refinement Modeling!. Crystals. What defines a crystal? 3D periodicity: anything (atom/molecule/void) present
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3. Crystals What defines a crystal? Atoms, lattice points, symmetry, space groups Diffraction B-factors R-factors Resolution Refinement Modeling!
Crystals What defines a crystal? 3D periodicity: anything (atom/molecule/void) present at some point in space, repeats at regular intervals, in three dimensions. X-rays ‘see’ electrons (r) = (r+X) (r): electron density at position r X: n1a + n2b + n3c n1, n2,n3: integers a, b, c: vectors
Crystals What defines a crystal? primary building block: the unit cell lattice: set of points with identical environment crystal
Crystals Which is the unit cell? primitive vs. centered lattice primitive cell: smallest possible volume 1 lattice point
Crystalsorganic versus inorganic * lattice points need not coincide with atoms * symmetry can be ‘low’ * unit cell dimensions: ca. 5-50Å, 200-5000Å3 NB: 1 Å = 10-10 m = 0.1 nm
Crystalssome terminology * solvates: crystalline mixtures of a compound plus solvent c a b - hydrate: solvent = aq - hemi-hydrate: 0.5 aq per molecule * polymorphs: different crystal packings of the same compound * lattice planes (h,k,l): series of planes that cut a, b, c into h, k, l parts respectively, e.g (0 2 0), (0 1 2), (0 1 –2)
Crystalscoordinate systems Coordinates: positions of the atoms in the unit cell ‘carthesian: using Ångstrøms, and an ortho-normal system of axes. Practical e.g. when calculating distances. example: (5.02, 9.21, 3.89) = the middle of the unit cell of estrone ‘fractional’: in fractions of the unit cell axes. Practical e.g. when calculating symmetry-related positions. examples: (½, ½, ½) = the middle of any unit cell (0.1, 0.2, 0.3) and (-0.2, 0.1, 0.3): symmetry related positions via axis of rotation along z-axis.
Crystalssymmetry • Why use it? • efficiency (fewer numbers, faster computation etc.) • less ‘noise’ (averaging) • finite objects: crystals • rotation axes () rotation axes (1,2,3,4,6) • mirror planes mirror planes • inversion centers inversion centers • rotation-inversion axes rotation-inversion axes • ----------------------------- + screw axes • point groups glide planes • translations • --------------------------- + • space groups
Crystalssymmetry and space groups symmetry elements * translation vector * rotation axis * screw axis * mirror plane * glide plane * inversion center
Crystalssymmetry and space groups symmetry elements * translation vector * rotation axis * screw axis * mirror plane * glide plane * inversion center examples (x, y, z) (x+½, y+½, z) (x, y, z) (-y, x, z) (x, y, z) (-y, x, z+½) (x, y, z) (x, y, -z) (x, y, z) (x+½, y, -z) (x, y, z) (-x, -y, -z) equivalent positions Set of symmetry elements present in a crystal: space group examples: P1; P1; P21; P21/c; C2/c Asymmetric unit: smallest part of the unit cell from which the whole crystal can be constructed, given the space group. -
CrystalsX-ray diffraction diffraction: scattering of X-rays by periodic electron density diffraction ~ reflection against lattice planes, if: 2dhklsin = n X ~ 0.5--2.0Å Cu: 1.54Å dhkl Data set: list of intensities I and angles path: 2dhklsin
Crystalsinformation contained in diffraction data • * lattice parameters (a, b, c, , , ) obtained from the directions of • the diffracted X-ray beams. • *electron densities in the unit cell, obtained from the intensitiesof the • diffracted X-ray beams. • Electron densities atomic coordinates (x, y, z) • Average over time and space • • Influence of movement due to temperature: atoms appear ‘smeared out’ • compared to the static model ADP’s (‘B-factors’). • Some atoms (e.g. solvent) not present in all cells occupancy factors. • Molecular conformation/orientation may differ between cells • disorder information.
Crystalsinformation contained in diffraction data * How well does the proposed structure correspond to the experimental data? R-factor consider all (typically 5000) reflections, and compare calculated structure factors to observed ones. R = | Fhklobserved - Fhklcalculated | Fhkl = Ihkl Fhklobserved OK if 0.02 < R < 0.06 (small molecules)
Crystals - doing calculations on a structure from the CSD We can search on e.g. compound name
Crystals - doing calculations on a structure from the CSD We can specify filters!
Crystals - doing calculations on a structure from the CSD • ‘refcodes’ • re-determinations • polymorphs • *anthraquinone*
Crystals - doing calculations on a structure from the CSD Z: molecules per cell Z’: molecules per asymmetric unit
Crystals - doing calculations on a structure from the CSDexporting from ConQuest/importing into Cerius Cerius2 CSD cif cssr fdat pdb Not all bond (-type) information in CSD data add that first!
Crystals - doing calculations on a structure from the CSDChecking for close contacts and voids how close is ‘too close’ default: ~0.9xRVdW minimal ‘void size’
Crystals - doing calculations on a structure from the CSDOptimizing the geometry CSD optimized*) a 7.86 7.76 b 3.94 4.36 c 15.75 15.12 90 90 102.6 107.4 90 90 ! * space-group symmetry imposed
Crystals - doing calculations on a structure from the CSDOptimizing the geometry CSD opt/spgr opt*) a 7.86 7.76 7.69 b 3.94 4.36 4.66 c 15.75 15.12 15.93 90 90 90 102.6 107.4 106.8 90 90 90 * space-group symmetry not imposed; Is it retained?
Crystals - doing calculations on a structure from the CSDOptimizing the geometry • Application of constraints during optimization: • space-group symmetry -- if assumed to be known • cell angles and/or axes -- e.g. from powder diffraction • positions of individual atoms -- e.g non-H, from diffraction • rigid bodies -- if molecule is rigid, or if it is too flexible...
Crystalssingle crystal versus powder diffraction Powder: large collection of small single crystals, in many orientations Single crystal all reflections (h,k,l) can be observed individually, leading to thousands of data points. Powder all reflections with the same overlap, leading to tens of data points. Diffraction data can easily be computed verification of proposed model, or refinement (Rietveld refinement)
Next week…. Modeling crystals: how does it differ from small systems? Applications: predicting morphology predicting crystal packing