Crystallography past, present and future

Transcription

1 Crystallography past, present and future Jenny P. Glusker Philadelphia, PA, U. S. A. International Year of Crystallography UNESCO, Paris, France 20 January 2014

2 QUARTZ CRYSTALS Quartz crystals found growing naturally. Note the crystal faces that are formed and the angles between two pairs of these faces

3 BIREFRINGENCE (double refraction) Calcite crystal. Notice the two images (birefringence).

4 LARGE CRYSTALS CAN BE GROWN Potassium dihydrogen phosphate. Large size. ISOMORPHISM Colorless potash alum grown on a crystal of violet chrome Alum, KCr(SO 4 ) 2.12H 2 O, embedded in colorless KAl(SO 4 ) 2.12H 2 O.

5 1665, THE INTERNAL STRUCTURE OF CRYSTALS Left: Robert Hooke in 1665 in his book, Micrographia, represented the internal structure of flint crystals by a close-packing of spheres. Spheres (pink) added to his diagram (top left).

6 CRYSTAL = LATTICE AND MOTIF crystal lattice structural motif crystal structure

7 TOBACCO NECROSIS VIRUS CRYSTALS Photograph from R. W. G. Wyckoff

8 X RAYS FOR VIEWING THE BODY X rays have enabled one to see bones in the human body. Röntgen reportedly photographed his wife s hand for 15 minutes, December Foot in a high-button shoe. Radiograph, 1896.

9 DIFFRACTION BY A SIEVE, SPACING, d n λ = 2 d sinθ Fine sieve. Wires closer together. Coarse sieve. Wires further apart. λ= wavelength of light, d = sieve wire spacing, θ = angle at which diffracted light beam hits the detector. Note that the diffraction for blue light is closer in than for red light (shorter wavelength for blue light).

10 DIFFRACTION PHOTOGRAPH OF ZINCBLENDE (ZnS) Laue, Friedrich and Knipping, 1912 Diffraction of X rays by crystalline zincblende. This photograph led to its crystal structure which contains a four-fold axis of symmetry.

11 X-RAY DIFFRACTION KCl X-RAY DIFFRACTION MYOGLOBIN From John Kendrew Positions of spots measured to give the unit-cell dimensions. Intensities of spots measured to give positions of atoms in each unit cell.

12 DNA DIFFRACTION PATTERN Pulled fibers of DNA A DNA structure Crystals of polynucleotides (portions of DNA) DNA helix DNA photograph courtesy Robert Langridge. Polynucleotide photographs courtesy Dick Dickerson.

13 SODIUM CHLORIDE CRYSTAL STRUCTURE Each sodium ion is surrounded by six chloride ions. Each chloride ion is surrounded by six sodium ions. No individual NaCl molecules are seen.

14 SEEING MOLECULES Electron microscopy X-ray analysis of crystals No X-ray lens currently available.

15 incident X rays 1 BRAGG S LAW nλ = 2d sinθ diffracted X rays crystal spacing The crystal has a periodic structure, repeating vertically at a distance d. The electrons around each atom scatter incident X rays. If the path difference of the two waves, 1 and 2, is an integral number of wavelengths, the intensity of the diffracted (scattered) beam will be increased (Young Bragg).

16 DIFFRACTION phase problem Aim to get observed and calculated intensities to agree in magnitude. electron-density map

17 EXPERIMENTAL SETUP This arrangement has not changed much in 100 years but each of the components are now greatly improved in capability and efficiency. crystal detection system source of X rays

18 OLD-TIME COMPUTING

19 HEXAMETHYLBENZENE (KATHLEEN LONSDALE, 1928) Benzene planar All C-C equal

20 STEROIDS (J. D. BERNAL, 1932) Wieland and Windaus formulae Bernal, Rosenheim King formula Will not fit into measured unit cell Wieland, Dane formula (also crystal structure) Fits into unit cell

21 POTASSIUM DIHYDROGEN PHOSPHATE Crystal structure Two orientations of the phosphate groups Patterson map

22

23 COPPER SULFATE PENTAHYDRATE Patterson map Cu-Cu and Cu-S vectors Crystal structure

24

25 BENZYLPENICILLIN (HODGKIN, 1949) Two possible formulae β-lactam oxazolone

26 PATTERSON MAPS: HEAVY ATOMS Patterson map Vectors at: 0,0 1/2-2x,-2y 1/2,1/2-2y -2x,1/2 Electrondensity map Atoms at: x,y 1/2-x,-y 1/2+x,1/2-y -x,1/2+y

27 FINDING ATOMS IN THE HEXAACID DERIVED FROM VITAMIN B 12 Cobalt only input 26 atoms input

28 ELECTRON-DENSITY MAPS AND RELATIVE PHASES Summing waves Effects of different relative phases

29 DIRECT METHODS: RELATIVE PHASES Choose the least negative background

30 HEXAMETHYLBENZENE 7-30 Kathleen Lonsdale,

31 RESOLUTION : WHAT WE CAN SEE 5.5 Å 2.5 Å 1.5 Å 0.8 Å

32 ANOMALOUS SCATTERING No anomalous scattering I (h k l ) = I (-h -k l ) Anomalous scattering I (h k l ) I (-h -k l ) Different path lengths as if the heavy atom had gulped

33 ABSOLUTE CONFIGURATION: ISOCITRATE Asymmetric carbon atom

34 BIOCHEMICAL REACTIONS 6 Li D H Absolute configuration of deuterated Li glycolate (action of lactate isomerase). Differences between intensities I (hkl) and I (-h k l) 6 Li is an anomalous scatterer for neutrons

35 INTERPRETING NEUTRON MAPS Element neutron X rays (fm) (electrons) H D C N O Mg Ca Mn Fe Co Ni Zn Å neutron map, blue positive, red negative. C O H on C not exchangeable H C H on N exchanged for D

36 CATALYTIC WATER MOLECULE Metal ion-carboxylate-water motif in D-xylose isomerase. The catalytic water is shown with heavy black bonds. Both protons are found to be present on that water W1018.

37 H-BONDING NETWORK BETWEEN SUBSTRATE AND ENZYME Oxygen red Nitrogen blue Hydrogen yellow

38 THE MANDELATE RACEMASE REACTION

39 INTERMOLECULAR INTERACTIONS Rosenfield JACS (1977)

40 GLYCOGEN PHOSPHORYLASE b Heptenitol plus phosphate gives heptulose-2-phosphate Note how the phosphate group becomes bound to the sugar as time progresses. Hadju, Machin, Campbell, Greenhough, Clifton, Zurek, Gover, Johnson, Elder. Nature 329, 178 (1987).

41 THE FUTURE OF CRYSTALLOGRAPHY Better methods for growing diffraction-quality crystals. Continuing the trend of solving structures of large biochemically relevant crystals and determining details of the reactions they undergo. Membrane proteins. Learning much more about electron density in molecules. Following the courses of chemical and biochemical reactions. More details of chemical bonding. Molecular motion and reactivity in crystals. Time-resolved X-ray diffraction. Studies of metals, alloys, polymers and ceramics and the relationship of their structure to their properties. Aperiodic and partially periodic structures. Shape memory alloys. New materials. Other new radiations for diffraction. Less than crystalline material. However, most scientific advances in the study of crystals in the next 100 years cannot be predicted at this time. The same was true in 1914.

42 Crystal SYNOPSIS Discovery of X rays 1895 Diffraction of X rays by crystals 1912 (periodicity) Solving the phase problem Patterson map 1934 Isomorphism Direct methods Direct phasing X-ray diffraction pattern can be interpreted in terms of the atomic arrangement in the crystal, 1914 Crystal structure determinations, scientific journals, databases Discovery of neutron diffraction 1945 Anomalous dispersion and absolute configuration 1949