1. Protein Structure Determination Lecture 4 -- Bragg’s Law and the Fourier Transform

2. Reflecting on mirrors Although sometimes drawn as a vector, X-rays are plane waves.

3. Consider: scattering by a plane The lines represent the crests of waves. Phase = 0.

4. Plane wave impacts the plane at different points on the plane at different phases.

5. Scatter from a point initiates a spherical wave

6. Waves scatter from points in all directions, creating interfering sphere waves. The phase of the sphere wave equals the phase of the incident wave at that point.

7. The combined sphere waves interfere destructively in all directions but one, the reflection angle.

8. Plane scatter geometry s0s0 s S  ...if, and only if, the angle of incidence equals the angle of scatter. Everywhere else, interference is destructive. All points on a plane scatter with the same path length...

9. d  n =2d sin  Points on parallel planes that have a integer number of wavelengths different path length scatter in phase.

10. d  n =2d sin 

11. Bragg planes Parallel planes that have a integer number of wavelengths difference in path length. Two unit vectors and a wavelength define a set of Bragg planes. 

12. Bragg’s law d  n =2d sin  Planes separated by d scatter in phase. If  is larger, d is smaller. d= /2sin  path length for this plane is shorter by Sir Lawrence Bragg, winner of 1914 Nobel Prize in Physics...than for this plane.

13. Path length differences d  path difference=2d sin  Therefore, n =2dsin    if waves add, then path difference = n 

14. Phase for points not on Bragg planes d  Path difference = 2(x*d) sin  Phase difference = 2  2(x*d) sin  radians   x*d therefore, phase difference = 2  x  radians but, d= /2sin 

15. Scattering from the Origin has phase 0 There is only one origin in the crystal (usually this is defined by crystal symmetry) The wave travels a distance a from the Xray source to the plane of the origin, and a distance b from the origin to the detector. s0s0 s origin of unit cell a b

16. Phase equals additional distance traveled... phase  a+rs 0 +b-rs - (a+b)]2  = 2  (rs 0 - rs)/ e-e- s0s0 s rs 0 -rs r origin of unit cell...divided by the wavelength Distance from source to e - = a + rs 0 Distance from e - to detector = b - rs a b

17. The scattering vector S We can simplify the equation for phase by noticing that (r 1 s - r 1 s 0 )/  r 1 (s - s 0 )/ So we define the “scattering vector” S S = (s - s 0 )/ Note the reciprocal Å units. These are the units of reciprocal space! Substituting S into expressions for phase: = 2  Sr 2 = 2  Sr 1 Simplifying slightly s0s0 s -s 0 / s/ S phase of a point r  2  (rs - rs 0 )/   = 2  (r 2 s - r 2 s 0 )/   = 2  (r 1 s - r 1 s 0 )/

18. Scattering factor for two or more e - Pick any two locations in space, r 1 and r 2, and a direction of scatter s (a unit vector). What is the amplitude and phase of the scattered X-rays?   = 2  Sr 2   = 2  Sr 1 e-e- e-e- r1r1 s0s0 s r2s0r2s0 r2sr2s r2r2 origin of unit cell F(s,s 0 )=A 1 e i  1 +A 2 e i  2 =  A k e i  k F(S)=  A k e i2  Sr k k k The exponent must be unit-less. Let’s check: r is in Å. S is in 1/Å. So units cancel!

19. Phase zero Bragg planes R i d  is proportional to the total number of e - on all of these planes.   ... planes extend throughout the crystal

20. Phase x Bragg planes R i  x  is proportional to the total number of e - on these planes.  x  Planes shifted by x = d/6 are phase shifted by 2  /6.

21. Integrating Bragg planes from x=0 to 1 R i The total F is the wave sum over all Bragg planes. R i F F=   (x)e 2  ix

22. Bragg planes versus crystal planes

23. Crystal planes

24. Bragg Planes are numbered according to how they intersect the crystal axes. Starting from the Origin and moving to the first Bragg plane, if it intersects the a axis at 1/h, the b axis at 1/k and the c axis at 1/l, then the Bragg planes are called the (h k l) reflection plane. Each set of Bragg planes defines a single diffracted spot, called a “reflection”. Reflections are also numbered using (h k l). NOTE: h k and l must be integers! (proof later)

25. (2 3 3) Bragg planes (4 6 6) Bragg planes 3D Bragg planes Phase-zero planes intersect the cell axes at multiples of fractional coordinates (1/h,0,0), (0,1/k,0),(0,0,1/l)

26. Proof: The only Bragg planes that diffract X-rays are those that match crystal planes In other words, if we have seen a reflection on the film, that reflection corresponds to a set of crystal planes. Since all crystal planes pass through the unit cell origins, and since the phase of the Origin can be set to zero, all (observable) Bragg planes of phase zero pass through the Origins

27. 1. Bragg planes are either aligned with the Unit Cell Origins, or they are not. If the Bragg planes don’t all go through the Origins, then phase of every Origin is different, depending on the distance to the Bragg plane. If the Bragg planes all pass through the Origins, the phase of every Origin is zero. Proof: All Bragg planes of phase zero pass through the Origins aligned not aligned phase at origin=0° phase at origin=180°

28. 2. All planes that pass through the Origins have the same number of electrons The angle and intercept with the Unit Cell determine with atoms are on the plane. Proof: All Bragg planes of phase zero pass through the Origins 3. All planes that pass through the Origins contribute the same amplitude....because amplitude is proportional to number of electrons, and (statement 2).

29. 4. Total amplitude is the sum of the amplitudes of the planes if the planes have the same phase. Amplitude contributed by origin planes is 10K times the amplitude of one such plane, if there are 10K unit cells. Proof: All Bragg planes of phase zero pass through the Origins 5. Total amplitude is approximately zero if the planes have different phases. Phase shifts by a constant for each unit cell. Vectors sum in a circle. Summed over 10K unit cells, vector length is small. i R i R

30. Conclusion: Bragg planes that pass through all of the Origins diffract X-rays. Bragg planes that do not pass through all of the origins do not diffract X-rays. Proof: All Bragg planes of phase zero pass through the Origins 6. Any point in the Unit Cell can be the Origin. 7. All equivalent positions by lattice symmetry have the same phase. Because (statement 6), statements 1-5 apply to any point in the Unit cell. 8. If the Bragg planes do not pass through all Origins, the diffraction amplitude is zero. Because the total diffraction amplitude is the wave sum over all points in the Unit Cell.

31. 2 1 0 Where the first Bragg plane cuts the axes The n=1 Bragg plane (normal to S at distance d) cuts the unit cell axes at 1/h1/k1/l

32. If indeces hkl are doubled, Bragg distance d is halved. 2 1 0 All unit cell origins have phase zero. But not all phase-zero Bragg planes must go through a unit cell origin. For example, the n=odd Bragg planes for the 0 2 0 reflection does not touch a single unit cell origin. 4 2 0 0 1 0 0 2 0

33. Calculating the structure factors Draw a plane that intersects the unit cell axes at 1/h, 1/k, and 1/l (careful to consider the sign of h,k,l) Measure the phase of each atom as its distance from the nearest Bragg plane, divided by d and multiplied by 360°. Draw the scattering factor for that atom, and sum the scattering factors to get the structure factor.

34. Calculate structure factors: F( 1 1 0) F(-1 1 0) F(-2 1 0) For a unit cell with two atoms: carbon (amplitude 6) @ (0.5, 0.2, 0.0) oxygen (amplitude 8) @ (0.3, 0.4, 0.0) a b In class exercise:

35. Calculating the density Given the structure factors F(hkl), find the point(s) of maximum e-density. F(hkl) = |F(hkl)|e i  Draw Bragg planes with phase =  ( Measure phase in the direction (h,k,l) ) Erase Bragg planes with phase =  +180° After drawing and erasing all F’s, the darkest areas are the locations of the atoms.

36. Find the maximum density point given the following structure factors: F( 1 1 0) = 1 e i(108°) F(0 1 0) = 1 e i(180°) F(1 1 0) = 1 e i(-60°) F(-1 1 0) = 1 e i(60°) F(-2 1 0) = 1 e i(-10°) a b In class exercise: