1. Chem 125 Lecture 7 9/20/06 Projected material This material is for the exclusive use of Chem 125 students at Yale and may not be copied or distributed further. It is not readily understood without reference to notes from the lecture.

2. Exam 1 - Friday, Sept. 29 ! Covers Lectures through next Wednesday Including: Functional Groups X-Ray Diffraction 1-Dimensional Quantum Mechanics (Sections I-IV of webpage & Erwin Meets Goldilocks)Erwin Meets Goldilocks Get-aquainted session Friday afternoon 4-5:30 in 160 SCL

3. TAs Gözde Josh Brian David All in WLH 114 7-9 Tuesday 8-10 Sunday 7-9 Thursday

4. In 1895 Röntgen Discovers X-Rays Shadow of Frau Röntgen's Hand (1895) In 1912 Laue Invents X-Ray Diffraction CuSO 4 Diffraction (1912)

5. Wm. Lawrence Bragg (1890-1971) Determined structure of ZnS from Laue's X-ray diffraction pattern (1912) Youngest Nobel Laureate (1915)

6. Tungsten Interconnect in Computer Chip Nanotomography Comes of Age, Nature, August 10, 2006 “They then use tomographic methods to combine images taken at different incident X-ray angles, allowing internal structures and - given sufficent spectral resolution - chemical bondings to be discerned with a spatial resolution of around 60 nanometers.”

7. "Seeing" Individual Molecules, Atoms, Bonds Collectively by X-Ray Crystallography

8. Blurring Problem Blurring Problem from Motion and Defects Time Averaging Space Averaging in Diffraction (Cooperative Scattering) Advantage for SPM (Operates in Real Space)

9. What can X-ray diffraction show? How does diffraction work? Like all light, X-rays are waves. Atoms?Molecules?Bonds?

10. Interference of Ripples

11. Wave Machines

12. Bragg Machine http://www.eserc.stonybrook.edu/ProjectJava/Bragg/ Breaks?

13. Real Space "Reciprocal" Space Material Diffraction Photo Molecular Structure Fuzzy Pattern Crystal Lattice Viewing Holes Decreasing Spacing Increasing Spacing

14. Direct Two Scattering Directions are Always Exactly in Phase “scattering vector” Specular perpendicular to scattering vector All electrons on a plane perpendicular to the scattering vector scatter in-phase at the specular angle ! Specular

15. Simplification from Electrons-on-a-Plane Trick scattering vector 3 2 4 1

16. 10 Simplification from Electrons-on-a-Plane Trick 3 +2 +4 +1 1 2 3 Net in-phase scattering Total Electrons 3 2 4 1

17. Water Oil “Thickness” ~ 200 nm Path Difference = 400 nm = 0.5 Strong 400 nm Scattering No 800 nm Scattering = 1

18. scattering vector Simplification from Electrons-on-a-Plane Trick 10 3 +2 +4 +1 Net in-phase scattering Total Electrons 1 2 3 Suppose first path difference is half a wavelength. (increase or decrease angle) 3 +2 -4 0 0.5 1 1.5 3 2 4 1

19. Benzene Snowflake Slide with Random (but Oriented) "Benzenes"

20. Benzene Snowflake Isolated “Benzenes”

21. Benzene Snowflake 1 √3 [1] Reciprocal Isolated “Benzenes” Closely-spaced planes give high angles.

22. Benzene Snowflake Isolated “Benzenes”

23. 2D Lattice of “Benzenes”

24. Filament Light Bulb Filament (helix)

25. Filament Light Bulb Filament (helix) X angle tells helix pitch Spot spacing tells scale Spot spacing tells scale Spots weaken successively (from wire thickness) (given & screen dist)

26. HELIX w S S vw S Curious Intensity Sequence B-DNA R. Franklin (1952)

27. Even Double Helix Would cancel "Odd # reflections"

28. w S S vw S Curious Intensity Sequence B-DNA R. Franklin (1952)

29. Offset Double Helix

30. BASE STACKING B-DNA R. Franklin (1952) w S S vw S MAJOR & MINOR GROOVES HELIX DIAMETER

31. End