Chemistry 125: Lecture 5 Sept. 10, 2010 X-Ray Diffraction In the last 25 years various manifestations of Scanning Probe Microscopy, such as AFM, STM, and SNOM, have enabled chemists to “feel” individual molecules and atoms. SPM techniques are not quite good enough yet to study how electrons are distributed in bonds. Because light is scattered predominantly by the charged particles with the smallest mass, the electron distribution in molecules can be determined by x-ray diffraction. The roles of molecular pattern and crystal lattice repetition can be illustrated by shining a visible laser through diffraction masks to generate scattering patterns reminiscent of those encountered in X-ray studies of ordered solids. For copyright notice see final page of this file

Despite Earnshaw, might there still be shared-pair bonds and lone pairs?

Gold coated Si Chip 1.4 mm Atomic Force Microscopy The smallest scale division is 20  m Hair Only one of these five cantilevers is used in any one experiment. They differ in stiffness and ability to twist.

Scanning Electron Micrographs of AFM Cantilever ©The IN-VSEE Project; Arizona State University Tip 1m1m Radius of curvature ~20 nm

Cantilever/Chip Holder Tips

Cantilever/Chip Holder Sensitive to < 1 molecule change in height !

AFM traces at 1 min intervals of part of the surface of a benzoin crystal dissolving in 95% water / 5% n-propanol. Each ledge is one “unit cell” (1.7 nm) high. The larger pit is 5.1 nm deep. 5  m (~600 molecules) fast slow slower Ledge Dissolution Rate

Scanning Tunneling Microscopy (1999) Geo. Flynn D. Yablon (Columbia Univ) Br O Br(CH 2 ) 11 COOH on graphite Graphite

Permission limited by IBM Click to link to copyright webpage Quantum corral STM Image of Fe atoms on Cu (1993) Reprint Courtesy of International Business Machines Corporation, copyright 1993 © International Business Machines Corporation

High Resolution Requires Small Probe Rolling Wheel with Chalk on Axle to Trace Chalk-Trough Profile No Barriers Horizontal Line Distant Barriers Distorted Humps Close Barriers One Broad Hump

Cu Pentacene on Cu Scanned with a Single-Atom Tip at 5K L. Gross, et al., Science, Aug. 28, v10 10 v/m!

SNOM Scanning Near-Field Optical Microscope Scanning Near-Field Optical Microscope Glass Fiber Aluminum Coating 100 nm Aperture Lens Emitted Light Detector Sample (scanned) Light

SNOM image of nanofabricated material W. Brocklesby by permissionwww.orc.soton.ac.uk  m scale red wavelength

Scanning Probe Microscopies (AFM, STM, SNOM) are really powerful. Sharp points can resolve individual molecules and even atoms but not bonds

Lux

A lonely architectural curiosity on Sterling Chemistry Laboratory at Yale University (1923)

Micrographia Robert Hooke (1665) “But Nature is not to be limited by our narrow comprehension; future improvements of glasses may yet further enlighten our understanding, and ocular inspection may demonstrate that which as yet we may think too extravagant either to feign or suppose.”

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

Hooke: Observ. IX. Of the Colours observable in Muscovy Glass, and other thin Bodies. Confus’d Pulses of Light

Chris Incarvito’s New Toys

User Operated - CCD Detector X-Ray Tube ~$200K

Image Plate ~$350K

"Seeing" Individual Molecules, Atoms, and Bonds? Problem:

What IS light?

In What Way is Light a Wave? Force on Charge at One Position Up Down 0 Time Charged Particle

Charged Particle In What Way is Light a Wave? Force at Different Positions - OneTime Up Down 0 Position

Accelerated Electrons “Scatter” Light Why don’t protons or other nuclei scatter light? Too heavy! direct beam

Interference of Ripples Angular Intensity Distribution at great distance depends on Scatterer Distribution at the origin

By refocussing, a lens can reassemble the information from the scattered wave into an image of the scatterers. But a lens for x-rays is hard to come by. Be sure to read the webpage on x-ray diffraction.

"Seeing" Molecules, Atoms, Bonds Collectively by X-Ray Crystallography SPM “feels” them Individually

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

In 1895 Röntgen Discovers X-Rays Shadow of Frau Röentgen’s hand (1896) In 1912 Laue Invents X-Ray Diffraction CuSO 4 Diffraction (1912)

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

B-DNA R. Franklin (1952)

Science, 11 August 2000

25 nm (250 Å) >100,000 atoms + hydrogens!

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

Wave Machines

by permission, Konstantin Lukin Bragg Machine Breaks? in & out same phase

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

scattering vector Electrons-on-Evenly-Spaced-Planes Trick

10 scattering vector Net in-phase scattering Total Electrons Suppose & angle such that: Electrons-on-Evenly-Spaced-Planes Trick

10 scattering vector Suppose first path difference is half a wavelength, because of change in (or angle) Net in-phase scattering Total Electrons Electrons-on-Evenly-Spaced-Planes Trick

View from Ceiling 10.6 m 633 nm DIFFRACTION MASK (courtesy T. R. Welberry, Canberra) ………………….. spot spacing = 10.8 cm Q. What is the line spacing?

To see and understand these diffraction images, study the course X-ray website: and particularly the section:

End of Lecture 5 Sept 11, 2009 Copyright © J. M. McBride Some rights reserved. Except for cited third-party materials, and those used by visiting speakers, all content is licensed under a Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0).Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0) Use of this content constitutes your acceptance of the noted license and the terms and conditions of use. Materials from Wikimedia Commons are denoted by the symbol. Third party materials may be subject to additional intellectual property notices, information, or restrictions. The following attribution may be used when reusing material that is not identified as third-party content: J. M. McBride, Chem 125. License: Creative Commons BY-NC-SA 3.0