X-Ray Diffraction and Electron Density Maps

Have you ever wandered how chemists determine the shape of molecules and ionic compounds?
How can they measure bond angles and bond lengths?
One of the most important ways to do this is to use X-ray diffraction.
AUS-e-TUTE has just added a new tutorial, game, test and exam to help you understand X-ray diffraction and electron density maps and to apply that understanding to solving problems in chemistry. AUS-e-TUTE Members should log-in to use these resources (under the Solid State Chemistry topic heading).
If you are not yet an AUS-e-TUTE Member then you can access the "free to view" tutorial at
https://www.ausetute.com.au/xdiffraction.html

Rosalind Franklin and the Structure of DNA

Three men, James Dewey Watson,  Francis Harry Compton Crick and Maurice Hugh Frederick Wilkins, shared the The Nobel Prize in Physiology or Medicine 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.", that is, they  modeled DNA as a double helix, each strand of the helix has a backbone of  sugar molecules held together by phosphate groups. The two strands are twisted together and held together by hydrogen bonds. But how did they learn what DNA was made up of?

 This is where Rosalind Elsie Franklin enters the story of DNA. In 1951 she was a Research Associate at Kings College London where she worked on  X-ray diffraction studies with her colleague Maurice Wilkins. Her x-ray diffraction images of DNA led to the discovery of the DNA helix. The image on the left is known as "photograph 51" and was an x-ray diffraction image of DNA obtained by Franklin's Ph.D student Raymond Gosling.

X-ray diffraction is an instrumental technique used to elucidate the structure of crystals of chemical compounds. Incoming x-rays are diffracted by the crystal lattice and they exit the crystal at different angles. An x-ray crystallographer like Franklin can measure the angles and intensities of these diffracted x-rays to produce a 3-dimensional picture of the density of electrons in the crystal lattice. The electron density can then be used to determine the locations of atoms within the crystal lattice.

Without Franklin's knowledge, Maurice Wilkins showed this image to James Watson who used it, along with other evidence, to develop a model of DNA. Science historians still debate whether Franklin would have determined the structure of DNA on her own had her images not been shared with Watson.

Rosalind Franklin made important scientific contributions, not only to the discovery of the structure of DNA and RNA, but also in helping us to understand the structure of viruses, coal and graphite.
Unfortunately, Rosalind Franklin died of ovarian cancer in 1958. Nobel Prizes are not generally awarded posthumously so her contribution to the elucidation of the structure of DNA is not well-known.


Further Reading:
Chemistry of DNA
Intramolecular Forces
Intermolecular Forces

Suggested Study Questions:

1. Explain the terms crystalline and amorphous.
2. Give an example of a crystalline substance and an example of an amorphous substance.
3. Explain why DNA had to be crystallised before useful information could be obtained using x-ray diffraction.
4. What does the abbreviation DNA stand for?
5. What are the 4 principle bases that make up DNA?
6. These principle bases occur in pairs; what are these 2 pairs?
7. What kind of chemical bonds act between the atoms making up each base in a strand of DNA?
8. What kind of chemical forces join one of the bases on one strand of DNA to its corresponding pair on the other strand of DNA?
9. If you wanted to separate the 2 strands of a DNA double helix, what sort of chemical bonds would you need to break?
10. If you wanted to separated each base from the backbone of sugar molecules, what sort of chemical bonds would you need to break?

Stripping Neon

The Linac Coherent Light Source (LCLS) delivers an intense pulse of X-rays designed to image atoms and molecules.
When the LCLS X-rays are tightly focused by mirrors, each pulse destroys any sample it hits.

LCLS pulses have been used to strip electrons away from atoms of neon one at a time.
Using a shorter pulse, fewer electrons are stripped away and less damage is done.
By varying the photon energies of the pulses, the electrons can be removed from the outside in, or, from the inside out creating so-called " hollow atoms".

The 2 electrons in the innermost electron shell closest to the nucleus are the hardest to strip away, but they also most readily absorb photons of X-ray light and so are the most vulnerable to being stripped away by intense X-rays. At low photon energies, the outer electrons are removed, leaving the inner electrons untouched. At higher photon energies the inner electrons are the first to be ejected, then the outer electrons cascade into the empty inner core, only to be kicked out by later parts of the same X-ray pulse.

Reference:
L. Young, E. P. Kanter, B. Krässig, Y. Li, A. M. March, S. T. Pratt, R. Santra, S. H. Southworth, N. Rohringer, L. F. DiMauro, G. Doumy, C. A. Roedig, N. Berrah, L. Fang, M. Hoener, P. H. Bucksbaum, J. P. Cryan, S. Ghimire, J. M. Glownia, D. A. Reis, J. D. Bozek, C. Bostedt, M. Messerschmidt. Femtosecond electronic response of atoms to ultra-intense X-rays. Nature, 2010; 466 (7302): 56 DOI: 10.1038/nature09177

Study Questions

1. What is the name given to the removal of electrons from a gaseous atom?
2. What is the charge resulting from the removal of an electron from a neon atom?
3. Write the electron configuration for the neon atom and for the species produced after an electron has been removed.
   
4. Write an equation to show the removal of an electron from a gaseous neon atom.
5. In a similar set of experiments, nitrogen was used instead of neon. Write the electron configuration of a nitrogen atom and of the species produced after an electron has been removed.
6. Do you think it would be easier to remove an electron from an atom of neon or from an atom of nitrogen? Explain your answer.
7. Why do you think the researchers chose to use neon and nitrogen gases for these experiments?
   

Chemistry of Archaeopteryx

A fossil specimen of the half-dinosaur/half-bird, archaeopteryx, has been placed under the X-ray beam at the Stanford Synchrotron Radiation Lightsource(SSRL). By recording how the X-rays interacted with the fossil, the scientists have been able to identify the precise locations of chemical elements hidden within. The concentration of elements in the fossil differs significantly from those in the surrounding rock, ruling out the possibility that the elements have leached from the surrounding rock into the fossil.

The results show that portions of the feathers are not just impressions of long-decomposed organic material as previously believed, but are actually fossilized feathers containing phosphorous and sulfur, the elements found in modern bird feathers. Trace amounts of copper and zinc have been found in the fossil's bones, just as in the bones of modern birds.

Reference:
U. Bergmann, R. W. Morton, P. L. Manning, W. I. Sellers, S. Farrar, K. G. Huntley, R. A. Wogelius, P. Larson. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging. Proceedings of National Academy of Sciences, 2010; DOI: 10.1073/pnas.1001569107