(Premium) Gist of Science Reporter Magazine: February 2013

Premium - Gist of Science Reporter: February 2013

Contents

A CENTURY OF X-RAY DIFFRACTION

The discovery of X-ray diffraction was a central event in modern science. While the technique of X-ray diffraction (XRD) began by identifying the symmetries in the crystals of minerals, it eventually evolved into a unique and powerful method of finding even the molecular structures in chemistry and biology. The observation of X-ray diffraction by Friedrich, Knipping and Laue is one of the most important discoveries in the history of science, and one with monumental consequences, It opened the path for the development of modern solid-state physics and materials science, including mineralogy, chemistry and molecular biology. In fact, all the science describing the material world around us has use for XRD and there is hardly any field in basic or applied research that has not employed XRD for achieving its ends. It continues to widen its net even today.

Though the mysterious radiation discovered by Roentgen was named ‘X-ray’ the debate was on for a few years whether they were waves or corpuscles (i.e. particles). A wave is expected to provide diffraction. Roentgen worked hard to get such an effect but could not.

DIFFRACTION

When a wave hits an object, they cannot reach the region immediately behind that object. Shadows are formed due to this. Since the waves of light are blocked, the region immediately behind the object is darker.

But shadows are sharper close to an object than they are further from it. This is due to diffraction. Waves that pass the object change their direction of travel slightly. The wave that just missed the object spreads in a circle or sphere. into the space behind the object. This is why shadows become more blurred further away from the object that casts them. Eventually the spherically spreading waves from each edge of the obstacle may even meet up.

BRAGG DIFFRACTION

To understand Braggs’ equation. let us look at an imaginary lattice array with atoms as shown in the figure here. Let a narrow beam of monoenergetic X-rays fall on this array of atoms. Monoenergetic signifies that the beam has only one wavelength e, unlike the experiments of Lane where the X-ray beam was a mixture of rays of various wavelengths. This can be obtained by appropriate filters. For Xrays, wavelength and energy are related; thus a single energy beam also means a single wavelength beam.

Diffraction is a two-step process: first a scattering and then interference of the scattered waves, either constructively or destructively. The single ray AO hits an atom and gets scattered in the direction OB; the ray A’O’ goes in OW direction. Notice the small cut marks on these waves which indicate location of a crest of the wave; the distance between two consecutive marks is wavelength a of the x-rays. The way marks placed on AO and A’O’ show that both the rays are in phase - their crests occur at the same time along the journey. Scattered waves OB and OW are also in phase. This is because the delay MO’ + O N is equal to one or more integer multiple of a wavelength. So the phase of the scattered ray is not disturbed and being at same phase OB and OW add the intensities on the way ahead. That gives a dark spot on the X-ray film or a peak in intensity of X- ays in a meter.

APPLICATIONS IN OTHER FIELDS

This new and ingenious method of crystallography found favour with scientists in other disciplines also. From the results of the work a realization was growing about the connection between the structure of materials and their properties as well as reactions. This was true for metallurgy and chemistry; somewhat later biology also joined the pursuit.

Cellulose structure was seen in 1920. The first organic structure determined was Hexamethylene Tetramine in 1923 (by Dickinson and Raymond). The nature of bonds in molecules could be understood from diffraction studies. The Benzene structure was understood in 1928 by Kathleen Lonsdale. C.G. Darwin (grandson of the famous Charles Darwin) gave a method to determine valency from the crystal structure. Later, a separate branch in chemistry called structural chemistry evolved. Metallurgy has derived maximum benefits from the application of XRD. Alloys could be better understood if the crystal structures were known. Graphical representations of alloy compositions at different temperatures are called phase diagrams; they are highly valuable tools to understand an alloy’s behavior. These could be generated with the help from the XRD. The modern XRD units facilitate dynamic study of structures by observing the changes in metallic phases in real time with changing temperatures. Even creating new alloys of desired properties is possible with the help of XRD and electron microscopes. If the material or a component is under stress - applied or left over after fabrication sequence - the lattice gets distorted. This results in a change in parameter ‘d’ and can be detected easily by XRD. This is a popular application of XRD in residual stress measurement in engineering.

APPLICATIONS IN BIOLOGY

Bioscientists were the last to get on board the XRD train. This is because XRD and crystallography were synonymous in those days. No biological substance, except bone, appeared to be crystalline, though later it came to be known that the X-ray techniques could be used for amorphous materials also, But biologists entered through a different route. They worked on crystallizing the proteins to study them. J.D. Bernal in England was the first to get X-ray photos of proteins in 1934, published in Nature (Vol. 133, p 794). Several biochemicals in our body are actually proteins: enzymes, hormones, haemoglobin or antibodies. They are large molecules and finding their structure was challenging. Sometimes it took five to seven years after obtaining the X-ray pictures to determine the exact structure in three dimensions.

After Bernal, his colleague Dorothy Crowfoot Hodgkin pursued this field of biomolecules throughout her life, deciphering Cholesterol, Penicillin and Vitamin B-12 etc. Her decoding of insulin came after she won the Nobel
Prize in 1964. Credit for solving haemoglobin goes to John Kendrew and Max Perutz, whose efforts were aided by improved instrumentation and evolved mathematics.

In this chain of workers came Rosalind Franklin at the King’s College London, as well as James Watson and Francis Crick at Cavendish Lab at Cambridge. The latter two gave the model of the hereditary material DNA (deoxyribonucleic acid). The molecular model was built up based on X-ray photos taken by Rosalind and Maurice Wilkins, though Watson and Crick did not acknowledge this fact till Rosalind was alive. It is an old and lively debate in the history of science. It is really a tribute to the long career of W.L. Bragg that he was the Head of Cavendish Lab when this most important molecule was reconstructed using the technique he invented 40 years earlier!!

The major impact of XRD work on human life has come through the achievements in biological science more than any other branch of science. The functioning of various proteins in the body depends on their shape; they connect to other chemicals at the open ends of the molecule to give effect to many a biological process. Thus, knowing their structure helps us to understand many processes and enables intervention. Take for instance drug design. Knowing the physiological basis of any ailment, one can construct a drug that has a molecular structure of one’s choice to go and nullify the malfunctioning molecule. Scientists at Squibb Institute of Medical Research were the first to collaborate with crystallographers for drug development, by targeting an enzyme for intentional latching. The first drug to come out this way was Captopril in 1975, used to alleviate hypertension. A branch of science called structural biology opened up to determine target structures responsible for morbidity, including enzymes, protein receptors, zones of DNA, RNA etc. These days, many drugs are designed in this way rather than invented by an accident or iterative trials. This became feasible because of better instrumentation for XRD technique, mathematical tools such as Fourier analysis and, above all, the progress in computer technology that permitted scientists to avail of the new theoretical concepts in a shorter time span. While Vitamin B-12 (C63 H 88N14 014P Co) with 181 atoms took eight years to resolve, today molecules comprising thousands of atoms can be resolved in a matter of months, thanks to help from computers.

NEWS BRIEFS

  • A team led by a physician-scientist and a chemist - from the fields of dermatology and nanotechnology - is the first to demonstrate the use of commercial moisturizers to deliver gene regulation technology that has great potential for life-saving therapies for skin cancers. Applied directly to the skin, the drug penetrates all of the skins layers and can selectively target diseasecausing genes while sparing normal genes. Once in cells, the drug simply flips the switch of the troublesome genes to “off.”

  • Latest research has found that people who consume fast food even once a week increase their risk of dying from coronary heart disease by 20% in comparison to people who avoid fast food. For people eating_ fast food two three times each week, the risk increases by 50% and the risk climbs to nearly 80% for people who consume last food items four or more times each week. A diet heavy in fast food increases the risk of developing Type2 diabetes and coronary heart disease.

  • Signals from natural intestinal bacteria are necessary for an effective immune response to various viral or bacterial germs. Trillions of bacteria residing in the intestines of healthy humans contribute to digestion and metabolism of vitamins and are of critical importance for the host organism. Research has shown that the intestinal flora also plays an important role in the formation of the immune system in the intestines and that changes to it can increase the risk of food allergies or chronic inflammatory intestinal diseases.

  • The first images of an upward surge of the Sun’s gases into quiescent coronal- P loops have been identified by scientists. The discovery is one more step towards understanding the origins of extreme space storms. which can destroy satellite communications and damage power grids on Earth. The observation will help to understand how solar structures are heated and maintained in the upper solar atmosphere. Extreme solar activity can lead to severe space storms that interfere with satellite communications and damage electric power transmission grids on Earth.

  • Scientists foresee a time when medical monitoring devices would he integrated seamlessly into the huma body to track a patient’s vita signs and transmit them t/ his doctors. With current technology, electronics are able to stretch a small amount, but many potential applications require a device to stretch like a rubber band. Researchers at the McCormick School of Engineering have recently developed a design that allows electronics to bend and stretch to more than 200% their original size, four times greater than is possible with today’s technology. The key is a combination of a porous polymer and liquid metal.

  • Most people are fascinated by the colourful and exotic coral reefs but human civilization is the top danger to these fragile ecosystems through climate change, oxygen depletion and ocean acidification. Now scientists have investigated how and why the corals die when exposed to sedimentation. According to their findings, oxygen depletion, together with an acidification of the environment, creates a chain reaction that leads to coral death.


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