Crystallography: The Universe as seen through a crystal

22/06/2020

How important are crystals in the Universe, the planets, the Earth, life, and everything around us, including the arts and humanities? Crystallography is the main technique by which we can analyze the atomic structure of almost everything, while it is very useful to find out why things behave the way they do.

Crystallography: The Universe as seen through a lens
Crystallography: The Universe as seen through a lens

Why does water boil at 100° C? Why is blood red and the grass green? Why is diamond hard and wax soft? Why do ice creams melt and nothing happens to steel if you hammer it?

The answers to all these questions are in structural analysis, which is why Max Perutz won the Nobel Prize for Chemistry in 1962, using X-ray diffraction to analyze protein crystals and later describing the molecular structure of hemoglobin (blood) using the same X-ray diffraction crystallography method.

Twenty-eight Nobel Prize winners have been associated with this discovery. Determining that the molecule of life, DNA, has a helical (helix) structure is perhaps one of the most revolutionary discoveries in science related to X-ray crystallography.

Giant Naica crystals

Naica is a mining town located in the north of Mexico, 112 km southeast of the capital of the state of Chihuahua. The name Naica, in the indigenous language of the Tarahumara, means "shaded place" because it refers to the shadow created by the mountain range over the desert. The mountain of Naica contains one of the largest deposits of lead, zinc, and silver in the world. Its entrails, rich in metallic sulfides, have been exploited since 1828.

The Mine

Approximately 26 million years ago, a mass of molten material emerged from the interior of the Earth to about two and a half kilometers from the surface, pushing the sedimentary rocks and thus creating the Naica mountain range, while covering it with very hot fluids rich in minerals.

Naica Cave Crystals. Photo: Wikipedia
Naica Cave Crystals. Photo: Wikipedia

The Cave of Giant Crystals was discovered at a depth of 290 meters, when a group of workers had the sensitivity to stop the excavation of a tunnel when they found a large hole with giant gypsum crystals. The company Peñoles, a world leader in silver production that is in charge of the operations of this mine, is proud of having made this discovery and of guarding it.

The Cave of Giant Crystals

The Cueva de los Cristales Gigantes is a limestone cavity ten meters wide by thirty meters long, approximately, in the shape of a U. Gypsum crystals are a late product of mineralization. The cave has a usual temperature between 45º and 50° C with a humidity of more than 90%.

The surface of the cavity is covered by huge crystalline blocks and giant prisms, which the miners call "beams". These are almost one meter wide and reach lengths of more than ten meters. Other crystals protrude from the walls and ceiling. The large plaster crystals are called selenites, after the moonlight.

The Formation

The caves were formed next to large faults and fractures where water circulated to dissolve the limestone rocks. At this depth, the caves were always full of salty water. After the formation of the metallic sulfides, the magma cooled down, the water mixed with the water filtered from the surface and the temperature of the rock reached 58° C.

Naica: location of the caves in the mine. Image: Wikipedia
Naica: location of the caves in the mine. Image: Wikipedia

It is precisely at this temperature that the transformation takes place: the anhydrite (dehydrated calcium sulfate) begins to dissolve and add sulfur and calcium molecules to the water that for millions of years had been placed in the caves in the form of selenite crystals (hydrated calcium sulfate), the largest and most beautiful in the world known to this day.

Crystals in everyday life

There is always something in the crystals that ends up seducing us, even fascinating us. It is probably the beauty of their symmetrical shapes, like those seen in a gem, or the mysteries of their growth, which sometimes occurs under great pressure inside the planet or in controlled conditions inside a laboratory.

Gallium, a metal that easily forms large crystals. Photo: Wikipedia
Gallium, a metal that easily forms large crystals. Photo: Wikipedia

The crystals are sometimes very large, so much so that there are even crystals of extraordinary dimensions that reach up to eleven meters. However, it is not always easy to recognize them, not all of them are of enormous magnitude.

There are also some crystals as small or smaller than a particle of dust and only by observing them through a microscope can their regular formations and faces or facets with specific angles be seen. An example of these crystals is the painkiller Aspirin, which at first sight looks like just dust compacted into a tablet, but under the microscope lens, you can see the tiny facets of the crystals that form it.

Crystals in living organisms

Some structures in the human body also have a crystalline structure, for example, bones and teeth. Hydroxyapatite crystals are found in the mineralized tissue of the teeth. This is very special because its formation is biologically induced by the living cells in the teeth.

Some human body parts also have a unique crystalline structure. Image: Needpix
Some human body parts also have a unique crystalline structure. Image: Needpix

In the bones, the crystalline structure of hydroxyapatite (calcium hydroxide) is integrated with an organic protein matrix to give it compressive strength and rigidity. In bone formation and repair, for example, when someone suffers a fracture, living cells - such as osteoblasts - and osteoclast cells regulate the formation of hydroxyapatite crystals that will re-solder the bone.

Crystals in the medicine cabinet and on the table

In a document released by UNESCO and the International Union of Crystallography, it is stressed that crystals are found everywhere in nature and also on our table. Some fundamental ingredients that we use in our food such as salt and sugar are also crystals. Salt is a crystal in which chlorine and sodium atoms form a cubic network. Sugar also has crystalline forms and it is known that in ancient times the Chinese and Hindus made sugar crystals from sugar cane juice.

Salt crystals. Image by kostkarubika005 from Pixabay
Salt crystals. Image by kostkarubika005 from Pixabay

Another crystal that forms part of our diet is chocolate. Cocoa butter crystallizes into six different forms, but only one of the six forms causes it to melt pleasantly in the mouth when eaten. This delicious crystalline form is not the most stable, so storing it for a long time recrystallizes it into another form that is not as appetizing.

Porous chocolate bar. Photo: Wallpaperflare.com
Porous chocolate bar. Photo: Wallpaperflare.com

Crystallography in our daily life

Crystallography studies have advanced rapidly over the years. At the beginning of the last century, the German scientist Max Von Laue proposed that when an X-ray beam is aimed at a crystal, a diffraction pattern is projected (light deflection when it encounters an obstacle). By analyzing the diffraction pattern with mathematical formulas, it is possible to infer the location of the atoms in the sample and, therefore, to determine the three-dimensional structure of the crystal. For example, using crystallography techniques it was possible to prove in 1913 that the carbon atoms in diamonds have an arrangement forming tetrahedrons that make the diamond a very hard material with which all kinds of solid material can be scratched.

Crystallography techniques allowed to reveal how the structure of a material is, have been of great importance to try to crystallize materials whose nature is not crystalline and thus know their structure. Some examples are the giant molecules, which are part of the cells or are related to them as lysosomes, ribosomes, or even viruses. Knowing the structure of these complicated biological molecules has a direct impact on drug design and health sciences in general.

A famous example of a molecule that was known using X-ray diffraction crystallography techniques is Deoxyribonucleic Acid (DNA). It is not found in crystalline form in the human body, but when it is crystallized in the laboratory by X-ray diffraction it can be seen that the molecules that make it up to fit together like a double helix like a spiral staircase. All this is possible thanks to X-ray crystallography techniques.

X-ray diffraction crystallography. Photo: Wikipedia
X-ray diffraction crystallography. Photo: Wikipedia

There is not a single day in life when we do not interact with crystals or the science that studies them. Everything around us from our bodies to the natural world and even high-tech products are made of crystalline matter. Humanity's understanding of the material nature of our world is based, in particular, on our knowledge of crystallography.

Crystals and technology

Present throughout nature, crystals have amazed men and women of all ages, not only because of their mesmerizing beauty but also because of their infinite possibilities in the various facets of everyday life: used for sumptuary decorations, as a work tool and even to salt or sweeten food. This fascination for crystals continues to this day: in the twenty-first century, crystals are also an essential part of scientific and technological development at the frontier.

Liquid crystals

In fact, crystals are present in the food industry as well as in the cosmetics industry, aeronautics, space technology, the design of new drugs, liquid crystal display technology, biosciences, agriculture, as well as in the development of new energies, new materials, and processes to improve water quality.

Texture in a polarizing microscope of a B7 bent-core phase of a liquid crystal. Image: Wikipedia
Texture in a polarizing microscope of a B7 bent-core phase of a liquid crystal. Image: Wikipedia

A crystal, according to the International Union of Crystallography, is a solid material whose atoms are organized in regular, symmetrical arrangements in three dimensions. However, not all crystals are solid. In 1888, the Austrian biologist Friedrich Raintizer discovered liquid crystals.

Liquid crystals can be found in nature, for example, in the cell wall or in the web. The beautiful colors of some beetles are due to the fact that their shells are made of cholesteric liquid crystals. There are also everyday products, such as soaps, which are also crystals. The material used in bulletproof vests called "kevlar" is made of polymer liquid crystal. Liquid crystals play a key role in everyday life. Can you imagine a world without computer screens or soap?

Liquid crystals are materials that combine the properties of liquids and solids. In an ordinary crystal like a diamond, the atoms are in fixed and regular positions in any direction. In this case, we say that the atoms have positional order and orientation. On the contrary, liquid crystals can flow and take the shape of the container that contains them. We know that in liquids the molecules have no order of position or orientation.

So why are they called liquid crystals? They are so-called because they are made up of organic molecules whose shape is elongated, similar to that of chopsticks. Just as in the game, the molecules can be arranged in bundles before they are released. In this case, we say that there is an order of orientation but not of position and in this case, liquid crystals are obtained.

When we drop the sticks on the table they become disordered and occupy random positions, then we say that we have an isotropic liquid. It is possible to make a transition from liquid crystal to isotropic liquid by thermal means and vice versa. These types of liquid crystals are known as thermotropic and are the most used in the industry.

Liquid crystals have several applications

Liquid crystals are present on TV screens and all types of displays. These crystals must have special properties to work properly. For this reason, they are synthesized in various laboratories around the world. Their synthesis is not cheap and few laboratories can produce the quantities required by the industry.

Liquid crystal display. Photo: Pexels
Liquid crystal display. Photo: Pexels

There are many laboratories around the world and in Mexico that can synthesize them, but in small quantities and not for commercial purposes. The cost of one gram of the simplest liquid crystal is approximately 100 dollars. Liquid crystals used in industry are not sold in small quantities because their price is high and companies are not interested in retailing them.

The advantages of liquid crystal displays over cathode ray and plasma displays are lower weight and volume, low power consumption, high image resolution, and a wide range of colors, allowing for impressive and even three-dimensional images. However, its future is not very promising due to the emergence of new technologies such as light-emitting diodes, or organic LEDs, which have produced new screens, displays, with higher resolution, lower weight, and lower power consumption.

Merck, the German pharmaceutical giant, controls approximately 70 percent of the world market for liquid crystals.

But liquid crystals have other applications: in temperature sensors, image processing, holography, and light polarization controllers. Potentially, they could be used as optical image processors; electronic optical devices, such as light couplers; light guides, etc.

Although liquid crystals are known and have been studied for over a hundred years, there is still a long way to go to understand their physics and chemistry. And they've shown great potential in scientific research.

Recently, cholesteric liquid crystals have been used to reduce the speed of light in that medium. This would lead to slow-light applications that could revolutionize telecommunications. New forms of the molecular arrangement have also been discovered in liquid crystals that function as photonic crystals whose applications have not even been analyzed. So liquid crystals still have a bright future ahead of them, although not in the display industry.

Diamonds in the Universe

Ten thousand billion nano-diamonds per gram of dust and gas from outer space. A billion-dollar dream come true.

Carbon is the most abundant element in the Universe, whose task is to form dust in the space between the stars, the so-called interstellar medium. It is also the chemical element that, in the presence of high temperatures and great pressure, converts its atomic structure into a crystalline network known as a diamond.

On Earth, diamonds arise deep in the crust, more than 150 km below the surface. Volcanic eruptions push the material to more superficial levels, where it can be extracted by humans.

Asteroids and cosmic dust

The existence of diamonds in outer space was postulated by Saslaw and Gaustad in a scientific article published in 1969. In 1987 Lewis and collaborators found a large number of nano or micro diamonds in studies they conducted, in other words, they found gems a few nanometers or micrometers in diameter on asteroids that had impacted the Earth (meteorites). They were up to 25,000 times smaller than a grain of sand. These studies revealed that up to 3 percent of the carbon present in the meteorites had the structure of diamond. Scientists estimated that diamonds could exist in interstellar dust in that same proportion, calculating their existence at about ten thousand billion (a ten followed by thirteen zeros) nano-diamonds for every gram of cosmic dust.

Asteroid Belt. Image: NASA Jet Propulsion Laboratory
Asteroid Belt. Image: NASA Jet Propulsion Laboratory

In complete contrast to terrestrial diamonds, space nano-diamonds are formed in gigantic molecular clouds (composed of gas and dust), where the pressure is millions of times lower than on Earth and temperatures are close to -240 ºC. The process of formation under such conditions is still the subject of debate among scientists, but it is known that their shape is cubic.

In a study by Bauschlicher and colleagues, they recommend observing the infrared wavelength of the surrounding material in the vicinity of other stars to detect nano-diamonds, because the ultraviolet light from the stars that strikes the diamonds is re-emitted in the infrared.

Stars

Diamonds have been found not only in the vicinity of the stars but also inside them. Stars eight times or less the mass of the Sun culminate their existence as white dwarf stars, they have their matter in a highly condensed state, where the main chemical components are carbon and oxygen.

Artist's conception of a multitude of tiny diamonds next to a hot star. Image: Wikipedia
Artist's conception of a multitude of tiny diamonds next to a hot star. Image: Wikipedia

In 2004 it was discovered that the white dwarf BPM 37093 is crystallized, that is, its molecular structure is crystal. Because the star is composed mainly of carbon, and thanks to the pressures and temperatures present in the star, a diamond core of 4 thousand kilometers in diameter has been created, surrounded by a tenuous atmosphere of hydrogen and helium.

The discovery was possible thanks to the study of the star's vibrations; the way in which the body vibrates made it possible to determine that its composition is 90% crystalline. BPM 37093 is located 53 light years away from the Earth, in the direction of the constellation Centaurus.

Extrasolar planets

55 Cancri e, the fifth planet around the star 55 Cancri, is about twice the diameter of the Earth and turns around its star every 18 hours. The pressure the planet generates on itself and the temperature of the star, together with its chemical composition, have led to the determination that at least one third of the planetary mass is pure diamond.

Artist’s impression of 55 Cancri e. Image: Wikipedia
Artist’s impression of 55 Cancri e. Image: Wikipedia

In the system PSR J1719-1438 there is a pulsar and a white dwarf. The pulsar is an extraordinarily compact object that emits radiation periodically, as if it were a lighthouse; it formed after the explosion of its parent star in a supernova. A red giant star, also in the last stage of its life, revolved around the pulsar. The giant evolved into a white dwarf, of very low density for its genus, which now orbits around the pulsar and is known as PSR J1719- 1438 b. Because of the characteristics of PSR J1719-1438 b, and because the pulsar's winds have left its core bare, it is believed that we are looking at an extrasolar planet composed of pure diamond. The system is located at a distance of 3,900 light years from the Earth, in the direction of the constellation Serpens.

The Solar System

In our neighborhood, observations of the storms on the planets Jupiter and Saturn, along with new laboratory experiments and computer models, show how the carbon in Saturn's atmosphere behaves under its extreme conditions. Data from space probes studying the interiors of the planets have made it possible to estimate the existence of large regions where diamonds can be produced.

The Solar System. Image: Needpix
The Solar System. Image: Needpix

The methane gas that exists in the atmosphere of the giant gaseous planets (Saturn, Jupiter, Uranus, and Neptune) can be converted into "drops" of diamond that rain towards their interiors. The lightning that is observed in the atmospheric storms of Jupiter and Saturn could break up the methane and convert it into carbon molecules, which fall from the upper atmosphere to deeper regions, where the higher pressure converts it into graphite. As it continues to fall, the temperature and pressure turn the graphite into diamond. It's estimated that on Saturn every year thousand tons of carbon are converted into diamonds.

On planets where the temperatures near the core are not so high, but the pressure is immense, it is believed that the conditions allow the gems to inhabit in a liquid state, creating oceans of a diamond. This is particularly true of Uranus and Neptune, where temperatures do not appear to be higher than 7,700°C in their cores.

Nicolas Copernicus (1473 - 1543)

"In the middle of it all is the sun. For who in this beautiful temple would put this lamp in a better place, from which everything could be illuminated?"

He was the first and perhaps the most important scientist in the Renaissance scene. He was also a clergyman, doctor, jurist, economist, and astronomer. He studied in Krakow and also in Bologna. In 1500, Copernicus received his doctorate in astronomy in Rome. The following year he obtained permission to study medicine at Padua (the university where Galileo taught almost a century later).

He was always interested in the problems presented by the geocentric planetary model, which had its antecedents in Ptolemy's Almagest. Later, around 1514, he had already outlined an alternative paradigm, a solar system with a fixed sun in the center, and where the Earth and the other planets were rotating around it, in addition, the Moon was orbiting our planet.

Just before his death in 1543, he published his theory in De revolutionibus orbium caelestium ("On the revolutions of the celestial orbs"). At first, his heliocentric thesis did not generate much interest or controversy, but half a century later, with the favorable observations of Brahe, Kepler, and Galileo (and his telescope), they reached important deductions that generated the so-called Copernican revolution in cosmology.

The relevance of the Copernican celebration

Nicolas Copernicus is considered the founder of modern astronomy because he revived and strengthened the heliocentric conception of the universe, proclaimed by the classics of antiquity. The booklet "Commentariolus" is registered in the private library of Mattias de Miechow in Krakow, with the date May 1, 1514.

It is in this work that Copernicus first postulates his basic astronomical considerations about a heliocentric system of the universe. With which it is opposed to the proposed one by Ptolomeo where the Earth is the center of the universe. But it maintains the consideration of the Greek thought about the uniform circular movement of the planets.

Copernicus' amazing astronomical considerations of a heliocentric system of the universe. Image: Wikimedia
Copernicus' amazing astronomical considerations of a heliocentric system of the universe. Image: Wikimedia

Therefore, due to the importance of Copernicus' contribution to the knowledge of the Solar System, in particular from his writing "Commentariolus" which by convention is associated to the date of registration in 1514, in this 2014 are fulfilled as indicated, 500 years from this date.

"To know that we know what we know and to know that we do not know what we do not know, that is true knowledge".

In Commentariolus he postulates seven axioms of his heliocentric system, namely

1. There is no single center for all the celestial spheres.

2. The center of the Earth is not the center of the Universe, but only the center of the lunar sphere.

3. All the spheres revolve around the Sun, which is in the middle of all of them, which is why the Sun is the center of the Universe.

4. The ratio between the distance of the Sun to the Earth and the distance at which the sphere of the fixed stars is situated is much smaller than the ratio between the radius of the Earth and the distance of the Earth from the Sun, so that the latter distance is imperceptible compared to the height of the firmament.

5. Any motion that seems to occur in the sphere of the fixed stars is not really due to any movement of the latter, but rather to the motion of the Earth. Thus, the earth, together with the surrounding elements, carries out a complete revolution around its axis every day, while the sphere of the stars and last sky remains motionless.

6. The movements with which the Sun is apparently endowed are not really due to it, but to the movement of the Earth and of our own sphere, with which we revolve around the Sun in exactly the same way as the other planets. The Earth, therefore, has more than one movement.

7. The apparently retrograde and direct movements of the planets are not really due to their own movement, but to the movement of the Earth. Therefore, this alone is sufficient to explain many of the apparent irregularities in the sky.