Friday , June 25 2021

Use a huge kilometer-long synchrotron to take atomic-size photographs of small crystals.



At 4 am, I finished work for about 20 hours straight away. A loud beep sounds and the red strobe light blinks. The stern voice displays "Station search B. Immediate end". It feels like an emergency, but it is not. In fact, the alarm has already passed 60 to 70 hours today. I am warning everyone nearby that they are trying to explode a high-performance X-ray beam into a small room full of electronic equipment and columns that vaporize liquid nitrogen.

In the middle of this room, called Room B, I placed a crystal that is not thicker than human hair on the tip of a small fiberglass. I have prepared dozens of crystals and am trying to analyze all of them.

The authors and colleagues prepared a crystalline sample to take to the synchrotron to determine the atomic level structure.
Courtesy of Kerry Lippi, CC BY-ND

The crystals are made from organic semiconductor materials used to make computer chips, LED lights, smartphone screens and solar panels. I want to know where each atom in the crystal is located, how tightly packed it is and how it interacts with each other. This information will help you predict how well the electricity will flow.

I need the help of a synchrotron to see these atoms and determine their structure. This requires the help of a synchrotron. It is a giant scientific tool in which a kilometer-long ring of electrons is magnified near the speed of light. Microscopes, gyroscopes, liquid nitrogen, lucky people, talented colleagues and tricycles are needed.

Hold the crystal in place

The first step of this experiment is to place microcrystalline crystals on the glass fiber ends. I use a needle to scratch the pile on a glass slide and put it under a microscope. The crystal is beautiful – faceted like a gorgeous little gem. I often look at a microscopic eye that has lost my limbs and refocus my gaze before carefully wrapping around the end of the fiberglass.

Once the crystals are attached to the optical fiber, the crystal is centered on the end of the gyroscope inside Station B. It is often frustrating to start working with the crystal slowly and continuously rotating the X-ray image from all sides of it.

On the left, there is a gyroscope designed to rotate a series of crystals at different angles of the gyroscope (X-ray beam). Behind this is a detector panel that records diffraction spots. The right side is an enlarged view of the single crystal attached to the glass fiber attached to the tip of the gyroscope.
Kerry Ripie, CC BY-ND

When it rotates, liquid nitrogen vapor is used to cool it: even at room temperature, atoms oscillate back and forth, making it difficult to get a clear image of them. When the crystal is cooled to minus 196 degrees Celsius (liquid nitrogen temperature), the atoms will not move too much.

X-ray picture

Once the crystal is centered and cooled, the B station is closed and the sample is x-rayed from the computer control hub outside. The resulting image, called a diffraction pattern, appears as a bright spot on an orange background.

This is the diffraction pattern that occurs when taking a single-crystal X-ray beam.
Kerry Ripie, CC BY-ND

What I am doing is not much different from taking pictures with camera and flash. I send a beam of light to the object and record how the light is reflected. However, you can not shoot atoms using visible light. The wavelength of visible light is too large because it is too small. X-rays have shorter wavelengths and therefore diffract or reflect atoms.

Unlike cameras, however, diffracted X-rays can not be focused with simple lenses. Instead of an image like a photo, the data I collect is an out-of-focus pattern where X-rays protruding from the atoms of the crystal go. A complete set of data for one crystal consists of these images taken from all angles around the crystal as the gyroscope rotates.

Advanced mathematics

Colleague Nicholas DeWeerd analyzes the data set he has already collected and is nearby. He ignores sparkling alarms and flashing lights for hours, sees the diffraction image on the screen, and virtually turns the x-ray image into crystal-inside atomic photos on all sides of the crystal.

In the past, this process was a careful calculation of years of manual computation, but now computer modeling is used to group all the pieces together. He is an informal expert of our research group in this part of the puzzle, and he likes it. "It's like Christmas!" I heard him mumbling while twirling the sparkling image of the diffraction pattern.

Solving the diffraction pattern set produces an atomic-level crystal figure showing how to combine with individual molecules (left) to form a crystal structure.
Kerry Rippy, CC BY-ND

I smile at the passion I have kept so late at night. I launch a synchrotron to get a crystal picture of Station B. I will breathe out the diffraction pattern on the screen at the first few angles. . Even if everything is set perfectly, not all crystals are diffracted. Because each decision is made up of much smaller crystals sticking together. Or because crystals containing too much impurities form repetitive crystal patterns that we can solve mathematically.

If this photo does not deliver a clear image, you'll need to start over. Fortunately, the first few images that pop up in this case represent bright, clear diffraction spots. I smile and sit down and gather the rest of the data set. As the gyroscope rotates and the X-ray beam emits the sample, you can take a few minutes to relax.

I drink coffee for warnings, but I am already shaking off caffeine overload. Instead, I call Nick: "I will kneel." I walk to a group of tricycles sitting nearby. I have found that it is equally helpful to desperate attempts to wake up with exercise because it is commonly used to travel around large buildings that typically contain synchrotron.

As I ride, I think about the crystal mounted on the gyroscope. I spent several months synthesizing it, and soon I will have a picture of it. From the picture, you will gain an understanding of whether the modifications made with slightly different modifications to other materials I made in the past have improved it at all. Evidence of better packaging or increased intermolecular interactions may mean that this molecule is a good candidate for testing in electronic devices.

It is exhausted, but I am happy because I am collecting useful data. I stepped on the pedals slowly around the loop and found that the synchrotron was in high demand. I work all night because the beam line runs 24/7. I was lucky I did not get the timetable. On other stations, other researchers like me are working late at night.

Ride a tricycle to get on from a high-grade photon source.

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