Dynamics of Atoms and Molecules at Work in the Background of Chemical Phenomena

Figure 1  A researcher who initiates an "action" gets a "reaction". What is the chemical "reality"?

If you are a high-school student and you hear the word ¨chemistry,¨ you may think of observing reactions in experiments. Certainly, when conducting an experiment, we initiate an "action," get a "reaction" and then examine the "reality," which is a mechanism of the chemical phenomenon. Alternatively, we use the "reality" to get the desired substance. Well, what is that "reality?" Do you want to take a peek at the mechanism in the black box? There must be a reason and a scientific theory that can offer an acceptable explanation.

"I want to see what cannot be seen and measure what cannot be measured." This type of curiosity motivates us in our research.

The "reality" of chemistry exists in a space at the atomic and molecular level (10^-8 to 10^-10 m). A chemical reaction is nothing more or less than a change in the atomic bonding combination, and this dynamic phenomenon is caused by the force applied to the atom or molecule. In fact, the force derives from electrons around the atom or molecule. Change in the electron distribution applies force to the atom and causes the chemical phenomenon.

 

How do You Use Computers to Research Chemistry?

Understanding the electron distribution leads to finding out the force acting on the atom, which paves the way to understanding the chemical phenomenon. Here, quantum chemistry is used. By solving the electron equation using the Schrödinger equation, the electron distribution and energy can be obtained. This process includes, as shown in Figure 2, creating a program for solving the electron equation, executing the program and analyzing the result.

Figure 2  Creating a computer program (left), executing the calculation using computers (middle) and analyzing the result (right)

Figure 3  Electron distribution in retinal molecule

For example, we found that the retinal molecule that controls the perceiving function in the retina has a distribution of electrons that responds to light, as shown in Figure 3. When this molecule receives light, the electron is transformed from HOMO to LUMO. Specifically, this refers to a change where the electron moves from the left side to the right side.

 

What Kind of Research are You Conducting

Chemical phenomena occur in complex systems where the molecule plays the leading role and mutually interacts with the environment, which plays the supporting role. It is not uncommon for the environment to adjust and take the leading role through this interaction. Figure 4 shows a human’s perception of color, where the fluorescent protein of coral and of a firefly are used as an example. The electron must change its shape in order to absorb or emit light, and the energy magnitude required for that shape change corresponds to the difference between colors. As a result of our analysis, we found that the energy magnitude depends on the electrical environment that the protein creates. In addition, we found that the variation in protein changes the electrical environment and that the light absorption or light emission color has systematic effects. As a result, we were able to identify the protein region that controlled a human’s perception of color.

Figure 4  Color tuning of light absorption and light emission has a common physical mechanism (left). In the fluorescent protein derived from coral (middle) and the retinal being a visual substance (right), the energy required to change the electron depends on electrical environment that the protein creates.

Currently, we are conducting more complex research in catalytic chemistry. A catalyst has a function that facilitates a chemical reaction very efficiently. But a substance in such a highly active state is pluralistically complex. Figure 5 shows an example of a catalyst that fixes carbon dioxide. This catalyst has a long alkyl chain that seems to be unnecessary. As a result of our analysis, however, we found that this long alkyl chain helps play a role in the reaction process, by facilitating flexible structural change and stabilizing a charge transfer during the reaction. Also, developing a theoretical calculation method that can handle such complex catalysts is an important research topic, and this field of research requires more involvement from young energetic researchers.

Figure 5  CO₂ fixation catalyst (left). Cellobiose and adsorption structure on carbon surface (middle). A Pt catalyst that hydrogenates carbonyl (right)

 

References

(1) Jun-ya Hasegawa, Quantum Chemistry of Color Tuning in Optically Functional Protein (hikarikinousei tanpakushitsu ni okeru kara^ chu^ningu no ryoshi rikigaku), Molecular Science, 4, A0031 (2010).