Seeing the essence of chemical reactions
25 April 2008 (Volume 3 Issue 4)
“When I was in high school, I was really interested in the first few pages of a textbook on chemistry, in which some molecular structures and chemical formulae were described,” says Toshinori Suzuki, Chief Scientist in the Chemical Dynamics Laboratory at the RIKEN Discovery Research Institute. “Why can we understand chemical structures when nobody has ever directly seen them? Why do chemical reactions occur as indicated in the formulae? I wanted to find answers to these questions.” Suzuki uses unique methods for visualizing chemical reactions to derive universal rules that commonly govern various chemical reactions, thus contributing to creating new chemical substances or gaining a better understanding of life phenomena.
“I got into the study of chemistry because I was inspired by Professor Yoshito Amako when I took his quantum chemistry course. Then, I was a first-year student at Tohoku University,” says Suzuki, looking back on his college years. Quantum chemistry is a field of research that aims to elucidate molecular structures and chemical reactions using quantum mechanics, which is a tool for explaining the microscopic world. “We usually learn quantum chemistry at the junior level,” explains Suzuki. “Professor Amako, however, tried to teach quantum chemistry to students who had only just graduated from high school. We had great difficulty in understanding his lectures. It seemed that Professor Amako was trying to see how many students could keep up with his lectures.” Suzuki recalls how after class, he would make a copy of his lecture notes in his apartment, and try to add to the notes with what he had found out for himself. “In this way, I managed to decipher the lectures one step at a time. As a result, I noticed, clearly, that chemistry is very logical.”
Thus, Suzuki began to pursue the study of elucidating the mechanism of chemical reactions. “Professor Amako told us first-year students that no textbooks were available for us because we should become researchers who explore the frontiers of science and for whom no textbook is available. We should be the ones who write the textbooks for future students. His words are still ringing in my ears.”
Bombarding molecules in a vacuum with other molecules
It is difficult even for modern chemists to understand the detailed mechanisms in chemistry.
Suzuki points out, “This is because we cannot directly see the molecular structures or processes of chemical reactions.” Molecules are very small, with a size of about 1 nanometer (where nano indicates 10–9). Chemical reactions are phenomena that occur in a very short period ranging from 10 femtoseconds (where femto indicates 10–15) to 10 nanoseconds. Chemical dynamics researchers aim to visualize as many chemical reaction processes as possible to understand the mechanisms involved.
The following rule prevails in many chemical reactions: molecule A bombarded with a molecule B produces molecules C and D. At present, there is no known method that enables the dynamics of this process to be observed as a movie. Such observations would require us to bombard A with B in a very short period of time to within an accuracy of 1 picosecond (10–12 seconds), which is the timescale in which most chemical reactions occur. “However,” adds Suzuki, “No such techniques are available, anywhere in the world.”
In the 1950s, to investigate chemical reaction processes, scientists began to develop the ‘crossed molecular beam scattering method’, which is a method for observing the direction and speed of the two new molecules created as a result of one molecule being bombarded by another molecule. In 1969, Dudley Herschbach of Harvard University in the USA and Yuan-Tseh Lee, a member of the Research Advisory Council (RAC—an international RIKEN external assessment committee), completed an apparatus that enabled the measurement of not only the direction and speed, but also the mass of newly created molecules, and to estimate what kind of molecules were created when two molecules bombarded each other. Thus, chemical reactions started to be investigated in detail. They were awarded the Nobel Prize in Chemistry for their work in 1986.
“Chemical reactions mainly occur in liquids and gases,” says Suzuki. He adds that, for example, in aqueous solution, there are many water molecules surrounding the molecules that cause the chemical reaction, and these water molecules significantly affect the reaction. “The first step we should take, however, is to eliminate the molecules in ‘supporting roles’, such as water molecules, and only pay attention to the molecules in ‘leading roles’, because this could lead to more simplified presentations of chemical reactions.” He explains that the crossed molecular beam scattering method is used to investigate how newly created molecules scatter when two leading-role molecules bombard each other in the absence of supporting-role molecules, such as water molecules. This may be compared to ‘tracing the memory of chemical reactions’, because the procedure is to estimate the chemical reaction that would have occurred at the moment of collision on the basis of how the newly created molecules are scattered.
Conventional crossed molecular beam scattering methods, however, are not available for observing how newly created molecules rotate and vibrate while they are being scattered. Thus, these methods failed to offer sufficient information to elucidate the chemical reactions.
In 1992, Suzuki tried to combine the crossed molecular beam scattering method with laser spectroscopy to develop the ‘crossed molecular beam scattering imaging method’, which enabled the observation of both the rotation and vibration of molecules. “In 2001, we presented the observation results to the US journal Science. We spent nearly 10 years developing the apparatus.” (See Fig. 1)
Figure 1: Crossed molecular beam scattering imaging instrument.
The two cylinders are used to produce two different beams of atoms or molecules (a supersonic molecular beam), which are then crossed causing a chemical reaction between them. The newly created molecules are ionized by a laser beam, and then a voltage is applied so that the ionized molecules collide with a screen for visualization. Selecting a special wavelength allows only the molecules in a special vibrational and rotational state to be ionized and visualized.
The following shows the results of some observations of chemical reactions between an oxygen atom radical and a deuterated methane molecule. There can be two kinds of channel in this chemical reaction (Fig. 2). One channel is the insertion-type mechanism, in which an oxygen atom is fused with a methane molecule to form a methanol-type intermediate, which is, in turn, separated into a methyl radical and OD (where O is oxygen and D is deuterated hydroxyl radical) radical molecules. The other is the abstraction-type mechanism, in which an oxygen atom pulls a hydrogen atom out of a methane molecule to form a methyl radical, and an OD radical. The chemical reactions in the two channels are reflected in the observed images.
A methane molecule consisting of a single carbon atom and four hydrogen atoms has a tetrahedral shape, whereas a methyl radical, which is a methane molecule minus one hydrogen atom, has a planar shape. “The methane molecule seems to vibrate violently when it is bombarded with a radical oxygen atom, causing a quick configurational change of orbitals and the loss of a hydrogen atom,” says Suzuki. “But in reality this is not the case.” Observed images showed that the vibration of the methyl radical is very small, and that the majority of the energy is converted into the vibrational energy of the OD radical. Thus, it is possible to physically elucidate chemical reactions only by observing the collision and scattering of molecules in detail, with the use of laser light sources and an imaging technique.
Figure 2: Chemical reaction between radical oxygen atoms and deuterated methane.
The scattering image looks like a diamond ring, in which the brighter diamond part corresponds to forward scattering, whereas the ring part corresponds to backward scattering. Backscattered methane radicals CD3 move at discrete velocities. This corresponds to the fact that OD radicals occupy discrete vibrational energy levels when they are created in pairs and vibrationally excited.
At present the Chemical Dynamics Laboratory at RIKEN is leading the research groups around the world in visualizing the chemical reaction and scattering of molecules and elucidating their dynamics.
Seeing electrons that cause chemical reactions
As another major subject of study, the Chemical Dynamics Laboratory is also conducting research using ‘ultrafast photo-electron imaging’. This is a technique that enables us to track, in real time, the motion of electrons caused by chemical reactions. “Although a molecule consists of electrons and nuclei, electrons have a leading role in chemical reactions. Thus, the change in the motion of electrons is the essence of chemical reactions.”
However, as mentioned before, there are no techniques that enable the real-time observation of the whole process in which molecule A is bombarded with molecule B to create molecules C and D. Laser-beam pulses are used to irradiate the combined state of molecules A and B at 100 femtosecond intervals—a timescale shorter than the timescale for chemical reactions—thus initiating the chemical reaction for creating molecules C and D. This process is called ‘half-collision’, because it only refers to the process following the bombardment of A with B. The laser pulses are used to knock the valence electrons—which are in the outmost orbit of the atoms and play an important role in this chemical reaction—out of the molecule, and to project the valence electrons onto a screen. The change in the motion of the electrons that cause chemical reactions is reflected in the projected electron distribution.
“In the spring of 1998 while I was developing this new experimental idea, I was invited by the Royal Society of Chemistry to a Faraday Discussion that was to be held in July of the following year,” says Suzuki. “I was expected to submit my paper to the Discussion in advance, and to deliver a presentation for several minutes on the day, as well as answer a bombardment of questions.” He describes how much he wanted to prepare interesting study results for the event. “Thus I finally completed the apparatus by December, and tried to make a thorough measurement of molecules available in the laboratory. I gave up my New Year’s holidays to continue the experiments, and finally obtained interesting observation results in March. However, I broke down from overwork immediately after I had obtained the successful results.”
It was a molecule called pyrazine that brought about the interesting results. Electrons have a physical property called ‘spin angular momentum’, which is similar to the spinning of the Earth. In terms of angular momentum, electrons can be in one of two spin states: either in the clockwise or counter-clockwise directions. When pyrazine molecules are irradiated by light, the spin state of the electrons is reversed, for example, from clockwise to counter-clockwise. The energy of the electrons is then reduced, causing the electrons to change their orbits. The reduced energy is converted into the vibrational energy of the molecules. The molecule disintegrates long afterward. Suzuki succeeded in observing the change in the motion of the electrons that occurs only momentarily, over about 100 picoseconds. At present, only Suzuki and members of the Laboratory are capable of conducting such detailed observations. The time resolution is now approaching 10 femtoseconds (Fig. 3).
Figure 3: Ultrafast photo-electron imaging.
When pyrazine molecules are subjected to 320 nm ultraviolet light, an electron is excited. The electron is then spin-reversed within about 100 picoseconds. The energy of the electron is reduced and the electron changes its orbit. The figure shows an observed cross-sectional image of a pyrazine molecule while its electrons are knocked out of the molecule by the light used for observation. The electronic distribution tends to become more concentrated at the center as the time it is exposed to the observation light increases, reflecting the change in electronic-spin motion.
“When I was in graduate school,” he says, “I had a chance to listen to a lecture given by Dr Kenichi Fukui, a Nobel Prize Laureate.” Suzuki recalls how after the lecture, a question was asked as to how to conduct good research. In answer to the question, Fukui said, “You should choose your molecules carefully.” Suzuki adds, “At the time I wondered why he told us to choose our molecules carefully when we were pursuing universal rules that govern every chemical reaction.” Suzuki then points out that in actual research activities, there is an opportunity to find molecules that can clearly provide the information needed or unexpected hints. “Thus we should listen to and try to thoroughly explore what the molecules tell us. In fact, that is the shortest way to detect universal rules in chemistry,” he continues. “We should explore, from a breakthrough with a specific molecule, the essence of chemistry located at the core of diversity, because chemistry is the study of science that deals with the diversity of materials.”
In the current ultrafast photo-electron imaging method, the valence electrons in the outmost orbit of atoms are knocked out of the molecules. “The valence electrons play the most important role in chemical reactions. However, we also need to observe electrons that lie deep in the molecule and close to the nuclei, so as to obtain structural information concerning specific atoms in the molecule.”
In order to knock deep-lying electrons out of the molecule, an extremely powerful laser beam with a shorter wavelength is needed. The X-ray Free Electron Laser (XFEL), which is now under construction at the RIKEN Harima Institute, would enable such observations. Suzuki and Laboratory members are planning to use the XFEL to extend further the ultrafast photo-electron imaging method.
Understanding how proteins act in water
Suzuki has successfully formed a very small liquid droplet, 10 nanometers in diameter. They have also begun to knock electrons that cause chemical reactions out of the tiny droplet, thus observing in detail the chemical reactions in it.
Figure 4: Suzuki, Chief Scientist (right); Alnama, Contract Researcher (middle); and Liu, Asia Program Associate (left).
The Chemical Dynamics Laboratory, from which 5 out of 10 scientists will be foreign nationals from April 2008, typifies international institutes like RIKEN. The photograph shows an apparatus to observe chemical reactions in solution. This apparatus will be brought into the RIKEN Harima Institute to conduct experiments using the XFEL.
The above-mentioned observations are all based on chemical reactions in a vacuum environment. However, most research on the development of new chemical substances is based on chemical reactions in solutions. In addition, biological molecules, such as proteins, which build and maintain our bodies, cause various chemical reactions in water. Thus it is essential to explore chemical reactions in water so as to make effective use of research into the mechanism of chemical reactions, for creating new chemical substances and developing life-science technologies. Furthermore, as the chemical reaction is driven by electron motion, we need to capture the motion of electrons in solutions. The measurement can be performed by using a very small liquid droplet.
Suzuki has launched a research project to explore the interaction between water and biological molecules, in collaboration with researchers working in physics, biology, and computer simulation at RIKEN. “We plan to observe, at the electronic level, how biological molecules function in water. Within an organism, water molecules are no longer in supporting roles. The dynamics of chemical reactions blended with solvent molecules is a very hard subject to deal with, but a challenge worth attempting because it affects the basis of life phenomena.”
Finally Suzuki related his dream as follows: “Chemistry is an important field of study for establishing our views on the world and the matter that forms it. We would like to give a complete picture of chemistry so that everyone can understand it. Through our research, we would like to rewrite textbooks on chemistry to make them more attractive.”
About the Researcher
Toshinori Suzuki
Toshinori Suzuki was born in Yamagata, Japan, in 1961. He graduated from the Department of Chemistry, Faculty of Science, Tohoku University, in 1984, and obtained his PhD degree in 1988 from the same university for stimulated emission spectroscopy of jet-cooled molecules. He then became a research associate at the Institute for Molecular Science (IMS) in Okazaki, Japan, between 1988 and 1990, and a JSPS fellow for research abroad to carry out research on molecular beam scattering at Cornell University and the University of California, Berkeley, between 1990 and 1992. He returned to Japan as an associate professor at IMS, where he started his independent research group on chemical reaction dynamics in 1992. He moved to RIKEN to become a chief scientist and the director of the chemical dynamics laboratory in 2002. He has received the Broida Award from the international symposium on free radicals, the JSPS Award, and the IBM Science Award for his achievements in chemical reaction dynamics.
