When computer is as important as a test tube

The laureates made classical physics work side-by-side with the fundamentally different quantum physics

October 09, 2013 03:24 pm | Updated November 16, 2021 11:05 pm IST - Stockholm

Chemists all over the world devise and carry out experiments on their computers on a daily basis. With the help of the methods that Martin Karplus, Michael Levitt and Arieh Warshel began to develop in the 1970s, they examined every tiny step in complex chemical processes invisible to the naked eye.

For example, if you can mimic photosynthesis you will be able create more efficient solar cells. When water molecules are split oxygen is created, but also hydrogen that could be used to power our vehicles.

So, go online and find a three dimensional image of the proteins that govern photosynthesis. You can twist and turn the image on your computer. It unveils gigantic protein molecules consisting of thousands of atoms. Somewhere in the middle, there is a region called the reaction centre, where the water molecules are split. However, only a few atoms are directly involved in the reaction. The image shows how atoms and ions are positioned in relation to each other, but it says nothing about what these atoms and ions do. Somehow, electrons must be extracted from the water and four protons need to be taken care of.

The details of this process are virtually impossible to map using traditional methods of chemistry. Things happen in fractions of milliseconds — ruling out most kinds of test tube experiments. The image that you have only shows the proteins in a state of rest. When sunlight hits the leaves, the proteins are filled with energy and the entire atomic structure is changed. To understand the chemical reaction you need to know what this energy-filled state looks like.

Using of the Nobel Laureates’ software you can calculate various plausible reaction pathways. When you have a plausible reaction path it is easier to carry out experiments that can verify the computer’s results. These experiments can then yield new clues that lead to even better simulations; theory and practice cross-fertilize each other. Thus, chemists now spend as much time in front of their computers as they do among test tubes.

Previously, software at scientists’ disposal was based upon either classical Newtonian physical theories or quantum physics, both with strengths and weaknesses. Classical programs gave chemists a good representation of how the atoms were positioned in the molecules but only displayed molecules in a state of rest. During reactions, molecules are filled with energy; they become excited. Classical physics simply have no understanding for such states – a severe limitation.

When scientists wanted to simulate chemical reactions, they turned to quantum physics, the theory where electrons can be both particles and waves simultaneously. It is unbiased and excludes any of the scientist’s preconceptions, making simulations more realistic. The downside: these calculations require enormous computing power because they yield detailed descriptions of chemical processes.

So, classical and quantum chemistry were two fundamentally different rivalling worlds. But the Nobel Laureates in Chemistry 2013 have opened a gate between these worlds. In their computer models, Newton and his apple collaborate with Schrödinger and his cat.

Quantum chemistry collaborating with classical physics

The collaboration was born in Martin Karplus’ laboratory at Harvard University in Cambridge, USA, in the early 1970s. Karplus and his research group developed computer programs that could simulate chemical reactions with the help of quantum physics. He had also developed the “Karplus equation” used in nuclear magnetic resonance (NMR) – a method well-known to chemists that builds on the quantum chemical properties of molecules. In 1970, Arieh Warshel arrived at Karplus’ laboratory after finishing his PhD at the Weizmann Institute of Science in Rehovot, Israel.

The institute had a powerful computer with whose help Arieh Warshel and Michael Levitt had developed a ground-breaking computer program based on classical theories. The program enabled modelling of all kinds of molecules, even really large ones.

When Arieh Warshel joined Martin Karplus at Harvard, he brought his classical computer program with him. Using that, he and Karplus began developing a new program that performed different kinds of calculations on different electrons.

In most molecules each electron orbits a particular atomic nucleus. In some molecules, certain electrons can move unhindered between several atomic nuclei. Such “free electrons” can be found, for instance, in retinal, a molecule embedded in the retina of the eye. When light hits the retina, the free electrons in retinal are filled with energy, altering the shape of the molecule. This is the first stage of human vision.

Eventually, Karplus and Warshel developed a computer program that drew on quantum physics when it performed calculations on free electrons, and applied simpler classical theories for all other electrons and atomic nuclei. In 1972, they published their ground-breaking results. This was the first time anyone had managed to bring about a chemically relevant collaboration between classical and quantum physics. But the program had one limitation: it could only handle molecules with mirror symmetry.

After two years at Harvard, Arieh Warshel reunited with Michael Levitt, who had finished his doctoral training at Cambridge University, UK. He had used his classical computer program to gain a better understanding of what biological molecules looked like. However, it could only examine molecules in a state of rest.

Levitt and Warshel wanted to develop a program that could be used to study enzymes; proteins that govern and simplify chemical reactions in living organisms. It is the cooperation between enzymes that makes life possible. In order to be able to simulate enzymatic reactions, Levitt and Warshel were required to make classical and quantum physics collaborate more smoothly. It took them several years to overcome all obstacles.

In 1976, they reached their goal and published the first computerized model of an enzymatic reaction. Their program was revolutionary because it could be used for any kind of molecule. Size was no longer an issue.

When chemists model chemical processes today, they perform demanding quantum physical calculations on electrons and atomic nuclei that directly impact the chemical process. The other parts of the molecules are modelled using classical equations.

To make things more efficient, Levitt and Warshel have showed that it is possible to merge several atoms during calculations. In modern calculations, scientists add a third layer to the simulation. They bundle atoms and molecules into a single homogenous mass called a dielectric medium.

Scientists these days can use computers to carry out experiments to yield a much deeper understanding of how chemical processes play out. The strength of the methods that the Laureates developed is that they are universal.

Progress will not stop here. In one of his publications, Levitt writes about one of his dreams: to simulate a living organism on a molecular level – a tantalizing thought.

( Edited excerpts from Nobelprize.org )

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