Research in the 1970s by Martin Karplus, Michael Levitt and Arieh Warshel has led to programs that unveil chemical processes such as how exhaust fumes are purified or how photosynthesis takes place in green leaves, the Royal Swedish Academy of Sciences said. That kind of knowledge makes it possible to find the best design for things like new drugs, solar cells or catalytic converters for cars.
The strength of the winning work is that it can be used to study all kinds of chemistry, the academy said.
"This year's prize is about taking the chemical experiment to cyberspace," said Staffan Normark, the academy's secretary.
All three scientists became US citizens. Karplus, an 83-year-old US and Austrian citizen, splits his time between the University of Strasbourg, France, and Harvard University. The academy said Levitt, 66, is a British, US, and Israeli citizen and a professor at Stanford University School of Medicine. Warshel, 72, is a US and Israeli citizen affiliated with the University of Southern California in Los Angeles.
Levitt told The Associated Press the award recognized him for work he had done when he was 20, before he even had his PhD.
"It was just me being in the right place at the right time and maybe having a few good ideas," he said, speaking by telephone from his home in Stanford, California.
Arieh Warshel talks on the phone with Israeli President Shimon Peres after hearing he won the Nobel chemistry prize in Los Angeles.(Reuters photo)
"It's sort of nice in more general terms to see that computational science, computational biology is being recognized," he added. "It's become a very large field and it's always in some ways been the poor sister, or the ugly sister, to experimental biology."
Jokingly, he said the biggest immediate impact of the Nobel Prize would be his need for dance lessons before appearing at the Nobel banquet.
A look at the winners of Nobel Prize in chemistry
"I would say the only real change in my life is I need to learn how to dance because when you go to Stockholm you have to do ballroom dancing," Levitt said. "This is the big problem I have right now."
Karplus told the AP the 5am call from the Nobel judges had him worried that the caller might be bearing bad news.
Michael Levitt during an interview at his home in Stanford.(Reuters photo)
"Usually you think when you get a call at 5 o'clock in the morning it's going to be bad news, you know, something's happened. My daughter, you know, who is in Israel, might have been run over by a car or something or other.
"But it turned out to be good news and, after a while, I finally understood it was a call from Sweden and . I had been awarded a Nobel Prize in chemistry with two other people," Karplus said.
Read more: Nobel laureate Martin Karplus escaped Nazis when a small boy
Warshel, speaking by telephone to a news conference in Stockholm, said he was "extremely happy" to have been woken up in the middle of the night in Los Angeles to find out he would share the $1.2 million prize, and looks forward to collecting it in the Swedish capital.
"In short, what we developed is a way which requires computers to look, to take the structure of the protein and then to eventually understand how exactly it does what it does," Warshel said.
A draft is displayed on a screen during a press conference to announce the laureates of the 2013 Nobel Prize in chemistry.(AFP photo)
When scientists wanted to simulate complex chemical processes on computers, they used to have to choose between software that was based on quantum physics, which applies on the scale of an atom, or classical Newtonian physics, which operates at larger scales. The academy said the three laureates developed computer models that "opened a gate between these two worlds."
While quantum mechanics is more accurate, it's impossible to use on large molecules because the equations are too complex to solve.
By using quantum mechanics only for key parts of molecules and classical physics for the rest, the blended approach delivers the accuracy of the quantum approach with manageable computations.
Working together at Harvard in the early 1970s, Karplus and Warshel developed a computer program that brought together classical and quantum physics.
Warshel later joined forces with Levitt at the Weizmann institute in Rehovot, Israel, and at the University of Cambridge in Britain, to develop a program that could be used to study enzymes.
A webpage shows the laureates Martin Karplus, Michael Levitt and Arieh Warshel as winners of the 2013 Nobel Prize in chemistry. (AP photo)
Jeremy Berg, a professor of computational and systems biology at the University of Pittsburgh, said the winning work gives scientists a way to understand complicated reactions that involve thousands to millions of atoms.
"There are thousands of laboratories around the world using these methods, both for basic biochemistry and for things like drug design," said Berg, former director of the National Institute of General Medical Sciences in Bethesda.
Many drug companies use computer simulations to screen substances for their potential as medicines, which lets them focus their chemistry lab work on those that look promising, he said.
Marinda Li Wu, president of the American Chemical Society, was equally enthusiastic about the award.
"I think it's fabulous," she said in a telephone interview. "They're talking about the partnering of theoreticians with experimentalists, and how this has led to greater understanding."
That is "bringing better understanding to problems that couldn't be solved experimentally," she said. "We're starting as scientists to better understand things like how pharmaceutical drugs interact with proteins in our body to treat diseases. This is very, very exciting."
Earlier this week, three Americans won the Nobel Prize in medicine for discoveries about how key substances are moved around within cells and the physics award went to British and Belgian scientists whose theories help explain how matter formed in the universe after the Big Bang.
The Nobel Prize in literature will be announced on Thursday, the Nobel Peace Prize on Friday and the economics prize on Monday.
All Nobel Prizes will be presented to the winners on Dec. 10, the anniversary of prize founder Alfred Nobel's death in 1896.