The configuration found in quasicrystals was considered impossible and Shechtman fought fiercely against established science about how atoms were packed inside crystals, the academy said Wednesday in a release.
"The Nobel Prize in Chemistry 2011 has fundamentally altered how chemists conceive of solid matter," the release said.
Shechtman, 70, now a distinguished professor in the Philip Tobias Chair at Technion, the Israel Institute of Technology in Haifa, said he was "excited" to be honored.
Shechtman's discovery in 1982 that atoms in a crystal could be packed in so they cannot be repeated challenged the belief that atoms were packed inside crystals in symmetrical patterns that could repeat.
"His discovery was extremely controversial. In the course of defending his findings, he was asked to leave his research group," the release said. "However, his battle eventually forced scientists to reconsider their conception of the very nature of matter."
Describing Shechtman's quasicrystals includes the golden ratio, a concept from mathematics and art, the academy said. In quasicrystals, the ratio of various distances between atoms is related to the golden mean.
Hundreds of quasicrystals have since been synthesized in laboratories and two years ago scientists reported the first naturally occurring quasicrystals in a mineral sample from Russia, Britain's Daily Telegraph reported.
Quasicrystals are useful as so-called thermoelectric materials, which convert heat into electricity, and also create non-stick surfaces.
Their qualities have made them useful in everything from diesel engines to frying pans, the Nobel committee said.
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