Karplus was born into a Jewish family in Vienna in 1930 and narrowly escaped Austria when Germany took control of the country in 1938, he wrote in a lengthy article in the Annual Review of Biophysics and Biomolecular Structure in 2006.
Karplus described how attitudes towards him and his family changed even before the Nazi takeover of Austria, and how two boys he and his brother had considered their best friends began bullying them.
"In the spring of 1937, they suddenly refused to have anything to do with us and began taunting us by calling us 'dirty Jew boys' when we foolishly continued to try to interact with them," he wrote.
When Nazi German troops rolled into Austria in March 1938, Karplus was able to escape to Switzerland with his brother and mother.
But in what he described as a "traumatic" aspect of the departure, his father was prevented from leaving and locked up in a Viennese jail.
"In part, he was kept as a hostage so that any money we had would not be spirited out of the country," he wrote.
As the small family secured passage to the United States and was preparing to embark on a trans-Atlantic journey at the French port of Le Havre, there was still no news of his father.
"He miraculously turned up at Le Havre a few days before our ship, the Ile de France, was scheduled to depart for New York," he wrote.
Karplus later learned that his uncle had signed a $5,000 bond for his release.
While Karplus, now 83, and his family were able to escape, many other Austrians Jews met a much more sinister fate.
"As history has recorded, many were not able to leave and died in concentration camps," he wrote.
Karplus went on to pursue a stellar academic career in the United States, getting a PhD in 1953 before making the discoveries that earned him the world's most prestigious award for the chemical science on Wednesday.