Back in the United States, Pauling was trying to work his magic again with DNA, in an attempt to replicate his feat with proteins. The available X-ray photos showed a strong reflection at about 3.4 angstroms, but nothing much else. As a starting point, Pauling reexamined Ronwin’s paper. Even though he was convinced that Ronwin’s proposed structure for the DNA, with the phosphorus atom connected to five oxygen atoms, was completely wrong, something in Ronwin’s suggestion attracted his attention. Ronwin had the four bases on the outside of the structure and the phosphates down the middle. This seemed to make sense to Pauling, precisely for the same reason that Watson and Crick placed the bases on the outside in their first attempt. (Pauling was unaware of that totally off-target model.) Following this line of thought, Pauling embarked again on what has become known as his “stochastic method.” The idea was to use chemical principles to pare down the list of possible structures to the most plausible ones and then to construct three-dimensional models of those in order to eliminate configurations that were packed either too tightly or too loosely. He could then check the emerging “best-bet” arrangement against the experimental X-ray diffraction pattern.

Having had great success with this method on previous occasions, Pauling thought that he knew exactly which steps to follow. First, he had little doubt that the molecule was helical, and the Astbury-Bell photographs seemed to be generally consistent with this assumption. Second, two of the bases were double ringed and two were single ringed. The different constructions and dimensions made it difficult, at least at first glance, to have the core of a helix—which appeared to be regular—be composed of the bases. The next step was to figure out how many strands the helix should have. Pauling decided to attack this problem by calculating the density of the structure. However, before he was even able to start, an unexpected distraction stopped him in his tracks.

In the Cold War atmosphere that followed World War II, and in particular after the passage of the Internal Security Act of 1950, the US State Department’s Passport Division was given almost unlimited authority to deny passports to anyone it deemed to be too “leftist.” Pauling applied to renew his passport in January 1952, as he was preparing to attend a Royal Society meeting in London the following May. Pauling and Corey had both been invited to present their work on proteins and the alpha-helix at that conference, and Pauling was also planning to take advantage of this trip to Europe to visit a few universities in Spain and France. Then on February 14, 1952, Ruth B. Shipley, head of the Passport Division, sent Pauling a letter that could hardly be considered a Valentine’s Day card. She informed him that his passport could not be issued, since the department was of the opinion that his travel “would not be in the best interest of the United States.”

In the then-prevailing mood, given Pauling’s many pacifist speeches, his activism against nuclear weapons, and his declaration that “the world now stands at a branch in the road, leading to a glorious future for all humanity or to the complete destruction of civilization,” it was perhaps not entirely shocking that Shipley would surmise that “there is good reason to believe that Dr. Pauling is a Communist.”

At first, Pauling regarded the refusal merely as an annoying inconvenience, and he was convinced that the problem would be resolved easily. To speed things up, he immediately sent a letter to President Harry Truman, to which he attached a copy of his 1948 Presidential Medal for Merit, signed by Truman. Pauling wrote in frustration, “I am confident that no harm whatever would be done to the Nation by my proposed travel.” The president’s secretary replied politely that the Passport Division had been asked to reevaluate its judgment. Still, the decision was not reversed. In April, with an increasing sense of urgency, Pauling took a series of actions: First, he asked for the assistance of a lawyer. Second, he supplied the Passport Office with loyalty oaths and affidavits declaring he was not a Communist. Finally, he arranged to meet in person with Ruth Shipley. All of this was to no avail. The conclusive denial of the appeal was announced on April 28, and the next day, Pauling notified the organizers of the Royal Society meeting of his inability to attend.