The New York Times’s examination of the Uranium One deal is based on dozens of interviews, as well as a review of public records and securities filings in Canada, Russia and the United States. Some of the connections between Uranium One and the Clinton Foundation were unearthed by Peter Schweizer, a former fellow at the right-leaning Hoover Institution and author of the forthcoming book “Clinton Cash.” Mr. Schweizer provided a preview of material in the book to The Times, which scrutinized his information and built upon it with its own reporting.

Whether the donations played any role in the approval of the uranium deal is unknown. But the episode underscores the special ethical challenges presented by the Clinton Foundation, headed by a former president who relied heavily on foreign cash to accumulate $250 million in assets even as his wife helped steer American foreign policy as secretary of state, presiding over decisions with the potential to benefit the foundation’s donors.

In a statement, Brian Fallon, a spokesman for Mrs. Clinton’s presidential campaign, said no one “has ever produced a shred of evidence supporting the theory that Hillary Clinton ever took action as secretary of state to support the interests of donors to the Clinton Foundation.” He emphasized that multiple United States agencies, as well as the Canadian government, had signed off on the deal and that, in general, such matters were handled at a level below the secretary. “To suggest the State Department, under then-Secretary Clinton, exerted undue influence in the U.S. government’s review of the sale of Uranium One is utterly baseless,” he added.

American political campaigns are barred from accepting foreign donations. But foreigners may give to foundations in the United States. In the days since Mrs. Clinton announced her candidacy for president, the Clinton Foundation has announced changes meant to quell longstanding concerns about potential conflicts of interest in such donations; it has limited donations from foreign governments, with many, like Russia’s, barred from giving to all but its health care initiatives. That policy stops short of a more stringent agreement between Mrs. Clinton and the Obama administration that was in effect while she was secretary of state.

Either way, the Uranium One deal highlights the limits of such prohibitions. The foundation will continue to accept contributions from foreign sources whose interests, like Uranium One’s, may overlap with those of foreign governments, some of which may be at odds with the United States.

When the Uranium One deal was approved, the geopolitical backdrop was far different from today’s. The Obama administration was seeking to “reset” strained relations with Russia. The deal was strategically important to Mr. Putin, who shortly after the Americans gave their blessing sat down for a staged interview with Rosatom’s chief executive, Sergei Kiriyenko. “Few could have imagined in the past that we would own 20 percent of U.S. reserves,” Mr. Kiriyenko told Mr. Putin.