Earlier, the Iranian state-run Press TV reported: "The explosion took place near the professor's home in Qeytariyeh neighbourhood, in northern Tehran".
It said Mohammadi was a "staunch supporter" of Iran's 1979 revolution and that he was "assassinated in a terrorist act by counter-revolutionary elements".
The broadcaster said police and security officials have launched an investigation.
Iranian media reports described Mohammadi as a nuclear energy professor, citing Abbas Jafari Dolatabadi, the Tehran prosecutor.
"Massoud Ali-Mohammadi was a professor in the nuclear field and there has so far been no arrests of those behind this incident," the Fars News Agency reported.
Al Jazeera's Alireza Ronaghi, reporting from Tehran, said Mohammadi might have had links to Iran's disputed nuclear programme.
"Authorities who decided to remain unnamed tell me that Mohammadi had some connections with Iran's nuclear programme and this [the murder] could be related," he said.
He said it was unclear who might have been behind the bombing.
"Anyone who is connected to Iran's nuclear programme could be an easy target for [foreign] intelligence services.
"Iran tries to protect its nuclear scientists very well but sometimes things get out of hand, and incidents like this happen."
Baqer Moin, an Iranian author and journalist in London, said Iranian media have accused "Zionist agents" as being behind the blast.
"They are looking towards people who are interested in delaying the Iranian nuclear programme. Websites close to the [Iranian] authorities are making these statements," he told Al Jazeera.
"There have been in the past reports that many nuclear scientists or people who wanted to join the Iranian nuclear organisation have been intimidated.
"There also were claims of other assassinations. But this is the first time in recent months that in Tehran such an occurrence has happened."
Western powers, including the US, accuse Iran of covertly seeking to develop atomic weapons.
They demand that Iran accept a UN brokered offer that would delay Iran's ability to make a nuclear weapon as well as engage in broader talks with the ultimate goal of persuading it to stop its enrichment programme.
Iran says its nuclear programme is for peaceful purposes.