AQ Khan under scrutiny after reports he tried to help Iran develop atomic weapons.
Qureshi said that there was “a 180-degree difference” in relations after the “stratgeic dialogue” go under way.
“There were no more question marks, there was no suspicion, there was no ‘do more,'” he said. “There was appreciation for what we had already done.”
Qureshi pledged support for action against extremism but said that Pakistan has key requests for the US.
“Pakistan is committed to doing its part to facilitate the world community’s effort for peace and stability in Afghanistan,” he said.
“We hope the world community will be equally responsive to our legitimate concerns and help advance common interests.”
Qureshi also said that Washington had agreed to pay $2bn owed for Islamabad’s role in past military operations by the end of June.
Pakistan had earlier presented a wish list to the US, including requests for military equipment and nuclear co-operation to be discussed during the talks on Wednesday and Thursday.
The 56-page document also sets out other priorities, such as water and electricity requirements for energy-starved Pakistan and better access to US markets.
Humayun Gauhar, a political columnist and editor-in-chief for Blue Chip Magazine, Pakistan’s leading business periodical, said the success of the wish list would be a sign of how far Washington was willing top go to improve ties.
“It all depends on how desperate America is in this new strategic partnership that it is trying to form with Pakistan, and the new responsibility and role it wants Pakistan to acquire,” he told Al Jazeera.
“It also depends on how hard [Pakistan] bargains.
“Pakistan has been at a moment like this many times in the past, where it went out of its way to do something for the world and the United States and the West, but got very little in return primarily because [it] asked for very little.”
On the security front, the US is considering ways to improve Pakistan’s ability to fight pro-Taliban and al-Qaeda forces along its border with Afghanistan.
“We hope non-discriminatory access to vital energy resources will also be made available to us”
Shah Mehmood Qureshi, Pakistan’s foreign minister
According to a senior defence official, who spoke to news agencies on condition of anonymity, Islamabad could be supplied with some unmanned drones for surveillance and intelligence gathering.
Although it does not confirm such attacks, the US military and CIA spy agency are believed to have used the drones to carry out more than 90 drone raids in Pakistan since August 2008, killing more than 830 people, according to local sources.
US officials say they have killed senior al-Qaeda and Taliban fighters in the attacks, but the Pakistani government wants more control over military operations in its own country.
Meanwhile in Pakistan, at least 21 Taliban fighters were killed on Wednesday during a military assault on suspected Taliban hideouts in the Orakzai tribal region near the Afghan border, military officials said.
The operation began hours after a suspected US drone aircraft fired two missiles into a compound in the North Waziristan tribal district, killing at least six suspected fighters, the AFP news agency reported, citing Pakistani officials.
Pakistani officials have also made it clear they would like a similar nuclear co-operation deal granted to neighbouring India by the previous US administration.
“We hope non-discriminatory access to vital energy resources will also be made available to us, so that we too can pursue our economic and industrial development plans,” Qureshi said during the talks on Wednesday.
However, Clinton has said that India’s arrangement came after “many, many years” of dialogue.
“I think on the energy issue specifically, there are more immediate steps that can be taken that have to help with the grid, have to help with other sources of energy, to upgrade power plants,” she told Pakistan’s Express TV earlier.
Kamal Matinuddin, a nuclear and security analyst in Islamabad, told Al Jazeera he did not see a nuclear deal with the US being made.
“The nuclear issue is not so much about Pakistan being recognised as nuclear power … it wants a nuclear deal for peaceful purposes because it is an energy deficient country,” Matinuddin said.
“Even if a deal is made, it would take many years [to implement]. It took five years for India to get the nuclear deal, similarly Pakistan would have to wait for another 5-7 years for them [US] to even accept Pakistan’s point of view [on this].”