NEW YORK —  Fifteen years ago Aafia Siddiqui — the MIT graduate recently caught carrying a list of American targets and charged with the attempted killing of U.S. agents in Afghanistan — had a day job helping elementary schools with their science experiments.

But at the same time, FOXNews.com has learned, the now-suspected Al Qaeda operative may have been concocting more explosive schemes: raising funds for machine guns, military supplies and terrorist operations for Al Qaeda.

In 1993, Siddiqui, a triple biology, anthropology and archaeology major, was one of 14 undergraduates awarded a $1,200 City Days fellowship by MIT’s public service program to assist public school teachers in developing science curricula. According to university records and publications, the fellowship required 40 hours of work each week inside elementary school classrooms in Cambridge, Mass., where MIT is located.

But e-mails obtained by FOXNews.com show messages sent by Siddiqui, during the same period that match two of her MIT addresses, soliciting money for Al-Kifah Refugee Center — a known Al Qaeda charitable front tied to Usama bin Laden and the 1993 World Trade Center bombing.

Al-Kifah was considered Al Qaeda’s U.S operational headquarters, a sort of underground railroad that was funneling funds and supplies to the terror group, according to government investigators. The U.S. government froze its assets shortly after the September 11 terror attacks.

In the e-mails — sent to students through various Middle Eastern and European Islamic newsgroups — Siddiqui said that the funds were being raised on behalf of Bosnian orphans and widows, but she asked for checks to be cut to Al-Kifah.

In one thread entitled "women available for marriage" dated March 15, 1993, less than a month after the first World Trade Center bombing, Siddiqui wrote:

“Kindly fill the pledge form and return to Al-Kifah. If I don't hear from you, I will assume that things are fine and taken care of.

“To those of you who had volunteered to find other sponsors within your community as well, kindly send at least one sponsor's info. (if you have not already done so) so I can mail you one form initially which you can use to inform others and get more commitments.

“Please keep up the spirit and motivate others as well!!!!!! The Muslims of our Ummah need ALL the help we can provide them.”

She signed this e-mail, “humbly, your sister Aafia.”

Siddiqui's lawyer Elaine Whitfield Sharp said she could not authenticate the e-mail and said she seriously questioned the source of the "document."

"Even if this e-mail were sent by Aafia, attempting to collect money for widows and orphans is not a crime and, indeed, it is a basic mission of Christendom, Islam, Judaism and all other religions," Sharp wrote in an email.

She added: "The poor will always be with us — and so will the oppressed. To publish this e-mail in a nefarious light would be an affront to Muslim-Americans and Muslims everywhere."

Terrorism expert Steven Emerson, head of The Investigative Project on Terrorism, said he wasn't aware of the e-mail but that the apparent link to Al Kifah fits, considering what's known by federal investigators about Siddiqui's role as the group's fundraiser.

“She was active in trying to resuscitate Al Kifah after the 1993 World Trade Center bombing," Emerson said. "After all the scrutiny from law enforcement, Al Kifah suffered a big hit then.”

In other e-mail, Siddiqui added a verse from the Koran about charity that stated:

"O you who believe! let not your riches or your children divert you fromthe remembrance of Allah. If any act thus, the loss is their own.

And spend something (in charity) out of the substance which We havebestowed on you, before Death should come to any of you and he should say,"O my Lord! Why did you not give me respite for a little while? I shouldthen have given (largely) in charity, and I should have been one of thedoers of good."

But to no soul will Allah grant respite when the time appointed (for it)has come; and Allah is well acquainted with (all) that you do."

(Qur'an, Surah Munafiqoon v.9-11)

In the mid 1990s, after graduating from MIT, Siddiqui continued her double life. She began a Ph.D. program in neuroscience at nearby Brandeis University, all the while raising funds for charity groups bankrolling Al Qaeda operations, according to government and court records.

According to Brandeis records, Siddiqui continued to teach at the university. In the spring of 1999, she taught 22 students General Biology Lab, a course required for undergraduate biology majors, pre-med and pre-dental students.

By 2003, Siddiqui was being investigated by federal agents after she was named by 9/11 mastermind Khalid Sheikh Mohammed as an Al Qaeda operative in Boston.

At a 2004 news conference, then-Attorney General John Ashcroft and FBI Director Robert Mueller III identified Siddiqui as one of seven people the FBI wanted to question about suspected ties to Al Qaeda.

Though they never alleged she was a full-fledged member of Al Qaeda, authorities said they believed Siddiqui could be a "fixer," someone with knowledge of the U.S. who supported other operatives trying to slip into the country and plot attacks.

Siddiqui, now 36, is being held in New York on charges of attempted murder of U.S. and military officials. She was stopped by Afghan police on July 17 and later interrogated by U.S. officials, whom she allegedly shot at during the interrogation.

She was found with lists of U.S. targets, including the Statue of Liberty, Times Square and the New York subway system, and recipes for biological and radioactive weapons in her purse, according to the complaint filed in U.S. Federal Court on July 31 and interviews with government sources.

Siddiqui is due in court next month where she faces charges of attempting to kill U.S. officers and employees and one count of assaulting U.S. officers and employees. If convicted, she faces a maximum sentence of 20 years in prison on each charge.

The Associated Press contributed to this report.