WASHINGTON — The Barack Obama Foundation has major problems with the University of Chicago bid for the Obama presidential library and museum and is uneasy about the bid from the University of Illinois at Chicago, leaving Columbia University in New York the front-runner for the project.

A source close to the foundation told me that the University of Chicago bid is in jeopardy because it does not own — and has no definite path to acquiring at present — any of the South Side sites the school proposed in its Dec. 11 bid. The land is owned by the Chicago Park District.

“There are major concerns with the three potential sites in the University of Chicago proposal given the fact that neither the school nor the City of Chicago control the sites,” the source said.

The jolt from the foundation, led by Marty Nesbitt, a friend of President Barack Obama’s, puts pressure on Mayor Rahm Emanuel, Obama’s former chief of staff. “The point is the city needs to solve the problem as much as the University of Chicago,” the source said.

“Clearly, the city has made no secret of its determination to make sure the Obama library is in Chicago. So given that, it is not unrealistic for the foundation to believe that the city can resolve the issues in a timely fashion.”

Emanuel adviser David Spielfogel told me that the foundation has discussed with City Hall its concerns about land acquisition and its desire for the sites to be under city control.

Later, Spielfogel said in a statement: “We are currently looking at all options to meet their requirements and their quick timeline, but the mayor will only consider potential sites that ensure parkland remains under public control and that the surrounding communities have a say in the process.”

As for UIC, the foundation board and staff is worried about the “unsettled nature of future leadership” there. The University of Illinois system is getting a new president and a new board chairman, and UIC a new chancellor next year, and the “leadership transition” raises questions because of  “the uncertainty that accompanies it,” the source told me.

At issue is whether the incoming new leaders “have the same high level of commitment” to the project as did the people they are replacing. Also, the public university is affected by the state of Illinois’ fiscal woes.

On Tuesday, UIC issued a strong joint statement from old and new leadership – including President Robert A. Easter, President-elect Timothy L. Killeen, UIC Chancellor Paula Allen-Meares, and UIC Chancellor-elect Michael D. Amiridis — reaffirming its commitment to the project.

“The Obama Foundation should feel confident in the University leadership’s ongoing support,” UIC said.

In contrast, Columbia University owns the land it is offering to the foundation, has stable leadership and the mega financial muscle at least the equal to the University of Chicago.

I have earlier reported that the University of Hawaii is in line for the foundation to grant the state where President Barack Obama was born a presidential “center,” to be run through a partnership with the foundation and the winning bidder in Chicago or New York.

As I’ve been reporting throughout the year – not based on official University of Chicago sources — the University of Chicago proposed sites, at the South Shore Cultural Center and in Jackson and Washington Parks, are owned by the Chicago Park District.

This means that the University of Chicago strategy to win the library and museum – never officially asking the Chicago Park District for the land and keeping its sites secret until recently in order not to stir up public protest — is on track to backfire and prevent the school from even being in the running.

Land acquisition is a crucial component for the foundation. The bid is supposed to contain a “detailed proposed process to obtain control of the site and convey it to the foundation,” according to the bid document – called a “request for proposal”  — that the foundation issued on Sept. 15.

The University of Chicago bid was submitted without that process in place.

The foundation board and staff have been working with the three schools. “Not negotiations as much as an ongoing dialogue around proposals and specifics that could be changed. It’s a very two-way process,” the source said.

Susan Sher, the University of Chicago executive in charge of the school’s drive to win the library and museum, told me earlier this month that the university is offering to restore other parklands and replace the lost acres someplace else in exchange for the sites.

But because the university has been so secretive, the public has no idea how many acres are involved or the locations of other parcels in the city that can be converted to parks.

Sher said in a statement Tuesday, “We will continue to do whatever we can to ensure a smooth public process, focused on producing tangible benefits for our communities and building lasting partnerships that will sustain the presidential library far into the future.”

Another factor that may complicate land acquisition for the university is the proposed George Lucas museum on Chicago Park District land south of Soldier Field. City Hall faces a lawsuit filed by Friends of the Park claiming that the city does not have the authority to give away the land.

I reported earlier this month that Friends of the Park president Cassandra Francis told me, “We do not believe the parks are the University of Chicago’s to offer up to the library.”

On Tuesday, the Friends of the Park leadership sent a letter to the president and first lady asking them not to locate their facility “at the expense of parks or public open space.”

I reported on Dec. 2 that park district board President Bryan Traubert, the husband of Commerce Secretary Penny Pritzker, recused himself in November from voting on any library land matter, passing the baton to board Vice President Avis LaVelle. Traubert and Pritzker are potential major donors to the foundation.

LaVelle told me she would seek public input over giving up parkland. But nothing official — meaning on the public record — has yet to come to the board.

I’m told the University of Chicago has been aware of the problem for some time – but never picked a site it has control over to include as an option. The school rejected an offer of empty, privately owned parcels at 79th and Lake Michigan on the Southeast Side that the owners were offering for free.

Nesbitt and the Obama family are vacationing in Hawaii. The White House staff the foundation coordinates with — Senior Adviser Valerie Jarrett, Michelle Obama’s Chief of Staff Tina Tchen and Deputy Chief of Staff Anita Decker Breckenridge, all with deep Chicago ties — are “well aware of the issues,” the source said.

The foundation set a deadline for making recommendations to Obama and the first lady by the end of March. The delay in knowing whether the University of Chicago and City Hall can acquire the sites may push back the deadline.

Because of the enormous wealth of the University of Chicago and its deep-pocketed trustees – and the many connections it has to the Obamas, whose Kenwood home is not far from the Hyde Park campus – the school has been seen as the front-runner since the foundation was launched last Jan. 31.

But no more.

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