No.  In the example you suggest, the $499,000 payment is not a charitable contribution.  The very language of your question shows that the property is given “in return for” the balance of the purchase price.  (The directors of the charity would probably be breaching their fiduciary duty to the organization if they gave the property away for $1 without the commitment to get the other $499,000.)

For a donor to claim a charitable contribution deduction, the donor is required to obtain an acknowledgment from the charity stating whether any goods or services were received in return for the payment and, if so, the value of such goods or services.  The charity cannot give statement that no goods or services were received in return for the $499,000.  The property was received “in return for” the payment.  No charity wants to get involved in the kind of tax fraud that would be involved if the donor in your example tried to claim a contribution deduction.