Can the purchase agreement be used to negotiate the commission offered to a cooperating broker?

No. It is important to keep in mind that the purchase agreement is a contract between seller and buyer. Commissions are a broker-to-broker issue. Article 16 (Standard of Practice 16-16) of the Code of Ethics states that REALTORS® shall not use the terms of an offer to attempt to modify the listing broker’s offer of compensation to a cooperating broker. If a cooperating broker is seeking additional compensation, there should be a broker-to-broker conversation about that issue and a separate agreement between the brokers confirming that arrangement.