Is it permissible for a purchasing agent to take the difference between the price at which he bought an item and the price he was asked for, without informing the company?

The company's representative is an agent for the employer, and any increase earned by the agent belongs to his principal. Therefore, it is not permissible for your brother to take this increase unless he agrees with the employer that he is commissioned to buy an item at a specific price, and that he is allowed to try to obtain it for less, with the difference being his. If the employer agrees to that, then it is permissible.