Is it permissible to deduct a percentage from the profit of a deal for a material that the company does not deal with, for the benefit of the employee who concluded it without the company's knowledge?

Your question has two parts: The first part concerns the purchase of the material. If you were authorized to do so, there is no harm in it for you. Otherwise, your action is gratuitous (unauthorized). If the company ratifies it, then it is valid and binding upon them. If they do not ratify it, then it is their right to do so, and the sale is binding upon you. As for the second part, which is your taking a portion of the profit without the company's knowledge: if the transaction was for the company, then you are not permitted to take anything from the profit without their permission, because all the profit belongs to the principal, as mentioned in the hadith of Urwah ibn Al-Ja'd Al-Bariqi. However, if the company did not approve the transaction, then the profit is yours alone.