The high stability of gold makes its surface an attractive substrate for the deposition of molecular materials and their functioning in devices. There are many substantial and profound experimental and theoretical issues that the use of any metal interacting with molecules requires to address. Here, we examine in some detail a semi-empirical computational model able to describe the metal-molecules interactions and provide an overview of the measure of success that it has reached. A number of specific examples are illustrated for a variety of rather large molecular systems. Challenges and future goals are also discussed.