By means of density functional theory calculations, we investigate work functions, energy level alignments, charge transfers, and tunneling characteristics of CH3- and CF3-terminated alkane- and diphenylthiol monolayers on Au(111). While the alignments of the energy levels and the charge transfers at the metal-molecule interface are found to be determined by the value of the clean Au surface work function relative to the HOMO ionization potential (IP) at the thiolate end of the monolayer, the change of work function for the modified Au( 111) surface is dominated by the properties of the thiolate monolayer, including the character, saturated or conjugated, of the molecule and the chemical nature and orientation of the terminal group. The tunneling currents through the adsorbed molecular monolayers are calculated using the Tersoff-Hamann approach. The computed difference between the I-V characteristics for the CH3- and CF3-terminated alkanethiol monolayers agree well with available experimental data. The energy barrier at the metal-molecule interface, the molecular electronic structure, and the IP of the terminal group are the key parameters which determine the tunneling properties.