We develop a theoretical model for how organic molecules can control the electronic and transport properties of an underlying transistor channel to whose surface they are chemically bonded. The influence arises from a combination of long-ranged dipolar electrostatics due to the molecular headgroups, as well as short-ranged charge transfer and interfacial dipole driven by equilibrium bandalignment between the molecular backbone and the reconstructed semiconductor surface atoms.Inorganic semiconductors have traditionally dominated as the material players in the electronics industry. While their organic counterparts have been studied extensively as alternate channel materials [1], the development of a stand-alone molecular electronics technology has been stymied by the inordinate difficulty of contacting small molecules reproducibly, their insufficient mobilities, large RC constants and poor gateability. Perhaps a more promising approach is to envisage hybrid organosemiconductor devices, combining the established infrastructure of the semiconductor integrated industry with the 'bottom-up' self-assembly and chemical tunability of molecular monolayers. A particularly interesting possibility is to use organic molecules to control the surface properties of deeply scaled, backgated silicon transistors, by tying up deleterious surface states and charge transfer 'doping'. In addition, monitoring the transistor dynamics, such as the shift in its threshold voltage, can be used to detect a single molecule adsorption event [2]. It is thus critical to properly understand the physical factors that determine how a molecule controls a transistor, and how the transistor, in turn, senses the molecule.In this paper, we develop a quantitative theory for the threshold voltage control of low-doped silicon channels by surface bonded organic monolayers with varying dipole moments. We focus in particular on a recent series of experiments [4] that involved the grafting of molecular monolayers atop oxide free H-passivated silicon surfaces. The choice of the molecules followed an important logic. An identical set of molecules was used, with the exception of one substituent group. This allowed a systematic study of the effect of the molecules on the electrical properties of the device. While organic molecules attached to semiconductor surfaces have been studied extensively [5,6,7], albeit phenomenologically, our principal challenge is to develop a quantitative, 'first principles' model that combines atomistic charge-transfer processes with macroscale electrostatics. We employ Density Functional Theory (DFT) to extract the molecular adsorption geometry, interfacial dipole and band-alignment at the atomistically reconstructed silicon surface. These quantities are then incorporated as inputs into a macroscopic Poisson solver to compute the band-bending in the transistor channel. The calculated threshold voltage shifts and band-alignments are in excellent agreement with experi-