Fluorine based additives have a tremendously beneficial effect on the performance of lithium ion batteries, yet the origin of this phenomenon is unclear. In this paper we show that the formation of a solid electrolyte interphase (SEI) on the anode surface in the first 5 charge / discharge cycles is affected by the stereochemistry of the electrolyte molecules on the anode surface starting at open circuit potential. We have studied an anode specific model system, the reduction of 1,2-diethoxy ethane with LiTFSI, lithium Bis(trifluoromethane)sulfonimide, as salt on amorphous silicon anode and compared the electrochemical response and SEI formation to its fluorinated version BTFEOE, Bis(2,2,2-trifluoroethoxy) ethane by sum frequency generation (SFG) vibrational spectroscopy under reaction conditions. Our SFG results suggest that the -CF3 end groups of the linear ether BTFEOE change its adsorption orientation on the a-Si surface at open circuit potential, leading to a better protective layer. Supporting evidence from ex situ scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) depth profiling measurements show that the fluorinated ether, BTFEOE, yields a smooth SEI on the a-Si surface and enables lithium ion to intercalate deeper into the a-Si bulk.