We discuss several proposed explanations for the switching and negative differential resistance (NDR).behavior seen in some molecular junctions. Several theoretical models are discussed, and we present results of electronic structure calculations on a series of substituted oligo(phenylene ethynylene) molecules. It is shown that a previously proposed polaron model is successful in predicting NDR behavior, and the model is elaborated with image charge effects and parameters from electronic structure calculations. This model now incorporates substituent effects and includes the effects of conformational change, charging, and image charge stabilization.