The adverse effects of nanomaterials on the living system have attracted considerable attention in the past few years. Such effects may come from either the core nanomaterials or the chemical agents used to modify the nanomaterials - the latter being largely overlooked. In a free form, these modifying agents might have little impact on living cells; however, they may exhibit distinct biological effects when they assemble into a larger dimension. Here, we report that (3-aminopropyl)triethoxysilane - a small molecule compound ubiquitously employed to functionalise nanosilica surface - could decrease the viability of human umbilical vein endothelial cells when it was grafted onto the nanosilica surface. However, intriguingly, such effect was not found in 3-aminopropyl)triethoxysilane itself, the unmodified silica nanoparticles or the 3-aminopropyl)triethoxysilane-modified microparticles. Change of surface charge was excluded as a cause and apoptosis was not observed. Nevertheless, the 3-aminopropyl)triethoxysilane-modified nanoparticles could exclusively arrest cell cycle at G1 phase. Our findings suggest that substances could gain 'new' functions at the nanoscale, which may not be found in their larger or smaller counterparts. Understanding of such effects will provide critical insights for better evaluation and thus safer use of nanomaterials, in particular those having been pre-modified with other agents.