Dip-pen nanolithography (DPN), the direct transport of a ''molecular ink'' onto a substrate from an AFM tip, is of interest both as a potential industrial patterning tool and as a means to study molecular behavior. We investigated DPN for the patterning of both octadecanethiol (ODT) and mercaptohexadecanoic acid (MHA). The molecular transport of ODT and MHA does not require a water meniscus but takes place because the molecules are individually mobile. The effects of relative humidity and temperature on the patterning of each molecule were investigated. While the molecular transport rate for MHA increases slightly with increased relative humidity, the rate of molecular transport for ODT exhibits no dependence on relative humidity (although relative humidity affects the resulting molecular distribution). The transport rate of both molecules increases exponentially with temperature, consistent with an activation barrier of about 0.75 eV. Although the molecular fluxes of MHA and ODT vary with tip preparation and atmospheric conditions, both molecules diffuse from an AFM tip at a rate of about 10(5) molecules/s, corresponding to a patterning time of 100 years/cm(2).