Methods for performing patterned chemistry

A method of making an array of molecules, comprising:

• providing a substrate having a surface wherein the surface has a plurality of features, each of the features being defined and outlined by an electrically neutral perimeter wall to reduce lateral diffusion of reagents and at least some of the features comprising a first plurality of active sites, wherein the electrically neutral perimeter wall comprises a metal chosen from the group consisting of gold, chrome and tin, and wherein the surface of the feature comprises a different material than the electrically neutral perimeter wall,
• applying a first chemical reaction mixture onto the surface such that the first chemical reaction mixture is evenly distributed across the first plurality of active sites, wherein the first chemical reaction mixture comprises a first molecule having a first functional group capable of attaching to the active site, a second functional group capable of forming a covalent bond and a protecting group capping the second functional group, whereby the first molecule is coupled to the first plurality of active sites.