This dataset contains data related to the geometric optimization calculations for systems composed of hydrogen-passivated nanowire surfaces functionalized with various types of chemisorbed organic molecules. We share input and output files from Quantum Espresso relax calculations obtained for several orientations of the chemisorbed organic molecules. The folder structure is organized into multiple levels: 1° Folder name: Nanowire element and surface orientation (, e.g., Si111) 2° Folder name: Surface and functional molecule type (_, e.g., Si111_alkanes) 3° Folder name: Length of organic molecule (C<#C_atoms>, e.g., C6) 4° Input file: theta_phi.in; Output file: theta_phi.out; Phi and Theta define the orientation of the related functional molecule as depicted in the figure contained in the DataSummary.xls file.