A new generation of radiation detectors relies on the crystalline Si and amorphous B (c-Si/a-B) junctions that are prepared through chemical vapor deposition of diborane (B2H6) on Si at low temperature (~400 °C). The Si wafer surface is dominated by the Si{0 0 1}3  ×  1 domains that consist of two different Si species at low temperature. Here we investigate the geometry, stability and electronic properties of the hydrogen passivated Si{0 0 1}3  ×  1 surfaces with deposited BH n (n  =  0 to 3) radicals using parameter-free first-principles approaches. Ab initio molecular dynamics simulations using the density functional theory (DFT) including van der Waals interaction reveal that in the initial stage the BH3 molecules/radicals deposit on the Si(–H), forming (–Si)BH4 radicals which then decompose into (–Si)BH2 with release of H2 molecules. Structural optimizations provide strong local relaxation and reconstructions at the deposited Si surface. Electronic structure calculations reveal the formation of various defect states in the forbidden gap. This indicates limitations of the presently used rigid electron-counting and band-filling models. The attained information enhances our understanding of the initial stage of the PureB process and the electric properties of the products.