The chemical bonding interactions of molecular pentacene with the Si(100) surface were investigated by high resolution core level photoemission spectroscopy and by scanning tunneling microscopy (STM). Thin films of pentacene were deposited from a thermal evaporator onto the atomically clean Si(100) surface in ultrahigh vacuum. Analysis of the Si 2p core level spectra reveal evidence of a strong chemical interaction between the molecule and the surface. Three chemically shifted components at kinetic energies-0.27, -0.65, and -1.1 eV with respect the bulk peak-are required to consistently fit the Si 2p core level. The -0.27 eV chemically shifted component resulting from the bonding interaction suggests the formation of Si-C bonds between the pentacene and the silicon surface. The other two components are attributed to different adsorption sites on the surface. Annealing the pentacene covered surface in the 100-200 degreesC temperature range results in the desorption of molecular layers which had been deposited on top of this chemically reacted layer, leaving a monolayer coverage intact. Valence band spectra of the annealed surface indicate that the bonding interaction occurs between the pi orbitals of the pentacene and the silicon surface. By acquiring valence band spectra of thicker layers with s and p polarized light it was possible to conclude that the pentacene molecules absorb molecularly on top of the reacted layer with the plane of the molecule lying parallel to the Si(100) surface. The STM studies of submonolayer coverages of pentacene on the clean Si surface allow three distinct molecular orientations to be identified. Adsorption taken place both on top of, and between, the dimer rows with the molecule aligned parallel to the dimer row axis. Molecular adsorption perpendicular to the dimer rows is also observed.