The understanding of the chemistry of silicon surfaces has been one of the major contributors in development and improvement of silicon based microelectronic devices in the past several decades. Progressively, the dimensions of devices have reduced by several orders of magnitude, presently at the length scale of few tens of nanometers, and are expected to decrease in size even more. For chemistry based film growth methods such as chemical vapor deposition (CVD) or atomic layer deposition (ALD), control of film structure and composition in this spatial regime requires a very detailed nanoscopic understanding of silicon surface chemistry. A combined experimental and theoretical approach, utilizing ultra high vacuum scanning tunneling microscopy (UHV-STM) and density functional theory (DFT), to understanding the surface chemistry of Si(100) is illustrated in the context of ALD development for high dielectric constant metal oxides. As a first possible route to controllably deposit monolayer thick metal layer, the reaction of the metal-organic molecule with bare silicon surface is considered. The interaction of the protonated b-diketonate ligand, 2,2,6,6-tetramethyl-3,5-heptanedione (dpmH), which is a byproduct of the strontium metal-organic precursor vaporization, with Si(100)-2x1 surface is investigated. Two aspects of the molecule's interactions were addressed: the adsorption at room temperature as well as its thermal decomposition. By combination of the experiments with DFT calculations of adsorbate geometry, STM image simulations, and reaction pathways it was possible to propose unique binding configurations that match the experimentally observed adsorption features. Theoretical analysis of multiple competing reaction pathways showed that hydroxyl dissociation via a 1,7 H-shift mechanism is the dominant adsorption pathway. Several other pathways including [2+4] addition, [2+2] C=O intra-dimer addition, [2+2] C=O intra-dimer addition with OH dissociation on an adjacent dimer, [2+2] C=C intra-dimer addition, and "ene" addition are found to be barrierless with respect to the entrance channel, and have small barriers relative to a hypothesized adsorption precursor intermediate. Pathways involving 1,3 and 1,2 intra-molecular H-shifts are found to be highly activated and are expected to be inaccessible at room temperature. Several state inter-conversions are found to be unlikely as well. These results provide insight to the competitive adsorption pathways for multifunctional molecules on silicon. Investigations of thermally induced decomposition of adsorbed dpmH molecules showed that there are no significant products of desorption of carbon containing fragments of the molecule, i.e. most of the carbon atoms incorporate into the silicon surface causing it to reconstruct to a c(4x4) phase at exposures below ~ 0.15 L. At higher exposures formation of SiC islands is observed. These findings demonstrate that schemes to deposit materials from organometallic compounds containing b-diketone ligands onto clean Si(100)-2x1 surface cannot result in an ordered interfacial structure as carbon incorporation into the substrate is inevitable. An alternative strategy for depositing metal template layer is proposed, where the initial reacting surface will be terminated by water at room temperature. The stability of surface hydroxyl groups and mechanisms of their decomposition in 300-600K temperature range are analyzed. It is found that surface oxidation does not follow first order kinetics with respect to the hydroxyl groups. DFT calculations of oxygen insertion pathways point towards a catalytic effect of the dangling bonds and suggest that in the 500-550K range the insertion events should occur predominantly next to unoccupied surface silicon sites. A model is proposed, where diffusing dangling bonds act as moving catalysts for hydroxyl group decomposition. Kinetic Monte Carlo (kMC) simulations are used to compare the results of this model with experimental data. A strategy to increase hydroxyl group stability is demonstrated where the initial concentration of surface dangling bonds is decreased by water termination at 130K.